Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	validation_status	validation_method	validation_tumor_sample	validation_alt_allele
Unknown	0	broad.mit.edu	37	1	102960	102960	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:102960delT	uc010nxt.1	-											Homo sapiens cDNA FLJ43258 fis, clone HHDPC1000001.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	537589	537599	+	IGR	DEL	TCTCTCCATCC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:537589_537599delTCTCTCCATCC								OR4F29 (168994 upstream) : LOC100133331 (123541 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	651212	651212	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:651212delA								OR4F29 (282617 upstream) : LOC100133331 (9928 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	726606	726615	+	IGR	DEL	GAATGGAATG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:726606_726615delGAATGGAATG								LOC100133331 (46870 upstream) : NCRNA00115 (34972 downstream)																																			---	---	---	---
LOC643837	643837	broad.mit.edu	37	1	766849	766849	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:766849delG	uc009vjn.1	+						LOC643837_uc001abp.1_Intron|LOC643837_uc001abq.1_Intron|LOC643837_uc009vjo.1_Intron|LOC643837_uc001abr.1_Intron					Homo sapiens cDNA: FLJ23220 fis, clone ADSU01957.												0																		---	---	---	---
NOC2L	26155	broad.mit.edu	37	1	889004	889004	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:889004delG	uc001abz.3	-						NOC2L_uc001aby.3_Intron|NOC2L_uc009vjq.2_Intron	NM_015658	NP_056473			nucleolar complex associated 2 homolog							nucleolus	protein binding			ovary(1)|skin(1)	2	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.86e-38)|OV - Ovarian serous cystadenocarcinoma(86;6.08e-23)|Colorectal(212;0.000161)|COAD - Colon adenocarcinoma(227;0.000194)|BRCA - Breast invasive adenocarcinoma(365;0.000475)|Kidney(185;0.00231)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0344)|Lung(427;0.2)														---	---	---	---
TTLL10	254173	broad.mit.edu	37	1	1116223	1116223	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1116223delG	uc001acy.2	+	8	889	c.738delG	c.(736-738)CCGfs	p.P246fs	uc001acx.1_5'Flank|TTLL10_uc010nyg.1_Frame_Shift_Del_p.P246fs|TTLL10_uc001acz.1_Frame_Shift_Del_p.P173fs	NM_001130045	NP_001123517	Q6ZVT0	TTL10_HUMAN	tubulin tyrosine ligase-like family, member 10	246	TTL.				protein modification process		ATP binding|tubulin-tyrosine ligase activity			large_intestine(1)	1	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;4.75e-36)|OV - Ovarian serous cystadenocarcinoma(86;5.82e-22)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)														---	---	---	---
TNFRSF18	8784	broad.mit.edu	37	1	1139982	1139983	+	Intron	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1139982_1139983insC	uc001adc.2	-						TNFRSF18_uc001ada.2_Intron|TNFRSF18_uc001adb.2_Intron|TNFRSF18_uc001add.2_Intron	NM_004195	NP_004186			tumor necrosis factor receptor superfamily,						anti-apoptosis|apoptosis	extracellular region|integral to plasma membrane	tumor necrosis factor receptor activity				0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;3.73e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.01e-21)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)														---	---	---	---
SDF4	51150	broad.mit.edu	37	1	1154584	1154584	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1154584delC	uc001adh.3	-						SDF4_uc001adg.2_RNA|SDF4_uc001adi.3_Intron|SDF4_uc009vjv.2_Intron|SDF4_uc009vjw.2_Intron	NM_016176	NP_057260			stromal cell derived factor 4 isoform 2						cerebellum development|fat cell differentiation|response to ethanol|UV protection|zymogen granule exocytosis	bleb|Golgi lumen|late endosome|soluble fraction	calcium ion binding|calcium ion binding|identical protein binding|protein binding			upper_aerodigestive_tract(1)|large_intestine(1)	2	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;7.85e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.42e-21)|Colorectal(212;4.79e-05)|COAD - Colon adenocarcinoma(227;4.83e-05)|Kidney(185;0.00252)|BRCA - Breast invasive adenocarcinoma(365;0.00263)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0368)|Lung(427;0.204)														---	---	---	---
SDF4	51150	broad.mit.edu	37	1	1165843	1165844	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1165843_1165844delTT	uc001adh.3	-						SDF4_uc001adi.3_Intron|SDF4_uc009vjv.2_Intron|SDF4_uc009vjw.2_Intron|B3GALT6_uc001adk.2_5'Flank	NM_016176	NP_057260			stromal cell derived factor 4 isoform 2						cerebellum development|fat cell differentiation|response to ethanol|UV protection|zymogen granule exocytosis	bleb|Golgi lumen|late endosome|soluble fraction	calcium ion binding|calcium ion binding|identical protein binding|protein binding			upper_aerodigestive_tract(1)|large_intestine(1)	2	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;7.85e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.42e-21)|Colorectal(212;4.79e-05)|COAD - Colon adenocarcinoma(227;4.83e-05)|Kidney(185;0.00252)|BRCA - Breast invasive adenocarcinoma(365;0.00263)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0368)|Lung(427;0.204)														---	---	---	---
MXRA8	54587	broad.mit.edu	37	1	1290110	1290111	+	Frame_Shift_Del	DEL	GG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1290110_1290111delGG	uc001aew.2	-	5	931_932	c.900_901delCC	c.(898-903)CCCCGGfs	p.P300fs	MXRA8_uc001aex.3_Frame_Shift_Del_p.P300fs|MXRA8_uc001aey.3_Frame_Shift_Del_p.P300fs|MXRA8_uc010nyl.1_Frame_Shift_Del_p.P300fs|MXRA8_uc001aez.2_Frame_Shift_Del_p.P199fs|MXRA8_uc001afa.2_Frame_Shift_Del_p.P291fs	NM_032348	NP_115724	Q9BRK3	MXRA8_HUMAN	matrix-remodelling associated 8 precursor	300_301	Extracellular (Potential).					integral to membrane					0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	1318078	1318078	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1318078delC								AURKAIP1 (7260 upstream) : CCNL2 (3013 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	1318117	1318117	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1318117delC								AURKAIP1 (7299 upstream) : CCNL2 (2974 downstream)																																			---	---	---	---
ATAD3B	83858	broad.mit.edu	37	1	1424139	1424139	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1424139delA	uc001afv.2	+						ATAD3B_uc001afx.2_Intron|ATAD3B_uc001afy.2_5'Flank	NM_031921	NP_114127			AAA-ATPase  TOB3								ATP binding|nucleoside-triphosphatase activity				0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	1434349	1434352	+	IGR	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1434349_1434352delTTTT								ATAD3B (2768 upstream) : ATAD3A (13203 downstream)																																			---	---	---	---
CDK11B	984	broad.mit.edu	37	1	1586978	1586978	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1586978delT	uc001agv.1	-						CDK11B_uc001ags.1_Intron|CDK11B_uc001agt.1_Intron|CDK11B_uc001aha.1_Intron|CDK11B_uc001agw.1_Intron|CDK11B_uc001agy.1_Intron|CDK11B_uc001agx.1_Intron|CDK11B_uc001agz.1_Intron|uc001ahc.1_Intron	NM_033486	NP_277021			cell division cycle 2-like 1 (PITSLRE proteins)						apoptosis|cell proliferation|mitosis|regulation of cell growth|regulation of mRNA processing|regulation of transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|cyclin-dependent protein kinase activity|protein binding			skin(1)	1																		---	---	---	---
SLC35E2B	728661	broad.mit.edu	37	1	1675460	1675460	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1675460delA	uc001ahh.3	-						SLC35E2_uc001ahy.2_Intron|SLC35E2_uc001ahz.2_Intron|SLC35E2_uc001aib.1_Intron	NM_001110781	NP_001104251			similar to solute carrier family 35, member E2							integral to membrane					0																		---	---	---	---
GNB1	2782	broad.mit.edu	37	1	1769889	1769889	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1769889delT	uc001aif.2	-						GNB1_uc009vky.2_Intron	NM_002074	NP_002065			guanine nucleotide-binding protein, beta-1						cellular response to glucagon stimulus|energy reserve metabolic process|muscarinic acetylcholine receptor signaling pathway|platelet activation|Ras protein signal transduction|synaptic transmission	heterotrimeric G-protein complex	GTPase activity|GTPase binding|signal transducer activity				0	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.62e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.14e-35)|OV - Ovarian serous cystadenocarcinoma(86;7.31e-23)|GBM - Glioblastoma multiforme(42;3.1e-07)|COAD - Colon adenocarcinoma(227;0.000323)|Colorectal(212;0.000374)|Kidney(185;0.00392)|BRCA - Breast invasive adenocarcinoma(365;0.00573)|STAD - Stomach adenocarcinoma(132;0.0072)|KIRC - Kidney renal clear cell carcinoma(229;0.0482)|Lung(427;0.236)														---	---	---	---
PRKCZ	5590	broad.mit.edu	37	1	2078442	2078445	+	Intron	DEL	CATC	-	-	rs196128		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2078442_2078445delCATC	uc001aiq.2	+						PRKCZ_uc001air.2_Intron|PRKCZ_uc010nyw.1_Intron|PRKCZ_uc001ais.2_Intron|PRKCZ_uc009vla.2_Intron|PRKCZ_uc010nyx.1_Intron|PRKCZ_uc009vlb.2_Intron	NM_002744	NP_002735			protein kinase C, zeta isoform 1						anti-apoptosis|intracellular signal transduction|negative regulation of insulin receptor signaling pathway|negative regulation of peptidyl-tyrosine phosphorylation|negative regulation of protein complex assembly|peptidyl-serine phosphorylation|platelet activation	endosome	ATP binding|protein kinase C activity|zinc ion binding			central_nervous_system(4)|large_intestine(2)	6	all_cancers(77;0.000177)|all_epithelial(69;6.41e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;1.14e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.96e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.3e-23)|GBM - Glioblastoma multiforme(42;2.85e-08)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00294)|BRCA - Breast invasive adenocarcinoma(365;0.00493)|STAD - Stomach adenocarcinoma(132;0.00669)|KIRC - Kidney renal clear cell carcinoma(229;0.0411)|Lung(427;0.213)														---	---	---	---
PRKCZ	5590	broad.mit.edu	37	1	2100888	2100888	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2100888delG	uc001aiq.2	+						PRKCZ_uc001air.2_Intron|PRKCZ_uc010nyw.1_Intron|PRKCZ_uc001ais.2_Intron|PRKCZ_uc009vla.2_Intron|PRKCZ_uc010nyx.1_Intron|PRKCZ_uc001ait.2_Frame_Shift_Del_p.V150fs	NM_002744	NP_002735			protein kinase C, zeta isoform 1						anti-apoptosis|intracellular signal transduction|negative regulation of insulin receptor signaling pathway|negative regulation of peptidyl-tyrosine phosphorylation|negative regulation of protein complex assembly|peptidyl-serine phosphorylation|platelet activation	endosome	ATP binding|protein kinase C activity|zinc ion binding			central_nervous_system(4)|large_intestine(2)	6	all_cancers(77;0.000177)|all_epithelial(69;6.41e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;1.14e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.96e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.3e-23)|GBM - Glioblastoma multiforme(42;2.85e-08)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00294)|BRCA - Breast invasive adenocarcinoma(365;0.00493)|STAD - Stomach adenocarcinoma(132;0.00669)|KIRC - Kidney renal clear cell carcinoma(229;0.0411)|Lung(427;0.213)														---	---	---	---
PEX10	5192	broad.mit.edu	37	1	2341763	2341764	+	Intron	INS	-	GT	GT			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2341763_2341764insGT	uc001ajh.2	-						PEX10_uc001ajg.2_Intron	NM_002617	NP_002608			peroxisome biogenesis factor 10 isoform 2						protein import into peroxisome matrix|protein import into peroxisome matrix	integral to peroxisomal membrane|peroxisomal membrane	protein binding|protein C-terminus binding|zinc ion binding|zinc ion binding			central_nervous_system(1)	1	all_cancers(77;0.000247)|all_epithelial(69;9.96e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;5.35e-20)|all_lung(118;2.78e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.1e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.02e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00102)|BRCA - Breast invasive adenocarcinoma(365;0.00435)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0169)|Lung(427;0.199)														---	---	---	---
PANK4	55229	broad.mit.edu	37	1	2452494	2452494	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2452494delG	uc001ajm.1	-						PANK4_uc010nza.1_Intron	NM_018216	NP_060686			pantothenate kinase 4						coenzyme A biosynthetic process	cytoplasm	ATP binding|pantothenate kinase activity			upper_aerodigestive_tract(1)|large_intestine(1)|ovary(1)	3	all_cancers(77;0.000158)|all_epithelial(69;8.01e-05)|all_lung(157;0.0212)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;3.18e-20)|all_lung(118;1.67e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;1.54e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.95e-23)|GBM - Glioblastoma multiforme(42;2.81e-08)|Colorectal(212;4.25e-05)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.00445)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.201)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	2616116	2616116	+	IGR	DEL	G	-	-	rs6683769	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2616116delG								MMEL1 (51635 upstream) : ACTRT2 (321930 downstream)																																			---	---	---	---
PRDM16	63976	broad.mit.edu	37	1	3070642	3070645	+	Intron	DEL	TGTC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3070642_3070645delTGTC	uc001akf.2	+						PRDM16_uc001akc.2_Intron|PRDM16_uc001akd.2_Intron|PRDM16_uc001ake.2_Intron|PRDM16_uc009vlh.2_Intron	NM_022114	NP_071397			PR domain containing 16 isoform 1						brown fat cell differentiation|negative regulation of granulocyte differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of cellular respiration|transcription, DNA-dependent	transcriptional repressor complex	protein binding|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			lung(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)				T	EVI1	MDS|AML								---	---	---	---
PRDM16	63976	broad.mit.edu	37	1	3268312	3268312	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3268312delC	uc001akf.2	+						PRDM16_uc001akc.2_Intron|PRDM16_uc001akd.2_Intron|PRDM16_uc001ake.2_Intron|PRDM16_uc009vlh.2_Intron	NM_022114	NP_071397			PR domain containing 16 isoform 1						brown fat cell differentiation|negative regulation of granulocyte differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of cellular respiration|transcription, DNA-dependent	transcriptional repressor complex	protein binding|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			lung(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)				T	EVI1	MDS|AML								---	---	---	---
PRDM16	63976	broad.mit.edu	37	1	3280527	3280527	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3280527delC	uc001akf.2	+						PRDM16_uc001akc.2_Intron|PRDM16_uc001akd.2_Intron|PRDM16_uc001ake.2_Intron|PRDM16_uc009vlh.2_Intron	NM_022114	NP_071397			PR domain containing 16 isoform 1						brown fat cell differentiation|negative regulation of granulocyte differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of cellular respiration|transcription, DNA-dependent	transcriptional repressor complex	protein binding|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			lung(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)				T	EVI1	MDS|AML								---	---	---	---
MEGF6	1953	broad.mit.edu	37	1	3502708	3502709	+	Intron	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3502708_3502709delTG	uc001akl.2	-							NM_001409	NP_001400			EGF-like-domain, multiple 3 precursor							extracellular region	calcium ion binding			large_intestine(1)	1	all_cancers(77;0.00681)|all_epithelial(69;0.00301)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.105)	all_epithelial(116;7.41e-22)|all_lung(118;8.3e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.78e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.86e-22)|GBM - Glioblastoma multiforme(42;1.96e-12)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000448)|BRCA - Breast invasive adenocarcinoma(365;0.000779)|KIRC - Kidney renal clear cell carcinoma(229;0.00645)|STAD - Stomach adenocarcinoma(132;0.00669)|Lung(427;0.213)														---	---	---	---
MEGF6	1953	broad.mit.edu	37	1	3515068	3515069	+	Intron	INS	-	C	C	rs138056953	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3515068_3515069insC	uc001akl.2	-							NM_001409	NP_001400			EGF-like-domain, multiple 3 precursor							extracellular region	calcium ion binding			large_intestine(1)	1	all_cancers(77;0.00681)|all_epithelial(69;0.00301)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.105)	all_epithelial(116;7.41e-22)|all_lung(118;8.3e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.78e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.86e-22)|GBM - Glioblastoma multiforme(42;1.96e-12)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000448)|BRCA - Breast invasive adenocarcinoma(365;0.000779)|KIRC - Kidney renal clear cell carcinoma(229;0.00645)|STAD - Stomach adenocarcinoma(132;0.00669)|Lung(427;0.213)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	4416976	4416976	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4416976delC								LOC100133612 (583099 upstream) : LOC284661 (55135 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	4681105	4681105	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4681105delT								LOC284661 (196361 upstream) : AJAP1 (34000 downstream)																																			---	---	---	---
AJAP1	55966	broad.mit.edu	37	1	4809966	4809966	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4809966delT	uc001alm.1	+						AJAP1_uc001aln.2_Intron	NM_001042478	NP_001035943			adherens junction associated protein 1						cell adhesion	adherens junction|apical plasma membrane|basolateral plasma membrane|integral to membrane				lung(1)	1	all_cancers(77;0.071)|Ovarian(185;0.0721)	all_cancers(23;1.77e-36)|all_epithelial(116;1.26e-21)|all_lung(118;3.51e-08)|Lung NSC(185;3.47e-06)|all_neural(13;8.84e-06)|all_hematologic(16;7.61e-05)|Breast(487;0.000507)|Renal(390;0.0007)|Colorectal(325;0.00117)|Hepatocellular(190;0.0071)|Glioma(11;0.0155)|Myeloproliferative disorder(586;0.0258)|Ovarian(437;0.0409)|Lung SC(97;0.133)|Medulloblastoma(700;0.215)		Epithelial(90;3.89e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.97e-19)|GBM - Glioblastoma multiforme(42;3.71e-19)|Colorectal(212;4.57e-06)|COAD - Colon adenocarcinoma(227;0.00019)|Kidney(185;0.000969)|BRCA - Breast invasive adenocarcinoma(365;0.00122)|STAD - Stomach adenocarcinoma(132;0.00578)|KIRC - Kidney renal clear cell carcinoma(229;0.0126)|READ - Rectum adenocarcinoma(331;0.0689)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	4877857	4877857	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4877857delA								AJAP1 (34007 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	4949124	4949125	+	IGR	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4949124_4949125insC								AJAP1 (105274 upstream) : NPHP4 (973745 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	5090863	5090863	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5090863delC								AJAP1 (247013 upstream) : NPHP4 (832007 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	5532620	5532621	+	IGR	DEL	GT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5532620_5532621delGT								AJAP1 (688770 upstream) : NPHP4 (390249 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	5713679	5713679	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5713679delA	uc001alp.1	-											Homo sapiens cDNA FLJ43088 fis, clone BRTHA3025826.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	5735266	5735266	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:5735266delC								AJAP1 (891416 upstream) : NPHP4 (187604 downstream)																																			---	---	---	---
RPL22	6146	broad.mit.edu	37	1	6257785	6257785	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6257785delT	uc001amd.2	-	2	90	c.44delA	c.(43-45)AAGfs	p.K15fs	RPL22_uc001ame.2_Frame_Shift_Del_p.K15fs	NM_000983	NP_000974	P35268	RL22_HUMAN	ribosomal protein L22 proprotein	15					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	heparin binding|RNA binding|structural constituent of ribosome				0	Ovarian(185;0.0634)	all_cancers(23;2.78e-38)|all_epithelial(116;8.88e-22)|all_lung(118;7.95e-08)|Lung NSC(185;1.6e-06)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211)		Epithelial(90;4.53e-38)|GBM - Glioblastoma multiforme(13;3.33e-32)|OV - Ovarian serous cystadenocarcinoma(86;2.8e-19)|Colorectal(212;6.8e-08)|COAD - Colon adenocarcinoma(227;8.04e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00311)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)				T	RUNX1	AML|CML								---	---	---	---
ICMT	23463	broad.mit.edu	37	1	6282496	6282496	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6282496delA	uc001amk.2	-	5					ICMT_uc001aml.2_3'UTR	NM_012405	NP_036537			isoprenylcysteine carboxyl methyltransferase						protein targeting to membrane	endoplasmic reticulum membrane|integral to membrane|membrane fraction	protein C-terminal S-isoprenylcysteine carboxyl O-methyltransferase activity				0	Ovarian(185;0.0634)	all_cancers(23;5.85e-39)|all_epithelial(116;2.4e-22)|all_lung(118;2.65e-08)|Lung NSC(185;6.45e-07)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000688)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211)		Epithelial(90;5.52e-38)|GBM - Glioblastoma multiforme(13;6.51e-32)|OV - Ovarian serous cystadenocarcinoma(86;3.03e-19)|Colorectal(212;7.08e-08)|COAD - Colon adenocarcinoma(227;8.35e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(365;0.00109)|STAD - Stomach adenocarcinoma(132;0.00313)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)														---	---	---	---
ICMT	23463	broad.mit.edu	37	1	6297516	6297516	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6297516delT	uc001amk.2	-						ICMT_uc001aml.2_5'Flank|uc001amm.2_5'Flank	NM_012405	NP_036537			isoprenylcysteine carboxyl methyltransferase						protein targeting to membrane	endoplasmic reticulum membrane|integral to membrane|membrane fraction	protein C-terminal S-isoprenylcysteine carboxyl O-methyltransferase activity				0	Ovarian(185;0.0634)	all_cancers(23;5.85e-39)|all_epithelial(116;2.4e-22)|all_lung(118;2.65e-08)|Lung NSC(185;6.45e-07)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000688)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211)		Epithelial(90;5.52e-38)|GBM - Glioblastoma multiforme(13;6.51e-32)|OV - Ovarian serous cystadenocarcinoma(86;3.03e-19)|Colorectal(212;7.08e-08)|COAD - Colon adenocarcinoma(227;8.35e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(365;0.00109)|STAD - Stomach adenocarcinoma(132;0.00313)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)														---	---	---	---
ESPN	83715	broad.mit.edu	37	1	6510453	6510454	+	Intron	INS	-	C	C	rs9435259		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6510453_6510454insC	uc001amy.2	+						ESPN_uc001amz.2_Intron	NM_031475	NP_113663			espin						sensory perception of sound	brush border|cytoplasm|filamentous actin|stereocilium	actin filament binding|SH3 domain binding				0	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;3.6e-37)|all_epithelial(116;2.56e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|all_hematologic(16;6.92e-06)|Colorectal(325;4.47e-05)|Acute lymphoblastic leukemia(12;4.92e-05)|Breast(487;7.61e-05)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)		Epithelial(90;1.82e-35)|GBM - Glioblastoma multiforme(13;3e-28)|Kidney(185;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(229;5.63e-08)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;1.41e-05)|BRCA - Breast invasive adenocarcinoma(365;0.000109)|STAD - Stomach adenocarcinoma(132;0.00167)|Lung(427;0.0108)|LUSC - Lung squamous cell carcinoma(448;0.0253)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
PLEKHG5	57449	broad.mit.edu	37	1	6580572	6580572	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6580572delT	uc001anp.1	-						PLEKHG5_uc001anq.1_5'Flank	NM_198681	NP_941374			pleckstrin homology domain containing family G						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|perinuclear region of cytoplasm	Rho guanyl-nucleotide exchange factor activity|signal transducer activity			liver(1)	1	Ovarian(185;0.02)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;5.51e-35)|GBM - Glioblastoma multiforme(13;3.57e-27)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00159)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
THAP3	90326	broad.mit.edu	37	1	6693977	6693977	+	Intron	DEL	A	-	-	rs3215503		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6693977delA	uc001aoe.1	+							NM_138350	NP_612359			THAP domain containing, apoptosis associated								DNA binding|metal ion binding				0	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;7.39e-28)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;1.29e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000513)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0642)														---	---	---	---
DNAJC11	55735	broad.mit.edu	37	1	6742975	6742975	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6742975delA	uc001aof.2	-						DNAJC11_uc010nzt.1_5'Flank|DNAJC11_uc001aog.2_Intron|DNAJC11_uc010nzu.1_Intron	NM_018198	NP_060668			DnaJ (Hsp40) homolog, subfamily C, member 11						protein folding		heat shock protein binding|unfolded protein binding			ovary(1)|skin(1)	2	Ovarian(185;0.0265)|all_lung(157;0.154)	all_cancers(23;1.97e-27)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;2.34e-07)|COAD - Colon adenocarcinoma(227;2.05e-05)|Kidney(185;7.67e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000639)|KIRC - Kidney renal clear cell carcinoma(229;0.00128)|STAD - Stomach adenocarcinoma(132;0.00179)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
CAMTA1	23261	broad.mit.edu	37	1	7063679	7063680	+	Intron	INS	-	TG	TG	rs147407695	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7063679_7063680insTG	uc001aoi.2	+							NM_015215	NP_056030			calmodulin-binding transcription activator 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)														---	---	---	---
CAMTA1	23261	broad.mit.edu	37	1	7196587	7196587	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7196587delA	uc001aoi.2	+							NM_015215	NP_056030			calmodulin-binding transcription activator 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)														---	---	---	---
CAMTA1	23261	broad.mit.edu	37	1	7219773	7219773	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7219773delA	uc001aoi.2	+							NM_015215	NP_056030			calmodulin-binding transcription activator 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)														---	---	---	---
CAMTA1	23261	broad.mit.edu	37	1	7543762	7543762	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7543762delG	uc001aoi.2	+							NM_015215	NP_056030			calmodulin-binding transcription activator 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)														---	---	---	---
CAMTA1	23261	broad.mit.edu	37	1	7719594	7719594	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7719594delA	uc001aoi.2	+							NM_015215	NP_056030			calmodulin-binding transcription activator 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)														---	---	---	---
CAMTA1	23261	broad.mit.edu	37	1	7799276	7799276	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7799276delA	uc001aoi.2	+						CAMTA1_uc010nzv.1_Intron|CAMTA1_uc001aok.3_Intron|CAMTA1_uc001aoj.2_Intron	NM_015215	NP_056030			calmodulin-binding transcription activator 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	8065713	8065714	+	IGR	DEL	TT	-	-	rs71567341		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8065713_8065714delTT								PARK7 (20372 upstream) : ERRFI1 (6066 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	8110461	8110461	+	IGR	DEL	T	-	-	rs113270512		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8110461delT								ERRFI1 (24068 upstream) : SLC45A1 (273929 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	8257017	8257017	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8257017delA								ERRFI1 (170624 upstream) : SLC45A1 (127373 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	8348323	8348324	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8348323_8348324delTT								ERRFI1 (261930 upstream) : SLC45A1 (36066 downstream)																																			---	---	---	---
RERE	473	broad.mit.edu	37	1	8568551	8568551	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8568551delA	uc001ape.2	-						RERE_uc001apf.2_Intron|RERE_uc010nzx.1_Intron|RERE_uc001aph.1_Intron	NM_012102	NP_036234			atrophin-1 like protein isoform a						multicellular organismal development|NLS-bearing substrate import into nucleus	mitochondrion	poly-glutamine tract binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	8910086	8910086	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8910086delT								RERE (32387 upstream) : ENO1 (10977 downstream)																																			---	---	---	---
SLC25A33	84275	broad.mit.edu	37	1	9633515	9633515	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9633515delT	uc001apw.2	+						SLC25A33_uc001apx.2_Intron	NM_032315	NP_115691			mitochondrial carrier protein MGC4399						transport	integral to membrane|mitochondrial inner membrane					0	all_lung(157;0.246)	all_epithelial(116;1.16e-18)|all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Breast(348;0.00191)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.01e-08)|COAD - Colon adenocarcinoma(227;1.44e-05)|Kidney(185;0.000262)|KIRC - Kidney renal clear cell carcinoma(229;0.000957)|BRCA - Breast invasive adenocarcinoma(304;0.0019)|STAD - Stomach adenocarcinoma(132;0.00355)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
PIK3CD	5293	broad.mit.edu	37	1	9755031	9755032	+	Intron	DEL	AG	-	-	rs113822530		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9755031_9755032delAG	uc001aqb.3	+						PIK3CD_uc001aqa.2_Intron|PIK3CD_uc010oaf.1_Intron	NM_005026	NP_005017			catalytic phosphatidylinositol 3-kinase delta						phosphatidylinositol-mediated signaling|protein phosphorylation	phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			lung(4)|skin(2)|central_nervous_system(1)	7	all_lung(157;0.222)	all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0231)|Colorectal(212;7.52e-08)|COAD - Colon adenocarcinoma(227;1.78e-05)|Kidney(185;0.000322)|KIRC - Kidney renal clear cell carcinoma(229;0.00114)|BRCA - Breast invasive adenocarcinoma(304;0.0021)|STAD - Stomach adenocarcinoma(132;0.00395)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
CLSTN1	22883	broad.mit.edu	37	1	9829518	9829518	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9829518delA	uc001aqh.2	-						CLSTN1_uc001aqi.2_Intron|CLSTN1_uc010oag.1_Intron	NM_001009566	NP_001009566			calsyntenin 1 isoform 1						homophilic cell adhesion	cell junction|cell projection|endoplasmic reticulum membrane|Golgi membrane|integral to membrane|nucleus|postsynaptic membrane	calcium ion binding			skin(1)	1	all_lung(157;0.222)	all_lung(284;4.03e-05)|Lung NSC(185;6.93e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;8.36e-08)|COAD - Colon adenocarcinoma(227;1.93e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|STAD - Stomach adenocarcinoma(132;0.00644)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
CLSTN1	22883	broad.mit.edu	37	1	9859709	9859710	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9859709_9859710delAA	uc001aqh.2	-						CLSTN1_uc001aqi.2_Intron|CLSTN1_uc010oag.1_Intron	NM_001009566	NP_001009566			calsyntenin 1 isoform 1						homophilic cell adhesion	cell junction|cell projection|endoplasmic reticulum membrane|Golgi membrane|integral to membrane|nucleus|postsynaptic membrane	calcium ion binding			skin(1)	1	all_lung(157;0.222)	all_lung(284;4.03e-05)|Lung NSC(185;6.93e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;8.36e-08)|COAD - Colon adenocarcinoma(227;1.93e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|STAD - Stomach adenocarcinoma(132;0.00644)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
NMNAT1	64802	broad.mit.edu	37	1	10044970	10044970	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10044970delT	uc001aqp.2	+	5						NM_022787	NP_073624			nicotinamide mononucleotide adenylyltransferase						water-soluble vitamin metabolic process	nucleoplasm	ATP binding|nicotinamide-nucleotide adenylyltransferase activity|nicotinate-nucleotide adenylyltransferase activity|protein binding				0		all_lung(284;0.000407)|Renal(390;0.000469)|Lung NSC(185;0.000577)|Colorectal(325;0.0062)|Breast(348;0.00686)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.31e-08)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(185;0.00028)|BRCA - Breast invasive adenocarcinoma(304;0.00032)|KIRC - Kidney renal clear cell carcinoma(229;0.00101)|STAD - Stomach adenocarcinoma(132;0.00908)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	10083151	10083151	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10083151delT								RBP7 (7074 upstream) : UBE4B (9865 downstream)																																			---	---	---	---
KIF1B	23095	broad.mit.edu	37	1	10297601	10297601	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10297601delT	uc001aqx.3	+						KIF1B_uc001aqv.3_Intron|KIF1B_uc001aqw.3_Intron|KIF1B_uc001aqy.2_Intron|KIF1B_uc001aqz.2_Intron|KIF1B_uc001ara.2_Intron|KIF1B_uc001arb.2_Intron|KIF1B_uc009vmt.2_Intron	NM_015074	NP_055889			kinesin family member 1B isoform b						anterograde axon cargo transport|apoptosis|neuromuscular synaptic transmission|neuron-neuron synaptic transmission	cytoplasmic vesicle membrane|microtubule|microtubule associated complex|mitochondrion	ATP binding|ATPase activity|kinesin binding|microtubule motor activity|protein binding			ovary(2)|upper_aerodigestive_tract(1)	3	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)														---	---	---	---
KIF1B	23095	broad.mit.edu	37	1	10391153	10391155	+	Intron	DEL	AAA	-	-	rs112706072		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10391153_10391155delAAA	uc001aqx.3	+						KIF1B_uc001aqw.3_Intron|KIF1B_uc001aqy.2_Intron|KIF1B_uc001aqz.2_Intron|KIF1B_uc001ara.2_Intron|KIF1B_uc001arb.2_Intron	NM_015074	NP_055889			kinesin family member 1B isoform b						anterograde axon cargo transport|apoptosis|neuromuscular synaptic transmission|neuron-neuron synaptic transmission	cytoplasmic vesicle membrane|microtubule|microtubule associated complex|mitochondrion	ATP binding|ATPase activity|kinesin binding|microtubule motor activity|protein binding			ovary(2)|upper_aerodigestive_tract(1)	3	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)														---	---	---	---
PGD	5226	broad.mit.edu	37	1	10463298	10463298	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10463298delT	uc001arc.2	+						PGD_uc001ard.2_Intron|PGD_uc010oak.1_Intron|PGD_uc010oal.1_Intron	NM_002631	NP_002622			phosphogluconate dehydrogenase						pentose-phosphate shunt, oxidative branch	cytosol	NADP binding|phosphogluconate dehydrogenase (decarboxylating) activity|protein binding			ovary(1)	1	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.14e-07)|COAD - Colon adenocarcinoma(227;7.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000294)|Kidney(185;0.000728)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(132;0.00832)|READ - Rectum adenocarcinoma(331;0.0487)														---	---	---	---
MASP2	10747	broad.mit.edu	37	1	11105065	11105065	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11105065delG	uc001aru.2	-						MASP2_uc001arv.2_Intron|MASP2_uc001arw.2_3'UTR	NM_006610	NP_006601			mannan-binding lectin serine protease 2 isoform						complement activation, classical pathway|complement activation, lectin pathway|proteolysis	extracellular region	calcium ion binding|calcium-dependent protein binding|serine-type endopeptidase activity			ovary(2)|pancreas(1)|skin(1)	4	Ovarian(185;0.249)	Lung NSC(185;1.04e-05)|all_lung(284;1.31e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.071)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.12e-07)|COAD - Colon adenocarcinoma(227;7.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|READ - Rectum adenocarcinoma(331;0.0487)|STAD - Stomach adenocarcinoma(313;0.192)														---	---	---	---
MTOR	2475	broad.mit.edu	37	1	11187619	11187619	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11187619delT	uc001asd.2	-						MTOR_uc001asc.2_Intron	NM_004958	NP_004949			FK506 binding protein 12-rapamycin associated						cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(7)|lung(6)|ovary(6)|skin(3)|kidney(3)|large_intestine(2)|breast(2)	29																		---	---	---	---
MTOR	2475	broad.mit.edu	37	1	11314203	11314204	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11314203_11314204delTT	uc001asd.2	-							NM_004958	NP_004949			FK506 binding protein 12-rapamycin associated						cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(7)|lung(6)|ovary(6)|skin(3)|kidney(3)|large_intestine(2)|breast(2)	29																		---	---	---	---
MTOR	2475	broad.mit.edu	37	1	11319566	11319566	+	Intron	DEL	T	-	-	rs17229137		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11319566delT	uc001asd.2	-							NM_004958	NP_004949			FK506 binding protein 12-rapamycin associated						cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(7)|lung(6)|ovary(6)|skin(3)|kidney(3)|large_intestine(2)|breast(2)	29																		---	---	---	---
PTCHD2	57540	broad.mit.edu	37	1	11541096	11541099	+	Intron	DEL	TCTC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11541096_11541099delTCTC	uc001ash.3	+						PTCHD2_uc009vmz.1_Intron	NM_020780	NP_065831			patched domain containing 2						cholesterol homeostasis|regulation of lipid transport|smoothened signaling pathway	endoplasmic reticulum|integral to membrane|nuclear membrane	hedgehog receptor activity			skin(3)|ovary(2)|pancreas(1)|breast(1)	7	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)														---	---	---	---
MTHFR	4524	broad.mit.edu	37	1	11862400	11862400	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11862400delA	uc001atc.1	-						MTHFR_uc001atb.1_Intron	NM_005957	NP_005948			5,10-methylenetetrahydrofolate reductase						blood circulation|folic acid metabolic process	cytosol	methylenetetrahydrofolate reductase (NADPH) activity|protein binding				0	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Benazepril(DB00542)|Cyanocobalamin(DB00115)|Folic Acid(DB00158)|L-Methionine(DB00134)|Menadione(DB00170)|Methotrexate(DB00563)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165)|Raltitrexed(DB00293)|Riboflavin(DB00140)|S-Adenosylmethionine(DB00118)|Tetrahydrofolic acid(DB00116)													---	---	---	---
KIAA2013	90231	broad.mit.edu	37	1	11987198	11987198	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11987198delA	uc001atk.2	-						KIAA2013_uc001atl.1_5'Flank	NM_138346	NP_612355			hypothetical protein LOC90231 precursor							integral to membrane				ovary(1)	1	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00149)|all_lung(284;0.00189)|Breast(348;0.00586)|Colorectal(325;0.0062)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0556)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.88e-06)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	11991166	11991166	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11991166delA								KIAA2013 (4686 upstream) : PLOD1 (3580 downstream)																																			---	---	---	---
MFN2	9927	broad.mit.edu	37	1	12066563	12066563	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12066563delC	uc001atn.3	+						MFN2_uc009vni.2_Intron	NM_014874	NP_055689			mitofusin 2						blood coagulation|mitochondrial fusion|mitochondrial membrane organization|mitochondrion localization|negative regulation of Ras protein signal transduction|negative regulation of smooth muscle cell proliferation|protein targeting to mitochondrion	cytosol|integral to membrane|intrinsic to mitochondrial outer membrane	GTP binding|GTPase activity|ubiquitin protein ligase binding			ovary(1)	1	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;7.25e-06)|COAD - Colon adenocarcinoma(227;0.000302)|BRCA - Breast invasive adenocarcinoma(304;0.000329)|Kidney(185;0.000896)|KIRC - Kidney renal clear cell carcinoma(229;0.00274)|STAD - Stomach adenocarcinoma(313;0.00773)|READ - Rectum adenocarcinoma(331;0.0656)														---	---	---	---
TNFRSF8	943	broad.mit.edu	37	1	12148389	12148389	+	Intron	DEL	G	-	-	rs34475937		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12148389delG	uc001atq.2	+						TNFRSF8_uc010obc.1_Intron	NM_001243	NP_001234			tumor necrosis factor receptor superfamily,						cellular response to mechanical stimulus|negative regulation of cell proliferation|positive regulation of apoptosis|positive regulation of TRAIL biosynthetic process|positive regulation of tumor necrosis factor biosynthetic process	cytoplasm|integral to membrane|plasma membrane				skin(2)|ovary(1)|pancreas(1)|central_nervous_system(1)	5	Ovarian(185;0.249)	Lung NSC(185;8.71e-05)|all_lung(284;9.89e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	12211550	12211552	+	IGR	DEL	CTC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12211550_12211552delCTC								TNFRSF8 (7288 upstream) : TNFRSF1B (15508 downstream)																																			---	---	---	---
VPS13D	55187	broad.mit.edu	37	1	12378663	12378664	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12378663_12378664delTT	uc001atv.2	+						VPS13D_uc001atw.2_Intron|VPS13D_uc001atx.2_Intron|VPS13D_uc001aty.1_Intron	NM_015378	NP_056193			vacuolar protein sorting 13D isoform 1						protein localization					ovary(4)|pancreas(1)	5	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	12574658	12574658	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12574658delT								VPS13D (2562 upstream) : DHRS3 (53282 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	12594167	12594168	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12594167_12594168insT								VPS13D (22071 upstream) : DHRS3 (33772 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	12597265	12597265	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12597265delT								VPS13D (25169 upstream) : DHRS3 (30675 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	12619999	12619999	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12619999delT								VPS13D (47903 upstream) : DHRS3 (7941 downstream)																																			---	---	---	---
C1orf158	93190	broad.mit.edu	37	1	12808638	12808639	+	Intron	DEL	AA	-	-	rs145631958		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12808638_12808639delAA	uc001auh.2	+						C1orf158_uc010obe.1_Intron	NM_152290	NP_689503			hypothetical protein LOC93190											ovary(1)|central_nervous_system(1)|skin(1)	3	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.06e-06)|COAD - Colon adenocarcinoma(227;0.000273)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00575)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
PRAMEF1	65121	broad.mit.edu	37	1	12855339	12855340	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12855339_12855340delAA	uc001auj.1	+							NM_023013	NP_075389			PRAME family member 1												0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
PRAMEF11	440560	broad.mit.edu	37	1	12891095	12891096	+	Intron	DEL	GA	-	-	rs139889932		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12891095_12891096delGA	uc001auk.2	-							NM_001146344	NP_001139816			PRAME family member 11												0																		---	---	---	---
PRAMEF2	65122	broad.mit.edu	37	1	12914197	12914198	+	5'Flank	INS	-	T	T	rs147592762	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12914197_12914198insT	uc001aum.1	+							NM_023014	NP_075390			PRAME family member 2												0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
PRAMEF5	343068	broad.mit.edu	37	1	13012832	13012833	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13012832_13012833delAA	uc001aur.2	-							NM_001013407	NP_001013425			PRAME family member 5												0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	13123163	13123164	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13123163_13123164delAA								PRAMEF5 (5412 upstream) : LOC440563 (59797 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	13218499	13218499	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13218499delA								LOC440563 (34532 upstream) : PRAMEF3 (110334 downstream)																																			---	---	---	---
PRAMEF17	391004	broad.mit.edu	37	1	13719052	13719052	+	3'UTR	DEL	T	-	-	rs141370897	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13719052delT	uc009vnz.1	+	3						NM_001099851	NP_001093321			PRAME family member 17												0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;9.86e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|COAD - Colon adenocarcinoma(227;0.000502)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
PDPN	10630	broad.mit.edu	37	1	13924304	13924305	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13924304_13924305insA	uc001avd.2	+						PDPN_uc001avc.2_Intron|PDPN_uc009vob.2_Intron|PDPN_uc009voc.2_Intron|PDPN_uc001ave.2_Intron|PDPN_uc001avf.2_Intron	NM_006474	NP_006465			lung type-I cell membrane-associated						cell morphogenesis|lymphangiogenesis|regulation of cell shape	filopodium membrane|integral to plasma membrane|lamellipodium membrane|microvillus membrane|ruffle membrane				ovary(2)	2	Ovarian(185;0.249)	all_lung(284;2.29e-05)|Lung NSC(185;4.37e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00969)|Colorectal(212;4.48e-06)|COAD - Colon adenocarcinoma(227;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000347)|Kidney(185;0.00087)|KIRC - Kidney renal clear cell carcinoma(229;0.0027)|STAD - Stomach adenocarcinoma(313;0.00802)|READ - Rectum adenocarcinoma(331;0.0678)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	14424527	14424527	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14424527delT								PRDM2 (272955 upstream) : KAZ (500686 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	14429409	14429410	+	IGR	INS	-	T	T	rs55657165	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14429409_14429410insT								PRDM2 (277837 upstream) : KAZ (495803 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	14620826	14620826	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14620826delT								PRDM2 (469254 upstream) : KAZ (304387 downstream)																																			---	---	---	---
KAZ	23254	broad.mit.edu	37	1	15134269	15134269	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15134269delA	uc001avm.3	+						KAZ_uc009vog.1_Intron|KAZ_uc010obj.1_Intron	NM_201628	NP_963922			kazrin isoform E						keratinization	cornified envelope|cytoplasm|desmosome|nucleus					0																		---	---	---	---
KAZ	23254	broad.mit.edu	37	1	15323501	15323501	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15323501delT	uc001avm.3	+						KAZ_uc009vog.1_Intron|KAZ_uc010obj.1_Intron|KAZ_uc001avo.2_Intron|KAZ_uc001avp.2_Intron|KAZ_uc001avq.2_Intron|KAZ_uc001avr.2_Intron	NM_201628	NP_963922			kazrin isoform E						keratinization	cornified envelope|cytoplasm|desmosome|nucleus					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	15927145	15927145	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15927145delT								DNAJC16 (8273 upstream) : DDI2 (16925 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	16117306	16117306	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16117306delA								FBLIM1 (2875 upstream) : UQCRHL (16351 downstream)																																			---	---	---	---
CLCNKB	1188	broad.mit.edu	37	1	16383078	16383078	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16383078delG	uc001axw.3	+						FAM131C_uc010obz.1_Intron|CLCNKB_uc001axx.3_Intron|CLCNKB_uc001axy.3_Intron	NM_000085	NP_000076			chloride channel Kb isoform 1						excretion	chloride channel complex|integral to plasma membrane	voltage-gated chloride channel activity			skin(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)												OREG0013133	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
EPHA2	1969	broad.mit.edu	37	1	16457127	16457129	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16457127_16457129delTTT	uc001aya.1	-							NM_004431	NP_004422			ephrin receptor EphA2 precursor						activation of Rac GTPase activity|angiogenesis|apoptosis|cell chemotaxis|negative regulation of protein kinase B signaling cascade|positive regulation of establishment of protein localization in plasma membrane|protein kinase B signaling cascade|regulation of blood vessel endothelial cell migration|regulation of cell adhesion mediated by integrin|regulation of lamellipodium assembly|response to growth factor stimulus	focal adhesion|integral to plasma membrane|lamellipodium membrane|ruffle membrane	ATP binding|ephrin receptor activity|protein binding			lung(3)|central_nervous_system(3)|stomach(2)|ovary(2)	10		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649)	Dasatinib(DB01254)													---	---	---	---
EPHA2	1969	broad.mit.edu	37	1	16462199	16462199	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16462199delG	uc001aya.1	-	6	1516	c.1379delC	c.(1378-1380)CCGfs	p.P460fs	EPHA2_uc010oca.1_Frame_Shift_Del_p.P460fs	NM_004431	NP_004422	P29317	EPHA2_HUMAN	ephrin receptor EphA2 precursor	460	Extracellular (Potential).|Fibronectin type-III 2.				activation of Rac GTPase activity|angiogenesis|apoptosis|cell chemotaxis|negative regulation of protein kinase B signaling cascade|positive regulation of establishment of protein localization in plasma membrane|protein kinase B signaling cascade|regulation of blood vessel endothelial cell migration|regulation of cell adhesion mediated by integrin|regulation of lamellipodium assembly|response to growth factor stimulus	focal adhesion|integral to plasma membrane|lamellipodium membrane|ruffle membrane	ATP binding|ephrin receptor activity|protein binding			lung(3)|central_nervous_system(3)|stomach(2)|ovary(2)	10		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649)	Dasatinib(DB01254)													---	---	---	---
ARHGEF19	128272	broad.mit.edu	37	1	16533831	16533834	+	Intron	DEL	ATTC	-	-	rs113001974		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16533831_16533834delATTC	uc001ayc.1	-						ARHGEF19_uc009voo.1_5'Flank|ARHGEF19_uc001ayb.1_5'Flank	NM_153213	NP_694945			Rho guanine nucleotide exchange factor (GEF) 19						regulation of actin cytoskeleton organization	intracellular	GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			skin(2)|ovary(1)	3		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|Colorectal(212;3.48e-07)|COAD - Colon adenocarcinoma(227;2.19e-05)|BRCA - Breast invasive adenocarcinoma(304;9.46e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.0117)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	16548352	16548355	+	IGR	DEL	GGAT	-	-	rs144038097		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16548352_16548355delGGAT								ARHGEF19 (9248 upstream) : C1orf89 (9828 downstream)																																			---	---	---	---
C1orf144	26099	broad.mit.edu	37	1	16695982	16695982	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16695982delT	uc001aym.3	+						C1orf144_uc010ocb.1_Intron|C1orf144_uc001ayi.3_Intron|C1orf144_uc001ayk.3_Intron	NM_001114600	NP_001108072			putative MAPK activating protein PM20,PM21												0		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00475)|all_lung(284;0.00671)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(227;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;4.12e-05)|Kidney(64;0.00018)|KIRC - Kidney renal clear cell carcinoma(64;0.00267)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
SPATA21	374955	broad.mit.edu	37	1	16735795	16735795	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16735795delG	uc001ayn.2	-						SPATA21_uc001ayl.1_Intron|SPATA21_uc010occ.1_Intron	NM_198546	NP_940948			spermatogenesis associated 21								calcium ion binding			ovary(2)|breast(1)	3		Colorectal(325;0.000147)|Renal(390;0.00145)|Lung NSC(340;0.00215)|Breast(348;0.00224)|all_lung(284;0.00351)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(227;1.15e-05)|BRCA - Breast invasive adenocarcinoma(304;4.2e-05)|Kidney(64;0.000183)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.0122)|READ - Rectum adenocarcinoma(331;0.0651)														---	---	---	---
NBPF1	55672	broad.mit.edu	37	1	16926643	16926643	+	Intron	DEL	C	-	-	rs59187254		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16926643delC	uc009vos.1	-						NBPF1_uc001aza.3_RNA	NM_017940	NP_060410			hypothetical protein LOC55672							cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)														---	---	---	---
MST1P2	11209	broad.mit.edu	37	1	16976869	16976869	+	RNA	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16976869delT	uc010och.1	+	14		c.2590delT			MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_RNA|MST1P2_uc001azm.3_RNA	NR_027504				Homo sapiens cDNA FLJ43241 fis, clone HEART1000010, weakly  similar to Hepatocyte growth factor-like protein precursor.												0																		---	---	---	---
ESPNP	284729	broad.mit.edu	37	1	17025261	17025262	+	Intron	INS	-	A	A	rs148465149	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17025261_17025262insA	uc001azn.1	-							NR_026567				RecName: Full=Espin; AltName: Full=Ectoplasmic specialization protein; AltName: Full=Autosomal recessive deafness type 36 protein;												0																		---	---	---	---
ESPNP	284729	broad.mit.edu	37	1	17027202	17027203	+	Intron	INS	-	C	C	rs141013108	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17027202_17027203insC	uc001azn.1	-							NR_026567				RecName: Full=Espin; AltName: Full=Ectoplasmic specialization protein; AltName: Full=Autosomal recessive deafness type 36 protein;												0																		---	---	---	---
CROCC	9696	broad.mit.edu	37	1	17203051	17203051	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17203051delA	uc009voy.1	+											Homo sapiens mRNA for KIAA0445 protein, partial cds.						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)														---	---	---	---
CROCC	9696	broad.mit.edu	37	1	17205586	17205586	+	Intron	DEL	A	-	-	rs67126650		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17205586delA	uc009voy.1	+											Homo sapiens mRNA for KIAA0445 protein, partial cds.						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)														---	---	---	---
CROCC	9696	broad.mit.edu	37	1	17206240	17206240	+	Intron	DEL	A	-	-	rs111577845		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17206240delA	uc009voy.1	+											Homo sapiens mRNA for KIAA0445 protein, partial cds.						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)														---	---	---	---
CROCC	9696	broad.mit.edu	37	1	17254992	17254992	+	Intron	DEL	T	-	-	rs113967647		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17254992delT	uc001azt.2	+						CROCC_uc009voy.1_Intron|CROCC_uc009voz.1_Intron	NM_014675	NP_055490			ciliary rootlet coiled-coil						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)														---	---	---	---
CROCC	9696	broad.mit.edu	37	1	17268504	17268504	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17268504delT	uc001azt.2	+						CROCC_uc009voz.1_Intron|CROCC_uc001azu.2_Intron	NM_014675	NP_055490			ciliary rootlet coiled-coil						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)														---	---	---	---
CROCC	9696	broad.mit.edu	37	1	17272607	17272607	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17272607delT	uc001azt.2	+						CROCC_uc009voz.1_Intron|CROCC_uc001azu.2_Intron	NM_014675	NP_055490			ciliary rootlet coiled-coil						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)														---	---	---	---
CROCC	9696	broad.mit.edu	37	1	17284494	17284494	+	Intron	DEL	T	-	-	rs66678901		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17284494delT	uc001azt.2	+						CROCC_uc001azu.2_Intron	NM_014675	NP_055490			ciliary rootlet coiled-coil						cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)														---	---	---	---
SDHB	6390	broad.mit.edu	37	1	17368424	17368425	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17368424_17368425insT	uc001bae.2	-							NM_003000	NP_002991			succinate dehydrogenase complex, subunit B, iron						respiratory electron transport chain|transport|tricarboxylic acid cycle	mitochondrial respiratory chain complex II	2 iron, 2 sulfur cluster binding|3 iron, 4 sulfur cluster binding|4 iron, 4 sulfur cluster binding|electron carrier activity|metal ion binding|protein binding|succinate dehydrogenase (ubiquinone) activity|ubiquinone binding			breast(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00054)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0049)|COAD - Colon adenocarcinoma(227;1.18e-05)|BRCA - Breast invasive adenocarcinoma(304;2.41e-05)|Kidney(64;0.000188)|KIRC - Kidney renal clear cell carcinoma(64;0.00273)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.19)	Succinic acid(DB00139)			Mis|N|F			paraganglioma|pheochromocytoma			Familial_Paragangliomas|Carney-Stratakis_syndrome|Cowden_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	1	17528566	17528567	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17528566_17528567delTT								PADI2 (82618 upstream) : PADI1 (3054 downstream)																																			---	---	---	---
PADI6	353238	broad.mit.edu	37	1	17702471	17702471	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17702471delT	uc001bak.1	+							NM_207421	NP_997304			peptidylarginine deiminase type 6						peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm|nucleus	calcium ion binding|protein-arginine deiminase activity			breast(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;7.59e-06)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.0134)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)													---	---	---	---
PADI6	353238	broad.mit.edu	37	1	17707166	17707166	+	Intron	DEL	A	-	-	rs34518731		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17707166delA	uc001bak.1	+							NM_207421	NP_997304			peptidylarginine deiminase type 6						peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm|nucleus	calcium ion binding|protein-arginine deiminase activity			breast(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;7.59e-06)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.0134)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)													---	---	---	---
RCC2	55920	broad.mit.edu	37	1	17744180	17744180	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17744180delA	uc001bal.2	-						RCC2_uc001bam.2_Intron	NM_001136204	NP_001129676			regulator of chromosome condensation 2						cell division|mitotic prometaphase	chromosome, centromeric region|cytosol|microtubule|nucleolus|spindle					0		Colorectal(325;0.000147)|Breast(348;0.00122)|Renal(390;0.00145)|all_lung(284;0.0054)|Lung NSC(340;0.00566)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00492)|BRCA - Breast invasive adenocarcinoma(304;7.69e-06)|COAD - Colon adenocarcinoma(227;1.19e-05)|Kidney(64;0.000189)|KIRC - Kidney renal clear cell carcinoma(64;0.00273)|STAD - Stomach adenocarcinoma(196;0.0135)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.19)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	18067661	18067662	+	IGR	INS	-	TCAT	TCAT	rs138747149	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18067661_18067662insTCAT								ARHGEF10L (43292 upstream) : ACTL8 (14146 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	18239322	18239323	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18239322_18239323insT								ACTL8 (85766 upstream) : IGSF21 (194917 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	18756165	18756165	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18756165delT								IGSF21 (51189 upstream) : KLHDC7A (51259 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	19329963	19329963	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19329963delA								IFFO2 (47137 upstream) : UBR4 (68641 downstream)																																			---	---	---	---
UBR4	23352	broad.mit.edu	37	1	19457413	19457413	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19457413delT	uc001bbi.2	-						UBR4_uc001bbk.1_Intron	NM_020765	NP_065816			retinoblastoma-associated factor 600						interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(10)|ovary(7)|breast(4)|pancreas(2)|skin(2)	25		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)														---	---	---	---
UBR4	23352	broad.mit.edu	37	1	19494743	19494743	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19494743delA	uc001bbi.2	-						UBR4_uc001bbm.1_Intron	NM_020765	NP_065816			retinoblastoma-associated factor 600						interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(10)|ovary(7)|breast(4)|pancreas(2)|skin(2)	25		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)														---	---	---	---
UBR4	23352	broad.mit.edu	37	1	19514156	19514156	+	Intron	DEL	A	-	-	rs144801649		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19514156delA	uc001bbi.2	-							NM_020765	NP_065816			retinoblastoma-associated factor 600						interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(10)|ovary(7)|breast(4)|pancreas(2)|skin(2)	25		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)														---	---	---	---
MRTO4	51154	broad.mit.edu	37	1	19581443	19581446	+	Intron	DEL	AAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19581443_19581446delAAAA	uc001bbs.2	+							NM_016183	NP_057267			mRNA turnover 4 homolog						ribosome biogenesis	nuclear membrane|nucleolus					0		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.87e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00301)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
CAPZB	832	broad.mit.edu	37	1	19755363	19755363	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19755363delA	uc010ocz.1	-						CAPZB_uc001bce.2_Intron|CAPZB_uc009vpk.2_Intron	NM_004930	NP_004921			F-actin capping protein beta subunit						actin cytoskeleton organization|actin filament capping|blood coagulation|cellular component movement	cytosol|F-actin capping protein complex|WASH complex	actin binding				0		Colorectal(325;3.93e-05)|Renal(390;0.000147)|all_lung(284;0.000169)|Lung NSC(340;0.000202)|Breast(348;0.000496)|Ovarian(437;0.00428)|Myeloproliferative disorder(586;0.0262)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Kidney(64;8.63e-06)|BRCA - Breast invasive adenocarcinoma(304;4.06e-05)|KIRC - Kidney renal clear cell carcinoma(64;0.000175)|GBM - Glioblastoma multiforme(114;0.000525)|STAD - Stomach adenocarcinoma(196;0.00779)|READ - Rectum adenocarcinoma(331;0.103)|Lung(427;0.173)														---	---	---	---
NBL1	4681	broad.mit.edu	37	1	19942072	19942072	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19942072delT	uc009vpl.1	+						C1orf151_uc001bch.1_Intron|C1orf151_uc001bci.1_Intron	NM_005380	NP_005371			neuroblastoma, suppression of tumorigenicity 1 2							extracellular region				ovary(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00043)|Ovarian(437;0.00373)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;5.9e-05)|Kidney(64;0.000173)|GBM - Glioblastoma multiforme(114;0.0012)|KIRC - Kidney renal clear cell carcinoma(64;0.0026)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
TMCO4	255104	broad.mit.edu	37	1	20025182	20025183	+	Intron	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20025182_20025183delCT	uc001bcn.2	-						TMCO4_uc001bcm.2_Intron|TMCO4_uc001bco.1_Intron|TMCO4_uc001bcp.1_Intron	NM_181719	NP_859070			transmembrane and coiled-coil domains 4							integral to membrane					0		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00519)|Breast(348;0.00526)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00708)|COAD - Colon adenocarcinoma(152;2.28e-05)|BRCA - Breast invasive adenocarcinoma(304;5.8e-05)|Kidney(64;0.000367)|GBM - Glioblastoma multiforme(114;0.000377)|KIRC - Kidney renal clear cell carcinoma(64;0.00459)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0862)|Lung(427;0.223)														---	---	---	---
TMCO4	255104	broad.mit.edu	37	1	20081071	20081071	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20081071delA	uc001bcn.2	-						TMCO4_uc001bcm.2_Intron|TMCO4_uc001bco.1_Intron|TMCO4_uc001bcp.1_Intron|TMCO4_uc009vpn.1_Intron|TMCO4_uc001bcq.1_Intron	NM_181719	NP_859070			transmembrane and coiled-coil domains 4							integral to membrane					0		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00519)|Breast(348;0.00526)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00708)|COAD - Colon adenocarcinoma(152;2.28e-05)|BRCA - Breast invasive adenocarcinoma(304;5.8e-05)|Kidney(64;0.000367)|GBM - Glioblastoma multiforme(114;0.000377)|KIRC - Kidney renal clear cell carcinoma(64;0.00459)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0862)|Lung(427;0.223)														---	---	---	---
TMCO4	255104	broad.mit.edu	37	1	20097622	20097623	+	Intron	INS	-	AAGTC	AAGTC	rs141798917	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20097622_20097623insAAGTC	uc001bcn.2	-						TMCO4_uc001bcm.2_Intron|TMCO4_uc001bco.1_Intron|TMCO4_uc001bcp.1_Intron|TMCO4_uc009vpn.1_Intron|TMCO4_uc001bcq.1_Intron	NM_181719	NP_859070			transmembrane and coiled-coil domains 4							integral to membrane					0		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00519)|Breast(348;0.00526)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00708)|COAD - Colon adenocarcinoma(152;2.28e-05)|BRCA - Breast invasive adenocarcinoma(304;5.8e-05)|Kidney(64;0.000367)|GBM - Glioblastoma multiforme(114;0.000377)|KIRC - Kidney renal clear cell carcinoma(64;0.00459)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0862)|Lung(427;0.223)														---	---	---	---
PLA2G5	5322	broad.mit.edu	37	1	20363165	20363165	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20363165delT	uc001bcx.2	+						PLA2G5_uc001bcw.2_Intron	NM_000929	NP_000920			phospholipase A2, group V precursor						lipid catabolic process	extracellular region	calcium ion binding|calcium-dependent phospholipase A2 activity			skin(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000249)|Lung NSC(340;0.000287)|Breast(348;0.000812)|Ovarian(437;0.00328)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.22e-05)|BRCA - Breast invasive adenocarcinoma(304;8.15e-05)|Kidney(64;0.000184)|GBM - Glioblastoma multiforme(114;0.00089)|KIRC - Kidney renal clear cell carcinoma(64;0.0027)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0652)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	20724594	20724594	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20724594delT	uc009vpu.1	-						uc001bdf.1_Intron					Homo sapiens cDNA clone IMAGE:5269505.																														---	---	---	---
KIF17	57576	broad.mit.edu	37	1	21000027	21000028	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21000027_21000028delTT	uc001bdr.3	-						KIF17_uc001bdp.3_Intron|KIF17_uc001bdq.3_Intron|KIF17_uc009vpx.2_Intron|KIF17_uc001bds.3_Intron	NM_020816	NP_065867			kinesin family member 17 isoform a						microtubule-based movement|protein transport	cytoplasm|microtubule	ATP binding			ovary(3)|skin(1)	4		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)														---	---	---	---
HP1BP3	50809	broad.mit.edu	37	1	21087036	21087038	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21087036_21087038delAAA	uc001bdw.1	-						HP1BP3_uc001bdv.1_Intron|HP1BP3_uc010odh.1_Intron|HP1BP3_uc001bdy.1_Intron|HP1BP3_uc001bdz.2_Intron|HP1BP3_uc001bea.2_Intron|HP1BP3_uc010odf.1_Intron|HP1BP3_uc010odg.1_Intron	NM_016287	NP_057371			HP1-BP74						nucleosome assembly	nucleosome|nucleus	DNA binding			central_nervous_system(1)|skin(1)	2		all_lung(284;6.55e-06)|Lung NSC(340;6.59e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.26e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00015)|GBM - Glioblastoma multiforme(114;0.000521)|Kidney(64;0.000529)|STAD - Stomach adenocarcinoma(196;0.00311)|KIRC - Kidney renal clear cell carcinoma(64;0.00687)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.201)														---	---	---	---
EIF4G3	8672	broad.mit.edu	37	1	21450783	21450783	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21450783delA	uc001bef.2	-						EIF4G3_uc001bed.2_Intron|EIF4G3_uc001bee.2_Intron|EIF4G3_uc001beh.2_Intron	NM_003760	NP_003751			eukaryotic translation initiation factor 4						interspecies interaction between organisms|regulation of translational initiation|RNA metabolic process	eukaryotic translation initiation factor 4F complex	protein binding|RNA cap binding|translation initiation factor activity			skin(1)	1		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)														---	---	---	---
EIF4G3	8672	broad.mit.edu	37	1	21488942	21488945	+	Intron	DEL	AAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21488942_21488945delAAAA	uc001bef.2	-						EIF4G3_uc001bed.2_Intron|EIF4G3_uc001bee.2_Intron|EIF4G3_uc001beh.2_Intron	NM_003760	NP_003751			eukaryotic translation initiation factor 4						interspecies interaction between organisms|regulation of translational initiation|RNA metabolic process	eukaryotic translation initiation factor 4F complex	protein binding|RNA cap binding|translation initiation factor activity			skin(1)	1		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	21539989	21539989	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21539989delT								EIF4G3 (36649 upstream) : ECE1 (3751 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	21698088	21698088	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21698088delA								ECE1 (26054 upstream) : NBPF3 (68543 downstream)																																			---	---	---	---
NBPF3	84224	broad.mit.edu	37	1	21789741	21789742	+	Intron	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21789741_21789742insC	uc001ber.2	+						NBPF3_uc001bes.2_Intron|NBPF3_uc009vqb.2_Intron|NBPF3_uc010odm.1_Intron	NM_032264	NP_115640			neuroblastoma breakpoint family, member 3							cytoplasm				upper_aerodigestive_tract(1)|ovary(1)	2		all_lung(284;2.16e-05)|Lung NSC(340;2.19e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|OV - Ovarian serous cystadenocarcinoma(117;7.53e-27)|COAD - Colon adenocarcinoma(152;1.18e-05)|GBM - Glioblastoma multiforme(114;3.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000143)|STAD - Stomach adenocarcinoma(196;0.00306)|KIRC - Kidney renal clear cell carcinoma(1967;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	22131416	22131416	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22131416delA								USP48 (21728 upstream) : LDLRAD2 (7342 downstream)																																			---	---	---	---
HSPG2	3339	broad.mit.edu	37	1	22220368	22220369	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22220368_22220369delAA	uc001bfj.2	-						HSPG2_uc009vqd.2_Intron|HSPG2_uc009vqe.1_Intron	NM_005529	NP_005520			heparan sulfate proteoglycan 2 precursor						angiogenesis|cell adhesion|lipid metabolic process|lipoprotein metabolic process	basement membrane|extracellular space|plasma membrane	protein C-terminus binding			ovary(5)|large_intestine(2)|central_nervous_system(1)|skin(1)	9		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Becaplermin(DB00102)|Palifermin(DB00039)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	22269828	22269828	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22269828delT								HSPG2 (6078 upstream) : CELA3B (33590 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	22441094	22441094	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22441094delG								CDC42 (21659 upstream) : WNT4 (2706 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	22569991	22569998	+	IGR	DEL	GGCAGGCC	-	-	rs71958787		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22569991_22569998delGGCAGGCC								WNT4 (99606 upstream) : ZBTB40 (208346 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	22672439	22672439	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22672439delC								WNT4 (202054 upstream) : ZBTB40 (105905 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	22956634	22956634	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22956634delT								EPHA8 (26547 upstream) : C1QA (6484 downstream)																																			---	---	---	---
C1QC	714	broad.mit.edu	37	1	22973037	22973037	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22973037delT	uc001bgc.3	+						C1QC_uc001bga.3_Intron|C1QC_uc001bgb.2_Intron	NM_172369	NP_758957			complement component 1, q subcomponent, C chain						complement activation, classical pathway|innate immune response|negative regulation of granulocyte differentiation|negative regulation of macrophage differentiation	collagen					0		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;6.21e-27)|Colorectal(126;1.5e-07)|COAD - Colon adenocarcinoma(152;1.12e-05)|GBM - Glioblastoma multiforme(114;1.61e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000538)|KIRC - Kidney renal clear cell carcinoma(1967;0.00269)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.196)	Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)													---	---	---	---
EPHB2	2048	broad.mit.edu	37	1	23095187	23095188	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23095187_23095188delAA	uc009vqj.1	+						EPHB2_uc001bge.2_Intron|EPHB2_uc001bgf.2_Intron|EPHB2_uc010odu.1_Intron	NM_017449	NP_059145			ephrin receptor EphB2 isoform 1 precursor						axon guidance	integral to plasma membrane	ATP binding|transmembrane-ephrin receptor activity			ovary(3)|lung(1)|pancreas(1)	5		Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0348)|OV - Ovarian serous cystadenocarcinoma(117;3.67e-26)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|GBM - Glioblastoma multiforme(114;2.93e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000606)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.126)|Lung(427;0.153)										Hereditary_Prostate_Cancer				---	---	---	---
TCEA3	6920	broad.mit.edu	37	1	23721839	23721839	+	Intron	DEL	G	-	-	rs139820009	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23721839delG	uc001bgx.1	-						TCEA3_uc009vqm.1_5'Flank	NM_003196	NP_003187			transcription elongation factor A (SII), 3						regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription elongation, DNA-dependent	nucleus	DNA binding|translation elongation factor activity|zinc ion binding				0		Colorectal(325;3.46e-05)|Lung NSC(340;4.16e-05)|all_lung(284;6.68e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.0054)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.6e-25)|Colorectal(126;8.32e-08)|COAD - Colon adenocarcinoma(152;4.29e-06)|GBM - Glioblastoma multiforme(114;9e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00112)|KIRC - Kidney renal clear cell carcinoma(1967;0.00424)|STAD - Stomach adenocarcinoma(196;0.0145)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.0963)|LUSC - Lung squamous cell carcinoma(448;0.198)														---	---	---	---
ASAP3	55616	broad.mit.edu	37	1	23771987	23771987	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23771987delA	uc001bha.2	-						ASAP3_uc010odz.1_Intron|ASAP3_uc010oea.1_Intron|ASAP3_uc001bhc.1_Intron	NM_017707	NP_060177			ArfGAP with SH3 domain, ankyrin repeat and PH						regulation of ARF GTPase activity	cytoplasm	ARF GTPase activator activity|zinc ion binding			large_intestine(1)|ovary(1)|skin(1)	3																		---	---	---	---
ASAP3	55616	broad.mit.edu	37	1	23777528	23777529	+	Intron	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23777528_23777529insG	uc001bha.2	-						ASAP3_uc010odz.1_Intron|ASAP3_uc010oea.1_Intron|ASAP3_uc001bhc.1_Intron	NM_017707	NP_060177			ArfGAP with SH3 domain, ankyrin repeat and PH						regulation of ARF GTPase activity	cytoplasm	ARF GTPase activator activity|zinc ion binding			large_intestine(1)|ovary(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	23982881	23982881	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23982881delA								MDS2 (15825 upstream) : RPL11 (35413 downstream)																																			---	---	---	---
HMGCL	3155	broad.mit.edu	37	1	24148340	24148340	+	Intron	DEL	T	-	-	rs78959587	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24148340delT	uc001bib.2	-						HMGCL_uc010oec.1_Intron|HMGCL_uc009vqr.2_Intron|HMGCL_uc001bic.2_Intron|HMGCL_uc009vqs.1_Intron|HMGCL_uc001bid.1_Intron	NM_000191	NP_000182			3-hydroxy-3-methylglutaryl CoA lyase isoform 1						acetoacetic acid biosynthetic process|ketone body biosynthetic process	mitochondrial matrix	hydroxymethylglutaryl-CoA lyase activity|metal ion binding			central_nervous_system(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.0044)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.38e-24)|Colorectal(126;5.58e-08)|COAD - Colon adenocarcinoma(152;3.12e-06)|GBM - Glioblastoma multiforme(114;4.9e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000982)|KIRC - Kidney renal clear cell carcinoma(1967;0.0034)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0856)|LUSC - Lung squamous cell carcinoma(448;0.188)														---	---	---	---
FUCA1	2517	broad.mit.edu	37	1	24175456	24175458	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24175456_24175458delTTT	uc001bie.2	-							NM_000147	NP_000138			fucosidase, alpha-L-1, tissue precursor						fucose metabolic process|glycosaminoglycan catabolic process	lysosome	alpha-L-fucosidase activity|cation binding			breast(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.00957)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-24)|Colorectal(126;5.69e-08)|COAD - Colon adenocarcinoma(152;3.15e-06)|GBM - Glioblastoma multiforme(114;9.04e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000986)|KIRC - Kidney renal clear cell carcinoma(1967;0.00342)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.144)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	24545829	24545830	+	IGR	INS	-	T	T	rs149147224	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24545829_24545830insT								LOC284632 (7649 upstream) : GRHL3 (100051 downstream)																																			---	---	---	---
GRHL3	57822	broad.mit.edu	37	1	24665772	24665775	+	Intron	DEL	TTTT	-	-	rs68153413	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24665772_24665775delTTTT	uc001biy.2	+						GRHL3_uc001bix.2_Intron|GRHL3_uc001biz.2_Intron	NM_021180	NP_067003			sister-of-mammalian grainyhead protein isoform						regulation of actin cytoskeleton organization|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.00171)|all_lung(284;0.00226)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;8.72e-25)|Colorectal(126;4.38e-08)|COAD - Colon adenocarcinoma(152;1.84e-06)|GBM - Glioblastoma multiforme(114;0.000132)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00151)|KIRC - Kidney renal clear cell carcinoma(1967;0.00377)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.143)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	24818450	24818452	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24818450_24818452delTTT								NIPAL3 (18978 upstream) : RCAN3 (10935 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	25062814	25062815	+	IGR	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25062814_25062815delAG								SRRM1 (63043 upstream) : CLIC4 (8945 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	25322114	25322114	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25322114delC								RUNX3 (30502 upstream) : SYF2 (226653 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	25415869	25415869	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25415869delG								RUNX3 (124257 upstream) : SYF2 (132898 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	25432071	25432071	+	IGR	DEL	T	-	-	rs111771528		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25432071delT								RUNX3 (140459 upstream) : SYF2 (116696 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	25528553	25528553	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25528553delA								RUNX3 (236941 upstream) : SYF2 (20214 downstream)																																			---	---	---	---
MAN1C1	57134	broad.mit.edu	37	1	26014444	26014444	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26014444delT	uc001bkm.2	+						MAN1C1_uc009vry.1_Intron	NM_020379	NP_065112			mannosidase, alpha, class 1C, member 1						post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			skin(1)	1		Colorectal(325;3.78e-05)|Lung NSC(340;0.000181)|all_lung(284;0.000245)|Renal(390;0.000714)|Ovarian(437;0.00159)|Breast(348;0.0156)|Myeloproliferative disorder(586;0.0257)|all_neural(195;0.0515)|Esophageal squamous(538;0.232)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0574)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.15e-07)|COAD - Colon adenocarcinoma(152;4.31e-06)|STAD - Stomach adenocarcinoma(196;0.00125)|BRCA - Breast invasive adenocarcinoma(304;0.00141)|KIRC - Kidney renal clear cell carcinoma(1967;0.00146)|GBM - Glioblastoma multiforme(114;0.0149)|READ - Rectum adenocarcinoma(331;0.0803)														---	---	---	---
STMN1	3925	broad.mit.edu	37	1	26212738	26212738	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26212738delG	uc010oev.1	-						STMN1_uc001bky.2_Intron	NM_001145454	NP_001138926			stathmin 1 isoform b						cell differentiation|intracellular signal transduction|microtubule depolymerization|mitotic spindle organization|nervous system development|response to virus	cytoplasm|microtubule	signal transducer activity|tubulin binding				0		Colorectal(325;3.46e-05)|Lung NSC(340;0.000163)|all_lung(284;0.000234)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0505)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.85e-25)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000946)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.013)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
PDIK1L	149420	broad.mit.edu	37	1	26444549	26444550	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26444549_26444550delAA	uc010oew.1	+						PDIK1L_uc001blj.3_Intron|PDIK1L_uc009vsb.2_Intron	NM_152835	NP_690048			PDLIM1 interacting kinase 1 like							nucleus	ATP binding|protein serine/threonine kinase activity				0		Colorectal(325;0.000147)|Renal(390;0.00211)|Lung NSC(340;0.00239)|all_lung(284;0.00366)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;7.32e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000735)|BRCA - Breast invasive adenocarcinoma(304;0.000973)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.015)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	26463816	26463816	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26463816delA								PDIK1L (11792 upstream) : GRRP1 (21695 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	26545035	26545035	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26545035delT								CATSPER4 (16003 upstream) : CCDC21 (15658 downstream)																																			---	---	---	---
DHDDS	79947	broad.mit.edu	37	1	26773178	26773179	+	Intron	INS	-	GT	GT	rs138481581	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26773178_26773179insGT	uc001bml.2	+						DHDDS_uc001bmk.2_Intron|DHDDS_uc001bmm.2_Intron|DHDDS_uc001bmn.2_Intron|DHDDS_uc010ofd.1_Intron	NM_205861	NP_995583			dehydrodolichyl diphosphate synthase isoform b								protein binding|transferase activity, transferring alkyl or aryl (other than methyl) groups			breast(3)	3		all_cancers(24;2.04e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.0161)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.166)|LUSC - Lung squamous cell carcinoma(448;0.239)														---	---	---	---
ZDHHC18	84243	broad.mit.edu	37	1	27179541	27179541	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27179541delA	uc001bnb.2	+							NM_032283	NP_115659			zinc finger, DHHC-type containing 18							integral to membrane	zinc ion binding				0		all_cancers(24;5.82e-22)|all_epithelial(13;9.91e-20)|Colorectal(325;0.000147)|Breast(348;0.000706)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;5.71e-53)|Epithelial(14;4.73e-52)|OV - Ovarian serous cystadenocarcinoma(117;1.53e-29)|Colorectal(126;1.9e-09)|COAD - Colon adenocarcinoma(152;4.2e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000548)|STAD - Stomach adenocarcinoma(196;0.00065)|KIRC - Kidney renal clear cell carcinoma(1967;0.000779)|GBM - Glioblastoma multiforme(114;0.0265)|READ - Rectum adenocarcinoma(331;0.0455)|Lung(427;0.163)|LUSC - Lung squamous cell carcinoma(448;0.237)												OREG0013274	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
GPN2	54707	broad.mit.edu	37	1	27211489	27211489	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27211489delA	uc001bnd.1	-							NM_018066	NP_060536			ATP binding domain 1 family, member B								GTP binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	27490135	27490135	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27490135delG								SLC9A1 (8684 upstream) : WDTC1 (70872 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	27494230	27494231	+	IGR	DEL	TT	-	-	rs139897998		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27494230_27494231delTT								SLC9A1 (12779 upstream) : WDTC1 (66776 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	27503184	27503184	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27503184delA								SLC9A1 (21733 upstream) : WDTC1 (57823 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	27514467	27514467	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27514467delT								SLC9A1 (33016 upstream) : WDTC1 (46540 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	27523054	27523055	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27523054_27523055delTT								SLC9A1 (41603 upstream) : WDTC1 (37952 downstream)																																			---	---	---	---
FCN3	8547	broad.mit.edu	37	1	27702582	27702582	+	5'Flank	DEL	A	-	-	rs67700463		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27702582delA	uc001boa.2	-						FCN3_uc001bob.2_5'Flank	NM_003665	NP_003656			ficolin 3 isoform 1 precursor						complement activation, lectin pathway|signal transduction	collagen|extracellular space	receptor binding|sugar binding				0		all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;1.42e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00128)|KIRC - Kidney renal clear cell carcinoma(1967;0.00155)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
WASF2	10163	broad.mit.edu	37	1	27745045	27745045	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27745045delT	uc001bof.1	-						WASF2_uc010ofl.1_Intron	NM_006990	NP_008921			WAS protein family, member 2						actin cytoskeleton organization|G-protein signaling, coupled to cAMP nucleotide second messenger	actin cytoskeleton|lamellipodium	actin binding			skin(2)|ovary(1)	3		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0446)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.7e-08)|COAD - Colon adenocarcinoma(152;2e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00139)|KIRC - Kidney renal clear cell carcinoma(1967;0.00204)|STAD - Stomach adenocarcinoma(196;0.00325)|READ - Rectum adenocarcinoma(331;0.0481)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	27838211	27838211	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27838211delA								WASF2 (21542 upstream) : AHDC1 (22583 downstream)																																			---	---	---	---
EYA3	2140	broad.mit.edu	37	1	28304728	28304728	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28304728delA	uc001bpi.1	-						EYA3_uc010ofs.1_Intron|EYA3_uc010oft.1_Intron|EYA3_uc001bpj.2_Intron	NM_001990	NP_001981			eyes absent 3						anatomical structure morphogenesis|double-strand break repair|histone dephosphorylation|multicellular organismal development|positive regulation of DNA repair|regulation of transcription, DNA-dependent|response to ionizing radiation|transcription, DNA-dependent|visual perception	cytoplasm	metal ion binding|protein binding|protein tyrosine phosphatase activity			ovary(2)|skin(1)	3		Colorectal(325;3.46e-05)|all_lung(284;0.000414)|Lung NSC(340;0.000432)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0484)|OV - Ovarian serous cystadenocarcinoma(117;1.25e-24)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;2.8e-06)|STAD - Stomach adenocarcinoma(196;0.00364)|KIRC - Kidney renal clear cell carcinoma(1967;0.00378)|BRCA - Breast invasive adenocarcinoma(304;0.00718)|READ - Rectum adenocarcinoma(331;0.0642)														---	---	---	---
PTAFR	5724	broad.mit.edu	37	1	28477695	28477697	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28477695_28477697delTTT	uc001bpl.2	-						PTAFR_uc001bpm.3_Intron|PTAFR_uc009vte.2_Intron	NM_000952	NP_000943			platelet-activating factor receptor						chemotaxis|inflammatory response|interferon-gamma-mediated signaling pathway|phosphatidylinositol-mediated signaling	integral to plasma membrane|nucleus	phospholipid binding|platelet activating factor receptor activity				0		Colorectal(325;0.000147)|Renal(390;0.00357)|Lung NSC(340;0.00715)|all_lung(284;0.00732)|Breast(348;0.0174)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0545)|all_neural(195;0.0557)		UCEC - Uterine corpus endometrioid carcinoma (279;0.215)|OV - Ovarian serous cystadenocarcinoma(117;6e-22)|Colorectal(126;3.04e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00279)|BRCA - Breast invasive adenocarcinoma(304;0.00595)|STAD - Stomach adenocarcinoma(196;0.00678)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
PTAFR	5724	broad.mit.edu	37	1	28519686	28519687	+	Intron	INS	-	TG	TG	rs141778632	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28519686_28519687insTG	uc001bpm.3	-						PTAFR_uc009vte.2_Intron	NM_000952	NP_000943			platelet-activating factor receptor						chemotaxis|inflammatory response|interferon-gamma-mediated signaling pathway|phosphatidylinositol-mediated signaling	integral to plasma membrane|nucleus	phospholipid binding|platelet activating factor receptor activity				0		Colorectal(325;0.000147)|Renal(390;0.00357)|Lung NSC(340;0.00715)|all_lung(284;0.00732)|Breast(348;0.0174)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0545)|all_neural(195;0.0557)		UCEC - Uterine corpus endometrioid carcinoma (279;0.215)|OV - Ovarian serous cystadenocarcinoma(117;6e-22)|Colorectal(126;3.04e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00279)|BRCA - Breast invasive adenocarcinoma(304;0.00595)|STAD - Stomach adenocarcinoma(196;0.00678)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
ATPIF1	93974	broad.mit.edu	37	1	28564029	28564029	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28564029delT	uc001bpq.2	+						ATPIF1_uc001bpp.2_Intron|ATPIF1_uc001bpr.2_3'UTR	NM_016311	NP_057395			ATPase inhibitory factor 1 isoform 1 precursor						angiogenesis|generation of precursor metabolites and energy|negative regulation of endothelial cell proliferation|negative regulation of hydrolase activity|negative regulation of nucleotide metabolic process|protein homotetramerization	cell surface|mitochondrion	angiostatin binding|ATPase binding|ATPase inhibitor activity|calmodulin binding|protein homodimerization activity				0		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;4.76e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;2.36e-22)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00269)|BRCA - Breast invasive adenocarcinoma(304;0.00574)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	28677675	28677676	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28677675_28677676delTT								MED18 (15198 upstream) : PHACTR4 (18417 downstream)																																			---	---	---	---
PHACTR4	65979	broad.mit.edu	37	1	28817970	28817970	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28817970delA	uc001bpw.2	+						PHACTR4_uc001bpv.1_Intron|PHACTR4_uc001bpx.2_Intron|PHACTR4_uc001bpy.2_Intron|PHACTR4_uc001bpz.2_5'Flank	NM_001048183	NP_001041648			phosphatase and actin regulator 4 isoform 1								actin binding|protein phosphatase inhibitor activity				0		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
GMEB1	10691	broad.mit.edu	37	1	29037282	29037283	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29037282_29037283delAA	uc001bra.2	+						GMEB1_uc001bqz.2_Intron|GMEB1_uc001brb.2_Intron	NM_006582	NP_006573			glucocorticoid modulatory element binding						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|metal ion binding|transcription coactivator activity				0		Colorectal(325;3.46e-05)|Lung NSC(340;0.000451)|all_lung(284;0.00063)|Breast(348;0.00502)|Renal(390;0.00555)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0221)|KIRC - Kidney renal clear cell carcinoma(1967;0.0296)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
EPB41	2035	broad.mit.edu	37	1	29347174	29347174	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29347174delT	uc001brm.1	+						EPB41_uc001brg.1_Intron|EPB41_uc001brh.1_Intron|EPB41_uc001bri.1_Intron|EPB41_uc001brj.1_Intron|EPB41_uc009vtk.1_Intron|EPB41_uc001brk.2_Intron|EPB41_uc001brl.1_Intron|EPB41_uc009vtl.1_Intron|EPB41_uc009vtm.1_Intron	NM_203342	NP_976217			erythrocyte membrane protein band 4.1						blood circulation|cortical actin cytoskeleton organization|positive regulation of protein binding	extrinsic to membrane|Golgi apparatus|nucleus|plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	1-phosphatidylinositol binding|actin binding|spectrin binding|structural constituent of cytoskeleton			ovary(1)	1		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	30116437	30116439	+	IGR	DEL	AAA	-	-	rs11354640		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:30116437_30116439delAAA								PTPRU (463122 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	30812523	30812524	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:30812523_30812524delTT								None (None upstream) : MATN1 (371602 downstream)																																			---	---	---	---
LAPTM5	7805	broad.mit.edu	37	1	31222582	31222582	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31222582delA	uc001bsc.2	-							NM_006762	NP_006753			lysosomal protein transmembrane 5						transport	integral to plasma membrane|lysosomal membrane					0		Colorectal(325;0.0199)|Myeloproliferative disorder(586;0.0393)|all_neural(195;0.0966)|Medulloblastoma(700;0.151)|Ovarian(437;0.192)		STAD - Stomach adenocarcinoma(196;0.0196)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
NKAIN1	79570	broad.mit.edu	37	1	31668476	31668476	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31668476delA	uc010ogd.1	-							NM_024522	NP_078798			Na+/K+ transporting ATPase interacting 1							integral to membrane|plasma membrane				ovary(1)	1		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)|Breast(348;0.141)|all_neural(195;0.146)|Medulloblastoma(700;0.151)		STAD - Stomach adenocarcinoma(196;0.0184)|READ - Rectum adenocarcinoma(331;0.148)														---	---	---	---
NKAIN1	79570	broad.mit.edu	37	1	31673692	31673692	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31673692delT	uc010ogd.1	-							NM_024522	NP_078798			Na+/K+ transporting ATPase interacting 1							integral to membrane|plasma membrane				ovary(1)	1		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)|Breast(348;0.141)|all_neural(195;0.146)|Medulloblastoma(700;0.151)		STAD - Stomach adenocarcinoma(196;0.0184)|READ - Rectum adenocarcinoma(331;0.148)														---	---	---	---
SNRNP40	9410	broad.mit.edu	37	1	31766006	31766006	+	Intron	DEL	A	-	-	rs112391814		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31766006delA	uc001bso.2	-						SNRNP40_uc010oge.1_Intron	NM_004814	NP_004805			WD repeat domain 57 (U5 snRNP specific)							catalytic step 2 spliceosome|cytoplasm|nucleoplasm|small nucleolar ribonucleoprotein complex|U5 snRNP	protein binding				0																		---	---	---	---
ZCCHC17	51538	broad.mit.edu	37	1	31779039	31779039	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31779039delT	uc001bsp.1	+						ZCCHC17_uc001bsq.1_Intron|ZCCHC17_uc010ogf.1_Intron|ZCCHC17_uc009vtu.1_Intron|ZCCHC17_uc001bsr.1_Intron|ZCCHC17_uc009vtv.1_Intron	NM_016505	NP_057589			zinc finger, CCHC domain containing 17							nucleolus	RNA binding|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)|all_neural(195;0.146)|Medulloblastoma(700;0.151)|Breast(348;0.222)		STAD - Stomach adenocarcinoma(196;0.0215)|READ - Rectum adenocarcinoma(331;0.168)														---	---	---	---
ZCCHC17	51538	broad.mit.edu	37	1	31791791	31791792	+	Intron	INS	-	A	A	rs56053258		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31791791_31791792insA	uc001bsp.1	+						ZCCHC17_uc001bsq.1_Intron|ZCCHC17_uc010ogf.1_Intron|ZCCHC17_uc009vtu.1_Intron|ZCCHC17_uc001bsr.1_Intron|ZCCHC17_uc009vtv.1_Intron	NM_016505	NP_057589			zinc finger, CCHC domain containing 17							nucleolus	RNA binding|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)|all_neural(195;0.146)|Medulloblastoma(700;0.151)|Breast(348;0.222)		STAD - Stomach adenocarcinoma(196;0.0215)|READ - Rectum adenocarcinoma(331;0.168)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	31947492	31947493	+	IGR	DEL	AA	-	-	rs141158732		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31947492_31947493delAA								SERINC2 (39968 upstream) : LOC284551 (36543 downstream)																																			---	---	---	---
COL16A1	1307	broad.mit.edu	37	1	32131296	32131296	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32131296delG	uc001btk.1	-						COL16A1_uc001bti.1_Intron|COL16A1_uc001btj.1_Intron	NM_001856	NP_001847			alpha 1 type XVI collagen precursor						cell adhesion|female pregnancy|integrin-mediated signaling pathway	collagen type XVI	integrin binding|structural molecule activity			ovary(8)	8		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)														---	---	---	---
COL16A1	1307	broad.mit.edu	37	1	32139833	32139834	+	Intron	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32139833_32139834insG	uc001btk.1	-						COL16A1_uc001btj.1_Intron	NM_001856	NP_001847			alpha 1 type XVI collagen precursor						cell adhesion|female pregnancy|integrin-mediated signaling pathway	collagen type XVI	integrin binding|structural molecule activity			ovary(8)	8		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)														---	---	---	---
TMEM39B	55116	broad.mit.edu	37	1	32559403	32559403	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32559403delT	uc010ogv.1	+						TMEM39B_uc010ogt.1_Intron|TMEM39B_uc010ogu.1_Intron|TMEM39B_uc001bue.3_Intron|TMEM39B_uc001buf.3_Intron|TMEM39B_uc010ogw.1_Intron	NM_018056	NP_060526			transmembrane protein 39B							integral to membrane					0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)																---	---	---	---
LCK	3932	broad.mit.edu	37	1	32750903	32750903	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32750903delA	uc001bux.2	+						LCK_uc001buy.2_Intron|LCK_uc001buz.2_Intron|LCK_uc001bva.2_Intron	NM_005356	NP_005347			lymphocyte-specific protein tyrosine kinase						activation of caspase activity|cellular zinc ion homeostasis|induction of apoptosis|interspecies interaction between organisms|leukocyte migration|platelet activation|positive regulation of T cell receptor signaling pathway|regulation of defense response to virus by virus|release of sequestered calcium ion into cytosol|response to drug|T cell costimulation|T cell differentiation|T cell receptor signaling pathway|viral reproduction	cytosol|Golgi apparatus|membrane raft|pericentriolar material|plasma membrane	ATP binding|ATPase binding|CD4 receptor binding|CD8 receptor binding|glycoprotein binding|non-membrane spanning protein tyrosine kinase activity|phosphatidylinositol 3-kinase binding|protein C-terminus binding|protein kinase binding|protein serine/threonine phosphatase activity|SH2 domain binding			lung(3)|central_nervous_system(2)|ovary(1)	6		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.212)			Dasatinib(DB01254)			T	TRB@	T-ALL								---	---	---	---
HDAC1	3065	broad.mit.edu	37	1	32766166	32766166	+	Intron	DEL	A	-	-	rs75363503		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32766166delA	uc001bvb.1	+						HDAC1_uc010ohd.1_Intron|HDAC1_uc010ohe.1_Intron|HDAC1_uc010ohf.1_Intron	NM_004964	NP_004955			histone deacetylase 1						anti-apoptosis|blood coagulation|embryonic digit morphogenesis|epidermal cell differentiation|eyelid development in camera-type eye|fungiform papilla formation|hair follicle placode formation|histone H3 deacetylation|histone H4 deacetylation|negative regulation by host of viral transcription|negative regulation of androgen receptor signaling pathway|negative regulation of cell cycle|nerve growth factor receptor signaling pathway|odontogenesis of dentine-containing tooth|positive regulation of cell proliferation|positive regulation of receptor biosynthetic process|positive regulation of transcription from RNA polymerase II promoter	cytosol|NuRD complex|Sin3 complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|identical protein binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|RNA polymerase II transcription corepressor activity|sequence-specific DNA binding transcription factor activity			ovary(1)|lung(1)|breast(1)	3		Breast(348;0.000523)|Lung NSC(340;0.000992)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Lung SC(1967;0.113)		KIRC - Kidney renal clear cell carcinoma(1967;0.138)	Vorinostat(DB02546)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	32871785	32871788	+	IGR	DEL	AAAA	-	-	rs35032902		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32871785_32871788delAAAA								BSDC1 (11723 upstream) : ZBTB8A (58870 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	32891244	32891245	+	IGR	DEL	TT	-	-	rs113309430		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32891244_32891245delTT								BSDC1 (31182 upstream) : ZBTB8A (39413 downstream)																																			---	---	---	---
ZBTB8A	653121	broad.mit.edu	37	1	32983946	32983947	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32983946_32983947insA	uc001bvk.2	+							NM_001145720				zinc finger and BTB domain containing 8B						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
RBBP4	5928	broad.mit.edu	37	1	33117785	33117785	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33117785delT	uc001bvr.2	+						ZBTB8OS_uc001bvo.1_5'Flank|ZBTB8OS_uc001bvp.2_5'Flank|ZBTB8OS_uc001bvq.2_5'Flank|RBBP4_uc001bvs.2_Intron|RBBP4_uc010ohj.1_Intron|RBBP4_uc010ohk.1_Intron	NM_005610	NP_005601			retinoblastoma binding protein 4 isoform a						cell cycle|CenH3-containing nucleosome assembly at centromere|DNA replication|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	CAF-1 complex|ESC/E(Z) complex|NuRD complex|NURF complex|Sin3 complex	histone binding|histone deacetylase binding			ovary(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)																---	---	---	---
KIAA1522	57648	broad.mit.edu	37	1	33234187	33234187	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33234187delA	uc001bvv.2	+						KIAA1522_uc001bvu.1_Intron|KIAA1522_uc010ohm.1_Intron|KIAA1522_uc010ohn.1_Intron	NM_020888	NP_065939			hypothetical protein LOC57648												0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)																---	---	---	---
YARS	8565	broad.mit.edu	37	1	33241763	33241763	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33241763delG	uc001bvy.1	-						YARS_uc001bvw.1_Intron|YARS_uc001bvx.1_Intron	NM_003680	NP_003671			tyrosyl-tRNA synthetase						apoptosis|tyrosyl-tRNA aminoacylation	cytosol|extracellular space|nucleus|soluble fraction	ATP binding|interleukin-8 receptor binding|signal transducer activity|tRNA binding|tyrosine-tRNA ligase activity			skin(2)	2		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)			L-Tyrosine(DB00135)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	33324563	33324563	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33324563delG								S100PBP (88 upstream) : FNDC5 (3307 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	33387727	33387727	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33387727delA								TMEM54 (20774 upstream) : RNF19B (14325 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	33434949	33434949	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33434949delT								RNF19B (4663 upstream) : AK2 (38637 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	33437531	33437531	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33437531delT								RNF19B (7245 upstream) : AK2 (36055 downstream)																																			---	---	---	---
AK2	204	broad.mit.edu	37	1	33486747	33486749	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33486747_33486749delAAA	uc001bwp.1	-						uc001bwn.2_Intron|AK2_uc001bwo.1_Intron|AK2_uc010ohq.1_Intron|AK2_uc009vud.1_Intron|AK2_uc010ohr.1_Intron|AK2_uc001bwq.1_Intron	NM_001625	NP_001616			adenylate kinase 2 isoform a						nucleobase, nucleoside and nucleotide interconversion	mitochondrial intermembrane space	adenylate kinase activity|ATP binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	33687884	33687884	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33687884delC								TRIM62 (40213 upstream) : ZNF362 (34290 downstream)																																			---	---	---	---
ZNF362	149076	broad.mit.edu	37	1	33745854	33745854	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33745854delC	uc001bxc.1	+	5	649	c.479delC	c.(478-480)TCCfs	p.S160fs		NM_152493	NP_689706	Q5T0B9	ZN362_HUMAN	zinc finger protein 362	160					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)																---	---	---	---
ZNF362	149076	broad.mit.edu	37	1	33760658	33760658	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33760658delC	uc001bxc.1	+							NM_152493	NP_689706			zinc finger protein 362						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)														OREG0013342	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CSMD2	114784	broad.mit.edu	37	1	34406590	34406590	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34406590delT	uc001bxn.1	-						CSMD2_uc001bxm.1_Intron	NM_052896	NP_443128			CUB and Sushi multiple domains 2							integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)																---	---	---	---
DLGAP3	58512	broad.mit.edu	37	1	35370746	35370747	+	Frame_Shift_Ins	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35370746_35370747insC	uc001byc.2	-	1	238_239	c.238_239insG	c.(238-240)GCCfs	p.A80fs		NM_001080418	NP_001073887	O95886	DLGP3_HUMAN	discs, large (Drosophila) homolog-associated	80					cell-cell signaling	cell junction|postsynaptic density|postsynaptic membrane				ovary(3)	3		Myeloproliferative disorder(586;0.0393)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	35441528	35441529	+	3'UTR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35441528_35441529delTG	uc001byd.3	-	2										Homo sapiens full length insert cDNA clone YR69B11.																														---	---	---	---
ZMYM4	9202	broad.mit.edu	37	1	35731673	35731673	+	5'Flank	DEL	A	-	-	rs528084	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35731673delA	uc001byt.2	+						ZMYM4_uc009vuu.2_5'Flank|ZMYM4_uc001byu.2_5'Flank	NM_005095	NP_005086			zinc finger protein 262						multicellular organismal development		DNA binding|zinc ion binding			large_intestine(2)|ovary(1)|kidney(1)|skin(1)	5		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
PSMB2	5690	broad.mit.edu	37	1	36062984	36062984	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36062984delC	uc001bzd.1	-							NM_002794	NP_002785			proteasome beta 2 subunit						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome core complex	threonine-type endopeptidase activity				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)			Bortezomib(DB00188)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	36136150	36136150	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36136150delA								PSMB2 (29007 upstream) : C1orf216 (43327 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	36266562	36266565	+	IGR	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36266562_36266565delTTTT								CLSPN (31011 upstream) : EIF2C4 (7263 downstream)																																			---	---	---	---
EIF2C4	192670	broad.mit.edu	37	1	36301364	36301364	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36301364delT	uc001bzj.1	+							NM_017629	NP_060099			eukaryotic translation initiation factor 2C, 4						mRNA catabolic process|negative regulation of translation involved in gene silencing by miRNA	cytoplasmic mRNA processing body|cytosol	protein binding|RNA binding			ovary(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
EIF2C1	26523	broad.mit.edu	37	1	36388063	36388063	+	3'UTR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36388063delG	uc001bzl.2	+	19					EIF2C1_uc001bzk.2_3'UTR|EIF2C1_uc009vuy.2_RNA	NM_012199	NP_036331			eukaryotic translation initiation factor 2C, 1						negative regulation of translation involved in gene silencing by miRNA|nuclear-transcribed mRNA catabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|micro-ribonucleoprotein complex|polysome	protein binding|RNA binding			ovary(2)|skin(1)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
THRAP3	9967	broad.mit.edu	37	1	36703608	36703609	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36703608_36703609insT	uc001cae.3	+						THRAP3_uc001caf.3_Intron|THRAP3_uc001cag.1_5'Flank	NM_005119	NP_005110			thyroid hormone receptor associated protein 3						androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ATP binding|ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(5)|lung(3)|breast(1)	9		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)						T	USP6	aneurysmal bone cysts								---	---	---	---
Unknown	0	broad.mit.edu	37	1	37092659	37092659	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37092659delC								CSF3R (144150 upstream) : GRIK3 (168469 downstream)																																			---	---	---	---
GRIK3	2899	broad.mit.edu	37	1	37270378	37270378	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37270378delG	uc001caz.2	-						GRIK3_uc001cba.1_3'UTR	NM_000831	NP_000822			glutamate receptor, ionotropic, kainate 3						negative regulation of synaptic transmission, glutamatergic|regulation of membrane potential|synaptic transmission	cell junction|dendrite cytoplasm|integral to plasma membrane|perikaryon|postsynaptic membrane|terminal button	adenylate cyclase inhibiting metabotropic glutamate receptor activity|extracellular-glutamate-gated ion channel activity|G-protein-coupled receptor binding|kainate selective glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)|breast(1)	7		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)			L-Glutamic Acid(DB00142)													---	---	---	---
GRIK3	2899	broad.mit.edu	37	1	37307187	37307187	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37307187delC	uc001caz.2	-						GRIK3_uc001cba.1_Intron	NM_000831	NP_000822			glutamate receptor, ionotropic, kainate 3						negative regulation of synaptic transmission, glutamatergic|regulation of membrane potential|synaptic transmission	cell junction|dendrite cytoplasm|integral to plasma membrane|perikaryon|postsynaptic membrane|terminal button	adenylate cyclase inhibiting metabotropic glutamate receptor activity|extracellular-glutamate-gated ion channel activity|G-protein-coupled receptor binding|kainate selective glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)|breast(1)	7		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)			L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	37505582	37505582	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37505582delC								GRIK3 (5738 upstream) : ZC3H12A (434537 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	37584509	37584509	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37584509delG								GRIK3 (84665 upstream) : ZC3H12A (355610 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	37807366	37807366	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37807366delT								GRIK3 (307522 upstream) : ZC3H12A (132753 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	38104600	38104600	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38104600delC								RSPO1 (4109 upstream) : C1orf109 (42650 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	38145253	38145254	+	IGR	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38145253_38145254delAG								RSPO1 (44762 upstream) : C1orf109 (1996 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	38417944	38417945	+	IGR	DEL	AA	-	-	rs143946257		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38417944_38417945delAA								INPP5B (5215 upstream) : SF3A3 (4709 downstream)																																			---	---	---	---
FHL3	2275	broad.mit.edu	37	1	38471422	38471422	+	5'Flank	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38471422delC	uc001ccj.2	-						FHL3_uc001cck.2_5'Flank|FHL3_uc001ccl.2_5'Flank|FHL3_uc001ccm.2_5'Flank|FHL3_uc009vvl.1_5'Flank	NM_004468	NP_004459			four and a half LIM domains 3						muscle organ development		zinc ion binding				0	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	38498465	38498465	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38498465delA								UTP11L (7969 upstream) : POU3F1 (11058 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	38529535	38529536	+	IGR	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38529535_38529536delGA								POU3F1 (17085 upstream) : RRAGC (775479 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	38988987	38988987	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38988987delA								POU3F1 (476537 upstream) : RRAGC (316028 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	39083657	39083657	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39083657delA								POU3F1 (571207 upstream) : RRAGC (221358 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	39084326	39084327	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39084326_39084327delAA								POU3F1 (571876 upstream) : RRAGC (220688 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	39153026	39153027	+	IGR	INS	-	T	T	rs71278738		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39153026_39153027insT								POU3F1 (640576 upstream) : RRAGC (151988 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	39170298	39170298	+	IGR	DEL	A	-	-	rs111389645		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39170298delA								POU3F1 (657848 upstream) : RRAGC (134717 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	39206961	39206961	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39206961delG								POU3F1 (694511 upstream) : RRAGC (98054 downstream)																																			---	---	---	---
RRAGC	64121	broad.mit.edu	37	1	39322850	39322850	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39322850delA	uc001ccq.2	-						RRAGC_uc010oim.1_Intron|RRAGC_uc001ccr.2_Intron	NM_022157	NP_071440			Ras-related GTP binding C						apoptosis|cell growth|cellular protein localization|cellular response to amino acid stimulus|positive regulation of TOR signaling cascade|RNA splicing|small GTPase mediated signal transduction|transcription, DNA-dependent	lysosome|nucleus	GDP binding|GTP binding|GTPase activity|magnesium ion binding|protein heterodimerization activity			ovary(1)	1	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)																---	---	---	---
RHBDL2	54933	broad.mit.edu	37	1	39352117	39352117	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39352117delT	uc001ccu.1	-	8					RHBDL2_uc010oin.1_3'UTR|RHBDL2_uc010oio.1_3'UTR	NM_017821	NP_060291			rhomboid protease 2						proteolysis	integral to membrane|plasma membrane	serine-type endopeptidase activity				0	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;8.23e-17)															---	---	---	---
MACF1	23499	broad.mit.edu	37	1	39561547	39561548	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39561547_39561548delAA	uc010ois.1	+						MACF1_uc010oir.1_Intron	NM_012090	NP_036222			microfilament and actin filament cross-linker						cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)|skin(2)	16	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)															---	---	---	---
BMP8A	353500	broad.mit.edu	37	1	39988318	39988319	+	Intron	INS	-	TTG	TTG	rs139401553	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39988318_39988319insTTG	uc001cdi.2	+						PPIEL_uc001cdj.1_Intron|PPIEL_uc001cdk.2_Intron	NM_181809	NP_861525			bone morphogenetic protein 8A precursor						cartilage development|cell differentiation|growth|ossification	extracellular space	cytokine activity|growth factor activity				0	Lung NSC(20;2.08e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;9.69e-19)|Epithelial(16;9.34e-17)|all cancers(16;1.73e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	40046147	40046148	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40046147_40046148delTT								PABPC4 (3626 upstream) : HEYL (42956 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	40398596	40398596	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40398596delA								MYCL1 (30909 upstream) : MFSD2A (22188 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	40622317	40622318	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40622317_40622318delTG								PPT1 (59175 upstream) : RLF (4723 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	40707641	40707642	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40707641_40707642delTT								RLF (1049 upstream) : TMCO2 (5931 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	40809260	40809260	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40809260delA								COL9A2 (26200 upstream) : SMAP2 (30468 downstream)																																			---	---	---	---
SMAP2	64744	broad.mit.edu	37	1	40836958	40836958	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40836958delA	uc001cfj.2	+						SMAP2_uc010ojh.1_5'Flank	NM_022733	NP_073570			small ArfGAP2						regulation of ARF GTPase activity	cytoplasm|nucleus	ARF GTPase activator activity|zinc ion binding				0	Lung NSC(20;1.56e-05)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;1.04e-17)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	40933983	40933983	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40933983delA								ZNF643 (4631 upstream) : ZNF642 (9319 downstream)																																			---	---	---	---
NFYC	4802	broad.mit.edu	37	1	41235432	41235432	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41235432delT	uc001cge.2	+						NFYC_uc001cfx.3_Intron|NFYC_uc009vwd.2_Intron|NFYC_uc001cfz.2_Intron|NFYC_uc010ojn.1_Intron|NFYC_uc001cfy.3_Intron|NFYC_uc001cgc.2_Intron|NFYC_uc001cgb.2_Intron|NFYC_uc001cgd.3_Intron	NM_001142588	NP_001136060			nuclear transcription factor Y, gamma isoform 1						protein folding|regulation of transcription from RNA polymerase II promoter	CCAAT-binding factor complex	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			breast(2)|kidney(1)	3	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.72e-17)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	41436835	41436836	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41436835_41436836delTT								CITED4 (108817 upstream) : CTPS (8171 downstream)																																			---	---	---	---
CTPS	1503	broad.mit.edu	37	1	41468521	41468521	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41468521delA	uc001cgk.3	+						CTPS_uc010ojo.1_Intron|CTPS_uc001cgl.3_Intron|CTPS_uc010ojq.1_Intron|CTPS_uc009vwe.2_Intron	NM_001905	NP_001896			CTP synthase						CTP biosynthetic process|glutamine metabolic process|nucleobase, nucleoside and nucleotide interconversion|response to drug	cytosol	ATP binding|CTP synthase activity|protein binding				0	Ovarian(52;0.00579)|all_hematologic(146;0.0977)|Breast(333;0.1)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0255)			L-Glutamine(DB00130)													---	---	---	---
SCMH1	22955	broad.mit.edu	37	1	41580334	41580337	+	Intron	DEL	TCTC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41580334_41580337delTCTC	uc001cgo.2	-						SCMH1_uc010ojr.1_Intron|SCMH1_uc001cgp.2_Intron|SCMH1_uc001cgr.2_Intron|SCMH1_uc001cgs.2_Intron|SCMH1_uc001cgt.2_Intron|SCMH1_uc001cgq.2_Intron|SCMH1_uc010ojs.1_Intron	NM_001031694	NP_001026864			sex comb on midleg 1 isoform 1						anatomical structure morphogenesis|gene silencing|multicellular organismal development|negative regulation of transcription, DNA-dependent		DNA binding|sequence-specific DNA binding transcription factor activity				0	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)|Breast(333;0.162)	Myeloproliferative disorder(586;0.0393)																---	---	---	---
HIVEP3	59269	broad.mit.edu	37	1	42450648	42450650	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42450648_42450650delAAA	uc001chb.1	-											Homo sapiens kappa B and V(D)J recombination signal sequences binding protein (KRC) mRNA, complete cds.						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	42510159	42510159	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42510159delT								HIVEP3 (8563 upstream) : GUCA2B (108933 downstream)																																			---	---	---	---
FOXJ3	22887	broad.mit.edu	37	1	42785289	42785289	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42785289delA	uc001che.2	-						FOXJ3_uc001chf.2_Intron|FOXJ3_uc001chg.2_Intron|FOXJ3_uc001chh.1_Intron	NM_014947	NP_055762			forkhead box J3						embryo development|organ development|pattern specification process|positive regulation of transcription, DNA-dependent|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein domain specific binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			ovary(2)	2	Ovarian(52;0.01)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)																---	---	---	---
RIMKLA	284716	broad.mit.edu	37	1	42869711	42869712	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42869711_42869712delTT	uc001chi.2	+							NM_173642	NP_775913			ribosomal modification protein rimK-like family						protein modification process	cytoplasm	acid-amino acid ligase activity|ATP binding|metal ion binding				0																		---	---	---	---
CCDC30	728621	broad.mit.edu	37	1	43060690	43060690	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43060690delT	uc009vwk.1	+						CCDC30_uc001chm.2_Intron|CCDC30_uc001chn.2_Intron|CCDC30_uc001chp.2_3'UTR	NM_001080850	NP_001074319			coiled-coil domain containing 30												0																		---	---	---	---
CCDC30	728621	broad.mit.edu	37	1	43108032	43108032	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43108032delA	uc009vwk.1	+						CCDC30_uc001chm.2_Intron|CCDC30_uc001chn.2_Intron	NM_001080850	NP_001074319			coiled-coil domain containing 30												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	43327694	43327694	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43327694delA	uc001cij.1	+											Homo sapiens cDNA clone IMAGE:5170739.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	43474793	43474793	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43474793delA								SLC2A1 (49946 upstream) : FAM183A (138801 downstream)																																			---	---	---	---
FAM183A	440585	broad.mit.edu	37	1	43615028	43615028	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43615028delC	uc009vwo.2	+							NM_001101376	NP_001094846			hCG23177											ovary(3)	3																		---	---	---	---
MPL	4352	broad.mit.edu	37	1	43807554	43807554	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43807554delT	uc001ciw.2	+						MPL_uc001civ.2_Intron|MPL_uc009vwr.2_Intron	NM_005373	NP_005364			myeloproliferative leukemia virus oncogene						cell proliferation|platelet activation	integral to plasma membrane	cytokine receptor activity			haematopoietic_and_lymphoid_tissue(361)|upper_aerodigestive_tract(1)|pancreas(1)	363	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)						Mis		MPD	MPD	congenital amegakaryocytic thrombocytopenia						---	---	---	---
CDC20	991	broad.mit.edu	37	1	43828862	43828862	+	3'UTR	DEL	T	-	-	rs78262841		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43828862delT	uc001cix.2	+	11					CDC20_uc001ciy.2_3'UTR	NM_001255	NP_001246			cell division cycle 20						activation of anaphase-promoting complex activity|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of synapse maturation|positive regulation of synaptic plasticity|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle	cytosol|nucleoplasm|spindle	enzyme binding|protein C-terminus binding				0	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)																---	---	---	---
KIAA0467	23334	broad.mit.edu	37	1	43862179	43862179	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43862179delA	uc009vws.1	+						C1orf84_uc001cjh.2_Intron|C1orf84_uc001cji.1_Intron					Homo sapiens mRNA for KIAA0467 protein, partial cds.							peroxisome					0	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)																---	---	---	---
ST3GAL3	6487	broad.mit.edu	37	1	44231492	44231492	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44231492delT	uc001ckc.2	+						ST3GAL3_uc009vwu.1_Intron|ST3GAL3_uc010okj.1_Intron|ST3GAL3_uc001cjz.2_Intron|ST3GAL3_uc001cka.2_Intron|ST3GAL3_uc001ckb.2_Intron|ST3GAL3_uc001ckd.2_Intron|ST3GAL3_uc001cke.2_Intron|ST3GAL3_uc001ckf.2_Intron|ST3GAL3_uc001ckg.2_Intron|ST3GAL3_uc001ckh.2_Intron|ST3GAL3_uc001cki.2_Intron|ST3GAL3_uc009vwv.2_Intron|ST3GAL3_uc001ckj.2_Intron|ST3GAL3_uc009vww.2_Intron|ST3GAL3_uc001ckk.2_Intron|ST3GAL3_uc009vwy.2_Intron|ST3GAL3_uc009vwx.2_Intron|ST3GAL3_uc001ckm.2_Intron|ST3GAL3_uc001ckl.2_Intron|ST3GAL3_uc009vwz.2_Intron|ST3GAL3_uc001ckn.2_Intron|ST3GAL3_uc001ckp.2_Intron|ST3GAL3_uc001cko.2_Intron|ST3GAL3_uc009vxa.2_Intron|ST3GAL3_uc001ckq.2_Intron|ST3GAL3_uc001ckr.2_Intron|ST3GAL3_uc009vxb.2_Intron	NM_006279	NP_006270			sialyltransferase 6 isoform j						protein glycosylation	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	N-acetyllactosaminide alpha-2,3-sialyltransferase activity			ovary(3)	3	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0518)																---	---	---	---
SLC6A9	6536	broad.mit.edu	37	1	44467402	44467402	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44467402delT	uc001cll.2	-						SLC6A9_uc009vxe.2_Intron|SLC6A9_uc010okm.1_Intron|SLC6A9_uc001clm.2_Intron|SLC6A9_uc009vxd.2_Intron|SLC6A9_uc010okn.1_Intron|SLC6A9_uc001cln.2_Intron|SLC6A9_uc010oko.1_Intron|SLC6A9_uc010okp.1_Intron	NM_201649	NP_964012			solute carrier family 6 member 9 isoform 2							integral to plasma membrane|membrane fraction	glycine:sodium symporter activity|neurotransmitter:sodium symporter activity				0	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)			Glycine(DB00145)													---	---	---	---
KLF17	128209	broad.mit.edu	37	1	44589947	44589947	+	Intron	DEL	T	-	-	rs35585037		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44589947delT	uc001clp.2	+						KLF17_uc009vxf.1_Intron	NM_173484	NP_775755			zinc finger protein 393						regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	44603909	44603909	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44603909delA								KLF17 (3102 upstream) : DMAP1 (75216 downstream)																																			---	---	---	---
ERI3	79033	broad.mit.edu	37	1	44792085	44792085	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44792085delA	uc001clt.2	-						ERI3_uc010okv.1_Intron|ERI3_uc009vxg.2_Intron|ERI3_uc010okw.1_Intron|ERI3_uc001clu.2_Intron	NM_024066	NP_076971			prion protein interacting protein							intracellular	exonuclease activity|metal ion binding|nucleic acid binding			ovary(2)|large_intestine(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	44834865	44834865	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44834865delT								ERI3 (13926 upstream) : RNF220 (36095 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	45237694	45237694	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45237694delT								KIF2C (4258 upstream) : RPS8 (3552 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	45245946	45245946	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45245946delT								RPS8 (1535 upstream) : BEST4 (3313 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	45249064	45249065	+	IGR	INS	-	TG	TG	rs147696977	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45249064_45249065insTG								RPS8 (4653 upstream) : BEST4 (194 downstream)																																			---	---	---	---
EIF2B3	8891	broad.mit.edu	37	1	45366323	45366324	+	Intron	DEL	TA	-	-	rs263970	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45366323_45366324delTA	uc001cmt.1	-						EIF2B3_uc001cmu.1_Intron|EIF2B3_uc001cmv.1_Intron|EIF2B3_uc001cmw.2_Intron	NM_020365	NP_065098			eukaryotic translation initiation factor 2B,						negative regulation of translational initiation in response to stress|oligodendrocyte development|response to glucose stimulus|response to heat|response to peptide hormone stimulus	cytosol|eukaryotic translation initiation factor 2B complex	nucleotidyltransferase activity|protein binding|translation initiation factor activity			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
TOE1	114034	broad.mit.edu	37	1	45807064	45807064	+	Intron	DEL	G	-	-	rs3811432	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45807064delG	uc009vxq.2	+						MUTYH_uc001cnf.2_5'Flank|MUTYH_uc009vxo.2_5'Flank|MUTYH_uc001cng.2_5'Flank|MUTYH_uc001cnj.2_5'Flank|MUTYH_uc001cni.2_5'Flank|MUTYH_uc001cnh.2_5'Flank|MUTYH_uc001cno.2_5'Flank|MUTYH_uc001cnk.2_5'Flank|MUTYH_uc010oll.1_5'Flank|MUTYH_uc001cnm.2_5'Flank|MUTYH_uc001cnl.2_5'Flank|MUTYH_uc009vxp.2_5'Flank|MUTYH_uc001cnn.2_5'Flank|TOE1_uc001cnq.3_Intron|TOE1_uc010olm.1_Intron|TOE1_uc010oln.1_Intron|TOE1_uc001cnr.3_Intron	NM_025077	NP_079353			target of EGR1, member 1 (nuclear)							nuclear speck|nucleolus	nucleic acid binding|zinc ion binding			central_nervous_system(1)	1	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
TESK2	10420	broad.mit.edu	37	1	45821220	45821220	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45821220delT	uc001cns.1	-						TESK2_uc009vxr.1_Intron|TESK2_uc010olo.1_Intron|TESK2_uc009vxs.1_Intron	NM_007170	NP_009101			testis-specific protein kinase 2						actin cytoskeleton organization|focal adhesion assembly|spermatogenesis	nucleus	ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(2)|breast(2)|pancreas(1)	5	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
TESK2	10420	broad.mit.edu	37	1	45864059	45864060	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45864059_45864060insA	uc001cns.1	-						TESK2_uc009vxr.1_Intron|TESK2_uc010olo.1_Intron|TESK2_uc009vxs.1_Intron	NM_007170	NP_009101			testis-specific protein kinase 2						actin cytoskeleton organization|focal adhesion assembly|spermatogenesis	nucleus	ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(2)|breast(2)|pancreas(1)	5	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
IPP	3652	broad.mit.edu	37	1	46166007	46166007	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46166007delT	uc001cou.2	-						IPP_uc001cos.3_Intron	NM_005897	NP_005888			intracisternal A particle-promoted polypeptide							actin cytoskeleton|cytoplasm	actin binding			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
IPP	3652	broad.mit.edu	37	1	46206445	46206445	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46206445delA	uc001cou.2	-						IPP_uc001cos.3_Intron	NM_005897	NP_005888			intracisternal A particle-promoted polypeptide							actin cytoskeleton|cytoplasm	actin binding			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	46252476	46252476	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46252476delA								IPP (35991 upstream) : MAST2 (16809 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	46260823	46260823	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46260823delT								IPP (44338 upstream) : MAST2 (8462 downstream)																																			---	---	---	---
MAST2	23139	broad.mit.edu	37	1	46299542	46299542	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46299542delT	uc001cov.2	+						MAST2_uc001cow.2_Intron	NM_015112	NP_055927			microtubule associated serine/threonine kinase						regulation of interleukin-12 biosynthetic process|spermatid differentiation	cytoplasm|cytoskeleton|plasma membrane	ATP binding|magnesium ion binding|phosphatase binding|protein serine/threonine kinase activity			ovary(5)|lung(3)|stomach(2)|breast(1)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)																	---	---	---	---
MAST2	23139	broad.mit.edu	37	1	46375796	46375799	+	Intron	DEL	TTTC	-	-	rs57335268	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46375796_46375799delTTTC	uc001cov.2	+						MAST2_uc001cow.2_Intron|MAST2_uc001cox.1_Intron|MAST2_uc001coy.1_Intron	NM_015112	NP_055927			microtubule associated serine/threonine kinase						regulation of interleukin-12 biosynthetic process|spermatid differentiation	cytoplasm|cytoskeleton|plasma membrane	ATP binding|magnesium ion binding|phosphatase binding|protein serine/threonine kinase activity			ovary(5)|lung(3)|stomach(2)|breast(1)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)																	---	---	---	---
PIK3R3	8503	broad.mit.edu	37	1	46514397	46514398	+	Intron	INS	-	A	A	rs140041494	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46514397_46514398insA	uc001cpb.3	-						PIK3R3_uc009vyb.2_Intron|PIK3R3_uc009vyc.2_Intron|PIK3R3_uc001cpc.3_Intron|PIK3R3_uc010olw.1_Intron|PIK3R3_uc010olv.1_Intron	NM_003629	NP_003620			phosphoinositide-3-kinase, regulatory subunit 3						insulin receptor signaling pathway|platelet activation|T cell costimulation		1-phosphatidylinositol-3-kinase activity|protein binding				0	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
PIK3R3	8503	broad.mit.edu	37	1	46541684	46541684	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46541684delT	uc001cpb.3	-						PIK3R3_uc009vyb.2_Intron|PIK3R3_uc009vyc.2_Intron|PIK3R3_uc001cpc.3_Intron|PIK3R3_uc010olw.1_Intron	NM_003629	NP_003620			phosphoinositide-3-kinase, regulatory subunit 3						insulin receptor signaling pathway|platelet activation|T cell costimulation		1-phosphatidylinositol-3-kinase activity|protein binding				0	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
PIK3R3	8503	broad.mit.edu	37	1	46594746	46594748	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46594746_46594748delAAA	uc001cpb.3	-						PIK3R3_uc009vyb.2_Intron|PIK3R3_uc009vyc.2_Intron|PIK3R3_uc001cpc.3_Intron|PIK3R3_uc010olw.1_Intron	NM_003629	NP_003620			phosphoinositide-3-kinase, regulatory subunit 3						insulin receptor signaling pathway|platelet activation|T cell costimulation		1-phosphatidylinositol-3-kinase activity|protein binding				0	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
POMGNT1	55624	broad.mit.edu	37	1	46688564	46688564	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46688564delT	uc001cpg.2	-						POMGNT1_uc001cpf.2_5'Flank	NR_024332				SubName: Full=Protein O-linked mannose beta1,2-N-acetylglucosaminyltransferase;						protein N-linked glycosylation|protein O-linked glycosylation	Golgi membrane|integral to membrane|microsome	alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity|beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	46785644	46785644	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46785644delT								UQCRH (3199 upstream) : NSUN4 (20746 downstream)																																			---	---	---	---
MKNK1	8569	broad.mit.edu	37	1	47025655	47025655	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47025655delT	uc001cqb.2	-						MKNK1_uc010omd.1_Intron|MKNK1_uc001cqc.2_Intron|MKNK1_uc009vyi.2_Intron|MKNK1_uc010ome.1_Intron	NM_003684	NP_003675			MAP kinase-interacting serine/threonine kinase 1						intracellular protein kinase cascade|peptidyl-serine phosphorylation|regulation of translation	cytoplasm|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			lung(2)	2	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
MKNK1	8569	broad.mit.edu	37	1	47034601	47034601	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47034601delA	uc001cqb.2	-						MKNK1_uc010omd.1_Intron|MKNK1_uc001cqc.2_Intron|MKNK1_uc009vyi.2_Intron|MKNK1_uc010ome.1_Intron|MKNK1_uc009vyj.2_Intron|MKNK1_uc001cqd.2_Intron	NM_003684	NP_003675			MAP kinase-interacting serine/threonine kinase 1						intracellular protein kinase cascade|peptidyl-serine phosphorylation|regulation of translation	cytoplasm|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			lung(2)	2	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
CYP4B1	1580	broad.mit.edu	37	1	47270107	47270107	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47270107delT	uc001cqm.3	+						CYP4B1_uc009vyl.1_Intron|CYP4B1_uc001cqn.3_Intron|CYP4B1_uc009vym.2_Intron|CYP4B1_uc010omk.1_Intron	NM_000779	NP_000770			cytochrome P450, family 4, subfamily B,						xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding			ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
CYP4Z2P	163720	broad.mit.edu	37	1	47365870	47365870	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47365870delT	uc001cqo.1	-						CYP4Z2P_uc009vyn.1_Intron	NR_002788				Homo sapiens cDNA FLJ40054 fis, clone TBAES2000315, weakly similar to CYTOCHROME P450 4A1 (EC 1.14.15.3).												0																		---	---	---	---
CYP4Z1	199974	broad.mit.edu	37	1	47581122	47581122	+	Intron	DEL	A	-	-	rs7547893	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47581122delA	uc001cqu.1	+							NM_178134	NP_835235			cytochrome P450 4Z1							endoplasmic reticulum membrane|integral to membrane|microsome	aromatase activity|electron carrier activity|heme binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	47595465	47595467	+	IGR	DEL	AAT	-	-	rs150236130		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47595465_47595467delAAT								CYP4Z1 (11473 upstream) : CYP4A22 (7640 downstream)																																			---	---	---	---
PDZK1IP1	10158	broad.mit.edu	37	1	47650220	47650220	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47650220delT	uc001cqw.2	-							NM_005764	NP_005755			PDZK1 interacting protein 1							integral to membrane					0																		---	---	---	---
SPATA6	54558	broad.mit.edu	37	1	48790635	48790635	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:48790635delA	uc001crr.1	-						SPATA6_uc001crs.1_Intron|SPATA6_uc010omv.1_Intron	NM_019073	NP_061946			spermatogenesis associated 6 precursor						cell differentiation|multicellular organismal development|spermatogenesis	extracellular region				ovary(1)	1																		---	---	---	---
AGBL4	84871	broad.mit.edu	37	1	49033964	49033965	+	Intron	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49033964_49033965delTC	uc001cru.2	-						AGBL4_uc010omw.1_Intron|AGBL4_uc010omx.1_Intron	NM_032785	NP_116174			ATP/GTP binding protein-like 4						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(1)|breast(1)	2				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)														---	---	---	---
AGBL4	84871	broad.mit.edu	37	1	49819666	49819666	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:49819666delA	uc001cru.2	-						AGBL4_uc010omw.1_Intron|AGBL4_uc010omx.1_Intron	NM_032785	NP_116174			ATP/GTP binding protein-like 4						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(1)|breast(1)	2				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)														---	---	---	---
AGBL4	84871	broad.mit.edu	37	1	50198707	50198707	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50198707delA	uc001cru.2	-						AGBL4_uc010omw.1_Intron|AGBL4_uc010omx.1_Intron	NM_032785	NP_116174			ATP/GTP binding protein-like 4						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(1)|breast(1)	2				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)														---	---	---	---
ELAVL4	1996	broad.mit.edu	37	1	50519196	50519196	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50519196delT	uc001cry.3	+							NM_001144777	NP_001138249			ELAV-like 4 isoform 5						mRNA processing		AU-rich element binding|mRNA 3'-UTR binding|nucleotide binding			ovary(1)|pancreas(1)	2																		---	---	---	---
ELAVL4	1996	broad.mit.edu	37	1	50601883	50601883	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50601883delA	uc001csb.2	+						ELAVL4_uc001cry.3_Intron|ELAVL4_uc001crz.3_Intron|ELAVL4_uc001csa.3_Intron|ELAVL4_uc001csc.3_Intron|ELAVL4_uc009vyu.2_Intron|ELAVL4_uc010omz.1_Intron	NM_021952	NP_068771			ELAV-like 4 isoform 1						mRNA processing		AU-rich element binding|mRNA 3'-UTR binding|nucleotide binding			ovary(1)|pancreas(1)	2																		---	---	---	---
FAF1	11124	broad.mit.edu	37	1	50957521	50957521	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50957521delA	uc009vyx.1	-						FAF1_uc009vyw.1_Intron|FAF1_uc001cse.1_Intron|FAF1_uc010onc.1_Intron	NM_007051	NP_008982			FAS-associated factor 1						apoptosis|cytoplasmic sequestering of NF-kappaB|positive regulation of apoptosis|positive regulation of protein complex assembly|proteasomal ubiquitin-dependent protein catabolic process|regulation of protein catabolic process	CD95 death-inducing signaling complex|cytosol|perinuclear region of cytoplasm	heat shock protein binding|NF-kappaB binding|protein kinase binding|protein kinase regulator activity			ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)														---	---	---	---
EPS15	2060	broad.mit.edu	37	1	51929725	51929725	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51929725delT	uc001csq.1	-						EPS15_uc009vyz.1_Intron	NM_001981	NP_001972			epidermal growth factor receptor pathway						cell proliferation|clathrin coat assembly|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|protein transport	cytosol|early endosome membrane	calcium ion binding|SH3 domain binding			lung(1)|kidney(1)	2								T	MLL	ALL								---	---	---	---
Unknown	0	broad.mit.edu	37	1	51994220	51994220	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51994220delA								EPS15 (9225 upstream) : OSBPL9 (48631 downstream)																																			---	---	---	---
OSBPL9	114883	broad.mit.edu	37	1	52200824	52200824	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52200824delA	uc001cst.2	+						OSBPL9_uc001css.2_Intron|OSBPL9_uc001csx.2_Intron|OSBPL9_uc009vza.2_Intron|OSBPL9_uc001csu.2_Intron|OSBPL9_uc001csv.2_Intron|OSBPL9_uc001csw.2_Intron|OSBPL9_uc001csy.2_Intron|OSBPL9_uc001csz.2_Intron|OSBPL9_uc001cta.2_Intron	NM_024586	NP_078862			oxysterol binding protein-like 9 isoform e						lipid transport		lipid binding			central_nervous_system(1)	1																		---	---	---	---
OSBPL9	114883	broad.mit.edu	37	1	52205662	52205662	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52205662delT	uc001cst.2	+						OSBPL9_uc001css.2_Intron|OSBPL9_uc001csx.2_Intron|OSBPL9_uc009vza.2_Intron|OSBPL9_uc001csu.2_Intron|OSBPL9_uc001csv.2_Intron|OSBPL9_uc001csw.2_Intron|OSBPL9_uc001csy.2_Intron|OSBPL9_uc001csz.2_Intron|OSBPL9_uc001cta.2_Intron	NM_024586	NP_078862			oxysterol binding protein-like 9 isoform e						lipid transport		lipid binding			central_nervous_system(1)	1																		---	---	---	---
NRD1	4898	broad.mit.edu	37	1	52301764	52301765	+	Intron	DEL	AA	-	-	rs115629064	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52301764_52301765delAA	uc001ctc.3	-						NRD1_uc009vzb.2_Intron|NRD1_uc001ctd.3_Intron|NRD1_uc001cte.2_Intron|NRD1_uc001ctf.2_Intron|NRD1_uc010ong.1_Intron|NRD1_uc009vzc.1_Intron	NM_002525	NP_002516			nardilysin isoform a						cell migration|cell proliferation|neuromuscular junction development|positive regulation of membrane protein ectodomain proteolysis|proteolysis|regulation of endopeptidase activity	cell surface|cytosol	epidermal growth factor binding|metalloendopeptidase activity|zinc ion binding				0																		---	---	---	---
NRD1	4898	broad.mit.edu	37	1	52341480	52341480	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52341480delC	uc001ctc.3	-						NRD1_uc001ctd.3_Intron|NRD1_uc001cte.2_Intron|NRD1_uc001ctf.2_Intron|NRD1_uc010ong.1_Intron|NRD1_uc009vzc.1_Intron	NM_002525	NP_002516			nardilysin isoform a						cell migration|cell proliferation|neuromuscular junction development|positive regulation of membrane protein ectodomain proteolysis|proteolysis|regulation of endopeptidase activity	cell surface|cytosol	epidermal growth factor binding|metalloendopeptidase activity|zinc ion binding				0																		---	---	---	---
RAB3B	5865	broad.mit.edu	37	1	52405998	52405998	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52405998delA	uc001cth.2	-							NM_002867	NP_002858			RAB3B, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding|GTPase activity			ovary(1)	1																		---	---	---	---
ZFYVE9	9372	broad.mit.edu	37	1	52810259	52810259	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52810259delT	uc001cto.2	+						ZFYVE9_uc001ctp.2_Intron	NM_004799	NP_004790			zinc finger, FYVE domain containing 9 isoform 3						endocytosis|SMAD protein complex assembly|SMAD protein import into nucleus|transforming growth factor beta receptor signaling pathway	early endosome membrane	metal ion binding|protein binding|receptor activity|serine-type peptidase activity			ovary(2)|lung(2)|central_nervous_system(2)|skin(2)	8																		---	---	---	---
ZCCHC11	23318	broad.mit.edu	37	1	52890675	52890675	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52890675delA	uc001ctx.2	-						ZCCHC11_uc001cty.2_Intron|ZCCHC11_uc001ctz.2_Intron	NM_015269	NP_056084			zinc finger, CCHC domain containing 11 isoform						miRNA catabolic process|pre-miRNA processing|RNA 3'-end processing|stem cell maintenance	cytoplasm|nucleolus	nucleic acid binding|protein binding|protein binding|RNA uridylyltransferase activity|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
ZCCHC11	23318	broad.mit.edu	37	1	52944667	52944667	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52944667delA	uc001ctx.2	-						ZCCHC11_uc001cty.2_Intron|ZCCHC11_uc001ctz.2_Intron|ZCCHC11_uc009vze.1_Intron|ZCCHC11_uc009vzf.1_Intron|ZCCHC11_uc001cub.2_Intron|ZCCHC11_uc001cuc.2_Intron	NM_015269	NP_056084			zinc finger, CCHC domain containing 11 isoform						miRNA catabolic process|pre-miRNA processing|RNA 3'-end processing|stem cell maintenance	cytoplasm|nucleolus	nucleic acid binding|protein binding|protein binding|RNA uridylyltransferase activity|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
C1orf163	65260	broad.mit.edu	37	1	53153917	53153917	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53153917delT	uc001cui.1	-							NM_023077	NP_075565			hypothetical protein LOC65260								binding				0																		---	---	---	---
ZYG11B	79699	broad.mit.edu	37	1	53255588	53255589	+	Intron	DEL	TT	-	-	rs67389144		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53255588_53255589delTT	uc001cuj.2	+						ZYG11B_uc009vzg.2_Intron|ZYG11B_uc010onj.1_Intron	NM_024646	NP_078922			zyg-11 homolog B								protein binding			upper_aerodigestive_tract(2)|ovary(1)|pancreas(1)	4																		---	---	---	---
ZYG11A	440590	broad.mit.edu	37	1	53310980	53310980	+	Intron	DEL	T	-	-	rs138948536		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53310980delT	uc001cuk.2	+						ZYG11A_uc001cul.2_Intron	NM_001004339	NP_001004339			zyg-11 homolog A								binding				0																		---	---	---	---
ZYG11A	440590	broad.mit.edu	37	1	53316716	53316716	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53316716delT	uc001cuk.2	+						ZYG11A_uc001cul.2_Intron	NM_001004339	NP_001004339			zyg-11 homolog A								binding				0																		---	---	---	---
ECHDC2	55268	broad.mit.edu	37	1	53377526	53377526	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53377526delG	uc001cup.3	-						ECHDC2_uc001cun.2_5'UTR|ECHDC2_uc001cuo.3_Intron|ECHDC2_uc010onk.1_Intron|ECHDC2_uc010onl.1_Intron|ECHDC2_uc010onm.1_Intron|ECHDC2_uc010onn.1_Intron	NM_018281	NP_060751			enoyl Coenzyme A hydratase domain containing 2						fatty acid metabolic process	mitochondrion	lyase activity			central_nervous_system(1)	1																		---	---	---	---
SCP2	6342	broad.mit.edu	37	1	53442196	53442196	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53442196delT	uc001cur.1	+						SCP2_uc001cus.1_Intron|SCP2_uc010ono.1_Intron|SCP2_uc010onp.1_Intron|SCP2_uc009vzi.1_Intron|SCP2_uc001cuq.1_Intron	NM_002979	NP_002970			sterol carrier protein 2 isoform 1 proprotein						bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase|lipid transport	mitochondrion|nucleus|peroxisomal matrix	propanoyl-CoA C-acyltransferase activity|propionyl-CoA C2-trimethyltridecanoyltransferase activity|protein binding|sterol binding			breast(1)	1																		---	---	---	---
SCP2	6342	broad.mit.edu	37	1	53442499	53442499	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53442499delC	uc001cur.1	+						SCP2_uc001cus.1_Intron|SCP2_uc010ono.1_Intron|SCP2_uc010onp.1_Intron|SCP2_uc009vzi.1_Intron|SCP2_uc001cuq.1_Intron	NM_002979	NP_002970			sterol carrier protein 2 isoform 1 proprotein						bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase|lipid transport	mitochondrion|nucleus|peroxisomal matrix	propanoyl-CoA C-acyltransferase activity|propionyl-CoA C2-trimethyltridecanoyltransferase activity|protein binding|sterol binding			breast(1)	1																		---	---	---	---
SCP2	6342	broad.mit.edu	37	1	53515429	53515429	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53515429delA	uc001cur.1	+						SCP2_uc001cus.1_Intron|SCP2_uc010ono.1_Intron|SCP2_uc010onp.1_Intron|SCP2_uc009vzi.1_Intron|SCP2_uc010onq.1_3'UTR|SCP2_uc001cut.1_Intron|SCP2_uc001cuu.1_Intron	NM_002979	NP_002970			sterol carrier protein 2 isoform 1 proprotein						bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase|lipid transport	mitochondrion|nucleus|peroxisomal matrix	propanoyl-CoA C-acyltransferase activity|propionyl-CoA C2-trimethyltridecanoyltransferase activity|protein binding|sterol binding			breast(1)	1																		---	---	---	---
C1orf123	54987	broad.mit.edu	37	1	53684324	53684324	+	Intron	DEL	A	-	-	rs3736118	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53684324delA	uc001cvd.2	-						C1orf123_uc001cvc.2_5'Flank|C1orf123_uc001cve.2_Intron	NM_017887	NP_060357			hypothetical protein LOC54987											pancreas(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	53858773	53858773	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53858773delA								LRP8 (64952 upstream) : FLJ40434 (45271 downstream)																																			---	---	---	---
GLIS1	148979	broad.mit.edu	37	1	53997898	53997898	+	Intron	DEL	G	-	-	rs143872857	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53997898delG	uc001cvr.1	-							NM_147193	NP_671726			GLIS family zinc finger 1						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding			skin(1)	1																		---	---	---	---
TMEM48	55706	broad.mit.edu	37	1	54269796	54269796	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54269796delA	uc001cvs.2	-						TMEM48_uc010onu.1_Intron|TMEM48_uc001cvt.2_Intron|TMEM48_uc009vzk.2_Intron|TMEM48_uc010onv.1_Intron	NM_018087	NP_060557			transmembrane protein 48						mRNA transport|nuclear pore complex assembly|nuclear pore distribution|protein transport|transmembrane transport	nuclear membrane|nuclear pore	protein binding|structural constituent of nuclear pore			ovary(1)|pancreas(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	54317102	54317102	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54317102delT								TMEM48 (12927 upstream) : YIPF1 (305 downstream)																																			---	---	---	---
SSBP3	23648	broad.mit.edu	37	1	54870482	54870484	+	Intron	DEL	GGG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54870482_54870484delGGG	uc001cxe.2	-						SSBP3_uc001cxf.2_Intron|SSBP3_uc001cxg.2_Intron	NM_145716	NP_663768			single stranded DNA binding protein 3 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	single-stranded DNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	54926295	54926296	+	IGR	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54926295_54926296delAC								SSBP3 (54203 upstream) : ACOT11 (81634 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	54941008	54941008	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54941008delT								SSBP3 (68916 upstream) : ACOT11 (66922 downstream)																																			---	---	---	---
ACOT11	26027	broad.mit.edu	37	1	55016334	55016334	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55016334delA	uc001cxm.1	+						ACOT11_uc001cxj.1_Intron|ACOT11_uc001cxk.2_Intron|ACOT11_uc001cxl.1_Intron	NM_015547	NP_056362			thioesterase, adipose associated isoform BFIT1						fatty acid metabolic process|intracellular signal transduction|response to cold		acyl-CoA thioesterase activity|carboxylesterase activity			central_nervous_system(1)	1																		---	---	---	---
C1orf175	374977	broad.mit.edu	37	1	55157460	55157465	+	Intron	DEL	AAAAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55157460_55157465delAAAAAA	uc010ooe.1	+						C1orf175_uc001cxq.2_Intron|C1orf175_uc010ooc.1_Intron|C1orf175_uc001cxs.2_Intron|C1orf175_uc010ood.1_Intron|C1orf175_uc010oof.1_Intron|C1orf175_uc001cxr.1_Intron|C1orf175_uc010oog.1_Intron|C1orf175_uc010ooh.1_Intron|C1orf175_uc009vzq.1_Intron|C1orf175_uc001cxt.1_Intron|C1orf175_uc009vzr.1_Intron|C1orf175_uc001cxu.2_Intron	NM_001039464	NP_001034553			hypothetical protein LOC374977							integral to membrane	binding				0																		---	---	---	---
C1orf177	163747	broad.mit.edu	37	1	55275558	55275558	+	Intron	DEL	C	-	-	rs67994040		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55275558delC	uc001cyb.3	+						C1orf177_uc001cya.3_Intron	NM_001110533	NP_001104003			hypothetical protein LOC163747 isoform 2												0																OREG0013501	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
USP24	23358	broad.mit.edu	37	1	55604597	55604597	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55604597delA	uc001cyg.3	-							NM_015306	NP_056121			ubiquitin specific protease 24						ubiquitin-dependent protein catabolic process		binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(6)|kidney(6)|breast(1)	13																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	56288035	56288035	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56288035delG								USP24 (607273 upstream) : PPAP2B (672398 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	56588720	56588720	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56588720delT								USP24 (907958 upstream) : PPAP2B (371713 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	56614587	56614587	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56614587delT								USP24 (933825 upstream) : PPAP2B (345846 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	56701705	56701706	+	IGR	DEL	CA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:56701705_56701706delCA								None (None upstream) : PPAP2B (258727 downstream)																																			---	---	---	---
PRKAA2	5563	broad.mit.edu	37	1	57158313	57158313	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57158313delT	uc001cyk.3	+							NM_006252	NP_006243			AMP-activated protein kinase alpha 2 catalytic						carnitine shuttle|cell cycle arrest|cholesterol biosynthetic process|energy reserve metabolic process|fatty acid biosynthetic process|insulin receptor signaling pathway|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation	cytosol|nucleoplasm	ATP binding|metal ion binding			breast(4)|ovary(1)|stomach(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	57303232	57303232	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57303232delT								C1orf168 (17863 upstream) : C8A (17211 downstream)																																			---	---	---	---
DAB1	1600	broad.mit.edu	37	1	57728794	57728795	+	Intron	DEL	TT	-	-	rs71968483		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57728794_57728795delTT	uc001cys.1	-						DAB1_uc001cyt.1_Intron|DAB1_uc001cyq.1_Intron|DAB1_uc001cyr.1_Intron|DAB1_uc009vzw.1_Intron|DAB1_uc009vzx.1_Intron	NM_021080	NP_066566			disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3																		---	---	---	---
DAB1	1600	broad.mit.edu	37	1	58127852	58127855	+	Intron	DEL	TTTG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58127852_58127855delTTTG	uc001cys.1	-						DAB1_uc001cyt.1_Intron	NM_021080	NP_066566			disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3																		---	---	---	---
DAB1	1600	broad.mit.edu	37	1	58224424	58224424	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58224424delT	uc001cys.1	-						DAB1_uc001cyt.1_Intron	NM_021080	NP_066566			disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3																		---	---	---	---
DAB1	1600	broad.mit.edu	37	1	58509065	58509066	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:58509065_58509066insA	uc001cys.1	-						DAB1_uc001cyt.1_Intron	NM_021080	NP_066566			disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3																		---	---	---	---
DAB1	1600	broad.mit.edu	37	1	59004990	59004990	+	Intron	DEL	A	-	-	rs79348154		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59004990delA	uc001cyt.1	-						OMA1_uc001cyx.1_5'Flank|OMA1_uc001cyy.2_Intron|OMA1_uc009vzz.2_Intron	NM_021080	NP_066566			disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	59229944	59229944	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59229944delG								MYSM1 (64197 upstream) : JUN (16520 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	59294909	59294909	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59294909delT	uc001czf.2	+						uc010oop.1_Intron					Homo sapiens cDNA FLJ30588 fis, clone BRAWH2008128.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	59309893	59309893	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59309893delT	uc001czf.2	+						uc010oop.1_Intron					Homo sapiens cDNA FLJ30588 fis, clone BRAWH2008128.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	59383355	59383355	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59383355delA								JUN (133570 upstream) : LOC729467 (214255 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	59400049	59400049	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59400049delT								JUN (150264 upstream) : LOC729467 (197561 downstream)																																			---	---	---	---
FGGY	55277	broad.mit.edu	37	1	59862073	59862073	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59862073delT	uc001czi.3	+						FGGY_uc001czg.2_Intron|FGGY_uc001czh.2_Intron|FGGY_uc009wac.2_Intron|FGGY_uc001czj.3_Intron|FGGY_uc001czk.3_Intron|FGGY_uc001czl.3_Intron	NM_018291	NP_060761			FGGY carbohydrate kinase domain containing						carbohydrate metabolic process|cell death|neuron homeostasis		kinase activity|phosphotransferase activity, alcohol group as acceptor			ovary(1)	1	all_cancers(7;7.36e-05)																	---	---	---	---
FGGY	55277	broad.mit.edu	37	1	59949609	59949609	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:59949609delA	uc001czi.3	+						FGGY_uc001czg.2_Intron|FGGY_uc001czh.2_Intron|FGGY_uc009wac.2_Intron|FGGY_uc001czj.3_Intron|FGGY_uc001czk.3_Intron|FGGY_uc001czl.3_Intron	NM_018291	NP_060761			FGGY carbohydrate kinase domain containing						carbohydrate metabolic process|cell death|neuron homeostasis		kinase activity|phosphotransferase activity, alcohol group as acceptor			ovary(1)	1	all_cancers(7;7.36e-05)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	60440014	60440015	+	IGR	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60440014_60440015delTC								CYP2J2 (47591 upstream) : C1orf87 (14809 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	60442634	60442635	+	IGR	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60442634_60442635insG								CYP2J2 (50211 upstream) : C1orf87 (12189 downstream)																																	OREG0013524	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	1	61142629	61142629	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61142629delA	uc001czt.1	-											Homo sapiens cDNA FLJ39874 fis, clone SPLEN2015815.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	61356838	61356839	+	IGR	DEL	GG	-	-	rs586443	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61356838_61356839delGG								C1orf87 (817412 upstream) : NFIA (186107 downstream)																																			---	---	---	---
NFIA	4774	broad.mit.edu	37	1	61588151	61588151	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61588151delA	uc001czw.2	+						NFIA_uc001czy.2_Intron|NFIA_uc010oos.1_Intron|NFIA_uc001czv.2_Intron	NM_001134673	NP_001128145			nuclear factor I/A isoform 1						DNA replication|viral genome replication	cell junction|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			pancreas(1)|skin(1)	2																		---	---	---	---
NFIA	4774	broad.mit.edu	37	1	61667193	61667194	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61667193_61667194delAA	uc001czw.2	+						NFIA_uc001czy.2_Intron|NFIA_uc010oos.1_Intron|NFIA_uc001czv.2_Intron	NM_001134673	NP_001128145			nuclear factor I/A isoform 1						DNA replication|viral genome replication	cell junction|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			pancreas(1)|skin(1)	2																		---	---	---	---
NFIA	4774	broad.mit.edu	37	1	61702294	61702295	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:61702294_61702295delTT	uc001czw.2	+						NFIA_uc001czy.2_Intron|NFIA_uc010oos.1_Intron|NFIA_uc001czv.2_Intron	NM_001134673	NP_001128145			nuclear factor I/A isoform 1						DNA replication|viral genome replication	cell junction|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			pancreas(1)|skin(1)	2																		---	---	---	---
INADL	10207	broad.mit.edu	37	1	62267609	62267609	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62267609delT	uc001dab.2	+						INADL_uc009waf.1_Intron|INADL_uc001daa.2_Intron|INADL_uc001dad.3_Intron	NM_176877	NP_795352			InaD-like						intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4																		---	---	---	---
INADL	10207	broad.mit.edu	37	1	62583430	62583430	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62583430delT	uc001dab.2	+						INADL_uc001dac.2_Intron|INADL_uc009wag.2_Intron	NM_176877	NP_795352			InaD-like						intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding			ovary(3)|skin(1)	4																		---	---	---	---
L1TD1	54596	broad.mit.edu	37	1	62668920	62668923	+	Intron	DEL	TTTC	-	-	rs76424229		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62668920_62668923delTTTC	uc001dae.3	+							NM_019079	NP_061952			LINE-1 type transposase domain containing 1											ovary(1)|skin(1)	2																		---	---	---	---
L1TD1	54596	broad.mit.edu	37	1	62677219	62677219	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62677219delA	uc001dae.3	+	4						NM_019079	NP_061952			LINE-1 type transposase domain containing 1											ovary(1)|skin(1)	2																		---	---	---	---
KANK4	163782	broad.mit.edu	37	1	62707844	62707844	+	Intron	DEL	G	-	-	rs66633397		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62707844delG	uc001dah.3	-						KANK4_uc001dai.3_Intron|KANK4_uc001daf.3_Intron|KANK4_uc001dag.3_Intron	NM_181712	NP_859063			ankyrin repeat domain 38											ovary(3)|skin(2)|lung(1)	6																		---	---	---	---
KANK4	163782	broad.mit.edu	37	1	62720238	62720238	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62720238delT	uc001dah.3	-						KANK4_uc001dai.3_Intron|KANK4_uc001daf.3_Intron|KANK4_uc001dag.3_Intron	NM_181712	NP_859063			ankyrin repeat domain 38											ovary(3)|skin(2)|lung(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	62837479	62837479	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62837479delT								KANK4 (52396 upstream) : USP1 (64496 downstream)																																			---	---	---	---
USP1	7398	broad.mit.edu	37	1	62900497	62900497	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62900497delT	uc001daj.1	+						USP1_uc001dak.1_5'Flank|USP1_uc001dal.1_5'Flank	NM_001017415	NP_001017415			ubiquitin specific protease 1						DNA repair|monoubiquitinated protein deubiquitination|regulation of DNA repair|response to UV|ubiquitin-dependent protein catabolic process	nucleoplasm	cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(1)	1		all_neural(321;0.0281)		BRCA - Breast invasive adenocarcinoma(111;8.01e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00245)|OV - Ovarian serous cystadenocarcinoma(397;0.0535)														---	---	---	---
DOCK7	85440	broad.mit.edu	37	1	62941104	62941104	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:62941104delA	uc001daq.2	-						DOCK7_uc001dan.2_Intron|DOCK7_uc001dao.2_Intron|DOCK7_uc001dap.2_Intron|DOCK7_uc001dam.2_Intron|DOCK7_uc010oov.1_Intron|DOCK7_uc001dar.1_Intron	NM_033407	NP_212132			dedicator of cytokinesis 7						activation of Rac GTPase activity|axonogenesis|establishment of neuroblast polarity|microtubule cytoskeleton organization|positive regulation of peptidyl-serine phosphorylation	axon|basal part of cell|growth cone	GTP binding|guanyl-nucleotide exchange factor activity|Rac GTPase binding			ovary(2)	2																		---	---	---	---
DOCK7	85440	broad.mit.edu	37	1	63106214	63106215	+	Intron	INS	-	GT	GT			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63106214_63106215insGT	uc001daq.2	-						DOCK7_uc001dan.2_Intron|DOCK7_uc001dao.2_Intron|DOCK7_uc001dap.2_Intron|DOCK7_uc009wah.1_Intron	NM_033407	NP_212132			dedicator of cytokinesis 7						activation of Rac GTPase activity|axonogenesis|establishment of neuroblast polarity|microtubule cytoskeleton organization|positive regulation of peptidyl-serine phosphorylation	axon|basal part of cell|growth cone	GTP binding|guanyl-nucleotide exchange factor activity|Rac GTPase binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	63584634	63584634	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63584634delA								ATG4C (254585 upstream) : FOXD3 (204096 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	63691859	63691859	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63691859delA	uc001daw.1	-											Homo sapiens cDNA clone IMAGE:4838722.																														---	---	---	---
ALG6	29929	broad.mit.edu	37	1	63893645	63893645	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63893645delT	uc010oow.1	+						ALG6_uc001daz.2_Intron|ALG6_uc009waj.2_Intron|ALG6_uc010oox.1_Intron	NM_013339	NP_037471			dolichyl pyrophosphate Man9GlcNAc2						dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	dolichyl-phosphate-glucose-glycolipid alpha-glucosyltransferase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	64771913	64771913	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64771913delA								UBE2U (61886 upstream) : CACHD1 (164563 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	64860355	64860355	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64860355delA								UBE2U (150328 upstream) : CACHD1 (76121 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	65187085	65187085	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65187085delT								CACHD1 (28344 upstream) : RAVER2 (23693 downstream)																																			---	---	---	---
JAK1	3716	broad.mit.edu	37	1	65343013	65343013	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65343013delT	uc001dbu.1	-						JAK1_uc009wam.1_Intron|JAK1_uc001dbv.2_RNA	NM_002227	NP_002218			janus kinase 1						interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to antibiotic|type I interferon-mediated signaling pathway	cytoskeleton|cytosol|endomembrane system|membrane|nucleus	ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity			haematopoietic_and_lymphoid_tissue(34)|prostate(7)|soft_tissue(6)|lung(4)|breast(3)|central_nervous_system(2)|liver(2)|large_intestine(1)|stomach(1)|ovary(1)	61				BRCA - Breast invasive adenocarcinoma(111;0.0485)				Mis		ALL								---	---	---	---
Unknown	0	broad.mit.edu	37	1	65469420	65469420	+	5'Flank	DEL	A	-	-	rs111269468		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65469420delA	uc001dbw.2	-											Homo sapiens cDNA FLJ44251 fis, clone TKIDN2004458.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	65561424	65561424	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65561424delT								MIR101-1 (37233 upstream) : AK3L1 (51808 downstream)																																			---	---	---	---
LEPR	3953	broad.mit.edu	37	1	66062116	66062116	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66062116delT	uc001dci.2	+						LEPR_uc001dcg.2_Intron|LEPR_uc001dch.2_Intron|LEPR_uc009waq.2_Intron|LEPR_uc001dcj.2_Intron|LEPR_uc001dck.2_Intron	NM_002303	NP_002294			leptin receptor isoform 1						energy reserve metabolic process|multicellular organismal development	extracellular region|integral to membrane|plasma membrane	cytokine receptor activity			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	66140083	66140083	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66140083delA								LEPR (37263 upstream) : PDE4B (118110 downstream)																																			---	---	---	---
PDE4B	5142	broad.mit.edu	37	1	66486001	66486001	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66486001delT	uc001dcn.2	+						PDE4B_uc009war.2_Intron|PDE4B_uc001dco.2_Intron|PDE4B_uc001dcp.2_Intron	NM_001037341	NP_001032418			phosphodiesterase 4B isoform 1						signal transduction	cytosol|insoluble fraction|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			ovary(2)|central_nervous_system(1)	3					Adenosine monophosphate(DB00131)|Amrinone(DB01427)|Caffeine(DB00201)|Cilostazol(DB01166)|Dyphylline(DB00651)|Enprofylline(DB00824)|Papaverine(DB01113)|Pentoxifylline(DB00806)|Theophylline(DB00277)													---	---	---	---
SERBP1	26135	broad.mit.edu	37	1	67881102	67881102	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67881102delA	uc001ddv.2	-						SERBP1_uc001ddx.2_Intron|SERBP1_uc001ddy.2_Intron|SERBP1_uc001ddw.2_Intron	NM_001018067	NP_001018077			SERPINE1 mRNA binding protein 1 isoform 1						regulation of mRNA stability	nucleus|perinuclear region of cytoplasm	mRNA 3'-UTR binding|protein binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	67976800	67976800	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67976800delT								SERBP1 (80677 upstream) : GADD45A (174083 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	68053218	68053218	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68053218delT								SERBP1 (157095 upstream) : GADD45A (97665 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	68137840	68137840	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68137840delA								SERBP1 (241717 upstream) : GADD45A (13043 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	68160804	68160805	+	IGR	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68160804_68160805delTC								GADD45A (6785 upstream) : GNG12 (6344 downstream)																																			---	---	---	---
WLS	79971	broad.mit.edu	37	1	68567857	68567859	+	Intron	DEL	CTC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:68567857_68567859delCTC	uc001dee.2	-						uc001deb.1_Intron|uc001dec.1_Intron	NM_001002292	NP_001002292			G protein-coupled receptor 177 isoform 2						multicellular organismal development|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|Wnt receptor signaling pathway	cytoplasmic vesicle membrane|Golgi membrane|integral to membrane	signal transducer activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	69042946	69042946	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:69042946delA								DEPDC1 (80147 upstream) : LRRC7 (989922 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	69287795	69287796	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:69287795_69287796delTT								DEPDC1 (324996 upstream) : LRRC7 (745072 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	69512965	69512965	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:69512965delA								DEPDC1 (550166 upstream) : LRRC7 (519903 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	69573550	69573551	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:69573550_69573551delAA								DEPDC1 (610751 upstream) : LRRC7 (459317 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	69731003	69731003	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:69731003delT								DEPDC1 (768204 upstream) : LRRC7 (301865 downstream)																																			---	---	---	---
LRRC7	57554	broad.mit.edu	37	1	70444730	70444730	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70444730delT	uc001dep.2	+						LRRC7_uc009wbg.2_Intron	NM_020794	NP_065845			leucine rich repeat containing 7							centrosome|focal adhesion|nucleolus	protein binding			ovary(9)|breast(2)|central_nervous_system(2)|liver(1)	14																		---	---	---	---
LRRC40	55631	broad.mit.edu	37	1	70668038	70668039	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70668038_70668039delAA	uc001der.1	-							NM_017768	NP_060238			leucine rich repeat containing 40											ovary(1)	1																		---	---	---	---
ANKRD13C	81573	broad.mit.edu	37	1	70808235	70808235	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70808235delA	uc001dex.3	-						ANKRD13C_uc009wbk.2_Intron	NM_030816	NP_110443			ankyrin repeat domain 13C						protein retention in ER lumen|regulation of anoikis|regulation of receptor biosynthetic process	endoplasmic reticulum membrane|perinuclear region of cytoplasm	receptor binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	71257054	71257055	+	IGR	DEL	TG	-	-	rs1536535	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:71257054_71257055delTG								CTH (351802 upstream) : PTGER3 (60981 downstream)																																			---	---	---	---
NEGR1	257194	broad.mit.edu	37	1	71910889	71910889	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:71910889delT	uc001dfw.2	-						NEGR1_uc001dfv.2_Intron|NEGR1_uc010oqs.1_Intron	NM_173808	NP_776169			neuronal growth regulator 1 precursor						cell adhesion	anchored to membrane|plasma membrane				ovary(1)	1		all_cancers(4;1.26e-06)|Renal(4;1.32e-08)|all_epithelial(4;5.39e-07)|Hepatocellular(141;0.117)		KIRC - Kidney renal clear cell carcinoma(4;0.00529)|Kidney(4;0.00609)|all cancers(265;0.022)|GBM - Glioblastoma multiforme(62;0.0382)|Epithelial(280;0.242)														---	---	---	---
NEGR1	257194	broad.mit.edu	37	1	72669980	72669980	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:72669980delA	uc001dfw.2	-						NEGR1_uc010oqs.1_Intron	NM_173808	NP_776169			neuronal growth regulator 1 precursor						cell adhesion	anchored to membrane|plasma membrane				ovary(1)	1		all_cancers(4;1.26e-06)|Renal(4;1.32e-08)|all_epithelial(4;5.39e-07)|Hepatocellular(141;0.117)		KIRC - Kidney renal clear cell carcinoma(4;0.00529)|Kidney(4;0.00609)|all cancers(265;0.022)|GBM - Glioblastoma multiforme(62;0.0382)|Epithelial(280;0.242)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	73320104	73320105	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:73320104_73320105insT								NEGR1 (571699 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	73327685	73327687	+	IGR	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:73327685_73327687delAAA								NEGR1 (579280 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	74080075	74080076	+	IGR	INS	-	A	A	rs142819715	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74080075_74080076insA								None (None upstream) : LRRIQ3 (411628 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	74300760	74300760	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74300760delA								None (None upstream) : LRRIQ3 (190944 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	74483353	74483353	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74483353delT								None (None upstream) : LRRIQ3 (8351 downstream)																																			---	---	---	---
TNNI3K	51086	broad.mit.edu	37	1	74986299	74986299	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74986299delA	uc001dgf.1	+						TNNI3K_uc001dge.1_Intron	NM_015978	NP_057062			TNNI3 interacting kinase isoform b							cytoplasm|nucleus	ATP binding|metal ion binding|protein C-terminus binding|protein serine/threonine kinase activity|troponin I binding			large_intestine(4)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	10																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	75549751	75549751	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75549751delT								TYW3 (317393 upstream) : LHX8 (44368 downstream)																																			---	---	---	---
SLC44A5	204962	broad.mit.edu	37	1	75685359	75685359	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75685359delA	uc001dgu.2	-						SLC44A5_uc001dgt.2_Intron|SLC44A5_uc001dgs.2_Intron|SLC44A5_uc001dgr.2_Intron|SLC44A5_uc010oqz.1_Intron|SLC44A5_uc010ora.1_Intron|SLC44A5_uc010orb.1_Intron	NM_152697	NP_689910			solute carrier family 44, member 5 isoform A							integral to membrane|plasma membrane	choline transmembrane transporter activity			ovary(2)|skin(2)	4																		---	---	---	---
SLC44A5	204962	broad.mit.edu	37	1	75698132	75698132	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75698132delT	uc001dgu.2	-						SLC44A5_uc001dgt.2_Intron|SLC44A5_uc001dgs.2_Intron|SLC44A5_uc001dgr.2_Intron|SLC44A5_uc010oqz.1_Intron|SLC44A5_uc010ora.1_Intron|SLC44A5_uc010orb.1_Intron	NM_152697	NP_689910			solute carrier family 44, member 5 isoform A							integral to membrane|plasma membrane	choline transmembrane transporter activity			ovary(2)|skin(2)	4																		---	---	---	---
SLC44A5	204962	broad.mit.edu	37	1	75795132	75795132	+	Intron	DEL	T	-	-	rs11307561		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75795132delT	uc001dgu.2	-						SLC44A5_uc001dgt.2_Intron|SLC44A5_uc001dgs.2_Intron|SLC44A5_uc001dgr.2_Intron|SLC44A5_uc010oqz.1_Intron|SLC44A5_uc010ora.1_Intron|SLC44A5_uc010orb.1_Intron	NM_152697	NP_689910			solute carrier family 44, member 5 isoform A							integral to membrane|plasma membrane	choline transmembrane transporter activity			ovary(2)|skin(2)	4																		---	---	---	---
ST6GALNAC3	256435	broad.mit.edu	37	1	76541396	76541397	+	Intron	INS	-	T	T	rs147299055		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:76541396_76541397insT	uc001dhh.2	+						ST6GALNAC3_uc001dhg.3_Intron|ST6GALNAC3_uc010orh.1_Intron	NM_152996	NP_694541			sialyltransferase 7C isoform 1						protein glycosylation	integral to Golgi membrane	sialyltransferase activity			ovary(3)|skin(2)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	77550363	77550364	+	IGR	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:77550363_77550364delCT								ST6GALNAC5 (18971 upstream) : PIGK (4305 downstream)																																			---	---	---	---
PIGK	10026	broad.mit.edu	37	1	77592187	77592187	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:77592187delA	uc001dhk.2	-						PIGK_uc010orj.1_Intron|PIGK_uc009wbx.2_Intron	NM_005482	NP_005473			phosphatidylinositol glycan anchor biosynthesis,						attachment of GPI anchor to protein|C-terminal protein lipidation|protein thiol-disulfide exchange|proteolysis	GPI-anchor transamidase complex	cysteine-type endopeptidase activity|GPI-anchor transamidase activity|protein binding			ovary(2)|pancreas(1)	3																		---	---	---	---
AK5	26289	broad.mit.edu	37	1	77948990	77948990	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:77948990delT	uc001dhn.2	+						AK5_uc001dho.2_Intron	NM_174858	NP_777283			adenylate kinase 5 isoform 1						ADP biosynthetic process|ATP metabolic process|dADP biosynthetic process|nucleobase, nucleoside and nucleotide interconversion|pyrimidine ribonucleotide biosynthetic process|signal transduction	centrosome|cytosol	adenylate kinase activity|ATP binding|cAMP-dependent protein kinase regulator activity|nucleoside kinase activity			skin(1)	1																		---	---	---	---
USP33	23032	broad.mit.edu	37	1	78187629	78187629	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78187629delA	uc001dht.2	-						USP33_uc001dhs.2_Intron|USP33_uc001dhu.2_Intron|USP33_uc001dhv.2_Intron|USP33_uc001dhw.2_Intron	NM_015017	NP_055832			ubiquitin specific protease 33 isoform 1						axon guidance|cell migration|endocytosis|protein K48-linked deubiquitination|protein K63-linked deubiquitination|regulation of G-protein coupled receptor protein signaling pathway|ubiquitin-dependent protein catabolic process	perinuclear region of cytoplasm|VCB complex	cysteine-type endopeptidase activity|G-protein-coupled receptor binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(2)|ovary(1)	3																		---	---	---	---
USP33	23032	broad.mit.edu	37	1	78225713	78225713	+	5'Flank	DEL	T	-	-	rs80254926		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78225713delT	uc001dht.2	-						USP33_uc001dhu.2_5'Flank|USP33_uc001dhw.2_5'Flank	NM_015017	NP_055832			ubiquitin specific protease 33 isoform 1						axon guidance|cell migration|endocytosis|protein K48-linked deubiquitination|protein K63-linked deubiquitination|regulation of G-protein coupled receptor protein signaling pathway|ubiquitin-dependent protein catabolic process	perinuclear region of cytoplasm|VCB complex	cysteine-type endopeptidase activity|G-protein-coupled receptor binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(2)|ovary(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	78502309	78502309	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78502309delG								DNAJB4 (19316 upstream) : GIPC2 (9280 downstream)																																			---	---	---	---
IFI44L	10964	broad.mit.edu	37	1	79102493	79102493	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79102493delT	uc010oro.1	+						IFI44L_uc010orp.1_Intron|IFI44L_uc010orq.1_Intron	NM_006820	NP_006811			interferon-induced protein 44-like							cytoplasm					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	79132403	79132405	+	IGR	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79132403_79132405delAAA								IFI44 (2642 upstream) : ELTD1 (223046 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	79292614	79292614	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79292614delT								IFI44 (162853 upstream) : ELTD1 (62837 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	79331518	79331518	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79331518delT								IFI44 (201757 upstream) : ELTD1 (23933 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	80750948	80750949	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:80750948_80750949delTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	81467784	81467785	+	IGR	DEL	AC	-	-	rs1030413		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:81467784_81467785delAC								None (None upstream) : LPHN2 (304060 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	81581380	81581380	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:81581380delG								None (None upstream) : LPHN2 (190465 downstream)																																			---	---	---	---
LPHN2	23266	broad.mit.edu	37	1	82103834	82103834	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82103834delA	uc001dis.2	+											SubName: Full=cDNA FLJ41428 fis, clone BRHIP2005236, highly similar to Latrophilin-2;						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|latrotoxin receptor activity|sugar binding			ovary(3)|lung(3)|breast(2)|central_nervous_system(1)	9				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)														---	---	---	---
LPHN2	23266	broad.mit.edu	37	1	82187977	82187977	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82187977delA	uc001dit.3	+						LPHN2_uc001dis.2_Intron	NM_012302	NP_036434			latrophilin 2 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|latrotoxin receptor activity|sugar binding			ovary(3)|lung(3)|breast(2)|central_nervous_system(1)	9				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)														---	---	---	---
LPHN2	23266	broad.mit.edu	37	1	82189512	82189512	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82189512delT	uc001dit.3	+						LPHN2_uc001dis.2_Intron	NM_012302	NP_036434			latrophilin 2 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|latrotoxin receptor activity|sugar binding			ovary(3)|lung(3)|breast(2)|central_nervous_system(1)	9				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	82472233	82472240	+	IGR	DEL	GTGTGTGC	-	-	rs3046463		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82472233_82472240delGTGTGTGC								LPHN2 (14127 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	82714561	82714561	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:82714561delT								LPHN2 (256455 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	83213379	83213379	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:83213379delA								LPHN2 (755273 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	83303777	83303777	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:83303777delT								LPHN2 (845671 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	84259638	84259638	+	Intron	DEL	A	-	-	rs111685871		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84259638delA	uc001diz.3	-											Homo sapiens cDNA clone IMAGE:4815396.																														---	---	---	---
SSX2IP	117178	broad.mit.edu	37	1	85120696	85120696	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85120696delA	uc001dkh.2	-						SSX2IP_uc001dkf.2_Intron|SSX2IP_uc001dkg.2_Intron|SSX2IP_uc010orz.1_Intron|SSX2IP_uc001dki.2_Intron|SSX2IP_uc010osa.1_Intron|SSX2IP_uc001dkj.2_Intron|SSX2IP_uc009wci.2_Intron	NM_014021	NP_054740			synovial sarcoma, X breakpoint 2 interacting						cell adhesion	nucleus|protein complex				ovary(2)	2				all cancers(265;0.0053)|Epithelial(280;0.0214)|OV - Ovarian serous cystadenocarcinoma(397;0.173)														---	---	---	---
LPAR3	23566	broad.mit.edu	37	1	85333798	85333798	+	5'Flank	DEL	T	-	-	rs113668388		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85333798delT	uc001dkl.2	-						LPAR3_uc009wcj.1_Intron	NM_012152	NP_036284			lysophosphatidic acid receptor 3						G-protein signaling, coupled to cyclic nucleotide second messenger|synaptic transmission	integral to plasma membrane|intracellular membrane-bounded organelle				lung(3)|ovary(2)	5																		---	---	---	---
MCOLN2	255231	broad.mit.edu	37	1	85412885	85412886	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85412885_85412886delAA	uc001dkm.2	-						MCOLN2_uc001dkn.2_Intron	NM_153259	NP_694991			mucolipin 2							integral to membrane	ion channel activity			ovary(3)|upper_aerodigestive_tract(1)	4				all cancers(265;0.0111)|Epithelial(280;0.0263)|OV - Ovarian serous cystadenocarcinoma(397;0.217)														---	---	---	---
WDR63	126820	broad.mit.edu	37	1	85553152	85553152	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85553152delA	uc001dkt.2	+						WDR63_uc009wcl.2_Intron	NM_145172	NP_660155			WD repeat domain 63											upper_aerodigestive_tract(2)|ovary(2)|skin(1)	5				all cancers(265;0.00391)|Epithelial(280;0.00922)|Colorectal(170;0.166)														---	---	---	---
DDAH1	23576	broad.mit.edu	37	1	85988468	85988469	+	Intron	INS	-	TA	TA	rs138199506	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:85988468_85988469insTA	uc001dlc.2	-							NM_001134445	NP_001127917			dimethylarginine dimethylaminohydrolase 1						arginine catabolic process|citrulline metabolic process|nitric oxide mediated signal transduction		dimethylargininase activity|metal ion binding				0				all cancers(265;0.0318)|Epithelial(280;0.0657)	L-Citrulline(DB00155)													---	---	---	---
DDAH1	23576	broad.mit.edu	37	1	86004091	86004092	+	Intron	DEL	AA	-	-	rs10553781		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86004091_86004092delAA	uc001dlc.2	-							NM_001134445	NP_001127917			dimethylarginine dimethylaminohydrolase 1						arginine catabolic process|citrulline metabolic process|nitric oxide mediated signal transduction		dimethylargininase activity|metal ion binding				0				all cancers(265;0.0318)|Epithelial(280;0.0657)	L-Citrulline(DB00155)													---	---	---	---
DDAH1	23576	broad.mit.edu	37	1	86005960	86005961	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86005960_86005961delTT	uc001dlc.2	-							NM_001134445	NP_001127917			dimethylarginine dimethylaminohydrolase 1						arginine catabolic process|citrulline metabolic process|nitric oxide mediated signal transduction		dimethylargininase activity|metal ion binding				0				all cancers(265;0.0318)|Epithelial(280;0.0657)	L-Citrulline(DB00155)													---	---	---	---
COL24A1	255631	broad.mit.edu	37	1	86482894	86482895	+	Intron	INS	-	G	G	rs147516626	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86482894_86482895insG	uc001dlj.2	-						COL24A1_uc010osd.1_Intron|COL24A1_uc001dlk.2_Intron|COL24A1_uc010ose.1_Intron|COL24A1_uc010osf.1_Intron	NM_152890	NP_690850			collagen, type XXIV, alpha 1 precursor						cell adhesion	collagen	extracellular matrix structural constituent			ovary(3)|central_nervous_system(1)|skin(1)	5				all cancers(265;0.0627)|Epithelial(280;0.0689)														---	---	---	---
COL24A1	255631	broad.mit.edu	37	1	86489955	86489955	+	Intron	DEL	T	-	-	rs140285550		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86489955delT	uc001dlj.2	-						COL24A1_uc010osd.1_Intron|COL24A1_uc001dlk.2_Intron|COL24A1_uc010ose.1_Intron|COL24A1_uc010osf.1_Intron	NM_152890	NP_690850			collagen, type XXIV, alpha 1 precursor						cell adhesion	collagen	extracellular matrix structural constituent			ovary(3)|central_nervous_system(1)|skin(1)	5				all cancers(265;0.0627)|Epithelial(280;0.0689)														---	---	---	---
SEP15	9403	broad.mit.edu	37	1	87352696	87352697	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87352696_87352697insT	uc010osi.1	-						SEP15_uc010osj.1_Intron	NM_004261	NP_004252			15 kDa selenoprotein isoform 1 precursor						'de novo' posttranslational protein folding	endoplasmic reticulum lumen	selenium binding				0		Lung NSC(277;0.153)		all cancers(265;0.00744)|Epithelial(280;0.0333)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	88135470	88135470	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88135470delT								LMO4 (320867 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	88143234	88143235	+	IGR	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88143234_88143235delTC								LMO4 (328631 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	88476736	88476737	+	IGR	INS	-	CA	CA	rs10922978	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88476736_88476737insCA								LMO4 (662133 upstream) : PKN2 (673185 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	88658022	88658029	+	IGR	DEL	ACACACAC	-	-	rs147801700		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88658022_88658029delACACACAC								LMO4 (843419 upstream) : PKN2 (491893 downstream)																																			---	---	---	---
PKN2	5586	broad.mit.edu	37	1	89270693	89270693	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89270693delT	uc001dmn.2	+						PKN2_uc001dmm.1_Intron|PKN2_uc010osp.1_Intron|PKN2_uc010osq.1_Intron|PKN2_uc009wcv.2_Intron|PKN2_uc010osr.1_Intron	NM_006256	NP_006247			protein kinase N2						signal transduction	cytoplasm	ATP binding|histone deacetylase binding|protein kinase C activity			large_intestine(1)|lung(1)|skin(1)	3		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)														---	---	---	---
PKN2	5586	broad.mit.edu	37	1	89301773	89301774	+	3'UTR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89301773_89301774insT	uc001dmn.2	+	22					PKN2_uc010osp.1_3'UTR|PKN2_uc010osq.1_3'UTR|PKN2_uc009wcv.2_3'UTR|PKN2_uc010osr.1_3'UTR	NM_006256	NP_006247			protein kinase N2						signal transduction	cytoplasm	ATP binding|histone deacetylase binding|protein kinase C activity			large_intestine(1)|lung(1)|skin(1)	3		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	89401060	89401061	+	IGR	DEL	AA	-	-	rs58882484		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89401060_89401061delAA								GTF2B (43759 upstream) : CCBL2 (395 downstream)																																			---	---	---	---
CCBL2	56267	broad.mit.edu	37	1	89444032	89444033	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89444032_89444033delTT	uc001dmp.2	-						CCBL2_uc001dmq.2_Intron|CCBL2_uc001dmr.2_Intron	NM_001008661	NP_001008661			kynurenine aminotransferase III isoform 1						biosynthetic process|kynurenine metabolic process|tryptophan catabolic process		cysteine-S-conjugate beta-lyase activity|kynurenine-glyoxylate transaminase activity|kynurenine-oxoglutarate transaminase activity|pyridoxal phosphate binding			ovary(1)	1		Lung NSC(277;0.123)		all cancers(265;0.0117)|Epithelial(280;0.0341)	L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)													---	---	---	---
GBP3	2635	broad.mit.edu	37	1	89478542	89478542	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89478542delT	uc001dmt.2	-						GBP3_uc010oss.1_Intron|GBP3_uc001dmu.2_Intron|GBP3_uc001dmv.2_Intron	NM_018284	NP_060754			guanylate binding protein 3							integral to membrane	GTP binding|GTPase activity			ovary(1)|pancreas(1)	2		Lung NSC(277;0.123)		all cancers(265;0.0103)|Epithelial(280;0.0293)														---	---	---	---
GBP1	2633	broad.mit.edu	37	1	89518866	89518867	+	3'UTR	DEL	TT	-	-	rs113952192		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89518866_89518867delTT	uc001dmx.2	-	11						NM_002053	NP_002044			guanylate binding protein 1,						interferon-gamma-mediated signaling pathway	plasma membrane	GTP binding|GTPase activity			ovary(1)|skin(1)	2		Lung NSC(277;0.123)		all cancers(265;0.0156)|Epithelial(280;0.0291)														---	---	---	---
GBP1	2633	broad.mit.edu	37	1	89519795	89519795	+	Intron	DEL	T	-	-	rs79499378		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89519795delT	uc001dmx.2	-							NM_002053	NP_002044			guanylate binding protein 1,						interferon-gamma-mediated signaling pathway	plasma membrane	GTP binding|GTPase activity			ovary(1)|skin(1)	2		Lung NSC(277;0.123)		all cancers(265;0.0156)|Epithelial(280;0.0291)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	89689243	89689244	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89689243_89689244insA								GBP4 (24610 upstream) : GBP5 (35392 downstream)																																			---	---	---	---
LRRC8C	84230	broad.mit.edu	37	1	90179647	90179647	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:90179647delC	uc001dnl.3	+	3	1760	c.1518delC	c.(1516-1518)CTCfs	p.L506fs		NM_032270	NP_115646	Q8TDW0	LRC8C_HUMAN	leucine rich repeat containing 8 family, member	506	LRR 5.					endoplasmic reticulum membrane|integral to membrane				ovary(3)|skin(3)|pancreas(1)|central_nervous_system(1)	8		all_lung(203;0.126)		all cancers(265;0.00756)|Epithelial(280;0.0313)														---	---	---	---
LRRC8D	55144	broad.mit.edu	37	1	90285085	90285086	+	5'Flank	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:90285085_90285086delTT	uc001dnm.2	+						LRRC8D_uc001dnn.2_5'Flank	NM_001134479	NP_001127951			leucine rich repeat containing 8 family, member							integral to membrane	protein binding			ovary(2)	2		all_lung(203;0.0894)|Lung NSC(277;0.227)		all cancers(265;0.0109)|Epithelial(280;0.0427)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	90419720	90419720	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:90419720delA								LRRC8D (17733 upstream) : GEMIN8P4 (39106 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	90705659	90705659	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:90705659delT								ZNF326 (211565 upstream) : BARHL2 (471921 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	91096543	91096543	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91096543delA								ZNF326 (602449 upstream) : BARHL2 (81037 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	91161536	91161537	+	IGR	INS	-	A	A	rs144961444	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91161536_91161537insA								ZNF326 (667442 upstream) : BARHL2 (16043 downstream)																																			---	---	---	---
BARHL2	343472	broad.mit.edu	37	1	91183879	91183879	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91183879delA	uc001dns.2	-							NM_020063	NP_064447			BarH-like homeobox 2							nucleus	sequence-specific DNA binding			ovary(1)	1		all_lung(203;0.0263)|Lung SC(238;0.128)		all cancers(265;0.000897)|Epithelial(280;0.00516)|OV - Ovarian serous cystadenocarcinoma(397;0.211)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	91364091	91364092	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91364091_91364092insA								BARHL2 (181297 upstream) : ZNF644 (16768 downstream)																																			---	---	---	---
ZNF644	84146	broad.mit.edu	37	1	91382293	91382293	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91382293delA	uc001dnw.2	-	6					ZNF644_uc001dnv.2_3'UTR|ZNF644_uc001dnx.2_3'UTR	NM_201269	NP_958357			zinc finger protein 644 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|breast(1)|skin(1)	3		all_lung(203;0.00206)|Lung NSC(277;0.0519)|Lung SC(238;0.101)		all cancers(265;0.00102)|Epithelial(280;0.00766)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)|OV - Ovarian serous cystadenocarcinoma(397;0.173)														---	---	---	---
ZNF644	84146	broad.mit.edu	37	1	91388538	91388538	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91388538delT	uc001dnw.2	-						ZNF644_uc001dnv.2_Intron|ZNF644_uc001dnx.2_Intron	NM_201269	NP_958357			zinc finger protein 644 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|breast(1)|skin(1)	3		all_lung(203;0.00206)|Lung NSC(277;0.0519)|Lung SC(238;0.101)		all cancers(265;0.00102)|Epithelial(280;0.00766)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)|OV - Ovarian serous cystadenocarcinoma(397;0.173)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	91618158	91618159	+	IGR	DEL	GA	-	-	rs2308037		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91618158_91618159delGA								ZNF644 (130487 upstream) : HFM1 (108165 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	91721633	91721633	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91721633delG								ZNF644 (233962 upstream) : HFM1 (4691 downstream)																																			---	---	---	---
HFM1	164045	broad.mit.edu	37	1	91855992	91855992	+	Intron	DEL	G	-	-	rs12143669		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91855992delG	uc001doa.3	-						HFM1_uc010osu.1_Intron|HFM1_uc010osv.1_Intron|HFM1_uc001doc.1_Intron	NM_001017975	NP_001017975			HFM1 protein								ATP binding|ATP-dependent helicase activity|nucleic acid binding				0		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	92024027	92024028	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92024027_92024028delTT								CDC7 (32707 upstream) : HSP90B3P (76540 downstream)																																			---	---	---	---
HSP90B3P	343477	broad.mit.edu	37	1	92101844	92101844	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92101844delT	uc010osx.1	+							NR_003130				SubName: Full=cDNA FLJ58812, highly similar to Endoplasmin (Heat shock protein 90kDa beta member 1);												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	92403432	92403433	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92403432_92403433insT								TGFBR3 (31873 upstream) : BRDT (11495 downstream)																																			---	---	---	---
BRDT	676	broad.mit.edu	37	1	92464325	92464325	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92464325delA	uc001dok.3	+						BRDT_uc001dol.3_Intron|BRDT_uc010osz.1_Intron|BRDT_uc009wdf.2_Intron|BRDT_uc010ota.1_Intron|BRDT_uc010otb.1_Intron|BRDT_uc001dom.3_Intron	NM_207189	NP_997072			testis-specific bromodomain protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein serine/threonine kinase activity|transcription coactivator activity			stomach(2)|ovary(1)|lung(1)	4		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)														---	---	---	---
BTBD8	284697	broad.mit.edu	37	1	92548405	92548406	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92548405_92548406delAA	uc001doo.2	+						BTBD8_uc010otc.1_Intron	NM_183242	NP_899065			BTB (POZ) domain containing 8							nucleus				ovary(1)	1		all_lung(203;0.0484)|Lung NSC(277;0.126)|Glioma(108;0.222)		all cancers(265;0.0153)|Epithelial(280;0.0982)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	92873951	92873951	+	IGR	DEL	C	-	-	rs11307401		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92873951delC								RPAP2 (20219 upstream) : GFI1 (66368 downstream)																																			---	---	---	---
EVI5	7813	broad.mit.edu	37	1	93146550	93146550	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93146550delG	uc001dox.2	-						EVI5_uc010otf.1_Intron|EVI5_uc001doy.1_Intron	NM_005665	NP_005656			ecotropic viral integration site 5						cell cycle|cell division|cell proliferation|multicellular organismal development	microtubule organizing center|nucleus|spindle	protein binding|Rab GTPase activator activity			ovary(1)|breast(1)	2		all_lung(203;0.00146)|Lung NSC(277;0.00565)|all_neural(321;0.185)|Melanoma(281;0.193)|Glioma(108;0.203)		Epithelial(280;8.09e-25)|OV - Ovarian serous cystadenocarcinoma(397;1.27e-22)|all cancers(265;1.74e-21)|GBM - Glioblastoma multiforme(16;0.00233)|BRCA - Breast invasive adenocarcinoma(282;0.211)														---	---	---	---
EVI5	7813	broad.mit.edu	37	1	93244531	93244531	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93244531delT	uc001dox.2	-						EVI5_uc010otf.1_Intron	NM_005665	NP_005656			ecotropic viral integration site 5						cell cycle|cell division|cell proliferation|multicellular organismal development	microtubule organizing center|nucleus|spindle	protein binding|Rab GTPase activator activity			ovary(1)|breast(1)	2		all_lung(203;0.00146)|Lung NSC(277;0.00565)|all_neural(321;0.185)|Melanoma(281;0.193)|Glioma(108;0.203)		Epithelial(280;8.09e-25)|OV - Ovarian serous cystadenocarcinoma(397;1.27e-22)|all cancers(265;1.74e-21)|GBM - Glioblastoma multiforme(16;0.00233)|BRCA - Breast invasive adenocarcinoma(282;0.211)														---	---	---	---
RPL5	6125	broad.mit.edu	37	1	93299389	93299389	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93299389delA	uc001doz.2	+						FAM69A_uc001dpc.2_Intron|RPL5_uc001dpa.2_Intron|RPL5_uc001dpb.2_Intron|RPL5_uc001dpd.2_5'Flank	NM_000969	NP_000960			ribosomal protein L5						endocrine pancreas development|ribosomal large subunit biogenesis|rRNA processing|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit|nucleolus	5S rRNA binding|protein binding|structural constituent of ribosome				0		all_lung(203;0.00265)|Lung NSC(277;0.0056)|all_neural(321;0.185)|Melanoma(281;0.192)|Glioma(108;0.203)		GBM - Glioblastoma multiforme(16;0.000305)|all cancers(265;0.000343)|Epithelial(280;0.0927)														---	---	---	---
FAM69A	388650	broad.mit.edu	37	1	93351887	93351887	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93351887delA	uc001dpg.2	-						FAM69A_uc001dpc.2_Intron	NM_001006605	NP_001006606			family with sequence similarity 69, member A							endoplasmic reticulum membrane|integral to membrane					0		all_lung(203;0.00265)|Lung NSC(277;0.00562)|all_neural(321;0.185)|Melanoma(281;0.192)|Glioma(108;0.203)		GBM - Glioblastoma multiforme(16;0.000563)|all cancers(265;0.000751)|Epithelial(280;0.127)														---	---	---	---
MTF2	22823	broad.mit.edu	37	1	93583739	93583739	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93583739delT	uc009wdj.2	+						MTF2_uc001dph.2_Intron|MTF2_uc010oth.1_Intron|MTF2_uc009wdk.2_Intron|MTF2_uc001dpi.3_Intron|MTF2_uc010oti.1_Intron|MTF2_uc001dpj.3_Intron|MTF2_uc001dpl.3_Intron	NM_007358	NP_031384			metal response element binding transcription							nucleus	DNA binding|zinc ion binding			ovary(2)	2		all_lung(203;0.00196)|Lung NSC(277;0.00902)|Melanoma(281;0.099)|Ovarian(761;0.109)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00076)|GBM - Glioblastoma multiforme(16;0.00157)|Epithelial(280;0.0886)														---	---	---	---
TMED5	50999	broad.mit.edu	37	1	93637872	93637872	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93637872delA	uc001dpn.2	-						TMED5_uc001dpo.2_Intron|TMED5_uc001dpp.2_Intron	NM_016040	NP_057124			transmembrane emp24 protein transport domain						transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment|integral to membrane				ovary(1)	1		all_lung(203;0.0223)|Lung NSC(277;0.071)|Melanoma(281;0.147)|Glioma(108;0.188)		all cancers(265;0.00108)|GBM - Glioblastoma multiforme(16;0.00407)|Epithelial(280;0.0797)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	93755950	93755951	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93755950_93755951insA	uc001dps.2	-											Homo sapiens cDNA FLJ42965 fis, clone BRSTN2014751.																														---	---	---	---
ARHGAP29	9411	broad.mit.edu	37	1	94643144	94643144	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94643144delT	uc001dqj.3	-						ARHGAP29_uc009wdq.1_Intron|ARHGAP29_uc001dqk.2_3'UTR	NM_004815	NP_004806			PTPL1-associated RhoGAP 1						Rho protein signal transduction	cytosol	metal ion binding|Rho GTPase activator activity			breast(4)|skin(3)|lung(2)|upper_aerodigestive_tract(1)|ovary(1)	11		all_lung(203;0.000732)|Lung NSC(277;0.00328)		all cancers(265;0.0187)|Epithelial(280;0.159)														---	---	---	---
RWDD3	25950	broad.mit.edu	37	1	95667654	95667654	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95667654delA	uc001drd.3	+						uc001dre.1_Intron	NM_152487	NP_689700			transmembrane protein 56							cytoplasm|nucleus	protein binding			ovary(1)	1		all_epithelial(167;5.99e-05)|all_lung(203;0.00168)|Lung NSC(277;0.00769)		all cancers(265;0.112)|Epithelial(280;0.229)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	95820084	95820084	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95820084delT								RWDD3 (107311 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	96170107	96170107	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96170107delA								RWDD3 (457334 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	96508336	96508338	+	IGR	DEL	AAA	-	-	rs79029879		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96508336_96508338delAAA								RWDD3 (795563 upstream) : PTBP2 (678837 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	96795228	96795228	+	IGR	DEL	T	-	-	rs35683612		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96795228delT								None (None upstream) : PTBP2 (391947 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	96884031	96884031	+	IGR	DEL	A	-	-	rs77096023		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96884031delA								None (None upstream) : PTBP2 (303144 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	96914049	96914049	+	IGR	DEL	C	-	-	rs1931180	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:96914049delC								None (None upstream) : PTBP2 (273126 downstream)																																			---	---	---	---
PTBP2	58155	broad.mit.edu	37	1	97213405	97213405	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:97213405delA	uc001drq.2	+						PTBP2_uc001drn.2_Intron|PTBP2_uc001dro.2_Intron|PTBP2_uc010otz.1_Intron|PTBP2_uc001drp.2_Intron|PTBP2_uc009wdw.2_Intron|PTBP2_uc001drr.2_Intron|PTBP2_uc010oua.1_Intron|PTBP2_uc001dru.2_Intron|PTBP2_uc001drm.2_Intron	NM_021190	NP_067013			polypyrimidine tract binding protein 2								nucleotide binding				0		all_epithelial(167;2.95e-05)|all_lung(203;0.000396)|Lung NSC(277;0.00171)		all cancers(265;0.0582)|Epithelial(280;0.0716)|Colorectal(170;0.0879)|KIRC - Kidney renal clear cell carcinoma(1967;0.202)														---	---	---	---
PTBP2	58155	broad.mit.edu	37	1	97279080	97279081	+	3'UTR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:97279080_97279081delTT	uc001drq.2	+	14					PTBP2_uc001drn.2_3'UTR|PTBP2_uc001dro.2_3'UTR|PTBP2_uc010otz.1_3'UTR|PTBP2_uc001drp.2_RNA|PTBP2_uc009wdw.2_3'UTR|PTBP2_uc001drr.2_3'UTR|PTBP2_uc010oua.1_3'UTR|PTBP2_uc001dru.2_RNA|PTBP2_uc001drs.1_3'UTR|PTBP2_uc001drt.2_3'UTR	NM_021190	NP_067013			polypyrimidine tract binding protein 2								nucleotide binding				0		all_epithelial(167;2.95e-05)|all_lung(203;0.000396)|Lung NSC(277;0.00171)		all cancers(265;0.0582)|Epithelial(280;0.0716)|Colorectal(170;0.0879)|KIRC - Kidney renal clear cell carcinoma(1967;0.202)														---	---	---	---
DPYD	1806	broad.mit.edu	37	1	97946791	97946791	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:97946791delT	uc001drv.2	-							NM_000110	NP_000101			dihydropyrimidine dehydrogenase isoform 1						'de novo' pyrimidine base biosynthetic process|purine base catabolic process|thymidine catabolic process|thymine catabolic process|UMP biosynthetic process|uracil catabolic process	cytosol	4 iron, 4 sulfur cluster binding|dihydroorotate oxidase activity|dihydropyrimidine dehydrogenase (NADP+) activity|electron carrier activity|flavin adenine dinucleotide binding|metal ion binding|NADP binding|protein homodimerization activity			ovary(3)|skin(3)|breast(2)	8		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Enfuvirtide(DB00109)													---	---	---	---
DPYD	1806	broad.mit.edu	37	1	97956384	97956385	+	Intron	DEL	AA	-	-	rs67444568		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:97956384_97956385delAA	uc001drv.2	-							NM_000110	NP_000101			dihydropyrimidine dehydrogenase isoform 1						'de novo' pyrimidine base biosynthetic process|purine base catabolic process|thymidine catabolic process|thymine catabolic process|UMP biosynthetic process|uracil catabolic process	cytosol	4 iron, 4 sulfur cluster binding|dihydroorotate oxidase activity|dihydropyrimidine dehydrogenase (NADP+) activity|electron carrier activity|flavin adenine dinucleotide binding|metal ion binding|NADP binding|protein homodimerization activity			ovary(3)|skin(3)|breast(2)	8		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Enfuvirtide(DB00109)													---	---	---	---
DPYD	1806	broad.mit.edu	37	1	98240540	98240540	+	Intron	DEL	A	-	-	rs114907527	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98240540delA	uc001drv.2	-						DPYD_uc010oub.1_Intron|DPYD_uc001drw.2_Intron	NM_000110	NP_000101			dihydropyrimidine dehydrogenase isoform 1						'de novo' pyrimidine base biosynthetic process|purine base catabolic process|thymidine catabolic process|thymine catabolic process|UMP biosynthetic process|uracil catabolic process	cytosol	4 iron, 4 sulfur cluster binding|dihydroorotate oxidase activity|dihydropyrimidine dehydrogenase (NADP+) activity|electron carrier activity|flavin adenine dinucleotide binding|metal ion binding|NADP binding|protein homodimerization activity			ovary(3)|skin(3)|breast(2)	8		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Enfuvirtide(DB00109)													---	---	---	---
LPPR5	163404	broad.mit.edu	37	1	99459789	99459789	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:99459789delA	uc001dsb.2	-						LPPR5_uc001dsc.2_Intron	NM_001037317	NP_001032394			phosphatidic acid phosphatase type 2d isoform 1							integral to membrane	hydrolase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	99608352	99608352	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:99608352delA	uc001dsd.1	+											Homo sapiens cDNA FLJ38225 fis, clone FCBBF2003528.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	99878627	99878627	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:99878627delA								LPPR4 (103491 upstream) : PALMD (232804 downstream)																																			---	---	---	---
FRRS1	391059	broad.mit.edu	37	1	100206567	100206567	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100206567delA	uc001dsh.1	-							NM_001013660	NP_001013682			stromal cell derived factor receptor 2 homolog						electron transport chain|transport	integral to membrane	ferric-chelate reductase activity|metal ion binding			skin(1)	1		all_epithelial(167;2.09e-06)|all_lung(203;0.000435)|Lung NSC(277;0.00201)		Epithelial(280;0.0718)|all cancers(265;0.126)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.206)														---	---	---	---
AGL	178	broad.mit.edu	37	1	100359743	100359743	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100359743delA	uc001dsi.1	+						AGL_uc001dsj.1_Intron|AGL_uc001dsk.1_Intron|AGL_uc001dsl.1_Intron|AGL_uc001dsm.1_Intron|AGL_uc001dsn.1_Intron	NM_000642	NP_000633			amylo-1,6-glucosidase,						glucose metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol|isoamylase complex|nucleus	4-alpha-glucanotransferase activity|amylo-alpha-1,6-glucosidase activity|cation binding			ovary(1)|central_nervous_system(1)|skin(1)	3		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)														---	---	---	---
HIAT1	64645	broad.mit.edu	37	1	100546397	100546397	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100546397delT	uc001dst.2	+							NM_033055	NP_149044			hippocampus abundant transcript 1						transmembrane transport	integral to membrane|plasma membrane	transporter activity				0		all_epithelial(167;2.96e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.0832)|all cancers(265;0.136)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.195)														---	---	---	---
LRRC39	127495	broad.mit.edu	37	1	100622540	100622540	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100622540delA	uc001dsw.1	-						LRRC39_uc001dsx.1_Intron|LRRC39_uc001dsy.1_Intron|LRRC39_uc001dsz.1_Intron	NM_144620	NP_653221			leucine rich repeat containing 39											ovary(2)|skin(1)	3		all_epithelial(167;0.000542)|all_lung(203;0.0154)|Lung NSC(277;0.0155)		Epithelial(280;0.0826)|all cancers(265;0.135)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.195)														---	---	---	---
CDC14A	8556	broad.mit.edu	37	1	100866351	100866351	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100866351delG	uc001dtg.3	+						CDC14A_uc009web.2_Intron|CDC14A_uc010oui.1_Intron|CDC14A_uc001dte.3_Intron|CDC14A_uc001dtf.2_Intron|CDC14A_uc009wed.1_Intron|CDC14A_uc009wee.2_Intron	NM_003672	NP_003663			CDC14 homolog A isoform 1						cell cycle|cell division|cell proliferation	centrosome|nucleus|spindle	protein binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			large_intestine(1)	1		all_epithelial(167;3.71e-06)|all_lung(203;0.00097)|Lung NSC(277;0.001)		Epithelial(280;0.0676)|all cancers(265;0.127)|COAD - Colon adenocarcinoma(174;0.201)|Lung(183;0.227)|Colorectal(144;0.241)														---	---	---	---
CDC14A	8556	broad.mit.edu	37	1	100973026	100973026	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100973026delT	uc001dtg.3	+						CDC14A_uc009wee.2_Intron	NM_003672	NP_003663			CDC14 homolog A isoform 1						cell cycle|cell division|cell proliferation	centrosome|nucleus|spindle	protein binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			large_intestine(1)	1		all_epithelial(167;3.71e-06)|all_lung(203;0.00097)|Lung NSC(277;0.001)		Epithelial(280;0.0676)|all cancers(265;0.127)|COAD - Colon adenocarcinoma(174;0.201)|Lung(183;0.227)|Colorectal(144;0.241)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	103088525	103088525	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103088525delC								OLFM3 (625735 upstream) : COL11A1 (253499 downstream)																																			---	---	---	---
COL11A1	1301	broad.mit.edu	37	1	103380471	103380471	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103380471delT	uc001dul.2	-						COL11A1_uc001duk.2_Intron|COL11A1_uc001dum.2_Intron|COL11A1_uc001dun.2_Intron|COL11A1_uc009weh.2_Intron	NM_001854	NP_001845			alpha 1 type XI collagen isoform A						collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	12		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)														---	---	---	---
COL11A1	1301	broad.mit.edu	37	1	103568727	103568727	+	Intron	DEL	A	-	-	rs2376281	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103568727delA	uc001dul.2	-						COL11A1_uc001dum.2_Intron|COL11A1_uc001dun.2_Intron|COL11A1_uc009weh.2_Intron	NM_001854	NP_001845			alpha 1 type XI collagen isoform A						collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	12		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	104737170	104737170	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104737170delA								AMY1A (529998 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	104766624	104766624	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:104766624delT								AMY1A (559452 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	105240372	105240372	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:105240372delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	105254875	105254875	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:105254875delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	105645468	105645468	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:105645468delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	106189877	106189878	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:106189877_106189878insA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	107622924	107622924	+	IGR	DEL	T	-	-	rs68131877		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:107622924delT								PRMT6 (21017 upstream) : NTNG1 (59705 downstream)																																			---	---	---	---
NTNG1	22854	broad.mit.edu	37	1	107901288	107901289	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:107901288_107901289delAA	uc001dvh.3	+						NTNG1_uc001dvf.3_Intron|NTNG1_uc010out.1_Intron|NTNG1_uc001dvc.3_Intron|NTNG1_uc001dvd.1_Intron	NM_001113226	NP_001106697			netrin G1 isoform 1						axonogenesis	anchored to plasma membrane	protein binding			large_intestine(2)|ovary(2)|skin(2)	6		all_epithelial(167;1.39e-05)|all_lung(203;0.000115)|Lung NSC(277;0.000238)|Breast(1374;0.243)		Lung(183;0.0946)|BRCA - Breast invasive adenocarcinoma(282;0.237)|Epithelial(280;0.245)														---	---	---	---
NTNG1	22854	broad.mit.edu	37	1	107902773	107902773	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:107902773delT	uc001dvh.3	+						NTNG1_uc001dvf.3_Intron|NTNG1_uc010out.1_Intron|NTNG1_uc001dvc.3_Intron|NTNG1_uc001dvd.1_Intron	NM_001113226	NP_001106697			netrin G1 isoform 1						axonogenesis	anchored to plasma membrane	protein binding			large_intestine(2)|ovary(2)|skin(2)	6		all_epithelial(167;1.39e-05)|all_lung(203;0.000115)|Lung NSC(277;0.000238)|Breast(1374;0.243)		Lung(183;0.0946)|BRCA - Breast invasive adenocarcinoma(282;0.237)|Epithelial(280;0.245)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	108066069	108066069	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108066069delT								NTNG1 (41598 upstream) : VAV3 (47713 downstream)																																			---	---	---	---
VAV3	10451	broad.mit.edu	37	1	108332706	108332706	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108332706delC	uc001dvk.1	-						VAV3_uc010ouw.1_Intron|VAV3_uc001dvl.1_Intron|VAV3_uc010oux.1_Intron	NM_006113	NP_006104			vav 3 guanine nucleotide exchange factor isoform						angiogenesis|apoptosis|B cell receptor signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of B cell proliferation|regulation of Rho protein signal transduction|response to DNA damage stimulus|response to drug|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(5)|lung(2)|breast(2)	9		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)														---	---	---	---
VAV3	10451	broad.mit.edu	37	1	108437745	108437745	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108437745delA	uc001dvk.1	-						VAV3_uc010ouw.1_Intron|VAV3_uc001dvl.1_Intron|VAV3_uc010oux.1_Intron	NM_006113	NP_006104			vav 3 guanine nucleotide exchange factor isoform						angiogenesis|apoptosis|B cell receptor signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of B cell proliferation|regulation of Rho protein signal transduction|response to DNA damage stimulus|response to drug|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(5)|lung(2)|breast(2)	9		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	108572165	108572165	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108572165delG								VAV3 (64620 upstream) : SLC25A24 (105284 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	108575319	108575319	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108575319delA								VAV3 (67774 upstream) : SLC25A24 (102130 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	108795307	108795308	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108795307_108795308delTT								NBPF4 (8604 upstream) : NBPF6 (197596 downstream)																																			---	---	---	---
KIAA1324	57535	broad.mit.edu	37	1	109745840	109745843	+	3'UTR	DEL	TTTG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109745840_109745843delTTTG	uc001dwq.2	+	23					KIAA1324_uc009wey.2_3'UTR|KIAA1324_uc010ovg.1_3'UTR|KIAA1324_uc001dwr.2_3'UTR	NM_020775	NP_065826			hypothetical protein LOC57535 precursor						macroautophagy|positive regulation of vacuole organization|regulation of apoptosis	integral to plasma membrane				ovary(2)|haematopoietic_and_lymphoid_tissue(1)|breast(1)|skin(1)	5		all_epithelial(167;0.000102)|all_lung(203;0.000323)|Lung NSC(277;0.00063)		Colorectal(144;0.0188)|Lung(183;0.0527)|COAD - Colon adenocarcinoma(174;0.14)|Epithelial(280;0.21)|all cancers(265;0.249)														---	---	---	---
AHCYL1	10768	broad.mit.edu	37	1	110551591	110551592	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110551591_110551592delAA	uc001dyx.2	+						AHCYL1_uc010ovw.1_Intron|AHCYL1_uc001dyy.2_Intron|AHCYL1_uc010ovx.1_Intron	NM_006621	NP_006612			S-adenosylhomocysteine hydrolase-like 1						one-carbon metabolic process	endoplasmic reticulum	adenosylhomocysteinase activity			ovary(1)	1		all_epithelial(167;3.58e-05)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0259)|Colorectal(144;0.123)|all cancers(265;0.134)|Epithelial(280;0.141)|LUSC - Lung squamous cell carcinoma(189;0.143)														---	---	---	---
KCNA10	3744	broad.mit.edu	37	1	111062336	111062337	+	5'Flank	INS	-	TA	TA	rs56239943		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111062336_111062337insTA	uc001dzt.1	-							NM_005549	NP_005540			potassium voltage-gated channel, shaker-related							voltage-gated potassium channel complex	intracellular cyclic nucleotide activated cation channel activity|voltage-gated potassium channel activity			ovary(3)|large_intestine(1)	4		all_cancers(81;4.57e-06)|all_epithelial(167;1.52e-05)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0238)|all cancers(265;0.0874)|Colorectal(144;0.103)|Epithelial(280;0.116)|LUSC - Lung squamous cell carcinoma(189;0.134)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	111571299	111571300	+	IGR	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111571299_111571300delTC								C1orf103 (64733 upstream) : DRAM2 (88655 downstream)																																			---	---	---	---
ADORA3	140	broad.mit.edu	37	1	112062160	112062161	+	Intron	DEL	GG	-	-	rs149188007	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112062160_112062161delGG	uc001ebg.3	-							NM_001081976	NP_001075445			adenosine A3 receptor isoform 3						activation of adenylate cyclase activity|inflammatory response|regulation of heart contraction	integral to plasma membrane	adenosine receptor activity, G-protein coupled			ovary(2)|large_intestine(1)|skin(1)	4		all_cancers(81;1.63e-06)|all_epithelial(167;5.01e-06)|all_lung(203;8.02e-05)|Lung NSC(277;0.000156)		all cancers(265;0.0185)|Colorectal(144;0.0186)|Lung(183;0.0238)|COAD - Colon adenocarcinoma(174;0.0644)|Epithelial(280;0.0872)|LUSC - Lung squamous cell carcinoma(189;0.134)	Adenosine(DB00640)|Aminophylline(DB01223)													---	---	---	---
ADORA3	140	broad.mit.edu	37	1	112076295	112076295	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112076295delC	uc001ebg.3	-							NM_001081976	NP_001075445			adenosine A3 receptor isoform 3						activation of adenylate cyclase activity|inflammatory response|regulation of heart contraction	integral to plasma membrane	adenosine receptor activity, G-protein coupled			ovary(2)|large_intestine(1)|skin(1)	4		all_cancers(81;1.63e-06)|all_epithelial(167;5.01e-06)|all_lung(203;8.02e-05)|Lung NSC(277;0.000156)		all cancers(265;0.0185)|Colorectal(144;0.0186)|Lung(183;0.0238)|COAD - Colon adenocarcinoma(174;0.0644)|Epithelial(280;0.0872)|LUSC - Lung squamous cell carcinoma(189;0.134)	Adenosine(DB00640)|Aminophylline(DB01223)													---	---	---	---
RAP1A	5906	broad.mit.edu	37	1	112141087	112141087	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112141087delT	uc001ebi.2	+							NM_002884	NP_002875			RAP1A, member of RAS oncogene family precursor						activation of MAPKK activity|blood coagulation|energy reserve metabolic process|nerve growth factor receptor signaling pathway|regulation of insulin secretion	cytosol|plasma membrane	GTP binding|GTPase activity				0		all_cancers(81;6.79e-06)|all_epithelial(167;2.42e-05)|all_lung(203;0.000105)|Lung NSC(277;0.00021)		Lung(183;0.0183)|Colorectal(144;0.0418)|LUSC - Lung squamous cell carcinoma(189;0.0966)|all cancers(265;0.098)|Epithelial(280;0.0981)|COAD - Colon adenocarcinoma(174;0.141)														---	---	---	---
RAP1A	5906	broad.mit.edu	37	1	112197969	112197969	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112197969delA	uc001ebi.2	+						RAP1A_uc001ebk.2_Intron|RAP1A_uc001ebl.2_Intron|RAP1A_uc001ebm.2_Intron	NM_002884	NP_002875			RAP1A, member of RAS oncogene family precursor						activation of MAPKK activity|blood coagulation|energy reserve metabolic process|nerve growth factor receptor signaling pathway|regulation of insulin secretion	cytosol|plasma membrane	GTP binding|GTPase activity				0		all_cancers(81;6.79e-06)|all_epithelial(167;2.42e-05)|all_lung(203;0.000105)|Lung NSC(277;0.00021)		Lung(183;0.0183)|Colorectal(144;0.0418)|LUSC - Lung squamous cell carcinoma(189;0.0966)|all cancers(265;0.098)|Epithelial(280;0.0981)|COAD - Colon adenocarcinoma(174;0.141)														---	---	---	---
RAP1A	5906	broad.mit.edu	37	1	112232301	112232301	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112232301delT	uc001ebi.2	+						RAP1A_uc001ebk.2_Intron|RAP1A_uc001ebl.2_Intron|RAP1A_uc001ebm.2_Intron	NM_002884	NP_002875			RAP1A, member of RAS oncogene family precursor						activation of MAPKK activity|blood coagulation|energy reserve metabolic process|nerve growth factor receptor signaling pathway|regulation of insulin secretion	cytosol|plasma membrane	GTP binding|GTPase activity				0		all_cancers(81;6.79e-06)|all_epithelial(167;2.42e-05)|all_lung(203;0.000105)|Lung NSC(277;0.00021)		Lung(183;0.0183)|Colorectal(144;0.0418)|LUSC - Lung squamous cell carcinoma(189;0.0966)|all cancers(265;0.098)|Epithelial(280;0.0981)|COAD - Colon adenocarcinoma(174;0.141)														---	---	---	---
KCND3	3752	broad.mit.edu	37	1	112347849	112347849	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112347849delA	uc001ebu.1	-						KCND3_uc001ebv.1_Intron	NM_004980	NP_004971			potassium voltage-gated channel, Shal-related							sarcolemma|voltage-gated potassium channel complex	A-type (transient outward) potassium channel activity|metal ion binding			ovary(2)|large_intestine(1)	3		all_cancers(81;8.52e-06)|all_epithelial(167;5.65e-06)|all_lung(203;2.72e-05)|Lung NSC(69;4.56e-05)		all cancers(265;0.056)|Lung(183;0.0576)|Colorectal(144;0.1)|Epithelial(280;0.104)|COAD - Colon adenocarcinoma(174;0.222)|LUSC - Lung squamous cell carcinoma(189;0.231)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	112930465	112930466	+	IGR	INS	-	AGGAAGGAAGGAAGGA	AGGAAGGAAGGAAGGA			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112930465_112930466insAGGAAGGAAGGAAGGA								KCND3 (398688 upstream) : CTTNBP2NL (8334 downstream)																																			---	---	---	---
CTTNBP2NL	55917	broad.mit.edu	37	1	112952505	112952505	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112952505delA	uc001ebx.2	+							NM_018704	NP_061174			CTTNBP2 N-terminal like							actin cytoskeleton	protein binding			central_nervous_system(2)|ovary(1)	3		all_cancers(81;0.00064)|all_epithelial(167;0.000415)|all_lung(203;0.00045)|Lung NSC(69;0.000705)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
ST7L	54879	broad.mit.edu	37	1	113083248	113083248	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113083248delA	uc001ecd.2	-						ST7L_uc009wgh.2_Intron|ST7L_uc001ecc.2_Intron|ST7L_uc010owg.1_Intron|ST7L_uc010owh.1_Intron|ST7L_uc001ece.2_Intron|ST7L_uc001ecf.2_Intron|ST7L_uc001ecg.2_Intron	NM_017744	NP_060214			suppression of tumorigenicity 7-like isoform 1						negative regulation of cell growth	integral to membrane	binding				0	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	113603261	113603262	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113603261_113603262delTT	uc001ede.1	-											Homo sapiens cDNA clone IMAGE:4798439.																														---	---	---	---
PHTF1	10745	broad.mit.edu	37	1	114267520	114267520	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114267520delA	uc009wgp.1	-						PHTF1_uc001edn.2_Intron|PHTF1_uc010own.1_Intron	NM_006608	NP_006599			putative homeodomain transcription factor 1							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
PHTF1	10745	broad.mit.edu	37	1	114267762	114267762	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114267762delA	uc009wgp.1	-						PHTF1_uc001edn.2_Intron|PHTF1_uc010own.1_Intron	NM_006608	NP_006599			putative homeodomain transcription factor 1							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
RSBN1	54665	broad.mit.edu	37	1	114319789	114319789	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114319789delA	uc001edq.2	-						RSBN1_uc001edr.2_Intron	NM_018364	NP_060834			round spermatid basic protein 1							nucleus				ovary(1)	1	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
PTPN22	26191	broad.mit.edu	37	1	114377352	114377352	+	Intron	DEL	A	-	-	rs79608028		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114377352delA	uc001eds.2	-						PTPN22_uc009wgq.2_Intron|PTPN22_uc010owo.1_Intron|PTPN22_uc001edt.2_Intron|PTPN22_uc009wgr.2_Intron|PTPN22_uc009wgs.2_Intron|PTPN22_uc001edu.2_Intron	NM_015967	NP_057051			protein tyrosine phosphatase, non-receptor type						negative regulation of T cell activation|negative regulation of T cell receptor signaling pathway|phosphoanandamide dephosphorylation|regulation of B cell receptor signaling pathway|regulation of natural killer cell proliferation|T cell differentiation	internal side of plasma membrane|nucleus|perinuclear region of cytoplasm	kinase binding|protein tyrosine phosphatase activity|SH3 domain binding			kidney(2)|lung(1)|skin(1)	4	Lung SC(450;0.184)	all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
PTPN22	26191	broad.mit.edu	37	1	114383852	114383852	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114383852delA	uc001eds.2	-						PTPN22_uc009wgq.2_Intron|PTPN22_uc010owo.1_Intron|PTPN22_uc001edt.2_Intron|PTPN22_uc009wgr.2_Intron|PTPN22_uc009wgs.2_Intron|PTPN22_uc001edu.2_Intron	NM_015967	NP_057051			protein tyrosine phosphatase, non-receptor type						negative regulation of T cell activation|negative regulation of T cell receptor signaling pathway|phosphoanandamide dephosphorylation|regulation of B cell receptor signaling pathway|regulation of natural killer cell proliferation|T cell differentiation	internal side of plasma membrane|nucleus|perinuclear region of cytoplasm	kinase binding|protein tyrosine phosphatase activity|SH3 domain binding			kidney(2)|lung(1)|skin(1)	4	Lung SC(450;0.184)	all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
PTPN22	26191	broad.mit.edu	37	1	114414022	114414022	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114414022delT	uc001eds.2	-						uc001edv.1_Intron|PTPN22_uc009wgq.2_Intron|PTPN22_uc010owo.1_Intron|PTPN22_uc001edt.2_Intron|PTPN22_uc009wgr.2_Intron|PTPN22_uc009wgs.2_Intron|PTPN22_uc001edu.2_Intron	NM_015967	NP_057051			protein tyrosine phosphatase, non-receptor type						negative regulation of T cell activation|negative regulation of T cell receptor signaling pathway|phosphoanandamide dephosphorylation|regulation of B cell receptor signaling pathway|regulation of natural killer cell proliferation|T cell differentiation	internal side of plasma membrane|nucleus|perinuclear region of cytoplasm	kinase binding|protein tyrosine phosphatase activity|SH3 domain binding			kidney(2)|lung(1)|skin(1)	4	Lung SC(450;0.184)	all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	114548805	114548805	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114548805delA								OLFML3 (23929 upstream) : SYT6 (83110 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	114806599	114806599	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114806599delG								SYT6 (110127 upstream) : TRIM33 (128802 downstream)																																			---	---	---	---
AMPD1	270	broad.mit.edu	37	1	115217930	115217930	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115217930delA	uc001efe.1	-						AMPD1_uc001eff.1_Intron	NM_000036	NP_000027			adenosine monophosphate deaminase 1 (isoform M)						purine base metabolic process|purine ribonucleoside monophosphate biosynthetic process|purine-containing compound salvage	cytosol	AMP deaminase activity|metal ion binding			ovary(2)|large_intestine(1)|skin(1)	4	all_epithelial(7;7.83e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	Adenosine monophosphate(DB00131)													---	---	---	---
SYCP1	6847	broad.mit.edu	37	1	115524252	115524252	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115524252delT	uc001efr.2	+						SYCP1_uc010owt.1_Intron|SYCP1_uc001efq.2_Intron|SYCP1_uc009wgw.2_Intron	NM_003176	NP_003167			synaptonemal complex protein 1						cell division|reciprocal meiotic recombination|spermatogenesis|synaptonemal complex assembly		DNA binding			skin(1)	1	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
SYCP1	6847	broad.mit.edu	37	1	115535246	115535246	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115535246delA	uc001efr.2	+						SYCP1_uc010owt.1_Intron|SYCP1_uc001efq.2_Intron|SYCP1_uc009wgw.2_Intron	NM_003176	NP_003167			synaptonemal complex protein 1						cell division|reciprocal meiotic recombination|spermatogenesis|synaptonemal complex assembly		DNA binding			skin(1)	1	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	116108154	116108154	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116108154delC								NGF (227297 upstream) : VANGL1 (76420 downstream)																																			---	---	---	---
SLC22A15	55356	broad.mit.edu	37	1	116569047	116569047	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116569047delA	uc001egb.3	+						SLC22A15_uc001ega.2_Intron	NM_018420	NP_060890			solute carrier family 22, member 15						ion transport	integral to membrane	transmembrane transporter activity			large_intestine(2)	2	Lung SC(450;0.184)	all_cancers(81;3.17e-06)|all_epithelial(167;2.32e-06)|all_lung(203;9.81e-06)|Lung NSC(69;5.94e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	116692538	116692538	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116692538delA								C1orf161 (14677 upstream) : ATP1A1 (222466 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	116973263	116973263	+	IGR	DEL	T	-	-	rs71896487		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116973263delT								C1orf203 (12019 upstream) : CD58 (83894 downstream)																																			---	---	---	---
CD58	965	broad.mit.edu	37	1	117078855	117078855	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117078855delA	uc001egm.2	-						CD58_uc001egn.2_Intron|CD58_uc010owy.1_Intron|CD58_uc001ego.1_Intron|CD58_uc001egp.3_Intron	NM_001779	NP_001770			CD58 molecule isoform 1						blood coagulation|cell-cell adhesion|leukocyte migration	anchored to membrane|integral to plasma membrane	protein binding				0	Lung SC(450;0.225)	all_cancers(81;0.000363)|all_lung(203;0.000118)|all_epithelial(167;0.000149)|Lung NSC(69;0.000577)		Lung(183;0.0086)|LUSC - Lung squamous cell carcinoma(189;0.0528)|Colorectal(144;0.0775)|all cancers(265;0.109)|Epithelial(280;0.118)|COAD - Colon adenocarcinoma(174;0.121)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	117218072	117218072	+	IGR	DEL	T	-	-	rs71582575		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117218072delT								MIR320B1 (3623 upstream) : CD2 (79014 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	117285582	117285584	+	IGR	DEL	AAA	-	-	rs5777285		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117285582_117285584delAAA								MIR320B1 (71133 upstream) : CD2 (11502 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	117389502	117389502	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117389502delA								CD2 (77652 upstream) : PTGFRN (63187 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	118283096	118283096	+	IGR	DEL	G	-	-	rs35632814		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118283096delG								FAM46C (112086 upstream) : GDAP2 (123012 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	118350229	118350229	+	IGR	DEL	G	-	-	rs35072320		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118350229delG								FAM46C (179219 upstream) : GDAP2 (55879 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	118396582	118396582	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118396582delT								FAM46C (225572 upstream) : GDAP2 (9526 downstream)																																			---	---	---	---
SPAG17	200162	broad.mit.edu	37	1	118699422	118699422	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118699422delT	uc001ehk.2	-							NM_206996	NP_996879			sperm associated antigen 17							cilium|flagellar axoneme|microtubule				upper_aerodigestive_tract(2)|ovary(2)|large_intestine(1)|skin(1)	6	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	118760582	118760585	+	IGR	DEL	GAGA	-	-	rs113617392		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118760582_118760585delGAGA								SPAG17 (32734 upstream) : TBX15 (665081 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	119325544	119325544	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119325544delA								SPAG17 (597696 upstream) : TBX15 (100122 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	119706411	119706413	+	Intron	DEL	TTT	-	-	rs111989746		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119706411_119706413delTTT	uc001ehp.1	+						uc009whk.1_Intron					Homo sapiens cDNA FLJ43771 fis, clone TESTI2049553.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	119774960	119774960	+	Intron	DEL	A	-	-	rs34387075		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:119774960delA	uc001ehp.1	+											Homo sapiens cDNA FLJ43771 fis, clone TESTI2049553.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	120004436	120004436	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120004436delT								HSD3B2 (15316 upstream) : HSD3B1 (45390 downstream)																																			---	---	---	---
NOTCH2	4853	broad.mit.edu	37	1	120470149	120470149	+	Intron	DEL	T	-	-	rs111292566		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120470149delT	uc001eik.2	-							NM_024408	NP_077719			notch 2 preproprotein						anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1)	27	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)				N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				---	---	---	---
FCGR1B	2210	broad.mit.edu	37	1	120929479	120929479	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120929479delT	uc001eip.2	-						FCGR1B_uc001eiq.2_Intron|FCGR1B_uc010oxl.1_Intron|FCGR1B_uc009whr.2_Intron	NM_001017986	NP_001017986			Fc fragment of IgG, high affinity Ib, receptor						interferon-gamma-mediated signaling pathway	integral to membrane|plasma membrane	IgG binding|immunoglobulin receptor activity				0	all_neural(166;0.181)	all_lung(203;7.27e-05)|Lung NSC(69;0.000389)|all_epithelial(167;0.068)		Lung(183;0.0327)|LUSC - Lung squamous cell carcinoma(189;0.19)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	121118973	121118975	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:121118973_121118975delAAA	uc001eis.2	+							NM_001042758	NP_001036223			SLIT-ROBO Rho GTPase activating protein 2																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	121387324	121387324	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:121387324delG								LOC647121 (73638 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	143425098	143425099	+	5'Flank	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143425098_143425099insA	hsa-mir-3118-3|MI0014133	-						uc001ejn.1_RNA																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	143932598	143932598	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143932598delT	uc010oxm.1	+											SubName: Full=Novel protein similar to SLIT-ROBO Rho GTPase activating protein 2 SRGAP2; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	143954491	143954493	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143954491_143954493delTTT	uc010oxm.1	+											SubName: Full=Novel protein similar to SLIT-ROBO Rho GTPase activating protein 2 SRGAP2; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	143984235	143984235	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:143984235delT	uc010oxm.1	+											SubName: Full=Novel protein similar to SLIT-ROBO Rho GTPase activating protein 2 SRGAP2; Flags: Fragment;																														---	---	---	---
NBPF9	400818	broad.mit.edu	37	1	144471831	144471832	+	Intron	INS	-	G	G	rs72701809		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144471831_144471832insG	uc010oxr.1	+						NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron	NM_001037675	NP_001032764			hypothetical protein LOC400818							cytoplasm					0																		---	---	---	---
NBPF9	400818	broad.mit.edu	37	1	144530876	144530877	+	Intron	INS	-	CC	CC	rs72257362		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144530876_144530877insCC	uc010oxr.1	+						NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron	NM_001037675	NP_001032764			hypothetical protein LOC400818							cytoplasm					0																		---	---	---	---
NBPF9	400818	broad.mit.edu	37	1	144681814	144681814	+	Intron	DEL	G	-	-	rs67467472		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144681814delG	uc009wig.1	+						NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxr.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc001eli.3_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF9_uc009wii.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron	NM_001037675	NP_001032764			hypothetical protein LOC400818							cytoplasm					0																		---	---	---	---
NBPF9	400818	broad.mit.edu	37	1	144844331	144844331	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144844331delA	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron					RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0																		---	---	---	---
PDE4DIP	9659	broad.mit.edu	37	1	144861754	144861755	+	Intron	INS	-	T	T	rs112244618		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144861754_144861755insT	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001elv.3_Intron	NM_014644	NP_055459			phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)				T	PDGFRB	MPD								---	---	---	---
PDE4DIP	9659	broad.mit.edu	37	1	144907405	144907405	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144907405delA	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001emc.1_Intron|PDE4DIP_uc001emd.1_Intron|PDE4DIP_uc001emb.1_Intron|PDE4DIP_uc001eme.1_Intron|PDE4DIP_uc001emf.1_Intron	NM_014644	NP_055459			phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)				T	PDGFRB	MPD								---	---	---	---
PDE4DIP	9659	broad.mit.edu	37	1	144992176	144992176	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144992176delA	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001emc.1_Intron|PDE4DIP_uc001emd.1_Intron|PDE4DIP_uc001emg.1_Intron|PDE4DIP_uc001emh.2_Intron	NM_014644	NP_055459			phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)				T	PDGFRB	MPD								---	---	---	---
PDE4DIP	9659	broad.mit.edu	37	1	145024583	145024590	+	Intron	DEL	ACACACAT	-	-	rs72171398		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145024583_145024590delACACACAT	uc001elx.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron	NM_014644	NP_055459			phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)				T	PDGFRB	MPD								---	---	---	---
NBPF9	400818	broad.mit.edu	37	1	145044040	145044041	+	Intron	DEL	AA	-	-	rs11451563		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145044040_145044041delAA	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron					RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0																		---	---	---	---
NBPF9	400818	broad.mit.edu	37	1	145045709	145045709	+	Intron	DEL	A	-	-	rs3978574		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145045709delA	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001emh.2_Intron					RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0																		---	---	---	---
NBPF9	400818	broad.mit.edu	37	1	145085808	145085809	+	Intron	INS	-	T	T	rs146743627		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145085808_145085809insT	uc010oye.1	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron					RecName: Full=Neuroblastoma breakpoint family member 8;							cytoplasm					0																		---	---	---	---
SEC22B	9554	broad.mit.edu	37	1	145116299	145116300	+	3'UTR	INS	-	TT	TT	rs71696722		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145116299_145116300insTT	uc001eml.1	+	7					NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron	NM_004892	NP_004883			SEC22 vesicle trafficking protein homolog B						ER to Golgi vesicle-mediated transport|protein transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane|melanosome	protein binding				0																		---	---	---	---
NBPF10	100132406	broad.mit.edu	37	1	145231038	145231042	+	Intron	DEL	AAAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145231038_145231042delAAAAA	uc001emp.3	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NOTCH2NL_uc001emn.3_Intron|NOTCH2NL_uc001emm.3_Intron|NOTCH2NL_uc001emo.2_Intron|NOTCH2NL_uc010oyh.1_Intron	NM_017940	NP_060410			hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)														---	---	---	---
NBPF10	100132406	broad.mit.edu	37	1	145302963	145302963	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145302963delT	uc001end.3	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|NBPF10_uc001emp.3_Intron|NBPF10_uc010oyi.1_Intron|NBPF10_uc001emq.1_Intron	NM_001039703	NP_001034792			hypothetical protein LOC100132406												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)														---	---	---	---
NBPF10	100132406	broad.mit.edu	37	1	145380919	145380921	+	Intron	DEL	CTT	-	-	rs55940905		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145380919_145380921delCTT	uc001emp.3	+							NM_017940	NP_060410			hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)														---	---	---	---
NBPF10	100132406	broad.mit.edu	37	1	145430334	145430335	+	Intron	DEL	AA	-	-	rs111654623		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145430334_145430335delAA	uc001emp.3	+							NM_017940	NP_060410			hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)														---	---	---	---
ITGA10	8515	broad.mit.edu	37	1	145531414	145531415	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145531414_145531415delAA	uc001eoa.2	+						NBPF10_uc001emp.3_Intron|ITGA10_uc010oyv.1_Intron|ITGA10_uc009wiw.2_Intron|ITGA10_uc010oyw.1_Intron	NM_003637	NP_003628			integrin, alpha 10 precursor						cell-matrix adhesion|integrin-mediated signaling pathway	integrin complex	collagen binding|receptor activity			lung(2)|ovary(2)|kidney(2)|large_intestine(1)|skin(1)	8	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)																	---	---	---	---
NBPF10	100132406	broad.mit.edu	37	1	145620825	145620825	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145620825delT	uc001emp.3	+						RNF115_uc001eoj.2_Intron|RNF115_uc001eok.2_Intron|RNF115_uc009wiy.2_Intron	NM_017940	NP_060410			hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)														---	---	---	---
NBPF10	100132406	broad.mit.edu	37	1	145646291	145646292	+	Intron	INS	-	GA	GA	rs147795554	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145646291_145646292insGA	uc001emp.3	+						RNF115_uc001eoj.2_Intron|RNF115_uc001eok.2_Intron|RNF115_uc009wiy.2_Intron	NM_017940	NP_060410			hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)														---	---	---	---
NBPF10	100132406	broad.mit.edu	37	1	145753599	145753600	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145753599_145753600delAA	uc001emp.3	+						PDZK1_uc001eon.1_Intron|PDZK1_uc001eoo.1_Intron|PDZK1_uc010oza.1_Intron	NM_017940	NP_060410			hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)														---	---	---	---
NBPF10	100132406	broad.mit.edu	37	1	145799077	145799078	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145799077_145799078delTT	uc001emp.3	+						GPR89A_uc001eor.2_Intron|GPR89A_uc010ozb.1_Intron|GPR89A_uc001eos.2_Intron|GPR89A_uc001eot.2_Intron|GPR89A_uc010ozc.1_Intron|GPR89A_uc010ozd.1_Intron|GPR89A_uc010oze.1_Intron	NM_017940	NP_060410			hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)														---	---	---	---
NBPF10	100132406	broad.mit.edu	37	1	145823365	145823365	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145823365delA	uc001emp.3	+						GPR89A_uc010ozb.1_Intron|GPR89A_uc001eos.2_Intron|GPR89A_uc001eot.2_Intron|GPR89A_uc010ozc.1_Intron|GPR89A_uc010ozd.1_Intron|GPR89A_uc010oze.1_Intron	NM_017940	NP_060410			hypothetical protein LOC55672												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)														---	---	---	---
PRKAB2	5565	broad.mit.edu	37	1	146645753	146645753	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146645753delA	uc001epe.2	-						PRKAB2_uc010ozm.1_5'Flank|PRKAB2_uc010ozn.1_5'Flank|PRKAB2_uc009wjf.1_5'Flank|uc001epf.1_Intron	NM_005399	NP_005390			AMP-activated protein kinase beta 2						carnitine shuttle|cell cycle arrest|energy reserve metabolic process|fatty acid biosynthetic process|insulin receptor signaling pathway|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation	cytosol|nucleoplasm				lung(2)|skin(1)	3	all_hematologic(923;0.0487)				Adenosine monophosphate(DB00131)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	146984232	146984232	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:146984232delA	uc001epp.2	-											Homo sapiens cDNA clone IMAGE:5266739.																														---	---	---	---
ACP6	51205	broad.mit.edu	37	1	147135409	147135409	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147135409delG	uc001epr.2	-						ACP6_uc009wjj.1_Intron	NM_016361	NP_057445			acid phosphatase 6, lysophosphatidic precursor						lipid metabolic process	extracellular region|mitochondrion	acid phosphatase activity|protein binding			ovary(4)	4	all_hematologic(923;0.0276)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	147275725	147275725	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147275725delA								GJA5 (30241 upstream) : GJA8 (99211 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	147391197	147391199	+	IGR	DEL	GGA	-	-	rs146981307		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147391197_147391199delGGA								GJA8 (9804 upstream) : GPR89B (9307 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	147393292	147393292	+	IGR	DEL	G	-	-	rs71083866		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147393292delG								GJA8 (11899 upstream) : GPR89B (7214 downstream)																																			---	---	---	---
LOC200030	200030	broad.mit.edu	37	1	148213507	148213507	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148213507delT	uc001eqf.2	-						LOC200030_uc001eqe.2_Intron|LOC200030_uc001eqg.2_Intron|NBPF14_uc010pab.1_Intron|NBPF14_uc010pac.1_Intron|NBPF14_uc001eqx.2_Intron|NBPF14_uc010pae.1_Intron|NBPF14_uc010paf.1_Intron|NBPF14_uc009wkf.1_Intron	NM_017940	NP_060410			hypothetical protein LOC55672							cytoplasm					0																		---	---	---	---
LOC200030	200030	broad.mit.edu	37	1	148220905	148220905	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148220905delA	uc001eqf.2	-						LOC200030_uc001eqe.2_Intron|LOC200030_uc001eqg.2_Intron|NBPF14_uc010pab.1_Intron|NBPF14_uc010pac.1_Intron|NBPF14_uc001eqx.2_Intron|NBPF14_uc010pae.1_Intron|NBPF14_uc010paf.1_Intron|NBPF14_uc009wkf.1_Intron	NM_017940	NP_060410			hypothetical protein LOC55672							cytoplasm					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	148871035	148871035	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148871035delA								NBPF16 (112724 upstream) : LOC645166 (57251 downstream)																																			---	---	---	---
LOC645166	645166	broad.mit.edu	37	1	148930861	148930862	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148930861_148930862insT	uc010pbc.1	+						LOC645166_uc010pbd.1_Intron|LOC645166_uc009wkw.1_Intron	NR_027355				Homo sapiens cDNA, FLJ18771.												0																		---	---	---	---
LOC645166	645166	broad.mit.edu	37	1	148944038	148944039	+	Intron	DEL	AA	-	-	rs76811044		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148944038_148944039delAA	uc010pbc.1	+						LOC645166_uc010pbd.1_Intron|LOC645166_uc009wkw.1_Intron	NR_027355				Homo sapiens cDNA, FLJ18771.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	149102851	149102851	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149102851delA								LOC645166 (149797 upstream) : LOC388692 (176625 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	149252674	149252675	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149252674_149252675insT								LOC645166 (299620 upstream) : LOC388692 (26801 downstream)																																			---	---	---	---
LOC388692	388692	broad.mit.edu	37	1	149283132	149283132	+	RNA	DEL	A	-	-	rs149398765		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149283132delA	uc010pbf.1	+	1		c.3657delA				NR_027002				Homo sapiens cDNA FLJ13580 fis, clone PLACE1008851.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	149313685	149313685	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149313685delA								LOC388692 (21943 upstream) : FCGR1C (55609 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	149862710	149862711	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149862710_149862711insA								HIST2H2AB (3244 upstream) : BOLA1 (8444 downstream)																																			---	---	---	---
VPS45	11311	broad.mit.edu	37	1	150057001	150057001	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150057001delT	uc001etp.2	+						VPS45_uc010pbp.1_Intron|VPS45_uc010pbq.1_Intron|VPS45_uc010pbs.1_Intron|VPS45_uc001etq.2_Intron|VPS45_uc009wlm.1_Intron	NM_007259	NP_009190			vacuolar protein sorting 45A						blood coagulation|intracellular protein transport|vesicle docking involved in exocytosis	endosome membrane|Golgi membrane|integral to membrane of membrane fraction				central_nervous_system(1)|skin(1)	2	Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
VPS45	11311	broad.mit.edu	37	1	150111065	150111065	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150111065delA	uc001etp.2	+						VPS45_uc010pbq.1_Intron|VPS45_uc010pbs.1_Intron|VPS45_uc001etq.2_Intron	NM_007259	NP_009190			vacuolar protein sorting 45A						blood coagulation|intracellular protein transport|vesicle docking involved in exocytosis	endosome membrane|Golgi membrane|integral to membrane of membrane fraction				central_nervous_system(1)|skin(1)	2	Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	150215858	150215858	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150215858delT								ANP32E (7354 upstream) : CA14 (14360 downstream)																																			---	---	---	---
PRPF3	9129	broad.mit.edu	37	1	150298611	150298611	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150298611delT	uc001eum.3	+						PRPF3_uc009wlo.2_Intron|PRPF3_uc009wlp.2_Intron|PRPF3_uc010pca.1_Intron|PRPF3_uc010pcb.1_Intron	NM_004698	NP_004689			PRP3 pre-mRNA processing factor 3 homolog						nuclear mRNA splicing, via spliceosome	Cajal body|cytoplasm|nuclear speck|spliceosomal complex	protein binding			ovary(1)	1	Lung NSC(24;5.57e-29)|Breast(34;0.000844)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)	Colorectal(1306;0.0149)														---	---	---	---
RPRD2	23248	broad.mit.edu	37	1	150383944	150383946	+	Intron	DEL	AAC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150383944_150383946delAAC	uc009wlr.2	+						RPRD2_uc010pcc.1_Intron|RPRD2_uc001eup.3_Intron	NM_015203	NP_056018			Regulation of nuclear pre-mRNA domain containing								protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	150510359	150510360	+	IGR	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150510359_150510360insG								ECM1 (24095 upstream) : ADAMTSL4 (11538 downstream)																																			---	---	---	---
CTSS	1520	broad.mit.edu	37	1	150711129	150711129	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150711129delA	uc001evn.2	-						CTSS_uc010pcj.1_Intron	NM_004079	NP_004070			cathepsin S preproprotein						immune response|proteolysis	extracellular region|lysosome	cysteine-type endopeptidase activity				0	all_cancers(9;6.17e-52)|all_epithelial(9;9.7e-43)|all_lung(15;5.74e-35)|Lung NSC(24;2.09e-31)|Breast(34;0.00146)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0485)|Epithelial(6;5.02e-21)|all cancers(9;1.28e-20)|OV - Ovarian serous cystadenocarcinoma(6;1.09e-14)|BRCA - Breast invasive adenocarcinoma(12;0.00501)|LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
SETDB1	9869	broad.mit.edu	37	1	150902735	150902735	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150902735delA	uc001evu.2	+						SETDB1_uc009wmf.2_Intron|SETDB1_uc001evv.2_Intron|SETDB1_uc001evw.3_Intron|SETDB1_uc009wmg.1_Intron	NM_001145415	NP_001138887			SET domain, bifurcated 1 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|Golgi apparatus|nucleus|plasma membrane	DNA binding|histone-lysine N-methyltransferase activity|protein binding|zinc ion binding			ovary(2)|upper_aerodigestive_tract(1)	3	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|BRCA - Breast invasive adenocarcinoma(12;0.0152)|LUSC - Lung squamous cell carcinoma(543;0.211)															---	---	---	---
PRUNE	58497	broad.mit.edu	37	1	150990220	150990221	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150990220_150990221delAA	uc001ewh.1	+						PRUNE_uc001ewi.1_Intron|PRUNE_uc010pco.1_Intron|PRUNE_uc001ewj.1_Intron	NM_021222	NP_067045			prune							cytoplasm|focal adhesion|nucleus	inorganic diphosphatase activity|manganese ion binding|protein binding			ovary(1)	1	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)															---	---	---	---
PRUNE	58497	broad.mit.edu	37	1	150996972	150996972	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150996972delA	uc001ewh.1	+						PRUNE_uc001ewi.1_Intron|PRUNE_uc010pco.1_Intron|PRUNE_uc001ewj.1_Intron|PRUNE_uc001ewk.1_5'Flank	NM_021222	NP_067045			prune							cytoplasm|focal adhesion|nucleus	inorganic diphosphatase activity|manganese ion binding|protein binding			ovary(1)	1	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)															---	---	---	---
BNIPL	149428	broad.mit.edu	37	1	151009357	151009358	+	Intron	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151009357_151009358delTG	uc001ewl.2	+						BNIPL_uc009wmi.2_Intron|BNIPL_uc009wmj.2_5'Flank	NM_138278	NP_612122			BCL2/adenovirus E1B 19kD interacting protein						apoptosis|induction of apoptosis|negative regulation of cell proliferation|regulation of growth rate	cytosol|nucleus	identical protein binding				0	Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)															---	---	---	---
BNIPL	149428	broad.mit.edu	37	1	151010862	151010862	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151010862delA	uc001ewl.2	+						BNIPL_uc009wmi.2_Intron|BNIPL_uc009wmj.2_5'Flank	NM_138278	NP_612122			BCL2/adenovirus E1B 19kD interacting protein						apoptosis|induction of apoptosis|negative regulation of cell proliferation|regulation of growth rate	cytosol|nucleus	identical protein binding				0	Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)															---	---	---	---
GABPB2	126626	broad.mit.edu	37	1	151079397	151079397	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151079397delT	uc001ewr.2	+						GABPB2_uc001ews.2_Intron|GABPB2_uc001ewt.2_Intron	NM_144618	NP_653219			GA repeat binding protein, beta 2						positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	protein heterodimerization activity|transcription regulatory region DNA binding				0				all cancers(107;7.17e-05)|GBM - Glioblastoma multiforme(94;0.000662)														---	---	---	---
PIP5K1A	8394	broad.mit.edu	37	1	151180183	151180183	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151180183delT	uc001exj.2	+						PIP5K1A_uc001exi.2_Intron|PIP5K1A_uc010pcu.1_Intron|PIP5K1A_uc001exk.2_Intron	NM_001135638	NP_001129110			phosphatidylinositol-4-phosphate 5-kinase, type						phospholipid biosynthetic process|signal transduction	endomembrane system|Golgi stack|lamellipodium|nuclear speck	1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|kinase binding			ovary(1)|central_nervous_system(1)|skin(1)	3	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
PIP5K1A	8394	broad.mit.edu	37	1	151184588	151184589	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151184588_151184589delAA	uc001exj.2	+						PIP5K1A_uc001exi.2_Intron|PIP5K1A_uc010pcu.1_Intron|PIP5K1A_uc001exk.2_Intron	NM_001135638	NP_001129110			phosphatidylinositol-4-phosphate 5-kinase, type						phospholipid biosynthetic process|signal transduction	endomembrane system|Golgi stack|lamellipodium|nuclear speck	1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|kinase binding			ovary(1)|central_nervous_system(1)|skin(1)	3	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
PIP5K1A	8394	broad.mit.edu	37	1	151202396	151202396	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151202396delA	uc001exj.2	+						PIP5K1A_uc001exi.2_Intron|PIP5K1A_uc010pcu.1_Intron|PIP5K1A_uc001exk.2_Intron	NM_001135638	NP_001129110			phosphatidylinositol-4-phosphate 5-kinase, type						phospholipid biosynthetic process|signal transduction	endomembrane system|Golgi stack|lamellipodium|nuclear speck	1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|kinase binding			ovary(1)|central_nervous_system(1)|skin(1)	3	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
CGN	57530	broad.mit.edu	37	1	151492628	151492628	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151492628delT	uc009wmw.2	+							NM_020770	NP_065821			cingulin							myosin complex|tight junction	actin binding|motor activity			ovary(2)|pancreas(1)	3	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
TUFT1	7286	broad.mit.edu	37	1	151525574	151525575	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151525574_151525575delTT	uc001eyl.2	+						TUFT1_uc001eym.2_Intron|TUFT1_uc010pdf.1_Intron|TUFT1_uc010pdg.1_Intron	NM_020127	NP_064512			tuftelin 1 isoform 1						bone mineralization|odontogenesis	cytoplasm|extracellular region	structural constituent of tooth enamel				0	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
TUFT1	7286	broad.mit.edu	37	1	151530466	151530466	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151530466delA	uc001eyl.2	+						TUFT1_uc001eym.2_Intron|TUFT1_uc010pdf.1_Intron|TUFT1_uc010pdg.1_Intron	NM_020127	NP_064512			tuftelin 1 isoform 1						bone mineralization|odontogenesis	cytoplasm|extracellular region	structural constituent of tooth enamel				0	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
SNX27	81609	broad.mit.edu	37	1	151587834	151587835	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151587834_151587835delTT	uc001eyn.1	+							NM_030918	NP_112180			sorting nexin family member 27						cell communication|protein transport|signal transduction	cytosol|early endosome	phosphatidylinositol binding|protein binding			ovary(2)|central_nervous_system(1)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	152311111	152311111	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152311111delA	uc001ezv.2	+											Homo sapiens cDNA FLJ31869 fis, clone NT2RP7002151.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	152504704	152504704	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152504704delT								CRCT1 (16224 upstream) : LCE3E (33427 downstream)																																			---	---	---	---
SMCP	4184	broad.mit.edu	37	1	152855136	152855137	+	Intron	DEL	CA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152855136_152855137delCA	uc001fat.2	+							NM_030663	NP_109588			sperm mitochondria-associated cysteine-rich						penetration of zona pellucida|sperm motility	mitochondrial membrane					0	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	153158959	153158959	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153158959delT								SPRR2G (35532 upstream) : LELP1 (16960 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	153205958	153205958	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153205958delA								LELP1 (28364 upstream) : LOR (26221 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	153459056	153459056	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153459056delA								S100A7 (25919 upstream) : S100A6 (48020 downstream)																																			---	---	---	---
S100A14	57402	broad.mit.edu	37	1	153586745	153586745	+	3'UTR	DEL	T	-	-	rs139764022	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153586745delT	uc001fce.2	-	4					S100A16_uc001fcd.1_5'Flank	NM_020672	NP_065723			S100 calcium binding protein A14						calcium ion homeostasis|defense response to bacterium|positive regulation of granulocyte chemotaxis|positive regulation of monocyte chemotaxis|response to lipopolysaccharide|toll-like receptor 4 signaling pathway	cell junction|microtubule cytoskeleton|perinuclear region of cytoplasm	calcium ion binding|chemokine receptor binding				0	all_lung(78;1.84e-32)|Lung NSC(65;6.67e-31)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
INTS3	65123	broad.mit.edu	37	1	153729864	153729864	+	Intron	DEL	T	-	-	rs113019058		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153729864delT	uc009wom.2	+						INTS3_uc001fct.2_Intron|INTS3_uc001fcu.2_Intron|INTS3_uc001fcv.2_Intron|INTS3_uc010peb.1_Intron|INTS3_uc001fcw.2_Intron|INTS3_uc010pec.1_5'Flank	NM_023015	NP_075391			integrator complex subunit 3						DNA repair|G2/M transition checkpoint|response to ionizing radiation|snRNA processing	integrator complex|SOSS complex	protein binding			ovary(2)|upper_aerodigestive_tract(1)	3	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)															---	---	---	---
INTS3	65123	broad.mit.edu	37	1	153733986	153733987	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153733986_153733987insA	uc009wom.2	+						INTS3_uc001fct.2_Intron|INTS3_uc001fcu.2_Intron|INTS3_uc001fcv.2_Intron|INTS3_uc010peb.1_Intron|INTS3_uc001fcw.2_Intron|INTS3_uc010pec.1_Intron	NM_023015	NP_075391			integrator complex subunit 3						DNA repair|G2/M transition checkpoint|response to ionizing radiation|snRNA processing	integrator complex|SOSS complex	protein binding			ovary(2)|upper_aerodigestive_tract(1)	3	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)															---	---	---	---
GATAD2B	57459	broad.mit.edu	37	1	153779429	153779429	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153779429delA	uc001fdb.3	-	11						NM_020699	NP_065750			GATA zinc finger domain containing 2B							nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_lung(78;1.34e-32)|Lung NSC(65;1.04e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)															---	---	---	---
GATAD2B	57459	broad.mit.edu	37	1	153897055	153897056	+	5'Flank	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153897055_153897056delTT	uc001fdb.3	-						uc001fdc.1_Intron	NM_020699	NP_065750			GATA zinc finger domain containing 2B							nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_lung(78;1.34e-32)|Lung NSC(65;1.04e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)															---	---	---	---
DENND4B	9909	broad.mit.edu	37	1	153916853	153916853	+	5'UTR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153916853delC	uc001fdd.1	-	2						NM_014856	NP_055671			DENN/MADD domain containing 4B											ovary(1)	1	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)															---	---	---	---
NUP210L	91181	broad.mit.edu	37	1	153986807	153986807	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153986807delC	uc001fdw.2	-						NUP210L_uc009woq.2_Intron|NUP210L_uc010peh.1_Intron	NM_207308	NP_997191			nucleoporin 210kDa-like isoform 1							integral to membrane				skin(5)|ovary(4)|large_intestine(1)|central_nervous_system(1)	11	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)															---	---	---	---
NUP210L	91181	broad.mit.edu	37	1	153989019	153989019	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153989019delA	uc001fdw.2	-						NUP210L_uc009woq.2_Intron|NUP210L_uc010peh.1_Intron	NM_207308	NP_997191			nucleoporin 210kDa-like isoform 1							integral to membrane				skin(5)|ovary(4)|large_intestine(1)|central_nervous_system(1)	11	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)															---	---	---	---
NUP210L	91181	broad.mit.edu	37	1	154002587	154002587	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154002587delT	uc001fdw.2	-						NUP210L_uc009woq.2_Intron|NUP210L_uc010peh.1_Intron	NM_207308	NP_997191			nucleoporin 210kDa-like isoform 1							integral to membrane				skin(5)|ovary(4)|large_intestine(1)|central_nervous_system(1)	11	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)															---	---	---	---
NUP210L	91181	broad.mit.edu	37	1	154090899	154090899	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154090899delA	uc001fdw.2	-						NUP210L_uc009woq.2_Intron|NUP210L_uc010peh.1_Intron	NM_207308	NP_997191			nucleoporin 210kDa-like isoform 1							integral to membrane				skin(5)|ovary(4)|large_intestine(1)|central_nervous_system(1)	11	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)															---	---	---	---
TPM3	7170	broad.mit.edu	37	1	154152492	154152492	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154152492delA	uc001fec.1	-						TPM3_uc010pei.1_Intron|TPM3_uc001fdy.1_Intron|TPM3_uc001fdz.1_Intron|TPM3_uc001fea.1_Intron|TPM3_uc001feb.1_Intron|TPM3_uc010pej.1_Intron|TPM3_uc009wor.2_Intron|TPM3_uc001fed.1_Intron	NM_152263	NP_689476			tropomyosin 3 isoform 1						cellular component movement|muscle filament sliding|regulation of muscle contraction	cytosol|muscle thin filament tropomyosin|stress fiber	actin binding		TPM3/ALK(33)	haematopoietic_and_lymphoid_tissue(22)|soft_tissue(11)|skin(1)	34	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)							T	NTRK1|ALK	papillary thyroid|ALCL								---	---	---	---
Unknown	0	broad.mit.edu	37	1	154339738	154339739	+	IGR	DEL	AA	-	-	rs137875808		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154339738_154339739delAA								ATP8B2 (15959 upstream) : IL6R (37930 downstream)																																			---	---	---	---
ADAR	103	broad.mit.edu	37	1	154554555	154554555	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154554555delT	uc001ffh.2	-	15					ADAR_uc001ffj.2_3'UTR|ADAR_uc001ffi.2_3'UTR|ADAR_uc001ffk.2_3'UTR	NM_001111	NP_001102			adenosine deaminase, RNA-specific isoform a						adenosine to inosine editing|gene silencing by RNA|mRNA modification|mRNA processing|type I interferon-mediated signaling pathway	cytoplasm|nucleolus|nucleoplasm	DNA binding|double-stranded RNA adenosine deaminase activity|metal ion binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997)		LUSC - Lung squamous cell carcinoma(543;0.185)	Colorectal(1306;0.115)														---	---	---	---
KCNN3	3782	broad.mit.edu	37	1	154800704	154800705	+	Intron	INS	-	A	A	rs143524769	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154800704_154800705insA	uc001ffp.2	-						KCNN3_uc001ffo.2_Intron|KCNN3_uc009wox.1_Intron	NM_002249	NP_002240			small conductance calcium-activated potassium							integral to membrane	calmodulin binding			lung(1)	1	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	154892214	154892214	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154892214delA								KCNN3 (49460 upstream) : PMVK (4995 downstream)																																			---	---	---	---
PBXIP1	57326	broad.mit.edu	37	1	154916724	154916724	+	3'UTR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154916724delG	uc001ffr.2	-	11					PBXIP1_uc001ffs.2_3'UTR|PBXIP1_uc010pep.1_3'UTR	NM_020524	NP_065385			pre-B-cell leukemia homeobox interacting protein						cell differentiation|multicellular organismal development|negative regulation of transcription, DNA-dependent	cytosol|microtubule|nucleus	protein binding|transcription corepressor activity			large_intestine(1)	1	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)													OREG0013843	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	1	154967617	154967617	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154967617delT								LENEP (827 upstream) : ZBTB7B (7495 downstream)																																			---	---	---	---
DCST1	149095	broad.mit.edu	37	1	155014579	155014580	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155014579_155014580delTT	uc001fgn.1	+						DCST1_uc010per.1_Intron|DCST1_uc010pes.1_Intron	NM_152494	NP_689707			DC-STAMP domain containing 1 isoform 1							integral to membrane	zinc ion binding			ovary(1)|skin(1)	2	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)															---	---	---	---
RAG1AP1	55974	broad.mit.edu	37	1	155138251	155138251	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155138251delA	uc010pey.1	+							NM_018845				recombination activating gene 1 activating						positive regulation of gene expression, epigenetic	Golgi membrane|integral to membrane|plasma membrane	glucoside transmembrane transporter activity				0	all_epithelial(22;4.71e-30)|all_lung(78;3.15e-27)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;2.28e-10)|all cancers(21;6.16e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000395)|LUSC - Lung squamous cell carcinoma(543;0.193)															---	---	---	---
THBS3	7059	broad.mit.edu	37	1	155171127	155171127	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155171127delC	uc001fix.2	-						RAG1AP1_uc010pey.1_Intron|THBS3_uc009wqi.2_Intron|THBS3_uc001fiz.2_Intron|THBS3_uc001fiy.2_Intron|THBS3_uc010pfu.1_Intron|THBS3_uc010pfv.1_Intron|THBS3_uc001fja.2_Intron	NM_007112	NP_009043			thrombospondin 3 precursor						cell-matrix adhesion	extracellular region|perinuclear region of cytoplasm	calcium ion binding|heparin binding|structural molecule activity			breast(3)|ovary(2)	5	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)															---	---	---	---
FDPS	2224	broad.mit.edu	37	1	155284142	155284143	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155284142_155284143delTT	uc001fkc.2	+						RAG1AP1_uc010pey.1_Intron|FDPS_uc001fkd.2_Intron|FDPS_uc001fke.2_Intron|FDPS_uc001fkf.2_Intron	NM_002004	NP_001995			farnesyl diphosphate synthase isoform a						cholesterol biosynthetic process|interspecies interaction between organisms|isoprenoid biosynthetic process	cytosol|nucleus	dimethylallyltranstransferase activity|geranyltranstransferase activity|metal ion binding				0	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;2.03e-10)|all cancers(21;5.23e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)		Alendronate(DB00630)|Ibandronate(DB00710)|Pamidronate(DB00282)|Risedronate(DB00884)|Zoledronate(DB00399)													---	---	---	---
RUSC1	23623	broad.mit.edu	37	1	155298230	155298233	+	Intron	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155298230_155298233delTTTT	uc001fkj.2	+						RAG1AP1_uc010pey.1_Intron|RUSC1_uc001fkk.2_Intron|RUSC1_uc009wqn.1_Intron|RUSC1_uc009wqo.1_Intron|RUSC1_uc001fkl.2_Intron|RUSC1_uc001fkp.2_Intron|RUSC1_uc001fkq.2_Intron|RUSC1_uc010pgb.1_Intron|RUSC1_uc009wqp.1_Intron|RUSC1_uc001fkn.2_Intron|RUSC1_uc001fko.2_Intron|RUSC1_uc001fkr.2_Intron|RUSC1_uc001fks.2_Intron	NM_001105203	NP_001098673			RUN and SH3 domain containing 1 isoform a							cytoplasm|nucleolus	SH3/SH2 adaptor activity			ovary(2)	2	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;1.55e-10)|all cancers(21;4.15e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)															---	---	---	---
ASH1L	55870	broad.mit.edu	37	1	155347853	155347853	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155347853delA	uc009wqq.2	-						RAG1AP1_uc010pey.1_Intron|ASH1L_uc001fkt.2_Intron	NM_018489	NP_060959			absent, small, or homeotic 1-like						cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)															---	---	---	---
ASH1L	55870	broad.mit.edu	37	1	155386722	155386723	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155386722_155386723delTT	uc009wqq.2	-						ASH1L_uc001fkt.2_Intron	NM_018489	NP_060959			absent, small, or homeotic 1-like						cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)															---	---	---	---
ASH1L	55870	broad.mit.edu	37	1	155418136	155418137	+	Intron	INS	-	TTG	TTG	rs112178568		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155418136_155418137insTTG	uc009wqq.2	-						ASH1L_uc001fkt.2_Intron	NM_018489	NP_060959			absent, small, or homeotic 1-like						cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)															---	---	---	---
ASH1L	55870	broad.mit.edu	37	1	155423590	155423590	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155423590delA	uc009wqq.2	-						ASH1L_uc001fkt.2_Intron	NM_018489	NP_060959			absent, small, or homeotic 1-like						cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)															---	---	---	---
ASH1L	55870	broad.mit.edu	37	1	155464724	155464725	+	Intron	DEL	AG	-	-	rs77785760		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155464724_155464725delAG	uc009wqq.2	-						ASH1L_uc001fkt.2_Intron|ASH1L_uc009wqr.1_Intron	NM_018489	NP_060959			absent, small, or homeotic 1-like						cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	155556427	155556427	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155556427delT								LOC645676 (22695 upstream) : MSTO1 (23580 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	155585574	155585574	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155585574delT	uc001fle.1	-											full-length cDNA clone CS0CAP008YC15 of Thymus of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	155709960	155709960	+	IGR	DEL	T	-	-	rs72405320		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155709960delT								DAP3 (1643 upstream) : MSTO2P (5649 downstream)																																			---	---	---	---
ARHGEF2	9181	broad.mit.edu	37	1	155924927	155924927	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155924927delT	uc001fmt.2	-						ARHGEF2_uc001fmr.2_Intron|ARHGEF2_uc001fms.2_Intron|ARHGEF2_uc001fmu.2_Intron	NM_001162383	NP_001155855			Rho/Rac guanine nucleotide exchange factor 2						actin filament organization|apoptosis|cell division|cell morphogenesis|induction of apoptosis by extracellular signals|intracellular protein transport|mitosis|negative regulation of microtubule depolymerization|nerve growth factor receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|regulation of cell proliferation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|Golgi apparatus|microtubule|ruffle membrane|spindle|tight junction	microtubule binding|Rac GTPase binding|Rac guanyl-nucleotide exchange factor activity|zinc ion binding			ovary(1)	1	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	155968540	155968540	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155968540delT								ARHGEF2 (8676 upstream) : SSR2 (10300 downstream)																																			---	---	---	---
LMNA	4000	broad.mit.edu	37	1	156051821	156051822	+	5'Flank	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156051821_156051822delGA	uc001fnf.1	+						MEX3A_uc001fnd.3_5'Flank	NM_005572	NP_005563			lamin A/C isoform 2						cellular component disassembly involved in apoptosis|cellular response to hypoxia|establishment or maintenance of microtubule cytoskeleton polarity|muscle organ development|positive regulation of cell aging|regulation of apoptosis|regulation of cell migration	cytoplasm|lamin filament|nuclear envelope|nuclear envelope|perinuclear region of cytoplasm	protein binding|structural molecule activity|structural molecule activity			ovary(2)	2	Hepatocellular(266;0.158)													Werner_syndrome|Hutchinson-Gilford_Progeria_Syndrome				---	---	---	---
LMNA	4000	broad.mit.edu	37	1	156086714	156086714	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156086714delT	uc001fni.2	+						LMNA_uc001fnf.1_Intron|LMNA_uc001fng.2_Intron|LMNA_uc001fnh.2_Intron|LMNA_uc009wro.1_Intron	NM_170707	NP_733821			lamin A/C isoform 1 precursor						cellular component disassembly involved in apoptosis|cellular response to hypoxia|establishment or maintenance of microtubule cytoskeleton polarity|muscle organ development|positive regulation of cell aging|regulation of apoptosis|regulation of cell migration	cytoplasm|lamin filament|nuclear envelope|nuclear envelope|perinuclear region of cytoplasm	protein binding|structural molecule activity|structural molecule activity			ovary(2)	2	Hepatocellular(266;0.158)													Werner_syndrome|Hutchinson-Gilford_Progeria_Syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	1	156318588	156318588	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156318588delA								C1orf182 (1805 upstream) : RHBG (20415 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	156329884	156329887	+	IGR	DEL	TAAG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156329884_156329887delTAAG								C1orf182 (13101 upstream) : RHBG (9116 downstream)																																			---	---	---	---
MEF2D	4209	broad.mit.edu	37	1	156456183	156456183	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156456183delG	uc001fpc.2	-						MEF2D_uc001fpb.2_Intron|MEF2D_uc001fpd.2_Intron|MEF2D_uc001fpe.1_Intron|MEF2D_uc009wsa.2_Intron	NM_005920	NP_005911			myocyte enhancer factor 2D						apoptosis|muscle organ development|nervous system development|positive regulation of transcription from RNA polymerase II promoter	nucleus	activating transcription factor binding|histone deacetylase binding|RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity			ovary(1)	1	all_hematologic(923;0.088)|Hepatocellular(266;0.158)																	---	---	---	---
C1orf66	51093	broad.mit.edu	37	1	156702951	156702951	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156702951delT	uc001fpu.2	+						C1orf66_uc001fpv.2_Intron	NM_015997	NP_057081			hypothetical protein LOC51093 isoform 1							integral to membrane	rRNA (adenine-N6,N6-)-dimethyltransferase activity				0	all_hematologic(923;0.088)|Hepatocellular(266;0.158)																	---	---	---	---
NTRK1	4914	broad.mit.edu	37	1	156830533	156830534	+	5'Flank	DEL	GG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156830533_156830534delGG	uc001fqh.1	+						NTRK1_uc001fqf.1_Intron|NTRK1_uc009wsi.1_Intron|INSRR_uc010pht.1_5'Flank|INSRR_uc009wsj.1_5'Flank|NTRK1_uc001fqi.1_5'Flank|NTRK1_uc009wsk.1_5'Flank	NM_002529	NP_002520			neurotrophic tyrosine kinase, receptor, type 1						activation of adenylate cyclase activity|activation of MAPKK activity|activation of phospholipase C activity|cell differentiation|nerve growth factor receptor signaling pathway|nervous system development|phosphatidylinositol-mediated signaling|Ras protein signal transduction	endosome|integral to plasma membrane	ATP binding|neurotrophin receptor activity|transmembrane receptor protein serine/threonine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(9)|ovary(6)|stomach(1)|central_nervous_system(1)	17	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Imatinib(DB00619)			T	TPM3|TPR|TFG	papillary thyroid					TSP Lung(10;0.080)			---	---	---	---
NTRK1	4914	broad.mit.edu	37	1	156841200	156841200	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156841200delA	uc001fqh.1	+						NTRK1_uc001fqf.1_Intron|NTRK1_uc009wsi.1_Intron|NTRK1_uc001fqi.1_Intron|NTRK1_uc009wsk.1_Intron	NM_002529	NP_002520			neurotrophic tyrosine kinase, receptor, type 1						activation of adenylate cyclase activity|activation of MAPKK activity|activation of phospholipase C activity|cell differentiation|nerve growth factor receptor signaling pathway|nervous system development|phosphatidylinositol-mediated signaling|Ras protein signal transduction	endosome|integral to plasma membrane	ATP binding|neurotrophin receptor activity|transmembrane receptor protein serine/threonine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(9)|ovary(6)|stomach(1)|central_nervous_system(1)	17	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Imatinib(DB00619)			T	TPM3|TPR|TFG	papillary thyroid					TSP Lung(10;0.080)			---	---	---	---
ARHGEF11	9826	broad.mit.edu	37	1	156912858	156912859	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156912858_156912859delTT	uc001fqo.2	-						ARHGEF11_uc010phu.1_Intron|ARHGEF11_uc001fqn.2_Intron	NM_014784	NP_055599			Rho guanine nucleotide exchange factor (GEF) 11						actin cytoskeleton organization|apoptosis|axon guidance|cellular component movement|cytokinesis|establishment of cell polarity|G-protein coupled receptor protein signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|positive regulation of transcription, DNA-dependent|regulation of cell growth|regulation of Rho protein signal transduction|Rho protein signal transduction|striated muscle contraction	cytosol|Golgi apparatus|plasma membrane	G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			ovary(3)|skin(2)|pleura(1)|lung(1)|kidney(1)|pancreas(1)	9	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)																	---	---	---	---
ARHGEF11	9826	broad.mit.edu	37	1	156917459	156917459	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156917459delC	uc001fqo.2	-						ARHGEF11_uc010phu.1_Intron|ARHGEF11_uc001fqn.2_Intron	NM_014784	NP_055599			Rho guanine nucleotide exchange factor (GEF) 11						actin cytoskeleton organization|apoptosis|axon guidance|cellular component movement|cytokinesis|establishment of cell polarity|G-protein coupled receptor protein signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|positive regulation of transcription, DNA-dependent|regulation of cell growth|regulation of Rho protein signal transduction|Rho protein signal transduction|striated muscle contraction	cytosol|Golgi apparatus|plasma membrane	G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			ovary(3)|skin(2)|pleura(1)|lung(1)|kidney(1)|pancreas(1)	9	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	157252857	157252858	+	IGR	DEL	AA	-	-	rs142938413		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157252857_157252858delAA								ETV3 (144474 upstream) : FCRL5 (230310 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	157264693	157264693	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157264693delG								ETV3 (156310 upstream) : FCRL5 (218475 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	157336094	157336094	+	IGR	DEL	A	-	-	rs74523040	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157336094delA								ETV3 (227711 upstream) : FCRL5 (147074 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	157641062	157641063	+	IGR	INS	-	A	A	rs148564710		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157641062_157641063insA								FCRL4 (73192 upstream) : FCRL3 (5215 downstream)																																			---	---	---	---
KIRREL	55243	broad.mit.edu	37	1	158035803	158035805	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158035803_158035805delTTT	uc001frn.3	+						KIRREL_uc010pib.1_Intron	NM_018240	NP_060710			kin of IRRE like precursor							integral to membrane				ovary(1)	1	all_hematologic(112;0.0378)																	---	---	---	---
SPTA1	6708	broad.mit.edu	37	1	158582498	158582498	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158582498delA	uc001fst.1	-							NM_003126	NP_003117			spectrin, alpha, erythrocytic 1						actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)																	---	---	---	---
SPTA1	6708	broad.mit.edu	37	1	158613927	158613928	+	Intron	DEL	AA	-	-	rs77912388		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158613927_158613928delAA	uc001fst.1	-							NM_003126	NP_003117			spectrin, alpha, erythrocytic 1						actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	158700924	158700924	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158700924delA								OR6K3 (12971 upstream) : OR6K6 (23682 downstream)																																			---	---	---	---
MNDA	4332	broad.mit.edu	37	1	158817340	158817340	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158817340delA	uc001fsz.1	+							NM_002432	NP_002423			myeloid cell nuclear differentiation antigen						B cell receptor signaling pathway|cellular defense response|negative regulation of B cell proliferation|positive regulation of apoptosis|regulation of transcription, DNA-dependent|response to DNA damage stimulus|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(2)|skin(2)	4	all_hematologic(112;0.0378)																	---	---	---	---
AIM2	9447	broad.mit.edu	37	1	159049317	159049317	+	5'Flank	DEL	T	-	-	rs79162124		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159049317delT	uc001ftj.1	-							NM_004833	NP_004824			absent in melanoma 2						cellular response to drug|immune response|interleukin-1 beta secretion	mitochondrion|nucleus				ovary(2)|pancreas(1)	3	all_hematologic(112;0.0429)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	159348659	159348659	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159348659delT	uc001fts.3	-											Homo sapiens, clone IMAGE:3917623, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	159370934	159370934	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159370934delA	uc001fts.3	-											Homo sapiens, clone IMAGE:3917623, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	159516750	159516750	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159516750delA								OR10J5 (10953 upstream) : APCS (40866 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	159661684	159661684	+	IGR	DEL	A	-	-	rs74954970		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159661684delA								APCS (103024 upstream) : CRP (20396 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	159744140	159744141	+	IGR	INS	-	G	G	rs137879985	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159744140_159744141insG								CRP (59761 upstream) : DUSP23 (6618 downstream)																																			---	---	---	---
C1orf204	284677	broad.mit.edu	37	1	159821683	159821683	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159821683delT	uc001fug.1	-						C1orf204_uc001fuf.1_Intron	NM_001134233	NP_001127705			hypothetical protein LOC284677							integral to membrane					0																		---	---	---	---
DCAF8	50717	broad.mit.edu	37	1	160194944	160194944	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160194944delC	uc001fvo.2	-						DCAF8_uc001fvn.2_Intron|DCAF8_uc009wth.2_Intron|DCAF8_uc010pjb.1_Intron|DCAF8_uc010pjc.1_Intron	NM_015726	NP_056541			DDB1 and CUL4 associated factor 8							CUL4 RING ubiquitin ligase complex	protein binding			skin(2)	2																		---	---	---	---
DCAF8	50717	broad.mit.edu	37	1	160207493	160207493	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160207493delT	uc001fvo.2	-						DCAF8_uc001fvn.2_Intron|DCAF8_uc009wth.2_Intron|DCAF8_uc010pjb.1_Intron|DCAF8_uc010pjc.1_Intron|uc010pjd.1_5'Flank	NM_015726	NP_056541			DDB1 and CUL4 associated factor 8							CUL4 RING ubiquitin ligase complex	protein binding			skin(2)	2																		---	---	---	---
NCSTN	23385	broad.mit.edu	37	1	160326892	160326893	+	Frame_Shift_Ins	INS	-	GT	GT			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160326892_160326893insGT	uc001fvx.2	+	16	1980_1981	c.1856_1857insGT	c.(1855-1857)CGGfs	p.R619fs	NCSTN_uc001fvy.2_Frame_Shift_Ins_p.R599fs|NCSTN_uc010pjf.1_Frame_Shift_Ins_p.R481fs|NCSTN_uc001fvz.2_Frame_Shift_Ins_p.R399fs|NCSTN_uc010pjg.1_Frame_Shift_Ins_p.R361fs	NM_015331	NP_056146	Q92542	NICA_HUMAN	nicastrin precursor	619	Extracellular (Potential).				amyloid precursor protein catabolic process|apoptosis|induction of apoptosis by extracellular signals|membrane protein ectodomain proteolysis|membrane protein intracellular domain proteolysis|nerve growth factor receptor signaling pathway|Notch receptor processing|Notch signaling pathway|positive regulation of catalytic activity|protein processing	endoplasmic reticulum|Golgi apparatus|integral to plasma membrane|melanosome	protein binding			ovary(1)|lung(1)	2	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	160640798	160640798	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160640798delT								SLAMF1 (23717 upstream) : CD48 (7740 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	160685297	160685297	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160685297delA								CD48 (3712 upstream) : SLAMF7 (23780 downstream)																																			---	---	---	---
LY9	4063	broad.mit.edu	37	1	160788309	160788309	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160788309delA	uc001fwu.2	+						LY9_uc001fwv.2_Intron|LY9_uc001fww.2_Intron|LY9_uc001fwx.2_Intron|LY9_uc001fwy.1_Intron|LY9_uc001fwz.2_Intron	NM_002348	NP_002339			lymphocyte antigen 9 isoform a						cell adhesion|immunoglobulin mediated immune response	integral to membrane				ovary(1)	1	all_cancers(52;2.72e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)															---	---	---	---
ITLN1	55600	broad.mit.edu	37	1	160847959	160847960	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160847959_160847960delAA	uc001fxc.2	-							NM_017625	NP_060095			intelectin precursor						positive regulation of glucose import|positive regulation of protein phosphorylation|response to nematode|signal transduction	anchored to membrane|brush border membrane|extracellular region|membrane raft	receptor binding|sugar binding			ovary(2)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)|central_nervous_system(1)	7	all_cancers(52;2.99e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)															---	---	---	---
F11R	50848	broad.mit.edu	37	1	160986447	160986449	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160986447_160986449delAAA	uc009wtt.2	-						F11R_uc010pjv.1_Intron|F11R_uc001fxe.3_Intron|F11R_uc009wtu.2_Intron|F11R_uc010pjw.1_Intron|F11R_uc001fxf.3_Intron	NM_016946	NP_058642			F11 receptor precursor						blood coagulation|inflammatory response|interspecies interaction between organisms|leukocyte migration|tight junction assembly	integral to membrane|tight junction				ovary(2)	2	all_cancers(52;6.73e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00207)															---	---	---	---
F11R	50848	broad.mit.edu	37	1	161001704	161001704	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161001704delA	uc010pjw.1	-						F11R_uc001fxf.3_Intron	NM_016946	NP_058642			F11 receptor precursor						blood coagulation|inflammatory response|interspecies interaction between organisms|leukocyte migration|tight junction assembly	integral to membrane|tight junction				ovary(2)	2	all_cancers(52;6.73e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00207)															---	---	---	---
PVRL4	81607	broad.mit.edu	37	1	161048935	161048935	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161048935delA	uc001fxo.2	-						PVRL4_uc010pjz.1_5'Flank	NM_030916	NP_112178			poliovirus receptor-related 4 precursor						adherens junction organization|cell adhesion|cell junction assembly	adherens junction|extracellular region|integral to membrane				ovary(2)	2	all_cancers(52;8.9e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)															---	---	---	---
ADAMTS4	9507	broad.mit.edu	37	1	161165878	161165878	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161165878delC	uc001fyt.3	-						ADAMTS4_uc001fyu.2_3'UTR	NM_005099	NP_005090			ADAM metallopeptidase with thrombospondin type 1						proteolysis|skeletal system development	extracellular space|proteinaceous extracellular matrix	metalloendopeptidase activity|protease binding|zinc ion binding			ovary(4)|central_nervous_system(1)	5	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)															---	---	---	---
PCP4L1	654790	broad.mit.edu	37	1	161254688	161254688	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161254688delT	uc001gad.2	+	3						NM_001102566	NP_001096036			Purkinje cell protein 4 like 1												0	all_cancers(52;4.16e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	161361682	161361682	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161361682delT								C1orf192 (24018 upstream) : FCGR2A (113523 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	161394019	161394019	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161394019delT								C1orf192 (56355 upstream) : FCGR2A (81186 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	161450606	161450607	+	IGR	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161450606_161450607insC								C1orf192 (112942 upstream) : FCGR2A (24598 downstream)																																			---	---	---	---
FCGR3B	2215	broad.mit.edu	37	1	161603103	161603103	+	5'Flank	DEL	A	-	-	rs147171530	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161603103delA	uc009wul.2	-							NM_000570	NP_000561			low affinity immunoglobulin gamma Fc region						immune response	anchored to membrane|extracellular region|plasma membrane	IgG binding|receptor activity				0	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	161662010	161662010	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161662010delT								RPL31P11 (6968 upstream) : FCRLA (14752 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	162025192	162025192	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162025192delT								OLFML2B (31548 upstream) : NOS1AP (14389 downstream)																																			---	---	---	---
NOS1AP	9722	broad.mit.edu	37	1	162098858	162098858	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162098858delT	uc001gbv.2	+						NOS1AP_uc010pkr.1_Intron|NOS1AP_uc010pks.1_Intron|NOS1AP_uc001gbw.2_Intron	NM_014697	NP_055512			nitric oxide synthase 1 (neuronal) adaptor						regulation of apoptosis|regulation of nitric oxide biosynthetic process|regulation of nitric-oxide synthase activity		nitric-oxide synthase binding|PDZ domain binding			lung(2)|upper_aerodigestive_tract(1)	3	all_hematologic(112;0.203)		BRCA - Breast invasive adenocarcinoma(70;0.0537)															---	---	---	---
NOS1AP	9722	broad.mit.edu	37	1	162184060	162184063	+	Intron	DEL	TTCA	-	-	rs10551799		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162184060_162184063delTTCA	uc001gbv.2	+						NOS1AP_uc010pkr.1_Intron|NOS1AP_uc010pks.1_Intron|NOS1AP_uc001gbw.2_Intron	NM_014697	NP_055512			nitric oxide synthase 1 (neuronal) adaptor						regulation of apoptosis|regulation of nitric oxide biosynthetic process|regulation of nitric-oxide synthase activity		nitric-oxide synthase binding|PDZ domain binding			lung(2)|upper_aerodigestive_tract(1)	3	all_hematologic(112;0.203)		BRCA - Breast invasive adenocarcinoma(70;0.0537)															---	---	---	---
SH2D1B	117157	broad.mit.edu	37	1	162367116	162367116	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162367116delA	uc001gbz.1	-						SH2D1B_uc001gca.1_Intron	NM_053282	NP_444512			SH2 domain containing 1B											pancreas(1)	1	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)															---	---	---	---
UHMK1	127933	broad.mit.edu	37	1	162476656	162476657	+	Intron	INS	-	A	A	rs74933664		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162476656_162476657insA	uc001gcc.1	+						UHMK1_uc001gcb.1_Intron|UHMK1_uc009wuu.1_Intron	NM_175866	NP_787062			kinase interacting stathmin						cell cycle arrest|neuron projection development|peptidyl-serine phosphorylation|positive regulation of translational initiation|protein autophosphorylation|regulation of protein export from nucleus	axon|dendrite cytoplasm|neuronal RNA granule|nucleus	protein binding|protein serine/threonine kinase activity|ribonucleoprotein binding|RNA binding				0	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)															---	---	---	---
UHMK1	127933	broad.mit.edu	37	1	162478493	162478494	+	Intron	DEL	AA	-	-	rs77667397		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162478493_162478494delAA	uc001gcc.1	+						UHMK1_uc001gcb.1_Intron|UHMK1_uc009wuu.1_Intron	NM_175866	NP_787062			kinase interacting stathmin						cell cycle arrest|neuron projection development|peptidyl-serine phosphorylation|positive regulation of translational initiation|protein autophosphorylation|regulation of protein export from nucleus	axon|dendrite cytoplasm|neuronal RNA granule|nucleus	protein binding|protein serine/threonine kinase activity|ribonucleoprotein binding|RNA binding				0	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)															---	---	---	---
UAP1	6675	broad.mit.edu	37	1	162558826	162558827	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162558826_162558827delTT	uc001gce.3	+							NM_003115	NP_003106			UDP-N-acetylglucosamine pyrophosphorylase 1						dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine|UDP-N-acetylglucosamine biosynthetic process	cytosol|nucleus|plasma membrane	UDP-N-acetylglucosamine diphosphorylase activity			ovary(2)|skin(2)|kidney(1)	5	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)															---	---	---	---
DDR2	4921	broad.mit.edu	37	1	162648957	162648957	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162648957delT	uc001gcf.2	+						DDR2_uc001gcg.2_Intron	NM_001014796	NP_001014796			discoidin domain receptor family, member 2						cell adhesion	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(2)|central_nervous_system(2)|ovary(1)|kidney(1)	6	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.113)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	163064277	163064277	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163064277delA								RGS4 (17686 upstream) : RGS5 (47821 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	163075842	163075842	+	IGR	DEL	A	-	-	rs34351472		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163075842delA								RGS4 (29251 upstream) : RGS5 (36256 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	163486811	163486811	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:163486811delA								NUF2 (161258 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	164289768	164289768	+	IGR	DEL	A	-	-	rs143997762		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164289768delA								NUF2 (964215 upstream) : PBX1 (239034 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	164454679	164454680	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164454679_164454680delAA								None (None upstream) : PBX1 (74122 downstream)																																			---	---	---	---
PBX1	5087	broad.mit.edu	37	1	164553601	164553602	+	Intron	DEL	AG	-	-	rs72455099		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164553601_164553602delAG	uc001gct.2	+						PBX1_uc010pku.1_Intron|PBX1_uc010pkv.1_Intron|PBX1_uc001gcs.2_Intron	NM_002585	NP_002576			pre-B-cell leukemia homeobox 1						negative regulation of sequence-specific DNA binding transcription factor activity|sex differentiation|steroid biosynthetic process	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription factor binding		EWSR1/PBX1(3)	soft_tissue(3)|lung(1)|skin(1)	5								T	TCF3|EWSR1	pre B-ALL|myoepithelioma								---	---	---	---
PBX1	5087	broad.mit.edu	37	1	164620056	164620056	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164620056delA	uc001gct.2	+						PBX1_uc010pku.1_Intron|PBX1_uc010pkv.1_Intron|PBX1_uc001gcs.2_Intron|PBX1_uc010pkw.1_Intron|uc001gcu.1_Intron	NM_002585	NP_002576			pre-B-cell leukemia homeobox 1						negative regulation of sequence-specific DNA binding transcription factor activity|sex differentiation|steroid biosynthetic process	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription factor binding		EWSR1/PBX1(3)	soft_tissue(3)|lung(1)|skin(1)	5								T	TCF3|EWSR1	pre B-ALL|myoepithelioma								---	---	---	---
PBX1	5087	broad.mit.edu	37	1	164739107	164739108	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164739107_164739108insT	uc001gct.2	+						PBX1_uc010pku.1_Intron|PBX1_uc010pkv.1_Intron|PBX1_uc001gcs.2_Intron|PBX1_uc010pkw.1_Intron	NM_002585	NP_002576			pre-B-cell leukemia homeobox 1						negative regulation of sequence-specific DNA binding transcription factor activity|sex differentiation|steroid biosynthetic process	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription factor binding		EWSR1/PBX1(3)	soft_tissue(3)|lung(1)|skin(1)	5								T	TCF3|EWSR1	pre B-ALL|myoepithelioma								---	---	---	---
PBX1	5087	broad.mit.edu	37	1	164772000	164772003	+	Intron	DEL	CATT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164772000_164772003delCATT	uc001gct.2	+						PBX1_uc010pku.1_Intron|PBX1_uc010pkv.1_Intron|PBX1_uc001gcs.2_Intron|PBX1_uc010pkw.1_Intron	NM_002585	NP_002576			pre-B-cell leukemia homeobox 1						negative regulation of sequence-specific DNA binding transcription factor activity|sex differentiation|steroid biosynthetic process	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription factor binding		EWSR1/PBX1(3)	soft_tissue(3)|lung(1)|skin(1)	5								T	TCF3|EWSR1	pre B-ALL|myoepithelioma								---	---	---	---
Unknown	0	broad.mit.edu	37	1	164906305	164906305	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:164906305delG								PBX1 (52005 upstream) : LMX1A (264800 downstream)																																			---	---	---	---
LMX1A	4009	broad.mit.edu	37	1	165285305	165285305	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165285305delC	uc001gcy.1	-						LMX1A_uc001gcz.1_Intron	NM_177398	NP_796372			LIM homeobox transcription factor 1, alpha							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(3)|upper_aerodigestive_tract(1)|pancreas(1)	5	all_hematologic(923;0.248)																	---	---	---	---
RXRG	6258	broad.mit.edu	37	1	165412509	165412509	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165412509delG	uc001gda.2	-						RXRG_uc001gdb.1_Intron	NM_006917	NP_008848			retinoid X receptor, gamma isoform a						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	retinoid-X receptor activity|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding				0	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)				Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Tretinoin(DB00755)													---	---	---	---
ALDH9A1	223	broad.mit.edu	37	1	165664744	165664748	+	Intron	DEL	TTTTC	-	-	rs143194829		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165664744_165664748delTTTTC	uc001gdh.1	-						ALDH9A1_uc010pky.1_Intron|ALDH9A1_uc010pkz.1_Intron|ALDH9A1_uc010pla.1_Intron	NM_000696	NP_000687			aldehyde dehydrogenase 9A1						carnitine biosynthetic process|cellular aldehyde metabolic process|hormone metabolic process|neurotransmitter biosynthetic process	cytosol|plasma membrane	3-chloroallyl aldehyde dehydrogenase activity|4-trimethylammoniobutyraldehyde dehydrogenase activity|aldehyde dehydrogenase (NAD) activity|aminobutyraldehyde dehydrogenase activity				0	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)				NADH(DB00157)													---	---	---	---
UCK2	7371	broad.mit.edu	37	1	165807992	165807992	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165807992delA	uc001gdp.2	+						UCK2_uc010plb.1_Intron	NM_012474	NP_036606			uridine-cytidine kinase 2						pyrimidine base metabolic process|pyrimidine nucleoside salvage	cytosol	ATP binding|phosphotransferase activity, alcohol group as acceptor|uridine kinase activity			ovary(1)	1	all_hematologic(923;0.048)|Acute lymphoblastic leukemia(8;0.155)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	165877653	165877653	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:165877653delT								UCK2 (316 upstream) : FAM78B (151763 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	166246957	166246957	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166246957delT								FAM78B (110751 upstream) : FMO9P (326196 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	166635127	166635127	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166635127delA								FMO9P (40656 upstream) : POGK (173597 downstream)																																			---	---	---	---
TADA1	117143	broad.mit.edu	37	1	166841911	166841912	+	Intron	DEL	AA	-	-	rs79635554		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166841911_166841912delAA	uc001gdw.2	-						TADA1_uc009wve.2_Intron	NM_053053	NP_444281			transcriptional adaptor 1-like						histone H3 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	STAGA complex	transcription coactivator activity			ovary(1)	1																		---	---	---	---
ILDR2	387597	broad.mit.edu	37	1	166894253	166894253	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166894253delA	uc001gdx.1	-							NM_199351	NP_955383			immunoglobulin-like domain containing receptor							integral to membrane				ovary(1)	1																		---	---	---	---
DUSP27	92235	broad.mit.edu	37	1	167066048	167066048	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167066048delT	uc001geb.1	+							NM_001080426	NP_001073895			dual specificity phosphatase 27						protein dephosphorylation		protein tyrosine/serine/threonine phosphatase activity			ovary(3)	3																		---	---	---	---
POU2F1	5451	broad.mit.edu	37	1	167200472	167200472	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167200472delT	uc001gec.2	+						POU2F1_uc010plg.1_Intron|POU2F1_uc001ged.2_Intron|POU2F1_uc001gee.2_Intron|POU2F1_uc010plh.1_Intron	NM_002697	NP_002688			POU class 2 homeobox 1						negative regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|skin(2)|breast(1)	5																		---	---	---	---
POU2F1	5451	broad.mit.edu	37	1	167306561	167306561	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167306561delA	uc001gec.2	+						POU2F1_uc010plg.1_Intron|POU2F1_uc001ged.2_Intron|POU2F1_uc001gee.2_Intron|POU2F1_uc010plh.1_Intron|POU2F1_uc001gef.2_Intron	NM_002697	NP_002688			POU class 2 homeobox 1						negative regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|skin(2)|breast(1)	5																		---	---	---	---
POU2F1	5451	broad.mit.edu	37	1	167306930	167306933	+	Intron	DEL	AAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167306930_167306933delAAAA	uc001gec.2	+						POU2F1_uc010plg.1_Intron|POU2F1_uc001ged.2_Intron|POU2F1_uc001gee.2_Intron|POU2F1_uc010plh.1_Intron|POU2F1_uc001gef.2_Intron	NM_002697	NP_002688			POU class 2 homeobox 1						negative regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|skin(2)|breast(1)	5																		---	---	---	---
RCSD1	92241	broad.mit.edu	37	1	167659923	167659924	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167659923_167659924insA	uc001gem.2	+						RCSD1_uc010pli.1_Intron	NM_052862	NP_443094			RCSD domain containing 1											ovary(2)|central_nervous_system(2)|skin(1)	5	all_hematologic(923;0.215)																	---	---	---	---
DCAF6	55827	broad.mit.edu	37	1	167948566	167948566	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167948566delT	uc001gew.2	+						DCAF6_uc001gev.2_Intron|DCAF6_uc001gex.2_Intron|DCAF6_uc010plk.1_Intron|DCAF6_uc001gey.2_Intron	NM_001017977	NP_001017977			IQ motif and WD repeats 1 isoform b						positive regulation of transcription from RNA polymerase II promoter	CUL4 RING ubiquitin ligase complex|nucleus	ligand-dependent nuclear receptor transcription coactivator activity			ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
TBX19	9095	broad.mit.edu	37	1	168203631	168203631	+	Intron	DEL	A	-	-	rs74538572		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168203631delA	uc001gfj.3	+						SFT2D2_uc001gfi.3_Intron	NM_005149	NP_005140			T-box 19						anatomical structure morphogenesis	nucleus	DNA binding				0	all_hematologic(923;0.215)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	168483930	168483930	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168483930delT								MIR557 (139071 upstream) : XCL2 (26075 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	168617678	168617678	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168617678delA								XCL1 (66363 upstream) : DPT (47029 downstream)																																			---	---	---	---
MGC4473	79100	broad.mit.edu	37	1	168760767	168760768	+	Intron	DEL	CA	-	-	rs111741142		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168760767_168760768delCA	uc001gfq.2	+							NR_024160				Homo sapiens hypothetical protein MGC4473, mRNA (cDNA clone IMAGE:2961346), partial cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	169037661	169037664	+	IGR	DEL	AAAC	-	-	rs67286335		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169037661_169037664delAAAC								MGC4473 (275541 upstream) : ATP1B1 (38283 downstream)																																			---	---	---	---
NME7	29922	broad.mit.edu	37	1	169138318	169138318	+	Intron	DEL	T	-	-	rs4656657	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169138318delT	uc001gfu.2	-						NME7_uc010plq.1_Intron|NME7_uc001gft.2_Intron	NM_013330	NP_037462			nucleoside diphosphate kinase 7 isoform a						CTP biosynthetic process|GTP biosynthetic process|UTP biosynthetic process	centrosome	ATP binding|metal ion binding|nucleoside diphosphate kinase activity			central_nervous_system(1)	1	all_hematologic(923;0.208)																	---	---	---	---
NME7	29922	broad.mit.edu	37	1	169218124	169218125	+	Intron	INS	-	AAATTT	AAATTT	rs71635613		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169218124_169218125insAAATTT	uc001gfu.2	-						NME7_uc010plq.1_Intron|NME7_uc001gft.2_Intron	NM_013330	NP_037462			nucleoside diphosphate kinase 7 isoform a						CTP biosynthetic process|GTP biosynthetic process|UTP biosynthetic process	centrosome	ATP binding|metal ion binding|nucleoside diphosphate kinase activity			central_nervous_system(1)	1	all_hematologic(923;0.208)																	---	---	---	---
C1orf114	57821	broad.mit.edu	37	1	169366387	169366387	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169366387delT	uc001gga.1	-						C1orf114_uc001gfz.1_Intron|C1orf114_uc009wvq.1_Intron	NM_021179	NP_067002			hypothetical protein LOC57821												0	all_hematologic(923;0.208)																	---	---	---	---
SELE	6401	broad.mit.edu	37	1	169698253	169698253	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169698253delT	uc001ggm.3	-						C1orf112_uc001ggj.2_Intron	NM_000450	NP_000441			selectin E precursor						actin filament-based process|activation of phospholipase C activity|calcium-mediated signaling|heterophilic cell-cell adhesion|leukocyte migration involved in inflammatory response|leukocyte tethering or rolling|positive regulation of receptor internalization|regulation of inflammatory response|response to interleukin-1|response to lipopolysaccharide|response to tumor necrosis factor	caveola|coated pit|cortical cytoskeleton|extracellular space|integral to membrane|perinuclear region of cytoplasm	oligosaccharide binding|phospholipase binding|sialic acid binding|transmembrane receptor activity			ovary(3)|skin(2)	5	all_hematologic(923;0.208)																	---	---	---	---
C1orf112	55732	broad.mit.edu	37	1	169790714	169790714	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169790714delT	uc001ggp.2	+						C1orf112_uc001ggj.2_Intron|C1orf112_uc001ggq.2_Intron|C1orf112_uc009wvt.2_Intron|C1orf112_uc010plu.1_Intron|C1orf112_uc009wvu.1_Intron|C1orf112_uc001ggr.2_Intron|C1orf112_uc010plv.1_Intron	NM_018186	NP_060656			hypothetical protein LOC55732												0	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)																	---	---	---	---
C1orf112	55732	broad.mit.edu	37	1	169801720	169801720	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169801720delT	uc001ggp.2	+						C1orf112_uc001ggj.2_Intron|C1orf112_uc001ggq.2_Intron|C1orf112_uc009wvt.2_Intron|C1orf112_uc009wvu.1_Intron|C1orf112_uc001ggr.2_Intron|C1orf112_uc010plv.1_Intron	NM_018186	NP_060656			hypothetical protein LOC55732												0	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)																	---	---	---	---
METTL11B	149281	broad.mit.edu	37	1	170123396	170123397	+	Intron	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170123396_170123397insC	uc009wvv.1	+						hsa-mir-3119-1|MI0014134_5'Flank	NM_001136107	NP_001129579			methyltransferase like 11B								methyltransferase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	170453591	170453591	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170453591delT	uc001ggy.1	-											Homo sapiens cDNA FLJ39010 fis, clone NT2RI2026758.																														---	---	---	---
PRRX1	5396	broad.mit.edu	37	1	170678721	170678721	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170678721delT	uc001ghf.2	+						PRRX1_uc001ghe.2_Intron	NM_022716	NP_073207			paired mesoderm homeobox 1 isoform pmx-1b							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(1)	1	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	170756909	170756909	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170756909delA								PRRX1 (48369 upstream) : C1orf129 (147703 downstream)																																			---	---	---	---
C1orf129	80133	broad.mit.edu	37	1	170985631	170985632	+	Intron	DEL	TT	-	-	rs76595205		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170985631_170985632delTT	uc010plz.1	+							NM_001163629	NP_001157101			hypothetical protein LOC80133 isoform 1								binding			pancreas(1)	1	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	171336655	171336657	+	IGR	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171336655_171336657delAAA								FMO4 (25433 upstream) : BAT2L2 (118009 downstream)																																			---	---	---	---
BAT2L2	23215	broad.mit.edu	37	1	171536062	171536062	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171536062delT	uc010pmg.1	+						BAT2L2_uc010pmh.1_Intron|BAT2L2_uc010pmi.1_Intron	NM_015172	NP_055987			HBxAg transactivated protein 2								protein C-terminus binding				0																		---	---	---	---
VAMP4	8674	broad.mit.edu	37	1	171690186	171690186	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171690186delA	uc001ghx.1	-						VAMP4_uc001ghw.1_Intron|VAMP4_uc001ghy.1_Intron	NM_003762	NP_003753			vesicle-associated membrane protein 4						vesicle-mediated transport	endosome|Golgi membrane|integral to membrane|lysosome					0	all_cancers(6;1.42e-10)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)																	---	---	---	---
DNM3	26052	broad.mit.edu	37	1	171870381	171870381	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171870381delA	uc001gie.2	+						DNM3_uc001gid.3_Intron|DNM3_uc009wwb.2_Intron|DNM3_uc001gif.2_Intron	NM_015569	NP_056384			dynamin 3 isoform a						endocytosis|filopodium assembly|synapse assembly	dendritic spine|microtubule|perinuclear region of cytoplasm|postsynaptic density	GTP binding|GTPase activity|protein binding			breast(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	172447729	172447730	+	IGR	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172447729_172447730delAG								C1orf105 (9764 upstream) : C1orf9 (54530 downstream)																																			---	---	---	---
C1orf9	51430	broad.mit.edu	37	1	172538309	172538309	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172538309delT	uc001giq.3	+						C1orf9_uc010pmm.1_Intron|C1orf9_uc009wwd.2_Intron|C1orf9_uc010pmn.1_Intron|C1orf9_uc010pmo.1_Intron	NM_014283	NP_055098			chromosome 1 open reading frame 9 protein						multicellular organismal development|ossification	integral to membrane|rough endoplasmic reticulum membrane				ovary(2)	2		Breast(1374;0.212)		Colorectal(1306;3.98e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00544)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	172613821	172613821	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:172613821delT								C1orf9 (32850 upstream) : FASLG (14364 downstream)																																			---	---	---	---
SLC9A11	284525	broad.mit.edu	37	1	173523646	173523646	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173523646delA	uc001giz.2	-						SLC9A11_uc009wwe.2_Intron|SLC9A11_uc010pmq.1_Intron	NM_178527	NP_848622			solute carrier family 9, member 11						sodium ion transport	integral to membrane	ion channel activity|solute:hydrogen antiporter activity			ovary(2)	2																		---	---	---	---
SLC9A11	284525	broad.mit.edu	37	1	173556683	173556683	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173556683delA	uc001giz.2	-						SLC9A11_uc010pmq.1_Intron	NM_178527	NP_848622			solute carrier family 9, member 11						sodium ion transport	integral to membrane	ion channel activity|solute:hydrogen antiporter activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	173663305	173663305	+	IGR	DEL	T	-	-	rs59858609	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173663305delT								ANKRD45 (24304 upstream) : KLHL20 (20775 downstream)																																			---	---	---	---
KLHL20	27252	broad.mit.edu	37	1	173702733	173702733	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173702733delA	uc001gjc.2	+						KLHL20_uc010pmr.1_Intron|KLHL20_uc009wwf.2_Intron|KLHL20_uc001gjd.2_Intron	NM_014458	NP_055273			kelch-like 20						cytoskeleton organization|negative regulation of apoptosis|proteasomal ubiquitin-dependent protein catabolic process|response to interferon-alpha	actin cytoskeleton|cell surface|Cul3-RING ubiquitin ligase complex|Golgi apparatus|perinuclear region of cytoplasm|PML body	actin binding|interferon-gamma binding|ubiquitin-protein ligase activity			ovary(1)	1																		---	---	---	---
DARS2	55157	broad.mit.edu	37	1	173802912	173802912	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173802912delT	uc001gjh.1	+							NM_018122	NP_060592			aspartyl-tRNA synthetase 2, mitochondrial						tRNA aminoacylation for protein translation	mitochondrial matrix|nucleus	aspartate-tRNA ligase activity|ATP binding|nucleic acid binding			central_nervous_system(2)	2					L-Aspartic Acid(DB00128)													---	---	---	---
SERPINC1	462	broad.mit.edu	37	1	173879832	173879832	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173879832delG	uc001gjt.2	-							NM_000488	NP_000479			serpin peptidase inhibitor, clade C, member 1						blood coagulation|regulation of proteolysis	extracellular space|plasma membrane	heparin binding|protease binding|serine-type endopeptidase inhibitor activity			ovary(1)	1					Enoxaparin(DB01225)|Fondaparinux sodium(DB00569)|Heparin(DB01109)													---	---	---	---
RABGAP1L	9910	broad.mit.edu	37	1	174255747	174255747	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174255747delT	uc001gjx.2	+						RABGAP1L_uc009wwq.1_Intron|RABGAP1L_uc001gjw.2_Intron|RABGAP1L_uc001gjy.2_Intron|RABGAP1L_uc001gjz.2_Intron	NM_014857	NP_055672			RAB GTPase activating protein 1-like isoform A						regulation of protein localization	early endosome|Golgi apparatus|nucleus	Rab GTPase activator activity			ovary(2)|lung(1)|kidney(1)	4																		---	---	---	---
RABGAP1L	9910	broad.mit.edu	37	1	174617200	174617200	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174617200delT	uc001gjx.2	+							NM_014857	NP_055672			RAB GTPase activating protein 1-like isoform A						regulation of protein localization	early endosome|Golgi apparatus|nucleus	Rab GTPase activator activity			ovary(2)|lung(1)|kidney(1)	4																		---	---	---	---
RABGAP1L	9910	broad.mit.edu	37	1	174721308	174721308	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174721308delA	uc001gjx.2	+						RABGAP1L_uc001gkb.3_Intron|RABGAP1L_uc001gkc.3_Intron|RABGAP1L_uc001gkd.3_Intron	NM_014857	NP_055672			RAB GTPase activating protein 1-like isoform A						regulation of protein localization	early endosome|Golgi apparatus|nucleus	Rab GTPase activator activity			ovary(2)|lung(1)|kidney(1)	4																		---	---	---	---
RABGAP1L	9910	broad.mit.edu	37	1	174948083	174948083	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:174948083delT	uc001gkd.3	+						RABGAP1L_uc001gkb.3_Intron|RABGAP1L_uc001gkc.3_Intron|RABGAP1L_uc001gke.3_Intron|RABGAP1L_uc001gkh.3_Intron|uc010pmv.1_Intron					RecName: Full=RAB GTPase-activating protein 1-like;						regulation of protein localization	early endosome|Golgi apparatus|nucleus	Rab GTPase activator activity			ovary(2)|lung(1)|kidney(1)	4																		---	---	---	---
TNN	63923	broad.mit.edu	37	1	175072778	175072778	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175072778delT	uc001gkl.1	+							NM_022093	NP_071376			tenascin N precursor						cell growth|cell migration|signal transduction	extracellular space|proteinaceous extracellular matrix				large_intestine(5)|ovary(3)|central_nervous_system(1)	9		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)														---	---	---	---
TNR	7143	broad.mit.edu	37	1	175336947	175336947	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175336947delT	uc001gkp.1	-						TNR_uc009wwu.1_Intron	NM_003285	NP_003276			tenascin R precursor						axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	175857627	175857628	+	IGR	DEL	TT	-	-	rs76992365		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:175857627_175857628delTT								TNR (144875 upstream) : RFWD2 (56339 downstream)																																	OREG0013999	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
RFWD2	64326	broad.mit.edu	37	1	176132127	176132127	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176132127delA	uc001gku.1	-						RFWD2_uc001gkv.1_Intron|RFWD2_uc001gkw.1_Intron|RFWD2_uc009wwv.2_5'Flank|RFWD2_uc001gkt.1_Intron	NM_022457	NP_071902			ring finger and WD repeat domain 2 isoform a						DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest	centrosome|cytosol|focal adhesion|nuclear speck	protein binding|ubiquitin-protein ligase activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	176200270	176200273	+	IGR	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176200270_176200273delTTTT								RFWD2 (23900 upstream) : PAPPA2 (232034 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	176254365	176254365	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176254365delT								RFWD2 (77995 upstream) : PAPPA2 (177942 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	176341472	176341472	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176341472delT								RFWD2 (165102 upstream) : PAPPA2 (90835 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	176372199	176372200	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176372199_176372200insT								RFWD2 (195829 upstream) : PAPPA2 (60107 downstream)																																			---	---	---	---
PAPPA2	60676	broad.mit.edu	37	1	176736317	176736317	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176736317delA	uc001gkz.2	+						PAPPA2_uc009www.2_Intron	NM_020318	NP_064714			pappalysin 2 isoform 1						cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|skin(2)|lung(1)|breast(1)	16																		---	---	---	---
PAPPA2	60676	broad.mit.edu	37	1	176797354	176797354	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176797354delT	uc001gkz.2	+						PAPPA2_uc009www.2_Intron	NM_020318	NP_064714			pappalysin 2 isoform 1						cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|skin(2)|lung(1)|breast(1)	16																		---	---	---	---
ASTN1	460	broad.mit.edu	37	1	176994611	176994611	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176994611delT	uc001glc.2	-						ASTN1_uc001glb.1_Intron|ASTN1_uc001gld.1_Intron|ASTN1_uc009wwx.1_Intron|ASTN1_uc001gle.3_Intron	NM_004319	NP_004310			astrotactin isoform 1						cell migration|neuron cell-cell adhesion	integral to membrane				ovary(6)|skin(5)|central_nervous_system(2)|large_intestine(1)|lung(1)	15																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	177588224	177588224	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177588224delA								FAM5B (336667 upstream) : SEC16B (309265 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	177634065	177634068	+	IGR	DEL	AAAA	-	-	rs75372885		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177634065_177634068delAAAA								FAM5B (382508 upstream) : SEC16B (263421 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	177682074	177682074	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177682074delC								FAM5B (430517 upstream) : SEC16B (215415 downstream)																																			---	---	---	---
SEC16B	89866	broad.mit.edu	37	1	177898365	177898365	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177898365delA	uc001gli.1	-	26					SEC16B_uc001glk.1_3'UTR|SEC16B_uc009wwy.1_3'UTR|SEC16B_uc001glh.1_3'UTR|SEC16B_uc009wwz.1_3'UTR|SEC16B_uc001glj.1_3'UTR	NM_033127	NP_149118			leucine zipper transcription regulator 2						protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|Golgi membrane				ovary(3)|central_nervous_system(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	178021814	178021815	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178021814_178021815delAA								SEC16B (14672 upstream) : LOC100302401 (38828 downstream)																																			---	---	---	---
RASAL2	9462	broad.mit.edu	37	1	178371093	178371093	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178371093delC	uc001glr.2	+						RASAL2_uc009wxb.2_Intron|RASAL2_uc001glq.2_Intron	NM_004841	NP_004832			RAS protein activator like 2 isoform 1						negative regulation of Ras protein signal transduction|signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	Ras GTPase activator activity			ovary(2)|breast(2)|large_intestine(1)	5																		---	---	---	---
RASAL2	9462	broad.mit.edu	37	1	178433967	178433980	+	Intron	DEL	TTTTTTTTTTTTTT	-	-	rs71951077		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178433967_178433980delTTTTTTTTTTTTTT	uc001glr.2	+						RASAL2_uc001glq.2_Intron|RASAL2_uc009wxc.2_Intron	NM_004841	NP_004832			RAS protein activator like 2 isoform 1						negative regulation of Ras protein signal transduction|signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	Ras GTPase activator activity			ovary(2)|breast(2)|large_intestine(1)	5																		---	---	---	---
RALGPS2	55103	broad.mit.edu	37	1	178784618	178784618	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178784618delT	uc001glz.2	+						RALGPS2_uc001gly.1_Intron|RALGPS2_uc010pnb.1_Intron	NM_152663	NP_689876			Ral GEF with PH domain and SH3 binding motif 2						small GTPase mediated signal transduction	cytoplasm|plasma membrane	guanyl-nucleotide exchange factor activity|protein binding				0																		---	---	---	---
ABL2	27	broad.mit.edu	37	1	179153898	179153898	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179153898delT	uc001gmj.3	-						ABL2_uc010pnf.1_Intron|ABL2_uc010png.1_Intron|ABL2_uc010pnh.1_Intron|ABL2_uc009wxe.2_Intron	NM_007314	NP_009298			arg tyrosine kinase isoform b						axon guidance|cell adhesion|peptidyl-tyrosine phosphorylation|positive regulation of oxidoreductase activity|signal transduction	cytoskeleton|cytosol	ATP binding|magnesium ion binding|manganese ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(8)|breast(3)|ovary(2)|central_nervous_system(1)	14					Adenosine triphosphate(DB00171)|Dasatinib(DB01254)			T	ETV6	AML								---	---	---	---
C1orf125	126859	broad.mit.edu	37	1	179405990	179405991	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179405990_179405991delAA	uc001gmo.2	+						C1orf125_uc009wxg.2_Intron|C1orf125_uc001gmn.1_Intron|C1orf125_uc010pnl.1_Intron|C1orf125_uc001gmp.2_Intron	NM_144696	NP_653297			hypothetical protein LOC126859 isoform 1												0																		---	---	---	---
C1orf125	126859	broad.mit.edu	37	1	179433085	179433085	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179433085delT	uc001gmo.2	+						C1orf125_uc009wxg.2_Intron|C1orf125_uc001gmn.1_Intron|C1orf125_uc010pnl.1_Intron|C1orf125_uc001gmp.2_Intron	NM_144696	NP_653297			hypothetical protein LOC126859 isoform 1												0																		---	---	---	---
C1orf125	126859	broad.mit.edu	37	1	179472860	179472860	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179472860delC	uc001gmo.2	+						C1orf125_uc009wxg.2_Intron|C1orf125_uc001gmp.2_Intron|C1orf125_uc009wxh.2_Intron	NM_144696	NP_653297			hypothetical protein LOC126859 isoform 1												0																		---	---	---	---
TDRD5	163589	broad.mit.edu	37	1	179587713	179587713	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179587713delT	uc001gnf.1	+						TDRD5_uc010pnp.1_Intron|TDRD5_uc001gnh.1_Intron	NM_173533	NP_775804			tudor domain containing 5						DNA methylation involved in gamete generation|P granule organization|spermatid development	chromatoid body|pi-body	nucleic acid binding			ovary(2)|skin(2)|central_nervous_system(1)	5																		---	---	---	---
TDRD5	163589	broad.mit.edu	37	1	179604781	179604781	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179604781delT	uc001gnf.1	+						TDRD5_uc010pnp.1_Intron|TDRD5_uc001gnh.1_Intron	NM_173533	NP_775804			tudor domain containing 5						DNA methylation involved in gamete generation|P granule organization|spermatid development	chromatoid body|pi-body	nucleic acid binding			ovary(2)|skin(2)|central_nervous_system(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	179679274	179679274	+	IGR	DEL	A	-	-	rs34563635		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179679274delA								TDRD5 (18876 upstream) : FAM163A (17641 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	179804779	179804779	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179804779delA								FAM163A (19453 upstream) : TOR1AIP2 (9175 downstream)																																			---	---	---	---
TOR1AIP2	163590	broad.mit.edu	37	1	179844102	179844103	+	Intron	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179844102_179844103delTC	uc001gnk.2	-						TOR1AIP2_uc001gnl.2_Intron|TOR1AIP2_uc001gnn.2_Intron	NM_145034	NP_659471			torsin A interacting protein 2							endoplasmic reticulum membrane|integral to membrane	protein binding			ovary(1)	1																		---	---	---	---
TOR1AIP1	26092	broad.mit.edu	37	1	179873275	179873276	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179873275_179873276insA	uc001gnq.2	+						TOR1AIP1_uc001gnp.1_Intron	NM_015602	NP_056417			lamina-associated polypeptide 1B							integral to membrane|nuclear inner membrane				breast(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	179904131	179904131	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179904131delT								TOR1AIP1 (14920 upstream) : CEP350 (19777 downstream)																																			---	---	---	---
CEP350	9857	broad.mit.edu	37	1	179961369	179961370	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179961369_179961370delAA	uc001gnt.2	+						CEP350_uc001gnr.1_Intron|CEP350_uc009wxl.2_Intron	NM_014810	NP_055625			centrosome-associated protein 350							centrosome|nucleus|spindle				ovary(4)	4																		---	---	---	---
CEP350	9857	broad.mit.edu	37	1	179993414	179993414	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179993414delA	uc001gnt.2	+						CEP350_uc009wxl.2_Intron|CEP350_uc001gnu.2_Intron	NM_014810	NP_055625			centrosome-associated protein 350							centrosome|nucleus|spindle				ovary(4)	4																		---	---	---	---
CEP350	9857	broad.mit.edu	37	1	180011138	180011138	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180011138delA	uc001gnt.2	+						CEP350_uc009wxl.2_Intron	NM_014810	NP_055625			centrosome-associated protein 350							centrosome|nucleus|spindle				ovary(4)	4																		---	---	---	---
CEP350	9857	broad.mit.edu	37	1	180077635	180077635	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180077635delA	uc001gnt.2	+						CEP350_uc009wxl.2_Intron|CEP350_uc001gnv.2_Intron|CEP350_uc001gnw.1_Intron|CEP350_uc001gnx.1_Intron	NM_014810	NP_055625			centrosome-associated protein 350							centrosome|nucleus|spindle				ovary(4)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	180496325	180496327	+	IGR	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180496325_180496327delAAA								ACBD6 (24303 upstream) : XPR1 (104819 downstream)																																			---	---	---	---
XPR1	9213	broad.mit.edu	37	1	180615532	180615532	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180615532delT	uc001goi.2	+						XPR1_uc009wxm.2_Intron|XPR1_uc009wxn.2_Intron	NM_004736	NP_004727			xenotropic and polytropic retrovirus receptor							integral to plasma membrane	G-protein coupled receptor activity				0																		---	---	---	---
XPR1	9213	broad.mit.edu	37	1	180651970	180651971	+	Intron	DEL	GT	-	-	rs78896344		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180651970_180651971delGT	uc001goi.2	+						XPR1_uc009wxm.2_Intron|XPR1_uc009wxn.2_Intron	NM_004736	NP_004727			xenotropic and polytropic retrovirus receptor							integral to plasma membrane	G-protein coupled receptor activity				0																		---	---	---	---
XPR1	9213	broad.mit.edu	37	1	180835348	180835348	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180835348delA	uc001goi.2	+						XPR1_uc009wxn.2_Intron	NM_004736	NP_004727			xenotropic and polytropic retrovirus receptor							integral to plasma membrane	G-protein coupled receptor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	180995159	180995160	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180995159_180995160delTG								STX6 (3113 upstream) : MR1 (7979 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	181121042	181121042	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181121042delT								IER5 (61065 upstream) : CACNA1E (331674 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	181331426	181331426	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181331426delT								IER5 (271449 upstream) : CACNA1E (121290 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	181416497	181416497	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181416497delA								IER5 (356520 upstream) : CACNA1E (36219 downstream)																																			---	---	---	---
CACNA1E	777	broad.mit.edu	37	1	181474046	181474046	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181474046delT	uc001gow.2	+							NM_000721	NP_000712			calcium channel, voltage-dependent, R type,						energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6																		---	---	---	---
CACNA1E	777	broad.mit.edu	37	1	181503090	181503090	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181503090delT	uc001gow.2	+						CACNA1E_uc009wxr.2_Intron|CACNA1E_uc009wxs.2_Intron	NM_000721	NP_000712			calcium channel, voltage-dependent, R type,						energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6																		---	---	---	---
CACNA1E	777	broad.mit.edu	37	1	181516286	181516286	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181516286delC	uc001gow.2	+						CACNA1E_uc009wxr.2_Intron|CACNA1E_uc009wxs.2_Intron	NM_000721	NP_000712			calcium channel, voltage-dependent, R type,						energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6																		---	---	---	---
CACNA1E	777	broad.mit.edu	37	1	181519854	181519855	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181519854_181519855delTT	uc001gow.2	+						CACNA1E_uc009wxr.2_Intron|CACNA1E_uc009wxs.2_Intron	NM_000721	NP_000712			calcium channel, voltage-dependent, R type,						energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6																		---	---	---	---
CACNA1E	777	broad.mit.edu	37	1	181529362	181529362	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181529362delT	uc001gow.2	+						CACNA1E_uc009wxr.2_Intron|CACNA1E_uc009wxs.2_Intron	NM_000721	NP_000712			calcium channel, voltage-dependent, R type,						energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6																		---	---	---	---
CACNA1E	777	broad.mit.edu	37	1	181748956	181748957	+	Intron	DEL	AC	-	-	rs147270838		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181748956_181748957delAC	uc001gow.2	+						CACNA1E_uc009wxs.2_Intron|CACNA1E_uc009wxt.2_Intron	NM_000721	NP_000712			calcium channel, voltage-dependent, R type,						energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	182044944	182044944	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182044944delA								ZNF648 (14097 upstream) : GLUL (306725 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	182397270	182397270	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182397270delA								TEDDM1 (27519 upstream) : RGSL1 (21986 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	182577425	182577425	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182577425delT								RGS16 (3877 upstream) : RGS8 (38367 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	182678502	182678503	+	IGR	DEL	CA	-	-	rs138657076	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182678502_182678503delCA								RGS8 (36435 upstream) : NPL (80369 downstream)																																			---	---	---	---
C1orf14	81626	broad.mit.edu	37	1	182921127	182921127	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182921127delA	uc001gpu.2	-						C1orf14_uc001gpv.2_Intron|C1orf14_uc010pnz.1_Intron|C1orf14_uc001gpw.2_Intron	NM_030933	NP_112195			chromosome 1 open reading frame 14												0				Colorectal(1306;1.64e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00267)														---	---	---	---
LAMC1	3915	broad.mit.edu	37	1	183024956	183024956	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183024956delA	uc001gpy.3	+						LAMC1_uc001gpx.2_Intron	NM_002293	NP_002284			laminin, gamma 1 precursor						axon guidance|cell migration|endoderm development|extracellular matrix disassembly|hemidesmosome assembly|positive regulation of epithelial cell proliferation|protein complex assembly|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	extracellular matrix structural constituent			ovary(3)|large_intestine(1)|kidney(1)	5					Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
NMNAT2	23057	broad.mit.edu	37	1	183357429	183357429	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183357429delA	uc001gqc.1	-							NM_015039	NP_055854			nicotinamide mononucleotide adenylyltransferase						water-soluble vitamin metabolic process	Golgi membrane|nucleus	ATP binding|nicotinamide-nucleotide adenylyltransferase activity|nicotinate-nucleotide adenylyltransferase activity			skin(1)	1																		---	---	---	---
RGL1	23179	broad.mit.edu	37	1	183689051	183689051	+	Intron	DEL	A	-	-	rs79595901		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183689051delA	uc001gqm.2	+						RGL1_uc010pof.1_Intron|RGL1_uc010pog.1_Intron|RGL1_uc010poh.1_Intron	NM_015149	NP_055964			ral guanine nucleotide dissociation						cellular lipid metabolic process|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular	protein binding|Ral guanyl-nucleotide exchange factor activity			breast(5)|ovary(4)|lung(2)	11																		---	---	---	---
TSEN15	116461	broad.mit.edu	37	1	184035548	184035548	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184035548delT	uc001gqt.3	+						TSEN15_uc009wyg.2_Intron|TSEN15_uc001gqu.3_Intron	NM_052965	NP_443197			tRNA splicing endonuclease 15 isoform 1						mRNA processing|tRNA processing	nucleolus	protein binding				0																		---	---	---	---
C1orf21	81563	broad.mit.edu	37	1	184447361	184447361	+	Intron	DEL	T	-	-	rs76591155		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184447361delT	uc001gqv.1	+							NM_030806	NP_110433			chromosome 1 open reading frame 21												0		Breast(1374;0.00262)		Colorectal(1306;4.8e-08)|KIRC - Kidney renal clear cell carcinoma(1967;0.00314)														---	---	---	---
FAM129A	116496	broad.mit.edu	37	1	184940801	184940801	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184940801delA	uc001gra.2	-						FAM129A_uc009wyh.1_Intron|FAM129A_uc009wyi.1_Intron	NM_052966	NP_443198			niban protein isoform 2						negative regulation of protein phosphorylation|positive regulation of protein phosphorylation|positive regulation of translation|response to endoplasmic reticulum stress	cytoplasm|nucleus|plasma membrane				ovary(3)|skin(1)	4																		---	---	---	---
RNF2	6045	broad.mit.edu	37	1	185043814	185043814	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185043814delA	uc001grc.1	+						RNF2_uc001grd.1_Intron	NM_007212	NP_009143			ring finger protein 2						histone H2A monoubiquitination|transcription, DNA-dependent	MLL1 complex|PcG protein complex|ubiquitin ligase complex	RING-like zinc finger domain binding|zinc ion binding			breast(1)	1		Breast(1374;0.000496)		Colorectal(1306;6.9e-08)|KIRC - Kidney renal clear cell carcinoma(1967;8.12e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	185076332	185076332	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185076332delA								RNF2 (4592 upstream) : C1orf25 (10887 downstream)																																			---	---	---	---
C1orf26	54823	broad.mit.edu	37	1	185140797	185140797	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185140797delT	uc001grg.3	+						C1orf26_uc001grh.3_Intron	NM_001105518	NP_001098988			hypothetical protein LOC54823												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	185667414	185667415	+	IGR	INS	-	TT	TT			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185667414_185667415insTT								IVNS1ABP (380953 upstream) : HMCN1 (36268 downstream)																																			---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	186062999	186062999	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186062999delT	uc001grq.1	+							NM_031935	NP_114141			hemicentin 1 precursor						response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23																		---	---	---	---
PRG4	10216	broad.mit.edu	37	1	186280090	186280090	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186280090delT	uc001gru.3	+						PRG4_uc001grt.3_Intron|PRG4_uc009wyl.2_Intron|PRG4_uc009wym.2_Intron|PRG4_uc010poo.1_Intron	NM_005807	NP_005798			proteoglycan 4 isoform A						cell proliferation|immune response	extracellular region	polysaccharide binding|protein binding|scavenger receptor activity			skin(1)	1																		---	---	---	---
TPR	7175	broad.mit.edu	37	1	186289561	186289561	+	Intron	DEL	A	-	-	rs74500854	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186289561delA	uc001grv.2	-							NM_003292	NP_003283			nuclear pore complex-associated protein TPR						carbohydrate metabolic process|glucose transport|mitotic cell cycle spindle assembly checkpoint|mRNA transport|protein import into nucleus|regulation of glucose transport|seryl-tRNA aminoacylation|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytoplasm|nuclear membrane|nuclear pore|nucleoplasm	ATP binding|protein binding|serine-tRNA ligase activity			ovary(2)|lung(2)|urinary_tract(1)|central_nervous_system(1)|skin(1)	7		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)				T	NTRK1	papillary thyroid								---	---	---	---
TPR	7175	broad.mit.edu	37	1	186307132	186307132	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186307132delT	uc001grv.2	-							NM_003292	NP_003283			nuclear pore complex-associated protein TPR						carbohydrate metabolic process|glucose transport|mitotic cell cycle spindle assembly checkpoint|mRNA transport|protein import into nucleus|regulation of glucose transport|seryl-tRNA aminoacylation|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytoplasm|nuclear membrane|nuclear pore|nucleoplasm	ATP binding|protein binding|serine-tRNA ligase activity			ovary(2)|lung(2)|urinary_tract(1)|central_nervous_system(1)|skin(1)	7		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)				T	NTRK1	papillary thyroid								---	---	---	---
C1orf27	54953	broad.mit.edu	37	1	186370598	186370599	+	Intron	INS	-	TCTG	TCTG	rs142302628	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186370598_186370599insTCTG	uc001grw.2	+						C1orf27_uc010poq.1_Intron|C1orf27_uc010por.1_Intron	NM_017847	NP_060317			odorant response abnormal 4 isoform 1							integral to membrane	oxidoreductase activity|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	187051388	187051388	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:187051388delT								PLA2G4A (93283 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	187068446	187068446	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:187068446delT								PLA2G4A (110341 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	187113367	187113367	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:187113367delA								PLA2G4A (155262 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	187330497	187330497	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:187330497delT								PLA2G4A (372392 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	187521497	187521497	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:187521497delA								PLA2G4A (563392 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	187856378	187856378	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:187856378delT								PLA2G4A (898273 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	188080632	188080635	+	IGR	DEL	ATTA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:188080632_188080635delATTA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	188211718	188211718	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:188211718delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	188238512	188238512	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:188238512delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	188416136	188416139	+	IGR	DEL	TTCC	-	-	rs112749943		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:188416136_188416139delTTCC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	188562065	188562065	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:188562065delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	188849638	188849638	+	IGR	DEL	T	-	-	rs35837851		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:188849638delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	189356719	189356720	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:189356719_189356720delTT								None (None upstream) : FAM5C (710077 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	189556919	189556919	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:189556919delT								None (None upstream) : FAM5C (509878 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	189648635	189648637	+	IGR	DEL	ACA	-	-	rs148654398		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:189648635_189648637delACA								None (None upstream) : FAM5C (418160 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	189826929	189826929	+	IGR	DEL	T	-	-	rs35747024		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:189826929delT								None (None upstream) : FAM5C (239868 downstream)																																			---	---	---	---
FAM5C	339479	broad.mit.edu	37	1	190210596	190210597	+	Intron	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:190210596_190210597delTC	uc001gse.1	-						FAM5C_uc010pot.1_Intron	NM_199051	NP_950252			family with sequence similarity 5, member C							extracellular region				lung(2)|ovary(1)|kidney(1)|skin(1)	5	Prostate(682;0.198)																	---	---	---	---
FAM5C	339479	broad.mit.edu	37	1	190267002	190267002	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:190267002delA	uc001gse.1	-						FAM5C_uc010pot.1_Intron	NM_199051	NP_950252			family with sequence similarity 5, member C							extracellular region				lung(2)|ovary(1)|kidney(1)|skin(1)	5	Prostate(682;0.198)																	---	---	---	---
FAM5C	339479	broad.mit.edu	37	1	190408663	190408664	+	Intron	DEL	GT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:190408663_190408664delGT	uc001gse.1	-						FAM5C_uc010pot.1_Intron	NM_199051	NP_950252			family with sequence similarity 5, member C							extracellular region				lung(2)|ovary(1)|kidney(1)|skin(1)	5	Prostate(682;0.198)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	191087197	191087197	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:191087197delT								FAM5C (640438 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	191133622	191133622	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:191133622delC								FAM5C (686863 upstream) : RGS18 (993970 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	191870663	191870663	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:191870663delT								None (None upstream) : RGS18 (256929 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	192007494	192007496	+	IGR	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192007494_192007496delAAA								None (None upstream) : RGS18 (120096 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	192187678	192187678	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192187678delT								RGS18 (32735 upstream) : RGS21 (98444 downstream)																																			---	---	---	---
RGS21	431704	broad.mit.edu	37	1	192321502	192321502	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192321502delT	uc001gsh.2	+							NM_001039152	NP_001034241			regulator of G-protein signaling 21						negative regulation of signal transduction	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	192360007	192360008	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192360007_192360008insT								RGS21 (23595 upstream) : RGS1 (184849 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	192918421	192918421	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:192918421delT								RGS2 (137015 upstream) : UCHL5 (66479 downstream)																																			---	---	---	---
CDC73	79577	broad.mit.edu	37	1	193108403	193108403	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193108403delT	uc001gtb.2	+							NM_024529	NP_078805			parafibromin						cell cycle|histone H2B ubiquitination|histone monoubiquitination|transcription, DNA-dependent	Cdc73/Paf1 complex	protein binding			parathyroid(46)|ovary(1)|breast(1)|pancreas(1)	49														Hyperparathyroidism_Familial_Isolated|Hyperparathyroidism-Jaw_Tumor_Syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	1	193421510	193421511	+	IGR	INS	-	TCT	TCT	rs146534813	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193421510_193421511insTCT								CDC73 (197570 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	194374361	194374361	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:194374361delC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	194494118	194494119	+	IGR	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:194494118_194494119delGA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	195095835	195095836	+	IGR	INS	-	TG	TG			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:195095835_195095836insTG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	195447416	195447416	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:195447416delT								None (None upstream) : KCNT2 (747497 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	195714526	195714526	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:195714526delT								None (None upstream) : KCNT2 (480387 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	196111339	196111339	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196111339delA								None (None upstream) : KCNT2 (83574 downstream)																																			---	---	---	---
KCNT2	343450	broad.mit.edu	37	1	196453450	196453451	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196453450_196453451delTT	uc001gtd.1	-						KCNT2_uc001gte.1_Intron|KCNT2_uc001gtf.1_Intron|KCNT2_uc001gtg.1_Intron|KCNT2_uc009wyu.2_Intron|KCNT2_uc009wyv.1_Intron	NM_198503	NP_940905			potassium channel, subfamily T, member 2							voltage-gated potassium channel complex	ATP binding|calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(5)|breast(1)|skin(1)	7																		---	---	---	---
KCNT2	343450	broad.mit.edu	37	1	196456540	196456541	+	Intron	DEL	GT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196456540_196456541delGT	uc001gtd.1	-						KCNT2_uc001gte.1_Intron|KCNT2_uc001gtf.1_Intron|KCNT2_uc001gtg.1_Intron|KCNT2_uc009wyu.2_Intron|KCNT2_uc009wyv.1_Intron	NM_198503	NP_940905			potassium channel, subfamily T, member 2							voltage-gated potassium channel complex	ATP binding|calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(5)|breast(1)|skin(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	196595201	196595202	+	IGR	INS	-	GA	GA	rs138451257	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196595201_196595202insGA								KCNT2 (17702 upstream) : CFH (25806 downstream)																																			---	---	---	---
CFH	3075	broad.mit.edu	37	1	196683153	196683153	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196683153delA	uc001gtj.3	+							NM_000186	NP_000177			complement factor H isoform a precursor						complement activation, alternative pathway	extracellular space				skin(4)|ovary(1)|breast(1)	6																		---	---	---	---
CFH	3075	broad.mit.edu	37	1	196711351	196711351	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196711351delA	uc001gtj.3	+							NM_000186	NP_000177			complement factor H isoform a precursor						complement activation, alternative pathway	extracellular space				skin(4)|ovary(1)|breast(1)	6																		---	---	---	---
CFHR3	10878	broad.mit.edu	37	1	196759036	196759037	+	Intron	DEL	AG	-	-	rs374905	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196759036_196759037delAG	uc001gtl.2	+						CFHR3_uc001gtk.2_3'UTR|CFHR3_uc010poy.1_Intron|CFHR1_uc001gtm.2_Intron	NM_021023	NP_066303			complement factor H-related 3 precursor							extracellular space					0																		---	---	---	---
CFHR4	10877	broad.mit.edu	37	1	196875839	196875839	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196875839delA	uc001gto.2	+						CFHR4_uc009wyy.2_Intron|CFHR4_uc001gtp.2_Intron	NM_006684	NP_006675			complement factor H-related 4 precursor							extracellular region	lipid transporter activity			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	196929932	196929932	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196929932delT								CFHR2 (1576 upstream) : CFHR5 (16735 downstream)																																			---	---	---	---
ASPM	259266	broad.mit.edu	37	1	197091176	197091176	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197091176delA	uc001gtu.2	-						ASPM_uc001gtv.2_Intron|ASPM_uc001gtw.3_Intron	NM_018136	NP_060606			asp (abnormal spindle)-like, microcephaly						mitosis	cytoplasm|nucleus	calmodulin binding			ovary(4)|central_nervous_system(2)	6																		---	---	---	---
DENND1B	163486	broad.mit.edu	37	1	197616863	197616863	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197616863delG	uc001guf.3	-						DENND1B_uc010ppe.1_Intron|DENND1B_uc010ppf.1_Intron|DENND1B_uc001gue.3_Intron|DENND1B_uc001gug.3_Intron	NM_144977	NP_659414			DENN/MADD domain containing 1B isoform 2							clathrin-coated vesicle|cytosol	guanyl-nucleotide exchange factor activity				0																		---	---	---	---
DENND1B	163486	broad.mit.edu	37	1	197629182	197629182	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197629182delA	uc001guf.3	-						DENND1B_uc010ppe.1_Intron|DENND1B_uc010ppf.1_Intron|DENND1B_uc001gue.3_Intron|DENND1B_uc001gug.3_5'Flank	NM_144977	NP_659414			DENN/MADD domain containing 1B isoform 2							clathrin-coated vesicle|cytosol	guanyl-nucleotide exchange factor activity				0																		---	---	---	---
DENND1B	163486	broad.mit.edu	37	1	197718538	197718538	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197718538delA	uc001guf.3	-						DENND1B_uc010ppe.1_Intron|DENND1B_uc010ppf.1_Intron|DENND1B_uc001gue.3_Intron	NM_144977	NP_659414			DENN/MADD domain containing 1B isoform 2							clathrin-coated vesicle|cytosol	guanyl-nucleotide exchange factor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	198114223	198114223	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198114223delG								LHX9 (212508 upstream) : NEK7 (11885 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	198540304	198540304	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198540304delT								ATP6V1G3 (30229 upstream) : PTPRC (67833 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	198936950	198936950	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198936950delA								MIR181A1 (108668 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	198979974	198979974	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198979974delT	uc001gva.3	-											Homo sapiens, clone IMAGE:5583320, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	199400536	199400536	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:199400536delT								MIR181A1 (572254 upstream) : NR5A2 (596234 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	199510432	199510432	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:199510432delA								MIR181A1 (682150 upstream) : NR5A2 (486338 downstream)																																			---	---	---	---
NR5A2	2494	broad.mit.edu	37	1	200067285	200067285	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200067285delG	uc001gvb.2	+						NR5A2_uc001gvc.2_Intron|NR5A2_uc009wzh.2_Intron|NR5A2_uc010pph.1_Intron	NM_205860	NP_995582			nuclear receptor subfamily 5, group A, member 2						embryo development|positive regulation of viral genome replication|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	lipid binding|protein binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|steroid hormone receptor activity|transcription regulatory region DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2	Prostate(682;0.19)																	---	---	---	---
NR5A2	2494	broad.mit.edu	37	1	200133210	200133211	+	Intron	INS	-	CT	CT			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200133210_200133211insCT	uc001gvb.2	+						NR5A2_uc001gvc.2_Intron|NR5A2_uc009wzh.2_Intron|NR5A2_uc010pph.1_Intron	NM_205860	NP_995582			nuclear receptor subfamily 5, group A, member 2						embryo development|positive regulation of viral genome replication|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	lipid binding|protein binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|steroid hormone receptor activity|transcription regulatory region DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2	Prostate(682;0.19)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	200516576	200516577	+	IGR	DEL	CA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200516576_200516577delCA								ZNF281 (137410 upstream) : KIF14 (4048 downstream)																																			---	---	---	---
DDX59	83479	broad.mit.edu	37	1	200613352	200613353	+	3'UTR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200613352_200613353insA	uc009wzk.2	-	8					DDX59_uc010ppl.1_Intron	NM_001031725	NP_001026895			DEAD (Asp-Glu-Ala-Asp) box polypeptide 59							intracellular	ATP binding|ATP-dependent helicase activity|metal ion binding|RNA binding			ovary(2)|breast(1)|central_nervous_system(1)	4																		---	---	---	---
DDX59	83479	broad.mit.edu	37	1	200632979	200632979	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200632979delA	uc009wzk.2	-						DDX59_uc010ppl.1_Intron	NM_001031725	NP_001026895			DEAD (Asp-Glu-Ala-Asp) box polypeptide 59							intracellular	ATP binding|ATP-dependent helicase activity|metal ion binding|RNA binding			ovary(2)|breast(1)|central_nervous_system(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	200667750	200667751	+	IGR	DEL	AA	-	-	rs72012731		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200667750_200667751delAA								DDX59 (28624 upstream) : CAMSAP1L1 (40935 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	200902825	200902825	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200902825delT	uc001gvp.1	+											Homo sapiens C1orf81 mRNA, partial sequence.																														---	---	---	---
KIF21B	23046	broad.mit.edu	37	1	200948193	200948193	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200948193delA	uc001gvs.1	-						KIF21B_uc001gvr.1_Intron|KIF21B_uc009wzl.1_Intron|KIF21B_uc010ppn.1_Intron	NM_017596	NP_060066			kinesin family member 21B						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)|skin(3)	6																		---	---	---	---
CACNA1S	779	broad.mit.edu	37	1	201019881	201019882	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201019881_201019882delAA	uc001gvv.2	-							NM_000069	NP_000060			calcium channel, voltage-dependent, L type,						axon guidance	I band|T-tubule|voltage-gated calcium channel complex	high voltage-gated calcium channel activity			ovary(3)|central_nervous_system(1)|skin(1)	5					Magnesium Sulfate(DB00653)|Verapamil(DB00661)													---	---	---	---
CACNA1S	779	broad.mit.edu	37	1	201046507	201046508	+	Intron	INS	-	CC	CC			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201046507_201046508insCC	uc001gvv.2	-							NM_000069	NP_000060			calcium channel, voltage-dependent, L type,						axon guidance	I band|T-tubule|voltage-gated calcium channel complex	high voltage-gated calcium channel activity			ovary(3)|central_nervous_system(1)|skin(1)	5					Magnesium Sulfate(DB00653)|Verapamil(DB00661)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	201103141	201103141	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201103141delT								CACNA1S (21447 upstream) : TMEM9 (760 downstream)																																			---	---	---	---
TMEM9	252839	broad.mit.edu	37	1	201121290	201121291	+	Intron	DEL	GT	-	-	rs34970698		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201121290_201121291delGT	uc001gvw.2	-						TMEM9_uc001gvx.2_Intron|TMEM9_uc001gvy.2_Intron|TMEM9_uc010ppo.1_Intron|TMEM9_uc001gvz.2_Intron|TMEM9_uc001gwa.2_Intron|TMEM9_uc010ppp.1_Intron	NM_016456	NP_057540			transmembrane protein 9 precursor						transport	integral to membrane|late endosome membrane|lysosomal membrane					0		Breast(1374;0.000301)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	201423981	201423982	+	IGR	INS	-	TG	TG	rs140609786	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201423981_201423982insTG								TNNI1 (24987 upstream) : PHLDA3 (10641 downstream)																																			---	---	---	---
RPS10P7	376693	broad.mit.edu	37	1	201486095	201486095	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201486095delT	uc009wzz.1	+						RPS10P7_uc010ppt.1_5'Flank					Homo sapiens cDNA FLJ31028 fis, clone HLUNG2000570, weakly similar to 40S RIBOSOMAL PROTEIN S10.												0																		---	---	---	---
NAV1	89796	broad.mit.edu	37	1	201636202	201636202	+	Intron	DEL	A	-	-	rs71689466		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201636202delA	uc001gwu.2	+							NM_020443	NP_065176			neuron navigator 1						cell differentiation|nervous system development	cytoplasm|microtubule	nucleoside-triphosphatase activity|nucleotide binding			central_nervous_system(3)|ovary(1)	4																		---	---	---	---
IPO9	55705	broad.mit.edu	37	1	201807204	201807204	+	Intron	DEL	A	-	-	rs76237986		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201807204delA	uc001gwz.2	+							NM_018085	NP_060555			importin 9						protein import into nucleus	cytoplasm|nucleus	histone binding|protein transporter activity			ovary(2)	2																		---	---	---	---
TIMM17A	10440	broad.mit.edu	37	1	201927266	201927266	+	Intron	DEL	A	-	-	rs78249899		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201927266delA	uc001gxc.2	+							NM_006335	NP_006326			translocase of inner mitochondrial membrane 17						protein targeting to mitochondrion	integral to membrane|mitochondrial inner membrane presequence translocase complex	P-P-bond-hydrolysis-driven protein transmembrane transporter activity				0																		---	---	---	---
PTPN7	5778	broad.mit.edu	37	1	202127662	202127662	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202127662delT	uc001gxm.1	-						PTPN7_uc001gxl.1_Intron|PTPN7_uc001gxn.1_Intron|PTPN7_uc010ppv.1_Intron|PTPN7_uc010ppw.1_Intron|PTPN7_uc010ppx.1_Intron|PTPN7_uc010ppy.1_Intron|PTPN7_uc001gxo.1_5'Flank	NM_002832	NP_002823			protein tyrosine phosphatase, non-receptor type							cytosol|internal side of plasma membrane	protein binding|protein tyrosine phosphatase activity			skin(1)	1																		---	---	---	---
PTPRVP	148713	broad.mit.edu	37	1	202136518	202136518	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202136518delT	uc010ppz.1	+							NR_002930				Homo sapiens PTPRV pseudogene.												0																		---	---	---	---
LGR6	59352	broad.mit.edu	37	1	202201799	202201800	+	Intron	INS	-	A	A	rs140473199	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202201799_202201800insA	uc001gxu.2	+						LGR6_uc001gxv.2_Intron|LGR6_uc009xab.2_Intron|LGR6_uc001gxw.2_Intron	NM_001017403	NP_001017403			leucine-rich repeat-containing G protein-coupled							integral to membrane|plasma membrane	protein-hormone receptor activity			large_intestine(4)|ovary(3)|skin(2)|pancreas(1)	10																		---	---	---	---
LGR6	59352	broad.mit.edu	37	1	202222436	202222438	+	Intron	DEL	TTT	-	-	rs75437944		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202222436_202222438delTTT	uc001gxu.2	+						LGR6_uc001gxv.2_Intron|LGR6_uc009xab.2_Intron|LGR6_uc001gxw.2_Intron|LGR6_uc009xac.1_Intron	NM_001017403	NP_001017403			leucine-rich repeat-containing G protein-coupled							integral to membrane|plasma membrane	protein-hormone receptor activity			large_intestine(4)|ovary(3)|skin(2)|pancreas(1)	10																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	202295682	202295682	+	IGR	DEL	A	-	-	rs71704998		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202295682delA								LGR6 (6794 upstream) : UBE2T (5104 downstream)																																			---	---	---	---
UBE2T	29089	broad.mit.edu	37	1	202304194	202304195	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202304194_202304195insA	uc001gxx.3	-							NM_014176	NP_054895			ubiquitin-conjugating enzyme E2T						DNA repair|protein K11-linked ubiquitination|protein K27-linked ubiquitination|protein K29-linked ubiquitination|protein K48-linked ubiquitination|protein K6-linked ubiquitination|protein K63-linked ubiquitination	nucleoplasm	ATP binding|ubiquitin-protein ligase activity				0																		---	---	---	---
PPP1R12B	4660	broad.mit.edu	37	1	202349728	202349728	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202349728delC	uc001gya.1	+						PPP1R12B_uc001gxy.2_Intron|PPP1R12B_uc009xad.1_Intron|PPP1R12B_uc009xae.1_Intron|PPP1R12B_uc001gxz.1_Intron	NM_002481	NP_002472			protein phosphatase 1, regulatory (inhibitor)						regulation of muscle contraction|signal transduction	cytoplasm	enzyme activator activity			ovary(3)	3			BRCA - Breast invasive adenocarcinoma(75;0.166)															---	---	---	---
TMEM183A	92703	broad.mit.edu	37	1	202991831	202991834	+	Intron	DEL	AAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202991831_202991834delAAAA	uc001gyu.1	+						TMEM183A_uc001gyv.1_Intron|TMEM183A_uc001gyw.1_Intron|TMEM183A_uc001gyx.1_Intron|TMEM183A_uc001gyy.2_5'Flank	NM_001079809	NP_001073277			transmembrane protein 183B							integral to membrane					0			BRCA - Breast invasive adenocarcinoma(75;0.18)															---	---	---	---
ADORA1	134	broad.mit.edu	37	1	203119000	203119001	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203119000_203119001insT	uc001gze.1	+						ADORA1_uc001gzf.1_Intron|ADORA1_uc010pqg.1_Intron|ADORA1_uc009xak.1_Intron|ADORA1_uc010pqh.1_Intron	NM_000674	NP_000665			adenosine A1 receptor						induction of apoptosis by extracellular signals|inflammatory response|nervous system development|phagocytosis	integral to plasma membrane				large_intestine(1)	1					Aminophylline(DB01223)|Caffeine(DB00201)|Defibrotide(DB04932)|Gabapentin(DB00996)|Imipramine(DB00458)|Pegademase bovine(DB00061)|Theophylline(DB00277)													---	---	---	---
FMOD	2331	broad.mit.edu	37	1	203217201	203217201	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203217201delG	uc010pqi.1	-						CHIT1_uc001gzm.1_Intron	NM_002023				fibromodulin precursor						transforming growth factor beta receptor complex assembly	extracellular space|proteinaceous extracellular matrix				ovary(2)|breast(1)	3			BRCA - Breast invasive adenocarcinoma(75;0.171)															---	---	---	---
FMOD	2331	broad.mit.edu	37	1	203259060	203259060	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203259060delT	uc010pqi.1	-							NM_002023				fibromodulin precursor						transforming growth factor beta receptor complex assembly	extracellular space|proteinaceous extracellular matrix				ovary(2)|breast(1)	3			BRCA - Breast invasive adenocarcinoma(75;0.171)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	203400712	203400713	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203400712_203400713insT								FMOD (80423 upstream) : PRELP (44170 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	203429981	203429981	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203429981delA								FMOD (109692 upstream) : PRELP (14902 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	203554279	203554280	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203554279_203554280insT								OPTC (76202 upstream) : ATP2B4 (41648 downstream)																																			---	---	---	---
ATP2B4	493	broad.mit.edu	37	1	203617421	203617422	+	Intron	DEL	TA	-	-	rs63709060	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203617421_203617422delTA	uc001gzw.2	+						ATP2B4_uc001gzv.2_Intron	NM_001684	NP_001675			plasma membrane calcium ATPase 4 isoform 4b						ATP biosynthetic process|platelet activation	integral to plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding|protein binding			ovary(2)|skin(1)	3	all_cancers(21;0.071)|all_epithelial(62;0.228)		BRCA - Breast invasive adenocarcinoma(75;0.109)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	204037228	204037228	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204037228delA								C1orf157 (26836 upstream) : SOX13 (5018 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	204037506	204037506	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204037506delT								C1orf157 (27114 upstream) : SOX13 (4740 downstream)																																			---	---	---	---
SOX13	9580	broad.mit.edu	37	1	204065993	204065995	+	Intron	DEL	TTC	-	-	rs112430179		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204065993_204065995delTTC	uc001ham.2	+						SOX13_uc001hal.2_Intron	NM_005686	NP_005677			SRY-box 13						anatomical structure morphogenesis	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)|central_nervous_system(1)	2	all_cancers(21;0.0754)|Breast(84;0.116)|all_epithelial(62;0.189)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.109)															---	---	---	---
PLEKHA6	22874	broad.mit.edu	37	1	204280620	204280620	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204280620delA	uc001hau.2	-							NM_014935	NP_055750			phosphoinositol 3-phosphate-binding protein-3											ovary(3)|pancreas(1)	4	all_cancers(21;0.0222)|Breast(84;0.179)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.229)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	204363980	204363982	+	IGR	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204363980_204363982delAAA								LOC127841 (25133 upstream) : PPP1R15B (8512 downstream)																																			---	---	---	---
PIK3C2B	5287	broad.mit.edu	37	1	204430270	204430270	+	Intron	DEL	A	-	-	rs76503937		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204430270delA	uc001haw.2	-						PIK3C2B_uc010pqv.1_Intron|PIK3C2B_uc001hax.1_Intron|PIK3C2B_uc009xbd.1_Intron	NM_002646	NP_002637			phosphoinositide-3-kinase, class 2 beta						cell communication|phosphatidylinositol-mediated signaling	endoplasmic reticulum|microsome|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity|protein binding			lung(2)|breast(2)|stomach(1)|prostate(1)|central_nervous_system(1)	7	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)															---	---	---	---
PIK3C2B	5287	broad.mit.edu	37	1	204448441	204448442	+	Intron	INS	-	CTCT	CTCT	rs145442411	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204448441_204448442insCTCT	uc001haw.2	-						PIK3C2B_uc010pqv.1_Intron|PIK3C2B_uc001hax.1_Intron|PIK3C2B_uc009xbd.1_Intron	NM_002646	NP_002637			phosphoinositide-3-kinase, class 2 beta						cell communication|phosphatidylinositol-mediated signaling	endoplasmic reticulum|microsome|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity|protein binding			lung(2)|breast(2)|stomach(1)|prostate(1)|central_nervous_system(1)	7	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)															---	---	---	---
MDM4	4194	broad.mit.edu	37	1	204553102	204553102	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204553102delA	uc001hbd.1	+						MDM4_uc001hbc.2_Intron	NM_002393				mouse double minute 4 homolog						apoptosis|cell proliferation|cellular response to hypoxia|G0 to G1 transition|negative regulation of apoptosis|negative regulation of cell cycle arrest|negative regulation of cell proliferation|negative regulation of protein catabolic process|negative regulation of transcription from RNA polymerase II promoter|protein complex assembly|protein stabilization	nucleus	enzyme binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	all_cancers(21;0.00146)|all_neural(3;0.0218)|Glioma(3;0.0382)|Breast(84;0.112)|all_epithelial(62;0.118)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;3.15e-47)|all cancers(3;3.56e-32)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|Epithelial(59;0.143)|BRCA - Breast invasive adenocarcinoma(75;0.143)					A		GBM|bladder|retinoblastoma								---	---	---	---
LRRN2	10446	broad.mit.edu	37	1	204632060	204632060	+	Intron	DEL	A	-	-	rs111337144		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204632060delA	uc001hbe.1	-						MDM4_uc001hbd.1_Intron|LRRN2_uc001hbf.1_Intron|LRRN2_uc009xbf.1_Intron	NM_006338	NP_006329			leucine rich repeat neuronal 2 precursor						cell adhesion	integral to membrane	receptor activity			central_nervous_system(2)	2	all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)															---	---	---	---
NFASC	23114	broad.mit.edu	37	1	204947238	204947238	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204947238delC	uc001hbj.2	+						NFASC_uc010pra.1_Intron|NFASC_uc001hbi.2_Intron|NFASC_uc010prb.1_Intron|NFASC_uc010prc.1_Intron|NFASC_uc001hbk.1_Intron	NM_001005388	NP_001005388			neurofascin isoform 1 precursor						axon guidance|cell adhesion|myelination|peripheral nervous system development	integral to membrane|node of Ranvier|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)															---	---	---	---
CDK18	5129	broad.mit.edu	37	1	205488061	205488061	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205488061delG	uc001hcr.2	+						CDK18_uc009xbk.1_Intron|CDK18_uc009xbl.1_Intron|CDK18_uc010pri.1_Intron|CDK18_uc001hcp.2_Intron|CDK18_uc001hcq.2_Intron|CDK18_uc010prj.1_Intron	NM_212503	NP_997668			PCTAIRE protein kinase 3 isoform a								ATP binding|cyclin-dependent protein kinase activity|protein binding|signal transducer activity			stomach(2)	2																		---	---	---	---
CDK18	5129	broad.mit.edu	37	1	205492638	205492639	+	Frame_Shift_Ins	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205492638_205492639insC	uc001hcr.2	+	3	377_378	c.158_159insC	c.(157-159)GACfs	p.D53fs	CDK18_uc009xbk.1_RNA|CDK18_uc009xbl.1_RNA|CDK18_uc010pri.1_Frame_Shift_Ins_p.R73fs|CDK18_uc001hcp.2_Frame_Shift_Ins_p.D53fs|CDK18_uc001hcq.2_Frame_Shift_Ins_p.D53fs|CDK18_uc010prj.1_5'UTR|CDK18_uc001hcs.2_5'UTR|CDK18_uc009xbm.1_5'UTR	NM_212503	NP_997668	Q07002	CDK18_HUMAN	PCTAIRE protein kinase 3 isoform a	51							ATP binding|cyclin-dependent protein kinase activity|protein binding|signal transducer activity			stomach(2)	2																		---	---	---	---
MFSD4	148808	broad.mit.edu	37	1	205561496	205561496	+	Intron	DEL	C	-	-	rs34928918		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205561496delC	uc001hcv.3	+						MFSD4_uc010prk.1_Intron|MFSD4_uc010prl.1_Intron|MFSD4_uc010prm.1_Intron|MFSD4_uc009xbn.2_Intron	NM_181644	NP_857595			major facilitator superfamily domain containing						transmembrane transport	integral to membrane				skin(2)|central_nervous_system(1)	3	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0908)															---	---	---	---
SLC45A3	85414	broad.mit.edu	37	1	205636993	205636993	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205636993delC	uc001hda.1	-						SLC45A3_uc010prp.1_Intron|ELK4_uc010prq.1_Intron	NM_033102	NP_149093			prostein						transmembrane transport	integral to membrane			SLC45A3/BRAF(2)	ovary(2)|prostate(2)	4	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0194)					T	ETV1|ETV5|ELK4|ERG	prostate 								---	---	---	---
NUCKS1	64710	broad.mit.edu	37	1	205713589	205713589	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205713589delT	uc001hdb.2	-							NM_022731	NP_073568			nuclear casein kinase and cyclin-dependent							nucleus					0	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0194)															---	---	---	---
SLC26A9	115019	broad.mit.edu	37	1	205913992	205913992	+	5'Flank	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205913992delC	uc001hdq.2	-						SLC26A9_uc001hdp.2_5'Flank	NM_052934	NP_443166			solute carrier family 26, member 9 isoform a							integral to membrane	chloride channel activity|secondary active sulfate transmembrane transporter activity			ovary(1)|skin(1)	2	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0458)															---	---	---	---
SRGAP2	23380	broad.mit.edu	37	1	206520609	206520611	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206520609_206520611delAAA	uc001hdy.2	+						SRGAP2_uc009xbt.2_Intron|SRGAP2_uc010prt.1_Intron|SRGAP2_uc001hdx.2_Intron|SRGAP2_uc010pru.1_Intron	NM_015326	NP_056141			SLIT-ROBO Rho GTPase activating protein 2						axon guidance|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding				0	Breast(84;0.137)																	---	---	---	---
SRGAP2	23380	broad.mit.edu	37	1	206532062	206532062	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206532062delA	uc001hdy.2	+						SRGAP2_uc009xbt.2_Intron|SRGAP2_uc010prt.1_Intron|SRGAP2_uc001hdx.2_Intron|SRGAP2_uc010pru.1_Intron	NM_015326	NP_056141			SLIT-ROBO Rho GTPase activating protein 2						axon guidance|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding				0	Breast(84;0.137)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	207064009	207064009	+	IGR	DEL	G	-	-	rs11312938		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207064009delG								IL20 (21442 upstream) : IL24 (6780 downstream)																																			---	---	---	---
FCAMR	83953	broad.mit.edu	37	1	207135373	207135373	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207135373delT	uc001hfa.3	-						FCAMR_uc001hfb.2_Intron|FCAMR_uc009xca.1_Intron|FCAMR_uc001hfc.2_Intron	NM_001122980	NP_001116452			Fc receptor, IgA, IgM, high affinity isoform 2							integral to membrane|plasma membrane	receptor activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	207150944	207150945	+	IGR	INS	-	TTCA	TTCA	rs142910716	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207150944_207150945insTTCA								FCAMR (6974 upstream) : C1orf116 (40921 downstream)																																			---	---	---	---
CD46	4179	broad.mit.edu	37	1	207941221	207941222	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207941221_207941222insT	uc001hgc.2	+						CD46_uc001hgd.2_Intron|CD46_uc001hge.2_Intron|CD46_uc001hgf.2_Intron|CD46_uc001hgg.2_Intron|CD46_uc001hgh.2_Intron|CD46_uc001hgi.2_Intron|CD46_uc001hgj.2_Intron|CD46_uc001hgk.2_Intron|CD46_uc001hgl.2_Intron|CD46_uc001hgm.2_Intron|CD46_uc001hgn.2_Intron|CD46_uc001hgo.2_Intron|CD46_uc001hgp.2_Intron	NM_002389	NP_002380			CD46 antigen, complement regulatory protein						complement activation, classical pathway|innate immune response|interspecies interaction between organisms|single fertilization	inner acrosomal membrane|integral to plasma membrane	protein binding|receptor activity			large_intestine(2)|lung(1)|central_nervous_system(1)	4																		---	---	---	---
CD34	947	broad.mit.edu	37	1	208062456	208062456	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208062456delC	uc001hgw.1	-						CD34_uc001hgv.1_Intron|CD34_uc001hgx.1_Intron|CD34_uc010psj.1_Intron	NM_001025109	NP_001020280			CD34 antigen isoform a						cell-cell adhesion|leukocyte migration|regulation of immune response	integral to membrane	carbohydrate binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	208469006	208469006	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208469006delT								PLXNA2 (51341 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	208544212	208544212	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208544212delT								PLXNA2 (126547 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	208964552	208964553	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:208964552_208964553insA								PLXNA2 (546887 upstream) : LOC642587 (637615 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	209366685	209366686	+	IGR	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209366685_209366686delTC								PLXNA2 (949020 upstream) : LOC642587 (235482 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	209414771	209414771	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209414771delG								PLXNA2 (997106 upstream) : LOC642587 (187397 downstream)																																			---	---	---	---
IRF6	3664	broad.mit.edu	37	1	209966562	209966562	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209966562delT	uc001hhq.1	-						IRF6_uc010psm.1_Intron|IRF6_uc009xct.1_Intron	NM_006147	NP_006138			interferon regulatory factor 6						cell cycle arrest|interferon-gamma-mediated signaling pathway|mammary gland epithelial cell differentiation|negative regulation of cell proliferation|positive regulation of transcription, DNA-dependent|type I interferon-mediated signaling pathway	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0351)											HNSCC(57;0.16)			---	---	---	---
Unknown	0	broad.mit.edu	37	1	210349551	210349551	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210349551delT								SYT14 (11920 upstream) : C1orf133 (55253 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	210432518	210432518	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210432518delT								SERTAD4 (16080 upstream) : HHAT (69088 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	210442648	210442649	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210442648_210442649delAA								SERTAD4 (26210 upstream) : HHAT (58957 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	211425451	211425451	+	IGR	DEL	T	-	-	rs67936298		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211425451delT								KCNH1 (117994 upstream) : RCOR3 (7257 downstream)																																			---	---	---	---
RCOR3	55758	broad.mit.edu	37	1	211458643	211458643	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211458643delT	uc001hig.2	+						RCOR3_uc010psv.1_Intron|RCOR3_uc001hie.2_Intron|RCOR3_uc010psw.1_Intron|RCOR3_uc001hif.2_Intron	NM_018254	NP_060724			REST corepressor 3 isoform d						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.00961)|all cancers(67;0.0999)|Epithelial(68;0.171)														---	---	---	---
TRAF5	7188	broad.mit.edu	37	1	211508942	211508942	+	Intron	DEL	G	-	-	rs149345244	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211508942delG	uc001hih.2	+						TRAF5_uc001hii.2_Intron|TRAF5_uc010psx.1_Intron|TRAF5_uc010psy.1_Intron	NM_004619	NP_004610			TNF receptor-associated factor 5						apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis	CD40 receptor complex|centrosome|internal side of plasma membrane	protein binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)|breast(2)|ovary(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.00946)|all cancers(67;0.0808)|Epithelial(68;0.144)														---	---	---	---
TRAF5	7188	broad.mit.edu	37	1	211538512	211538512	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211538512delA	uc001hih.2	+						TRAF5_uc001hii.2_Intron|TRAF5_uc010psx.1_Intron|TRAF5_uc010psy.1_Intron|TRAF5_uc001hij.2_Intron	NM_004619	NP_004610			TNF receptor-associated factor 5						apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis	CD40 receptor complex|centrosome|internal side of plasma membrane	protein binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)|breast(2)|ovary(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.00946)|all cancers(67;0.0808)|Epithelial(68;0.144)														---	---	---	---
INTS7	25896	broad.mit.edu	37	1	212141426	212141426	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212141426delA	uc001hiw.1	-						INTS7_uc009xdb.1_Intron|INTS7_uc001hix.1_Intron|INTS7_uc001hiy.1_Intron|INTS7_uc010pta.1_Intron	NM_015434	NP_056249			integrator complex subunit 7						snRNA processing	integrator complex	protein binding				0				OV - Ovarian serous cystadenocarcinoma(81;0.00584)|all cancers(67;0.0318)|Epithelial(68;0.0852)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	212318718	212318719	+	IGR	INS	-	T	T	rs144123963	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212318718_212318719insT								DTL (40532 upstream) : PPP2R5A (140160 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	212441975	212441975	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212441975delT								DTL (163789 upstream) : PPP2R5A (16904 downstream)																																			---	---	---	---
PPP2R5A	5525	broad.mit.edu	37	1	212503890	212503890	+	Intron	DEL	A	-	-	rs76114599		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212503890delA	uc001hjb.2	+						PPP2R5A_uc010ptd.1_Intron	NM_006243	NP_006234			protein phosphatase 2, regulatory subunit B						negative regulation of establishment of protein localization in plasma membrane|negative regulation of lipid kinase activity|positive regulation of protein dephosphorylation|signal transduction	chromosome, centromeric region|cytoplasm|nucleus|protein phosphatase type 2A complex	kinase binding|protein phosphatase type 2A regulator activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0125)|all cancers(67;0.029)|Epithelial(68;0.154)|GBM - Glioblastoma multiforme(131;0.155)														---	---	---	---
PPP2R5A	5525	broad.mit.edu	37	1	212525797	212525798	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212525797_212525798delTT	uc001hjb.2	+						PPP2R5A_uc010ptd.1_Intron|SNORA16B_uc009xdf.1_5'Flank	NM_006243	NP_006234			protein phosphatase 2, regulatory subunit B						negative regulation of establishment of protein localization in plasma membrane|negative regulation of lipid kinase activity|positive regulation of protein dephosphorylation|signal transduction	chromosome, centromeric region|cytoplasm|nucleus|protein phosphatase type 2A complex	kinase binding|protein phosphatase type 2A regulator activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0125)|all cancers(67;0.029)|Epithelial(68;0.154)|GBM - Glioblastoma multiforme(131;0.155)														---	---	---	---
TMEM206	55248	broad.mit.edu	37	1	212563385	212563385	+	Intron	DEL	A	-	-	rs78587328		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212563385delA	uc001hjc.3	-						TMEM206_uc010pte.1_Intron	NM_018252	NP_060722			transmembrane protein 206							integral to membrane				breast(1)	1				all cancers(67;0.012)|OV - Ovarian serous cystadenocarcinoma(81;0.0121)|GBM - Glioblastoma multiforme(131;0.0377)|Epithelial(68;0.148)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	212630599	212630600	+	IGR	DEL	AA	-	-	rs145323231		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212630599_212630600delAA								NENF (10880 upstream) : ATF3 (108097 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	212645570	212645570	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212645570delA								NENF (25851 upstream) : ATF3 (93127 downstream)																																			---	---	---	---
ATF3	467	broad.mit.edu	37	1	212747014	212747014	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212747014delT	uc001hjf.2	+							NM_001030287	NP_001025458			activating transcription factor 3 isoform 1							nucleolus	identical protein binding|protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity				0				OV - Ovarian serous cystadenocarcinoma(81;0.00628)|all cancers(67;0.0097)|GBM - Glioblastoma multiforme(131;0.0388)|Epithelial(68;0.0933)														---	---	---	---
ATF3	467	broad.mit.edu	37	1	212766780	212766781	+	Intron	DEL	AA	-	-	rs80312077	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212766780_212766781delAA	uc001hjf.2	+							NM_001030287	NP_001025458			activating transcription factor 3 isoform 1							nucleolus	identical protein binding|protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity				0				OV - Ovarian serous cystadenocarcinoma(81;0.00628)|all cancers(67;0.0097)|GBM - Glioblastoma multiforme(131;0.0388)|Epithelial(68;0.0933)														---	---	---	---
NSL1	25936	broad.mit.edu	37	1	212963364	212963364	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212963364delT	uc001hjn.2	-						NSL1_uc001hjm.2_Intron|NSL1_uc010pti.1_Intron|TATDN3_uc001hjo.2_5'Flank|TATDN3_uc010ptj.1_5'Flank|TATDN3_uc010ptk.1_5'Flank|TATDN3_uc001hjp.2_5'Flank|TATDN3_uc010ptl.1_5'Flank	NM_015471	NP_056286			NSL1, MIND kinetochore complex component isoform						cell division|chromosome segregation|mitotic prometaphase	cytosol|MIS12/MIND type complex|nucleus	protein binding			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.00597)|all cancers(67;0.00893)|GBM - Glioblastoma multiforme(131;0.0514)|Epithelial(68;0.102)														---	---	---	---
C1orf227	149643	broad.mit.edu	37	1	213019594	213019595	+	Intron	INS	-	T	T	rs78907254		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213019594_213019595insT	uc001hjq.2	-							NM_001024601	NP_001019772			hypothetical protein LOC149643												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	213113462	213113463	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213113462_213113463insT								FLVCR1 (43265 upstream) : VASH2 (10424 downstream)																																			---	---	---	---
VASH2	79805	broad.mit.edu	37	1	213127423	213127423	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213127423delA	uc001hjy.2	+						VASH2_uc001hju.2_Intron|VASH2_uc001hjv.2_Intron|VASH2_uc001hjx.2_Intron|VASH2_uc010ptn.1_Intron|VASH2_uc001hjw.2_Intron	NM_001136475	NP_001129947			vasohibin 2 isoform 3						positive regulation of angiogenesis|positive regulation of endothelial cell proliferation	cytoplasm					0				OV - Ovarian serous cystadenocarcinoma(81;0.00479)|all cancers(67;0.00844)|GBM - Glioblastoma multiforme(131;0.0496)|Epithelial(68;0.0986)														---	---	---	---
VASH2	79805	broad.mit.edu	37	1	213140505	213140505	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213140505delT	uc001hjy.2	+						VASH2_uc001hju.2_3'UTR|VASH2_uc001hjv.2_Intron|VASH2_uc001hjx.2_Intron|VASH2_uc010ptn.1_Intron|VASH2_uc001hjw.2_Intron	NM_001136475	NP_001129947			vasohibin 2 isoform 3						positive regulation of angiogenesis|positive regulation of endothelial cell proliferation	cytoplasm					0				OV - Ovarian serous cystadenocarcinoma(81;0.00479)|all cancers(67;0.00844)|GBM - Glioblastoma multiforme(131;0.0496)|Epithelial(68;0.0986)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	213638123	213638123	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213638123delT								RPS6KC1 (191316 upstream) : PROX1 (523163 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	214144523	214144523	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214144523delT								RPS6KC1 (697716 upstream) : PROX1 (16763 downstream)																																			---	---	---	---
PROX1	5629	broad.mit.edu	37	1	214172218	214172218	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214172218delT	uc001hkh.2	+							NM_002763	NP_002754			prospero homeobox 1						aorta smooth muscle tissue morphogenesis|atrial cardiac muscle tissue morphogenesis|brain development|dorsal spinal cord development|embryonic retina morphogenesis in camera-type eye|endocardium formation|hepatocyte differentiation|kidney development|lens fiber cell morphogenesis|lung development|lymphangiogenesis|negative regulation of bile acid biosynthetic process|negative regulation of cell proliferation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of viral genome replication|neural tube development|olfactory placode formation|optic placode formation involved in camera-type eye formation|otic placode formation|pancreas development|positive regulation of cyclin-dependent protein kinase activity|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of heart growth|positive regulation of S phase of mitotic cell cycle|positive regulation of sarcomere organization|positive regulation of transcription, DNA-dependent|regulation of transcription involved in lymphatic endothelial cell fate commitment|skeletal muscle thin filament assembly|venous blood vessel morphogenesis|ventricular cardiac muscle tissue morphogenesis|ventricular cardiac myofibril development|ventricular septum morphogenesis	cytoplasm|nucleus	DBD domain binding|LBD domain binding|ligand-dependent nuclear receptor binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription corepressor activity|transcription regulatory region DNA binding			ovary(3)|lung(1)|central_nervous_system(1)|skin(1)	6				OV - Ovarian serous cystadenocarcinoma(81;0.0179)|all cancers(67;0.0488)|GBM - Glioblastoma multiforme(131;0.188)|Epithelial(68;0.219)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	214282141	214282142	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214282141_214282142delTT								PROX1 (72381 upstream) : SMYD2 (172423 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	214349560	214349560	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214349560delT								PROX1 (139800 upstream) : SMYD2 (105005 downstream)																																			---	---	---	---
CENPF	1063	broad.mit.edu	37	1	214802687	214802687	+	Intron	DEL	T	-	-	rs115144504	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214802687delT	uc001hkm.2	+							NM_016343	NP_057427			centromere protein F						cell differentiation|cell division|cell proliferation|DNA replication|G2 phase of mitotic cell cycle|kinetochore assembly|metaphase plate congression|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|muscle organ development|negative regulation of transcription, DNA-dependent|protein transport|regulation of G2/M transition of mitotic cell cycle|regulation of striated muscle tissue development|response to drug	condensed chromosome outer kinetochore|cytosol|midbody|nuclear envelope|nuclear matrix|perinuclear region of cytoplasm|spindle pole	chromatin binding|dynein binding|protein C-terminus binding|protein homodimerization activity|transcription factor binding			ovary(6)|central_nervous_system(4)|large_intestine(2)|skin(1)	13				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)														---	---	---	---
CENPF	1063	broad.mit.edu	37	1	214811439	214811439	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214811439delT	uc001hkm.2	+							NM_016343	NP_057427			centromere protein F						cell differentiation|cell division|cell proliferation|DNA replication|G2 phase of mitotic cell cycle|kinetochore assembly|metaphase plate congression|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|muscle organ development|negative regulation of transcription, DNA-dependent|protein transport|regulation of G2/M transition of mitotic cell cycle|regulation of striated muscle tissue development|response to drug	condensed chromosome outer kinetochore|cytosol|midbody|nuclear envelope|nuclear matrix|perinuclear region of cytoplasm|spindle pole	chromatin binding|dynein binding|protein C-terminus binding|protein homodimerization activity|transcription factor binding			ovary(6)|central_nervous_system(4)|large_intestine(2)|skin(1)	13				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)														---	---	---	---
KCNK2	3776	broad.mit.edu	37	1	215316138	215316138	+	Intron	DEL	T	-	-	rs79707664		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215316138delT	uc001hkq.2	+						KCNK2_uc001hko.2_Intron|KCNK2_uc009xdm.2_Intron|KCNK2_uc001hkp.2_Intron|KCNK2_uc010pua.1_Intron|KCNK2_uc001hkr.3_Intron	NM_001017425	NP_001017425			potassium channel, subfamily K, member 2 isoform								outward rectifier potassium channel activity				0				OV - Ovarian serous cystadenocarcinoma(81;0.0399)|all cancers(67;0.0556)|GBM - Glioblastoma multiforme(131;0.068)	Dofetilide(DB00204)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	215448011	215448011	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215448011delC								KCNK2 (37576 upstream) : KCTD3 (292724 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	215653765	215653765	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215653765delT								KCNK2 (243330 upstream) : KCTD3 (86970 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	215731671	215731671	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215731671delT								KCNK2 (321236 upstream) : KCTD3 (9064 downstream)																																			---	---	---	---
USH2A	7399	broad.mit.edu	37	1	215812319	215812320	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215812319_215812320insA	uc001hku.1	-							NM_206933	NP_996816			usherin isoform B						maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)											HNSCC(13;0.011)			---	---	---	---
USH2A	7399	broad.mit.edu	37	1	215993628	215993628	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:215993628delC	uc001hku.1	-							NM_206933	NP_996816			usherin isoform B						maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)											HNSCC(13;0.011)			---	---	---	---
USH2A	7399	broad.mit.edu	37	1	216009262	216009262	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216009262delT	uc001hku.1	-							NM_206933	NP_996816			usherin isoform B						maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)											HNSCC(13;0.011)			---	---	---	---
USH2A	7399	broad.mit.edu	37	1	216071928	216071928	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216071928delA	uc001hku.1	-							NM_206933	NP_996816			usherin isoform B						maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)											HNSCC(13;0.011)			---	---	---	---
USH2A	7399	broad.mit.edu	37	1	216495187	216495187	+	Intron	DEL	T	-	-	rs79650190		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216495187delT	uc001hku.1	-						USH2A_uc001hkv.2_Intron	NM_206933	NP_996816			usherin isoform B						maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)											HNSCC(13;0.011)			---	---	---	---
ESRRG	2104	broad.mit.edu	37	1	216743270	216743270	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216743270delT	uc001hkw.1	-						ESRRG_uc001hky.1_Intron|ESRRG_uc009xdp.1_Intron|ESRRG_uc001hkz.1_Intron|ESRRG_uc010puc.1_Intron|ESRRG_uc001hla.1_Intron|ESRRG_uc001hlb.1_Intron|ESRRG_uc010pud.1_Intron|ESRRG_uc001hlc.1_Intron|ESRRG_uc001hld.1_Intron|ESRRG_uc001hkx.1_Intron|ESRRG_uc009xdo.1_Intron|ESRRG_uc001hle.1_Intron	NM_001438	NP_001429			estrogen-related receptor gamma isoform 1						positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	AF-2 domain binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|kidney(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)													---	---	---	---
ESRRG	2104	broad.mit.edu	37	1	217215815	217215816	+	Intron	INS	-	ACAC	ACAC	rs140559927	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217215815_217215816insACAC	uc010puc.1	-						ESRRG_uc001hkz.1_Intron|ESRRG_uc001hla.1_Intron|ESRRG_uc001hlb.1_Intron|ESRRG_uc010pud.1_Intron|ESRRG_uc001hlc.1_Intron|ESRRG_uc001hld.1_Intron	NM_206595	NP_996318			estrogen-related receptor gamma isoform 2						positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	AF-2 domain binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|kidney(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	217365299	217365300	+	IGR	DEL	CA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217365299_217365300delCA								ESRRG (54202 upstream) : GPATCH2 (238534 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	217549593	217549593	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217549593delA								ESRRG (238496 upstream) : GPATCH2 (54241 downstream)																																			---	---	---	---
SPATA17	128153	broad.mit.edu	37	1	217886597	217886597	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:217886597delT	uc001hlh.1	+						SPATA17_uc009xdr.1_Intron|SPATA17_uc001hli.2_Intron	NM_138796	NP_620151			spermatogenesis associated 17							cytoplasm	calmodulin binding			pancreas(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0516)|all cancers(67;0.0891)|GBM - Glioblastoma multiforme(131;0.117)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	218249834	218249834	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:218249834delA								SPATA17 (209332 upstream) : RRP15 (208795 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	219032948	219032948	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:219032948delA								TGFB2 (414989 upstream) : LYPLAL1 (314244 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	219162688	219162688	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:219162688delT								TGFB2 (544729 upstream) : LYPLAL1 (184504 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	219234243	219234243	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:219234243delA								TGFB2 (616284 upstream) : LYPLAL1 (112949 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	219785370	219785370	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:219785370delA								LYPLAL1 (399164 upstream) : SLC30A10 (73399 downstream)																																			---	---	---	---
IARS2	55699	broad.mit.edu	37	1	220291457	220291457	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220291457delA	uc001hmc.2	+						MIR215_hsa-mir-215|MI0000291_5'Flank|uc010pui.1_5'Flank	NM_018060	NP_060530			mitochondrial isoleucine tRNA synthetase						isoleucyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|isoleucine-tRNA ligase activity			ovary(2)|skin(2)	4				GBM - Glioblastoma multiforme(131;0.0554)	L-Isoleucine(DB00167)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	220474887	220474888	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220474887_220474888insT								RAB3GAP2 (29044 upstream) : MARK1 (226680 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	220907453	220907453	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220907453delT								C1orf115 (34954 upstream) : MOSC2 (14223 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	221000466	221000466	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221000466delT	uc001hmu.2	+											Homo sapiens cDNA clone IMAGE:5298101.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	221097947	221097947	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221097947delT								HLX (39549 upstream) : LOC400804 (405323 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	221276830	221276830	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221276830delA								HLX (218432 upstream) : LOC400804 (226440 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	222047579	222047579	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222047579delA								DUSP10 (132118 upstream) : HHIPL2 (648023 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	222358700	222358700	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222358700delT								DUSP10 (443239 upstream) : HHIPL2 (336902 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	222435596	222435596	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222435596delT								DUSP10 (520135 upstream) : HHIPL2 (260006 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	222480173	222480173	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222480173delT								DUSP10 (564712 upstream) : HHIPL2 (215429 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	222607995	222607995	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222607995delC								DUSP10 (692534 upstream) : HHIPL2 (87607 downstream)																																			---	---	---	---
TAF1A	9015	broad.mit.edu	37	1	222754129	222754129	+	Intron	DEL	G	-	-	rs149973233	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222754129delG	uc009xdz.1	-						TAF1A_uc001hni.1_Intron|TAF1A_uc001hnj.2_Intron|TAF1A_uc001hnk.2_Intron|TAF1A_uc010pur.1_Intron	NM_139352	NP_647603			TBP-associated factor 1A isoform 2						regulation of transcription, DNA-dependent|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter	RNA polymerase I transcription factor complex	DNA binding				0				GBM - Glioblastoma multiforme(131;0.0186)														---	---	---	---
AIDA	64853	broad.mit.edu	37	1	222844941	222844941	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222844941delA	uc001hnn.2	-						AIDA_uc001hno.2_Intron|AIDA_uc010pus.1_Intron	NM_022831	NP_073742			axin interactor, dorsalization associated						dorsal/ventral pattern formation|negative regulation of JNK cascade|negative regulation of JUN kinase activity|regulation of protein homodimerization activity						0																		---	---	---	---
AIDA	64853	broad.mit.edu	37	1	222876706	222876706	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222876706delA	uc001hnn.2	-						AIDA_uc001hno.2_Intron|AIDA_uc010pus.1_Intron	NM_022831	NP_073742			axin interactor, dorsalization associated						dorsal/ventral pattern formation|negative regulation of JNK cascade|negative regulation of JUN kinase activity|regulation of protein homodimerization activity						0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	223023854	223023854	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223023854delT								FAM177B (99853 upstream) : DISP1 (77929 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	223069947	223069950	+	IGR	DEL	AAAA	-	-	rs143783223		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223069947_223069950delAAAA								FAM177B (145946 upstream) : DISP1 (31833 downstream)																																			---	---	---	---
SUSD4	55061	broad.mit.edu	37	1	223397848	223397848	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223397848delA	uc001hnx.2	-						SUSD4_uc001hny.3_Intron|SUSD4_uc010puw.1_Intron	NM_017982	NP_060452			sushi domain containing 4 isoform a							integral to membrane					0				GBM - Glioblastoma multiforme(131;0.0611)														---	---	---	---
CAPN2	824	broad.mit.edu	37	1	223903689	223903689	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223903689delA	uc001hob.3	+						CAPN2_uc010puy.1_Intron	NM_001748	NP_001739			calpain 2 isoform 1						proteolysis	cytoplasm|plasma membrane				lung(3)|breast(1)|skin(1)	5				GBM - Glioblastoma multiforme(131;0.109)														---	---	---	---
TP53BP2	7159	broad.mit.edu	37	1	223980974	223980974	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223980974delA	uc010pvb.1	-						TP53BP2_uc001hod.2_Intron|TP53BP2_uc010puz.1_Intron|TP53BP2_uc010pva.1_Intron	NM_001031685	NP_001026855			tumor protein p53 binding protein, 2 isoform 1						apoptosis|cell cycle|induction of apoptosis|negative regulation of cell cycle|signal transduction	nucleus|perinuclear region of cytoplasm	NF-kappaB binding|protein binding|SH3 domain binding|SH3/SH2 adaptor activity			ovary(2)|lung(1)	3				GBM - Glioblastoma multiforme(131;0.0958)														---	---	---	---
NVL	4931	broad.mit.edu	37	1	224440755	224440755	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224440755delT	uc001hok.2	-						NVL_uc001hol.2_Intron|NVL_uc010pvd.1_Intron|NVL_uc010pve.1_Intron|NVL_uc010pvf.1_Intron	NM_002533	NP_002524			nuclear VCP-like isoform 1							aggresome|cytoplasm|nucleolus	ATP binding|nucleoside-triphosphatase activity			skin(2)	2				GBM - Glioblastoma multiforme(131;0.00501)														---	---	---	---
NVL	4931	broad.mit.edu	37	1	224518599	224518599	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224518599delA	uc001hok.2	-						NVL_uc001hol.2_5'Flank|NVL_uc010pvd.1_5'Flank|NVL_uc010pve.1_5'Flank|NVL_uc010pvf.1_5'Flank|NVL_uc010pvg.1_5'Flank	NM_002533	NP_002524			nuclear VCP-like isoform 1							aggresome|cytoplasm|nucleolus	ATP binding|nucleoside-triphosphatase activity			skin(2)	2				GBM - Glioblastoma multiforme(131;0.00501)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	224768793	224768794	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224768793_224768794insT								WDR26 (147061 upstream) : CNIH3 (35385 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	225111370	225111370	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225111370delT								CNIH3 (183121 upstream) : DNAH14 (5986 downstream)																																			---	---	---	---
LBR	3930	broad.mit.edu	37	1	225590888	225590888	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225590888delA	uc001hoy.2	-	14					LBR_uc001hoz.2_3'UTR	NM_002296	NP_002287			lamin B receptor						cholesterol biosynthetic process	integral to nuclear inner membrane	chromo shadow domain binding|delta14-sterol reductase activity|DNA binding|lamin binding|receptor activity			ovary(1)|skin(1)	2	Breast(184;0.165)			GBM - Glioblastoma multiforme(131;0.117)														---	---	---	---
LBR	3930	broad.mit.edu	37	1	225607376	225607377	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225607376_225607377delAA	uc001hoy.2	-						LBR_uc001hoz.2_Intron|LBR_uc001hpa.1_Intron	NM_002296	NP_002287			lamin B receptor						cholesterol biosynthetic process	integral to nuclear inner membrane	chromo shadow domain binding|delta14-sterol reductase activity|DNA binding|lamin binding|receptor activity			ovary(1)|skin(1)	2	Breast(184;0.165)			GBM - Glioblastoma multiforme(131;0.117)														---	---	---	---
LBR	3930	broad.mit.edu	37	1	225616136	225616136	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225616136delT	uc001hoy.2	-						LBR_uc001hoz.2_Intron|LBR_uc001hpa.1_5'Flank	NM_002296	NP_002287			lamin B receptor						cholesterol biosynthetic process	integral to nuclear inner membrane	chromo shadow domain binding|delta14-sterol reductase activity|DNA binding|lamin binding|receptor activity			ovary(1)|skin(1)	2	Breast(184;0.165)			GBM - Glioblastoma multiforme(131;0.117)														---	---	---	---
LBR	3930	broad.mit.edu	37	1	225616613	225616613	+	5'Flank	DEL	T	-	-	rs80100107		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225616613delT	uc001hoy.2	-						LBR_uc001hoz.2_5'Flank|LBR_uc001hpa.1_5'Flank	NM_002296	NP_002287			lamin B receptor						cholesterol biosynthetic process	integral to nuclear inner membrane	chromo shadow domain binding|delta14-sterol reductase activity|DNA binding|lamin binding|receptor activity			ovary(1)|skin(1)	2	Breast(184;0.165)			GBM - Glioblastoma multiforme(131;0.117)														---	---	---	---
ENAH	55740	broad.mit.edu	37	1	225718042	225718042	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:225718042delA	uc001hpc.1	-						ENAH_uc001hpd.1_Intron	NM_001008493	NP_001008493			enabled homolog isoform a						axon guidance|intracellular transport|T cell receptor signaling pathway	cytosol|filopodium|focal adhesion|lamellipodium|synapse	actin binding|SH3 domain binding|WW domain binding			ovary(1)|skin(1)	2	Breast(184;0.206)			GBM - Glioblastoma multiforme(131;0.19)														---	---	---	---
TMEM63A	9725	broad.mit.edu	37	1	226036149	226036149	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226036149delA	uc001hpm.1	-							NM_014698	NP_055513			transmembrane protein 63A							integral to membrane|lysosomal membrane	nucleotide binding			ovary(1)|breast(1)	2	Breast(184;0.197)																	---	---	---	---
LIN9	286826	broad.mit.edu	37	1	226475508	226475508	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226475508delA	uc001hqa.2	-						LIN9_uc001hqb.2_Intron|LIN9_uc001hqc.2_Intron|LIN9_uc009xel.1_Intron	NM_173083	NP_775106			lin-9 homolog						cell cycle|DNA replication	nucleoplasm					0	Breast(184;0.158)			GBM - Glioblastoma multiforme(131;0.131)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	226504399	226504399	+	IGR	DEL	A	-	-	rs149383378	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226504399delA								LIN9 (6829 upstream) : PARP1 (43994 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	226518885	226518886	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226518885_226518886delTT								LIN9 (21315 upstream) : PARP1 (29507 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	226644321	226644321	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226644321delT								PARP1 (48520 upstream) : C1orf95 (92180 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	226815111	226815111	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226815111delA								C1orf95 (21808 upstream) : ITPKB (4281 downstream)																																			---	---	---	---
CDC42BPA	8476	broad.mit.edu	37	1	227359375	227359375	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227359375delT	uc001hqr.2	-						CDC42BPA_uc001hqs.2_Intron|CDC42BPA_uc009xes.2_Intron|CDC42BPA_uc010pvs.1_Intron	NM_003607	NP_003598			CDC42-binding protein kinase alpha isoform B						actin cytoskeleton reorganization|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm	ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1)	11		all_cancers(173;0.156)|Prostate(94;0.0792)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	227617130	227617130	+	RNA	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227617130delA	uc001hqv.2	+	4		c.365delA								Homo sapiens cDNA clone IMAGE:5270051.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	228100245	228100245	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228100245delT								PRSS38 (66076 upstream) : WNT9A (8920 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	228707640	228707641	+	IGR	DEL	CA	-	-	rs111341592		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228707640_228707641delCA								RNF187 (23752 upstream) : DUSP5P (73016 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	228859788	228859789	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228859788_228859789delTT								DUSP5P (71629 upstream) : RHOU (11080 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	229008304	229008304	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229008304delT								RHOU (125895 upstream) : RAB4A (398575 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	229154134	229154134	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229154134delT								RHOU (271725 upstream) : RAB4A (252745 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	229290278	229290278	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229290278delA								RHOU (407869 upstream) : RAB4A (116601 downstream)																																			---	---	---	---
NUP133	55746	broad.mit.edu	37	1	229605770	229605770	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229605770delC	uc001htn.2	-							NM_018230	NP_060700			nucleoporin 133kDa						carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|nuclear pore organization|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			breast(4)|skin(2)|ovary(1)	7	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	229855206	229855210	+	IGR	DEL	TTTTT	-	-	rs113766723		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229855206_229855210delTTTTT								URB2 (59260 upstream) : GALNT2 (338326 downstream)																																			---	---	---	---
GALNT2	2590	broad.mit.edu	37	1	230232320	230232320	+	Intron	DEL	T	-	-	rs77034196	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230232320delT	uc010pwa.1	+						GALNT2_uc010pvy.1_Intron|GALNT2_uc010pvz.1_Intron	NM_004481	NP_004472			polypeptide N-acetylgalactosaminyltransferase 2						immunoglobulin biosynthetic process|protein O-linked glycosylation via serine|protein O-linked glycosylation via threonine	extracellular region|Golgi cisterna membrane|integral to Golgi membrane|perinuclear region of cytoplasm	manganese ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)	2	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)																---	---	---	---
PGBD5	79605	broad.mit.edu	37	1	230481796	230481797	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230481796_230481797insT	uc010pwb.1	-						PGBD5_uc001htv.2_Intron	NM_024554	NP_078830			piggyBac transposable element derived 5							integral to membrane				ovary(2)|central_nervous_system(1)|skin(1)	4	Breast(184;0.0397)	Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;0.201)														---	---	---	---
COG2	22796	broad.mit.edu	37	1	230823194	230823195	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230823194_230823195delTT	uc001htw.2	+						COG2_uc001htx.2_Intron|COG2_uc010pwc.1_Intron	NM_007357	NP_031383			component of oligomeric golgi complex 2 isoform						Golgi organization|intra-Golgi vesicle-mediated transport|intracellular protein transport|oligosaccharide biosynthetic process|protein glycosylation	Golgi membrane|Golgi stack|Golgi transport complex	protein binding|protein transporter activity				0	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)																---	---	---	---
COG2	22796	broad.mit.edu	37	1	230828972	230828972	+	Intron	DEL	T	-	-	rs111313789		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230828972delT	uc001htw.2	+						COG2_uc001htx.2_Intron|COG2_uc010pwc.1_Intron	NM_007357	NP_031383			component of oligomeric golgi complex 2 isoform						Golgi organization|intra-Golgi vesicle-mediated transport|intracellular protein transport|oligosaccharide biosynthetic process|protein glycosylation	Golgi membrane|Golgi stack|Golgi transport complex	protein binding|protein transporter activity				0	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)																---	---	---	---
CAPN9	10753	broad.mit.edu	37	1	230930228	230930228	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230930228delA	uc001htz.1	+						CAPN9_uc009xfg.1_Intron|CAPN9_uc001hua.1_Intron	NM_006615	NP_006606			calpain 9 isoform 1						digestion|proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			ovary(1)	1	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	231019654	231019654	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231019654delG								C1orf198 (14319 upstream) : TTC13 (22336 downstream)																																			---	---	---	---
TTC13	79573	broad.mit.edu	37	1	231052933	231052933	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231052933delA	uc001huf.3	-						TTC13_uc009xfi.2_Intron|TTC13_uc009xfj.2_Intron|TTC13_uc001hug.3_Intron|TTC13_uc009xfk.1_Intron	NM_024525	NP_078801			tetratricopeptide repeat domain 13 isoform a								binding			ovary(1)|skin(1)	2	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)		COAD - Colon adenocarcinoma(196;0.243)												OREG0014319	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	1	231141907	231141907	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231141907delA								ARV1 (5436 upstream) : FAM89A (12797 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	231242828	231242828	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231242828delT								FAM89A (66833 upstream) : TRIM67 (55846 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	231266860	231266860	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231266860delT								FAM89A (90865 upstream) : TRIM67 (31814 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	231441928	231441928	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231441928delG								GNPAT (28210 upstream) : EXOC8 (26555 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	231588390	231588390	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231588390delA								EGLN1 (27600 upstream) : TSNAX-DISC1 (76009 downstream)																																			---	---	---	---
TSNAX-DISC1	100303453	broad.mit.edu	37	1	231723508	231723509	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231723508_231723509insT	uc010pwg.1	+						TSNAX-DISC1_uc010pwe.1_Intron|TSNAX-DISC1_uc010pwf.1_Intron|TSNAX-DISC1_uc010pwh.1_Intron|TSNAX-DISC1_uc010pwi.1_Intron|TSNAX-DISC1_uc010pwj.1_Intron|TSNAX-DISC1_uc010pwk.1_Intron|TSNAX-DISC1_uc010pwl.1_Intron	NM_001012959	NP_001012977			disrupted in schizophrenia 1 isoform S												0																		---	---	---	---
TSNAX-DISC1	100303453	broad.mit.edu	37	1	231745950	231745950	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231745950delT	uc010pwg.1	+						TSNAX-DISC1_uc010pwe.1_Intron|TSNAX-DISC1_uc010pwf.1_Intron|TSNAX-DISC1_uc010pwh.1_Intron|TSNAX-DISC1_uc010pwi.1_Intron|TSNAX-DISC1_uc010pwj.1_Intron|TSNAX-DISC1_uc010pwk.1_Intron|TSNAX-DISC1_uc010pwl.1_Intron	NM_001012959	NP_001012977			disrupted in schizophrenia 1 isoform S												0																		---	---	---	---
TSNAX-DISC1	100303453	broad.mit.edu	37	1	231761309	231761310	+	Intron	DEL	AA	-	-	rs112836010		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231761309_231761310delAA	uc010pwg.1	+						TSNAX-DISC1_uc010pwe.1_Intron|TSNAX-DISC1_uc010pwf.1_Intron|TSNAX-DISC1_uc010pwh.1_Intron|TSNAX-DISC1_uc010pwi.1_Intron|TSNAX-DISC1_uc010pwj.1_Intron|TSNAX-DISC1_uc010pwk.1_Intron|TSNAX-DISC1_uc010pwl.1_Intron|DISC1_uc010pwo.1_5'Flank|DISC1_uc010pwp.1_5'Flank|DISC1_uc010pwq.1_5'Flank|DISC1_uc010pwr.1_5'Flank|DISC1_uc010pws.1_5'Flank|DISC1_uc010pwt.1_5'Flank|DISC1_uc010pwu.1_5'Flank|DISC1_uc010pwv.1_5'Flank|DISC1_uc010pww.1_5'Flank|DISC1_uc010pwx.1_5'Flank|DISC1_uc010pwy.1_5'Flank|DISC1_uc010pwz.1_5'Flank|DISC1_uc010pxa.1_5'Flank|DISC1_uc001huy.2_5'Flank|DISC1_uc010pxb.1_5'Flank|DISC1_uc010pxc.1_5'Flank|DISC1_uc010pxd.1_5'Flank|DISC1_uc010pxe.1_5'Flank|DISC1_uc009xfr.2_5'Flank|DISC1_uc010pxf.1_5'Flank|DISC1_uc010pxg.1_5'Flank|DISC1_uc010pxh.1_5'Flank|DISC1_uc010pxi.1_5'Flank|DISC1_uc010pxj.1_5'Flank|DISC1_uc010pxk.1_5'Flank|DISC1_uc010pxl.1_5'Flank|DISC1_uc010pxm.1_5'Flank|DISC1_uc010pxn.1_5'Flank|DISC1_uc001huz.2_5'Flank|DISC1_uc001hva.2_5'Flank|DISC1_uc010pwm.1_5'Flank|DISC1_uc001hux.1_5'Flank|DISC1_uc001hvc.3_5'Flank|DISC1_uc010pwn.1_5'Flank	NM_001012959	NP_001012977			disrupted in schizophrenia 1 isoform S												0																		---	---	---	---
DISC1	27185	broad.mit.edu	37	1	231764655	231764656	+	Intron	DEL	TT	-	-	rs74867880		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231764655_231764656delTT	uc001huz.2	+						TSNAX-DISC1_uc010pwe.1_Intron|TSNAX-DISC1_uc010pwf.1_Intron|TSNAX-DISC1_uc010pwg.1_Intron|TSNAX-DISC1_uc010pwh.1_Intron|TSNAX-DISC1_uc010pwi.1_Intron|TSNAX-DISC1_uc010pwj.1_Intron|TSNAX-DISC1_uc010pwk.1_Intron|TSNAX-DISC1_uc010pwl.1_Intron|DISC1_uc010pwo.1_Intron|DISC1_uc010pwp.1_Intron|DISC1_uc010pwq.1_Intron|DISC1_uc010pwr.1_Intron|DISC1_uc010pws.1_Intron|DISC1_uc010pwt.1_Intron|DISC1_uc010pwu.1_Intron|DISC1_uc010pwv.1_Intron|DISC1_uc010pww.1_Intron|DISC1_uc010pwx.1_Intron|DISC1_uc010pwy.1_Intron|DISC1_uc010pwz.1_Intron|DISC1_uc010pxa.1_Intron|DISC1_uc001huy.2_Intron|DISC1_uc010pxb.1_Intron|DISC1_uc010pxc.1_Intron|DISC1_uc010pxd.1_Intron|DISC1_uc010pxe.1_Intron|DISC1_uc009xfr.2_Intron|DISC1_uc010pxf.1_Intron|DISC1_uc010pxg.1_Intron|DISC1_uc010pxh.1_Intron|DISC1_uc010pxi.1_Intron|DISC1_uc010pxj.1_Intron|DISC1_uc010pxk.1_Intron|DISC1_uc010pxl.1_Intron|DISC1_uc010pxm.1_Intron|DISC1_uc010pxn.1_Intron|DISC1_uc001hva.2_Intron|DISC1_uc010pwm.1_Intron|DISC1_uc001hux.1_Intron|DISC1_uc001hvc.3_Intron|DISC1_uc010pwn.1_Intron	NM_018662	NP_061132			disrupted in schizophrenia 1 isoform L						microtubule cytoskeleton organization|neuron migration|positive regulation of neuroblast proliferation|positive regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway	centrosome|microtubule	protein binding			skin(1)	1		all_cancers(173;0.0208)|Prostate(94;0.0975)																---	---	---	---
DISC1	27185	broad.mit.edu	37	1	232166945	232166946	+	Intron	INS	-	AA	AA	rs145210522	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232166945_232166946insAA	uc001huz.2	+						DISC1_uc001hva.2_Intron	NM_018662	NP_061132			disrupted in schizophrenia 1 isoform L						microtubule cytoskeleton organization|neuron migration|positive regulation of neuroblast proliferation|positive regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway	centrosome|microtubule	protein binding			skin(1)	1		all_cancers(173;0.0208)|Prostate(94;0.0975)																---	---	---	---
Unknown	0	broad.mit.edu	37	1	232302629	232302629	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232302629delT								DISC1 (125613 upstream) : SIPA1L2 (231085 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	232381089	232381091	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232381089_232381091delTTT								DISC1 (204073 upstream) : SIPA1L2 (152623 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	232689128	232689128	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232689128delG								SIPA1L2 (37885 upstream) : KIAA1383 (251510 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	232829116	232829117	+	IGR	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:232829116_232829117delGA								SIPA1L2 (177873 upstream) : KIAA1383 (111521 downstream)																																			---	---	---	---
C1orf57	84284	broad.mit.edu	37	1	233105315	233105315	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233105315delA	uc001hvj.1	+						C1orf57_uc001hvi.2_Intron|C1orf57_uc009xft.1_Intron	NM_032324	NP_115700			nucleoside-triphosphatase C1orf57								ATP binding|nucleoside-triphosphatase activity|nucleotide phosphatase activity|transferase activity				0		all_cancers(173;0.0818)|Prostate(94;0.137)																---	---	---	---
KCNK1	3775	broad.mit.edu	37	1	233749418	233749419	+	5'Flank	INS	-	AC	AC	rs147044709	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233749418_233749419insAC	uc010pxo.1	+							NM_002245	NP_002236			potassium channel, subfamily K, member 1							voltage-gated potassium channel complex	inward rectifier potassium channel activity			central_nervous_system(1)	1		all_cancers(173;0.00217)|all_epithelial(177;0.121)|Prostate(94;0.122)|Acute lymphoblastic leukemia(190;0.175)			Ibutilide(DB00308)|Quinidine(DB00908)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	233861792	233861792	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233861792delA								KCNK1 (53534 upstream) : SLC35F3 (178887 downstream)																																			---	---	---	---
SLC35F3	148641	broad.mit.edu	37	1	234438508	234438509	+	Intron	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234438508_234438509delTC	uc001hwa.1	+						SLC35F3_uc001hvy.1_Intron	NM_173508	NP_775779			solute carrier family 35, member F3						transport	integral to membrane				ovary(2)	2	Ovarian(103;0.0454)	all_cancers(173;0.145)|Prostate(94;0.0885)	OV - Ovarian serous cystadenocarcinoma(106;0.00531)															---	---	---	---
TARBP1	6894	broad.mit.edu	37	1	234543947	234543950	+	Intron	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234543947_234543950delTTTT	uc001hwd.2	-							NM_005646	NP_005637			TAR RNA binding protein 1						regulation of transcription from RNA polymerase II promoter|RNA processing	nucleus	RNA binding|RNA methyltransferase activity			ovary(2)|skin(1)	3	Ovarian(103;0.0339)	all_cancers(173;0.00995)|Prostate(94;0.0115)|all_epithelial(177;0.172)	OV - Ovarian serous cystadenocarcinoma(106;0.000263)															---	---	---	---
TARBP1	6894	broad.mit.edu	37	1	234608725	234608726	+	Intron	INS	-	T	T	rs141043621	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234608725_234608726insT	uc001hwd.2	-							NM_005646	NP_005637			TAR RNA binding protein 1						regulation of transcription from RNA polymerase II promoter|RNA processing	nucleus	RNA binding|RNA methyltransferase activity			ovary(2)|skin(1)	3	Ovarian(103;0.0339)	all_cancers(173;0.00995)|Prostate(94;0.0115)|all_epithelial(177;0.172)	OV - Ovarian serous cystadenocarcinoma(106;0.000263)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	235094804	235094805	+	Intron	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235094804_235094805insC	uc001hwk.3	-											Homo sapiens, clone IMAGE:3896086, mRNA.																														---	---	---	---
RBM34	23029	broad.mit.edu	37	1	235321364	235321364	+	Intron	DEL	T	-	-	rs72756041	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235321364delT	uc001hwn.2	-						RBM34_uc001hwo.2_Intron|ARID4B_uc001hwp.2_Intron|RBM34_uc010pxp.1_Intron	NM_015014	NP_055829			RNA binding motif protein 34 isoform 1							nucleolus	nucleotide binding|RNA binding			central_nervous_system(1)	1	Ovarian(103;0.0398)	all_cancers(173;0.177)|Prostate(94;0.0166)	OV - Ovarian serous cystadenocarcinoma(106;5.43e-05)|Epithelial(3;0.000121)															---	---	---	---
GGPS1	9453	broad.mit.edu	37	1	235505913	235505913	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235505913delA	uc001hwv.2	+	4	813	c.729delA	c.(727-729)ATAfs	p.I243fs	GGPS1_uc001hww.2_Frame_Shift_Del_p.I243fs|GGPS1_uc001hwx.2_Frame_Shift_Del_p.I189fs|GGPS1_uc001hwy.2_Frame_Shift_Del_p.I243fs	NM_001037277	NP_001032354	O95749	GGPPS_HUMAN	geranylgeranyl diphosphate synthase 1 isoform A	243					cholesterol biosynthetic process|isoprenoid biosynthetic process	cytosol|soluble fraction	dimethylallyltranstransferase activity|farnesyltranstransferase activity|geranyltranstransferase activity|metal ion binding			central_nervous_system(1)	1	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00192)|Prostate(94;0.0294)|all_epithelial(177;0.155)|Lung SC(1967;0.238)	OV - Ovarian serous cystadenocarcinoma(106;1.39e-05)															---	---	---	---
B3GALNT2	148789	broad.mit.edu	37	1	235616773	235616773	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235616773delT	uc001hxc.2	-							NM_152490	NP_689703			beta-1,3-N-acetylgalactosaminyltransferase 2						protein glycosylation	Golgi membrane|integral to membrane	galactosyltransferase activity			breast(1)	1	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.0539)|Prostate(94;0.0353)	OV - Ovarian serous cystadenocarcinoma(106;0.000117)															---	---	---	---
GNG4	2786	broad.mit.edu	37	1	235799624	235799624	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235799624delA	uc001hxe.3	-						GNG4_uc009xfz.2_Intron|GNG4_uc001hxh.3_Intron	NM_001098722	NP_001092192			guanine nucleotide binding protein (G protein),						cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|negative regulation of cell growth|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	heterotrimeric G-protein complex	signal transducer activity				0	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00168)|Prostate(94;0.0776)|Acute lymphoblastic leukemia(190;0.23)	OV - Ovarian serous cystadenocarcinoma(106;0.000882)															---	---	---	---
LYST	1130	broad.mit.edu	37	1	235897978	235897978	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235897978delT	uc001hxj.2	-						LYST_uc001hxi.2_Frame_Shift_Del_p.K4fs	NM_000081	NP_000072			lysosomal trafficking regulator						defense response to bacterium|defense response to protozoan|defense response to virus|endosome to lysosome transport via multivesicular body sorting pathway|leukocyte chemotaxis|mast cell secretory granule organization|melanosome organization|natural killer cell mediated cytotoxicity|protein transport	cytoplasm|microtubule cytoskeleton	protein binding			ovary(6)|breast(4)|central_nervous_system(2)	12	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)											Chediak-Higashi_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	1	236097409	236097410	+	IGR	INS	-	T	T	rs144746919	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236097409_236097410insT								LYST (50469 upstream) : NID1 (41731 downstream)																																			---	---	---	---
NID1	4811	broad.mit.edu	37	1	236180690	236180690	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236180690delT	uc001hxo.2	-						NID1_uc009xgd.2_Intron	NM_002508	NP_002499			nidogen 1 precursor						cell-matrix adhesion	basement membrane	calcium ion binding			large_intestine(1)|pancreas(1)	2	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Becaplermin(DB00102)|Urokinase(DB00013)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	236248205	236248205	+	IGR	DEL	A	-	-	rs12184333		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236248205delA								NID1 (19724 upstream) : GPR137B (57627 downstream)																																			---	---	---	---
ERO1LB	56605	broad.mit.edu	37	1	236393400	236393400	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236393400delT	uc001hxt.2	-							NM_019891	NP_063944			endoplasmic reticulum oxidoreductin 1-Lbeta						electron transport chain|protein thiol-disulfide exchange|transport	endoplasmic reticulum membrane	flavin adenine dinucleotide binding|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor|unfolded protein binding				0	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.123)|Acute lymphoblastic leukemia(190;0.205)|Prostate(94;0.219)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)															---	---	---	---
ERO1LB	56605	broad.mit.edu	37	1	236409635	236409635	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236409635delT	uc001hxt.2	-						ERO1LB_uc010pxt.1_Intron	NM_019891	NP_063944			endoplasmic reticulum oxidoreductin 1-Lbeta						electron transport chain|protein thiol-disulfide exchange|transport	endoplasmic reticulum membrane	flavin adenine dinucleotide binding|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor|unfolded protein binding				0	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.123)|Acute lymphoblastic leukemia(190;0.205)|Prostate(94;0.219)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	236657498	236657498	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236657498delT								EDARADD (9490 upstream) : LGALS8 (24067 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	236799143	236799144	+	IGR	INS	-	TC	TC			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236799143_236799144insTC								HEATR1 (31329 upstream) : ACTN2 (50626 downstream)																																			---	---	---	---
ACTN2	88	broad.mit.edu	37	1	236876877	236876877	+	Intron	DEL	A	-	-	rs71532031		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236876877delA	uc001hyf.2	+						ACTN2_uc001hyg.2_Intron|ACTN2_uc009xgi.1_Intron	NM_001103	NP_001094			actinin, alpha 2						focal adhesion assembly|microspike assembly|muscle filament sliding|platelet activation|platelet degranulation|protein homotetramerization|regulation of apoptosis|synaptic transmission	actin filament|cytosol|dendritic spine|extracellular region|filopodium|focal adhesion|nucleolus|platelet alpha granule lumen|pseudopodium|Z disc	actin binding|calcium ion binding|FATZ 1 binding|identical protein binding|integrin binding|protein dimerization activity|structural constituent of muscle|titin binding|titin Z domain binding|ZASP binding			ovary(4)|skin(1)	5	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.00661)|Acute lymphoblastic leukemia(190;0.109)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00168)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	237127469	237127469	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237127469delA								MTR (60189 upstream) : RYR2 (78233 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	237135002	237135002	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237135002delT								MTR (67722 upstream) : RYR2 (70700 downstream)																																			---	---	---	---
RYR2	6262	broad.mit.edu	37	1	237819091	237819091	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237819091delT	uc001hyl.1	+							NM_001035	NP_001026			cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)															---	---	---	---
RYR2	6262	broad.mit.edu	37	1	237875200	237875200	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237875200delT	uc001hyl.1	+						RYR2_uc010pxz.1_Intron	NM_001035	NP_001026			cardiac muscle ryanodine receptor						cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	238375302	238375302	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238375302delA								LOC100130331 (283685 upstream) : LOC339535 (268384 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	238534701	238534702	+	IGR	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238534701_238534702delAG								LOC100130331 (443084 upstream) : LOC339535 (108984 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	238623206	238623206	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238623206delA								LOC100130331 (531589 upstream) : LOC339535 (20480 downstream)																																			---	---	---	---
LOC339535	339535	broad.mit.edu	37	1	238648694	238648695	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238648694_238648695delAA	uc001hyn.2	-							NR_015407				Homo sapiens cDNA clone IMAGE:5186761.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	1	238701638	238701638	+	IGR	DEL	T	-	-	rs80007507		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238701638delT								LOC339535 (52321 upstream) : CHRM3 (848227 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	239074190	239074190	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239074190delA								LOC339535 (424873 upstream) : CHRM3 (475675 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	239315710	239315711	+	IGR	INS	-	AC	AC	rs144466530	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239315710_239315711insAC								LOC339535 (666393 upstream) : CHRM3 (234154 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	239322551	239322551	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239322551delT								LOC339535 (673234 upstream) : CHRM3 (227314 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	239351626	239351626	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239351626delA								LOC339535 (702309 upstream) : CHRM3 (198239 downstream)																																			---	---	---	---
CHRM3	1131	broad.mit.edu	37	1	239890409	239890409	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239890409delA	uc001hyp.2	+						CHRM3_uc001hyo.1_Intron	NM_000740	NP_000731			cholinergic receptor, muscarinic 3						cell proliferation|energy reserve metabolic process|nervous system development|protein modification process|regulation of insulin secretion	basolateral plasma membrane|cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|phosphatidylinositol phospholipase C activity			ovary(4)|skin(1)	5	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Cevimeline(DB00185)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Darifenacin(DB00496)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Homatropine Methylbromide(DB00725)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Solifenacin(DB01591)|Thiethylperazine(DB00372)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tridihexethyl(DB00505)													---	---	---	---
CHRM3	1131	broad.mit.edu	37	1	239894840	239894840	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239894840delT	uc001hyp.2	+						CHRM3_uc001hyo.1_Intron	NM_000740	NP_000731			cholinergic receptor, muscarinic 3						cell proliferation|energy reserve metabolic process|nervous system development|protein modification process|regulation of insulin secretion	basolateral plasma membrane|cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|phosphatidylinositol phospholipase C activity			ovary(4)|skin(1)	5	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Cevimeline(DB00185)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Darifenacin(DB00496)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Homatropine Methylbromide(DB00725)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Solifenacin(DB01591)|Thiethylperazine(DB00372)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tridihexethyl(DB00505)													---	---	---	---
CHRM3	1131	broad.mit.edu	37	1	239949515	239949516	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:239949515_239949516insT	uc001hyp.2	+						CHRM3_uc001hyo.1_Intron	NM_000740	NP_000731			cholinergic receptor, muscarinic 3						cell proliferation|energy reserve metabolic process|nervous system development|protein modification process|regulation of insulin secretion	basolateral plasma membrane|cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|phosphatidylinositol phospholipase C activity			ovary(4)|skin(1)	5	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Cevimeline(DB00185)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Darifenacin(DB00496)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Homatropine Methylbromide(DB00725)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Solifenacin(DB01591)|Thiethylperazine(DB00372)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tridihexethyl(DB00505)													---	---	---	---
CHRM3	1131	broad.mit.edu	37	1	240072444	240072444	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240072444delA	uc001hyp.2	+	5	2472	c.1693delA	c.(1693-1695)AAAfs	p.K565fs		NM_000740	NP_000731	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	565	Cytoplasmic (By similarity).				cell proliferation|energy reserve metabolic process|nervous system development|protein modification process|regulation of insulin secretion	basolateral plasma membrane|cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|phosphatidylinositol phospholipase C activity			ovary(4)|skin(1)	5	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Cevimeline(DB00185)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Darifenacin(DB00496)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Homatropine Methylbromide(DB00725)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Solifenacin(DB01591)|Thiethylperazine(DB00372)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tridihexethyl(DB00505)													---	---	---	---
Unknown	0	broad.mit.edu	37	1	240212080	240212080	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240212080delA								CHRM3 (139365 upstream) : FMN2 (43105 downstream)																																			---	---	---	---
FMN2	56776	broad.mit.edu	37	1	240414269	240414270	+	Intron	INS	-	TC	TC	rs145904188	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240414269_240414270insTC	uc010pyd.1	+						FMN2_uc010pye.1_Intron|FMN2_uc010pyf.1_Intron|FMN2_uc010pyg.1_Intron	NM_020066	NP_064450			formin 2						actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1)	12	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)															---	---	---	---
GREM2	64388	broad.mit.edu	37	1	240684880	240684881	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240684880_240684881insA	uc001hys.2	-							NM_022469	NP_071914			gremlin 2 precursor						BMP signaling pathway	extracellular space	cytokine activity				0		all_cancers(173;0.0196)	OV - Ovarian serous cystadenocarcinoma(106;0.0123)															---	---	---	---
RGS7	6000	broad.mit.edu	37	1	240948277	240948278	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240948277_240948278insT	uc001hyv.2	-						RGS7_uc010pyh.1_Intron|RGS7_uc010pyj.1_Intron|RGS7_uc001hyu.2_Intron|RGS7_uc009xgn.1_Intron|RGS7_uc001hyw.2_Intron|RGS7_uc010pyi.1_Intron|RGS7_uc001hyt.2_Intron	NM_002924	NP_002915			regulator of G-protein signaling 7						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|protein binding|signal transducer activity			ovary(4)|skin(2)|kidney(1)	7		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)															---	---	---	---
RGS7	6000	broad.mit.edu	37	1	241189889	241189889	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241189889delA	uc001hyv.2	-						RGS7_uc010pyh.1_Intron|RGS7_uc010pyj.1_Intron|RGS7_uc001hyu.2_Intron|RGS7_uc009xgn.1_Intron|RGS7_uc001hyw.2_Intron	NM_002924	NP_002915			regulator of G-protein signaling 7						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|protein binding|signal transducer activity			ovary(4)|skin(2)|kidney(1)	7		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)															---	---	---	---
EXO1	9156	broad.mit.edu	37	1	242023510	242023510	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242023510delA	uc001hzh.2	+						EXO1_uc001hzi.2_Intron|EXO1_uc001hzj.2_Intron|EXO1_uc009xgq.2_Intron	NM_130398	NP_569082			exonuclease 1 isoform b						meiosis|mismatch repair	nucleus	double-stranded DNA specific 5'-3' exodeoxyribonuclease activity|flap endonuclease activity|metal ion binding|protein binding|protein binding|ribonuclease H activity|single-stranded DNA specific 5'-3' exodeoxyribonuclease activity			ovary(2)|lung(2)|skin(1)	5	Ovarian(103;0.103)	all_cancers(173;0.0555)	OV - Ovarian serous cystadenocarcinoma(106;0.0107)										Direct_reversal_of_damage|Editing_and_processing_nucleases					---	---	---	---
PLD5	200150	broad.mit.edu	37	1	242253557	242253557	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242253557delA	uc001hzn.1	-						PLD5_uc001hzl.3_Intron|PLD5_uc001hzm.3_Intron|PLD5_uc001hzo.1_Intron					RecName: Full=Inactive phospholipase D5;          Short=Inactive PLD 5; AltName: Full=Inactive choline phosphatase 5; AltName: Full=Inactive phosphatidylcholine-hydrolyzing phospholipase D5; AltName: Full=PLDc;							integral to membrane	catalytic activity			ovary(6)	6	Melanoma(84;0.242)		OV - Ovarian serous cystadenocarcinoma(106;0.0329)															---	---	---	---
PLD5	200150	broad.mit.edu	37	1	242363942	242363945	+	Intron	DEL	AAAT	-	-	rs5782222		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242363942_242363945delAAAT	uc001hzn.1	-						PLD5_uc001hzl.3_Intron|PLD5_uc001hzm.3_Intron|PLD5_uc001hzo.1_Intron					RecName: Full=Inactive phospholipase D5;          Short=Inactive PLD 5; AltName: Full=Inactive choline phosphatase 5; AltName: Full=Inactive phosphatidylcholine-hydrolyzing phospholipase D5; AltName: Full=PLDc;							integral to membrane	catalytic activity			ovary(6)	6	Melanoma(84;0.242)		OV - Ovarian serous cystadenocarcinoma(106;0.0329)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	242701111	242701113	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242701111_242701113delTTT								PLD5 (13113 upstream) : CEP170 (586618 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	242797576	242797577	+	IGR	DEL	AA	-	-	rs138172286		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242797576_242797577delAA								PLD5 (109578 upstream) : CEP170 (490154 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	242845787	242845787	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242845787delA								PLD5 (157789 upstream) : CEP170 (441944 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	243097397	243097398	+	IGR	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243097397_243097398delTC								PLD5 (409399 upstream) : CEP170 (190333 downstream)																																			---	---	---	---
SDCCAG8	10806	broad.mit.edu	37	1	243640320	243640321	+	Intron	INS	-	CG	CG	rs146929535	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243640320_243640321insCG	uc001hzw.2	+						SDCCAG8_uc010pyk.1_Intron|SDCCAG8_uc010pyl.1_Intron|SDCCAG8_uc001hzx.2_Intron	NM_006642	NP_006633			serologically defined colon cancer antigen 8						establishment of cell polarity|G2/M transition of mitotic cell cycle|tube formation	cell-cell junction|centriole|cytosol	protein binding				0	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)	COAD - Colon adenocarcinoma(196;0.145)														---	---	---	---
AKT3	10000	broad.mit.edu	37	1	243951257	243951257	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243951257delA	uc001iab.1	-						AKT3_uc001hzz.1_Intron	NM_005465	NP_005456			AKT3 kinase isoform 1						signal transduction	Golgi apparatus|nucleus|plasma membrane	ATP binding|protein binding|protein serine/threonine kinase activity			stomach(1)|lung(1)|breast(1)|central_nervous_system(1)	4	all_cancers(71;0.000307)|all_epithelial(71;0.000374)|all_lung(81;0.0323)|Ovarian(71;0.0619)|all_neural(11;0.101)|Lung NSC(105;0.168)	all_cancers(173;0.0274)	all cancers(7;4.3e-08)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00196)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	244083509	244083509	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244083509delA	uc001iac.2	+											Homo sapiens cDNA clone IMAGE:5244187.																														---	---	---	---
Unknown	0	broad.mit.edu	37	1	244424380	244424381	+	IGR	DEL	TA	-	-	rs35119785		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244424380_244424381delTA								ZNF238 (203604 upstream) : C1orf100 (91556 downstream)																																			---	---	---	---
C1orf101	257044	broad.mit.edu	37	1	244790875	244790875	+	Intron	DEL	A	-	-	rs79951235		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244790875delA	uc001iam.2	+						C1orf101_uc001ial.2_Intron|C1orf101_uc010pym.1_Intron|C1orf101_uc010pyn.1_Intron	NM_001130957	NP_001124429			hypothetical protein LOC257044 isoform 1							integral to membrane				ovary(1)|breast(1)	2	all_cancers(71;2.99e-05)|all_epithelial(71;0.00015)|all_neural(11;0.0269)|Breast(184;0.0654)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0874)|Lung NSC(105;0.121)		all cancers(7;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(106;0.001)|GBM - Glioblastoma multiforme(7;0.0154)															---	---	---	---
PPPDE1	51029	broad.mit.edu	37	1	244847174	244847174	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:244847174delT	uc001iao.2	+						PPPDE1_uc001iap.2_Intron	NM_016076	NP_057160			PPPDE peptidase domain containing 1											breast(3)	3																		---	---	---	---
EFCAB2	84288	broad.mit.edu	37	1	245170881	245170881	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245170881delA	uc001ibd.2	+						EFCAB2_uc001ibc.2_Intron|EFCAB2_uc010pyo.1_Intron|EFCAB2_uc010pyp.1_Intron|EFCAB2_uc001ibe.2_Intron	NR_026586				RecName: Full=EF-hand calcium-binding domain-containing protein 2;								calcium ion binding				0	all_cancers(71;2.93e-06)|all_epithelial(71;2.13e-05)|all_lung(81;0.0337)|Lung NSC(105;0.0472)|Ovarian(71;0.0584)|Breast(184;0.0716)|all_neural(11;0.0982)		OV - Ovarian serous cystadenocarcinoma(106;0.015)															---	---	---	---
KIF26B	55083	broad.mit.edu	37	1	245326857	245326858	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245326857_245326858delTT	uc001ibf.1	+						KIF26B_uc010pyq.1_Intron	NM_018012	NP_060482			kinesin family member 26B						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)															---	---	---	---
KIF26B	55083	broad.mit.edu	37	1	245565219	245565219	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245565219delA	uc001ibf.1	+						KIF26B_uc010pyq.1_Intron	NM_018012	NP_060482			kinesin family member 26B						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)															---	---	---	---
KIF26B	55083	broad.mit.edu	37	1	245667675	245667682	+	Intron	DEL	TCCCTCCT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245667675_245667682delTCCCTCCT	uc001ibf.1	+						KIF26B_uc010pyq.1_Intron	NM_018012	NP_060482			kinesin family member 26B						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)															---	---	---	---
KIF26B	55083	broad.mit.edu	37	1	245789961	245789961	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245789961delT	uc001ibf.1	+						KIF26B_uc010pyq.1_Intron|KIF26B_uc001ibg.1_Intron	NM_018012	NP_060482			kinesin family member 26B						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)															---	---	---	---
KIF26B	55083	broad.mit.edu	37	1	245847716	245847716	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245847716delG	uc001ibf.1	+						KIF26B_uc001ibg.1_Intron|KIF26B_uc001ibh.1_Intron	NM_018012	NP_060482			kinesin family member 26B						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)															---	---	---	---
SMYD3	64754	broad.mit.edu	37	1	246091340	246091340	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246091340delA	uc001ibl.2	-						SMYD3_uc001ibk.2_Intron|SMYD3_uc001ibi.2_Intron|SMYD3_uc001ibj.2_Intron	NM_022743	NP_073580			SET and MYND domain containing 3							cytoplasm|nucleus	histone-lysine N-methyltransferase activity|protein binding|zinc ion binding				0	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)														---	---	---	---
SMYD3	64754	broad.mit.edu	37	1	246292273	246292273	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246292273delT	uc001ibl.2	-						SMYD3_uc001ibk.2_Intron	NM_022743	NP_073580			SET and MYND domain containing 3							cytoplasm|nucleus	histone-lysine N-methyltransferase activity|protein binding|zinc ion binding				0	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)														---	---	---	---
SMYD3	64754	broad.mit.edu	37	1	246342127	246342128	+	Intron	DEL	AA	-	-	rs11362321		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246342127_246342128delAA	uc001ibl.2	-						SMYD3_uc001ibk.2_Intron	NM_022743	NP_073580			SET and MYND domain containing 3							cytoplasm|nucleus	histone-lysine N-methyltransferase activity|protein binding|zinc ion binding				0	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)														---	---	---	---
SCCPDH	51097	broad.mit.edu	37	1	246889334	246889334	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246889334delT	uc001ibr.2	+							NM_016002	NP_057086			saccharopine dehydrogenase (putative)							midbody	binding|saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity			ovary(1)	1	all_cancers(71;6.8e-05)|all_epithelial(71;7.93e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0545)|Lung NSC(105;0.0618)	all_cancers(173;0.0343)	OV - Ovarian serous cystadenocarcinoma(106;0.00323)	GBM - Glioblastoma multiforme(49;0.0896)														---	---	---	---
ZNF124	7678	broad.mit.edu	37	1	247307269	247307270	+	Intron	DEL	AG	-	-	rs35531017		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247307269_247307270delAG	uc001ici.2	-						uc001ich.2_Intron					Homo sapiens cDNA FLJ30085 fis, clone BGGI12001714, highly similar to Homo sapiens zinc finger protein 124 (HZF-16) (ZNF124), mRNA.						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)	1	all_cancers(71;5.07e-05)|all_epithelial(71;8.72e-06)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0488)|Lung NSC(105;0.053)		OV - Ovarian serous cystadenocarcinoma(106;0.00739)															---	---	---	---
ZNF124	7678	broad.mit.edu	37	1	247308245	247308245	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247308245delT	uc001ici.2	-						uc001ich.2_Intron					Homo sapiens cDNA FLJ30085 fis, clone BGGI12001714, highly similar to Homo sapiens zinc finger protein 124 (HZF-16) (ZNF124), mRNA.						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)	1	all_cancers(71;5.07e-05)|all_epithelial(71;8.72e-06)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0488)|Lung NSC(105;0.053)		OV - Ovarian serous cystadenocarcinoma(106;0.00739)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	247442566	247442566	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247442566delA								VN1R5 (22120 upstream) : ZNF496 (21057 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	247501599	247501599	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247501599delT								ZNF496 (6437 upstream) : NLRP3 (77859 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	247519305	247519305	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247519305delA								ZNF496 (24143 upstream) : NLRP3 (60153 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	247534835	247534835	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247534835delG								ZNF496 (39673 upstream) : NLRP3 (44623 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	247546219	247546221	+	IGR	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247546219_247546221delAAA								ZNF496 (51057 upstream) : NLRP3 (33237 downstream)																																			---	---	---	---
C1orf150	148823	broad.mit.edu	37	1	247705591	247705591	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247705591delA	uc009xgw.2	+						C1orf150_uc001ida.3_Intron|C1orf150_uc001idb.3_Intron|C1orf150_uc009xgx.2_Intron					Homo sapiens cDNA FLJ41804 fis, clone NOVAR2000710.												0	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.0241)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	247780996	247780997	+	IGR	DEL	GT	-	-	rs67123644		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247780996_247780997delGT								OR2G3 (11180 upstream) : OR13G1 (54423 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	247899464	247899465	+	IGR	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247899464_247899465insC								OR6F1 (23407 upstream) : OR1C1 (21301 downstream)																																			---	---	---	---
TRIM58	25893	broad.mit.edu	37	1	248024472	248024472	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248024472delT	uc001ido.2	+							NM_015431	NP_056246			tripartite motif-containing 58							intracellular	zinc ion binding			skin(3)|ovary(1)|pancreas(1)|lung(1)|central_nervous_system(1)	7	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0286)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)															---	---	---	---
TRIM58	25893	broad.mit.edu	37	1	248030993	248030993	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248030993delA	uc001ido.2	+						OR2W3_uc001idp.1_5'Flank	NM_015431	NP_056246			tripartite motif-containing 58							intracellular	zinc ion binding			skin(3)|ovary(1)|pancreas(1)|lung(1)|central_nervous_system(1)	7	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0286)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	248795053	248795053	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248795053delT								OR2T11 (4624 upstream) : OR2T35 (6535 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	291508	291508	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:291508delT								FAM150B (3200 upstream) : TMEM18 (376467 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	329186	329186	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:329186delT								FAM150B (40878 upstream) : TMEM18 (338789 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	331227	331228	+	IGR	INS	-	A	A	rs139299243	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:331227_331228insA								FAM150B (42919 upstream) : TMEM18 (336747 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	830685	830685	+	Intron	DEL	A	-	-	rs113059780		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:830685delA	uc002qwn.1	-						uc002qwo.1_Intron					Homo sapiens cDNA clone IMAGE:5174186.																														---	---	---	---
SNTG2	54221	broad.mit.edu	37	2	1154800	1154801	+	Intron	DEL	TC	-	-	rs66470757		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1154800_1154801delTC	uc002qwq.2	+						SNTG2_uc002qwp.2_Intron|SNTG2_uc010ewi.2_Intron	NM_018968	NP_061841			syntrophin, gamma 2						central nervous system development	cytoplasm|cytoskeleton|sarcolemma|syntrophin complex	actin binding|PDZ domain binding			ovary(1)|large_intestine(1)|breast(1)	3	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)														---	---	---	---
SNTG2	54221	broad.mit.edu	37	2	1194154	1194154	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1194154delA	uc002qwq.2	+						SNTG2_uc010ewi.2_Intron	NM_018968	NP_061841			syntrophin, gamma 2						central nervous system development	cytoplasm|cytoskeleton|sarcolemma|syntrophin complex	actin binding|PDZ domain binding			ovary(1)|large_intestine(1)|breast(1)	3	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	1598574	1598575	+	IGR	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1598574_1598575insC								TPO (52076 upstream) : PXDN (37085 downstream)																																			---	---	---	---
PXDN	7837	broad.mit.edu	37	2	1665309	1665321	+	Intron	DEL	GGATGCAGGTGGA	-	-	rs6146592		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1665309_1665321delGGATGCAGGTGGA	uc002qxa.2	-						PXDN_uc002qxb.1_Intron	NM_012293	NP_036425			peroxidasin precursor						extracellular matrix organization|hydrogen peroxide catabolic process|immune response	endoplasmic reticulum|extracellular space|proteinaceous extracellular matrix	extracellular matrix structural constituent|heme binding|interleukin-1 receptor antagonist activity|peroxidase activity			pancreas(6)|ovary(2)	8	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)														---	---	---	---
MYT1L	23040	broad.mit.edu	37	2	1906371	1906371	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1906371delA	uc002qxe.2	-						MYT1L_uc002qxd.2_Intron|MYT1L_uc010ewl.1_Intron	NM_015025	NP_055840			myelin transcription factor 1-like						cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)														---	---	---	---
MYT1L	23040	broad.mit.edu	37	2	1998069	1998069	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1998069delG	uc002qxe.2	-						MYT1L_uc002qxd.2_Intron|MYT1L_uc002qxf.1_Intron	NM_015025	NP_055840			myelin transcription factor 1-like						cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)														---	---	---	---
MYT1L	23040	broad.mit.edu	37	2	2154558	2154559	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2154558_2154559insT	uc002qxe.2	-						MYT1L_uc002qxd.2_Intron|MYT1L_uc002qxf.1_Intron	NM_015025	NP_055840			myelin transcription factor 1-like						cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	2428356	2428356	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:2428356delA								MYT1L (93311 upstream) : TSSC1 (764385 downstream)																																			---	---	---	---
TSSC1	7260	broad.mit.edu	37	2	3319833	3319834	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3319833_3319834insT	uc002qxj.2	-						TSSC1_uc002qxi.2_Intron	NM_003310	NP_003301			tumor suppressing subtransferable candidate 1								protein binding				0	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.212)		OV - Ovarian serous cystadenocarcinoma(76;0.00877)|Epithelial(75;0.0283)|all cancers(51;0.0464)														---	---	---	---
TTC15	51112	broad.mit.edu	37	2	3465149	3465149	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3465149delG	uc002qxm.1	+						TTC15_uc002qxn.1_Intron|TTC15_uc010ewm.1_Intron	NM_016030	NP_057114			tetratricopeptide repeat domain 15								binding			ovary(2)|breast(1)|pancreas(1)	4	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.214)		OV - Ovarian serous cystadenocarcinoma(76;0.0402)|Epithelial(75;0.0986)|all cancers(51;0.149)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	3693356	3693358	+	IGR	DEL	TTT	-	-	rs71845698		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3693356_3693358delTTT								COLEC11 (1311 upstream) : ALLC (12428 downstream)																																			---	---	---	---
ALLC	55821	broad.mit.edu	37	2	3718511	3718512	+	Intron	INS	-	T	T	rs146599821	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3718511_3718512insT	uc010ewt.2	+							NM_018436	NP_060906			allantoicase isoform a								allantoicase activity			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.088)	all_cancers(51;0.24)		OV - Ovarian serous cystadenocarcinoma(76;0.088)|all cancers(51;0.151)|Epithelial(75;0.206)											HNSCC(21;0.051)			---	---	---	---
Unknown	0	broad.mit.edu	37	2	4115281	4115282	+	IGR	DEL	CT	-	-	rs10180014	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:4115281_4115282delCT								ALLC (365023 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	4700879	4700880	+	Intron	DEL	GT	-	-	rs71839494		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:4700879_4700880delGT	uc002qyi.2	-											Homo sapiens cDNA, FLJ97272.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	5278539	5278540	+	IGR	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:5278539_5278540delCT								None (None upstream) : SOX11 (554259 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	5434569	5434569	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:5434569delG								None (None upstream) : SOX11 (398230 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	5810407	5810407	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:5810407delA								None (None upstream) : SOX11 (22392 downstream)																																			---	---	---	---
SOX11	6664	broad.mit.edu	37	2	5832794	5832794	+	5'Flank	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:5832794delG	uc002qyj.2	+							NM_003108	NP_003099			SRY-box 11						cardiac ventricle formation|closure of optic fissure|cornea development in camera-type eye|embryonic digestive tract morphogenesis|embryonic skeletal system morphogenesis|eyelid development in camera-type eye|glial cell proliferation|hard palate development|lens morphogenesis in camera-type eye|limb bud formation|lung morphogenesis|negative regulation of cell death|negative regulation of glial cell proliferation|negative regulation of lymphocyte proliferation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription regulatory region DNA binding|neural crest cell development|neural tube formation|neuroepithelial cell differentiation|noradrenergic neuron differentiation|outflow tract morphogenesis|positive regulation of BMP signaling pathway|positive regulation of hippo signaling cascade|positive regulation of hormone secretion|positive regulation of neurogenesis|positive regulation of neuron differentiation|positive regulation of ossification|positive regulation of osteoblast differentiation|positive regulation of stem cell proliferation|regulation of transforming growth factor beta receptor signaling pathway|signal transduction involved in G1/S transition checkpoint|soft palate development|somite development|spinal cord development|sympathetic nervous system development|ventricular septum morphogenesis	cytoplasm|nucleolus	enhancer sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|RNA polymerase II transcription coactivator activity|translation factor activity, nucleic acid binding			central_nervous_system(3)	3	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			OV - Ovarian serous cystadenocarcinoma(76;0.132)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	6197943	6197943	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6197943delT								LOC400940 (69579 upstream) : CMPK2 (782560 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	6321638	6321638	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6321638delT								LOC400940 (193274 upstream) : CMPK2 (658865 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	6570223	6570223	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6570223delT								LOC400940 (441859 upstream) : CMPK2 (410280 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	6709127	6709127	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6709127delT								LOC400940 (580763 upstream) : CMPK2 (271376 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	6969089	6969090	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6969089_6969090delAA								LOC400940 (840725 upstream) : CMPK2 (11413 downstream)																																			---	---	---	---
RNF144A	9781	broad.mit.edu	37	2	7077965	7077966	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7077965_7077966insA	uc002qys.2	+						RNF144A_uc002qyt.2_Intron|RNF144A_uc002qyu.2_Intron	NM_014746	NP_055561			ring finger protein 144							Golgi apparatus|integral to membrane	ligase activity|zinc ion binding			ovary(1)|kidney(1)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;0.226)		OV - Ovarian serous cystadenocarcinoma(76;0.195)														---	---	---	---
RNF144A	9781	broad.mit.edu	37	2	7099571	7099572	+	Intron	DEL	TG	-	-	rs138677365		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7099571_7099572delTG	uc002qys.2	+						RNF144A_uc002qyt.2_Intron	NM_014746	NP_055561			ring finger protein 144							Golgi apparatus|integral to membrane	ligase activity|zinc ion binding			ovary(1)|kidney(1)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;0.226)		OV - Ovarian serous cystadenocarcinoma(76;0.195)														---	---	---	---
RNF144A	9781	broad.mit.edu	37	2	7145044	7145044	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7145044delA	uc002qys.2	+						RNF144A_uc002qyt.2_Intron	NM_014746	NP_055561			ring finger protein 144							Golgi apparatus|integral to membrane	ligase activity|zinc ion binding			ovary(1)|kidney(1)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;0.226)		OV - Ovarian serous cystadenocarcinoma(76;0.195)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	7200649	7200649	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7200649delC								RNF144A (16342 upstream) : LOC339788 (861909 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	7323702	7323702	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7323702delA								RNF144A (139395 upstream) : LOC339788 (738856 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	8038194	8038195	+	IGR	INS	-	AAAG	AAAG			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8038194_8038195insAAAG								RNF144A (853887 upstream) : LOC339788 (24363 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	8538184	8538185	+	IGR	DEL	CA	-	-	rs111912936	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8538184_8538185delCA								LOC339788 (421207 upstream) : ID2 (281155 downstream)																																			---	---	---	---
KIDINS220	57498	broad.mit.edu	37	2	8875667	8875667	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8875667delA	uc002qzc.2	-						KIDINS220_uc010yiv.1_Intron|KIDINS220_uc002qzd.2_Intron|KIDINS220_uc010yiw.1_Intron|KIDINS220_uc002qzb.2_Intron	NM_020738	NP_065789			kinase D-interacting substrate of 220 kDa						activation of MAPKK activity|nerve growth factor receptor signaling pathway	cytosol|integral to membrane				ovary(3)|central_nervous_system(1)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
KIDINS220	57498	broad.mit.edu	37	2	8887029	8887029	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8887029delA	uc002qzc.2	-						KIDINS220_uc010yiv.1_Intron|KIDINS220_uc002qzd.2_Intron|KIDINS220_uc010yiw.1_Intron|KIDINS220_uc002qzb.2_Intron|KIDINS220_uc002qze.2_3'UTR	NM_020738	NP_065789			kinase D-interacting substrate of 220 kDa						activation of MAPKK activity|nerve growth factor receptor signaling pathway	cytosol|integral to membrane				ovary(3)|central_nervous_system(1)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
MBOAT2	129642	broad.mit.edu	37	2	9007191	9007192	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9007191_9007192insT	uc002qzg.1	-						MBOAT2_uc010yix.1_Intron	NM_138799	NP_620154			O-acyltransferase (membrane bound) domain						phospholipid biosynthetic process	integral to membrane	1-acylglycerol-3-phosphate O-acyltransferase activity				0	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
ADAM17	6868	broad.mit.edu	37	2	9661885	9661885	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9661885delA	uc002qzu.2	-						ADAM17_uc010ewy.2_Intron|ADAM17_uc010ewz.2_Intron|ADAM17_uc010exa.2_RNA	NM_003183	NP_003174			a disintegrin and metalloprotease domain 17						B cell differentiation|cell adhesion mediated by integrin|epidermal growth factor receptor signaling pathway|epidermal growth factor receptor transactivation by G-protein coupled receptor signaling pathway|germinal center formation|membrane protein intracellular domain proteolysis|negative regulation of interleukin-8 production|nerve growth factor receptor signaling pathway|Notch signaling pathway|PMA-inducible membrane protein ectodomain proteolysis|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of chemokine production|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of protein phosphorylation|positive regulation of T cell chemotaxis|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of mast cell apoptosis|response to drug|response to high density lipoprotein particle stimulus|response to hypoxia|response to lipopolysaccharide|spleen development|T cell differentiation in thymus|wound healing, spreading of epidermal cells	actin cytoskeleton|apical plasma membrane|cell surface|cytoplasm|integral to plasma membrane|membrane raft	integrin binding|interleukin-6 receptor binding|metalloendopeptidase activity|PDZ domain binding|SH3 domain binding|zinc ion binding			lung(1)|kidney(1)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.225)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	9698923	9698924	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9698923_9698924delAA								ADAM17 (3006 upstream) : YWHAQ (25183 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	9912792	9912792	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9912792delC								YWHAQ (141686 upstream) : TAF1B (70779 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	10271864	10271864	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10271864delA								RRM2 (318 upstream) : C2orf48 (9645 downstream)																																			---	---	---	---
HPCAL1	3241	broad.mit.edu	37	2	10454952	10454952	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10454952delT	uc002raj.2	+						HPCAL1_uc002rak.2_Intron|HPCAL1_uc002ral.2_Intron	NM_002149	NP_002140			hippocalcin-like 1								calcium ion binding			pancreas(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.214)														---	---	---	---
HPCAL1	3241	broad.mit.edu	37	2	10523499	10523499	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10523499delT	uc002raj.2	+						HPCAL1_uc002rak.2_Intron|HPCAL1_uc002ral.2_Intron|HPCAL1_uc010exe.2_Intron|HPCAL1_uc010exf.2_Intron	NM_002149	NP_002140			hippocalcin-like 1								calcium ion binding			pancreas(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.214)														---	---	---	---
HPCAL1	3241	broad.mit.edu	37	2	10523803	10523803	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10523803delA	uc002raj.2	+						HPCAL1_uc002rak.2_Intron|HPCAL1_uc002ral.2_Intron|HPCAL1_uc010exe.2_Intron|HPCAL1_uc010exf.2_Intron	NM_002149	NP_002140			hippocalcin-like 1								calcium ion binding			pancreas(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.214)														---	---	---	---
HPCAL1	3241	broad.mit.edu	37	2	10556828	10556831	+	Intron	DEL	TTTT	-	-	rs7576888		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10556828_10556831delTTTT	uc002raj.2	+						HPCAL1_uc002rak.2_Intron|HPCAL1_uc002ral.2_Intron|HPCAL1_uc010exe.2_Intron|HPCAL1_uc010exf.2_Intron	NM_002149	NP_002140			hippocalcin-like 1								calcium ion binding			pancreas(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.214)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	10568252	10568252	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10568252delT								HPCAL1 (510 upstream) : ODC1 (12256 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	10857132	10857133	+	IGR	DEL	GG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10857132_10857133delGG								NOL10 (27020 upstream) : ATP6V1C2 (4642 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	11131854	11131856	+	IGR	DEL	GAG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11131854_11131856delGAG								KCNF1 (77504 upstream) : C2orf50 (141323 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	11188997	11188998	+	IGR	DEL	GT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11188997_11188998delGT								KCNF1 (134647 upstream) : C2orf50 (84181 downstream)																																			---	---	---	---
PQLC3	130814	broad.mit.edu	37	2	11300855	11300855	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11300855delG	uc002rbc.2	+						PQLC3_uc010yjk.1_Intron	NM_152391	NP_689604			PQ loop repeat containing 3 precursor							integral to membrane					0	all_hematologic(175;0.0797)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.0978)|OV - Ovarian serous cystadenocarcinoma(76;0.132)														---	---	---	---
ROCK2	9475	broad.mit.edu	37	2	11351719	11351719	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11351719delA	uc002rbd.1	-							NM_004850	NP_004841			Rho-associated, coiled-coil containing protein						axon guidance|cytokinesis|intracellular signal transduction	cytosol|plasma membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|structural molecule activity			stomach(2)|skin(2)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)														---	---	---	---
ROCK2	9475	broad.mit.edu	37	2	11402501	11402501	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11402501delA	uc002rbd.1	-							NM_004850	NP_004841			Rho-associated, coiled-coil containing protein						axon guidance|cytokinesis|intracellular signal transduction	cytosol|plasma membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|structural molecule activity			stomach(2)|skin(2)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	12570620	12570620	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12570620delA	uc002rbu.1	+											Homo sapiens cDNA FLJ10696 fis, clone NT2RP3000484.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	12758313	12758313	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12758313delC								LPIN1 (790782 upstream) : TRIB2 (98685 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	12783330	12783330	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:12783330delT								LPIN1 (815799 upstream) : TRIB2 (73668 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	13145794	13145795	+	Intron	DEL	CA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:13145794_13145795delCA	uc002rbw.1	-											Homo sapiens cDNA FLJ41125 fis, clone BRACE2015969.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	13264839	13264839	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:13264839delA								TRIB2 (381983 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	13415468	13415469	+	IGR	DEL	TG	-	-	rs72398479		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:13415468_13415469delTG								TRIB2 (532612 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	13535644	13535644	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:13535644delA								TRIB2 (652788 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	13615541	13615541	+	IGR	DEL	T	-	-	rs76583415		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:13615541delT								TRIB2 (732685 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	13995292	13995292	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:13995292delA								None (None upstream) : FAM84A (777564 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	14160585	14160587	+	IGR	DEL	AAA	-	-	rs72392757		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:14160585_14160587delAAA								None (None upstream) : FAM84A (612269 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	14961039	14961039	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:14961039delT								FAM84A (170106 upstream) : NBAS (345993 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	15010763	15010763	+	IGR	DEL	A	-	-	rs74605612		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15010763delA								FAM84A (219830 upstream) : NBAS (296269 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	15209958	15209958	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15209958delA								FAM84A (419025 upstream) : NBAS (97074 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	15289620	15289621	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15289620_15289621insT								FAM84A (498687 upstream) : NBAS (17411 downstream)																																			---	---	---	---
NBAS	51594	broad.mit.edu	37	2	15359202	15359202	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15359202delT	uc002rcc.1	-						NBAS_uc002rcb.1_Intron|NBAS_uc010exl.1_Intron|NBAS_uc002rcd.1_Intron	NM_015909	NP_056993			neuroblastoma-amplified protein											ovary(2)|liver(1)|skin(1)	4																		---	---	---	---
NBAS	51594	broad.mit.edu	37	2	15611064	15611064	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15611064delA	uc002rcc.1	-						NBAS_uc002rcd.1_Intron	NM_015909	NP_056993			neuroblastoma-amplified protein											ovary(2)|liver(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	15847021	15847022	+	Intron	INS	-	A	A	rs77552974	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15847021_15847022insA	uc002rcf.1	+											Homo sapiens cDNA FLJ36206 fis, clone TESTI2028662.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	16065599	16065600	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16065599_16065600insA								DDX1 (294375 upstream) : MYCNOS (14420 downstream)																																			---	---	---	---
MYCN	4613	broad.mit.edu	37	2	16086265	16086265	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16086265delT	uc002rci.2	+	3					MYCN_uc010yjr.1_3'UTR	NM_005378	NP_005369			v-myc myelocytomatosis viral related oncogene,						regulation of transcription from RNA polymerase II promoter	chromatin|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|ovary(1)|lung(1)|skin(1)	5	all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197)		GBM - Glioblastoma multiforme(3;0.000332)					A		neuroblastoma								---	---	---	---
Unknown	0	broad.mit.edu	37	2	16643208	16643208	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16643208delG								MYCN (556080 upstream) : FAM49A (90693 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	16659714	16659714	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16659714delT								MYCN (572586 upstream) : FAM49A (74187 downstream)																																			---	---	---	---
FAM49A	81553	broad.mit.edu	37	2	16738812	16738812	+	Intron	DEL	A	-	-	rs35620535		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16738812delA	uc010exm.1	-						FAM49A_uc002rck.1_Intron	NM_030797	NP_110424			family with sequence similarity 49, member A							intracellular					0	Acute lymphoblastic leukemia(172;0.0734)|all_hematologic(175;0.088)		GBM - Glioblastoma multiforme(3;0.00969)															---	---	---	---
FAM49A	81553	broad.mit.edu	37	2	16794171	16794171	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16794171delC	uc010exm.1	-						FAM49A_uc002rck.1_Intron	NM_030797	NP_110424			family with sequence similarity 49, member A							intracellular					0	Acute lymphoblastic leukemia(172;0.0734)|all_hematologic(175;0.088)		GBM - Glioblastoma multiforme(3;0.00969)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	16916527	16916527	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16916527delC								FAM49A (69431 upstream) : RAD51AP2 (775459 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	17217511	17217512	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17217511_17217512insT								FAM49A (370415 upstream) : RAD51AP2 (474474 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	17608154	17608154	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:17608154delC								FAM49A (761058 upstream) : RAD51AP2 (83832 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	18907901	18907901	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18907901delA								NT5C1B (137063 upstream) : OSR1 (643346 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	19107630	19107630	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19107630delA								NT5C1B (336792 upstream) : OSR1 (443617 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	19638491	19638491	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19638491delA								OSR1 (80119 upstream) : TTC32 (458027 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	19756034	19756034	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19756034delA								OSR1 (197662 upstream) : TTC32 (340484 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	19786148	19786148	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:19786148delA								OSR1 (227776 upstream) : TTC32 (310370 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	20077458	20077459	+	Intron	DEL	AA	-	-	rs111415712		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20077458_20077459delAA	uc002rdf.2	+											Homo sapiens cDNA FLJ12334 fis, clone MAMMA1002209.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	20392219	20392220	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20392219_20392220insT								LAPTM4A (140430 upstream) : SDC1 (8338 downstream)																																			---	---	---	---
SDC1	6382	broad.mit.edu	37	2	20405078	20405078	+	Intron	DEL	G	-	-	rs74334882	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20405078delG	uc002rdo.1	-						SDC1_uc002rdp.1_Intron|SDC1_uc010exv.2_Intron|SDC1_uc010exw.1_Intron	NM_002997	NP_002988			syndecan 1 precursor						lipid metabolic process|lipoprotein metabolic process|myoblast development|striated muscle cell development	cytoplasm|extracellular region|focal adhesion|integral to plasma membrane	cytoskeletal protein binding|protein C-terminus binding			ovary(4)|skin(1)	5	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)			OV - Ovarian serous cystadenocarcinoma(76;0.221)														---	---	---	---
PUM2	23369	broad.mit.edu	37	2	20454512	20454512	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20454512delA	uc002rds.1	-						PUM2_uc002rdq.1_Intron|PUM2_uc002rdt.1_Intron|PUM2_uc002rdr.2_Intron|PUM2_uc010yjy.1_Intron|PUM2_uc002rdu.1_Intron|PUM2_uc010yjz.1_Intron	NM_015317	NP_056132			pumilio homolog 2						regulation of translation	perinuclear region of cytoplasm|stress granule	protein binding|RNA binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
PUM2	23369	broad.mit.edu	37	2	20510916	20510917	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20510916_20510917delAA	uc002rds.1	-						PUM2_uc002rdt.1_Intron|PUM2_uc002rdr.2_Intron|PUM2_uc010yjy.1_Intron|PUM2_uc002rdu.1_Intron|PUM2_uc010yjz.1_Intron	NM_015317	NP_056132			pumilio homolog 2						regulation of translation	perinuclear region of cytoplasm|stress granule	protein binding|RNA binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	20883653	20883657	+	IGR	DEL	GTGAA	-	-	rs150267980		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20883653_20883657delGTGAA								GDF7 (12403 upstream) : C2orf43 (146 downstream)																																			---	---	---	---
C2orf43	60526	broad.mit.edu	37	2	20893919	20893920	+	Intron	INS	-	C	C	rs142359947	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20893919_20893920insC	uc002rec.2	-						C2orf43_uc002rea.1_Intron|C2orf43_uc002reb.1_Intron|C2orf43_uc010yka.1_Intron|C2orf43_uc010ykb.1_Intron|C2orf43_uc010ykc.1_Intron|C2orf43_uc010ykd.1_Intron|C2orf43_uc010yke.1_Intron|C2orf43_uc010ykf.1_Intron	NM_021925	NP_068744			hypothetical protein LOC60526												0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	22066052	22066053	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:22066052_22066053delAA								APOB (799107 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	22425451	22425451	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:22425451delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	23037159	23037160	+	IGR	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23037159_23037160delCT								None (None upstream) : KLHL29 (718295 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	23601116	23601116	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23601116delA								None (None upstream) : KLHL29 (154339 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	23656106	23656106	+	IGR	DEL	T	-	-	rs56313665		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:23656106delT								None (None upstream) : KLHL29 (99349 downstream)																																			---	---	---	---
ATAD2B	54454	broad.mit.edu	37	2	24063161	24063161	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24063161delA	uc002rek.3	-						ATAD2B_uc010yki.1_Intron	NM_017552	NP_060022			ATPase family, AAA domain containing 2B								ATP binding|nucleoside-triphosphatase activity			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
MFSD2B	388931	broad.mit.edu	37	2	24246272	24246272	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24246272delG	uc002reo.1	+							NM_001080473	NP_001073942			major facilitator superfamily domain containing						transport	integral to membrane				ovary(2)	2																		---	---	---	---
FKBP1B	2281	broad.mit.edu	37	2	24279221	24279222	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24279221_24279222delTT	uc002rer.2	+						FKBP1B_uc002res.2_Intron|FKBP1B_uc002ret.2_Intron|FKBP1B_uc002reu.2_Intron	NM_004116	NP_004107			FK506 binding protein 1B, 12.6 kDa isoform a						'de novo' protein folding|negative regulation of heart rate|negative regulation of protein phosphatase type 2B activity|protein maturation by protein folding|protein refolding|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|regulation of ryanodine-sensitive calcium-release channel activity|response to redox state	calcium channel complex|sarcoplasmic reticulum membrane	FK506 binding|peptidyl-prolyl cis-trans isomerase activity|receptor binding				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
LOC375190	375190	broad.mit.edu	37	2	24344299	24344299	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24344299delA	uc010ykl.1	+						LOC375190_uc002rew.2_Intron|LOC375190_uc002rfb.2_5'Flank|PFN4_uc002rfa.1_Intron	NM_001145710	NP_001139182			hypothetical protein LOC375190												0																		---	---	---	---
ADCY3	109	broad.mit.edu	37	2	25139550	25139551	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25139550_25139551delAA	uc002rfs.3	-						ADCY3_uc010ykm.1_Intron	NM_004036	NP_004027			adenylate cyclase 3						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|sensory perception of smell|synaptic transmission|transmembrane transport|water transport	cytoplasm|integral to plasma membrane	ATP binding|calmodulin binding|metal ion binding			breast(3)|ovary(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	25418502	25418502	+	IGR	DEL	A	-	-	rs74912817		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25418502delA								POMC (26943 upstream) : DNMT3A (37344 downstream)																																			---	---	---	---
DTNB	1838	broad.mit.edu	37	2	25815005	25815006	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25815005_25815006delTT	uc002rgh.2	-						DTNB_uc010yko.1_Intron|DTNB_uc010ykp.1_Intron|DTNB_uc002rgo.2_Intron|DTNB_uc002rgi.2_Intron|DTNB_uc002rgj.2_Intron|DTNB_uc002rgk.2_Intron|DTNB_uc002rgl.2_Intron|DTNB_uc002rgq.2_Intron|DTNB_uc002rgm.2_Intron|DTNB_uc002rgn.2_Intron|DTNB_uc002rgr.1_Intron|DTNB_uc010ykq.1_Intron	NM_021907	NP_068707			dystrobrevin, beta isoform 1							cytoplasm	calcium ion binding|zinc ion binding			large_intestine(2)|ovary(2)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
DTNB	1838	broad.mit.edu	37	2	25874748	25874748	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25874748delA	uc002rgh.2	-						DTNB_uc010yko.1_5'Flank|DTNB_uc010ykp.1_Intron|DTNB_uc002rgo.2_Intron|DTNB_uc002rgi.2_Intron|DTNB_uc002rgj.2_Intron|DTNB_uc002rgk.2_Intron|DTNB_uc002rgl.2_Intron|DTNB_uc002rgq.2_Intron|DTNB_uc002rgm.2_Intron|DTNB_uc002rgn.2_Intron|DTNB_uc002rgr.1_Intron|DTNB_uc010ykq.1_Intron	NM_021907	NP_068707			dystrobrevin, beta isoform 1							cytoplasm	calcium ion binding|zinc ion binding			large_intestine(2)|ovary(2)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
ASXL2	55252	broad.mit.edu	37	2	26026854	26026854	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26026854delT	uc002rgs.2	-							NM_018263	NP_060733			additional sex combs like 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|protein binding			pancreas(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
KIF3C	3797	broad.mit.edu	37	2	26164426	26164427	+	Intron	DEL	AA	-	-	rs13023705	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26164426_26164427delAA	uc002rgu.2	-						KIF3C_uc010eyj.1_Intron|KIF3C_uc010ykr.1_Intron	NM_002254	NP_002245			kinesin family member 3C						blood coagulation|microtubule-based movement	cytosol|kinesin complex|microtubule	ATP binding|microtubule motor activity			ovary(3)|skin(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
EPT1	85465	broad.mit.edu	37	2	26600140	26600140	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26600140delT	uc010ykz.1	+						EPT1_uc010eyl.1_Intron	NM_033505	NP_277040			selenoprotein I						phospholipid biosynthetic process	integral to membrane	ethanolaminephosphotransferase activity|metal ion binding				0																		---	---	---	---
MAPRE3	22924	broad.mit.edu	37	2	27227952	27227952	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27227952delA	uc002rhw.2	+						MAPRE3_uc002rhx.2_Intron	NM_012326	NP_036458			microtubule-associated protein, RP/EB family,						cell division|mitosis|positive regulation of transcription, DNA-dependent	cytoplasm|cytoplasmic microtubule|microtubule|midbody|perinuclear region of cytoplasm	microtubule binding|protein binding|small GTPase regulator activity			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	27298485	27298485	+	IGR	DEL	T	-	-	rs116506287	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27298485delT								OST4 (3918 upstream) : EMILIN1 (3021 downstream)																																			---	---	---	---
CAD	790	broad.mit.edu	37	2	27442217	27442217	+	Intron	DEL	T	-	-	rs66822219		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27442217delT	uc002rji.2	+						CAD_uc010eyw.2_Intron	NM_004341	NP_004332			carbamoylphosphate synthetase 2/aspartate						'de novo' pyrimidine base biosynthetic process|drug metabolic process|glutamine metabolic process|peptidyl-threonine phosphorylation|protein autophosphorylation|pyrimidine nucleoside biosynthetic process|pyrimidine nucleotide biosynthetic process	cytosol|neuronal cell body|nuclear matrix|terminal button	aspartate binding|aspartate carbamoyltransferase activity|ATP binding|carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity|dihydroorotase activity|enzyme binding|identical protein binding|metal ion binding|protein kinase activity			ovary(4)|large_intestine(2)|kidney(2)|lung(1)|pancreas(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				L-Aspartic Acid(DB00128)|L-Glutamine(DB00130)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	27760358	27760358	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27760358delT								GCKR (13810 upstream) : C2orf16 (39031 downstream)																																			---	---	---	---
ZNF512	84450	broad.mit.edu	37	2	27816063	27816074	+	Intron	DEL	ACACACACACAC	-	-	rs72332920		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27816063_27816074delACACACACACAC	uc002rla.2	+						ZNF512_uc010ylv.1_Intron|ZNF512_uc010ylw.1_Intron|ZNF512_uc002rlb.2_Intron|ZNF512_uc010ylx.1_Intron|ZNF512_uc002rlc.2_Intron|ZNF512_uc010yly.1_Intron|ZNF512_uc010ylz.1_Intron	NM_032434	NP_115810			zinc finger protein 512						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	28687507	28687508	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28687507_28687508insA								FOSL2 (49993 upstream) : PLB1 (31474 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	28692580	28692580	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28692580delG								FOSL2 (55066 upstream) : PLB1 (26402 downstream)																																			---	---	---	---
PPP1CB	5500	broad.mit.edu	37	2	28986318	28986320	+	Intron	DEL	AAA	-	-	rs11419223		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28986318_28986320delAAA	uc002rmg.2	+						PPP1CB_uc010ymj.1_Intron|PPP1CB_uc010ymk.1_Intron|PPP1CB_uc010yml.1_Intron|PPP1CB_uc002rmh.2_Intron	NM_206876	NP_996759			protein phosphatase 1, catalytic subunit, beta						cell cycle|cell division|glycogen metabolic process|triglyceride catabolic process	MLL5-L complex|nucleolus|PTW/PP1 phosphatase complex	metal ion binding|myosin phosphatase activity|myosin-light-chain-phosphatase activity|protein binding			skin(1)	1	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
SPDYA	245711	broad.mit.edu	37	2	29062250	29062251	+	Intron	DEL	TG	-	-	rs145407151		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29062250_29062251delTG	uc002rmj.2	+						SPDYA_uc002rmi.2_Intron|SPDYA_uc002rmk.2_Intron|SPDYA_uc002rml.2_Intron	NM_182756	NP_877433			speedy homolog A isoform 1						G1/S transition of mitotic cell cycle|multicellular organismal development|positive regulation of cell proliferation|response to DNA damage stimulus	nucleus	protein kinase binding			upper_aerodigestive_tract(1)|ovary(1)	2	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
WDR43	23160	broad.mit.edu	37	2	29158318	29158318	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29158318delT	uc002rmo.2	+							NM_015131	NP_055946			WD repeat domain 43							nucleolus				ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
CLIP4	79745	broad.mit.edu	37	2	29361356	29361356	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29361356delT	uc002rmv.2	+						CLIP4_uc002rmu.2_Intron|CLIP4_uc010ezm.1_Intron|CLIP4_uc002rmw.2_Intron|CLIP4_uc010ymn.1_Intron	NM_024692	NP_078968			CAP-GLY domain containing linker protein family,											ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
CLIP4	79745	broad.mit.edu	37	2	29376364	29376365	+	Intron	INS	-	T	T	rs142567119	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29376364_29376365insT	uc002rmv.2	+						CLIP4_uc002rmu.2_Intron|CLIP4_uc010ezm.1_Intron|CLIP4_uc002rmw.2_Intron|CLIP4_uc010ymn.1_Intron	NM_024692	NP_078968			CAP-GLY domain containing linker protein family,											ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
ALK	238	broad.mit.edu	37	2	29525391	29525391	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29525391delA	uc002rmy.2	-							NM_004304	NP_004295			anaplastic lymphoma kinase precursor						protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity		NPM1/ALK(632)|EML4/ALK(246)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(16)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(262)|autonomic_ganglia(148)|soft_tissue(61)|breast(4)|kidney(4)|large_intestine(3)|skin(3)|ovary(3)|thyroid(2)|central_nervous_system(1)|pancreas(1)	1218	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)			T|Mis|A	NPM1|TPM3|TFG|TPM4|ATIC|CLTC|MSN|ALO17|CARS|EML4	ALCL|NSCLC|Neuroblastoma	neuroblastoma			Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	2	30542061	30542063	+	IGR	DEL	GAG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30542061_30542063delGAG								LBH (59162 upstream) : LCLAT1 (128060 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	30648064	30648064	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30648064delC								LBH (165165 upstream) : LCLAT1 (22059 downstream)																																			---	---	---	---
LCLAT1	253558	broad.mit.edu	37	2	30846445	30846445	+	Intron	DEL	A	-	-	rs12185696	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30846445delA	uc002rnj.2	+						LCLAT1_uc010ymp.1_Intron|LCLAT1_uc002rnl.2_Intron|LCLAT1_uc010ymq.1_Intron	NM_182551	NP_872357			lysocardiolipin acyltransferase 1 isoform 1						multicellular organismal development|phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	1-acylglycerol-3-phosphate O-acyltransferase activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	31055133	31055133	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31055133delT								CAPN13 (24822 upstream) : GALNT14 (78201 downstream)																																			---	---	---	---
GALNT14	79623	broad.mit.edu	37	2	31358385	31358385	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31358385delA	uc002rnr.2	-						GALNT14_uc002rns.2_Intron|GALNT14_uc010ymr.1_Intron|GALNT14_uc010ezo.1_Intron|GALNT14_uc010ezp.1_Intron	NM_024572	NP_078848			N-acetylgalactosaminyltransferase 14							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			upper_aerodigestive_tract(2)|skin(1)	3	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
SRD5A2	6716	broad.mit.edu	37	2	31778118	31778118	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31778118delA	uc002rnw.1	-							NM_000348	NP_000339			3-oxo-5 alpha-steroid 4-dehydrogenase 2						androgen biosynthetic process|cell differentiation|cell-cell signaling|male gonad development	endoplasmic reticulum membrane|integral to membrane|microsome	3-oxo-5-alpha-steroid 4-dehydrogenase activity|sterol 5-alpha reductase activity				0	Acute lymphoblastic leukemia(172;0.155)				Azelaic Acid(DB00548)|Dutasteride(DB01126)													---	---	---	---
MEMO1	51072	broad.mit.edu	37	2	32241706	32241706	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32241706delT	uc002rnz.2	-						MEMO1_uc010ymv.1_Intron					Homo sapiens C2orf4a mRNA, complete cds, chromosome 2 open reading frame 4a.						regulation of microtubule-based process	cytosol|nucleus				ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
SPAST	6683	broad.mit.edu	37	2	32350594	32350594	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32350594delT	uc002roc.2	+						SPAST_uc002rod.2_Intron	NM_014946	NP_055761			spastin isoform 1						cell cycle|cell death|cell differentiation|cytokinesis, completion of separation|ER to Golgi vesicle-mediated transport|microtubule bundle formation|microtubule severing|nervous system development|protein hexamerization|protein homooligomerization	endoplasmic reticulum|endosome|integral to membrane|microtubule|microtubule organizing center|nucleus|perinuclear region of cytoplasm|spindle	alpha-tubulin binding|ATP binding|beta-tubulin binding|microtubule binding|microtubule-severing ATPase activity			breast(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)																	---	---	---	---
SPAST	6683	broad.mit.edu	37	2	32364907	32364909	+	Intron	DEL	AAA	-	-	rs77971769		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32364907_32364909delAAA	uc002roc.2	+						SPAST_uc002rod.2_Intron	NM_014946	NP_055761			spastin isoform 1						cell cycle|cell death|cell differentiation|cytokinesis, completion of separation|ER to Golgi vesicle-mediated transport|microtubule bundle formation|microtubule severing|nervous system development|protein hexamerization|protein homooligomerization	endoplasmic reticulum|endosome|integral to membrane|microtubule|microtubule organizing center|nucleus|perinuclear region of cytoplasm|spindle	alpha-tubulin binding|ATP binding|beta-tubulin binding|microtubule binding|microtubule-severing ATPase activity			breast(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)																	---	---	---	---
SPAST	6683	broad.mit.edu	37	2	32372162	32372162	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32372162delT	uc002roc.2	+						SPAST_uc002rod.2_Intron	NM_014946	NP_055761			spastin isoform 1						cell cycle|cell death|cell differentiation|cytokinesis, completion of separation|ER to Golgi vesicle-mediated transport|microtubule bundle formation|microtubule severing|nervous system development|protein hexamerization|protein homooligomerization	endoplasmic reticulum|endosome|integral to membrane|microtubule|microtubule organizing center|nucleus|perinuclear region of cytoplasm|spindle	alpha-tubulin binding|ATP binding|beta-tubulin binding|microtubule binding|microtubule-severing ATPase activity			breast(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)																	---	---	---	---
YIPF4	84272	broad.mit.edu	37	2	32517177	32517177	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32517177delT	uc002rok.2	+							NM_032312	NP_115688			Yip1 domain family, member 4							endoplasmic reticulum|integral to membrane	protein binding				0	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
BIRC6	57448	broad.mit.edu	37	2	32770120	32770120	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32770120delA	uc010ezu.2	+							NM_016252	NP_057336			baculoviral IAP repeat-containing 6						anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
BIRC6	57448	broad.mit.edu	37	2	32793912	32793915	+	Intron	DEL	AAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32793912_32793915delAAAA	uc010ezu.2	+							NM_016252	NP_057336			baculoviral IAP repeat-containing 6						anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
TTC27	55622	broad.mit.edu	37	2	32983770	32983770	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32983770delT	uc002rom.2	+						TTC27_uc010ymx.1_Intron|TTC27_uc002ron.2_Intron	NM_017735	NP_060205			tetratricopeptide repeat domain 27								protein binding			central_nervous_system(1)	1																		---	---	---	---
TTC27	55622	broad.mit.edu	37	2	32989515	32989515	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32989515delA	uc002rom.2	+						TTC27_uc010ymx.1_Intron|TTC27_uc002ron.2_Intron	NM_017735	NP_060205			tetratricopeptide repeat domain 27								protein binding			central_nervous_system(1)	1																		---	---	---	---
TTC27	55622	broad.mit.edu	37	2	33004290	33004290	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33004290delA	uc002rom.2	+						TTC27_uc010ymx.1_Intron|TTC27_uc002ron.2_Intron	NM_017735	NP_060205			tetratricopeptide repeat domain 27								protein binding			central_nervous_system(1)	1																		---	---	---	---
LTBP1	4052	broad.mit.edu	37	2	33210001	33210002	+	Intron	INS	-	AAAACAAAAC	AAAACAAAAC	rs149430632	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33210001_33210002insAAAACAAAAC	uc002ros.2	+							NM_206943	NP_996826			latent transforming growth factor beta binding						negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta	proteinaceous extracellular matrix	calcium ion binding|growth factor binding|transforming growth factor beta receptor activity			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)	8	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)																---	---	---	---
LTBP1	4052	broad.mit.edu	37	2	33389035	33389035	+	Intron	DEL	T	-	-	rs77110027		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33389035delT	uc002ros.2	+						LTBP1_uc002rot.2_Intron|LTBP1_uc002rou.2_Intron|LTBP1_uc002rov.2_Intron|LTBP1_uc010ymz.1_Intron|LTBP1_uc010yna.1_Intron	NM_206943	NP_996826			latent transforming growth factor beta binding						negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta	proteinaceous extracellular matrix	calcium ion binding|growth factor binding|transforming growth factor beta receptor activity			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)	8	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)																---	---	---	---
RASGRP3	25780	broad.mit.edu	37	2	33740066	33740066	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33740066delT	uc002rox.2	+						RASGRP3_uc010ync.1_Intron|RASGRP3_uc002roy.2_Intron	NM_170672	NP_733772			RAS guanyl releasing protein 3 (calcium and						MAPKKK cascade|small GTPase mediated signal transduction	integral to plasma membrane|intracellular	calcium ion binding|diacylglycerol binding|guanyl-nucleotide exchange factor activity|protein binding|Rap GTPase activator activity|signal transducer activity			lung(3)|ovary(1)|pancreas(1)	5	all_hematologic(175;0.115)																	---	---	---	---
RASGRP3	25780	broad.mit.edu	37	2	33757477	33757477	+	Intron	DEL	T	-	-	rs77194148		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33757477delT	uc002rox.2	+						RASGRP3_uc010ync.1_Intron|RASGRP3_uc002roy.2_Intron	NM_170672	NP_733772			RAS guanyl releasing protein 3 (calcium and						MAPKKK cascade|small GTPase mediated signal transduction	integral to plasma membrane|intracellular	calcium ion binding|diacylglycerol binding|guanyl-nucleotide exchange factor activity|protein binding|Rap GTPase activator activity|signal transducer activity			lung(3)|ovary(1)|pancreas(1)	5	all_hematologic(175;0.115)																	---	---	---	---
FAM98A	25940	broad.mit.edu	37	2	33820417	33820417	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33820417delA	uc002rpa.1	-						FAM98A_uc010yne.1_Intron	NM_015475	NP_056290			hypothetical protein LOC25940											ovary(1)	1	all_hematologic(175;0.115)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	34868957	34868958	+	IGR	INS	-	A	A	rs138609031	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:34868957_34868958insA								MYADML (915673 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	35042329	35042330	+	IGR	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:35042329_35042330delAC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	35631521	35631521	+	IGR	DEL	T	-	-	rs113221483		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:35631521delT								None (None upstream) : CRIM1 (951876 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	36185999	36185999	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36185999delT								None (None upstream) : CRIM1 (397398 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	36208007	36208007	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36208007delA								None (None upstream) : CRIM1 (375390 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	36479025	36479025	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:36479025delA								None (None upstream) : CRIM1 (104372 downstream)																																			---	---	---	---
VIT	5212	broad.mit.edu	37	2	37019080	37019080	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37019080delA	uc002rpl.2	+						VIT_uc002rpm.2_Intron|VIT_uc010ezv.2_Intron|VIT_uc010ezw.2_Intron	NM_053276	NP_444506			vitrin							proteinaceous extracellular matrix				ovary(1)|pancreas(1)	2		all_hematologic(82;0.248)																---	---	---	---
HEATR5B	54497	broad.mit.edu	37	2	37308370	37308370	+	Intron	DEL	T	-	-	rs75036290		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37308370delT	uc002rpp.1	-							NM_019024	NP_061897			HEAT repeat containing 5B								binding			ovary(5)|skin(2)|breast(1)	8		all_hematologic(82;0.21)																---	---	---	---
CCDC75	253635	broad.mit.edu	37	2	37315175	37315175	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37315175delA	uc010ezz.2	+						CCDC75_uc002rpr.3_Intron	NM_174931	NP_777591			coiled-coil domain containing 75							intracellular	nucleic acid binding				0		all_hematologic(82;0.21)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	37392240	37392240	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37392240delT								EIF2AK2 (8050 upstream) : SULT6B1 (2724 downstream)																																			---	---	---	---
C2orf56	55471	broad.mit.edu	37	2	37469699	37469699	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37469699delT	uc002rqa.3	+						C2orf56_uc010ynj.1_Intron|C2orf56_uc002rqc.3_Intron|C2orf56_uc010ynk.1_Intron|C2orf56_uc010ynl.1_Intron|C2orf56_uc010fah.2_Intron	NM_144736	NP_653337			hypothetical protein LOC55471 isoform 1						mitochondrial respiratory chain complex I assembly	mitochondrion	enzyme binding|methyltransferase activity			central_nervous_system(1)	1		all_hematologic(82;0.21)																---	---	---	---
C2orf56	55471	broad.mit.edu	37	2	37469850	37469850	+	Intron	DEL	A	-	-	rs142499241	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37469850delA	uc002rqa.3	+						C2orf56_uc010ynj.1_Intron|C2orf56_uc002rqc.3_Intron|C2orf56_uc010ynk.1_Intron|C2orf56_uc010ynl.1_Intron|C2orf56_uc010fah.2_Intron	NM_144736	NP_653337			hypothetical protein LOC55471 isoform 1						mitochondrial respiratory chain complex I assembly	mitochondrion	enzyme binding|methyltransferase activity			central_nervous_system(1)	1		all_hematologic(82;0.21)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	37712353	37712358	+	IGR	DEL	CTCCTC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37712353_37712358delCTCCTC								QPCT (111889 upstream) : CDC42EP3 (158385 downstream)																																			---	---	---	---
CDC42EP3	10602	broad.mit.edu	37	2	37887712	37887712	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37887712delT	uc002rqi.1	-							NM_006449	NP_006440			Cdc42 effector protein 3						regulation of cell shape|signal transduction	actin cytoskeleton|cytoplasm|endomembrane system|membrane	cytoskeletal regulatory protein binding				0		all_hematologic(82;0.172)																---	---	---	---
FAM82A1	151393	broad.mit.edu	37	2	38282449	38282449	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38282449delA	uc002rqn.1	+							NM_144713	NP_653314			family with sequence similarity 82, member A1							cytoplasm|integral to membrane|microtubule|spindle pole	binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	38441354	38441354	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38441354delA								C2orf58 (32363 upstream) : ATL2 (80677 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	38486567	38486567	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38486567delT								C2orf58 (77576 upstream) : ATL2 (35464 downstream)																																			---	---	---	---
ATL2	64225	broad.mit.edu	37	2	38527241	38527242	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38527241_38527242delAA	uc002rqq.2	-						ATL2_uc010ynm.1_Intron|ATL2_uc010ynn.1_Intron|ATL2_uc010yno.1_Intron|ATL2_uc002rqs.2_Intron|ATL2_uc002rqr.2_Intron	NM_001135673	NP_001129145			atlastin GTPase 2 isoform 2						endoplasmic reticulum organization|Golgi organization|protein homooligomerization	endoplasmic reticulum membrane|integral to membrane	GTP binding|GTPase activity|identical protein binding			ovary(1)|kidney(1)|skin(1)	3																		---	---	---	---
GALM	130589	broad.mit.edu	37	2	38896190	38896191	+	Intron	INS	-	T	T	rs140982755	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38896190_38896191insT	uc002rqy.2	+							NM_138801	NP_620156			galactose mutarotase						hexose metabolic process	cytoplasm	aldose 1-epimerase activity|carbohydrate binding				0		all_hematologic(82;0.248)																---	---	---	---
GALM	130589	broad.mit.edu	37	2	38910715	38910715	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38910715delT	uc002rqy.2	+							NM_138801	NP_620156			galactose mutarotase						hexose metabolic process	cytoplasm	aldose 1-epimerase activity|carbohydrate binding				0		all_hematologic(82;0.248)																---	---	---	---
GALM	130589	broad.mit.edu	37	2	38925093	38925094	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:38925093_38925094delTT	uc002rqy.2	+							NM_138801	NP_620156			galactose mutarotase						hexose metabolic process	cytoplasm	aldose 1-epimerase activity|carbohydrate binding				0		all_hematologic(82;0.248)																---	---	---	---
DHX57	90957	broad.mit.edu	37	2	39074919	39074919	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39074919delA	uc002rrf.2	-						DHX57_uc002rrd.3_Intron|DHX57_uc002rre.2_Intron	NM_198963	NP_945314			DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57								ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding|zinc ion binding			ovary(1)|lung(1)|skin(1)	3		all_hematologic(82;0.248)																---	---	---	---
ARHGEF33	100271715	broad.mit.edu	37	2	39167431	39167431	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39167431delT	uc010ynq.1	+							NM_001145451	NP_001138923			DH and coiled-coil domain-containing protein												0																		---	---	---	---
SOS1	6654	broad.mit.edu	37	2	39294567	39294567	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39294567delA	uc002rrk.3	-						SOS1_uc010ynr.1_Intron	NM_005633	NP_005624			son of sevenless homolog 1						apoptosis|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	cytosol	DNA binding|protein binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			ovary(4)|breast(3)|lung(2)|central_nervous_system(1)	10		all_hematologic(82;0.21)												Noonan_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	2	40016337	40016337	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40016337delA								THUMPD2 (9921 upstream) : SLC8A1 (322950 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	40932997	40932997	+	IGR	DEL	T	-	-	rs75959954		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40932997delT								SLC8A1 (193422 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	41278960	41278961	+	IGR	DEL	AC	-	-	rs62139045		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:41278960_41278961delAC								SLC8A1 (539385 upstream) : PKDCC (996200 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	41597905	41597906	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:41597905_41597906insA								SLC8A1 (858330 upstream) : PKDCC (677255 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	41861704	41861704	+	IGR	DEL	A	-	-	rs35647171		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:41861704delA								None (None upstream) : PKDCC (413457 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	42313986	42313986	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42313986delC								PKDCC (28320 upstream) : EML4 (82504 downstream)																																	OREG0014567	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
EML4	27436	broad.mit.edu	37	2	42430856	42430856	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42430856delA	uc002rsi.2	+						EML4_uc002rsh.3_Intron|EML4_uc010fap.2_Intron	NM_019063	NP_061936			echinoderm microtubule associated protein like 4						microtubule-based process|mitosis	cytoplasm|microtubule	protein binding		EML4/ALK(246)	lung(246)|ovary(2)|central_nervous_system(1)|skin(1)	250								T	ALK	NSCLC								---	---	---	---
MTA3	57504	broad.mit.edu	37	2	42747723	42747723	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42747723delT	uc002rso.1	+							NM_020744	NP_065795			metastasis associated 1 family, member 3							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2																		---	---	---	---
MTA3	57504	broad.mit.edu	37	2	42802701	42802701	+	Intron	DEL	A	-	-	rs60646215		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42802701delA	uc002rso.1	+						MTA3_uc002rsp.1_Intron|MTA3_uc002rsq.2_Intron|MTA3_uc002rsr.2_Intron	NM_020744	NP_065795			metastasis associated 1 family, member 3							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2																		---	---	---	---
MTA3	57504	broad.mit.edu	37	2	42968755	42968756	+	Intron	INS	-	A	A	rs144784589	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42968755_42968756insA	uc002rso.1	+						MTA3_uc002rsp.1_Intron	NM_020744	NP_065795			metastasis associated 1 family, member 3							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2																		---	---	---	---
HAAO	23498	broad.mit.edu	37	2	43002086	43002087	+	Intron	INS	-	AC	AC	rs146530543	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43002086_43002087insAC	uc002rst.3	-						HAAO_uc010ynw.1_Intron	NM_012205	NP_036337			3-hydroxyanthranilate 3,4-dioxygenase						neuron homeostasis|pyridine nucleotide biosynthetic process|quinolinate biosynthetic process|response to cadmium ion|response to zinc ion|tryptophan catabolic process	cytosol|soluble fraction	3-hydroxyanthranilate 3,4-dioxygenase activity|electron carrier activity|ferrous iron binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	43285436	43285436	+	IGR	DEL	C	-	-	rs143041007	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43285436delC								HAAO (265685 upstream) : ZFP36L2 (164106 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	43371212	43371212	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43371212delT								HAAO (351461 upstream) : ZFP36L2 (78330 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	43387262	43387262	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43387262delT								HAAO (367511 upstream) : ZFP36L2 (62280 downstream)																																			---	---	---	---
ABCG5	64240	broad.mit.edu	37	2	44054969	44054969	+	Intron	DEL	A	-	-	rs112929080	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44054969delA	uc002rtn.2	-						ABCG5_uc002rtm.2_Intron|ABCG5_uc002rto.2_Intron|ABCG5_uc002rtp.2_Intron	NM_022436	NP_071881			ATP-binding cassette sub-family G member 5						cholesterol efflux|cholesterol homeostasis|excretion|lipid metabolic process|negative regulation of intestinal cholesterol absorption|negative regulation of intestinal phytosterol absorption	apical plasma membrane|integral to membrane	ATP binding|ATPase activity|protein heterodimerization activity			ovary(1)|skin(1)	2		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)																---	---	---	---
ABCG8	64241	broad.mit.edu	37	2	44101866	44101866	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44101866delA	uc002rtq.2	+						ABCG8_uc010yoa.1_Intron	NM_022437	NP_071882			ATP-binding cassette sub-family G member 8						cholesterol efflux|cholesterol homeostasis|excretion|lipid metabolic process|negative regulation of intestinal cholesterol absorption|negative regulation of intestinal phytosterol absorption	apical plasma membrane|integral to membrane	ATP binding|ATPase activity|protein heterodimerization activity			skin(3)|ovary(1)	4		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)																---	---	---	---
C2orf34	79823	broad.mit.edu	37	2	44729362	44729362	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44729362delA	uc002rum.2	+							NM_024766	NP_079042			hypothetical protein LOC79823							cytoplasm	calmodulin-lysine N-methyltransferase activity				0		all_hematologic(82;0.0892)|Acute lymphoblastic leukemia(82;0.17)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	45342987	45342987	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45342987delA								SIX2 (106444 upstream) : SRBD1 (272833 downstream)																																			---	---	---	---
SRBD1	55133	broad.mit.edu	37	2	45657293	45657293	+	Intron	DEL	A	-	-	rs138437911		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45657293delA	uc002rus.2	-						SRBD1_uc010yoc.1_Intron	NM_018079	NP_060549			S1 RNA binding domain 1						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		hydrolase activity, acting on ester bonds|RNA binding			central_nervous_system(1)	1		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	LUSC - Lung squamous cell carcinoma(58;0.0917)|Lung(47;0.154)															---	---	---	---
SRBD1	55133	broad.mit.edu	37	2	45838600	45838600	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45838600delT	uc002rus.2	-							NM_018079	NP_060549			S1 RNA binding domain 1						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		hydrolase activity, acting on ester bonds|RNA binding			central_nervous_system(1)	1		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	LUSC - Lung squamous cell carcinoma(58;0.0917)|Lung(47;0.154)															---	---	---	---
PRKCE	5581	broad.mit.edu	37	2	46301153	46301153	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46301153delT	uc002rut.2	+							NM_005400	NP_005391			protein kinase C, epsilon						activation of phospholipase C activity|induction of apoptosis|intracellular signal transduction|nerve growth factor receptor signaling pathway|platelet activation	cytosol|endoplasmic reticulum|plasma membrane	ATP binding|enzyme activator activity|metal ion binding|signal transducer activity			lung(4)|ovary(3)|kidney(1)|breast(1)|large_intestine(1)	10		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)															---	---	---	---
PRKCE	5581	broad.mit.edu	37	2	46388426	46388426	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46388426delA	uc002rut.2	+							NM_005400	NP_005391			protein kinase C, epsilon						activation of phospholipase C activity|induction of apoptosis|intracellular signal transduction|nerve growth factor receptor signaling pathway|platelet activation	cytosol|endoplasmic reticulum|plasma membrane	ATP binding|enzyme activator activity|metal ion binding|signal transducer activity			lung(4)|ovary(3)|kidney(1)|breast(1)|large_intestine(1)	10		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)															---	---	---	---
PRKCE	5581	broad.mit.edu	37	2	46394204	46394205	+	Intron	INS	-	CT	CT			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:46394204_46394205insCT	uc002rut.2	+							NM_005400	NP_005391			protein kinase C, epsilon						activation of phospholipase C activity|induction of apoptosis|intracellular signal transduction|nerve growth factor receptor signaling pathway|platelet activation	cytosol|endoplasmic reticulum|plasma membrane	ATP binding|enzyme activator activity|metal ion binding|signal transducer activity			lung(4)|ovary(3)|kidney(1)|breast(1)|large_intestine(1)	10		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)															---	---	---	---
LOC100134259	100134259	broad.mit.edu	37	2	47064937	47064938	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47064937_47064938delTT	uc002rvi.3	+							NR_024452				Homo sapiens cDNA FLJ35178 fis, clone PLACE6014043.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	47117611	47117611	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47117611delA								LOC100134259 (31466 upstream) : MCFD2 (11406 downstream)																																			---	---	---	---
MCFD2	90411	broad.mit.edu	37	2	47134512	47134513	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47134512_47134513delTT	uc002rvk.2	-						MCFD2_uc002rvl.2_Intron|MCFD2_uc010fba.2_Intron|MCFD2_uc010yof.1_Intron	NM_139279	NP_644808			multiple coagulation factor deficiency 2						post-translational protein modification|protein N-linked glycosylation via asparagine|protein transport|vesicle-mediated transport	endoplasmic reticulum|ER to Golgi transport vesicle membrane|ER-Golgi intermediate compartment|Golgi apparatus	calcium ion binding			central_nervous_system(1)	1		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)		Antihemophilic Factor(DB00025)													---	---	---	---
TTC7A	57217	broad.mit.edu	37	2	47176347	47176347	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47176347delG	uc002rvo.2	+						TTC7A_uc002rvm.2_Intron|TTC7A_uc002rvn.1_Intron|TTC7A_uc010fbb.2_Intron|TTC7A_uc010fbc.2_Intron|TTC7A_uc002rvp.2_5'Flank	NM_020458	NP_065191			tetratricopeptide repeat domain 7A								binding			breast(1)|skin(1)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)															---	---	---	---
TTC7A	57217	broad.mit.edu	37	2	47283921	47283921	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47283921delA	uc002rvo.2	+						TTC7A_uc002rvm.2_Intron|TTC7A_uc010fbb.2_Intron|TTC7A_uc010fbc.2_Intron|TTC7A_uc002rvp.2_Intron|TTC7A_uc002rvq.2_Intron|TTC7A_uc002rvr.2_Intron	NM_020458	NP_065191			tetratricopeptide repeat domain 7A								binding			breast(1)|skin(1)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)															---	---	---	---
C2orf61	285051	broad.mit.edu	37	2	47352560	47352560	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47352560delA	uc010yog.1	-						C2orf61_uc010fbd.2_Intron	NM_001163561	NP_001157033			hypothetical protein LOC285051 isoform 1												0		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)															---	---	---	---
MSH6	2956	broad.mit.edu	37	2	48030692	48030692	+	Frame_Shift_Del	DEL	T	-	-	rs2020910	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48030692delT	uc002rwd.3	+	5	3458	c.3306delT	c.(3304-3306)ACTfs	p.T1102fs	MSH6_uc010fbj.2_Frame_Shift_Del_p.T800fs|MSH6_uc010yoi.1_Frame_Shift_Del_p.T972fs|MSH6_uc010yoj.1_Frame_Shift_Del_p.T800fs	NM_000179	NP_000170	P52701	MSH6_HUMAN	mutS homolog 6	1102					determination of adult lifespan|DNA damage response, signal transduction resulting in induction of apoptosis|isotype switching|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|response to UV|somatic hypermutation of immunoglobulin genes	MutSalpha complex	ATP binding|DNA-dependent ATPase activity|protein binding			large_intestine(53)|central_nervous_system(28)|endometrium(28)|stomach(22)|haematopoietic_and_lymphoid_tissue(9)|lung(7)|skin(6)|urinary_tract(5)|breast(5)|ovary(3)|thyroid(1)|upper_aerodigestive_tract(1)	168		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)					Mis|N|F|S		colorectal	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	2	48220755	48220755	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48220755delA								FBXO11 (87941 upstream) : FOXN2 (321040 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	48290703	48290704	+	IGR	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48290703_48290704delAG								FBXO11 (157889 upstream) : FOXN2 (251091 downstream)																																			---	---	---	---
STON1	11037	broad.mit.edu	37	2	48780572	48780573	+	Intron	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48780572_48780573delTC	uc002rwo.3	+						STON1_uc010fbm.2_Intron	NM_006873	NP_006864			stonin 1						endocytosis|intracellular protein transport|regulation of endocytosis	clathrin adaptor complex				skin(1)	1		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)															---	---	---	---
STON1-GTF2A1L	286749	broad.mit.edu	37	2	48860096	48860096	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48860096delA	uc010yol.1	+						STON1-GTF2A1L_uc002rwp.1_Intron|GTF2A1L_uc002rws.1_Intron|GTF2A1L_uc010yom.1_Intron|GTF2A1L_uc002rwt.2_Intron	NM_006873	NP_006864			stonin 1						endocytosis|intracellular protein transport|transcription initiation from RNA polymerase II promoter	clathrin adaptor complex|transcription factor TFIIA complex				ovary(3)|pancreas(1)|skin(1)	5		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)															---	---	---	---
LHCGR	3973	broad.mit.edu	37	2	48935854	48935854	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:48935854delT	uc002rwu.3	-						GTF2A1L_uc002rwt.2_Intron|LHCGR_uc002rwv.2_Intron	NM_000233	NP_000224			luteinizing hormone/choriogonadotropin receptor						male genitalia development|male gonad development	endosome|integral to plasma membrane	luteinizing hormone receptor activity			ovary(3)|lung(2)|breast(2)|skin(1)	8		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Cetrorelix(DB00050)|Choriogonadotropin alfa(DB00097)|Goserelin(DB00014)|Lutropin alfa(DB00044)|Menotropins(DB00032)									Familial_Male-Limited_Precocious_Puberty				---	---	---	---
FSHR	2492	broad.mit.edu	37	2	49195930	49195930	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49195930delT	uc002rww.2	-	9	835	c.761delA	c.(760-762)AAGfs	p.K254fs	FSHR_uc002rwx.2_Intron|FSHR_uc010fbn.2_Frame_Shift_Del_p.K228fs	NM_000145	NP_000136	P23945	FSHR_HUMAN	follicle stimulating hormone receptor isoform 1	254	Extracellular (Potential).|LRR 9.				female gamete generation|male gonad development|spermatogenesis	integral to membrane|plasma membrane	follicle-stimulating hormone receptor activity|protein binding			ovary(4)|lung(2)|central_nervous_system(1)|skin(1)	8		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Urofollitropin(DB00094)									Gonadal_Dysgenesis_46_XX				---	---	---	---
FSHR	2492	broad.mit.edu	37	2	49239550	49239550	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49239550delT	uc002rww.2	-						FSHR_uc002rwx.2_Intron|FSHR_uc010fbn.2_Intron|FSHR_uc010fbo.1_Intron	NM_000145	NP_000136			follicle stimulating hormone receptor isoform 1						female gamete generation|male gonad development|spermatogenesis	integral to membrane|plasma membrane	follicle-stimulating hormone receptor activity|protein binding			ovary(4)|lung(2)|central_nervous_system(1)|skin(1)	8		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Urofollitropin(DB00094)									Gonadal_Dysgenesis_46_XX				---	---	---	---
Unknown	0	broad.mit.edu	37	2	49742484	49742485	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49742484_49742485insT								FSHR (360854 upstream) : NRXN1 (403159 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	49841694	49841694	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49841694delA								FSHR (460064 upstream) : NRXN1 (303950 downstream)																																			---	---	---	---
NRXN1	9378	broad.mit.edu	37	2	50207045	50207045	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50207045delT	uc010fbp.2	-						NRXN1_uc002rxb.3_Intron|NRXN1_uc010fbq.2_Intron|NRXN1_uc002rxe.3_Intron	NM_138735	NP_620072			neurexin 1 isoform beta precursor						angiogenesis|neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)															---	---	---	---
NRXN1	9378	broad.mit.edu	37	2	51010091	51010091	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:51010091delT	uc010fbq.2	-						NRXN1_uc002rxe.3_Intron	NM_001135659	NP_001129131			neurexin 1 isoform alpha2 precursor						angiogenesis|neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)															---	---	---	---
NRXN1	9378	broad.mit.edu	37	2	51135501	51135502	+	Intron	DEL	AC	-	-	rs34878919		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:51135501_51135502delAC	uc010fbq.2	-						NRXN1_uc002rxe.3_Intron	NM_001135659	NP_001129131			neurexin 1 isoform alpha2 precursor						angiogenesis|neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	51644207	51644207	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:51644207delA								NRXN1 (384533 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	53308912	53308913	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53308912_53308913insA								None (None upstream) : ASB3 (588205 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	53878934	53878935	+	IGR	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:53878934_53878935delTC								None (None upstream) : ASB3 (18183 downstream)																																			---	---	---	---
PSME4	23198	broad.mit.edu	37	2	54093154	54093154	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54093154delA	uc002rxp.2	-						PSME4_uc010yop.1_Intron|PSME4_uc010yoq.1_Intron|PSME4_uc010fbu.1_Intron|PSME4_uc010fbv.1_Intron|PSME4_uc010fbt.1_Intron	NM_014614	NP_055429			proteasome (prosome, macropain) activator						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|M/G1 transition of mitotic cell cycle|mRNA metabolic process|multicellular organismal development|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|spermatogenesis|viral reproduction	nuclear speck|proteasome complex	binding			ovary(2)|breast(2)|pancreas(1)	5			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)															---	---	---	---
PSME4	23198	broad.mit.edu	37	2	54135789	54135789	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54135789delA	uc002rxp.2	-						PSME4_uc010yop.1_Intron|PSME4_uc010yoq.1_Intron|PSME4_uc010fbu.1_Intron|PSME4_uc010fbv.1_Intron	NM_014614	NP_055429			proteasome (prosome, macropain) activator						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|M/G1 transition of mitotic cell cycle|mRNA metabolic process|multicellular organismal development|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|spermatogenesis|viral reproduction	nuclear speck|proteasome complex	binding			ovary(2)|breast(2)|pancreas(1)	5			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)															---	---	---	---
PSME4	23198	broad.mit.edu	37	2	54186518	54186518	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54186518delA	uc002rxp.2	-						PSME4_uc010fbu.1_Intron|PSME4_uc010fbv.1_Intron	NM_014614	NP_055429			proteasome (prosome, macropain) activator						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|M/G1 transition of mitotic cell cycle|mRNA metabolic process|multicellular organismal development|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|spermatogenesis|viral reproduction	nuclear speck|proteasome complex	binding			ovary(2)|breast(2)|pancreas(1)	5			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	54309380	54309380	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54309380delT								PSME4 (111403 upstream) : ACYP2 (33030 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	54669556	54669556	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54669556delT								C2orf73 (80842 upstream) : SPTBN1 (13898 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	54925276	54925276	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54925276delA								SPTBN1 (26694 upstream) : EML6 (26873 downstream)																																			---	---	---	---
EML6	400954	broad.mit.edu	37	2	55170577	55170577	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55170577delA	uc002ryb.3	+							NM_001039753	NP_001034842			echinoderm microtubule associated protein like							cytoplasm|microtubule					0																		---	---	---	---
EML6	400954	broad.mit.edu	37	2	55176077	55176077	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55176077delA	uc002ryb.3	+	28	4113	c.4063delA	c.(4063-4065)AAAfs	p.K1355fs		NM_001039753	NP_001034842	Q6ZMW3	EMAL6_HUMAN	echinoderm microtubule associated protein like	1355	Poly-Lys.					cytoplasm|microtubule					0																		---	---	---	---
RTN4	57142	broad.mit.edu	37	2	55267564	55267564	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55267564delA	uc002rye.2	-						RTN4_uc002ryd.2_Intron|RTN4_uc002ryf.2_Intron|RTN4_uc002ryg.2_Intron	NM_020532	NP_065393			reticulon 4 isoform A						apoptosis|axonal fasciculation|cerebral cortex radial glia guided migration|endoplasmic reticulum tubular network organization|negative regulation of anti-apoptosis|negative regulation of axon extension|nerve growth factor receptor signaling pathway|regulation of apoptosis|regulation of branching morphogenesis of a nerve|regulation of cell migration	integral to endoplasmic reticulum membrane|nuclear envelope|plasma membrane	protein binding			ovary(2)|large_intestine(1)	3																		---	---	---	---
MTIF2	4528	broad.mit.edu	37	2	55479363	55479363	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55479363delA	uc002ryn.2	-						MTIF2_uc010yox.1_Intron|MTIF2_uc002ryo.2_Intron	NM_001005369	NP_001005369			mitochondrial translational initiation factor 2						regulation of translational initiation	mitochondrion	GTP binding|GTPase activity|ribosomal small subunit binding|translation initiation factor activity			ovary(1)	1																		---	---	---	---
CCDC88A	55704	broad.mit.edu	37	2	55523308	55523308	+	Intron	DEL	C	-	-	rs141740382	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55523308delC	uc002ryv.2	-						CCDC88A_uc010yoz.1_Intron|CCDC88A_uc010ypa.1_Intron|CCDC88A_uc002ryt.2_Intron|CCDC88A_uc010fbw.2_Intron|CCDC88A_uc002ryu.2_Intron|CCDC88A_uc002rys.2_Intron|CCDC88A_uc002ryw.2_Intron|CCDC88A_uc010fby.1_Intron	NM_001135597	NP_001129069			coiled-coil domain containing 88A isoform 1						activation of protein kinase B activity|cell migration|cellular membrane organization|DNA replication|lamellipodium assembly|microtubule cytoskeleton organization|regulation of actin cytoskeleton organization|regulation of cell proliferation|regulation of DNA replication|regulation of neuron projection development|TOR signaling cascade	cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|Golgi apparatus|lamellipodium|plasma membrane	actin binding|microtubule binding|phosphatidylinositol binding|protein homodimerization activity|protein kinase B binding			ovary(2)|skin(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	55855157	55855157	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55855157delA								SMEK2 (10044 upstream) : PNPT1 (6041 downstream)																																			---	---	---	---
PNPT1	87178	broad.mit.edu	37	2	55910980	55910980	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55910980delA	uc002rzf.2	-						PNPT1_uc002rzg.2_Intron	NM_033109	NP_149100			polyribonucleotide nucleotidyltransferase 1						mRNA catabolic process|RNA processing	plasma membrane	3'-5'-exoribonuclease activity|polyribonucleotide nucleotidyltransferase activity|RNA binding				0			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	56377694	56377694	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56377694delT	uc002rzk.2	+											Homo sapiens, clone IMAGE:3873411, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	56956516	56956516	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56956516delA								CCDC85A (343208 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	56978990	56978990	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:56978990delA								CCDC85A (365682 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	57697708	57697708	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:57697708delT								None (None upstream) : VRK2 (437078 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	57886989	57886989	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:57886989delT								None (None upstream) : VRK2 (247797 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	58107244	58107245	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58107244_58107245delTT								None (None upstream) : VRK2 (27541 downstream)																																			---	---	---	---
VRK2	7444	broad.mit.edu	37	2	58246461	58246461	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58246461delT	uc002rzo.2	+						VRK2_uc010fcb.2_Intron	NM_001130482	NP_001123954			vaccinia related kinase 2 isoform 2							integral to membrane	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(1)	1																		---	---	---	---
VRK2	7444	broad.mit.edu	37	2	58353281	58353281	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58353281delA	uc002rzo.2	+						VRK2_uc010fcb.2_Intron|VRK2_uc002rzs.2_Intron|VRK2_uc002rzr.2_Intron|VRK2_uc010fcc.2_Intron|VRK2_uc002rzv.2_Intron|VRK2_uc010fcd.2_Intron|VRK2_uc002rzp.2_Intron|VRK2_uc010ypg.1_Intron|VRK2_uc002rzq.2_Intron|VRK2_uc002rzu.2_Intron|VRK2_uc002rzt.2_Intron|VRK2_uc010yph.1_Intron	NM_001130482	NP_001123954			vaccinia related kinase 2 isoform 2							integral to membrane	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	58687298	58687298	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:58687298delT								FANCL (218783 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	59385351	59385351	+	IGR	DEL	A	-	-	rs72032388		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:59385351delA								FANCL (916836 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	59385444	59385444	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:59385444delA								FANCL (916929 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	60378109	60378109	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60378109delA								None (None upstream) : BCL11A (300194 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	60509425	60509425	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60509425delG								None (None upstream) : BCL11A (168878 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	60548201	60548201	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60548201delT								None (None upstream) : BCL11A (130102 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	60550605	60550605	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60550605delA								None (None upstream) : BCL11A (127698 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	60667962	60667963	+	IGR	DEL	AC	-	-	rs72354426		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60667962_60667963delAC								None (None upstream) : BCL11A (10340 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	60881178	60881179	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60881178_60881179delAA								BCL11A (100545 upstream) : PAPOLG (102204 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	60941792	60941794	+	IGR	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60941792_60941794delAAA								BCL11A (161159 upstream) : PAPOLG (41589 downstream)																																			---	---	---	---
PUS10	150962	broad.mit.edu	37	2	61186021	61186021	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61186021delA	uc010fci.2	-						PUS10_uc002sao.2_Intron|PUS10_uc010ypk.1_Intron	NM_144709	NP_653310			pseudouridylate synthase 10						pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding			ovary(2)|large_intestine(1)|kidney(1)	4			LUSC - Lung squamous cell carcinoma(5;1.56e-06)|Lung(5;2.48e-05)|Epithelial(17;0.113)															---	---	---	---
PUS10	150962	broad.mit.edu	37	2	61216772	61216772	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61216772delT	uc010fci.2	-						PUS10_uc002sao.2_Intron|PUS10_uc010ypk.1_Intron	NM_144709	NP_653310			pseudouridylate synthase 10						pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding			ovary(2)|large_intestine(1)|kidney(1)	4			LUSC - Lung squamous cell carcinoma(5;1.56e-06)|Lung(5;2.48e-05)|Epithelial(17;0.113)															---	---	---	---
KIAA1841	84542	broad.mit.edu	37	2	61336547	61336547	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61336547delA	uc002saw.3	+						KIAA1841_uc002sax.3_Intron|KIAA1841_uc002say.2_Intron	NM_001129993	NP_001123465			KIAA1841 protein isoform a												0			Epithelial(17;0.193)															---	---	---	---
USP34	9736	broad.mit.edu	37	2	61447729	61447729	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61447729delT	uc002sbe.2	-							NM_014709	NP_055524			ubiquitin specific protease 34						positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)															---	---	---	---
USP34	9736	broad.mit.edu	37	2	61577527	61577527	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61577527delA	uc002sbe.2	-							NM_014709	NP_055524			ubiquitin specific protease 34						positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)															---	---	---	---
XPO1	7514	broad.mit.edu	37	2	61713321	61713321	+	Intron	DEL	T	-	-	rs11438336		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61713321delT	uc002sbj.2	-						XPO1_uc010fcl.2_Intron|XPO1_uc010ypn.1_Intron|XPO1_uc002sbk.2_Intron|XPO1_uc002sbg.2_5'Flank|XPO1_uc002sbh.2_Intron	NM_003400	NP_003391			exportin 1						intracellular protein transport|mitotic prometaphase|mRNA metabolic process|mRNA transport|viral genome transport in host cell|viral infectious cycle	annulate lamellae|Cajal body|cytosol|kinetochore|nuclear envelope|nucleolus|ribonucleoprotein complex	protein binding|protein transporter activity|RNA binding			ovary(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	4			LUSC - Lung squamous cell carcinoma(7;5.71e-05)|Epithelial(17;0.0662)|all cancers(80;0.226)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	61842114	61842115	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61842114_61842115insT								XPO1 (76696 upstream) : FAM161A (209870 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	61848705	61848706	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61848705_61848706delAA								XPO1 (83287 upstream) : FAM161A (203279 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	62002016	62002016	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62002016delT								XPO1 (236598 upstream) : FAM161A (49969 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	62016987	62016987	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62016987delA								XPO1 (251569 upstream) : FAM161A (34998 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	62020544	62020546	+	IGR	DEL	AAA	-	-	rs74791580		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62020544_62020546delAAA								XPO1 (255126 upstream) : FAM161A (31439 downstream)																																			---	---	---	---
COMMD1	150684	broad.mit.edu	37	2	62340000	62340000	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62340000delT	uc002sbp.2	+						uc002sbr.2_Intron	NM_152516	NP_689729			MURR1						copper ion homeostasis|negative regulation of NF-kappaB transcription factor activity|positive regulation of protein ubiquitination|regulation of proteasomal ubiquitin-dependent protein catabolic process	cell junction|Cul2-RING ubiquitin ligase complex|cytoplasm|nucleolus	copper ion binding|protein homodimerization activity			ovary(1)	1	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;4.73e-07)|Epithelial(17;0.0216)|all cancers(80;0.0934)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	62395542	62395542	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62395542delA								COMMD1 (32338 upstream) : B3GNT2 (27720 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	62411400	62411400	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:62411400delA								COMMD1 (48196 upstream) : B3GNT2 (11862 downstream)																																			---	---	---	---
C2orf86	51057	broad.mit.edu	37	2	63621512	63621513	+	Intron	DEL	AA	-	-	rs145280348		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:63621512_63621513delAA	uc002sch.2	-						C2orf86_uc002sce.2_Intron|C2orf86_uc002scf.2_Intron|C2orf86_uc010ypu.1_Intron|C2orf86_uc002scg.2_Intron|C2orf86_uc002sci.1_Intron	NM_015910	NP_056994			hypothetical protein LOC51057 isoform 2						cilium morphogenesis|regulation of embryonic cell shape|regulation of protein localization|septin cytoskeleton organization	cilium axoneme|cytoplasm|cytoskeleton|plasma membrane					0																		---	---	---	---
UGP2	7360	broad.mit.edu	37	2	64094391	64094391	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64094391delT	uc002scm.2	+						UGP2_uc002scl.2_Intron|UGP2_uc010ypx.1_Intron	NM_006759	NP_006750			UDP-glucose pyrophosphorylase 2 isoform a						glycogen biosynthetic process|phosphorylation|UDP-glucose metabolic process|UDP-glucuronate biosynthetic process|xenobiotic metabolic process	cytosol	metal ion binding|protein binding|UTP:glucose-1-phosphate uridylyltransferase activity				0																		---	---	---	---
UGP2	7360	broad.mit.edu	37	2	64113202	64113202	+	Intron	DEL	G	-	-	rs34145077	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64113202delG	uc002scm.2	+						UGP2_uc002scl.2_Intron|UGP2_uc010ypx.1_Intron	NM_006759	NP_006750			UDP-glucose pyrophosphorylase 2 isoform a						glycogen biosynthetic process|phosphorylation|UDP-glucose metabolic process|UDP-glucuronate biosynthetic process|xenobiotic metabolic process	cytosol	metal ion binding|protein binding|UTP:glucose-1-phosphate uridylyltransferase activity				0																		---	---	---	---
VPS54	51542	broad.mit.edu	37	2	64202181	64202181	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64202181delT	uc002scq.2	-						VPS54_uc002scp.2_Intron|VPS54_uc010fct.2_5'UTR	NM_016516	NP_057600			vacuolar protein sorting 54 isoform 1						protein transport|retrograde transport, endosome to Golgi						0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	64465189	64465189	+	Intron	DEL	T	-	-	rs111436614		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64465189delT	uc002scv.1	+											full-length cDNA clone CS0DI020YI19 of Placenta Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	64660396	64660396	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64660396delT								PELI1 (288791 upstream) : HSPC159 (20931 downstream)																																			---	---	---	---
HSPC159	29094	broad.mit.edu	37	2	64683729	64683729	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64683729delA	uc002scy.3	+							NM_014181	NP_054900			galectin-related protein							intracellular	sugar binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	64705874	64705874	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64705874delA								HSPC159 (17363 upstream) : AFTPH (45591 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	64724688	64724688	+	IGR	DEL	A	-	-	rs68153716		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64724688delA								HSPC159 (36177 upstream) : AFTPH (26777 downstream)																																			---	---	---	---
SERTAD2	9792	broad.mit.edu	37	2	64880265	64880265	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64880265delA	uc002sde.1	-							NM_014755	NP_055570			SERTA domain containing 2						negative regulation of cell growth|transcription, DNA-dependent	cytoplasm|nucleus					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	65068180	65068182	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65068180_65068182delTTT								SERTAD2 (187134 upstream) : SLC1A4 (147397 downstream)																																			---	---	---	---
RAB1A	5861	broad.mit.edu	37	2	65325295	65325295	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65325295delA	uc002sdm.2	-						RAB1A_uc002sdn.2_Intron|RAB1A_uc010yqe.1_Intron|RAB1A_uc002sdo.2_Intron	NM_004161	NP_004152			RAB1A, member RAS oncogene family isoform 1						protein transport|small GTPase mediated signal transduction|vesicle-mediated transport	endoplasmic reticulum|Golgi apparatus	GTP binding|GTPase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	65406979	65406980	+	IGR	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65406979_65406980delGA								RAB1A (49544 upstream) : ACTR2 (47849 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	65667637	65667637	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65667637delA	uc010fcy.1	+											Homo sapiens cDNA FLJ16124 fis, clone BRACE2011677.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	65811152	65811152	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65811152delT	uc010fcy.1	+											Homo sapiens cDNA FLJ16124 fis, clone BRACE2011677.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	65975417	65975418	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65975417_65975418insT	uc010fcy.1	+						uc010fcz.1_Intron					Homo sapiens cDNA FLJ16124 fis, clone BRACE2011677.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	66009651	66009652	+	Intron	INS	-	AG	AG			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66009651_66009652insAG	uc010fcy.1	+											Homo sapiens cDNA FLJ16124 fis, clone BRACE2011677.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	66503787	66503787	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66503787delT								SPRED2 (844131 upstream) : MEIS1 (158745 downstream)																																			---	---	---	---
MEIS1	4211	broad.mit.edu	37	2	66719202	66719203	+	Intron	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66719202_66719203delTG	uc002sdu.2	+						MEIS1_uc002sdt.2_Intron|MEIS1_uc002sdv.2_Intron|MEIS1_uc010yqh.1_Intron|MEIS1_uc010yqi.1_Intron|MEIS1_uc002sdw.1_Intron	NM_002398	NP_002389			Meis homeobox 1								sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	67251088	67251088	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67251088delC								MEIS1 (451198 upstream) : ETAA1 (373354 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	67710069	67710069	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67710069delA								ETAA1 (72536 upstream) : C1D (559264 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	67764627	67764627	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67764627delT								ETAA1 (127094 upstream) : C1D (504706 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	67884173	67884176	+	IGR	DEL	AAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67884173_67884176delAAAA								ETAA1 (246640 upstream) : C1D (385157 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	67939364	67939365	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:67939364_67939365insA								ETAA1 (301831 upstream) : C1D (329968 downstream)																																			---	---	---	---
FBXO48	554251	broad.mit.edu	37	2	68691329	68691329	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68691329delT	uc002seo.2	-	4						NM_001024680	NP_001019851			F-box protein 48												0																		---	---	---	---
ARHGAP25	9938	broad.mit.edu	37	2	68973840	68973842	+	Intron	DEL	CCT	-	-	rs13010123	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68973840_68973842delCCT	uc002seu.2	+						ARHGAP25_uc010yqk.1_Intron|ARHGAP25_uc010fdg.2_Intron|ARHGAP25_uc010yql.1_Intron	NM_001007231	NP_001007232			Rho GTPase activating protein 25 isoform a						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(2)|breast(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	69172285	69172285	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69172285delT								BMP10 (73636 upstream) : GKN2 (80 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	69508577	69508577	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69508577delC								ANTXR1 (32120 upstream) : GFPT1 (38328 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	69536072	69536072	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69536072delG								ANTXR1 (59615 upstream) : GFPT1 (10833 downstream)																																			---	---	---	---
ANXA4	307	broad.mit.edu	37	2	70030916	70030916	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70030916delA	uc002sfr.3	+						ANXA4_uc010yqn.1_Intron|ANXA4_uc002sfs.3_Intron|ANXA4_uc010yqo.1_Intron	NM_001153	NP_001144			annexin IV						anti-apoptosis|signal transduction	cytoplasm	calcium ion binding|calcium-dependent phospholipid binding|phospholipase inhibitor activity				0																		---	---	---	---
ASPRV1	151516	broad.mit.edu	37	2	70280497	70280497	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70280497delG	uc002sga.2	-						uc002sgb.1_Intron|uc002sgc.2_Intron|uc002sgd.2_Intron|uc002sge.1_Intron					Homo sapiens cDNA FLJ32260 fis, clone PROST1000334.						protein maturation by peptide bond cleavage|skin development		aspartic-type endopeptidase activity			ovary(1)	1																		---	---	---	---
ASPRV1	151516	broad.mit.edu	37	2	70301427	70301427	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70301427delT	uc002sga.2	-						uc002sgb.1_Intron|uc002sgd.2_Intron|uc002sge.1_Intron					Homo sapiens cDNA FLJ32260 fis, clone PROST1000334.						protein maturation by peptide bond cleavage|skin development		aspartic-type endopeptidase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	70351109	70351109	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70351109delA								PCBP1 (34777 upstream) : LOC100133985 (60 downstream)																																			---	---	---	---
C2orf42	54980	broad.mit.edu	37	2	70389779	70389779	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70389779delA	uc002sgh.2	-							NM_017880	NP_060350			hypothetical protein LOC54980												0																		---	---	---	---
TIA1	7072	broad.mit.edu	37	2	70442886	70442887	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70442886_70442887delTT	uc002sgj.3	-						TIA1_uc002sgk.3_Intron|TIA1_uc002sgl.3_Intron	NM_022173	NP_071505			TIA1 cytotoxic granule-associated RNA binding						apoptosis|induction of apoptosis|regulation of nuclear mRNA splicing, via spliceosome	nucleus	nucleotide binding|poly(A) RNA binding|protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	70567170	70567170	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70567170delT								FAM136A (37950 upstream) : TGFA (107249 downstream)																																			---	---	---	---
ADD2	119	broad.mit.edu	37	2	70985994	70985994	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70985994delG	uc002sgz.2	-						ADD2_uc010fds.1_Intron|ADD2_uc002sgy.2_Intron|ADD2_uc002sha.2_Intron|ADD2_uc002shc.1_Intron|ADD2_uc002shd.1_Intron|ADD2_uc010fdu.1_Intron	NM_001617	NP_001608			adducin 2 isoform a						actin filament bundle assembly|barbed-end actin filament capping|positive regulation of protein binding	cytoplasm|F-actin capping protein complex|plasma membrane	actin filament binding|calmodulin binding|metal ion binding|protein heterodimerization activity|protein homodimerization activity|spectrin binding			ovary(2)|pancreas(1)	3																		---	---	---	---
DYSF	8291	broad.mit.edu	37	2	71786422	71786422	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71786422delC	uc002sie.2	+						DYSF_uc010feg.2_Intron|DYSF_uc010feh.2_Intron|DYSF_uc002sig.3_Intron|DYSF_uc010yqx.1_Intron|DYSF_uc010fee.2_Intron|DYSF_uc010fef.2_Intron|DYSF_uc010fei.2_Intron|DYSF_uc010fek.2_Intron|DYSF_uc010fej.2_Intron|DYSF_uc010fel.2_Intron|DYSF_uc010feo.2_Intron|DYSF_uc010fem.2_Intron|DYSF_uc010fen.2_Intron|DYSF_uc002sif.2_Intron	NM_003494	NP_003485			dysferlin isoform 8							cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)|skin(1)	7																		---	---	---	---
DYSF	8291	broad.mit.edu	37	2	71791037	71791037	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71791037delG	uc002sie.2	+						DYSF_uc010feg.2_Intron|DYSF_uc010feh.2_Intron|DYSF_uc002sig.3_Intron|DYSF_uc010yqx.1_Intron|DYSF_uc010fee.2_Intron|DYSF_uc010fef.2_Intron|DYSF_uc010fei.2_Intron|DYSF_uc010fek.2_Intron|DYSF_uc010fej.2_Intron|DYSF_uc010fel.2_Intron|DYSF_uc010feo.2_Intron|DYSF_uc010fem.2_Intron|DYSF_uc010fen.2_Intron|DYSF_uc002sif.2_Intron	NM_003494	NP_003485			dysferlin isoform 8							cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)|skin(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	71920737	71920737	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71920737delC								DYSF (6845 upstream) : CYP26B1 (435630 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	71951253	71951253	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71951253delT								DYSF (37361 upstream) : CYP26B1 (405114 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	72259201	72259201	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72259201delG								DYSF (345309 upstream) : CYP26B1 (97166 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	72334629	72334629	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72334629delT								DYSF (420737 upstream) : CYP26B1 (21738 downstream)																																			---	---	---	---
EXOC6B	23233	broad.mit.edu	37	2	72516285	72516287	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72516285_72516287delAAA	uc010fep.2	-							NM_015189	NP_056004			SEC15-like 2						protein transport|vesicle docking involved in exocytosis	exocyst				central_nervous_system(2)	2																		---	---	---	---
EXOC6B	23233	broad.mit.edu	37	2	72864919	72864923	+	Intron	DEL	AAAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72864919_72864923delAAAAA	uc010fep.2	-						EXOC6B_uc002sij.2_Intron	NM_015189	NP_056004			SEC15-like 2						protein transport|vesicle docking involved in exocytosis	exocyst				central_nervous_system(2)	2																		---	---	---	---
EXOC6B	23233	broad.mit.edu	37	2	72968233	72968233	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:72968233delA	uc010fep.2	-						EXOC6B_uc002sij.2_Intron	NM_015189	NP_056004			SEC15-like 2						protein transport|vesicle docking involved in exocytosis	exocyst				central_nervous_system(2)	2																		---	---	---	---
EXOC6B	23233	broad.mit.edu	37	2	73038160	73038160	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73038160delA	uc010fep.2	-						EXOC6B_uc002sij.2_Intron	NM_015189	NP_056004			SEC15-like 2						protein transport|vesicle docking involved in exocytosis	exocyst				central_nervous_system(2)	2																		---	---	---	---
RAB11FIP5	26056	broad.mit.edu	37	2	73308448	73308448	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73308448delG	uc002siu.3	-						RAB11FIP5_uc002sis.3_5'Flank|RAB11FIP5_uc002sit.3_Intron|uc002siv.2_5'Flank	NM_015470	NP_056285			RAB11 family interacting protein 5 (class I)						protein transport	mitochondrial outer membrane|recycling endosome membrane	gamma-tubulin binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	73513939	73513939	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73513939delT	uc002sjc.1	+	2										Homo sapiens cDNA FLJ43061 fis, clone BRTHA3008143.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	73583866	73583866	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73583866delA								EGR4 (63037 upstream) : ALMS1 (29020 downstream)																																			---	---	---	---
STAMBP	10617	broad.mit.edu	37	2	74076334	74076334	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74076334delT	uc002sjs.2	+						STAMBP_uc002sjt.2_Intron|STAMBP_uc002sju.2_Intron|STAMBP_uc002sjv.2_Intron	NM_201647	NP_964010			STAM binding protein						JAK-STAT cascade|positive regulation of cell proliferation	early endosome|membrane|nucleus	metal ion binding|metallopeptidase activity|protein binding			ovary(1)|lung(1)|breast(1)|pancreas(1)	4																		---	---	---	---
TET3	200424	broad.mit.edu	37	2	74313507	74313509	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74313507_74313509delAAA	uc002skb.3	+							NM_144993	NP_659430			tet oncogene family member 3								metal ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0																		---	---	---	---
MOBKL1B	55233	broad.mit.edu	37	2	74394389	74394389	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74394389delT	uc002skh.3	-						MOBKL1B_uc002ski.2_Intron	NM_018221	NP_060691			Mob4B protein						hippo signaling cascade		metal ion binding|protein binding				0																		---	---	---	---
CCDC142	84865	broad.mit.edu	37	2	74704250	74704251	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74704250_74704251delTT	uc002slr.2	-						CCDC142_uc002slo.2_Intron|CCDC142_uc002slq.2_Intron|CCDC142_uc002slp.2_Intron	NM_032779	NP_116168			coiled-coil domain containing 142											central_nervous_system(1)	1																		---	---	---	---
DQX1	165545	broad.mit.edu	37	2	74751023	74751023	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74751023delT	uc010yrw.1	-						DQX1_uc002smc.2_5'Flank	NM_133637	NP_598376			DEAQ box polypeptide 1 (RNA-dependent ATPase)							nucleus	ATP binding|helicase activity|nucleic acid binding			ovary(2)	2																		---	---	---	---
SEMA4F	10505	broad.mit.edu	37	2	74904563	74904563	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74904563delA	uc002sna.1	+						SEMA4F_uc010ffr.1_Intron|SEMA4F_uc002snb.1_Intron|SEMA4F_uc002snc.1_Intron	NM_004263	NP_004254			semaphorin W precursor						cell-cell signaling	endoplasmic reticulum|integral to plasma membrane	receptor activity			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
HK2	3099	broad.mit.edu	37	2	75059745	75059747	+	5'Flank	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75059745_75059747delAAA	uc002snd.2	+							NM_000189	NP_000180			hexokinase 2						apoptotic mitochondrial changes|glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane	ATP binding|glucokinase activity			ovary(1)|lung(1)	2																		---	---	---	---
HK2	3099	broad.mit.edu	37	2	75081242	75081244	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75081242_75081244delTTT	uc002snd.2	+							NM_000189	NP_000180			hexokinase 2						apoptotic mitochondrial changes|glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane	ATP binding|glucokinase activity			ovary(1)|lung(1)	2																		---	---	---	---
HK2	3099	broad.mit.edu	37	2	75094527	75094527	+	Intron	DEL	A	-	-	rs151230031		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75094527delA	uc002snd.2	+							NM_000189	NP_000180			hexokinase 2						apoptotic mitochondrial changes|glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane	ATP binding|glucokinase activity			ovary(1)|lung(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	75501069	75501069	+	IGR	DEL	T	-	-	rs79598097		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75501069delT								TACR1 (74424 upstream) : FAM176A (218375 downstream)																																			---	---	---	---
C2orf3	6936	broad.mit.edu	37	2	75900439	75900440	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75900439_75900440delAA	uc002sno.2	-						C2orf3_uc010ffs.2_Intron|C2orf3_uc002snn.2_Intron|C2orf3_uc010fft.2_Intron	NM_003203	NP_003194			hypothetical protein LOC6936						negative regulation of transcription, DNA-dependent	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	76251071	76251071	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:76251071delT								C2orf3 (312960 upstream) : LRRTM4 (723787 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	76363546	76363546	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:76363546delT								C2orf3 (425435 upstream) : LRRTM4 (611312 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	76500437	76500437	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:76500437delT								C2orf3 (562326 upstream) : LRRTM4 (474421 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	76556320	76556321	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:76556320_76556321insT								C2orf3 (618209 upstream) : LRRTM4 (418537 downstream)																																			---	---	---	---
LRRTM4	80059	broad.mit.edu	37	2	77465914	77465914	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:77465914delA	uc002snr.2	-						LRRTM4_uc002snq.2_Intron	NM_001134745	NP_001128217			leucine rich repeat transmembrane neuronal 4							integral to membrane				pancreas(3)|ovary(1)	4				Colorectal(11;0.059)														---	---	---	---
LRRTM4	80059	broad.mit.edu	37	2	77523506	77523507	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:77523506_77523507insT	uc002snr.2	-						LRRTM4_uc002snq.2_Intron	NM_001134745	NP_001128217			leucine rich repeat transmembrane neuronal 4							integral to membrane				pancreas(3)|ovary(1)	4				Colorectal(11;0.059)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	78080812	78080812	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:78080812delA								LRRTM4 (331310 upstream) : SNAR-H (101221 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	78164684	78164685	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:78164684_78164685delTT								LRRTM4 (415182 upstream) : SNAR-H (17348 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	78258665	78258665	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:78258665delA	uc002snu.3	-											Homo sapiens cDNA clone IMAGE:4816654.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	78382007	78382008	+	Intron	DEL	TT	-	-	rs71383194		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:78382007_78382008delTT	uc002snu.3	-											Homo sapiens cDNA clone IMAGE:4816654.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	79129675	79129675	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79129675delA								SNAR-H (947523 upstream) : REG3G (123151 downstream)																																			---	---	---	---
REG1A	5967	broad.mit.edu	37	2	79348504	79348504	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79348504delT	uc002snz.2	+						REG1A_uc010ffx.1_Intron|REG1A_uc010ysd.1_Intron	NM_002909	NP_002900			regenerating islet-derived 1 alpha precursor						positive regulation of cell proliferation	extracellular region	growth factor activity|sugar binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	79396225	79396226	+	IGR	DEL	CT	-	-	rs111977343		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79396225_79396226delCT								REG3A (9346 upstream) : CTNNA2 (16131 downstream)																																			---	---	---	---
CTNNA2	1496	broad.mit.edu	37	2	79584465	79584466	+	Intron	INS	-	A	A	rs143955849	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79584465_79584466insA	uc010yse.1	+							NM_004389	NP_004380			catenin, alpha 2 isoform 1						axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9																		---	---	---	---
CTNNA2	1496	broad.mit.edu	37	2	80133420	80133421	+	Intron	DEL	AC	-	-	rs67271469		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:80133420_80133421delAC	uc010ysh.1	+						CTNNA2_uc010yse.1_Intron|CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron	NM_004389	NP_004380			catenin, alpha 2 isoform 1						axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			pancreas(4)|lung(3)|breast(1)|skin(1)	9																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	81261712	81261712	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:81261712delT								CTNNA2 (385808 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	81321407	81321407	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:81321407delT								CTNNA2 (445503 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	81882853	81882854	+	IGR	INS	-	G	G	rs150432257	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:81882853_81882854insG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	81966981	81966981	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:81966981delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	82166627	82166631	+	IGR	DEL	AAAAC	-	-	rs72137105		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:82166627_82166631delAAAAC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	83263497	83263497	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:83263497delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	84194501	84194502	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84194501_84194502delTT								None (None upstream) : FUNDC2P2 (323304 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	84354796	84354796	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84354796delT								None (None upstream) : FUNDC2P2 (163010 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	84427422	84427423	+	IGR	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84427422_84427423delTC								None (None upstream) : FUNDC2P2 (90383 downstream)																																			---	---	---	---
DNAH6	1768	broad.mit.edu	37	2	84777275	84777275	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84777275delA	uc010fgb.2	+						DNAH6_uc002soo.2_Intron|DNAH6_uc002sop.2_Intron	NM_001370	NP_001361			dynein, axonemal, heavy polypeptide 6						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			central_nervous_system(1)	1																		---	---	---	---
DNAH6	1768	broad.mit.edu	37	2	84912421	84912422	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84912421_84912422delTT	uc010fgb.2	+						DNAH6_uc002sor.2_Intron	NM_001370	NP_001361			dynein, axonemal, heavy polypeptide 6						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			central_nervous_system(1)	1																		---	---	---	---
C2orf89	129293	broad.mit.edu	37	2	85097203	85097203	+	Intron	DEL	T	-	-	rs35902901		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85097203delT	uc010ysl.1	-						C2orf89_uc002sou.3_Intron|C2orf89_uc010fgc.1_Intron	NM_001080824	NP_001074293			hypothetical protein LOC129293 precursor							integral to membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	85115030	85115030	+	IGR	DEL	A	-	-	rs113555175		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85115030delA								C2orf89 (6778 upstream) : TMSB10 (17733 downstream)																																			---	---	---	---
KCMF1	56888	broad.mit.edu	37	2	85255969	85255969	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85255969delA	uc002sox.3	+							NM_020122	NP_064507			potassium channel modulatory factor 1							intracellular	ligase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	85287455	85287456	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85287455_85287456delTT								KCMF1 (861 upstream) : TCF7L1 (73278 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	85291059	85291062	+	IGR	DEL	CACA	-	-	rs10533673		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85291059_85291062delCACA								KCMF1 (4465 upstream) : TCF7L1 (69672 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	85325799	85325799	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85325799delA								KCMF1 (39205 upstream) : TCF7L1 (34935 downstream)																																			---	---	---	---
ELMOD3	84173	broad.mit.edu	37	2	85615287	85615287	+	Intron	DEL	T	-	-	rs6707822		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85615287delT	uc002spf.3	+						ELMOD3_uc002spg.3_Intron|ELMOD3_uc002sph.3_Intron|ELMOD3_uc010ysn.1_Intron|ELMOD3_uc010yso.1_Intron|ELMOD3_uc010ysp.1_Intron	NM_001135021	NP_001128493			ELMO/CED-12 domain containing 3 isoform b						phagocytosis	cytoskeleton				ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	85751882	85751882	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85751882delT								SH2D6 (87732 upstream) : MAT2A (14406 downstream)																																			---	---	---	---
VAMP5	10791	broad.mit.edu	37	2	85814385	85814387	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85814385_85814387delTTT	uc002spu.1	+							NM_006634	NP_006625			vesicle-associated membrane protein 5						cell differentiation|vesicle-mediated transport	endomembrane system					0																		---	---	---	---
USP39	10713	broad.mit.edu	37	2	85851477	85851477	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85851477delT	uc002sqe.2	+						USP39_uc002sqb.2_Intron|USP39_uc010ysu.1_Intron|USP39_uc010ysv.1_Intron|USP39_uc010fgn.1_Intron|USP39_uc002sqf.2_Intron|USP39_uc002sqg.2_Intron|USP39_uc010fgo.2_Intron	NM_006590	NP_006581			ubiquitin specific protease 39						spliceosome assembly|ubiquitin-dependent protein catabolic process	nucleus	protein binding|ubiquitin thiolesterase activity|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	85899144	85899144	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85899144delA								SFTPB (3770 upstream) : GNLY (22270 downstream)																																			---	---	---	---
PTCD3	55037	broad.mit.edu	37	2	86358372	86358372	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86358372delT	uc002sqw.2	+						PTCD3_uc002sqx.1_Intron	NM_017952	NP_060422			pentatricopeptide repeat domain 3 precursor							mitochondrion	protein binding			ovary(1)	1																		---	---	---	---
REEP1	65055	broad.mit.edu	37	2	86464974	86464974	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86464974delA	uc002srh.3	-						REEP1_uc010ytg.1_Intron|REEP1_uc010yth.1_Intron|REEP1_uc010yti.1_Intron	NM_022912	NP_075063			receptor accessory protein 1 isoform 2						cell death|protein insertion into membrane	integral to membrane|mitochondrial membrane	olfactory receptor binding				0																		---	---	---	---
RMND5A	64795	broad.mit.edu	37	2	86971101	86971104	+	Intron	DEL	AAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86971101_86971104delAAAA	uc010ytm.1	+						RMND5A_uc002srs.3_Intron|RMND5A_uc002srr.2_Intron	NM_022780	NP_073617			required for meiotic nuclear division 5 homolog											ovary(1)|skin(1)	2																		---	---	---	---
RMND5A	64795	broad.mit.edu	37	2	87305593	87305593	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87305593delT	uc002srs.3	+						LOC285074_uc010fgw.2_5'Flank|LOC285074_uc002ssf.3_5'Flank					SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	88495084	88495084	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88495084delA								THNSL2 (8939 upstream) : FOXI3 (252642 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	88553744	88553744	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88553744delA								THNSL2 (67599 upstream) : FOXI3 (193982 downstream)																																			---	---	---	---
EIF2AK3	9451	broad.mit.edu	37	2	88892666	88892667	+	Intron	DEL	AT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88892666_88892667delAT	uc002stc.3	-							NM_004836	NP_004827			eukaryotic translation initiation factor 2-alpha						activation of caspase activity|bone mineralization|calcium-mediated signaling|chondrocyte development|endocrine pancreas development|endoplasmic reticulum organization|endoplasmic reticulum unfolded protein response|ER overload response|insulin secretion|insulin-like growth factor receptor signaling pathway|negative regulation of myelination|negative regulation of translational initiation in response to stress|protein autophosphorylation|protein homooligomerization	endoplasmic reticulum membrane|integral to membrane	ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|identical protein binding			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	89152888	89152888	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89152888delT								FLJ40330 (46763 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	89277834	89277834	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89277834delT	uc010ytr.1	-						uc002stl.2_Intron					Parts of antibodies, mostly variable regions.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	89330359	89330360	+	Intron	DEL	TT	-	-	rs66530729		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89330359_89330360delTT	uc010ytr.1	-						uc002stl.2_Intron					Parts of antibodies, mostly variable regions.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	89407971	89407974	+	Intron	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89407971_89407974delTTTT	uc010ytr.1	-						uc002stl.2_Intron					Parts of antibodies, mostly variable regions.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	90011388	90011388	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90011388delT	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	90371692	90371693	+	Intron	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90371692_90371693delGA	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	90417245	90417247	+	Intron	DEL	GAG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90417245_90417247delGAG	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	90481670	90481670	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90481670delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	91696118	91696119	+	IGR	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91696118_91696119delTC								None (None upstream) : LOC654342 (109073 downstream)																																			---	---	---	---
LOC654342	654342	broad.mit.edu	37	2	91836306	91836307	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91836306_91836307insT	uc002sts.3	-						LOC654342_uc002stt.2_Intron|LOC654342_uc010yub.1_Intron					Homo sapiens cDNA clone IMAGE:4801360.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	91973598	91973600	+	IGR	DEL	AGA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91973598_91973600delAGA								GGT8P (3445 upstream) : FKSG73 (155559 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	92041822	92041823	+	IGR	DEL	AC	-	-	rs74533162		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92041822_92041823delAC								GGT8P (71669 upstream) : FKSG73 (87336 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	92071842	92071842	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92071842delT								GGT8P (101689 upstream) : FKSG73 (57317 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	92089509	92089509	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92089509delA								GGT8P (119356 upstream) : FKSG73 (39650 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	95669165	95669165	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95669165delA								TEKT4 (126597 upstream) : MAL (22314 downstream)																																			---	---	---	---
KCNIP3	30818	broad.mit.edu	37	2	96039793	96039793	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96039793delG	uc002sup.2	+						KCNIP3_uc002suq.2_Intron	NM_013434	NP_038462			Kv channel interacting protein 3 isoform 1						apoptosis|signal transduction|transcription, DNA-dependent	endoplasmic reticulum|Golgi apparatus|nucleus|plasma membrane	calcium ion binding|DNA binding|potassium channel activity|transcription corepressor activity|voltage-gated ion channel activity			breast(2)|ovary(1)	3				READ - Rectum adenocarcinoma(193;0.13)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	96061337	96061337	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96061337delC								KCNIP3 (9513 upstream) : FAHD2A (7111 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	96183238	96183239	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96183238_96183239delTT								FAHD2A (104360 upstream) : TRIM43 (74527 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	96205466	96205466	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96205466delA								FAHD2A (126588 upstream) : TRIM43 (52300 downstream)																																			---	---	---	---
TRIM43	129868	broad.mit.edu	37	2	96265407	96265408	+	3'UTR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96265407_96265408insT	uc002suv.2	+	7						NM_138800	NP_620155			tripartite motif-containing 43							intracellular	zinc ion binding			ovary(1)	1																		---	---	---	---
SNRNP200	23020	broad.mit.edu	37	2	96972450	96972450	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96972450delT	uc002svu.2	-							NM_014014	NP_054733			activating signal cointegrator 1 complex subunit							catalytic step 2 spliceosome|nucleoplasm|U5 snRNP	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			ovary(5)|skin(4)|large_intestine(1)	10																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	97052975	97052975	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97052975delT								NCAPH (11701 upstream) : NEURL3 (110410 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	97072058	97072058	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97072058delT								NCAPH (30784 upstream) : NEURL3 (91327 downstream)																																			---	---	---	---
LMAN2L	81562	broad.mit.edu	37	2	97373577	97373577	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97373577delA	uc002swu.2	-						LMAN2L_uc002swv.2_Intron|LMAN2L_uc010yut.1_Intron|LMAN2L_uc010yuu.1_Intron|LMAN2L_uc010yuv.1_Intron|LMAN2L_uc010yuw.1_Intron|LMAN2L_uc002sww.2_Intron|LMAN2L_uc010yux.1_Intron	NM_030805	NP_110432			lectin, mannose-binding 2-like isoform 2						ER to Golgi vesicle-mediated transport|protein folding|protein transport	endoplasmic reticulum membrane|ER to Golgi transport vesicle|Golgi membrane|integral to membrane	mannose binding|metal ion binding				0																		---	---	---	---
FAM178B	51252	broad.mit.edu	37	2	97570791	97570791	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97570791delA	uc002sxl.3	-						FAM178B_uc002sxk.3_Intron	NM_001122646	NP_001116118			hypothetical protein LOC51252 isoform A												0																		---	---	---	---
ANKRD36B	57730	broad.mit.edu	37	2	98129604	98129605	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98129604_98129605delAA	uc010yvc.1	-						ANKRD36B_uc010fid.1_5'Flank|ANKRD36B_uc002sxx.1_5'Flank|ANKRD36B_uc010yvd.1_Intron	NM_025190	NP_079466			ankyrin repeat domain 36B												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	98252866	98252866	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98252866delA								ANKRD36B (46438 upstream) : COX5B (9655 downstream)																																			---	---	---	---
TMEM131	23505	broad.mit.edu	37	2	98409753	98409753	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98409753delT	uc002syh.3	-							NM_015348	NP_056163			RW1 protein							integral to membrane				ovary(4)|central_nervous_system(2)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	98628253	98628253	+	IGR	DEL	C	-	-	rs112561889	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98628253delC								TMEM131 (15899 upstream) : VWA3B (75342 downstream)																																			---	---	---	---
VWA3B	200403	broad.mit.edu	37	2	98799913	98799913	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98799913delA	uc002syo.2	+						VWA3B_uc010yvh.1_Intron|VWA3B_uc002syj.2_Intron|VWA3B_uc002syk.1_Intron|VWA3B_uc002syl.1_Intron|VWA3B_uc002sym.2_Intron|VWA3B_uc002syn.1_Intron|VWA3B_uc010yvi.1_Intron	NM_144992	NP_659429			von Willebrand factor A domain containing 3B											ovary(3)|large_intestine(2)|skin(1)	6																		---	---	---	---
INPP4A	3631	broad.mit.edu	37	2	99183010	99183010	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99183010delG	uc002syy.2	+						INPP4A_uc010yvj.1_Intron|INPP4A_uc010yvk.1_Intron|INPP4A_uc002syx.2_Intron|INPP4A_uc010fik.2_Intron	NM_001134224	NP_001127696			inositol polyphosphate-4-phosphatase, type 1						signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			kidney(1)	1																		---	---	---	---
MGAT4A	11320	broad.mit.edu	37	2	99315969	99315971	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99315969_99315971delTTT	uc002sze.2	-						MGAT4A_uc010fil.2_Intron	NM_012214	NP_036346			alpha-1,3-mannosyl-glycoprotein						N-glycan processing|post-translational protein modification|protein N-linked glycosylation via asparagine	extracellular region|Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity|metal ion binding			skin(1)	1																		---	---	---	---
MGAT4A	11320	broad.mit.edu	37	2	99333367	99333368	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99333367_99333368insA	uc002sze.2	-						MGAT4A_uc010fil.2_Intron	NM_012214	NP_036346			alpha-1,3-mannosyl-glycoprotein						N-glycan processing|post-translational protein modification|protein N-linked glycosylation via asparagine	extracellular region|Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity|metal ion binding			skin(1)	1																		---	---	---	---
C2orf55	343990	broad.mit.edu	37	2	99443770	99443770	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99443770delT	uc002szf.1	-							NM_207362	NP_997245			hypothetical protein LOC343990												0																		---	---	---	---
EIF5B	9669	broad.mit.edu	37	2	99999545	99999547	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99999545_99999547delTTT	uc002tab.2	+							NM_015904	NP_056988			eukaryotic translation initiation factor 5B						regulation of translational initiation	cytosol	GTP binding|GTPase activity|protein binding|translation initiation factor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
AFF3	3899	broad.mit.edu	37	2	100185025	100185025	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100185025delA	uc002tag.2	-						AFF3_uc002taf.2_Intron	NM_002285	NP_002276			AF4/FMR2 family, member 3 isoform 1						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6																		---	---	---	---
AFF3	3899	broad.mit.edu	37	2	100508291	100508291	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100508291delT	uc002tag.2	-						AFF3_uc002taf.2_Intron|AFF3_uc010fiq.1_Intron|AFF3_uc010yvr.1_Intron|AFF3_uc002tah.1_Intron|AFF3_uc010fir.1_Intron	NM_002285	NP_002276			AF4/FMR2 family, member 3 isoform 1						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	100942656	100942657	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100942656_100942657delAA								LONRF2 (3461 upstream) : CHST10 (65666 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	101218659	101218659	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101218659delA								PDCL3 (25458 upstream) : NPAS2 (217954 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	101252596	101252596	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101252596delG								PDCL3 (59395 upstream) : NPAS2 (184017 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	101263603	101263604	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101263603_101263604delTT								PDCL3 (70402 upstream) : NPAS2 (173009 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	101383814	101383815	+	IGR	DEL	AT	-	-	rs150359782		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101383814_101383815delAT								PDCL3 (190613 upstream) : NPAS2 (52798 downstream)																																			---	---	---	---
NPAS2	4862	broad.mit.edu	37	2	101584647	101584647	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101584647delT	uc002tap.1	+						NPAS2_uc010yvt.1_Intron	NM_002518	NP_002509			neuronal PAS domain protein 2						central nervous system development|positive regulation of transcription from RNA polymerase II promoter|rhythmic process	transcription factor complex	DNA binding|Hsp90 protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(3)|upper_aerodigestive_tract(1)	4																		---	---	---	---
TBC1D8	11138	broad.mit.edu	37	2	101640087	101640087	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101640087delT	uc010fiv.2	-						TBC1D8_uc002tau.3_Intron	NM_001102426	NP_001095896			TBC1 domain family, member 8						blood circulation|positive regulation of cell proliferation	intracellular|membrane	calcium ion binding|Rab GTPase activator activity			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	101808473	101808474	+	IGR	DEL	TT	-	-	rs111957502		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101808473_101808474delTT								TBC1D8 (40627 upstream) : C2orf29 (60871 downstream)																																			---	---	---	---
RNF149	284996	broad.mit.edu	37	2	101913995	101913995	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101913995delT	uc002taz.1	-						RNF149_uc002tax.1_Intron	NM_173647	NP_775918			ring finger protein 149 precursor							integral to membrane	ligase activity|zinc ion binding			ovary(1)|breast(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	102100039	102100039	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102100039delT								RFX8 (8874 upstream) : MAP4K4 (214449 downstream)																																			---	---	---	---
MAP4K4	9448	broad.mit.edu	37	2	102448112	102448112	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102448112delT	uc002tbg.2	+						MAP4K4_uc002tbc.2_Intron|MAP4K4_uc002tbd.2_Intron|MAP4K4_uc002tbe.2_Intron|MAP4K4_uc002tbf.2_Intron|MAP4K4_uc010yvy.1_Intron|MAP4K4_uc002tbh.2_Intron|MAP4K4_uc002tbi.2_Intron|MAP4K4_uc010yvz.1_Intron|MAP4K4_uc010fiw.1_Intron|MAP4K4_uc002tbj.1_Intron	NM_145687	NP_663720			mitogen-activated protein kinase kinase kinase						intracellular protein kinase cascade|regulation of JNK cascade|response to stress	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			stomach(1)|lung(1)|central_nervous_system(1)|skin(1)	4																OREG0014845	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
MAP4K4	9448	broad.mit.edu	37	2	102452476	102452476	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102452476delT	uc002tbg.2	+						MAP4K4_uc002tbc.2_Intron|MAP4K4_uc002tbd.2_Intron|MAP4K4_uc002tbe.2_Intron|MAP4K4_uc002tbf.2_Intron|MAP4K4_uc010yvy.1_Intron|MAP4K4_uc002tbh.2_Intron|MAP4K4_uc002tbi.2_Intron|MAP4K4_uc010yvz.1_Intron|MAP4K4_uc010fiw.1_Intron|MAP4K4_uc002tbj.1_Intron	NM_145687	NP_663720			mitogen-activated protein kinase kinase kinase						intracellular protein kinase cascade|regulation of JNK cascade|response to stress	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			stomach(1)|lung(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
MAP4K4	9448	broad.mit.edu	37	2	102493939	102493941	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102493939_102493941delTTT	uc002tbg.2	+						MAP4K4_uc002tbc.2_Intron|MAP4K4_uc002tbd.2_Intron|MAP4K4_uc002tbe.2_Intron|MAP4K4_uc002tbf.2_Intron|MAP4K4_uc010yvy.1_Intron|MAP4K4_uc002tbh.2_Intron|MAP4K4_uc002tbi.2_Intron|MAP4K4_uc010yvz.1_Intron|MAP4K4_uc002tbk.2_Intron|MAP4K4_uc002tbl.2_Intron	NM_145687	NP_663720			mitogen-activated protein kinase kinase kinase						intracellular protein kinase cascade|regulation of JNK cascade|response to stress	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			stomach(1)|lung(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	102591965	102591965	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102591965delC								MAP4K4 (80814 upstream) : IL1R2 (16341 downstream)																																			---	---	---	---
IL1RL2	8808	broad.mit.edu	37	2	102835403	102835403	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102835403delT	uc002tbs.2	+						IL1RL2_uc002tbt.2_Intron	NM_003854	NP_003845			interleukin 1 receptor-like 2 precursor						cellular defense response|innate immune response	integral to plasma membrane	interleukin-1, Type I, activating receptor activity			ovary(2)	2																		---	---	---	---
IL1RL2	8808	broad.mit.edu	37	2	102851247	102851247	+	Intron	DEL	A	-	-	rs72526182		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102851247delA	uc002tbs.2	+						IL1RL2_uc002tbt.2_Intron	NM_003854	NP_003845			interleukin 1 receptor-like 2 precursor						cellular defense response|innate immune response	integral to plasma membrane	interleukin-1, Type I, activating receptor activity			ovary(2)	2																		---	---	---	---
SLC9A2	6549	broad.mit.edu	37	2	103293758	103293759	+	Intron	DEL	AA	-	-	rs72353099		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103293758_103293759delAA	uc002tca.2	+							NM_003048	NP_003039			solute carrier family 9 (sodium/hydrogen							integral to membrane|plasma membrane	sodium:hydrogen antiporter activity			central_nervous_system(3)|skin(3)|breast(2)	8																		---	---	---	---
MFSD9	84804	broad.mit.edu	37	2	103343084	103343085	+	Intron	DEL	CA	-	-	rs112803412		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103343084_103343085delCA	uc002tcb.2	-						MFSD9_uc010fja.2_Intron	NM_032718	NP_116107			major facilitator superfamily domain containing						transmembrane transport	integral to membrane|plasma membrane	transporter activity			ovary(2)|breast(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	103500138	103500138	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103500138delG								TMEM182 (66002 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	103778982	103778982	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103778982delC								TMEM182 (344846 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	103897035	103897035	+	IGR	DEL	A	-	-	rs75660767		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103897035delA								TMEM182 (462899 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	103913375	103913376	+	IGR	DEL	CA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103913375_103913376delCA								TMEM182 (479239 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	104160544	104160544	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:104160544delT								TMEM182 (726408 upstream) : LOC150568 (890261 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	105019779	105019779	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105019779delG	uc010ywf.1	-											SubName: Full=cDNA FLJ59030;																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	105032762	105032762	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105032762delA								None (None upstream) : LOC150568 (18043 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	105155259	105155259	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105155259delT								LOC150568 (26045 upstream) : POU3F3 (316710 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	106246607	106246607	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106246607delA								FHL2 (191377 upstream) : NCK2 (114747 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	106675579	106675579	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106675579delT								NCK2 (164853 upstream) : C2orf40 (6534 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	106950469	106950470	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106950469_106950470insT								UXS1 (139674 upstream) : PLGLA (52299 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	107198126	107198127	+	IGR	DEL	GT	-	-	rs67277155		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107198126_107198127delGT								RGPD3 (113325 upstream) : ST6GAL2 (219931 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	107315190	107315190	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107315190delA								RGPD3 (230389 upstream) : ST6GAL2 (102868 downstream)																																			---	---	---	---
ST6GAL2	84620	broad.mit.edu	37	2	107476338	107476338	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107476338delA	uc002tdq.2	-						ST6GAL2_uc002tdr.2_Intron|ST6GAL2_uc002tds.3_Intron	NM_001142351	NP_001135823			ST6 beta-galactosamide						growth|multicellular organismal development|oligosaccharide metabolic process|protein glycosylation	Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,6-sialyltransferase activity			pancreas(6)|ovary(4)|skin(1)	11																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	107777900	107777900	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107777900delT								ST6GAL2 (274337 upstream) : LOC729121 (661620 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	107807026	107807026	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107807026delA								ST6GAL2 (303463 upstream) : LOC729121 (632494 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	107887917	107887917	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107887917delT								ST6GAL2 (384354 upstream) : LOC729121 (551603 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	108094829	108094829	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108094829delA								ST6GAL2 (591266 upstream) : LOC729121 (344691 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	108160522	108160522	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108160522delA								ST6GAL2 (656959 upstream) : LOC729121 (278998 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	108592630	108592630	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108592630delA								RGPD4 (83631 upstream) : SLC5A7 (10365 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	108635237	108635237	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108635237delA								SLC5A7 (4798 upstream) : SULT1C3 (228414 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	108655629	108655629	+	IGR	DEL	A	-	-	rs79116185		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108655629delA								SLC5A7 (25190 upstream) : SULT1C3 (208022 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	108940582	108940584	+	IGR	DEL	AAA	-	-	rs111955452		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:108940582_108940584delAAA								SULT1C2 (14212 upstream) : SULT1C4 (53837 downstream)																																			---	---	---	---
LIMS1	3987	broad.mit.edu	37	2	109167414	109167415	+	Intron	DEL	AA	-	-	rs77711513		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109167414_109167415delAA	uc002tef.2	+							NM_004987	NP_004978			LIM and senescent cell antigen-like domains 1						cell aging|cell junction assembly|cellular response to transforming growth factor beta stimulus|negative regulation of transcription, DNA-dependent	cytosol|focal adhesion|perinuclear region of cytoplasm	protein binding|zinc ion binding				0																		---	---	---	---
LIMS1	3987	broad.mit.edu	37	2	109181282	109181282	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109181282delA	uc002tef.2	+							NM_004987	NP_004978			LIM and senescent cell antigen-like domains 1						cell aging|cell junction assembly|cellular response to transforming growth factor beta stimulus|negative regulation of transcription, DNA-dependent	cytosol|focal adhesion|perinuclear region of cytoplasm	protein binding|zinc ion binding				0																		---	---	---	---
LIMS1	3987	broad.mit.edu	37	2	109276713	109276713	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109276713delA	uc002teg.2	+						LIMS1_uc002tef.2_Intron|LIMS1_uc002teh.2_Intron|LIMS1_uc002tei.2_Intron|LIMS1_uc002tej.2_Intron|LIMS1_uc002tek.3_Intron	NM_004987	NP_004978			LIM and senescent cell antigen-like domains 1						cell aging|cell junction assembly|cellular response to transforming growth factor beta stimulus|negative regulation of transcription, DNA-dependent	cytosol|focal adhesion|perinuclear region of cytoplasm	protein binding|zinc ion binding				0																		---	---	---	---
CCDC138	165055	broad.mit.edu	37	2	109490006	109490006	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109490006delA	uc002ten.1	+	14	1853	c.1793delA	c.(1792-1794)GAAfs	p.E598fs	CCDC138_uc002teo.1_Intron|CCDC138_uc002tep.1_Frame_Shift_Del_p.E282fs|CCDC138_uc010fjm.1_Intron	NM_144978	NP_659415	Q96M89	CC138_HUMAN	coiled-coil domain containing 138	598											0																		---	---	---	---
EDAR	10913	broad.mit.edu	37	2	109577059	109577059	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109577059delT	uc002teq.3	-						EDAR_uc010fjn.2_Intron|EDAR_uc010yws.1_Intron	NM_022336	NP_071731			ectodysplasin A receptor precursor						apoptosis|cell differentiation	integral to membrane	protein binding|transmembrane receptor activity			skin(1)	1																		---	---	---	---
SH3RF3	344558	broad.mit.edu	37	2	110066467	110066467	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110066467delT	uc010ywt.1	+							NM_001099289	NP_001092759			SH3 domain containing ring finger 3								zinc ion binding			ovary(1)	1																		---	---	---	---
NPHP1	4867	broad.mit.edu	37	2	110886672	110886673	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110886672_110886673delAA	uc002tfn.3	-						NPHP1_uc002tfm.3_Intron|NPHP1_uc002tfl.3_Intron|NPHP1_uc002tfo.3_Intron|NPHP1_uc010ywx.1_Intron|NPHP1_uc010fjv.1_Intron	NM_207181	NP_997064			nephrocystin 1 isoform 2						actin cytoskeleton organization|cell projection organization|cell-cell adhesion|excretion|retina development in camera-type eye|signal transduction|spermatid differentiation|visual behavior	adherens junction|cell-cell junction|cilium axoneme|cytoplasm|cytoskeleton|motile cilium|photoreceptor connecting cilium	protein binding|structural molecule activity			ovary(2)	2																		---	---	---	---
ACOXL	55289	broad.mit.edu	37	2	111588116	111588117	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:111588116_111588117delTT	uc002tgr.3	+						ACOXL_uc010fkc.2_Intron|ACOXL_uc010yxk.1_Intron	NM_001105516	NP_001098986			acyl-Coenzyme A oxidase-like 2						fatty acid beta-oxidation	peroxisome	acyl-CoA dehydrogenase activity|acyl-CoA oxidase activity				0																		---	---	---	---
LOC541471	541471	broad.mit.edu	37	2	112053455	112053465	+	Intron	DEL	TTTTTTTTTTT	-	-	rs113210524		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112053455_112053465delTTTTTTTTTTT	uc002the.2	-											Homo sapiens hypothetical LOC541471, mRNA (cDNA clone IMAGE:3459303).												0																		---	---	---	---
ANAPC1	64682	broad.mit.edu	37	2	112576822	112576822	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112576822delA	uc002thi.2	-							NM_022662	NP_073153			anaphase promoting complex subunit 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm				skin(2)	2																		---	---	---	---
ANAPC1	64682	broad.mit.edu	37	2	112610713	112610713	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112610713delT	uc002thi.2	-							NM_022662	NP_073153			anaphase promoting complex subunit 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm				skin(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	112647861	112647863	+	IGR	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112647861_112647863delAAA								ANAPC1 (6120 upstream) : MERTK (8328 downstream)																																			---	---	---	---
MERTK	10461	broad.mit.edu	37	2	112778786	112778786	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112778786delA	uc002thk.1	+						MERTK_uc002thl.1_Intron	NM_006343	NP_006334			MER receptor tyrosine kinase precursor						cell surface receptor linked signaling pathway|cell-cell signaling|leukocyte migration	integral to plasma membrane|soluble fraction	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(6)|upper_aerodigestive_tract(1)|stomach(1)|kidney(1)	9																		---	---	---	---
FBLN7	129804	broad.mit.edu	37	2	112919362	112919362	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112919362delT	uc002tho.1	+						FBLN7_uc002thn.2_Intron|FBLN7_uc010fki.1_Intron|FBLN7_uc010fkj.1_Intron	NM_153214	NP_694946			fibulin 7 isoform 1						cell adhesion	proteinaceous extracellular matrix	calcium ion binding|heparin binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
PSD4	23550	broad.mit.edu	37	2	113935794	113935794	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113935794delA	uc002tjc.2	+						PSD4_uc002tjd.2_Intron|PSD4_uc002tje.2_Intron	NM_012455	NP_036587			pleckstrin and Sec7 domain containing 4						regulation of ARF protein signal transduction	cytoplasm|plasma membrane	ARF guanyl-nucleotide exchange factor activity			ovary(2)	2																		---	---	---	---
WASH2P	375260	broad.mit.edu	37	2	114339317	114339318	+	5'Flank	DEL	CC	-	-	rs114363417		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114339317_114339318delCC	uc002tka.2	+						WASH2P_uc002tkb.2_5'Flank	NR_024077				Homo sapiens cDNA FLJ75027 complete cds, highly similar to Homo sapiens CXYorf1-related protein (MGC52000), mRNA.												0																		---	---	---	---
RABL2A	11159	broad.mit.edu	37	2	114388483	114388484	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114388483_114388484insT	uc002tkn.3	+						RABL2A_uc010flb.2_Intron|RABL2A_uc002tkl.3_Intron|RABL2A_uc002tkm.3_Intron|RABL2A_uc002tks.3_Intron|RABL2A_uc002tkr.2_Intron|RABL2A_uc002tkp.3_Intron|RABL2A_uc002tkq.2_Intron	NM_007082	NP_009013			RAB, member of RAS oncogene family-like 2A						small GTPase mediated signal transduction		GTP binding|GTPase activity			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	114986206	114986207	+	IGR	DEL	TG	-	-	rs10178287	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114986206_114986207delTG								ACTR3 (270039 upstream) : DPP10 (213692 downstream)																																			---	---	---	---
DPP10	57628	broad.mit.edu	37	2	115410603	115410610	+	Intron	DEL	GAGTGTGT	-	-	rs13387978	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:115410603_115410610delGAGTGTGT	uc002tla.1	+						DPP10_uc002tlb.1_Intron	NM_020868	NP_065919			dipeptidyl peptidase 10 isoform long						proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10																		---	---	---	---
DPP10	57628	broad.mit.edu	37	2	115754904	115754904	+	Intron	DEL	A	-	-	rs67289472		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:115754904delA	uc002tla.1	+						DPP10_uc002tlb.1_Intron	NM_020868	NP_065919			dipeptidyl peptidase 10 isoform long						proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10																		---	---	---	---
DPP10	57628	broad.mit.edu	37	2	116165250	116165250	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116165250delA	uc002tla.1	+						DPP10_uc002tlb.1_Intron|DPP10_uc002tlc.1_Intron|DPP10_uc002tle.2_Intron|DPP10_uc002tlf.1_Intron	NM_020868	NP_065919			dipeptidyl peptidase 10 isoform long						proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10																		---	---	---	---
DPP10	57628	broad.mit.edu	37	2	116415890	116415890	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116415890delT	uc002tla.1	+						DPP10_uc002tlb.1_Intron|DPP10_uc002tlc.1_Intron|DPP10_uc002tle.2_Intron|DPP10_uc002tlf.1_Intron	NM_020868	NP_065919			dipeptidyl peptidase 10 isoform long						proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10																		---	---	---	---
DPP10	57628	broad.mit.edu	37	2	116443955	116443955	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116443955delA	uc002tla.1	+						DPP10_uc002tlb.1_Intron|DPP10_uc002tlc.1_Intron|DPP10_uc002tle.2_Intron|DPP10_uc002tlf.1_Intron	NM_020868	NP_065919			dipeptidyl peptidase 10 isoform long						proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	117308061	117308061	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:117308061delA								DPP10 (706125 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	117515711	117515711	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:117515711delT								DPP10 (913775 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	117849609	117849609	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:117849609delT								None (None upstream) : DDX18 (722646 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	118165512	118165513	+	IGR	INS	-	TTCT	TTCT	rs142850732	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:118165512_118165513insTTCT								None (None upstream) : DDX18 (406742 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	119280426	119280426	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119280426delA								INSIG2 (412830 upstream) : EN1 (319322 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	119305674	119305676	+	IGR	DEL	AAA	-	-	rs34683946		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119305674_119305676delAAA								INSIG2 (438078 upstream) : EN1 (294072 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	119566424	119566424	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119566424delA								INSIG2 (698828 upstream) : EN1 (33324 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	119969570	119969570	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:119969570delT								C1QL2 (53099 upstream) : STEAP3 (11814 downstream)																																			---	---	---	---
TMEM177	80775	broad.mit.edu	37	2	120462156	120462156	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120462156delA	uc002tme.2	+											Homo sapiens cDNA FLJ32751 fis, clone TESTI2001621.							integral to membrane				ovary(1)	1	Colorectal(110;0.196)																	---	---	---	---
PTPN4	5775	broad.mit.edu	37	2	120707446	120707447	+	Intron	INS	-	AC	AC	rs139007582	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120707446_120707447insAC	uc002tmf.1	+						PTPN4_uc010flj.1_Intron|PTPN4_uc010yyr.1_Intron	NM_002830	NP_002821			protein tyrosine phosphatase, non-receptor type							cytoplasm|cytoskeleton|internal side of plasma membrane	cytoskeletal protein binding|non-membrane spanning protein tyrosine phosphatase activity			ovary(2)	2					Alendronate(DB00630)													---	---	---	---
EPB41L5	57669	broad.mit.edu	37	2	120779217	120779217	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120779217delA	uc002tmg.2	+						EPB41L5_uc010flk.2_Intron|EPB41L5_uc010fll.2_Intron|EPB41L5_uc002tmh.3_Intron	NM_020909	NP_065960			erythrocyte membrane protein band 4.1 like 5							cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding			ovary(1)	1																		---	---	---	---
EPB41L5	57669	broad.mit.edu	37	2	120857801	120857801	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120857801delT	uc002tmg.2	+						EPB41L5_uc010flk.2_Intron|EPB41L5_uc010fll.2_Intron|EPB41L5_uc002tmh.3_Intron|EPB41L5_uc010flm.2_Intron	NM_020909	NP_065960			erythrocyte membrane protein band 4.1 like 5							cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding			ovary(1)	1																		---	---	---	---
RALB	5899	broad.mit.edu	37	2	121004738	121004738	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121004738delG	uc010yys.1	+							NM_002881	NP_002872			v-ral simian leukemia viral oncogene homolog B						apoptosis|cell cycle|cytokinesis|nerve growth factor receptor signaling pathway|Ras protein signal transduction|regulation of exocyst assembly|regulation of exocyst localization	cytosol|midbody|plasma membrane	GTP binding|GTPase activity|protein binding			lung(3)	3		Prostate(154;0.122)																---	---	---	---
RALB	5899	broad.mit.edu	37	2	121047045	121047045	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121047045delT	uc002tmk.2	+						RALB_uc010yys.1_Intron|RALB_uc002tml.2_Intron|RALB_uc002tmm.2_Intron|RALB_uc010yyt.1_Intron	NM_002881	NP_002872			v-ral simian leukemia viral oncogene homolog B						apoptosis|cell cycle|cytokinesis|nerve growth factor receptor signaling pathway|Ras protein signal transduction|regulation of exocyst assembly|regulation of exocyst localization	cytosol|midbody|plasma membrane	GTP binding|GTPase activity|protein binding			lung(3)	3		Prostate(154;0.122)																---	---	---	---
Unknown	0	broad.mit.edu	37	2	121130589	121130590	+	IGR	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121130589_121130590delAC								INHBB (21206 upstream) : LOC84931 (91321 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	121352394	121352394	+	IGR	DEL	A	-	-	rs146893532		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121352394delA								LOC84931 (128469 upstream) : GLI2 (140805 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	121464907	121464907	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:121464907delG								LOC84931 (240982 upstream) : GLI2 (28292 downstream)																																			---	---	---	---
MKI67IP	84365	broad.mit.edu	37	2	122484977	122484977	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122484977delT	uc002tnk.2	-	7					uc002tnj.1_Intron	NM_032390	NP_115766			MKI67 interacting nucleolar phosphoprotein						protein complex assembly|rRNA metabolic process|rRNA transcription	condensed nuclear chromosome|cytoplasm|nucleolus|nucleoplasm	nucleotide binding|protein binding|RNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	122562015	122562016	+	IGR	INS	-	TG	TG	rs149545942	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122562015_122562016insTG								TSN (36589 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	122565296	122565297	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122565296_122565297delTT								TSN (39870 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	122683563	122683563	+	IGR	DEL	A	-	-	rs148215240		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122683563delA								TSN (158137 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	122752769	122752769	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122752769delT								TSN (227343 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	123183410	123183413	+	IGR	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:123183410_123183413delTTTT								TSN (657984 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	123240272	123240273	+	IGR	DEL	TT	-	-	rs78149157		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:123240272_123240273delTT								TSN (714846 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	123437238	123437241	+	IGR	DEL	TTTT	-	-	rs78193718		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:123437238_123437241delTTTT								TSN (911812 upstream) : None (None downstream)																																			---	---	---	---
CNTNAP5	129684	broad.mit.edu	37	2	125189780	125189780	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125189780delC	uc002tno.2	+						CNTNAP5_uc010flu.2_Intron	NM_130773	NP_570129			contactin associated protein-like 5 precursor						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)														---	---	---	---
CNTNAP5	129684	broad.mit.edu	37	2	125202201	125202201	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125202201delA	uc002tno.2	+						CNTNAP5_uc010flu.2_Intron	NM_130773	NP_570129			contactin associated protein-like 5 precursor						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)														---	---	---	---
CNTNAP5	129684	broad.mit.edu	37	2	125431022	125431023	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125431022_125431023delTT	uc002tno.2	+						CNTNAP5_uc010flu.2_Intron	NM_130773	NP_570129			contactin associated protein-like 5 precursor						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)														---	---	---	---
CNTNAP5	129684	broad.mit.edu	37	2	125480764	125480765	+	Intron	INS	-	A	A	rs139016539	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125480764_125480765insA	uc002tno.2	+						CNTNAP5_uc010flu.2_Intron	NM_130773	NP_570129			contactin associated protein-like 5 precursor						cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	125911410	125911410	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:125911410delA								CNTNAP5 (238549 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	126210886	126210887	+	IGR	INS	-	C	C	rs150645411	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:126210886_126210887insC								CNTNAP5 (538025 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	126242951	126242951	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:126242951delT								CNTNAP5 (570090 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	126288710	126288713	+	IGR	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:126288710_126288713delTTTT								CNTNAP5 (615849 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	127199850	127199850	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127199850delT								None (None upstream) : GYPC (213834 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	127261102	127261102	+	IGR	DEL	T	-	-	rs71961749		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127261102delT								None (None upstream) : GYPC (152582 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	127456206	127456207	+	IGR	DEL	CA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127456206_127456207delCA								GYPC (1961 upstream) : BIN1 (349400 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	127559234	127559234	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127559234delC								GYPC (104989 upstream) : BIN1 (246373 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	127764195	127764195	+	IGR	DEL	T	-	-	rs11397868		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127764195delT								GYPC (309950 upstream) : BIN1 (41412 downstream)																																			---	---	---	---
ERCC3	2071	broad.mit.edu	37	2	128035266	128035266	+	Intron	DEL	A	-	-	rs79528586		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128035266delA	uc002toh.1	-						ERCC3_uc002toe.1_Intron|ERCC3_uc002tof.1_Intron|ERCC3_uc002tog.1_Intron	NM_000122	NP_000113			excision repair cross-complementing rodent						cell cycle checkpoint|DNA topological change|hair cell differentiation|induction of apoptosis|interspecies interaction between organisms|mRNA capping|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA duplex unwinding|nucleotide-excision repair, DNA incision|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|protein localization|response to oxidative stress|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	holo TFIIH complex	3'-5' DNA helicase activity|ATP binding|damaged DNA binding|protein C-terminus binding|protein N-terminus binding|transcription factor binding			ovary(2)|lung(2)|breast(2)|kidney(1)	7	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.073)				Mis|S			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				---	---	---	---
MYO7B	4648	broad.mit.edu	37	2	128311504	128311504	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128311504delC	uc002top.2	+							NM_001080527	NP_001073996			myosin VIIB							apical plasma membrane|myosin complex	actin binding|ATP binding|motor activity			ovary(1)|pancreas(1)	2	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)														---	---	---	---
WDR33	55339	broad.mit.edu	37	2	128533443	128533443	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128533443delA	uc002tpg.1	-						WDR33_uc002tph.1_Intron|WDR33_uc002tpi.1_Intron	NM_018383	NP_060853			WD repeat domain 33 isoform 1						postreplication repair|spermatogenesis	collagen|nucleus	protein binding				0	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)														---	---	---	---
AMMECR1L	83607	broad.mit.edu	37	2	128634911	128634911	+	Intron	DEL	T	-	-	rs10559480		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128634911delT	uc002tpl.2	-						AMMECR1L_uc002tpm.2_Intron	NM_031445	NP_113633			AMME chromosomal region gene 1-like											central_nervous_system(1)	1	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.07)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	129017487	129017488	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129017487_129017488delTT								UGGT1 (64240 upstream) : HS6ST1 (5567 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	129456304	129456304	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129456304delA								HS6ST1 (380133 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	129484286	129484287	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129484286_129484287insA								HS6ST1 (408115 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	129908513	129908513	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129908513delA								HS6ST1 (832342 upstream) : LOC389033 (771922 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	130108335	130108337	+	IGR	DEL	AAG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130108335_130108337delAAG								None (None upstream) : LOC389033 (572098 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	130265089	130265089	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130265089delA								None (None upstream) : LOC389033 (415346 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	130342340	130342340	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130342340delA								None (None upstream) : LOC389033 (338095 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	130433516	130433516	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130433516delT								None (None upstream) : LOC389033 (246919 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	130625546	130625547	+	IGR	DEL	CA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130625546_130625547delCA								None (None upstream) : LOC389033 (54888 downstream)																																			---	---	---	---
POTEF	728378	broad.mit.edu	37	2	130840908	130840908	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130840908delA	uc010fmh.2	-							NM_001099771	NP_001093241			prostate, ovary, testis expressed protein on							cell cortex	ATP binding			skin(3)|ovary(2)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	130966645	130966645	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130966645delT								TUBA3E (10611 upstream) : CCDC115 (129171 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	131000154	131000154	+	IGR	DEL	T	-	-	rs77841472		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131000154delT								TUBA3E (44120 upstream) : CCDC115 (95662 downstream)																																			---	---	---	---
PTPN18	26469	broad.mit.edu	37	2	131125244	131125244	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131125244delA	uc002trc.2	+						PTPN18_uc002trd.2_Intron|PTPN18_uc002trb.2_Intron	NM_014369	NP_055184			protein tyrosine phosphatase, non-receptor type							cytoplasm|nucleus	non-membrane spanning protein tyrosine phosphatase activity			ovary(3)|kidney(1)	4	Colorectal(110;0.1)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	131205215	131205215	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131205215delC								PTPN18 (72234 upstream) : CFC1B (73621 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	131534203	131534205	+	IGR	DEL	AAG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131534203_131534205delAAG								FAM123C (8496 upstream) : ARHGEF4 (138581 downstream)																																			---	---	---	---
FAM168B	130074	broad.mit.edu	37	2	131840238	131840238	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131840238delA	uc002tsd.2	-							NM_001009993	NP_001009993			hypothetical protein LOC130074												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	132405756	132405756	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132405756delA								CCDC74A (114519 upstream) : C2orf27A (74308 downstream)																																			---	---	---	---
C2orf27B	408029	broad.mit.edu	37	2	132553833	132553833	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132553833delT	uc002ttg.1	-							NM_214461	NP_999626			hypothetical protein LOC408029												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	132704985	132704986	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132704985_132704986insA								C2orf27B (145751 upstream) : NCRNA00164 (200178 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	132775036	132775036	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132775036delT								C2orf27B (215802 upstream) : NCRNA00164 (130128 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	132819857	132819857	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:132819857delA								C2orf27B (260623 upstream) : NCRNA00164 (85307 downstream)																																			---	---	---	---
NCRNA00164	554226	broad.mit.edu	37	2	133001716	133001717	+	Intron	DEL	TT	-	-	rs79369156		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133001716_133001717delTT	uc002ttj.3	-							NR_027020				Homo sapiens non-protein coding RNA 164, mRNA (cDNA clone IMAGE:5169389), with apparent retained intron.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	133025014	133025017	+	IGR	DEL	GAGT	-	-	rs62166675		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133025014_133025017delGAGT								NCRNA00164 (9472 upstream) : GPR39 (149130 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	133027144	133027145	+	IGR	INS	-	AGAC	AGAC	rs150603360		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133027144_133027145insAGAC								NCRNA00164 (11602 upstream) : GPR39 (147002 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	133028586	133028587	+	IGR	INS	-	AGAG	AGAG			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133028586_133028587insAGAG								NCRNA00164 (13044 upstream) : GPR39 (145560 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	133098834	133098837	+	IGR	DEL	AAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133098834_133098837delAAAA								NCRNA00164 (83292 upstream) : GPR39 (75310 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	133101614	133101615	+	IGR	INS	-	TT	TT	rs61437831		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133101614_133101615insTT								NCRNA00164 (86072 upstream) : GPR39 (72532 downstream)																																			---	---	---	---
NCKAP5	344148	broad.mit.edu	37	2	133628887	133628891	+	Intron	DEL	AAACA	-	-	rs148470709		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133628887_133628891delAAACA	uc002ttp.2	-						NCKAP5_uc002ttq.2_Intron	NM_207363	NP_997246			Nck-associated protein 5 isoform 1								protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	134355276	134355276	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134355276delA								NCKAP5 (29245 upstream) : MGAT5 (656554 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	134518800	134518800	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134518800delA								NCKAP5 (192769 upstream) : MGAT5 (493030 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	134954319	134954319	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:134954319delT								NCKAP5 (628288 upstream) : MGAT5 (57511 downstream)																																			---	---	---	---
TMEM163	81615	broad.mit.edu	37	2	135417513	135417513	+	Intron	DEL	A	-	-	rs75134401	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135417513delA	uc002ttx.2	-						TMEM163_uc002tty.2_Intron	NM_030923	NP_112185			transmembrane protein 163							integral to membrane					0				BRCA - Breast invasive adenocarcinoma(221;0.154)														---	---	---	---
TMEM163	81615	broad.mit.edu	37	2	135426353	135426354	+	Intron	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135426353_135426354insG	uc002ttx.2	-						TMEM163_uc002tty.2_Intron	NM_030923	NP_112185			transmembrane protein 163							integral to membrane					0				BRCA - Breast invasive adenocarcinoma(221;0.154)														---	---	---	---
TMEM163	81615	broad.mit.edu	37	2	135474304	135474304	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135474304delA	uc002ttx.2	-						TMEM163_uc002tty.2_Intron	NM_030923	NP_112185			transmembrane protein 163							integral to membrane					0				BRCA - Breast invasive adenocarcinoma(221;0.154)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	135531512	135531512	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135531512delT								TMEM163 (6178 upstream) : ACMSD (64674 downstream)																																			---	---	---	---
ACMSD	130013	broad.mit.edu	37	2	135659283	135659284	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135659283_135659284insT	uc002ttz.2	+						ACMSD_uc002tua.2_Intron|uc010zbe.1_Intron	NM_138326	NP_612199			aminocarboxymuconate semialdehyde decarboxylase						quinolinate metabolic process|tryptophan catabolic process	cytosol	aminocarboxymuconate-semialdehyde decarboxylase activity|metal ion binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.115)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	135665993	135665993	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135665993delA	uc010zbe.1	-											Homo sapiens cDNA FLJ57500 complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	135953966	135953967	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135953966_135953967delTT								RAB3GAP1 (20002 upstream) : ZRANB3 (3609 downstream)																																			---	---	---	---
DARS	1615	broad.mit.edu	37	2	136673772	136673772	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136673772delA	uc002tux.1	-						DARS_uc010fnj.1_Intron	NM_001349	NP_001340			aspartyl-tRNA synthetase						aspartyl-tRNA aminoacylation|protein complex assembly	cytosol|nuclear membrane|plasma membrane|soluble fraction	aminoacylase activity|aspartate-tRNA ligase activity|ATP binding|nucleic acid binding|protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.168)	L-Aspartic Acid(DB00128)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	137011720	137011720	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137011720delA								CXCR4 (135995 upstream) : THSD7B (511395 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	137108737	137108737	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137108737delT								CXCR4 (233012 upstream) : THSD7B (414378 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	137204629	137204629	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137204629delT								CXCR4 (328904 upstream) : THSD7B (318486 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	137218312	137218313	+	IGR	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137218312_137218313delAG								CXCR4 (342587 upstream) : THSD7B (304802 downstream)																																			---	---	---	---
THSD7B	80731	broad.mit.edu	37	2	137540471	137540471	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137540471delA	uc010zbj.1	+											Homo sapiens mRNA for KIAA1679 protein, partial cds.											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)														---	---	---	---
THSD7B	80731	broad.mit.edu	37	2	138033617	138033617	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138033617delT	uc002tva.1	+						THSD7B_uc010zbj.1_Intron|THSD7B_uc002tvb.2_Intron	NM_001080427	NP_001073896			thrombospondin, type I, domain containing 7B											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)														---	---	---	---
HNMT	3176	broad.mit.edu	37	2	138742773	138742774	+	Intron	DEL	AA	-	-	rs35327551		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138742773_138742774delAA	uc002tvc.2	+						HNMT_uc002tvf.2_Intron	NM_006895	NP_008826			histamine N-methyltransferase isoform 1						respiratory gaseous exchange	cytoplasm	histamine N-methyltransferase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.125)	Amodiaquine(DB00613)|Histamine Phosphate(DB00667)|Quinacrine(DB01103)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	138815666	138815666	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:138815666delA								HNMT (41733 upstream) : SPOPL (443684 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	139415848	139415848	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139415848delC								SPOPL (85045 upstream) : NXPH2 (10881 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	140114142	140114142	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:140114142delT								NXPH2 (576331 upstream) : LRP1B (874854 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	140221449	140221449	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:140221449delT								NXPH2 (683638 upstream) : LRP1B (767547 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	140533695	140533695	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:140533695delT								NXPH2 (995884 upstream) : LRP1B (455301 downstream)																																			---	---	---	---
LRP1B	53353	broad.mit.edu	37	2	141526936	141526936	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141526936delG	uc002tvj.1	-							NM_018557	NP_061027			low density lipoprotein-related protein 1B						protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)											TSP Lung(27;0.18)			---	---	---	---
LRP1B	53353	broad.mit.edu	37	2	141631852	141631852	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141631852delT	uc002tvj.1	-						LRP1B_uc010fnl.1_Intron	NM_018557	NP_061027			low density lipoprotein-related protein 1B						protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)											TSP Lung(27;0.18)			---	---	---	---
LRP1B	53353	broad.mit.edu	37	2	141663524	141663524	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:141663524delA	uc002tvj.1	-						LRP1B_uc010fnl.1_Intron	NM_018557	NP_061027			low density lipoprotein-related protein 1B						protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)											TSP Lung(27;0.18)			---	---	---	---
LRP1B	53353	broad.mit.edu	37	2	142004972	142004972	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:142004972delT	uc002tvj.1	-						LRP1B_uc010fnl.1_Intron	NM_018557	NP_061027			low density lipoprotein-related protein 1B						protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)											TSP Lung(27;0.18)			---	---	---	---
Unknown	0	broad.mit.edu	37	2	143291973	143291973	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:143291973delA								LRP1B (402703 upstream) : KYNU (343222 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	143394309	143394310	+	IGR	DEL	GT	-	-	rs113147563		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:143394309_143394310delGT								LRP1B (505039 upstream) : KYNU (240885 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	143444860	143444860	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:143444860delA								LRP1B (555590 upstream) : KYNU (190335 downstream)																																			---	---	---	---
KYNU	8942	broad.mit.edu	37	2	143672227	143672227	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:143672227delT	uc002tvl.2	+						KYNU_uc002tvk.2_Intron|KYNU_uc010fnm.2_Intron	NM_003937	NP_003928			kynureninase (L-kynurenine hydrolase) isoform a						anthranilate metabolic process|NAD biosynthetic process|quinolinate biosynthetic process|response to interferon-gamma|response to vitamin B6	cytosol|mitochondrion|soluble fraction	kynureninase activity|protein homodimerization activity			skin(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.072)	L-Alanine(DB00160)|Pyridoxal Phosphate(DB00114)													---	---	---	---
GTDC1	79712	broad.mit.edu	37	2	145005252	145005252	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145005252delT	uc002tvp.2	-						GTDC1_uc002tvq.2_Intron|GTDC1_uc002tvr.2_Intron|GTDC1_uc010fnn.2_Intron|GTDC1_uc002tvs.2_Intron|GTDC1_uc010fno.2_Intron|GTDC1_uc002tvt.1_Intron	NM_001006636	NP_001006637			glycosyltransferase-like domain containing 1						biosynthetic process		transferase activity, transferring glycosyl groups			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.0914)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	145119026	145119026	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145119026delT								GTDC1 (28997 upstream) : ZEB2 (26559 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	145554635	145554635	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145554635delA	uc002twc.2	+											Homo sapiens hypothetical gene supported by BC043549; BX648102, mRNA (cDNA clone IMAGE:5172341).																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	145804107	145804108	+	Intron	INS	-	AC	AC			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145804107_145804108insAC	uc002twc.2	+						uc002twd.2_Intron|uc002twe.2_Intron					Homo sapiens hypothetical gene supported by BC043549; BX648102, mRNA (cDNA clone IMAGE:5172341).																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	145821682	145821682	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145821682delT	uc002twc.2	+						uc002twd.2_Intron|uc002twe.2_Intron					Homo sapiens hypothetical gene supported by BC043549; BX648102, mRNA (cDNA clone IMAGE:5172341).																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	145963481	145963481	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:145963481delT								ZEB2 (685550 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	146137945	146137946	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:146137945_146137946delAA								ZEB2 (860014 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	146341921	146341922	+	IGR	DEL	TT	-	-	rs5835060		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:146341921_146341922delTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	146446925	146446926	+	IGR	DEL	CA	-	-	rs149882697		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:146446925_146446926delCA								None (None upstream) : PABPC1P2 (897699 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	146862863	146862864	+	IGR	DEL	TT	-	-	rs111767252		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:146862863_146862864delTT								None (None upstream) : PABPC1P2 (481761 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	147917690	147917690	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:147917690delT								PABPC1P2 (569133 upstream) : ACVR2A (684396 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	148047222	148047223	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148047222_148047223delTT								PABPC1P2 (698665 upstream) : ACVR2A (554863 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	148061336	148061336	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148061336delT								PABPC1P2 (712779 upstream) : ACVR2A (540750 downstream)																																			---	---	---	---
ACVR2A	92	broad.mit.edu	37	2	148683686	148683686	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:148683686delA	uc002twg.2	+	11	1572	c.1303delA	c.(1303-1305)AAAfs	p.K435fs	ACVR2A_uc010zbn.1_Frame_Shift_Del_p.K327fs|ACVR2A_uc002twh.2_Frame_Shift_Del_p.K435fs	NM_001616	NP_001607	P27037	AVR2A_HUMAN	activin A receptor, type IIA precursor	435	Cytoplasmic (Potential).|Protein kinase.				activin receptor signaling pathway|BMP signaling pathway|positive regulation of activin receptor signaling pathway|positive regulation of bone mineralization|positive regulation of erythrocyte differentiation|positive regulation of osteoblast differentiation|positive regulation of protein phosphorylation	cytoplasm|inhibin-betaglycan-ActRII complex|integral to plasma membrane	ATP binding|coreceptor activity|inhibin beta-A binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|transforming growth factor beta receptor activity			stomach(8)|large_intestine(2)|lung(1)|breast(1)|kidney(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.0969)														---	---	---	---
MBD5	55777	broad.mit.edu	37	2	149050461	149050462	+	Intron	DEL	AA	-	-	rs79987303		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149050461_149050462delAA	uc002twm.3	+							NM_018328	NP_060798			methyl-CpG binding domain protein 5							chromosome|nucleus	chromatin binding|DNA binding			skin(3)|ovary(2)	5				BRCA - Breast invasive adenocarcinoma(221;0.0569)														---	---	---	---
KIF5C	3800	broad.mit.edu	37	2	149674207	149674207	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149674207delT	uc010zbu.1	+							NM_004522	NP_004513			kinesin family member 5C						microtubule-based movement|organelle organization	cytoplasm|kinesin complex|microtubule	ATP binding|microtubule motor activity			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.108)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	151558458	151558459	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151558458_151558459delTT								RND3 (214278 upstream) : RBM43 (546270 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	151811406	151811406	+	IGR	DEL	T	-	-	rs111289361		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151811406delT								RND3 (467226 upstream) : RBM43 (293323 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	151931514	151931514	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:151931514delA								RND3 (587334 upstream) : RBM43 (173215 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	152002756	152002756	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152002756delT								RND3 (658576 upstream) : RBM43 (101973 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	152205622	152205622	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152205622delA								NMI (59192 upstream) : TNFAIP6 (8483 downstream)																																			---	---	---	---
RIF1	55183	broad.mit.edu	37	2	152292282	152292283	+	Intron	DEL	TT	-	-	rs75364982	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152292282_152292283delTT	uc002txm.2	+						RIF1_uc002txl.2_Intron|RIF1_uc010fnv.1_Intron|RIF1_uc002txn.2_Intron|RIF1_uc002txo.2_Intron|RIF1_uc010zby.1_Intron	NM_018151	NP_060621			RAP1 interacting factor 1						cell cycle|response to DNA damage stimulus	chromosome, telomeric region|cytoplasm|nucleus|spindle	binding			ovary(5)|breast(4)|skin(3)|lung(2)|kidney(1)	15				BRCA - Breast invasive adenocarcinoma(221;0.0429)														---	---	---	---
RIF1	55183	broad.mit.edu	37	2	152334229	152334230	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152334229_152334230insT	uc002txp.2	+							NM_018151				RAP1 interacting factor 1						cell cycle|response to DNA damage stimulus	chromosome, telomeric region|cytoplasm|nucleus|spindle	binding			ovary(5)|breast(4)|skin(3)|lung(2)|kidney(1)	15				BRCA - Breast invasive adenocarcinoma(221;0.0429)														---	---	---	---
NEB	4703	broad.mit.edu	37	2	152363627	152363627	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152363627delA	uc010fnx.2	-						NEB_uc002txr.2_Intron|RIF1_uc002txp.2_Intron|NEB_uc010zca.1_5'Flank|NEB_uc010zcb.1_5'Flank|NEB_uc002txt.3_Intron	NM_004543	NP_004534			nebulin isoform 3						muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	153073357	153073358	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153073357_153073358delTT								STAM2 (40851 upstream) : FMNL2 (118393 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	153145240	153145240	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153145240delT								STAM2 (112734 upstream) : FMNL2 (46511 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	153146455	153146455	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153146455delG								STAM2 (113949 upstream) : FMNL2 (45296 downstream)																																			---	---	---	---
PRPF40A	55660	broad.mit.edu	37	2	153524505	153524506	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153524505_153524506delTT	uc002tyh.3	-						PRPF40A_uc002tyg.3_Intron|PRPF40A_uc010zcd.1_Intron	NM_017892	NP_060362			formin binding protein 3						mRNA processing|RNA splicing	nuclear matrix|nuclear speck	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	154053404	154053404	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:154053404delC								ARL6IP6 (435637 upstream) : RPRM (280448 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	154270735	154270735	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:154270735delA								ARL6IP6 (652968 upstream) : RPRM (63117 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	154491408	154491408	+	IGR	DEL	T	-	-	rs77468325		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:154491408delT								RPRM (156086 upstream) : GALNT13 (237018 downstream)																																			---	---	---	---
KCNJ3	3760	broad.mit.edu	37	2	155600251	155600251	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:155600251delT	uc002tyv.1	+						KCNJ3_uc010zce.1_Intron	NM_002239	NP_002230			potassium inwardly-rectifying channel J3						synaptic transmission	voltage-gated potassium channel complex	G-protein activated inward rectifier potassium channel activity|protein binding			upper_aerodigestive_tract(1)|pancreas(1)	2					Halothane(DB01159)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	155839527	155839527	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:155839527delA								KCNJ3 (126513 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	156459229	156459230	+	IGR	INS	-	TT	TT	rs112155074		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:156459229_156459230insTT								KCNJ3 (746215 upstream) : NR4A2 (721716 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	156605222	156605222	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:156605222delG								KCNJ3 (892208 upstream) : NR4A2 (575724 downstream)																																			---	---	---	---
GPD2	2820	broad.mit.edu	37	2	157340049	157340049	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157340049delA	uc002tzf.3	+						GPD2_uc010zch.1_Intron|GPD2_uc002tzd.3_Intron	NM_001083112	NP_001076581			glycerol-3-phosphate dehydrogenase 2,						cellular lipid metabolic process	glycerol-3-phosphate dehydrogenase complex|mitochondrial inner membrane	calcium ion binding|sn-glycerol-3-phosphate:ubiquinone-8 oxidoreductase activity			ovary(1)	1																		---	---	---	---
GPD2	2820	broad.mit.edu	37	2	157348096	157348096	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157348096delT	uc002tzf.3	+						GPD2_uc010zch.1_Intron|GPD2_uc002tzd.3_Intron	NM_001083112	NP_001076581			glycerol-3-phosphate dehydrogenase 2,						cellular lipid metabolic process	glycerol-3-phosphate dehydrogenase complex|mitochondrial inner membrane	calcium ion binding|sn-glycerol-3-phosphate:ubiquinone-8 oxidoreductase activity			ovary(1)	1																		---	---	---	---
ACVR1C	130399	broad.mit.edu	37	2	158481601	158481601	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158481601delC	uc002tzk.3	-						ACVR1C_uc002tzl.3_Intron|ACVR1C_uc010fof.2_Intron	NM_145259	NP_660302			activin A receptor, type IC isoform 1						apoptosis|cell differentiation|regulation of apoptosis	activin receptor complex	activin receptor activity, type I|ATP binding|transforming growth factor beta receptor activity			lung(3)|ovary(2)|skin(2)	7																		---	---	---	---
ACVR1	90	broad.mit.edu	37	2	158623546	158623547	+	Intron	DEL	TT	-	-	rs72201685		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158623546_158623547delTT	uc002tzm.3	-						ACVR1_uc002tzn.3_Intron|ACVR1_uc010fog.2_Intron	NM_001111067	NP_001104537			activin A receptor, type I precursor						BMP signaling pathway|G1/S transition of mitotic cell cycle|negative regulation of activin receptor signaling pathway|negative regulation of apoptosis|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway	activin receptor complex	activin binding|ATP binding|follistatin binding|metal ion binding|protein homodimerization activity|SMAD binding|transforming growth factor beta binding			ovary(2)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.104)	Adenosine triphosphate(DB00171)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	158747385	158747385	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158747385delG								ACVR1 (15011 upstream) : UPP2 (104306 downstream)																																			---	---	---	---
UPP2	151531	broad.mit.edu	37	2	158968967	158968967	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:158968967delA	uc002tzp.2	+						UPP2_uc002tzo.2_Intron	NM_173355	NP_775491			uridine phosphorylase 2 isoform a						nucleotide catabolic process|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process|pyrimidine nucleoside salvage|uridine metabolic process	cytosol|type III intermediate filament	uridine phosphorylase activity				0																		---	---	---	---
TANC1	85461	broad.mit.edu	37	2	159979762	159979762	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:159979762delT	uc002uag.2	+						TANC1_uc010fol.1_Intron|TANC1_uc010zcm.1_Intron|TANC1_uc010fom.1_Intron	NM_033394	NP_203752			tetratricopeptide repeat, ankyrin repeat and							cell junction|postsynaptic density|postsynaptic membrane	binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
BAZ2B	29994	broad.mit.edu	37	2	160283972	160283972	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160283972delA	uc002uao.2	-						BAZ2B_uc002uap.2_Intron|BAZ2B_uc002uaq.1_Intron|BAZ2B_uc002uar.1_Intron	NM_013450	NP_038478			bromodomain adjacent to zinc finger domain, 2B						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|skin(1)	4																		---	---	---	---
BAZ2B	29994	broad.mit.edu	37	2	160284756	160284756	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160284756delT	uc002uao.2	-						BAZ2B_uc002uap.2_Intron|BAZ2B_uc002uaq.1_Intron|BAZ2B_uc002uar.1_Intron	NM_013450	NP_038478			bromodomain adjacent to zinc finger domain, 2B						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|skin(1)	4																		---	---	---	---
BAZ2B	29994	broad.mit.edu	37	2	160318673	160318673	+	Intron	DEL	A	-	-	rs74547104		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160318673delA	uc002uao.2	-						BAZ2B_uc002uap.2_Intron|BAZ2B_uc002uas.1_Intron|BAZ2B_uc002uau.1_Intron|BAZ2B_uc002uat.3_Intron|BAZ2B_uc010fop.1_Intron	NM_013450	NP_038478			bromodomain adjacent to zinc finger domain, 2B						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|skin(1)	4																		---	---	---	---
PLA2R1	22925	broad.mit.edu	37	2	160818061	160818061	+	Intron	DEL	T	-	-	rs140691195	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160818061delT	uc002ube.1	-						PLA2R1_uc010zcp.1_Intron|PLA2R1_uc002ubf.2_Intron	NM_007366	NP_031392			phospholipase A2 receptor 1 isoform 1 precursor						endocytosis	extracellular space|integral to plasma membrane	receptor activity|sugar binding			skin(2)|ovary(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	161972902	161972902	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:161972902delT								RBMS1 (622584 upstream) : TANK (20564 downstream)																																			---	---	---	---
PSMD14	10213	broad.mit.edu	37	2	162169537	162169537	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162169537delT	uc002ubu.2	+							NM_005805	NP_005796			proteasome 26S subunit, non-ATPase 14						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K63-linked deubiquitination|regulation of apoptosis|regulation of cellular amino acid metabolic process|regulation of proteasomal protein catabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome complex	endopeptidase activator activity|metal ion binding|metallopeptidase activity|proteasome binding|ubiquitin thiolesterase activity			breast(1)	1																		---	---	---	---
TBR1	10716	broad.mit.edu	37	2	162272776	162272777	+	5'UTR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162272776_162272777delAA	uc002ubw.1	+	1					TBR1_uc010foy.2_5'Flank	NM_006593	NP_006584			T-box, brain, 1							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
SLC4A10	57282	broad.mit.edu	37	2	162480805	162480805	+	5'Flank	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162480805delG	uc002ubx.3	+						SLC4A10_uc010fpa.1_5'Flank|SLC4A10_uc010zcr.1_5'Flank|SLC4A10_uc002uby.3_5'Flank|SLC4A10_uc010zcs.1_5'Flank	NM_022058	NP_071341			solute carrier family 4, sodium bicarbonate						bicarbonate transport|chloride transport|sodium ion transport	integral to membrane|plasma membrane	inorganic anion exchanger activity|symporter activity			ovary(2)|lung(2)|pancreas(1)	5																		---	---	---	---
SLC4A10	57282	broad.mit.edu	37	2	162577335	162577336	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162577335_162577336delTT	uc002ubx.3	+						SLC4A10_uc010fpa.1_Intron|SLC4A10_uc010zcr.1_Intron|SLC4A10_uc002uby.3_Intron|SLC4A10_uc010zcs.1_Intron	NM_022058	NP_071341			solute carrier family 4, sodium bicarbonate						bicarbonate transport|chloride transport|sodium ion transport	integral to membrane|plasma membrane	inorganic anion exchanger activity|symporter activity			ovary(2)|lung(2)|pancreas(1)	5																		---	---	---	---
FAP	2191	broad.mit.edu	37	2	163087041	163087041	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163087041delA	uc002ucd.2	-						FAP_uc010zct.1_Intron|FAP_uc010fpd.2_Intron|FAP_uc010fpe.1_Intron	NM_004460	NP_004451			fibroblast activation protein, alpha subunit						endothelial cell migration|negative regulation of extracellular matrix disassembly|proteolysis	cell junction|integral to membrane|invadopodium membrane|lamellipodium membrane	dipeptidyl-peptidase activity|metalloendopeptidase activity|protein homodimerization activity|serine-type endopeptidase activity			ovary(3)	3																		---	---	---	---
IFIH1	64135	broad.mit.edu	37	2	163134716	163134716	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163134716delT	uc002uce.2	-	9	1986	c.1764delA	c.(1762-1764)AAAfs	p.K588fs		NM_022168	NP_071451	Q9BYX4	IFIH1_HUMAN	interferon induced with helicase C domain 1	588					detection of virus|innate immune response|interspecies interaction between organisms|negative regulation of type I interferon production|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|regulation of apoptosis	cytosol|nucleus	ATP binding|DNA binding|double-stranded RNA binding|helicase activity|protein binding|ribonucleoprotein binding|zinc ion binding			ovary(1)	1																		---	---	---	---
KCNH7	90134	broad.mit.edu	37	2	163276467	163276467	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163276467delA	uc002uch.1	-							NM_033272	NP_150375			potassium voltage-gated channel, subfamily H,						regulation of transcription, DNA-dependent	integral to membrane	protein binding|signal transducer activity			ovary(3)|skin(2)	5					Ibutilide(DB00308)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	163944727	163944727	+	IGR	DEL	T	-	-	rs11332724		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163944727delT								KCNH7 (249487 upstream) : FIGN (519391 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	164346265	164346265	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:164346265delA								KCNH7 (651025 upstream) : FIGN (117853 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	165346756	165346756	+	IGR	DEL	T	-	-	rs71393621		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165346756delT								FIGN (754243 upstream) : GRB14 (2577 downstream)																																			---	---	---	---
GRB14	2888	broad.mit.edu	37	2	165407237	165407237	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165407237delA	uc002ucl.2	-						GRB14_uc010zcv.1_Intron|GRB14_uc002ucm.2_Intron	NM_004490	NP_004481			growth factor receptor-bound protein 14						blood coagulation|leukocyte migration	cytosol|endosome membrane|Golgi membrane|microsome|plasma membrane	SH3/SH2 adaptor activity			ovary(5)|upper_aerodigestive_tract(1)|lung(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	165915240	165915240	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165915240delA								SLC38A11 (103205 upstream) : SCN3A (28792 downstream)																																			---	---	---	---
CSRNP3	80034	broad.mit.edu	37	2	166328485	166328485	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166328485delT	uc002udf.2	+							NM_024969	NP_079245			cysteine-serine-rich nuclear protein 3						apoptosis|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|large_intestine(1)|skin(1)	5																		---	---	---	---
CSRNP3	80034	broad.mit.edu	37	2	166481844	166481844	+	Intron	DEL	A	-	-	rs12470080		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166481844delA	uc002udf.2	+						CSRNP3_uc002udg.2_Intron	NM_024969	NP_079245			cysteine-serine-rich nuclear protein 3						apoptosis|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|large_intestine(1)|skin(1)	5																		---	---	---	---
TTC21B	79809	broad.mit.edu	37	2	166756519	166756525	+	Intron	DEL	AAAAAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166756519_166756525delAAAAAAA	uc002udk.2	-							NM_024753	NP_079029			tetratricopeptide repeat domain 21B							cilium axoneme|cytoplasm|cytoskeleton	binding			ovary(2)|pancreas(2)|breast(1)	5																		---	---	---	---
SCN1A	6323	broad.mit.edu	37	2	166868923	166868923	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166868923delT	uc010zcz.1	-						SCN1A_uc002udo.3_Intron|SCN1A_uc010fpk.2_Intron	NM_006920	NP_008851			sodium channel, voltage-gated, type I, alpha							voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|skin(6)|large_intestine(1)	13					Lamotrigine(DB00555)|Levetiracetam(DB01202)|Phenacemide(DB01121)|Phenytoin(DB00252)|Topiramate(DB00273)|Zonisamide(DB00909)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	167035453	167035453	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167035453delA	uc002udp.2	+											Homo sapiens, clone IMAGE:3681561, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	167438270	167438271	+	IGR	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167438270_167438271insG								SCN7A (87553 upstream) : XIRP2 (306726 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	167481036	167481036	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167481036delT								SCN7A (130319 upstream) : XIRP2 (263961 downstream)																																			---	---	---	---
XIRP2	129446	broad.mit.edu	37	2	167842319	167842319	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167842319delA	uc002udx.2	+						XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron	NM_152381	NP_689594			xin actin-binding repeat containing 2 isoform 1						actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	168747690	168747692	+	IGR	DEL	AGG	-	-	rs75064746	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168747690_168747692delAGG								B3GALT1 (20324 upstream) : STK39 (62839 downstream)																																			---	---	---	---
STK39	27347	broad.mit.edu	37	2	169038780	169038780	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169038780delA	uc002uea.2	-							NM_013233	NP_037365			serine threonine kinase 39 (STE20/SPS1 homolog,						response to stress	cytoplasm|nucleus	ATP binding|protein binding|receptor signaling protein serine/threonine kinase activity			central_nervous_system(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	169198533	169198533	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169198533delC								STK39 (94428 upstream) : LASS6 (114302 downstream)																																			---	---	---	---
LASS6	253782	broad.mit.edu	37	2	169502813	169502813	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169502813delT	uc002ueb.1	+						LASS6_uc002uec.1_Intron	NM_203463	NP_982288			longevity assurance homolog 6							endoplasmic reticulum membrane|integral to membrane|nuclear membrane	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sphingosine N-acyltransferase activity			skin(1)	1																		---	---	---	---
LASS6	253782	broad.mit.edu	37	2	169578894	169578894	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169578894delT	uc002ueb.1	+						LASS6_uc002uec.1_Intron	NM_203463	NP_982288			longevity assurance homolog 6							endoplasmic reticulum membrane|integral to membrane|nuclear membrane	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sphingosine N-acyltransferase activity			skin(1)	1																		---	---	---	---
LRP2	4036	broad.mit.edu	37	2	170058057	170058057	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170058057delT	uc002ues.2	-							NM_004525	NP_004516			low density lipoprotein-related protein 2						hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)													---	---	---	---
LRP2	4036	broad.mit.edu	37	2	170136168	170136168	+	Intron	DEL	T	-	-	rs17280868		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170136168delT	uc002ues.2	-						LRP2_uc010zdf.1_Intron	NM_004525	NP_004516			low density lipoprotein-related protein 2						hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	170277892	170277892	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170277892delA								LRP2 (58770 upstream) : BBS5 (58114 downstream)																																			---	---	---	---
KBTBD10	10324	broad.mit.edu	37	2	170371018	170371018	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170371018delT	uc002ueu.1	+						KBTBD10_uc010zdh.1_Intron	NM_006063	NP_006054			kelch repeat and BTB (POZ) domain containing 10						striated muscle contraction	centrosome|nucleolus|plasma membrane|pseudopodium|ruffle					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	170433856	170433856	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170433856delA								FASTKD1 (3432 upstream) : PPIG (6994 downstream)																																			---	---	---	---
METTL5	29081	broad.mit.edu	37	2	170668752	170668752	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170668752delT	uc002ufn.2	-						METTL5_uc002ufo.2_Intron|METTL5_uc002ufp.2_Intron|METTL5_uc002ufq.1_3'UTR	NM_014168	NP_054887			methyltransferase like 5								methyltransferase activity|nucleic acid binding			central_nervous_system(1)	1																		---	---	---	---
MYO3B	140469	broad.mit.edu	37	2	171258313	171258316	+	Intron	DEL	TTTT	-	-	rs146922053		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171258313_171258316delTTTT	uc002ufy.2	+						MYO3B_uc002ufv.2_Intron|MYO3B_uc010fqb.1_Intron|MYO3B_uc002ufz.2_Intron|MYO3B_uc002ufw.2_Intron|MYO3B_uc002ufx.2_Intron|MYO3B_uc002ugb.2_Intron	NM_138995	NP_620482			myosin IIIB isoform 2						response to stimulus|visual perception	cytoplasm|myosin complex	actin binding|ATP binding|motor activity|protein serine/threonine kinase activity			lung(8)|ovary(6)|skin(4)|central_nervous_system(1)	19																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	171662614	171662614	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171662614delG								SP5 (88117 upstream) : GAD1 (10586 downstream)																																			---	---	---	---
TLK1	9874	broad.mit.edu	37	2	171916563	171916563	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171916563delA	uc002ugn.2	-						TLK1_uc002ugo.2_Intron|TLK1_uc002ugp.2_Intron|TLK1_uc002ugq.2_Intron|TLK1_uc010zdn.1_Intron	NM_012290	NP_036422			tousled-like kinase 1 isoform 1						cell cycle|chromatin modification|intracellular protein transport|intracellular signal transduction|regulation of chromatin assembly or disassembly|response to DNA damage stimulus	nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(1)	1																		---	---	---	---
TLK1	9874	broad.mit.edu	37	2	172074778	172074779	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172074778_172074779insA	uc002ugp.2	-							NM_001136554	NP_001130026			tousled-like kinase 1 isoform 2						cell cycle|chromatin modification|intracellular protein transport|intracellular signal transduction|regulation of chromatin assembly or disassembly|response to DNA damage stimulus	nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	172107670	172107671	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172107670_172107671delAA								TLK1 (19846 upstream) : METTL8 (66244 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	172347829	172347829	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172347829delA								DCAF17 (6269 upstream) : CYBRD1 (31037 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	172374479	172374480	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172374479_172374480delTT								DCAF17 (32919 upstream) : CYBRD1 (4386 downstream)																																			---	---	---	---
CYBRD1	79901	broad.mit.edu	37	2	172379264	172379264	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172379264delG	uc002ugy.3	+						CYBRD1_uc002ugz.3_Intron	NM_024843	NP_079119			cytochrome b reductase 1 isoform 1						cellular iron ion homeostasis|electron transport chain|transmembrane transport	integral to membrane	ferric-chelate reductase activity|metal ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	172495805	172495805	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172495805delT								CYBRD1 (81162 upstream) : DYNC1I2 (48177 downstream)																																			---	---	---	---
SLC25A12	8604	broad.mit.edu	37	2	172749493	172749493	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172749493delA	uc002uhh.2	-						SLC25A12_uc010fqh.2_Intron|SLC25A12_uc010zdv.1_Intron	NM_003705	NP_003696			solute carrier family 25, member 12						gluconeogenesis|malate-aspartate shuttle|response to calcium ion	integral to membrane|mitochondrial inner membrane	calcium ion binding|L-aspartate transmembrane transporter activity|L-glutamate transmembrane transporter activity|protein binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.216)		L-Aspartic Acid(DB00128)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	172848929	172848932	+	IGR	DEL	TAAG	-	-	rs111501594		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172848929_172848932delTAAG								HAT1 (330 upstream) : MAP1D (15872 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	173107508	173107508	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173107508delT								DLX2 (140030 upstream) : ITGA6 (184574 downstream)																																			---	---	---	---
RAPGEF4	11069	broad.mit.edu	37	2	173747829	173747830	+	Intron	DEL	AA	-	-	rs144808138		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173747829_173747830delAA	uc002uhv.3	+						RAPGEF4_uc002uhu.2_Intron|RAPGEF4_uc002uhw.3_Intron|RAPGEF4_uc010zec.1_Intron|RAPGEF4_uc010zed.1_Intron	NM_007023	NP_008954			Rap guanine nucleotide exchange factor (GEF) 4						blood coagulation|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|regulation of insulin secretion|regulation of protein phosphorylation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cAMP-dependent protein kinase complex|membrane fraction|plasma membrane	cAMP binding|cAMP-dependent protein kinase regulator activity|Ras GTPase binding|Ras guanyl-nucleotide exchange factor activity			large_intestine(2)|skin(2)|kidney(1)|central_nervous_system(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.194)															---	---	---	---
ZAK	51776	broad.mit.edu	37	2	174074693	174074693	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174074693delT	uc002uhz.2	+						ZAK_uc002uhx.2_3'UTR|ZAK_uc002uhy.2_Intron|ZAK_uc010zei.1_Intron|ZAK_uc002uia.1_Intron|uc002uib.2_Intron	NM_016653	NP_057737			MLK-related kinase isoform 1						activation of JUN kinase activity|activation of MAPKK activity|cell cycle arrest|cell death|cell differentiation|cell proliferation|DNA damage checkpoint|positive regulation of apoptosis|response to radiation	cytoplasm|nucleus	ATP binding|identical protein binding|magnesium ion binding|MAP kinase kinase kinase activity|protein binding			lung(3)|stomach(1)|ovary(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.176)															---	---	---	---
ZAK	51776	broad.mit.edu	37	2	174128438	174128438	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174128438delT	uc002uhz.2	+						uc002uib.2_Intron	NM_016653	NP_057737			MLK-related kinase isoform 1						activation of JUN kinase activity|activation of MAPKK activity|cell cycle arrest|cell death|cell differentiation|cell proliferation|DNA damage checkpoint|positive regulation of apoptosis|response to radiation	cytoplasm|nucleus	ATP binding|identical protein binding|magnesium ion binding|MAP kinase kinase kinase activity|protein binding			lung(3)|stomach(1)|ovary(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.176)															---	---	---	---
CDCA7	83879	broad.mit.edu	37	2	174231277	174231277	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174231277delT	uc002uid.1	+						CDCA7_uc002uic.1_Intron|CDCA7_uc010zej.1_Intron|CDCA7_uc010zek.1_Intron	NM_145810	NP_665809			cell division cycle associated 7 isoform 2						regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.116)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	174489029	174489030	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:174489029_174489030delAA								CDCA7 (255311 upstream) : SP3 (284229 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	175164719	175164719	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175164719delA								OLA1 (51354 upstream) : SP9 (35102 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	175172640	175172640	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175172640delT								OLA1 (59275 upstream) : SP9 (27181 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	175571883	175571883	+	Intron	DEL	G	-	-	rs71407140		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175571883delG	uc002uiw.2	+											Homo sapiens cDNA FLJ11228 fis, clone PLACE1008329.																														---	---	---	---
CHN1	1123	broad.mit.edu	37	2	175787452	175787452	+	Intron	DEL	A	-	-	rs72923148	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175787452delA	uc002uji.2	-						CHN1_uc010zeq.1_Intron|CHN1_uc002ujj.2_Intron	NM_001822	NP_001813			chimerin (chimaerin) 1 isoform a						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(2)|skin(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.226)					T	TAF15	extraskeletal myxoid chondrosarcoma								---	---	---	---
Unknown	0	broad.mit.edu	37	2	175880906	175880921	+	IGR	DEL	GATAGATAGATAGATA	-	-	rs71407167		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175880906_175880921delGATAGATAGATAGATA								CHN1 (10736 upstream) : ATF2 (58087 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	176141195	176141196	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176141195_176141196delAA								ATP5G3 (94705 upstream) : KIAA1715 (649214 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	176222600	176222604	+	IGR	DEL	TTTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176222600_176222604delTTTTT								ATP5G3 (176110 upstream) : KIAA1715 (567806 downstream)																																			---	---	---	---
HOXD8	3234	broad.mit.edu	37	2	176995683	176995683	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176995683delT	uc002uko.2	+						uc002ukl.1_5'Flank|uc002ukm.1_5'Flank|HOXD8_uc002ukn.2_Intron|HOXD8_uc002ukp.2_Intron	NM_019558	NP_062458			homeobox D8						anterior/posterior axis specification, embryo	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.195)	Colorectal(32;0.0224)|READ - Rectum adenocarcinoma(9;0.0556)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	177238465	177238465	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:177238465delT								MTX2 (35714 upstream) : MIR1246 (227243 downstream)																																			---	---	---	---
NFE2L2	4780	broad.mit.edu	37	2	178120597	178120597	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178120597delT	uc002ulh.3	-						NFE2L2_uc002ulg.3_Intron|NFE2L2_uc010zfa.1_Intron|NFE2L2_uc002uli.3_Intron|NFE2L2_uc010fra.2_Intron|NFE2L2_uc010frb.2_Intron	NM_006164	NP_006155			nuclear factor erythroid 2-like 2 isoform 1						transcription from RNA polymerase II promoter	centrosome|cytosol|nucleus|plasma membrane	protein dimerization activity|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)					Mis		NSCLC|HNSCC					HNSCC(56;0.16)			---	---	---	---
NFE2L2	4780	broad.mit.edu	37	2	178136648	178136649	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178136648_178136649insT	uc002uli.3	-							NM_001145412	NP_001138884			nuclear factor erythroid 2-like 2 isoform 2						transcription from RNA polymerase II promoter	centrosome|cytosol|nucleus|plasma membrane	protein dimerization activity|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)					Mis		NSCLC|HNSCC					HNSCC(56;0.16)			---	---	---	---
NFE2L2	4780	broad.mit.edu	37	2	178238946	178238947	+	Intron	INS	-	TTG	TTG	rs142014738	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178238946_178238947insTTG	uc002uli.3	-						LOC100130691_uc002ulk.1_Intron	NM_001145412	NP_001138884			nuclear factor erythroid 2-like 2 isoform 2						transcription from RNA polymerase II promoter	centrosome|cytosol|nucleus|plasma membrane	protein dimerization activity|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)					Mis		NSCLC|HNSCC					HNSCC(56;0.16)			---	---	---	---
AGPS	8540	broad.mit.edu	37	2	178301396	178301396	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178301396delA	uc002ull.2	+						AGPS_uc010zfb.1_Intron	NM_003659	NP_003650			alkyldihydroxyacetone phosphate synthase						ether lipid biosynthetic process	peroxisomal matrix|peroxisomal membrane|plasma membrane	alkylglycerone-phosphate synthase activity|flavin adenine dinucleotide binding|oxidoreductase activity			ovary(2)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.0018)|Epithelial(96;0.00919)|all cancers(119;0.0358)															---	---	---	---
TTC30B	150737	broad.mit.edu	37	2	178415367	178415367	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178415367delT	uc002uln.2	-	1					TTC30B_uc010zfc.1_3'UTR	NM_152517	NP_689730			tetratricopeptide repeat domain 30B						cell projection organization	cilium	binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.00151)|Epithelial(96;0.00931)|all cancers(119;0.0362)															---	---	---	---
PDE11A	50940	broad.mit.edu	37	2	178934315	178934315	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178934315delA	uc002ulq.2	-						PDE11A_uc002ulr.2_Intron|PDE11A_uc002ult.1_Intron	NM_016953	NP_058649			phosphodiesterase 11A isoform 4						platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding			ovary(3)|large_intestine(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)											Primary_Pigmented_Nodular_Adrenocortical_Disease_Familial				---	---	---	---
PDE11A	50940	broad.mit.edu	37	2	178961622	178961622	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178961622delT	uc002ulr.2	-						PDE11A_uc002ult.1_Intron	NM_001077197	NP_001070665			phosphodiesterase 11A isoform 3						platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding			ovary(3)|large_intestine(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)											Primary_Pigmented_Nodular_Adrenocortical_Disease_Familial				---	---	---	---
TTN	7273	broad.mit.edu	37	2	179478747	179478748	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179478747_179478748delTT	uc010zfg.1	-						uc002ump.1_Intron|TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron	NM_133378	NP_596869			titin isoform N2-A								ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179558767	179558767	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179558767delT	uc010zfg.1	-						TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron|TTN_uc010fre.1_Intron	NM_133378	NP_596869			titin isoform N2-A								ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179639950	179639950	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179639950delA	uc010zfg.1	-						TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002unb.2_Intron|uc002unc.1_5'Flank	NM_133378	NP_596869			titin isoform N2-A								ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179669245	179669245	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179669245delA	uc002und.2	-						TTN_uc010zfg.1_Intron|TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002unb.2_Intron					Homo sapiens cDNA FLJ32040 fis, clone NTONG2000858, highly similar to H.sapiens mRNA for titin protein.								ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
CCDC141	285025	broad.mit.edu	37	2	179715301	179715302	+	Intron	INS	-	ATCTCCAGCCAA	ATCTCCAGCCAA	rs149213970	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179715301_179715302insATCTCCAGCCAA	uc002unf.1	-							NM_173648	NP_775919			coiled-coil domain containing 141								protein binding			ovary(7)|pancreas(2)|skin(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	179949205	179949208	+	IGR	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179949205_179949208delTTTT								CCDC141 (34419 upstream) : SESTD1 (17213 downstream)																																			---	---	---	---
ZNF385B	151126	broad.mit.edu	37	2	180562442	180562442	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180562442delT	uc002unn.3	-						ZNF385B_uc002unm.2_Intron	NM_152520	NP_689733			zinc finger protein 385B isoform 1							nucleus	nucleic acid binding|zinc ion binding			ovary(1)	1			Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201)															---	---	---	---
ZNF385B	151126	broad.mit.edu	37	2	180579519	180579519	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180579519delA	uc002unn.3	-						ZNF385B_uc002unm.2_Intron	NM_152520	NP_689733			zinc finger protein 385B isoform 1							nucleus	nucleic acid binding|zinc ion binding			ovary(1)	1			Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201)															---	---	---	---
ZNF385B	151126	broad.mit.edu	37	2	180634657	180634657	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180634657delA	uc002unn.3	-							NM_152520	NP_689733			zinc finger protein 385B isoform 1							nucleus	nucleic acid binding|zinc ion binding			ovary(1)	1			Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201)															---	---	---	---
ZNF385B	151126	broad.mit.edu	37	2	180682392	180682393	+	Intron	INS	-	TG	TG	rs143388441	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180682392_180682393insTG	uc002unn.3	-							NM_152520	NP_689733			zinc finger protein 385B isoform 1							nucleus	nucleic acid binding|zinc ion binding			ovary(1)	1			Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	181421783	181421784	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181421783_181421784delAA								CWC22 (549943 upstream) : UBE2E3 (423328 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	181764200	181764200	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181764200delG								CWC22 (892360 upstream) : UBE2E3 (80912 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	181775673	181775673	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181775673delT								CWC22 (903833 upstream) : UBE2E3 (69439 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	181810352	181810352	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181810352delT								CWC22 (938512 upstream) : UBE2E3 (34760 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	181976754	181976754	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:181976754delA								UBE2E3 (48604 upstream) : ITGA4 (344865 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	182236022	182236022	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:182236022delA	uc002uns.1	+											Homo sapiens cDNA FLJ43011 fis, clone BRTHA2015853.																														---	---	---	---
PDE1A	5136	broad.mit.edu	37	2	183110202	183110202	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183110202delA	uc002uos.2	-						PDE1A_uc010zfp.1_Intron|PDE1A_uc002uoq.1_Intron|PDE1A_uc010zfq.1_Intron|PDE1A_uc002uor.2_Intron	NM_001003683	NP_001003683			phosphodiesterase 1A isoform 2						activation of phospholipase C activity|nerve growth factor receptor signaling pathway|platelet activation	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			skin(2)|ovary(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.061)															---	---	---	---
FRZB	2487	broad.mit.edu	37	2	183708659	183708659	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183708659delA	uc002upa.1	-							NM_001463	NP_001454			frizzled-related protein precursor						brain development|cochlea morphogenesis|gonad development|mammary gland involution|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cartilage development|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of hepatocyte differentiation|positive regulation of apoptosis|positive regulation of fat cell differentiation|skeletal system development|vasculature development|Wnt receptor signaling pathway	cytoplasm|extracellular space|membrane	PDZ domain binding|Wnt receptor activity|Wnt-protein binding			ovary(2)|lung(1)|central_nervous_system(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.109)|Epithelial(96;0.231)															---	---	---	---
FRZB	2487	broad.mit.edu	37	2	183719139	183719140	+	Intron	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183719139_183719140insG	uc002upa.1	-							NM_001463	NP_001454			frizzled-related protein precursor						brain development|cochlea morphogenesis|gonad development|mammary gland involution|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cartilage development|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of hepatocyte differentiation|positive regulation of apoptosis|positive regulation of fat cell differentiation|skeletal system development|vasculature development|Wnt receptor signaling pathway	cytoplasm|extracellular space|membrane	PDZ domain binding|Wnt receptor activity|Wnt-protein binding			ovary(2)|lung(1)|central_nervous_system(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.109)|Epithelial(96;0.231)															---	---	---	---
NUP35	129401	broad.mit.edu	37	2	184008011	184008011	+	Intron	DEL	T	-	-	rs77074391		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:184008011delT	uc002upf.2	+						NUP35_uc010zfs.1_Intron|NUP35_uc010zft.1_Intron|NUP35_uc002upg.2_Intron	NM_138285	NP_612142			nucleoporin 35kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	intermediate filament cytoskeleton|nuclear membrane|nuclear pore|plasma membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	184519227	184519227	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:184519227delC								NUP35 (492820 upstream) : ZNF804A (943866 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	185252730	185252730	+	IGR	DEL	A	-	-	rs76497176		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:185252730delA								None (None upstream) : ZNF804A (210363 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	185412772	185412772	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:185412772delA								None (None upstream) : ZNF804A (50321 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	186701963	186701963	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:186701963delT								ZNF804A (897751 upstream) : ZC3H15 (648922 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	187052221	187052222	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187052221_187052222delAA								None (None upstream) : ZC3H15 (298663 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	187101719	187101720	+	IGR	DEL	CC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187101719_187101720delCC								None (None upstream) : ZC3H15 (249165 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	187446471	187446471	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187446471delT								ZC3H15 (72386 upstream) : ITGAV (8319 downstream)																																			---	---	---	---
ITGAV	3685	broad.mit.edu	37	2	187532575	187532575	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187532575delA	uc002upq.2	+						ITGAV_uc010frs.2_Intron|ITGAV_uc010zfv.1_Intron	NM_002210	NP_002201			integrin alpha-V isoform 1 precursor						angiogenesis|axon guidance|blood coagulation|cell-matrix adhesion|entry of bacterium into host cell|entry of symbiont into host cell by promotion of host phagocytosis|entry of virus into host cell|ERK1 and ERK2 cascade|integrin-mediated signaling pathway|leukocyte migration|negative regulation of apoptosis|negative regulation of lipid storage|negative regulation of lipid transport|negative regulation of lipoprotein metabolic process|negative regulation of low-density lipoprotein particle receptor biosynthetic process|negative regulation of macrophage derived foam cell differentiation|positive regulation of cell adhesion|positive regulation of cell proliferation|regulation of apoptotic cell clearance	integrin complex	receptor activity|transforming growth factor beta binding			ovary(2)|kidney(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0185)|Epithelial(96;0.072)|all cancers(119;0.189)	STAD - Stomach adenocarcinoma(3;0.106)|COAD - Colon adenocarcinoma(31;0.108)														---	---	---	---
FAM171B	165215	broad.mit.edu	37	2	187564804	187564805	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187564804_187564805delTT	uc002ups.2	+						FAM171B_uc002upr.1_Intron	NM_177454	NP_803237			KIAA1946							integral to membrane	DNA binding			ovary(6)|breast(3)|central_nervous_system(1)	10																		---	---	---	---
FAM171B	165215	broad.mit.edu	37	2	187603864	187603864	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187603864delT	uc002ups.2	+						FAM171B_uc002upr.1_Intron	NM_177454	NP_803237			KIAA1946							integral to membrane	DNA binding			ovary(6)|breast(3)|central_nervous_system(1)	10																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	187823737	187823737	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187823737delA								ZSWIM2 (109840 upstream) : CALCRL (384114 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	188131717	188131717	+	IGR	DEL	G	-	-	rs147418701		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:188131717delG								ZSWIM2 (417820 upstream) : CALCRL (76134 downstream)																																			---	---	---	---
CALCRL	10203	broad.mit.edu	37	2	188230591	188230591	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:188230591delA	uc002upv.3	-						CALCRL_uc010frt.2_Intron	NM_005795	NP_005786			calcitonin receptor-like precursor							integral to plasma membrane				lung(3)|ovary(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(96;0.227)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	188567606	188567606	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:188567606delA								TFPI (148387 upstream) : GULP1 (588998 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	190301478	190301478	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190301478delA								COL5A2 (256873 upstream) : WDR75 (4681 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	190366158	190366158	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190366158delT								WDR75 (25894 upstream) : SLC40A1 (59160 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	190515414	190515414	+	IGR	DEL	C	-	-	rs10710019		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190515414delC								SLC40A1 (66930 upstream) : ASNSD1 (10711 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	190870337	190870338	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190870337_190870338insT								PMS1 (127983 upstream) : MSTN (50089 downstream)																																			---	---	---	---
HIBCH	26275	broad.mit.edu	37	2	191142938	191142938	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191142938delT	uc002uru.2	-						HIBCH_uc002urv.2_Intron	NM_014362	NP_055177			3-hydroxyisobutyryl-Coenzyme A hydrolase isoform						branched chain family amino acid catabolic process	mitochondrial matrix	3-hydroxyisobutyryl-CoA hydrolase activity|protein binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.000586)|Epithelial(96;0.0286)|all cancers(119;0.0814)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	191736956	191736957	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191736956_191736957delTT								NAB1 (179465 upstream) : GLS (8590 downstream)																																			---	---	---	---
GLS	2744	broad.mit.edu	37	2	191797646	191797646	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191797646delT	uc002usf.2	+						GLS_uc002use.2_3'UTR|GLS_uc002usg.1_3'UTR|GLS_uc002ush.2_Intron|GLS_uc010zgi.1_Intron|GLS_uc010zgj.1_Intron	NM_014905	NP_055720			glutaminase precursor						cellular amino acid biosynthetic process|glutamate secretion|glutamine catabolic process|neurotransmitter secretion	mitochondrial matrix	glutaminase activity			ovary(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.00625)|Epithelial(96;0.0744)|all cancers(119;0.181)		L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)													---	---	---	---
STAT4	6775	broad.mit.edu	37	2	192033366	192033366	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192033366delA	uc010zgm.1	-						STAT4_uc010zgn.1_Intron|STAT4_uc010zgo.1_Intron					Homo sapiens cDNA FLJ60872 complete cds, moderately similar to Signal transducer and activator of transcription 4.						JAK-STAT cascade	cytoplasm|nucleus	calcium ion binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			breast(3)|skin(2)|lung(1)|ovary(1)|prostate(1)|pancreas(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.0864)|all cancers(119;0.204)															---	---	---	---
MYO1B	4430	broad.mit.edu	37	2	192152257	192152257	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:192152257delA	uc010fsg.2	+						MYO1B_uc002usq.2_Intron|MYO1B_uc002usr.2_Intron|MYO1B_uc002uss.1_Intron	NM_001130158	NP_001123630			myosin IB isoform 1							myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			central_nervous_system(5)|large_intestine(2)|ovary(1)	8			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236)															---	---	---	---
TMEFF2	23671	broad.mit.edu	37	2	193061411	193061412	+	5'Flank	DEL	TT	-	-	rs112398432		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193061411_193061412delTT	uc002utc.2	-						TMEFF2_uc002utd.1_5'Flank	NM_016192	NP_057276			transmembrane protein with EGF-like and two							extracellular region|integral to membrane				lung(2)|pancreas(1)|breast(1)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(117;0.0835)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	193077595	193077597	+	IGR	DEL	TTT	-	-	rs78149951		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193077595_193077597delTTT								TMEFF2 (17951 upstream) : PCGEM1 (536974 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	193265799	193265800	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193265799_193265800delTT								TMEFF2 (206155 upstream) : PCGEM1 (348771 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	193360611	193360612	+	IGR	INS	-	T	T	rs113496658		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193360611_193360612insT								TMEFF2 (300967 upstream) : PCGEM1 (253959 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	193555789	193555789	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193555789delT								TMEFF2 (496145 upstream) : PCGEM1 (58782 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	193594079	193594080	+	IGR	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:193594079_193594080delCT								TMEFF2 (534435 upstream) : PCGEM1 (20491 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	194092185	194092185	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:194092185delT								PCGEM1 (450564 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	194442440	194442440	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:194442440delA								PCGEM1 (800819 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	194595387	194595387	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:194595387delT								PCGEM1 (953766 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	194919272	194919272	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:194919272delG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	195324018	195324018	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:195324018delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	195512210	195512211	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:195512210_195512211delAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	195987717	195987717	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:195987717delT								None (None upstream) : SLC39A10 (533815 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	196230303	196230303	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196230303delA								None (None upstream) : SLC39A10 (291229 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	196515670	196515671	+	IGR	DEL	GG	-	-	rs10534487		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196515670_196515671delGG								None (None upstream) : SLC39A10 (5861 downstream)																																			---	---	---	---
DNAH7	56171	broad.mit.edu	37	2	196602560	196602560	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196602560delA	uc002utj.3	-	65					DNAH7_uc002uti.3_3'UTR	NM_018897	NP_061720			dynein, axonemal, heavy chain 7						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12																		---	---	---	---
DNAH7	56171	broad.mit.edu	37	2	196674803	196674803	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196674803delT	uc002utj.3	-							NM_018897	NP_061720			dynein, axonemal, heavy chain 7						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12																		---	---	---	---
DNAH7	56171	broad.mit.edu	37	2	196799630	196799630	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196799630delA	uc002utj.3	-							NM_018897	NP_061720			dynein, axonemal, heavy chain 7						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12																		---	---	---	---
DNAH7	56171	broad.mit.edu	37	2	196810682	196810682	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196810682delG	uc002utj.3	-							NM_018897	NP_061720			dynein, axonemal, heavy chain 7						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12																		---	---	---	---
DNAH7	56171	broad.mit.edu	37	2	196838172	196838173	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196838172_196838173insT	uc002utj.3	-							NM_018897	NP_061720			dynein, axonemal, heavy chain 7						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12																		---	---	---	---
DNAH7	56171	broad.mit.edu	37	2	196931205	196931205	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196931205delT	uc002utj.3	-							NM_018897	NP_061720			dynein, axonemal, heavy chain 7						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12																		---	---	---	---
HECW2	57520	broad.mit.edu	37	2	197182420	197182421	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197182420_197182421delAA	uc002utm.1	-						HECW2_uc002utl.1_Intron	NM_020760	NP_065811			HECT, C2 and WW domain containing E3 ubiquitin						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm	ubiquitin-protein ligase activity			skin(5)|ovary(5)|lung(4)|pancreas(2)|central_nervous_system(1)|kidney(1)	18																		---	---	---	---
HECW2	57520	broad.mit.edu	37	2	197413054	197413055	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197413054_197413055delAA	uc002utm.1	-							NM_020760	NP_065811			HECT, C2 and WW domain containing E3 ubiquitin						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm	ubiquitin-protein ligase activity			skin(5)|ovary(5)|lung(4)|pancreas(2)|central_nervous_system(1)|kidney(1)	18																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	197472654	197472654	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197472654delA								HECW2 (15319 upstream) : CCDC150 (31702 downstream)																																			---	---	---	---
CCDC150	284992	broad.mit.edu	37	2	197541991	197541991	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197541991delT	uc002utp.1	+						CCDC150_uc010zgq.1_Intron|CCDC150_uc010zgr.1_Intron|CCDC150_uc010zgs.1_Intron	NM_001080539	NP_001074008			coiled-coil domain containing 150												0																		---	---	---	---
PGAP1	80055	broad.mit.edu	37	2	197712538	197712538	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197712538delA	uc002utw.2	-						PGAP1_uc002utx.2_Intron|PGAP1_uc002uty.1_3'UTR|PGAP1_uc010fsi.2_5'Flank	NM_024989	NP_079265			GPI deacylase						attachment of GPI anchor to protein|C-terminal protein lipidation|intracellular protein transport|myo-inositol transport	integral to membrane|intrinsic to endoplasmic reticulum membrane	nuclease activity|phosphoric ester hydrolase activity			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
PGAP1	80055	broad.mit.edu	37	2	197735724	197735724	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197735724delA	uc002utw.2	-						PGAP1_uc002utx.2_Intron|PGAP1_uc002uty.1_Intron	NM_024989	NP_079265			GPI deacylase						attachment of GPI anchor to protein|C-terminal protein lipidation|intracellular protein transport|myo-inositol transport	integral to membrane|intrinsic to endoplasmic reticulum membrane	nuclease activity|phosphoric ester hydrolase activity			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
ANKRD44	91526	broad.mit.edu	37	2	197872490	197872490	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197872490delA	uc002uua.1	-						ANKRD44_uc002utz.3_Intron	NM_153697	NP_710181			ankyrin repeat domain 44								protein binding			ovary(4)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(117;0.246)															---	---	---	---
ANKRD44	91526	broad.mit.edu	37	2	197972241	197972242	+	Intron	DEL	TT	-	-	rs72237044		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197972241_197972242delTT	uc002uuc.2	-						ANKRD44_uc002utz.3_Intron|ANKRD44_uc002uua.1_Intron|ANKRD44_uc002uub.2_Intron|ANKRD44_uc010zgw.1_Intron	NM_153697	NP_710181			ankyrin repeat domain 44								protein binding			ovary(4)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(117;0.246)															---	---	---	---
BOLL	66037	broad.mit.edu	37	2	198593345	198593345	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198593345delA	uc002uus.2	-						uc002uup.2_Intron|BOLL_uc002uur.2_Intron|BOLL_uc002uut.2_Intron|BOLL_uc010zha.1_Intron|BOLL_uc002uuu.1_Intron	NM_033030	NP_149019			boule isoform 2						cell differentiation|meiosis|multicellular organismal development|positive regulation of translational initiation|spermatogenesis	cytoplasm	nucleotide binding|protein binding|RNA binding|translation activator activity			ovary(2)	2																		---	---	---	---
PLCL1	5334	broad.mit.edu	37	2	198927464	198927464	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198927464delA	uc010fsp.2	+						PLCL1_uc002uuv.3_Intron	NM_001114661	NP_001108133			RecName: Full=Inactive phospholipase C-like protein 1;          Short=PLC-L1; AltName: Full=Phospholipase C-deleted in lung carcinoma; AltName: Full=Phospholipase C-related but catalytically inactive protein;          Short=PRIP;						intracellular signal transduction|lipid metabolic process	cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|skin(1)	2					Quinacrine(DB01103)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	199157524	199157524	+	IGR	DEL	C	-	-	rs34798348		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:199157524delC								PLCL1 (142918 upstream) : SATB2 (976700 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	199647540	199647540	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:199647540delA								PLCL1 (632934 upstream) : SATB2 (486684 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	199789025	199789026	+	IGR	DEL	GT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:199789025_199789026delGT								PLCL1 (774419 upstream) : SATB2 (345198 downstream)																																			---	---	---	---
SATB2	23314	broad.mit.edu	37	2	200136824	200136825	+	3'UTR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200136824_200136825insA	uc002uuy.1	-	11					SATB2_uc010fsq.1_3'UTR|SATB2_uc002uuz.1_3'UTR|SATB2_uc002uva.1_3'UTR	NM_015265	NP_056080			SATB homeobox 2							cytoplasm|nuclear matrix	sequence-specific DNA binding transcription factor activity			ovary(1)	1																		---	---	---	---
C2orf60	129450	broad.mit.edu	37	2	200798091	200798091	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200798091delA	uc002uvi.3	-						C2orf60_uc002uvj.3_Intron|C2orf60_uc002uvk.3_Intron|C2orf60_uc010fss.2_Intron	NM_001039693	NP_001034782			hypothetical protein LOC129450						wybutosine biosynthetic process		iron ion binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein homodimerization activity|tRNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	200864467	200864467	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:200864467delT								C2orf47 (35622 upstream) : SPATS2L (306137 downstream)																																			---	---	---	---
AOX1	316	broad.mit.edu	37	2	201495240	201495241	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201495240_201495241delAA	uc002uvx.2	+						AOX1_uc010zhf.1_Intron|AOX1_uc010fsu.2_Intron	NM_001159	NP_001150			aldehyde oxidase 1						inflammatory response|reactive oxygen species metabolic process	cytoplasm	2 iron, 2 sulfur cluster binding|aldehyde oxidase activity|flavin adenine dinucleotide binding|iron ion binding|NAD binding|xanthine dehydrogenase activity			ovary(4)|pancreas(1)|skin(1)	6					Brimonidine(DB00484)|Chlorpromazine(DB00477)|Famciclovir(DB00426)|Menadione(DB00170)|Methotrexate(DB00563)|NADH(DB00157)|Palonosetron(DB00377)|Penciclovir(DB00299)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	201694714	201694717	+	IGR	DEL	AAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201694714_201694717delAAAA								BZW1 (6155 upstream) : CLK1 (23015 downstream)																																			---	---	---	---
FAM126B	285172	broad.mit.edu	37	2	201881949	201881951	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201881949_201881951delTTT	uc002uws.3	-						FAM126B_uc002uwu.2_Intron|FAM126B_uc002uwv.2_Intron|FAM126B_uc002uww.1_Intron	NM_173822	NP_776183			hypothetical protein LOC285172							intracellular				ovary(1)	1																		---	---	---	---
CASP8	841	broad.mit.edu	37	2	202099180	202099181	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202099180_202099181delTT	uc002uxr.1	+						CASP8_uc010ftc.1_Intron|CASP8_uc002uxo.1_Intron|CASP8_uc002uxp.1_Intron|CASP8_uc002uxq.1_Intron|CASP8_uc002uxn.2_Intron	NM_033355	NP_203519			caspase 8 isoform B precursor						activation of caspase activity|activation of pro-apoptotic gene products|cellular component disassembly involved in apoptosis|cellular response to mechanical stimulus|induction of apoptosis by extracellular signals|induction of apoptosis by intracellular signals|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteolysis involved in cellular protein catabolic process|response to tumor necrosis factor	centrosome|cytosol|mitochondrial outer membrane	cysteine-type endopeptidase activity|protein binding|protein binding			upper_aerodigestive_tract(2)|ovary(1)|breast(1)|skin(1)	5															HNSCC(4;0.00038)			---	---	---	---
ALS2	57679	broad.mit.edu	37	2	202580260	202580260	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202580260delT	uc002uyo.2	-						ALS2_uc010ftl.2_Intron	NM_020919	NP_065970			alsin isoform 1						cell death|endosome organization|positive regulation of Rac GTPase activity|regulation of endosome size	centrosome|cytosol|early endosome|growth cone|lamellipodium|protein complex|ruffle	protein homodimerization activity|protein serine/threonine kinase activator activity|Rab GTPase binding|Rab guanyl-nucleotide exchange factor activity|Rac guanyl-nucleotide exchange factor activity|Ran guanyl-nucleotide exchange factor activity			skin(5)|lung(1)|breast(1)	7																		---	---	---	---
CDK15	65061	broad.mit.edu	37	2	202672518	202672518	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202672518delA	uc002uyt.2	+						CDK15_uc010ftm.2_Intron|CDK15_uc002uys.2_Intron|CDK15_uc010ftn.1_Intron|CDK15_uc010fto.1_Intron	NM_139158	NP_631897			PFTAIRE protein kinase 2								ATP binding|cyclin-dependent protein kinase activity|metal ion binding|protein binding			breast(2)|ovary(1)|lung(1)|kidney(1)	5					Adenosine triphosphate(DB00171)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	202915269	202915271	+	IGR	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202915269_202915271delAAA								FZD7 (12109 upstream) : SUMO1 (155632 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	202930763	202930763	+	IGR	DEL	T	-	-	rs74914867		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202930763delT								FZD7 (27603 upstream) : SUMO1 (140140 downstream)																																			---	---	---	---
SUMO1	7341	broad.mit.edu	37	2	203084974	203084974	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203084974delA	uc002uyz.1	-						SUMO1_uc002uza.1_Intron	NM_001005781	NP_001005781			SMT3 suppressor of mif two 3 homolog 1 isoform a						DNA repair|interferon-gamma-mediated signaling pathway|negative regulation of DNA binding|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|palate development|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein complex assembly|protein sumoylation|regulation of interferon-gamma-mediated signaling pathway|regulation of protein localization	cytoplasm|nuclear membrane|nuclear pore|nuclear speck	ubiquitin protein ligase binding				0																		---	---	---	---
NOP58	51602	broad.mit.edu	37	2	203142921	203142921	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203142921delT	uc002uzb.2	+						NOP58_uc010zhv.1_Intron	NM_015934	NP_057018			NOP58 ribonucleoprotein homolog						cell growth|rRNA processing|snRNP protein import into nucleus	box C/D snoRNP complex|Cajal body|cytoplasm|pre-snoRNP complex	protein binding|snoRNA binding				0																		---	---	---	---
NOP58	51602	broad.mit.edu	37	2	203168133	203168133	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203168133delA	uc002uzb.2	+	15	1714	c.1564delA	c.(1564-1566)AAAfs	p.K522fs		NM_015934	NP_057018	Q9Y2X3	NOP58_HUMAN	NOP58 ribonucleoprotein homolog	522	Lys-rich.				cell growth|rRNA processing|snRNP protein import into nucleus	box C/D snoRNP complex|Cajal body|cytoplasm|pre-snoRNP complex	protein binding|snoRNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	203184162	203184165	+	IGR	DEL	AAAA	-	-	rs72445165		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203184162_203184165delAAAA								NOP58 (15780 upstream) : BMPR2 (56885 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	203191565	203191567	+	IGR	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203191565_203191567delAAA								NOP58 (23183 upstream) : BMPR2 (49483 downstream)																																			---	---	---	---
BMPR2	659	broad.mit.edu	37	2	203378636	203378636	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203378636delA	uc002uzf.3	+						BMPR2_uc010ftr.2_Intron	NM_001204	NP_001195			bone morphogenetic protein receptor type II						anterior/posterior pattern formation|BMP signaling pathway|cellular response to starvation|lung alveolus development|mesoderm formation|negative regulation of cell growth|negative regulation of systemic arterial blood pressure|negative regulation of vasoconstriction|positive regulation of BMP signaling pathway|positive regulation of bone mineralization|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of epithelial cell migration|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|regulation of lung blood pressure|transcription from RNA polymerase II promoter|vascular endothelial growth factor receptor signaling pathway	integral to plasma membrane	ATP binding|metal ion binding|transforming growth factor beta receptor activity			ovary(4)|breast(2)|large_intestine(1)|stomach(1)|pancreas(1)	9																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	203462898	203462898	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203462898delT								BMPR2 (30425 upstream) : FAM117B (37003 downstream)																																			---	---	---	---
FAM117B	150864	broad.mit.edu	37	2	203518515	203518515	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203518515delT	uc010zhx.1	+						FAM117B_uc010zhw.1_Intron	NM_173511	NP_775782			amyotrophic lateral sclerosis 2 (juvenile)											ovary(1)	1																		---	---	---	---
ALS2CR8	79800	broad.mit.edu	37	2	203829178	203829178	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203829178delT	uc002uzo.2	+						ALS2CR8_uc010zhy.1_Intron|ALS2CR8_uc010zhz.1_Intron|ALS2CR8_uc010ftu.1_Intron|ALS2CR8_uc010zia.1_Intron|ALS2CR8_uc010zib.1_Intron|ALS2CR8_uc010zic.1_Intron|ALS2CR8_uc002uzp.2_Intron	NM_001104586	NP_001098056			amyotrophic lateral sclerosis 2 (juvenile)											large_intestine(1)|ovary(1)	2																		---	---	---	---
CYP20A1	57404	broad.mit.edu	37	2	204144676	204144676	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204144676delT	uc002uzv.3	+						CYP20A1_uc002uzx.3_Intron|CYP20A1_uc010zif.1_Intron|CYP20A1_uc002uzy.3_Intron|CYP20A1_uc002uzw.3_Intron|CYP20A1_uc010ftw.2_Intron	NM_177538	NP_803882			cytochrome P450, family 20, subfamily A,							integral to membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	204528442	204528442	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204528442delT								RAPH1 (128384 upstream) : CD28 (42756 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	204643646	204643647	+	IGR	INS	-	A	A	rs111707441		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204643646_204643647insA								CD28 (41090 upstream) : CTLA4 (88862 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	204695699	204695699	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204695699delA								CD28 (93143 upstream) : CTLA4 (36810 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	204753728	204753728	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204753728delA								CTLA4 (15045 upstream) : ICOS (47743 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	205031250	205031256	+	IGR	DEL	AAAAAAA	-	-	rs72235500		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:205031250_205031256delAAAAAAA								ICOS (204954 upstream) : PARD3B (379260 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	205139531	205139533	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:205139531_205139533delTTT								ICOS (313235 upstream) : PARD3B (270983 downstream)																																			---	---	---	---
PARD3B	117583	broad.mit.edu	37	2	205445032	205445032	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:205445032delT	uc002var.1	+						PARD3B_uc010fub.1_Intron|PARD3B_uc002vao.1_Intron|PARD3B_uc002vap.1_Intron|PARD3B_uc002vaq.1_Intron	NM_152526	NP_689739			par-3 partitioning defective 3 homolog B isoform						cell cycle|cell division	endomembrane system|tight junction				skin(2)|ovary(1)|breast(1)	4		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)														---	---	---	---
PARD3B	117583	broad.mit.edu	37	2	205468276	205468277	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:205468276_205468277delTT	uc002var.1	+						PARD3B_uc010fub.1_Intron|PARD3B_uc002vao.1_Intron|PARD3B_uc002vap.1_Intron|PARD3B_uc002vaq.1_Intron	NM_152526	NP_689739			par-3 partitioning defective 3 homolog B isoform						cell cycle|cell division	endomembrane system|tight junction				skin(2)|ovary(1)|breast(1)	4		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)														---	---	---	---
PARD3B	117583	broad.mit.edu	37	2	205657268	205657268	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:205657268delT	uc002var.1	+						PARD3B_uc010fub.1_Intron|PARD3B_uc002vao.1_Intron|PARD3B_uc002vap.1_Intron|PARD3B_uc002vaq.1_Intron	NM_152526	NP_689739			par-3 partitioning defective 3 homolog B isoform						cell cycle|cell division	endomembrane system|tight junction				skin(2)|ovary(1)|breast(1)	4		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)														---	---	---	---
PARD3B	117583	broad.mit.edu	37	2	205810618	205810619	+	Intron	INS	-	T	T	rs146849433	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:205810618_205810619insT	uc002var.1	+						PARD3B_uc010fub.1_Intron|PARD3B_uc002vao.1_Intron|PARD3B_uc002vap.1_Intron|PARD3B_uc002vaq.1_Intron	NM_152526	NP_689739			par-3 partitioning defective 3 homolog B isoform						cell cycle|cell division	endomembrane system|tight junction				skin(2)|ovary(1)|breast(1)	4		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)														---	---	---	---
PARD3B	117583	broad.mit.edu	37	2	205889320	205889320	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:205889320delT	uc002var.1	+						PARD3B_uc010fub.1_Intron|PARD3B_uc002vao.1_Intron|PARD3B_uc002vap.1_Intron|PARD3B_uc002vaq.1_Intron	NM_152526	NP_689739			par-3 partitioning defective 3 homolog B isoform						cell cycle|cell division	endomembrane system|tight junction				skin(2)|ovary(1)|breast(1)	4		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)														---	---	---	---
PARD3B	117583	broad.mit.edu	37	2	206162457	206162457	+	Intron	DEL	T	-	-	rs35954752		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206162457delT	uc002var.1	+						PARD3B_uc010fub.1_Intron|PARD3B_uc002vao.1_Intron|PARD3B_uc002vap.1_Intron|PARD3B_uc002vaq.1_Intron	NM_152526	NP_689739			par-3 partitioning defective 3 homolog B isoform						cell cycle|cell division	endomembrane system|tight junction				skin(2)|ovary(1)|breast(1)	4		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)														---	---	---	---
NRP2	8828	broad.mit.edu	37	2	206629885	206629885	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206629885delC	uc002vaw.2	+						NRP2_uc002vau.2_Intron|NRP2_uc002vav.2_Intron|NRP2_uc002vax.2_Intron|NRP2_uc002vay.2_Intron	NM_201266	NP_957718			neuropilin 2 isoform 1 precursor						angiogenesis|axon guidance|cell adhesion	integral to membrane|membrane fraction|plasma membrane	heparin binding|metal ion binding|semaphorin receptor activity|vascular endothelial growth factor receptor activity			skin(2)|ovary(1)|central_nervous_system(1)	4																		---	---	---	---
INO80D	54891	broad.mit.edu	37	2	206872713	206872714	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206872713_206872714delTT	uc002vaz.3	-							NM_017759	NP_060229			INO80 complex subunit D						DNA recombination|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(1)	1																		---	---	---	---
INO80D	54891	broad.mit.edu	37	2	206931970	206931973	+	Intron	DEL	AAAA	-	-	rs77263877		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206931970_206931973delAAAA	uc002vaz.3	-							NM_017759	NP_060229			INO80 complex subunit D						DNA recombination|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	207087776	207087776	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207087776delT								GPR1 (5005 upstream) : ZDBF2 (51747 downstream)																																			---	---	---	---
ADAM23	8745	broad.mit.edu	37	2	207408475	207408476	+	Intron	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207408475_207408476delAC	uc002vbq.2	+						ADAM23_uc010ziv.1_Intron	NM_003812	NP_003803			ADAM metallopeptidase domain 23 preproprotein						cell adhesion|central nervous system development|proteolysis	extracellular region|integral to plasma membrane	integrin binding|metalloendopeptidase activity|zinc ion binding			skin(2)|ovary(1)	3				LUSC - Lung squamous cell carcinoma(261;0.0961)|Lung(261;0.182)|Epithelial(149;0.205)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	207919802	207919802	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207919802delA								CPO (85604 upstream) : KLF7 (25727 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	208081258	208081258	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208081258delA								KLF7 (49687 upstream) : MIR1302-4 (52741 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	208573245	208573246	+	IGR	DEL	TT	-	-	rs145818915		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208573245_208573246delTT								FAM119A (83180 upstream) : CCNYL1 (3018 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	208659863	208659864	+	IGR	INS	-	TC	TC			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208659863_208659864insTC								FZD5 (25720 upstream) : PLEKHM3 (26148 downstream)																																			---	---	---	---
PLEKHM3	389072	broad.mit.edu	37	2	208861732	208861733	+	Intron	DEL	AA	-	-	rs72190439		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208861732_208861733delAA	uc002vcl.2	-						PLEKHM3_uc002vcm.2_Intron	NM_001080475	NP_001073944			pleckstrin homology domain containing, family M,						intracellular signal transduction		metal ion binding			ovary(1)	1																		---	---	---	---
PLEKHM3	389072	broad.mit.edu	37	2	208892959	208892959	+	5'Flank	DEL	A	-	-	rs79092542		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208892959delA	uc002vcl.2	-						PLEKHM3_uc002vcm.2_5'Flank	NM_001080475	NP_001073944			pleckstrin homology domain containing, family M,						intracellular signal transduction		metal ion binding			ovary(1)	1																		---	---	---	---
PTH2R	5746	broad.mit.edu	37	2	209375603	209375603	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209375603delT	uc010fuo.1	+											Homo sapiens cDNA FLJ60238 complete cds, highly similar to Parathyroid hormone receptor precursor.							integral to plasma membrane	parathyroid hormone receptor activity			ovary(1)|breast(1)|skin(1)	3				Epithelial(149;0.0684)|Lung(261;0.0785)|LUSC - Lung squamous cell carcinoma(261;0.0836)														---	---	---	---
MAP2	4133	broad.mit.edu	37	2	210545255	210545255	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210545255delT	uc002vde.1	+						MAP2_uc002vdc.1_Intron|MAP2_uc002vdd.1_Intron|MAP2_uc002vdf.1_Intron|MAP2_uc002vdg.1_Intron|MAP2_uc002vdh.1_Intron|MAP2_uc002vdi.1_Intron	NM_002374	NP_002365			microtubule-associated protein 2 isoform 1						central nervous system neuron development|dendrite morphogenesis|negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	beta-dystroglycan binding|calmodulin binding|structural molecule activity			ovary(9)|upper_aerodigestive_tract(2)|large_intestine(2)|pancreas(2)|central_nervous_system(1)|skin(1)	17		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Estramustine(DB01196)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	211142508	211142509	+	IGR	INS	-	T	T	rs138806816	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211142508_211142509insT								ACADL (52293 upstream) : MYL1 (12360 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	211276816	211276816	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211276816delA								MYL1 (96921 upstream) : LANCL1 (19158 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	211758778	211758780	+	IGR	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211758778_211758780delAAA								CPS1 (214949 upstream) : ERBB4 (481662 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	211908118	211908118	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211908118delT								CPS1 (364289 upstream) : ERBB4 (332324 downstream)																																			---	---	---	---
ERBB4	2066	broad.mit.edu	37	2	212456065	212456065	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:212456065delT	uc002veg.1	-						ERBB4_uc002veh.1_Intron|ERBB4_uc010zji.1_Intron|ERBB4_uc010zjj.1_Intron|ERBB4_uc010fut.1_Intron	NM_005235	NP_005226			v-erb-a erythroblastic leukemia viral oncogene						cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent|transmembrane receptor protein tyrosine kinase signaling pathway	basolateral plasma membrane|cytoplasm|integral to membrane|nucleus	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(21)|skin(5)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	33		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)											TSP Lung(8;0.080)			---	---	---	---
Unknown	0	broad.mit.edu	37	2	213532415	213532415	+	IGR	DEL	A	-	-	rs36060781		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:213532415delA								ERBB4 (129063 upstream) : IKZF2 (331998 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	213769867	213769868	+	IGR	INS	-	GGG	GGG	rs143840421	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:213769867_213769868insGGG								ERBB4 (366515 upstream) : IKZF2 (94545 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	213805368	213805368	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:213805368delT								ERBB4 (402016 upstream) : IKZF2 (59045 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	214089389	214089390	+	IGR	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:214089389_214089390delAC								IKZF2 (73056 upstream) : SPAG16 (59726 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	214135072	214135074	+	IGR	DEL	AAA	-	-	rs78003063		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:214135072_214135074delAAA								IKZF2 (118739 upstream) : SPAG16 (14042 downstream)																																			---	---	---	---
SPAG16	79582	broad.mit.edu	37	2	214559501	214559504	+	Intron	DEL	TTCC	-	-	rs35547318		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:214559501_214559504delTTCC	uc002veq.2	+						SPAG16_uc010fuz.1_Intron|SPAG16_uc002ver.2_Intron|SPAG16_uc010zjk.1_Intron	NM_024532	NP_078808			sperm associated antigen 16 isoform 1						cilium assembly	cilium axoneme|flagellar axoneme				ovary(1)|skin(1)	2		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)														---	---	---	---
SPAG16	79582	broad.mit.edu	37	2	214968668	214968669	+	Intron	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:214968668_214968669delAG	uc002veq.2	+						SPAG16_uc010fuz.1_Intron|SPAG16_uc002ver.2_Intron|SPAG16_uc010zjk.1_Intron	NM_024532	NP_078808			sperm associated antigen 16 isoform 1						cilium assembly	cilium axoneme|flagellar axoneme				ovary(1)|skin(1)	2		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	215574738	215574739	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215574738_215574739delAA								VWC2L (134085 upstream) : BARD1 (18536 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	215712227	215712227	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215712227delA								BARD1 (37799 upstream) : ABCA12 (84040 downstream)																																			---	---	---	---
ABCA12	26154	broad.mit.edu	37	2	215866486	215866486	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215866486delA	uc002vew.2	-						ABCA12_uc002vev.2_Intron|ABCA12_uc010zjn.1_Intron	NM_173076	NP_775099			ATP-binding cassette, sub-family A, member 12						cellular homeostasis|lipid transport	integral to membrane	ATP binding|ATPase activity			ovary(6)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	11		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)														---	---	---	---
ABCA12	26154	broad.mit.edu	37	2	215873518	215873518	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215873518delA	uc002vew.2	-						ABCA12_uc002vev.2_Intron|ABCA12_uc010zjn.1_Intron	NM_173076	NP_775099			ATP-binding cassette, sub-family A, member 12						cellular homeostasis|lipid transport	integral to membrane	ATP binding|ATPase activity			ovary(6)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	11		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)														---	---	---	---
ATIC	471	broad.mit.edu	37	2	216211202	216211203	+	Intron	DEL	TT	-	-	rs112969952		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216211202_216211203delTT	uc002vex.3	+						ATIC_uc010zjo.1_Intron|ATIC_uc002vey.3_Intron	NM_004044	NP_004035			5-aminoimidazole-4-carboxamide ribonucleotide						IMP biosynthetic process|purine base metabolic process	cytosol	IMP cyclohydrolase activity|phosphoribosylaminoimidazolecarboxamide formyltransferase activity|protein homodimerization activity		ATIC/ALK(24)	haematopoietic_and_lymphoid_tissue(22)|ovary(2)|lung(2)|soft_tissue(2)|skin(1)	29		Renal(323;0.229)		Epithelial(149;2.02e-06)|all cancers(144;0.000316)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.0097)	Tetrahydrofolic acid(DB00116)			T	ALK	ALCL								---	---	---	---
ATIC	471	broad.mit.edu	37	2	216212413	216212413	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216212413delT	uc002vex.3	+						ATIC_uc010zjo.1_Intron|ATIC_uc002vey.3_Intron	NM_004044	NP_004035			5-aminoimidazole-4-carboxamide ribonucleotide						IMP biosynthetic process|purine base metabolic process	cytosol	IMP cyclohydrolase activity|phosphoribosylaminoimidazolecarboxamide formyltransferase activity|protein homodimerization activity		ATIC/ALK(24)	haematopoietic_and_lymphoid_tissue(22)|ovary(2)|lung(2)|soft_tissue(2)|skin(1)	29		Renal(323;0.229)		Epithelial(149;2.02e-06)|all cancers(144;0.000316)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.0097)	Tetrahydrofolic acid(DB00116)			T	ALK	ALCL								---	---	---	---
FN1	2335	broad.mit.edu	37	2	216237928	216237929	+	Intron	INS	-	A	A	rs2289199	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216237928_216237929insA	uc002vfa.2	-						FN1_uc002vfb.2_Intron|FN1_uc002vfc.2_Intron|FN1_uc002vfd.2_Intron|FN1_uc002vfe.2_Intron|FN1_uc002vff.2_Intron|FN1_uc002vfg.2_Intron|FN1_uc002vfh.2_Intron|FN1_uc002vfi.2_Intron|FN1_uc002vfj.2_Intron|FN1_uc002vez.2_Intron|FN1_uc010zjp.1_Intron|FN1_uc002vfk.1_Intron|FN1_uc010fva.1_Intron|FN1_uc010fvb.1_Intron|FN1_uc010fvc.1_Intron|FN1_uc010fvd.1_Intron	NM_212482	NP_997647			fibronectin 1 isoform 1 preproprotein						acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading	ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix	collagen binding|extracellular matrix structural constituent|heparin binding			central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1)	13		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	216590830	216590833	+	Intron	DEL	AAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216590830_216590833delAAAA	uc002vfm.1	-						uc002vfn.1_Intron					Homo sapiens cDNA FLJ34546 fis, clone HLUNG2008959.																														---	---	---	---
PECR	55825	broad.mit.edu	37	2	216913912	216913912	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216913912delA	uc002vft.2	-						PECR_uc010zjq.1_Intron|PECR_uc002vfr.2_Intron|PECR_uc002vfs.2_Intron	NM_018441	NP_060911			peroxisomal trans-2-enoyl-CoA reductase						fatty acid biosynthetic process|regulation of apoptosis	peroxisome	binding|trans-2-enoyl-CoA reductase (NADPH) activity				0		Renal(323;0.0327)		Epithelial(149;3.8e-06)|all cancers(144;0.000272)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Adenine(DB00173)													---	---	---	---
MARCH4	57574	broad.mit.edu	37	2	217179649	217179649	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217179649delA	uc002vgb.2	-							NM_020814	NP_065865			membrane-associated ring finger (C3HC4) 4							Golgi membrane|Golgi stack|integral to membrane|trans-Golgi network	ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		Renal(323;0.0854)		Epithelial(149;2.19e-05)|all cancers(144;0.00121)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0125)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	217271799	217271799	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217271799delC								MARCH4 (35049 upstream) : SMARCAL1 (5338 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	217380628	217380631	+	IGR	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217380628_217380631delTTTT								RPL37A (14442 upstream) : IGFBP2 (117496 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	217672196	217672196	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:217672196delT								IGFBP5 (111924 upstream) : TNP1 (51988 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	218108303	218108310	+	IGR	DEL	AACACACA	-	-	rs36231294		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218108303_218108310delAACACACA								TNP1 (383521 upstream) : DIRC3 (40438 downstream)																																			---	---	---	---
DIRC3	729582	broad.mit.edu	37	2	218172508	218172508	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218172508delT	uc002vgn.1	-						DIRC3_uc002vgo.2_Intron					Homo sapiens cDNA FLJ14199 fis, clone NT2RP3002713.												0																		---	---	---	---
DIRC3	729582	broad.mit.edu	37	2	218600536	218600536	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:218600536delG	uc002vgo.2	-							NR_026597				Homo sapiens cDNA FLJ14199 fis, clone NT2RP3002713.												0																		---	---	---	---
PNKD	25953	broad.mit.edu	37	2	219145117	219145117	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219145117delG	uc002vhn.2	+						TMBIM1_uc002vhp.1_Intron|TMBIM1_uc010zjz.1_Intron|TMBIM1_uc010zka.1_Intron|TMBIM1_uc002vho.1_Intron	NM_015488	NP_056303			myofibrillogenesis regulator 1 isoform 1							membrane|mitochondrion|nucleus	hydroxyacylglutathione hydrolase activity|zinc ion binding				0		Renal(207;0.0474)		Epithelial(149;7.33e-07)|all cancers(144;0.000133)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
C2orf62	375307	broad.mit.edu	37	2	219227356	219227357	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219227356_219227357insA	uc002vhr.2	+						C2orf62_uc002vhs.2_Intron	NM_198559	NP_940961			hypothetical protein LOC375307												0		Renal(207;0.0915)		Epithelial(149;8.08e-07)|all cancers(144;0.000146)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
RQCD1	9125	broad.mit.edu	37	2	219449944	219449944	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219449944delT	uc010zkh.1	+						RQCD1_uc002vih.1_Intron|RQCD1_uc010zki.1_Intron	NM_005444	NP_005435			RCD1 required for cell differentiation1 homolog						nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|sex differentiation|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|nucleus	protein binding			ovary(1)|skin(1)	2		Renal(207;0.0915)		Epithelial(149;1.13e-06)|all cancers(144;0.000192)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
RNF25	64320	broad.mit.edu	37	2	219535990	219535992	+	Intron	DEL	TTT	-	-	rs35556340		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219535990_219535992delTTT	uc002vit.2	-						STK36_uc002viu.2_5'Flank|STK36_uc002viv.2_5'Flank|RNF25_uc010fvw.2_Intron	NM_022453	NP_071898			ring finger protein 25						positive regulation of NF-kappaB transcription factor activity	cytosol|nucleus	NF-kappaB binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2		Renal(207;0.0474)		Epithelial(149;6.99e-07)|all cancers(144;0.000129)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	219774073	219774073	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219774073delC	uc002vje.1	-											Homo sapiens, clone IMAGE:5191738, mRNA.																														---	---	---	---
ABCB6	10058	broad.mit.edu	37	2	220077254	220077254	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220077254delT	uc002vkc.1	-						ABCB6_uc010fwe.1_Intron	NM_005689	NP_005680			ATP-binding cassette, sub-family B, member 6						cadmium ion transmembrane transport|cellular iron ion homeostasis|detoxification of cadmium ion|porphyrin biosynthetic process	ATP-binding cassette (ABC) transporter complex|Golgi apparatus|integral to mitochondrial outer membrane|plasma membrane|vacuolar membrane	ATP binding|efflux transmembrane transporter activity|heme binding|heme-transporting ATPase activity			breast(1)|central_nervous_system(1)	2		Renal(207;0.0474)		Epithelial(149;1.22e-06)|all cancers(144;0.000201)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
ATG9A	79065	broad.mit.edu	37	2	220090841	220090842	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220090841_220090842insT	uc002vke.1	-						ATG9A_uc002vkd.1_Intron|ATG9A_uc002vkf.1_Intron	NM_001077198	NP_001070666			APG9 autophagy 9-like 1						autophagic vacuole assembly|protein transport	autophagic vacuole membrane|cytoplasmic vesicle|Golgi apparatus|integral to membrane|late endosome membrane				skin(1)	1		Renal(207;0.0474)		Epithelial(149;1.37e-06)|all cancers(144;0.000222)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
DNPEP	23549	broad.mit.edu	37	2	220234703	220234703	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220234703delA	uc010zlf.1	-							NM_012100				aspartyl aminopeptidase						peptide metabolic process|proteolysis	cytoplasm	aminopeptidase activity|metallopeptidase activity|protein binding|zinc ion binding				0		Renal(207;0.0474)		Epithelial(149;1.09e-06)|all cancers(144;0.000179)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	L-Glutamic Acid(DB00142)													---	---	---	---
OBSL1	23363	broad.mit.edu	37	2	220429790	220429790	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220429790delA	uc010fwk.2	-						OBSL1_uc010zli.1_5'Flank|OBSL1_uc010fwl.1_Intron|OBSL1_uc002vmi.2_Intron|OBSL1_uc002vmj.2_Intron	NM_015311	NP_056126			obscurin-like 1						cardiac myofibril assembly	intercalated disc|M band|perinuclear region of cytoplasm|Z disc	cytoskeletal adaptor activity				0		Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	220974913	220974913	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220974913delG								SLC4A3 (468212 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	221369214	221369214	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:221369214delA								SLC4A3 (862513 upstream) : EPHA4 (913535 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	221841462	221841463	+	IGR	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:221841462_221841463insC								None (None upstream) : EPHA4 (441286 downstream)																																			---	---	---	---
PAX3	5077	broad.mit.edu	37	2	223077661	223077661	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223077661delT	uc010fwo.2	-						PAX3_uc002vmt.1_Intron|PAX3_uc002vmy.1_Intron|PAX3_uc002vmv.1_Intron|PAX3_uc002vmw.1_Intron|PAX3_uc002vmx.1_Intron	NM_181457	NP_852122			paired box 3 isoform PAX3						apoptosis|organ morphogenesis|positive regulation of transcription from RNA polymerase II promoter|sensory perception of sound|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		PAX3/FOXO1(749)|PAX3/NCOA1(8)|PAX3/NCOA2(4)	soft_tissue(761)|ovary(4)|skin(1)	766		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;1.85e-07)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)				T	FOXO1A|NCOA1	alveolar rhabdomyosarcoma		Waardenburg syndrome; craniofacial-deafness-hand syndrome						---	---	---	---
CCDC140	151278	broad.mit.edu	37	2	223167195	223167196	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223167195_223167196insT	uc002vnb.1	+							NM_153038	NP_694583			coiled-coil domain containing 140												0		Renal(207;0.0376)		Epithelial(121;4.03e-10)|all cancers(144;1.8e-07)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
ACSL3	2181	broad.mit.edu	37	2	223773360	223773360	+	Intron	DEL	A	-	-	rs80016908		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223773360delA	uc002vni.2	+						ACSL3_uc002vnj.2_Intron	NM_004457	NP_004448			acyl-CoA synthetase long-chain family member 3						long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane|peroxisomal membrane	ATP binding|fatty-acyl-CoA synthase activity|long-chain fatty acid-CoA ligase activity|protein binding			ovary(2)	2		Renal(207;0.0183)		Epithelial(121;1.28e-10)|all cancers(144;8.06e-08)|Lung(261;0.00834)|LUSC - Lung squamous cell carcinoma(224;0.00864)	Icosapent(DB00159)			T	ETV1	prostate								---	---	---	---
Unknown	0	broad.mit.edu	37	2	223840077	223840077	+	IGR	DEL	C	-	-	rs7575534		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223840077delC								ACSL3 (30723 upstream) : KCNE4 (76785 downstream)																																			---	---	---	---
WDFY1	57590	broad.mit.edu	37	2	224760080	224760081	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224760080_224760081insA	uc002vnq.2	-							NM_020830	NP_065881			WD repeat and FYVE domain containing 1							cytosol|early endosome|nucleus	1-phosphatidylinositol binding|zinc ion binding			lung(1)	1		all_lung(227;0.00682)|Lung NSC(271;0.00859)|Renal(207;0.0112)|all_hematologic(139;0.189)		Epithelial(121;5.34e-10)|all cancers(144;1.67e-07)|Lung(261;0.00807)|LUSC - Lung squamous cell carcinoma(224;0.00843)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	225496844	225496845	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225496844_225496845delAA								CUL3 (46734 upstream) : DOCK10 (132962 downstream)																																			---	---	---	---
DOCK10	55619	broad.mit.edu	37	2	225641350	225641352	+	Intron	DEL	AAA	-	-	rs142525317		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225641350_225641352delAAA	uc010fwz.1	-						DOCK10_uc002vob.2_Intron|DOCK10_uc002voa.2_Intron	NM_014689	NP_055504			dedicator of cytokinesis 10								GTP binding			ovary(2)	2		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	226085238	226085238	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:226085238delA								DOCK10 (177908 upstream) : KIAA1486 (180364 downstream)																																			---	---	---	---
KIAA1486	57624	broad.mit.edu	37	2	226366334	226366334	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:226366334delT	uc002voe.2	+						KIAA1486_uc010fxa.1_Intron	NM_020864	NP_065915			hypothetical protein LOC57624											ovary(2)|central_nervous_system(1)	3		Renal(207;0.0112)|all_lung(227;0.0477)|Lung NSC(271;0.0644)|all_hematologic(139;0.101)|Esophageal squamous(248;0.129)		Epithelial(121;6.73e-10)|all cancers(144;4.32e-07)|Lung(261;0.0161)|LUSC - Lung squamous cell carcinoma(224;0.0223)														---	---	---	---
KIAA1486	57624	broad.mit.edu	37	2	226559018	226559018	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:226559018delT	uc002vof.1	+							NM_020864	NP_065915			hypothetical protein LOC57624											ovary(2)|central_nervous_system(1)	3		Renal(207;0.0112)|all_lung(227;0.0477)|Lung NSC(271;0.0644)|all_hematologic(139;0.101)|Esophageal squamous(248;0.129)		Epithelial(121;6.73e-10)|all cancers(144;4.32e-07)|Lung(261;0.0161)|LUSC - Lung squamous cell carcinoma(224;0.0223)														---	---	---	---
IRS1	3667	broad.mit.edu	37	2	227623463	227623463	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227623463delA	uc002voh.3	-							NM_005544	NP_005535			insulin receptor substrate 1						fibroblast growth factor receptor signaling pathway|glucose homeostasis|insulin receptor signaling pathway|negative regulation of insulin receptor signaling pathway|negative regulation of insulin secretion|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity	caveola|cytosol|insulin receptor complex|microsome|nucleus	insulin receptor binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase binding|protein kinase C binding|SH2 domain binding|transmembrane receptor protein tyrosine kinase adaptor activity			lung(5)|central_nervous_system(4)|ovary(2)|pancreas(1)	12		Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23)		Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137)														---	---	---	---
RHBDD1	84236	broad.mit.edu	37	2	227788021	227788021	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227788021delT	uc002voi.2	+						RHBDD1_uc010fxc.2_Intron|RHBDD1_uc002voj.2_Intron	NM_032276	NP_115652			rhomboid domain containing 1							integral to membrane	serine-type endopeptidase activity			ovary(1)	1		Renal(207;0.023)|all_lung(227;0.13)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;1.47e-11)|all cancers(144;1.52e-08)|Lung(261;0.0128)|LUSC - Lung squamous cell carcinoma(224;0.0175)														---	---	---	---
COL4A4	1286	broad.mit.edu	37	2	227985652	227985652	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227985652delA	uc010zlt.1	-							NM_000092	NP_000083			alpha 4 type IV collagen precursor						axon guidance|glomerular basement membrane development	basal lamina|collagen type IV	extracellular matrix structural constituent|protein binding			ovary(5)|central_nervous_system(3)|pancreas(1)|breast(1)|skin(1)	11		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	228283415	228283415	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228283415delT								TM4SF20 (39393 upstream) : AGFG1 (53473 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	228297163	228297163	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228297163delT								TM4SF20 (53141 upstream) : AGFG1 (39725 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	228541596	228541597	+	IGR	INS	-	GTGT	GTGT	rs143803081	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228541596_228541597insGTGT								C2orf83 (43560 upstream) : SLC19A3 (8330 downstream)																																			---	---	---	---
SLC19A3	80704	broad.mit.edu	37	2	228561871	228561871	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228561871delA	uc002vpi.2	-						SLC19A3_uc002vpj.2_Intron|SLC19A3_uc010zlv.1_Intron	NM_025243	NP_079519			solute carrier family 19, member 3						thiamine-containing compound metabolic process	integral to membrane|plasma membrane	folic acid binding|reduced folate carrier activity|thiamine uptake transmembrane transporter activity			ovary(2)	2		Renal(207;0.0112)|all_lung(227;0.0335)|Lung NSC(271;0.142)|all_hematologic(139;0.21)|Esophageal squamous(248;0.236)		Epithelial(121;1.58e-10)|all cancers(144;8.55e-08)|Lung(261;0.00948)|LUSC - Lung squamous cell carcinoma(224;0.0125)	L-Cysteine(DB00151)													---	---	---	---
WDR69	164781	broad.mit.edu	37	2	228756854	228756854	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228756854delT	uc002vpn.1	+						WDR69_uc010zlw.1_Intron|WDR69_uc002vpo.1_Intron	NM_178821	NP_849143			WD repeat domain 69											breast(1)	1		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;1.22e-10)|all cancers(144;8.11e-08)|Lung(261;0.011)|LUSC - Lung squamous cell carcinoma(224;0.0148)														---	---	---	---
SPHKAP	80309	broad.mit.edu	37	2	228846310	228846310	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228846310delT	uc002vpq.2	-	12					SPHKAP_uc002vpp.2_3'UTR|SPHKAP_uc010zlx.1_3'UTR	NM_001142644	NP_001136116			sphingosine kinase type 1-interacting protein							cytoplasm	protein binding			skin(5)|ovary(4)|lung(1)	10		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	229380820	229380820	+	IGR	DEL	A	-	-	rs34672532		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:229380820delA								SPHKAP (334459 upstream) : PID1 (507870 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	229758313	229758314	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:229758313_229758314delTT								SPHKAP (711952 upstream) : PID1 (130376 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	229851437	229851438	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:229851437_229851438delTT								SPHKAP (805076 upstream) : PID1 (37252 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	230588947	230588948	+	IGR	DEL	CA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230588947_230588948delCA								DNER (9661 upstream) : TRIP12 (42982 downstream)																																			---	---	---	---
SLC16A14	151473	broad.mit.edu	37	2	230910277	230910277	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230910277delA	uc002vqd.1	-						FBXO36_uc010fxi.1_Intron	NM_152527	NP_689740			solute carrier family 16 (monocarboxylic acid							integral to membrane|plasma membrane	symporter activity			ovary(4)|skin(2)	6		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.149)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;7.31e-13)|all cancers(144;5.1e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00948)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	230972124	230972124	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230972124delT								FBXO36 (24108 upstream) : SP110 (61521 downstream)																																			---	---	---	---
SP110	3431	broad.mit.edu	37	2	231034021	231034021	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231034021delT	uc002vqh.3	-						SP110_uc002vqg.3_Intron	NM_004509	NP_004500			SP110 nuclear body protein isoform a						interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|signal transducer activity|zinc ion binding			ovary(2)|breast(2)	4		Renal(207;0.0112)|all_lung(227;0.0223)|Lung NSC(271;0.0983)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.169)		Epithelial(121;2.61e-12)|all cancers(144;6.39e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.0097)														---	---	---	---
SP100	6672	broad.mit.edu	37	2	231347251	231347251	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231347251delT	uc002vqt.2	+						SP100_uc002vqs.2_Intron|SP100_uc002vqu.1_Intron	NM_003113	NP_003104			nuclear antigen Sp100 isoform 2						DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|interspecies interaction between organisms|negative regulation of cellular component movement|negative regulation of DNA binding|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|negative regulation of transcription, DNA-dependent|negative regulation of viral transcription|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|response to cytokine stimulus|response to retinoic acid|response to type I interferon	cytoplasm|nuclear periphery|nucleolus|PML body	chromo shadow domain binding|DNA binding|identical protein binding|kinase binding|protein homodimerization activity|transcription coactivator activity|transcription corepressor activity|transcription factor binding			ovary(4)|central_nervous_system(1)	5		Renal(207;0.0112)|all_lung(227;0.0335)|all_hematologic(139;0.0749)|Lung NSC(271;0.142)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	231454791	231454791	+	IGR	DEL	A	-	-	rs35778997		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231454791delA								SP100 (44474 upstream) : CAB39 (122766 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	231467244	231467244	+	IGR	DEL	A	-	-	rs79431082		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231467244delA								SP100 (56927 upstream) : CAB39 (110313 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	231505248	231505248	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231505248delA								SP100 (94931 upstream) : CAB39 (72309 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	231513628	231513628	+	IGR	DEL	A	-	-	rs35445610		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231513628delA								SP100 (103311 upstream) : CAB39 (63929 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	231515144	231515144	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231515144delA								SP100 (104827 upstream) : CAB39 (62413 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	231559841	231559842	+	RNA	DEL	AA	-	-	rs77932103		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231559841_231559842delAA	uc002vqw.1	-	3		c.720_721delTT								Homo sapiens cDNA FLJ30454 fis, clone BRACE2009311.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	231850714	231850714	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231850714delC								GPR55 (25023 upstream) : SPATA3 (10125 downstream)																																			---	---	---	---
ARMC9	80210	broad.mit.edu	37	2	232065667	232065667	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232065667delG	uc002vrq.3	+						ARMC9_uc002vrp.3_Intron	NM_025139	NP_079415			armadillo repeat containing 9								binding			ovary(1)	1		Renal(207;0.0112)|all_lung(227;0.0744)|all_hematologic(139;0.0749)|Acute lymphoblastic leukemia(138;0.167)|Medulloblastoma(418;0.184)|Lung NSC(271;0.205)		Epithelial(121;1.43e-10)|LUSC - Lung squamous cell carcinoma(224;0.017)|Lung(119;0.0189)														---	---	---	---
ARMC9	80210	broad.mit.edu	37	2	232083471	232083471	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232083471delT	uc002vrq.3	+						ARMC9_uc002vrp.3_Intron	NM_025139	NP_079415			armadillo repeat containing 9								binding			ovary(1)	1		Renal(207;0.0112)|all_lung(227;0.0744)|all_hematologic(139;0.0749)|Acute lymphoblastic leukemia(138;0.167)|Medulloblastoma(418;0.184)|Lung NSC(271;0.205)		Epithelial(121;1.43e-10)|LUSC - Lung squamous cell carcinoma(224;0.017)|Lung(119;0.0189)														---	---	---	---
B3GNT7	93010	broad.mit.edu	37	2	232259830	232259830	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232259830delA	uc002vrs.2	+							NM_145236	NP_660279			UDP-GlcNAc:betaGal						protein glycosylation	Golgi membrane|integral to membrane	galactosyltransferase activity				0		Renal(207;0.025)|all_hematologic(139;0.094)|Acute lymphoblastic leukemia(138;0.164)|Medulloblastoma(418;0.232)		Epithelial(121;3.22e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0139)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	232292213	232292213	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232292213delT								B3GNT7 (26340 upstream) : NCL (27247 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	232421934	232421935	+	IGR	DEL	AC	-	-	rs150508019		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232421934_232421935delAC								NMUR1 (26752 upstream) : C2orf57 (35677 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	232501303	232501303	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232501303delA								C2orf57 (42311 upstream) : PTMA (71932 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	232684868	232684870	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232684868_232684870delTTT								COPS7B (11434 upstream) : MIR1471 (72082 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	233326576	233326576	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233326576delA								ALPI (1836 upstream) : ECEL1 (17961 downstream)																																			---	---	---	---
GIGYF2	26058	broad.mit.edu	37	2	233711877	233711877	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233711877delT	uc002vti.3	+						GIGYF2_uc002vtj.3_Intron|GIGYF2_uc002vtk.3_Intron|GIGYF2_uc002vth.3_Intron|GIGYF2_uc010zmk.1_Intron|GIGYF2_uc002vtq.3_Intron	NM_015575	NP_056390			GRB10 interacting GYF protein 2 isoform b						cell death		protein binding			ovary(4)|central_nervous_system(3)	7		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)														---	---	---	---
NGEF	25791	broad.mit.edu	37	2	233875286	233875286	+	Intron	DEL	T	-	-	rs5839464		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233875286delT	uc002vts.2	-							NM_019850	NP_062824			neuronal guanine nucleotide exchange factor						apoptosis|cell differentiation|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|growth cone|plasma membrane	Rho guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)|skin(1)	7		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.00793)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;8.65e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(119;0.00984)|GBM - Glioblastoma multiforme(43;0.0604)														---	---	---	---
INPP5D	3635	broad.mit.edu	37	2	234104167	234104167	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234104167delG	uc010zmo.1	+						INPP5D_uc010zmp.1_Intron	NM_001017915	NP_001017915			SH2 containing inositol phosphatase isoform a						apoptosis|blood coagulation|leukocyte migration|T cell receptor signaling pathway	cytosol	inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|SH3 domain binding			ovary(1)|central_nervous_system(1)	2		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0273)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0843)		Epithelial(121;1.16e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000479)|LUSC - Lung squamous cell carcinoma(224;0.00655)|Lung(119;0.00802)|GBM - Glioblastoma multiforme(43;0.0185)														---	---	---	---
SAG	6295	broad.mit.edu	37	2	234232016	234232016	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234232016delT	uc002vuh.2	+						SAG_uc010zmq.1_Intron	NM_000541	NP_000532			S-arrestin						rhodopsin mediated phototransduction|rhodopsin mediated signaling pathway		protein phosphatase inhibitor activity			ovary(1)	1		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.018)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.054)		Epithelial(121;2.86e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00608)|Lung(119;0.00714)|GBM - Glioblastoma multiforme(43;0.207)														---	---	---	---
SAG	6295	broad.mit.edu	37	2	234244221	234244222	+	Intron	INS	-	TTCA	TTCA	rs148663292	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234244221_234244222insTTCA	uc002vuh.2	+						SAG_uc010zmq.1_Intron	NM_000541	NP_000532			S-arrestin						rhodopsin mediated phototransduction|rhodopsin mediated signaling pathway		protein phosphatase inhibitor activity			ovary(1)	1		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.018)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.054)		Epithelial(121;2.86e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00608)|Lung(119;0.00714)|GBM - Glioblastoma multiforme(43;0.207)														---	---	---	---
DGKD	8527	broad.mit.edu	37	2	234303990	234303990	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234303990delT	uc002vui.1	+						DGKD_uc002vuj.1_Intron	NM_152879	NP_690618			diacylglycerol kinase, delta 130kDa isoform 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell growth|diacylglycerol metabolic process|endocytosis|epidermal growth factor receptor signaling pathway|multicellular organismal development|platelet activation|protein homooligomerization|protein transport|response to organic substance|second-messenger-mediated signaling	cytoplasm|cytoplasmic membrane-bounded vesicle|plasma membrane|plasma membrane	ATP binding|diacylglycerol binding|diacylglycerol kinase activity|metal ion binding|protein heterodimerization activity|protein homodimerization activity			central_nervous_system(2)|pancreas(1)|lung(1)|skin(1)	5		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0538)		Epithelial(121;1.31e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000416)|Lung(119;0.00285)|LUSC - Lung squamous cell carcinoma(224;0.00655)	Phosphatidylserine(DB00144)													---	---	---	---
Unknown	0	broad.mit.edu	37	2	234721412	234721412	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234721412delA								UGT1A10 (39463 upstream) : HJURP (24075 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	234945466	234945466	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234945466delA								TRPM8 (17301 upstream) : SPP2 (13880 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	235336346	235336346	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235336346delT								SPP2 (350570 upstream) : ARL4C (65342 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	236164209	236164210	+	IGR	DEL	AC	-	-	rs11895313		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236164209_236164210delAC								SH3BP4 (199853 upstream) : AGAP1 (238526 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	236209052	236209053	+	IGR	DEL	AA	-	-	rs10554722		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236209052_236209053delAA								SH3BP4 (244696 upstream) : AGAP1 (193683 downstream)																																			---	---	---	---
AGAP1	116987	broad.mit.edu	37	2	236507938	236507938	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236507938delG	uc002vvs.2	+						AGAP1_uc002vvt.2_Intron	NM_001037131	NP_001032208			centaurin, gamma 2 isoform 1						protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm	ARF GTPase activator activity|GTP binding|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
AGAP1	116987	broad.mit.edu	37	2	236720812	236720812	+	Intron	DEL	T	-	-	rs10715633		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236720812delT	uc002vvs.2	+						AGAP1_uc002vvt.2_Intron	NM_001037131	NP_001032208			centaurin, gamma 2 isoform 1						protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm	ARF GTPase activator activity|GTP binding|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
AGAP1	116987	broad.mit.edu	37	2	236819559	236819561	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236819559_236819561delAAA	uc002vvs.2	+						AGAP1_uc002vvt.2_Intron	NM_001037131	NP_001032208			centaurin, gamma 2 isoform 1						protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm	ARF GTPase activator activity|GTP binding|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
AGAP1	116987	broad.mit.edu	37	2	236954668	236954668	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236954668delG	uc002vvs.2	+						AGAP1_uc002vvt.2_Intron	NM_001037131	NP_001032208			centaurin, gamma 2 isoform 1						protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm	ARF GTPase activator activity|GTP binding|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
AGAP1	116987	broad.mit.edu	37	2	236957573	236957573	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236957573delT	uc002vvs.2	+						AGAP1_uc002vvt.2_Intron	NM_001037131	NP_001032208			centaurin, gamma 2 isoform 1						protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm	ARF GTPase activator activity|GTP binding|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
AGAP1	116987	broad.mit.edu	37	2	237013548	237013548	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237013548delA	uc002vvs.2	+						AGAP1_uc002vvt.2_Intron	NM_001037131	NP_001032208			centaurin, gamma 2 isoform 1						protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm	ARF GTPase activator activity|GTP binding|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	237041905	237041905	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237041905delA								AGAP1 (7791 upstream) : GBX2 (32402 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	237045103	237045103	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237045103delG								AGAP1 (10989 upstream) : GBX2 (29204 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	237058865	237058865	+	IGR	DEL	A	-	-	rs35670534		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237058865delA								AGAP1 (24751 upstream) : GBX2 (15442 downstream)																																			---	---	---	---
ASB18	401036	broad.mit.edu	37	2	237173538	237173539	+	5'Flank	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237173538_237173539delAA	uc010znh.1	-							NM_212556	NP_997721			ankyrin repeat and SOCS box-containing 18						intracellular signal transduction					ovary(1)	1		all_hematologic(139;0.00615)|Renal(207;0.00963)|Breast(86;0.0126)|Acute lymphoblastic leukemia(138;0.0815)		Epithelial(121;2.04e-26)|OV - Ovarian serous cystadenocarcinoma(60;1.47e-11)|BRCA - Breast invasive adenocarcinoma(100;2.88e-05)|Lung(119;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00644)|GBM - Glioblastoma multiforme(43;0.244)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	237502174	237502175	+	IGR	INS	-	TA	TA			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237502174_237502175insTA								CXCR7 (11182 upstream) : COPS8 (491909 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	237790312	237790312	+	IGR	DEL	T	-	-	rs11891045		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237790312delT								CXCR7 (299320 upstream) : COPS8 (203772 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	237862629	237862629	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237862629delA								CXCR7 (371637 upstream) : COPS8 (131455 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	238120851	238120852	+	IGR	INS	-	GTGTG	GTGTG			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238120851_238120852insGTGTG								COPS8 (113364 upstream) : COL6A3 (111803 downstream)																																			---	---	---	---
COL6A3	1293	broad.mit.edu	37	2	238234469	238234469	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238234469delA	uc002vwl.2	-						COL6A3_uc002vwo.2_Intron|COL6A3_uc010znj.1_Intron|COL6A3_uc002vwj.2_Intron	NM_004369	NP_004360			alpha 3 type VI collagen isoform 1 precursor						axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	18		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)														---	---	---	---
COL6A3	1293	broad.mit.edu	37	2	238277153	238277153	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238277153delA	uc002vwl.2	-						COL6A3_uc002vwo.2_Intron|COL6A3_uc010znj.1_Intron	NM_004369	NP_004360			alpha 3 type VI collagen isoform 1 precursor						axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	18		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)														---	---	---	---
RAB17	64284	broad.mit.edu	37	2	238501566	238501566	+	5'Flank	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238501566delC	uc002vwz.1	-						RAB17_uc002vxa.1_5'Flank|RAB17_uc002vxb.1_5'Flank	NM_022449	NP_071894			RAB17, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	intracellular|plasma membrane	GTP binding|protein binding				0		Renal(207;0.00272)|Breast(86;0.00297)|all_hematologic(139;0.182)|Ovarian(221;0.221)		Epithelial(121;9.36e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.26e-10)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000354)|Lung(119;0.011)|LUSC - Lung squamous cell carcinoma(224;0.026)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	238513651	238513651	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238513651delA								RAB17 (13915 upstream) : LRRFIP1 (22573 downstream)																																			---	---	---	---
SCLY	51540	broad.mit.edu	37	2	238925156	238925156	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238925156delT	uc002vxm.3	+						UBE2F_uc010znn.1_Intron|UBE2F_uc002vxk.2_Intron|UBE2F_uc002vxl.2_Intron|UBE2F_uc010zno.1_Intron|UBE2F_uc010znp.1_Intron	NM_016510	NP_057594			selenocysteine lyase						cellular amino acid metabolic process	cytosol	pyridoxal phosphate binding|selenocysteine lyase activity|transferase activity			ovary(2)	2		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285)														---	---	---	---
PER2	8864	broad.mit.edu	37	2	239168597	239168597	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239168597delT	uc002vyc.2	-						PER2_uc010znv.1_Intron	NM_022817	NP_073728			period 2						circadian rhythm|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	protein binding|signal transducer activity			upper_aerodigestive_tract(1)|breast(1)	2		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)														---	---	---	---
TWIST2	117581	broad.mit.edu	37	2	239779229	239779230	+	Intron	INS	-	CA	CA			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239779229_239779230insCA	uc010znx.1	+						TWIST2_uc010zny.1_Intron	NM_057179	NP_476527			twist homolog 2						negative regulation of osteoblast differentiation	cytoplasm	DNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	239942984	239942984	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239942984delT								TWIST2 (110747 upstream) : HDAC4 (26881 downstream)																																			---	---	---	---
HDAC4	9759	broad.mit.edu	37	2	240206372	240206372	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240206372delG	uc002vyk.3	-						HDAC4_uc010fyz.1_Intron|HDAC4_uc010zoa.1_Intron|HDAC4_uc010fza.2_Intron	NM_006037	NP_006028			histone deacetylase 4						B cell differentiation|cardiac muscle hypertrophy in response to stress|chromatin remodeling|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of glycolysis|negative regulation of myotube differentiation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nervous system development|peptidyl-lysine deacetylation|positive regulation of cell proliferation|positive regulation of protein sumoylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|response to denervation involved in regulation of muscle adaptation|response to interleukin-1|transcription, DNA-dependent	histone deacetylase complex|transcriptional repressor complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|potassium ion binding|repressing transcription factor binding|zinc ion binding			breast(3)|skin(2)|ovary(1)	6		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)														---	---	---	---
HDAC4	9759	broad.mit.edu	37	2	240287284	240287285	+	Intron	INS	-	AG	AG	rs138547361	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240287284_240287285insAG	uc002vyk.3	-						HDAC4_uc010fza.2_Intron	NM_006037	NP_006028			histone deacetylase 4						B cell differentiation|cardiac muscle hypertrophy in response to stress|chromatin remodeling|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of glycolysis|negative regulation of myotube differentiation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nervous system development|peptidyl-lysine deacetylation|positive regulation of cell proliferation|positive regulation of protein sumoylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|response to denervation involved in regulation of muscle adaptation|response to interleukin-1|transcription, DNA-dependent	histone deacetylase complex|transcriptional repressor complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|potassium ion binding|repressing transcription factor binding|zinc ion binding			breast(3)|skin(2)|ovary(1)	6		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	240349528	240349528	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240349528delT								HDAC4 (26182 upstream) : NDUFA10 (550630 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	240779232	240779232	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240779232delC								HDAC4 (455886 upstream) : NDUFA10 (120926 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	240859557	240859557	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240859557delG								HDAC4 (536211 upstream) : NDUFA10 (40601 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	240892566	240892566	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240892566delG								HDAC4 (569220 upstream) : NDUFA10 (7592 downstream)																																			---	---	---	---
NDUFA10	4705	broad.mit.edu	37	2	240958813	240958813	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240958813delT	uc002vyn.2	-						NDUFA10_uc010fzc.1_Intron|NDUFA10_uc002vyo.1_Intron|NDUFA10_uc002vyp.2_Intron	NM_004544	NP_004535			NADH dehydrogenase (ubiquinone) 1 alpha						mitochondrial electron transport, NADH to ubiquinone|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|transport	mitochondrial matrix|mitochondrial respiratory chain complex I	ATP binding|NADH dehydrogenase (ubiquinone) activity|phosphotransferase activity, alcohol group as acceptor			central_nervous_system(1)	1		all_epithelial(40;4.26e-15)|Breast(86;4.4e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0396)|Lung NSC(271;0.128)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(121;7.82e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.5e-13)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;2.39e-05)|Lung(119;0.00519)|LUSC - Lung squamous cell carcinoma(224;0.0202)	NADH(DB00157)													---	---	---	---
CAPN10	11132	broad.mit.edu	37	2	241529076	241529076	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241529076delG	uc002vzk.1	+						CAPN10_uc010zoh.1_Intron|CAPN10_uc002vzl.1_Intron|CAPN10_uc002vzm.1_Intron|CAPN10_uc002vzn.1_Intron|CAPN10_uc002vzo.1_Intron|CAPN10_uc010fzg.1_Intron|CAPN10_uc002vzp.1_Intron|CAPN10_uc002vzq.1_Intron	NM_023083	NP_075571			calpain 10 isoform a						actin cytoskeleton reorganization|cellular response to insulin stimulus|positive regulation of apoptosis|positive regulation of glucose import|positive regulation of insulin secretion|positive regulation of intracellular transport|proteolysis	cytosol|plasma membrane	calcium-dependent cysteine-type endopeptidase activity|cytoskeletal protein binding|SNARE binding			ovary(3)|large_intestine(2)|lung(1)	6		all_epithelial(40;1.72e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|all_neural(83;0.0459)|Lung NSC(271;0.094)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.13e-31)|all cancers(36;3.24e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.82e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;5.1e-06)|Lung(119;0.00168)|Colorectal(34;0.00495)|LUSC - Lung squamous cell carcinoma(224;0.00813)|COAD - Colon adenocarcinoma(134;0.032)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	241778192	241778192	+	IGR	DEL	A	-	-	rs34913339		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241778192delA								KIF1A (18568 upstream) : AGXT (29970 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	241907303	241907303	+	5'Flank	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241907303delC	uc002waf.2	-											Homo sapiens, clone IMAGE:5745636, mRNA.																														---	---	---	---
PASK	23178	broad.mit.edu	37	2	242047519	242047519	+	Intron	DEL	A	-	-	rs59710610	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242047519delA	uc002wao.1	-						PASK_uc010zol.1_Intron|PASK_uc010zom.1_Intron|PASK_uc010fzl.1_Intron|PASK_uc010zon.1_Intron	NM_015148	NP_055963			PAS domain containing serine/threonine kinase						regulation of transcription, DNA-dependent	Golgi apparatus	ATP binding|identical protein binding|protein serine/threonine kinase activity|signal transducer activity			ovary(4)|lung(1)|skin(1)	6		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)														---	---	---	---
HDLBP	3069	broad.mit.edu	37	2	242178792	242178792	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242178792delT	uc002waz.2	-						HDLBP_uc002wba.2_Intron|HDLBP_uc002wbb.2_Intron	NM_203346	NP_976221			high density lipoprotein binding protein						cholesterol metabolic process|lipid transport	cytoplasm|high-density lipoprotein particle|nucleus|plasma membrane	lipid binding|protein binding|RNA binding			breast(3)|skin(1)	4		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)														---	---	---	---
HDLBP	3069	broad.mit.edu	37	2	242213268	242213269	+	5'Flank	DEL	TT	-	-	rs111935616		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242213268_242213269delTT	uc002waz.2	-						HDLBP_uc002wba.2_Intron|HDLBP_uc002wbb.2_5'Flank|HDLBP_uc010fzn.1_5'Flank	NM_203346	NP_976221			high density lipoprotein binding protein						cholesterol metabolic process|lipid transport	cytoplasm|high-density lipoprotein particle|nucleus|plasma membrane	lipid binding|protein binding|RNA binding			breast(3)|skin(1)	4		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)														---	---	---	---
FARP2	9855	broad.mit.edu	37	2	242382670	242382671	+	Intron	DEL	TT	-	-	rs112563539		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242382670_242382671delTT	uc010zoq.1	+						FARP2_uc010zor.1_Intron|FARP2_uc002wbi.1_Intron|uc002wbj.2_3'UTR	NM_014808	NP_055623			FERM, RhoGEF and pleckstrin domain protein 2						axon guidance|neuron remodeling|Rac protein signal transduction|regulation of Rho protein signal transduction	cytoskeleton|cytosol|extrinsic to membrane	cytoskeletal protein binding|Rho guanyl-nucleotide exchange factor activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)														---	---	---	---
BOK	666	broad.mit.edu	37	2	242505718	242505719	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242505718_242505719delTT	uc002wbq.2	+							NM_032515	NP_115904			BCL2-related ovarian killer						activation of caspase activity|cell proliferation|signal transduction by p53 class mediator resulting in induction of apoptosis	mitochondrial membrane|nucleus				ovary(1)	1		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;2.04e-33)|all cancers(36;7.87e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.52e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.64e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0835)														---	---	---	---
Unknown	0	broad.mit.edu	37	2	242523790	242523790	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242523790delA								BOK (10239 upstream) : THAP4 (31 downstream)																																			---	---	---	---
ING5	84289	broad.mit.edu	37	2	242643984	242643984	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242643984delA	uc002wcd.2	+						ING5_uc002wcc.1_Intron	NM_032329	NP_115705			inhibitor of growth family, member 5						DNA replication|histone H3 acetylation|negative regulation of cell proliferation|negative regulation of growth|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex	protein binding|zinc ion binding				0		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;2.16e-33)|all cancers(36;4.99e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.6e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0839)														---	---	---	---
CHL1	10752	broad.mit.edu	37	3	357594	357595	+	Intron	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:357594_357595delGA	uc003bou.2	+						CHL1_uc003bot.2_Intron|CHL1_uc003bow.1_Intron	NM_006614	NP_006605			cell adhesion molecule with homology to L1CAM						axon guidance|cell adhesion|signal transduction	integral to membrane|plasma membrane|proteinaceous extracellular matrix				skin(5)|central_nervous_system(4)|large_intestine(2)|ovary(1)	12		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)														---	---	---	---
CNTN6	27255	broad.mit.edu	37	3	1213888	1213888	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:1213888delA	uc003boz.2	+						CNTN6_uc010hbo.2_Intron|CNTN6_uc011asj.1_Intron|CNTN6_uc003bpa.2_Intron	NM_014461	NP_055276			contactin 6 precursor						axon guidance|cell adhesion|central nervous system development|Notch signaling pathway	anchored to membrane|plasma membrane				skin(3)|lung(2)|breast(2)|pancreas(1)	8		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)														---	---	---	---
CNTN6	27255	broad.mit.edu	37	3	1289449	1289449	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:1289449delT	uc003boz.2	+						CNTN6_uc010hbo.2_Intron|CNTN6_uc011asj.1_Intron|CNTN6_uc003bpa.2_Intron	NM_014461	NP_055276			contactin 6 precursor						axon guidance|cell adhesion|central nervous system development|Notch signaling pathway	anchored to membrane|plasma membrane				skin(3)|lung(2)|breast(2)|pancreas(1)	8		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	1844562	1844562	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:1844562delC								CNTN6 (399285 upstream) : CNTN4 (295988 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	1930924	1930925	+	IGR	INS	-	A	A	rs146498352	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:1930924_1930925insA								CNTN6 (485647 upstream) : CNTN4 (209625 downstream)																																			---	---	---	---
CNTN4	152330	broad.mit.edu	37	3	2138879	2138879	+	5'Flank	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:2138879delG	uc003bpb.1	+							NM_175613	NP_783302			contactin 4 isoform c precursor						axon guidance|axonal fasciculation|brain development|negative regulation of neuron differentiation|neuron cell-cell adhesion|regulation of synaptic plasticity	anchored to membrane|axon|extracellular region|plasma membrane	protein binding			large_intestine(2)|ovary(2)|lung(1)|central_nervous_system(1)|pancreas(1)	7		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)														---	---	---	---
CNTN4	152330	broad.mit.edu	37	3	2906122	2906123	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:2906122_2906123insA	uc003bpc.2	+						CNTN4_uc003bpb.1_Intron|CNTN4_uc003bpd.1_Intron	NM_175607	NP_783200			contactin 4 isoform a precursor						axon guidance|axonal fasciculation|brain development|negative regulation of neuron differentiation|neuron cell-cell adhesion|regulation of synaptic plasticity	anchored to membrane|axon|extracellular region|plasma membrane	protein binding			large_intestine(2)|ovary(2)|lung(1)|central_nervous_system(1)|pancreas(1)	7		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)														---	---	---	---
IL5RA	3568	broad.mit.edu	37	3	3150830	3150831	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3150830_3150831insT	uc011ask.1	-						IL5RA_uc010hbs.2_Intron|IL5RA_uc011asl.1_Intron|IL5RA_uc011asm.1_Intron|IL5RA_uc010hbt.2_Intron|IL5RA_uc011asn.1_Intron|IL5RA_uc010hbu.2_Intron	NM_000564	NP_000555			interleukin 5 receptor, alpha isoform 1						cell proliferation	extracellular space|integral to membrane|plasma membrane	interleukin-5 receptor activity			ovary(1)	1				Epithelial(13;0.00278)|all cancers(10;0.00809)|OV - Ovarian serous cystadenocarcinoma(96;0.00944)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	3301574	3301575	+	IGR	INS	-	A	A	rs147463233	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3301574_3301575insA								CRBN (80184 upstream) : SUMF1 (521461 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	3642493	3642494	+	IGR	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3642493_3642494insG								CRBN (421103 upstream) : SUMF1 (180542 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	3678263	3678263	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3678263delT								CRBN (456873 upstream) : SUMF1 (144773 downstream)																																			---	---	---	---
SUMF1	285362	broad.mit.edu	37	3	4145141	4145141	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4145141delT	uc003bps.1	-							NM_182760				sulfatase modifying factor 1 isoform 1							endoplasmic reticulum lumen	metal ion binding|oxidoreductase activity			upper_aerodigestive_tract(1)	1		Melanoma(143;0.068)|Colorectal(144;0.233)		Epithelial(13;0.0147)|OV - Ovarian serous cystadenocarcinoma(96;0.0444)|all cancers(10;0.0549)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	4895840	4895840	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4895840delA								ITPR1 (6554 upstream) : BHLHE40 (125257 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	5049734	5049734	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5049734delA								BHLHE40 (22871 upstream) : ARL8B (114196 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	5115753	5115754	+	IGR	INS	-	A	A	rs111823556		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5115753_5115754insA								BHLHE40 (88890 upstream) : ARL8B (48176 downstream)																																			---	---	---	---
ARL8B	55207	broad.mit.edu	37	3	5197276	5197276	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5197276delT	uc003bqg.2	+						ARL8B_uc011asx.1_Intron|ARL8B_uc011asy.1_Intron	NM_018184	NP_060654			ADP-ribosylation factor-like 10C						cell cycle|cell division|chromosome segregation|small GTPase mediated signal transduction	late endosome membrane|lysosomal membrane|midbody|spindle midzone	alpha-tubulin binding|beta-tubulin binding|GDP binding|GTP binding|GTPase activity				0				OV - Ovarian serous cystadenocarcinoma(96;0.0717)|Epithelial(13;0.0777)														---	---	---	---
ARL8B	55207	broad.mit.edu	37	3	5201447	5201448	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5201447_5201448insT	uc003bqg.2	+						ARL8B_uc011asx.1_Intron|ARL8B_uc011asy.1_Intron	NM_018184	NP_060654			ADP-ribosylation factor-like 10C						cell cycle|cell division|chromosome segregation|small GTPase mediated signal transduction	late endosome membrane|lysosomal membrane|midbody|spindle midzone	alpha-tubulin binding|beta-tubulin binding|GDP binding|GTP binding|GTPase activity				0				OV - Ovarian serous cystadenocarcinoma(96;0.0717)|Epithelial(13;0.0777)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	5629588	5629589	+	IGR	INS	-	TA	TA			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:5629588_5629589insTA								EDEM1 (367939 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	6037386	6037386	+	IGR	DEL	A	-	-	rs11290389		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:6037386delA								EDEM1 (775737 upstream) : GRM7 (865416 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	6202228	6202229	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:6202228_6202229delAA								EDEM1 (940579 upstream) : GRM7 (700573 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	6327028	6327028	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:6327028delA								None (None upstream) : GRM7 (575774 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	6614314	6614314	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:6614314delT	uc003bqj.1	+											Homo sapiens clone P1 NTera2D1 teratocarcinoma mRNA.																														---	---	---	---
GRM7	2917	broad.mit.edu	37	3	7056823	7056823	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7056823delC	uc003bqm.2	+						GRM7_uc011ata.1_Intron|GRM7_uc011atb.1_Intron|GRM7_uc010hcf.2_Intron|GRM7_uc011atc.1_Intron|GRM7_uc010hcg.2_Intron|GRM7_uc003bql.2_Intron	NM_000844	NP_000835			glutamate receptor, metabotropic 7 isoform a						negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission	asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone	adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding			ovary(4)|lung(3)	7					L-Glutamic Acid(DB00142)													---	---	---	---
GRM7	2917	broad.mit.edu	37	3	7391565	7391565	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7391565delT	uc003bqm.2	+						GRM7_uc011ata.1_Intron|GRM7_uc011atb.1_Intron|GRM7_uc010hcf.2_Intron|GRM7_uc011atc.1_Intron|GRM7_uc010hcg.2_Intron|GRM7_uc003bql.2_Intron|GRM7_uc003bqn.1_Intron	NM_000844	NP_000835			glutamate receptor, metabotropic 7 isoform a						negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission	asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone	adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding			ovary(4)|lung(3)	7					L-Glutamic Acid(DB00142)													---	---	---	---
GRM7	2917	broad.mit.edu	37	3	7408989	7408989	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7408989delT	uc003bqm.2	+						GRM7_uc011ata.1_Intron|GRM7_uc011atb.1_Intron|GRM7_uc010hcf.2_Intron|GRM7_uc011atc.1_Intron|GRM7_uc010hcg.2_Intron|GRM7_uc003bql.2_Intron|GRM7_uc003bqn.1_Intron	NM_000844	NP_000835			glutamate receptor, metabotropic 7 isoform a						negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission	asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone	adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding			ovary(4)|lung(3)	7					L-Glutamic Acid(DB00142)													---	---	---	---
GRM7	2917	broad.mit.edu	37	3	7467814	7467814	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7467814delT	uc003bqm.2	+						GRM7_uc011ata.1_Intron|GRM7_uc011atb.1_Intron|GRM7_uc010hcf.2_Intron|GRM7_uc011atc.1_Intron|GRM7_uc010hcg.2_Intron|GRM7_uc003bql.2_Intron|GRM7_uc003bqn.1_Intron	NM_000844	NP_000835			glutamate receptor, metabotropic 7 isoform a						negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission	asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone	adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding			ovary(4)|lung(3)	7					L-Glutamic Acid(DB00142)													---	---	---	---
GRM7	2917	broad.mit.edu	37	3	7528408	7528409	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7528408_7528409insT	uc003bqm.2	+						GRM7_uc011ata.1_Intron|GRM7_uc011atb.1_Intron|GRM7_uc010hcf.2_Intron|GRM7_uc011atc.1_Intron|GRM7_uc010hcg.2_Intron|GRM7_uc003bql.2_Intron|GRM7_uc003bqn.1_Intron|GRM7_uc010hch.1_Intron	NM_000844	NP_000835			glutamate receptor, metabotropic 7 isoform a						negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission	asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone	adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding			ovary(4)|lung(3)	7					L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	7788409	7788409	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7788409delA								GRM7 (5191 upstream) : LMCD1 (755102 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	8355867	8355868	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:8355867_8355868insT	uc003bqp.2	-											Homo sapiens cDNA FLJ42094 fis, clone TESOP2002489.																														---	---	---	---
C3orf32	51066	broad.mit.edu	37	3	8711540	8711540	+	Intron	DEL	G	-	-	rs35261953		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:8711540delG	uc003bqz.2	-						C3orf32_uc003bqx.2_Intron|C3orf32_uc003bqy.2_Intron	NM_015931	NP_057015			hypothetical protein LOC51066											skin(1)	1																		---	---	---	---
SRGAP3	9901	broad.mit.edu	37	3	9061999	9061999	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9061999delT	uc003brf.1	-						SRGAP3_uc003brg.1_Intron|SRGAP3_uc003bri.1_Intron	NM_014850	NP_055665			SLIT-ROBO Rho GTPase activating protein 3						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding		SRGAP3/RAF1(4)	central_nervous_system(4)|skin(3)|urinary_tract(1)|breast(1)	9				OV - Ovarian serous cystadenocarcinoma(96;0.0563)				T	RAF1	pilocytic astrocytoma								---	---	---	---
Unknown	0	broad.mit.edu	37	3	9331795	9331796	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9331795_9331796delAA								SRGAP3 (40484 upstream) : LOC440944 (59578 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	9637586	9637586	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9637586delT								LHFPL4 (42100 upstream) : MTMR14 (53558 downstream)																																			---	---	---	---
MTMR14	64419	broad.mit.edu	37	3	9690580	9690580	+	5'Flank	DEL	T	-	-	rs113053674		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9690580delT	uc003brz.2	+						MTMR14_uc003bsa.2_5'Flank|MTMR14_uc003bsb.2_5'Flank|MTMR14_uc011ath.1_5'Flank|MTMR14_uc010hcl.2_5'Flank	NM_001077525	NP_001070993			jumpy isoform 2							perinuclear region of cytoplasm|ruffle	phosphatidylinositol-3-phosphatase activity|protein tyrosine phosphatase activity			skin(1)	1	Medulloblastoma(99;0.227)																	---	---	---	---
OGG1	4968	broad.mit.edu	37	3	9797996	9797997	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9797996_9797997delAA	uc003bsi.2	+						OGG1_uc003bsh.2_Intron|OGG1_uc003bsj.2_Intron|OGG1_uc003bsk.2_Intron|OGG1_uc003bsl.2_Intron|OGG1_uc003bsm.2_Intron|OGG1_uc003bsn.2_Intron|OGG1_uc003bso.2_Intron|OGG1_uc003bsp.1_Intron|OGG1_uc010hcm.1_Intron|OGG1_uc003bsq.1_Intron|OGG1_uc003bsr.1_Intron	NM_002542	NP_002533			8-oxoguanine DNA-glycosylase 1 isoform 1a						depurination|nucleotide-excision repair|regulation of protein import into nucleus, translocation|regulation of transcription, DNA-dependent|response to oxidative stress|response to radiation	mitochondrion|nuclear matrix|nuclear speck	damaged DNA binding|endonuclease activity|oxidized purine base lesion DNA N-glycosylase activity|protein binding				0	Medulloblastoma(99;0.227)												BER_DNA_glycosylases					---	---	---	---
FANCD2	2177	broad.mit.edu	37	3	10081677	10081677	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10081677delA	uc003buw.2	+						FANCD2_uc003bux.1_Intron|FANCD2_uc003buy.1_Intron|FANCD2_uc003buv.2_3'UTR	NM_033084	NP_149075			Fanconi anemia complementation group D2 isoform						DNA repair|response to gamma radiation	nucleoplasm	protein binding|protein binding			central_nervous_system(2)|ovary(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(96;0.148)				D|Mis|N|F			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
IRAK2	3656	broad.mit.edu	37	3	10216617	10216617	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10216617delA	uc003bve.1	+							NM_001570	NP_001561			interleukin-1 receptor-associated kinase 2						activation of MAPK activity|I-kappaB kinase/NF-kappaB cascade|inflammatory response|innate immune response|interleukin-1-mediated signaling pathway|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of NF-kappaB transcription factor activity|positive regulation of NF-kappaB transcription factor activity|regulation of cytokine-mediated signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cell surface|cytosol|endosome membrane|plasma membrane	ATP binding|NF-kappaB-inducing kinase activity|protein heterodimerization activity|protein homodimerization activity			lung(5)|breast(3)	8																		---	---	---	---
ATP2B2	491	broad.mit.edu	37	3	10528927	10528928	+	Intron	DEL	CA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10528927_10528928delCA	uc003bvt.2	-						ATP2B2_uc003bvv.2_Intron|ATP2B2_uc003bvw.2_Intron|ATP2B2_uc010hdp.2_Intron	NM_001001331	NP_001001331			plasma membrane calcium ATPase 2 isoform 1						ATP biosynthetic process|cytosolic calcium ion homeostasis|platelet activation	cytosol|integral to membrane|plasma membrane	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|calcium-transporting ATPase activity|calmodulin binding|calmodulin binding|metal ion binding|PDZ domain binding|protein C-terminus binding			ovary(3)|skin(2)|central_nervous_system(1)	6																		---	---	---	---
ATP2B2	491	broad.mit.edu	37	3	10634246	10634246	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10634246delT	uc003bvw.2	-							NM_001683	NP_001674			plasma membrane calcium ATPase 2 isoform 2						ATP biosynthetic process|cytosolic calcium ion homeostasis|platelet activation	cytosol|integral to membrane|plasma membrane	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|calcium-transporting ATPase activity|calmodulin binding|calmodulin binding|metal ion binding|PDZ domain binding|protein C-terminus binding			ovary(3)|skin(2)|central_nervous_system(1)	6																		---	---	---	---
SLC6A11	6538	broad.mit.edu	37	3	10960518	10960518	+	Intron	DEL	T	-	-	rs34883736		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10960518delT	uc003bvz.2	+							NM_014229	NP_055044			solute carrier family 6 (neurotransmitter						neurotransmitter secretion	integral to plasma membrane	gamma-aminobutyric acid:sodium symporter activity|neurotransmitter:sodium symporter activity			skin(3)|ovary(1)	4				OV - Ovarian serous cystadenocarcinoma(96;0.229)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	11014038	11014039	+	IGR	INS	-	TG	TG	rs7632186	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11014038_11014039insTG								SLC6A11 (33894 upstream) : SLC6A1 (20381 downstream)																																			---	---	---	---
HRH1	3269	broad.mit.edu	37	3	11284601	11284602	+	Intron	DEL	TT	-	-	rs113202543		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11284601_11284602delTT	uc010hdr.2	+						HRH1_uc010hds.2_Intron|HRH1_uc010hdt.2_Intron	NM_001098213	NP_001091683			histamine receptor H1						activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|inflammatory response	cytoplasm|integral to plasma membrane|nucleus	histamine receptor activity			large_intestine(1)|ovary(1)	2					Aceprometazine(DB01615)|Astemizole(DB00637)|Azatadine(DB00719)|Azelastine(DB00972)|Benzquinamide(DB00767)|Bepotastine(DB04890)|Bromodiphenhydramine(DB01237)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbinoxamine(DB00748)|Cetirizine(DB00341)|Chlophedianol(DB04837)|Chlorpheniramine(DB01114)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clemastine(DB00283)|Clozapine(DB00363)|Cyclizine(DB01176)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexbrompheniramine(DB00405)|Dimenhydrinate(DB00985)|Diphenhydramine(DB01075)|Diphenylpyraline(DB01146)|Doxepin(DB01142)|Doxylamine(DB00366)|Emedastine(DB01084)|Epinastine(DB00751)|Fexofenadine(DB00950)|Flunarizine(DB04841)|Histamine Phosphate(DB00667)|Hydroxyzine(DB00557)|Ketotifen(DB00920)|Levocabastine(DB01106)|Loratadine(DB00455)|Maprotiline(DB00934)|Meclizine(DB00737)|Mequitazine(DB01071)|Methdilazine(DB00902)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Nedocromil(DB00716)|Olanzapine(DB00334)|Olopatadine(DB00768)|Orphenadrine(DB01173)|Pemirolast(DB00885)|Phenindamine(DB01619)|Pheniramine(DB01620)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Terfenadine(DB00342)|Thiethylperazine(DB00372)|Trazodone(DB00656)|Trimeprazine(DB01246)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Ziprasidone(DB00246)													---	---	---	---
VGLL4	9686	broad.mit.edu	37	3	11639975	11639975	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11639975delT	uc003bwf.2	-						VGLL4_uc010hdx.1_Intron|VGLL4_uc003bwg.2_Intron|VGLL4_uc011aun.1_Intron	NM_014667	NP_055482			vestigial like 4 isoform b						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(1)	1				LUSC - Lung squamous cell carcinoma(1;0.089)|Lung(1;0.111)														---	---	---	---
VGLL4	9686	broad.mit.edu	37	3	11732123	11732123	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:11732123delA	uc003bwf.2	-						VGLL4_uc003bwg.2_Intron	NM_014667	NP_055482			vestigial like 4 isoform b						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(1)	1				LUSC - Lung squamous cell carcinoma(1;0.089)|Lung(1;0.111)														---	---	---	---
PPARG	5468	broad.mit.edu	37	3	12328138	12328138	+	5'Flank	DEL	A	-	-	rs73813169	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12328138delA	uc003bwr.2	+						PPARG_uc003bws.2_5'Flank|PPARG_uc003bwu.2_5'Flank|PPARG_uc003bwq.1_5'Flank|PPARG_uc010hdz.1_5'Flank|PPARG_uc003bwt.1_5'Flank	NM_138712	NP_619726			peroxisome proliferative activated receptor						activation of caspase activity|cell fate commitment|cell maturation|cellular response to insulin stimulus|epithelial cell differentiation|glucose homeostasis|induction of apoptosis|innate immune response|lipid homeostasis|lipoprotein transport|long-chain fatty acid transport|low-density lipoprotein particle receptor biosynthetic process|monocyte differentiation|negative regulation of cholesterol storage|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of macrophage derived foam cell differentiation|negative regulation of receptor biosynthetic process|negative regulation of sequestering of triglyceride|negative regulation of transcription from RNA polymerase II promoter|placenta development|positive regulation of fat cell differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of blood pressure|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to lipid|response to low-density lipoprotein particle stimulus|white fat cell differentiation	cytosol|nucleoplasm	activating transcription factor binding|arachidonic acid binding|drug binding|enzyme binding|prostaglandin receptor activity|retinoid X receptor binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)|kidney(1)	2					Atorvastatin(DB01076)|Icosapent(DB00159)|Pioglitazone(DB01132)|Rosiglitazone(DB00412)|Troglitazone(DB00197)			T	PAX8	follicular thyroid		Insulin resistance ; lipodystrophy|familial partial L;diabetes mellitus|insulin-resistantI|with acanthosis nigricans and hypertension						---	---	---	---
RAF1	5894	broad.mit.edu	37	3	12659890	12659890	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12659890delA	uc003bxf.3	-						RAF1_uc011auu.1_Intron	NM_002880	NP_002871			v-raf-1 murine leukemia viral oncogene homolog						activation of MAPKK activity|apoptosis|axon guidance|cell proliferation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|negative regulation of apoptosis|negative regulation of cell proliferation|negative regulation of protein complex assembly|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of peptidyl-serine phosphorylation|Ras protein signal transduction|synaptic transmission	cytosol|mitochondrial outer membrane|plasma membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|receptor signaling protein activity		ESRP1/RAF1(4)|SRGAP3/RAF1(4)	central_nervous_system(4)|prostate(4)|lung(2)|upper_aerodigestive_tract(1)|stomach(1)|liver(1)|ovary(1)	14					Sorafenib(DB00398)			T	SRGAP3	pilocytic astrocytoma				Noonan_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	3	12773823	12773823	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12773823delC								RAF1 (68123 upstream) : TMEM40 (1569 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	13261293	13261293	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13261293delG								IQSEC1 (146676 upstream) : NUP210 (96444 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	13307391	13307392	+	IGR	DEL	AA	-	-	rs113593638		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13307391_13307392delAA								IQSEC1 (192774 upstream) : NUP210 (50345 downstream)																																			---	---	---	---
FBLN2	2199	broad.mit.edu	37	3	13602477	13602477	+	Intron	DEL	C	-	-	rs4684956	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:13602477delC	uc011avb.1	+						FBLN2_uc011auz.1_Intron|FBLN2_uc011ava.1_Intron	NM_001998	NP_001989			fibulin 2 isoform b precursor							proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(1)	1			UCEC - Uterine corpus endometrioid carcinoma (1;0.00416)															---	---	---	---
C3orf20	84077	broad.mit.edu	37	3	14731483	14731484	+	Intron	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14731483_14731484delTC	uc003byy.2	+						C3orf20_uc003byz.2_Intron|C3orf20_uc003bza.2_Intron|C3orf20_uc003byx.1_Intron	NM_032137	NP_115513			hypothetical protein LOC84077							cytoplasm|integral to membrane				ovary(3)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	14845365	14845366	+	IGR	INS	-	CA	CA	rs149407655	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14845365_14845366insCA								C3orf20 (30825 upstream) : FGD5 (15103 downstream)																																			---	---	---	---
FGD5	152273	broad.mit.edu	37	3	14971558	14971558	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14971558delT	uc003bzc.2	+						FGD5_uc011avk.1_Intron|FGD5_uc003bzd.2_Intron	NM_152536	NP_689749			FYVE, RhoGEF and PH domain containing 5						actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(3)|kidney(1)|pancreas(1)	5																		---	---	---	---
DVWA	344875	broad.mit.edu	37	3	15208373	15208374	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15208373_15208374insT	uc010hel.1	-							NR_027927				Homo sapiens DIVA mRNA for Dual Intracellular Von Willebrand factor domain A, complete cds.												0																		---	---	---	---
CAPN7	23473	broad.mit.edu	37	3	15288152	15288152	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15288152delT	uc003bzn.2	+							NM_014296	NP_055111			calpain 7						proteolysis	nucleus	calcium-dependent cysteine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
SH3BP5	9467	broad.mit.edu	37	3	15352725	15352727	+	Intron	DEL	ACA	-	-	rs13326080	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15352725_15352727delACA	uc003bzp.1	-						SH3BP5_uc010hem.1_Intron|SH3BP5_uc003bzq.1_Intron|SH3BP5_uc003bzr.1_Intron	NM_004844	NP_004835			SH3-domain binding protein 5 (BTK-associated)						intracellular signal transduction	mitochondrion	protein kinase inhibitor activity|SH3 domain binding				0																		---	---	---	---
ANKRD28	23243	broad.mit.edu	37	3	15752582	15752582	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15752582delT	uc003caj.1	-						ANKRD28_uc003cai.1_Intron|ANKRD28_uc011avz.1_Intron|ANKRD28_uc003cak.1_Intron|ANKRD28_uc011awa.1_Intron|ANKRD28_uc003cal.1_Intron|ANKRD28_uc003cam.2_Intron	NM_015199	NP_056014			ankyrin repeat domain 28							nucleoplasm	protein binding			breast(1)	1																		---	---	---	---
GALNTL2	117248	broad.mit.edu	37	3	16174154	16174154	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16174154delA	uc003caq.3	+							NM_054110	NP_473451			UDP-N-acetyl-alpha-D-galactosamine:polypeptide							Golgi membrane|integral to membrane|transport vesicle	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(1)	1																		---	---	---	---
RFTN1	23180	broad.mit.edu	37	3	16456535	16456535	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16456535delA	uc003cay.2	-						RFTN1_uc010hes.2_Intron	NM_015150	NP_055965			raft-linking protein							plasma membrane				ovary(3)|central_nervous_system(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	17162367	17162367	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17162367delT								PLCL2 (30270 upstream) : TBC1D5 (36288 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	17835675	17835675	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17835675delT								TBC1D5 (51435 upstream) : SATB1 (553591 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	18169116	18169117	+	Intron	DEL	TT	-	-	rs73030625	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:18169116_18169117delTT	uc003cbg.2	+											Homo sapiens cDNA clone IMAGE:5584035.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	18876869	18876869	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:18876869delG								SATB1 (396617 upstream) : KCNH8 (313148 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	18948338	18948338	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:18948338delA								SATB1 (468086 upstream) : KCNH8 (241679 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	19100422	19100422	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19100422delA								SATB1 (620170 upstream) : KCNH8 (89595 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	19113392	19113392	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19113392delA								SATB1 (633140 upstream) : KCNH8 (76625 downstream)																																			---	---	---	---
KCNH8	131096	broad.mit.edu	37	3	19498222	19498222	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19498222delT	uc003cbk.1	+						KCNH8_uc010hex.1_Intron	NM_144633	NP_653234			potassium voltage-gated channel, subfamily H,							integral to membrane	two-component sensor activity			lung(4)|ovary(1)	5																		---	---	---	---
RAB5A	5868	broad.mit.edu	37	3	20014874	20014874	+	Intron	DEL	T	-	-	rs63327960		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20014874delT	uc003cbn.2	+						RAB5A_uc010hey.2_Intron|RAB5A_uc011awg.1_Intron	NM_004162	NP_004153			RAB5A, member RAS oncogene family						blood coagulation|protein transport|receptor internalization|regulation of filopodium assembly|small GTPase mediated signal transduction	early endosome membrane|melanosome|plasma membrane	GDP binding|GTP binding|GTPase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	20618650	20618650	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20618650delA								SGOL1 (390967 upstream) : VENTXP7 (828568 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	20795445	20795445	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20795445delG								SGOL1 (567762 upstream) : VENTXP7 (651773 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	21222557	21222558	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:21222557_21222558insT								SGOL1 (994874 upstream) : VENTXP7 (224660 downstream)																																			---	---	---	---
ZNF385D	79750	broad.mit.edu	37	3	21796106	21796106	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:21796106delT	uc010hfb.1	-											Homo sapiens cDNA: FLJ22419 fis, clone HRC08593.							nucleus	nucleic acid binding|zinc ion binding			large_intestine(2)|skin(2)|ovary(1)	5																		---	---	---	---
ZNF385D	79750	broad.mit.edu	37	3	22133083	22133083	+	Intron	DEL	A	-	-	rs71993159		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:22133083delA	uc010hfb.1	-											Homo sapiens cDNA: FLJ22419 fis, clone HRC08593.							nucleus	nucleic acid binding|zinc ion binding			large_intestine(2)|skin(2)|ovary(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	22617205	22617206	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:22617205_22617206delAA								ZNF385D (203082 upstream) : UBE2E2 (627447 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	22624066	22624066	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:22624066delA								ZNF385D (209943 upstream) : UBE2E2 (620587 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	23079703	23079703	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23079703delA								ZNF385D (665580 upstream) : UBE2E2 (164950 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	23231860	23231861	+	IGR	DEL	GT	-	-	rs141827581	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23231860_23231861delGT								ZNF385D (817737 upstream) : UBE2E2 (12792 downstream)																																			---	---	---	---
UBE2E2	7325	broad.mit.edu	37	3	23275692	23275693	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23275692_23275693delTT	uc003ccg.2	+						UBE2E2_uc010hfc.2_Intron	NM_152653	NP_689866			ubiquitin-conjugating enzyme E2E 2						ISG15-protein conjugation|protein K11-linked ubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination	nucleolus	ATP binding|ISG15 ligase activity|ubiquitin-protein ligase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	23808376	23808376	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:23808376delT								UBE2E2 (176080 upstream) : UBE2E1 (39063 downstream)																																			---	---	---	---
THRB	7068	broad.mit.edu	37	3	24381892	24381895	+	Intron	DEL	TCTC	-	-	rs62255381		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:24381892_24381895delTCTC	uc003ccx.3	-						THRB_uc010hfe.2_Intron|THRB_uc003ccy.3_Intron|THRB_uc003ccz.3_Intron|THRB_uc003cdc.2_Intron|THRB_uc003cdd.2_Intron|THRB_uc003cde.1_Intron	NM_001128176	NP_001121648			thyroid hormone receptor, beta						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	enzyme binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|thyroid hormone receptor activity|transcription corepressor activity|zinc ion binding			skin(2)|pancreas(1)	3					Levothyroxine(DB00451)|Liothyronine(DB00279)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	24625923	24625923	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:24625923delG								THRB (89470 upstream) : RARB (589900 downstream)																																			---	---	---	---
RARB	5915	broad.mit.edu	37	3	25225628	25225629	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25225628_25225629delTT	uc011awl.1	+							NM_016152	NP_057236			retinoic acid receptor, beta isoform 2						embryonic digestive tract development|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	protein binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|large_intestine(1)|pancreas(1)	3					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Tamibarotene(DB04942)|Tazarotene(DB00799)													---	---	---	---
RARB	5915	broad.mit.edu	37	3	25471157	25471157	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25471157delA	uc011awl.1	+						RARB_uc003cdi.1_Intron|RARB_uc003cdh.2_Intron	NM_016152	NP_057236			retinoic acid receptor, beta isoform 2						embryonic digestive tract development|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	protein binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|large_intestine(1)|pancreas(1)	3					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Tamibarotene(DB04942)|Tazarotene(DB00799)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	25712252	25712252	+	IGR	DEL	A	-	-	rs75861475		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25712252delA								TOP2B (6421 upstream) : NGLY1 (48184 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	25967253	25967253	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:25967253delA								OXSM (131229 upstream) : LRRC3B (697047 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	26015090	26015090	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:26015090delA								OXSM (179066 upstream) : LRRC3B (649210 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	26306649	26306650	+	IGR	DEL	AC	-	-	rs34469961		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:26306649_26306650delAC								OXSM (470625 upstream) : LRRC3B (357650 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	26327656	26327656	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:26327656delA								OXSM (491632 upstream) : LRRC3B (336644 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	27533465	27533466	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27533465_27533466insT								SLC4A7 (7627 upstream) : EOMES (224422 downstream)																																			---	---	---	---
EOMES	8320	broad.mit.edu	37	3	27759334	27759338	+	Intron	DEL	AAAAC	-	-	rs59348913	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27759334_27759338delAAAAC	uc003cdx.2	-						EOMES_uc003cdy.3_Intron|EOMES_uc010hfn.2_Intron|EOMES_uc011axc.1_Intron	NM_005442	NP_005433			eomesodermin						CD8-positive, alpha-beta T cell differentiation involved in immune response|cell differentiation involved in embryonic placenta development|endoderm formation|mesoderm formation|mesodermal to mesenchymal transition involved in gastrulation|positive regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|breast(1)	4																		---	---	---	---
EOMES	8320	broad.mit.edu	37	3	27761564	27761565	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27761564_27761565delAA	uc003cdx.2	-						EOMES_uc003cdy.3_Intron|EOMES_uc010hfn.2_Intron|EOMES_uc011axc.1_Intron	NM_005442	NP_005433			eomesodermin						CD8-positive, alpha-beta T cell differentiation involved in immune response|cell differentiation involved in embryonic placenta development|endoderm formation|mesoderm formation|mesodermal to mesenchymal transition involved in gastrulation|positive regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|breast(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	27826808	27826808	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27826808delT								EOMES (62602 upstream) : CMC1 (456316 downstream)																																			---	---	---	---
CMC1	152100	broad.mit.edu	37	3	28325042	28325043	+	Intron	INS	-	A	A	rs79469771		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:28325042_28325043insA	uc003cea.2	+							NM_182523	NP_872329			COX assembly mitochondrial protein homolog							mitochondrion	metal ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	28861592	28861592	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:28861592delA								ZCWPW2 (294962 upstream) : RBMS3 (461351 downstream)																																			---	---	---	---
RBMS3	27303	broad.mit.edu	37	3	29534216	29534216	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:29534216delA	uc003cel.2	+						RBMS3_uc003cek.2_Intron|RBMS3_uc010hfq.2_Intron|RBMS3_uc003cem.2_Intron|RBMS3_uc010hfr.2_Intron	NM_001003793	NP_001003793			RNA binding motif, single stranded interacting							cytoplasm	nucleotide binding|RNA binding			central_nervous_system(1)	1		Ovarian(412;0.0956)																---	---	---	---
Unknown	0	broad.mit.edu	37	3	30346513	30346513	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30346513delA								RBMS3 (299894 upstream) : TGFBR2 (301481 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	30526085	30526086	+	IGR	INS	-	TGTG	TGTG	rs145877383	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30526085_30526086insTGTG								RBMS3 (479466 upstream) : TGFBR2 (121908 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	30540676	30540676	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30540676delA								RBMS3 (494057 upstream) : TGFBR2 (107318 downstream)																																			---	---	---	---
GADL1	339896	broad.mit.edu	37	3	30832959	30832959	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:30832959delA	uc003cep.2	-							NM_207359	NP_997242			glutamate decarboxylase-like 1						carboxylic acid metabolic process		carboxy-lyase activity|pyridoxal phosphate binding				0					Pyridoxal Phosphate(DB00114)													---	---	---	---
OSBPL10	114884	broad.mit.edu	37	3	31771823	31771823	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:31771823delA	uc003cev.2	-						OSBPL10_uc003ceu.1_Intron|OSBPL10_uc011axf.1_Intron	NM_017784	NP_060254			oxysterol-binding protein-like protein 10						lipid transport		lipid binding			skin(1)	1				STAD - Stomach adenocarcinoma(1;0.00406)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	32035174	32035177	+	IGR	DEL	ACAC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32035174_32035177delACAC								ZNF860 (2054 upstream) : GPD1L (112967 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	32140695	32140696	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32140695_32140696insT								ZNF860 (107575 upstream) : GPD1L (7448 downstream)																																			---	---	---	---
GPD1L	23171	broad.mit.edu	37	3	32200958	32200960	+	Intron	DEL	AAA	-	-	rs35234737		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32200958_32200960delAAA	uc003cew.2	+							NM_015141	NP_055956			glycerol-3-phosphate dehydrogenase 1-like						glycerol-3-phosphate catabolic process	glycerol-3-phosphate dehydrogenase complex	glycerol-3-phosphate dehydrogenase|NAD binding|protein homodimerization activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	32222296	32222297	+	IGR	INS	-	G	G	rs146359824	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32222296_32222297insG								GPD1L (12100 upstream) : CMTM8 (57874 downstream)																																			---	---	---	---
DYNC1LI1	51143	broad.mit.edu	37	3	32571050	32571050	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32571050delT	uc003cfb.3	-	11	1376	c.1288delA	c.(1288-1290)ATTfs	p.I430fs	DYNC1LI1_uc011axh.1_Frame_Shift_Del_p.I314fs	NM_016141	NP_057225	Q9Y6G9	DC1L1_HUMAN	dynein, cytoplasmic 1, light intermediate chain	430					cell division|interspecies interaction between organisms|mitosis|positive regulation of mitotic cell cycle spindle assembly checkpoint|transport	centrosome|condensed chromosome kinetochore|cytoplasmic dynein complex|microtubule|plasma membrane|spindle pole	ATP binding|motor activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	32618551	32618552	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32618551_32618552delTT								DYNC1LI1 (6201 upstream) : CNOT10 (108146 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	32951121	32951124	+	IGR	DEL	TTTT	-	-	rs111510749		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32951121_32951124delTTTT								TRIM71 (17351 upstream) : CCR4 (41942 downstream)																																			---	---	---	---
GLB1	2720	broad.mit.edu	37	3	33065729	33065729	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33065729delT	uc003cfi.1	-						GLB1_uc003cfh.1_Intron|GLB1_uc003cfj.1_Intron|GLB1_uc011axk.1_Intron	NM_000404	NP_000395			galactosidase, beta 1 isoform a preproprotein						carbohydrate metabolic process	lysosome|perinuclear region of cytoplasm	beta-galactosidase activity|cation binding|protein binding			large_intestine(1)	1		Melanoma(143;0.104)																---	---	---	---
Unknown	0	broad.mit.edu	37	3	33144798	33144798	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33144798delA								GLB1 (6104 upstream) : CRTAP (10652 downstream)																																			---	---	---	---
FBXL2	25827	broad.mit.edu	37	3	33387904	33387904	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33387904delA	uc003cfp.2	+						FBXL2_uc011axm.1_Intron|FBXL2_uc011axn.1_Intron|FBXL2_uc011axo.1_Intron|FBXL2_uc011axp.1_Intron|FBXL2_uc011axq.1_Intron|FBXL2_uc011axr.1_Intron|FBXL2_uc011axs.1_Intron	NM_012157	NP_036289			F-box and leucine-rich repeat protein 2						interspecies interaction between organisms|proteolysis	cytoplasm|membrane	protein binding|ubiquitin-protein ligase activity			large_intestine(1)	1																		---	---	---	---
CLASP2	23122	broad.mit.edu	37	3	33602101	33602101	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33602101delA	uc003cfu.2	-						CLASP2_uc003cfs.2_Intron|CLASP2_uc003cft.2_Intron|CLASP2_uc010hgb.2_Intron|CLASP2_uc011axt.1_Intron	NM_015097	NP_055912			CLIP-associating protein 2											ovary(3)|central_nervous_system(1)	4																		---	---	---	---
CLASP2	23122	broad.mit.edu	37	3	33613127	33613129	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33613127_33613129delAAA	uc003cfu.2	-						CLASP2_uc003cfs.2_Intron|CLASP2_uc003cft.2_Intron|CLASP2_uc010hgb.2_Intron|CLASP2_uc011axt.1_Intron	NM_015097	NP_055912			CLIP-associating protein 2											ovary(3)|central_nervous_system(1)	4																		---	---	---	---
PDCD6IP	10015	broad.mit.edu	37	3	33877438	33877438	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33877438delT	uc003cfx.2	+						PDCD6IP_uc003cfy.2_Intron|PDCD6IP_uc011axw.1_Intron	NM_013374	NP_037506			programmed cell death 6 interacting protein						apoptosis|cell cycle|cell division|interspecies interaction between organisms|protein transport	cytosol|melanosome|microtubule organizing center	calcium-dependent protein binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	33958932	33958933	+	IGR	DEL	TT	-	-	rs71987248		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33958932_33958933delTT								PDCD6IP (47738 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	34058800	34058800	+	IGR	DEL	T	-	-	rs142542028		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:34058800delT								PDCD6IP (147606 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	35335803	35335804	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35335803_35335804delAA								None (None upstream) : ARPP21 (345277 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	35481841	35481841	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35481841delA								None (None upstream) : ARPP21 (199240 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	35570923	35570923	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35570923delA								None (None upstream) : ARPP21 (110158 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	35583486	35583493	+	IGR	DEL	TCTCTCTC	-	-	rs72220481		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35583486_35583493delTCTCTCTC								None (None upstream) : ARPP21 (97588 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	36266327	36266328	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36266327_36266328delTT								ARPP21 (430340 upstream) : STAC (155769 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	36638873	36638873	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36638873delG								STAC (49377 upstream) : DCLK3 (115040 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	36810381	36810382	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36810381_36810382delTT								DCLK3 (29029 upstream) : TRANK1 (57929 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	36952956	36952956	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36952956delA								TRANK1 (50545 upstream) : EPM2AIP1 (74402 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	36978118	36978118	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36978118delA								TRANK1 (75707 upstream) : EPM2AIP1 (49240 downstream)																																			---	---	---	---
GOLGA4	2803	broad.mit.edu	37	3	37349123	37349123	+	Intron	DEL	A	-	-	rs68166319		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37349123delA	uc003cgv.2	+						GOLGA4_uc010hgr.1_Intron|GOLGA4_uc003cgw.2_Intron|GOLGA4_uc010hgs.2_Intron|GOLGA4_uc003cgx.2_Intron	NM_002078	NP_002069			golgi autoantigen, golgin subfamily a, 4						Golgi to plasma membrane protein transport	Golgi membrane|trans-Golgi network	protein binding			ovary(2)|breast(1)|central_nervous_system(1)	4																		---	---	---	---
ITGA9	3680	broad.mit.edu	37	3	37589035	37589035	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37589035delA	uc003chd.2	+						ITGA9_uc003chc.2_Intron	NM_002207	NP_002198			integrin, alpha 9 precursor						axon guidance|cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			breast(3)|pancreas(1)|lung(1)|skin(1)	6				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)														---	---	---	---
ITGA9	3680	broad.mit.edu	37	3	37851915	37851915	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37851915delT	uc003chd.2	+						uc003che.2_Intron	NM_002207	NP_002198			integrin, alpha 9 precursor						axon guidance|cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			breast(3)|pancreas(1)|lung(1)|skin(1)	6				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	38486290	38486290	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38486290delC								XYLB (29823 upstream) : LOC100128640 (6234 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	38698461	38698461	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38698461delG								SCN5A (7297 upstream) : SCN10A (40377 downstream)																																			---	---	---	---
SCN10A	6336	broad.mit.edu	37	3	38790655	38790655	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38790655delT	uc003ciq.2	-							NM_006514	NP_006505			sodium channel, voltage-gated, type X, alpha						sensory perception	voltage-gated sodium channel complex				ovary(5)|skin(3)|large_intestine(1)|kidney(1)	10				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cocaine(DB00907)|Dibucaine(DB00527)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)													---	---	---	---
SCN11A	11280	broad.mit.edu	37	3	38948838	38948841	+	Intron	DEL	TATC	-	-	rs62242293		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38948838_38948841delTATC	uc011ays.1	-							NM_014139	NP_054858			sodium channel, voltage-gated, type XI, alpha						response to drug	voltage-gated sodium channel complex	voltage-gated sodium channel activity			skin(6)|ovary(1)|haematopoietic_and_lymphoid_tissue(1)|pancreas(1)	9				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)													---	---	---	---
WDR48	57599	broad.mit.edu	37	3	39121185	39121185	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39121185delT	uc003cit.2	+						WDR48_uc011ayt.1_Intron|WDR48_uc011ayu.1_Intron|WDR48_uc011ayv.1_Intron|WDR48_uc003ciu.2_Intron	NM_020839	NP_065890			WD repeat domain 48						interspecies interaction between organisms|protein deubiquitination	lysosome|nucleus	protein binding			ovary(1)|breast(1)	2				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	39376897	39376897	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39376897delA								CCR8 (1726 upstream) : SLC25A38 (47918 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	39439939	39439939	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39439939delT								SLC25A38 (1120 upstream) : RPSA (8265 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	39747392	39747392	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39747392delT								MOBP (179537 upstream) : MYRIP (103911 downstream)																																			---	---	---	---
MYRIP	25924	broad.mit.edu	37	3	39907699	39907699	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39907699delA	uc003cka.2	+						MYRIP_uc010hhu.2_Intron|MYRIP_uc010hhv.2_Intron|MYRIP_uc010hhw.2_Intron|MYRIP_uc010hhx.1_Intron	NM_015460	NP_056275			myosin VIIA and Rab interacting protein						intracellular protein transport		actin binding|zinc ion binding			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5				KIRC - Kidney renal clear cell carcinoma(284;0.174)|Kidney(284;0.206)														---	---	---	---
MYRIP	25924	broad.mit.edu	37	3	40044026	40044027	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40044026_40044027delAA	uc003cka.2	+						MYRIP_uc010hhu.2_Intron|MYRIP_uc010hhv.2_Intron|MYRIP_uc010hhw.2_Intron|MYRIP_uc010hhx.1_Intron	NM_015460	NP_056275			myosin VIIA and Rab interacting protein						intracellular protein transport		actin binding|zinc ion binding			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5				KIRC - Kidney renal clear cell carcinoma(284;0.174)|Kidney(284;0.206)														---	---	---	---
MYRIP	25924	broad.mit.edu	37	3	40211851	40211851	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40211851delT	uc003cka.2	+						MYRIP_uc010hhu.2_Intron|MYRIP_uc010hhv.2_Intron|MYRIP_uc010hhw.2_Intron|MYRIP_uc011ayz.1_Intron	NM_015460	NP_056275			myosin VIIA and Rab interacting protein						intracellular protein transport		actin binding|zinc ion binding			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5				KIRC - Kidney renal clear cell carcinoma(284;0.174)|Kidney(284;0.206)														---	---	---	---
MYRIP	25924	broad.mit.edu	37	3	40251104	40251104	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40251104delA	uc003cka.2	+						MYRIP_uc010hhu.2_Intron|MYRIP_uc010hhv.2_Intron|MYRIP_uc010hhw.2_Intron|MYRIP_uc011ayz.1_Intron|uc003ckb.2_Intron	NM_015460	NP_056275			myosin VIIA and Rab interacting protein						intracellular protein transport		actin binding|zinc ion binding			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5				KIRC - Kidney renal clear cell carcinoma(284;0.174)|Kidney(284;0.206)														---	---	---	---
RPL14	9045	broad.mit.edu	37	3	40501670	40501670	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40501670delT	uc003ckg.2	+						RPL14_uc003ckh.2_Intron|RPL14_uc003cki.2_Intron	NM_003973	NP_003964			ribosomal protein L14						endocrine pancreas development|ribosomal large subunit biogenesis|rRNA processing|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	protein binding|RNA binding|structural constituent of ribosome				0				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)														---	---	---	---
ZNF619	285267	broad.mit.edu	37	3	40523870	40523870	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40523870delC	uc011azb.1	+						ZNF619_uc010hhz.2_Intron|ZNF619_uc003ckj.2_Intron|ZNF619_uc011azc.1_Intron|ZNF619_uc011azd.1_Intron|ZNF619_uc011aza.1_Intron	NM_001145082	NP_001138554			zinc finger protein 619 isoform 1						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	40701337	40701337	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40701337delA								ZNF621 (120294 upstream) : CTNNB1 (535064 downstream)																																			---	---	---	---
CTNNB1	1499	broad.mit.edu	37	3	41265954	41265954	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41265954delT	uc010hia.1	+						CTNNB1_uc003ckp.2_Intron|CTNNB1_uc003ckq.2_Intron|CTNNB1_uc003ckr.2_Intron|CTNNB1_uc011azf.1_Intron|CTNNB1_uc011azg.1_Intron|uc010hib.1_Intron	NM_001904	NP_001895			beta-catenin						adherens junction assembly|androgen receptor signaling pathway|branching involved in ureteric bud morphogenesis|canonical Wnt receptor signaling pathway involved in negative regulation of apoptosis|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell-cell adhesion|cell-matrix adhesion|cellular component disassembly involved in apoptosis|cellular response to growth factor stimulus|cellular response to indole-3-methanol|central nervous system vasculogenesis|cytoskeletal anchoring at plasma membrane|determination of dorsal/ventral asymmetry|dorsal/ventral axis specification|ectoderm development|embryonic axis specification|embryonic foregut morphogenesis|embryonic leg joint morphogenesis|endodermal cell fate commitment|endothelial tube morphogenesis|epithelial to mesenchymal transition|gastrulation with mouth forming second|glial cell fate determination|hair follicle morphogenesis|hair follicle placode formation|hindbrain development|liver development|lung cell differentiation|lung induction|lung-associated mesenchyme development|male genitalia development|mesenchymal cell proliferation involved in lung development|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of cell proliferation|negative regulation of chondrocyte differentiation|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of osteoclast differentiation|negative regulation of transcription from RNA polymerase II promoter|nephron tubule formation|odontogenesis of dentine-containing tooth|oocyte development|pancreas development|positive regulation of anti-apoptosis|positive regulation of apoptosis|positive regulation of branching involved in lung morphogenesis|positive regulation of epithelial cell proliferation involved in prostate gland development|positive regulation of fibroblast growth factor receptor signaling pathway|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of MAPKKK cascade|positive regulation of muscle cell differentiation|positive regulation of osteoblast differentiation|positive regulation of transcription from RNA polymerase II promoter|protein localization at cell surface|proximal/distal pattern formation|regulation of angiogenesis|regulation of calcium ion import|regulation of centriole-centriole cohesion|regulation of centromeric sister chromatid cohesion|regulation of fibroblast proliferation|regulation of nephron tubule epithelial cell differentiation|regulation of protein localization at cell surface|regulation of smooth muscle cell proliferation|regulation of T cell proliferation|renal inner medulla development|renal outer medulla development|renal vesicle formation|response to drug|response to estradiol stimulus|Schwann cell proliferation|smooth muscle cell differentiation|synapse organization|synaptic vesicle transport|T cell differentiation in thymus|thymus development|trachea formation	APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin-TCF7L2 complex|catenin complex|cell cortex|cell-substrate adherens junction|centrosome|dendritic shaft|desmosome|fascia adherens|internal side of plasma membrane|lamellipodium|lateral plasma membrane|microvillus membrane|perinuclear region of cytoplasm|protein-DNA complex|synapse|transcription factor complex|Z disc|zonula adherens	alpha-catenin binding|androgen receptor binding|cadherin binding|estrogen receptor binding|I-SMAD binding|ion channel binding|protein binding|protein C-terminus binding|protein kinase binding|protein phosphatase binding|R-SMAD binding|RPTP-like protein binding|signal transducer activity|specific RNA polymerase II transcription factor activity|structural molecule activity|transcription coactivator activity|transcription regulatory region DNA binding	p.A5_A80del(3)|p.T3_A126del(2)|p.?(2)|p.A5fs*7(2)|p.M1_V173del(1)|p.A5_G80>(1)|p.M1_A87del(1)	CTNNB1/PLAG1(60)	liver(806)|soft_tissue(609)|large_intestine(243)|endometrium(222)|kidney(172)|stomach(157)|central_nervous_system(139)|ovary(104)|skin(97)|pancreas(91)|adrenal_gland(85)|pituitary(81)|salivary_gland(62)|haematopoietic_and_lymphoid_tissue(57)|thyroid(55)|biliary_tract(41)|lung(38)|prostate(24)|bone(20)|small_intestine(17)|cervix(9)|parathyroid(9)|urinary_tract(8)|breast(7)|oesophagus(5)|NS(3)|pleura(2)|upper_aerodigestive_tract(2)|eye(1)	3166				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)	Lithium(DB01356)		15	H|Mis|T	PLAG1	colorectal|cvarian| hepatoblastoma|others|pleomorphic salivary adenoma				Pilomatrixoma_Familial_Clustering_of				---	---	---	---
ULK4	54986	broad.mit.edu	37	3	41324181	41324181	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41324181delA	uc003ckv.3	-							NM_017886	NP_060356			unc-51-like kinase 4								ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)														---	---	---	---
ULK4	54986	broad.mit.edu	37	3	41796959	41796960	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:41796959_41796960insA	uc003ckv.3	-							NM_017886	NP_060356			unc-51-like kinase 4								ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)														---	---	---	---
TRAK1	22906	broad.mit.edu	37	3	42137204	42137205	+	Intron	INS	-	TCATCG	TCATCG	rs148593287	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42137204_42137205insTCATCG	uc003cky.2	+						TRAK1_uc011azh.1_Intron|TRAK1_uc011azi.1_Intron	NM_001042646	NP_001036111			OGT(O-Glc-NAc transferase)-interacting protein						endosome to lysosome transport|protein O-linked glycosylation|protein targeting|regulation of transcription from RNA polymerase II promoter	early endosome|mitochondrion|nucleus				ovary(1)	1																		---	---	---	---
TRAK1	22906	broad.mit.edu	37	3	42152623	42152623	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42152623delA	uc003cky.2	+						TRAK1_uc011azh.1_Intron|TRAK1_uc011azi.1_Intron	NM_001042646	NP_001036111			OGT(O-Glc-NAc transferase)-interacting protein						endosome to lysosome transport|protein O-linked glycosylation|protein targeting|regulation of transcription from RNA polymerase II promoter	early endosome|mitochondrion|nucleus				ovary(1)	1																		---	---	---	---
TRAK1	22906	broad.mit.edu	37	3	42156758	42156758	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42156758delT	uc003cky.2	+						TRAK1_uc011azh.1_Intron|TRAK1_uc011azi.1_Intron	NM_001042646	NP_001036111			OGT(O-Glc-NAc transferase)-interacting protein						endosome to lysosome transport|protein O-linked glycosylation|protein targeting|regulation of transcription from RNA polymerase II promoter	early endosome|mitochondrion|nucleus				ovary(1)	1																		---	---	---	---
NKTR	4820	broad.mit.edu	37	3	42645872	42645873	+	Intron	DEL	TT	-	-	rs34258304		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42645872_42645873delTT	uc003clo.2	+						NKTR_uc003cll.1_Intron|NKTR_uc003clm.1_Intron|NKTR_uc003clp.2_Intron|NKTR_uc011azp.1_Intron	NM_005385	NP_005376			natural killer-tumor recognition sequence						protein folding	membrane	cyclosporin A binding|peptidyl-prolyl cis-trans isomerase activity			ovary(2)|skin(1)	3				KIRC - Kidney renal clear cell carcinoma(284;0.24)														---	---	---	---
HHATL	57467	broad.mit.edu	37	3	42741498	42741499	+	Intron	INS	-	TG	TG			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42741498_42741499insTG	uc003clw.2	-						HHATL_uc003clx.2_Intron	NM_020707	NP_065758			hedgehog acyltransferase-like						negative regulation of N-terminal protein palmitoylation	endoplasmic reticulum membrane|integral to membrane|perinuclear region of cytoplasm				ovary(3)	3				KIRC - Kidney renal clear cell carcinoma(284;0.215)														---	---	---	---
CCBP2	1238	broad.mit.edu	37	3	42852729	42852729	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42852729delG	uc003cme.2	+						CCBP2_uc003cmc.1_Intron|CCBP2_uc003cmd.1_Intron|CCBP2_uc003cmf.2_Intron|CCBP2_uc003cmg.2_Intron	NM_001296	NP_001287			chemokine binding protein 2						chemotaxis|immune response|multicellular organismal development	integral to plasma membrane	C-X-C chemokine receptor activity			lung(4)|skin(1)	5				KIRC - Kidney renal clear cell carcinoma(284;0.241)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	43104050	43104050	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43104050delT								FAM198A (2347 upstream) : C3orf39 (16679 downstream)																																			---	---	---	---
ANO10	55129	broad.mit.edu	37	3	43549066	43549066	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43549066delA	uc003cmv.2	-						ANO10_uc011azs.1_Intron|ANO10_uc003cmw.2_Intron|ANO10_uc010hil.2_Intron|ANO10_uc011azt.1_Intron	NM_018075	NP_060545			transmembrane protein 16K						cell death	chloride channel complex	chloride channel activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	43897459	43897460	+	IGR	INS	-	GCA	GCA	rs150022097	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43897459_43897460insGCA								ABHD5 (133243 upstream) : MIR138-1 (258244 downstream)																																			---	---	---	---
ZNF445	353274	broad.mit.edu	37	3	44518401	44518401	+	Intron	DEL	A	-	-	rs63659460		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44518401delA	uc003cnf.2	-						ZNF445_uc011azw.1_Intron	NM_181489	NP_852466			zinc finger protein 445						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(197;0.0514)|Kidney(197;0.0646)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	44566507	44566507	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44566507delA								ZNF445 (5281 upstream) : ZNF167 (30197 downstream)																																			---	---	---	---
ZNF167	55888	broad.mit.edu	37	3	44617547	44617547	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44617547delT	uc010hio.2	+						ZNF167_uc003cni.2_Intron|ZNF167_uc003cnk.2_Intron|uc011azz.1_5'Flank	NM_018651	NP_061121			zinc finger protein 167 isoform 1						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2				KIRC - Kidney renal clear cell carcinoma(197;0.0486)|Kidney(197;0.0609)														---	---	---	---
ZNF167	55888	broad.mit.edu	37	3	44618007	44618007	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44618007delT	uc010hio.2	+						ZNF167_uc003cni.2_Intron|ZNF167_uc003cnk.2_Intron|uc011azz.1_5'Flank	NM_018651	NP_061121			zinc finger protein 167 isoform 1						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2				KIRC - Kidney renal clear cell carcinoma(197;0.0486)|Kidney(197;0.0609)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	44654583	44654583	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44654583delA								ZNF660 (17026 upstream) : ZNF197 (11928 downstream)																																			---	---	---	---
KIF15	56992	broad.mit.edu	37	3	44868054	44868054	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44868054delT	uc003cnx.3	+						KIF15_uc010hiq.2_Intron|KIF15_uc010hir.2_Intron	NM_020242	NP_064627			kinesin family member 15						blood coagulation|cell proliferation|microtubule-based movement|mitosis	centrosome|cytosol|microtubule|plus-end kinesin complex|spindle	ATP binding|DNA binding|microtubule motor activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)														---	---	---	---
EXOSC7	23016	broad.mit.edu	37	3	45021081	45021082	+	Intron	DEL	TT	-	-	rs79219358	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45021081_45021082delTT	uc003coi.2	+						EXOSC7_uc003coh.1_Intron|EXOSC7_uc011bae.1_Intron|EXOSC7_uc010his.1_Intron|EXOSC7_uc003coj.2_Intron	NM_015004	NP_055819			exosome component 7						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|rRNA processing	cytosol|exosome (RNase complex)|nucleolus	3'-5'-exoribonuclease activity|protein binding|RNA binding				0				BRCA - Breast invasive adenocarcinoma(193;0.00911)|KIRC - Kidney renal clear cell carcinoma(197;0.0509)|Kidney(197;0.064)														---	---	---	---
LARS2	23395	broad.mit.edu	37	3	45561625	45561626	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45561625_45561626delTT	uc003cop.1	+						LARS2_uc010hit.1_Intron	NM_015340	NP_056155			leucyl-tRNA synthetase 2, mitochondrial						leucyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|leucine-tRNA ligase activity			upper_aerodigestive_tract(1)|ovary(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.0122)|KIRC - Kidney renal clear cell carcinoma(197;0.0313)|Kidney(197;0.0372)	L-Leucine(DB00149)													---	---	---	---
LARS2	23395	broad.mit.edu	37	3	45564232	45564232	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45564232delA	uc003cop.1	+						LARS2_uc010hit.1_Intron	NM_015340	NP_056155			leucyl-tRNA synthetase 2, mitochondrial						leucyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|leucine-tRNA ligase activity			upper_aerodigestive_tract(1)|ovary(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.0122)|KIRC - Kidney renal clear cell carcinoma(197;0.0313)|Kidney(197;0.0372)	L-Leucine(DB00149)													---	---	---	---
SACM1L	22908	broad.mit.edu	37	3	45765062	45765062	+	Intron	DEL	A	-	-	rs34076210		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45765062delA	uc003cos.2	+						SACM1L_uc011bag.1_Intron|SACM1L_uc011bah.1_Intron	NM_014016	NP_054735			suppressor of actin 1							Golgi apparatus				ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.0102)|KIRC - Kidney renal clear cell carcinoma(197;0.0234)|Kidney(197;0.0277)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	46142712	46142713	+	IGR	INS	-	AAC	AAC	rs10629003		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46142712_46142713insAAC								XCR1 (73733 upstream) : CCR3 (62383 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	46146260	46146260	+	IGR	DEL	G	-	-	rs5848783		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46146260delG								XCR1 (77281 upstream) : CCR3 (58836 downstream)																																			---	---	---	---
CCR3	1232	broad.mit.edu	37	3	46253236	46253236	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46253236delT	uc003cpg.1	+							NM_178329	NP_847899			CC chemokine receptor 3 isoform 1						cell adhesion|cellular defense response|chemotaxis|elevation of cytosolic calcium ion concentration|G-protein signaling, coupled to cAMP nucleotide second messenger|inflammatory response|interspecies interaction between organisms|positive regulation of angiogenesis	integral to plasma membrane				ovary(3)|lung(3)|breast(1)|kidney(1)	8				BRCA - Breast invasive adenocarcinoma(193;0.00119)|KIRC - Kidney renal clear cell carcinoma(197;0.0183)|Kidney(197;0.0216)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	46443581	46443582	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46443581_46443582insT								CCR5 (25891 upstream) : CCRL2 (5139 downstream)																																			---	---	---	---
PTH1R	5745	broad.mit.edu	37	3	46936387	46936387	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46936387delA	uc003cqm.2	+						PTH1R_uc003cqn.2_Intron	NM_000316	NP_000307			parathyroid hormone receptor 1 precursor							cytoplasm|integral to plasma membrane|nucleus	parathyroid hormone receptor activity|peptide hormone binding|protein self-association			breast(1)	1														Ollier_disease_/_Maffuci_syndrome		OREG0015543	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CCDC12	151903	broad.mit.edu	37	3	47000546	47000546	+	Intron	DEL	A	-	-	rs34423565		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47000546delA	uc011baq.1	-						CCDC12_uc003cqo.2_Intron|CCDC12_uc011bar.1_Intron	NM_144716	NP_653317			coiled-coil domain containing 12												0		Prostate(884;0.0143)|Ovarian(412;0.0448)|Acute lymphoblastic leukemia(5;0.143)		OV - Ovarian serous cystadenocarcinoma(275;2.2e-56)|BRCA - Breast invasive adenocarcinoma(193;0.00136)|KIRC - Kidney renal clear cell carcinoma(197;0.00703)|Kidney(197;0.00809)														---	---	---	---
SETD2	29072	broad.mit.edu	37	3	47127923	47127923	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47127923delA	uc003cqs.2	-						SETD2_uc003cqv.2_Intron|SETD2_uc003cqt.1_5'Flank	NM_014159	NP_054878			SET domain containing 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	DNA binding|histone-lysine N-methyltransferase activity|oxidoreductase activity|transition metal ion binding			kidney(24)|ovary(5)|skin(1)|central_nervous_system(1)|breast(1)	32		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)				N|F|S|Mis		clear cell renal carcinoma								---	---	---	---
KLHL18	23276	broad.mit.edu	37	3	47368422	47368423	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47368422_47368423delAA	uc003crd.2	+						KLHL18_uc003crc.2_Intron|KLHL18_uc011bav.1_Intron	NM_025010	NP_079286			kelch-like 18												0		Acute lymphoblastic leukemia(5;0.164)		BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00645)|Kidney(197;0.00741)														---	---	---	---
C3orf75	54859	broad.mit.edu	37	3	47553863	47553863	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47553863delA	uc003crk.2	-						C3orf75_uc003crj.2_Intron|C3orf75_uc011bba.1_Intron|C3orf75_uc003crl.1_Intron	NM_001031703	NP_001026873			transmembrane protein 103												0																		---	---	---	---
ZNF589	51385	broad.mit.edu	37	3	48292887	48292887	+	Intron	DEL	A	-	-	rs113298003		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48292887delA	uc003csl.3	+						ZNF589_uc010hjt.1_Intron|ZNF589_uc003csn.2_Intron|ZNF589_uc011bbg.1_Intron|ZNF589_uc003csm.2_Intron	NM_016089	NP_057173			zinc finger protein 589						regulation of transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000649)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)														---	---	---	---
PFKFB4	5210	broad.mit.edu	37	3	48583738	48583739	+	Intron	INS	-	TG	TG	rs144720503	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48583738_48583739insTG	uc003ctv.2	-						PFKFB4_uc003ctw.2_Intron|PFKFB4_uc010hkc.2_Intron|PFKFB4_uc003ctx.2_Intron|PFKFB4_uc010hkb.2_Intron|PFKFB4_uc011bbm.1_Intron|PFKFB4_uc011bbn.1_Intron	NM_004567	NP_004558			6-phosphofructo-2-kinase/fructose-2,						fructose 2,6-bisphosphate metabolic process|glycolysis	cytosol	6-phosphofructo-2-kinase activity|ATP binding|fructose-2,6-bisphosphate 2-phosphatase activity			breast(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.0003)|KIRC - Kidney renal clear cell carcinoma(197;0.00596)|Kidney(197;0.00684)														---	---	---	---
COL7A1	1294	broad.mit.edu	37	3	48620631	48620632	+	Intron	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48620631_48620632delAG	uc003ctz.2	-							NM_000094	NP_000085			alpha 1 type VII collagen precursor						cell adhesion|epidermis development	basement membrane|collagen type VII	protein binding|serine-type endopeptidase inhibitor activity			ovary(4)|breast(3)|skin(3)|central_nervous_system(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)														---	---	---	---
CELSR3	1951	broad.mit.edu	37	3	48678465	48678465	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48678465delG	uc003cul.2	-						CELSR3_uc003cuf.1_Intron|CELSR3_uc010hkf.2_Intron|CELSR3_uc010hkg.2_Intron	NM_001407	NP_001398			cadherin EGF LAG seven-pass G-type receptor 3						homophilic cell adhesion|multicellular organismal development|neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(5)|upper_aerodigestive_tract(2)|central_nervous_system(2)|skin(2)	11				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)														---	---	---	---
ARIH2	10425	broad.mit.edu	37	3	48996142	48996142	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48996142delA	uc003cvb.2	+						ARIH2_uc003cvc.2_Intron|ARIH2_uc003cvf.2_Intron|ARIH2_uc010hkl.2_Intron|ARIH2_uc003cvd.1_Intron|ARIH2_uc003cve.1_Intron	NM_006321	NP_006312			ariadne homolog 2						developmental cell growth|hemopoietic stem cell proliferation|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	nucleic acid binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;9.42e-05)|Kidney(197;0.00258)|KIRC - Kidney renal clear cell carcinoma(197;0.00269)														---	---	---	---
ARIH2	10425	broad.mit.edu	37	3	48999809	48999809	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48999809delA	uc003cvb.2	+						ARIH2_uc003cvc.2_Intron|ARIH2_uc003cvf.2_Intron|ARIH2_uc010hkl.2_Intron	NM_006321	NP_006312			ariadne homolog 2						developmental cell growth|hemopoietic stem cell proliferation|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	nucleic acid binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;9.42e-05)|Kidney(197;0.00258)|KIRC - Kidney renal clear cell carcinoma(197;0.00269)														---	---	---	---
QRICH1	54870	broad.mit.edu	37	3	49083350	49083350	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49083350delT	uc010hkq.2	-						QRICH1_uc003cvu.2_Intron|QRICH1_uc003cvv.2_Intron	NM_198880	NP_942581			glutamine-rich 1											ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.88e-05)|Kidney(197;0.00239)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)														---	---	---	---
C3orf62	375341	broad.mit.edu	37	3	49309180	49309180	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49309180delA	uc003cwn.2	-						C3orf62_uc003cwm.2_Intron|hsa-mir-4271|MI0015879_5'Flank	NM_198562	NP_940964			hypothetical protein LOC375341												0				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)														---	---	---	---
USP4	7375	broad.mit.edu	37	3	49358912	49358912	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49358912delT	uc003cwq.2	-						USP4_uc003cwr.2_Intron	NM_003363	NP_003354			ubiquitin specific protease 4 isoform a						negative regulation of protein ubiquitination|protein deubiquitination|protein localization at cell surface|regulation of protein stability|ubiquitin-dependent protein catabolic process	lysosome|nucleus	adenosine receptor binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(2)|urinary_tract(1)|lung(1)	4		Ovarian(412;0.00308)|Myeloproliferative disorder(1037;0.0255)|Hepatocellular(537;0.121)		OV - Ovarian serous cystadenocarcinoma(275;4.74e-26)|Kidney(197;2.22e-07)|KIRC - Kidney renal clear cell carcinoma(197;5.14e-06)|BRCA - Breast invasive adenocarcinoma(193;9.46e-05)														---	---	---	---
USP4	7375	broad.mit.edu	37	3	49364972	49364972	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49364972delA	uc003cwq.2	-						USP4_uc003cwr.2_Intron	NM_003363	NP_003354			ubiquitin specific protease 4 isoform a						negative regulation of protein ubiquitination|protein deubiquitination|protein localization at cell surface|regulation of protein stability|ubiquitin-dependent protein catabolic process	lysosome|nucleus	adenosine receptor binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(2)|urinary_tract(1)|lung(1)	4		Ovarian(412;0.00308)|Myeloproliferative disorder(1037;0.0255)|Hepatocellular(537;0.121)		OV - Ovarian serous cystadenocarcinoma(275;4.74e-26)|Kidney(197;2.22e-07)|KIRC - Kidney renal clear cell carcinoma(197;5.14e-06)|BRCA - Breast invasive adenocarcinoma(193;9.46e-05)														---	---	---	---
RHOA	387	broad.mit.edu	37	3	49411308	49411308	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49411308delA	uc003cwu.2	-						RHOA_uc010hku.2_Intron	NM_001664	NP_001655			ras homolog gene family, member A precursor						axon guidance|interspecies interaction between organisms|negative regulation of axonogenesis|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of axonogenesis|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of neuron differentiation|positive regulation of NF-kappaB import into nucleus|positive regulation of stress fiber assembly|regulation of cell migration|regulation of small GTPase mediated signal transduction|Rho protein signal transduction|spindle assembly involved in mitosis	cytoskeleton|cytosol|plasma membrane	GTP binding|GTPase activity|myosin binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;8.58e-05)|Kidney(197;0.0023)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)	Atorvastatin(DB01076)|Simvastatin(DB00641)													---	---	---	---
DAG1	1605	broad.mit.edu	37	3	49511017	49511017	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49511017delT	uc003cxc.3	+							NM_004393	NP_004384			dystroglycan 1 preproprotein						cytoskeletal anchoring at plasma membrane|interspecies interaction between organisms|microtubule anchoring|negative regulation of cell migration|negative regulation of MAPKKK cascade|negative regulation of protein kinase B signaling cascade	basement membrane|contractile ring|cytoplasm|cytoskeleton|dystrophin-associated glycoprotein complex|extracellular space|filopodium|integral to membrane|integral to membrane of membrane fraction|lamellipodium|nucleoplasm	actin binding|alpha-actinin binding|calcium ion binding|laminin-1 binding|receptor activity|structural constituent of muscle|tubulin binding|vinculin binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.00241)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)														---	---	---	---
BSN	8927	broad.mit.edu	37	3	49646263	49646266	+	Intron	DEL	GAAA	-	-	rs7646288	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49646263_49646266delGAAA	uc003cxe.3	+							NM_003458	NP_003449			bassoon protein						synaptic transmission	cell junction|cytoplasm|cytoskeleton|nucleus|synaptosome	metal ion binding			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)														---	---	---	---
GMPPB	29925	broad.mit.edu	37	3	49760750	49760750	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49760750delC	uc003cxk.1	-						GMPPB_uc003cxl.1_Intron	NM_021971	NP_068806			GDP-mannose pyrophosphorylase B isoform 2						dolichol-linked oligosaccharide biosynthetic process|GDP-mannose biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine		GTP binding|mannose-1-phosphate guanylyltransferase activity				0				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)														---	---	---	---
IP6K1	9807	broad.mit.edu	37	3	49804097	49804097	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49804097delA	uc003cxm.1	-						IP6K1_uc003cxn.1_Intron|IP6K1_uc011bcv.1_Intron|IP6K1_uc003cxo.2_Intron	NM_153273	NP_695005			inositol hexakisphosphate kinase 1 isoform 1						phosphatidylinositol phosphorylation	cytoplasm|nucleus	ATP binding|inositol hexakisphosphate 5-kinase activity|inositol trisphosphate 3-kinase activity				0																		---	---	---	---
TRAIP	10293	broad.mit.edu	37	3	49887635	49887636	+	Intron	INS	-	AG	AG	rs143295074	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49887635_49887636insAG	uc003cxs.1	-						TRAIP_uc010hla.1_Intron|TRAIP_uc011bcx.1_Intron	NM_005879	NP_005870			TRAF interacting protein						cell proliferation|induction of apoptosis	perinuclear region of cytoplasm	protein binding|zinc ion binding			lung(4)|upper_aerodigestive_tract(1)|ovary(1)	6				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)														---	---	---	---
RBM6	10180	broad.mit.edu	37	3	50068361	50068361	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50068361delG	uc003cyc.2	+						RBM6_uc011bdh.1_Intron|RBM6_uc010hlc.1_Intron|RBM6_uc003cyd.2_Intron|RBM6_uc003cye.2_Intron|RBM6_uc011bdi.1_Intron|RBM6_uc010hld.1_Intron|RBM6_uc010hle.1_Intron|RBM6_uc010hlf.1_Intron	NM_005777	NP_005768			RNA binding motif protein 6						RNA processing	nucleus	DNA binding|nucleotide binding|RNA binding|zinc ion binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)														---	---	---	---
RBM6	10180	broad.mit.edu	37	3	50088785	50088785	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50088785delT	uc003cyc.2	+						RBM6_uc011bdh.1_Intron|RBM6_uc010hlc.1_Intron|RBM6_uc003cyd.2_Intron|RBM6_uc003cye.2_Intron|RBM6_uc011bdi.1_Intron|RBM6_uc010hld.1_Intron|RBM6_uc010hle.1_Intron|RBM6_uc010hlf.1_Intron	NM_005777	NP_005768			RNA binding motif protein 6						RNA processing	nucleus	DNA binding|nucleotide binding|RNA binding|zinc ion binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	50579536	50579537	+	IGR	DEL	GG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50579536_50579537delGG								CACNA2D2 (38644 upstream) : C3orf18 (15926 downstream)																																			---	---	---	---
C3orf18	51161	broad.mit.edu	37	3	50596381	50596381	+	3'UTR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50596381delG	uc003das.2	-	5					C3orf18_uc003dar.2_3'UTR|C3orf18_uc011bdr.1_RNA|C3orf18_uc010hlo.2_3'UTR|C3orf18_uc010hlp.2_Frame_Shift_Del_p.P66fs|C3orf18_uc003dat.2_3'UTR	NM_016210	NP_057294			hypothetical protein LOC51161							integral to membrane				pancreas(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.0175)|Kidney(197;0.0207)														---	---	---	---
MAPKAPK3	7867	broad.mit.edu	37	3	50655080	50655080	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50655080delG	uc003day.1	+	4	680	c.84delG	c.(82-84)CCGfs	p.P28fs	MAPKAPK3_uc003daz.1_Frame_Shift_Del_p.P28fs|MAPKAPK3_uc003dba.1_Frame_Shift_Del_p.P28fs|MAPKAPK3_uc010hlr.1_Frame_Shift_Del_p.P28fs	NM_004635	NP_004626	Q16644	MAPK3_HUMAN	mitogen-activated protein kinase-activated	28			P -> S (in a glioblastoma multiforme sample; somatic mutation).		activation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|Ras protein signal transduction|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase kinase activity|protein serine/threonine kinase activity	p.P28S(1)		ovary(1)|central_nervous_system(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.0188)|Kidney(197;0.0223)														---	---	---	---
DOCK3	1795	broad.mit.edu	37	3	50988390	50988391	+	Intron	DEL	TC	-	-	rs67826845		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50988390_50988391delTC	uc011bds.1	+							NM_004947	NP_004938			dedicator of cytokinesis 3							cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding				0				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)														---	---	---	---
DOCK3	1795	broad.mit.edu	37	3	51243993	51243994	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51243993_51243994insA	uc011bds.1	+							NM_004947	NP_004938			dedicator of cytokinesis 3							cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding				0				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)														---	---	---	---
DOCK3	1795	broad.mit.edu	37	3	51417604	51417604	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51417604delC	uc011bds.1	+	52	5572	c.5549delC	c.(5548-5550)ACCfs	p.T1850fs		NM_004947	NP_004938	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	1850						cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding				0				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)														---	---	---	---
MANF	7873	broad.mit.edu	37	3	51426551	51426551	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51426551delA	uc003dbc.2	+	4					RBM15B_uc003dbd.2_5'Flank	NM_006010	NP_006001			mesencephalic astrocyte-derived neurotrophic						response to unfolded protein	extracellular region	growth factor activity				0																OREG0015594	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
VPRBP	9730	broad.mit.edu	37	3	51465638	51465638	+	Intron	DEL	T	-	-	rs78922608		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51465638delT	uc003dbe.1	-							NM_014703	NP_055518			HIV-1 Vpr binding protein						interspecies interaction between organisms	cytoplasm|nucleus	protein binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.000272)|Kidney(197;0.000729)|KIRC - Kidney renal clear cell carcinoma(197;0.000875)														---	---	---	---
GRM2	2912	broad.mit.edu	37	3	51746309	51746310	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51746309_51746310insA	uc010hlv.2	+						GRM2_uc003dbo.3_Intron|GRM2_uc010hlu.2_Intron	NM_000839	NP_000830			glutamate receptor, metabotropic 2 isoform a						synaptic transmission	integral to plasma membrane				lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Acamprosate(DB00659)|Nicotine(DB00184)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	51792021	51792021	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51792021delT								GRM2 (39398 upstream) : IQCF6 (20557 downstream)																																			---	---	---	---
GPR62	118442	broad.mit.edu	37	3	51987148	51987149	+	5'Flank	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51987148_51987149delAA	uc003dca.3	+							NM_080865	NP_543141			G protein-coupled receptor 62							integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)														---	---	---	---
ALAS1	211	broad.mit.edu	37	3	52236382	52236382	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52236382delA	uc003dcy.1	+						ALAS1_uc003dcx.1_Intron|ALAS1_uc003dcz.1_Intron|ALAS1_uc011bec.1_Intron	NM_000688	NP_000679			5-aminolevulinate synthase 1 precursor						heme biosynthetic process	mitochondrial matrix	5-aminolevulinate synthase activity|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups			ovary(2)|upper_aerodigestive_tract(1)	3				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.000583)|KIRC - Kidney renal clear cell carcinoma(197;0.000751)	Glycine(DB00145)|Pyridoxal Phosphate(DB00114)													---	---	---	---
ALAS1	211	broad.mit.edu	37	3	52241490	52241490	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52241490delT	uc003dcy.1	+						ALAS1_uc003dcz.1_Intron|ALAS1_uc011bec.1_Intron	NM_000688	NP_000679			5-aminolevulinate synthase 1 precursor						heme biosynthetic process	mitochondrial matrix	5-aminolevulinate synthase activity|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups			ovary(2)|upper_aerodigestive_tract(1)	3				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.000583)|KIRC - Kidney renal clear cell carcinoma(197;0.000751)	Glycine(DB00145)|Pyridoxal Phosphate(DB00114)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	52251943	52251946	+	IGR	DEL	AAAA	-	-	rs66943294		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52251943_52251946delAAAA								ALAS1 (3600 upstream) : TLR9 (3152 downstream)																																			---	---	---	---
DNAH1	25981	broad.mit.edu	37	3	52421303	52421303	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52421303delG	uc011bef.1	+						DNAH1_uc003ddv.2_Intron	NM_015512	NP_056327			dynein, axonemal, heavy chain 1						ciliary or flagellar motility|microtubule-based movement|response to mechanical stimulus	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			large_intestine(3)	3				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	52465910	52465912	+	IGR	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52465910_52465912delAAA								PHF7 (8254 upstream) : SEMA3G (1356 downstream)																																			---	---	---	---
PBRM1	55193	broad.mit.edu	37	3	52606555	52606555	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52606555delT	uc003des.2	-						PBRM1_uc003dex.2_Intron|PBRM1_uc003deq.2_Intron|PBRM1_uc003der.2_Intron|PBRM1_uc003det.2_Intron|PBRM1_uc003deu.2_Intron|PBRM1_uc003dev.2_Intron|PBRM1_uc003dew.2_Intron|PBRM1_uc010hmk.1_Intron|PBRM1_uc003dey.2_Intron|PBRM1_uc003dez.1_Intron	NM_181042	NP_060635			polybromo 1 isoform 4						chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)				Mis|N|F|S|D|O		clear cell renal carcinoma|breast								---	---	---	---
PBRM1	55193	broad.mit.edu	37	3	52668500	52668500	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52668500delA	uc003des.2	-						PBRM1_uc003dex.2_Intron|PBRM1_uc003deq.2_Intron|PBRM1_uc003der.2_Intron|PBRM1_uc003det.2_Intron|PBRM1_uc003deu.2_Intron|PBRM1_uc003dev.2_Intron|PBRM1_uc003dew.2_Intron|PBRM1_uc010hmk.1_Intron|PBRM1_uc003dey.2_Intron|PBRM1_uc003dez.1_Intron|PBRM1_uc003dfb.1_Intron	NM_181042	NP_060635			polybromo 1 isoform 4						chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)				Mis|N|F|S|D|O		clear cell renal carcinoma|breast								---	---	---	---
NEK4	6787	broad.mit.edu	37	3	52768925	52768925	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52768925delA	uc003dfq.3	-						NEK4_uc011bej.1_Intron	NM_003157	NP_003148			NIMA-related kinase 4						cell division|mitosis	nucleus	ATP binding|metal ion binding|protein serine/threonine kinase activity			large_intestine(1)	1				BRCA - Breast invasive adenocarcinoma(193;7.44e-05)|Kidney(197;0.000711)|KIRC - Kidney renal clear cell carcinoma(197;0.00086)|OV - Ovarian serous cystadenocarcinoma(275;0.0513)														---	---	---	---
TMEM110	375346	broad.mit.edu	37	3	52925697	52925698	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52925697_52925698delTT	uc003dge.2	-						TMEM110_uc003dgc.3_Intron	NM_198563	NP_940965			transmembrane protein 110							integral to membrane				large_intestine(1)	1				BRCA - Breast invasive adenocarcinoma(193;7.72e-05)|Kidney(197;0.000777)|KIRC - Kidney renal clear cell carcinoma(197;0.000915)|OV - Ovarian serous cystadenocarcinoma(275;0.0541)														---	---	---	---
SFMBT1	51460	broad.mit.edu	37	3	52939993	52939993	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52939993delA	uc003dgf.2	-						SFMBT1_uc010hmr.2_Intron|SFMBT1_uc003dgg.2_Intron|SFMBT1_uc003dgh.2_Intron	NM_001005159	NP_001005159			Scm-like with four mbt domains 1						regulation of transcription, DNA-dependent	nucleus				ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;9.91e-05)|Kidney(197;0.000644)|KIRC - Kidney renal clear cell carcinoma(197;0.000792)|OV - Ovarian serous cystadenocarcinoma(275;0.113)														---	---	---	---
SFMBT1	51460	broad.mit.edu	37	3	53028454	53028455	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53028454_53028455delAA	uc003dgf.2	-						SFMBT1_uc003dgg.2_Intron|SFMBT1_uc003dgh.2_Intron	NM_001005159	NP_001005159			Scm-like with four mbt domains 1						regulation of transcription, DNA-dependent	nucleus				ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;9.91e-05)|Kidney(197;0.000644)|KIRC - Kidney renal clear cell carcinoma(197;0.000792)|OV - Ovarian serous cystadenocarcinoma(275;0.113)														---	---	---	---
TKT	7086	broad.mit.edu	37	3	53280307	53280307	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53280307delA	uc003dgo.2	-						TKT_uc011beo.1_Intron|TKT_uc003dgq.2_Intron|TKT_uc011beq.1_Intron|TKT_uc011ber.1_Intron|TKT_uc011bep.1_Intron	NM_001135055	NP_001128527			transketolase isoform 1						energy reserve metabolic process|xylulose biosynthetic process	cytosol	protein binding|transketolase activity			ovary(2)	2		Prostate(884;0.0959)		BRCA - Breast invasive adenocarcinoma(193;0.000159)|OV - Ovarian serous cystadenocarcinoma(275;0.000314)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)	Thiamine(DB00152)													---	---	---	---
DCP1A	55802	broad.mit.edu	37	3	53323036	53323036	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53323036delT	uc003dgs.3	-						DCP1A_uc003dgt.3_Intron	NM_018403	NP_060873			DCP1 decapping enzyme homolog A						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytoplasmic mRNA processing body|cytosol|nucleus	hydrolase activity|protein binding				0				BRCA - Breast invasive adenocarcinoma(193;0.000164)|KIRC - Kidney renal clear cell carcinoma(197;0.00525)|Kidney(197;0.00579)|OV - Ovarian serous cystadenocarcinoma(275;0.0647)														---	---	---	---
CACNA1D	776	broad.mit.edu	37	3	53526787	53526788	+	5'Flank	INS	-	AA	AA	rs11430200		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53526787_53526788insAA	uc003dgv.3	+						CACNA1D_uc003dgu.3_5'Flank|CACNA1D_uc003dgy.3_5'Flank	NM_001128840	NP_001122312			calcium channel, voltage-dependent, L type,						axon guidance|energy reserve metabolic process|regulation of insulin secretion	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(6)|upper_aerodigestive_tract(2)|liver(1)|central_nervous_system(1)|skin(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Verapamil(DB00661)													---	---	---	---
CACNA1D	776	broad.mit.edu	37	3	53531143	53531143	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53531143delA	uc003dgv.3	+						CACNA1D_uc003dgu.3_Intron|CACNA1D_uc003dgy.3_Intron	NM_001128840	NP_001122312			calcium channel, voltage-dependent, L type,						axon guidance|energy reserve metabolic process|regulation of insulin secretion	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(6)|upper_aerodigestive_tract(2)|liver(1)|central_nervous_system(1)|skin(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Verapamil(DB00661)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	54007470	54007471	+	IGR	INS	-	GATG	GATG	rs142885510	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54007470_54007471insGATG								SELK (81481 upstream) : CACNA2D3 (149222 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	54031773	54031773	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54031773delA								SELK (105784 upstream) : CACNA2D3 (124920 downstream)																																			---	---	---	---
WNT5A	7474	broad.mit.edu	37	3	55513599	55513599	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:55513599delG	uc003dhn.2	-						WNT5A_uc003dhm.2_Intron|WNT5A_uc010hmw.2_Intron|WNT5A_uc010hmx.2_Intron	NM_003392	NP_003383			wingless-type MMTV integration site family,						activation of JUN kinase activity|activation of protein kinase B activity|axon guidance|cartilage development|cellular protein localization|cellular response to calcium ion|cellular response to interferon-gamma|cellular response to lipopolysaccharide|cellular response to retinoic acid|cellular response to transforming growth factor beta stimulus|cervix development|cochlea morphogenesis|convergent extension involved in organogenesis|dopaminergic neuron differentiation|dorsal/ventral axis specification|embryonic digit morphogenesis|embryonic skeletal system development|epithelial cell proliferation involved in mammary gland duct elongation|epithelial to mesenchymal transition|face development|genitalia development|heart looping|hemopoietic stem cell proliferation|keratinocyte differentiation|lateral sprouting involved in mammary gland duct morphogenesis|lens development in camera-type eye|male gonad development|mammary gland branching involved in thelarche|negative regulation of apoptosis|negative regulation of BMP signaling pathway|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of fat cell differentiation|negative regulation of fibroblast growth factor receptor signaling pathway|negative regulation of mesenchymal cell proliferation|negative regulation of transcription, DNA-dependent|neural tube closure|olfactory bulb interneuron development|optic cup formation involved in camera-type eye development|palate development|positive regulation of angiogenesis|positive regulation of cartilage development|positive regulation of cGMP metabolic process|positive regulation of chemokine biosynthetic process|positive regulation of cytokine secretion involved in immune response|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of fibroblast proliferation|positive regulation of inflammatory response|positive regulation of interleukin-1 beta secretion|positive regulation of interleukin-6 production|positive regulation of JNK cascade|positive regulation of macrophage activation|positive regulation of macrophage cytokine production|positive regulation of mesenchymal cell proliferation|positive regulation of neuron projection development|positive regulation of NF-kappaB transcription factor activity|positive regulation of ossification|positive regulation of protein catabolic process|positive regulation of protein kinase C signaling cascade|positive regulation of T cell chemotaxis|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of type I interferon-mediated signaling pathway|primitive streak formation|regulation of branching involved in mammary gland duct morphogenesis|somitogenesis|tail morphogenesis|type B pancreatic cell development|urinary bladder development|uterus development|vagina development|Wnt receptor signaling pathway, calcium modulating pathway|wound healing	extracellular space|membrane fraction|plasma membrane|proteinaceous extracellular matrix	frizzled binding|frizzled-2 binding|receptor tyrosine kinase-like orphan receptor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding				0				KIRC - Kidney renal clear cell carcinoma(284;0.00377)|Kidney(284;0.00408)|OV - Ovarian serous cystadenocarcinoma(275;0.204)														---	---	---	---
ERC2	26059	broad.mit.edu	37	3	56295726	56295726	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56295726delT	uc003dhr.1	-							NM_015576	NP_056391			cytomatrix protein p110							cell junction|cytoplasm|cytoskeleton|growth cone|presynaptic membrane|synaptosome	protein binding			ovary(2)	2				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)														---	---	---	---
CCDC66	285331	broad.mit.edu	37	3	56591278	56591279	+	Frame_Shift_Ins	INS	-	GGGGTAAGCA	GGGGTAAGCA	rs150150392	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56591278_56591279insGGGGTAAGCA	uc003dhz.2	+	1	95_96	c.8_9insGGGGTAAGCA	c.(7-9)TTGfs	p.L3fs	CCDC66_uc003dhy.2_5'UTR|CCDC66_uc003dhu.2_Intron|CCDC66_uc003dhx.2_RNA|CCDC66_uc003dhv.2_RNA|CCDC66_uc003dhw.2_Frame_Shift_Ins_p.L3fs	NM_001141947	NP_001135419	A2RUB6	CCD66_HUMAN	coiled-coil domain containing 66 isoform 1	3										breast(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0478)|Kidney(284;0.0597)|OV - Ovarian serous cystadenocarcinoma(275;0.233)														---	---	---	---
C3orf63	23272	broad.mit.edu	37	3	56709206	56709207	+	Intron	DEL	TT	-	-	rs111854641		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56709206_56709207delTT	uc003did.3	-						C3orf63_uc003die.3_Intron	NM_015224	NP_056039			retinoblastoma-associated protein 140 isoform b											ovary(3)|kidney(1)|central_nervous_system(1)	5				KIRC - Kidney renal clear cell carcinoma(284;0.0126)|Kidney(284;0.0147)														---	---	---	---
ARHGEF3	50650	broad.mit.edu	37	3	56808955	56808955	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56808955delA	uc003dig.2	-						ARHGEF3_uc011bew.1_Intron|ARHGEF3_uc003dih.2_Intron|ARHGEF3_uc011bev.1_Intron|ARHGEF3_uc003dif.2_Intron|ARHGEF3_uc010hmy.1_Intron|ARHGEF3_uc003dii.2_Intron	NM_019555	NP_062455			Rho guanine nucleotide exchange factor 3 isoform						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|Rho protein signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0161)|Kidney(284;0.019)|OV - Ovarian serous cystadenocarcinoma(275;0.193)														---	---	---	---
DNAH12	201625	broad.mit.edu	37	3	57494742	57494742	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57494742delT	uc003dit.2	-						DNAH12_uc003diu.2_Intron	NM_178504	NP_848599			dynein heavy chain domain 2 isoform 1						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			pancreas(1)|skin(1)	2																		---	---	---	---
DNAH12	201625	broad.mit.edu	37	3	57504279	57504280	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57504279_57504280insA	uc003dit.2	-						DNAH12_uc003diu.2_Intron	NM_178504	NP_848599			dynein heavy chain domain 2 isoform 1						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			pancreas(1)|skin(1)	2																		---	---	---	---
DNAH12	201625	broad.mit.edu	37	3	57509313	57509313	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57509313delT	uc003dit.2	-	4	457	c.276delA	c.(274-276)AAAfs	p.K92fs	DNAH12_uc003diu.2_Frame_Shift_Del_p.K92fs	NM_178504	NP_848599	Q6ZR08	DYH12_HUMAN	dynein heavy chain domain 2 isoform 1	92	Stem (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			pancreas(1)|skin(1)	2																		---	---	---	---
FAM116A	201627	broad.mit.edu	37	3	57645136	57645139	+	Intron	DEL	AAGC	-	-	rs80026743		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57645136_57645139delAAGC	uc003dja.2	-							NM_152678	NP_689891			hypothetical protein LOC201627											pancreas(1)	1				BRCA - Breast invasive adenocarcinoma(55;0.000621)|KIRC - Kidney renal clear cell carcinoma(284;0.0485)|Kidney(284;0.0607)														---	---	---	---
FAM116A	201627	broad.mit.edu	37	3	57646215	57646215	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57646215delA	uc003dja.2	-							NM_152678	NP_689891			hypothetical protein LOC201627											pancreas(1)	1				BRCA - Breast invasive adenocarcinoma(55;0.000621)|KIRC - Kidney renal clear cell carcinoma(284;0.0485)|Kidney(284;0.0607)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	57922694	57922694	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:57922694delG								SLMAP (7800 upstream) : FLNB (71433 downstream)																																			---	---	---	---
FLNB	2317	broad.mit.edu	37	3	58001788	58001789	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58001788_58001789delTT	uc003djj.2	+						FLNB_uc010hne.2_Intron|FLNB_uc003djk.2_Intron|FLNB_uc010hnf.2_Intron	NM_001457	NP_001448			filamin B isoform 2						actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction	cell cortex|integral to membrane|nucleus|sarcomere	actin binding			breast(8)|ovary(5)|lung(3)|skin(2)|central_nervous_system(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)														---	---	---	---
FLNB	2317	broad.mit.edu	37	3	58118376	58118376	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58118376delT	uc003djj.2	+						FLNB_uc010hne.2_Intron|FLNB_uc003djk.2_Intron|FLNB_uc010hnf.2_Intron|FLNB_uc003djl.2_Intron|FLNB_uc003djm.2_Intron	NM_001457	NP_001448			filamin B isoform 2						actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction	cell cortex|integral to membrane|nucleus|sarcomere	actin binding			breast(8)|ovary(5)|lung(3)|skin(2)|central_nervous_system(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)														---	---	---	---
PXK	54899	broad.mit.edu	37	3	58368235	58368237	+	Intron	DEL	TTA	-	-	rs71287201		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58368235_58368237delTTA	uc003djz.1	+						PXK_uc003djx.1_Intron|PXK_uc003djy.1_Intron|PXK_uc003dka.1_Intron|PXK_uc003dkb.1_Intron|PXK_uc003dkc.1_Intron|PXK_uc011bfe.1_Intron|PXK_uc010hnj.1_Intron|PXK_uc003dkd.1_Intron|PXK_uc010hnk.1_5'Flank	NM_017771	NP_060241			PX domain containing serine/threonine kinase						cell communication|inflammatory response|negative regulation of ATPase activity|negative regulation of ion transport|regulation of synaptic transmission	centrosome|cytoplasm|nucleus|plasma membrane	actin binding|ATP binding|phosphatidylinositol binding|phosphatidylinositol binding|protein C-terminus binding|protein kinase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(55;0.000249)|KIRC - Kidney renal clear cell carcinoma(10;0.00346)|Kidney(10;0.00368)|OV - Ovarian serous cystadenocarcinoma(275;0.22)														---	---	---	---
PXK	54899	broad.mit.edu	37	3	58395502	58395502	+	Intron	DEL	A	-	-	rs72406989		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58395502delA	uc003djz.1	+						PXK_uc003djx.1_Intron|PXK_uc003djy.1_Intron|PXK_uc003dka.1_Intron|PXK_uc003dkb.1_Intron|PXK_uc003dkc.1_Intron|PXK_uc011bfe.1_Intron|PXK_uc010hnj.1_Intron|PXK_uc003dkd.1_Intron|PXK_uc010hnk.1_Intron	NM_017771	NP_060241			PX domain containing serine/threonine kinase						cell communication|inflammatory response|negative regulation of ATPase activity|negative regulation of ion transport|regulation of synaptic transmission	centrosome|cytoplasm|nucleus|plasma membrane	actin binding|ATP binding|phosphatidylinositol binding|phosphatidylinositol binding|protein C-terminus binding|protein kinase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(55;0.000249)|KIRC - Kidney renal clear cell carcinoma(10;0.00346)|Kidney(10;0.00368)|OV - Ovarian serous cystadenocarcinoma(275;0.22)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	58546722	58546723	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58546722_58546723delTT								ACOX2 (23793 upstream) : FAM107A (3124 downstream)																																			---	---	---	---
FAM107A	11170	broad.mit.edu	37	3	58565949	58565950	+	5'Flank	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58565949_58565950delTT	uc003dkm.2	-						FAM107A_uc003dko.2_Intron|FAM107A_uc003dkn.2_5'Flank|FAM107A_uc010hnm.2_Intron|FAM107A_uc003dkp.1_5'Flank	NM_007177	NP_009108			downregulated in renal cell carcinoma						regulation of cell growth	nucleus	protein binding				0				BRCA - Breast invasive adenocarcinoma(55;0.000189)|Kidney(10;0.000536)|KIRC - Kidney renal clear cell carcinoma(10;0.000716)|OV - Ovarian serous cystadenocarcinoma(275;0.154)														---	---	---	---
C3orf67	200844	broad.mit.edu	37	3	58739692	58739692	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58739692delT	uc003dkt.1	-						C3orf67_uc003dkr.1_Intron|C3orf67_uc003dks.1_Intron	NM_198463	NP_940865			hypothetical protein LOC200844												0		all_cancers(2;0.000156)|all_epithelial(2;0.000493)|Breast(2;0.00446)|all_lung(2;0.074)|Lung NSC(2;0.248)		BRCA - Breast invasive adenocarcinoma(55;5.93e-06)|Kidney(10;0.00155)|KIRC - Kidney renal clear cell carcinoma(10;0.00172)|OV - Ovarian serous cystadenocarcinoma(275;0.23)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	59230208	59230209	+	IGR	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:59230208_59230209delCT								C3orf67 (194450 upstream) : FHIT (504829 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	59358180	59358180	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:59358180delA								C3orf67 (322422 upstream) : FHIT (376858 downstream)																																			---	---	---	---
FHIT	2272	broad.mit.edu	37	3	61100387	61100387	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:61100387delT	uc003dkx.3	-						FHIT_uc003dky.2_Intron|FHIT_uc010hnn.1_Intron	NM_002012	NP_002003			fragile histidine triad gene						nucleotide metabolic process		bis(5'-adenosyl)-triphosphatase activity|protein binding				0		all_cancers(2;2.37e-314)|all_epithelial(2;5.17e-286)|Colorectal(2;1.24e-68)|all_lung(2;1.31e-45)|Lung NSC(2;1.79e-44)|all_hematologic(2;1.59e-23)|Renal(2;1.03e-13)|Breast(2;1.06e-10)|Esophageal squamous(2;6.31e-09)|Melanoma(2;1.83e-07)|Acute lymphoblastic leukemia(2;5.46e-05)|all_neural(2;0.00118)|Medulloblastoma(2;0.00263)|Hepatocellular(2;0.0245)|Ovarian(2;0.0408)		UCEC - Uterine corpus endometrioid carcinoma (45;0.0887)|Epithelial(1;9.28e-70)|all cancers(1;3.07e-60)|Colorectal(1;2.33e-53)|STAD - Stomach adenocarcinoma(1;7.22e-48)|COAD - Colon adenocarcinoma(3;1.05e-44)|READ - Rectum adenocarcinoma(3;2.41e-08)|KIRC - Kidney renal clear cell carcinoma(10;0.000109)|Kidney(10;0.000125)|Lung(1;0.000161)|LUSC - Lung squamous cell carcinoma(1;0.000742)|OV - Ovarian serous cystadenocarcinoma(275;0.00372)|BRCA - Breast invasive adenocarcinoma(55;0.00448)				T	HMGA2	pleomorphic salivary gland adenoma				Renal_Cell_Cancer_associated_with_constitutional_translocation_of_chromosome_3				---	---	---	---
Unknown	0	broad.mit.edu	37	3	61328400	61328401	+	IGR	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:61328400_61328401delTC								FHIT (91267 upstream) : PTPRG (218842 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	61466086	61466087	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:61466086_61466087delAA								FHIT (228953 upstream) : PTPRG (81156 downstream)																																			---	---	---	---
PTPRG	5793	broad.mit.edu	37	3	61561076	61561076	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:61561076delA	uc003dlb.2	+						PTPRG_uc003dlc.2_Intron|PTPRG_uc003dla.3_Intron	NM_002841	NP_002832			protein tyrosine phosphatase, receptor type, G						transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	identical protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(5)|lung(2)	7				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)														---	---	---	---
PTPRG	5793	broad.mit.edu	37	3	61646747	61646748	+	Intron	DEL	TT	-	-	rs6792090	by1000genomes;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:61646747_61646748delTT	uc003dlb.2	+						PTPRG_uc003dlc.2_Intron|PTPRG_uc003dla.3_Intron	NM_002841	NP_002832			protein tyrosine phosphatase, receptor type, G						transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	identical protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(5)|lung(2)	7				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)														---	---	---	---
PTPRG	5793	broad.mit.edu	37	3	62119657	62119657	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62119657delA	uc003dlb.2	+						PTPRG_uc003dlc.2_Intron	NM_002841	NP_002832			protein tyrosine phosphatase, receptor type, G						transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	identical protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(5)|lung(2)	7				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	62322164	62322164	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62322164delT								C3orf14 (2846 upstream) : FEZF2 (33183 downstream)																																			---	---	---	---
CADPS	8618	broad.mit.edu	37	3	62469827	62469827	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62469827delT	uc003dll.2	-						CADPS_uc003dlj.1_5'Flank|CADPS_uc003dlk.1_Intron|CADPS_uc003dlm.2_Intron|CADPS_uc003dln.2_Intron	NM_003716	NP_003707			Ca2+-dependent secretion activator isoform 1						exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|cytosol|synapse	lipid binding|metal ion binding			central_nervous_system(2)|ovary(1)	3		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)														---	---	---	---
CADPS	8618	broad.mit.edu	37	3	62776635	62776635	+	Intron	DEL	T	-	-	rs35894606		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62776635delT	uc003dll.2	-						CADPS_uc003dlm.2_Intron|CADPS_uc003dln.2_Intron	NM_003716	NP_003707			Ca2+-dependent secretion activator isoform 1						exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|cytosol|synapse	lipid binding|metal ion binding			central_nervous_system(2)|ovary(1)	3		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	63705800	63705800	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63705800delA								SNTN (54919 upstream) : C3orf49 (99241 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	63764846	63764846	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63764846delG								SNTN (113965 upstream) : C3orf49 (40195 downstream)																																			---	---	---	---
C3orf49	132200	broad.mit.edu	37	3	63828401	63828401	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63828401delA	uc003dls.3	+						THOC7_uc003dlt.3_Intron|THOC7_uc003dlu.3_Intron	NR_026866				RecName: Full=Putative uncharacterized protein C3orf49;												0																		---	---	---	---
ATXN7	6314	broad.mit.edu	37	3	63886408	63886410	+	Intron	DEL	AGA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63886408_63886410delAGA	uc003dlw.3	+						ATXN7_uc003dlv.2_Intron|ATXN7_uc010hnv.2_Intron|ATXN7_uc010hnu.1_Intron	NM_000333	NP_000324			ataxin 7 isoform a						cell death|histone deubiquitination|nucleus organization|regulation of transcription, DNA-dependent|transcription, DNA-dependent|visual perception	cytoplasm|nuclear matrix|nucleolus	protein binding|zinc ion binding				0		Prostate(884;0.0181)		BRCA - Breast invasive adenocarcinoma(55;0.000614)|KIRC - Kidney renal clear cell carcinoma(15;0.00294)|Kidney(15;0.00305)														---	---	---	---
ATXN7	6314	broad.mit.edu	37	3	63940388	63940391	+	Intron	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63940388_63940391delTTTT	uc003dlw.3	+						ATXN7_uc003dlv.2_Intron|ATXN7_uc010hnv.2_Intron	NM_000333	NP_000324			ataxin 7 isoform a						cell death|histone deubiquitination|nucleus organization|regulation of transcription, DNA-dependent|transcription, DNA-dependent|visual perception	cytoplasm|nuclear matrix|nucleolus	protein binding|zinc ion binding				0		Prostate(884;0.0181)		BRCA - Breast invasive adenocarcinoma(55;0.000614)|KIRC - Kidney renal clear cell carcinoma(15;0.00294)|Kidney(15;0.00305)														---	---	---	---
ATXN7	6314	broad.mit.edu	37	3	63974140	63974142	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63974140_63974142delAAA	uc003dlw.3	+						ATXN7_uc003dlv.2_Intron|ATXN7_uc010hnv.2_Intron|ATXN7_uc011bfn.1_Intron	NM_000333	NP_000324			ataxin 7 isoform a						cell death|histone deubiquitination|nucleus organization|regulation of transcription, DNA-dependent|transcription, DNA-dependent|visual perception	cytoplasm|nuclear matrix|nucleolus	protein binding|zinc ion binding				0		Prostate(884;0.0181)		BRCA - Breast invasive adenocarcinoma(55;0.000614)|KIRC - Kidney renal clear cell carcinoma(15;0.00294)|Kidney(15;0.00305)														---	---	---	---
ATXN7	6314	broad.mit.edu	37	3	63981832	63981832	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63981832delC	uc003dlw.3	+	12	2887	c.2334delC	c.(2332-2334)GGCfs	p.G778fs	ATXN7_uc003dlv.2_Frame_Shift_Del_p.G778fs|ATXN7_uc010hnv.2_Frame_Shift_Del_p.G778fs|ATXN7_uc011bfn.1_Frame_Shift_Del_p.G633fs	NM_000333	NP_000324	O15265	ATX7_HUMAN	ataxin 7 isoform a	778	Ser-rich.				cell death|histone deubiquitination|nucleus organization|regulation of transcription, DNA-dependent|transcription, DNA-dependent|visual perception	cytoplasm|nuclear matrix|nucleolus	protein binding|zinc ion binding				0		Prostate(884;0.0181)		BRCA - Breast invasive adenocarcinoma(55;0.000614)|KIRC - Kidney renal clear cell carcinoma(15;0.00294)|Kidney(15;0.00305)														---	---	---	---
PRICKLE2	166336	broad.mit.edu	37	3	64189671	64189672	+	Intron	DEL	AT	-	-	rs829524	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64189671_64189672delAT	uc003dmf.2	-							NM_198859	NP_942559			prickle-like 2							cytoplasm|nuclear membrane	zinc ion binding			ovary(4)|skin(1)	5		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000971)|KIRC - Kidney renal clear cell carcinoma(15;0.00443)|Kidney(15;0.00497)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	64358169	64358172	+	IGR	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64358169_64358172delTTTT								PRICKLE2 (147038 upstream) : ADAMTS9 (143161 downstream)																																			---	---	---	---
ADAMTS9	56999	broad.mit.edu	37	3	64554386	64554386	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64554386delA	uc003dmg.2	-						ADAMTS9_uc011bfo.1_Intron|ADAMTS9_uc003dmh.1_Intron|ADAMTS9_uc011bfp.1_Intron|uc003dmi.1_Intron	NM_182920	NP_891550			ADAM metallopeptidase with thrombospondin type 1						glycoprotein catabolic process|multicellular organismal development|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|urinary_tract(1)|skin(1)	4		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	65090870	65090871	+	IGR	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65090870_65090871insG								ADAMTS9 (417505 upstream) : MAGI1 (249036 downstream)																																			---	---	---	---
MAGI1	9223	broad.mit.edu	37	3	65908144	65908145	+	Intron	INS	-	T	T	rs144794138	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65908144_65908145insT	uc003dmn.2	-						MAGI1_uc003dmm.2_Intron|MAGI1_uc003dmo.2_Intron|MAGI1_uc003dmp.2_Intron|MAGI1_uc003dmr.2_Intron	NM_001033057	NP_001028229			membrane associated guanylate kinase, WW and PDZ						cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly	tight junction	ATP binding|protein C-terminus binding			lung(2)|skin(1)|breast(1)|kidney(1)|pancreas(1)	6		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	66098344	66098345	+	IGR	INS	-	TCA	TCA			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66098344_66098345insTCA								MAGI1 (73835 upstream) : SLC25A26 (20940 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	66649900	66649902	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:66649900_66649902delTTT								LRIG1 (99055 upstream) : KBTBD8 (398825 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	67006990	67006991	+	IGR	DEL	GT	-	-	rs10545785	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:67006990_67006991delGT								LRIG1 (456145 upstream) : KBTBD8 (41736 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	67192894	67192894	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:67192894delA								KBTBD8 (131264 upstream) : SUCLG2 (232251 downstream)																																			---	---	---	---
SUCLG2	8801	broad.mit.edu	37	3	67570955	67570955	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:67570955delC	uc003dna.3	-	5	549	c.521delG	c.(520-522)GGCfs	p.G174fs	SUCLG2_uc010hob.2_Frame_Shift_Del_p.G55fs	NM_003848	NP_003839	Q96I99	SUCB2_HUMAN	succinate-CoA ligase, GDP-forming beta subunit	174	ATP-grasp.			GV -> RS (in Ref. 2; AAC64397).	succinyl-CoA metabolic process|tricarboxylic acid cycle	mitochondrial matrix	ATP binding|GTP binding|succinate-CoA ligase (GDP-forming) activity			central_nervous_system(1)|skin(1)	2		Renal(2;0.00294)|Lung NSC(201;0.012)|Hepatocellular(537;0.121)		BRCA - Breast invasive adenocarcinoma(55;3.53e-05)|Epithelial(33;0.000153)	Succinic acid(DB00139)													---	---	---	---
SUCLG2	8801	broad.mit.edu	37	3	67655073	67655074	+	Intron	INS	-	AGA	AGA	rs148744938	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:67655073_67655074insAGA	uc003dna.3	-							NM_003848	NP_003839			succinate-CoA ligase, GDP-forming beta subunit						succinyl-CoA metabolic process|tricarboxylic acid cycle	mitochondrial matrix	ATP binding|GTP binding|succinate-CoA ligase (GDP-forming) activity			central_nervous_system(1)|skin(1)	2		Renal(2;0.00294)|Lung NSC(201;0.012)|Hepatocellular(537;0.121)		BRCA - Breast invasive adenocarcinoma(55;3.53e-05)|Epithelial(33;0.000153)	Succinic acid(DB00139)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	67750551	67750551	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:67750551delA	uc003dnb.2	+						uc003dnc.2_Intron					Homo sapiens mRNA; cDNA DKFZp686F1220 (from clone DKFZp686F1220).																														---	---	---	---
FAM19A1	407738	broad.mit.edu	37	3	68084865	68084866	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:68084865_68084866insA	uc003dnd.2	+						FAM19A1_uc003dne.2_Intron|FAM19A1_uc003dng.2_Intron	NM_213609	NP_998774			family with sequence similarity 19 (chemokine							endoplasmic reticulum|extracellular region				ovary(1)	1		Lung NSC(201;0.0117)		BRCA - Breast invasive adenocarcinoma(55;7.7e-05)|Epithelial(33;0.000937)|KIRC - Kidney renal clear cell carcinoma(39;0.0579)|Kidney(39;0.0743)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	68683716	68683717	+	IGR	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:68683716_68683717delCT								FAM19A1 (88947 upstream) : FAM19A4 (97200 downstream)																																			---	---	---	---
FAM19A4	151647	broad.mit.edu	37	3	68852168	68852168	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:68852168delT	uc003dnh.1	-						FAM19A4_uc003dni.1_Intron	NM_182522	NP_872328			family with sequence similarity 19 (chemokine							extracellular region				skin(2)	2		Lung NSC(201;0.0198)		BRCA - Breast invasive adenocarcinoma(55;1.38e-05)|Epithelial(33;0.000124)|LUSC - Lung squamous cell carcinoma(21;0.0248)|KIRC - Kidney renal clear cell carcinoma(39;0.0729)|Kidney(39;0.0904)														---	---	---	---
FRMD4B	23150	broad.mit.edu	37	3	69296810	69296810	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69296810delT	uc003dnv.2	-						FRMD4B_uc003dnw.2_Intron|FRMD4B_uc003dnx.1_Intron|FRMD4B_uc011bga.1_Intron	NM_015123	NP_055938			FERM domain containing 4B							cytoplasm|cytoskeleton	binding			ovary(3)|central_nervous_system(1)	4		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)														---	---	---	---
FRMD4B	23150	broad.mit.edu	37	3	69307144	69307145	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69307144_69307145delTT	uc003dnv.2	-						FRMD4B_uc003dnw.2_Intron|FRMD4B_uc003dnx.1_Intron	NM_015123	NP_055938			FERM domain containing 4B							cytoplasm|cytoskeleton	binding			ovary(3)|central_nervous_system(1)	4		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	69739689	69739692	+	IGR	DEL	CACA	-	-	rs10576100		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69739689_69739692delCACA								FRMD4B (147956 upstream) : MITF (48941 downstream)																																			---	---	---	---
MITF	4286	broad.mit.edu	37	3	69815731	69815731	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69815731delA	uc003dnz.2	+						MITF_uc011bgb.1_Intron|MITF_uc003doa.2_Intron	NM_198159	NP_937802			microphthalmia-associated transcription factor						melanocyte differentiation|multicellular organismal development|protein complex assembly	nucleus|protein complex	DNA binding|protein binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription			ovary(2)	2		Lung NSC(201;0.0384)|Prostate(884;0.0526)		BRCA - Breast invasive adenocarcinoma(55;3.07e-05)|Epithelial(33;0.000138)|LUSC - Lung squamous cell carcinoma(21;0.008)|Lung(16;0.0107)|KIRC - Kidney renal clear cell carcinoma(39;0.204)|Kidney(39;0.239)				A		melanoma 		Waardenburg syndrome type 2|Tietz syndrome						---	---	---	---
Unknown	0	broad.mit.edu	37	3	70186659	70186659	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:70186659delT								MITF (169173 upstream) : FOXP1 (818078 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	70317181	70317183	+	IGR	DEL	CTC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:70317181_70317183delCTC								MITF (299695 upstream) : FOXP1 (687554 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	70629571	70629571	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:70629571delA								MITF (612085 upstream) : FOXP1 (375166 downstream)																																			---	---	---	---
FOXP1	27086	broad.mit.edu	37	3	71090807	71090807	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71090807delT	uc003dol.2	-						FOXP1_uc003dom.2_Intron|FOXP1_uc003don.2_Intron|FOXP1_uc003doo.2_Intron|FOXP1_uc003dop.2_Intron|FOXP1_uc003doq.1_Intron|FOXP1_uc003doi.2_Intron|FOXP1_uc003doj.2_Intron|FOXP1_uc003dok.2_Intron|FOXP1_uc003dor.1_5'Flank	NM_032682	NP_116071			forkhead box P1 isoform 1						cardiac muscle cell differentiation|embryo development|immunoglobulin V(D)J recombination|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of immunoglobulin production|positive regulation of mesenchymal cell proliferation|pre-B cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|skeletal muscle tissue development|smooth muscle tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)				T	PAX5	ALL								---	---	---	---
FOXP1	27086	broad.mit.edu	37	3	71188061	71188062	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71188061_71188062delAA	uc003dol.2	-						FOXP1_uc003dom.2_Intron|FOXP1_uc003don.2_Intron|FOXP1_uc003doo.2_Intron|FOXP1_uc003dop.2_Intron|FOXP1_uc003doq.1_Intron	NM_032682	NP_116071			forkhead box P1 isoform 1						cardiac muscle cell differentiation|embryo development|immunoglobulin V(D)J recombination|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of immunoglobulin production|positive regulation of mesenchymal cell proliferation|pre-B cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|skeletal muscle tissue development|smooth muscle tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)				T	PAX5	ALL								---	---	---	---
FOXP1	27086	broad.mit.edu	37	3	71479664	71479666	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71479664_71479666delAAA	uc003dop.2	-						FOXP1_uc003don.2_Intron|FOXP1_uc003doo.2_Intron|FOXP1_uc003dos.2_Intron	NM_032682	NP_116071			forkhead box P1 isoform 1						cardiac muscle cell differentiation|embryo development|immunoglobulin V(D)J recombination|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of immunoglobulin production|positive regulation of mesenchymal cell proliferation|pre-B cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|skeletal muscle tissue development|smooth muscle tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)				T	PAX5	ALL								---	---	---	---
EIF4E3	317649	broad.mit.edu	37	3	71733616	71733616	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71733616delT	uc003dov.3	-	7					EIF4E3_uc011bgc.1_3'UTR|EIF4E3_uc003dox.2_3'UTR|EIF4E3_uc011bgd.1_3'UTR|EIF4E3_uc010hoc.2_3'UTR	NM_001134651	NP_001128123			eukaryotic translation initiation factor 4E						regulation of translation	cytoplasm|mRNA cap binding complex	translation initiation factor activity				0		Prostate(10;0.0166)		BRCA - Breast invasive adenocarcinoma(55;2.56e-05)|Epithelial(33;2.9e-05)|Lung(16;9.28e-05)|LUSC - Lung squamous cell carcinoma(21;0.00227)														---	---	---	---
EIF4E3	317649	broad.mit.edu	37	3	71739006	71739007	+	Intron	DEL	AA	-	-	rs57050022		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71739006_71739007delAA	uc003dov.3	-						EIF4E3_uc011bgc.1_Intron|EIF4E3_uc003dox.2_Intron|EIF4E3_uc011bgd.1_Intron|EIF4E3_uc010hoc.2_Intron	NM_001134651	NP_001128123			eukaryotic translation initiation factor 4E						regulation of translation	cytoplasm|mRNA cap binding complex	translation initiation factor activity				0		Prostate(10;0.0166)		BRCA - Breast invasive adenocarcinoma(55;2.56e-05)|Epithelial(33;2.9e-05)|Lung(16;9.28e-05)|LUSC - Lung squamous cell carcinoma(21;0.00227)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	72068222	72068222	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72068222delT								PROK2 (233865 upstream) : RYBP (355529 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	72342100	72342102	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72342100_72342102delTTT								PROK2 (507743 upstream) : RYBP (81649 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	72773654	72773654	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72773654delT								RYBP (277880 upstream) : SHQ1 (24776 downstream)																																			---	---	---	---
SHQ1	55164	broad.mit.edu	37	3	72890504	72890505	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:72890504_72890505delAA	uc003dpf.2	-						SHQ1_uc010hod.2_Intron	NM_018130	NP_060600			SHQ1 homolog						ribonucleoprotein complex assembly	cytosol|nucleoplasm	protein binding			ovary(2)|large_intestine(1)	3		Prostate(10;0.00482)|Lung NSC(201;0.0339)|Myeloproliferative disorder(1037;0.204)		BRCA - Breast invasive adenocarcinoma(55;9.68e-05)|Epithelial(33;0.000563)|LUSC - Lung squamous cell carcinoma(21;0.00229)|Lung(16;0.00688)|KIRC - Kidney renal clear cell carcinoma(39;0.018)|Kidney(39;0.0213)														---	---	---	---
PDZRN3	23024	broad.mit.edu	37	3	73489194	73489194	+	Intron	DEL	T	-	-	rs112630598		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73489194delT	uc003dpl.1	-						PDZRN3_uc011bgh.1_Intron|PDZRN3_uc010hoe.1_Intron|PDZRN3_uc011bgg.1_Intron	NM_015009	NP_055824			PDZ domain containing ring finger 3								ubiquitin-protein ligase activity|zinc ion binding			pancreas(2)|ovary(2)|skin(2)|large_intestine(1)	7		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)														---	---	---	---
PDZRN3	23024	broad.mit.edu	37	3	73656840	73656840	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73656840delT	uc003dpl.1	-							NM_015009	NP_055824			PDZ domain containing ring finger 3								ubiquitin-protein ligase activity|zinc ion binding			pancreas(2)|ovary(2)|skin(2)|large_intestine(1)	7		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	73896815	73896815	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:73896815delT								PDZRN3 (222743 upstream) : CNTN3 (414907 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	74293704	74293704	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74293704delA								PDZRN3 (619632 upstream) : CNTN3 (18018 downstream)																																			---	---	---	---
CNTN3	5067	broad.mit.edu	37	3	74549529	74549530	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74549529_74549530insA	uc003dpm.1	-							NM_020872	NP_065923			contactin 3 precursor						cell adhesion	anchored to membrane|plasma membrane	protein binding			breast(3)|ovary(1)|skin(1)	5		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	74601747	74601747	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74601747delT								CNTN3 (31404 upstream) : FAM86D (868958 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	74929459	74929459	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74929459delA								CNTN3 (359116 upstream) : FAM86D (541246 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	75912912	75912915	+	IGR	DEL	AGTG	-	-	rs9631536	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:75912912_75912915delAGTG								ZNF717 (78242 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	76971986	76971987	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:76971986_76971987insA								None (None upstream) : ROBO2 (117307 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	77002971	77002972	+	IGR	INS	-	TG	TG	rs151038669	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:77002971_77002972insTG								None (None upstream) : ROBO2 (86322 downstream)																																			---	---	---	---
ROBO2	6092	broad.mit.edu	37	3	77255295	77255296	+	Intron	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:77255295_77255296delTC	uc003dpy.3	+						ROBO2_uc003dpz.2_Intron|ROBO2_uc011bgj.1_Intron|ROBO2_uc011bgk.1_Intron	NM_002942	NP_002933			roundabout, axon guidance receptor, homolog 2						apoptosis involved in luteolysis|axon midline choice point recognition|cellular response to hormone stimulus|homophilic cell adhesion|metanephros development|negative regulation of negative chemotaxis|negative regulation of synaptogenesis|olfactory bulb interneuron development|positive regulation of axonogenesis|retinal ganglion cell axon guidance|ureteric bud development	axolemma|cell surface|integral to membrane	axon guidance receptor activity|identical protein binding			lung(5)|skin(3)|ovary(1)|large_intestine(1)|liver(1)	11				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)														---	---	---	---
ROBO2	6092	broad.mit.edu	37	3	77502527	77502528	+	Intron	DEL	TT	-	-	rs71629652		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:77502527_77502528delTT	uc003dpy.3	+						ROBO2_uc003dpz.2_Intron|ROBO2_uc011bgj.1_Intron|ROBO2_uc011bgk.1_Intron	NM_002942	NP_002933			roundabout, axon guidance receptor, homolog 2						apoptosis involved in luteolysis|axon midline choice point recognition|cellular response to hormone stimulus|homophilic cell adhesion|metanephros development|negative regulation of negative chemotaxis|negative regulation of synaptogenesis|olfactory bulb interneuron development|positive regulation of axonogenesis|retinal ganglion cell axon guidance|ureteric bud development	axolemma|cell surface|integral to membrane	axon guidance receptor activity|identical protein binding			lung(5)|skin(3)|ovary(1)|large_intestine(1)|liver(1)	11				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	78146817	78146820	+	IGR	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:78146817_78146820delTTTT								ROBO2 (450156 upstream) : ROBO1 (499568 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	78378626	78378626	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:78378626delT								ROBO2 (681965 upstream) : ROBO1 (267762 downstream)																																			---	---	---	---
ROBO1	6091	broad.mit.edu	37	3	79163673	79163673	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:79163673delT	uc003dqe.2	-							NM_002941	NP_002932			roundabout 1 isoform a						activation of caspase activity|axon midline choice point recognition|cell migration involved in sprouting angiogenesis|chemorepulsion involved in postnatal olfactory bulb interneuron migration|homophilic cell adhesion|negative regulation of chemokine-mediated signaling pathway|negative regulation of mammary gland epithelial cell proliferation|negative regulation of negative chemotaxis|positive regulation of axonogenesis|Roundabout signaling pathway	cell surface|cytoplasm|integral to plasma membrane	axon guidance receptor activity|identical protein binding|LRR domain binding			large_intestine(2)	2		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)														---	---	---	---
ROBO1	6091	broad.mit.edu	37	3	79337942	79337942	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:79337942delT	uc003dqe.2	-							NM_002941	NP_002932			roundabout 1 isoform a						activation of caspase activity|axon midline choice point recognition|cell migration involved in sprouting angiogenesis|chemorepulsion involved in postnatal olfactory bulb interneuron migration|homophilic cell adhesion|negative regulation of chemokine-mediated signaling pathway|negative regulation of mammary gland epithelial cell proliferation|negative regulation of negative chemotaxis|positive regulation of axonogenesis|Roundabout signaling pathway	cell surface|cytoplasm|integral to plasma membrane	axon guidance receptor activity|identical protein binding|LRR domain binding			large_intestine(2)	2		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	80092217	80092217	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:80092217delT								ROBO1 (275158 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	80452909	80452910	+	IGR	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:80452909_80452910delTC								ROBO1 (635850 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	81323826	81323827	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81323826_81323827insA								None (None upstream) : GBE1 (215023 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	81342557	81342557	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81342557delT								None (None upstream) : GBE1 (196293 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	81510228	81510228	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81510228delG								None (None upstream) : GBE1 (28622 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	81834197	81834197	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81834197delA								GBE1 (23247 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	82186902	82186902	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:82186902delT	uc003dqh.1	+											Homo sapiens cDNA clone IMAGE:5271111.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	82508840	82508840	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:82508840delT	uc003dqh.1	+											Homo sapiens cDNA clone IMAGE:5271111.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	83519248	83519248	+	IGR	DEL	G	-	-	rs138814388	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:83519248delG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	83537466	83537466	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:83537466delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	83992035	83992035	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:83992035delC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	84104979	84104979	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:84104979delT								None (None upstream) : CADM2 (903154 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	85004929	85004929	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:85004929delA								None (None upstream) : CADM2 (3204 downstream)																																			---	---	---	---
CADM2	253559	broad.mit.edu	37	3	85224094	85224094	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:85224094delT	uc003dqj.2	+						CADM2_uc003dqk.2_Intron	NM_153184	NP_694854			immunoglobulin superfamily, member 4D						adherens junction organization|cell junction assembly	integral to membrane|plasma membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)														---	---	---	---
CADM2	253559	broad.mit.edu	37	3	85284171	85284172	+	Intron	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:85284171_85284172delCT	uc003dqj.2	+						CADM2_uc003dqk.2_Intron	NM_153184	NP_694854			immunoglobulin superfamily, member 4D						adherens junction organization|cell junction assembly	integral to membrane|plasma membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)														---	---	---	---
CADM2	253559	broad.mit.edu	37	3	85294849	85294849	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:85294849delA	uc003dqj.2	+						CADM2_uc003dqk.2_Intron	NM_153184	NP_694854			immunoglobulin superfamily, member 4D						adherens junction organization|cell junction assembly	integral to membrane|plasma membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)														---	---	---	---
CADM2	253559	broad.mit.edu	37	3	85536790	85536792	+	Intron	DEL	GAG	-	-	rs112613086		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:85536790_85536792delGAG	uc003dqj.2	+						CADM2_uc003dqk.2_Intron	NM_153184	NP_694854			immunoglobulin superfamily, member 4D						adherens junction organization|cell junction assembly	integral to membrane|plasma membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)														---	---	---	---
CADM2	253559	broad.mit.edu	37	3	86112807	86112807	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:86112807delT	uc003dqj.2	+						CADM2_uc003dqk.2_Intron|CADM2_uc003dql.2_Intron	NM_153184	NP_694854			immunoglobulin superfamily, member 4D						adherens junction organization|cell junction assembly	integral to membrane|plasma membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	86235043	86235043	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:86235043delA								CADM2 (117095 upstream) : VGLL3 (752082 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	87157847	87157847	+	IGR	DEL	A	-	-	rs72470772		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:87157847delA								VGLL3 (117590 upstream) : CHMP2B (118566 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	87545217	87545218	+	IGR	DEL	TC	-	-	rs144423121	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:87545217_87545218delTC								POU1F1 (219480 upstream) : HTR1F (486508 downstream)																																			---	---	---	---
CGGBP1	8545	broad.mit.edu	37	3	88108817	88108817	+	5'Flank	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:88108817delG	uc003dqs.2	-						CGGBP1_uc003dqt.2_5'Flank|CGGBP1_uc003dqu.2_Intron	NM_001008390	NP_001008391			CGG triplet repeat binding protein 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	double-stranded DNA binding				0		Lung NSC(201;0.0283)		LUSC - Lung squamous cell carcinoma(29;0.00359)|Lung(72;0.00677)														---	---	---	---
CGGBP1	8545	broad.mit.edu	37	3	88160014	88160014	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:88160014delA	uc003dqu.2	-							NM_003663	NP_003654			CGG triplet repeat binding protein 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	double-stranded DNA binding				0		Lung NSC(201;0.0283)		LUSC - Lung squamous cell carcinoma(29;0.00359)|Lung(72;0.00677)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	89104690	89104691	+	IGR	INS	-	T	T	rs140202129	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:89104690_89104691insT								C3orf38 (897577 upstream) : EPHA3 (51983 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	89629289	89629289	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:89629289delT								EPHA3 (98007 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	90071762	90071762	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:90071762delA								EPHA3 (540480 upstream) : None (None downstream)																																			---	---	---	---
PROS1	5627	broad.mit.edu	37	3	93644431	93644431	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:93644431delT	uc003drb.3	-						PROS1_uc010hoo.2_Intron|PROS1_uc003dqz.3_Intron	NM_000313	NP_000304			protein S, alpha preproprotein						leukocyte migration|peptidyl-glutamic acid carboxylation|platelet activation|platelet degranulation|post-translational protein modification|proteolysis	endoplasmic reticulum membrane|extracellular region|Golgi lumen|Golgi membrane|platelet alpha granule lumen	calcium ion binding|endopeptidase inhibitor activity			large_intestine(1)	1					Antihemophilic Factor(DB00025)|Drotrecogin alfa(DB00055)|Menadione(DB00170)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	94333972	94333973	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:94333972_94333973delTT								NSUN3 (488342 upstream) : LOC255025 (323134 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	95026798	95026798	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:95026798delT								LOC255025 (131719 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	95420125	95420126	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:95420125_95420126insA								LOC255025 (525046 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	95631101	95631101	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:95631101delC								LOC255025 (736022 upstream) : EPHA6 (902324 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	95674124	95674124	+	IGR	DEL	A	-	-	rs76015596		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:95674124delA								LOC255025 (779045 upstream) : EPHA6 (859301 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	95675687	95675688	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:95675687_95675688delTG								LOC255025 (780608 upstream) : EPHA6 (857737 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	96031743	96031743	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96031743delA								None (None upstream) : EPHA6 (501682 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	96152254	96152254	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96152254delG								None (None upstream) : EPHA6 (381171 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	96468368	96468368	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96468368delA								None (None upstream) : EPHA6 (65057 downstream)																																			---	---	---	---
EPHA6	285220	broad.mit.edu	37	3	96847364	96847364	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96847364delT	uc010how.1	+						EPHA6_uc003drp.1_Intron	NM_001080448	NP_001073917			EPH receptor A6 isoform a							integral to plasma membrane	ATP binding|ephrin receptor activity			stomach(5)|lung(4)|central_nervous_system(3)|breast(1)|skin(1)|ovary(1)|kidney(1)	16																		---	---	---	---
EPHA6	285220	broad.mit.edu	37	3	96888969	96888969	+	Intron	DEL	A	-	-	rs68162597		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96888969delA	uc010how.1	+						EPHA6_uc003drp.1_Intron	NM_001080448	NP_001073917			EPH receptor A6 isoform a							integral to plasma membrane	ATP binding|ephrin receptor activity			stomach(5)|lung(4)|central_nervous_system(3)|breast(1)|skin(1)|ovary(1)|kidney(1)	16																		---	---	---	---
EPHA6	285220	broad.mit.edu	37	3	96912859	96912859	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96912859delA	uc010how.1	+						EPHA6_uc003drp.1_Intron	NM_001080448	NP_001073917			EPH receptor A6 isoform a							integral to plasma membrane	ATP binding|ephrin receptor activity			stomach(5)|lung(4)|central_nervous_system(3)|breast(1)|skin(1)|ovary(1)|kidney(1)	16																		---	---	---	---
ARL6	84100	broad.mit.edu	37	3	97499620	97499620	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97499620delT	uc003drv.2	+						ARL6_uc003drw.2_Intron|ARL6_uc003dru.2_Intron|ARL6_uc010hoy.2_Intron	NM_177976	NP_816931			ADP-ribosylation factor-like 6						cilium assembly|determination of left/right symmetry|melanosome transport|protein polymerization|protein targeting to membrane|small GTPase mediated signal transduction|visual perception|Wnt receptor signaling pathway	axonemal microtubule|cilium axoneme|cilium membrane|membrane coat|microtubule basal body	GTP binding|metal ion binding|phospholipid binding|protein binding				0		Lung NSC(201;0.0193)|Prostate(884;0.174)		LUSC - Lung squamous cell carcinoma(29;0.0118)|Lung(72;0.0189)										Bardet-Biedl_syndrome				---	---	---	---
ARL6	84100	broad.mit.edu	37	3	97511820	97511820	+	Intron	DEL	A	-	-	rs73138803	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97511820delA	uc003drv.2	+						ARL6_uc003drw.2_Intron|ARL6_uc003dru.2_Intron|ARL6_uc010hoy.2_Intron	NM_177976	NP_816931			ADP-ribosylation factor-like 6						cilium assembly|determination of left/right symmetry|melanosome transport|protein polymerization|protein targeting to membrane|small GTPase mediated signal transduction|visual perception|Wnt receptor signaling pathway	axonemal microtubule|cilium axoneme|cilium membrane|membrane coat|microtubule basal body	GTP binding|metal ion binding|phospholipid binding|protein binding				0		Lung NSC(201;0.0193)|Prostate(884;0.174)		LUSC - Lung squamous cell carcinoma(29;0.0118)|Lung(72;0.0189)										Bardet-Biedl_syndrome				---	---	---	---
ARL6	84100	broad.mit.edu	37	3	97513036	97513037	+	Intron	INS	-	GA	GA			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97513036_97513037insGA	uc003drv.2	+						ARL6_uc003drw.2_Intron|ARL6_uc003dru.2_Intron|ARL6_uc010hoy.2_Intron	NM_177976	NP_816931			ADP-ribosylation factor-like 6						cilium assembly|determination of left/right symmetry|melanosome transport|protein polymerization|protein targeting to membrane|small GTPase mediated signal transduction|visual perception|Wnt receptor signaling pathway	axonemal microtubule|cilium axoneme|cilium membrane|membrane coat|microtubule basal body	GTP binding|metal ion binding|phospholipid binding|protein binding				0		Lung NSC(201;0.0193)|Prostate(884;0.174)		LUSC - Lung squamous cell carcinoma(29;0.0118)|Lung(72;0.0189)										Bardet-Biedl_syndrome				---	---	---	---
CPOX	1371	broad.mit.edu	37	3	98304724	98304724	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98304724delT	uc003dsx.2	-							NM_000097	NP_000088			coproporphyrinogen oxidase precursor							mitochondrial intermembrane space	coproporphyrinogen oxidase activity|protein homodimerization activity				0																		---	---	---	---
ST3GAL6	10402	broad.mit.edu	37	3	98462746	98462746	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98462746delC	uc003dsz.2	+						ST3GAL6_uc003dsy.2_Intron|ST3GAL6_uc003dta.2_Intron|ST3GAL6_uc003dtb.2_Intron|ST3GAL6_uc003dtc.2_Intron|ST3GAL6_uc010hpd.2_Intron	NM_006100	NP_006091			alpha2,3-sialyltransferase VI						amino sugar metabolic process|glycolipid metabolic process|protein glycosylation|protein lipoylation	integral to Golgi membrane	sialyltransferase activity			ovary(1)	1																		---	---	---	---
ST3GAL6	10402	broad.mit.edu	37	3	98482011	98482011	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98482011delA	uc003dsz.2	+						ST3GAL6_uc003dsy.2_Intron|ST3GAL6_uc003dta.2_Intron|ST3GAL6_uc003dtb.2_Intron|ST3GAL6_uc003dtc.2_Intron|ST3GAL6_uc010hpd.2_Intron	NM_006100	NP_006091			alpha2,3-sialyltransferase VI						amino sugar metabolic process|glycolipid metabolic process|protein glycosylation|protein lipoylation	integral to Golgi membrane	sialyltransferase activity			ovary(1)	1																		---	---	---	---
ST3GAL6	10402	broad.mit.edu	37	3	98501234	98501234	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98501234delA	uc003dsz.2	+						ST3GAL6_uc003dsy.2_Intron|ST3GAL6_uc003dta.2_Intron|ST3GAL6_uc003dtb.2_Intron|ST3GAL6_uc003dtc.2_Intron|ST3GAL6_uc010hpd.2_Intron	NM_006100	NP_006091			alpha2,3-sialyltransferase VI						amino sugar metabolic process|glycolipid metabolic process|protein glycosylation|protein lipoylation	integral to Golgi membrane	sialyltransferase activity			ovary(1)	1																		---	---	---	---
ST3GAL6	10402	broad.mit.edu	37	3	98503990	98503990	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98503990delT	uc003dsz.2	+						ST3GAL6_uc003dsy.2_Intron|ST3GAL6_uc003dta.2_Intron|ST3GAL6_uc003dtb.2_Intron|ST3GAL6_uc003dtc.2_Intron|ST3GAL6_uc010hpd.2_Intron	NM_006100	NP_006091			alpha2,3-sialyltransferase VI						amino sugar metabolic process|glycolipid metabolic process|protein glycosylation|protein lipoylation	integral to Golgi membrane	sialyltransferase activity			ovary(1)	1																		---	---	---	---
DCBLD2	131566	broad.mit.edu	37	3	98571726	98571727	+	Intron	INS	-	ACT	ACT	rs143201379	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98571726_98571727insACT	uc003dtd.2	-						DCBLD2_uc003dte.2_Intron|DCBLD2_uc003dtf.1_Intron	NM_080927	NP_563615			discoidin, CUB and LCCL domain containing 2						cell adhesion|intracellular receptor mediated signaling pathway|negative regulation of cell growth|wound healing	cell surface|integral to plasma membrane				ovary(2)|central_nervous_system(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	98666454	98666454	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98666454delT								DCBLD2 (45921 upstream) : COL8A1 (691000 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	98837266	98837266	+	IGR	DEL	G	-	-	rs62743460		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98837266delG								DCBLD2 (216733 upstream) : COL8A1 (520188 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	98876554	98876554	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98876554delT								DCBLD2 (256021 upstream) : COL8A1 (480900 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	99162696	99162696	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99162696delT								DCBLD2 (542163 upstream) : COL8A1 (194758 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	99307298	99307298	+	IGR	DEL	A	-	-	rs35989848		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99307298delA								DCBLD2 (686765 upstream) : COL8A1 (50156 downstream)																																			---	---	---	---
COL8A1	1295	broad.mit.edu	37	3	99496464	99496464	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99496464delA	uc003dtg.1	+						COL8A1_uc003dth.1_Intron|COL8A1_uc003dti.1_Intron	NM_001850	NP_001841			alpha 1 type VIII collagen precursor						angiogenesis|cell adhesion	basement membrane|collagen type VIII					0																		---	---	---	---
FILIP1L	11259	broad.mit.edu	37	3	99682454	99682455	+	Intron	INS	-	T	T	rs140480534	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99682454_99682455insT	uc003dtm.2	-						C3orf26_uc003dtk.1_Intron|C3orf26_uc003dtl.2_Intron|FILIP1L_uc003dto.2_Intron	NM_182909	NP_878913			filamin A interacting protein 1-like isoform 1							cytoplasm|membrane|myosin complex|nucleus				ovary(1)	1																		---	---	---	---
FILIP1L	11259	broad.mit.edu	37	3	99776653	99776653	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99776653delT	uc003dtm.2	-						C3orf26_uc003dtl.2_Intron|FILIP1L_uc003dto.2_Intron	NM_182909	NP_878913			filamin A interacting protein 1-like isoform 1							cytoplasm|membrane|myosin complex|nucleus				ovary(1)	1																		---	---	---	---
C3orf26	84319	broad.mit.edu	37	3	99839680	99839680	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:99839680delA	uc003dtl.2	+							NM_032359	NP_115735			hypothetical protein LOC84319								ATP binding|ATP-dependent helicase activity|nucleic acid binding			skin(1)	1																		---	---	---	---
TBC1D23	55773	broad.mit.edu	37	3	100042414	100042414	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100042414delT	uc003dtt.2	+						TBC1D23_uc003dts.2_Intron|TBC1D23_uc003dtu.2_Intron	NM_018309	NP_060779			TBC1 domain family, member 23							intracellular	Rab GTPase activator activity			ovary(1)|liver(1)	2																		---	---	---	---
TOMM70A	9868	broad.mit.edu	37	3	100086754	100086754	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100086754delT	uc003dtw.2	-							NM_014820	NP_055635			translocase of outer mitochondrial membrane 70						protein targeting to mitochondrion	integral to membrane|mitochondrial outer membrane translocase complex	protein binding|protein transmembrane transporter activity			ovary(1)	1																		---	---	---	---
GPR128	84873	broad.mit.edu	37	3	100388167	100388167	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100388167delA	uc003duc.2	+						GPR128_uc011bhc.1_Intron|GPR128_uc003dud.2_Intron	NM_032787	NP_116176			G protein-coupled receptor 128 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(3)|skin(1)	4																		---	---	---	---
TFG	10342	broad.mit.edu	37	3	100451189	100451190	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100451189_100451190insA	uc003due.2	+						TFG_uc003duf.2_Intron|TFG_uc003dug.2_Intron|TFG_uc003duh.2_Intron|TFG_uc003dui.2_Intron	NM_006070	NP_006061			TRK-fused						positive regulation of I-kappaB kinase/NF-kappaB cascade	cytoplasm	signal transducer activity		TFG/ALK(7)	haematopoietic_and_lymphoid_tissue(7)|lung(2)|large_intestine(1)|prostate(1)	11								T	NTRK1|ALK	papillary thyroid|ALCL|NSCLC								---	---	---	---
Unknown	0	broad.mit.edu	37	3	100759549	100759550	+	IGR	DEL	CA	-	-	rs113530288		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100759549_100759550delCA								ABI3BP (47215 upstream) : IMPG2 (185738 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	100768776	100768776	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100768776delT								ABI3BP (56442 upstream) : IMPG2 (176512 downstream)																																			---	---	---	---
SENP7	57337	broad.mit.edu	37	3	101198451	101198452	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101198451_101198452delAA	uc003dut.2	-						SENP7_uc003duu.2_Intron|SENP7_uc003duv.2_Intron|SENP7_uc003duw.2_Intron|SENP7_uc003dux.2_Intron	NM_020654	NP_065705			sentrin/SUMO-specific protease 7 isoform 1						proteolysis	nucleus	cysteine-type peptidase activity			ovary(3)|lung(2)	5																		---	---	---	---
ZBTB11	27107	broad.mit.edu	37	3	101376352	101376353	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101376352_101376353delAA	uc003dve.3	-							NM_014415	NP_055230			zinc finger protein ZNF-U69274						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1																		---	---	---	---
NFKBIZ	64332	broad.mit.edu	37	3	101552282	101552282	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101552282delA	uc003dvo.2	+						NFKBIZ_uc010hpo.2_Intron	NM_001005474	NP_001005474			nuclear factor of kappa light polypeptide gene						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	101778037	101778037	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101778037delT								LOC152225 (61267 upstream) : ZPLD1 (40051 downstream)																																			---	---	---	---
ZPLD1	131368	broad.mit.edu	37	3	101929918	101929918	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:101929918delT	uc003dvs.1	+							NM_175056	NP_778226			zona pellucida-like domain containing 1							integral to membrane				ovary(2)|skin(2)|central_nervous_system(1)	5																		---	---	---	---
ZPLD1	131368	broad.mit.edu	37	3	102173881	102173881	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:102173881delA	uc003dvs.1	+						ZPLD1_uc003dvt.1_Intron|ZPLD1_uc011bhg.1_Intron	NM_175056	NP_778226			zona pellucida-like domain containing 1							integral to membrane				ovary(2)|skin(2)|central_nervous_system(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	102222424	102222426	+	IGR	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:102222424_102222426delAAA								ZPLD1 (23739 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	103008746	103008746	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:103008746delT								ZPLD1 (810061 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	104664936	104664936	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:104664936delT								None (None upstream) : ALCAM (420777 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	105960427	105960427	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:105960427delA								CBLB (372161 upstream) : LOC100302640 (595233 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	106207720	106207720	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106207720delT								CBLB (619454 upstream) : LOC100302640 (347940 downstream)																																			---	---	---	---
LOC100302640	100302640	broad.mit.edu	37	3	106838541	106838541	+	Intron	DEL	A	-	-	rs11310984		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:106838541delA	uc003dwf.3	-						LOC100302640_uc011bhk.1_Intron					Homo sapiens cDNA clone IMAGE:5284861.												0																		---	---	---	---
BBX	56987	broad.mit.edu	37	3	107501678	107501678	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:107501678delT	uc010hpr.2	+						BBX_uc003dwk.3_Intron|BBX_uc003dwl.3_Intron|BBX_uc003dwm.3_Intron|BBX_uc003dwo.3_Intron	NM_001142568	NP_001136040			HMG-BOX transcription factor BBX isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(3)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(3;0.112)															---	---	---	---
KIAA1524	57650	broad.mit.edu	37	3	108287039	108287039	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108287039delT	uc003dxb.3	-	10	1505	c.1236delA	c.(1234-1236)AAAfs	p.K412fs	KIAA1524_uc010hpv.1_5'Flank|KIAA1524_uc003dxc.1_Frame_Shift_Del_p.K253fs|KIAA1524_uc010hpw.1_Frame_Shift_Del_p.K253fs	NM_020890	NP_065941	Q8TCG1	CIP2A_HUMAN	p90 autoantigen	412				KCER -> NVKG (in Ref. 3; CAD28489).		cytoplasm|integral to membrane	protein binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
DZIP3	9666	broad.mit.edu	37	3	108365888	108365888	+	Intron	DEL	A	-	-	rs76287412		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108365888delA	uc003dxd.2	+						DZIP3_uc003dxf.1_Intron|DZIP3_uc011bhm.1_Intron|DZIP3_uc003dxe.1_Intron|DZIP3_uc003dxg.1_Intron	NM_014648	NP_055463			DAZ interacting protein 3, zinc finger						protein polyubiquitination	cytoplasm	polyubiquitin binding|RNA binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	108424647	108424647	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108424647delA								DZIP3 (10955 upstream) : RETNLB (49839 downstream)																																			---	---	---	---
MORC1	27136	broad.mit.edu	37	3	108818455	108818456	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108818455_108818456delTT	uc003dxl.2	-						MORC1_uc011bhn.1_Intron	NM_014429	NP_055244			MORC family CW-type zinc finger 1						cell differentiation|multicellular organismal development|spermatogenesis	nucleus	ATP binding|zinc ion binding			ovary(3)|skin(3)|breast(2)	8																		---	---	---	---
MORC1	27136	broad.mit.edu	37	3	108819090	108819091	+	Intron	DEL	AA	-	-	rs78907417		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108819090_108819091delAA	uc003dxl.2	-						MORC1_uc011bhn.1_Intron	NM_014429	NP_055244			MORC family CW-type zinc finger 1						cell differentiation|multicellular organismal development|spermatogenesis	nucleus	ATP binding|zinc ion binding			ovary(3)|skin(3)|breast(2)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	109384560	109384560	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:109384560delA								FLJ25363 (170546 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	110756728	110756728	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:110756728delA								None (None upstream) : PVRL3 (34137 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	111136296	111136297	+	IGR	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111136296_111136297delCT								PVRL3 (223923 upstream) : CD96 (124629 downstream)																																			---	---	---	---
PHLDB2	90102	broad.mit.edu	37	3	111573951	111573951	+	Intron	DEL	A	-	-	rs71714747		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111573951delA	uc003dyc.2	+							NM_001134437	NP_001127909			pleckstrin homology-like domain, family B,							cytoplasm|intermediate filament cytoskeleton|plasma membrane				ovary(4)|skin(2)	6																		---	---	---	---
PHLDB2	90102	broad.mit.edu	37	3	111671328	111671328	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111671328delT	uc010hqa.2	+						PHLDB2_uc003dyc.2_Intron|PHLDB2_uc003dyd.2_Intron|PHLDB2_uc003dyg.2_Intron|PHLDB2_uc003dyh.2_Intron|PHLDB2_uc003dyi.2_Intron	NM_001134438	NP_001127910			pleckstrin homology-like domain, family B,							cytoplasm|intermediate filament cytoskeleton|plasma membrane				ovary(4)|skin(2)	6																		---	---	---	---
ABHD10	55347	broad.mit.edu	37	3	111700978	111700979	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111700978_111700979insA	uc003dyk.3	+						ABHD10_uc011bhq.1_Intron	NM_018394	NP_060864			abhydrolase domain containing 10 precursor							mitochondrion	serine-type peptidase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	112167496	112167496	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112167496delT								CD200 (85840 upstream) : BTLA (15319 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	112697094	112697095	+	IGR	INS	-	ACAC	ACAC	rs143543153	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112697094_112697095insACAC								CD200R1 (3157 upstream) : GTPBP8 (12705 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	112787557	112787557	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112787557delA								C3orf17 (49002 upstream) : BOC (142855 downstream)																																			---	---	---	---
BOC	91653	broad.mit.edu	37	3	113005754	113005754	+	3'UTR	DEL	A	-	-	rs5022662	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113005754delA	uc003dzx.2	+	20					BOC_uc003dzy.2_3'UTR|BOC_uc003dzz.2_3'UTR|BOC_uc003eab.2_3'UTR|BOC_uc003eac.2_Intron	NM_033254	NP_150279			brother of CDO precursor						cell adhesion|muscle cell differentiation|positive regulation of myoblast differentiation	integral to membrane|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|pancreas(1)	6			Epithelial(53;0.227)															---	---	---	---
WDR52	55779	broad.mit.edu	37	3	113079774	113079775	+	Intron	DEL	AA	-	-	rs111698499		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113079774_113079775delAA	uc003ead.1	-											RecName: Full=WD repeat protein 52.; Flags: Fragment;											central_nervous_system(1)	1																		---	---	---	---
WDR52	55779	broad.mit.edu	37	3	113122994	113122994	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113122994delA	uc003eae.1	-							NM_018338	NP_060808			WD repeat domain 52 isoform 2											central_nervous_system(1)	1																		---	---	---	---
WDR52	55779	broad.mit.edu	37	3	113154706	113154707	+	Intron	DEL	GT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113154706_113154707delGT	uc003eae.1	-							NM_018338	NP_060808			WD repeat domain 52 isoform 2											central_nervous_system(1)	1																		---	---	---	---
ATP6V1A	523	broad.mit.edu	37	3	113514112	113514112	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113514112delA	uc003eao.2	+						ATP6V1A_uc011bik.1_Intron	NM_001690	NP_001681			ATPase, H+ transporting, lysosomal V1 subunit A						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytosol|integral to plasma membrane|proton-transporting V-type ATPase, V1 domain	ATP binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|proton-transporting ATPase activity, rotational mechanism			ovary(2)|skin(1)	3																		---	---	---	---
GRAMD1C	54762	broad.mit.edu	37	3	113569031	113569032	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113569031_113569032delTT	uc003eaq.3	+						GRAMD1C_uc011bil.1_Intron|GRAMD1C_uc011bim.1_Intron	NM_017577	NP_060047			GRAM domain containing 1C							integral to membrane				ovary(2)|skin(1)	3																		---	---	---	---
QTRTD1	79691	broad.mit.edu	37	3	113799338	113799338	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113799338delT	uc003eay.2	+						QTRTD1_uc003eaz.2_Intron|QTRTD1_uc011biq.1_Intron|QTRTD1_uc011bir.1_Intron	NM_024638	NP_078914			queuine tRNA-ribosyltransferase domain						queuosine biosynthetic process	mitochondrion	metal ion binding|queuine tRNA-ribosyltransferase activity			central_nervous_system(1)|skin(1)	2																		---	---	---	---
DRD3	1814	broad.mit.edu	37	3	113895457	113895457	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113895457delA	uc003ebd.2	-						DRD3_uc010hqn.1_Intron|DRD3_uc003ebb.1_Intron|DRD3_uc003ebc.1_Intron	NM_000796	NP_000787			dopamine receptor D3 isoform a						activation of adenylate cyclase activity by dopamine receptor signaling pathway|arachidonic acid secretion|behavioral response to cocaine|cellular calcium ion homeostasis|circadian regulation of gene expression|G-protein coupled receptor internalization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|locomotory behavior|musculoskeletal movement, spinal reflex action|negative regulation of blood pressure|negative regulation of oligodendrocyte differentiation|negative regulation of protein kinase B signaling cascade|negative regulation of protein secretion|positive regulation of dopamine receptor signaling pathway|positive regulation of mitosis|prepulse inhibition|regulation of dopamine secretion|response to drug|response to histamine|response to morphine|social behavior|visual learning	integral to plasma membrane	dopamine D3 receptor activity|drug binding			ovary(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4					Apomorphine(DB00714)|Chlorprothixene(DB01239)|Cocaine(DB00907)|Methotrimeprazine(DB01403)|Olanzapine(DB00334)|Pramipexole(DB00413)|Ropinirole(DB00268)|Ziprasidone(DB00246)													---	---	---	---
ZBTB20	26137	broad.mit.edu	37	3	114058003	114058004	+	Frame_Shift_Del	DEL	GG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114058003_114058004delGG	uc003ebi.2	-	5	2254_2255	c.2074_2075delCC	c.(2074-2076)CCTfs	p.P692fs	ZBTB20_uc003ebj.2_Frame_Shift_Del_p.P619fs|ZBTB20_uc010hqp.2_Frame_Shift_Del_p.P619fs|ZBTB20_uc003ebk.2_Frame_Shift_Del_p.P619fs|ZBTB20_uc003ebl.2_Frame_Shift_Del_p.P619fs|ZBTB20_uc003ebm.2_Frame_Shift_Del_p.P619fs|ZBTB20_uc003ebn.2_Frame_Shift_Del_p.P619fs	NM_015642	NP_056457	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20 isoform	692					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)														---	---	---	---
ZBTB20	26137	broad.mit.edu	37	3	114234852	114234855	+	Intron	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114234852_114234855delTTTT	uc003ebj.2	-						ZBTB20_uc010hqp.2_Intron|ZBTB20_uc003ebk.2_Intron|ZBTB20_uc003ebl.2_Intron|ZBTB20_uc003ebm.2_Intron|ZBTB20_uc003ebn.2_Intron	NM_015642	NP_056457			zinc finger and BTB domain containing 20 isoform						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)														---	---	---	---
ZBTB20	26137	broad.mit.edu	37	3	114380752	114380754	+	Intron	DEL	TTT	-	-	rs75942254		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114380752_114380754delTTT	uc003ebk.2	-						ZBTB20_uc003ebl.2_Intron|ZBTB20_uc003ebm.2_Intron|ZBTB20_uc003ebn.2_Intron	NM_015642	NP_056457			zinc finger and BTB domain containing 20 isoform						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)														---	---	---	---
ZBTB20	26137	broad.mit.edu	37	3	114388474	114388475	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114388474_114388475delAA	uc003ebk.2	-						ZBTB20_uc003ebl.2_Intron|ZBTB20_uc003ebm.2_Intron|ZBTB20_uc003ebn.2_Intron	NM_015642	NP_056457			zinc finger and BTB domain containing 20 isoform						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)														---	---	---	---
ZBTB20	26137	broad.mit.edu	37	3	114494321	114494321	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114494321delT	uc003ebm.2	-						ZBTB20_uc003ebn.2_Intron|ZBTB20_uc003ebp.2_Intron	NM_015642	NP_056457			zinc finger and BTB domain containing 20 isoform						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)														---	---	---	---
ZBTB20	26137	broad.mit.edu	37	3	114513031	114513031	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114513031delC	uc003ebm.2	-						ZBTB20_uc003ebn.2_Intron|ZBTB20_uc003ebp.2_Intron	NM_015642	NP_056457			zinc finger and BTB domain containing 20 isoform						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)														---	---	---	---
ZBTB20	26137	broad.mit.edu	37	3	114686441	114686441	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114686441delA	uc003ebm.2	-						ZBTB20_uc003ebn.2_Intron|ZBTB20_uc003ebp.2_Intron	NM_015642	NP_056457			zinc finger and BTB domain containing 20 isoform						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	115006243	115006244	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115006243_115006244insT								ZBTB20 (140116 upstream) : GAP43 (335907 downstream)																																			---	---	---	---
GAP43	2596	broad.mit.edu	37	3	115342811	115342811	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115342811delT	uc003ebq.2	+						GAP43_uc003ebr.2_Intron	NM_002045	NP_002036			growth associated protein 43 isoform 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell differentiation|nervous system development|regulation of filopodium assembly|regulation of growth|response to wounding	cell junction|filopodium membrane|growth cone membrane|synapse	calmodulin binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.164)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	115507453	115507455	+	IGR	DEL	AAA	-	-	rs111467666		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115507453_115507455delAAA								GAP43 (67119 upstream) : LSAMP (13767 downstream)																																			---	---	---	---
LSAMP	4045	broad.mit.edu	37	3	115680307	115680307	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:115680307delT	uc003ebt.2	-						LSAMP_uc011bis.1_Intron	NM_002338	NP_002329			limbic system-associated membrane protein						cell adhesion|nervous system development	anchored to membrane|plasma membrane					0		all_cancers(1;0.00189)|all_epithelial(1;0.0366)|Myeloproliferative disorder(1037;0.17)|all_neural(597;0.208)|Lung NSC(201;0.215)		GBM - Glioblastoma multiforme(114;0.00117)|LUSC - Lung squamous cell carcinoma(41;0.0407)|Lung(219;0.152)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	116383073	116383074	+	IGR	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:116383073_116383074delGA								LSAMP (859055 upstream) : LOC285194 (45561 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	116582869	116582869	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:116582869delT								LOC285194 (146984 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	117688745	117688746	+	IGR	DEL	AA	-	-	rs75158538		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:117688745_117688746delAA								None (None upstream) : IGSF11 (930735 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	118227458	118227459	+	Frame_Shift_Ins	INS	-	TC	TC			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118227458_118227459insTC	uc011biu.1	-	4	394_395	c.384_385insGA	c.(382-387)AGACACfs	p.R128fs						Homo sapiens clone HA_003061 mRNA sequence.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	118528377	118528377	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118528377delT	uc011biu.1	-											Homo sapiens clone HA_003061 mRNA sequence.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	118536545	118536546	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118536545_118536546delAA								None (None upstream) : IGSF11 (82935 downstream)																																			---	---	---	---
IGSF11	152404	broad.mit.edu	37	3	118741809	118741809	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118741809delA	uc003ebw.2	-						IGSF11_uc011biv.1_Intron|IGSF11_uc003ebx.2_Intron|IGSF11_uc003eby.2_Intron|IGSF11_uc003ebz.2_Intron|IGSF11_uc010hqs.2_Intron	NM_001015887	NP_001015887			immunoglobulin superfamily, member 11 isoform b						cell adhesion|regulation of growth	integral to membrane|plasma membrane	receptor activity				0																		---	---	---	---
IGSF11	152404	broad.mit.edu	37	3	118746915	118746915	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118746915delA	uc003ebw.2	-						IGSF11_uc011biv.1_Intron|IGSF11_uc003ebx.2_Intron|IGSF11_uc003eby.2_Intron|IGSF11_uc003ebz.2_Intron|IGSF11_uc010hqs.2_Intron	NM_001015887	NP_001015887			immunoglobulin superfamily, member 11 isoform b						cell adhesion|regulation of growth	integral to membrane|plasma membrane	receptor activity				0																		---	---	---	---
IGSF11	152404	broad.mit.edu	37	3	118798208	118798208	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118798208delA	uc003eby.2	-						IGSF11_uc003ebz.2_Intron|IGSF11_uc010hqs.2_Intron	NM_152538	NP_689751			immunoglobulin superfamily, member 11 isoform a						cell adhesion|regulation of growth	integral to membrane|plasma membrane	receptor activity				0																		---	---	---	---
UPK1B	7348	broad.mit.edu	37	3	118906002	118906003	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:118906002_118906003insT	uc003ecc.2	+						UPK1B_uc011bix.1_Intron|UPK1B_uc003ecd.2_Intron	NM_006952	NP_008883			uroplakin 1B						epithelial cell differentiation	integral to membrane	structural molecule activity				0				GBM - Glioblastoma multiforme(114;0.222)														---	---	---	---
ARHGAP31	57514	broad.mit.edu	37	3	119021224	119021224	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119021224delT	uc003ecj.3	+							NM_020754	NP_065805			Cdc42 GTPase-activating protein						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|focal adhesion|lamellipodium	GTPase activator activity			ovary(2)	2																		---	---	---	---
ARHGAP31	57514	broad.mit.edu	37	3	119050146	119050146	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119050146delA	uc003ecj.3	+							NM_020754	NP_065805			Cdc42 GTPase-activating protein						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|focal adhesion|lamellipodium	GTPase activator activity			ovary(2)	2																		---	---	---	---
ARHGAP31	57514	broad.mit.edu	37	3	119083982	119083982	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119083982delT	uc003ecj.3	+							NM_020754	NP_065805			Cdc42 GTPase-activating protein						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|focal adhesion|lamellipodium	GTPase activator activity			ovary(2)	2																		---	---	---	---
TMEM39A	55254	broad.mit.edu	37	3	119180142	119180142	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119180142delA	uc003eck.1	-						TMEM39A_uc003ecl.1_Intron	NM_018266	NP_060736			transmembrane protein 39A							integral to membrane				ovary(1)|breast(1)	2				GBM - Glioblastoma multiforme(114;0.244)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	119290923	119290924	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119290923_119290924delTT								CD80 (12442 upstream) : ADPRH (7599 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	119853924	119853924	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119853924delT	uc003edp.2	+											Homo sapiens cDNA clone IMAGE:4827879.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	119871258	119871260	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119871258_119871260delTTT								GSK3B (57994 upstream) : GPR156 (14620 downstream)																																			---	---	---	---
GPR156	165829	broad.mit.edu	37	3	119930853	119930853	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119930853delT	uc011bjf.1	-						GPR156_uc011bjg.1_Intron	NM_153002	NP_694547			G protein-coupled receptor 156							integral to membrane|plasma membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(1)|skin(1)	2				GBM - Glioblastoma multiforme(114;0.19)														---	---	---	---
GPR156	165829	broad.mit.edu	37	3	119954923	119954923	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119954923delT	uc011bjf.1	-						GPR156_uc011bjg.1_Intron	NM_153002	NP_694547			G protein-coupled receptor 156							integral to membrane|plasma membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(1)|skin(1)	2				GBM - Glioblastoma multiforme(114;0.19)														---	---	---	---
LRRC58	116064	broad.mit.edu	37	3	120063749	120063749	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120063749delA	uc003edr.2	-							NM_001099678	NP_001093148			leucine rich repeat containing 58												0				GBM - Glioblastoma multiforme(114;0.147)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	120192921	120192923	+	IGR	DEL	TTT	-	-	rs77884971		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120192921_120192923delTTT								FSTL1 (23003 upstream) : NDUFB4 (122205 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	120286881	120286881	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120286881delT								FSTL1 (116963 upstream) : NDUFB4 (28247 downstream)																																			---	---	---	---
RABL3	285282	broad.mit.edu	37	3	120419132	120419133	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120419132_120419133insA	uc003edx.2	-							NM_173825	NP_776186			RAB, member of RAS oncogene family-like 3						small GTPase mediated signal transduction		GTP binding				0				GBM - Glioblastoma multiforme(114;0.151)														---	---	---	---
ARGFX	503582	broad.mit.edu	37	3	121286803	121286804	+	5'UTR	INS	-	AG	AG			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121286803_121286804insAG	uc003eef.2	+	1						NM_001012659	NP_001012677			arginine-fifty homeobox							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(2)|ovary(1)	3				GBM - Glioblastoma multiforme(114;0.152)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	121350075	121350075	+	IGR	DEL	A	-	-	rs111509389		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121350075delA								FBXO40 (936 upstream) : HCLS1 (172 downstream)																																			---	---	---	---
GOLGB1	2804	broad.mit.edu	37	3	121383889	121383889	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121383889delA	uc003eei.3	-						GOLGB1_uc010hrc.2_Intron|GOLGB1_uc003eej.3_Intron	NM_004487	NP_004478			golgi autoantigen, golgin subfamily b,						Golgi organization	ER-Golgi intermediate compartment|Golgi membrane|Golgi stack|integral to membrane	protein binding			ovary(6)|breast(2)|skin(2)	10				GBM - Glioblastoma multiforme(114;0.0989)														---	---	---	---
SLC15A2	6565	broad.mit.edu	37	3	121639131	121639131	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121639131delT	uc003eep.2	+						SLC15A2_uc011bjn.1_Intron	NM_021082	NP_066568			peptide transporter 2 isoform a						protein transport	integral to plasma membrane	peptide:hydrogen symporter activity|protein binding			skin(1)	1				GBM - Glioblastoma multiforme(114;0.0967)	Cefadroxil(DB01140)													---	---	---	---
ILDR1	286676	broad.mit.edu	37	3	121724127	121724127	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121724127delC	uc003ees.2	-	3	449	c.343delG	c.(343-345)GTAfs	p.V115fs	ILDR1_uc003eeq.2_Frame_Shift_Del_p.V127fs|ILDR1_uc003eer.2_Frame_Shift_Del_p.V115fs|ILDR1_uc010hrg.2_Frame_Shift_Del_p.V115fs	NM_175924	NP_787120	Q86SU0	ILDR1_HUMAN	immunoglobulin-like domain containing receptor	115	Extracellular (Potential).|Ig-like V-type.					cytosol|integral to membrane|plasma membrane	receptor activity			skin(1)	1				GBM - Glioblastoma multiforme(114;0.156)														---	---	---	---
CD86	942	broad.mit.edu	37	3	121825017	121825017	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121825017delT	uc003eet.2	+						CD86_uc011bjo.1_Intron|CD86_uc011bjp.1_Intron|CD86_uc003eeu.2_Intron	NM_175862	NP_787058			CD86 antigen isoform 1						interspecies interaction between organisms|positive regulation of cell proliferation|positive regulation of interleukin-2 biosynthetic process|positive regulation of interleukin-4 biosynthetic process|positive regulation of lymphotoxin A biosynthetic process|positive regulation of T-helper 2 cell differentiation|positive regulation of transcription, DNA-dependent|T cell costimulation		coreceptor activity|protein binding			pancreas(1)|skin(1)	2				GBM - Glioblastoma multiforme(114;0.156)	Abatacept(DB01281)													---	---	---	---
CASR	846	broad.mit.edu	37	3	121973380	121973380	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121973380delT	uc003eev.3	+						CASR_uc003eew.3_Intron	NM_000388	NP_000379			calcium-sensing receptor precursor						anatomical structure morphogenesis|calcium ion import|cellular calcium ion homeostasis|chemosensory behavior|detection of calcium ion|ossification	integral to plasma membrane	G-protein coupled receptor activity|phosphatidylinositol phospholipase C activity			ovary(4)|skin(2)|upper_aerodigestive_tract(1)	7				GBM - Glioblastoma multiforme(114;0.226)	Cinacalcet(DB01012)													---	---	---	---
PARP14	54625	broad.mit.edu	37	3	122414253	122414253	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122414253delT	uc003efq.3	+						PARP14_uc010hrk.2_5'Flank	NM_017554	NP_060024			poly (ADP-ribose) polymerase family, member 14						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	NAD+ ADP-ribosyltransferase activity			ovary(2)|breast(2)|lung(1)|pancreas(1)	6				GBM - Glioblastoma multiforme(114;0.0531)														---	---	---	---
PARP14	54625	broad.mit.edu	37	3	122432999	122433000	+	Intron	DEL	TT	-	-	rs72248506		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122432999_122433000delTT	uc003efq.3	+						PARP14_uc010hrk.2_Intron|PARP14_uc003efr.2_Intron|PARP14_uc003efs.1_Intron	NM_017554	NP_060024			poly (ADP-ribose) polymerase family, member 14						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	NAD+ ADP-ribosyltransferase activity			ovary(2)|breast(2)|lung(1)|pancreas(1)	6				GBM - Glioblastoma multiforme(114;0.0531)														---	---	---	---
DIRC2	84925	broad.mit.edu	37	3	122552150	122552150	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122552150delT	uc003efw.3	+						DIRC2_uc010hrl.2_Intron|DIRC2_uc010hrm.2_Intron	NM_032839	NP_116228			disrupted in renal carcinoma 2						transport	integral to membrane					0				GBM - Glioblastoma multiforme(114;0.0614)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	122780093	122780093	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122780093delG								SEMA5B (32641 upstream) : PDIA5 (5872 downstream)																																			---	---	---	---
PDIA5	10954	broad.mit.edu	37	3	122826991	122826991	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122826991delT	uc003egc.1	+						PDIA5_uc003egd.1_Intron	NM_006810	NP_006801			protein disulfide isomerase A5 precursor						cell redox homeostasis|glycerol ether metabolic process|protein folding|response to stress	endoplasmic reticulum lumen	electron carrier activity|protein disulfide isomerase activity|protein disulfide oxidoreductase activity			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.0427)														---	---	---	---
ADCY5	111	broad.mit.edu	37	3	123038224	123038224	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123038224delA	uc003egh.1	-						ADCY5_uc003egg.1_Intron|ADCY5_uc003egi.1_Intron	NM_183357	NP_899200			adenylate cyclase 5						activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)	4				GBM - Glioblastoma multiforme(114;0.0342)														---	---	---	---
ADCY5	111	broad.mit.edu	37	3	123051611	123051611	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123051611delT	uc003egh.1	-						ADCY5_uc003egg.1_Intron|ADCY5_uc003egi.1_Intron	NM_183357	NP_899200			adenylate cyclase 5						activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)	4				GBM - Glioblastoma multiforme(114;0.0342)														---	---	---	---
ADCY5	111	broad.mit.edu	37	3	123087600	123087601	+	Intron	DEL	AA	-	-	rs138058637		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123087600_123087601delAA	uc003egh.1	-						ADCY5_uc003egg.1_Intron|ADCY5_uc003egi.1_Intron	NM_183357	NP_899200			adenylate cyclase 5						activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)	4				GBM - Glioblastoma multiforme(114;0.0342)														---	---	---	---
PTPLB	201562	broad.mit.edu	37	3	123245381	123245381	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123245381delT	uc003egj.2	-							NM_198402	NP_940684			protein tyrosine phosphatase-like (proline						fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	lyase activity|protein binding			kidney(1)	1				GBM - Glioblastoma multiforme(114;0.1)														---	---	---	---
PTPLB	201562	broad.mit.edu	37	3	123301217	123301217	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123301217delA	uc003egj.2	-							NM_198402	NP_940684			protein tyrosine phosphatase-like (proline						fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	lyase activity|protein binding			kidney(1)	1				GBM - Glioblastoma multiforme(114;0.1)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	123318833	123318833	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123318833delC	uc003egk.2	+											Homo sapiens cDNA clone IMAGE:5288594.																														---	---	---	---
MYLK	4638	broad.mit.edu	37	3	123400652	123400652	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123400652delG	uc003ego.2	-						MYLK_uc011bjv.1_Intron|MYLK_uc011bjw.1_Intron|MYLK_uc003egp.2_Intron|MYLK_uc003egq.2_Intron|MYLK_uc003egr.2_Intron|MYLK_uc003egs.2_Intron|MYLK_uc003egt.2_3'UTR	NM_053025	NP_444253			myosin light chain kinase isoform 1						aorta smooth muscle tissue morphogenesis|muscle contraction	cytosol	actin binding|ATP binding|calmodulin binding|metal ion binding|myosin light chain kinase activity			ovary(6)|skin(2)|stomach(1)	9		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)														---	---	---	---
MYLK	4638	broad.mit.edu	37	3	123508507	123508508	+	Intron	DEL	AA	-	-	rs34326373		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123508507_123508508delAA	uc003ego.2	-						MYLK_uc011bjw.1_Intron|MYLK_uc003egp.2_Intron|MYLK_uc003egq.2_Intron|MYLK_uc003egr.2_Intron|MYLK_uc003egs.2_Intron|MYLK_uc010hrs.1_Intron|MYLK_uc003egu.1_Intron	NM_053025	NP_444253			myosin light chain kinase isoform 1						aorta smooth muscle tissue morphogenesis|muscle contraction	cytosol	actin binding|ATP binding|calmodulin binding|metal ion binding|myosin light chain kinase activity			ovary(6)|skin(2)|stomach(1)	9		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)														---	---	---	---
ROPN1	54763	broad.mit.edu	37	3	123703596	123703596	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123703596delA	uc003eha.2	-						ROPN1_uc003ehb.1_Intron|ROPN1_uc003ehc.1_Intron	NM_017578	NP_060048			ropporin						signal transduction		cAMP-dependent protein kinase regulator activity			ovary(1)|skin(1)	2				GBM - Glioblastoma multiforme(114;0.148)														---	---	---	---
KALRN	8997	broad.mit.edu	37	3	124048962	124048962	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124048962delT	uc003ehg.2	+						KALRN_uc010hrv.1_Intron|KALRN_uc003ehf.1_Intron|KALRN_uc011bjy.1_Intron	NM_001024660	NP_001019831			kalirin, RhoGEF kinase isoform 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
KALRN	8997	broad.mit.edu	37	3	124075539	124075539	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124075539delT	uc003ehg.2	+						KALRN_uc010hrv.1_Intron|KALRN_uc003ehf.1_Intron|KALRN_uc011bjy.1_Intron	NM_001024660	NP_001019831			kalirin, RhoGEF kinase isoform 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
KALRN	8997	broad.mit.edu	37	3	124177192	124177192	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124177192delT	uc003ehg.2	+						KALRN_uc010hrv.1_Intron|KALRN_uc003ehf.1_Intron|KALRN_uc011bjy.1_Intron|KALRN_uc003ehh.1_Intron	NM_001024660	NP_001019831			kalirin, RhoGEF kinase isoform 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	124479939	124479940	+	IGR	DEL	TT	-	-	rs35822111		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124479939_124479940delTT								UMPS (15901 upstream) : ITGB5 (1856 downstream)																																			---	---	---	---
HEG1	57493	broad.mit.edu	37	3	124714941	124714941	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124714941delT	uc003ehs.3	-						HEG1_uc003ehr.3_Intron|HEG1_uc011bke.1_Intron	NM_020733	NP_065784			HEG homolog 1 precursor							extracellular region|integral to membrane	calcium ion binding			ovary(2)	2																		---	---	---	---
HEG1	57493	broad.mit.edu	37	3	124743919	124743922	+	Intron	DEL	CTCT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124743919_124743922delCTCT	uc003ehs.3	-						HEG1_uc011bke.1_Intron	NM_020733	NP_065784			HEG homolog 1 precursor							extracellular region|integral to membrane	calcium ion binding			ovary(2)	2																		---	---	---	---
SLC12A8	84561	broad.mit.edu	37	3	124843179	124843179	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124843179delT	uc003ehv.3	-						SLC12A8_uc003ehw.3_Intron|SLC12A8_uc010hrz.1_Intron|SLC12A8_uc003ehu.3_5'Flank|SLC12A8_uc010hry.2_5'Flank	NM_024628	NP_078904			solute carrier family 12, member 8						potassium ion transport	integral to membrane	symporter activity				0																		---	---	---	---
SNX4	8723	broad.mit.edu	37	3	125178714	125178715	+	Intron	INS	-	TT	TT	rs141734856	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125178714_125178715insTT	uc003eib.2	-						SNX4_uc011bkf.1_Intron	NM_003794	NP_003785			sorting nexin 4						cell communication|endocytic recycling|endocytosis|protein transport	cytoplasmic dynein complex|early endosome membrane	phosphatidylinositol binding|protein binding			breast(2)|ovary(1)|central_nervous_system(1)	4																		---	---	---	---
SNX4	8723	broad.mit.edu	37	3	125199226	125199227	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125199226_125199227insA	uc003eib.2	-						SNX4_uc011bkf.1_Intron	NM_003794	NP_003785			sorting nexin 4						cell communication|endocytic recycling|endocytosis|protein transport	cytoplasmic dynein complex|early endosome membrane	phosphatidylinositol binding|protein binding			breast(2)|ovary(1)|central_nervous_system(1)	4																		---	---	---	---
SNX4	8723	broad.mit.edu	37	3	125223328	125223328	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125223328delA	uc003eib.2	-						SNX4_uc011bkf.1_Intron	NM_003794	NP_003785			sorting nexin 4						cell communication|endocytic recycling|endocytosis|protein transport	cytoplasmic dynein complex|early endosome membrane	phosphatidylinositol binding|protein binding			breast(2)|ovary(1)|central_nervous_system(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	125370928	125370928	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125370928delT								OSBPL11 (56547 upstream) : MIR548I1 (138319 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	125390085	125390085	+	IGR	DEL	T	-	-	rs112155366		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125390085delT								OSBPL11 (75704 upstream) : MIR548I1 (119162 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	125405831	125405831	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125405831delC								OSBPL11 (91450 upstream) : MIR548I1 (103416 downstream)																																			---	---	---	---
MIR548I1	100302204	broad.mit.edu	37	3	125511090	125511090	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125511090delA	hsa-mir-548i-1|MI0006421	-																							0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	125555433	125555434	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125555433_125555434insA								MIR548I1 (46038 upstream) : LOC100125556 (80010 downstream)																																			---	---	---	---
LOC100125556	100125556	broad.mit.edu	37	3	125639002	125639002	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125639002delC	uc003eif.3	+						LOC100125556_uc003eid.3_Intron|LOC100125556_uc003eie.3_Intron	NR_024251				Homo sapiens family with sequence similarity 86, member A pseudogene, mRNA (cDNA clone IMAGE:4425123).												0																		---	---	---	---
ALG1L	200810	broad.mit.edu	37	3	125651237	125651237	+	Intron	DEL	A	-	-	rs112489594		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125651237delA	uc003eig.1	-							NM_001015050	NP_001015050			asparagine-linked glycosylation 1-like								transferase activity, transferring glycosyl groups				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	125921650	125921654	+	Intron	DEL	AAAAG	-	-	rs6438985		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125921650_125921654delAAAAG	uc003eiq.2	+											Homo sapiens cDNA FLJ40189 fis, clone TESTI2018974.																														---	---	---	---
KLF15	28999	broad.mit.edu	37	3	126062510	126062510	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126062510delA	uc011bkk.1	-	3						NM_014079	NP_054798			Kruppel-like factor 15							nucleus	DNA binding|zinc ion binding			lung(1)	1				GBM - Glioblastoma multiforme(114;0.147)														---	---	---	---
UROC1	131669	broad.mit.edu	37	3	126210924	126210925	+	Intron	INS	-	C	C	rs146668711	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126210924_126210925insC	uc003eiz.1	-						UROC1_uc010hsi.1_Intron	NM_144639	NP_653240			urocanase domain containing 1 isoform 1						histidine catabolic process	cytosol	urocanate hydratase activity			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.17)														---	---	---	---
C3orf22	152065	broad.mit.edu	37	3	126275771	126275774	+	Intron	DEL	ACAT	-	-	rs141113743		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126275771_126275774delACAT	uc003ejb.2	-							NM_152533	NP_689746			hypothetical protein LOC152065												0				GBM - Glioblastoma multiforme(114;0.147)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	126806912	126806912	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126806912delA								PLXNA1 (50684 upstream) : TPRA1 (484996 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	126939874	126939874	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126939874delA								PLXNA1 (183646 upstream) : TPRA1 (352034 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	127032759	127032759	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127032759delA								PLXNA1 (276531 upstream) : TPRA1 (259149 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	127065011	127065012	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127065011_127065012insA	uc003ejj.2	-											Homo sapiens, clone IMAGE:4618125, mRNA.																														---	---	---	---
RPN1	6184	broad.mit.edu	37	3	128378220	128378220	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128378220delA	uc011bkq.1	-							NM_002950	NP_002941			ribophorin I precursor						post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|melanosome|oligosaccharyltransferase complex|rough microsome	dolichyl-diphosphooligosaccharide-protein glycotransferase activity|protein binding			ovary(2)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(114;0.189)				T	EVI1	AML								---	---	---	---
CNBP	7555	broad.mit.edu	37	3	128898137	128898137	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128898137delA	uc003elq.3	-						CNBP_uc003elr.3_Intron|CNBP_uc011bku.1_Intron	NM_003418	NP_003409			zinc finger protein 9 isoform 3						cholesterol biosynthetic process	endoplasmic reticulum	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0																		---	---	---	---
COPG	22820	broad.mit.edu	37	3	128974331	128974331	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128974331delT	uc003els.2	+						COPG_uc010htb.2_Intron	NM_016128	NP_057212			coatomer protein complex, subunit gamma 1						COPI coating of Golgi vesicle|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol	protein binding|structural molecule activity			ovary(3)|breast(1)	4																		---	---	---	---
COPG	22820	broad.mit.edu	37	3	128986065	128986065	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128986065delA	uc003els.2	+						COPG_uc010htb.2_Intron	NM_016128	NP_057212			coatomer protein complex, subunit gamma 1						COPI coating of Golgi vesicle|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol	protein binding|structural molecule activity			ovary(3)|breast(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	129028908	129028908	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129028908delT								C3orf37 (4775 upstream) : H1FX (4707 downstream)																																			---	---	---	---
IFT122	55764	broad.mit.edu	37	3	129174023	129174023	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129174023delT	uc003emm.2	+						IFT122_uc003eml.2_Intron|IFT122_uc003emn.2_Intron|IFT122_uc003emo.2_Intron|IFT122_uc003emp.2_Intron|IFT122_uc010htc.2_Intron|IFT122_uc011bky.1_Intron|IFT122_uc003emq.2_Intron|IFT122_uc011bkx.1_Intron	NM_052989	NP_443715			WD repeat domain 10 isoform 2						camera-type eye morphogenesis|cilium morphogenesis|embryonic body morphogenesis|embryonic heart tube development|limb development|neural tube closure	microtubule basal body|photoreceptor connecting cilium				ovary(1)|skin(1)	2																		---	---	---	---
IFT122	55764	broad.mit.edu	37	3	129178373	129178373	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129178373delT	uc003emm.2	+						IFT122_uc003eml.2_Intron|IFT122_uc003emn.2_Intron|IFT122_uc003emo.2_Intron|IFT122_uc003emp.2_Intron|IFT122_uc010htc.2_Intron|IFT122_uc011bky.1_Intron|IFT122_uc003emq.2_Intron|IFT122_uc011bkx.1_Intron|IFT122_uc011bkz.1_5'Flank	NM_052989	NP_443715			WD repeat domain 10 isoform 2						camera-type eye morphogenesis|cilium morphogenesis|embryonic body morphogenesis|embryonic heart tube development|limb development|neural tube closure	microtubule basal body|photoreceptor connecting cilium				ovary(1)|skin(1)	2																		---	---	---	---
IFT122	55764	broad.mit.edu	37	3	129229086	129229086	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129229086delC	uc003emm.2	+						IFT122_uc003eml.2_Intron|IFT122_uc003emn.2_Intron|IFT122_uc003emo.2_Intron|IFT122_uc003emp.2_Intron|IFT122_uc010htc.2_Intron|IFT122_uc011bky.1_Intron|IFT122_uc003emq.2_Intron|IFT122_uc003emr.2_Intron|IFT122_uc011bla.1_Intron|IFT122_uc010hte.2_Intron|IFT122_uc003ems.2_Intron|IFT122_uc011bkx.1_Intron	NM_052989	NP_443715			WD repeat domain 10 isoform 2						camera-type eye morphogenesis|cilium morphogenesis|embryonic body morphogenesis|embryonic heart tube development|limb development|neural tube closure	microtubule basal body|photoreceptor connecting cilium				ovary(1)|skin(1)	2																		---	---	---	---
PLXND1	23129	broad.mit.edu	37	3	129294507	129294507	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129294507delG	uc003emx.2	-							NM_015103	NP_055918			plexin D1 precursor						axon guidance	integral to membrane|intracellular|plasma membrane				large_intestine(1)	1																		---	---	---	---
TMCC1	23023	broad.mit.edu	37	3	129540173	129540173	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129540173delT	uc003emz.3	-						TMCC1_uc010htg.2_Intron	NM_001017395	NP_001017395			transmembrane and coiled-coil domain family 1							integral to membrane				skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	129719781	129719781	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129719781delT								TRH (23005 upstream) : ALG1L2 (80893 downstream)																																			---	---	---	---
COL29A1	256076	broad.mit.edu	37	3	130122553	130122554	+	Intron	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130122553_130122554delAC	uc010htj.1	+						COL29A1_uc010hti.1_Intron	NM_153264	NP_694996			collagen, type XXIX, alpha 1						axon guidance|cell adhesion	collagen					0																		---	---	---	---
COL6A6	131873	broad.mit.edu	37	3	130367861	130367861	+	Intron	DEL	T	-	-	rs72391450		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130367861delT	uc010htl.2	+						COL6A6_uc003eni.3_Intron	NM_001102608	NP_001096078			collagen type VI alpha 6 precursor						axon guidance|cell adhesion	collagen				ovary(6)|central_nervous_system(1)|pancreas(1)	8																		---	---	---	---
NEK11	79858	broad.mit.edu	37	3	130765373	130765373	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130765373delT	uc003eny.2	+						NEK11_uc003enx.2_Intron|NEK11_uc003eoa.2_Intron|NEK11_uc003enz.2_Intron|NEK11_uc010htn.2_Intron|NEK11_uc011blk.1_Intron|NEK11_uc011bll.1_Intron|NEK11_uc003enw.1_Intron|NEK11_uc011blm.1_Intron	NM_024800	NP_079076			NIMA-related kinase 11 isoform 1						cell cycle|intra-S DNA damage checkpoint|intracellular protein kinase cascade	nucleolus	ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity			large_intestine(4)|stomach(1)|central_nervous_system(1)	6																		---	---	---	---
NEK11	79858	broad.mit.edu	37	3	130817670	130817670	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130817670delT	uc003eny.2	+						NEK11_uc003enx.2_Intron|NEK11_uc003eoa.2_Intron|NEK11_uc003enz.2_Intron|NEK11_uc010htn.2_Intron|NEK11_uc011blk.1_Intron|NEK11_uc011bll.1_Intron|NEK11_uc003enw.1_Intron|NEK11_uc011blm.1_Intron|NEK11_uc010hto.1_Intron	NM_024800	NP_079076			NIMA-related kinase 11 isoform 1						cell cycle|intra-S DNA damage checkpoint|intracellular protein kinase cascade	nucleolus	ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity			large_intestine(4)|stomach(1)|central_nervous_system(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	131149500	131149501	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131149500_131149501delAA								NUDT16 (44571 upstream) : MRPL3 (31545 downstream)																																			---	---	---	---
CPNE4	131034	broad.mit.edu	37	3	131611408	131611408	+	Intron	DEL	T	-	-	rs60226759		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:131611408delT	uc003eok.2	-						CPNE4_uc011blq.1_Intron|CPNE4_uc003eol.2_Intron|CPNE4_uc003eom.2_Intron	NM_130808	NP_570720			copine IV											upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
ACPP	55	broad.mit.edu	37	3	132055587	132055587	+	Intron	DEL	A	-	-	rs73215917	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132055587delA	uc010htp.2	+						ACPP_uc003eon.3_Intron|ACPP_uc003eop.3_Intron	NM_001099	NP_001090			acid phosphatase, prostate short isoform							extracellular region|lysosomal membrane	5'-nucleotidase activity|acid phosphatase activity			ovary(1)	1																		---	---	---	---
NPHP3	27031	broad.mit.edu	37	3	132417745	132417745	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132417745delT	uc003epe.1	-						NPHP3_uc003epd.1_Intron	NM_153240	NP_694972			nephrocystin 3						maintenance of organ identity|negative regulation of canonical Wnt receptor signaling pathway|photoreceptor cell maintenance|regulation of Wnt receptor signaling pathway, planar cell polarity pathway|Wnt receptor signaling pathway	cilium	protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	132687669	132687669	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132687669delT								NCRNA00119 (94619 upstream) : TMEM108 (69502 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	132710680	132710680	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132710680delT								NCRNA00119 (117630 upstream) : TMEM108 (46491 downstream)																																			---	---	---	---
TMEM108	66000	broad.mit.edu	37	3	132891407	132891407	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132891407delT	uc003eph.2	+						TMEM108_uc003epi.2_Intron|TMEM108_uc003epj.1_Intron|TMEM108_uc003epk.2_Intron	NM_023943	NP_076432			transmembrane protein 108 precursor							integral to membrane				ovary(2)|skin(2)	4																		---	---	---	---
TOPBP1	11073	broad.mit.edu	37	3	133342879	133342879	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133342879delA	uc003eps.2	-						TOPBP1_uc003ept.1_Intron	NM_007027	NP_008958			topoisomerase (DNA) II binding protein 1						DNA repair|response to ionizing radiation	microtubule organizing center|PML body|spindle pole	DNA binding|protein C-terminus binding			ovary(2)|kidney(2)|skin(1)|lung(1)|pancreas(1)	7													Other_conserved_DNA_damage_response_genes					---	---	---	---
RAB6B	51560	broad.mit.edu	37	3	133557659	133557659	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133557659delA	uc003epy.2	-						RAB6B_uc011blu.1_Intron	NM_016577	NP_057661			RAB6B, member RAS oncogene family						protein transport|retrograde vesicle-mediated transport, Golgi to ER|small GTPase mediated signal transduction	cytoplasmic membrane-bounded vesicle|Golgi membrane	GTP binding|GTPase activity|protein binding			pancreas(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	134435573	134435573	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134435573delC								KY (65095 upstream) : EPHB1 (78687 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	134439835	134439835	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134439835delT								KY (69357 upstream) : EPHB1 (74425 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	134492532	134492532	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134492532delC								KY (122054 upstream) : EPHB1 (21728 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	135056743	135056743	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135056743delA								EPHB1 (77438 upstream) : PPP2R3A (627824 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	135583010	135583010	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135583010delT								EPHB1 (603705 upstream) : PPP2R3A (101557 downstream)																																			---	---	---	---
PPP2R3A	5523	broad.mit.edu	37	3	135804975	135804975	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135804975delA	uc003eqv.1	+						PPP2R3A_uc011blz.1_Intron|PPP2R3A_uc003eqw.1_Intron	NM_002718	NP_002709			protein phosphatase 2, regulatory subunit B'',						protein dephosphorylation	protein phosphatase type 2A complex	calcium ion binding|protein binding|protein phosphatase type 2A regulator activity			ovary(3)|pancreas(1)|lung(1)|breast(1)|skin(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	135930783	135930783	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:135930783delT								MSL2 (16095 upstream) : PCCB (38384 downstream)																																			---	---	---	---
STAG1	10274	broad.mit.edu	37	3	136135575	136135575	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136135575delA	uc003era.1	-						STAG1_uc003erb.1_Intron|STAG1_uc003erc.1_Intron	NM_005862	NP_005853			stromal antigen 1						cell division|chromosome segregation|mitotic metaphase/anaphase transition|mitotic prometaphase	cell junction|chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	136795738	136795738	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136795738delA								IL20RB (65818 upstream) : SOX14 (687841 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	136822556	136822557	+	IGR	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136822556_136822557delCT								IL20RB (92636 upstream) : SOX14 (661022 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	136905179	136905180	+	IGR	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136905179_136905180delGA								IL20RB (175259 upstream) : SOX14 (578399 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	137167366	137167366	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137167366delT								IL20RB (437446 upstream) : SOX14 (316213 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	137190745	137190745	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137190745delC								IL20RB (460825 upstream) : SOX14 (292834 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	137392288	137392288	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137392288delT								IL20RB (662368 upstream) : SOX14 (91291 downstream)																																			---	---	---	---
A4GNT	51146	broad.mit.edu	37	3	137848929	137848929	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137848929delT	uc003ers.2	-							NM_016161	NP_057245			alpha-1,4-N-acetylglucosaminyltransferase						protein O-linked glycosylation	Golgi membrane|Golgi stack|integral to membrane|membrane fraction	acetylglucosaminyltransferase activity|galactosyltransferase activity			central_nervous_system(1)	1																		---	---	---	---
ARMC8	25852	broad.mit.edu	37	3	137907029	137907029	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137907029delT	uc003esa.1	+						ARMC8_uc003erw.2_Intron|ARMC8_uc003erx.2_Intron|ARMC8_uc003ery.2_Intron|ARMC8_uc003erz.2_Intron|ARMC8_uc011bmf.1_Intron|ARMC8_uc011bmg.1_Intron|ARMC8_uc011bmh.1_Intron|ARMC8_uc003esb.1_5'Flank	NM_015396	NP_056211			armadillo repeat containing 8 isoform 2								binding				0																		---	---	---	---
ARMC8	25852	broad.mit.edu	37	3	137988856	137988856	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137988856delT	uc003esa.1	+						TXNDC6_uc003esd.1_Intron|TXNDC6_uc010huf.1_Intron|TXNDC6_uc003ese.1_Intron|ARMC8_uc011bmf.1_Intron|ARMC8_uc011bmg.1_Intron|ARMC8_uc011bmh.1_Intron|ARMC8_uc003esb.1_Intron|ARMC8_uc003esc.1_Intron|ARMC8_uc003esf.1_Intron	NM_015396	NP_056211			armadillo repeat containing 8 isoform 2								binding				0																		---	---	---	---
ARMC8	25852	broad.mit.edu	37	3	138012379	138012379	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138012379delA	uc003esa.1	+						TXNDC6_uc003esd.1_Intron|TXNDC6_uc010huf.1_Intron|TXNDC6_uc003ese.1_Intron|ARMC8_uc011bmf.1_Intron|ARMC8_uc011bmg.1_Intron|ARMC8_uc011bmh.1_Intron|ARMC8_uc003esb.1_Intron|ARMC8_uc003esc.1_Intron|ARMC8_uc003esf.1_Intron	NM_015396	NP_056211			armadillo repeat containing 8 isoform 2								binding				0																		---	---	---	---
MRAS	22808	broad.mit.edu	37	3	138123869	138123869	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138123869delT	uc003esh.3	+	6					MRAS_uc011bmi.1_3'UTR|MRAS_uc003esi.3_3'UTR|MRAS_uc011bmj.1_3'UTR	NM_012219	NP_036351			muscle RAS oncogene homolog precursor						actin cytoskeleton organization|muscle organ development|Ras protein signal transduction	intracellular|plasma membrane	GTP binding|GTP-dependent protein binding|GTPase activity			lung(2)|upper_aerodigestive_tract(1)|ovary(1)	4																		---	---	---	---
FAIM	55179	broad.mit.edu	37	3	138333290	138333291	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138333290_138333291delAA	uc003esr.2	+						FAIM_uc003eso.1_Intron|FAIM_uc003esp.2_Intron|FAIM_uc003esq.2_Intron|FAIM_uc003ess.2_Intron	NM_001033032	NP_001028204			Fas apoptotic inhibitory molecule isoform c						apoptosis	cytoplasm					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	138492239	138492239	+	IGR	DEL	A	-	-	rs79007918		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138492239delA								PIK3CB (14054 upstream) : FOXL2 (170828 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	138525327	138525327	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138525327delA								PIK3CB (47142 upstream) : FOXL2 (137740 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	138681802	138681802	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138681802delT								C3orf72 (8972 upstream) : PRR23A (41003 downstream)																																			---	---	---	---
BPESC1	60467	broad.mit.edu	37	3	138821778	138821778	+	5'Flank	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138821778delC	uc003eta.2	+							NR_026783				Homo sapiens blepharophimosis, epicanthus inversus and ptosis, candidate 1 (BPESC1) mRNA, complete cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	138896163	138896164	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:138896163_138896164delTT								BPESC1 (52160 upstream) : PISRT1 (55671 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	139531398	139531398	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139531398delT								NMNAT3 (134558 upstream) : CLSTN2 (122629 downstream)																																			---	---	---	---
CLSTN2	64084	broad.mit.edu	37	3	139811947	139811948	+	Intron	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139811947_139811948delGA	uc003etn.2	+						CLSTN2_uc003etm.2_Intron	NM_022131	NP_071414			calsyntenin 2 precursor						homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			skin(3)|large_intestine(2)|pancreas(1)|central_nervous_system(1)	7															HNSCC(16;0.037)			---	---	---	---
CLSTN2	64084	broad.mit.edu	37	3	139859244	139859245	+	Intron	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139859244_139859245delGA	uc003etn.2	+						CLSTN2_uc003etm.2_Intron	NM_022131	NP_071414			calsyntenin 2 precursor						homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			skin(3)|large_intestine(2)|pancreas(1)|central_nervous_system(1)	7															HNSCC(16;0.037)			---	---	---	---
CLSTN2	64084	broad.mit.edu	37	3	139932086	139932087	+	Intron	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:139932086_139932087delTG	uc003etn.2	+						CLSTN2_uc003etm.2_Intron	NM_022131	NP_071414			calsyntenin 2 precursor						homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			skin(3)|large_intestine(2)|pancreas(1)|central_nervous_system(1)	7															HNSCC(16;0.037)			---	---	---	---
Unknown	0	broad.mit.edu	37	3	140296725	140296725	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140296725delC								CLSTN2 (9808 upstream) : TRIM42 (100156 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	140600014	140600014	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140600014delA								TRIM42 (180023 upstream) : SLC25A36 (60648 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	140901176	140901176	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140901176delC								SPSB4 (33724 upstream) : ACPL2 (49506 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	141024547	141024548	+	IGR	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141024547_141024548delTC								ACPL2 (11062 upstream) : ZBTB38 (18507 downstream)																																			---	---	---	---
RASA2	5922	broad.mit.edu	37	3	141208072	141208072	+	Intron	DEL	A	-	-	rs139520839		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141208072delA	uc003etz.1	+						RASA2_uc010huq.1_Intron|RASA2_uc003eua.1_Intron	NM_006506	NP_006497			RAS p21 protein activator 2						intracellular signal transduction|negative regulation of Ras protein signal transduction	intracellular membrane-bounded organelle|intrinsic to internal side of plasma membrane|perinuclear region of cytoplasm	metal ion binding|Ras GTPase activator activity			ovary(2)|lung(2)|breast(1)|skin(1)	6																		---	---	---	---
XRN1	54464	broad.mit.edu	37	3	142138167	142138167	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142138167delA	uc003eus.2	-						XRN1_uc003eut.2_Intron|XRN1_uc003euu.2_Intron|XRN1_uc003euv.1_Intron|XRN1_uc003euw.2_Intron|XRN1_uc011bnh.1_Intron	NM_019001	NP_061874			5'-3' exoribonuclease 1 isoform a						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|histone mRNA catabolic process|nuclear mRNA surveillance|rRNA catabolic process	cytosol|Golgi apparatus|intermediate filament cytoskeleton|plasma membrane	5'-3' exonuclease activity|DNA binding|protein binding|RNA binding			ovary(3)	3																		---	---	---	---
PLS1	5357	broad.mit.edu	37	3	142317843	142317845	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142317843_142317845delAAA	uc010huv.2	+							NM_001145319	NP_001138791			plastin 1							cytoplasm	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(1)	1																		---	---	---	---
PCOLCE2	26577	broad.mit.edu	37	3	142577456	142577456	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142577456delG	uc003evd.2	-							NM_013363	NP_037495			procollagen C-endopeptidase enhancer 2							extracellular region	collagen binding|heparin binding|peptidase activator activity			ovary(2)|skin(1)	3																		---	---	---	---
SLC9A9	285195	broad.mit.edu	37	3	143150734	143150734	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143150734delT	uc003evn.2	-							NM_173653	NP_775924			solute carrier family 9 (sodium/hydrogen						regulation of pH	integral to membrane|late endosome membrane|recycling endosome	sodium:hydrogen antiporter activity			ovary(2)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	143878667	143878667	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143878667delA								C3orf58 (167458 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	143976879	143976879	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143976879delA								C3orf58 (265670 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	144556704	144556704	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:144556704delT								C3orf58 (845495 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	144881066	144881069	+	IGR	DEL	AGTC	-	-	rs67488414		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:144881066_144881069delAGTC								None (None upstream) : PLOD2 (906159 downstream)																																			---	---	---	---
PLSCR5	389158	broad.mit.edu	37	3	146306565	146306565	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:146306565delA	uc003ewb.2	-						PLSCR5_uc010hvb.2_Intron|PLSCR5_uc010hvc.2_Intron	NM_001085420	NP_001078889			phospholipid scramblase family, member 5												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	146357728	146357728	+	IGR	DEL	T	-	-	rs112221388		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:146357728delT								PLSCR5 (33725 upstream) : ZIC4 (746109 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	146588405	146588405	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:146588405delA								PLSCR5 (264402 upstream) : ZIC4 (515432 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	146714231	146714231	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:146714231delG								PLSCR5 (390228 upstream) : ZIC4 (389606 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	147021057	147021058	+	IGR	DEL	AA	-	-	rs10709703		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147021057_147021058delAA								PLSCR5 (697054 upstream) : ZIC4 (82779 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	147135212	147135212	+	IGR	DEL	T	-	-	rs79890191		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147135212delT								ZIC1 (708 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	147351788	147351788	+	IGR	DEL	T	-	-	rs66501449		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147351788delT								ZIC1 (217284 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	147826957	147826957	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147826957delA								ZIC1 (692453 upstream) : AGTR1 (588701 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	147859550	147859552	+	IGR	DEL	AGG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:147859550_147859552delAGG								ZIC1 (725046 upstream) : AGTR1 (556106 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	148147791	148147791	+	IGR	DEL	T	-	-	rs112920564		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148147791delT								None (None upstream) : AGTR1 (267867 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	148405382	148405383	+	IGR	INS	-	T	T	rs144650978	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148405382_148405383insT								None (None upstream) : AGTR1 (10275 downstream)																																			---	---	---	---
CPA3	1359	broad.mit.edu	37	3	148582960	148582961	+	5'Flank	DEL	AA	-	-	rs143382113		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148582960_148582961delAA	uc003ewm.2	+							NM_001870	NP_001861			carboxypeptidase A3 precursor						proteolysis	stored secretory granule|transport vesicle	metallocarboxypeptidase activity|zinc ion binding			breast(1)|skin(1)	2			LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	148686561	148686561	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148686561delA								CPA3 (71691 upstream) : GYG1 (22814 downstream)																																			---	---	---	---
HPS3	84343	broad.mit.edu	37	3	148886826	148886827	+	Intron	DEL	GT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:148886826_148886827delGT	uc003ewu.1	+						CP_uc011bnr.1_Intron|HPS3_uc011bnq.1_Intron|HPS3_uc003ewv.1_Intron	NM_032383	NP_115759			Hermansky-Pudlak syndrome 3 protein							cytoplasm				ovary(5)|large_intestine(1)	6			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)											Hermansky-Pudlak_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	3	149167795	149167797	+	IGR	DEL	CTC	-	-	rs150354925		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149167795_149167797delCTC								TM4SF1 (72227 upstream) : TM4SF4 (24637 downstream)																																			---	---	---	---
TM4SF4	7104	broad.mit.edu	37	3	149199315	149199315	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149199315delA	uc003exd.1	+							NM_004617	NP_004608			transmembrane 4 superfamily member 4							integral to membrane					0			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)															---	---	---	---
WWTR1	25937	broad.mit.edu	37	3	149346728	149346728	+	Intron	DEL	A	-	-	rs63693160		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:149346728delA	uc003exe.2	-						WWTR1_uc003exf.2_Intron|WWTR1_uc011bns.1_Intron|WWTR1_uc003exh.2_Intron	NM_015472	NP_056287			WW domain containing transcription regulator 1						hippo signaling cascade|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of protein kinase activity|negative regulation of protein phosphorylation|positive regulation of cell proliferation|positive regulation of epithelial to mesenchymal transition|regulation of SMAD protein import into nucleus|stem cell division|transcription, DNA-dependent	cytoplasm	transcription coactivator activity			breast(3)|skin(1)	4			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)															---	---	---	---
EIF2A	83939	broad.mit.edu	37	3	150269355	150269356	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150269355_150269356delAA	uc003eya.2	+						SERP1_uc003exz.2_Intron|EIF2A_uc003eyb.2_Intron|EIF2A_uc003eyc.2_Intron|EIF2A_uc011bnv.1_Intron|EIF2A_uc011bnw.1_Intron|EIF2A_uc003eyd.2_5'Flank	NM_032025	NP_114414			eukaryotic translation initiation factor 2A						regulation of translation|ribosome assembly	eukaryotic translation initiation factor 2 complex	ribosome binding|translation initiation factor activity|tRNA binding				0		Melanoma(1037;0.0575)	LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)															---	---	---	---
FAM194A	131831	broad.mit.edu	37	3	150393143	150393143	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150393143delT	uc003eyg.2	-						FAM194A_uc003eyh.2_Intron	NM_152394	NP_689607			hypothetical protein LOC131831											skin(2)|ovary(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	150492643	150492643	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150492643delC								SIAH2 (11380 upstream) : CLRN1OS (77628 downstream)																																			---	---	---	---
CLRN1OS	116933	broad.mit.edu	37	3	150634919	150634919	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150634919delA	uc011bny.1	+											Homo sapiens usher critical region protein (UCRP) pseudogene mRNA, complete sequence.												0																		---	---	---	---
MED12L	116931	broad.mit.edu	37	3	150828347	150828347	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:150828347delT	uc003eyp.2	+						MED12L_uc011bnz.1_Intron|MED12L_uc003eym.1_Intron|MED12L_uc003eyn.2_Intron|MED12L_uc003eyo.2_Intron	NM_053002	NP_443728			mediator of RNA polymerase II transcription,						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)															---	---	---	---
MED12L	116931	broad.mit.edu	37	3	151021860	151021860	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151021860delG	uc003eyp.2	+						MED12L_uc011bnz.1_Intron|GPR87_uc003eyt.2_Intron	NM_053002	NP_443728			mediator of RNA polymerase II transcription,						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)															---	---	---	---
MED12L	116931	broad.mit.edu	37	3	151123996	151123996	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151123996delT	uc003eyp.2	+						MED12L_uc011bnz.1_Intron	NM_053002	NP_443728			mediator of RNA polymerase II transcription,						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)															---	---	---	---
MED12L	116931	broad.mit.edu	37	3	151150682	151150682	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151150682delT	uc003eyp.2	+	43					MED12L_uc011bnz.1_3'UTR	NM_053002	NP_443728			mediator of RNA polymerase II transcription,						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	151961371	151961372	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151961371_151961372delTT								SUCNR1 (361721 upstream) : LOC401093 (19041 downstream)																																			---	---	---	---
MBNL1	4154	broad.mit.edu	37	3	152048997	152048998	+	Intron	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152048997_152048998delAC	uc003ezm.2	+						MBNL1_uc003ezh.2_Intron|MBNL1_uc003ezi.2_Intron|MBNL1_uc003ezj.2_Intron|MBNL1_uc003ezl.2_Intron|MBNL1_uc003ezp.2_Intron|MBNL1_uc003ezn.2_Intron|MBNL1_uc003ezo.2_Intron	NM_207293	NP_997176			muscleblind-like 1 isoform c						embryonic limb morphogenesis|in utero embryonic development|myoblast differentiation|nervous system development	nucleus|stress granule	double-stranded RNA binding|protein binding|zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	152428327	152428327	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152428327delA								MBNL1 (244759 upstream) : P2RY1 (124409 downstream)																																			---	---	---	---
P2RY1	5028	broad.mit.edu	37	3	152553722	152553722	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152553722delT	uc003ezq.2	+	1	987	c.151delT	c.(151-153)TTTfs	p.F51fs		NM_002563	NP_002554	P47900	P2RY1_HUMAN	purinergic receptor P2Y1	51	Extracellular (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|platelet activation	integral to plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			lung(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0628)|Lung(72;0.11)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	152738598	152738598	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152738598delA								P2RY1 (182757 upstream) : RAP2B (141431 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	152989479	152989480	+	IGR	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:152989479_152989480delAG								RAP2B (103218 upstream) : C3orf79 (212804 downstream)																																			---	---	---	---
C3orf79	152118	broad.mit.edu	37	3	153217143	153217143	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:153217143delT	uc003ezt.2	+							NM_001101337	NP_001094807			chromosome 3 open reading frame 79												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	153614376	153614376	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:153614376delT								C3orf79 (393893 upstream) : SGEF (224773 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	153741961	153741961	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:153741961delA								C3orf79 (521478 upstream) : SGEF (97188 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	153838403	153838403	+	Intron	DEL	T	-	-	rs1727885	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:153838403delT	uc003ezu.1	-						SGEF_uc011bog.1_5'Flank|SGEF_uc011boh.1_5'Flank					Homo sapiens cDNA clone IMAGE:4823793.																														---	---	---	---
GPR149	344758	broad.mit.edu	37	3	154119456	154119456	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154119456delA	uc003faa.2	-							NM_001038705	NP_001033794			G protein-coupled receptor 149							integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(6)	6			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	154219506	154219506	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154219506delA								GPR149 (72002 upstream) : MME (522407 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	154299398	154299399	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154299398_154299399delTG								GPR149 (151894 upstream) : MME (442514 downstream)																																			---	---	---	---
MME	4311	broad.mit.edu	37	3	154760434	154760434	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154760434delT	uc010hvr.1	+							NM_007289	NP_009220			membrane metallo-endopeptidase						cell-cell signaling|proteolysis	integral to plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			ovary(2)|central_nervous_system(1)	3		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)													---	---	---	---
MME	4311	broad.mit.edu	37	3	154834153	154834153	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154834153delT	uc010hvr.1	+						MME_uc003fab.1_Intron|MME_uc003fac.1_Intron|MME_uc003fad.1_Intron|MME_uc003fae.1_Intron	NM_007289	NP_009220			membrane metallo-endopeptidase						cell-cell signaling|proteolysis	integral to plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			ovary(2)|central_nervous_system(1)	3		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	155045515	155045515	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155045515delA								MME (143997 upstream) : PLCH1 (152156 downstream)																																			---	---	---	---
PLCH1	23007	broad.mit.edu	37	3	155211804	155211804	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155211804delA	uc011bok.1	-						PLCH1_uc011boj.1_Intron|PLCH1_uc011bol.1_Intron	NM_001130960	NP_001124432			phospholipase C eta 1 isoform a						lipid catabolic process|phosphatidylinositol-mediated signaling	membrane	calcium ion binding|calcium-dependent phospholipase C activity|phosphatidylinositol phospholipase C activity|signal transducer activity			skin(3)|ovary(1)	4			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)															---	---	---	---
PLCH1	23007	broad.mit.edu	37	3	155358984	155358987	+	Intron	DEL	AAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155358984_155358987delAAAA	uc011bok.1	-						PLCH1_uc011boj.1_Intron|PLCH1_uc011bol.1_Intron	NM_001130960	NP_001124432			phospholipase C eta 1 isoform a						lipid catabolic process|phosphatidylinositol-mediated signaling	membrane	calcium ion binding|calcium-dependent phospholipase C activity|phosphatidylinositol phospholipase C activity|signal transducer activity			skin(3)|ovary(1)	4			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	155477313	155477313	+	IGR	DEL	A	-	-	rs76970216		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155477313delA								PLCH1 (55316 upstream) : C3orf33 (3088 downstream)																																			---	---	---	---
GMPS	8833	broad.mit.edu	37	3	155632554	155632554	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155632554delT	uc003faq.2	+						GMPS_uc011bom.1_Intron	NM_003875	NP_003866			guanine monophosphate synthetase						glutamine metabolic process|purine base biosynthetic process	cytosol	ATP binding|GMP synthase (glutamine-hydrolyzing) activity|GMP synthase activity			ovary(2)|lung(1)	3			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)		L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)			T	MLL	AML								---	---	---	---
KCNAB1	7881	broad.mit.edu	37	3	156140687	156140687	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156140687delA	uc003far.2	+						KCNAB1_uc011bon.1_Intron|KCNAB1_uc003fas.2_Intron|KCNAB1_uc003fat.2_Intron|KCNAB1_uc010hvt.1_Intron	NM_172160	NP_751892			potassium voltage-gated channel, shaker-related							cytoplasm|integral to membrane	oxidoreductase activity|potassium channel regulator activity|voltage-gated potassium channel activity			ovary(3)|skin(1)	4			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	156329983	156329984	+	IGR	INS	-	CT	CT			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156329983_156329984insCT								SSR3 (57048 upstream) : LOC100287227 (60980 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	156435978	156435979	+	IGR	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156435978_156435979insG								TIPARP (11449 upstream) : PA2G4P4 (91081 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	156486915	156486915	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156486915delA	uc003fax.1	-											Homo sapiens cDNA FLJ31839 fis, clone NT2RP7000086.																														---	---	---	---
VEPH1	79674	broad.mit.edu	37	3	157126887	157126887	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157126887delT	uc003fbj.1	-						VEPH1_uc003fbk.1_Intron|VEPH1_uc010hvu.1_Intron	NM_024621	NP_078897			ventricular zone expressed PH domain homolog 1							plasma membrane				breast(3)|ovary(1)|lung(1)	5			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	157396849	157396849	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157396849delA								C3orf55 (77830 upstream) : SHOX2 (416952 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	157556864	157556864	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157556864delA								C3orf55 (237845 upstream) : SHOX2 (256937 downstream)																																			---	---	---	---
RSRC1	51319	broad.mit.edu	37	3	157888692	157888692	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157888692delC	uc003fbt.2	+						RSRC1_uc011bou.1_Intron|RSRC1_uc003fbu.1_Intron|RSRC1_uc003fbv.2_Intron	NM_016625	NP_057709			arginine/serine-rich coiled-coil 1						nucleocytoplasmic transport	cytoplasm|nuclear speck	protein binding				0			Lung(72;0.00416)|LUSC - Lung squamous cell carcinoma(72;0.00575)															---	---	---	---
RSRC1	51319	broad.mit.edu	37	3	157960507	157960507	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157960507delT	uc003fbt.2	+						RSRC1_uc011bou.1_Intron|RSRC1_uc003fbu.1_Intron|RSRC1_uc003fbv.2_Intron	NM_016625	NP_057709			arginine/serine-rich coiled-coil 1						nucleocytoplasmic transport	cytoplasm|nuclear speck	protein binding				0			Lung(72;0.00416)|LUSC - Lung squamous cell carcinoma(72;0.00575)															---	---	---	---
MFSD1	64747	broad.mit.edu	37	3	158531731	158531731	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158531731delT	uc003fcl.1	+						MFSD1_uc003fcm.1_Intron|MFSD1_uc003fcn.1_Intron|MFSD1_uc011bow.1_Intron|MFSD1_uc011box.1_Intron	NM_022736	NP_073573			major facilitator superfamily domain containing						transmembrane transport	integral to membrane					0			Lung(72;0.00372)|LUSC - Lung squamous cell carcinoma(72;0.00523)															---	---	---	---
SCHIP1	29970	broad.mit.edu	37	3	158844559	158844559	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158844559delT	uc003fcq.1	+						IQCJ_uc003fco.2_Intron|IQCJ_uc010hvy.1_Intron|IQCJ_uc003fcp.1_Intron	NM_014575	NP_055390			schwannomin interacting protein 1							cytoplasm	identical protein binding|protein binding			ovary(1)|central_nervous_system(1)	2			LUSC - Lung squamous cell carcinoma(72;0.00523)|Lung(72;0.00534)															---	---	---	---
IFT80	57560	broad.mit.edu	37	3	160049801	160049801	+	Intron	DEL	C	-	-	rs142923847		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160049801delC	uc011boy.1	-						IFT80_uc003fda.2_Intron|IFT80_uc003fdb.1_Intron|IFT80_uc003fdd.1_Intron|IFT80_uc003fde.1_Intron	NM_020800	NP_065851			WD repeat domain 56							cilium axoneme|microtubule basal body				ovary(1)	1			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)															---	---	---	---
IFT80	57560	broad.mit.edu	37	3	160102250	160102250	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160102250delA	uc011boy.1	-						IFT80_uc003fda.2_Intron|IFT80_uc003fdb.1_5'UTR|IFT80_uc003fdd.1_5'UTR|IFT80_uc003fde.1_5'UTR	NM_020800	NP_065851			WD repeat domain 56							cilium axoneme|microtubule basal body				ovary(1)	1			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)															---	---	---	---
KPNA4	3840	broad.mit.edu	37	3	160248733	160248733	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160248733delA	uc003fdn.2	-							NM_002268	NP_002259			karyopherin alpha 4						NLS-bearing substrate import into nucleus	cytoplasm|nuclear pore	protein binding				0			Lung(72;0.00149)|LUSC - Lung squamous cell carcinoma(72;0.00216)															---	---	---	---
NMD3	51068	broad.mit.edu	37	3	160951131	160951131	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160951131delT	uc003feb.1	+						NMD3_uc003fec.2_Intron|NMD3_uc003fed.1_Intron|NMD3_uc010hwh.2_5'Flank	NM_015938	NP_057022			NMD3 homolog						protein transport	cytoplasm|nucleolus|nucleoplasm				ovary(1)	1			Lung(72;0.00111)|LUSC - Lung squamous cell carcinoma(72;0.00156)															---	---	---	---
NMD3	51068	broad.mit.edu	37	3	160960578	160960578	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160960578delT	uc003feb.1	+						NMD3_uc003fec.2_Intron|NMD3_uc003fed.1_Intron|NMD3_uc010hwh.2_Intron	NM_015938	NP_057022			NMD3 homolog						protein transport	cytoplasm|nucleolus|nucleoplasm				ovary(1)	1			Lung(72;0.00111)|LUSC - Lung squamous cell carcinoma(72;0.00156)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	161658180	161658180	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:161658180delT								OTOL1 (436452 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	162482540	162482540	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:162482540delT	uc003feg.2	+											Homo sapiens, clone IMAGE:2905387, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	162915684	162915684	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:162915684delT	uc003feg.2	+						uc003feh.2_Intron					Homo sapiens, clone IMAGE:2905387, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	163358509	163358509	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:163358509delA								None (None upstream) : MIR1263 (530750 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	163415646	163415646	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:163415646delC								None (None upstream) : MIR1263 (473613 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	163519515	163519515	+	IGR	DEL	C	-	-	rs11321394		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:163519515delC								None (None upstream) : MIR1263 (369744 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	163654371	163654371	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:163654371delA								None (None upstream) : MIR1263 (234888 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	164336640	164336640	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164336640delT								MIR720 (277402 upstream) : SI (360047 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	164541224	164541225	+	IGR	DEL	GT	-	-	rs72050433		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164541224_164541225delGT								MIR720 (481986 upstream) : SI (155462 downstream)																																			---	---	---	---
SI	6476	broad.mit.edu	37	3	164758105	164758106	+	Intron	DEL	AG	-	-	rs71833654		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164758105_164758106delAG	uc003fei.2	-							NM_001041	NP_001032			sucrase-isomaltase						carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity			ovary(7)|upper_aerodigestive_tract(4)|skin(2)|pancreas(1)	14		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)										HNSCC(35;0.089)			---	---	---	---
Unknown	0	broad.mit.edu	37	3	164804943	164804944	+	IGR	DEL	AC	-	-	rs139362445		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164804943_164804944delAC								SI (8661 upstream) : SLITRK3 (99574 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	165695034	165695037	+	IGR	DEL	GTGC	-	-	rs58738986		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:165695034_165695037delGTGC								BCHE (139781 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	166024045	166024046	+	IGR	DEL	AC	-	-	rs71632442		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:166024045_166024046delAC								BCHE (468792 upstream) : ZBBX (934035 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	166160532	166160533	+	IGR	DEL	TT	-	-	rs78330324		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:166160532_166160533delTT								BCHE (605279 upstream) : ZBBX (797548 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	166319502	166319502	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:166319502delA								BCHE (764249 upstream) : ZBBX (638579 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	166427454	166427456	+	IGR	DEL	AAC	-	-	rs142148374	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:166427454_166427456delAAC								BCHE (872201 upstream) : ZBBX (530625 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	166488028	166488028	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:166488028delT								BCHE (932775 upstream) : ZBBX (470053 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	166897925	166897925	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:166897925delA								None (None upstream) : ZBBX (60156 downstream)																																			---	---	---	---
ZBBX	79740	broad.mit.edu	37	3	166984054	166984054	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:166984054delT	uc003fep.2	-						ZBBX_uc011bpc.1_Intron|ZBBX_uc003feq.2_Intron	NM_024687	NP_078963			zinc finger, B-box domain containing							intracellular	zinc ion binding			ovary(2)	2																		---	---	---	---
SERPINI2	5276	broad.mit.edu	37	3	167170830	167170830	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167170830delA	uc003fer.1	-						SERPINI2_uc003fes.1_Intron|SERPINI2_uc003fet.1_Intron	NM_006217	NP_006208			serpin peptidase inhibitor, clade I (pancpin),						cellular component movement|regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			skin(2)|urinary_tract(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	167682545	167682545	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167682545delT								SERPINI1 (139189 upstream) : GOLIM4 (45109 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	167943994	167943994	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167943994delA								GOLIM4 (130577 upstream) : MIR551B (325648 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	168011308	168011308	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168011308delC								GOLIM4 (197891 upstream) : MIR551B (258334 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	168020630	168020630	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168020630delA								GOLIM4 (207213 upstream) : MIR551B (249012 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	168064022	168064022	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168064022delT								GOLIM4 (250605 upstream) : MIR551B (205620 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	168158215	168158216	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168158215_168158216insT								GOLIM4 (344798 upstream) : MIR551B (111426 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	168195525	168195525	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168195525delA								GOLIM4 (382108 upstream) : MIR551B (74117 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	168248545	168248547	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168248545_168248547delTTT								GOLIM4 (435128 upstream) : MIR551B (21095 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	168344171	168344172	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168344171_168344172delTT								MIR551B (74434 upstream) : C3orf50 (183412 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	168371161	168371161	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168371161delA								MIR551B (101424 upstream) : C3orf50 (156423 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	168577115	168577115	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168577115delA								C3orf50 (28743 upstream) : MECOM (224172 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	168605104	168605104	+	IGR	DEL	A	-	-	rs112652406		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168605104delA								C3orf50 (56732 upstream) : MECOM (196183 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	168766240	168766240	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:168766240delA								C3orf50 (217868 upstream) : MECOM (35047 downstream)																																			---	---	---	---
MYNN	55892	broad.mit.edu	37	3	169501506	169501506	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169501506delT	uc003fft.2	+						MYNN_uc011bpm.1_Intron|MYNN_uc003ffu.2_Intron|MYNN_uc003ffv.2_Intron|MYNN_uc010hwo.2_Intron|MYNN_uc003ffw.1_Intron	NM_018657	NP_061127			myoneurin							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1	all_cancers(22;9.55e-22)|all_epithelial(15;2.04e-26)|all_lung(20;5.05e-16)|Lung NSC(18;2.19e-15)|Ovarian(172;0.000223)|Breast(254;0.197)		Epithelial(2;4.03e-64)|all cancers(2;2.19e-58)|Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00676)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	169905197	169905198	+	IGR	DEL	TT	-	-	rs72356327		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169905197_169905198delTT								PHC3 (5660 upstream) : PRKCI (35022 downstream)																																			---	---	---	---
PRKCI	5584	broad.mit.edu	37	3	169941408	169941408	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169941408delT	uc003fgs.2	+							NM_002740	NP_002731			protein kinase C, iota						anti-apoptosis|cellular membrane organization|cellular response to insulin stimulus|establishment or maintenance of epithelial cell apical/basal polarity|intracellular signal transduction|nerve growth factor receptor signaling pathway|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|protein targeting to membrane|secretion|tight junction assembly|vesicle-mediated transport	cytosol|endosome|nucleus|polarisome	ATP binding|phospholipid binding|protein binding|protein kinase C activity|zinc ion binding			lung(2)|ovary(1)|breast(1)|skin(1)	5	all_cancers(22;6.45e-23)|all_epithelial(15;8.52e-28)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)															---	---	---	---
PRKCI	5584	broad.mit.edu	37	3	169957530	169957533	+	Intron	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169957530_169957533delTTTT	uc003fgs.2	+							NM_002740	NP_002731			protein kinase C, iota						anti-apoptosis|cellular membrane organization|cellular response to insulin stimulus|establishment or maintenance of epithelial cell apical/basal polarity|intracellular signal transduction|nerve growth factor receptor signaling pathway|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|protein targeting to membrane|secretion|tight junction assembly|vesicle-mediated transport	cytosol|endosome|nucleus|polarisome	ATP binding|phospholipid binding|protein binding|protein kinase C activity|zinc ion binding			lung(2)|ovary(1)|breast(1)|skin(1)	5	all_cancers(22;6.45e-23)|all_epithelial(15;8.52e-28)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)															---	---	---	---
EIF5A2	56648	broad.mit.edu	37	3	170624844	170624844	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170624844delT	uc003fhd.2	-	3	334	c.204delA	c.(202-204)AAAfs	p.K68fs		NM_020390	NP_065123	Q9GZV4	IF5A2_HUMAN	eIF-5A2 protein	68					mRNA transport|peptidyl-lysine modification to hypusine|polyamine homeostasis|positive regulation of cell proliferation|positive regulation of translational elongation|positive regulation of translational termination|post-translational protein modification|protein transport|spermatogenesis|translational frameshifting|transmembrane transport	cytosol|endoplasmic reticulum membrane|nuclear pore	protein binding|ribosome binding|translation elongation factor activity				0	all_cancers(22;1.61e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;9.8e-16)|Lung(28;4.28e-15)															---	---	---	---
SLC2A2	6514	broad.mit.edu	37	3	170718428	170718428	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170718428delT	uc003fhe.1	-						SLC2A2_uc003fhf.1_Intron|SLC2A2_uc011bpu.1_Intron	NM_000340	NP_000331			solute carrier family 2 (facilitated glucose						carbohydrate metabolic process|cellular lipid metabolic process|endocrine pancreas development|energy reserve metabolic process|regulation of insulin secretion	integral to plasma membrane|membrane fraction	D-glucose transmembrane transporter activity			ovary(1)|central_nervous_system(1)	2	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)															---	---	---	---
SLC2A2	6514	broad.mit.edu	37	3	170736123	170736123	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:170736123delT	uc003fhe.1	-						SLC2A2_uc003fhf.1_Intron|SLC2A2_uc011bpu.1_Intron	NM_000340	NP_000331			solute carrier family 2 (facilitated glucose						carbohydrate metabolic process|cellular lipid metabolic process|endocrine pancreas development|energy reserve metabolic process|regulation of insulin secretion	integral to plasma membrane|membrane fraction	D-glucose transmembrane transporter activity			ovary(1)|central_nervous_system(1)	2	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)															---	---	---	---
TNIK	23043	broad.mit.edu	37	3	171063505	171063505	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171063505delT	uc003fhh.2	-						TNIK_uc003fhi.2_Intron|TNIK_uc003fhj.2_Intron|TNIK_uc003fhk.2_Intron|TNIK_uc003fhl.2_Intron|TNIK_uc003fhm.2_Intron|TNIK_uc003fhn.2_Intron|TNIK_uc003fho.2_Intron	NM_015028	NP_055843			TRAF2 and NCK interacting kinase isoform 1						actin cytoskeleton reorganization|activation of JNKK activity|protein autophosphorylation|regulation of dendrite morphogenesis|Wnt receptor signaling pathway	cytoskeleton|nucleus|recycling endosome	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(4)|large_intestine(1)	5	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)															---	---	---	---
TNIK	23043	broad.mit.edu	37	3	171150482	171150482	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171150482delA	uc003fhh.2	-						TNIK_uc003fhi.2_Intron|TNIK_uc003fhj.2_Intron|TNIK_uc003fhk.2_Intron|TNIK_uc003fhl.2_Intron|TNIK_uc003fhm.2_Intron|TNIK_uc003fhn.2_Intron|TNIK_uc003fho.2_Intron|TNIK_uc003fhq.2_Intron	NM_015028	NP_055843			TRAF2 and NCK interacting kinase isoform 1						actin cytoskeleton reorganization|activation of JNKK activity|protein autophosphorylation|regulation of dendrite morphogenesis|Wnt receptor signaling pathway	cytoskeleton|nucleus|recycling endosome	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(4)|large_intestine(1)	5	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	171532308	171532308	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171532308delT								PLD1 (4035 upstream) : TMEM212 (28851 downstream)																																			---	---	---	---
FNDC3B	64778	broad.mit.edu	37	3	172054949	172054950	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172054949_172054950insT	uc003fhy.2	+						FNDC3B_uc003fhz.3_Intron|FNDC3B_uc003fia.2_Intron	NM_022763	NP_073600			fibronectin type III domain containing 3B							endoplasmic reticulum|integral to membrane				ovary(2)|breast(1)	3	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	172247155	172247155	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172247155delA								TNFSF10 (5886 upstream) : NCEH1 (101281 downstream)																																			---	---	---	---
NCEH1	57552	broad.mit.edu	37	3	172370661	172370664	+	Intron	DEL	TTTT	-	-	rs33937237		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172370661_172370664delTTTT	uc011bpx.1	-						NCEH1_uc003fig.2_Intron|NCEH1_uc011bpw.1_Intron|NCEH1_uc011bpy.1_Intron	NM_001146276	NP_001139748			arylacetamide deacetylase-like 1 isoform a						lipid catabolic process	endoplasmic reticulum|integral to membrane|microsome	carboxylesterase activity				0																		---	---	---	---
SPATA16	83893	broad.mit.edu	37	3	172860173	172860174	+	5'Flank	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172860173_172860174insA	uc003fin.3	-							NM_031955	NP_114161			spermatogenesis associated 16						cell differentiation|multicellular organismal development|spermatogenesis	Golgi apparatus	binding			ovary(2)|skin(1)	3	Ovarian(172;0.00319)|Breast(254;0.197)		LUSC - Lung squamous cell carcinoma(14;1.48e-14)|Lung(28;6.63e-14)															---	---	---	---
NLGN1	22871	broad.mit.edu	37	3	173141331	173141331	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173141331delA	uc003fio.1	+							NM_014932	NP_055747			neuroligin 1						calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of excitatory postsynaptic membrane potential|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of N-methyl-D-aspartate selective glutamate receptor activity|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)|ovary(1)|pancreas(1)	7	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)															---	---	---	---
NLGN1	22871	broad.mit.edu	37	3	173220873	173220874	+	Intron	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173220873_173220874delTG	uc003fio.1	+							NM_014932	NP_055747			neuroligin 1						calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of excitatory postsynaptic membrane potential|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of N-methyl-D-aspartate selective glutamate receptor activity|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)|ovary(1)|pancreas(1)	7	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)															---	---	---	---
NLGN1	22871	broad.mit.edu	37	3	173672745	173672745	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173672745delT	uc003fio.1	+						NLGN1_uc010hww.1_Intron|NLGN1_uc003fip.1_Intron	NM_014932	NP_055747			neuroligin 1						calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of excitatory postsynaptic membrane potential|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of N-methyl-D-aspartate selective glutamate receptor activity|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)|ovary(1)|pancreas(1)	7	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)															---	---	---	---
NLGN1	22871	broad.mit.edu	37	3	173841192	173841194	+	Intron	DEL	TTG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:173841192_173841194delTTG	uc003fio.1	+						NLGN1_uc010hww.1_Intron|NLGN1_uc003fip.1_Intron	NM_014932	NP_055747			neuroligin 1						calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of excitatory postsynaptic membrane potential|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of N-methyl-D-aspartate selective glutamate receptor activity|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)|ovary(1)|pancreas(1)	7	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)															---	---	---	---
NAALADL2	254827	broad.mit.edu	37	3	174972939	174972940	+	Intron	INS	-	ATAA	ATAA	rs149285858	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:174972939_174972940insATAA	uc003fit.2	+						NAALADL2_uc003fiu.1_Intron|NAALADL2_uc010hwy.1_Intron|NAALADL2_uc010hwz.1_5'Flank	NM_207015	NP_996898			N-acetylated alpha-linked acidic dipeptidase 2						proteolysis	integral to membrane	peptidase activity			pancreas(1)	1	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	175580326	175580326	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175580326delA								NAALADL2 (56900 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	175848077	175848077	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:175848077delA								NAALADL2 (324651 upstream) : TBL1XR1 (890466 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	176311869	176311869	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176311869delT								NAALADL2 (788443 upstream) : TBL1XR1 (426674 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	176380685	176380685	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:176380685delT								NAALADL2 (857259 upstream) : TBL1XR1 (357858 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	177429544	177429544	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177429544delT								TBL1XR1 (514496 upstream) : KCNMB2 (824680 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	177612244	177612245	+	Intron	INS	-	AA	AA			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177612244_177612245insAA	uc003fiz.1	+											Homo sapiens cDNA FLJ31690 fis, clone NT2RI2005621.																														---	---	---	---
Unknown	0	broad.mit.edu	37	3	177749582	177749582	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177749582delA								TBL1XR1 (834534 upstream) : KCNMB2 (504642 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	177765823	177765828	+	IGR	DEL	TGTGTG	-	-	rs76951388		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:177765823_177765828delTGTGTG								TBL1XR1 (850775 upstream) : KCNMB2 (488396 downstream)																																			---	---	---	---
KCNMB2	10242	broad.mit.edu	37	3	178258393	178258393	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178258393delA	uc003fjd.2	+						uc003fjb.1_Intron|uc003fjc.1_Intron	NM_181361	NP_852006			calcium-activated potassium channel beta 2						detection of calcium ion|platelet activation|regulation of action potential in neuron|regulation of vasoconstriction	voltage-gated potassium channel complex	calcium-activated potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(1)	1	all_cancers(143;5.38e-18)|Ovarian(172;0.00769)|Breast(254;0.125)		OV - Ovarian serous cystadenocarcinoma(80;1.32e-27)|GBM - Glioblastoma multiforme(14;0.0321)|BRCA - Breast invasive adenocarcinoma(182;0.0841)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	178599180	178599180	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178599180delT								KCNMB2 (36964 upstream) : ZMAT3 (142347 downstream)																																			---	---	---	---
ACTL6A	86	broad.mit.edu	37	3	179298542	179298542	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179298542delA	uc003fjw.2	+						ACTL6A_uc003fjx.2_Intron|ACTL6A_uc003fjy.2_Intron	NM_004301	NP_004292			actin-like 6A isoform 1						chromatin remodeling|DNA recombination|DNA repair|histone H2A acetylation|histone H4 acetylation|nervous system development|regulation of growth|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	Ino80 complex|npBAF complex|NuA4 histone acetyltransferase complex|plasma membrane|SWI/SNF complex	ATP binding|chromatin binding			ovary(1)	1	all_cancers(143;3.94e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)															---	---	---	---
PEX5L	51555	broad.mit.edu	37	3	179550891	179550891	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179550891delG	uc003fki.1	-						PEX5L_uc011bqd.1_Intron|PEX5L_uc011bqe.1_Intron|PEX5L_uc011bqf.1_Intron|PEX5L_uc003fkj.1_Intron|PEX5L_uc010hxd.1_Intron|PEX5L_uc011bqg.1_Intron|PEX5L_uc011bqh.1_Intron	NM_016559	NP_057643			peroxisomal biogenesis factor 5-like						protein import into peroxisome matrix|regulation of cAMP-mediated signaling	cytosol|peroxisomal membrane	peroxisome matrix targeting signal-1 binding			ovary(3)|large_intestine(1)	4	all_cancers(143;3.94e-14)|Ovarian(172;0.0338)|Breast(254;0.183)		OV - Ovarian serous cystadenocarcinoma(80;1.75e-26)|GBM - Glioblastoma multiforme(14;0.000518)															---	---	---	---
PEX5L	51555	broad.mit.edu	37	3	179742478	179742479	+	Intron	DEL	GA	-	-	rs59205301	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179742478_179742479delGA	uc003fki.1	-						PEX5L_uc003fkj.1_Intron|PEX5L_uc010hxd.1_Intron|PEX5L_uc011bqg.1_Intron|PEX5L_uc011bqh.1_Intron	NM_016559	NP_057643			peroxisomal biogenesis factor 5-like						protein import into peroxisome matrix|regulation of cAMP-mediated signaling	cytosol|peroxisomal membrane	peroxisome matrix targeting signal-1 binding			ovary(3)|large_intestine(1)	4	all_cancers(143;3.94e-14)|Ovarian(172;0.0338)|Breast(254;0.183)		OV - Ovarian serous cystadenocarcinoma(80;1.75e-26)|GBM - Glioblastoma multiforme(14;0.000518)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	180129457	180129457	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180129457delT								PEX5L (374940 upstream) : TTC14 (190461 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	180160705	180160705	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180160705delA								PEX5L (406188 upstream) : TTC14 (159213 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	180291085	180291085	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180291085delT								PEX5L (536568 upstream) : TTC14 (28833 downstream)																																			---	---	---	---
CCDC39	339829	broad.mit.edu	37	3	180379570	180379570	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180379570delA	uc010hxe.2	-						CCDC39_uc003fkn.2_Intron	NM_181426	NP_852091			coiled-coil domain containing 39						axonemal dynein complex assembly|ciliary cell motility|cilium movement involved in determination of left/right asymmetry|flagellar cell motility	cilium axoneme|cytoplasm|cytoskeleton				ovary(4)	4	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)															---	---	---	---
FXR1	8087	broad.mit.edu	37	3	180652986	180652986	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180652986delA	uc003fkq.2	+	3	187	c.165delA	c.(163-165)ATAfs	p.I55fs	FXR1_uc003fkp.2_5'UTR|FXR1_uc003fkr.2_Frame_Shift_Del_p.I55fs|FXR1_uc011bqj.1_5'UTR|FXR1_uc003fks.2_Intron|FXR1_uc011bqk.1_Intron|FXR1_uc011bql.1_Frame_Shift_Del_p.I42fs	NM_005087	NP_005078	P51114	FXR1_HUMAN	fragile X mental retardation-related protein 1	55					apoptosis|cell differentiation|muscle organ development	nucleolus|polysome				breast(1)	1	all_cancers(143;6.07e-14)|Ovarian(172;0.0212)		Epithelial(37;3.05e-35)|OV - Ovarian serous cystadenocarcinoma(80;2.4e-22)															---	---	---	---
FXR1	8087	broad.mit.edu	37	3	180671370	180671370	+	Intron	DEL	T	-	-	rs75916673		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:180671370delT	uc003fkq.2	+						FXR1_uc003fkp.2_Intron|FXR1_uc003fkr.2_Intron|FXR1_uc011bqj.1_Intron|FXR1_uc003fks.2_Intron|FXR1_uc011bqk.1_Intron|FXR1_uc011bql.1_Intron	NM_005087	NP_005078			fragile X mental retardation-related protein 1						apoptosis|cell differentiation|muscle organ development	nucleolus|polysome				breast(1)	1	all_cancers(143;6.07e-14)|Ovarian(172;0.0212)		Epithelial(37;3.05e-35)|OV - Ovarian serous cystadenocarcinoma(80;2.4e-22)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	181601684	181601685	+	IGR	DEL	TT	-	-	rs111389994		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181601684_181601685delTT								SOX2OT (142681 upstream) : ATP11B (909606 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	181771931	181771932	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181771931_181771932insA								SOX2OT (312928 upstream) : ATP11B (739359 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	181941634	181941635	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181941634_181941635insT								SOX2OT (482631 upstream) : ATP11B (569656 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	181961095	181961095	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:181961095delA								SOX2OT (502092 upstream) : ATP11B (550196 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	182219013	182219014	+	IGR	INS	-	TG	TG	rs143883440	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182219013_182219014insTG								SOX2OT (760010 upstream) : ATP11B (292277 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	182405465	182405466	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182405465_182405466insA								SOX2OT (946462 upstream) : ATP11B (105825 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	182431577	182431577	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182431577delA								SOX2OT (972574 upstream) : ATP11B (79714 downstream)																																			---	---	---	---
MCCC1	56922	broad.mit.edu	37	3	182807402	182807402	+	Intron	DEL	A	-	-	rs75056919		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182807402delA	uc003fle.2	-						MCCC1_uc010hxi.2_Intron|MCCC1_uc011bqo.1_Intron|MCCC1_uc003flf.2_Intron|MCCC1_uc003flg.2_Intron|MCCC1_uc011bqp.1_Intron|MCCC1_uc011bqq.1_Intron	NM_020166	NP_064551			methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)						biotin metabolic process|leucine catabolic process	mitochondrial inner membrane|mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|metal ion binding|methylcrotonoyl-CoA carboxylase activity			ovary(1)|central_nervous_system(1)|skin(1)	3	all_cancers(143;1.84e-14)|Ovarian(172;0.0355)		all cancers(12;1.8e-44)|Epithelial(37;3.23e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;5.07e-21)		Biotin(DB00121)													---	---	---	---
YEATS2	55689	broad.mit.edu	37	3	183471705	183471706	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183471705_183471706insT	uc003fly.2	+							NM_018023	NP_060493			YEATS domain containing 2						histone H3 acetylation|negative regulation of transcription from RNA polymerase II promoter	Ada2/Gcn5/Ada3 transcription activator complex	TBP-class protein binding			ovary(3)|large_intestine(1)	4	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)															---	---	---	---
DVL3	1857	broad.mit.edu	37	3	183888381	183888381	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183888381delC	uc003fms.2	+	15	2129	c.1989delC	c.(1987-1989)GGCfs	p.G663fs	DVL3_uc011bqw.1_Frame_Shift_Del_p.G646fs|DVL3_uc003fmt.2_Frame_Shift_Del_p.G334fs|DVL3_uc003fmu.2_Frame_Shift_Del_p.G495fs	NM_004423	NP_004414	Q92997	DVL3_HUMAN	dishevelled 3	663					canonical Wnt receptor signaling pathway|intracellular signal transduction|positive regulation of JUN kinase activity|positive regulation of protein phosphorylation|positive regulation of transcription, DNA-dependent	cytoplasm	beta-catenin binding|frizzled binding|protease binding|protein heterodimerization activity|signal transducer activity			ovary(1)|lung(1)|breast(1)	3	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.08e-34)|OV - Ovarian serous cystadenocarcinoma(80;1.31e-22)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	184166415	184166415	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184166415delC								CHRD (58796 upstream) : EPHB3 (113172 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	184364048	184364049	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184364048_184364049delTT								EPHB3 (63853 upstream) : MAGEF1 (64107 downstream)																																			---	---	---	---
VPS8	23355	broad.mit.edu	37	3	184754370	184754370	+	Intron	DEL	T	-	-	rs149707850		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184754370delT	uc003fpb.1	+						VPS8_uc010hyd.1_Intron|VPS8_uc010hye.1_Intron	NM_015303	NP_056118			vacuolar protein sorting 8 homolog isoform b								zinc ion binding			ovary(1)	1	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)															---	---	---	---
IGF2BP2	10644	broad.mit.edu	37	3	185540912	185540912	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185540912delA	uc003fpo.2	-						IGF2BP2_uc010hyi.2_5'Flank|IGF2BP2_uc010hyj.2_5'Flank|IGF2BP2_uc010hyk.2_5'Flank|IGF2BP2_uc010hyl.2_5'Flank|IGF2BP2_uc003fpp.2_Intron|IGF2BP2_uc003fpq.2_Intron	NM_006548	NP_006539			insulin-like growth factor 2 mRNA binding						anatomical structure morphogenesis|negative regulation of translation	cytoskeletal part|cytosol|nucleus	mRNA 3'-UTR binding|mRNA 5'-UTR binding|nucleotide binding|protein binding|translation regulator activity				0	all_cancers(143;5.84e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)															---	---	---	---
DGKG	1608	broad.mit.edu	37	3	185867773	185867774	+	3'UTR	INS	-	TG	TG	rs139132455	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185867773_185867774insTG	uc003fqa.2	-	25					DGKG_uc003fqb.2_3'UTR|DGKG_uc003fqc.2_3'UTR|DGKG_uc011brx.1_3'UTR	NM_001346	NP_001337			diacylglycerol kinase gamma isoform 1						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity			breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)													---	---	---	---
AHSG	197	broad.mit.edu	37	3	186335013	186335013	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186335013delC	uc003fqk.3	+	4	528	c.447delC	c.(445-447)TGCfs	p.C149fs	AHSG_uc003fqj.2_Frame_Shift_Del_p.C149fs|AHSG_uc003fql.3_Frame_Shift_Del_p.C150fs|AHSG_uc003fqm.3_Frame_Shift_Del_p.C148fs|AHSG_uc010hyp.2_Frame_Shift_Del_p.C112fs	NM_001622	NP_001613	P02765	FETUA_HUMAN	alpha-2-HS-glycoprotein	149	Cystatin fetuin-A-type 2.				acute-phase response|negative regulation of bone mineralization|negative regulation of insulin receptor signaling pathway|pinocytosis|positive regulation of phagocytosis|regulation of inflammatory response|skeletal system development	extracellular space	cysteine-type endopeptidase inhibitor activity|protein binding				0	all_cancers(143;3.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.27e-20)	GBM - Glioblastoma multiforme(93;0.0463)												OREG0015968	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
KNG1	3827	broad.mit.edu	37	3	186438059	186438059	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186438059delT	uc011bsa.1	+						KNG1_uc003fqr.2_Intron	NM_001102416	NP_001095886			kininogen 1 isoform 1						blood coagulation, intrinsic pathway|elevation of cytosolic calcium ion concentration|inflammatory response|negative regulation of blood coagulation|negative regulation of cell adhesion|platelet activation|platelet degranulation|positive regulation of apoptosis|positive regulation of renal sodium excretion|positive regulation of urine volume|smooth muscle contraction|vasodilation	extracellular space|plasma membrane|platelet alpha granule lumen	cysteine-type endopeptidase inhibitor activity|heparin binding|receptor binding|zinc ion binding			skin(1)	1	all_cancers(143;8.96e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.12e-20)	GBM - Glioblastoma multiforme(93;0.0798)	Ouabain(DB01092)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	186632463	186632463	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186632463delT								ADIPOQ (56213 upstream) : ST6GAL1 (16053 downstream)																																			---	---	---	---
MASP1	5648	broad.mit.edu	37	3	186951171	186951171	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186951171delT	uc003frh.1	-							NM_001879	NP_001870			mannan-binding lectin serine protease 1 isoform						complement activation, lectin pathway|negative regulation of complement activation|proteolysis	extracellular space	calcium ion binding|calcium-dependent protein binding|protein binding|protein homodimerization activity|serine-type endopeptidase activity			ovary(2)|breast(1)|liver(1)	4	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.49e-18)	GBM - Glioblastoma multiforme(93;0.0366)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	187141216	187141216	+	IGR	DEL	A	-	-	rs80024997		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:187141216delA								RTP4 (51849 upstream) : SST (245480 downstream)																																			---	---	---	---
LPP	4026	broad.mit.edu	37	3	188096879	188096879	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188096879delT	uc003frs.1	+						LPP_uc011bsg.1_Intron|LPP_uc011bsi.1_Intron|LPP_uc003frt.2_Intron	NM_005578	NP_005569			LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)				T	HMGA2|MLL|C12orf9	lipoma|leukemia								---	---	---	---
LPP	4026	broad.mit.edu	37	3	188193821	188193821	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188193821delT	uc003frs.1	+						LPP_uc011bsg.1_Intron|LPP_uc011bsi.1_Intron|LPP_uc003frt.2_Intron	NM_005578	NP_005569			LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)				T	HMGA2|MLL|C12orf9	lipoma|leukemia								---	---	---	---
LPP	4026	broad.mit.edu	37	3	188441495	188441495	+	Intron	DEL	A	-	-	rs147125668		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188441495delA	uc003frs.1	+						LPP_uc011bsg.1_Intron|LPP_uc011bsi.1_Intron|LPP_uc011bsj.1_Intron	NM_005578	NP_005569			LIM domain containing preferred translocation						cell adhesion	cytoplasm|focal adhesion|nucleus	protein binding|zinc ion binding		HMGA2/LPP(161)	soft_tissue(134)|bone(27)|lung(2)|ovary(1)|breast(1)	165	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)				T	HMGA2|MLL|C12orf9	lipoma|leukemia								---	---	---	---
TPRG1	285386	broad.mit.edu	37	3	188715761	188715761	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188715761delA	uc003frv.1	+							NM_198485	NP_940887			tumor protein p63 regulated 1												0	all_cancers(143;6.12e-12)|all_hematologic(3;0.0359)|Ovarian(172;0.0925)	all_lung(153;8.23e-09)|Lung NSC(153;3.55e-06)|all_neural(597;0.0019)|Myeloproliferative disorder(1037;0.0255)	Lung(62;6.93e-06)	GBM - Glioblastoma multiforme(93;4.77e-14)														---	---	---	---
TPRG1	285386	broad.mit.edu	37	3	188869959	188869959	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188869959delT	uc003frv.1	+							NM_198485	NP_940887			tumor protein p63 regulated 1												0	all_cancers(143;6.12e-12)|all_hematologic(3;0.0359)|Ovarian(172;0.0925)	all_lung(153;8.23e-09)|Lung NSC(153;3.55e-06)|all_neural(597;0.0019)|Myeloproliferative disorder(1037;0.0255)	Lung(62;6.93e-06)	GBM - Glioblastoma multiforme(93;4.77e-14)														---	---	---	---
TPRG1	285386	broad.mit.edu	37	3	188903012	188903013	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188903012_188903013insT	uc003frv.1	+						TPRG1_uc003frw.1_Intron	NM_198485	NP_940887			tumor protein p63 regulated 1												0	all_cancers(143;6.12e-12)|all_hematologic(3;0.0359)|Ovarian(172;0.0925)	all_lung(153;8.23e-09)|Lung NSC(153;3.55e-06)|all_neural(597;0.0019)|Myeloproliferative disorder(1037;0.0255)	Lung(62;6.93e-06)	GBM - Glioblastoma multiforme(93;4.77e-14)														---	---	---	---
TPRG1	285386	broad.mit.edu	37	3	188948224	188948224	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:188948224delA	uc003frv.1	+						TPRG1_uc003frw.1_Intron	NM_198485	NP_940887			tumor protein p63 regulated 1												0	all_cancers(143;6.12e-12)|all_hematologic(3;0.0359)|Ovarian(172;0.0925)	all_lung(153;8.23e-09)|Lung NSC(153;3.55e-06)|all_neural(597;0.0019)|Myeloproliferative disorder(1037;0.0255)	Lung(62;6.93e-06)	GBM - Glioblastoma multiforme(93;4.77e-14)														---	---	---	---
LEPREL1	55214	broad.mit.edu	37	3	189683759	189683760	+	Intron	DEL	AA	-	-	rs78912968		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189683759_189683760delAA	uc011bsk.1	-						LEPREL1_uc003fsg.2_Intron	NM_018192	NP_060662			leprecan-like 1 isoform a						collagen metabolic process|negative regulation of cell proliferation|peptidyl-proline hydroxylation	basement membrane|endoplasmic reticulum|Golgi apparatus	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-proline 3-dioxygenase activity			breast(3)|ovary(1)	4	all_cancers(143;4.01e-10)|Ovarian(172;0.0925)		Lung(62;4.35e-05)	GBM - Glioblastoma multiforme(93;0.02)	L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)													---	---	---	---
LEPREL1	55214	broad.mit.edu	37	3	189700671	189700671	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189700671delT	uc011bsk.1	-						LEPREL1_uc003fsg.2_Intron	NM_018192	NP_060662			leprecan-like 1 isoform a						collagen metabolic process|negative regulation of cell proliferation|peptidyl-proline hydroxylation	basement membrane|endoplasmic reticulum|Golgi apparatus	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-proline 3-dioxygenase activity			breast(3)|ovary(1)	4	all_cancers(143;4.01e-10)|Ovarian(172;0.0925)		Lung(62;4.35e-05)	GBM - Glioblastoma multiforme(93;0.02)	L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)													---	---	---	---
Unknown	0	broad.mit.edu	37	3	189892564	189892564	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189892564delT								LEPREL1 (52338 upstream) : CLDN1 (130939 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	189994858	189994858	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189994858delT								LEPREL1 (154632 upstream) : CLDN1 (28645 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	190757618	190757618	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190757618delT								SNAR-I (161779 upstream) : OSTN (172704 downstream)																																			---	---	---	---
FGF12	2257	broad.mit.edu	37	3	192199121	192199122	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192199121_192199122delAA	uc003fsy.2	-							NM_004113	NP_004104			fibroblast growth factor 12 isoform 2						cell-cell signaling|heart development|JNK cascade|nervous system development|signal transduction	extracellular space|nucleus	growth factor activity|heparin binding			ovary(1)|skin(1)|lung(1)|pancreas(1)	4	all_cancers(143;1.72e-08)|Ovarian(172;0.0634)|Breast(254;0.247)	Lung NSC(153;0.21)	LUSC - Lung squamous cell carcinoma(58;5.45e-06)|Lung(62;6.17e-06)	GBM - Glioblastoma multiforme(46;0.00032)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	192470441	192470444	+	IGR	DEL	AAAA	-	-	rs113979900		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192470441_192470444delAAAA								FGF12 (25053 upstream) : C3orf59 (44163 downstream)																																			---	---	---	---
C3orf59	151963	broad.mit.edu	37	3	192633097	192633097	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192633097delA	uc011bsp.1	-							NM_178496	NP_848591			hypothetical protein LOC151963												0	all_cancers(143;1.56e-08)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.8e-18)|LUSC - Lung squamous cell carcinoma(58;8.04e-06)|Lung(62;8.62e-06)	GBM - Glioblastoma multiforme(46;3.86e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	192773314	192773314	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:192773314delA								C3orf59 (137364 upstream) : HRASLS (185604 downstream)																																			---	---	---	---
ATP13A5	344905	broad.mit.edu	37	3	193001209	193001209	+	Intron	DEL	A	-	-	rs5855477		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193001209delA	uc011bsq.1	-							NM_198505	NP_940907			ATPase type 13A5						ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(5)|skin(4)|large_intestine(2)	11	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)														---	---	---	---
ATP13A5	344905	broad.mit.edu	37	3	193092088	193092089	+	Intron	INS	-	AG	AG	rs59002589		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193092088_193092089insAG	uc011bsq.1	-							NM_198505	NP_940907			ATPase type 13A5						ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(5)|skin(4)|large_intestine(2)	11	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)														---	---	---	---
ATP13A4	84239	broad.mit.edu	37	3	193208798	193208798	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193208798delA	uc003ftd.2	-						ATP13A4_uc003fte.1_Intron|ATP13A4_uc011bsr.1_Intron	NM_032279	NP_115655			ATPase type 13A4						ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(2)	2	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)														---	---	---	---
OPA1	4976	broad.mit.edu	37	3	193366428	193366428	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193366428delA	uc003ftm.2	+						OPA1_uc003ftg.2_Intron|OPA1_uc003fth.2_Intron|OPA1_uc003fti.2_Intron|OPA1_uc003ftj.2_Intron|OPA1_uc003ftk.2_Intron|OPA1_uc003ftl.2_Intron|OPA1_uc003ftn.2_Intron	NM_015560	NP_056375			optic atrophy 1 isoform 1						apoptosis|axon transport of mitochondrion|inner mitochondrial membrane organization|mitochondrial fission|mitochondrial fusion|positive regulation of anti-apoptosis|response to stimulus|visual perception	dendrite|integral to membrane|mitochondrial crista|mitochondrial intermembrane space|mitochondrial outer membrane	GTP binding|GTPase activity|magnesium ion binding|protein binding				0	all_cancers(143;9.56e-09)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;9.19e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000162)														---	---	---	---
OPA1	4976	broad.mit.edu	37	3	193382502	193382502	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193382502delA	uc003ftm.2	+						OPA1_uc003ftg.2_Intron|OPA1_uc003fth.2_Intron|OPA1_uc003fti.2_Intron|OPA1_uc003ftj.2_Intron|OPA1_uc003ftk.2_Intron|OPA1_uc003ftl.2_Intron|OPA1_uc003ftn.2_Intron	NM_015560	NP_056375			optic atrophy 1 isoform 1						apoptosis|axon transport of mitochondrion|inner mitochondrial membrane organization|mitochondrial fission|mitochondrial fusion|positive regulation of anti-apoptosis|response to stimulus|visual perception	dendrite|integral to membrane|mitochondrial crista|mitochondrial intermembrane space|mitochondrial outer membrane	GTP binding|GTPase activity|magnesium ion binding|protein binding				0	all_cancers(143;9.56e-09)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;9.19e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000162)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	193797459	193797460	+	IGR	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193797459_193797460delAG								LOC100128023 (85432 upstream) : HES1 (56474 downstream)																																			---	---	---	---
CPN2	1370	broad.mit.edu	37	3	194073592	194073593	+	5'Flank	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194073592_194073593delTG	uc003fts.2	-							NM_001080513	NP_001073982			carboxypeptidase N, polypeptide 2						protein stabilization	extracellular region	enzyme regulator activity			ovary(5)	5	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.65e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	194248590	194248594	+	IGR	DEL	TCCCC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194248590_194248594delTCCCC								ATP13A3 (59622 upstream) : TMEM44 (59809 downstream)																																			---	---	---	---
TMEM44	93109	broad.mit.edu	37	3	194315249	194315249	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194315249delA	uc010hzn.2	-						TMEM44_uc010hzm.2_Intron|TMEM44_uc003fuc.2_Intron|TMEM44_uc003fue.2_Intron|TMEM44_uc003fud.2_Intron|TMEM44_uc003fuf.2_Intron|TMEM44_uc011bsv.1_Intron|TMEM44_uc003fuh.1_Intron	NM_001011655	NP_001011655			transmembrane protein 44 isoform b							integral to membrane					0	all_cancers(143;1.41e-08)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;4.34e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;9.06e-06)														---	---	---	---
LSG1	55341	broad.mit.edu	37	3	194363097	194363097	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194363097delC	uc003fui.2	-							NM_018385	NP_060855			large subunit GTPase 1						nuclear export|protein transport	Cajal body|endoplasmic reticulum	GTP binding|hydrolase activity				0	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;4.34e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;7.55e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	194594089	194594089	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194594089delT								FAM43A (184325 upstream) : C3orf21 (194926 downstream)																																			---	---	---	---
C3orf21	152002	broad.mit.edu	37	3	194863118	194863118	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194863118delC	uc003fum.3	-						C3orf21_uc003ful.2_Intron	NM_152531	NP_689744			hypothetical protein LOC152002							integral to membrane	transferase activity, transferring glycosyl groups				0	all_cancers(143;9.33e-09)|Ovarian(172;0.0634)		Epithelial(36;1.73e-20)|all cancers(36;1.42e-18)|OV - Ovarian serous cystadenocarcinoma(49;1.56e-17)|Lung(62;0.000117)|LUSC - Lung squamous cell carcinoma(58;0.000146)	GBM - Glioblastoma multiforme(46;1.36e-05)														---	---	---	---
C3orf21	152002	broad.mit.edu	37	3	194925206	194925207	+	Intron	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194925206_194925207delCT	uc003fum.3	-						C3orf21_uc011bsw.1_Intron	NM_152531	NP_689744			hypothetical protein LOC152002							integral to membrane	transferase activity, transferring glycosyl groups				0	all_cancers(143;9.33e-09)|Ovarian(172;0.0634)		Epithelial(36;1.73e-20)|all cancers(36;1.42e-18)|OV - Ovarian serous cystadenocarcinoma(49;1.56e-17)|Lung(62;0.000117)|LUSC - Lung squamous cell carcinoma(58;0.000146)	GBM - Glioblastoma multiforme(46;1.36e-05)														---	---	---	---
C3orf21	152002	broad.mit.edu	37	3	194989328	194989330	+	Intron	DEL	ACA	-	-	rs141983303	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194989328_194989330delACA	uc003fum.3	-							NM_152531	NP_689744			hypothetical protein LOC152002							integral to membrane	transferase activity, transferring glycosyl groups				0	all_cancers(143;9.33e-09)|Ovarian(172;0.0634)		Epithelial(36;1.73e-20)|all cancers(36;1.42e-18)|OV - Ovarian serous cystadenocarcinoma(49;1.56e-17)|Lung(62;0.000117)|LUSC - Lung squamous cell carcinoma(58;0.000146)	GBM - Glioblastoma multiforme(46;1.36e-05)														---	---	---	---
ACAP2	23527	broad.mit.edu	37	3	195106512	195106523	+	Intron	DEL	TGTAACTTCCCC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195106512_195106523delTGTAACTTCCCC	uc003fun.3	-						ACAP2_uc003fuo.2_Intron	NM_012287	NP_036419			centaurin, beta 2						regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding			large_intestine(1)|ovary(1)	2																		---	---	---	---
ACAP2	23527	broad.mit.edu	37	3	195118335	195118336	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195118335_195118336delAA	uc003fun.3	-						ACAP2_uc003fuo.2_Intron	NM_012287	NP_036419			centaurin, beta 2						regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding			large_intestine(1)|ovary(1)	2																		---	---	---	---
APOD	347	broad.mit.edu	37	3	195310559	195310559	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195310559delA	uc003fur.2	-						APOD_uc011bsx.1_Intron	NM_001647	NP_001638			apolipoprotein D precursor						lipid metabolic process	extracellular space	lipid binding|lipid transporter activity|protein binding			ovary(2)	2	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)														---	---	---	---
SDHAP2	727956	broad.mit.edu	37	3	195392917	195392917	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195392917delT	uc003fuw.2	+						SDHAP2_uc003fut.3_Intron|SDHAP2_uc003fuu.3_Intron|SDHAP2_uc011btb.1_Intron|SDHAP2_uc011btc.1_Intron|SDHAP2_uc003fuv.2_Intron					SubName: Full=cDNA FLJ16373 fis, clone THYMU3000269, highly similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial (EC 1.3.5.1);												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	195468951	195468954	+	IGR	DEL	TTAA	-	-	rs71637179		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195468951_195468954delTTAA								MUC20 (4412 upstream) : MUC4 (4686 downstream)																																			---	---	---	---
MUC4	4585	broad.mit.edu	37	3	195497376	195497376	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195497376delT	uc011bto.1	-						MUC4_uc003fuz.2_Intron|MUC4_uc003fva.2_Intron|MUC4_uc003fvb.2_Intron|MUC4_uc003fvc.2_Intron|MUC4_uc003fvd.2_Intron|MUC4_uc003fve.2_Intron|MUC4_uc010hzr.2_Intron|MUC4_uc011btf.1_Intron|MUC4_uc011btg.1_Intron|MUC4_uc011bth.1_Intron|MUC4_uc011bti.1_Intron|MUC4_uc011btj.1_Intron|MUC4_uc011btk.1_Intron|MUC4_uc011btl.1_Intron|MUC4_uc011btm.1_Intron|MUC4_uc011btn.1_Intron|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876			mucin 4 isoform a						cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	196318557	196318557	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196318557delA								FBXO45 (2629 upstream) : LRRC33 (48099 downstream)																																			---	---	---	---
LRRC33	375387	broad.mit.edu	37	3	196364791	196364792	+	5'Flank	INS	-	GA	GA	rs145710230	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196364791_196364792insGA	uc003fwv.2	+							NM_198565	NP_940967			leucine rich repeat containing 33 precursor							integral to membrane				ovary(2)|central_nervous_system(1)	3	all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.9e-23)|all cancers(36;1.76e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00326)														---	---	---	---
DLG1	1739	broad.mit.edu	37	3	196781203	196781204	+	Intron	INS	-	TTTC	TTTC	rs141364309	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196781203_196781204insTTTC	uc003fxo.3	-						DLG1_uc011bub.1_Intron|DLG1_uc011buc.1_Intron|DLG1_uc011bud.1_Intron|DLG1_uc003fxn.3_Intron|DLG1_uc011bue.1_Intron|DLG1_uc010ial.2_Intron	NM_001098424	NP_001091894			discs, large homolog 1 isoform 1						actin filament organization|axon guidance|cell-cell adhesion|cortical actin cytoskeleton organization|endothelial cell proliferation|establishment or maintenance of cell polarity|interspecies interaction between organisms|mitotic cell cycle G1/S transition checkpoint|negative regulation of mitotic cell cycle|protein localization in plasma membrane|synaptic transmission|tight junction assembly	basolateral plasma membrane|cytosol|endoplasmic reticulum membrane|immunological synapse|MPP7-DLG1-LIN7 complex|nucleus|postsynaptic density|postsynaptic membrane|sarcolemma|tight junction	cytoskeletal protein binding|guanylate kinase activity|L27 domain binding|phosphatase binding|phosphoprotein phosphatase activity|potassium channel regulator activity|protein binding|protein C-terminus binding|protein kinase binding			ovary(3)	3	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)														---	---	---	---
DLG1	1739	broad.mit.edu	37	3	196793772	196793772	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196793772delA	uc003fxo.3	-						DLG1_uc011bub.1_Intron|DLG1_uc011buc.1_Intron|DLG1_uc011bud.1_Intron|DLG1_uc003fxn.3_Intron|DLG1_uc011bue.1_Intron|DLG1_uc010ial.2_Intron	NM_001098424	NP_001091894			discs, large homolog 1 isoform 1						actin filament organization|axon guidance|cell-cell adhesion|cortical actin cytoskeleton organization|endothelial cell proliferation|establishment or maintenance of cell polarity|interspecies interaction between organisms|mitotic cell cycle G1/S transition checkpoint|negative regulation of mitotic cell cycle|protein localization in plasma membrane|synaptic transmission|tight junction assembly	basolateral plasma membrane|cytosol|endoplasmic reticulum membrane|immunological synapse|MPP7-DLG1-LIN7 complex|nucleus|postsynaptic density|postsynaptic membrane|sarcolemma|tight junction	cytoskeletal protein binding|guanylate kinase activity|L27 domain binding|phosphatase binding|phosphoprotein phosphatase activity|potassium channel regulator activity|protein binding|protein C-terminus binding|protein kinase binding			ovary(3)	3	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)														---	---	---	---
DLG1	1739	broad.mit.edu	37	3	196795255	196795255	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196795255delA	uc003fxo.3	-						DLG1_uc011bub.1_Intron|DLG1_uc011buc.1_Intron|DLG1_uc011bud.1_Intron|DLG1_uc003fxn.3_Intron|DLG1_uc011bue.1_Intron|DLG1_uc010ial.2_Intron	NM_001098424	NP_001091894			discs, large homolog 1 isoform 1						actin filament organization|axon guidance|cell-cell adhesion|cortical actin cytoskeleton organization|endothelial cell proliferation|establishment or maintenance of cell polarity|interspecies interaction between organisms|mitotic cell cycle G1/S transition checkpoint|negative regulation of mitotic cell cycle|protein localization in plasma membrane|synaptic transmission|tight junction assembly	basolateral plasma membrane|cytosol|endoplasmic reticulum membrane|immunological synapse|MPP7-DLG1-LIN7 complex|nucleus|postsynaptic density|postsynaptic membrane|sarcolemma|tight junction	cytoskeletal protein binding|guanylate kinase activity|L27 domain binding|phosphatase binding|phosphoprotein phosphatase activity|potassium channel regulator activity|protein binding|protein C-terminus binding|protein kinase binding			ovary(3)	3	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)														---	---	---	---
Unknown	0	broad.mit.edu	37	3	197064991	197064991	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197064991delA								DLG1 (38848 upstream) : BDH1 (171664 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	197150689	197150690	+	IGR	INS	-	T	T	rs145869557	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197150689_197150690insT								DLG1 (124546 upstream) : BDH1 (85965 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	3	197511670	197511670	+	IGR	DEL	A	-	-	rs72425216		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197511670delA								FYTTD1 (353 upstream) : LRCH3 (6475 downstream)																																			---	---	---	---
LMLN	89782	broad.mit.edu	37	3	197744009	197744010	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197744009_197744010delAA	uc011buo.1	+						LMLN_uc003fyt.2_Intron|LMLN_uc010iar.2_Intron|LMLN_uc010ias.2_Intron|LMLN_uc003fyu.2_Intron	NM_033029	NP_149018			leishmanolysin-like isoform 2						cell adhesion|cell division|mitosis|proteolysis	cytoplasm|membrane	metalloendopeptidase activity|zinc ion binding			skin(1)	1	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;9.84e-24)|all cancers(36;3.18e-22)|OV - Ovarian serous cystadenocarcinoma(49;5.35e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.111)														---	---	---	---
ZNF595	152687	broad.mit.edu	37	4	67191	67191	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:67191delA	uc003fzv.1	+						ZNF595_uc003fzu.1_Intron|ZNF718_uc003fzt.3_Intron|ZNF595_uc010iay.1_Intron|ZNF595_uc011bus.1_Intron|ZNF595_uc011but.1_Intron	NM_182524	NP_872330			zinc finger protein 595						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)														---	---	---	---
ZNF718	255403	broad.mit.edu	37	4	116081	116081	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:116081delT	uc003fzt.3	+						ZNF595_uc003fzu.1_Intron	NM_001039127	NP_001034216			zinc finger protein 718						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0681)|Epithelial(2;0.0838)|all cancers(2;0.135)|LUSC - Lung squamous cell carcinoma(95;0.18)														---	---	---	---
ABCA11P	79963	broad.mit.edu	37	4	428113	428113	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:428113delT	uc003gae.2	-						ABCA11P_uc003gac.2_Intron|ABCA11P_uc003gad.2_Intron|ABCA11P_uc011buv.1_Intron|ABCA11P_uc010ibd.1_Intron					RecName: Full=Putative ATP-binding cassette sub-family A member 11;												0																		---	---	---	---
PIGG	54872	broad.mit.edu	37	4	524075	524075	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:524075delG	uc003gak.3	+						PIGG_uc003gaj.3_Intron|PIGG_uc011bux.1_Intron|PIGG_uc010ibf.2_Intron|PIGG_uc003gal.3_Intron	NM_001127178	NP_001120650			phosphatidylinositol glycan anchor biosynthesis,						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	CP2 mannose-ethanolamine phosphotransferase activity			central_nervous_system(2)|ovary(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	608399	608399	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:608399delT								PIGG (75080 upstream) : PDE6B (10964 downstream)																																			---	---	---	---
PDE6B	5158	broad.mit.edu	37	4	633104	633104	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:633104delT	uc003gap.2	+						PDE6B_uc003gao.3_Intron	NM_000283	NP_000274			phosphodiesterase 6B isoform 1						cytosolic calcium ion homeostasis|GMP metabolic process|phototransduction, visible light|platelet activation|visual perception	cytosol|membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding				0																		---	---	---	---
PDE6B	5158	broad.mit.edu	37	4	650964	650964	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:650964delC	uc003gap.2	+						PDE6B_uc003gao.3_Intron|PDE6B_uc011buy.1_Intron|uc003gaq.1_5'Flank	NM_000283	NP_000274			phosphodiesterase 6B isoform 1						cytosolic calcium ion homeostasis|GMP metabolic process|phototransduction, visible light|platelet activation|visual perception	cytosol|membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding				0																		---	---	---	---
CTBP1	1487	broad.mit.edu	37	4	1238143	1238143	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1238143delG	uc003gcv.1	-						CTBP1_uc003gcu.1_Intron|CTBP1_uc003gcx.1_5'Flank	NM_001328	NP_001319			C-terminal binding protein 1 isoform 1						interspecies interaction between organisms|negative regulation of cell proliferation|negative regulation of histone H4 acetylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of histone deacetylation|protein phosphorylation|regulation of cell cycle|regulation of transcription by chromatin organization|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|viral genome replication|white fat cell differentiation	cytoplasm|transcriptional repressor complex	NAD binding|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor|protein C-terminus binding|protein domain specific binding|transcription factor binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(23;0.00818)	Colorectal(103;0.2)														---	---	---	---
TACC3	10460	broad.mit.edu	37	4	1738645	1738645	+	Intron	DEL	A	-	-	rs76165080		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1738645delA	uc003gdo.2	+						TACC3_uc010ibz.2_Intron|TACC3_uc003gdp.2_Intron|TACC3_uc010ica.2_Intron	NM_006342	NP_006333			transforming, acidic coiled-coil containing							centrosome				ovary(1)|central_nervous_system(1)	2		Breast(71;0.212)|all_epithelial(65;0.241)	OV - Ovarian serous cystadenocarcinoma(23;0.00765)|Epithelial(3;0.0126)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	1760827	1760828	+	IGR	INS	-	AC	AC	rs148957908	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1760827_1760828insAC								TACC3 (13932 upstream) : FGFR3 (34211 downstream)																																			---	---	---	---
WHSC1	7468	broad.mit.edu	37	4	1911961	1911961	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1911961delT	uc003gdz.3	+						WHSC1_uc003geb.3_Intron|WHSC1_uc003gec.3_Intron|WHSC1_uc003ged.3_Intron|WHSC1_uc003gee.3_Intron|WHSC1_uc003gef.3_Intron|WHSC1_uc003gdx.2_Intron|WHSC1_uc003gdy.1_Intron|WHSC1_uc010icd.1_Intron|WHSC1_uc003gea.1_Intron|WHSC1_uc010ice.1_Intron|WHSC1_uc003geg.1_Intron|WHSC1_uc003geh.1_Intron	NM_001042424	NP_001035889			Wolf-Hirschhorn syndrome candidate 1 protein						anatomical structure morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|cytoplasm|nuclear membrane|nucleolus	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			ovary(3)|lung(3)|skin(2)|pancreas(1)	9		all_epithelial(65;1.34e-05)	OV - Ovarian serous cystadenocarcinoma(23;0.00606)	STAD - Stomach adenocarcinoma(129;0.232)				T	IGH@	MM								---	---	---	---
POLN	353497	broad.mit.edu	37	4	2081319	2081319	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2081319delT	uc003ger.2	-						POLN_uc010icg.1_Intron|POLN_uc010ich.1_3'UTR	NM_181808	NP_861524			DNA-directed DNA polymerase nu						DNA repair|DNA replication	nucleus	DNA binding|DNA-directed DNA polymerase activity			kidney(2)|ovary(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(23;0.0955)										DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
POLN	353497	broad.mit.edu	37	4	2146935	2146935	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2146935delA	uc003ger.2	-						POLN_uc010icg.1_Intron|POLN_uc010ich.1_Intron	NM_181808	NP_861524			DNA-directed DNA polymerase nu						DNA repair|DNA replication	nucleus	DNA binding|DNA-directed DNA polymerase activity			kidney(2)|ovary(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(23;0.0955)										DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
HAUS3	79441	broad.mit.edu	37	4	2242634	2242634	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2242634delT	uc003ges.1	-	2	270	c.40delA	c.(40-42)ATTfs	p.I14fs	POLN_uc011bvi.1_Intron|HAUS3_uc011bvj.1_Frame_Shift_Del_p.I14fs|HAUS3_uc003get.1_Frame_Shift_Del_p.I14fs	NM_024511	NP_078787	Q68CZ6	HAUS3_HUMAN	HAUS augmin-like complex, subunit 3	14					cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|spindle				large_intestine(2)|breast(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	2544822	2544822	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2544822delT								RNF4 (27241 upstream) : FAM193A (53006 downstream)																																			---	---	---	---
FAM193A	8603	broad.mit.edu	37	4	2661593	2661593	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2661593delC	uc010icl.2	+	8	1035	c.684delC	c.(682-684)GACfs	p.D228fs	FAM193A_uc010ick.2_Frame_Shift_Del_p.D428fs|FAM193A_uc003gfd.2_Frame_Shift_Del_p.D228fs|FAM193A_uc011bvm.1_Frame_Shift_Del_p.D252fs|FAM193A_uc011bvn.1_Frame_Shift_Del_p.D228fs|FAM193A_uc011bvo.1_RNA|FAM193A_uc010icm.2_RNA|FAM193A_uc003gfe.2_Frame_Shift_Del_p.D82fs	NM_003704	NP_003695	P78312	F193A_HUMAN	hypothetical protein LOC8603	228										ovary(3)	3																		---	---	---	---
FAM193A	8603	broad.mit.edu	37	4	2703506	2703506	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2703506delT	uc010icl.2	+						FAM193A_uc010ick.2_Intron|FAM193A_uc003gfd.2_Intron|FAM193A_uc011bvm.1_Intron|FAM193A_uc011bvn.1_Intron|FAM193A_uc011bvo.1_Intron|FAM193A_uc010icm.2_Intron	NM_003704	NP_003695			hypothetical protein LOC8603											ovary(3)	3																		---	---	---	---
FAM193A	8603	broad.mit.edu	37	4	2720032	2720032	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2720032delA	uc010icl.2	+						FAM193A_uc010ick.2_Intron|FAM193A_uc003gfd.2_Intron|FAM193A_uc011bvm.1_Intron|FAM193A_uc011bvn.1_Intron|FAM193A_uc011bvo.1_Intron|FAM193A_uc010icm.2_Intron	NM_003704	NP_003695			hypothetical protein LOC8603											ovary(3)	3																		---	---	---	---
FAM193A	8603	broad.mit.edu	37	4	2728280	2728280	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2728280delT	uc010icl.2	+						FAM193A_uc010ick.2_Intron|FAM193A_uc003gfd.2_Intron|FAM193A_uc011bvm.1_Intron|FAM193A_uc011bvn.1_Intron|FAM193A_uc011bvo.1_Intron|FAM193A_uc010icm.2_Intron	NM_003704	NP_003695			hypothetical protein LOC8603											ovary(3)	3																		---	---	---	---
ADD1	118	broad.mit.edu	37	4	2896576	2896576	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2896576delA	uc003gfr.2	+						ADD1_uc003gfn.2_Intron|ADD1_uc010ico.1_Intron|ADD1_uc003gfo.2_Intron|ADD1_uc003gfp.2_Intron|ADD1_uc003gfq.2_Intron|ADD1_uc003gfs.2_Intron|ADD1_uc003gft.3_Intron|ADD1_uc003gfu.2_Intron	NM_001119	NP_001110			adducin 1 (alpha) isoform a						actin filament bundle assembly|barbed-end actin filament capping|cellular component disassembly involved in apoptosis|positive regulation of protein binding	cytosol|F-actin capping protein complex|nucleus|plasma membrane	actin filament binding|calmodulin binding|metal ion binding|protein heterodimerization activity|protein homodimerization activity|spectrin binding|transcription factor binding			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)														---	---	---	---
NOP14	8602	broad.mit.edu	37	4	2958218	2958218	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2958218delA	uc003ggj.1	-						C4orf10_uc003ggi.1_Intron|NOP14_uc010icp.2_5'Flank|NOP14_uc003ggk.3_Intron|NOP14_uc003ggl.2_Intron|NOP14_uc010icq.1_Intron	NM_003703	NP_003694			probable nucleolar complex protein 14						endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	mitochondrion|Noc4p-Nop14p complex|small-subunit processome	snoRNA binding			pancreas(1)	1																		---	---	---	---
GRK4	2868	broad.mit.edu	37	4	2990908	2990909	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2990908_2990909delAA	uc003ggn.1	+						GRK4_uc003ggo.1_Intron|GRK4_uc003ggp.1_Intron|GRK4_uc003ggq.1_Intron	NM_182982	NP_892027			G protein-coupled receptor kinase 4 isoform							cell cortex	ATP binding|G-protein coupled receptor kinase activity|signal transducer activity			lung(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)														---	---	---	---
HTT	3064	broad.mit.edu	37	4	3088650	3088650	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3088650delT	uc011bvq.1	+							NM_002111	NP_002102			huntingtin						establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule	autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex	beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding			skin(2)|ovary(1)|lung(1)	4		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)														---	---	---	---
HTT	3064	broad.mit.edu	37	4	3108410	3108411	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3108410_3108411delTT	uc011bvq.1	+							NM_002111	NP_002102			huntingtin						establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule	autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex	beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding			skin(2)|ovary(1)|lung(1)	4		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)														---	---	---	---
HTT	3064	broad.mit.edu	37	4	3144480	3144480	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3144480delT	uc011bvq.1	+							NM_002111	NP_002102			huntingtin						establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule	autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex	beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding			skin(2)|ovary(1)|lung(1)	4		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)														---	---	---	---
RGS12	6002	broad.mit.edu	37	4	3430399	3430399	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3430399delA	uc003ggw.2	+	16	4430	c.3526delA	c.(3526-3528)AAAfs	p.K1176fs	RGS12_uc003ggv.2_Frame_Shift_Del_p.K1176fs|RGS12_uc003ggy.1_Intron|RGS12_uc003ggz.2_Frame_Shift_Del_p.K528fs|RGS12_uc011bvs.1_Intron|RGS12_uc003gha.2_Frame_Shift_Del_p.K518fs|RGS12_uc010icv.2_Frame_Shift_Del_p.K375fs	NM_198229	NP_937872	O14924	RGS12_HUMAN	regulator of G-protein signalling 12 isoform 1	1176						condensed nuclear chromosome|cytoplasm|plasma membrane	GTPase activator activity|receptor signaling protein activity			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)														---	---	---	---
DOK7	285489	broad.mit.edu	37	4	3494969	3494970	+	Frame_Shift_Ins	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3494969_3494970insC	uc003ghd.2	+	7	1326_1327	c.1256_1257insC	c.(1255-1257)AGCfs	p.S419fs	DOK7_uc003ghe.2_Frame_Shift_Ins_p.S281fs|DOK7_uc003ghf.2_Frame_Shift_Ins_p.A161fs|DOK7_uc003ghg.1_Frame_Shift_Ins_p.S109fs	NM_173660	NP_775931	Q18PE1	DOK7_HUMAN	downstream of tyrosine kinase 7 isoform 1	419					positive regulation of protein tyrosine kinase activity	cell junction|synapse	insulin receptor binding|protein kinase binding			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	3624858	3624863	+	IGR	DEL	ATGTGG	-	-	rs143759719		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3624858_3624863delATGTGG								LRPAP1 (90634 upstream) : ADRA2C (143212 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	3631469	3631471	+	IGR	DEL	TAC	-	-	rs142611164		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3631469_3631471delTAC								LRPAP1 (97245 upstream) : ADRA2C (136604 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	3687680	3687680	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3687680delC								LRPAP1 (153456 upstream) : ADRA2C (80395 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	3794963	3794964	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3794963_3794964delTT								ADRA2C (24712 upstream) : LOC348926 (148706 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	3990385	3990387	+	IGR	DEL	TTA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3990385_3990387delTTA								LOC348926 (33237 upstream) : OTOP1 (200143 downstream)																																			---	---	---	---
LYAR	55646	broad.mit.edu	37	4	4275973	4275973	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4275973delA	uc011bvy.1	-						LYAR_uc011bvx.1_Intron|LYAR_uc003ght.2_Intron	NM_001145725	NP_001139197			Ly1 antibody reactive homolog							nucleolus	metal ion binding|protein binding				0				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	4657296	4657296	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4657296delA	uc003gid.2	+											Homo sapiens, clone IMAGE:5204729, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	4762366	4762366	+	5'Flank	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4762366delG	uc003gie.1	+											Homo sapiens cDNA FLJ31519 fis, clone NT2RI2000116.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	4846952	4846952	+	IGR	DEL	G	-	-	rs11285303		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:4846952delG								STX18 (303177 upstream) : MSX1 (14440 downstream)																																			---	---	---	---
STK32B	55351	broad.mit.edu	37	4	5281922	5281922	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5281922delT	uc003gih.1	+						STK32B_uc010ida.1_Intron	NM_018401	NP_060871			serine/threonine kinase 32B								ATP binding|metal ion binding|protein serine/threonine kinase activity			breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
EVC2	132884	broad.mit.edu	37	4	5649749	5649749	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5649749delT	uc003gij.2	-						EVC2_uc011bwb.1_Intron|EVC2_uc003gik.2_Intron	NM_147127	NP_667338			limbin							integral to membrane				large_intestine(3)|ovary(2)	5																		---	---	---	---
CRMP1	1400	broad.mit.edu	37	4	5829348	5829349	+	Intron	DEL	CA	-	-	rs142436178	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5829348_5829349delCA	uc003gip.2	-						EVC_uc003gim.1_Intron|CRMP1_uc003gin.1_Intron|CRMP1_uc003giq.2_Intron|CRMP1_uc003gir.2_Intron|CRMP1_uc003gis.2_Intron	NM_001313	NP_001304			collapsin response mediator protein 1 isoform 2						axon guidance|pyrimidine base catabolic process	cytosol|microtubule organizing center|spindle	dihydropyrimidinase activity|protein binding			ovary(2)	2				Colorectal(103;0.0721)														---	---	---	---
CRMP1	1400	broad.mit.edu	37	4	5830665	5830666	+	Intron	INS	-	T	T	rs149294408	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5830665_5830666insT	uc003gip.2	-						EVC_uc003gim.1_RNA|CRMP1_uc003gin.1_Intron|CRMP1_uc003giq.2_Intron|CRMP1_uc003gir.2_Intron|CRMP1_uc003gis.2_Intron	NM_001313	NP_001304			collapsin response mediator protein 1 isoform 2						axon guidance|pyrimidine base catabolic process	cytosol|microtubule organizing center|spindle	dihydropyrimidinase activity|protein binding			ovary(2)	2				Colorectal(103;0.0721)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	5928350	5928350	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5928350delT								CRMP1 (33565 upstream) : C4orf50 (30495 downstream)																																			---	---	---	---
JAKMIP1	152789	broad.mit.edu	37	4	6052288	6052288	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6052288delC	uc010idb.1	-						JAKMIP1_uc010idc.1_Intron|JAKMIP1_uc010idd.1_Intron	NM_001099433	NP_001092903			janus kinase and microtubule interacting protein						protein transport	cytoplasm|membrane|microtubule|peripheral to membrane of membrane fraction|ribonucleoprotein complex	GABA receptor binding|RNA binding			large_intestine(1)|pancreas(1)|ovary(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	6762302	6762304	+	IGR	DEL	TCC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6762302_6762304delTCC								CNO (42915 upstream) : KIAA0232 (22155 downstream)																																			---	---	---	---
TBC1D14	57533	broad.mit.edu	37	4	6925986	6925990	+	Intron	DEL	AATCC	-	-	rs57881179		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6925986_6925990delAATCC	uc011bwg.1	+						TBC1D14_uc003gjs.3_Intron	NM_001113361	NP_001106832			TBC1 domain family, member 14 isoform a							intracellular	Rab GTPase activator activity			ovary(1)|pancreas(1)	2																		---	---	---	---
SORCS2	57537	broad.mit.edu	37	4	7296851	7296852	+	Intron	INS	-	CCCTCC	CCCTCC			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7296851_7296852insCCCTCC	uc003gkb.3	+							NM_020777	NP_065828			VPS10 domain receptor protein SORCS 2 precursor							integral to membrane	neuropeptide receptor activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
SORCS2	57537	broad.mit.edu	37	4	7356435	7356436	+	Intron	INS	-	AG	AG	rs145745168	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7356435_7356436insAG	uc003gkb.3	+							NM_020777	NP_065828			VPS10 domain receptor protein SORCS 2 precursor							integral to membrane	neuropeptide receptor activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
AFAP1	60312	broad.mit.edu	37	4	7883508	7883508	+	Intron	DEL	A	-	-	rs71875997		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7883508delA	uc003gkg.1	-						AFAP1_uc011bwk.1_Intron	NM_198595	NP_940997			actin filament associated protein 1							actin cytoskeleton|cytoplasm|focal adhesion	actin binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	8821855	8821855	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8821855delG								CPZ (200369 upstream) : HMX1 (46918 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	9014588	9014589	+	IGR	DEL	CT	-	-	rs2368728		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9014588_9014589delCT								LOC650293 (62462 upstream) : USP17 (345520 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	9163806	9163807	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9163806_9163807insT								LOC650293 (211680 upstream) : USP17 (196302 downstream)																																			---	---	---	---
SLC2A9	56606	broad.mit.edu	37	4	9884536	9884536	+	Intron	DEL	T	-	-	rs6449090	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9884536delT	uc003gmc.2	-						SLC2A9_uc003gmd.2_Intron	NM_020041	NP_064425			solute carrier family 2, member 9 protein						glucose transport|urate metabolic process	integral to membrane|plasma membrane	sugar:hydrogen symporter activity			ovary(3)	3																		---	---	---	---
SLC2A9	56606	broad.mit.edu	37	4	10002124	10002124	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10002124delC	uc003gmc.2	-						SLC2A9_uc003gmd.2_Intron	NM_020041	NP_064425			solute carrier family 2, member 9 protein						glucose transport|urate metabolic process	integral to membrane|plasma membrane	sugar:hydrogen symporter activity			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	10924353	10924353	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10924353delT								CLNK (237967 upstream) : MIR572 (446098 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	11457622	11457622	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:11457622delA								HS3ST1 (27085 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	11458550	11458550	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:11458550delT								HS3ST1 (28013 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	11671187	11671187	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:11671187delT								HS3ST1 (240650 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	11707010	11707011	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:11707010_11707011insT								HS3ST1 (276473 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	11943179	11943179	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:11943179delA								HS3ST1 (512642 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	12238464	12238465	+	Intron	INS	-	G	G	rs150031438	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:12238464_12238465insG	uc003gmr.2	+											Homo sapiens cDNA clone IMAGE:4830086.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	12534993	12534996	+	IGR	DEL	AAAA	-	-	rs113094530		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:12534993_12534996delAAAA								None (None upstream) : HSP90AB2P (800041 downstream)																																			---	---	---	---
RAB28	9364	broad.mit.edu	37	4	13475851	13475852	+	Intron	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13475851_13475852delTG	uc003gmu.2	-						RAB28_uc003gmt.2_Intron|RAB28_uc011bwz.1_Intron|RAB28_uc003gmv.2_Intron	NM_001017979	NP_001017979			RAB28, member RAS oncogene family isoform 1						small GTPase mediated signal transduction	plasma membrane	GDP binding|GTP binding|GTPase activity			ovary(1)|skin(1)	2																		---	---	---	---
RAB28	9364	broad.mit.edu	37	4	13485808	13485808	+	5'UTR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13485808delG	uc003gmu.2	-	1					RAB28_uc003gmt.2_5'UTR|RAB28_uc011bwz.1_5'UTR|RAB28_uc003gmv.2_RNA	NM_001017979	NP_001017979			RAB28, member RAS oncogene family isoform 1						small GTPase mediated signal transduction	plasma membrane	GDP binding|GTP binding|GTPase activity			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	13742143	13742143	+	Intron	DEL	T	-	-	rs75359471		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13742143delT	uc003gna.1	+											Homo sapiens cDNA FLJ34570 fis, clone KIDNE2008072.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	13749090	13749090	+	Intron	DEL	T	-	-	rs78267549		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:13749090delT	uc003gna.1	+											Homo sapiens cDNA FLJ34570 fis, clone KIDNE2008072.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	14101443	14101443	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:14101443delT								BOD1L (472115 upstream) : CPEB2 (904079 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	14915197	14915197	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:14915197delT	uc003gng.3	-											Homo sapiens cDNA FLJ35938 fis, clone TESTI2011549.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	15105337	15105337	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15105337delA								CPEB2 (33563 upstream) : C1QTNF7 (236223 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	15267121	15267122	+	IGR	DEL	TC	-	-	rs111764708		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15267121_15267122delTC								CPEB2 (195347 upstream) : C1QTNF7 (74438 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	16332340	16332340	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16332340delT								FLJ39653 (72530 upstream) : LDB2 (170827 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	16487802	16487802	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16487802delA								FLJ39653 (227992 upstream) : LDB2 (15365 downstream)																																			---	---	---	---
LDB2	9079	broad.mit.edu	37	4	16584474	16584475	+	Intron	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:16584474_16584475insG	uc003goz.2	-						LDB2_uc003gpa.2_Intron|LDB2_uc003gpb.2_Intron|LDB2_uc011bxh.1_Intron|LDB2_uc010iee.2_Intron|LDB2_uc003goy.2_Intron|LDB2_uc011bxi.1_Intron	NM_001290	NP_001281			LIM domain binding 2 isoform a								LIM domain binding|transcription cofactor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	17000384	17000384	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17000384delC								LDB2 (99960 upstream) : QDPR (487636 downstream)																																			---	---	---	---
MED28	80306	broad.mit.edu	37	4	17623198	17623198	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17623198delT	uc003gpi.1	+						MED28_uc003gpj.2_Intron	NM_025205	NP_079481			mediator complex subunit 28						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|membrane|nucleus	actin binding				0																		---	---	---	---
FAM184B	27146	broad.mit.edu	37	4	17658328	17658328	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17658328delT	uc003gpm.3	-							NM_015688	NP_056503			hypothetical protein LOC27146											central_nervous_system(1)	1																		---	---	---	---
LCORL	254251	broad.mit.edu	37	4	17954617	17954618	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17954617_17954618delTT	uc003gpq.2	-						LCORL_uc011bxk.1_Intron	NM_153686	NP_710153			ligand dependent nuclear receptor						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	18068212	18068212	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:18068212delT								LCORL (44827 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	18212621	18212621	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:18212621delT								LCORL (189236 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	18332256	18332256	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:18332256delC								LCORL (308871 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	19997271	19997271	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:19997271delA								None (None upstream) : SLIT2 (257964 downstream)																																			---	---	---	---
KCNIP4	80333	broad.mit.edu	37	4	21719106	21719106	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:21719106delA	uc003gqi.1	-							NM_147182	NP_671711			Kv channel interacting protein 4 isoform 3							plasma membrane	calcium ion binding|potassium channel activity|protein binding|voltage-gated ion channel activity				0		Breast(46;0.134)																---	---	---	---
KCNIP4	80333	broad.mit.edu	37	4	21852622	21852622	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:21852622delA	uc003gqi.1	-						NCRNA00099_uc003gqj.1_RNA	NM_147182	NP_671711			Kv channel interacting protein 4 isoform 3							plasma membrane	calcium ion binding|potassium channel activity|protein binding|voltage-gated ion channel activity				0		Breast(46;0.134)																---	---	---	---
GPR125	166647	broad.mit.edu	37	4	22440088	22440088	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22440088delA	uc003gqm.1	-						GPR125_uc010ieo.1_Intron|GPR125_uc003gqn.1_Intron|GPR125_uc003gqo.2_Intron	NM_145290	NP_660333			G protein-coupled receptor 125 precursor						neuropeptide signaling pathway	integral to membrane	G-protein coupled receptor activity			skin(1)	1		Breast(46;0.198)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	22635447	22635447	+	IGR	DEL	C	-	-	rs11337835		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22635447delC								GPR125 (117775 upstream) : GBA3 (59101 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	23029304	23029304	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23029304delA	uc003gqr.1	+											full-length cDNA clone CS0DB009YA06 of Neuroblastoma Cot 10-normalized of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	23215783	23215783	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23215783delT								GBA3 (394592 upstream) : PPARGC1A (577862 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	23300913	23300913	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23300913delA								GBA3 (479722 upstream) : PPARGC1A (492732 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	23470656	23470657	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23470656_23470657insA								GBA3 (649465 upstream) : PPARGC1A (322988 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	23664647	23664648	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23664647_23664648insA								GBA3 (843456 upstream) : PPARGC1A (128997 downstream)																																			---	---	---	---
PPARGC1A	10891	broad.mit.edu	37	4	23842079	23842079	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23842079delT	uc003gqs.2	-						PPARGC1A_uc003gqt.2_Intron|PPARGC1A_uc011bxp.1_Intron|PPARGC1A_uc010ier.1_Intron	NM_013261	NP_037393			peroxisome proliferator-activated receptor						androgen receptor signaling pathway|brown fat cell differentiation|cellular glucose homeostasis|digestion|fatty acid oxidation|gluconeogenesis|mitochondrion organization|mRNA processing|neuron death|positive regulation of fatty acid oxidation|positive regulation of gluconeogenesis|positive regulation of histone acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|protein complex assembly|protein stabilization|response to muscle activity|response to starvation|RNA splicing|temperature homeostasis|transcription initiation from RNA polymerase II promoter	DNA-directed RNA polymerase II, core complex	androgen receptor binding|DNA binding|ligand-dependent nuclear receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|nucleotide binding|RNA binding|RNA polymerase II transcription cofactor activity|transcription factor binding			ovary(2)|lung(2)|kidney(2)|skin(2)	8		Breast(46;0.0503)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	24066397	24066397	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24066397delT								PPARGC1A (174697 upstream) : MIR573 (455418 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	24802565	24802565	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24802565delT								SOD3 (99 upstream) : CCDC149 (5175 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	24992763	24992764	+	IGR	DEL	TG	-	-	rs60384714		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24992763_24992764delTG								CCDC149 (10993 upstream) : LGI2 (7707 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	25951439	25951439	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25951439delG								C4orf52 (19939 upstream) : RBPJ (369893 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	26545418	26545419	+	IGR	INS	-	TTTTG	TTTTG	rs138527472	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26545418_26545419insTTTTG								CCKAR (53376 upstream) : TBC1D19 (40127 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	26580198	26580199	+	IGR	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26580198_26580199delAG								CCKAR (88156 upstream) : TBC1D19 (5347 downstream)																																			---	---	---	---
TBC1D19	55296	broad.mit.edu	37	4	26703367	26703367	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26703367delA	uc003gsf.3	+						TBC1D19_uc010iew.2_Intron|TBC1D19_uc011bxu.1_Intron	NM_018317	NP_060787			TBC1 domain family, member 19							intracellular	Rab GTPase activator activity			breast(1)	1		Breast(46;0.0503)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	26771688	26771688	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26771688delA								TBC1D19 (14773 upstream) : STIM2 (90676 downstream)																																			---	---	---	---
STIM2	57620	broad.mit.edu	37	4	27019137	27019137	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27019137delT	uc003gsh.3	+						STIM2_uc003gsg.3_Intron|STIM2_uc010iex.2_Intron|STIM2_uc010iey.2_Intron	NM_020860	NP_065911			stromal interaction molecule 2						activation of store-operated calcium channel activity|calcium ion transport|cellular calcium ion homeostasis|negative regulation of calcium ion transport via store-operated calcium channel activity	endoplasmic reticulum membrane|integral to membrane|plasma membrane	calcium channel regulator activity|calcium ion binding|protein binding			central_nervous_system(1)|skin(1)	2		Breast(46;0.0503)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	27641238	27641240	+	IGR	DEL	ATC	-	-	rs297284	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27641238_27641240delATC								STIM2 (615430 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	27754801	27754801	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27754801delA								STIM2 (728993 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	28047381	28047381	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:28047381delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	28876146	28876148	+	IGR	DEL	AAA	-	-	rs148606420		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:28876146_28876148delAAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	29137832	29137833	+	IGR	DEL	TT	-	-	rs33937847		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:29137832_29137833delTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	30049505	30049505	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:30049505delT								None (None upstream) : PCDH7 (672532 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	30663162	30663163	+	IGR	DEL	AA	-	-	rs112854399		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:30663162_30663163delAA								None (None upstream) : PCDH7 (58874 downstream)																																			---	---	---	---
PCDH7	5099	broad.mit.edu	37	4	30798900	30798901	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:30798900_30798901insT	uc011bxx.1	+						PCDH7_uc011bxw.1_Intron	NM_002589	NP_002580			protocadherin 7 isoform a precursor						homophilic cell adhesion	integral to plasma membrane	calcium ion binding			upper_aerodigestive_tract(1)|ovary(1)|liver(1)|skin(1)	4																		---	---	---	---
PCDH7	5099	broad.mit.edu	37	4	30813019	30813019	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:30813019delA	uc011bxx.1	+						PCDH7_uc011bxw.1_Intron	NM_002589	NP_002580			protocadherin 7 isoform a precursor						homophilic cell adhesion	integral to plasma membrane	calcium ion binding			upper_aerodigestive_tract(1)|ovary(1)|liver(1)|skin(1)	4																		---	---	---	---
PCDH7	5099	broad.mit.edu	37	4	30830456	30830456	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:30830456delT	uc011bxx.1	+						PCDH7_uc011bxw.1_Intron	NM_002589	NP_002580			protocadherin 7 isoform a precursor						homophilic cell adhesion	integral to plasma membrane	calcium ion binding			upper_aerodigestive_tract(1)|ovary(1)|liver(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	32123252	32123252	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:32123252delA								PCDH7 (974831 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	32230880	32230881	+	IGR	INS	-	ACAC	ACAC	rs143199865	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:32230880_32230881insACAC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	33242373	33242373	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:33242373delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	33435954	33435954	+	IGR	DEL	T	-	-	rs113462683		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:33435954delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	33769218	33769218	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:33769218delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	34366999	34367000	+	IGR	INS	-	A	A	rs138879904	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:34366999_34367000insA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	34439181	34439182	+	IGR	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:34439181_34439182delGA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	35303161	35303161	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:35303161delC								None (None upstream) : ARAP2 (646683 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	35461401	35461401	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:35461401delT								None (None upstream) : ARAP2 (488443 downstream)																																			---	---	---	---
ARAP2	116984	broad.mit.edu	37	4	36195430	36195431	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:36195430_36195431insA	uc003gsq.1	-						ARAP2_uc003gsr.1_Intron	NM_015230	NP_056045			ArfGAP with RhoGAP domain, ankyrin repeat and PH						regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytosol	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	36896502	36896503	+	IGR	INS	-	A	A	rs142641991	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:36896502_36896503insA								MIR1255B-1 (468452 upstream) : KIAA1239 (350187 downstream)																																			---	---	---	---
KIAA1239	57495	broad.mit.edu	37	4	37330661	37330662	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37330661_37330662delAA	uc011bxz.1	+							NM_001144990	NP_001138462			hypothetical protein LOC57495												0																		---	---	---	---
KIAA1239	57495	broad.mit.edu	37	4	37399411	37399414	+	Intron	DEL	CTCT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37399411_37399414delCTCT	uc011bxz.1	+							NM_001144990	NP_001138462			hypothetical protein LOC57495												0																		---	---	---	---
KIAA1239	57495	broad.mit.edu	37	4	37446089	37446089	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37446089delT	uc011bxz.1	+	7	2479	c.2479delT	c.(2479-2481)TTTfs	p.F827fs		NM_001144990	NP_001138462	Q9ULI1	K1239_HUMAN	hypothetical protein LOC57495	827											0																		---	---	---	---
C4orf19	55286	broad.mit.edu	37	4	37590393	37590393	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37590393delA	uc003gsw.3	+						C4orf19_uc003gsy.3_Intron	NM_001104629	NP_001098099			hypothetical protein LOC55286												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	37750568	37750569	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37750568_37750569insA								RELL1 (62569 upstream) : PGM2 (77713 downstream)																																			---	---	---	---
TBC1D1	23216	broad.mit.edu	37	4	37909850	37909850	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37909850delG	uc003gtb.2	+						TBC1D1_uc011byd.1_Intron|TBC1D1_uc010ifd.2_Intron	NM_015173	NP_055988			TBC1 (tre-2/USP6, BUB2, cdc16) domain family,							nucleus	Rab GTPase activator activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	38144960	38144960	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38144960delA								TBC1D1 (4167 upstream) : FLJ13197 (469362 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	38291754	38291755	+	IGR	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38291754_38291755delAC								TBC1D1 (150961 upstream) : FLJ13197 (322567 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	38410256	38410256	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38410256delA								TBC1D1 (269463 upstream) : FLJ13197 (204066 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	38470069	38470069	+	IGR	DEL	T	-	-	rs111460865		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38470069delT								TBC1D1 (329276 upstream) : FLJ13197 (144253 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	38820243	38820243	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38820243delG								TLR1 (13831 upstream) : TLR6 (8165 downstream)																																			---	---	---	---
TMEM156	80008	broad.mit.edu	37	4	38990181	38990182	+	Intron	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38990181_38990182delTC	uc003gto.2	-						TMEM156_uc010ifj.2_Intron	NM_024943	NP_079219			transmembrane protein 156							integral to membrane				skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	39153693	39153693	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39153693delA								KLHL5 (29865 upstream) : WDR19 (30331 downstream)																																			---	---	---	---
WDR19	57728	broad.mit.edu	37	4	39255399	39255400	+	Intron	DEL	AA	-	-	rs75042299		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39255399_39255400delAA	uc003gtv.2	+						WDR19_uc011byi.1_Intron|WDR19_uc003gtw.1_Intron	NM_025132	NP_079408			WD repeat domain 19						cell projection organization	microtubule basal body|motile cilium|photoreceptor connecting cilium	binding			large_intestine(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	39376818	39376818	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39376818delT								RFC1 (8823 upstream) : KLB (31655 downstream)																																			---	---	---	---
UGDH	7358	broad.mit.edu	37	4	39505928	39505928	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39505928delA	uc003guk.1	-						UGDH_uc011byp.1_Intron|UGDH_uc003gul.1_Intron	NM_003359	NP_003350			UDP-glucose dehydrogenase						glycosaminoglycan biosynthetic process|UDP-glucose metabolic process|UDP-glucuronate biosynthetic process|xenobiotic metabolic process	cytosol	electron carrier activity|NAD binding|UDP-glucose 6-dehydrogenase activity			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4					NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	39546247	39546247	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39546247delA	uc003gum.1	+											Homo sapiens cDNA FLJ31996 fis, clone NT2RP7009253.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	39684922	39684922	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39684922delT								C4orf34 (44441 upstream) : UBE2K (14742 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	39806457	39806457	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39806457delT								UBE2K (22049 upstream) : PDS5A (18027 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	40328713	40328713	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40328713delT								RHOH (82432 upstream) : CHRNA9 (8756 downstream)																																			---	---	---	---
RBM47	54502	broad.mit.edu	37	4	40505208	40505209	+	Intron	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40505208_40505209delTG	uc003gvc.2	-						RBM47_uc003gvd.2_Intron|RBM47_uc003gve.2_Intron|RBM47_uc011bys.1_Intron|RBM47_uc003gvg.1_Intron	NM_001098634	NP_001092104			RNA binding motif protein 47 isoform a							nucleus	nucleotide binding|RNA binding			breast(3)	3																		---	---	---	---
RBM47	54502	broad.mit.edu	37	4	40620253	40620253	+	Intron	DEL	A	-	-	rs34659484		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40620253delA	uc003gvc.2	-						RBM47_uc003gve.2_Intron|RBM47_uc011bys.1_Intron	NM_001098634	NP_001092104			RNA binding motif protein 47 isoform a							nucleus	nucleotide binding|RNA binding			breast(3)	3																		---	---	---	---
NSUN7	79730	broad.mit.edu	37	4	40753847	40753847	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40753847delA	uc003gvj.3	+						NSUN7_uc003gvh.2_Intron|NSUN7_uc003gvi.3_Intron	NM_024677	NP_078953			NOL1/NOP2/Sun domain family, member 7												0																		---	---	---	---
NSUN7	79730	broad.mit.edu	37	4	40778355	40778355	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40778355delT	uc003gvj.3	+						NSUN7_uc003gvi.3_Intron	NM_024677	NP_078953			NOL1/NOP2/Sun domain family, member 7												0																		---	---	---	---
APBB2	323	broad.mit.edu	37	4	40866495	40866496	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40866495_40866496insA	uc003gvl.2	-						APBB2_uc010ifu.2_Intron|APBB2_uc003gvm.2_Intron|APBB2_uc003gvn.2_Intron	NM_173075	NP_775098			amyloid beta A4 precursor protein-binding,						cell cycle arrest|intracellular signal transduction|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|regulation of transcription, DNA-dependent	growth cone|lamellipodium|membrane|nucleus|synapse	beta-amyloid binding|transcription factor binding			ovary(2)|large_intestine(1)	3																		---	---	---	---
APBB2	323	broad.mit.edu	37	4	40897200	40897200	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40897200delA	uc003gvl.2	-						APBB2_uc010ifu.2_Intron|APBB2_uc003gvm.2_Intron|APBB2_uc003gvn.2_Intron|APBB2_uc011byt.1_Intron	NM_173075	NP_775098			amyloid beta A4 precursor protein-binding,						cell cycle arrest|intracellular signal transduction|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|regulation of transcription, DNA-dependent	growth cone|lamellipodium|membrane|nucleus|synapse	beta-amyloid binding|transcription factor binding			ovary(2)|large_intestine(1)	3																		---	---	---	---
LIMCH1	22998	broad.mit.edu	37	4	41615397	41615397	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41615397delT	uc003gvu.3	+						LIMCH1_uc003gvt.1_Intron|LIMCH1_uc003gvv.3_Intron|LIMCH1_uc003gvw.3_Intron|LIMCH1_uc003gvx.3_Intron|LIMCH1_uc003gwe.3_Intron|LIMCH1_uc003gvy.3_Intron|LIMCH1_uc003gwa.3_Intron|LIMCH1_uc003gvz.3_Intron|LIMCH1_uc011byu.1_Intron|LIMCH1_uc003gwc.3_Intron|LIMCH1_uc003gwd.3_Intron|LIMCH1_uc011byv.1_5'Flank|LIMCH1_uc003gwb.1_Intron	NM_014988	NP_055803			LIM and calponin homology domains 1 isoform a						actomyosin structure organization		actin binding|zinc ion binding			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	41702605	41702605	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41702605delT								LIMCH1 (546 upstream) : PHOX2B (43495 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	41805178	41805179	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:41805178_41805179delAA								PHOX2B (54191 upstream) : TMEM33 (131958 downstream)																																			---	---	---	---
SLC30A9	10463	broad.mit.edu	37	4	42065768	42065768	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42065768delT	uc003gwl.2	+						SLC30A9_uc011byx.1_Intron	NM_006345	NP_006336			solute carrier family 30 (zinc transporter),						nucleotide-excision repair|zinc ion transport	cytoskeleton|integral to membrane|nucleus	cation transmembrane transporter activity|nucleotide binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
SLC30A9	10463	broad.mit.edu	37	4	42080153	42080153	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42080153delT	uc003gwl.2	+						SLC30A9_uc011byx.1_Intron	NM_006345	NP_006336			solute carrier family 30 (zinc transporter),						nucleotide-excision repair|zinc ion transport	cytoskeleton|integral to membrane|nucleus	cation transmembrane transporter activity|nucleotide binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
BEND4	389206	broad.mit.edu	37	4	42131308	42131308	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42131308delA	uc003gwn.2	-						BEND4_uc003gwm.2_Intron|BEND4_uc011byy.1_Intron	NM_207406	NP_997289			BEN domain containing 4 isoform a												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	42164716	42164716	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42164716delT								BEND4 (9821 upstream) : SHISA3 (235140 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	42184978	42184978	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42184978delT								BEND4 (30083 upstream) : SHISA3 (214878 downstream)																																			---	---	---	---
ATP8A1	10396	broad.mit.edu	37	4	42644007	42644007	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42644007delT	uc003gwr.2	-						ATP8A1_uc003gws.2_Intron|ATP8A1_uc011byz.1_Intron	NM_006095	NP_006086			ATPase, aminophospholipid transporter (APLT),						ATP biosynthetic process	chromaffin granule membrane|integral to membrane|plasma membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			skin(2)|central_nervous_system(1)	3					Phosphatidylserine(DB00144)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	42769793	42769793	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42769793delG								ATP8A1 (110671 upstream) : GRXCR1 (125491 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	43127752	43127752	+	IGR	DEL	T	-	-	rs111350736		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:43127752delT								GRXCR1 (95079 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	43412012	43412012	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:43412012delT								GRXCR1 (379339 upstream) : KCTD8 (763910 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	44122467	44122467	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:44122467delT								None (None upstream) : KCTD8 (53455 downstream)																																			---	---	---	---
KCTD8	386617	broad.mit.edu	37	4	44240215	44240215	+	Intron	DEL	G	-	-	rs28642794	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:44240215delG	uc003gwu.2	-							NM_198353	NP_938167			potassium channel tetramerisation domain							cell junction|postsynaptic membrane|presynaptic membrane|voltage-gated potassium channel complex	voltage-gated potassium channel activity			central_nervous_system(2)|ovary(1)	3															HNSCC(17;0.042)			---	---	---	---
KCTD8	386617	broad.mit.edu	37	4	44342323	44342325	+	Intron	DEL	TTG	-	-	rs2636402	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:44342323_44342325delTTG	uc003gwu.2	-							NM_198353	NP_938167			potassium channel tetramerisation domain							cell junction|postsynaptic membrane|presynaptic membrane|voltage-gated potassium channel complex	voltage-gated potassium channel activity			central_nervous_system(2)|ovary(1)	3															HNSCC(17;0.042)			---	---	---	---
KCTD8	386617	broad.mit.edu	37	4	44411862	44411862	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:44411862delA	uc003gwu.2	-							NM_198353	NP_938167			potassium channel tetramerisation domain							cell junction|postsynaptic membrane|presynaptic membrane|voltage-gated potassium channel complex	voltage-gated potassium channel activity			central_nervous_system(2)|ovary(1)	3															HNSCC(17;0.042)			---	---	---	---
GUF1	60558	broad.mit.edu	37	4	44700615	44700615	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:44700615delA	uc003gww.3	+	17	2134	c.1927delA	c.(1927-1929)AAAfs	p.K643fs	GUF1_uc011bza.1_Frame_Shift_Del_p.K50fs	NM_021927	NP_068746	Q8N442	GUF1_HUMAN	GUF1 GTPase homolog	643					translation	mitochondrial inner membrane	GTP binding|GTPase activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	44821444	44821444	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:44821444delA								GNPDA2 (92832 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	44969233	44969236	+	IGR	DEL	TGTT	-	-	rs35345808		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:44969233_44969236delTGTT								GNPDA2 (240621 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	45015280	45015283	+	IGR	DEL	TTAT	-	-	rs33930788		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:45015280_45015283delTTAT								GNPDA2 (286668 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	45554168	45554168	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:45554168delA								GNPDA2 (825556 upstream) : GABRG1 (483621 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	45851447	45851447	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:45851447delT								None (None upstream) : GABRG1 (186342 downstream)																																			---	---	---	---
ATP10D	57205	broad.mit.edu	37	4	47574595	47574595	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47574595delA	uc003gxk.1	+						ATP10D_uc003gxl.1_Intron	NM_020453	NP_065186			ATPase, class V, type 10D						ATP biosynthetic process|cation transport	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|pancreas(1)	3																		---	---	---	---
ATP10D	57205	broad.mit.edu	37	4	47582226	47582226	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47582226delT	uc003gxk.1	+						ATP10D_uc003gxl.1_Intron	NM_020453	NP_065186			ATPase, class V, type 10D						ATP biosynthetic process|cation transport	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|pancreas(1)	3																		---	---	---	---
CORIN	10699	broad.mit.edu	37	4	47695103	47695103	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47695103delA	uc003gxm.2	-						CORIN_uc011bzf.1_Intron|CORIN_uc011bzg.1_Intron|CORIN_uc011bzh.1_Intron|CORIN_uc011bzi.1_Intron|CORIN_uc003gxn.3_Intron	NM_006587	NP_006578			corin						peptide hormone processing|regulation of systemic arterial blood pressure by atrial natriuretic peptide	integral to membrane|plasma membrane	scavenger receptor activity|serine-type endopeptidase activity|serine-type exopeptidase activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
CORIN	10699	broad.mit.edu	37	4	47723184	47723185	+	Intron	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47723184_47723185delAG	uc003gxm.2	-						CORIN_uc011bzf.1_Intron|CORIN_uc011bzg.1_Intron|CORIN_uc011bzh.1_Intron|CORIN_uc011bzi.1_Intron|CORIN_uc003gxn.3_Intron	NM_006587	NP_006578			corin						peptide hormone processing|regulation of systemic arterial blood pressure by atrial natriuretic peptide	integral to membrane|plasma membrane	scavenger receptor activity|serine-type endopeptidase activity|serine-type exopeptidase activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
CORIN	10699	broad.mit.edu	37	4	47787535	47787535	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47787535delT	uc003gxm.2	-						CORIN_uc011bzf.1_Intron|CORIN_uc011bzg.1_Intron|CORIN_uc011bzh.1_Intron|CORIN_uc011bzi.1_Intron|CORIN_uc003gxn.3_Intron	NM_006587	NP_006578			corin						peptide hormone processing|regulation of systemic arterial blood pressure by atrial natriuretic peptide	integral to membrane|plasma membrane	scavenger receptor activity|serine-type endopeptidase activity|serine-type exopeptidase activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
NFXL1	152518	broad.mit.edu	37	4	47879126	47879126	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47879126delA	uc010igh.2	-						NFXL1_uc003gxo.2_Intron|NFXL1_uc003gxp.2_Intron|NFXL1_uc003gxq.3_RNA|NFXL1_uc010igi.2_Intron	NM_152995	NP_694540			nuclear transcription factor, X-box binding-like							integral to membrane|nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)|skin(1)	3																		---	---	---	---
NFXL1	152518	broad.mit.edu	37	4	47893954	47893954	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47893954delA	uc010igh.2	-						NFXL1_uc003gxp.2_Intron|NFXL1_uc003gxq.3_Intron|NFXL1_uc010igi.2_Intron	NM_152995	NP_694540			nuclear transcription factor, X-box binding-like							integral to membrane|nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)|skin(1)	3																		---	---	---	---
NFXL1	152518	broad.mit.edu	37	4	47899965	47899965	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47899965delA	uc010igh.2	-						NFXL1_uc003gxp.2_Intron|NFXL1_uc003gxq.3_Intron|NFXL1_uc010igi.2_Intron	NM_152995	NP_694540			nuclear transcription factor, X-box binding-like							integral to membrane|nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)|skin(1)	3																		---	---	---	---
NFXL1	152518	broad.mit.edu	37	4	47907496	47907496	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:47907496delT	uc010igh.2	-						NFXL1_uc003gxp.2_Intron|NFXL1_uc003gxq.3_Intron|NFXL1_uc010igi.2_Intron	NM_152995	NP_694540			nuclear transcription factor, X-box binding-like							integral to membrane|nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	48053730	48053730	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48053730delT								NIPAL1 (14652 upstream) : TXK (14682 downstream)																																			---	---	---	---
TXK	7294	broad.mit.edu	37	4	48096365	48096365	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48096365delC	uc003gxx.3	-						TXK_uc003gxy.1_Intron	NM_003328	NP_003319			TXK tyrosine kinase							cytoplasm	ATP binding|non-membrane spanning protein tyrosine kinase activity				0																		---	---	---	---
TXK	7294	broad.mit.edu	37	4	48097244	48097244	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48097244delA	uc003gxx.3	-						TXK_uc003gxy.1_Intron	NM_003328	NP_003319			TXK tyrosine kinase							cytoplasm	ATP binding|non-membrane spanning protein tyrosine kinase activity				0																		---	---	---	---
TXK	7294	broad.mit.edu	37	4	48137723	48137723	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48137723delA	uc003gxx.3	-						TXK_uc003gxy.1_5'Flank	NM_003328	NP_003319			TXK tyrosine kinase							cytoplasm	ATP binding|non-membrane spanning protein tyrosine kinase activity				0																		---	---	---	---
TEC	7006	broad.mit.edu	37	4	48208170	48208171	+	Intron	INS	-	T	T	rs146635255	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48208170_48208171insT	uc003gxz.2	-							NM_003215	NP_003206			tec protein tyrosine kinase						intracellular protein kinase cascade	cytosol	ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(4)|stomach(1)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)	9																		---	---	---	---
TEC	7006	broad.mit.edu	37	4	48229307	48229307	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48229307delA	uc003gxz.2	-							NM_003215	NP_003206			tec protein tyrosine kinase						intracellular protein kinase cascade	cytosol	ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(4)|stomach(1)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)	9																		---	---	---	---
FRYL	285527	broad.mit.edu	37	4	48625114	48625114	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48625114delA	uc003gyh.1	-						FRYL_uc003gyk.2_Intron|FRYL_uc003gyl.1_Intron|FRYL_uc003gym.1_Intron	NM_015030	NP_055845			furry-like						regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			skin(1)	1																		---	---	---	---
FRYL	285527	broad.mit.edu	37	4	48625211	48625213	+	Intron	DEL	AAC	-	-	rs776579	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48625211_48625213delAAC	uc003gyh.1	-						FRYL_uc003gyk.2_Intron|FRYL_uc003gyl.1_Intron|FRYL_uc003gym.1_Intron	NM_015030	NP_055845			furry-like						regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			skin(1)	1																		---	---	---	---
OCIAD1	54940	broad.mit.edu	37	4	48859543	48859543	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48859543delT	uc003gyo.2	+						OCIAD1_uc003gyr.2_Intron|OCIAD1_uc003gyp.2_Intron|OCIAD1_uc003gys.2_Intron|OCIAD1_uc003gyq.2_Intron|OCIAD1_uc010igk.2_Intron	NM_017830	NP_060300			OCIA domain containing 1 isoform 1							endosome	protein binding				0																		---	---	---	---
OCIAD2	132299	broad.mit.edu	37	4	48892270	48892270	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48892270delA	uc003gyt.2	-						OCIAD2_uc003gyu.2_Intron	NM_001014446	NP_001014446			OCIA domain containing 2 isoform 1							endosome					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	49090257	49090257	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49090257delT								CWH43 (26164 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	49133566	49133570	+	IGR	DEL	TTTCG	-	-	rs150882409	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49133566_49133570delTTTCG								CWH43 (69473 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	49534615	49534616	+	IGR	INS	-	C	C	rs68121402		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49534615_49534616insC								CWH43 (470522 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	49577818	49577818	+	5'Flank	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49577818delC	uc003gzb.1	+											DQ596206																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	49588794	49588795	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:49588794_49588795insA								CWH43 (524701 upstream) : None (None downstream)																																			---	---	---	---
DCUN1D4	23142	broad.mit.edu	37	4	52731147	52731147	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:52731147delT	uc003gze.2	+						DCUN1D4_uc003gzf.2_Intron|DCUN1D4_uc011bzn.1_Intron|DCUN1D4_uc003gzg.2_Intron|DCUN1D4_uc003gzh.2_Intron|DCUN1D4_uc011bzo.1_Intron	NM_001040402	NP_001035492			DCN1, defective in cullin neddylation 1, domain											ovary(2)	2			GBM - Glioblastoma multiforme(4;1.93e-11)|LUSC - Lung squamous cell carcinoma(32;0.00654)															---	---	---	---
SPATA18	132671	broad.mit.edu	37	4	52926826	52926826	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:52926826delT	uc003gzl.2	+						SPATA18_uc010igl.1_Intron|SPATA18_uc011bzq.1_Intron|SPATA18_uc003gzk.1_Intron	NM_145263	NP_660306			spermatogenesis associated 18 homolog						mitochondrial protein catabolic process|mitochondrion degradation by induced vacuole formation|response to DNA damage stimulus	mitochondrial outer membrane	protein binding			ovary(2)|skin(2)	4			GBM - Glioblastoma multiforme(4;1.77e-13)|LUSC - Lung squamous cell carcinoma(32;0.00204)															---	---	---	---
SPATA18	132671	broad.mit.edu	37	4	52935037	52935037	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:52935037delT	uc003gzl.2	+						SPATA18_uc010igl.1_Intron|SPATA18_uc011bzq.1_Intron|SPATA18_uc003gzk.1_Intron	NM_145263	NP_660306			spermatogenesis associated 18 homolog						mitochondrial protein catabolic process|mitochondrion degradation by induced vacuole formation|response to DNA damage stimulus	mitochondrial outer membrane	protein binding			ovary(2)|skin(2)	4			GBM - Glioblastoma multiforme(4;1.77e-13)|LUSC - Lung squamous cell carcinoma(32;0.00204)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	53163409	53163409	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53163409delA								SPATA18 (199952 upstream) : USP46 (293720 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	53286038	53286038	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53286038delA								SPATA18 (322581 upstream) : USP46 (171091 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	53623447	53623449	+	IGR	DEL	AAG	-	-	rs9999908	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53623447_53623449delAAG								KIAA0114 (43142 upstream) : RASL11B (105046 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	53632066	53632066	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:53632066delT								KIAA0114 (51761 upstream) : RASL11B (96429 downstream)																																			---	---	---	---
PDGFRA	5156	broad.mit.edu	37	4	54266168	54266168	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54266168delT	uc003haa.2	+						FIP1L1_uc003gzx.3_Intron|FIP1L1_uc011bzt.1_Intron|FIP1L1_uc003gzy.2_Intron|FIP1L1_uc011bzu.1_Intron|FIP1L1_uc003gzz.2_Intron|FIP1L1_uc003hab.2_Intron|FIP1L1_uc003hac.2_Intron|FIP1L1_uc010ign.2_Intron	NM_006206	NP_006197			platelet-derived growth factor receptor alpha						cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			---	---	---	---
PDGFRA	5156	broad.mit.edu	37	4	54549054	54549054	+	Intron	DEL	T	-	-	rs79742162		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54549054delT	uc003haa.2	+							NM_006206	NP_006197			platelet-derived growth factor receptor alpha						cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			---	---	---	---
PDGFRA	5156	broad.mit.edu	37	4	54673606	54673607	+	Intron	INS	-	TG	TG	rs149989556	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54673606_54673607insTG	uc003haa.2	+							NM_006206	NP_006197			platelet-derived growth factor receptor alpha						cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			---	---	---	---
PDGFRA	5156	broad.mit.edu	37	4	54811426	54811426	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:54811426delT	uc003haa.2	+							NM_006206	NP_006197			platelet-derived growth factor receptor alpha						cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			---	---	---	---
Unknown	0	broad.mit.edu	37	4	55189683	55189683	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55189683delA								PDGFRA (25272 upstream) : KIT (334412 downstream)																																	OREG0016197	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	4	55241301	55241302	+	IGR	INS	-	T	T	rs142584237	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55241301_55241302insT								PDGFRA (76890 upstream) : KIT (282793 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	55498511	55498511	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55498511delG								PDGFRA (334100 upstream) : KIT (25584 downstream)																																			---	---	---	---
KIT	3815	broad.mit.edu	37	4	55556225	55556228	+	Intron	DEL	GGGG	-	-	rs58899968	by1000genomes;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55556225_55556228delGGGG	uc010igr.2	+						KIT_uc010igs.2_Intron	NM_000222	NP_000213			v-kit Hardy-Zuckerman 4 feline sarcoma viral						male gonad development|transmembrane receptor protein tyrosine kinase signaling pathway	extracellular space|integral to membrane	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity			soft_tissue(3273)|haematopoietic_and_lymphoid_tissue(1572)|skin(99)|testis(49)|bone(21)|genital_tract(18)|kidney(17)|ovary(16)|salivary_gland(15)|large_intestine(11)|thymus(6)|lung(6)|central_nervous_system(4)|NS(3)|eye(2)|endometrium(2)|breast(1)|stomach(1)|autonomic_ganglia(1)|pancreas(1)	5118	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Sorafenib(DB00398)|Sunitinib(DB01268)		1	Mis|O		GIST|AML|TGCT|mastocytosis|mucosal melanoma	GIST|epithelioma	Piebald trait		Mast_Cell_disease_Familial_Clustering_of|Piebaldism|Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Gastrointestinal_Stromal_Tumors				---	---	---	---
CEP135	9662	broad.mit.edu	37	4	56884135	56884135	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:56884135delT	uc003hbi.2	+						CEP135_uc003hbj.2_Intron	NM_025009	NP_079285			centrosome protein 4						centriole replication|centriole-centriole cohesion|G2/M transition of mitotic cell cycle	centriole|cytosol	protein C-terminus binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5	Glioma(25;0.08)|all_neural(26;0.101)																	---	---	---	---
KIAA1211	57482	broad.mit.edu	37	4	57099294	57099295	+	Intron	INS	-	TTTG	TTTG	rs34664446		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57099294_57099295insTTTG	uc003hbk.2	+							NM_020722	NP_065773			hypothetical protein LOC57482											ovary(1)|skin(1)	2	Glioma(25;0.08)|all_neural(26;0.101)																	---	---	---	---
KIAA1211	57482	broad.mit.edu	37	4	57170591	57170591	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57170591delT	uc003hbk.2	+						KIAA1211_uc010iha.2_Intron	NM_020722	NP_065773			hypothetical protein LOC57482											ovary(1)|skin(1)	2	Glioma(25;0.08)|all_neural(26;0.101)																	---	---	---	---
AASDH	132949	broad.mit.edu	37	4	57211107	57211111	+	Intron	DEL	TTTTT	-	-	rs35522451		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57211107_57211111delTTTTT	uc003hbn.2	-						AASDH_uc010ihb.2_Intron|AASDH_uc011caa.1_Intron|AASDH_uc003hbo.2_Intron|AASDH_uc011cab.1_Intron|AASDH_uc010ihc.2_Intron	NM_181806	NP_861522			aminoadipate-semialdehyde dehydrogenase						fatty acid metabolic process		acid-thiol ligase activity|acyl carrier activity|ATP binding|cofactor binding			ovary(4)	4	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)																---	---	---	---
PPAT	5471	broad.mit.edu	37	4	57268218	57268218	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57268218delA	uc003hbr.2	-							NM_002703	NP_002694			phosphoribosyl pyrophosphate amidotransferase						glutamine metabolic process|nucleoside metabolic process|purine base biosynthetic process|purine ribonucleoside monophosphate biosynthetic process	cytosol	4 iron, 4 sulfur cluster binding|amidophosphoribosyltransferase activity|metal ion binding				0	Glioma(25;0.08)|all_neural(26;0.101)				L-Glutamine(DB00130)|Thioguanine(DB00352)													---	---	---	---
PPAT	5471	broad.mit.edu	37	4	57268999	57269016	+	Intron	DEL	AAAAAAAAAAAAAAAAGG	-	-	rs72259300		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57268999_57269016delAAAAAAAAAAAAAAAAGG	uc003hbr.2	-							NM_002703	NP_002694			phosphoribosyl pyrophosphate amidotransferase						glutamine metabolic process|nucleoside metabolic process|purine base biosynthetic process|purine ribonucleoside monophosphate biosynthetic process	cytosol	4 iron, 4 sulfur cluster binding|amidophosphoribosyltransferase activity|metal ion binding				0	Glioma(25;0.08)|all_neural(26;0.101)				L-Glutamine(DB00130)|Thioguanine(DB00352)													---	---	---	---
PPAT	5471	broad.mit.edu	37	4	57292568	57292569	+	Intron	DEL	AA	-	-	rs113640946		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57292568_57292569delAA	uc003hbr.2	-							NM_002703	NP_002694			phosphoribosyl pyrophosphate amidotransferase						glutamine metabolic process|nucleoside metabolic process|purine base biosynthetic process|purine ribonucleoside monophosphate biosynthetic process	cytosol	4 iron, 4 sulfur cluster binding|amidophosphoribosyltransferase activity|metal ion binding				0	Glioma(25;0.08)|all_neural(26;0.101)				L-Glutamine(DB00130)|Thioguanine(DB00352)													---	---	---	---
SRP72	6731	broad.mit.edu	37	4	57337867	57337867	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57337867delT	uc003hbv.2	+						SRP72_uc010ihe.2_Intron|SRP72_uc003hbw.1_5'Flank	NM_006947	NP_008878			signal recognition particle 72kDa						response to drug|SRP-dependent cotranslational protein targeting to membrane	cytosol|nucleolus|plasma membrane|signal recognition particle, endoplasmic reticulum targeting	7S RNA binding|signal recognition particle binding			ovary(1)	1	Glioma(25;0.08)|all_neural(26;0.101)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	57811076	57811077	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57811076_57811077delAA								REST (12737 upstream) : C4orf14 (18440 downstream)																																			---	---	---	---
POLR2B	5431	broad.mit.edu	37	4	57852961	57852963	+	Intron	DEL	AAA	-	-	rs34549456		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57852961_57852963delAAA	uc003hcl.1	+						POLR2B_uc011cae.1_Intron|POLR2B_uc011caf.1_Intron	NM_000938	NP_000929			DNA directed RNA polymerase II polypeptide B						mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|protein binding|ribonucleoside binding			ovary(2)	2	Glioma(25;0.08)|all_neural(26;0.181)																	---	---	---	---
POLR2B	5431	broad.mit.edu	37	4	57863274	57863275	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57863274_57863275insA	uc003hcl.1	+						POLR2B_uc011cae.1_Intron|POLR2B_uc011caf.1_Intron	NM_000938	NP_000929			DNA directed RNA polymerase II polypeptide B						mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|protein binding|ribonucleoside binding			ovary(2)	2	Glioma(25;0.08)|all_neural(26;0.181)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	58171015	58171015	+	IGR	DEL	A	-	-	rs113095306		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:58171015delA								IGFBP7 (194476 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	58281184	58281184	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:58281184delA								IGFBP7 (304645 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	59060583	59060584	+	IGR	DEL	GT	-	-	rs150717687		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:59060583_59060584delGT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	59135390	59135390	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:59135390delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	59177981	59177981	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:59177981delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	60128408	60128408	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:60128408delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	60576194	60576195	+	IGR	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:60576194_60576195delTC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	60710694	60710694	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:60710694delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	60894230	60894233	+	IGR	DEL	TCTC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:60894230_60894233delTCTC								None (None upstream) : None (None downstream)																																			---	---	---	---
LPHN3	23284	broad.mit.edu	37	4	62791351	62791352	+	Intron	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62791351_62791352delAG	uc010ihh.2	+						LPHN3_uc003hcq.3_Intron|LPHN3_uc003hct.2_Intron|LPHN3_uc003hcs.1_Intron	NM_015236	NP_056051			latrophilin 3 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1)	18																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	63039401	63039401	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:63039401delT								LPHN3 (101234 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	63041581	63041582	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:63041581_63041582insT								LPHN3 (103414 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	63282051	63282051	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:63282051delA								LPHN3 (343884 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	63474772	63474773	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:63474772_63474773delTT								LPHN3 (536605 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	63512666	63512666	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:63512666delA								LPHN3 (574499 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	63639441	63639442	+	IGR	INS	-	AC	AC	rs150574993	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:63639441_63639442insAC								LPHN3 (701274 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	63911485	63911486	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:63911485_63911486insA								LPHN3 (973318 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	63961686	63961686	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:63961686delC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	64080152	64080152	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:64080152delT								None (None upstream) : None (None downstream)																																			---	---	---	---
TECRL	253017	broad.mit.edu	37	4	65162092	65162092	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:65162092delT	uc003hcv.2	-							NM_001010874	NP_001010874			steroid 5 alpha-reductase 2-like 2						lipid metabolic process	cytoplasm|integral to membrane	oxidoreductase activity, acting on the CH-CH group of donors				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	65568973	65568973	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:65568973delA								TECRL (293795 upstream) : EPHA5 (616309 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	66169083	66169083	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:66169083delA								TECRL (893905 upstream) : EPHA5 (16199 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	67580093	67580093	+	IGR	DEL	A	-	-	rs111492055		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:67580093delA								MIR1269 (437447 upstream) : CENPC1 (757896 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	67636533	67636534	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:67636533_67636534delTT								MIR1269 (493887 upstream) : CENPC1 (701455 downstream)																																			---	---	---	---
TMPRSS11D	9407	broad.mit.edu	37	4	68725581	68725581	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68725581delT	uc003hdq.2	-						LOC550112_uc003hdl.3_Intron|TMPRSS11D_uc011caj.1_Intron	NM_004262	NP_004253			transmembrane protease, serine 11D						proteolysis|respiratory gaseous exchange	extracellular region|integral to plasma membrane	serine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
TMPRSS11F	389208	broad.mit.edu	37	4	68929077	68929077	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:68929077delT	uc003hdt.1	-						LOC550112_uc003hdl.3_Intron|uc011cak.1_Intron|SYT14L_uc010ihn.2_5'Flank	NM_207407	NP_997290			transmembrane protease, serine 11F						proteolysis	extracellular region|integral to plasma membrane	serine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
YTHDC1	91746	broad.mit.edu	37	4	69197919	69197919	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69197919delA	uc003hdx.2	-						YTHDC1_uc003hdy.2_Intron	NM_001031732	NP_001026902			splicing factor YT521-B isoform 1											upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	69821033	69821033	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69821033delA								UGT2A3 (3524 upstream) : UGT2B7 (141160 downstream)																																			---	---	---	---
UGT2B7	7364	broad.mit.edu	37	4	69968844	69968847	+	Intron	DEL	TAAG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69968844_69968847delTAAG	uc003heg.3	+						UGT2B7_uc010ihq.2_Intron	NM_001074	NP_001065			UDP glucuronosyltransferase 2B7 precursor						lipid metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			ovary(1)|skin(1)	2																		---	---	---	---
UGT2A1	10941	broad.mit.edu	37	4	70462252	70462252	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70462252delT	uc003hem.3	-						UGT2A1_uc011caq.1_Intron|UGT2A1_uc010ihu.2_Intron|UGT2A1_uc010iht.2_Intron|UGT2A1_uc010ihs.2_Intron	NM_006798	NP_006789			UDP glucuronosyltransferase 2 family,						detection of chemical stimulus|sensory perception of smell	integral to membrane	glucuronosyltransferase activity|glucuronosyltransferase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	70570329	70570329	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70570329delG								UGT2A1 (51362 upstream) : SULT1B1 (22359 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	71374314	71374315	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71374314_71374315delAA								MUC7 (25601 upstream) : AMTN (9983 downstream)																																			---	---	---	---
DCK	1633	broad.mit.edu	37	4	71889231	71889231	+	Intron	DEL	T	-	-	rs3833976		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71889231delT	uc003hfx.2	+						DCK_uc011cbb.1_Intron	NM_000788	NP_000779			deoxycytidine kinase						purine base metabolic process|purine-containing compound salvage|pyrimidine base metabolic process|pyrimidine nucleoside salvage|pyrimidine nucleotide metabolic process	cytosol|nucleus	ATP binding|deoxycytidine kinase activity|drug binding|phosphotransferase activity, alcohol group as acceptor|protein homodimerization activity			ovary(1)	1			Lung(101;0.235)		Cladribine(DB00242)|Clofarabine(DB00631)|Decitabine(DB01262)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Pemetrexed(DB00642)|Zalcitabine(DB00943)													---	---	---	---
SLC4A4	8671	broad.mit.edu	37	4	72102101	72102101	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72102101delG	uc003hfy.2	+						SLC4A4_uc010iic.2_Intron|SLC4A4_uc010iib.2_Intron|SLC4A4_uc003hfz.2_5'Flank	NM_001098484	NP_001091954			solute carrier family 4, sodium bicarbonate							basolateral plasma membrane|integral to plasma membrane	inorganic anion exchanger activity|protein binding|sodium:bicarbonate symporter activity			ovary(3)|kidney(1)|skin(1)	5			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)															---	---	---	---
SLC4A4	8671	broad.mit.edu	37	4	72187994	72187994	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72187994delT	uc003hfy.2	+						SLC4A4_uc010iic.2_Intron|SLC4A4_uc010iib.2_Intron|SLC4A4_uc003hfz.2_Intron|SLC4A4_uc003hga.2_Intron	NM_001098484	NP_001091954			solute carrier family 4, sodium bicarbonate							basolateral plasma membrane|integral to plasma membrane	inorganic anion exchanger activity|protein binding|sodium:bicarbonate symporter activity			ovary(3)|kidney(1)|skin(1)	5			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	72558133	72558133	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72558133delA								SLC4A4 (120330 upstream) : GC (49280 downstream)																																			---	---	---	---
NPFFR2	10886	broad.mit.edu	37	4	73010210	73010210	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73010210delT	uc003hgg.2	+						NPFFR2_uc010iig.1_Intron|NPFFR2_uc003hgi.2_Intron|NPFFR2_uc003hgh.2_Intron|NPFFR2_uc003hgj.2_5'Flank	NM_004885	NP_004876			neuropeptide FF receptor 2 isoform 1						detection of abiotic stimulus	actin cytoskeleton|integral to plasma membrane	neuropeptide receptor activity			ovary(2)|central_nervous_system(1)	3			Lung(101;0.0935)|LUSC - Lung squamous cell carcinoma(112;0.138)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	73095116	73095116	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73095116delT								NPFFR2 (76368 upstream) : ADAMTS3 (51571 downstream)																																			---	---	---	---
ADAMTS3	9508	broad.mit.edu	37	4	73158464	73158465	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73158464_73158465insT	uc003hgk.1	-							NM_014243	NP_055058			ADAM metallopeptidase with thrombospondin type 1						collagen catabolic process|collagen fibril organization|proteolysis	proteinaceous extracellular matrix	heparin binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)	2			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	73651517	73651517	+	IGR	DEL	A	-	-	rs113640198		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73651517delA								ADAMTS3 (217001 upstream) : COX18 (268899 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	73871196	73871196	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73871196delA								ADAMTS3 (436680 upstream) : COX18 (49220 downstream)																																			---	---	---	---
ANKRD17	26057	broad.mit.edu	37	4	73941878	73941878	+	3'UTR	DEL	T	-	-	rs63678862		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73941878delT	uc003hgp.2	-	34					ANKRD17_uc003hgo.2_3'UTR|ANKRD17_uc003hgq.2_3'UTR|ANKRD17_uc003hgr.2_3'UTR	NM_032217	NP_115593			ankyrin repeat domain protein 17 isoform a						interspecies interaction between organisms	cytoplasm|nucleus	RNA binding			ovary(5)|skin(3)|upper_aerodigestive_tract(1)|lung(1)	10	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)															---	---	---	---
ANKRD17	26057	broad.mit.edu	37	4	74030513	74030515	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74030513_74030515delAAA	uc003hgp.2	-						ANKRD17_uc003hgo.2_Intron|ANKRD17_uc003hgq.2_Intron|ANKRD17_uc003hgr.2_Intron	NM_032217	NP_115593			ankyrin repeat domain protein 17 isoform a						interspecies interaction between organisms	cytoplasm|nucleus	RNA binding			ovary(5)|skin(3)|upper_aerodigestive_tract(1)|lung(1)	10	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	74910877	74910877	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74910877delA								CXCL3 (6387 upstream) : PPBPL2 (8878 downstream)																																			---	---	---	---
MTHFD2L	441024	broad.mit.edu	37	4	75008866	75008867	+	Intron	INS	-	AA	AA			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:75008866_75008867insAA	uc003hhn.1	+						MTHFD2L_uc011cbj.1_Intron|MTHFD2L_uc003hho.2_Intron	NM_001144978	NP_001138450			methylenetetrahydrofolate dehydrogenase 2-like						folic acid-containing compound biosynthetic process|histidine biosynthetic process|methionine biosynthetic process|one-carbon metabolic process|purine nucleotide biosynthetic process		binding|methenyltetrahydrofolate cyclohydrolase activity|methylenetetrahydrofolate dehydrogenase (NAD+) activity			ovary(1)|central_nervous_system(1)	2			all cancers(17;0.0101)|Lung(101;0.196)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	75574455	75574455	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:75574455delA								AREG (93824 upstream) : BTC (96993 downstream)																																			---	---	---	---
BTC	685	broad.mit.edu	37	4	75721694	75721694	+	5'Flank	DEL	C	-	-	rs11733938	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:75721694delC	uc003hig.2	-							NM_001729	NP_001720			betacellulin precursor						positive regulation of cell division|positive regulation of cell proliferation	extracellular space|integral to membrane|plasma membrane|soluble fraction	epidermal growth factor receptor binding|growth factor activity			central_nervous_system(1)|skin(1)	2			Lung(101;0.219)															---	---	---	---
PARM1	25849	broad.mit.edu	37	4	75946655	75946655	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:75946655delT	uc003hih.1	+							NM_015393	NP_056208			prostatic androgen-repressed message-1						positive regulation of telomerase activity	early endosome|endosome membrane|Golgi membrane|integral to membrane|late endosome|plasma membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	76751560	76751560	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76751560delA								USO1 (16196 upstream) : PPEF2 (29468 downstream)																																			---	---	---	---
CCDC158	339965	broad.mit.edu	37	4	77304580	77304581	+	Intron	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77304580_77304581delTC	uc003hkb.3	-						CCDC158_uc003hkd.2_Intron	NM_001042784	NP_001036249			coiled-coil domain containing 158											skin(3)|ovary(2)|pancreas(1)	6																		---	---	---	---
SHROOM3	57619	broad.mit.edu	37	4	77535186	77535187	+	Intron	INS	-	TTTG	TTTG	rs150463465	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77535186_77535187insTTTG	uc011cbx.1	+						uc011cby.1_Intron	NM_020859	NP_065910			shroom family member 3 protein						apical protein localization|cell morphogenesis|cellular pigment accumulation|pattern specification process|regulation of cell shape	adherens junction|apical junction complex|apical plasma membrane|cytoplasm|microtubule	actin binding			skin(2)|ovary(1)	3			Lung(101;0.0903)															---	---	---	---
Unknown	0	broad.mit.edu	37	4	77795209	77795209	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77795209delT								SHROOM3 (90806 upstream) : ANKRD56 (20874 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	78055039	78055040	+	IGR	INS	-	C	C	rs142477461	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78055039_78055040insC								CCNI (57914 upstream) : CCNG2 (23317 downstream)																																			---	---	---	---
CNOT6L	246175	broad.mit.edu	37	4	78636848	78636848	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78636848delT	uc011ccd.1	-	12					CNOT6L_uc003hks.2_3'UTR	NM_144571	NP_653172			CCR4-NOT transcription complex, subunit 6-like						nuclear-transcribed mRNA poly(A) tail shortening	cytosol	exonuclease activity|protein binding			large_intestine(1)	1																		---	---	---	---
CNOT6L	246175	broad.mit.edu	37	4	78695895	78695895	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78695895delA	uc011ccd.1	-						CNOT6L_uc003hks.2_Intron|CNOT6L_uc011cce.1_Intron	NM_144571	NP_653172			CCR4-NOT transcription complex, subunit 6-like						nuclear-transcribed mRNA poly(A) tail shortening	cytosol	exonuclease activity|protein binding			large_intestine(1)	1																		---	---	---	---
MRPL1	65008	broad.mit.edu	37	4	78818525	78818525	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78818525delA	uc003hku.2	+						MRPL1_uc010iji.1_Intron	NM_020236	NP_064621			mitochondrial ribosomal protein L1 precursor								RNA binding				0																		---	---	---	---
FRAS1	80144	broad.mit.edu	37	4	78993959	78993959	+	Intron	DEL	T	-	-	rs35214420		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:78993959delT	uc003hlb.2	+						FRAS1_uc003hkw.2_Intron	NM_025074	NP_079350			Fraser syndrome 1						cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5																		---	---	---	---
FRAS1	80144	broad.mit.edu	37	4	79322049	79322049	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79322049delT	uc003hlb.2	+						FRAS1_uc003hkw.2_Intron	NM_025074	NP_079350			Fraser syndrome 1						cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5																		---	---	---	---
BMP2K	55589	broad.mit.edu	37	4	79782784	79782784	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79782784delT	uc003hlk.2	+						BMP2K_uc010ijl.1_Intron|BMP2K_uc003hlj.2_Intron	NM_198892	NP_942595			BMP-2 inducible kinase isoform a							nucleus	ATP binding|protein serine/threonine kinase activity			lung(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	80110676	80110676	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:80110676delG	uc003hlr.1	+											Homo sapiens full length insert cDNA clone YY75G10.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	80619170	80619171	+	IGR	DEL	GT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:80619170_80619171delGT								GK2 (289798 upstream) : GDEP (129454 downstream)																																			---	---	---	---
C4orf22	255119	broad.mit.edu	37	4	81398115	81398116	+	Intron	DEL	GT	-	-	rs72214889		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:81398115_81398116delGT	uc003hmf.2	+						C4orf22_uc010ijp.2_Intron	NM_152770	NP_689983			hypothetical protein LOC255119											skin(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	82000841	82000841	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82000841delT								BMP3 (22157 upstream) : PRKG2 (8996 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	82008187	82008188	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82008187_82008188delTT								BMP3 (29503 upstream) : PRKG2 (1649 downstream)																																			---	---	---	---
RASGEF1B	153020	broad.mit.edu	37	4	82369488	82369488	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82369488delC	uc003hmi.1	-						RASGEF1B_uc003hmj.1_Intron|RASGEF1B_uc010ijq.1_Intron	NM_152545	NP_689758			RasGEF domain family, member 1B						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular	Ras guanyl-nucleotide exchange factor activity				0																		---	---	---	---
RASGEF1B	153020	broad.mit.edu	37	4	82384472	82384472	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82384472delA	uc003hmi.1	-						RASGEF1B_uc003hmj.1_Intron|RASGEF1B_uc010ijq.1_Intron|RASGEF1B_uc003hmk.2_Intron	NM_152545	NP_689758			RasGEF domain family, member 1B						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular	Ras guanyl-nucleotide exchange factor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	82414248	82414249	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82414248_82414249delAA								RASGEF1B (21187 upstream) : HNRNPD (860218 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	82618317	82618317	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:82618317delA								RASGEF1B (225256 upstream) : HNRNPD (656150 downstream)																																			---	---	---	---
SCD5	79966	broad.mit.edu	37	4	83575670	83575670	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83575670delT	uc003hna.2	-							NM_001037582	NP_001032671			stearoyl-CoA desaturase 5 isoform a						fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	iron ion binding|stearoyl-CoA 9-desaturase activity			ovary(1)	1		Colorectal(4;0.0323)|Hepatocellular(203;0.115)																---	---	---	---
SCD5	79966	broad.mit.edu	37	4	83695451	83695451	+	Intron	DEL	A	-	-	rs75468704		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83695451delA	uc003hna.2	-						SCD5_uc003hnb.3_Intron|SCD5_uc003hnc.2_Intron	NM_001037582	NP_001032671			stearoyl-CoA desaturase 5 isoform a						fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	iron ion binding|stearoyl-CoA 9-desaturase activity			ovary(1)	1		Colorectal(4;0.0323)|Hepatocellular(203;0.115)																---	---	---	---
SEC31A	22872	broad.mit.edu	37	4	83784550	83784550	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83784550delA	uc003hnf.2	-						SEC31A_uc003hne.2_Intron|SEC31A_uc011ccl.1_Intron|SEC31A_uc003hnl.2_Intron|SEC31A_uc003hng.2_Intron|SEC31A_uc003hnh.2_Intron|SEC31A_uc003hni.2_Intron|SEC31A_uc003hnj.2_Intron|SEC31A_uc011ccm.1_Intron|SEC31A_uc011ccn.1_Intron|SEC31A_uc003hnk.2_Intron|SEC31A_uc003hnm.2_Intron|SEC31A_uc003hnn.1_Intron|SEC31A_uc003hno.2_Intron	NM_001077207	NP_001070675			SEC31 homolog A isoform 1						COPII vesicle coating|post-translational protein modification|protein N-linked glycosylation via asparagine|protein transport|response to calcium ion	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|perinuclear region of cytoplasm	calcium-dependent protein binding		SEC31A/JAK2(4)|SEC31A/ALK(3)	haematopoietic_and_lymphoid_tissue(4)|soft_tissue(3)|breast(1)	8		Hepatocellular(203;0.114)																---	---	---	---
COPS4	51138	broad.mit.edu	37	4	83977952	83977952	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83977952delA	uc003hoa.2	+						COPS4_uc003hob.2_Intron|COPS4_uc010ijw.2_Intron|COPS4_uc010ijx.2_Intron	NM_016129	NP_057213			COP9 signalosome subunit 4						cullin deneddylation	cytoplasm|signalosome	protein binding			kidney(1)	1		Hepatocellular(203;0.114)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	84063051	84063051	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84063051delT								PLAC8 (27140 upstream) : COQ2 (119638 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	84078902	84078902	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84078902delT								PLAC8 (42991 upstream) : COQ2 (103787 downstream)																																			---	---	---	---
AGPAT9	84803	broad.mit.edu	37	4	84511241	84511242	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84511241_84511242delAA	uc003how.2	+						AGPAT9_uc003hox.2_Intron|AGPAT9_uc003hoy.2_Intron	NM_032717	NP_116106			1-acylglycerol-3-phosphate O-acyltransferase 9						phospholipid biosynthetic process|regulation of TOR signaling cascade|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane	glycerol-3-phosphate O-acyltransferase activity			skin(1)	1		Hepatocellular(203;0.114)																---	---	---	---
AGPAT9	84803	broad.mit.edu	37	4	84517996	84517996	+	Intron	DEL	T	-	-	rs79149035		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84517996delT	uc003how.2	+						AGPAT9_uc003hox.2_Intron|AGPAT9_uc003hoy.2_Intron	NM_032717	NP_116106			1-acylglycerol-3-phosphate O-acyltransferase 9						phospholipid biosynthetic process|regulation of TOR signaling cascade|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane	glycerol-3-phosphate O-acyltransferase activity			skin(1)	1		Hepatocellular(203;0.114)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	84786288	84786288	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84786288delT	uc010ikd.1	-											Homo sapiens cDNA FLJ37966 fis, clone CTONG2009871.																														---	---	---	---
NKX6-1	4825	broad.mit.edu	37	4	85419122	85419122	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85419122delG	uc003hpa.1	-	1	266	c.260delC	c.(259-261)CCGfs	p.P87fs		NM_006168	NP_006159	P78426	NKX61_HUMAN	NK6 transcription factor related, locus 1	87					detection of glucose|negative regulation of transcription from RNA polymerase II promoter|organ morphogenesis|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of type B pancreatic cell development|type B pancreatic cell maturation	nucleus					0		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.0013)														---	---	---	---
WDFY3	23001	broad.mit.edu	37	4	85674763	85674763	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85674763delA	uc003hpd.2	-							NM_014991	NP_055806			WD repeat and FYVE domain containing 3 isoform							cytoplasmic part|extrinsic to membrane|nuclear envelope	1-phosphatidylinositol binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)														---	---	---	---
C4orf12	404201	broad.mit.edu	37	4	85896698	85896699	+	Intron	INS	-	CA	CA	rs142195208	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:85896698_85896699insCA	uc003hph.2	+						C4orf12_uc003hpg.2_Intron	NR_015359				Homo sapiens C4ORF12 protein (C4ORF12) mRNA, complete cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	86145452	86145452	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:86145452delG								C4orf12 (217284 upstream) : ARHGAP24 (250832 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	86180954	86180957	+	IGR	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:86180954_86180957delTTTT								C4orf12 (252786 upstream) : ARHGAP24 (215327 downstream)																																			---	---	---	---
MAPK10	5602	broad.mit.edu	37	4	87080311	87080311	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87080311delT	uc003hpq.2	-						MAPK10_uc010ikg.2_Intron|MAPK10_uc003hpr.2_Intron|MAPK10_uc003hps.2_Intron|MAPK10_uc003hpt.2_Intron|MAPK10_uc003hpu.2_Intron|MAPK10_uc003hpv.2_Intron|MAPK10_uc010ikh.1_Intron|uc003hpw.2_Intron	NM_138982	NP_620448			mitogen-activated protein kinase 10 isoform 2						innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|regulation of sequence-specific DNA binding transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|JUN kinase activity|MAP kinase kinase activity|protein binding			stomach(1)|breast(1)|central_nervous_system(1)	3		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.243)		OV - Ovarian serous cystadenocarcinoma(123;0.002)														---	---	---	---
AFF1	4299	broad.mit.edu	37	4	87973777	87973777	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87973777delT	uc003hqj.3	+						AFF1_uc003hqh.1_Intron|AFF1_uc011ccy.1_Intron|AFF1_uc011ccz.1_Intron|AFF1_uc003hqk.3_Intron|AFF1_uc011cda.1_Intron	NM_005935	NP_005926			myeloid/lymphoid or mixed-lineage leukemia							nucleus	sequence-specific DNA binding transcription factor activity			breast(1)	1		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)														---	---	---	---
AFF1	4299	broad.mit.edu	37	4	87986663	87986664	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87986663_87986664delAA	uc003hqj.3	+						AFF1_uc003hqh.1_Intron|AFF1_uc011ccy.1_Intron|AFF1_uc011ccz.1_Intron|AFF1_uc003hqk.3_Intron|AFF1_uc011cda.1_Intron	NM_005935	NP_005926			myeloid/lymphoid or mixed-lineage leukemia							nucleus	sequence-specific DNA binding transcription factor activity			breast(1)	1		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)														---	---	---	---
AFF1	4299	broad.mit.edu	37	4	88034443	88034443	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88034443delT	uc003hqj.3	+						AFF1_uc011ccz.1_Intron|AFF1_uc003hqk.3_Intron|AFF1_uc011cda.1_Intron	NM_005935	NP_005926			myeloid/lymphoid or mixed-lineage leukemia							nucleus	sequence-specific DNA binding transcription factor activity			breast(1)	1		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)														---	---	---	---
KLHL8	57563	broad.mit.edu	37	4	88083118	88083118	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88083118delT	uc011cdb.1	-	10					KLHL8_uc003hql.1_3'UTR|KLHL8_uc003hqm.1_3'UTR|KLHL8_uc003hqn.1_3'UTR|KLHL8_uc010ikj.1_3'UTR	NM_020803	NP_065854			kelch-like 8												0		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)														---	---	---	---
KLHL8	57563	broad.mit.edu	37	4	88102746	88102748	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88102746_88102748delAAA	uc011cdb.1	-						KLHL8_uc003hql.1_Intron|KLHL8_uc003hqm.1_Intron|KLHL8_uc003hqn.1_Intron|KLHL8_uc010ikj.1_Intron	NM_020803	NP_065854			kelch-like 8												0		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	88180869	88180875	+	IGR	DEL	TTTCTTT	-	-	rs72429385		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88180869_88180875delTTTCTTT								KLHL8 (39195 upstream) : HSD17B13 (44066 downstream)																																			---	---	---	---
HSD17B13	345275	broad.mit.edu	37	4	88226474	88226474	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88226474delA	uc003hqo.2	-						HSD17B13_uc010ikk.2_Intron	NM_178135	NP_835236			hydroxysteroid (17-beta) dehydrogenase 13							extracellular region	binding|oxidoreductase activity				0		Acute lymphoblastic leukemia(40;0.244)|all_hematologic(202;0.248)		OV - Ovarian serous cystadenocarcinoma(123;0.000308)														---	---	---	---
SPARCL1	8404	broad.mit.edu	37	4	88423821	88423822	+	Intron	INS	-	T	T	rs138666989	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88423821_88423822insT	uc010ikm.2	-						SPARCL1_uc011cdc.1_Intron|SPARCL1_uc003hqs.3_Intron|SPARCL1_uc011cdd.1_Intron|SPARCL1_uc003hqt.2_Intron	NM_001128310	NP_001121782			SPARC-like 1 precursor						signal transduction	extracellular space|proteinaceous extracellular matrix	calcium ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(123;0.00118)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	88455311	88455312	+	IGR	INS	-	A	A	rs149905472	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88455311_88455312insA								SPARCL1 (4656 upstream) : DSPP (74369 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	88660523	88660524	+	IGR	INS	-	ATC	ATC	rs147498957	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88660523_88660524insATC								DMP1 (75013 upstream) : IBSP (60178 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	89269443	89269443	+	IGR	DEL	G	-	-	rs2196938	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89269443delG								PPM1K (63555 upstream) : HERC6 (30448 downstream)																																			---	---	---	---
HERC5	51191	broad.mit.edu	37	4	89425218	89425220	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89425218_89425220delAAA	uc003hrt.2	+						HERC5_uc011cdm.1_Intron	NM_016323	NP_057407			hect domain and RLD 5						innate immune response|ISG15-protein conjugation|negative regulation of type I interferon production|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of cyclin-dependent protein kinase activity|regulation of defense response to virus|response to virus	cytosol|perinuclear region of cytoplasm	ISG15 ligase activity|protein binding|ubiquitin-protein ligase activity			ovary(4)|lung(3)|skin(2)	9		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000209)														---	---	---	---
HERC3	8916	broad.mit.edu	37	4	89511418	89511419	+	5'Flank	INS	-	A	A	rs35519732		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89511418_89511419insA	uc003hrw.1	+						HERC3_uc003hrv.2_5'Flank|HERC3_uc011cdn.1_5'Flank	NM_014606	NP_055421			hect domain and RLD 3						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasmic membrane-bounded vesicle	ubiquitin-protein ligase activity			lung(2)|prostate(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(123;0.000319)														---	---	---	---
HERC3	8916	broad.mit.edu	37	4	89528323	89528324	+	Intron	INS	-	GT	GT	rs145067863	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89528323_89528324insGT	uc003hrw.1	+						HERC3_uc003hrv.2_Intron|HERC3_uc011cdn.1_Intron	NM_014606	NP_055421			hect domain and RLD 3						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasmic membrane-bounded vesicle	ubiquitin-protein ligase activity			lung(2)|prostate(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(123;0.000319)														---	---	---	---
FAM13A	10144	broad.mit.edu	37	4	89824025	89824025	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89824025delA	uc003hse.1	-						FAM13A_uc003hsf.1_Intron|FAM13A_uc003hsh.1_Intron	NM_014883	NP_055698			family with sequence similarity 13, member A1						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(1)|liver(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	90448728	90448728	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90448728delA								GPRIN3 (219567 upstream) : SNCA (196523 downstream)																																			---	---	---	---
SNCA	6622	broad.mit.edu	37	4	90696852	90696853	+	Intron	DEL	GT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90696852_90696853delGT	uc003hsq.2	-						SNCA_uc010ikt.2_Intron|SNCA_uc003hso.2_Intron|SNCA_uc003hsp.2_Intron|SNCA_uc003hsr.2_Intron	NM_001146054	NP_001139526			alpha-synuclein isoform NACP140						activation of caspase activity|anti-apoptosis|negative regulation of dopamine uptake|negative regulation of exocytosis|negative regulation of histone acetylation|negative regulation of microtubule polymerization|negative regulation of monooxygenase activity|negative regulation of norepinephrine uptake|negative regulation of platelet-derived growth factor receptor signaling pathway|negative regulation of serotonin uptake|negative regulation of thrombin receptor signaling pathway|negative regulation of transporter activity|positive regulation of endocytosis|positive regulation of inositol phosphate biosynthetic process|positive regulation of peptidyl-serine phosphorylation|positive regulation of protein serine/threonine kinase activity|positive regulation of receptor recycling|positive regulation of release of sequestered calcium ion into cytosol|receptor internalization|regulation of phospholipase activity|response to interferon-gamma|response to interleukin-1|response to iron(II) ion|response to lipopolysaccharide|response to magnesium ion|synaptic vesicle endocytosis	actin cytoskeleton|axon|cell cortex|cell junction|cytosol|fibril|growth cone|nucleus|synapse	alpha-tubulin binding|calcium ion binding|caspase inhibitor activity|dynein binding|ferrous iron binding|histone binding|Hsp70 protein binding|kinesin binding|magnesium ion binding|phosphoprotein binding|tau protein binding|zinc ion binding				0		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;7.42e-05)	Melatonin(DB01065)													---	---	---	---
MMRN1	22915	broad.mit.edu	37	4	90849243	90849243	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90849243delT	uc003hst.2	+						MMRN1_uc010iku.2_Intron|MMRN1_uc011cds.1_Intron	NM_007351	NP_031377			multimerin 1						cell adhesion|platelet activation|platelet degranulation	extracellular region|platelet alpha granule lumen				ovary(4)	4		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)														---	---	---	---
FAM190A	401145	broad.mit.edu	37	4	91676432	91676432	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:91676432delT	uc003hsv.3	+						FAM190A_uc010ikv.2_Intron|FAM190A_uc003hsw.2_Intron|FAM190A_uc003hsx.2_Intron	NM_001145065	NP_001138537			KIAA1680 protein isoform 1											large_intestine(1)|ovary(1)	2																		---	---	---	---
FAM190A	401145	broad.mit.edu	37	4	92124801	92124801	+	Intron	DEL	A	-	-	rs66685434		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:92124801delA	uc003hsv.3	+							NM_001145065	NP_001138537			KIAA1680 protein isoform 1											large_intestine(1)|ovary(1)	2																		---	---	---	---
FAM190A	401145	broad.mit.edu	37	4	92187411	92187411	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:92187411delT	uc003hsv.3	+							NM_001145065	NP_001138537			KIAA1680 protein isoform 1											large_intestine(1)|ovary(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	93208584	93208584	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:93208584delG								FAM190A (685215 upstream) : GRID2 (16966 downstream)																																			---	---	---	---
GRID2	2895	broad.mit.edu	37	4	94092006	94092008	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94092006_94092008delTTT	uc011cdt.1	+						GRID2_uc010ikx.2_Intron|GRID2_uc011cdu.1_Intron|GRID2_uc011cdv.1_Intron	NM_001510	NP_001501			glutamate receptor, ionotropic, delta 2						glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)													---	---	---	---
GRID2	2895	broad.mit.edu	37	4	94182305	94182305	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94182305delA	uc011cdt.1	+						GRID2_uc011cdu.1_Intron|GRID2_uc010ikz.1_Intron	NM_001510	NP_001501			glutamate receptor, ionotropic, delta 2						glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)													---	---	---	---
GRID2	2895	broad.mit.edu	37	4	94384350	94384350	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94384350delA	uc011cdt.1	+						GRID2_uc011cdu.1_Intron	NM_001510	NP_001501			glutamate receptor, ionotropic, delta 2						glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)													---	---	---	---
GRID2	2895	broad.mit.edu	37	4	94432931	94432931	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94432931delT	uc011cdt.1	+						GRID2_uc011cdu.1_Intron	NM_001510	NP_001501			glutamate receptor, ionotropic, delta 2						glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)													---	---	---	---
GRID2	2895	broad.mit.edu	37	4	94441491	94441492	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94441491_94441492delAA	uc011cdt.1	+						GRID2_uc011cdu.1_Intron	NM_001510	NP_001501			glutamate receptor, ionotropic, delta 2						glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)													---	---	---	---
GRID2	2895	broad.mit.edu	37	4	94580315	94580315	+	Intron	DEL	A	-	-	rs74384371		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94580315delA	uc011cdt.1	+						GRID2_uc011cdu.1_Intron	NM_001510	NP_001501			glutamate receptor, ionotropic, delta 2						glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)													---	---	---	---
SMARCAD1	56916	broad.mit.edu	37	4	95163097	95163098	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95163097_95163098insT	uc003htc.3	+						SMARCAD1_uc003htb.3_Intron|SMARCAD1_uc003htd.3_Intron|SMARCAD1_uc010ila.2_Intron	NM_020159	NP_064544			SWI/SNF-related, matrix-associated						chromatin modification|nucleotide metabolic process|positive regulation of transcription, DNA-dependent|protein homooligomerization|regulation of DNA recombination	nuclear matrix	ATP binding|DNA binding|helicase activity			skin(2)|ovary(1)|breast(1)	4				OV - Ovarian serous cystadenocarcinoma(123;4.33e-08)														---	---	---	---
HPGDS	27306	broad.mit.edu	37	4	95254148	95254148	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95254148delA	uc003hte.1	-							NM_014485	NP_055300			prostaglandin D2 synthase, hematopoietic						locomotory behavior|prostaglandin biosynthetic process|signal transduction	cytoplasm|nucleus	calcium ion binding|glutathione transferase activity|magnesium ion binding|prostaglandin-D synthase activity|protein homodimerization activity			ovary(1)	1					Glutathione(DB00143)													---	---	---	---
PDLIM5	10611	broad.mit.edu	37	4	95550485	95550485	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95550485delA	uc003hti.2	+						PDLIM5_uc011cdx.1_Intron|PDLIM5_uc003hth.2_Intron|PDLIM5_uc003htj.2_Intron|PDLIM5_uc003htk.2_Intron|PDLIM5_uc011cdy.1_Intron|PDLIM5_uc003htl.2_Intron	NM_006457	NP_006448			PDZ and LIM domain 5 isoform a						regulation of dendritic spine morphogenesis|regulation of synaptogenesis	actin cytoskeleton|cell junction|cytosol|postsynaptic density|postsynaptic membrane|synaptosome	actin binding|actinin binding|protein kinase C binding|zinc ion binding			ovary(1)|skin(1)	2		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.84e-09)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	95658955	95658956	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95658955_95658956delAA								PDLIM5 (69579 upstream) : BMPR1B (20172 downstream)																																			---	---	---	---
UNC5C	8633	broad.mit.edu	37	4	96225726	96225726	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:96225726delT	uc003htp.1	-						UNC5C_uc010ilc.1_Intron|UNC5C_uc003htq.2_Intron	NM_003728	NP_003719			unc5C precursor						apoptosis|axon guidance|brain development	integral to membrane	netrin receptor activity			ovary(3)|pancreas(1)	4		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)														---	---	---	---
UNC5C	8633	broad.mit.edu	37	4	96279254	96279254	+	Intron	DEL	A	-	-	rs76935495		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:96279254delA	uc003htp.1	-						UNC5C_uc010ilc.1_Intron|UNC5C_uc003htq.2_Intron	NM_003728	NP_003719			unc5C precursor						apoptosis|axon guidance|brain development	integral to membrane	netrin receptor activity			ovary(3)|pancreas(1)	4		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	96825247	96825247	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:96825247delA								PDHA2 (62623 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	96910004	96910004	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:96910004delT								PDHA2 (147380 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	96956640	96956640	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:96956640delT								PDHA2 (194016 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	97352939	97352939	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:97352939delT								PDHA2 (590315 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	97564651	97564652	+	IGR	DEL	TT	-	-	rs33922461		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:97564651_97564652delTT								PDHA2 (802027 upstream) : C4orf37 (915382 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	97827402	97827402	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:97827402delA								None (None upstream) : C4orf37 (652632 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	98183542	98183542	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:98183542delA								None (None upstream) : C4orf37 (296492 downstream)																																			---	---	---	---
C4orf37	285555	broad.mit.edu	37	4	98947473	98947473	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:98947473delA	uc003htt.1	-							NM_174952	NP_777612			hypothetical protein LOC285555												0				OV - Ovarian serous cystadenocarcinoma(123;2.27e-08)														---	---	---	---
C4orf37	285555	broad.mit.edu	37	4	98982969	98982969	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:98982969delA	uc003htt.1	-							NM_174952	NP_777612			hypothetical protein LOC285555												0				OV - Ovarian serous cystadenocarcinoma(123;2.27e-08)														---	---	---	---
EIF4E	1977	broad.mit.edu	37	4	99836461	99836463	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99836461_99836463delAAA	uc003hue.2	-						EIF4E_uc011cea.1_Intron|EIF4E_uc011ceb.1_Intron|EIF4E_uc011cec.1_Intron	NM_001968	NP_001959			eukaryotic translation initiation factor 4E						G1/S transition of mitotic cell cycle|insulin receptor signaling pathway|interspecies interaction between organisms|mRNA export from nucleus|nuclear-transcribed mRNA poly(A) tail shortening|positive regulation of mitotic cell cycle|regulation of translation	cytoplasmic mRNA processing body|cytosol|eukaryotic translation initiation factor 4F complex|mRNA cap binding complex|RNA-induced silencing complex	protein binding|RNA cap binding|translation initiation factor activity			lung(1)|central_nervous_system(1)	2				OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)|LUSC - Lung squamous cell carcinoma(721;0.00227)														---	---	---	---
METAP1	23173	broad.mit.edu	37	4	99960366	99960367	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99960366_99960367insT	uc003huf.3	+						METAP1_uc003hug.2_Intron	NM_015143	NP_055958			methionyl aminopeptidase 1						N-terminal protein amino acid modification|peptidyl-methionine modification|proteolysis|regulation of translation	cytoplasm	aminopeptidase activity|metal ion binding|metalloexopeptidase activity|protein binding				0				OV - Ovarian serous cystadenocarcinoma(123;3.12e-07)														---	---	---	---
MTTP	4547	broad.mit.edu	37	4	100512170	100512170	+	Intron	DEL	A	-	-	rs34244951		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100512170delA	uc003hvc.3	+						MTTP_uc011cej.1_Intron	NM_000253	NP_000244			microsomal triglyceride transfer protein large						lipid metabolic process|lipoprotein metabolic process	endoplasmic reticulum lumen	lipid binding|lipid transporter activity			ovary(3)|central_nervous_system(1)	4				OV - Ovarian serous cystadenocarcinoma(123;6.04e-09)	Hesperetin(DB01094)													---	---	---	---
DAPP1	27071	broad.mit.edu	37	4	100789086	100789087	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100789086_100789087delAA	uc003hvf.3	+						DAPP1_uc010ilh.2_Intron	NM_014395	NP_055210			dual adaptor of phosphotyrosine and						signal transduction	cytoplasm|plasma membrane	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|protein tyrosine phosphatase activity				0				OV - Ovarian serous cystadenocarcinoma(123;7.04e-09)														---	---	---	---
DNAJB14	79982	broad.mit.edu	37	4	100829887	100829887	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100829887delA	uc003hvl.2	-	4	769	c.618delT	c.(616-618)TTTfs	p.F206fs	DNAJB14_uc003hvk.2_Frame_Shift_Del_p.F121fs|DNAJB14_uc010ili.2_Frame_Shift_Del_p.F139fs	NM_001031723	NP_001026893	Q8TBM8	DJB14_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 14	206					protein folding	integral to membrane	heat shock protein binding|unfolded protein binding				0				OV - Ovarian serous cystadenocarcinoma(123;4.59e-09)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	101216255	101216255	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:101216255delT								DDIT4L (104642 upstream) : EMCN (100245 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	101751402	101751403	+	IGR	DEL	CT	-	-	rs72280798		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:101751402_101751403delCT								EMCN (312152 upstream) : PPP3CA (193184 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	101902973	101902974	+	IGR	DEL	AA	-	-	rs11415329		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:101902973_101902974delAA								EMCN (463723 upstream) : PPP3CA (41613 downstream)																																			---	---	---	---
PPP3CA	5530	broad.mit.edu	37	4	101953593	101953593	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:101953593delA	uc011cen.1	-						PPP3CA_uc003hvu.2_Intron|PPP3CA_uc010ilj.2_Intron|PPP3CA_uc003hvt.2_Intron|PPP3CA_uc003hvs.2_Intron|PPP3CA_uc010ilk.2_Intron	NM_000944	NP_000935			protein phosphatase 3, catalytic subunit, alpha						protein dephosphorylation	calcineurin complex|cytosol|nucleus	calcium ion binding|calmodulin binding			ovary(1)|skin(1)	2				OV - Ovarian serous cystadenocarcinoma(123;6.79e-08)														---	---	---	---
PPP3CA	5530	broad.mit.edu	37	4	102211760	102211760	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:102211760delA	uc011cen.1	-						PPP3CA_uc003hvu.2_Intron|PPP3CA_uc010ilj.2_Intron|PPP3CA_uc003hvt.2_Intron|PPP3CA_uc003hvs.2_Intron|PPP3CA_uc010ilk.2_Intron	NM_000944	NP_000935			protein phosphatase 3, catalytic subunit, alpha						protein dephosphorylation	calcineurin complex|cytosol|nucleus	calcium ion binding|calmodulin binding			ovary(1)|skin(1)	2				OV - Ovarian serous cystadenocarcinoma(123;6.79e-08)														---	---	---	---
BANK1	55024	broad.mit.edu	37	4	102357037	102357037	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:102357037delT	uc003hvx.3	+							NM_001083907	NP_001077376			B-cell scaffold protein with ankyrin repeats 1						B cell activation					ovary(2)|skin(1)	3		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)														---	---	---	---
BANK1	55024	broad.mit.edu	37	4	102460645	102460645	+	Intron	DEL	A	-	-	rs146698769		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:102460645delA	uc003hvx.3	+							NM_001083907	NP_001077376			B-cell scaffold protein with ankyrin repeats 1						B cell activation					ovary(2)|skin(1)	3		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)														---	---	---	---
BANK1	55024	broad.mit.edu	37	4	102476522	102476522	+	Intron	DEL	A	-	-	rs5860681		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:102476522delA	uc003hvx.3	+							NM_001083907	NP_001077376			B-cell scaffold protein with ankyrin repeats 1						B cell activation					ovary(2)|skin(1)	3		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)														---	---	---	---
BANK1	55024	broad.mit.edu	37	4	102514174	102514174	+	Intron	DEL	G	-	-	rs34222436		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:102514174delG	uc003hvx.3	+							NM_001083907	NP_001077376			B-cell scaffold protein with ankyrin repeats 1						B cell activation					ovary(2)|skin(1)	3		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)														---	---	---	---
BANK1	55024	broad.mit.edu	37	4	102571443	102571443	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:102571443delA	uc003hvx.3	+							NM_001083907	NP_001077376			B-cell scaffold protein with ankyrin repeats 1						B cell activation					ovary(2)|skin(1)	3		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)														---	---	---	---
BANK1	55024	broad.mit.edu	37	4	102894214	102894214	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:102894214delT	uc003hvy.3	+						BANK1_uc003hvx.3_Intron|BANK1_uc010ill.2_Intron|BANK1_uc003hvz.3_Intron	NM_017935	NP_060405			B-cell scaffold protein with ankyrin repeats 1						B cell activation					ovary(2)|skin(1)	3		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)														---	---	---	---
BANK1	55024	broad.mit.edu	37	4	102965187	102965187	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:102965187delT	uc003hvy.3	+						BANK1_uc003hvx.3_Intron|BANK1_uc010ill.2_Intron|BANK1_uc003hvz.3_Intron	NM_017935	NP_060405			B-cell scaffold protein with ankyrin repeats 1						B cell activation					ovary(2)|skin(1)	3		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	103163283	103163284	+	IGR	INS	-	T	T	rs151212536	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103163283_103163284insT								BANK1 (167316 upstream) : SLC39A8 (8914 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	103388071	103388071	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103388071delA								SLC39A8 (121416 upstream) : NFKB1 (34415 downstream)																																			---	---	---	---
NFKB1	4790	broad.mit.edu	37	4	103501922	103501923	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:103501922_103501923insA	uc011ceq.1	+						NFKB1_uc011cep.1_Intron|NFKB1_uc011cer.1_Intron	NM_003998	NP_003989			nuclear factor kappa-B, subunit 1 isoform 1						anti-apoptosis|apoptosis|cellular response to mechanical stimulus|inflammatory response|innate immune response|membrane protein intracellular domain proteolysis|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of calcidiol 1-monooxygenase activity|nerve growth factor receptor signaling pathway|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription, DNA-dependent|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transcription from RNA polymerase II promoter	cytosol|I-kappaB/NF-kappaB complex|mitochondrion|nucleoplasm	protein binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			ovary(2)|breast(2)|skin(1)	5		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.59e-08)	Dexamethasone(DB01234)|Pranlukast(DB01411)|Thalidomide(DB01041)													---	---	---	---
CENPE	1062	broad.mit.edu	37	4	104073426	104073426	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104073426delA	uc003hxb.1	-						CENPE_uc003hxc.1_Intron	NM_001813	NP_001804			centromere protein E						blood coagulation|cell division|kinetochore assembly|microtubule-based movement|mitotic chromosome movement towards spindle pole|mitotic metaphase|mitotic metaphase plate congression|mitotic prometaphase|multicellular organismal development|positive regulation of protein kinase activity	condensed chromosome kinetochore|cytosol|microtubule|nucleus|spindle	ATP binding|kinetochore binding|microtubule motor activity			ovary(5)|breast(4)	9				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	104289604	104289604	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104289604delT								CENPE (170038 upstream) : TACR3 (221021 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	105596789	105596790	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:105596789_105596790insT	uc003hxh.1	+											Homo sapiens cDNA FLJ37242 fis, clone BRAMY2004335.																														---	---	---	---
TET2	54790	broad.mit.edu	37	4	106149879	106149879	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106149879delT	uc003hxk.2	+						TET2_uc011cez.1_Intron|TET2_uc010ilp.1_Intron|TET2_uc003hxi.1_Intron	NM_001127208	NP_001120680			tet oncogene family member 2 isoform a						cell cycle|myeloid cell differentiation		metal ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			haematopoietic_and_lymphoid_tissue(732)|pancreas(1)	733		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)				Mis N|F		MDS								---	---	---	---
GSTCD	79807	broad.mit.edu	37	4	106692290	106692290	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106692290delT	uc003hxz.3	+						GSTCD_uc003hxx.2_Intron|GSTCD_uc003hxy.3_Intron|GSTCD_uc011cfb.1_Intron	NM_001031720	NP_001026890			glutathione S-transferase, C-terminal domain							cytoplasm	rRNA methyltransferase activity			breast(1)|central_nervous_system(1)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.15e-07)|READ - Rectum adenocarcinoma(30;0.139)														---	---	---	---
TBCK	93627	broad.mit.edu	37	4	106977723	106977725	+	Intron	DEL	TTT	-	-	rs71586121		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106977723_106977725delTTT	uc010ilv.2	-						TBCK_uc003hyb.2_Intron|TBCK_uc003hye.2_Intron|TBCK_uc003hyc.2_Intron|TBCK_uc003hyd.2_Intron|TBCK_uc003hyf.2_Intron	NM_001163435	NP_001156907			TBC domain-containing protein kinase-like							intracellular	Rab GTPase activator activity			large_intestine(2)|upper_aerodigestive_tract(1)|stomach(1)|ovary(1)	5																		---	---	---	---
TBCK	93627	broad.mit.edu	37	4	107080192	107080193	+	Intron	DEL	AA	-	-	rs74774924		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:107080192_107080193delAA	uc010ilv.2	-						TBCK_uc003hyb.2_Intron|TBCK_uc003hye.2_Intron|TBCK_uc003hyc.2_Intron|TBCK_uc003hyd.2_Intron|TBCK_uc003hyf.2_Intron	NM_001163435	NP_001156907			TBC domain-containing protein kinase-like							intracellular	Rab GTPase activator activity			large_intestine(2)|upper_aerodigestive_tract(1)|stomach(1)|ovary(1)	5																		---	---	---	---
AIMP1	9255	broad.mit.edu	37	4	107258917	107258917	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:107258917delT	uc011cfg.1	+						AIMP1_uc003hyg.2_Intron|AIMP1_uc003hyh.2_Intron	NM_001142415	NP_001135887			small inducible cytokine subfamily E, member 1						angiogenesis|apoptosis|cell adhesion|cell-cell signaling|chemotaxis|glucose metabolic process|inflammatory response|leukocyte migration|negative regulation of endothelial cell proliferation|signal transduction|tRNA aminoacylation for protein translation	aminoacyl-tRNA synthetase multienzyme complex|cytosol|endoplasmic reticulum|extracellular space|Golgi apparatus|nucleus|transport vesicle	cell surface binding|cytokine activity|protein homodimerization activity|tRNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	107342446	107342446	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:107342446delT								AIMP1 (72067 upstream) : DKK2 (500514 downstream)																																			---	---	---	---
DKK2	27123	broad.mit.edu	37	4	107883754	107883754	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:107883754delA	uc003hyi.2	-						DKK2_uc010ilw.1_Intron|DKK2_uc003hyj.1_Intron	NM_014421	NP_055236			dickkopf homolog 2 precursor						multicellular organismal development|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	extracellular space				ovary(3)|lung(1)|skin(1)	5		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.34e-06)														---	---	---	---
PAPSS1	9061	broad.mit.edu	37	4	108536250	108536251	+	Intron	DEL	TC	-	-	rs142730607	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:108536250_108536251delTC	uc003hyk.2	-							NM_005443	NP_005434			3'-phosphoadenosine 5'-phosphosulfate synthase						3'-phosphoadenosine 5'-phosphosulfate biosynthetic process|skeletal system development|sulfate assimilation|xenobiotic metabolic process	cytosol	adenylylsulfate kinase activity|ATP binding|sulfate adenylyltransferase (ATP) activity			ovary(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.49e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	109116575	109116576	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109116575_109116576delTT								LEF1 (26997 upstream) : LOC285456 (342770 downstream)																																			---	---	---	---
RPL34	6164	broad.mit.edu	37	4	109546421	109546421	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109546421delT	uc003hyz.2	+						RPL34_uc003hza.2_Intron	NM_000995	NP_000986			ribosomal protein L34						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	protein binding|RNA binding|structural constituent of ribosome				0		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000286)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	109653854	109653857	+	IGR	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109653854_109653857delTTTT								OSTC (64874 upstream) : AGXT2L1 (9347 downstream)																																			---	---	---	---
COL25A1	84570	broad.mit.edu	37	4	109752263	109752264	+	Intron	INS	-	T	T	rs140722957	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109752263_109752264insT	uc003hze.1	-						COL25A1_uc003hzg.2_Intron|COL25A1_uc003hzd.2_Intron|COL25A1_uc003hzf.2_Intron	NM_198721	NP_942014			collagen, type XXV, alpha 1 isoform 1							collagen|extracellular space	beta-amyloid binding|heparin binding			ovary(2)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)														---	---	---	---
COL25A1	84570	broad.mit.edu	37	4	109852959	109852959	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109852959delA	uc003hze.1	-						COL25A1_uc003hzg.2_Intron|COL25A1_uc003hzd.2_Intron|COL25A1_uc003hzf.2_Intron	NM_198721	NP_942014			collagen, type XXV, alpha 1 isoform 1							collagen|extracellular space	beta-amyloid binding|heparin binding			ovary(2)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)														---	---	---	---
COL25A1	84570	broad.mit.edu	37	4	109981365	109981365	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109981365delA	uc003hze.1	-						COL25A1_uc003hzg.2_Intron|COL25A1_uc003hzh.1_Intron	NM_198721	NP_942014			collagen, type XXV, alpha 1 isoform 1							collagen|extracellular space	beta-amyloid binding|heparin binding			ovary(2)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)														---	---	---	---
SEC24B	10427	broad.mit.edu	37	4	110442149	110442149	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110442149delA	uc003hzk.2	+						SEC24B_uc003hzl.2_Intron|SEC24B_uc011cfp.1_Intron|SEC24B_uc011cfq.1_Intron|SEC24B_uc011cfr.1_Intron	NM_006323	NP_006314			SEC24 (S. cerevisiae) homolog B isoform a						COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|Golgi membrane|perinuclear region of cytoplasm	protein binding|transporter activity|zinc ion binding			ovary(2)|large_intestine(1)	3		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)														---	---	---	---
SEC24B	10427	broad.mit.edu	37	4	110449587	110449590	+	Intron	DEL	AAAA	-	-	rs35976480		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110449587_110449590delAAAA	uc003hzk.2	+						SEC24B_uc003hzl.2_Intron|SEC24B_uc011cfp.1_Intron|SEC24B_uc011cfq.1_Intron|SEC24B_uc011cfr.1_Intron	NM_006323	NP_006314			SEC24 (S. cerevisiae) homolog B isoform a						COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|Golgi membrane|perinuclear region of cytoplasm	protein binding|transporter activity|zinc ion binding			ovary(2)|large_intestine(1)	3		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)														---	---	---	---
SEC24B	10427	broad.mit.edu	37	4	110457008	110457008	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110457008delA	uc003hzk.2	+						SEC24B_uc003hzl.2_Intron|SEC24B_uc011cfp.1_Intron|SEC24B_uc011cfq.1_Intron|SEC24B_uc011cfr.1_Intron	NM_006323	NP_006314			SEC24 (S. cerevisiae) homolog B isoform a						COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|Golgi membrane|perinuclear region of cytoplasm	protein binding|transporter activity|zinc ion binding			ovary(2)|large_intestine(1)	3		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.03e-05)														---	---	---	---
CASP6	839	broad.mit.edu	37	4	110610300	110610300	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110610300delT	uc003hzn.1	-	7					CASP6_uc003hzo.1_3'UTR	NM_001226	NP_001217			caspase 6 isoform alpha preproprotein						cellular component disassembly involved in apoptosis|induction of apoptosis|proteolysis	cytosol|nucleoplasm	cysteine-type endopeptidase activity|protein binding			ovary(1)|breast(1)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000171)														---	---	---	---
RRH	10692	broad.mit.edu	37	4	110756944	110756944	+	Intron	DEL	T	-	-	rs71595523		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110756944delT	uc003hzv.2	+							NM_006583	NP_006574			peropsin						phototransduction|protein-chromophore linkage|visual perception	integral to plasma membrane	G-protein coupled receptor activity|photoreceptor activity			ovary(1)	1		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00109)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	112406569	112406570	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:112406569_112406570delAA								MIR297 (624766 upstream) : C4orf32 (659983 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	112653102	112653102	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:112653102delA								MIR297 (871299 upstream) : C4orf32 (413451 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	112814173	112814174	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:112814173_112814174delTG								None (None upstream) : C4orf32 (252379 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	112844419	112844419	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:112844419delT								None (None upstream) : C4orf32 (222134 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	113374226	113374227	+	IGR	DEL	AC	-	-	rs138531506		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113374226_113374227delAC								ALPK1 (10465 upstream) : NEUROG2 (60447 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	113451700	113451700	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113451700delT								NEUROG2 (14372 upstream) : C4orf21 (8790 downstream)																																			---	---	---	---
C4orf21	55345	broad.mit.edu	37	4	113540916	113540916	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113540916delA	uc003iau.2	-						C4orf21_uc003iaw.2_Intron	NM_018392	NP_060862			prematurely terminated mRNA decay factor-like							integral to membrane	zinc ion binding				0		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)														---	---	---	---
LARP7	51574	broad.mit.edu	37	4	113569800	113569801	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113569800_113569801insT	uc003iay.2	+						LARP7_uc003iaz.2_Intron|LARP7_uc003iba.2_Intron|LARP7_uc003ibb.2_Intron|uc011cfy.1_5'Flank|MIR367_hsa-mir-367|MI0000775_5'Flank|MIR302D_hsa-mir-302d|MI0000774_5'Flank|uc011cfz.1_5'Flank|MIR302A_hsa-mir-302a|MI0000738_5'Flank|MIR302C_hsa-mir-302c|MI0000773_5'Flank|MIR302B_hsa-mir-302b|MI0000772_5'Flank|uc011cga.1_5'Flank	NM_016648	NP_057732			La ribonucleoprotein domain family, member 7						RNA processing	nucleoplasm|ribonucleoprotein complex	nucleotide binding|RNA binding			ovary(3)	3		Ovarian(17;0.0443)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)														---	---	---	---
LARP7	51574	broad.mit.edu	37	4	113570754	113570754	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113570754delA	uc003iay.2	+	9	1484	c.1206delA	c.(1204-1206)TTAfs	p.L402fs	LARP7_uc003iaz.2_Frame_Shift_Del_p.L409fs|LARP7_uc003iba.2_Frame_Shift_Del_p.L323fs|LARP7_uc003ibb.2_Frame_Shift_Del_p.L402fs|uc011cfy.1_5'Flank|MIR367_hsa-mir-367|MI0000775_5'Flank|MIR302D_hsa-mir-302d|MI0000774_5'Flank|uc011cfz.1_5'Flank|MIR302A_hsa-mir-302a|MI0000738_5'Flank|MIR302C_hsa-mir-302c|MI0000773_5'Flank|MIR302B_hsa-mir-302b|MI0000772_5'Flank|uc011cga.1_5'Flank	NM_016648	NP_057732	Q4G0J3	LARP7_HUMAN	La ribonucleoprotein domain family, member 7	402					RNA processing	nucleoplasm|ribonucleoprotein complex	nucleotide binding|RNA binding			ovary(3)	3		Ovarian(17;0.0443)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	113612319	113612321	+	IGR	DEL	AAA	-	-	rs77152482		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113612319_113612321delAAA								LARP7 (33578 upstream) : ANK2 (126918 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	114712960	114712960	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114712960delA								CAMK2D (29877 upstream) : ARSJ (108480 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	115260251	115260251	+	IGR	DEL	A	-	-	rs35904961		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115260251delA								ARSJ (359373 upstream) : UGT8 (259360 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	115621750	115621751	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115621750_115621751insA								UGT8 (23548 upstream) : NDST4 (127180 downstream)																																			---	---	---	---
NDST4	64579	broad.mit.edu	37	4	115825221	115825221	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115825221delA	uc003ibu.2	-						NDST4_uc010imw.2_Intron	NM_022569	NP_072091			heparan sulfate N-deacetylase/N-sulfotransferase							Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			skin(3)|ovary(1)	4		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000562)														---	---	---	---
NDST4	64579	broad.mit.edu	37	4	115843110	115843110	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115843110delT	uc003ibu.2	-						NDST4_uc010imw.2_Intron	NM_022569	NP_072091			heparan sulfate N-deacetylase/N-sulfotransferase							Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			skin(3)|ovary(1)	4		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000562)														---	---	---	---
NDST4	64579	broad.mit.edu	37	4	115999841	115999841	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115999841delA	uc003ibu.2	-						NDST4_uc010imw.2_Intron	NM_022569	NP_072091			heparan sulfate N-deacetylase/N-sulfotransferase							Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			skin(3)|ovary(1)	4		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000562)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	116723510	116723511	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:116723510_116723511insT								NDST4 (688478 upstream) : MIR1973 (497370 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	117069011	117069011	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:117069011delA								None (None upstream) : MIR1973 (151870 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	117738544	117738545	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:117738544_117738545delAA								MIR1973 (517620 upstream) : TRAM1L1 (266171 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	117981846	117981846	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:117981846delT								MIR1973 (760922 upstream) : TRAM1L1 (22870 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	118151835	118151835	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:118151835delA								TRAM1L1 (145099 upstream) : NDST3 (802938 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	118651851	118651851	+	IGR	DEL	T	-	-	rs111620190	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:118651851delT								TRAM1L1 (645115 upstream) : NDST3 (302922 downstream)																																			---	---	---	---
NDST3	9348	broad.mit.edu	37	4	119153789	119153789	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119153789delA	uc003ibx.2	+						NDST3_uc011cgf.1_Intron	NM_004784	NP_004775			N-deacetylase/N-sulfotransferase (heparan							Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			large_intestine(1)	1																		---	---	---	---
PRSS12	8492	broad.mit.edu	37	4	119266691	119266691	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119266691delA	uc003ica.1	-							NM_003619	NP_003610			neurotrypsin precursor							membrane	scavenger receptor activity			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	119430009	119430009	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119430009delT								PRSS12 (156087 upstream) : CEP170L (7486 downstream)																																			---	---	---	---
MYOZ2	51778	broad.mit.edu	37	4	120089822	120089822	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120089822delA	uc003icp.3	+							NM_016599	NP_057683			myozenin 2								protein phosphatase 2B binding				0																		---	---	---	---
MYOZ2	51778	broad.mit.edu	37	4	120106340	120106340	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120106340delT	uc003icp.3	+							NM_016599	NP_057683			myozenin 2								protein phosphatase 2B binding				0																		---	---	---	---
PDE5A	8654	broad.mit.edu	37	4	120483779	120483779	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120483779delA	uc003idh.2	-						PDE5A_uc003idf.2_Intron|PDE5A_uc003idg.2_Intron	NM_001083	NP_001074			phosphodiesterase 5A isoform 1						platelet activation|signal transduction	cytosol	3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|zinc ion binding				0					Dipyridamole(DB00975)|Pentoxifylline(DB00806)|Sildenafil(DB00203)|Tadalafil(DB00820)|Theophylline(DB00277)|Vardenafil(DB00862)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	121018940	121018942	+	IGR	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:121018940_121018942delAAA								MAD2L1 (30927 upstream) : PRDM5 (596988 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	121420845	121420845	+	IGR	DEL	C	-	-	rs112928328		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:121420845delC								MAD2L1 (432832 upstream) : PRDM5 (195085 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	122632990	122632990	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122632990delA								ANXA5 (14843 upstream) : TMEM155 (47095 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	122694105	122694105	+	IGR	DEL	A	-	-	rs113647146		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122694105delA								LOC100192379 (6143 upstream) : EXOSC9 (28367 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	122969128	122969128	+	IGR	DEL	T	-	-	rs77090075		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122969128delT								TRPC3 (96219 upstream) : KIAA1109 (122630 downstream)																																			---	---	---	---
KIAA1109	84162	broad.mit.edu	37	4	123164876	123164876	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123164876delA	uc003ieh.2	+						KIAA1109_uc003iek.2_Intron	NM_015312	NP_056127			fragile site-associated protein						regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12																		---	---	---	---
KIAA1109	84162	broad.mit.edu	37	4	123193663	123193664	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123193663_123193664delTT	uc003ieh.2	+						KIAA1109_uc003iel.1_Intron|KIAA1109_uc003iek.2_Intron	NM_015312	NP_056127			fragile site-associated protein						regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12																		---	---	---	---
KIAA1109	84162	broad.mit.edu	37	4	123234945	123234945	+	Intron	DEL	A	-	-	rs72925991	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123234945delA	uc003ieh.2	+						KIAA1109_uc003iel.1_Intron	NM_015312	NP_056127			fragile site-associated protein						regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12																		---	---	---	---
ADAD1	132612	broad.mit.edu	37	4	123301135	123301135	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123301135delG	uc003ieo.2	+						ADAD1_uc003iep.2_Intron|ADAD1_uc003ieq.2_Intron	NM_139243	NP_640336			adenosine deaminase domain containing 1						multicellular organismal development|RNA processing	nucleus	adenosine deaminase activity|double-stranded RNA binding				0																		---	---	---	---
SPATA5	166378	broad.mit.edu	37	4	123856628	123856628	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123856628delT	uc003iez.3	+						SPATA5_uc003iey.2_Intron	NM_145207	NP_660208			spermatogenesis associated 5						cell differentiation|multicellular organismal development|spermatogenesis	mitochondrion	ATP binding|nucleoside-triphosphatase activity				0																		---	---	---	---
SPATA5	166378	broad.mit.edu	37	4	123968730	123968730	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123968730delT	uc003iez.3	+							NM_145207	NP_660208			spermatogenesis associated 5						cell differentiation|multicellular organismal development|spermatogenesis	mitochondrion	ATP binding|nucleoside-triphosphatase activity				0																		---	---	---	---
SPATA5	166378	broad.mit.edu	37	4	124052219	124052219	+	Intron	DEL	T	-	-	rs35545092		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:124052219delT	uc003iez.3	+							NM_145207	NP_660208			spermatogenesis associated 5						cell differentiation|multicellular organismal development|spermatogenesis	mitochondrion	ATP binding|nucleoside-triphosphatase activity				0																		---	---	---	---
LOC285419	285419	broad.mit.edu	37	4	124826671	124826671	+	Intron	DEL	G	-	-	rs112054922		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:124826671delG	uc011cgn.1	+							NR_027105				Homo sapiens mRNA; cDNA DKFZp686P12109 (from clone DKFZp686P12109).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	124939702	124939702	+	IGR	DEL	T	-	-	rs112094577		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:124939702delT								LOC285419 (88184 upstream) : ANKRD50 (645766 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	125788530	125788530	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:125788530delT								ANKRD50 (154643 upstream) : FAT4 (449037 downstream)																																			---	---	---	---
FAT4	79633	broad.mit.edu	37	4	126297057	126297057	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126297057delT	uc003ifj.3	+							NM_024582	NP_078858			FAT tumor suppressor homolog 4 precursor						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18																		---	---	---	---
FAT4	79633	broad.mit.edu	37	4	126398215	126398215	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126398215delA	uc003ifj.3	+						FAT4_uc011cgp.1_Intron|FAT4_uc003ifi.1_Intron	NM_024582	NP_078858			FAT tumor suppressor homolog 4 precursor						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	126471802	126471802	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126471802delA								MIR2054 (43340 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	127155337	127155338	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:127155337_127155338insT								MIR2054 (726875 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	127155342	127155342	+	IGR	DEL	C	-	-	rs112995722		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:127155342delC								MIR2054 (726880 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	127676064	127676065	+	IGR	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:127676064_127676065delAG								None (None upstream) : INTU (878055 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	128269505	128269505	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128269505delA								None (None upstream) : INTU (284615 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	128518976	128518976	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128518976delA								None (None upstream) : INTU (35144 downstream)																																			---	---	---	---
SLC25A31	83447	broad.mit.edu	37	4	128665964	128665964	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128665964delT	uc003ifl.2	+							NM_031291	NP_112581			solute carrier family 25 (mitochondrial carrier;						transmembrane transport	cilium|flagellum|integral to membrane|mitochondrial inner membrane	binding|transporter activity				0																		---	---	---	---
HSPA4L	22824	broad.mit.edu	37	4	128722470	128722470	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128722470delT	uc003ifm.2	+						HSPA4L_uc010iny.1_Intron|HSPA4L_uc011cgr.1_Intron	NM_014278	NP_055093			heat shock 70kDa protein 4-like						protein folding|response to unfolded protein	cytoplasm|nucleus	ATP binding|protein binding			ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
MFSD8	256471	broad.mit.edu	37	4	128851731	128851731	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128851731delA	uc003ifp.2	-						MFSD8_uc011cgu.1_Intron|MFSD8_uc011cgv.1_Intron|MFSD8_uc011cgw.1_Intron	NM_152778	NP_689991			major facilitator superfamily domain containing						cell death|transmembrane transport	integral to membrane|lysosomal membrane				ovary(1)|liver(1)	2																		---	---	---	---
C4orf29	80167	broad.mit.edu	37	4	128894537	128894537	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128894537delT	uc003ifr.2	+						C4orf29_uc003ifq.1_Intron|C4orf29_uc003ifs.2_Intron	NM_001039717	NP_001034806			hypothetical protein LOC80167 precursor							extracellular region				ovary(1)	1																		---	---	---	---
C4orf33	132321	broad.mit.edu	37	4	130021082	130021083	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:130021082_130021083delAA	uc003igu.3	+						C4orf33_uc010ioc.1_Intron|C4orf33_uc010iod.2_Intron	NM_173487	NP_775758			hypothetical protein LOC132321											upper_aerodigestive_tract(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	131784610	131784610	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:131784610delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	132264280	132264280	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:132264280delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	133177277	133177277	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:133177277delA								None (None upstream) : PCDH10 (893193 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	133289039	133289042	+	IGR	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:133289039_133289042delTTTT								None (None upstream) : PCDH10 (781428 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	134179289	134179289	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134179289delT								PCDH10 (66558 upstream) : PABPC4L (938202 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	134407204	134407205	+	IGR	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134407204_134407205delAC								PCDH10 (294473 upstream) : PABPC4L (710286 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	135664560	135664560	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:135664560delA								PABPC4L (541657 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	135897290	135897291	+	IGR	INS	-	G	G	rs138689081	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:135897290_135897291insG								PABPC4L (774387 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	136430706	136430707	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:136430706_136430707delAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	136717839	136717839	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:136717839delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	136774639	136774640	+	IGR	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:136774639_136774640delAC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	137261113	137261116	+	IGR	DEL	AAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:137261113_137261116delAAAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	137308749	137308750	+	IGR	INS	-	T	T	rs11309308		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:137308749_137308750insT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	137444573	137444573	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:137444573delA								None (None upstream) : PCDH18 (995503 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	137774413	137774416	+	IGR	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:137774413_137774416delTTTT								None (None upstream) : PCDH18 (665660 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	138236170	138236170	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:138236170delT								None (None upstream) : PCDH18 (203906 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	139066054	139066054	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139066054delT	uc003ihi.1	+											Homo sapiens hypothetical protein LOC641364, mRNA (cDNA clone IMAGE:5273158).																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	139384541	139384542	+	IGR	INS	-	T	T	rs145167857	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139384541_139384542insT								SLC7A11 (221038 upstream) : CCRN4L (552401 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	139786778	139786781	+	IGR	DEL	GGAA	-	-	rs112477691		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139786778_139786781delGGAA								SLC7A11 (623275 upstream) : CCRN4L (150162 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	139839233	139839233	+	IGR	DEL	T	-	-	rs12711280	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139839233delT								SLC7A11 (675730 upstream) : CCRN4L (97710 downstream)																																			---	---	---	---
CCRN4L	25819	broad.mit.edu	37	4	139956284	139956284	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139956284delT	uc003ihl.2	+						CCRN4L_uc003ihk.1_Intron	NM_012118	NP_036250			CCR4 carbon catabolite repression 4-like						rhythmic process|transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding transcription factor activity			ovary(1)	1	all_hematologic(180;0.162)																	---	---	---	---
ELF2	1998	broad.mit.edu	37	4	139991452	139991454	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:139991452_139991454delTTT	uc003ihp.1	-						ELF2_uc003ihm.1_Intron|ELF2_uc003ihn.1_Intron|ELF2_uc003iho.1_Intron|ELF2_uc010ioh.2_Intron	NM_201999	NP_973728			E74-like factor 2 (ets domain transcription						negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter	cytoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity			ovary(1)|skin(1)	2	all_hematologic(180;0.162)																	---	---	---	---
ELF2	1998	broad.mit.edu	37	4	140036422	140036422	+	Intron	DEL	T	-	-	rs7661947		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140036422delT	uc003ihp.1	-						ELF2_uc003ihq.2_Intron	NM_201999	NP_973728			E74-like factor 2 (ets domain transcription						negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter	cytoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity			ovary(1)|skin(1)	2	all_hematologic(180;0.162)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	140142185	140142185	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140142185delA								ELF2 (43813 upstream) : C4orf49 (45132 downstream)																																			---	---	---	---
NAA15	80155	broad.mit.edu	37	4	140263951	140263951	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140263951delA	uc003ihu.1	+							NM_057175	NP_476516			NMDA receptor regulated 1						angiogenesis|cell differentiation|N-terminal protein amino acid acetylation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|transcription factor complex	protein binding			ovary(1)|skin(1)	2																		---	---	---	---
NAA15	80155	broad.mit.edu	37	4	140273100	140273101	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140273100_140273101insT	uc003ihu.1	+							NM_057175	NP_476516			NMDA receptor regulated 1						angiogenesis|cell differentiation|N-terminal protein amino acid acetylation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|transcription factor complex	protein binding			ovary(1)|skin(1)	2																		---	---	---	---
MGST2	4258	broad.mit.edu	37	4	140632168	140632170	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140632168_140632170delTTT	uc010ioi.1	+											Homo sapiens cDNA FLJ27438 fis, clone TST09249, highly similar to Homo sapiens microsomal glutathione S-transferase 2 (MGST2).						glutathione biosynthetic process|leukotriene biosynthetic process|leukotriene production involved in inflammatory response|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome|nuclear membrane|plasma membrane	enzyme activator activity|glutathione peroxidase activity|glutathione transferase activity|leukotriene-C4 synthase activity			ovary(1)	1	all_hematologic(180;0.162)				Glutathione(DB00143)													---	---	---	---
SCOC	60592	broad.mit.edu	37	4	141207343	141207343	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141207343delA	uc003iib.2	+						uc003iic.1_Intron	NM_032547	NP_115936			short coiled-coil protein isoform 4							Golgi apparatus|nucleus	protein binding				0	all_hematologic(180;0.162)																	---	---	---	---
ELMOD2	255520	broad.mit.edu	37	4	141466291	141466291	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141466291delT	uc003iik.2	+							NM_153702	NP_714913			ELMO/CED-12 domain containing 2						phagocytosis|regulation of defense response to virus|response to virus	cytoskeleton	GTPase activator activity			ovary(1)	1	all_hematologic(180;0.162)																	---	---	---	---
UCP1	7350	broad.mit.edu	37	4	141484372	141484372	+	Intron	DEL	A	-	-	rs111460010		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141484372delA	uc011chj.1	-						UCP1_uc011chk.1_Intron	NM_021833	NP_068605			uncoupling protein 1						brown fat cell differentiation|cellular lipid metabolic process|respiratory electron transport chain	integral to membrane|mitochondrial inner membrane	binding			ovary(1)	1	all_hematologic(180;0.162)																	---	---	---	---
TBC1D9	23158	broad.mit.edu	37	4	141549102	141549103	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141549102_141549103insA	uc010ioj.2	-							NM_015130	NP_055945			TBC1 domain family, member 9 (with GRAM domain)							intracellular	calcium ion binding|Rab GTPase activator activity			ovary(1)	1	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)																---	---	---	---
TBC1D9	23158	broad.mit.edu	37	4	141607766	141607767	+	Intron	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141607766_141607767delAC	uc010ioj.2	-							NM_015130	NP_055945			TBC1 domain family, member 9 (with GRAM domain)							intracellular	calcium ion binding|Rab GTPase activator activity			ovary(1)	1	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	141711268	141711268	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141711268delT								TBC1D9 (33797 upstream) : RNF150 (75457 downstream)																																			---	---	---	---
RNF150	57484	broad.mit.edu	37	4	141859441	141859441	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141859441delT	uc003iio.1	-						RNF150_uc010iok.1_Intron|RNF150_uc003iip.1_Intron	NM_020724	NP_065775			ring finger protein 150 precursor							integral to membrane	zinc ion binding			ovary(1)	1	all_hematologic(180;0.162)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	142314286	142314287	+	IGR	INS	-	T	T	rs144045898	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:142314286_142314287insT								ZNF330 (158438 upstream) : IL15 (243467 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	142540345	142540345	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:142540345delA								ZNF330 (384497 upstream) : IL15 (17409 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	142707180	142707180	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:142707180delT								IL15 (52569 upstream) : INPP4B (242004 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	142717186	142717186	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:142717186delC								IL15 (62575 upstream) : INPP4B (231998 downstream)																																			---	---	---	---
INPP4B	8821	broad.mit.edu	37	4	143111547	143111547	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143111547delA	uc003iix.3	-						INPP4B_uc003iiw.3_Intron|INPP4B_uc011chm.1_Intron|INPP4B_uc011chn.1_Intron|INPP4B_uc011cho.1_Intron|INPP4B_uc011chp.1_Intron	NM_003866	NP_003857			inositol polyphosphate-4-phosphatase, type II,						signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			ovary(1)|lung(1)	2	all_hematologic(180;0.158)																	---	---	---	---
INPP4B	8821	broad.mit.edu	37	4	143437919	143437920	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143437919_143437920delTT	uc003iix.3	-						INPP4B_uc003iiw.3_Intron|INPP4B_uc011cho.1_5'Flank	NM_003866	NP_003857			inositol polyphosphate-4-phosphatase, type II,						signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			ovary(1)|lung(1)	2	all_hematologic(180;0.158)																	---	---	---	---
INPP4B	8821	broad.mit.edu	37	4	143722245	143722245	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143722245delA	uc003iix.3	-						INPP4B_uc003iiw.3_Intron	NM_003866	NP_003857			inositol polyphosphate-4-phosphatase, type II,						signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			ovary(1)|lung(1)	2	all_hematologic(180;0.158)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	143882847	143882848	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143882847_143882848delAA								INPP4B (115243 upstream) : USP38 (223222 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	144146476	144146477	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144146476_144146477insT								USP38 (3336 upstream) : GAB1 (111506 downstream)																																			---	---	---	---
SMARCA5	8467	broad.mit.edu	37	4	144442477	144442477	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144442477delT	uc003ijg.2	+							NM_003601	NP_003592			SWI/SNF-related matrix-associated						CenH3-containing nucleosome assembly at centromere|nucleosome positioning|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	condensed chromosome|nucleolus|nucleoplasm|NURF complex|RSF complex	ATP binding|ATPase activity|DNA binding|helicase activity|nucleosome binding|protein binding			skin(1)	1	all_hematologic(180;0.158)																	---	---	---	---
SMARCA5	8467	broad.mit.edu	37	4	144469373	144469373	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144469373delA	uc003ijg.2	+							NM_003601	NP_003592			SWI/SNF-related matrix-associated						CenH3-containing nucleosome assembly at centromere|nucleosome positioning|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	condensed chromosome|nucleolus|nucleoplasm|NURF complex|RSF complex	ATP binding|ATPase activity|DNA binding|helicase activity|nucleosome binding|protein binding			skin(1)	1	all_hematologic(180;0.158)																	---	---	---	---
SMARCA5	8467	broad.mit.edu	37	4	144471021	144471021	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144471021delT	uc003ijg.2	+							NM_003601	NP_003592			SWI/SNF-related matrix-associated						CenH3-containing nucleosome assembly at centromere|nucleosome positioning|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	condensed chromosome|nucleolus|nucleoplasm|NURF complex|RSF complex	ATP binding|ATPase activity|DNA binding|helicase activity|nucleosome binding|protein binding			skin(1)	1	all_hematologic(180;0.158)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	144589033	144589033	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:144589033delT								LOC441046 (99720 upstream) : GYPE (202987 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	146491620	146491620	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146491620delG								SMAD1 (11297 upstream) : MMAA (48920 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	147087546	147087547	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147087546_147087547insT								ZNF827 (227939 upstream) : LSM6 (9288 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	147567908	147567909	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147567908_147567909insT								POU4F2 (4286 upstream) : TTC29 (60271 downstream)																																			---	---	---	---
TTC29	83894	broad.mit.edu	37	4	147831547	147831548	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147831547_147831548insA	uc003ikw.3	-						TTC29_uc010ipc.2_Intron|TTC29_uc003ikx.3_Intron|TTC29_uc010ipd.1_Intron	NM_031956	NP_114162			tetratricopeptide repeat domain 29								binding				0	all_hematologic(180;0.151)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	147883336	147883337	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147883336_147883337delTG								TTC29 (16302 upstream) : MIR548G (382444 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	147988558	147988558	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147988558delT								TTC29 (121524 upstream) : MIR548G (277223 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	148096866	148096866	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148096866delA								TTC29 (229832 upstream) : MIR548G (168915 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	148156320	148156321	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148156320_148156321delTG								TTC29 (289286 upstream) : MIR548G (109460 downstream)																																			---	---	---	---
EDNRA	1909	broad.mit.edu	37	4	148453478	148453490	+	Intron	DEL	AAAAAAAAAAAAA	-	-	rs34658974		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148453478_148453490delAAAAAAAAAAAAA	uc003iky.2	+						EDNRA_uc011cid.1_Intron|EDNRA_uc010ipe.1_Intron|EDNRA_uc010ipf.1_Intron|EDNRA_uc010ipg.1_Intron	NM_001957	NP_001948			endothelin receptor type A isoform a precursor						activation of adenylate cyclase activity|artery smooth muscle contraction|cell proliferation|glucose transport|respiratory gaseous exchange	integral to plasma membrane	endothelin-A receptor activity|phosphatidylinositol phospholipase C activity			ovary(1)|breast(1)	2	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.154)	Bosentan(DB00559)													---	---	---	---
PRMT10	90826	broad.mit.edu	37	4	148605499	148605499	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148605499delT	uc003ilc.2	-						PRMT10_uc003ild.2_5'Flank	NM_138364	NP_612373			protein arginine methyltransferase 10							cytoplasm	binding|protein methyltransferase activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
ARHGAP10	79658	broad.mit.edu	37	4	148828655	148828655	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148828655delA	uc003ilf.2	+						ARHGAP10_uc003ilg.2_Intron	NM_024605	NP_078881			Rho GTPase activating protein 10						apoptosis|filopodium assembly|regulation of apoptosis|small GTPase mediated signal transduction	cytosol|perinuclear region of cytoplasm|plasma membrane	cytoskeletal adaptor activity|SH3 domain binding			skin(2)|pancreas(1)|lung(1)	4	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	149727131	149727139	+	IGR	DEL	GGTTTTCTG	-	-	rs113835757		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:149727131_149727139delGGTTTTCTG								NR3C2 (363488 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	149894886	149894886	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:149894886delT								NR3C2 (531243 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	149938871	149938872	+	IGR	INS	-	CT	CT	rs146768566	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:149938871_149938872insCT								NR3C2 (575228 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	150440798	150440799	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:150440798_150440799delAA	uc003ill.2	-											Homo sapiens cDNA clone IMAGE:5295442.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	150573786	150573786	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:150573786delA	uc003ill.2	-											Homo sapiens cDNA clone IMAGE:5295442.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	150879775	150879776	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:150879775_150879776delTG								None (None upstream) : DCLK2 (120304 downstream)																																			---	---	---	---
LRBA	987	broad.mit.edu	37	4	151905662	151905662	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151905662delA	uc010ipj.2	-						LRBA_uc003ilu.3_Intron	NM_006726	NP_006717			LPS-responsive vesicle trafficking, beach and							endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)|skin(1)	7	all_hematologic(180;0.151)																	---	---	---	---
LRBA	987	broad.mit.edu	37	4	151935472	151935473	+	Intron	INS	-	A	A	rs144803488	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151935472_151935473insA	uc010ipj.2	-						LRBA_uc003ilu.3_Intron|LRBA_uc003ilx.1_3'UTR	NM_006726	NP_006717			LPS-responsive vesicle trafficking, beach and							endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)|skin(1)	7	all_hematologic(180;0.151)																	---	---	---	---
Unknown	0	broad.mit.edu	37	4	153018561	153018562	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153018561_153018562delAA								PET112L (336415 upstream) : FBXW7 (223849 downstream)														p.?(1)																					---	---	---	---
Unknown	0	broad.mit.edu	37	4	153052173	153052174	+	IGR	DEL	TA	-	-	rs6833616	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153052173_153052174delTA								PET112L (370027 upstream) : FBXW7 (190237 downstream)														p.?(1)																					---	---	---	---
Unknown	0	broad.mit.edu	37	4	153473441	153473441	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153473441delA								FBXW7 (17098 upstream) : TMEM154 (73830 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	154872088	154872088	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154872088delA								SFRP2 (161860 upstream) : DCHS2 (283439 downstream)																																			---	---	---	---
PLRG1	5356	broad.mit.edu	37	4	155470090	155470091	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155470090_155470091delAA	uc003iny.2	-						PLRG1_uc003inz.2_Intron|PLRG1_uc011cil.1_Intron	NM_002669	NP_002660			pleiotropic regulator 1 (PRL1 homolog,							catalytic step 2 spliceosome|nuclear speck	protein binding|signal transducer activity|transcription corepressor activity				0	all_hematologic(180;0.215)	Renal(120;0.0854)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	156361742	156361742	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156361742delT								MAP9 (63620 upstream) : GUCY1A3 (226120 downstream)																																			---	---	---	---
ACCN5	51802	broad.mit.edu	37	4	156765767	156765768	+	Intron	INS	-	TG	TG	rs147269130	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156765767_156765768insTG	uc003ipe.1	-							NM_017419	NP_059115			amiloride-sensitive cation channel 5,							integral to membrane|plasma membrane				ovary(2)|skin(1)	3	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.0464)|Kidney(143;0.058)|COAD - Colon adenocarcinoma(41;0.141)														---	---	---	---
ACCN5	51802	broad.mit.edu	37	4	156773541	156773541	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156773541delT	uc003ipe.1	-							NM_017419	NP_059115			amiloride-sensitive cation channel 5,							integral to membrane|plasma membrane				ovary(2)|skin(1)	3	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.0464)|Kidney(143;0.058)|COAD - Colon adenocarcinoma(41;0.141)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	157240685	157240692	+	IGR	DEL	GTATAGTG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:157240685_157240692delGTATAGTG								CTSO (365637 upstream) : PDGFC (442072 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	157546073	157546073	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:157546073delA								CTSO (671025 upstream) : PDGFC (136691 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	157661642	157661642	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:157661642delA								CTSO (786594 upstream) : PDGFC (21122 downstream)																																			---	---	---	---
PDGFC	56034	broad.mit.edu	37	4	157708825	157708825	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:157708825delA	uc003iph.1	-						PDGFC_uc003ipi.1_Intron|PDGFC_uc011cis.1_Intron|PDGFC_uc011cir.1_Intron	NM_016205	NP_057289			platelet-derived growth factor C precursor						central nervous system development|platelet-derived growth factor receptor signaling pathway|positive regulation of cell division|positive regulation of DNA replication|positive regulation of fibroblast proliferation|vascular endothelial growth factor receptor signaling pathway	endoplasmic reticulum lumen|extracellular space|Golgi membrane|nucleus	cell surface binding|growth factor activity|platelet-derived growth factor receptor binding|protein homodimerization activity			ovary(1)|lung(1)|skin(1)	3	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.08)|Kidney(143;0.0977)|COAD - Colon adenocarcinoma(41;0.212)														---	---	---	---
PDGFC	56034	broad.mit.edu	37	4	157740400	157740400	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:157740400delA	uc003iph.1	-						PDGFC_uc003ipi.1_Intron|PDGFC_uc011cis.1_Intron|PDGFC_uc011cir.1_Intron	NM_016205	NP_057289			platelet-derived growth factor C precursor						central nervous system development|platelet-derived growth factor receptor signaling pathway|positive regulation of cell division|positive regulation of DNA replication|positive regulation of fibroblast proliferation|vascular endothelial growth factor receptor signaling pathway	endoplasmic reticulum lumen|extracellular space|Golgi membrane|nucleus	cell surface binding|growth factor activity|platelet-derived growth factor receptor binding|protein homodimerization activity			ovary(1)|lung(1)|skin(1)	3	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.08)|Kidney(143;0.0977)|COAD - Colon adenocarcinoma(41;0.212)														---	---	---	---
GLRB	2743	broad.mit.edu	37	4	158052443	158052443	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158052443delT	uc003ipj.2	+							NM_000824	NP_000815			glycine receptor, beta isoform A precursor						nervous system development|neuropeptide signaling pathway|startle response	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	extracellular-glycine-gated chloride channel activity|protein binding|receptor activity			skin(2)	2	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.0564)|COAD - Colon adenocarcinoma(41;0.0642)|Kidney(143;0.0707)	Glycine(DB00145)													---	---	---	---
GRIA2	2891	broad.mit.edu	37	4	158241102	158241102	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158241102delA	uc003ipm.3	+						GRIA2_uc011cit.1_Intron|GRIA2_uc003ipl.3_Intron|GRIA2_uc003ipk.3_Intron|GRIA2_uc010iqh.1_Intron	NM_001083619	NP_001077088			glutamate receptor, ionotropic, AMPA 2 isoform 2						synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|endoplasmic reticulum membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			central_nervous_system(3)|ovary(1)	4	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	158303316	158303316	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158303316delA								GRIA2 (16092 upstream) : LOC340017 (190326 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	158718005	158718005	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158718005delT								LOC340017 (220710 upstream) : FAM198B (327728 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	158766697	158766697	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158766697delT								LOC340017 (269402 upstream) : FAM198B (279036 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	158828672	158828672	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:158828672delA								LOC340017 (331377 upstream) : FAM198B (217061 downstream)																																			---	---	---	---
TMEM144	55314	broad.mit.edu	37	4	159137982	159137984	+	Intron	DEL	AAA	-	-	rs35913363		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159137982_159137984delAAA	uc003ipx.2	+						TMEM144_uc010iqi.2_Intron	NM_018342	NP_060812			transmembrane protein 144							integral to membrane					0	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0539)														---	---	---	---
TMEM144	55314	broad.mit.edu	37	4	159155693	159155695	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159155693_159155695delAAA	uc003ipx.2	+						TMEM144_uc010iqi.2_Intron	NM_018342	NP_060812			transmembrane protein 144							integral to membrane					0	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0539)														---	---	---	---
RXFP1	59350	broad.mit.edu	37	4	159569825	159569825	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159569825delT	uc003ipz.2	+	17	2013	c.1931delT	c.(1930-1932)ATTfs	p.I644fs	RXFP1_uc011cja.1_Frame_Shift_Del_p.I539fs|RXFP1_uc010iqo.2_Frame_Shift_Del_p.I596fs|RXFP1_uc011cjb.1_Frame_Shift_Del_p.I542fs|RXFP1_uc010iqk.2_Frame_Shift_Del_p.I512fs|RXFP1_uc011cjc.1_Frame_Shift_Del_p.I563fs|RXFP1_uc011cjd.1_Frame_Shift_Del_p.I563fs|RXFP1_uc010iql.2_Frame_Shift_Del_p.I488fs|RXFP1_uc011cje.1_Frame_Shift_Del_p.I671fs|RXFP1_uc010iqm.2_Frame_Shift_Del_p.I611fs|RXFP1_uc011cjf.1_Frame_Shift_Del_p.I513fs|RXFP1_uc010iqn.2_Frame_Shift_Del_p.I589fs	NM_021634	NP_067647	Q9HBX9	RXFP1_HUMAN	relaxin/insulin-like family peptide receptor 1	644	Helical; Name=6; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity|metal ion binding				0	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0219)														---	---	---	---
RAPGEF2	9693	broad.mit.edu	37	4	160253031	160253031	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160253031delT	uc003iqg.3	+							NM_014247	NP_055062			Rap guanine nucleotide exchange factor 2						cAMP-mediated signaling|MAPKKK cascade|small GTPase mediated signal transduction	integral to plasma membrane|intracellular	calcium ion binding|diacylglycerol binding|Rap GTPase activator activity|Rap guanyl-nucleotide exchange factor activity|signal transducer activity			lung(2)|upper_aerodigestive_tract(1)|skin(1)	4	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	160619795	160619796	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160619795_160619796insT								RAPGEF2 (338496 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	161224344	161224344	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:161224344delT								RAPGEF2 (943045 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	162130524	162130524	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:162130524delA								None (None upstream) : FSTL5 (174527 downstream)																																			---	---	---	---
FSTL5	56884	broad.mit.edu	37	4	163048902	163048903	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:163048902_163048903insA	uc003iqh.2	-						FSTL5_uc003iqi.2_Intron|FSTL5_uc010iqv.2_Intron	NM_020116	NP_064501			follistatin-like 5 isoform a							extracellular region	calcium ion binding			ovary(2)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|skin(1)	8	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)														---	---	---	---
FSTL5	56884	broad.mit.edu	37	4	163054276	163054276	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:163054276delT	uc003iqh.2	-						FSTL5_uc003iqi.2_Intron|FSTL5_uc010iqv.2_Intron	NM_020116	NP_064501			follistatin-like 5 isoform a							extracellular region	calcium ion binding			ovary(2)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|skin(1)	8	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)														---	---	---	---
MARCH1	55016	broad.mit.edu	37	4	164580860	164580860	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164580860delA	uc003iqs.1	-							NM_017923	NP_060393			membrane-associated RING-CH protein I						antigen processing and presentation of peptide antigen via MHC class II|immune response	cytoplasmic vesicle membrane|early endosome membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|plasma membrane	MHC protein binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)	2	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)																---	---	---	---
MARCH1	55016	broad.mit.edu	37	4	164812816	164812816	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164812816delC	uc003iqs.1	-							NM_017923	NP_060393			membrane-associated RING-CH protein I						antigen processing and presentation of peptide antigen via MHC class II|immune response	cytoplasmic vesicle membrane|early endosome membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|plasma membrane	MHC protein binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)	2	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)																---	---	---	---
Unknown	0	broad.mit.edu	37	4	165663802	165663807	+	IGR	DEL	TCTGTA	-	-	rs68035788		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165663802_165663807delTCTGTA								MARCH1 (358600 upstream) : TRIM61 (211793 downstream)																																			---	---	---	---
TRIM60	166655	broad.mit.edu	37	4	165961700	165961700	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165961700delA	uc003iqy.1	+	3	646	c.476delA	c.(475-477)GAAfs	p.E159fs	TRIM60_uc010iqx.1_Frame_Shift_Del_p.E159fs	NM_152620	NP_689833	Q495X7	TRI60_HUMAN	ring finger protein 129	159						intracellular	zinc ion binding			skin(1)	1	all_hematologic(180;0.221)	Prostate(90;0.0959)|Melanoma(52;0.18)		GBM - Glioblastoma multiforme(119;0.0844)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	165983346	165983346	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:165983346delT								TRIM60 (20450 upstream) : TMEM192 (13885 downstream)																																			---	---	---	---
KLHL2	11275	broad.mit.edu	37	4	166184958	166184959	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166184958_166184959delTT	uc003irb.2	+						KLHL2_uc011cjm.1_Intron|KLHL2_uc003irc.2_Intron|KLHL2_uc010ira.2_Intron	NM_007246	NP_009177			kelch-like 2, Mayven isoform 1						intracellular protein transport	actin cytoskeleton|cytoplasm	actin binding|transporter activity				0	all_hematologic(180;0.221)			GBM - Glioblastoma multiforme(119;2.94e-27)|COAD - Colon adenocarcinoma(41;1.4e-05)|Kidney(143;4.95e-05)|KIRC - Kidney renal clear cell carcinoma(143;0.000927)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	166282410	166282410	+	IGR	DEL	A	-	-	rs111251442		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166282410delA								SC4MOL (18186 upstream) : CPE (17687 downstream)																																			---	---	---	---
CPE	1363	broad.mit.edu	37	4	166385414	166385414	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166385414delT	uc003irg.3	+							NM_001873	NP_001864			carboxypeptidase E preproprotein						cardiac left ventricle morphogenesis|neuropeptide signaling pathway|protein modification process	extracellular region|nucleus|plasma membrane	metallocarboxypeptidase activity|protein binding|zinc ion binding			large_intestine(1)|ovary(1)|skin(1)	3	all_hematologic(180;0.221)	Prostate(90;0.0962)|Melanoma(52;0.18)		GBM - Glioblastoma multiforme(119;0.137)	Glucagon recombinant(DB00040)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	166663052	166663052	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166663052delT								CPE (243571 upstream) : TLL1 (131358 downstream)																																			---	---	---	---
TLL1	7092	broad.mit.edu	37	4	166794335	166794335	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166794335delT	uc003irh.1	+						TLL1_uc011cjn.1_5'Flank|TLL1_uc011cjo.1_5'Flank	NM_012464	NP_036596			tolloid-like 1 precursor						cell differentiation|proteolysis|skeletal system development	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	167042664	167042664	+	IGR	DEL	T	-	-	rs71933141		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:167042664delT								TLL1 (17671 upstream) : SPOCK3 (611872 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	167551980	167551983	+	IGR	DEL	TGAT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:167551980_167551983delTGAT								TLL1 (526987 upstream) : SPOCK3 (102553 downstream)																																			---	---	---	---
SPOCK3	50859	broad.mit.edu	37	4	167746061	167746061	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:167746061delA	uc003iri.1	-						SPOCK3_uc011cjp.1_Intron|SPOCK3_uc011cjq.1_Intron|SPOCK3_uc011cjr.1_Intron|SPOCK3_uc003irj.1_Intron|SPOCK3_uc011cjs.1_Intron|SPOCK3_uc011cjt.1_Intron|SPOCK3_uc011cju.1_Intron|SPOCK3_uc011cjv.1_Intron|SPOCK3_uc003irk.3_Intron	NM_016950	NP_058646			testican 3 isoform 2						signal transduction	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase inhibitor activity			large_intestine(1)|ovary(1)|central_nervous_system(1)	3	all_hematologic(180;0.221)	Prostate(90;0.0181)|Renal(120;0.0184)|Melanoma(52;0.0198)		GBM - Glioblastoma multiforme(119;0.02)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	168859368	168859368	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:168859368delA								SPOCK3 (703627 upstream) : ANXA10 (154339 downstream)																																			---	---	---	---
DDX60	55601	broad.mit.edu	37	4	169211653	169211654	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169211653_169211654delTT	uc003irp.2	-							NM_017631	NP_060101			DEAD (Asp-Glu-Ala-Asp) box polypeptide 60								ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0485)														---	---	---	---
DDX60L	91351	broad.mit.edu	37	4	169337603	169337604	+	Intron	INS	-	TA	TA	rs142137108	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169337603_169337604insTA	uc003irq.3	-						DDX60L_uc003irr.1_Intron|DDX60L_uc003irs.1_Intron	NM_001012967	NP_001012985			DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like								ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)														---	---	---	---
PALLD	23022	broad.mit.edu	37	4	169661218	169661218	+	Intron	DEL	A	-	-	rs76075804		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169661218delA	uc011cjx.1	+						PALLD_uc003iru.2_Intron|PALLD_uc003irv.2_Intron	NM_016081	NP_057165			palladin isoform 2						cytoskeleton organization	actin filament|focal adhesion|lamellipodium|nucleus|ruffle|sarcomere	actin binding|muscle alpha-actinin binding			ovary(1)	1		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)										Pancreatic_Cancer_Familial_Clustering_of				---	---	---	---
PALLD	23022	broad.mit.edu	37	4	169821069	169821069	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169821069delA	uc011cjx.1	+						CBR4_uc011cjy.1_Intron|PALLD_uc003iru.2_Intron|PALLD_uc003irv.2_Intron|PALLD_uc003irw.2_Intron|PALLD_uc003irx.2_Intron	NM_016081	NP_057165			palladin isoform 2						cytoskeleton organization	actin filament|focal adhesion|lamellipodium|nucleus|ruffle|sarcomere	actin binding|muscle alpha-actinin binding			ovary(1)	1		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)										Pancreatic_Cancer_Familial_Clustering_of				---	---	---	---
Unknown	0	broad.mit.edu	37	4	170284878	170284879	+	IGR	INS	-	T	T	rs140460537		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170284878_170284879insT								SH3RF1 (92629 upstream) : NEK1 (29550 downstream)																																			---	---	---	---
NEK1	4750	broad.mit.edu	37	4	170403790	170403790	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170403790delT	uc003isb.1	-						NEK1_uc003isc.1_Intron|NEK1_uc003isd.1_Intron|NEK1_uc003ise.1_Intron|NEK1_uc003isf.1_Intron	NM_012224	NP_036356			NIMA-related kinase 1						cell division|cilium assembly|mitosis	nucleus|pericentriolar material	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(3)|ovary(2)|large_intestine(1)	6		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)														---	---	---	---
CLCN3	1182	broad.mit.edu	37	4	170557052	170557053	+	Intron	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170557052_170557053insC	uc003isi.2	+						CLCN3_uc003ish.2_Intron|CLCN3_uc011cjz.1_Intron|CLCN3_uc011cka.1_Intron	NM_001829	NP_001820			chloride channel 3 isoform b						endosomal lumen acidification	cell surface|early endosome membrane|Golgi membrane|integral to membrane|late endosome membrane|transport vesicle membrane	antiporter activity|ATP binding|PDZ domain binding|protein heterodimerization activity|protein homodimerization activity|voltage-gated chloride channel activity			breast(2)|ovary(1)	3		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0233)|LUSC - Lung squamous cell carcinoma(193;0.131)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	172205936	172205936	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:172205936delT								None (None upstream) : GALNTL6 (528639 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	172597667	172597667	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:172597667delA								None (None upstream) : GALNTL6 (136908 downstream)																																			---	---	---	---
GALNTL6	442117	broad.mit.edu	37	4	172871634	172871634	+	Intron	DEL	T	-	-	rs10556434		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:172871634delT	uc003isv.2	+							NM_001034845	NP_001030017			N-acetylgalactosaminyltransferase-like 6							Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(2)|ovary(1)|skin(1)	4																		---	---	---	---
GALNTL6	442117	broad.mit.edu	37	4	173253521	173253522	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:173253521_173253522insT	uc003isv.2	+							NM_001034845	NP_001030017			N-acetylgalactosaminyltransferase-like 6							Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(2)|ovary(1)|skin(1)	4																		---	---	---	---
GALNTL6	442117	broad.mit.edu	37	4	173661094	173661094	+	Intron	DEL	A	-	-	rs35229715		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:173661094delA	uc003isv.2	+							NM_001034845	NP_001030017			N-acetylgalactosaminyltransferase-like 6							Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(2)|ovary(1)|skin(1)	4																		---	---	---	---
GALNTL6	442117	broad.mit.edu	37	4	173952771	173952772	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:173952771_173952772delAA	uc003isv.2	+							NM_001034845	NP_001030017			N-acetylgalactosaminyltransferase-like 6							Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(2)|ovary(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	4	174801310	174801311	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174801310_174801311delTT								MORF4 (263516 upstream) : FBXO8 (356501 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	175112411	175112411	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175112411delT	uc003ito.1	-											Homo sapiens cDNA FLJ43267 fis, clone IMR322007704.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	175328966	175328966	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175328966delT								KIAA1712 (74435 upstream) : HPGD (82362 downstream)																																			---	---	---	---
GLRA3	8001	broad.mit.edu	37	4	175598519	175598519	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175598519delT	uc003ity.1	-						GLRA3_uc003itz.1_Intron	NM_006529	NP_006520			glycine receptor, alpha 3 isoform a						synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	extracellular-glycine-gated chloride channel activity|glycine binding|receptor activity|transmitter-gated ion channel activity			ovary(3)	3		Prostate(90;0.00601)|Breast(14;0.0091)|Melanoma(52;0.00959)|Renal(120;0.0183)|all_neural(102;0.0891)|all_hematologic(60;0.107)		all cancers(43;4.99e-18)|Epithelial(43;1.18e-16)|OV - Ovarian serous cystadenocarcinoma(60;5.88e-09)|STAD - Stomach adenocarcinoma(60;0.00442)|GBM - Glioblastoma multiforme(59;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0421)	Glycine(DB00145)													---	---	---	---
GPM6A	2823	broad.mit.edu	37	4	176594562	176594563	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:176594562_176594563delAA	uc003iuf.2	-						GPM6A_uc011ckj.1_Intron|GPM6A_uc003iug.2_Intron|GPM6A_uc003iuh.2_Intron	NM_201591	NP_963885			glycoprotein M6A isoform 2							cell surface|integral to membrane					0		Breast(14;7.35e-05)|Melanoma(52;0.00909)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;9.21e-19)|Epithelial(43;3.01e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.02e-09)|STAD - Stomach adenocarcinoma(60;0.00083)|GBM - Glioblastoma multiforme(59;0.00168)|LUSC - Lung squamous cell carcinoma(193;0.0388)														---	---	---	---
GPM6A	2823	broad.mit.edu	37	4	176680449	176680449	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:176680449delG	uc003iuf.2	-						GPM6A_uc011ckj.1_Intron|GPM6A_uc003iug.2_Intron|GPM6A_uc003iuh.2_Intron	NM_201591	NP_963885			glycoprotein M6A isoform 2							cell surface|integral to membrane					0		Breast(14;7.35e-05)|Melanoma(52;0.00909)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;9.21e-19)|Epithelial(43;3.01e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.02e-09)|STAD - Stomach adenocarcinoma(60;0.00083)|GBM - Glioblastoma multiforme(59;0.00168)|LUSC - Lung squamous cell carcinoma(193;0.0388)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	177276057	177276059	+	IGR	DEL	AAA	-	-	rs140155152		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177276057_177276059delAAA								SPCS3 (22663 upstream) : VEGFC (328632 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	177775611	177775611	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177775611delT								VEGFC (61716 upstream) : NEIL3 (455380 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	178311523	178311523	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178311523delT								NEIL3 (27431 upstream) : AGA (40401 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	178326839	178326839	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178326839delA								NEIL3 (42747 upstream) : AGA (25085 downstream)																																			---	---	---	---
LOC285501	285501	broad.mit.edu	37	4	178753121	178753121	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178753121delG	uc010iru.2	+							NR_028342				Homo sapiens cDNA clone IMAGE:4828874.												0		all_lung(41;6.03e-08)|Lung NSC(41;4.26e-07)|Breast(14;0.00066)|Melanoma(52;0.00168)|Prostate(90;0.0129)|all_hematologic(60;0.0202)|Renal(120;0.0246)|Colorectal(36;0.0508)|Hepatocellular(41;0.236)		all cancers(43;9.24e-25)|Epithelial(43;6.28e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.29e-10)|LUSC - Lung squamous cell carcinoma(1;2.61e-05)|Lung(1;3.22e-05)|GBM - Glioblastoma multiforme(59;0.000185)|Colorectal(24;0.000244)|STAD - Stomach adenocarcinoma(60;0.000777)|COAD - Colon adenocarcinoma(29;0.000884)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	178929810	178929810	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178929810delA								LOC285501 (17907 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	178951563	178951563	+	IGR	DEL	G	-	-	rs2615591	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178951563delG								LOC285501 (39660 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	179772899	179772900	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:179772899_179772900delTT								LOC285501 (860996 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	180344650	180344651	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:180344650_180344651delTG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	180585202	180585203	+	IGR	DEL	CA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:180585202_180585203delCA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	180637761	180637761	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:180637761delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	181170846	181170847	+	IGR	INS	-	A	A	rs11445930		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:181170846_181170847insA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	181202745	181202745	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:181202745delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	181322400	181322400	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:181322400delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	181524165	181524166	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:181524165_181524166insT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	182956434	182956434	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:182956434delC	uc003iva.1	-											Homo sapiens cDNA FLJ31634 fis, clone NT2RI2003419.																														---	---	---	---
ODZ3	55714	broad.mit.edu	37	4	183238615	183238615	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183238615delT	uc010irv.1	+											Homo sapiens ODZ3 (ODZ3) mRNA, partial cds.						signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	183740175	183740175	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183740175delG								ODZ3 (15998 upstream) : DCTD (71070 downstream)																																			---	---	---	---
WWC2	80014	broad.mit.edu	37	4	184159019	184159020	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184159019_184159020delTT	uc010irx.2	+						WWC2_uc003ivk.3_Intron|WWC2_uc003ivl.3_Intron|WWC2_uc010iry.2_Intron|uc003ivm.2_Intron	NM_024949	NP_079225			WW and C2 domain containing 2											ovary(2)|lung(1)	3		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	184344586	184344586	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184344586delT								WWC2 (102659 upstream) : CDKN2AIP (21203 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	184641725	184641725	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184641725delT								C4orf41 (6981 upstream) : STOX2 (184784 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	184650258	184650258	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184650258delT								C4orf41 (15514 upstream) : STOX2 (176251 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	184666526	184666526	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184666526delT								C4orf41 (31782 upstream) : STOX2 (159983 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	184788175	184788176	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184788175_184788176delTT								C4orf41 (153431 upstream) : STOX2 (38333 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	185175909	185175914	+	IGR	DEL	AAAAAT	-	-	rs72111107	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185175909_185175914delAAAAAT								ENPP6 (36795 upstream) : IRF2 (132964 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	185246879	185246881	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185246879_185246881delTTT								ENPP6 (107765 upstream) : IRF2 (61997 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	185405674	185405675	+	IGR	INS	-	A	A	rs140263720	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185405674_185405675insA								IRF2 (9948 upstream) : CASP3 (143177 downstream)																																			---	---	---	---
CCDC111	201973	broad.mit.edu	37	4	185578560	185578560	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185578560delA	uc003iwk.2	+						CCDC111_uc010isd.1_Intron|CCDC111_uc003iwj.2_Intron|CCDC111_uc003iwl.2_Intron|CCDC111_uc003iwm.2_Intron|CCDC111_uc003iwn.2_Intron	NM_152683	NP_689896			coiled-coil domain containing 111						DNA replication, synthesis of RNA primer		DNA primase activity			central_nervous_system(1)	1		all_lung(41;9.65e-12)|Lung NSC(41;1.64e-11)|Colorectal(36;0.00531)|Hepatocellular(41;0.00932)|Renal(120;0.0246)|Prostate(90;0.0283)|all_hematologic(60;0.0749)|all_neural(102;0.131)		all cancers(43;5.84e-27)|Epithelial(43;2.2e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.28e-11)|STAD - Stomach adenocarcinoma(60;2.66e-05)|GBM - Glioblastoma multiforme(59;3.03e-05)|Colorectal(24;7.57e-05)|BRCA - Breast invasive adenocarcinoma(30;0.000249)|COAD - Colon adenocarcinoma(29;0.000502)|LUSC - Lung squamous cell carcinoma(40;0.00995)|READ - Rectum adenocarcinoma(43;0.173)														---	---	---	---
ACSL1	2180	broad.mit.edu	37	4	185698936	185698937	+	Intron	DEL	AG	-	-	rs67023515		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185698936_185698937delAG	uc003iww.2	-						ACSL1_uc011ckm.1_Intron|ACSL1_uc003iwt.1_Intron|ACSL1_uc003iwu.1_Intron|ACSL1_uc011ckn.1_Intron|ACSL1_uc003iwv.1_Intron	NM_001995	NP_001986			acyl-CoA synthetase long-chain family member 1						digestion|fatty acid metabolic process|long-chain fatty-acyl-CoA biosynthetic process|regulation of fatty acid oxidation|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane|peroxisomal membrane	ATP binding|long-chain fatty acid-CoA ligase activity			ovary(2)	2		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Colorectal(36;0.00172)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0315)|all_neural(102;0.107)|Medulloblastoma(177;0.146)		all cancers(43;1.33e-28)|Epithelial(43;5.3e-25)|OV - Ovarian serous cystadenocarcinoma(60;4.88e-11)|Colorectal(24;3.59e-06)|STAD - Stomach adenocarcinoma(60;2.72e-05)|GBM - Glioblastoma multiforme(59;2.83e-05)|BRCA - Breast invasive adenocarcinoma(30;7.66e-05)|COAD - Colon adenocarcinoma(29;0.000538)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.0419)	Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)													---	---	---	---
SORBS2	8470	broad.mit.edu	37	4	186810513	186810514	+	Intron	DEL	TT	-	-	rs72447539		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186810513_186810514delTT	uc003iyl.2	-						SORBS2_uc003iym.2_Intron|SORBS2_uc011cky.1_Intron	NM_021069	NP_066547			sorbin and SH3 domain containing 2 isoform 2							actin cytoskeleton|nucleus|perinuclear region of cytoplasm|Z disc	cytoskeletal adaptor activity|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(1)	1		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	186979793	186979793	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186979793delA								SORBS2 (101923 upstream) : TLR3 (10516 downstream)																																			---	---	---	---
FAM149A	25854	broad.mit.edu	37	4	187067152	187067152	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187067152delA	uc003iyt.3	+						FAM149A_uc011cla.1_Intron|FAM149A_uc010isj.2_Intron|FAM149A_uc010isk.2_Intron|FAM149A_uc003iyu.3_Intron	NM_015398	NP_056213			hypothetical protein LOC25854											breast(1)	1		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.19e-10)|BRCA - Breast invasive adenocarcinoma(30;1.22e-05)|GBM - Glioblastoma multiforme(59;0.000122)|STAD - Stomach adenocarcinoma(60;0.000288)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.166)														---	---	---	---
F11	2160	broad.mit.edu	37	4	187197260	187197260	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187197260delA	uc003iza.1	+							NM_000128	NP_000119			coagulation factor XI precursor						blood coagulation, intrinsic pathway|plasminogen activation|positive regulation of fibrinolysis	extracellular space|plasma membrane	heparin binding|serine-type endopeptidase activity				0		all_cancers(14;6.2e-52)|all_epithelial(14;1.62e-38)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Colorectal(36;0.0161)|all_neural(102;0.202)		OV - Ovarian serous cystadenocarcinoma(60;2.13e-11)|BRCA - Breast invasive adenocarcinoma(30;4.59e-06)|GBM - Glioblastoma multiforme(59;0.000149)|STAD - Stomach adenocarcinoma(60;0.000314)|LUSC - Lung squamous cell carcinoma(40;0.00112)|READ - Rectum adenocarcinoma(43;0.176)	Coagulation Factor IX(DB00100)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	187301846	187301846	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187301846delA	uc003izb.1	-											Homo sapiens coagulation factor XI (plasma thromboplastin antecedent), mRNA (cDNA clone IMAGE:4831055).																														---	---	---	---
FAT1	2195	broad.mit.edu	37	4	187549136	187549136	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187549136delA	uc003izf.2	-							NM_005245	NP_005236			FAT tumor suppressor 1 precursor						actin filament organization|anatomical structure morphogenesis|cell migration|cell-cell signaling|establishment or maintenance of cell polarity|homophilic cell adhesion	cell-cell junction|integral to plasma membrane|nucleus|perinuclear region of cytoplasm	calcium ion binding|protein binding			ovary(10)|central_nervous_system(1)|pancreas(1)	12															HNSCC(5;0.00058)			---	---	---	---
Unknown	0	broad.mit.edu	37	4	187742759	187742760	+	IGR	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187742759_187742760insC								FAT1 (94909 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	188765521	188765521	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:188765521delA								None (None upstream) : ZFP42 (151404 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	188855989	188855989	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:188855989delA								None (None upstream) : ZFP42 (60936 downstream)																																			---	---	---	---
TRIML2	205860	broad.mit.edu	37	4	189019278	189019284	+	Intron	DEL	AAAAAAA	-	-	rs77035135		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189019278_189019284delAAAAAAA	uc003izl.2	-						TRIML2_uc003izj.1_Intron|TRIML2_uc003izk.1_Intron|TRIML2_uc011cle.1_Intron	NM_173553	NP_775824			tripartite motif family-like 2								ligase activity			central_nervous_system(2)	2		all_cancers(14;3.11e-44)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|all_hematologic(60;0.0202)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)		OV - Ovarian serous cystadenocarcinoma(60;1.79e-11)|BRCA - Breast invasive adenocarcinoma(30;4.52e-06)|GBM - Glioblastoma multiforme(59;1.62e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.0091)|READ - Rectum adenocarcinoma(43;0.163)														---	---	---	---
TRIML2	205860	broad.mit.edu	37	4	189031555	189031555	+	5'Flank	DEL	T	-	-	rs10532491		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189031555delT	uc011clf.1	-							NM_173553	NP_775824			tripartite motif family-like 2								ligase activity			central_nervous_system(2)	2		all_cancers(14;3.11e-44)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|all_hematologic(60;0.0202)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)		OV - Ovarian serous cystadenocarcinoma(60;1.79e-11)|BRCA - Breast invasive adenocarcinoma(30;4.52e-06)|GBM - Glioblastoma multiforme(59;1.62e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.0091)|READ - Rectum adenocarcinoma(43;0.163)														---	---	---	---
Unknown	0	broad.mit.edu	37	4	189354086	189354086	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189354086delT	uc003izo.1	+											Homo sapiens cDNA FLJ38649 fis, clone HHDPC2007302.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	189769029	189769029	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:189769029delT								TRIML1 (700380 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190076556	190076557	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190076556_190076557insT								None (None upstream) : FRG1 (785417 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190152987	190152989	+	IGR	DEL	CAC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190152987_190152989delCAC								None (None upstream) : FRG1 (708985 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190598155	190598156	+	IGR	DEL	CA	-	-	rs66488551		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190598155_190598156delCA								None (None upstream) : FRG1 (263818 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190627455	190627455	+	IGR	DEL	A	-	-	rs68065627		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190627455delA								None (None upstream) : FRG1 (234519 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	190825928	190825928	+	Intron	DEL	T	-	-	rs113376083		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190825928delT	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	190840895	190840895	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190840895delG	uc003izq.2	-											Homo sapiens cDNA clone IMAGE:30384438.																														---	---	---	---
Unknown	0	broad.mit.edu	37	4	190909182	190909183	+	IGR	DEL	TT	-	-	rs79611741		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:190909182_190909183delTT								TUBB4Q (3158 upstream) : LOC653545 (99383 downstream)																																			---	---	---	---
LRRC14B	389257	broad.mit.edu	37	5	193252	193252	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:193252delG	uc003jal.1	+							NM_001080478	NP_001073947			leucine rich repeat containing 14B											skin(1)	1																		---	---	---	---
EXOC3	11336	broad.mit.edu	37	5	443615	443615	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:443615delC	uc003jba.2	+						C5orf55_uc010ita.2_5'Flank	NM_007277	NP_009208			Sec6 protein						exocytosis|protein transport						0		Ovarian(839;0.0563)	Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	551565	551566	+	IGR	DEL	AA	-	-	rs67344157		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:551565_551566delAA								SLC9A3 (27016 upstream) : CEP72 (60839 downstream)																																			---	---	---	---
CEP72	55722	broad.mit.edu	37	5	620722	620722	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:620722delC	uc003jbf.2	+						CEP72_uc011clz.1_Intron	NM_018140	NP_060610			centrosomal protein 72 kDa						G2/M transition of mitotic cell cycle|gamma-tubulin complex localization|spindle organization	centrosome|cytosol				ovary(1)	1			Epithelial(17;0.000339)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|Lung(60;0.0863)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	859964	859964	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:859964delG								ZDHHC11 (8863 upstream) : BRD9 (3887 downstream)																																			---	---	---	---
TRIP13	9319	broad.mit.edu	37	5	896984	896984	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:896984delG	uc003jbr.2	+						TRIP13_uc010ite.1_Intron	NM_004237	NP_004228			thyroid hormone receptor interactor 13						double-strand break repair|reciprocal meiotic recombination|synaptonemal complex assembly|transcription from RNA polymerase II promoter		ATP binding|identical protein binding|nucleoside-triphosphatase activity|transcription cofactor activity				0			Epithelial(17;0.00147)|OV - Ovarian serous cystadenocarcinoma(19;0.00271)|all cancers(22;0.00622)|Lung(60;0.165)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	978779	978779	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:978779delT								TRIP13 (60621 upstream) : NKD2 (30389 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	1127139	1127139	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1127139delT								SLC12A7 (14967 upstream) : SLC6A19 (74571 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	1137064	1137066	+	IGR	DEL	ACC	-	-	rs146508637		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1137064_1137066delACC								SLC12A7 (24892 upstream) : SLC6A19 (64644 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	1177953	1177953	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1177953delA	uc003jbv.1	-											Homo sapiens cDNA FLJ34472 fis, clone HLUNG2003691.																														---	---	---	---
SLC6A18	348932	broad.mit.edu	37	5	1230076	1230076	+	Intron	DEL	C	-	-	rs151076146	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1230076delC	uc003jby.1	+							NM_182632	NP_872438			solute carrier family 6, member 18						cellular nitrogen compound metabolic process	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity			ovary(1)	1	all_cancers(3;2.99e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.76e-10)		Epithelial(17;0.000356)|all cancers(22;0.00124)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)															---	---	---	---
CLPTM1L	81037	broad.mit.edu	37	5	1321591	1321591	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1321591delT	uc003jch.2	-						CLPTM1L_uc003jcg.2_Intron	NM_030782	NP_110409			CLPTM1-like						apoptosis	integral to membrane				breast(1)|central_nervous_system(1)	2	Lung NSC(6;5.78e-14)|all_lung(6;4.47e-13)|all_epithelial(6;4.47e-09)		Epithelial(17;0.00931)|OV - Ovarian serous cystadenocarcinoma(19;0.0116)|all cancers(22;0.0181)	KIRC - Kidney renal clear cell carcinoma(5;0.177)|Kidney(13;0.208)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	1528721	1528721	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1528721delA								LPCAT1 (4645 upstream) : SDHAP3 (39916 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	1562340	1562341	+	IGR	INS	-	AC	AC	rs139946135	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1562340_1562341insAC								LPCAT1 (38264 upstream) : SDHAP3 (6296 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	1703622	1703622	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1703622delC								LOC728613 (69502 upstream) : MRPL36 (94878 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	1876118	1876118	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1876118delT								NDUFS6 (59955 upstream) : IRX4 (1423 downstream)																																			---	---	---	---
IRX4	50805	broad.mit.edu	37	5	1879665	1879665	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1879665delC	uc003jcz.2	-	4	808	c.689delG	c.(688-690)GGCfs	p.G230fs	IRX4_uc011cmf.1_Frame_Shift_Del_p.G91fs	NM_016358	NP_057442	P78413	IRX4_HUMAN	iroquois homeobox 4	230					heart development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0				GBM - Glioblastoma multiforme(108;0.242)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	1922600	1922601	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1922600_1922601delAA								IRX4 (39720 upstream) : IRX2 (823680 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	2080903	2080904	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2080903_2080904insT								IRX4 (198023 upstream) : IRX2 (665377 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	2129071	2129071	+	IGR	DEL	T	-	-	rs33913124		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2129071delT								IRX4 (246191 upstream) : IRX2 (617210 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	2145935	2145936	+	IGR	INS	-	C	C	rs144120416		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2145935_2145936insC								IRX4 (263055 upstream) : IRX2 (600345 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	2146339	2146340	+	IGR	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2146339_2146340insC								IRX4 (263459 upstream) : IRX2 (599941 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	2291499	2291500	+	IGR	INS	-	C	C	rs78379745		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2291499_2291500insC								IRX4 (408619 upstream) : IRX2 (454781 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	2398595	2398595	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2398595delA								IRX4 (515715 upstream) : IRX2 (347686 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	2433456	2433457	+	IGR	DEL	AG	-	-	rs315902		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2433456_2433457delAG								IRX4 (550576 upstream) : IRX2 (312824 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	2585448	2585449	+	IGR	INS	-	GATG	GATG	rs28742164	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2585448_2585449insGATG								IRX4 (702568 upstream) : IRX2 (160832 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	2612775	2612776	+	IGR	DEL	AA	-	-	rs73735834	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2612775_2612776delAA								IRX4 (729895 upstream) : IRX2 (133505 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	2783892	2783892	+	IGR	DEL	C	-	-	rs34215414		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2783892delC								C5orf38 (28380 upstream) : IRX1 (812276 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	2997023	2997023	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:2997023delC								C5orf38 (241511 upstream) : IRX1 (599145 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	3111366	3111366	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3111366delT								C5orf38 (355854 upstream) : IRX1 (484802 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	3413300	3413301	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3413300_3413301delTG								C5orf38 (657788 upstream) : IRX1 (182867 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	3425293	3425293	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3425293delA	uc003jdd.2	-											Homo sapiens cDNA clone IMAGE:4823480.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	3533188	3533188	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3533188delT	uc003jdd.2	-											Homo sapiens cDNA clone IMAGE:4823480.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	3561741	3561741	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3561741delT								C5orf38 (806229 upstream) : IRX1 (34427 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	3577130	3577130	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3577130delC								C5orf38 (821618 upstream) : IRX1 (19038 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	3601622	3601623	+	IGR	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3601622_3601623delAG								IRX1 (106 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	3961387	3961388	+	IGR	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3961387_3961388delAG								IRX1 (359871 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	3970886	3970886	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:3970886delG								IRX1 (369370 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	4010857	4010857	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4010857delT								IRX1 (409341 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	4056965	4056965	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4056965delA								IRX1 (455449 upstream) : LOC340094 (977507 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	4073344	4073344	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4073344delT								IRX1 (471828 upstream) : LOC340094 (961128 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	4277083	4277083	+	IGR	DEL	A	-	-	rs11362055		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4277083delA								IRX1 (675567 upstream) : LOC340094 (757389 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	4286927	4286927	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4286927delT								IRX1 (685411 upstream) : LOC340094 (747545 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	4400837	4400838	+	IGR	INS	-	AAAG	AAAG	rs144804283	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4400837_4400838insAAAG								IRX1 (799321 upstream) : LOC340094 (633634 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	4404051	4404052	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4404051_4404052delTG								IRX1 (802535 upstream) : LOC340094 (630420 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	4691292	4691293	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4691292_4691293insA								None (None upstream) : LOC340094 (343179 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	4758291	4758292	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4758291_4758292delTG								None (None upstream) : LOC340094 (276180 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	4922343	4922344	+	IGR	DEL	AC	-	-	rs1562956		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4922343_4922344delAC								None (None upstream) : LOC340094 (112128 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	4985887	4985887	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:4985887delA								None (None upstream) : LOC340094 (48585 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	5110898	5110898	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5110898delA								LOC340094 (40789 upstream) : ADAMTS16 (29545 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	5670505	5670505	+	IGR	DEL	T	-	-	rs60633970		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5670505delT								KIAA0947 (180168 upstream) : FLJ33360 (640049 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	5843877	5843877	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5843877delT								KIAA0947 (353540 upstream) : FLJ33360 (466677 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	5847373	5847373	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5847373delT								KIAA0947 (357036 upstream) : FLJ33360 (463181 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	5937211	5937211	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5937211delT								KIAA0947 (446874 upstream) : FLJ33360 (373343 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	6044743	6044743	+	IGR	DEL	A	-	-	rs171588	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6044743delA								KIAA0947 (554406 upstream) : FLJ33360 (265811 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	6207419	6207419	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6207419delG								KIAA0947 (717082 upstream) : FLJ33360 (103135 downstream)																																			---	---	---	---
UBE2QL1	134111	broad.mit.edu	37	5	6447816	6447817	+	5'Flank	INS	-	CA	CA			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6447816_6447817insCA	uc003jdp.3	+							NM_001145161	NP_001138633			ubiquitin-conjugating enzyme E2Q family-like 1								ATP binding|ubiquitin-protein ligase activity				0																		---	---	---	---
UBE2QL1	134111	broad.mit.edu	37	5	6488920	6488921	+	Intron	DEL	AA	-	-	rs75358166		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6488920_6488921delAA	uc003jdp.3	+							NM_001145161	NP_001138633			ubiquitin-conjugating enzyme E2Q family-like 1								ATP binding|ubiquitin-protein ligase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	6498728	6498728	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6498728delA								UBE2QL1 (6023 upstream) : LOC255167 (83559 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	6519443	6519444	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6519443_6519444delAA								UBE2QL1 (26738 upstream) : LOC255167 (62843 downstream)																																			---	---	---	---
NSUN2	54888	broad.mit.edu	37	5	6604807	6604807	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6604807delA	uc003jdu.2	-						NSUN2_uc003jds.2_Frame_Shift_Del_p.Y23fs|NSUN2_uc003jdt.2_Intron|NSUN2_uc011cmk.1_Intron|NSUN2_uc003jdv.2_Intron	NM_017755	NP_060225			NOL1/NOP2/Sun domain family, member 2							cytoplasm|nucleolus	tRNA (cytosine-5-)-methyltransferase activity|tRNA binding			ovary(1)	1																		---	---	---	---
NSUN2	54888	broad.mit.edu	37	5	6620711	6620711	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6620711delA	uc003jdu.2	-						NSUN2_uc003jdt.2_5'UTR|NSUN2_uc011cmk.1_Intron|NSUN2_uc003jdv.2_Intron	NM_017755	NP_060225			NOL1/NOP2/Sun domain family, member 2							cytoplasm|nucleolus	tRNA (cytosine-5-)-methyltransferase activity|tRNA binding			ovary(1)	1																		---	---	---	---
PAPD7	11044	broad.mit.edu	37	5	6750912	6750913	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6750912_6750913delAA	uc003jdx.1	+						PAPD7_uc011cmn.1_Intron|PAPD7_uc010itl.1_Intron	NM_006999	NP_008930			DNA polymerase sigma						cell division|DNA replication|double-strand break repair|mitotic chromosome condensation|response to drug|sister chromatid cohesion	nucleus	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|SMC protein binding			ovary(1)	1																		---	---	---	---
PAPD7	11044	broad.mit.edu	37	5	6755012	6755013	+	Frame_Shift_Ins	INS	-	AC	AC			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6755012_6755013insAC	uc003jdx.1	+	13	1712_1713	c.1583_1584insAC	c.(1582-1584)AAAfs	p.K528fs	PAPD7_uc011cmn.1_Frame_Shift_Ins_p.K518fs|PAPD7_uc010itl.1_Frame_Shift_Ins_p.K348fs	NM_006999	NP_008930	Q5XG87	PAPD7_HUMAN	DNA polymerase sigma	528					cell division|DNA replication|double-strand break repair|mitotic chromosome condensation|response to drug|sister chromatid cohesion	nucleus	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|SMC protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	6792375	6792376	+	IGR	DEL	TG	-	-	rs71606079		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6792375_6792376delTG								PAPD7 (35214 upstream) : ADCY2 (603967 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	6795237	6795242	+	IGR	DEL	TTTTTT	-	-	rs71606080		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6795237_6795242delTTTTTT								PAPD7 (38076 upstream) : ADCY2 (601101 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	7021526	7021528	+	IGR	DEL	ATT	-	-	rs150706572		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7021526_7021528delATT								PAPD7 (264365 upstream) : ADCY2 (374815 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	7049287	7049287	+	IGR	DEL	A	-	-	rs140661967		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7049287delA								PAPD7 (292126 upstream) : ADCY2 (347056 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	7135946	7135946	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7135946delT								PAPD7 (378785 upstream) : ADCY2 (260397 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	7155501	7155501	+	IGR	DEL	T	-	-	rs77770801		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7155501delT								PAPD7 (398340 upstream) : ADCY2 (240842 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	7208602	7208602	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7208602delC								PAPD7 (451441 upstream) : ADCY2 (187741 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	7323474	7323474	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7323474delA								PAPD7 (566313 upstream) : ADCY2 (72869 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	7371098	7371098	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7371098delA								PAPD7 (613937 upstream) : ADCY2 (25245 downstream)																																			---	---	---	---
ADCY2	108	broad.mit.edu	37	5	7457906	7457909	+	Intron	DEL	AAGT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7457906_7457909delAAGT	uc003jdz.1	+							NM_020546	NP_065433			adenylate cyclase 2						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)|skin(1)	7																		---	---	---	---
ADCY2	108	broad.mit.edu	37	5	7628936	7628939	+	Intron	DEL	AAAA	-	-	rs72250823		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7628936_7628939delAAAA	uc003jdz.1	+							NM_020546	NP_065433			adenylate cyclase 2						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)|skin(1)	7																		---	---	---	---
ADCY2	108	broad.mit.edu	37	5	7633239	7633239	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7633239delA	uc003jdz.1	+							NM_020546	NP_065433			adenylate cyclase 2						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)|skin(1)	7																		---	---	---	---
ADCY2	108	broad.mit.edu	37	5	7755520	7755520	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7755520delA	uc003jdz.1	+						ADCY2_uc011cmo.1_Intron	NM_020546	NP_065433			adenylate cyclase 2						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)|skin(1)	7																		---	---	---	---
ADCY2	108	broad.mit.edu	37	5	7806427	7806427	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7806427delA	uc003jdz.1	+						ADCY2_uc011cmo.1_Intron|ADCY2_uc010itm.1_Intron	NM_020546	NP_065433			adenylate cyclase 2						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)|skin(1)	7																		---	---	---	---
ADCY2	108	broad.mit.edu	37	5	7813023	7813023	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7813023delA	uc003jdz.1	+						ADCY2_uc011cmo.1_Intron|ADCY2_uc010itm.1_Intron	NM_020546	NP_065433			adenylate cyclase 2						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)|skin(1)	7																		---	---	---	---
ADCY2	108	broad.mit.edu	37	5	7826747	7826747	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7826747delT	uc003jdz.1	+						ADCY2_uc011cmo.1_Intron|ADCY2_uc010itm.1_Intron	NM_020546	NP_065433			adenylate cyclase 2						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)|skin(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	7971776	7971776	+	IGR	DEL	T	-	-	rs2021827	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7971776delT								MTRR (70543 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	8200170	8200171	+	IGR	INS	-	GA	GA			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8200170_8200171insGA								MTRR (298937 upstream) : SEMA5A (834967 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	8257552	8257553	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8257552_8257553delTT								MTRR (356319 upstream) : SEMA5A (777585 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	8348634	8348634	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8348634delA	uc003jeh.1	-											Homo sapiens cDNA clone IMAGE:5297486.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	8506686	8506686	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8506686delA								MTRR (605453 upstream) : SEMA5A (528452 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	8844200	8844201	+	Intron	INS	-	GT	GT	rs148909600	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8844200_8844201insGT	uc003jej.2	+											Homo sapiens cDNA clone IMAGE:5259428.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	8925323	8925323	+	IGR	DEL	T	-	-	rs34286559		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:8925323delT								None (None upstream) : SEMA5A (109815 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	9025264	9025264	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9025264delA								None (None upstream) : SEMA5A (9874 downstream)																																			---	---	---	---
SEMA5A	9037	broad.mit.edu	37	5	9044550	9044550	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9044550delG	uc003jek.2	-	22	3752	c.3040delC	c.(3040-3042)CTTfs	p.L1014fs		NM_003966	NP_003957	Q13591	SEM5A_HUMAN	semaphorin 5A precursor	1014	Cytoplasmic (Potential).				cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
SEMA5A	9037	broad.mit.edu	37	5	9068808	9068808	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9068808delA	uc003jek.2	-							NM_003966	NP_003957			semaphorin 5A precursor						cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
SEMA5A	9037	broad.mit.edu	37	5	9101073	9101073	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9101073delA	uc003jek.2	-							NM_003966	NP_003957			semaphorin 5A precursor						cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
SEMA5A	9037	broad.mit.edu	37	5	9203933	9203933	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9203933delA	uc003jek.2	-							NM_003966	NP_003957			semaphorin 5A precursor						cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
SEMA5A	9037	broad.mit.edu	37	5	9319564	9319565	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9319564_9319565insA	uc003jek.2	-							NM_003966	NP_003957			semaphorin 5A precursor						cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
SEMA5A	9037	broad.mit.edu	37	5	9324751	9324751	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9324751delA	uc003jek.2	-							NM_003966	NP_003957			semaphorin 5A precursor						cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
SEMA5A	9037	broad.mit.edu	37	5	9469818	9469818	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9469818delT	uc003jek.2	-							NM_003966	NP_003957			semaphorin 5A precursor						cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
SEMA5A	9037	broad.mit.edu	37	5	9477226	9477227	+	Intron	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9477226_9477227delTC	uc003jek.2	-							NM_003966	NP_003957			semaphorin 5A precursor						cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
LOC285692	285692	broad.mit.edu	37	5	9713103	9713103	+	5'Flank	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9713103delC	uc010itq.1	-						LOC285692_uc003jen.2_Intron					Homo sapiens clone TEE10 Cri-du-chat region mRNA.												0																		---	---	---	---
LOC285692	285692	broad.mit.edu	37	5	9743012	9743012	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9743012delA	uc003jen.2	-							NR_027112				Homo sapiens clone TEE10 Cri-du-chat region mRNA.												0																		---	---	---	---
LOC285692	285692	broad.mit.edu	37	5	9862313	9862313	+	Intron	DEL	A	-	-	rs34827790		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9862313delA	uc003jen.2	-							NR_027112				Homo sapiens clone TEE10 Cri-du-chat region mRNA.												0																		---	---	---	---
LOC285692	285692	broad.mit.edu	37	5	9893321	9893323	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9893321_9893323delTTT	uc003jen.2	-							NR_027112				Homo sapiens clone TEE10 Cri-du-chat region mRNA.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	10031686	10031686	+	IGR	DEL	T	-	-	rs66634096		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10031686delT								LOC285692 (127750 upstream) : FAM173B (194752 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	10107274	10107274	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10107274delA								LOC285692 (203338 upstream) : FAM173B (119164 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	10132553	10132553	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10132553delA								LOC285692 (228617 upstream) : FAM173B (93885 downstream)																																			---	---	---	---
CMBL	134147	broad.mit.edu	37	5	10291779	10291780	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10291779_10291780delAA	uc003jes.2	-							NM_138809	NP_620164			carboxymethylenebutenolidase							cytosol	hydrolase activity|protein binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	10343442	10343442	+	IGR	DEL	A	-	-	rs77784857		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10343442delA								CMBL (35274 upstream) : MARCH6 (10386 downstream)																																			---	---	---	---
MARCH6	10299	broad.mit.edu	37	5	10405856	10405856	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10405856delT	uc003jet.1	+						MARCH6_uc011cmu.1_Intron|MARCH6_uc003jeu.1_Intron|MARCH6_uc011cmv.1_Intron	NM_005885	NP_005876			membrane-associated ring finger (C3HC4) 6						protein K48-linked ubiquitination	integral to endoplasmic reticulum membrane	ubiquitin conjugating enzyme binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|breast(1)	2																		---	---	---	---
MARCH6	10299	broad.mit.edu	37	5	10415851	10415851	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10415851delT	uc003jet.1	+						MARCH6_uc011cmu.1_Intron|MARCH6_uc003jeu.1_Intron|MARCH6_uc011cmv.1_Intron	NM_005885	NP_005876			membrane-associated ring finger (C3HC4) 6						protein K48-linked ubiquitination	integral to endoplasmic reticulum membrane	ubiquitin conjugating enzyme binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|breast(1)	2																		---	---	---	---
MARCH6	10299	broad.mit.edu	37	5	10424069	10424070	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10424069_10424070delTT	uc003jet.1	+						MARCH6_uc011cmu.1_Intron|MARCH6_uc003jeu.1_Intron|MARCH6_uc011cmv.1_Intron	NM_005885	NP_005876			membrane-associated ring finger (C3HC4) 6						protein K48-linked ubiquitination	integral to endoplasmic reticulum membrane	ubiquitin conjugating enzyme binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|breast(1)	2																		---	---	---	---
MARCH6	10299	broad.mit.edu	37	5	10427740	10427740	+	Intron	DEL	A	-	-	rs78606808	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10427740delA	uc003jet.1	+						MARCH6_uc011cmu.1_Intron|MARCH6_uc003jeu.1_Intron|MARCH6_uc011cmv.1_Intron	NM_005885	NP_005876			membrane-associated ring finger (C3HC4) 6						protein K48-linked ubiquitination	integral to endoplasmic reticulum membrane	ubiquitin conjugating enzyme binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|breast(1)	2																		---	---	---	---
DAP	1611	broad.mit.edu	37	5	10683952	10683952	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10683952delT	uc003jez.3	-						DAP_uc011cmw.1_Intron	NM_004394	NP_004385			death-associated protein						activation of caspase activity|cellular response to amino acid starvation|induction of apoptosis by extracellular signals|negative regulation of autophagy|negative regulation of NF-kappaB transcription factor activity|negative regulation of transcription, DNA-dependent		death domain binding				0		Ovarian(839;1.34e-05)|Breast(839;0.0634)|Lung NSC(810;0.0804)																---	---	---	---
Unknown	0	broad.mit.edu	37	5	10884723	10884723	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10884723delA								DAP (123336 upstream) : CTNND2 (87229 downstream)																																			---	---	---	---
CTNND2	1501	broad.mit.edu	37	5	10990564	10990564	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10990564delC	uc003jfa.1	-						CTNND2_uc010itt.2_Intron|CTNND2_uc011cmy.1_Intron|CTNND2_uc011cmz.1_Intron|CTNND2_uc010itu.1_Intron|CTNND2_uc011cmx.1_Intron	NM_001332	NP_001323			catenin (cadherin-associated protein), delta 2						multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8																		---	---	---	---
CTNND2	1501	broad.mit.edu	37	5	11182056	11182056	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11182056delG	uc003jfa.1	-						CTNND2_uc010itt.2_Intron|CTNND2_uc011cmy.1_Intron|CTNND2_uc011cmz.1_Intron|CTNND2_uc010itu.1_Intron|CTNND2_uc011cmx.1_Intron	NM_001332	NP_001323			catenin (cadherin-associated protein), delta 2						multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8																		---	---	---	---
CTNND2	1501	broad.mit.edu	37	5	11183249	11183249	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11183249delA	uc003jfa.1	-						CTNND2_uc010itt.2_Intron|CTNND2_uc011cmy.1_Intron|CTNND2_uc011cmz.1_Intron|CTNND2_uc010itu.1_Intron|CTNND2_uc011cmx.1_Intron	NM_001332	NP_001323			catenin (cadherin-associated protein), delta 2						multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8																		---	---	---	---
CTNND2	1501	broad.mit.edu	37	5	11312112	11312113	+	Intron	DEL	CA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11312112_11312113delCA	uc003jfa.1	-						CTNND2_uc010itt.2_Intron|CTNND2_uc011cmy.1_Intron|CTNND2_uc011cmz.1_Intron|CTNND2_uc010itu.1_Intron|CTNND2_uc011cmx.1_Intron	NM_001332	NP_001323			catenin (cadherin-associated protein), delta 2						multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8																		---	---	---	---
CTNND2	1501	broad.mit.edu	37	5	11345921	11345921	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11345921delA	uc003jfa.1	-						CTNND2_uc010itt.2_Intron|CTNND2_uc011cmy.1_Intron|CTNND2_uc011cmz.1_Intron|CTNND2_uc010itu.1_Intron|CTNND2_uc011cmx.1_Intron	NM_001332	NP_001323			catenin (cadherin-associated protein), delta 2						multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8																		---	---	---	---
CTNND2	1501	broad.mit.edu	37	5	11378897	11378897	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11378897delT	uc003jfa.1	-						CTNND2_uc010itt.2_Intron|CTNND2_uc011cmy.1_Intron|CTNND2_uc011cmz.1_Intron|CTNND2_uc010itu.1_Intron|CTNND2_uc011cmx.1_Intron	NM_001332	NP_001323			catenin (cadherin-associated protein), delta 2						multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8																		---	---	---	---
CTNND2	1501	broad.mit.edu	37	5	11384949	11384949	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11384949delG	uc003jfa.1	-	7	1150	c.1005delC	c.(1003-1005)CCCfs	p.P335fs	CTNND2_uc010itt.2_Frame_Shift_Del_p.P244fs|CTNND2_uc011cmy.1_Intron|CTNND2_uc011cmz.1_Intron|CTNND2_uc010itu.1_Intron|CTNND2_uc011cmx.1_5'UTR	NM_001332	NP_001323	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	335					multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8																		---	---	---	---
CTNND2	1501	broad.mit.edu	37	5	11477494	11477495	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11477494_11477495delTT	uc003jfa.1	-						CTNND2_uc010itt.2_Intron|CTNND2_uc011cmy.1_Intron|CTNND2_uc011cmz.1_Intron|CTNND2_uc010itu.1_Intron	NM_001332	NP_001323			catenin (cadherin-associated protein), delta 2						multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8																		---	---	---	---
CTNND2	1501	broad.mit.edu	37	5	11484158	11484158	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11484158delC	uc003jfa.1	-						CTNND2_uc010itt.2_Intron|CTNND2_uc011cmy.1_Intron|CTNND2_uc011cmz.1_Intron|CTNND2_uc010itu.1_Intron	NM_001332	NP_001323			catenin (cadherin-associated protein), delta 2						multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8																		---	---	---	---
CTNND2	1501	broad.mit.edu	37	5	11551480	11551480	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11551480delT	uc003jfa.1	-						CTNND2_uc010itt.2_Intron|CTNND2_uc011cmy.1_Intron|CTNND2_uc011cmz.1_Intron|CTNND2_uc010itu.1_Intron	NM_001332	NP_001323			catenin (cadherin-associated protein), delta 2						multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8																		---	---	---	---
CTNND2	1501	broad.mit.edu	37	5	11628887	11628887	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11628887delA	uc003jfa.1	-						CTNND2_uc011cmz.1_Intron|CTNND2_uc010itu.1_Intron	NM_001332	NP_001323			catenin (cadherin-associated protein), delta 2						multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8																		---	---	---	---
CTNND2	1501	broad.mit.edu	37	5	11726206	11726206	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11726206delT	uc003jfa.1	-						CTNND2_uc011cmz.1_Intron|CTNND2_uc010itu.1_Intron	NM_001332	NP_001323			catenin (cadherin-associated protein), delta 2						multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8																		---	---	---	---
CTNND2	1501	broad.mit.edu	37	5	11752753	11752753	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11752753delT	uc003jfa.1	-						CTNND2_uc011cmz.1_Intron|CTNND2_uc010itu.1_Intron	NM_001332	NP_001323			catenin (cadherin-associated protein), delta 2						multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	12239047	12239048	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:12239047_12239048delAA								CTNND2 (334937 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	12275117	12275117	+	IGR	DEL	T	-	-	rs72294044		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:12275117delT								CTNND2 (371007 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	12356531	12356531	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:12356531delT								CTNND2 (452421 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	12604379	12604379	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:12604379delT	uc003jfb.1	+						uc010itv.1_Intron					Homo sapiens TAG1 mRNA, complete sequence.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	12657173	12657174	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:12657173_12657174insA	uc003jfb.1	+						uc010itv.1_Intron					Homo sapiens TAG1 mRNA, complete sequence.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	12666691	12666691	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:12666691delC	uc003jfb.1	+						uc010itv.1_Intron					Homo sapiens TAG1 mRNA, complete sequence.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	12838158	12838160	+	IGR	DEL	TTT	-	-	rs138421732		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:12838158_12838160delTTT								CTNND2 (934048 upstream) : DNAH5 (852277 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	12967810	12967812	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:12967810_12967812delTTT								None (None upstream) : DNAH5 (722625 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	13119504	13119504	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13119504delA								None (None upstream) : DNAH5 (570933 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	13125272	13125272	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13125272delA								None (None upstream) : DNAH5 (565165 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	13155706	13155706	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13155706delT								None (None upstream) : DNAH5 (534731 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	13201217	13201217	+	IGR	DEL	A	-	-	rs76533242		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13201217delA								None (None upstream) : DNAH5 (489220 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	13211249	13211250	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13211249_13211250insA								None (None upstream) : DNAH5 (479187 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	13428551	13428551	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13428551delT								None (None upstream) : DNAH5 (261886 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	13556654	13556654	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13556654delA								None (None upstream) : DNAH5 (133783 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	13593893	13593893	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13593893delT								None (None upstream) : DNAH5 (96544 downstream)																																			---	---	---	---
DNAH5	1767	broad.mit.edu	37	5	13708059	13708059	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13708059delA	uc003jfd.2	-						DNAH5_uc003jfc.2_Intron	NM_001369	NP_001360			dynein, axonemal, heavy chain 5						microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)													Kartagener_syndrome				---	---	---	---
DNAH5	1767	broad.mit.edu	37	5	13732485	13732485	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13732485delT	uc003jfd.2	-						DNAH5_uc003jfc.2_Intron	NM_001369	NP_001360			dynein, axonemal, heavy chain 5						microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)													Kartagener_syndrome				---	---	---	---
DNAH5	1767	broad.mit.edu	37	5	13872998	13872999	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13872998_13872999delAA	uc003jfd.2	-							NM_001369	NP_001360			dynein, axonemal, heavy chain 5						microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)													Kartagener_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	5	14007457	14007457	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14007457delT								DNAH5 (62868 upstream) : TRIO (136372 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	14063328	14063328	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14063328delT								DNAH5 (118739 upstream) : TRIO (80501 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	14079316	14079316	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14079316delT								DNAH5 (134727 upstream) : TRIO (64513 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	14123382	14123382	+	IGR	DEL	A	-	-	rs115220583	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14123382delA								DNAH5 (178793 upstream) : TRIO (20447 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	14123699	14123699	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14123699delA								DNAH5 (179110 upstream) : TRIO (20130 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	14136576	14136577	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14136576_14136577insA								DNAH5 (191987 upstream) : TRIO (7252 downstream)																																			---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14143357	14143357	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14143357delT	uc003jff.2	+						TRIO_uc003jfg.2_5'Flank	NM_007118	NP_009049			triple functional domain (PTPRF interacting)						apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)																	---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14184091	14184091	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14184091delA	uc003jff.2	+						TRIO_uc003jfg.2_Intron|TRIO_uc011cna.1_Intron	NM_007118	NP_009049			triple functional domain (PTPRF interacting)						apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)																	---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14247172	14247172	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14247172delC	uc003jff.2	+						TRIO_uc003jfg.2_Intron|TRIO_uc011cna.1_Intron	NM_007118	NP_009049			triple functional domain (PTPRF interacting)						apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)																	---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14287249	14287249	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14287249delT	uc003jff.2	+						TRIO_uc003jfg.2_Intron|TRIO_uc011cna.1_Intron	NM_007118	NP_009049			triple functional domain (PTPRF interacting)						apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)																	---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14309911	14309911	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14309911delT	uc003jff.2	+						TRIO_uc003jfg.2_Intron|TRIO_uc011cna.1_Intron|TRIO_uc003jfh.1_Intron	NM_007118	NP_009049			triple functional domain (PTPRF interacting)						apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)																	---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14330443	14330443	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14330443delA	uc003jff.2	+						TRIO_uc003jfg.2_Intron|TRIO_uc011cna.1_Intron|TRIO_uc003jfh.1_Intron	NM_007118	NP_009049			triple functional domain (PTPRF interacting)						apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)																	---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14377266	14377266	+	Intron	DEL	T	-	-	rs112812791		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14377266delT	uc003jff.2	+						TRIO_uc003jfg.2_Intron|TRIO_uc011cna.1_Intron|TRIO_uc003jfh.1_Intron	NM_007118	NP_009049			triple functional domain (PTPRF interacting)						apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)																	---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14382964	14382965	+	Intron	INS	-	TG	TG	rs139747773	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14382964_14382965insTG	uc003jff.2	+						TRIO_uc003jfg.2_Intron|TRIO_uc011cna.1_Intron|TRIO_uc003jfh.1_Intron	NM_007118	NP_009049			triple functional domain (PTPRF interacting)						apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)																	---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14383051	14383052	+	Intron	INS	-	GT	GT			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14383051_14383052insGT	uc003jff.2	+						TRIO_uc003jfg.2_Intron|TRIO_uc011cna.1_Intron|TRIO_uc003jfh.1_Intron	NM_007118	NP_009049			triple functional domain (PTPRF interacting)						apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)																	---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14489275	14489276	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14489275_14489276delAA	uc003jff.2	+						TRIO_uc003jfg.2_Intron	NM_007118	NP_009049			triple functional domain (PTPRF interacting)						apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)																	---	---	---	---
Unknown	0	broad.mit.edu	37	5	14546358	14546359	+	IGR	INS	-	GT	GT	rs145256474	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14546358_14546359insGT								TRIO (36908 upstream) : FAM105A (35532 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	14559216	14559216	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14559216delG								TRIO (49766 upstream) : FAM105A (22675 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	14576902	14576902	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14576902delA								TRIO (67452 upstream) : FAM105A (4989 downstream)																																			---	---	---	---
FAM105A	54491	broad.mit.edu	37	5	14586985	14586985	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14586985delA	uc003jfj.2	+							NM_019018	NP_061891			hypothetical protein LOC54491											ovary(1)	1	Lung NSC(4;0.00592)																	---	---	---	---
Unknown	0	broad.mit.edu	37	5	14625171	14625172	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14625171_14625172delAA								FAM105A (8886 upstream) : FAM105B (39611 downstream)																																			---	---	---	---
FAM105B	90268	broad.mit.edu	37	5	14670881	14670882	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14670881_14670882delTT	uc003jfk.2	+							NM_138348	NP_612357			hypothetical protein LOC90268											ovary(2)	2	Lung NSC(4;0.00696)																	---	---	---	---
FAM105B	90268	broad.mit.edu	37	5	14697156	14697157	+	3'UTR	DEL	GT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14697156_14697157delGT	uc003jfk.2	+	7						NM_138348	NP_612357			hypothetical protein LOC90268											ovary(2)	2	Lung NSC(4;0.00696)																	---	---	---	---
ANKH	56172	broad.mit.edu	37	5	14769313	14769313	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14769313delA	uc003jfm.3	-							NM_054027	NP_473368			progressive ankylosis protein						locomotory behavior|regulation of bone mineralization|skeletal system development	integral to plasma membrane|outer membrane	inorganic diphosphate transmembrane transporter activity|inorganic phosphate transmembrane transporter activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	14887435	14887435	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14887435delT								ANKH (15548 upstream) : FBXL7 (612870 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	14937711	14937711	+	IGR	DEL	T	-	-	rs112706492		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14937711delT								ANKH (65824 upstream) : FBXL7 (562594 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	14963347	14963348	+	IGR	DEL	TT	-	-	rs112928907		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14963347_14963348delTT								ANKH (91460 upstream) : FBXL7 (536957 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	14983823	14983827	+	IGR	DEL	TTTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14983823_14983827delTTTTT								ANKH (111936 upstream) : FBXL7 (516478 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	15041755	15041755	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15041755delT								ANKH (169868 upstream) : FBXL7 (458550 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	15348638	15348638	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15348638delT								ANKH (476751 upstream) : FBXL7 (151667 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	15375659	15375660	+	IGR	DEL	AA	-	-	rs149141223	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15375659_15375660delAA								ANKH (503772 upstream) : FBXL7 (124645 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	15376177	15376177	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15376177delT								ANKH (504290 upstream) : FBXL7 (124128 downstream)																																			---	---	---	---
FBXL7	23194	broad.mit.edu	37	5	15555332	15555332	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15555332delC	uc003jfn.1	+							NM_012304	NP_036436			F-box and leucine-rich repeat protein 7						ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(1)	3																		---	---	---	---
FBXL7	23194	broad.mit.edu	37	5	15597917	15597918	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15597917_15597918insA	uc003jfn.1	+							NM_012304	NP_036436			F-box and leucine-rich repeat protein 7						ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(1)	3																		---	---	---	---
FBXL7	23194	broad.mit.edu	37	5	15615946	15615946	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15615946delA	uc003jfn.1	+							NM_012304	NP_036436			F-box and leucine-rich repeat protein 7						ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(1)	3																		---	---	---	---
FBXL7	23194	broad.mit.edu	37	5	15760536	15760536	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:15760536delA	uc003jfn.1	+							NM_012304	NP_036436			F-box and leucine-rich repeat protein 7						ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	16310597	16310598	+	IGR	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16310597_16310598delCT								MARCH11 (130700 upstream) : ZNF622 (141031 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	16446849	16446849	+	IGR	DEL	A	-	-	rs80053380		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16446849delA								MARCH11 (266952 upstream) : ZNF622 (4780 downstream)																																			---	---	---	---
FAM134B	54463	broad.mit.edu	37	5	16614021	16614021	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16614021delA	uc003jfs.2	-							NM_001034850	NP_001030022			hypothetical protein LOC54463 isoform 1						sensory perception of pain	cis-Golgi network|endoplasmic reticulum|integral to membrane				ovary(2)|breast(1)	3																		---	---	---	---
MYO10	4651	broad.mit.edu	37	5	16682910	16682912	+	Intron	DEL	AAT	-	-	rs2401986	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16682910_16682912delAAT	uc003jft.3	-						MYO10_uc011cnb.1_5'Flank|MYO10_uc011cnc.1_Intron|MYO10_uc011cnd.1_Intron|MYO10_uc011cne.1_Intron|MYO10_uc010itx.2_Intron	NM_012334	NP_036466			myosin X						axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
MYO10	4651	broad.mit.edu	37	5	16682911	16682912	+	Intron	DEL	AT	-	-	rs2401986	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16682911_16682912delAT	uc003jft.3	-						MYO10_uc011cnb.1_5'Flank|MYO10_uc011cnc.1_Intron|MYO10_uc011cnd.1_Intron|MYO10_uc011cne.1_Intron|MYO10_uc010itx.2_Intron	NM_012334	NP_036466			myosin X						axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
MYO10	4651	broad.mit.edu	37	5	16714407	16714407	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16714407delA	uc003jft.3	-						MYO10_uc011cnd.1_Intron|MYO10_uc011cne.1_Intron|MYO10_uc010itx.2_Intron	NM_012334	NP_036466			myosin X						axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
MYO10	4651	broad.mit.edu	37	5	16740462	16740462	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16740462delA	uc003jft.3	-						MYO10_uc011cnd.1_5'Flank|MYO10_uc011cne.1_Intron|MYO10_uc010itx.2_Intron	NM_012334	NP_036466			myosin X						axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
MYO10	4651	broad.mit.edu	37	5	16801042	16801042	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16801042delA	uc003jft.3	-						MYO10_uc003jfu.2_Intron	NM_012334	NP_036466			myosin X						axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
MYO10	4651	broad.mit.edu	37	5	16818442	16818443	+	Intron	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16818442_16818443delTC	uc003jft.3	-						MYO10_uc003jfu.2_Intron|MYO10_uc003jfv.2_Intron	NM_012334	NP_036466			myosin X						axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
MYO10	4651	broad.mit.edu	37	5	16827310	16827310	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16827310delA	uc003jft.3	-						MYO10_uc003jfu.2_Intron|MYO10_uc003jfv.2_Intron	NM_012334	NP_036466			myosin X						axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
MYO10	4651	broad.mit.edu	37	5	16888711	16888711	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16888711delA	uc003jft.3	-						MYO10_uc003jfu.2_Intron|MYO10_uc003jfv.2_Intron	NM_012334	NP_036466			myosin X						axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
MYO10	4651	broad.mit.edu	37	5	16904258	16904258	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16904258delA	uc003jft.3	-						MYO10_uc003jfu.2_Intron|MYO10_uc003jfv.2_Intron	NM_012334	NP_036466			myosin X						axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	16946603	16946604	+	IGR	DEL	AA	-	-	rs113545792		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16946603_16946604delAA								MYO10 (10218 upstream) : LOC285696 (183533 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	16958052	16958052	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16958052delC								MYO10 (21667 upstream) : LOC285696 (172085 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	17104555	17104556	+	IGR	DEL	TC	-	-	rs67381352		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17104555_17104556delTC								MYO10 (168170 upstream) : LOC285696 (25581 downstream)																																			---	---	---	---
LOC285696	285696	broad.mit.edu	37	5	17173243	17173243	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17173243delA	uc003jfw.2	-							NR_027253				Homo sapiens cDNA FLJ34047 fis, clone FCBBF3000001.												0																		---	---	---	---
BASP1	10409	broad.mit.edu	37	5	17225381	17225381	+	Intron	DEL	A	-	-	rs3215105		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17225381delA	uc003jfx.2	+							NM_006317	NP_006308			brain abundant, membrane attached signal protein						glomerular visceral epithelial cell differentiation|negative regulation of transcription, DNA-dependent	cytoplasm|cytoskeleton|growth cone|nuclear speck|plasma membrane	protein domain specific binding|transcription corepressor activity|transcription regulatory region DNA binding				0																		---	---	---	---
BASP1	10409	broad.mit.edu	37	5	17233877	17233878	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17233877_17233878delTT	uc003jfx.2	+							NM_006317	NP_006308			brain abundant, membrane attached signal protein						glomerular visceral epithelial cell differentiation|negative regulation of transcription, DNA-dependent	cytoplasm|cytoskeleton|growth cone|nuclear speck|plasma membrane	protein domain specific binding|transcription corepressor activity|transcription regulatory region DNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	17676986	17676986	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17676986delT								BASP1 (400051 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	17745028	17745029	+	IGR	INS	-	TG	TG	rs142984710	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17745028_17745029insTG								BASP1 (468093 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	17761360	17761360	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17761360delT								BASP1 (484425 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	17870670	17870671	+	Intron	INS	-	T	T	rs145743736	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17870670_17870671insT	uc003jgb.2	+											Homo sapiens cDNA clone IMAGE:5201079.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	17894851	17894853	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17894851_17894853delTTT	uc003jgb.2	+											Homo sapiens cDNA clone IMAGE:5201079.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	17929749	17929749	+	RNA	DEL	T	-	-	rs146489835		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17929749delT	uc003jgb.2	+	7		c.959delT								Homo sapiens cDNA clone IMAGE:5201079.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	17950351	17950351	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:17950351delT								BASP1 (673416 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	18056603	18056603	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18056603delA								BASP1 (779668 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	18123155	18123155	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18123155delA								BASP1 (846220 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	18187629	18187629	+	IGR	DEL	T	-	-	rs75669003	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18187629delT								BASP1 (910694 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	18239268	18239268	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18239268delT								BASP1 (962333 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	18251707	18251708	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18251707_18251708insA								BASP1 (974772 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	18259068	18259068	+	IGR	DEL	A	-	-	rs71953292		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18259068delA								BASP1 (982133 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	18351455	18351457	+	IGR	DEL	ACA	-	-	rs142039737		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18351455_18351457delACA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	18363291	18363293	+	IGR	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18363291_18363293delAAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	18468754	18468754	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18468754delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	18570942	18570942	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18570942delA								None (None upstream) : CDH18 (902215 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	18650648	18650649	+	IGR	INS	-	GT	GT	rs140458001	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18650648_18650649insGT								None (None upstream) : CDH18 (822508 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	18731495	18731495	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18731495delT								None (None upstream) : CDH18 (741662 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	18745147	18745149	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18745147_18745149delTTT								None (None upstream) : CDH18 (728008 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	18934822	18934825	+	IGR	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:18934822_18934825delTTTT								None (None upstream) : CDH18 (538332 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	19031875	19031875	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19031875delA								None (None upstream) : CDH18 (441282 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	19046383	19046383	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19046383delT								None (None upstream) : CDH18 (426774 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	19086395	19086396	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19086395_19086396insA								None (None upstream) : CDH18 (386761 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	19109089	19109089	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19109089delT								None (None upstream) : CDH18 (364068 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	19255031	19255031	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19255031delA								None (None upstream) : CDH18 (218126 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	19368125	19368126	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19368125_19368126delAA								None (None upstream) : CDH18 (105031 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	19396615	19396616	+	IGR	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19396615_19396616delCT								None (None upstream) : CDH18 (76541 downstream)																																			---	---	---	---
CDH18	1016	broad.mit.edu	37	5	19537573	19537574	+	Intron	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19537573_19537574delAC	uc003jgc.2	-						CDH18_uc003jgd.2_Intron|CDH18_uc011cnm.1_Intron	NM_004934	NP_004925			cadherin 18, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)																	---	---	---	---
CDH18	1016	broad.mit.edu	37	5	19606013	19606013	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19606013delA	uc003jgc.2	-						CDH18_uc003jgd.2_Intron|CDH18_uc011cnm.1_Intron	NM_004934	NP_004925			cadherin 18, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)																	---	---	---	---
CDH18	1016	broad.mit.edu	37	5	19625432	19625432	+	Intron	DEL	T	-	-	rs72739139	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19625432delT	uc003jgc.2	-						CDH18_uc003jgd.2_Intron|CDH18_uc011cnm.1_Intron	NM_004934	NP_004925			cadherin 18, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)																	---	---	---	---
CDH18	1016	broad.mit.edu	37	5	19732206	19732206	+	Intron	DEL	A	-	-	rs11292049		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19732206delA	uc003jgc.2	-						CDH18_uc003jgd.2_Intron|CDH18_uc011cnm.1_Intron	NM_004934	NP_004925			cadherin 18, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)																	---	---	---	---
CDH18	1016	broad.mit.edu	37	5	19741549	19741549	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19741549delT	uc003jgc.2	-						CDH18_uc003jgd.2_Intron|CDH18_uc011cnm.1_Intron	NM_004934	NP_004925			cadherin 18, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)																	---	---	---	---
CDH18	1016	broad.mit.edu	37	5	19744612	19744613	+	Intron	INS	-	AC	AC	rs146975713	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19744612_19744613insAC	uc003jgc.2	-						CDH18_uc003jgd.2_Intron|CDH18_uc011cnm.1_Intron	NM_004934	NP_004925			cadherin 18, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)																	---	---	---	---
CDH18	1016	broad.mit.edu	37	5	19811270	19811271	+	Intron	DEL	GG	-	-	rs10473177	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19811270_19811271delGG	uc003jgc.2	-						CDH18_uc003jgd.2_Intron|CDH18_uc011cnm.1_Intron	NM_004934	NP_004925			cadherin 18, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)																	---	---	---	---
CDH18	1016	broad.mit.edu	37	5	19828532	19828534	+	Intron	DEL	CAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19828532_19828534delCAA	uc003jgc.2	-						CDH18_uc003jgd.2_Intron|CDH18_uc011cnm.1_Intron	NM_004934	NP_004925			cadherin 18, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)																	---	---	---	---
CDH18	1016	broad.mit.edu	37	5	19851861	19851862	+	Intron	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19851861_19851862delTG	uc003jgc.2	-						CDH18_uc003jgd.2_Intron|CDH18_uc011cnm.1_Intron	NM_004934	NP_004925			cadherin 18, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)																	---	---	---	---
CDH18	1016	broad.mit.edu	37	5	19925602	19925602	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19925602delT	uc003jgc.2	-						CDH18_uc003jgd.2_Intron|CDH18_uc011cnm.1_Intron	NM_004934	NP_004925			cadherin 18, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)																	---	---	---	---
Unknown	0	broad.mit.edu	37	5	20108640	20108640	+	IGR	DEL	T	-	-	rs147318780	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:20108640delT								CDH18 (120333 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	20131984	20131984	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:20131984delT								CDH18 (143677 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	20351361	20351362	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:20351361_20351362delTT								CDH18 (363054 upstream) : GUSBP1 (990580 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	20463412	20463413	+	IGR	DEL	AA	-	-	rs140023840		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:20463412_20463413delAA								CDH18 (475105 upstream) : GUSBP1 (878529 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	20475396	20475396	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:20475396delT								CDH18 (487089 upstream) : GUSBP1 (866546 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	20720543	20720543	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:20720543delA	uc003jge.1	+											Homo sapiens cDNA FLJ36043 fis, clone TESTI2017582.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	21033652	21033652	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21033652delA								None (None upstream) : GUSBP1 (308290 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	21096362	21096362	+	IGR	DEL	T	-	-	rs72226376		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21096362delT								None (None upstream) : GUSBP1 (245580 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	21246585	21246585	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21246585delT								None (None upstream) : GUSBP1 (95357 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	21322646	21322646	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21322646delA								None (None upstream) : GUSBP1 (19296 downstream)																																			---	---	---	---
GUSBP1	728411	broad.mit.edu	37	5	21494754	21494754	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21494754delT	uc010iub.2	+						GUSBP1_uc011cnn.1_Intron|GUSBP1_uc003jgh.3_Intron	NR_027028				SubName: Full=Putative uncharacterized protein GUSBL2;												0																		---	---	---	---
GUSBP1	728411	broad.mit.edu	37	5	21535641	21535641	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21535641delA	uc011cnn.1	+						GUSBP1_uc003jgh.3_Intron					Homo sapiens cDNA FLJ38337 fis, clone FCBBF3026692, moderately similar to Homo sapiens WD repeat domain 70 (WDR70), mRNA.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	21620426	21620426	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21620426delA	uc003jgj.2	+											Homo sapiens, clone IMAGE:5171606, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	21719655	21719656	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21719655_21719656delAA	uc003jgj.2	+											Homo sapiens, clone IMAGE:5171606, mRNA.																														---	---	---	---
CDH12	1010	broad.mit.edu	37	5	21755645	21755645	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21755645delA	uc010iuc.2	-						CDH12_uc011cno.1_Intron|CDH12_uc003jgk.2_Intron|uc003jgj.2_Intron	NM_004061	NP_004052			cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2															HNSCC(59;0.17)			---	---	---	---
CDH12	1010	broad.mit.edu	37	5	21820201	21820201	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21820201delA	uc010iuc.2	-						CDH12_uc011cno.1_Intron|CDH12_uc003jgk.2_Intron	NM_004061	NP_004052			cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2															HNSCC(59;0.17)			---	---	---	---
CDH12	1010	broad.mit.edu	37	5	21965705	21965705	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21965705delT	uc010iuc.2	-						CDH12_uc011cno.1_Intron|CDH12_uc003jgk.2_Intron	NM_004061	NP_004052			cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2															HNSCC(59;0.17)			---	---	---	---
CDH12	1010	broad.mit.edu	37	5	22143016	22143016	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22143016delT	uc010iuc.2	-						CDH12_uc011cno.1_Intron|CDH12_uc003jgk.2_Intron|PMCHL1_uc011cnp.1_Intron|PMCHL1_uc010iud.2_Intron|PMCHL1_uc011cnq.1_Intron|PMCHL1_uc011cnr.1_Intron|PMCHL1_uc003jgl.2_Intron|PMCHL1_uc011cns.1_Intron|PMCHL1_uc003jgn.2_Intron|PMCHL1_uc003jgm.2_RNA|PMCHL1_uc010iue.2_Intron|PMCHL1_uc011cnt.1_Intron	NM_004061	NP_004052			cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2															HNSCC(59;0.17)			---	---	---	---
CDH12	1010	broad.mit.edu	37	5	22229970	22229971	+	Intron	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22229970_22229971delAC	uc003jgk.2	-							NM_004061	NP_004052			cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2															HNSCC(59;0.17)			---	---	---	---
CDH12	1010	broad.mit.edu	37	5	22275446	22275446	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22275446delA	uc003jgk.2	-							NM_004061	NP_004052			cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2															HNSCC(59;0.17)			---	---	---	---
CDH12	1010	broad.mit.edu	37	5	22276085	22276085	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22276085delT	uc003jgk.2	-							NM_004061	NP_004052			cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2															HNSCC(59;0.17)			---	---	---	---
CDH12	1010	broad.mit.edu	37	5	22290433	22290434	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22290433_22290434insA	uc003jgk.2	-							NM_004061	NP_004052			cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2															HNSCC(59;0.17)			---	---	---	---
CDH12	1010	broad.mit.edu	37	5	22297100	22297101	+	Intron	DEL	TC	-	-	rs143413177	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22297100_22297101delTC	uc003jgk.2	-							NM_004061	NP_004052			cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2															HNSCC(59;0.17)			---	---	---	---
CDH12	1010	broad.mit.edu	37	5	22490678	22490678	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22490678delA	uc003jgk.2	-							NM_004061	NP_004052			cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2															HNSCC(59;0.17)			---	---	---	---
CDH12	1010	broad.mit.edu	37	5	22544924	22544925	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22544924_22544925delAA	uc003jgk.2	-							NM_004061	NP_004052			cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2															HNSCC(59;0.17)			---	---	---	---
CDH12	1010	broad.mit.edu	37	5	22562453	22562453	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22562453delA	uc003jgk.2	-							NM_004061	NP_004052			cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2															HNSCC(59;0.17)			---	---	---	---
CDH12	1010	broad.mit.edu	37	5	22570630	22570630	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22570630delA	uc003jgk.2	-							NM_004061	NP_004052			cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2															HNSCC(59;0.17)			---	---	---	---
CDH12	1010	broad.mit.edu	37	5	22574500	22574500	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22574500delT	uc003jgk.2	-							NM_004061	NP_004052			cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2															HNSCC(59;0.17)			---	---	---	---
CDH12	1010	broad.mit.edu	37	5	22626247	22626248	+	Intron	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22626247_22626248insC	uc003jgk.2	-							NM_004061	NP_004052			cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2															HNSCC(59;0.17)			---	---	---	---
Unknown	0	broad.mit.edu	37	5	22970976	22970977	+	IGR	DEL	AG	-	-	rs148536334		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22970976_22970977delAG								CDH12 (117245 upstream) : PRDM9 (536747 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	23001541	23001542	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23001541_23001542insA								CDH12 (147810 upstream) : PRDM9 (506182 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	23110932	23110932	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23110932delA								CDH12 (257201 upstream) : PRDM9 (396792 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	23160349	23160350	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23160349_23160350delTT								CDH12 (306618 upstream) : PRDM9 (347374 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	23191539	23191539	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23191539delA								CDH12 (337808 upstream) : PRDM9 (316185 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	23235771	23235771	+	IGR	DEL	A	-	-	rs73741958	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23235771delA								CDH12 (382040 upstream) : PRDM9 (271953 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	23319163	23319163	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23319163delT								CDH12 (465432 upstream) : PRDM9 (188561 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	23403291	23403291	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23403291delT								CDH12 (549560 upstream) : PRDM9 (104433 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	23451386	23451386	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23451386delA								CDH12 (597655 upstream) : PRDM9 (56338 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	23859218	23859218	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23859218delT								PRDM9 (330514 upstream) : CDH10 (627992 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	23863631	23863631	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:23863631delT								PRDM9 (334927 upstream) : CDH10 (623579 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	24251243	24251243	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24251243delT								PRDM9 (722539 upstream) : CDH10 (235967 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	24251645	24251646	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24251645_24251646delTT								PRDM9 (722941 upstream) : CDH10 (235564 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	24396548	24396548	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24396548delT								PRDM9 (867844 upstream) : CDH10 (90662 downstream)																																			---	---	---	---
CDH10	1008	broad.mit.edu	37	5	24521922	24521922	+	Intron	DEL	A	-	-	rs34883769		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24521922delA	uc003jgr.1	-						CDH10_uc011cnu.1_Intron	NM_006727	NP_006718			cadherin 10, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|pancreas(4)|breast(2)	12				STAD - Stomach adenocarcinoma(35;0.0556)											HNSCC(23;0.051)			---	---	---	---
CDH10	1008	broad.mit.edu	37	5	24537329	24537329	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24537329delT	uc003jgr.1	-						CDH10_uc011cnu.1_Intron	NM_006727	NP_006718			cadherin 10, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|pancreas(4)|breast(2)	12				STAD - Stomach adenocarcinoma(35;0.0556)											HNSCC(23;0.051)			---	---	---	---
CDH10	1008	broad.mit.edu	37	5	24550492	24550492	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24550492delA	uc003jgr.1	-						CDH10_uc011cnu.1_Intron	NM_006727	NP_006718			cadherin 10, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|pancreas(4)|breast(2)	12				STAD - Stomach adenocarcinoma(35;0.0556)											HNSCC(23;0.051)			---	---	---	---
Unknown	0	broad.mit.edu	37	5	24712952	24712952	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24712952delT								CDH10 (68041 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	24797175	24797175	+	IGR	DEL	T	-	-	rs11318322		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24797175delT								CDH10 (152264 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	25030573	25030573	+	IGR	DEL	T	-	-	rs78787009		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:25030573delT								CDH10 (385662 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	25105728	25105728	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:25105728delA								CDH10 (460817 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	25251023	25251023	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:25251023delA								CDH10 (606112 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	25271008	25271008	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:25271008delT								CDH10 (626097 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	25297835	25297835	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:25297835delA								CDH10 (652924 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	25371433	25371433	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:25371433delA								CDH10 (726522 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	25377797	25377798	+	IGR	INS	-	T	T	rs34449232		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:25377797_25377798insT								CDH10 (732886 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	25469613	25469614	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:25469613_25469614insA								CDH10 (824702 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	25496274	25496274	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:25496274delT								CDH10 (851363 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	26858388	26858388	+	IGR	DEL	A	-	-	rs34540612		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:26858388delA								None (None upstream) : CDH9 (22321 downstream)																																			---	---	---	---
CDH9	1007	broad.mit.edu	37	5	26897299	26897299	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:26897299delA	uc003jgs.1	-							NM_016279	NP_057363			cadherin 9, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|skin(2)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)	9																		---	---	---	---
CDH9	1007	broad.mit.edu	37	5	26943457	26943457	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:26943457delA	uc003jgs.1	-						CDH9_uc010iug.2_Intron	NM_016279	NP_057363			cadherin 9, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|skin(2)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)	9																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	27142408	27142408	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27142408delT								CDH9 (103719 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	27160093	27160093	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27160093delA								CDH9 (121404 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	27187813	27187813	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27187813delA								CDH9 (149124 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	27198484	27198487	+	IGR	DEL	TGTG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27198484_27198487delTGTG								CDH9 (159795 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	27292897	27292897	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27292897delA								CDH9 (254208 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	27348823	27348824	+	IGR	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27348823_27348824delAG								CDH9 (310134 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	27386986	27386986	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27386986delT								CDH9 (348297 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	27587234	27587234	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27587234delT								CDH9 (548545 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	27628098	27628099	+	IGR	DEL	CC	-	-	rs139621511	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27628098_27628099delCC								CDH9 (589409 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	27783780	27783780	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27783780delT								CDH9 (745091 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	27847538	27847539	+	IGR	DEL	GT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:27847538_27847539delGT								CDH9 (808849 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	28090608	28090609	+	IGR	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:28090608_28090609delAG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	28112946	28112947	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:28112946_28112947delAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	28115848	28115848	+	IGR	DEL	A	-	-	rs34800734		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:28115848delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	28663629	28663630	+	IGR	DEL	AC	-	-	rs13157149	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:28663629_28663630delAC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	28705267	28705267	+	IGR	DEL	T	-	-	rs74583572	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:28705267delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	28768599	28768600	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:28768599_28768600insT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	28870060	28870060	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:28870060delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	28968452	28968452	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:28968452delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	29175374	29175374	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:29175374delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	29433994	29433994	+	IGR	DEL	A	-	-	rs73071370	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:29433994delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	30122703	30122703	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:30122703delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	30147049	30147049	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:30147049delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	30428575	30428575	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:30428575delT								None (None upstream) : CDH6 (765221 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	30516146	30516147	+	IGR	DEL	AA	-	-	rs77702004		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:30516146_30516147delAA								None (None upstream) : CDH6 (677649 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	30536086	30536086	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:30536086delA								None (None upstream) : CDH6 (657710 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	30563512	30563512	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:30563512delA								None (None upstream) : CDH6 (630284 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	30747940	30747940	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:30747940delT								None (None upstream) : CDH6 (445856 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	30802929	30802929	+	IGR	DEL	T	-	-	rs34033218		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:30802929delT								None (None upstream) : CDH6 (390867 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	31183528	31183528	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31183528delA								None (None upstream) : CDH6 (10268 downstream)																																			---	---	---	---
CDH6	1004	broad.mit.edu	37	5	31290073	31290073	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31290073delA	uc003jhe.1	+						CDH6_uc003jhd.1_Intron	NM_004932	NP_004923			cadherin 6, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	cytoplasm|integral to membrane|nucleus|plasma membrane	calcium ion binding			ovary(4)|skin(2)|large_intestine(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	31346242	31346242	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31346242delT								CDH6 (21005 upstream) : RNASEN (54360 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	31386112	31386112	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31386112delA								CDH6 (60875 upstream) : RNASEN (14490 downstream)																																			---	---	---	---
RNASEN	29102	broad.mit.edu	37	5	31429552	31429552	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31429552delA	uc003jhg.2	-						RNASEN_uc003jhh.2_Intron|RNASEN_uc003jhi.2_Intron	NM_013235	NP_037367			ribonuclease III, nuclear isoform 1						gene silencing by RNA|ribosome biogenesis|RNA processing	nucleolus|nucleoplasm	double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity				0																		---	---	---	---
RNASEN	29102	broad.mit.edu	37	5	31435976	31435976	+	Intron	DEL	A	-	-	rs77666632		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31435976delA	uc003jhg.2	-						RNASEN_uc003jhh.2_Intron|RNASEN_uc003jhi.2_Intron	NM_013235	NP_037367			ribonuclease III, nuclear isoform 1						gene silencing by RNA|ribosome biogenesis|RNA processing	nucleolus|nucleoplasm	double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity				0																		---	---	---	---
RNASEN	29102	broad.mit.edu	37	5	31505441	31505441	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31505441delA	uc003jhg.2	-						RNASEN_uc003jhh.2_Intron|RNASEN_uc003jhi.2_Intron|RNASEN_uc010iui.1_Intron	NM_013235	NP_037367			ribonuclease III, nuclear isoform 1						gene silencing by RNA|ribosome biogenesis|RNA processing	nucleolus|nucleoplasm	double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity				0																		---	---	---	---
C5orf22	55322	broad.mit.edu	37	5	31538753	31538754	+	Frame_Shift_Ins	INS	-	T	T	rs143742555		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31538753_31538754insT	uc003jhj.3	+	4	891_892	c.764_765insT	c.(763-765)GATfs	p.D255fs	C5orf22_uc011cnw.1_RNA|C5orf22_uc003jhk.3_5'UTR	NM_018356	NP_060826	Q49AR2	CE022_HUMAN	hypothetical protein LOC55322	255										ovary(2)	2																		---	---	---	---
C5orf22	55322	broad.mit.edu	37	5	31545171	31545173	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31545171_31545173delTTT	uc003jhj.3	+						C5orf22_uc011cnw.1_Intron|C5orf22_uc003jhk.3_Intron|C5orf22_uc010iuj.2_5'Flank	NM_018356	NP_060826			hypothetical protein LOC55322											ovary(2)	2																		---	---	---	---
PDZD2	23037	broad.mit.edu	37	5	31646153	31646153	+	Intron	DEL	G	-	-	rs78083202		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31646153delG	uc003jhl.2	+							NM_178140	NP_835260			PDZ domain containing 2						cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9																		---	---	---	---
PDZD2	23037	broad.mit.edu	37	5	31663962	31663963	+	Intron	DEL	GT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31663962_31663963delGT	uc003jhl.2	+							NM_178140	NP_835260			PDZ domain containing 2						cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9																		---	---	---	---
PDZD2	23037	broad.mit.edu	37	5	31823086	31823086	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31823086delT	uc003jhl.2	+						PDZD2_uc003jhm.2_Intron	NM_178140	NP_835260			PDZ domain containing 2						cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9																		---	---	---	---
PDZD2	23037	broad.mit.edu	37	5	31941068	31941068	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31941068delA	uc003jhl.2	+						PDZD2_uc003jhm.2_Intron|PDZD2_uc011cnx.1_Intron	NM_178140	NP_835260			PDZ domain containing 2						cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9																		---	---	---	---
PDZD2	23037	broad.mit.edu	37	5	31962030	31962030	+	Intron	DEL	T	-	-	rs11329169		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:31962030delT	uc003jhl.2	+						PDZD2_uc003jhm.2_Intron|PDZD2_uc011cnx.1_Intron	NM_178140	NP_835260			PDZ domain containing 2						cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9																		---	---	---	---
MTMR12	54545	broad.mit.edu	37	5	32294415	32294415	+	Intron	DEL	T	-	-	rs113079004		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32294415delT	uc003jhq.2	-						MTMR12_uc010iuk.2_Intron|MTMR12_uc010iul.2_Intron	NM_001040446	NP_001035536			myotubularin related protein 12							cytoplasm	phosphatase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	32345055	32345056	+	IGR	DEL	AA	-	-	rs77690049		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32345055_32345056delAA								MTMR12 (31941 upstream) : ZFR (9400 downstream)																																			---	---	---	---
ZFR	51663	broad.mit.edu	37	5	32406709	32406709	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32406709delT	uc003jhr.1	-							NM_016107	NP_057191			zinc finger RNA binding protein						multicellular organismal development	chromosome|cytoplasm|nucleus	DNA binding|RNA binding|zinc ion binding				0				STAD - Stomach adenocarcinoma(35;0.19)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	32515515	32515515	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32515515delT								ZFR (70671 upstream) : SUB1 (70090 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	32542235	32542235	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32542235delA								ZFR (97391 upstream) : SUB1 (43370 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	32604369	32604369	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32604369delT								SUB1 (184 upstream) : NPR3 (106391 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	32674923	32674924	+	IGR	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32674923_32674924insC								SUB1 (70738 upstream) : NPR3 (35836 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	32686576	32686576	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32686576delA								SUB1 (82391 upstream) : NPR3 (24184 downstream)																																			---	---	---	---
NPR3	4883	broad.mit.edu	37	5	32739290	32739291	+	Intron	DEL	TT	-	-	rs79938890		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32739290_32739291delTT	uc003jhv.2	+						NPR3_uc010iuo.2_Intron|NPR3_uc011cnz.1_Intron|NPR3_uc003jhu.2_Intron	NM_000908	NP_000899			natriuretic peptide receptor C/guanylate cyclase						osteoclast proliferation|positive regulation of urine volume|regulation of blood pressure|regulation of osteoblast proliferation|skeletal system development	integral to membrane	hormone binding|natriuretic peptide receptor activity			ovary(1)|central_nervous_system(1)	2					Nesiritide(DB04899)													---	---	---	---
NPR3	4883	broad.mit.edu	37	5	32773370	32773370	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32773370delT	uc003jhv.2	+						NPR3_uc010iuo.2_Intron|NPR3_uc011cnz.1_Intron|NPR3_uc003jhu.2_Intron	NM_000908	NP_000899			natriuretic peptide receptor C/guanylate cyclase						osteoclast proliferation|positive regulation of urine volume|regulation of blood pressure|regulation of osteoblast proliferation|skeletal system development	integral to membrane	hormone binding|natriuretic peptide receptor activity			ovary(1)|central_nervous_system(1)	2					Nesiritide(DB04899)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	32828597	32828600	+	IGR	DEL	TGTG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32828597_32828600delTGTG								C5orf23 (36778 upstream) : TARS (612202 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	32859303	32859304	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32859303_32859304insT								C5orf23 (67484 upstream) : TARS (581498 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	32900765	32900767	+	IGR	DEL	GCT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32900765_32900767delGCT								C5orf23 (108946 upstream) : TARS (540035 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	32915996	32915996	+	IGR	DEL	T	-	-	rs75960758		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32915996delT								C5orf23 (124177 upstream) : TARS (524806 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	33184648	33184648	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33184648delC								C5orf23 (392829 upstream) : TARS (256154 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	33332382	33332382	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33332382delA								C5orf23 (540563 upstream) : TARS (108420 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	33337747	33337748	+	IGR	DEL	AC	-	-	rs139496369	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33337747_33337748delAC								C5orf23 (545928 upstream) : TARS (103054 downstream)																																			---	---	---	---
ADAMTS12	81792	broad.mit.edu	37	5	33546481	33546481	+	Intron	DEL	A	-	-	rs74463306		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33546481delA	uc003jia.1	-						ADAMTS12_uc010iuq.1_Intron	NM_030955	NP_112217			ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	9															HNSCC(64;0.19)			---	---	---	---
ADAMTS12	81792	broad.mit.edu	37	5	33585144	33585147	+	Intron	DEL	ATCC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33585144_33585147delATCC	uc003jia.1	-						ADAMTS12_uc010iuq.1_Intron	NM_030955	NP_112217			ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	9															HNSCC(64;0.19)			---	---	---	---
ADAMTS12	81792	broad.mit.edu	37	5	33816757	33816758	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33816757_33816758insA	uc003jia.1	-						ADAMTS12_uc010iuq.1_Intron|ADAMTS12_uc003jib.1_Intron	NM_030955	NP_112217			ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	9															HNSCC(64;0.19)			---	---	---	---
Unknown	0	broad.mit.edu	37	5	34011849	34011849	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34011849delA								AMACR (3643 upstream) : C1QTNF3 (6115 downstream)																																			---	---	---	---
C1QTNF3	114899	broad.mit.edu	37	5	34028696	34028696	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34028696delA	uc003jin.2	-						C1QTNF3_uc003jim.2_Intron|C1QTNF3_uc003jio.2_Intron	NM_030945	NP_112207			C1q and tumor necrosis factor related protein 3							collagen					0	all_lung(31;0.0207)																	---	---	---	---
Unknown	0	broad.mit.edu	37	5	34174855	34174856	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34174855_34174856insT								C1QTNF3 (131538 upstream) : RAI14 (481577 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	34236496	34236496	+	IGR	DEL	A	-	-	rs144323307		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34236496delA								C1QTNF3 (193179 upstream) : RAI14 (419937 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	34303479	34303479	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34303479delT								C1QTNF3 (260162 upstream) : RAI14 (352954 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	34650723	34650723	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34650723delA								C1QTNF3 (607406 upstream) : RAI14 (5710 downstream)																																			---	---	---	---
RAI14	26064	broad.mit.edu	37	5	34750578	34750578	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34750578delT	uc003jir.2	+						RAI14_uc010iur.2_Intron|RAI14_uc011coj.1_Intron|RAI14_uc010ius.1_Intron|RAI14_uc003jis.2_Intron|RAI14_uc003jit.2_Intron|RAI14_uc011cok.1_Intron	NM_015577	NP_056392			retinoic acid induced 14 isoform a							cell cortex|cytoskeleton	protein binding			ovary(1)	1	all_lung(31;0.000191)																	---	---	---	---
RAI14	26064	broad.mit.edu	37	5	34759374	34759374	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34759374delA	uc003jir.2	+						RAI14_uc010iur.2_Intron|RAI14_uc011coj.1_Intron|RAI14_uc010ius.1_Intron|RAI14_uc003jis.2_Intron|RAI14_uc003jit.2_Intron|RAI14_uc011cok.1_Intron	NM_015577	NP_056392			retinoic acid induced 14 isoform a							cell cortex|cytoskeleton	protein binding			ovary(1)	1	all_lung(31;0.000191)																	---	---	---	---
RAI14	26064	broad.mit.edu	37	5	34822965	34822965	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34822965delT	uc003jir.2	+						RAI14_uc010iur.2_Intron|RAI14_uc011coj.1_Intron|RAI14_uc003jis.2_Intron|RAI14_uc003jit.2_Intron|RAI14_uc011cok.1_Intron	NM_015577	NP_056392			retinoic acid induced 14 isoform a							cell cortex|cytoskeleton	protein binding			ovary(1)	1	all_lung(31;0.000191)																	---	---	---	---
TTC23L	153657	broad.mit.edu	37	5	34861084	34861085	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34861084_34861085delTT	uc003jiu.2	+							NM_144725	NP_653326			tetratricopeptide repeat domain 23-like								binding			central_nervous_system(1)	1																		---	---	---	---
DNAJC21	134218	broad.mit.edu	37	5	34937382	34937382	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34937382delA	uc003jjc.2	+						DNAJC21_uc003jjb.2_Intron|DNAJC21_uc010iuu.1_Intron	NM_001012339	NP_001012339			DnaJ homology subfamily A member 5 isoform 2						protein folding	ribosome	heat shock protein binding|nucleic acid binding|unfolded protein binding|zinc ion binding			breast(1)|skin(1)	2	all_lung(31;7.08e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	34996830	34996831	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34996830_34996831insT								DNAJC21 (37762 upstream) : AGXT2 (1375 downstream)																																			---	---	---	---
AGXT2	64902	broad.mit.edu	37	5	35038695	35038695	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35038695delG	uc003jjf.2	-						AGXT2_uc011com.1_Intron|AGXT2_uc011con.1_Intron	NM_031900	NP_114106			alanine-glyoxylate aminotransferase 2 precursor						glyoxylate metabolic process|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process	mitochondrial matrix	(R)-3-amino-2-methylpropionate-pyruvate transaminase activity|alanine-glyoxylate transaminase activity|pyridoxal phosphate binding			ovary(3)|skin(1)	4	all_lung(31;4.52e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)	GBM - Glioblastoma multiforme(108;0.181)	Glycine(DB00145)|L-Alanine(DB00160)|Pyridoxal Phosphate(DB00114)|Pyruvic acid(DB00119)													---	---	---	---
PRLR	5618	broad.mit.edu	37	5	35083523	35083524	+	Intron	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35083523_35083524delTC	uc003jjm.2	-						PRLR_uc003jjg.1_Intron|PRLR_uc003jjh.1_Intron|PRLR_uc003jji.1_Intron|PRLR_uc003jjj.1_Intron|PRLR_uc003jjk.1_Intron|PRLR_uc003jjl.3_Intron|PRLR_uc010iuw.1_Intron	NM_000949	NP_000940			prolactin receptor precursor						activation of JAK2 kinase activity|activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|embryo implantation|lactation|steroid biosynthetic process|T cell activation	cell surface|extracellular region|integral to membrane	metal ion binding|ornithine decarboxylase activator activity|peptide hormone binding|prolactin receptor activity|protein homodimerization activity			ovary(2)|skin(1)	3	all_lung(31;3.83e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)		Dromostanolone(DB00858)|Fluoxymesterone(DB01185)|Pegvisomant(DB00082)|Somatropin recombinant(DB00052)													---	---	---	---
PRLR	5618	broad.mit.edu	37	5	35210822	35210822	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35210822delT	uc003jjm.2	-							NM_000949	NP_000940			prolactin receptor precursor						activation of JAK2 kinase activity|activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|embryo implantation|lactation|steroid biosynthetic process|T cell activation	cell surface|extracellular region|integral to membrane	metal ion binding|ornithine decarboxylase activator activity|peptide hormone binding|prolactin receptor activity|protein homodimerization activity			ovary(2)|skin(1)	3	all_lung(31;3.83e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)		Dromostanolone(DB00858)|Fluoxymesterone(DB01185)|Pegvisomant(DB00082)|Somatropin recombinant(DB00052)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	35237116	35237116	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35237116delT								PRLR (6322 upstream) : SPEF2 (380873 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	35348912	35348912	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35348912delT								PRLR (118118 upstream) : SPEF2 (269077 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	35551701	35551701	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35551701delT								PRLR (320907 upstream) : SPEF2 (66288 downstream)																																			---	---	---	---
SPEF2	79925	broad.mit.edu	37	5	35618974	35618974	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35618974delT	uc003jjo.2	+						SPEF2_uc003jjn.1_Intron|SPEF2_uc003jjq.3_Intron	NM_024867	NP_079143			KPL2 protein isoform 1						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|protein dimerization activity			skin(2)|ovary(1)|central_nervous_system(1)	4	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
IL7R	3575	broad.mit.edu	37	5	35876845	35876845	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35876845delA	uc003jjs.2	+	8					IL7R_uc011cop.1_RNA	NM_002185	NP_002176			interleukin 7 receptor precursor						immune response|regulation of DNA recombination	extracellular region|integral to membrane	antigen binding|interleukin-7 receptor activity			ovary(3)|breast(1)|skin(1)	5	all_lung(31;0.00015)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.187)|Colorectal(62;0.202)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	35952681	35952681	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35952681delG								CAPSL (13800 upstream) : UGT3A1 (529 downstream)																																			---	---	---	---
UGT3A1	133688	broad.mit.edu	37	5	35998187	35998187	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35998187delA	uc003jjy.1	-							NM_152404	NP_689617			UDP glycosyltransferase 3 family, polypeptide A1							integral to membrane	glucuronosyltransferase activity			ovary(2)|central_nervous_system(1)	3	all_lung(31;0.000197)		Epithelial(62;0.107)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	36484857	36484857	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36484857delT								RANBP3L (182846 upstream) : SLC1A3 (121600 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	36520091	36520091	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36520091delT								RANBP3L (218080 upstream) : SLC1A3 (86366 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	36576560	36576560	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36576560delA								RANBP3L (274549 upstream) : SLC1A3 (29897 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	36588956	36588956	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36588956delA								RANBP3L (286945 upstream) : SLC1A3 (17501 downstream)																																			---	---	---	---
NIPBL	25836	broad.mit.edu	37	5	37020837	37020837	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37020837delA	uc003jkl.3	+						NIPBL_uc003jkk.3_Intron	NM_133433	NP_597677			delangin isoform A						brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis	SMC loading complex	chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding			ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1)	9	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	37070908	37070908	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37070908delT								NIPBL (4988 upstream) : C5orf42 (35422 downstream)																																			---	---	---	---
C5orf42	65250	broad.mit.edu	37	5	37123800	37123800	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37123800delT	uc011cpa.1	-						C5orf42_uc003jko.1_5'Flank|C5orf42_uc003jkp.1_Intron|C5orf42_uc011coy.1_Intron|C5orf42_uc003jks.2_Intron|C5orf42_uc011coz.1_Intron	NM_023073	NP_075561			hypothetical protein LOC65250											ovary(4)|breast(2)|skin(1)	7	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)															---	---	---	---
C5orf42	65250	broad.mit.edu	37	5	37169770	37169770	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37169770delA	uc011cpa.1	-						C5orf42_uc011coy.1_Intron|C5orf42_uc003jks.2_Intron|C5orf42_uc011coz.1_Intron|C5orf42_uc003jkr.1_Intron	NM_023073	NP_075561			hypothetical protein LOC65250											ovary(4)|breast(2)|skin(1)	7	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)															---	---	---	---
C5orf42	65250	broad.mit.edu	37	5	37180363	37180363	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37180363delT	uc011cpa.1	-						C5orf42_uc011coy.1_Intron|C5orf42_uc003jks.2_Intron|C5orf42_uc011coz.1_Intron	NM_023073	NP_075561			hypothetical protein LOC65250											ovary(4)|breast(2)|skin(1)	7	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)															---	---	---	---
C5orf42	65250	broad.mit.edu	37	5	37224916	37224917	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37224916_37224917delTT	uc011cpa.1	-							NM_023073	NP_075561			hypothetical protein LOC65250											ovary(4)|breast(2)|skin(1)	7	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)															---	---	---	---
C5orf42	65250	broad.mit.edu	37	5	37225360	37225360	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37225360delT	uc011cpa.1	-							NM_023073	NP_075561			hypothetical protein LOC65250											ovary(4)|breast(2)|skin(1)	7	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)															---	---	---	---
NUP155	9631	broad.mit.edu	37	5	37305222	37305222	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37305222delT	uc003jku.1	-	26	3112	c.2994delA	c.(2992-2994)AAAfs	p.K998fs	NUP155_uc003jkt.1_Frame_Shift_Del_p.K939fs|NUP155_uc010iuz.1_Frame_Shift_Del_p.K934fs	NM_153485	NP_705618	O75694	NU155_HUMAN	nucleoporin 155kDa isoform 1	998					carbohydrate metabolic process|glucose transport|mRNA transport|nucleocytoplasmic transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear membrane|nuclear pore	protein binding|structural constituent of nuclear pore|transporter activity			ovary(1)	1	all_lung(31;0.000137)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
NUP155	9631	broad.mit.edu	37	5	37345254	37345254	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37345254delA	uc003jku.1	-						NUP155_uc003jkt.1_Intron|NUP155_uc010iuz.1_Intron	NM_153485	NP_705618			nucleoporin 155kDa isoform 1						carbohydrate metabolic process|glucose transport|mRNA transport|nucleocytoplasmic transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear membrane|nuclear pore	protein binding|structural constituent of nuclear pore|transporter activity			ovary(1)	1	all_lung(31;0.000137)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
NUP155	9631	broad.mit.edu	37	5	37353693	37353693	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37353693delA	uc003jku.1	-						NUP155_uc003jkt.1_Intron|NUP155_uc010iuz.1_Intron	NM_153485	NP_705618			nucleoporin 155kDa isoform 1						carbohydrate metabolic process|glucose transport|mRNA transport|nucleocytoplasmic transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear membrane|nuclear pore	protein binding|structural constituent of nuclear pore|transporter activity			ovary(1)	1	all_lung(31;0.000137)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
WDR70	55100	broad.mit.edu	37	5	37410154	37410156	+	Intron	DEL	TTT	-	-	rs112303347		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37410154_37410156delTTT	uc003jkv.2	+						WDR70_uc010iva.1_Intron	NM_018034	NP_060504			WD repeat domain 70											ovary(1)|central_nervous_system(1)	2	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
WDR70	55100	broad.mit.edu	37	5	37455261	37455262	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37455261_37455262insT	uc003jkv.2	+						WDR70_uc010iva.1_Intron	NM_018034	NP_060504			WD repeat domain 70											ovary(1)|central_nervous_system(1)	2	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
WDR70	55100	broad.mit.edu	37	5	37482992	37482993	+	Intron	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37482992_37482993delGA	uc003jkv.2	+						WDR70_uc010iva.1_Intron	NM_018034	NP_060504			WD repeat domain 70											ovary(1)|central_nervous_system(1)	2	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
WDR70	55100	broad.mit.edu	37	5	37499221	37499221	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37499221delT	uc003jkv.2	+						WDR70_uc010iva.1_Intron	NM_018034	NP_060504			WD repeat domain 70											ovary(1)|central_nervous_system(1)	2	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
WDR70	55100	broad.mit.edu	37	5	37554740	37554741	+	Intron	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37554740_37554741delAC	uc003jkv.2	+						WDR70_uc010iva.1_Intron	NM_018034	NP_060504			WD repeat domain 70											ovary(1)|central_nervous_system(1)	2	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
WDR70	55100	broad.mit.edu	37	5	37588489	37588490	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37588489_37588490insT	uc003jkv.2	+						WDR70_uc010iva.1_Intron	NM_018034	NP_060504			WD repeat domain 70											ovary(1)|central_nervous_system(1)	2	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
WDR70	55100	broad.mit.edu	37	5	37602738	37602738	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37602738delA	uc003jkv.2	+						WDR70_uc010iva.1_Intron	NM_018034	NP_060504			WD repeat domain 70											ovary(1)|central_nervous_system(1)	2	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
WDR70	55100	broad.mit.edu	37	5	37616231	37616231	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37616231delT	uc003jkv.2	+						WDR70_uc010iva.1_Intron	NM_018034	NP_060504			WD repeat domain 70											ovary(1)|central_nervous_system(1)	2	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
WDR70	55100	broad.mit.edu	37	5	37645286	37645286	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37645286delT	uc003jkv.2	+						WDR70_uc010iva.1_Intron	NM_018034	NP_060504			WD repeat domain 70											ovary(1)|central_nervous_system(1)	2	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
WDR70	55100	broad.mit.edu	37	5	37724697	37724697	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37724697delA	uc003jkv.2	+							NM_018034	NP_060504			WD repeat domain 70											ovary(1)|central_nervous_system(1)	2	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	37764255	37764256	+	IGR	DEL	TT	-	-	rs140022561		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37764255_37764256delTT								WDR70 (11483 upstream) : GDNF (51498 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	37845366	37845367	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37845366_37845367delTG								GDNF (5584 upstream) : EGFLAM (413166 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	37905676	37905676	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37905676delT								GDNF (65894 upstream) : EGFLAM (352857 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	37976180	37976180	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37976180delT								GDNF (136398 upstream) : EGFLAM (282353 downstream)																																			---	---	---	---
EGFLAM	133584	broad.mit.edu	37	5	38257358	38257359	+	5'Flank	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38257358_38257359delTG	uc003jlc.1	+						EGFLAM_uc003jlb.1_5'Flank	NM_152403	NP_689616			EGF-like, fibronectin type III and laminin G							cell junction|proteinaceous extracellular matrix|synapse				pancreas(3)|skin(3)|ovary(1)	7	all_lung(31;0.000385)																	---	---	---	---
EGFLAM	133584	broad.mit.edu	37	5	38371794	38371794	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38371794delA	uc003jlc.1	+						EGFLAM_uc003jlb.1_Intron	NM_152403	NP_689616			EGF-like, fibronectin type III and laminin G							cell junction|proteinaceous extracellular matrix|synapse				pancreas(3)|skin(3)|ovary(1)	7	all_lung(31;0.000385)																	---	---	---	---
LIFR	3977	broad.mit.edu	37	5	38549272	38549272	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38549272delT	uc010ive.1	-						LIFR_uc003jli.2_Intron	NM_001127671	NP_001121143			leukemia inhibitory factor receptor precursor						positive regulation of cell proliferation	extracellular region|integral to plasma membrane	ciliary neurotrophic factor receptor binding|growth factor binding|leukemia inhibitory factor receptor activity			ovary(3)|large_intestine(1)	4	all_lung(31;0.00021)							T	PLAG1	salivary adenoma								---	---	---	---
Unknown	0	broad.mit.edu	37	5	38622076	38622076	+	Intron	DEL	T	-	-	rs111379328		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38622076delT	uc003jlj.2	+											Homo sapiens cDNA clone IMAGE:4829282.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	38750903	38750903	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38750903delT								LIFR (155396 upstream) : OSMR (95225 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	38814340	38814340	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38814340delA	uc003jlk.1	-											full-length cDNA clone CS0DI053YO12 of Placenta Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	38830555	38830556	+	Intron	INS	-	G	G	rs144221239	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38830555_38830556insG	uc003jlk.1	-											full-length cDNA clone CS0DI053YO12 of Placenta Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
RICTOR	253260	broad.mit.edu	37	5	38958957	38958958	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38958957_38958958delAA	uc003jlp.2	-						RICTOR_uc003jlo.2_Intron|RICTOR_uc010ivf.2_Intron	NM_152756	NP_689969			rapamycin-insensitive companion of mTOR						actin cytoskeleton reorganization|embryo development|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of TOR signaling cascade|regulation of protein kinase B signaling cascade|T cell costimulation	cytosol|TORC2 complex	protein binding			ovary(3)|lung(3)|skin(2)|kidney(1)|central_nervous_system(1)	10	all_lung(31;0.000396)																	---	---	---	---
RICTOR	253260	broad.mit.edu	37	5	38999394	38999394	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38999394delA	uc003jlp.2	-						RICTOR_uc003jlo.2_Intron|RICTOR_uc010ivf.2_Intron|RICTOR_uc003jlq.1_Intron|RICTOR_uc011cpk.1_Intron	NM_152756	NP_689969			rapamycin-insensitive companion of mTOR						actin cytoskeleton reorganization|embryo development|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of TOR signaling cascade|regulation of protein kinase B signaling cascade|T cell costimulation	cytosol|TORC2 complex	protein binding			ovary(3)|lung(3)|skin(2)|kidney(1)|central_nervous_system(1)	10	all_lung(31;0.000396)																	---	---	---	---
RICTOR	253260	broad.mit.edu	37	5	38999721	38999721	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38999721delA	uc003jlp.2	-						RICTOR_uc003jlo.2_Intron|RICTOR_uc010ivf.2_Intron|RICTOR_uc003jlq.1_Intron|RICTOR_uc011cpk.1_Intron	NM_152756	NP_689969			rapamycin-insensitive companion of mTOR						actin cytoskeleton reorganization|embryo development|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of TOR signaling cascade|regulation of protein kinase B signaling cascade|T cell costimulation	cytosol|TORC2 complex	protein binding			ovary(3)|lung(3)|skin(2)|kidney(1)|central_nervous_system(1)	10	all_lung(31;0.000396)																	---	---	---	---
FYB	2533	broad.mit.edu	37	5	39130175	39130175	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39130175delA	uc003jls.2	-						FYB_uc003jlt.2_Intron|FYB_uc003jlu.2_Intron|FYB_uc011cpl.1_Intron	NM_199335	NP_955367			FYN binding protein (FYB-120/130) isoform 2						cell junction assembly|immune response|intracellular protein kinase cascade|NLS-bearing substrate import into nucleus|protein phosphorylation|T cell receptor signaling pathway	cytosol|nucleus	protein binding			ovary(2)	2	all_lung(31;0.000343)		Epithelial(62;0.235)															---	---	---	---
FYB	2533	broad.mit.edu	37	5	39258389	39258390	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39258389_39258390insT	uc011cpl.1	-							NM_001465	NP_001456			FYN binding protein (FYB-120/130) isoform 1						cell junction assembly|immune response|intracellular protein kinase cascade|NLS-bearing substrate import into nucleus|protein phosphorylation|T cell receptor signaling pathway	cytosol|nucleus	protein binding			ovary(2)	2	all_lung(31;0.000343)		Epithelial(62;0.235)															---	---	---	---
DAB2	1601	broad.mit.edu	37	5	39374289	39374290	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39374289_39374290delAA	uc003jlx.2	-						DAB2_uc003jlw.2_Intron	NM_001343	NP_001334			disabled homolog 2						cell proliferation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of protein binding|negative regulation of transcription, DNA-dependent|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of transcription, DNA-dependent|positive regulation of Wnt receptor signaling pathway, planar cell polarity pathway	clathrin coated vesicle membrane|coated pit	protein C-terminus binding			kidney(2)|skin(1)	3	all_lung(31;0.000197)		Epithelial(62;0.137)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	39508473	39508474	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39508473_39508474insA								DAB2 (83138 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	40246527	40246527	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40246527delA								DAB2 (821192 upstream) : PTGER4 (433505 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	40300669	40300669	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40300669delT								DAB2 (875334 upstream) : PTGER4 (379363 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	40636891	40636891	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40636891delA								None (None upstream) : PTGER4 (43141 downstream)																																			---	---	---	---
PTGER4	5734	broad.mit.edu	37	5	40686817	40686817	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40686817delA	uc003jlz.2	+							NM_000958	NP_000949			prostaglandin E receptor 4, subtype EP4						G-protein signaling, coupled to cAMP nucleotide second messenger|immune response	integral to membrane|plasma membrane	prostaglandin E receptor activity			lung(2)	2																		---	---	---	---
PRKAA1	5562	broad.mit.edu	37	5	40800044	40800044	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40800044delA	uc003jmc.2	-						PRKAA1_uc003jmb.2_5'Flank	NM_006251	NP_006242			protein kinase, AMP-activated, alpha 1 catalytic						activation of MAPK activity|cell cycle arrest|cholesterol biosynthetic process|fatty acid biosynthetic process|insulin receptor signaling pathway|negative regulation of glucosylceramide biosynthetic process|positive regulation of anti-apoptosis|positive regulation of cholesterol biosynthetic process|regulation of fatty acid oxidation|response to hypoxia	cytosol	ATP binding|cAMP-dependent protein kinase activity|metal ion binding|protein binding			breast(1)	1					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Phenformin(DB00914)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	40804456	40804457	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40804456_40804457delAA								PRKAA1 (6159 upstream) : RPL37 (26973 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	40879296	40879296	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40879296delA								CARD6 (23842 upstream) : C7 (30303 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	40902347	40902347	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40902347delT								CARD6 (46893 upstream) : C7 (7252 downstream)																																			---	---	---	---
C6	729	broad.mit.edu	37	5	41168742	41168742	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41168742delT	uc003jmk.2	-						C6_uc003jml.1_Intron	NM_000065	NP_000056			complement component 6 precursor						complement activation, classical pathway|cytolysis|innate immune response	membrane attack complex	protein binding			ovary(3)|central_nervous_system(2)|skin(2)	7		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)																---	---	---	---
Unknown	0	broad.mit.edu	37	5	41267729	41267730	+	IGR	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41267729_41267730delGA								C6 (6189 upstream) : PLCXD3 (39318 downstream)																																			---	---	---	---
PLCXD3	345557	broad.mit.edu	37	5	41307607	41307607	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41307607delA	uc003jmm.1	-	3						NM_001005473	NP_001005473			phosphatidylinositol-specific phospholipase C, X						intracellular signal transduction|lipid catabolic process		phospholipase C activity|signal transducer activity			skin(2)|urinary_tract(1)|ovary(1)|lung(1)|central_nervous_system(1)	6																		---	---	---	---
PLCXD3	345557	broad.mit.edu	37	5	41429512	41429513	+	Intron	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41429512_41429513delGA	uc003jmm.1	-							NM_001005473	NP_001005473			phosphatidylinositol-specific phospholipase C, X						intracellular signal transduction|lipid catabolic process		phospholipase C activity|signal transducer activity			skin(2)|urinary_tract(1)|ovary(1)|lung(1)|central_nervous_system(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	41600918	41600918	+	IGR	DEL	C	-	-	rs6867292	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41600918delC								PLCXD3 (90188 upstream) : OXCT1 (129250 downstream)																																			---	---	---	---
OXCT1	5019	broad.mit.edu	37	5	41781539	41781541	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41781539_41781541delTTT	uc003jmn.2	-						OXCT1_uc011cpo.1_Intron|OXCT1_uc011cpp.1_Intron	NM_000436	NP_000427			3-oxoacid CoA transferase 1 precursor						cellular lipid metabolic process|ketone body catabolic process	mitochondrial matrix	3-oxoacid CoA-transferase activity|protein homodimerization activity			ovary(2)|large_intestine(1)	3					Succinic acid(DB00139)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	41876111	41876112	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41876111_41876112delAA								OXCT1 (5320 upstream) : C5orf51 (28358 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	41956662	41956663	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41956662_41956663insT								FBXO4 (14999 upstream) : GHR (467363 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	41986438	41986438	+	IGR	DEL	A	-	-	rs76325041	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41986438delA								FBXO4 (44775 upstream) : GHR (437588 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	42017881	42017883	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42017881_42017883delTTT								FBXO4 (76218 upstream) : GHR (406143 downstream)																																			---	---	---	---
GHR	2690	broad.mit.edu	37	5	42441617	42441618	+	Intron	DEL	TT	-	-	rs35357870		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42441617_42441618delTT	uc003jmt.2	+						uc003jmu.2_Intron|uc003jmv.1_Intron	NM_000163	NP_000154			growth hormone receptor precursor						2-oxoglutarate metabolic process|activation of JAK2 kinase activity|activation of MAPK activity|allantoin metabolic process|citrate metabolic process|creatine metabolic process|creatinine metabolic process|endocytosis|fatty acid metabolic process|growth hormone receptor signaling pathway|insulin-like growth factor receptor signaling pathway|isoleucine metabolic process|JAK-STAT cascade|multicellular organismal metabolic process|oxaloacetate metabolic process|positive regulation of multicellular organism growth|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of tyrosine phosphorylation of Stat5 protein|receptor internalization|response to cycloheximide|response to estradiol stimulus|succinate metabolic process|taurine metabolic process|valine metabolic process	cell surface|extracellular space|growth hormone receptor complex|integral to plasma membrane	growth factor binding|peptide hormone binding|proline-rich region binding|protein homodimerization activity|protein kinase binding			lung(4)|kidney(1)|skin(1)	6		Myeloproliferative disorder(839;0.00878)			Pegvisomant(DB00082)|Somatropin recombinant(DB00052)													---	---	---	---
GHR	2690	broad.mit.edu	37	5	42456627	42456627	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42456627delA	uc003jmt.2	+						uc003jmu.2_Intron|uc003jmv.1_Intron	NM_000163	NP_000154			growth hormone receptor precursor						2-oxoglutarate metabolic process|activation of JAK2 kinase activity|activation of MAPK activity|allantoin metabolic process|citrate metabolic process|creatine metabolic process|creatinine metabolic process|endocytosis|fatty acid metabolic process|growth hormone receptor signaling pathway|insulin-like growth factor receptor signaling pathway|isoleucine metabolic process|JAK-STAT cascade|multicellular organismal metabolic process|oxaloacetate metabolic process|positive regulation of multicellular organism growth|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of tyrosine phosphorylation of Stat5 protein|receptor internalization|response to cycloheximide|response to estradiol stimulus|succinate metabolic process|taurine metabolic process|valine metabolic process	cell surface|extracellular space|growth hormone receptor complex|integral to plasma membrane	growth factor binding|peptide hormone binding|proline-rich region binding|protein homodimerization activity|protein kinase binding			lung(4)|kidney(1)|skin(1)	6		Myeloproliferative disorder(839;0.00878)			Pegvisomant(DB00082)|Somatropin recombinant(DB00052)													---	---	---	---
GHR	2690	broad.mit.edu	37	5	42531581	42531582	+	Intron	DEL	TT	-	-	rs68103582		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42531581_42531582delTT	uc003jmt.2	+							NM_000163	NP_000154			growth hormone receptor precursor						2-oxoglutarate metabolic process|activation of JAK2 kinase activity|activation of MAPK activity|allantoin metabolic process|citrate metabolic process|creatine metabolic process|creatinine metabolic process|endocytosis|fatty acid metabolic process|growth hormone receptor signaling pathway|insulin-like growth factor receptor signaling pathway|isoleucine metabolic process|JAK-STAT cascade|multicellular organismal metabolic process|oxaloacetate metabolic process|positive regulation of multicellular organism growth|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of tyrosine phosphorylation of Stat5 protein|receptor internalization|response to cycloheximide|response to estradiol stimulus|succinate metabolic process|taurine metabolic process|valine metabolic process	cell surface|extracellular space|growth hormone receptor complex|integral to plasma membrane	growth factor binding|peptide hormone binding|proline-rich region binding|protein homodimerization activity|protein kinase binding			lung(4)|kidney(1)|skin(1)	6		Myeloproliferative disorder(839;0.00878)			Pegvisomant(DB00082)|Somatropin recombinant(DB00052)													---	---	---	---
GHR	2690	broad.mit.edu	37	5	42687944	42687944	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42687944delA	uc003jmt.2	+						GHR_uc011cpq.1_Intron	NM_000163	NP_000154			growth hormone receptor precursor						2-oxoglutarate metabolic process|activation of JAK2 kinase activity|activation of MAPK activity|allantoin metabolic process|citrate metabolic process|creatine metabolic process|creatinine metabolic process|endocytosis|fatty acid metabolic process|growth hormone receptor signaling pathway|insulin-like growth factor receptor signaling pathway|isoleucine metabolic process|JAK-STAT cascade|multicellular organismal metabolic process|oxaloacetate metabolic process|positive regulation of multicellular organism growth|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of tyrosine phosphorylation of Stat5 protein|receptor internalization|response to cycloheximide|response to estradiol stimulus|succinate metabolic process|taurine metabolic process|valine metabolic process	cell surface|extracellular space|growth hormone receptor complex|integral to plasma membrane	growth factor binding|peptide hormone binding|proline-rich region binding|protein homodimerization activity|protein kinase binding			lung(4)|kidney(1)|skin(1)	6		Myeloproliferative disorder(839;0.00878)			Pegvisomant(DB00082)|Somatropin recombinant(DB00052)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	42859713	42859714	+	IGR	INS	-	T	T	rs150723674	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:42859713_42859714insT								SEPP1 (33715 upstream) : C5orf39 (179469 downstream)																																			---	---	---	---
C5orf39	389289	broad.mit.edu	37	5	43041748	43041751	+	5'Flank	DEL	AAAA	-	-	rs35130164		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43041748_43041751delAAAA	uc003jnf.2	-						C5orf39_uc010ivj.1_Intron|LOC153684_uc003jng.2_RNA|LOC153684_uc003jni.2_5'Flank	NM_001014279	NP_001014301			annexin II receptor								receptor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	43047764	43047764	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43047764delA								LOC153684 (2394 upstream) : ZNF131 (73221 downstream)																																			---	---	---	---
ZNF131	7690	broad.mit.edu	37	5	43149363	43149364	+	Intron	DEL	AA	-	-	rs36054171		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43149363_43149364delAA	uc011cpw.1	+						ZNF131_uc010ivl.1_Intron|ZNF131_uc003jnj.3_Intron|ZNF131_uc003jnk.2_Intron|ZNF131_uc003jnn.3_Intron|ZNF131_uc003jnl.1_Intron|ZNF131_uc010ivm.1_Intron	NM_003432	NP_003423			zinc finger protein 131							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0																		---	---	---	---
ZNF131	7690	broad.mit.edu	37	5	43172835	43172835	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43172835delT	uc011cpw.1	+						ZNF131_uc003jnj.3_Intron|ZNF131_uc003jnk.2_Intron|ZNF131_uc003jnn.3_Intron|ZNF131_uc003jnl.1_Intron|ZNF131_uc010ivm.1_Intron	NM_003432	NP_003423			zinc finger protein 131							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0																		---	---	---	---
MGC42105	167359	broad.mit.edu	37	5	43230957	43230957	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43230957delT	uc003jno.2	+							NM_153361	NP_699192			serine/threonine-protein kinase NIM1								ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(4)|ovary(2)|stomach(1)|large_intestine(1)|breast(1)	9																		---	---	---	---
MGC42105	167359	broad.mit.edu	37	5	43252224	43252225	+	Intron	DEL	AA	-	-	rs78891437		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43252224_43252225delAA	uc003jno.2	+							NM_153361	NP_699192			serine/threonine-protein kinase NIM1								ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(4)|ovary(2)|stomach(1)|large_intestine(1)|breast(1)	9																		---	---	---	---
MGC42105	167359	broad.mit.edu	37	5	43273973	43273973	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43273973delT	uc003jno.2	+							NM_153361	NP_699192			serine/threonine-protein kinase NIM1								ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(4)|ovary(2)|stomach(1)|large_intestine(1)|breast(1)	9																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	43336510	43336510	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43336510delA								HMGCS1 (22915 upstream) : CCL28 (40240 downstream)																																			---	---	---	---
CCL28	56477	broad.mit.edu	37	5	43399952	43399954	+	Intron	DEL	TTT	-	-	rs11462172		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43399952_43399954delTTT	uc003jnu.2	-						CCL28_uc003jns.2_Intron|CCL28_uc003jnt.2_Intron|CCL28_uc010ivn.2_5'Flank	NM_148672	NP_683513			chemokine (C-C motif) ligand 28 precursor						chemotaxis|immune response	extracellular space	chemokine activity			ovary(1)|kidney(1)	2																		---	---	---	---
PAIP1	10605	broad.mit.edu	37	5	43535227	43535227	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43535227delA	uc003job.2	-						PAIP1_uc003joa.2_Intron|PAIP1_uc010ivp.2_Intron|PAIP1_uc010ivo.2_Intron|PAIP1_uc003joc.2_Intron	NM_006451	NP_006442			poly(A) binding protein interacting protein 1						mRNA stabilization|nuclear-transcribed mRNA poly(A) tail shortening|translational initiation	cytosol	protein binding|RNA binding|translation activator activity			ovary(1)	1	Lung NSC(6;2.07e-05)																	---	---	---	---
NNT	23530	broad.mit.edu	37	5	43600134	43600134	+	5'Flank	DEL	T	-	-	rs143326631		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43600134delT	uc003joe.2	+						uc003jod.1_Intron	NM_012343	NP_036475			nicotinamide nucleotide transhydrogenase						tricarboxylic acid cycle	integral to membrane|mitochondrial respiratory chain	NAD binding|NAD(P)+ transhydrogenase (AB-specific) activity|NAD(P)+ transhydrogenase (B-specific) activity|NADP binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(6;2.58e-06)				NADH(DB00157)													---	---	---	---
NNT	23530	broad.mit.edu	37	5	43666736	43666736	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43666736delT	uc003joe.2	+						NNT_uc003jof.2_Intron	NM_012343	NP_036475			nicotinamide nucleotide transhydrogenase						tricarboxylic acid cycle	integral to membrane|mitochondrial respiratory chain	NAD binding|NAD(P)+ transhydrogenase (AB-specific) activity|NAD(P)+ transhydrogenase (B-specific) activity|NADP binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(6;2.58e-06)				NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	43945364	43945364	+	IGR	DEL	A	-	-	rs35817642		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43945364delA								NNT (239697 upstream) : FGF10 (359733 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	44019184	44019184	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:44019184delA								NNT (313517 upstream) : FGF10 (285913 downstream)																																			---	---	---	---
FGF10	2255	broad.mit.edu	37	5	44341597	44341597	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:44341597delA	uc003jog.1	-							NM_004465	NP_004456			fibroblast growth factor 10 precursor						actin cytoskeleton reorganization|activation of MAPK activity|bud outgrowth involved in lung branching|ERK1 and ERK2 cascade|fibroblast growth factor receptor signaling pathway involved in mammary gland specification|insulin receptor signaling pathway|lacrimal gland development|lung saccule development|mesonephros development|negative regulation of cell cycle arrest|positive regulation of ATPase activity|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of DNA repair|positive regulation of DNA replication|positive regulation of epithelial cell migration|positive regulation of epithelial cell proliferation involved in wound healing|positive regulation of ERK1 and ERK2 cascade|positive regulation of hair follicle cell proliferation|positive regulation of keratinocyte migration|positive regulation of keratinocyte proliferation|positive regulation of lymphocyte proliferation|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of Ras protein signal transduction|positive regulation of transcription, DNA-dependent|positive regulation of urothelial cell proliferation|protein localization at cell surface|radial glial cell differentiation|regulation of saliva secretion|response to protein stimulus|secretion by lung epithelial cell involved in lung growth|tear secretion|thymus development|urothelial cell proliferation	cell surface|extracellular space|nucleus|plasma membrane	chemoattractant activity|growth factor activity|heparin binding|type 2 fibroblast growth factor receptor binding			lung(3)	3	Lung NSC(6;1.12e-06)																	---	---	---	---
Unknown	0	broad.mit.edu	37	5	44405935	44405935	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:44405935delA								FGF10 (17151 upstream) : MRPS30 (403092 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	44711971	44711971	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:44711971delA								FGF10 (323187 upstream) : MRPS30 (97056 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	44937341	44937341	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:44937341delA								MRPS30 (121727 upstream) : HCN1 (322012 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	45078956	45078957	+	IGR	INS	-	GT	GT			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45078956_45078957insGT								MRPS30 (263342 upstream) : HCN1 (180396 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	45110130	45110130	+	IGR	DEL	G	-	-	rs112967717	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45110130delG								MRPS30 (294516 upstream) : HCN1 (149223 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	45122119	45122124	+	IGR	DEL	AAAAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45122119_45122124delAAAAAA								MRPS30 (306505 upstream) : HCN1 (137229 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	45177976	45177976	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45177976delT								MRPS30 (362362 upstream) : HCN1 (81377 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	45224623	45224623	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45224623delT								MRPS30 (409009 upstream) : HCN1 (34730 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	45237129	45237130	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45237129_45237130delTT								MRPS30 (421515 upstream) : HCN1 (22223 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	45252607	45252608	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45252607_45252608delTT								MRPS30 (436993 upstream) : HCN1 (6745 downstream)																																			---	---	---	---
HCN1	348980	broad.mit.edu	37	5	45313213	45313213	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45313213delC	uc003jok.2	-							NM_021072	NP_066550			hyperpolarization activated cyclic							integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1																		---	---	---	---
HCN1	348980	broad.mit.edu	37	5	45438692	45438694	+	Intron	DEL	AAA	-	-	rs78404932		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45438692_45438694delAAA	uc003jok.2	-							NM_021072	NP_066550			hyperpolarization activated cyclic							integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1																		---	---	---	---
HCN1	348980	broad.mit.edu	37	5	45605258	45605259	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45605258_45605259insT	uc003jok.2	-							NM_021072	NP_066550			hyperpolarization activated cyclic							integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1																		---	---	---	---
HCN1	348980	broad.mit.edu	37	5	45649684	45649684	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45649684delT	uc003jok.2	-							NM_021072	NP_066550			hyperpolarization activated cyclic							integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	46251003	46251004	+	IGR	INS	-	A	A	rs140927102	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:46251003_46251004insA								HCN1 (554783 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	46349465	46349466	+	IGR	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:46349465_46349466insC								HCN1 (653245 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	46391795	46391795	+	IGR	DEL	A	-	-	rs34574350		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:46391795delA								HCN1 (695575 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	49517168	49517169	+	IGR	DEL	TG	-	-	rs3070351		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:49517168_49517169delTG								None (None upstream) : EMB (174864 downstream)																																			---	---	---	---
EMB	133418	broad.mit.edu	37	5	49696346	49696346	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:49696346delA	uc003jom.2	-						EMB_uc010ivq.2_Intron|EMB_uc003jol.2_Intron|EMB_uc011cpy.1_Intron|EMB_uc010ivr.2_Intron	NM_198449	NP_940851			embigin precursor							integral to membrane					0	Lung SC(58;0.218)	Lung NSC(810;0.0795)																---	---	---	---
EMB	133418	broad.mit.edu	37	5	49715383	49715384	+	Intron	DEL	AC	-	-	rs66621835		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:49715383_49715384delAC	uc003jom.2	-						EMB_uc011cpy.1_Intron|EMB_uc010ivr.2_Intron	NM_198449	NP_940851			embigin precursor							integral to membrane					0	Lung SC(58;0.218)	Lung NSC(810;0.0795)																---	---	---	---
Unknown	0	broad.mit.edu	37	5	50475529	50475529	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:50475529delT								PARP8 (337360 upstream) : ISL1 (203429 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	51322329	51322329	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:51322329delA								ISL1 (631772 upstream) : ITGA1 (761445 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	51773124	51773124	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:51773124delT								None (None upstream) : ITGA1 (310650 downstream)																																			---	---	---	---
ITGA1	3672	broad.mit.edu	37	5	52145084	52145084	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52145084delT	uc003jou.2	+						ITGA1_uc003jov.2_Intron	NM_181501	NP_852478			integrin, alpha 1 precursor						axon guidance|cell-matrix adhesion|integrin-mediated signaling pathway|muscle contraction	integrin complex	collagen binding|receptor activity			ovary(2)|lung(1)	3		Lung NSC(810;5.05e-05)|Breast(144;0.0851)																---	---	---	---
Unknown	0	broad.mit.edu	37	5	52254061	52254061	+	RNA	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52254061delA	uc003jox.1	+	1		c.2875delA								Homo sapiens cDNA FLJ39969 fis, clone SPLEN2027868.																														---	---	---	---
ITGA2	3673	broad.mit.edu	37	5	52335819	52335819	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52335819delT	uc003joy.2	+						ITGA2_uc011cqa.1_Intron|ITGA2_uc011cqb.1_Intron|ITGA2_uc011cqc.1_Intron|ITGA2_uc011cqd.1_Intron|ITGA2_uc011cqe.1_Intron	NM_002203	NP_002194			integrin alpha 2 precursor						axon guidance|blood coagulation|cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|organ morphogenesis	integrin complex	collagen binding|identical protein binding|receptor activity			lung(1)	1		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)																---	---	---	---
ITGA2	3673	broad.mit.edu	37	5	52346165	52346166	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52346165_52346166insT	uc003joy.2	+						ITGA2_uc011cqa.1_Intron|ITGA2_uc011cqb.1_Intron|ITGA2_uc011cqc.1_Intron|ITGA2_uc011cqd.1_Intron|ITGA2_uc011cqe.1_Intron	NM_002203	NP_002194			integrin alpha 2 precursor						axon guidance|blood coagulation|cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|organ morphogenesis	integrin complex	collagen binding|identical protein binding|receptor activity			lung(1)	1		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)																---	---	---	---
Unknown	0	broad.mit.edu	37	5	52536586	52536586	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52536586delA								MOCS2 (130988 upstream) : FST (240009 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	52736315	52736315	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52736315delA								MOCS2 (330717 upstream) : FST (40280 downstream)																																			---	---	---	---
NDUFS4	4724	broad.mit.edu	37	5	52856354	52856354	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52856354delT	uc003jpe.2	+							NM_002495	NP_002486			NADH dehydrogenase (ubiquinone) Fe-S protein 4						brain development|cAMP-mediated signaling|mitochondrial electron transport, NADH to ubiquinone|mitochondrial respiratory chain complex I assembly|positive regulation of fibroblast proliferation|reactive oxygen species metabolic process|regulation of protein phosphorylation|response to cAMP|transport	mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity			central_nervous_system(1)	1		Lung NSC(810;8.27e-05)|Breast(144;0.0848)			NADH(DB00157)													---	---	---	---
NDUFS4	4724	broad.mit.edu	37	5	52868480	52868480	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52868480delT	uc003jpe.2	+							NM_002495	NP_002486			NADH dehydrogenase (ubiquinone) Fe-S protein 4						brain development|cAMP-mediated signaling|mitochondrial electron transport, NADH to ubiquinone|mitochondrial respiratory chain complex I assembly|positive regulation of fibroblast proliferation|reactive oxygen species metabolic process|regulation of protein phosphorylation|response to cAMP|transport	mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity			central_nervous_system(1)	1		Lung NSC(810;8.27e-05)|Breast(144;0.0848)			NADH(DB00157)													---	---	---	---
ARL15	54622	broad.mit.edu	37	5	53194108	53194108	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53194108delT	uc003jpg.1	-						ARL15_uc010ivs.1_Intron	NM_019087	NP_061960			ADP-ribosylation factor-like 15								GTP binding			ovary(1)	1		Lung NSC(810;0.000779)																---	---	---	---
ARL15	54622	broad.mit.edu	37	5	53405769	53405769	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53405769delT	uc003jpg.1	-						ARL15_uc010ivs.1_Intron	NM_019087	NP_061960			ADP-ribosylation factor-like 15								GTP binding			ovary(1)	1		Lung NSC(810;0.000779)																---	---	---	---
ARL15	54622	broad.mit.edu	37	5	53513768	53513768	+	Intron	DEL	A	-	-	rs3842039		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53513768delA	uc003jpg.1	-						ARL15_uc010ivs.1_Intron	NM_019087	NP_061960			ADP-ribosylation factor-like 15								GTP binding			ovary(1)	1		Lung NSC(810;0.000779)																---	---	---	---
Unknown	0	broad.mit.edu	37	5	53697309	53697310	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53697309_53697310delAA								ARL15 (90906 upstream) : HSPB3 (54135 downstream)																																			---	---	---	---
HSPB3	8988	broad.mit.edu	37	5	53750939	53750940	+	5'Flank	INS	-	TTTG	TTTG	rs146707918	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:53750939_53750940insTTTG	uc003jph.1	+							NM_006308	NP_006299			heat shock 27kDa protein 3						cell death|response to heat|response to unfolded protein	cytoplasm|nucleus					0		Lung NSC(810;0.00104)																---	---	---	---
SKIV2L2	23517	broad.mit.edu	37	5	54721292	54721292	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54721292delA	uc003jpy.3	+	27					SKIV2L2_uc011cqi.1_3'UTR|PPAP2A_uc003jpz.2_Intron|PPAP2A_uc003jqa.2_Intron|PPAP2A_uc003jqb.2_Intron	NM_015360	NP_056175			superkiller viralicidic activity 2-like 2						maturation of 5.8S rRNA	catalytic step 2 spliceosome|nucleolus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			ovary(1)|skin(1)	2		Lung NSC(810;0.000744)|Breast(144;0.181)|Prostate(74;0.194)																---	---	---	---
Unknown	0	broad.mit.edu	37	5	54877892	54877892	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54877892delA								PPAP2A (47019 upstream) : SLC38A9 (43784 downstream)																																			---	---	---	---
ANKRD55	79722	broad.mit.edu	37	5	55487944	55487945	+	Intron	DEL	CT	-	-	rs71906215		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55487944_55487945delCT	uc003jqu.2	-							NM_024669	NP_078945			ankyrin repeat domain 55 isoform 1											skin(1)	1		Lung NSC(810;8.69e-05)|Prostate(74;0.00634)|Breast(144;0.0334)|Ovarian(174;0.223)																---	---	---	---
Unknown	0	broad.mit.edu	37	5	55965807	55965807	+	IGR	DEL	T	-	-	rs75848760	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:55965807delT								ANKRD55 (436621 upstream) : MAP3K1 (145093 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	56405309	56405316	+	IGR	DEL	GAAGGAAG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56405309_56405316delGAAGGAAG								MIER3 (137808 upstream) : GPBP1 (64459 downstream)																																			---	---	---	---
GPBP1	65056	broad.mit.edu	37	5	56500089	56500089	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56500089delT	uc003jrh.3	+						GPBP1_uc010iwg.2_Intron|GPBP1_uc003jri.3_Intron|GPBP1_uc003jrj.3_Intron	NM_022913	NP_075064			GC-rich promoter binding protein 1 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			large_intestine(1)|central_nervous_system(1)	2		Lung NSC(810;0.000861)|Prostate(74;0.0305)|Breast(144;0.222)		OV - Ovarian serous cystadenocarcinoma(10;7.64e-39)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	56633921	56633921	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56633921delT								GPBP1 (74511 upstream) : ACTBL2 (141923 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	56736177	56736177	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56736177delA								GPBP1 (176767 upstream) : ACTBL2 (39667 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	56940066	56940066	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56940066delT								ACTBL2 (161430 upstream) : PLK2 (809746 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	57466824	57466826	+	IGR	DEL	AAA	-	-	rs34622519		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:57466824_57466826delAAA								ACTBL2 (688188 upstream) : PLK2 (282986 downstream)																																			---	---	---	---
RAB3C	115827	broad.mit.edu	37	5	57921684	57921685	+	Intron	DEL	AA	-	-	rs146672110		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:57921684_57921685delAA	uc003jrp.2	+							NM_138453	NP_612462			RAB3C, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding			ovary(1)|central_nervous_system(1)	2		all_cancers(5;9.93e-10)|all_epithelial(5;1.49e-10)|all_lung(5;8.97e-05)|Lung NSC(5;0.000139)|Prostate(74;0.0664)		OV - Ovarian serous cystadenocarcinoma(10;1.8e-34)														---	---	---	---
RAB3C	115827	broad.mit.edu	37	5	58050713	58050713	+	Intron	DEL	T	-	-	rs35414718		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:58050713delT	uc003jrp.2	+							NM_138453	NP_612462			RAB3C, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding			ovary(1)|central_nervous_system(1)	2		all_cancers(5;9.93e-10)|all_epithelial(5;1.49e-10)|all_lung(5;8.97e-05)|Lung NSC(5;0.000139)|Prostate(74;0.0664)		OV - Ovarian serous cystadenocarcinoma(10;1.8e-34)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	58147565	58147566	+	IGR	INS	-	TGTG	TGTG	rs139614048	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:58147565_58147566insTGTG								RAB3C (160 upstream) : PDE4D (117300 downstream)																																			---	---	---	---
PDE4D	5144	broad.mit.edu	37	5	58586754	58586754	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:58586754delT	uc003jsa.2	-						PDE4D_uc003jrx.2_Intron|PDE4D_uc003jry.2_Intron|PDE4D_uc003jrz.2_Intron|PDE4D_uc003jsb.2_Intron|PDE4D_uc003jsc.2_Intron|PDE4D_uc003jrw.2_Intron	NM_001104631	NP_001098101			phosphodiesterase 4D isoform 1						signal transduction	cytosol|insoluble fraction|membrane|microtubule organizing center|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Dyphylline(DB00651)													---	---	---	---
PDE4D	5144	broad.mit.edu	37	5	58622851	58622851	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:58622851delT	uc003jsa.2	-						PDE4D_uc003jrx.2_Intron|PDE4D_uc003jry.2_Intron|PDE4D_uc003jrz.2_Intron|PDE4D_uc003jsb.2_Intron|PDE4D_uc003jsc.2_Intron|PDE4D_uc003jrw.2_Intron	NM_001104631	NP_001098101			phosphodiesterase 4D isoform 1						signal transduction	cytosol|insoluble fraction|membrane|microtubule organizing center|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Dyphylline(DB00651)													---	---	---	---
PDE4D	5144	broad.mit.edu	37	5	59110662	59110662	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59110662delA	uc003jsa.2	-						PDE4D_uc003jsb.2_Intron	NM_001104631	NP_001098101			phosphodiesterase 4D isoform 1						signal transduction	cytosol|insoluble fraction|membrane|microtubule organizing center|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Dyphylline(DB00651)													---	---	---	---
PDE4D	5144	broad.mit.edu	37	5	59168089	59168098	+	Intron	DEL	ACACACACAC	-	-	rs71606610		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59168089_59168098delACACACACAC	uc003jsa.2	-						PDE4D_uc003jsb.2_Intron	NM_001104631	NP_001098101			phosphodiesterase 4D isoform 1						signal transduction	cytosol|insoluble fraction|membrane|microtubule organizing center|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Dyphylline(DB00651)													---	---	---	---
PDE4D	5144	broad.mit.edu	37	5	59252302	59252302	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59252302delA	uc003jsb.2	-							NM_006203	NP_006194			phosphodiesterase 4D isoform 2						signal transduction	cytosol|insoluble fraction|membrane|microtubule organizing center|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Dyphylline(DB00651)													---	---	---	---
PDE4D	5144	broad.mit.edu	37	5	59670120	59670120	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:59670120delA	uc003jsb.2	-						PDE4D_uc010iwj.1_Intron	NM_006203	NP_006194			phosphodiesterase 4D isoform 2						signal transduction	cytosol|insoluble fraction|membrane|microtubule organizing center|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Dyphylline(DB00651)													---	---	---	---
ELOVL7	79993	broad.mit.edu	37	5	60071448	60071448	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60071448delA	uc003jsi.3	-						ELOVL7_uc011cqo.1_Intron|ELOVL7_uc010iwk.2_Intron|ELOVL7_uc003jsj.3_Intron	NM_024930	NP_079206			elongation of very long chain fatty acids-like						fatty acid elongation, polyunsaturated fatty acid|fatty acid elongation, saturated fatty acid|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process|very long-chain fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	fatty acid elongase activity|protein binding				0		Lung NSC(810;2.56e-06)|Prostate(74;0.0115)|Breast(144;0.0244)|Ovarian(174;0.0481)																---	---	---	---
ERCC8	1161	broad.mit.edu	37	5	60171526	60171526	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60171526delT	uc003jsm.3	-						ERCC8_uc003jsk.2_Intron|ERCC8_uc003jsl.3_Intron|ERCC8_uc011cqp.1_Intron	NM_000082	NP_000073			excision repair cross-complementing rodent						positive regulation of DNA repair|proteasomal ubiquitin-dependent protein catabolic process|protein autoubiquitination|protein polyubiquitination|response to oxidative stress|response to UV|response to UV|transcription-coupled nucleotide-excision repair	Cul4A-RING ubiquitin ligase complex|nuclear matrix|nucleoplasm|nucleotide-excision repair complex|soluble fraction	protein binding|protein complex binding				0		Lung NSC(810;1.51e-06)|Prostate(74;0.0322)|Ovarian(174;0.0481)|Breast(144;0.077)											Direct_reversal_of_damage|NER					---	---	---	---
FLJ37543	285668	broad.mit.edu	37	5	60987054	60987055	+	Intron	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:60987054_60987055delGA	uc003jst.1	+						uc003jsv.2_Intron	NM_173667	NP_775938			hypothetical protein LOC285668 precursor							extracellular region					0		Lung NSC(810;0.000468)|Prostate(74;0.0283)|Breast(144;0.237)																---	---	---	---
Unknown	0	broad.mit.edu	37	5	61135748	61135749	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61135748_61135749delTT								FLJ37543 (133386 upstream) : KIF2A (466240 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	61520902	61520902	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61520902delT								FLJ37543 (518540 upstream) : KIF2A (81087 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	61547790	61547790	+	IGR	DEL	C	-	-	rs34287763		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61547790delC								FLJ37543 (545428 upstream) : KIF2A (54199 downstream)																																			---	---	---	---
KIF2A	3796	broad.mit.edu	37	5	61642858	61642858	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61642858delT	uc003jsy.3	+						KIF2A_uc003jsz.3_Intron|KIF2A_uc010iwp.2_Intron|KIF2A_uc003jsx.3_Intron|KIF2A_uc010iwq.2_5'Flank	NM_004520	NP_004511			kinesin heavy chain member 2 isoform 1						blood coagulation|cell differentiation|cell division|microtubule-based movement|mitotic prometaphase|mitotic spindle organization|nervous system development	centrosome|cytosol|microtubule|spindle pole	ATP binding|microtubule motor activity|protein binding				0		Lung NSC(810;8.94e-06)|Prostate(74;0.0132)|Ovarian(174;0.051)|Breast(144;0.077)		Lung(70;0.14)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	62456342	62456342	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:62456342delA								ISCA1P1 (383172 upstream) : HTR1A (799937 downstream)																																			---	---	---	---
RNF180	285671	broad.mit.edu	37	5	63626252	63626252	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:63626252delA	uc003jti.2	+							NM_001113561	NP_001107033			ring finger protein 180 isoform 1							integral to membrane|nuclear envelope	zinc ion binding				0		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0848)|Colorectal(97;0.234)		Lung(70;0.114)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	63720103	63720103	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:63720103delA								RNF180 (51409 upstream) : RGS7BP (82349 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	63758894	63758894	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:63758894delA								RNF180 (90200 upstream) : RGS7BP (43558 downstream)																																			---	---	---	---
RGS7BP	401190	broad.mit.edu	37	5	63830081	63830082	+	Intron	DEL	GA	-	-	rs142555885		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:63830081_63830082delGA	uc003jtj.2	+							NM_001029875	NP_001025046			regulator of G-protein signaling 7 binding						negative regulation of signal transduction	cytoplasm|nucleus|plasma membrane					0		Lung NSC(810;0.000518)|Prostate(74;0.0435)|Ovarian(174;0.186)		Lung(70;0.147)														---	---	---	---
SFRS12IP1	285672	broad.mit.edu	37	5	64023941	64023941	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64023941delT	uc003jtk.2	-	4	423	c.271delA	c.(271-273)AGGfs	p.R91fs		NM_173829	NP_776190	Q8N9Q2	SR1IP_HUMAN	P18SRP protein	91	Lys-rich.				mRNA processing|RNA splicing		nucleic acid binding|zinc ion binding				0		Lung NSC(167;1.66e-05)|Prostate(74;0.0138)|Ovarian(174;0.0545)|Colorectal(97;0.234)		Lung(70;0.119)														---	---	---	---
SFRS12IP1	285672	broad.mit.edu	37	5	64050779	64050780	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64050779_64050780insA	uc003jtk.2	-							NM_173829	NP_776190			P18SRP protein						mRNA processing|RNA splicing		nucleic acid binding|zinc ion binding				0		Lung NSC(167;1.66e-05)|Prostate(74;0.0138)|Ovarian(174;0.0545)|Colorectal(97;0.234)		Lung(70;0.119)														---	---	---	---
ADAMTS6	11174	broad.mit.edu	37	5	64698796	64698796	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:64698796delT	uc003jtp.2	-						ADAMTS6_uc003jto.2_Intron|ADAMTS6_uc003jtq.2_Intron|ADAMTS6_uc003jtr.1_Intron	NM_197941	NP_922932			ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0		Lung NSC(167;2.44e-06)|Prostate(74;0.014)|Ovarian(174;0.0549)|Breast(144;0.111)|Colorectal(97;0.235)		Lung(70;0.00942)														---	---	---	---
NLN	57486	broad.mit.edu	37	5	65101911	65101911	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65101911delA	uc003juf.2	+						NLN_uc003jug.2_Intron|NLN_uc010iww.2_Intron	NM_020726	NP_065777			neurolysin precursor						proteolysis	mitochondrial intermembrane space	metal ion binding|metalloendopeptidase activity			central_nervous_system(1)	1		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0743)|Lung(70;0.00616)														---	---	---	---
NLN	57486	broad.mit.edu	37	5	65103266	65103267	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65103266_65103267delTT	uc003juf.2	+						NLN_uc003jug.2_Intron|NLN_uc010iww.2_Intron	NM_020726	NP_065777			neurolysin precursor						proteolysis	mitochondrial intermembrane space	metal ion binding|metalloendopeptidase activity			central_nervous_system(1)	1		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0743)|Lung(70;0.00616)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	65498990	65498991	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65498990_65498991insT								SFRS12 (22278 upstream) : MAST4 (393185 downstream)																																			---	---	---	---
MAST4	375449	broad.mit.edu	37	5	65939961	65939961	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:65939961delT	uc003jur.3	+						MAST4_uc010iwz.2_Intron	NM_198828	NP_942123			microtubule associated serine/threonine kinase							cytoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(6)|ovary(2)|kidney(2)|breast(2)|central_nervous_system(1)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)														---	---	---	---
MAST4	375449	broad.mit.edu	37	5	66357343	66357344	+	Intron	DEL	GT	-	-	rs28394164	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66357343_66357344delGT	uc003jut.1	+						MAST4_uc003jus.2_Intron|MAST4_uc003juu.1_Intron|MAST4_uc011cra.1_Intron|MAST4_uc010ixa.2_Intron|MAST4_uc003juv.2_Intron|MAST4_uc003juw.2_Intron	NM_015183	NP_055998			microtubule associated serine/threonine kinase							cytoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(6)|ovary(2)|kidney(2)|breast(2)|central_nervous_system(1)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	66469694	66469694	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66469694delA								MAST4 (6602 upstream) : CD180 (8410 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	66515101	66515103	+	IGR	DEL	ATT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66515101_66515103delATT								CD180 (22484 upstream) : PIK3R1 (996501 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	66996231	66996232	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66996231_66996232delTT								CD180 (503614 upstream) : PIK3R1 (515372 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	67195705	67195705	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67195705delA								CD180 (703088 upstream) : PIK3R1 (315899 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	67268247	67268248	+	IGR	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67268247_67268248delCT								CD180 (775630 upstream) : PIK3R1 (243356 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	68306671	68306671	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68306671delT	uc003jvf.1	-											Homo sapiens cDNA FLJ46633 fis, clone TRACH2025705.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	68346284	68346284	+	IGR	DEL	T	-	-	rs77343244		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68346284delT								PIK3R1 (748637 upstream) : SLC30A5 (43534 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	68775896	68775896	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68775896delT								MARVELD2 (36060 upstream) : OCLN (12223 downstream)																																			---	---	---	---
GUSBP3	653188	broad.mit.edu	37	5	69461999	69461999	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:69461999delA	uc003jxm.2	-						uc011crh.1_Intron|uc011crl.1_Intron|LOC100170939_uc010ixu.2_Intron|LOC100170939_uc003jyl.2_Intron|LOC100170939_uc003jyo.1_Intron					Homo sapiens cDNA FLJ36702 fis, clone UTERU2009206.												0																		---	---	---	---
GTF2H2B	653238	broad.mit.edu	37	5	69730715	69730715	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:69730715delT	uc003jzb.3	+						uc011crh.1_Intron|uc011crl.1_Intron|LOC100170939_uc010ixu.2_Intron|uc003jyr.1_Intron|LOC100170939_uc003jys.2_Intron|LOC100170939_uc011crn.1_Intron|uc011cro.1_Intron|GTF2H2B_uc011crp.1_Intron	NM_001098729	NP_001092199			general transcription factor IIH, polypeptide												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	70707224	70707224	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70707224delT	uc010iyu.1	-						uc003kbl.1_Intron					Homo sapiens cDNA FLJ41874 fis, clone OCBBF2019327.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	70973131	70973132	+	IGR	DEL	CA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70973131_70973132delCA								MCCC2 (18603 upstream) : CARTPT (41862 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	71139028	71139028	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71139028delT								CARTPT (122156 upstream) : MAP1B (264090 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	71153402	71153402	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71153402delT								CARTPT (136530 upstream) : MAP1B (249716 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	71323360	71323360	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71323360delA								CARTPT (306488 upstream) : MAP1B (79758 downstream)																																			---	---	---	---
MAP1B	4131	broad.mit.edu	37	5	71501438	71501439	+	3'UTR	INS	-	GA	GA			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71501438_71501439insGA	uc003kbw.3	+	7						NM_005909	NP_005900			microtubule-associated protein 1B							microtubule|microtubule associated complex	structural molecule activity			large_intestine(2)|ovary(1)|central_nervous_system(1)|pancreas(1)	5		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)														---	---	---	---
MRPS27	23107	broad.mit.edu	37	5	71611385	71611386	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71611385_71611386delAA	uc003kbz.3	-						MRPS27_uc003kca.3_Intron|MRPS27_uc011cse.1_Intron|MRPS27_uc010iza.2_Intron	NM_015084	NP_055899			mitochondrial ribosomal protein S27							mitochondrion|ribosome					0		Lung NSC(167;0.00237)|Ovarian(174;0.0175)|Prostate(461;0.141)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.46e-53)														---	---	---	---
ZNF366	167465	broad.mit.edu	37	5	71756732	71756733	+	Frame_Shift_Ins	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71756732_71756733insT	uc003kce.1	-	2	777_778	c.591_592insA	c.(589-594)CCCTTCfs	p.P197fs		NM_152625	NP_689838	Q8N895	ZN366_HUMAN	zinc finger protein 366	197_198					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)|skin(1)	2		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)														---	---	---	---
TNPO1	3842	broad.mit.edu	37	5	72136259	72136259	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72136259delA	uc003kck.3	+						TNPO1_uc011csi.1_Intron|TNPO1_uc011csj.1_Intron	NM_002270	NP_002261			transportin 1 isoform 1						interspecies interaction between organisms|mRNA metabolic process|protein import into nucleus, translocation	cytosol|nucleus	nuclear localization sequence binding|protein binding|protein transporter activity			skin(3)|urinary_tract(1)|ovary(1)|kidney(1)|central_nervous_system(1)	7		Lung NSC(167;0.0053)|Ovarian(174;0.0175)		OV - Ovarian serous cystadenocarcinoma(47;6.14e-54)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	72219067	72219068	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72219067_72219068delTT								TNPO1 (8853 upstream) : FCHO2 (32740 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	72702896	72702896	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72702896delT								TMEM174 (231928 upstream) : FOXD1 (39191 downstream)																																			---	---	---	---
BTF3	689	broad.mit.edu	37	5	72801223	72801223	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72801223delT	uc003kcr.1	+	6					BTF3_uc003kcq.1_3'UTR|BTF3_uc003kcs.1_RNA|BTF3_uc003kct.1_RNA	NM_001037637	NP_001032726			basic transcription factor 3 isoform A						regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	protein binding				0		Lung NSC(167;0.00405)|Ovarian(174;0.0175)		OV - Ovarian serous cystadenocarcinoma(47;2.73e-54)														---	---	---	---
UTP15	84135	broad.mit.edu	37	5	72871552	72871553	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72871552_72871553delTT	uc003kcw.1	+						UTP15_uc011cso.1_Intron|UTP15_uc011csp.1_Intron|UTP15_uc010ize.1_Intron	NM_032175	NP_115551			UTP15, U3 small nucleolar ribonucleoprotein,						rRNA processing	cytoplasm|nucleolus					0		Lung NSC(167;0.00405)|Ovarian(174;0.0129)		OV - Ovarian serous cystadenocarcinoma(47;7.76e-55)														---	---	---	---
UTP15	84135	broad.mit.edu	37	5	72874391	72874391	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72874391delT	uc003kcw.1	+						UTP15_uc011cso.1_Intron|UTP15_uc011csp.1_Intron|UTP15_uc010ize.1_Intron	NM_032175	NP_115551			UTP15, U3 small nucleolar ribonucleoprotein,						rRNA processing	cytoplasm|nucleolus					0		Lung NSC(167;0.00405)|Ovarian(174;0.0129)		OV - Ovarian serous cystadenocarcinoma(47;7.76e-55)														---	---	---	---
RGNEF	64283	broad.mit.edu	37	5	72953965	72953968	+	Intron	DEL	AAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:72953965_72953968delAAAA	uc003kcx.2	+							NM_001080479	NP_001073948			Rho-guanine nucleotide exchange factor						cell differentiation|intracellular signal transduction|regulation of Rho protein signal transduction	cytoplasm|plasma membrane	metal ion binding|Rho guanyl-nucleotide exchange factor activity|RNA binding				0		Lung NSC(167;0.0378)|all_lung(232;0.04)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;1.25e-51)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	73346104	73346104	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73346104delT								RGNEF (108691 upstream) : ENC1 (577131 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	73375026	73375026	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73375026delT								RGNEF (137613 upstream) : ENC1 (548209 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	73402662	73402662	+	IGR	DEL	T	-	-	rs288852	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73402662delT								RGNEF (165249 upstream) : ENC1 (520573 downstream)																																			---	---	---	---
HEXB	3074	broad.mit.edu	37	5	74011542	74011544	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74011542_74011544delAAA	uc003kdf.3	+						HEXB_uc003kdd.2_Intron|HEXB_uc010izh.2_Intron|HEXB_uc003kdg.1_5'Flank|HEXB_uc010izi.1_5'Flank	NM_000521	NP_000512			hexosaminidase B preproprotein						cell death	lysosome	cation binding|protein heterodimerization activity|protein homodimerization activity			ovary(1)	1		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.72e-57)														---	---	---	---
GFM2	84340	broad.mit.edu	37	5	74043422	74043422	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74043422delA	uc003kdh.1	-						GFM2_uc003kdi.1_Intron|GFM2_uc010izj.1_Intron|GFM2_uc010izk.1_Intron|GFM2_uc003kdj.1_Intron|GFM2_uc010izl.1_Intron	NM_032380	NP_115756			mitochondrial elongation factor G2 isoform 1						mitochondrial translation|ribosome disassembly	mitochondrion	GTP binding|GTPase activity				0		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.86e-56)														---	---	---	---
FAM169A	26049	broad.mit.edu	37	5	74135799	74135799	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74135799delA	uc003kdm.2	-						FAM169A_uc010izm.2_Intron|FAM169A_uc003kdl.2_Intron	NM_015566	NP_056381			hypothetical protein LOC26049												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	74203469	74203469	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74203469delT								FAM169A (11681 upstream) : GCNT4 (119821 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	74391299	74391300	+	IGR	DEL	AA	-	-	rs78904658		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74391299_74391300delAA								GCNT4 (64575 upstream) : ANKRD31 (51762 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	74429163	74429163	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74429163delA								GCNT4 (102439 upstream) : ANKRD31 (13899 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	74563856	74563856	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74563856delA								ANKRD31 (31153 upstream) : HMGCR (68298 downstream)																																			---	---	---	---
HMGCR	3156	broad.mit.edu	37	5	74652094	74652095	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74652094_74652095insA	uc003kdp.2	+						HMGCR_uc011cst.1_Intron|HMGCR_uc003kdq.2_Intron|HMGCR_uc010izo.2_5'Flank|HMGCR_uc010izp.2_5'Flank	NM_000859	NP_000850			3-hydroxy-3-methylglutaryl-Coenzyme A reductase						cholesterol biosynthetic process|coenzyme A metabolic process|germ cell migration|gonad development|isoprenoid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|peroxisomal membrane	hydroxymethylglutaryl-CoA reductase (NADPH) activity|NADP binding			ovary(1)	1		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;2.24e-54)	Atorvastatin(DB01076)|Bezafibrate(DB01393)|Cerivastatin(DB00439)|Fluvastatin(DB01095)|Lovastatin(DB00227)|NADH(DB00157)|Pravastatin(DB00175)|Rosuvastatin(DB01098)|Simvastatin(DB00641)													---	---	---	---
POLK	51426	broad.mit.edu	37	5	74872584	74872584	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74872584delT	uc003kdw.2	+						POLK_uc003kdx.2_Intron|POLK_uc003kdy.2_Intron|POLK_uc003kea.2_Intron|POLK_uc003keb.2_Intron|POLK_uc010izq.2_Intron|POLK_uc003kec.2_Intron|POLK_uc010izr.2_Intron|POLK_uc010izs.2_Intron|POLK_uc003ked.2_Intron|POLK_uc003kee.2_Intron|POLK_uc003kef.2_Intron	NM_016218	NP_057302			DNA-directed DNA polymerase kappa						DNA replication|nucleotide-excision repair, DNA gap filling	nucleus	damaged DNA binding|DNA-directed DNA polymerase activity|metal ion binding			ovary(2)|kidney(2)	4		all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;2.9e-54)|all cancers(79;1.27e-42)									DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
POC5	134359	broad.mit.edu	37	5	74991485	74991486	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74991485_74991486insA	uc003keh.3	-						POC5_uc010izu.2_Intron|POC5_uc003keg.3_Intron	NM_001099271	NP_001092741			proteome of centriole 5 isoform 1						cell cycle	centriole				lung(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	75143628	75143628	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75143628delA								POC5 (130315 upstream) : SV2C (235677 downstream)																																			---	---	---	---
SV2C	22987	broad.mit.edu	37	5	75577223	75577227	+	Intron	DEL	AAAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75577223_75577227delAAAAA	uc003kei.1	+							NM_014979	NP_055794			synaptic vesicle glycoprotein 2C						neurotransmitter transport	cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			skin(1)	1		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)														---	---	---	---
IQGAP2	10788	broad.mit.edu	37	5	75795766	75795767	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75795766_75795767delAA	uc003kek.2	+							NM_006633	NP_006624			IQ motif containing GTPase activating protein 2						small GTPase mediated signal transduction	actin cytoskeleton	actin binding|calmodulin binding|GTPase inhibitor activity|Ras GTPase activator activity			ovary(6)|central_nervous_system(1)	7		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)														---	---	---	---
PDE8B	8622	broad.mit.edu	37	5	76563265	76563267	+	Intron	DEL	AAA	-	-	rs78677953		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76563265_76563267delAAA	uc003kfa.2	+						PDE8B_uc003kfb.2_Intron|PDE8B_uc003kfc.2_Intron|PDE8B_uc003kfd.2_Intron|PDE8B_uc003kfe.2_Intron	NM_003719	NP_003710			phosphodiesterase 8B isoform 1						cyclic nucleotide metabolic process|regulation of transcription, DNA-dependent	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|two-component response regulator activity				0		all_lung(232;0.00043)|Lung NSC(167;0.00114)|Ovarian(174;0.0107)|Prostate(461;0.0605)		OV - Ovarian serous cystadenocarcinoma(54;2.21e-49)|Epithelial(54;5.82e-43)|all cancers(79;4.06e-38)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	76820439	76820439	+	IGR	DEL	T	-	-	rs72273842		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76820439delT								WDR41 (32107 upstream) : OTP (104099 downstream)																																			---	---	---	---
AP3B1	8546	broad.mit.edu	37	5	77334907	77334907	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77334907delT	uc003kfj.2	-	23	2894	c.2769delA	c.(2767-2769)AAAfs	p.K923fs		NM_003664	NP_003655	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1	923					endocytosis|melanosome organization	clathrin coated vesicle membrane|Golgi apparatus|membrane coat	protein phosphatase binding|protein transporter activity			central_nervous_system(1)	1		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)										Hermansky-Pudlak_syndrome				---	---	---	---
AP3B1	8546	broad.mit.edu	37	5	77453583	77453583	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77453583delT	uc003kfj.2	-							NM_003664	NP_003655			adaptor-related protein complex 3, beta 1						endocytosis|melanosome organization	clathrin coated vesicle membrane|Golgi apparatus|membrane coat	protein phosphatase binding|protein transporter activity			central_nervous_system(1)	1		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)										Hermansky-Pudlak_syndrome				---	---	---	---
AP3B1	8546	broad.mit.edu	37	5	77540244	77540244	+	Intron	DEL	A	-	-	rs77569828		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77540244delA	uc003kfj.2	-							NM_003664	NP_003655			adaptor-related protein complex 3, beta 1						endocytosis|melanosome organization	clathrin coated vesicle membrane|Golgi apparatus|membrane coat	protein phosphatase binding|protein transporter activity			central_nervous_system(1)	1		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)										Hermansky-Pudlak_syndrome				---	---	---	---
LHFPL2	10184	broad.mit.edu	37	5	77886025	77886027	+	Intron	DEL	AAC	-	-	rs34565791		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77886025_77886027delAAC	uc003kfo.2	-							NM_005779	NP_005770			lipoma HMGIC fusion partner-like 2							integral to membrane					0		all_lung(232;0.000409)|Lung NSC(167;0.00108)|Ovarian(174;0.0107)|Prostate(461;0.218)		OV - Ovarian serous cystadenocarcinoma(54;6.48e-46)|Epithelial(54;8.43e-42)|all cancers(79;1.42e-36)														---	---	---	---
LHFPL2	10184	broad.mit.edu	37	5	77915024	77915024	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:77915024delT	uc003kfo.2	-							NM_005779	NP_005770			lipoma HMGIC fusion partner-like 2							integral to membrane					0		all_lung(232;0.000409)|Lung NSC(167;0.00108)|Ovarian(174;0.0107)|Prostate(461;0.218)		OV - Ovarian serous cystadenocarcinoma(54;6.48e-46)|Epithelial(54;8.43e-42)|all cancers(79;1.42e-36)														---	---	---	---
ARSB	411	broad.mit.edu	37	5	78092488	78092488	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78092488delT	uc003kfq.2	-							NM_000046	NP_000037			arylsulfatase B isoform 1 precursor						lysosomal transport|lysosome organization	lysosome	arylsulfatase activity|metal ion binding|N-acetylgalactosamine-4-sulfatase activity			upper_aerodigestive_tract(1)	1		all_lung(232;0.000637)|Lung NSC(167;0.00173)|Ovarian(174;0.0105)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;4.24e-44)|Epithelial(54;3.12e-39)|all cancers(79;3.02e-34)														---	---	---	---
ARSB	411	broad.mit.edu	37	5	78247334	78247334	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78247334delA	uc003kfq.2	-						ARSB_uc003kfr.3_Intron	NM_000046	NP_000037			arylsulfatase B isoform 1 precursor						lysosomal transport|lysosome organization	lysosome	arylsulfatase activity|metal ion binding|N-acetylgalactosamine-4-sulfatase activity			upper_aerodigestive_tract(1)	1		all_lung(232;0.000637)|Lung NSC(167;0.00173)|Ovarian(174;0.0105)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;4.24e-44)|Epithelial(54;3.12e-39)|all cancers(79;3.02e-34)														---	---	---	---
JMY	133746	broad.mit.edu	37	5	78588151	78588152	+	Intron	INS	-	TTG	TTG			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78588151_78588152insTTG	uc003kfx.3	+						JMY_uc003kfw.1_Intron	NM_152405	NP_689618			junction-mediating and regulatory protein						'de novo' actin filament nucleation|actin polymerization-dependent cell motility|Arp2/3 complex-mediated actin nucleation|cell cycle arrest|DNA repair|induction of apoptosis|positive regulation of sequence-specific DNA binding transcription factor activity|regulation of transcription from RNA polymerase II promoter	cell leading edge|cytoplasm|cytoskeleton|nucleus	actin binding|transcription coactivator activity				0		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;4.45e-45)|Epithelial(54;5.85e-40)|all cancers(79;2.89e-35)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	79234760	79234760	+	IGR	DEL	T	-	-	rs71601540		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79234760delT								CMYA5 (138712 upstream) : MTX3 (37781 downstream)																																			---	---	---	---
THBS4	7060	broad.mit.edu	37	5	79378155	79378155	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79378155delC	uc003kgh.2	+						uc003kgi.3_Intron	NM_003248	NP_003239			thrombospondin 4 precursor						endothelial cell-cell adhesion|myoblast migration|negative regulation of angiogenesis|positive regulation of endothelial cell proliferation|positive regulation of neutrophil chemotaxis|positive regulation of peptidyl-tyrosine phosphorylation	basement membrane|extracellular space	calcium ion binding|heparin binding|integrin binding|structural molecule activity				0		Lung NSC(167;0.00328)|all_lung(232;0.00355)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;6.3e-45)|Epithelial(54;1.77e-39)|all cancers(79;3.2e-34)														---	---	---	---
SERINC5	256987	broad.mit.edu	37	5	79473234	79473234	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79473234delA	uc003kgj.2	-						SERINC5_uc003kgk.2_Intron|SERINC5_uc003kgl.2_Intron|SERINC5_uc003kgm.2_Intron|SERINC5_uc011ctj.1_Intron	NM_178276	NP_840060			developmentally regulated protein TPO1						phosphatidylserine metabolic process|phospholipid biosynthetic process|positive regulation of transferase activity	endoplasmic reticulum membrane|integral to membrane				ovary(1)	1		Lung NSC(167;0.00328)|all_lung(232;0.00356)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;2.93e-46)|Epithelial(54;5.59e-40)|all cancers(79;1.89e-34)														---	---	---	---
FAM151B	167555	broad.mit.edu	37	5	79809324	79809324	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79809324delT	uc003kgv.1	+						FAM151B_uc010jal.1_Intron	NM_205548	NP_991111			hypothetical protein LOC167555												0		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;8.21e-47)|Epithelial(54;8.3e-42)|all cancers(79;1.97e-36)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	79895405	79895405	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79895405delC								ANKRD34B (29307 upstream) : DHFR (26640 downstream)																																			---	---	---	---
MSH3	4437	broad.mit.edu	37	5	80077298	80077298	+	Intron	DEL	T	-	-	rs71659599		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80077298delT	uc003kgz.2	+							NM_002439	NP_002430			mutS homolog 3						maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments	MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding			lung(2)|ovary(1)|breast(1)	4		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)									MMR					---	---	---	---
SSBP2	23635	broad.mit.edu	37	5	80716503	80716503	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80716503delA	uc003kho.2	-						RNU5E_uc011cto.1_Intron|SSBP2_uc010jar.2_Intron|SSBP2_uc003khn.2_Intron|SSBP2_uc003khp.2_Intron|SSBP2_uc011ctp.1_Intron|SSBP2_uc011ctq.1_Intron|SSBP2_uc011ctr.1_Intron	NM_012446	NP_036578			single-stranded DNA binding protein 2						regulation of transcription, DNA-dependent	cytoplasm|nucleus	single-stranded DNA binding		SSBP2/JAK2(4)	haematopoietic_and_lymphoid_tissue(4)|skin(1)	5		Lung NSC(167;0.00154)|all_lung(232;0.00179)|Ovarian(174;0.0338)		OV - Ovarian serous cystadenocarcinoma(54;1.07e-41)|Epithelial(54;2.79e-35)|all cancers(79;1.18e-29)														---	---	---	---
SSBP2	23635	broad.mit.edu	37	5	80733496	80733496	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80733496delT	uc003kho.2	-						RNU5E_uc011cto.1_Intron|SSBP2_uc010jar.2_Intron|SSBP2_uc003khn.2_Intron|SSBP2_uc003khp.2_Intron|SSBP2_uc011ctp.1_Intron|SSBP2_uc011ctq.1_Intron|SSBP2_uc011ctr.1_Intron	NM_012446	NP_036578			single-stranded DNA binding protein 2						regulation of transcription, DNA-dependent	cytoplasm|nucleus	single-stranded DNA binding		SSBP2/JAK2(4)	haematopoietic_and_lymphoid_tissue(4)|skin(1)	5		Lung NSC(167;0.00154)|all_lung(232;0.00179)|Ovarian(174;0.0338)		OV - Ovarian serous cystadenocarcinoma(54;1.07e-41)|Epithelial(54;2.79e-35)|all cancers(79;1.18e-29)														---	---	---	---
ATG10	83734	broad.mit.edu	37	5	81470378	81470378	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81470378delT	uc003khs.2	+						ATG10_uc003khr.2_Intron|ATG10_uc010jas.2_Intron	NM_001131028	NP_001124500			APG10 autophagy 10-like						autophagy in response to ER overload|positive regulation of protein modification process|protein lipidation|protein modification by small protein conjugation|protein transport	cytoplasm	Atg12 ligase activity|protein binding				0		Lung NSC(167;0.0258)|all_lung(232;0.0294)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;9.94e-41)|Epithelial(54;6.3e-36)|all cancers(79;2.31e-30)														---	---	---	---
ATG10	83734	broad.mit.edu	37	5	81550382	81550389	+	3'UTR	DEL	AAAAAAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81550382_81550389delAAAAAAAA	uc003khs.2	+	9					ATG10_uc003khr.2_3'UTR|ATG10_uc010jas.2_3'UTR	NM_001131028	NP_001124500			APG10 autophagy 10-like						autophagy in response to ER overload|positive regulation of protein modification process|protein lipidation|protein modification by small protein conjugation|protein transport	cytoplasm	Atg12 ligase activity|protein binding				0		Lung NSC(167;0.0258)|all_lung(232;0.0294)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;9.94e-41)|Epithelial(54;6.3e-36)|all cancers(79;2.31e-30)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	81614226	81614226	+	IGR	DEL	A	-	-	rs71756795		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81614226delA								ATP6AP1L (80 upstream) : TMEM167A (734441 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	81934940	81934943	+	IGR	DEL	TTTT	-	-	rs34486657		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:81934940_81934943delTTTT								ATP6AP1L (320794 upstream) : TMEM167A (413724 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	82005312	82005313	+	IGR	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82005312_82005313delTC								ATP6AP1L (391166 upstream) : TMEM167A (343354 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	82024224	82024226	+	IGR	DEL	AAA	-	-	rs77317361		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82024224_82024226delAAA								ATP6AP1L (410078 upstream) : TMEM167A (324441 downstream)																																			---	---	---	---
TMEM167A	153339	broad.mit.edu	37	5	82360945	82360945	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82360945delA	uc003khx.3	-						SCARNA18_uc003khz.2_5'Flank	NM_174909	NP_777569			transmembrane protein 167A precursor							Golgi membrane|integral to membrane					0																		---	---	---	---
TMEM167A	153339	broad.mit.edu	37	5	82372898	82372898	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82372898delT	uc003khx.3	-						XRCC4_uc003kia.1_5'Flank|XRCC4_uc003kib.2_5'Flank|XRCC4_uc003kid.2_5'Flank|XRCC4_uc003kic.2_5'Flank|XRCC4_uc003kie.2_5'Flank	NM_174909	NP_777569			transmembrane protein 167A precursor							Golgi membrane|integral to membrane					0																		---	---	---	---
VCAN	1462	broad.mit.edu	37	5	82821765	82821767	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82821765_82821767delTTT	uc003kii.3	+						VCAN_uc003kij.3_Intron|VCAN_uc010jau.2_Intron|VCAN_uc003kik.3_Intron	NM_004385	NP_004376			versican isoform 1 precursor						cell adhesion|cell recognition|glial cell migration	extracellular space|proteinaceous extracellular matrix	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(7)|skin(6)|lung(2)|central_nervous_system(1)	16		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	84159657	84159659	+	IGR	DEL	TTT	-	-	rs113407266		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:84159657_84159659delTTT								EDIL3 (479046 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	84726321	84726321	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:84726321delT								None (None upstream) : NBPF22P (851941 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	84861936	84861936	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:84861936delT								None (None upstream) : NBPF22P (716326 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	84923000	84923001	+	IGR	DEL	TG	-	-	rs71607762		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:84923000_84923001delTG								None (None upstream) : NBPF22P (655261 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	86014095	86014095	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86014095delT								COX7C (97514 upstream) : RASA1 (550056 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	86485194	86485194	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86485194delT	uc003kit.2	+											Homo sapiens cDNA clone IMAGE:5444809, **** WARNING: chimeric clone ****.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	87059963	87059963	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87059963delG								CCNH (351127 upstream) : TMEM161B (431061 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	87264189	87264189	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87264189delA								CCNH (555353 upstream) : TMEM161B (226835 downstream)																																			---	---	---	---
TMEM161B	153396	broad.mit.edu	37	5	87491918	87491918	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87491918delT	uc003kjc.2	-	12					TMEM161B_uc011cty.1_3'UTR|TMEM161B_uc010jax.2_RNA|TMEM161B_uc011ctx.1_3'UTR	NM_153354	NP_699185			transmembrane protein 161B							integral to membrane				skin(2)	2		all_cancers(142;0.000275)|Lung NSC(167;0.00901)|all_lung(232;0.0111)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;6.24e-36)|Epithelial(54;6.8e-31)|all cancers(79;1.07e-26)														---	---	---	---
TMEM161B	153396	broad.mit.edu	37	5	87527815	87527815	+	Intron	DEL	T	-	-	rs137980672	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87527815delT	uc003kjc.2	-						TMEM161B_uc011cty.1_Intron|TMEM161B_uc010jax.2_Intron|TMEM161B_uc011ctz.1_Intron	NM_153354	NP_699185			transmembrane protein 161B							integral to membrane				skin(2)	2		all_cancers(142;0.000275)|Lung NSC(167;0.00901)|all_lung(232;0.0111)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;6.24e-36)|Epithelial(54;6.8e-31)|all cancers(79;1.07e-26)														---	---	---	---
LOC645323	645323	broad.mit.edu	37	5	87898998	87898998	+	Intron	DEL	A	-	-	rs11959094		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:87898998delA	uc011cua.1	-							NR_015436				Homo sapiens cDNA FLJ34037 fis, clone FCBBF2005439.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	88258119	88258119	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88258119delT	uc003kjn.1	+											Homo sapiens mRNA; cDNA DKFZp586I041 (from clone DKFZp586I041).																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	88476277	88476278	+	IGR	DEL	GT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88476277_88476278delGT								MEF2C (276408 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	88658445	88658445	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88658445delA								MEF2C (458576 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	88961509	88961510	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88961509_88961510delTG								MEF2C (761640 upstream) : CETN3 (728021 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	89485401	89485401	+	IGR	DEL	A	-	-	rs33936305		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89485401delA								None (None upstream) : CETN3 (204130 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	89494776	89494776	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89494776delA								None (None upstream) : CETN3 (194755 downstream)																																			---	---	---	---
CETN3	1070	broad.mit.edu	37	5	89701343	89701344	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89701343_89701344insA	uc003kjo.2	-							NM_004365	NP_004356			centrin 3						cell division|centrosome cycle|mitosis	centriole	calcium ion binding				0		all_cancers(142;7.93e-09)|all_epithelial(76;2.13e-11)|Lung NSC(167;2.46e-05)|all_lung(232;3.25e-05)|Ovarian(174;0.00832)|Colorectal(57;0.122)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(54;1.42e-32)|Epithelial(54;1.45e-26)|all cancers(79;2.87e-23)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	89831809	89831809	+	IGR	DEL	A	-	-	rs11346827		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89831809delA								LYSMD3 (6408 upstream) : GPR98 (22808 downstream)																																			---	---	---	---
GPR98	84059	broad.mit.edu	37	5	89932611	89932611	+	Intron	DEL	T	-	-	rs78277883		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89932611delT	uc003kju.2	+						GPR98_uc003kjt.2_Intron	NM_032119	NP_115495			G protein-coupled receptor 98 precursor						cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)														---	---	---	---
GPR98	84059	broad.mit.edu	37	5	90010094	90010094	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90010094delT	uc003kju.2	+						GPR98_uc003kjt.2_Intron|GPR98_uc003kjv.2_Intron	NM_032119	NP_115495			G protein-coupled receptor 98 precursor						cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)														---	---	---	---
GPR98	84059	broad.mit.edu	37	5	90025688	90025689	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90025688_90025689delTT	uc003kju.2	+						GPR98_uc003kjt.2_Intron|GPR98_uc003kjv.2_Intron	NM_032119	NP_115495			G protein-coupled receptor 98 precursor						cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)														---	---	---	---
GPR98	84059	broad.mit.edu	37	5	90086591	90086591	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90086591delT	uc003kju.2	+						GPR98_uc003kjt.2_Intron|GPR98_uc003kjw.2_Intron	NM_032119	NP_115495			G protein-coupled receptor 98 precursor						cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)														---	---	---	---
GPR98	84059	broad.mit.edu	37	5	90278563	90278564	+	Intron	INS	-	T	T	rs72545412	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:90278563_90278564insT	uc003kju.2	+						GPR98_uc003kjt.2_Intron|GPR98_uc003kjw.2_Intron|GPR98_uc003kjx.2_Intron	NM_032119	NP_115495			G protein-coupled receptor 98 precursor						cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	91014511	91014511	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:91014511delT								LOC100129716 (297980 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	91604022	91604022	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:91604022delA	uc003kkb.1	+											Homo sapiens cDNA FLJ31923 fis, clone NT2RP7005323.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	92249857	92249857	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:92249857delA								None (None upstream) : FLJ42709 (495208 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	92434998	92434999	+	IGR	DEL	GA	-	-	rs34266609		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:92434998_92434999delGA								None (None upstream) : FLJ42709 (310066 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	92490739	92490739	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:92490739delA								None (None upstream) : FLJ42709 (254326 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	92569949	92569949	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:92569949delA								None (None upstream) : FLJ42709 (175116 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	92659553	92659553	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:92659553delA								None (None upstream) : FLJ42709 (85512 downstream)																																			---	---	---	---
FAM172A	83989	broad.mit.edu	37	5	93019526	93019526	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:93019526delT	uc010jbd.2	-						FAM172A_uc011cuf.1_Intron|FAM172A_uc011cug.1_Intron|FAM172A_uc011cuh.1_Intron|FAM172A_uc011cui.1_Intron|FAM172A_uc011cuj.1_Intron	NM_032042	NP_114431			hypothetical protein LOC83989 isoform 1							endoplasmic reticulum|extracellular region					0																		---	---	---	---
FAM172A	83989	broad.mit.edu	37	5	93359949	93359949	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:93359949delA	uc010jbd.2	-						FAM172A_uc011cuf.1_Intron|FAM172A_uc011cug.1_Intron|FAM172A_uc011cuh.1_Intron|FAM172A_uc011cui.1_Intron|FAM172A_uc011cuj.1_Intron|FAM172A_uc003kkm.3_Intron	NM_032042	NP_114431			hypothetical protein LOC83989 isoform 1							endoplasmic reticulum|extracellular region					0																		---	---	---	---
C5orf36	285600	broad.mit.edu	37	5	93828172	93828172	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:93828172delA	uc011cuk.1	-							NM_001145678	NP_001139150			hypothetical protein LOC285600 isoform 1												0		all_cancers(142;2.12e-08)|all_epithelial(76;5.95e-11)|all_lung(232;0.000996)|Lung NSC(167;0.0108)|Ovarian(174;0.0218)|Colorectal(57;0.0329)|Breast(839;0.214)|Lung SC(612;0.236)		all cancers(79;3.96e-19)														---	---	---	---
C5orf36	285600	broad.mit.edu	37	5	93858130	93858130	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:93858130delT	uc011cuk.1	-						C5orf36_uc003kkp.2_Intron	NM_001145678	NP_001139150			hypothetical protein LOC285600 isoform 1												0		all_cancers(142;2.12e-08)|all_epithelial(76;5.95e-11)|all_lung(232;0.000996)|Lung NSC(167;0.0108)|Ovarian(174;0.0218)|Colorectal(57;0.0329)|Breast(839;0.214)|Lung SC(612;0.236)		all cancers(79;3.96e-19)														---	---	---	---
MCTP1	79772	broad.mit.edu	37	5	94090392	94090392	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94090392delT	uc003kkx.2	-						MCTP1_uc003kkv.2_Intron|MCTP1_uc003kkw.2_Intron|MCTP1_uc003kku.2_Intron	NM_024717	NP_078993			multiple C2 domains, transmembrane 1 isoform L						calcium-mediated signaling	integral to membrane|membrane fraction	calcium ion binding			ovary(2)	2		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)														---	---	---	---
MCTP1	79772	broad.mit.edu	37	5	94317059	94317059	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94317059delA	uc003kkx.2	-						MCTP1_uc003kkv.2_Intron|MCTP1_uc003kkw.2_Intron|MCTP1_uc003kkz.2_Intron	NM_024717	NP_078993			multiple C2 domains, transmembrane 1 isoform L						calcium-mediated signaling	integral to membrane|membrane fraction	calcium ion binding			ovary(2)	2		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)														---	---	---	---
FAM81B	153643	broad.mit.edu	37	5	94755802	94755805	+	Intron	DEL	CAAA	-	-	rs145960524		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94755802_94755805delCAAA	uc003kla.1	+						FAM81B_uc010jbe.1_Intron	NM_152548	NP_689761			hypothetical protein LOC153643											ovary(1)|skin(1)	2		all_cancers(142;1.1e-06)|all_epithelial(76;1.48e-09)|all_lung(232;0.000696)|Lung NSC(167;0.000947)|Ovarian(225;0.00473)		all cancers(79;1.04e-16)														---	---	---	---
TTC37	9652	broad.mit.edu	37	5	94807246	94807247	+	Intron	DEL	TT	-	-	rs147754036		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94807246_94807247delTT	uc003klb.2	-							NM_014639	NP_055454			tetratricopeptide repeat domain 37								binding			ovary(3)|pancreas(1)	4																		---	---	---	---
TTC37	9652	broad.mit.edu	37	5	94853658	94853658	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94853658delT	uc003klb.2	-							NM_014639	NP_055454			tetratricopeptide repeat domain 37								binding			ovary(3)|pancreas(1)	4																		---	---	---	---
TTC37	9652	broad.mit.edu	37	5	94877400	94877403	+	Intron	DEL	AAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94877400_94877403delAAAA	uc003klb.2	-						TTC37_uc010jbf.1_Intron	NM_014639	NP_055454			tetratricopeptide repeat domain 37								binding			ovary(3)|pancreas(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	95039735	95039735	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95039735delA								SPATA9 (21021 upstream) : RHOBTB3 (13602 downstream)																																			---	---	---	---
RHOBTB3	22836	broad.mit.edu	37	5	95058888	95058888	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95058888delA	uc003klk.1	+							NM_014899	NP_055714			rho-related BTB domain containing 3						retrograde transport, endosome to Golgi	Golgi apparatus	ATP binding|ATPase activity|Rab GTPase binding			lung(1)|skin(1)	2		all_cancers(142;2.58e-06)|all_epithelial(76;4.19e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0164)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.79e-16)														---	---	---	---
RHOBTB3	22836	broad.mit.edu	37	5	95067839	95067839	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95067839delT	uc003klm.2	+						RHOBTB3_uc003klk.1_Intron|RHOBTB3_uc003kll.2_Frame_Shift_Del_p.P93fs	NM_014899	NP_055714			rho-related BTB domain containing 3						retrograde transport, endosome to Golgi	Golgi apparatus	ATP binding|ATPase activity|Rab GTPase binding			lung(1)|skin(1)	2		all_cancers(142;2.58e-06)|all_epithelial(76;4.19e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0164)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.79e-16)														---	---	---	---
RHOBTB3	22836	broad.mit.edu	37	5	95075362	95075362	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95075362delC	uc003klm.2	+						RHOBTB3_uc003klk.1_Intron	NM_014899	NP_055714			rho-related BTB domain containing 3						retrograde transport, endosome to Golgi	Golgi apparatus	ATP binding|ATPase activity|Rab GTPase binding			lung(1)|skin(1)	2		all_cancers(142;2.58e-06)|all_epithelial(76;4.19e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0164)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.79e-16)														---	---	---	---
ELL2	22936	broad.mit.edu	37	5	95296130	95296130	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95296130delT	uc003klr.3	-							NM_012081	NP_036213			elongation factor, RNA polymerase II, 2						regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter	transcription elongation factor complex				central_nervous_system(1)	1		all_cancers(142;2.04e-06)|all_epithelial(76;3.1e-09)|all_lung(232;0.00309)|Lung NSC(167;0.00454)|Ovarian(225;0.0165)|Colorectal(57;0.0343)|Breast(839;0.198)		all cancers(79;2.16e-15)												OREG0016709	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ELL2	22936	broad.mit.edu	37	5	95296579	95296579	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95296579delC	uc003klr.3	-							NM_012081	NP_036213			elongation factor, RNA polymerase II, 2						regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter	transcription elongation factor complex				central_nervous_system(1)	1		all_cancers(142;2.04e-06)|all_epithelial(76;3.1e-09)|all_lung(232;0.00309)|Lung NSC(167;0.00454)|Ovarian(225;0.0165)|Colorectal(57;0.0343)|Breast(839;0.198)		all cancers(79;2.16e-15)												OREG0016709	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	5	95313849	95313849	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95313849delT								ELL2 (16074 upstream) : MIR583 (100993 downstream)																																			---	---	---	---
CAST	831	broad.mit.edu	37	5	96050610	96050610	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96050610delT	uc003klz.1	+						CAST_uc003klt.2_Intron|CAST_uc003klu.2_Intron|CAST_uc003klv.2_Intron|CAST_uc003klw.2_Intron|CAST_uc003klx.2_Intron|CAST_uc003kly.2_Intron|CAST_uc011cuo.1_Intron|CAST_uc011cup.1_Intron|CAST_uc011cuq.1_Intron|CAST_uc011cur.1_Intron|CAST_uc011cus.1_Intron|CAST_uc003kma.1_Intron|CAST_uc011cut.1_Intron|CAST_uc003kmb.2_Intron|CAST_uc003kmc.2_Intron|CAST_uc003kmd.2_Intron|CAST_uc003kme.2_Intron|CAST_uc003kmf.2_Intron	NM_001042443	NP_001035908			calpastatin isoform i								calcium-dependent cysteine-type endopeptidase inhibitor activity|protein binding			central_nervous_system(3)|ovary(1)|kidney(1)	5		all_cancers(142;5.27e-07)|all_epithelial(76;8.21e-10)|all_lung(232;0.000396)|Lung NSC(167;0.000539)|Ovarian(225;0.024)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;6.85e-15)														---	---	---	---
CAST	831	broad.mit.edu	37	5	96082019	96082019	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96082019delT	uc003klz.1	+						CAST_uc003klt.2_Intron|CAST_uc003klu.2_Intron|CAST_uc003klv.2_Intron|CAST_uc003klw.2_Intron|CAST_uc003klx.2_Intron|CAST_uc003kly.2_Intron|CAST_uc011cuo.1_Intron|CAST_uc011cuq.1_Intron|CAST_uc011cur.1_Intron|CAST_uc011cus.1_Intron|CAST_uc003kma.1_Intron|CAST_uc011cut.1_Intron|CAST_uc003kmb.2_Intron|CAST_uc003kmc.2_Intron|CAST_uc003kmd.2_Intron|CAST_uc003kme.2_Intron|CAST_uc003kmf.2_Intron|CAST_uc003kmh.2_Intron|CAST_uc010jbj.2_Intron|CAST_uc010jbk.2_Intron|CAST_uc010jbl.1_Intron|CAST_uc003kmi.2_Intron|CAST_uc003kmj.2_Intron	NM_001042443	NP_001035908			calpastatin isoform i								calcium-dependent cysteine-type endopeptidase inhibitor activity|protein binding			central_nervous_system(3)|ovary(1)|kidney(1)	5		all_cancers(142;5.27e-07)|all_epithelial(76;8.21e-10)|all_lung(232;0.000396)|Lung NSC(167;0.000539)|Ovarian(225;0.024)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;6.85e-15)														---	---	---	---
ERAP1	51752	broad.mit.edu	37	5	96120905	96120905	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96120905delA	uc003kmm.2	-						ERAP1_uc003kml.2_Intron|ERAP1_uc010jbm.1_Intron|ERAP1_uc003kmn.2_Intron	NM_001040458	NP_001035548			type 1 tumor necrosis factor receptor shedding						angiogenesis|antigen processing and presentation of endogenous peptide antigen via MHC class I|fat cell differentiation|membrane protein ectodomain proteolysis|regulation of blood pressure|regulation of innate immune response|response to bacterium	cytosol|endoplasmic reticulum lumen|endoplasmic reticulum membrane|extracellular region|integral to membrane	aminopeptidase activity|interleukin-1, Type II receptor binding|interleukin-6 receptor binding|metalloexopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)	2		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	96203710	96203711	+	Intron	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96203710_96203711delAG	uc003kmo.1	-											Homo sapiens cDNA FLJ37666 fis, clone BRHIP2011576.																														---	---	---	---
LNPEP	4012	broad.mit.edu	37	5	96357945	96357945	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96357945delT	uc003kmv.1	+						LNPEP_uc003kmw.1_Intron	NM_005575	NP_005566			leucyl/cystinyl aminopeptidase isoform 1						cell-cell signaling|female pregnancy|proteolysis	extracellular region|integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(3)|breast(1)	4		all_cancers(142;7e-07)|all_epithelial(76;9.52e-10)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0269)|Breast(839;0.244)		COAD - Colon adenocarcinoma(37;0.072)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	97763504	97763505	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:97763504_97763505delTT								None (None upstream) : RGMB (341494 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	98138639	98138639	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98138639delT								RGMB (6443 upstream) : CHD1 (52270 downstream)																																			---	---	---	---
CHD1	1105	broad.mit.edu	37	5	98240928	98240928	+	Intron	DEL	A	-	-	rs35910253		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98240928delA	uc003knf.2	-							NM_001270	NP_001261			chromodomain helicase DNA binding protein 1						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|methylated histone residue binding			lung(2)|ovary(1)|breast(1)|pancreas(1)	5		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	99302139	99302139	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:99302139delA								None (None upstream) : LOC100133050 (413070 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	99565881	99565882	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:99565881_99565882insA								None (None upstream) : LOC100133050 (149327 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	99622449	99622449	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:99622449delA								None (None upstream) : LOC100133050 (92760 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	99787081	99787081	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:99787081delA	uc003kni.2	-											full-length cDNA clone CS0DJ013YK21 of T cells (Jurkat cell line) Cot 10-normalized of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	100042894	100042894	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:100042894delT								FAM174A (120454 upstream) : ST8SIA4 (99746 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	100884680	100884680	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:100884680delA								ST8SIA4 (645693 upstream) : SLCO4C1 (685014 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	100944703	100944705	+	IGR	DEL	AAA	-	-	rs33982416		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:100944703_100944705delAAA								ST8SIA4 (705716 upstream) : SLCO4C1 (624989 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	101327219	101327219	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:101327219delT								None (None upstream) : SLCO4C1 (242475 downstream)																																			---	---	---	---
SLCO6A1	133482	broad.mit.edu	37	5	101760015	101760016	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:101760015_101760016insA	uc003knn.2	-						SLCO6A1_uc003kno.2_Intron|SLCO6A1_uc003knp.2_Intron|SLCO6A1_uc003knq.2_Intron	NM_173488	NP_775759			solute carrier organic anion transporter family,							integral to membrane|plasma membrane	transporter activity			ovary(3)|skin(3)|central_nervous_system(1)	7		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)														---	---	---	---
PAM	5066	broad.mit.edu	37	5	102347083	102347084	+	Intron	DEL	CA	-	-	rs71886397		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102347083_102347084delCA	uc003knw.2	+						PAM_uc003kns.2_Intron|PAM_uc003knt.2_Intron|PAM_uc003knu.2_Intron|PAM_uc003knv.2_Intron|PAM_uc011cuz.1_Intron|PAM_uc003knz.2_Intron	NM_000919	NP_000910			peptidylglycine alpha-amidating monooxygenase						peptide metabolic process|protein modification process	extracellular region|integral to membrane|stored secretory granule	L-ascorbic acid binding|peptidylamidoglycolate lyase activity|peptidylglycine monooxygenase activity|protein binding				0		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)													---	---	---	---
PPIP5K2	23262	broad.mit.edu	37	5	102484798	102484799	+	Intron	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102484798_102484799delAC	uc003kod.3	+						PPIP5K2_uc011cva.1_Intron|PPIP5K2_uc003koe.2_Intron|PPIP5K2_uc010jbo.1_Intron	NM_015216	NP_056031			Histidine acid phosphatase domain containing 1						inositol metabolic process	cytosol	acid phosphatase activity|ATP binding|diphosphoinositol-pentakisphosphate kinase activity|inositol 1,3,4,5,6-pentakisphosphate kinase activity|inositol hexakisphosphate 5-kinase activity			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	102642404	102642404	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102642404delT								C5orf30 (28043 upstream) : NUDT12 (242153 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	102945414	102945414	+	IGR	DEL	T	-	-	rs67183514		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:102945414delT								NUDT12 (46924 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	104071423	104071424	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:104071423_104071424delTT								None (None upstream) : RAB9BP1 (363751 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	104399547	104399548	+	IGR	INS	-	TG	TG			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:104399547_104399548insTG								None (None upstream) : RAB9BP1 (35627 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	104856700	104856700	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:104856700delA								RAB9BP1 (420902 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	105209214	105209214	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:105209214delA								RAB9BP1 (773416 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	106224488	106224488	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:106224488delG								None (None upstream) : EFNA5 (488103 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	106654567	106654567	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:106654567delA								None (None upstream) : EFNA5 (58024 downstream)																																			---	---	---	---
EFNA5	1946	broad.mit.edu	37	5	106980415	106980416	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:106980415_106980416insT	uc003kol.2	-						EFNA5_uc010jbr.1_Intron	NM_001962	NP_001953			ephrin-A5 precursor						cell-cell signaling	anchored to plasma membrane|caveola|extracellular space	ephrin receptor binding				0		all_cancers(142;5.15e-06)|all_epithelial(76;4.39e-07)|Prostate(80;0.00726)|Lung NSC(167;0.0736)|Ovarian(225;0.0797)|all_lung(232;0.0854)|Colorectal(57;0.241)		Epithelial(69;1.25e-12)|OV - Ovarian serous cystadenocarcinoma(64;1.32e-11)|BRCA - Breast invasive adenocarcinoma(61;0.0376)|COAD - Colon adenocarcinoma(37;0.109)														---	---	---	---
FBXL17	64839	broad.mit.edu	37	5	107377524	107377524	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:107377524delT	uc011cvc.1	-						FBXL17_uc003kon.3_Intron	NM_001163315	NP_001156787			F-box and leucine-rich repeat protein 17												0		all_cancers(142;0.00273)|all_epithelial(76;0.000362)|Prostate(80;0.0115)|Myeloproliferative disorder(839;0.0393)|Ovarian(225;0.232)		OV - Ovarian serous cystadenocarcinoma(64;9.63e-11)|Epithelial(69;4.02e-10)														---	---	---	---
FBXL17	64839	broad.mit.edu	37	5	107552462	107552462	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:107552462delA	uc011cvc.1	-						FBXL17_uc003kon.3_Intron	NM_001163315	NP_001156787			F-box and leucine-rich repeat protein 17												0		all_cancers(142;0.00273)|all_epithelial(76;0.000362)|Prostate(80;0.0115)|Myeloproliferative disorder(839;0.0393)|Ovarian(225;0.232)		OV - Ovarian serous cystadenocarcinoma(64;9.63e-11)|Epithelial(69;4.02e-10)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	107841563	107841564	+	IGR	DEL	AG	-	-	rs10563555		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:107841563_107841564delAG								FBXL17 (123764 upstream) : FER (241959 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	107944134	107944134	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:107944134delA								FBXL17 (226335 upstream) : FER (139389 downstream)																																			---	---	---	---
FER	2241	broad.mit.edu	37	5	108121299	108121300	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108121299_108121300delAA	uc003kop.1	+						FER_uc011cve.1_Intron|FER_uc011cvf.1_Intron|FER_uc003koq.2_Intron|FER_uc011cvg.1_Intron	NM_005246	NP_005237			fer (fps/fes related) tyrosine kinase						intracellular signal transduction|peptidyl-tyrosine phosphorylation	cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|kidney(1)	5		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	108542241	108542242	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108542241_108542242insA								FER (18868 upstream) : PJA2 (128169 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	108617997	108617997	+	IGR	DEL	G	-	-	rs77140591	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108617997delG								FER (94624 upstream) : PJA2 (52414 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	108847089	108847096	+	IGR	DEL	CTTCCTTG	-	-	rs77986172	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108847089_108847096delCTTCCTTG								PJA2 (101414 upstream) : MAN2A1 (178060 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	109418683	109418683	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109418683delG								MAN2A1 (215254 upstream) : TMEM232 (206251 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	109426735	109426735	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109426735delT								MAN2A1 (223306 upstream) : TMEM232 (198199 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	109555779	109555779	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109555779delT								MAN2A1 (352350 upstream) : TMEM232 (69155 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	110159925	110159925	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110159925delC								SLC25A46 (61443 upstream) : TSLP (245853 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	110391633	110391633	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110391633delT								SLC25A46 (293151 upstream) : TSLP (14145 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	110859952	110859952	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:110859952delT								STARD4 (11719 upstream) : C5orf13 (138371 downstream)																																			---	---	---	---
C5orf13	9315	broad.mit.edu	37	5	111166880	111166880	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111166880delT	uc011cvr.1	-						C5orf13_uc011cvs.1_Intron	NM_001142475	NP_001135947			neuronal protein 3.1 isoform c							cytoplasm				skin(1)	1		all_cancers(142;0.00597)|all_epithelial(76;0.000144)|Prostate(80;0.0115)|Colorectal(10;0.0446)|Ovarian(225;0.156)		OV - Ovarian serous cystadenocarcinoma(64;5.45e-09)|Epithelial(69;2e-08)|all cancers(49;1.9e-06)|COAD - Colon adenocarcinoma(37;0.0514)|Colorectal(14;0.0629)														---	---	---	---
C5orf13	9315	broad.mit.edu	37	5	111307121	111307121	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111307121delA	uc011cvr.1	-						C5orf13_uc011cvs.1_Intron	NM_001142475	NP_001135947			neuronal protein 3.1 isoform c							cytoplasm				skin(1)	1		all_cancers(142;0.00597)|all_epithelial(76;0.000144)|Prostate(80;0.0115)|Colorectal(10;0.0446)|Ovarian(225;0.156)		OV - Ovarian serous cystadenocarcinoma(64;5.45e-09)|Epithelial(69;2e-08)|all cancers(49;1.9e-06)|COAD - Colon adenocarcinoma(37;0.0514)|Colorectal(14;0.0629)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	111857377	111857378	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111857377_111857378insT								FLJ11235 (100704 upstream) : APC (185840 downstream)																																			---	---	---	---
APC	324	broad.mit.edu	37	5	112086153	112086154	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112086153_112086154delTT	uc010jby.2	+						APC_uc011cvt.1_Intron|APC_uc003kpz.3_Intron|APC_uc003kpy.3_Intron|APC_uc010jbz.2_Intron	NM_001127511	NP_001120983			adenomatous polyposis coli						canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly	adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction	beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity			large_intestine(2123)|stomach(123)|soft_tissue(55)|small_intestine(34)|breast(26)|pancreas(25)|urinary_tract(20)|lung(19)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|skin(7)|upper_aerodigestive_tract(6)|adrenal_gland(6)|bone(6)|NS(5)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1)	2515		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)			12	D|Mis|N|F|S		colorectal|pancreatic|desmoid|hepatoblastoma|glioma|other CNS	colorectal|pancreatic|desmoid|hepatoblastoma|glioma|other CNS			Hereditary_Desmoid_Disease|Familial_Adenomatous_Polyposis|Turcot_syndrome	TSP Lung(16;0.13)			---	---	---	---
SRP19	6728	broad.mit.edu	37	5	112226937	112226937	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112226937delT	uc011cvv.1	+						SRP19_uc011cvu.1_Intron|REEP5_uc011cvw.1_Intron|REEP5_uc003kqe.1_Intron|REEP5_uc011cvx.1_Intron|REEP5_uc011cvy.1_Intron|REEP5_uc011cvz.1_Intron					SubName: Full=Zinc finger (CCCH type), RNA-binding motif and serine/arginine rich 2;						response to drug|SRP-dependent cotranslational protein targeting to membrane	cytosol|mitochondrion|nucleolus|signal recognition particle, endoplasmic reticulum targeting	7S RNA binding				0		all_cancers(142;0.00328)|all_epithelial(76;6.39e-05)|Prostate(80;0.00174)|Colorectal(10;0.00372)|Ovarian(225;0.156)		Epithelial(69;1.7e-09)|OV - Ovarian serous cystadenocarcinoma(64;1.17e-08)|all cancers(49;3.96e-07)|Colorectal(14;0.0056)|COAD - Colon adenocarcinoma(37;0.0104)														---	---	---	---
MCC	4163	broad.mit.edu	37	5	112477671	112477671	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112477671delA	uc003kqj.3	-						MCC_uc003kqk.3_Intron|MCC_uc003kql.3_Intron|MCC_uc011cwb.1_Intron|MCC_uc010jcd.1_Intron	NM_002387	NP_002378			mutated in colorectal cancers isoform 2						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|Wnt receptor signaling pathway	cytoplasm|nucleus|plasma membrane	protein binding|receptor activity			ovary(1)	1		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)														---	---	---	---
YTHDC2	64848	broad.mit.edu	37	5	112915100	112915100	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112915100delT	uc003kqn.2	+							NM_022828	NP_073739			YTH domain containing 2								ATP binding|ATP-dependent helicase activity|nucleic acid binding			skin(2)|central_nervous_system(1)	3		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	113207778	113207778	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:113207778delA								YTHDC2 (276799 upstream) : KCNN2 (490238 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	113932745	113932745	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:113932745delA	uc003kqr.1	-											Homo sapiens cDNA FLJ40367 fis, clone TESTI2034785.																														---	---	---	---
TRIM36	55521	broad.mit.edu	37	5	114513228	114513229	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:114513228_114513229insA	uc003kqs.2	-						TRIM36_uc003kqt.2_Intron|TRIM36_uc003kqu.2_Intron	NM_018700	NP_061170			tripartite motif-containing 36 isoform 1							acrosomal vesicle|cytoskeleton	ligase activity|zinc ion binding			ovary(4)|lung(2)|breast(2)	8		all_cancers(142;0.00133)|all_epithelial(76;2.41e-05)|Prostate(80;0.00955)|Ovarian(225;0.0443)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;3.62e-08)|Epithelial(69;7.69e-08)|all cancers(49;9.33e-06)														---	---	---	---
PGGT1B	5229	broad.mit.edu	37	5	114587536	114587538	+	Intron	DEL	AAT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:114587536_114587538delAAT	uc003kqw.3	-						PGGT1B_uc003kqx.3_Intron|PGGT1B_uc010jch.2_Intron	NM_005023	NP_005014			geranylgeranyltransferase type 1 beta						protein geranylgeranylation	CAAX-protein geranylgeranyltransferase complex	CAAX-protein geranylgeranyltransferase activity				0		all_cancers(142;0.000523)|all_epithelial(76;6.45e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)		Epithelial(69;2.95e-08)|OV - Ovarian serous cystadenocarcinoma(64;4.98e-08)|all cancers(49;3.1e-06)	Pravastatin(DB00175)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	115104789	115104789	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115104789delT								TMED7-TICAM2 (142919 upstream) : CDO1 (35643 downstream)																																			---	---	---	---
AQPEP	206338	broad.mit.edu	37	5	115361334	115361335	+	Intron	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115361334_115361335insG	uc003kro.2	+						AQPEP_uc003krp.2_Intron|AQPEP_uc003krq.2_Intron|AQPEP_uc003krr.2_Intron|AQPEP_uc003krs.2_Intron	NM_173800	NP_776161			laeverin						proteolysis	integral to membrane	metallopeptidase activity|zinc ion binding				0																		---	---	---	---
COMMD10	51397	broad.mit.edu	37	5	115426966	115426966	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115426966delT	uc003krt.1	+							NM_016144	NP_057228			COMM domain containing 10								protein binding			ovary(1)	1		all_cancers(142;0.0834)|all_epithelial(76;0.00314)|Prostate(80;0.0102)|Ovarian(225;0.232)		OV - Ovarian serous cystadenocarcinoma(64;4.3e-07)|Epithelial(69;8.06e-07)|all cancers(49;4.06e-05)														---	---	---	---
SEMA6A	57556	broad.mit.edu	37	5	115822792	115822793	+	Intron	DEL	AA	-	-	rs111384042		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115822792_115822793delAA	uc010jck.2	-						SEMA6A_uc003krx.3_Intron	NM_020796	NP_065847			sema domain, transmembrane domain (TM), and						apoptosis|axon guidance|cell surface receptor linked signaling pathway|cytoskeleton organization|organ morphogenesis	axon|integral to membrane|plasma membrane	receptor activity			ovary(2)	2		all_cancers(142;0.00316)|all_epithelial(76;5.71e-05)|Prostate(80;0.00845)|Ovarian(225;0.0796)|Lung NSC(810;0.171)|all_lung(232;0.203)		OV - Ovarian serous cystadenocarcinoma(64;1.59e-08)|Epithelial(69;2e-08)|all cancers(49;5.7e-08)|COAD - Colon adenocarcinoma(49;0.151)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	116086667	116086668	+	IGR	INS	-	ATC	ATC			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116086667_116086668insATC								SEMA6A (176116 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	116269870	116269870	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116269870delA								SEMA6A (359319 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	116351245	116351248	+	IGR	DEL	TTTT	-	-	rs71891250		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116351245_116351248delTTTT								SEMA6A (440694 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	116459820	116459820	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116459820delA								SEMA6A (549269 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	116623625	116623625	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116623625delT								SEMA6A (713074 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	116623643	116623643	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116623643delT								SEMA6A (713092 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	116818498	116818499	+	Intron	DEL	TT	-	-	rs67919989		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:116818498_116818499delTT	uc003kry.2	+											Homo sapiens cDNA clone IMAGE:5297581.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	117312499	117312499	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:117312499delT								None (None upstream) : DTWD2 (860072 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	117344540	117344540	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:117344540delA								None (None upstream) : DTWD2 (828031 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	117775156	117775156	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:117775156delA								None (None upstream) : DTWD2 (397415 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	117929419	117929420	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:117929419_117929420delTG								None (None upstream) : DTWD2 (243151 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	117999849	117999849	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:117999849delT								None (None upstream) : DTWD2 (172722 downstream)																																			---	---	---	---
DTWD2	285605	broad.mit.edu	37	5	118310505	118310505	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118310505delA	uc003ksa.2	-							NM_173666	NP_775937			DTW domain containing 2												0		all_epithelial(76;0.0982)|Prostate(80;0.121)		OV - Ovarian serous cystadenocarcinoma(64;0.000228)|Epithelial(69;0.000941)|all cancers(49;0.00939)														---	---	---	---
DMXL1	1657	broad.mit.edu	37	5	118534382	118534383	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118534382_118534383insA	uc003ksd.2	+						DMXL1_uc010jcl.1_Intron	NM_005509	NP_005500			Dmx-like 1											ovary(2)	2		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)														---	---	---	---
TNFAIP8	25816	broad.mit.edu	37	5	118653902	118653902	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118653902delT	uc003ksg.2	+						TNFAIP8_uc003ksf.1_Intron	NM_001077654	NP_001071122			tumor necrosis factor, alpha-induced protein 8						anti-apoptosis|apoptosis|negative regulation of anti-apoptosis	cytoplasm	caspase inhibitor activity|protein binding			ovary(1)	1		all_cancers(142;0.0317)|Prostate(80;0.111)|Breast(839;0.231)		Epithelial(69;4.63e-83)|OV - Ovarian serous cystadenocarcinoma(64;1.39e-82)|all cancers(49;4.88e-75)|GBM - Glioblastoma multiforme(465;0.00338)|BRCA - Breast invasive adenocarcinoma(61;0.0148)|COAD - Colon adenocarcinoma(49;0.0829)														---	---	---	---
TNFAIP8	25816	broad.mit.edu	37	5	118677400	118677400	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118677400delT	uc011cwf.1	+						TNFAIP8_uc003ksf.1_Intron|TNFAIP8_uc003ksg.2_Intron	NM_001077654	NP_001071122			tumor necrosis factor, alpha-induced protein 8						anti-apoptosis|apoptosis|negative regulation of anti-apoptosis	cytoplasm	caspase inhibitor activity|protein binding			ovary(1)	1		all_cancers(142;0.0317)|Prostate(80;0.111)|Breast(839;0.231)		Epithelial(69;4.63e-83)|OV - Ovarian serous cystadenocarcinoma(64;1.39e-82)|all cancers(49;4.88e-75)|GBM - Glioblastoma multiforme(465;0.00338)|BRCA - Breast invasive adenocarcinoma(61;0.0148)|COAD - Colon adenocarcinoma(49;0.0829)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	118769226	118769227	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118769226_118769227insA								TNFAIP8 (38933 upstream) : HSD17B4 (18921 downstream)																																			---	---	---	---
HSD17B4	3295	broad.mit.edu	37	5	118856080	118856080	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118856080delT	uc003ksj.2	+						HSD17B4_uc011cwg.1_Intron|HSD17B4_uc011cwh.1_Intron|HSD17B4_uc011cwi.1_Intron|HSD17B4_uc003ksk.3_Intron|HSD17B4_uc011cwj.1_Intron|HSD17B4_uc010jcn.1_Intron	NM_000414	NP_000405			hydroxysteroid (17-beta) dehydrogenase 4						bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase	peroxisomal matrix	3-hydroxyacyl-CoA dehydrogenase activity|3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity|estradiol 17-beta-dehydrogenase activity|isomerase activity|long-chain-enoyl-CoA hydratase activity|protein binding|sterol binding|sterol transporter activity			ovary(1)|pancreas(1)	2		all_cancers(142;0.0206)|Prostate(80;0.0322)		OV - Ovarian serous cystadenocarcinoma(64;0.000247)|Epithelial(69;0.000849)|all cancers(49;0.0122)	NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	119015012	119015013	+	IGR	INS	-	G	G	rs138260814	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:119015012_119015013insG								FAM170A (43496 upstream) : PRR16 (785006 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	119073223	119073223	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:119073223delT								FAM170A (101707 upstream) : PRR16 (726796 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	120138305	120138305	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:120138305delT								PRR16 (115343 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	120585020	120585020	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:120585020delT								PRR16 (562058 upstream) : FTMT (602630 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	121231069	121231069	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121231069delA								FTMT (42548 upstream) : SRFBP1 (66587 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	121950464	121950464	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121950464delA								SNCAIP (150670 upstream) : SNX2 (160286 downstream)																																			---	---	---	---
SNX2	6643	broad.mit.edu	37	5	122165208	122165208	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122165208delT	uc003kte.2	+						SNX2_uc011cwn.1_Intron	NM_003100	NP_003091			sorting nexin 2						cell communication|endocytosis|intracellular protein transport	early endosome membrane	phosphatidylinositol binding|protein binding|protein transporter activity			kidney(1)	1		all_cancers(142;1.14e-44)|all_lung(232;1.03e-13)|Lung NSC(810;2.5e-13)|Breast(839;0.000812)|Myeloproliferative disorder(839;0.0122)|Prostate(80;0.0235)|all_hematologic(541;0.0592)|all_neural(839;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	all cancers(49;2.13e-24)|Epithelial(69;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(64;5.6e-11)|BRCA - Breast invasive adenocarcinoma(61;0.00013)|GBM - Glioblastoma multiforme(465;0.000357)|COAD - Colon adenocarcinoma(49;0.000887)|Lung(113;0.0109)														---	---	---	---
SNX24	28966	broad.mit.edu	37	5	122269525	122269526	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122269525_122269526delTT	uc011cwo.1	+						SNX24_uc003ktf.2_Intron|SNX24_uc010jcy.2_Intron	NM_014035	NP_054754			SBBI31 protein						cell communication|protein transport	cytoplasmic vesicle membrane	phosphatidylinositol binding				0		Prostate(80;0.0387)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	OV - Ovarian serous cystadenocarcinoma(64;0.000654)|Epithelial(69;0.0016)|all cancers(49;0.0139)														---	---	---	---
PRDM6	93166	broad.mit.edu	37	5	122483068	122483068	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122483068delT	uc003kti.2	+						PRDM6_uc003ktj.2_Intron	NM_001136239	NP_001129711			PR domain containing 6						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	histone-lysine N-methyltransferase activity|nucleic acid binding|zinc ion binding				0																		---	---	---	---
CEP120	153241	broad.mit.edu	37	5	122751561	122751562	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122751561_122751562insA	uc003ktk.2	-						CEP120_uc011cwq.1_Intron|CEP120_uc010jcz.1_Intron	NM_153223	NP_694955			coiled-coil domain containing 100							centrosome				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	122838544	122838547	+	IGR	DEL	AAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122838544_122838547delAAAA								CEP120 (79292 upstream) : CSNK1G3 (9246 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	123448952	123448952	+	IGR	DEL	T	-	-	rs33976198		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123448952delT								CSNK1G3 (496490 upstream) : ZNF608 (523658 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	123629603	123629603	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123629603delA								CSNK1G3 (677141 upstream) : ZNF608 (343007 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	123810160	123810160	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123810160delA								CSNK1G3 (857698 upstream) : ZNF608 (162450 downstream)																																			---	---	---	---
ZNF608	57507	broad.mit.edu	37	5	123998506	123998507	+	Intron	DEL	AC	-	-	rs35528084		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123998506_123998507delAC	uc003ktq.1	-						ZNF608_uc003ktr.1_Intron|ZNF608_uc003kts.1_Intron|ZNF608_uc003ktt.1_Intron	NM_020747	NP_065798			zinc finger protein 608							intracellular	zinc ion binding			skin(3)|ovary(2)|lung(1)	6		all_cancers(142;0.186)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	124240668	124240668	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124240668delT								ZNF608 (156168 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	124282335	124282335	+	IGR	DEL	T	-	-	rs60828100	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124282335delT								ZNF608 (197835 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	124493683	124493683	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124493683delA								ZNF608 (409183 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	124677449	124677450	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124677449_124677450insT								ZNF608 (592949 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	124852785	124852785	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124852785delT								ZNF608 (768285 upstream) : GRAMD3 (843003 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	125388147	125388147	+	IGR	DEL	G	-	-	rs72160672		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125388147delG								None (None upstream) : GRAMD3 (307641 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	125572729	125572729	+	IGR	DEL	C	-	-	rs67917845		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125572729delC								None (None upstream) : GRAMD3 (123059 downstream)																																			---	---	---	---
GRAMD3	65983	broad.mit.edu	37	5	125775713	125775713	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125775713delT	uc003ktu.2	+						GRAMD3_uc011cwt.1_Intron|GRAMD3_uc011cwv.1_Intron|GRAMD3_uc011cww.1_Intron|GRAMD3_uc011cwx.1_Intron|GRAMD3_uc011cwu.1_Intron	NM_023927	NP_076416			GRAM domain containing 3 isoform 2											central_nervous_system(1)	1		Prostate(80;0.0928)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0401)|OV - Ovarian serous cystadenocarcinoma(64;0.0604)|all cancers(49;0.108)														---	---	---	---
GRAMD3	65983	broad.mit.edu	37	5	125801275	125801275	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125801275delT	uc003ktu.2	+						GRAMD3_uc011cwt.1_Intron|GRAMD3_uc011cwv.1_Intron|GRAMD3_uc011cww.1_Intron|GRAMD3_uc011cwx.1_Intron|GRAMD3_uc011cwy.1_Intron|GRAMD3_uc011cwz.1_Intron|GRAMD3_uc011cwu.1_Intron	NM_023927	NP_076416			GRAM domain containing 3 isoform 2											central_nervous_system(1)	1		Prostate(80;0.0928)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0401)|OV - Ovarian serous cystadenocarcinoma(64;0.0604)|all cancers(49;0.108)														---	---	---	---
MEGF10	84466	broad.mit.edu	37	5	126705551	126705551	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:126705551delT	uc003kuh.3	+						MEGF10_uc010jdc.1_Intron|MEGF10_uc010jdd.1_Intron|MEGF10_uc003kui.3_Intron	NM_032446	NP_115822			multiple EGF-like-domains 10 precursor						cell adhesion|phagocytosis	basolateral plasma membrane|cell projection|integral to membrane|phagocytic cup				ovary(4)	4		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	127009345	127009347	+	IGR	DEL	AGA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127009345_127009347delAGA								CTXN3 (15024 upstream) : FLJ33630 (266788 downstream)																																			---	---	---	---
SLC12A2	6558	broad.mit.edu	37	5	127493887	127493887	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127493887delT	uc003kus.2	+						SLC12A2_uc010jdf.2_Intron|SLC12A2_uc010jdg.2_Intron|SLC12A2_uc003kut.1_Intron	NM_001046	NP_001037			solute carrier family 12						potassium ion transport|sodium ion transport|transepithelial ammonium transport|transepithelial chloride transport	integral to plasma membrane|membrane fraction	ammonia transmembrane transporter activity|sodium:potassium:chloride symporter activity			ovary(3)	3		all_cancers(142;0.0972)|Prostate(80;0.151)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978)	Bumetanide(DB00887)|Potassium Chloride(DB00761)													---	---	---	---
SLC27A6	28965	broad.mit.edu	37	5	128323903	128323903	+	Intron	DEL	C	-	-	rs51666	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128323903delC	uc003kuy.2	+						SLC27A6_uc003kuz.2_Intron	NM_014031	NP_054750			solute carrier family 27 (fatty acid						long-chain fatty acid transport|transmembrane transport|very long-chain fatty acid metabolic process	integral to membrane|sarcolemma	fatty acid transporter activity|long-chain fatty acid-CoA ligase activity|nucleotide binding				0		all_cancers(142;0.0483)|Prostate(80;0.055)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.171)|OV - Ovarian serous cystadenocarcinoma(64;0.186)														---	---	---	---
SLC27A6	28965	broad.mit.edu	37	5	128358651	128358651	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128358651delG	uc003kuy.2	+						SLC27A6_uc003kuz.2_Intron	NM_014031	NP_054750			solute carrier family 27 (fatty acid						long-chain fatty acid transport|transmembrane transport|very long-chain fatty acid metabolic process	integral to membrane|sarcolemma	fatty acid transporter activity|long-chain fatty acid-CoA ligase activity|nucleotide binding				0		all_cancers(142;0.0483)|Prostate(80;0.055)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.171)|OV - Ovarian serous cystadenocarcinoma(64;0.186)														---	---	---	---
ADAMTS19	171019	broad.mit.edu	37	5	128799191	128799194	+	Intron	DEL	TATG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128799191_128799194delTATG	uc003kvb.1	+						ADAMTS19_uc003kvc.1_Intron	NM_133638	NP_598377			ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|breast(2)|lung(1)|skin(1)	9		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)														---	---	---	---
ADAMTS19	171019	broad.mit.edu	37	5	128848600	128848600	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:128848600delT	uc003kvb.1	+						ADAMTS19_uc003kvc.1_Intron	NM_133638	NP_598377			ADAM metallopeptidase with thrombospondin type 1						proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|breast(2)|lung(1)|skin(1)	9		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	129099779	129099779	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129099779delA								ADAMTS19 (25403 upstream) : CHSY3 (140744 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	129616737	129616737	+	IGR	DEL	T	-	-	rs77332700		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129616737delT								CHSY3 (94411 upstream) : HINT1 (878138 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	130022547	130022547	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130022547delA								CHSY3 (500221 upstream) : HINT1 (472328 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	130027383	130027383	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130027383delA								CHSY3 (505057 upstream) : HINT1 (467492 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	130221306	130221306	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130221306delT								CHSY3 (698980 upstream) : HINT1 (273569 downstream)																																			---	---	---	---
LYRM7	90624	broad.mit.edu	37	5	130535735	130535736	+	3'UTR	DEL	CA	-	-	rs10586320		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130535735_130535736delCA	uc003kvg.1	+	5						NM_181705	NP_859056			Lyrm7 homolog												0		all_cancers(142;0.0377)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
CDC42SE2	56990	broad.mit.edu	37	5	130699389	130699393	+	Intron	DEL	TTTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130699389_130699393delTTTTT	uc003kvh.2	+						CDC42SE2_uc003kvi.2_Intron|CDC42SE2_uc003kvj.2_Intron|CDC42SE2_uc003kvk.2_Intron|CDC42SE2_uc003kvl.2_Intron	NM_020240	NP_064625			CDC42 small effector 2						phagocytosis|regulation of cell shape|regulation of signal transduction	cell projection|cytoplasm|cytoskeleton|phagocytic cup	protein binding|structural molecule activity				0		all_cancers(142;0.0525)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	130734831	130734831	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130734831delT								CDC42SE2 (4451 upstream) : RAPGEF6 (26773 downstream)																																			---	---	---	---
RAPGEF6	51735	broad.mit.edu	37	5	130764956	130764956	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130764956delA	uc003kvn.1	-						RAPGEF6_uc003kvp.1_Intron|RAPGEF6_uc003kvo.1_Intron|RAPGEF6_uc010jdi.1_Intron|RAPGEF6_uc010jdj.1_Intron|RAPGEF6_uc003kvm.1_Intron	NM_016340	NP_057424			PDZ domain-containing guanine nucleotide						Ras protein signal transduction|regulation of GTPase activity|regulation of small GTPase mediated signal transduction	cytoplasm|plasma membrane	GTP-dependent protein binding|guanyl-nucleotide exchange factor activity|Ras GTPase binding			ovary(1)|lung(1)|central_nervous_system(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)														---	---	---	---
RAPGEF6	51735	broad.mit.edu	37	5	130838416	130838416	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130838416delA	uc003kvn.1	-						RAPGEF6_uc003kvp.1_Intron|RAPGEF6_uc003kvo.1_Intron|RAPGEF6_uc010jdi.1_Intron|RAPGEF6_uc010jdj.1_Intron|RAPGEF6_uc003kvq.2_Intron|RAPGEF6_uc003kvr.2_Intron|RAPGEF6_uc011cxe.1_Intron|RAPGEF6_uc010jdk.2_Intron	NM_016340	NP_057424			PDZ domain-containing guanine nucleotide						Ras protein signal transduction|regulation of GTPase activity|regulation of small GTPase mediated signal transduction	cytoplasm|plasma membrane	GTP-dependent protein binding|guanyl-nucleotide exchange factor activity|Ras GTPase binding			ovary(1)|lung(1)|central_nervous_system(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)														---	---	---	---
RAD50	10111	broad.mit.edu	37	5	131924364	131924364	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131924364delT	uc003kxi.2	+						RAD50_uc003kxh.2_Intron	NM_005732	NP_005723			RAD50 homolog isoform 1						DNA duplex unwinding|double-strand break repair via homologous recombination|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|telomere maintenance via telomerase	Mre11 complex|nuclear chromosome, telomeric region|nucleoplasm	ATP binding|DNA binding|nuclease activity|protein binding, bridging|zinc ion binding			lung(2)|ovary(1)|skin(1)	4		all_cancers(142;0.0368)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)										Homologous_recombination					---	---	---	---
Unknown	0	broad.mit.edu	37	5	132374960	132374961	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132374960_132374961delTT								ZCCHC10 (12720 upstream) : HSPA4 (12701 downstream)																																			---	---	---	---
FSTL4	23105	broad.mit.edu	37	5	132698867	132698868	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132698867_132698868insA	uc003kyn.1	-							NM_015082	NP_055897			follistatin-like 4 precursor							extracellular region	calcium ion binding			central_nervous_system(1)|skin(1)	2		all_cancers(142;0.244)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
FSTL4	23105	broad.mit.edu	37	5	132819681	132819681	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132819681delC	uc003kyn.1	-							NM_015082	NP_055897			follistatin-like 4 precursor							extracellular region	calcium ion binding			central_nervous_system(1)|skin(1)	2		all_cancers(142;0.244)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
DDX46	9879	broad.mit.edu	37	5	134116711	134116711	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134116711delA	uc003kzw.2	+						DDX46_uc003kzv.1_Intron	NM_014829	NP_055644			DEAD (Asp-Glu-Ala-Asp) box polypeptide 46						mRNA processing|RNA splicing	Cajal body|nuclear speck	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
DDX46	9879	broad.mit.edu	37	5	134118927	134118927	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134118927delT	uc003kzw.2	+						DDX46_uc003kzv.1_Intron	NM_014829	NP_055644			DEAD (Asp-Glu-Ala-Asp) box polypeptide 46						mRNA processing|RNA splicing	Cajal body|nuclear speck	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
DDX46	9879	broad.mit.edu	37	5	134141903	134141904	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134141903_134141904delAA	uc003kzw.2	+						DDX46_uc003kzv.1_Intron	NM_014829	NP_055644			DEAD (Asp-Glu-Ala-Asp) box polypeptide 46						mRNA processing|RNA splicing	Cajal body|nuclear speck	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
DDX46	9879	broad.mit.edu	37	5	134146034	134146035	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134146034_134146035delTT	uc003kzw.2	+						DDX46_uc003kzv.1_Intron	NM_014829	NP_055644			DEAD (Asp-Glu-Ala-Asp) box polypeptide 46						mRNA processing|RNA splicing	Cajal body|nuclear speck	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	134422299	134422299	+	Intron	DEL	C	-	-	rs2342145	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134422299delC	uc003laj.1	+											Homo sapiens cDNA: FLJ23312 fis, clone HEP11874.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	134802082	134802082	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134802082delT								TIFAB (13993 upstream) : NEUROG1 (67898 downstream)																																	OREG0016798	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	5	134850724	134850724	+	IGR	DEL	T	-	-	rs148962355		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134850724delT								TIFAB (62635 upstream) : NEUROG1 (19256 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	135225585	135225585	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135225585delT								LOC153328 (1261 upstream) : IL9 (2350 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	135911122	135911122	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135911122delA								TRPC7 (218049 upstream) : SPOCK1 (399866 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	135961064	135961064	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135961064delT								TRPC7 (267991 upstream) : SPOCK1 (349924 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	136015353	136015353	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136015353delT								TRPC7 (322280 upstream) : SPOCK1 (295635 downstream)																																			---	---	---	---
SPOCK1	6695	broad.mit.edu	37	5	136328035	136328035	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136328035delT	uc003lbo.2	-						SPOCK1_uc003lbp.2_Intron	NM_004598	NP_004589			sparc/osteonectin, cwcv and kazal-like domains						cell adhesion|cell proliferation|cellular component movement|nervous system development|signal transduction	proteinaceous extracellular matrix	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
SPOCK1	6695	broad.mit.edu	37	5	136587444	136587444	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136587444delA	uc003lbo.2	-						SPOCK1_uc003lbp.2_Intron	NM_004598	NP_004589			sparc/osteonectin, cwcv and kazal-like domains						cell adhesion|cell proliferation|cellular component movement|nervous system development|signal transduction	proteinaceous extracellular matrix	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
SPOCK1	6695	broad.mit.edu	37	5	136684312	136684312	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136684312delA	uc003lbo.2	-						SPOCK1_uc003lbp.2_Intron	NM_004598	NP_004589			sparc/osteonectin, cwcv and kazal-like domains						cell adhesion|cell proliferation|cellular component movement|nervous system development|signal transduction	proteinaceous extracellular matrix	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
KLHL3	26249	broad.mit.edu	37	5	137009531	137009532	+	Intron	INS	-	AGT	AGT	rs142079310		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137009531_137009532insAGT	uc010jek.2	-						KLHL3_uc011cyc.1_5'Flank|KLHL3_uc003lbr.3_Intron|KLHL3_uc011cyd.1_Intron|KLHL3_uc010jel.1_5'UTR|KLHL3_uc010jem.1_Intron|KLHL3_uc010jen.1_Intron|KLHL3_uc003lbs.1_Intron	NM_017415	NP_059111			kelch-like 3							cytoplasm|cytoskeleton	actin binding|structural molecule activity				0		all_hematologic(541;3.67e-07)|Breast(839;7.61e-05)|Prostate(281;0.000825)|Ovarian(839;0.0481)|all_lung(232;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)	GBM - Glioblastoma multiforme(465;0.0223)														---	---	---	---
PKD2L2	27039	broad.mit.edu	37	5	137253534	137253534	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137253534delT	uc003lby.2	+						PKD2L2_uc003lbw.1_Intron|PKD2L2_uc003lbx.2_Intron|PKD2L2_uc011cyi.1_Intron	NM_014386	NP_055201			polycystic kidney disease 2-like 2							integral to membrane	calcium ion binding|ion channel activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)															---	---	---	---
PKD2L2	27039	broad.mit.edu	37	5	137260513	137260513	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137260513delC	uc003lby.2	+						PKD2L2_uc003lbw.1_Intron|PKD2L2_uc003lbx.2_Intron|PKD2L2_uc011cyi.1_Intron	NM_014386	NP_055201			polycystic kidney disease 2-like 2							integral to membrane	calcium ion binding|ion channel activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)															---	---	---	---
FAM13B	51306	broad.mit.edu	37	5	137298018	137298018	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137298018delA	uc003lbz.2	-						FAM13B_uc003lcb.2_Intron|FAM13B_uc003lca.2_Intron	NM_016603	NP_057687			hypothetical protein LOC51306 isoform 1						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0																		---	---	---	---
GFRA3	2676	broad.mit.edu	37	5	137598663	137598664	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137598663_137598664insT	uc003lcn.2	-						GFRA3_uc003lco.2_Intron	NM_001496	NP_001487			GDNF family receptor alpha 3 preproprotein						peripheral nervous system development	anchored to membrane|cytoplasm|extrinsic to membrane|intracellular membrane-bounded organelle	receptor binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)															---	---	---	---
CDC25C	995	broad.mit.edu	37	5	137662042	137662042	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137662042delT	uc003lcp.1	-						CDC25C_uc003lcq.1_Intron|CDC25C_uc003lcr.1_Intron|CDC25C_uc011cyp.1_Intron|CDC25C_uc003lcs.1_Intron|CDC25C_uc010jet.1_Intron|CDC25C_uc003lct.1_Intron|CDC25C_uc003lcu.1_Intron	NM_001790	NP_001781			cell division cycle 25C isoform a						cell cycle checkpoint|cell division|cell proliferation|DNA replication|G2/M transition of mitotic cell cycle|interspecies interaction between organisms|mitosis|regulation of cyclin-dependent protein kinase activity|regulation of mitosis|traversing start control point of mitotic cell cycle	cytosol|nucleoplasm	protein tyrosine phosphatase activity|WW domain binding			lung(3)	3			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)															---	---	---	---
KDM3B	51780	broad.mit.edu	37	5	137741202	137741202	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137741202delA	uc003lcy.1	+						KDM3B_uc010jew.1_Intron|KDM3B_uc011cys.1_Intron	NM_016604	NP_057688			jumonji domain containing 1B						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			ovary(3)|upper_aerodigestive_tract(2)|lung(2)|kidney(2)|central_nervous_system(1)|skin(1)	11																		---	---	---	---
SIL1	64374	broad.mit.edu	37	5	138387909	138387910	+	Intron	INS	-	CAGT	CAGT	rs142967461	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138387909_138387910insCAGT	uc003ldm.2	-						SIL1_uc003ldn.2_Intron|SIL1_uc003ldo.2_Intron|SIL1_uc003ldp.2_Intron	NM_022464	NP_071909			SIL1 protein precursor						intracellular protein transport|protein folding|transmembrane transport	endoplasmic reticulum lumen	unfolded protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)											Marinesco-Sj_gren_syndrome				---	---	---	---
MATR3	9782	broad.mit.edu	37	5	138620295	138620296	+	Intron	DEL	AA	-	-	rs77498730		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138620295_138620296delAA	uc003ldu.2	+						MATR3_uc003lds.2_Intron|MATR3_uc010jfb.2_Intron|MATR3_uc003ldt.2_Intron	NM_199189	NP_954659			matrin 3							nuclear inner membrane|nuclear matrix	nucleotide binding|protein binding|RNA binding|structural molecule activity|zinc ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)															---	---	---	---
MATR3	9782	broad.mit.edu	37	5	138643062	138643062	+	5'UTR	DEL	T	-	-	rs12153162	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138643062delT	uc003ldu.2	+	5					MATR3_uc003lds.2_5'UTR|MATR3_uc010jfb.2_5'UTR|MATR3_uc003ldt.2_Intron|MATR3_uc003ldw.2_5'UTR|MATR3_uc003ldx.2_5'UTR|MATR3_uc010jfc.2_5'UTR|MATR3_uc003ldy.2_Intron|MATR3_uc011czb.1_Intron|MATR3_uc003ldz.2_5'UTR|MATR3_uc003lea.2_5'UTR	NM_199189	NP_954659			matrin 3							nuclear inner membrane|nuclear matrix	nucleotide binding|protein binding|RNA binding|structural molecule activity|zinc ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)															---	---	---	---
MATR3	9782	broad.mit.edu	37	5	138660882	138660882	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138660882delA	uc003ldu.2	+						MATR3_uc003ldt.2_Intron|MATR3_uc003ldw.2_Intron|MATR3_uc003ldx.2_Intron|MATR3_uc010jfc.2_Intron|MATR3_uc011czb.1_Intron|MATR3_uc003ldz.2_Intron|MATR3_uc003lea.2_Intron|MATR3_uc003leb.2_Intron|MATR3_uc003lec.2_Intron	NM_199189	NP_954659			matrin 3							nuclear inner membrane|nuclear matrix	nucleotide binding|protein binding|RNA binding|structural molecule activity|zinc ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)															---	---	---	---
UBE2D2	7322	broad.mit.edu	37	5	138961852	138961852	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138961852delT	uc003ler.2	+						UBE2D2_uc003leq.2_Intron	NM_003339	NP_003330			ubiquitin-conjugating enzyme E2D 2 isoform 1						protein K48-linked ubiquitination|ubiquitin-dependent protein catabolic process		ATP binding|protein binding|ubiquitin-protein ligase activity			central_nervous_system(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)															---	---	---	---
PSD2	84249	broad.mit.edu	37	5	139184149	139184150	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139184149_139184150insT	uc003leu.1	+							NM_032289	NP_115665			pleckstrin and Sec7 domain containing 2						regulation of ARF protein signal transduction	cytoplasm|integral to membrane	ARF guanyl-nucleotide exchange factor activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
NRG2	9542	broad.mit.edu	37	5	139263008	139263009	+	Intron	INS	-	G	G	rs146436302	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139263008_139263009insG	uc003lex.1	-						NRG2_uc003lev.1_Intron|NRG2_uc003lew.1_Intron|NRG2_uc003ley.1_Intron	NM_004883	NP_004874			neuregulin 2 isoform 1						embryo development	extracellular region|integral to membrane|plasma membrane	growth factor activity			pancreas(2)|breast(2)|ovary(1)|skin(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
SLC4A9	83697	broad.mit.edu	37	5	139740267	139740267	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139740267delG	uc003lfm.2	+						SLC4A9_uc003lfj.2_Intron|SLC4A9_uc011czg.1_Intron|SLC4A9_uc003lfl.2_Intron|SLC4A9_uc003lfk.2_Intron	NM_031467	NP_113655			solute carrier family 4, sodium bicarbonate							integral to membrane|plasma membrane	inorganic anion exchanger activity|sodium:bicarbonate symporter activity			large_intestine(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
ANKHD1-EIF4EBP3	404734	broad.mit.edu	37	5	139893392	139893393	+	Intron	DEL	AA	-	-	rs150381798		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139893392_139893393delAA	uc003lfs.1	+						ANKHD1_uc003lfq.1_Intron|ANKHD1_uc003lfr.2_Intron|ANKHD1_uc003lft.1_Intron|ANKHD1_uc003lfu.1_Intron|ANKHD1_uc003lfv.1_Intron|ANKHD1-EIF4EBP3_uc011czh.1_Intron|ANKHD1_uc003lfw.2_Intron	NM_020690	NP_065741			ANKHD1-EIF4EBP3 protein							cytoplasm|nucleus	RNA binding			ovary(6)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
HARS	3035	broad.mit.edu	37	5	140058448	140058448	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140058448delA	uc003lgv.2	-						HARS_uc003lgu.2_Intron|HARS_uc011czm.1_Intron|HARS_uc003lgw.2_Intron|HARS_uc011czn.1_Intron|HARS_uc010jfu.2_Intron|HARS_uc011czo.1_Intron|HARS_uc011czp.1_Intron|HARS_uc011czq.1_Intron	NM_002109	NP_002100			histidyl-tRNA synthetase						histidyl-tRNA aminoacylation	cytosol	ATP binding|histidine-tRNA ligase activity			ovary(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		L-Histidine(DB00117)													---	---	---	---
PCDHAC2	56134	broad.mit.edu	37	5	140385974	140385974	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140385974delT	uc003lii.2	+						PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc003lia.2_Intron|PCDHA12_uc003lic.2_Intron|PCDHA13_uc003lie.1_Intron|PCDHA13_uc003lif.2_Intron|PCDHAC1_uc003lih.2_Intron	NM_018899	NP_061722			protocadherin alpha subfamily C, 2 isoform 1						homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(2)|skin(2)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHGA10	56106	broad.mit.edu	37	5	140795209	140795209	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140795209delA	uc003lkl.1	+						PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc011day.1_Frame_Shift_Del_p.K823fs|PCDHGB7_uc003lkm.2_5'Flank|PCDHGB7_uc003lkn.1_5'Flank	NM_018913	NP_061736			protocadherin gamma subfamily A, 10 isoform 1						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
KIAA0141	9812	broad.mit.edu	37	5	141311092	141311092	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141311092delG	uc003lls.2	+						KIAA0141_uc003llt.2_Intron|KIAA0141_uc003llu.1_5'Flank	NM_001142603	NP_001136075			hypothetical protein LOC9812 precursor						apoptosis|regulation of caspase activity	mitochondrion	protein binding			skin(1)	1		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
RNF14	9604	broad.mit.edu	37	5	141354197	141354197	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141354197delT	uc003lly.2	+						RNF14_uc003llz.2_Intron|RNF14_uc003lma.2_Intron|RNF14_uc003lmb.2_Intron|RNF14_uc003lmc.2_Intron|RNF14_uc011dbg.1_Intron|RNF14_uc011dbh.1_Intron|RNF14_uc003lmd.2_Intron	NM_183399	NP_899646			ring finger protein 14 isoform 1						androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|protein ubiquitination|regulation of androgen receptor signaling pathway|regulation of transcription from RNA polymerase II promoter|response to estradiol stimulus|transcription, DNA-dependent	cytoplasm|nucleus	androgen receptor binding|small conjugating protein ligase activity|transcription coactivator activity|zinc ion binding				0		all_hematologic(541;0.0536)|Ovarian(839;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.0407)														---	---	---	---
SPRY4	81848	broad.mit.edu	37	5	141699961	141699961	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141699961delA	uc003lml.2	-						SPRY4_uc010jgi.1_Intron	NM_001127496	NP_001120968			sprouty homolog 4 isoform 2						multicellular organismal development	cytoplasm|ruffle membrane	protein binding			ovary(1)|lung(1)	2		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											Testicular_Cancer_Familial_Clustering_of				---	---	---	---
Unknown	0	broad.mit.edu	37	5	141856766	141856767	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141856766_141856767delTT								SPRY4 (152146 upstream) : FGF1 (114977 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	141885052	141885052	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141885052delA								SPRY4 (180432 upstream) : FGF1 (86692 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	141944285	141944285	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141944285delA								SPRY4 (239665 upstream) : FGF1 (27459 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	142112090	142112090	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142112090delT								FGF1 (34455 upstream) : ARHGAP26 (38202 downstream)																																			---	---	---	---
ARHGAP26	23092	broad.mit.edu	37	5	142158012	142158012	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142158012delT	uc011dbj.1	+						ARHGAP26_uc003lmt.2_Intron|ARHGAP26_uc003lmw.2_Intron	NM_015071	NP_055886			GTPase regulator associated with the focal						actin cytoskeleton organization|filopodium assembly|nervous system development|small GTPase mediated signal transduction	cytoskeleton|cytosol|focal adhesion	cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding			ovary(1)	1		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
ARHGAP26	23092	broad.mit.edu	37	5	142549261	142549261	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142549261delG	uc011dbj.1	+						ARHGAP26_uc003lmt.2_Intron|ARHGAP26_uc003lmw.2_Intron	NM_015071	NP_055886			GTPase regulator associated with the focal						actin cytoskeleton organization|filopodium assembly|nervous system development|small GTPase mediated signal transduction	cytoskeleton|cytosol|focal adhesion	cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding			ovary(1)	1		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
NR3C1	2908	broad.mit.edu	37	5	142801104	142801105	+	Intron	INS	-	T	T	rs140492655	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142801104_142801105insT	uc003lnf.2	-						NR3C1_uc003lnc.2_Intron|NR3C1_uc003lnd.2_Intron|NR3C1_uc003lne.2_Intron	NM_001024094	NP_001019265			glucocorticoid receptor isoform gamma						chromatin modification|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to protein stimulus|transcription from RNA polymerase II promoter	mitochondrial matrix|nucleoplasm	glucocorticoid receptor activity|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|zinc ion binding			ovary(2)	2		Acute lymphoblastic leukemia(2;3.2e-05)|all_hematologic(2;0.000361)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)		Amcinonide(DB00288)|Betamethasone(DB00443)|Budesonide(DB01222)|Dexamethasone(DB01234)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluticasone Propionate(DB00588)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Loteprednol Etabonate(DB00873)|Methylprednisolone(DB00959)|Mifepristone(DB00834)|Mometasone(DB00764)|Prednisone(DB00635)													---	---	---	---
HMHB1	57824	broad.mit.edu	37	5	143198346	143198346	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:143198346delT	uc003lnj.2	+							NM_021182	NP_067005			minor histocompatibility antigen HB-1												0		Acute lymphoblastic leukemia(2;0.0236)|all_hematologic(2;0.041)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	143232671	143232671	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:143232671delA								HMHB1 (32389 upstream) : YIPF5 (305060 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	143266928	143266928	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:143266928delT								HMHB1 (66646 upstream) : YIPF5 (270803 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	143330584	143330585	+	IGR	DEL	TT	-	-	rs71793075		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:143330584_143330585delTT								HMHB1 (130302 upstream) : YIPF5 (207146 downstream)																																			---	---	---	---
TCERG1	10915	broad.mit.edu	37	5	145825410	145825410	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145825410delT	uc003lob.2	+						TCERG1_uc003loc.2_5'Flank|TCERG1_uc011dbt.1_5'Flank	NM_006706	NP_006697			transcription elongation regulator 1 isoform 1						regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	protein binding|transcription coactivator activity			ovary(1)|skin(1)	2		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
TCERG1	10915	broad.mit.edu	37	5	145834133	145834134	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145834133_145834134delTT	uc003lob.2	+						TCERG1_uc003loc.2_Intron|TCERG1_uc011dbt.1_Intron	NM_006706	NP_006697			transcription elongation regulator 1 isoform 1						regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	protein binding|transcription coactivator activity			ovary(1)|skin(1)	2		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
PPP2R2B	5521	broad.mit.edu	37	5	146390862	146390863	+	Intron	INS	-	C	C	rs141651279	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146390862_146390863insC	uc011dbv.1	-						PPP2R2B_uc003loi.3_Intron|PPP2R2B_uc003loh.3_Intron|PPP2R2B_uc003loj.3_Intron|PPP2R2B_uc003lok.3_Intron|PPP2R2B_uc011dbu.1_Intron	NM_181675	NP_858061			beta isoform of regulatory subunit B55, protein						apoptosis|signal transduction	cytoskeleton|mitochondrial outer membrane|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(1)|prostate(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
PPP2R2B	5521	broad.mit.edu	37	5	146435335	146435335	+	5'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146435335delA	uc003loi.3	-	1					PPP2R2B_uc003loh.3_5'UTR|PPP2R2B_uc003loj.3_Intron|PPP2R2B_uc003lok.3_Intron|PPP2R2B_uc011dbu.1_Intron|PPP2R2B_uc011dbv.1_Intron	NM_181676	NP_858062			beta isoform of regulatory subunit B55, protein						apoptosis|signal transduction	cytoskeleton|mitochondrial outer membrane|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(1)|prostate(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	146610654	146610655	+	IGR	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146610654_146610655insC								PPP2R2B (149600 upstream) : STK32A (3924 downstream)																																			---	---	---	---
DPYSL3	1809	broad.mit.edu	37	5	146884805	146884805	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:146884805delT	uc003loo.2	-							NM_001387	NP_001378			dihydropyrimidinase-like 3						axon guidance|pyrimidine base catabolic process|signal transduction	cytosol|growth cone	dihydropyrimidinase activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	147296841	147296841	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147296841delA								C5orf46 (10740 upstream) : SPINK5 (146694 downstream)																																			---	---	---	---
HTR4	3360	broad.mit.edu	37	5	147932777	147932777	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147932777delA	uc003lpn.2	-						HTR4_uc010jgu.1_Intron|HTR4_uc003lpi.1_Intron|HTR4_uc003lpj.1_Intron|HTR4_uc003lpk.2_Intron|HTR4_uc011dby.1_Intron|HTR4_uc003lpl.2_Intron|HTR4_uc003lpm.2_Intron|HTR4_uc010jgv.2_Intron|HTR4_uc003lpo.1_Intron|SH3TC2_uc003lpp.1_Intron	NM_000870	NP_000861			serotonin 5-HT4 receptor isoform b						G-protein signaling, coupled to cyclic nucleotide second messenger|positive regulation of cell proliferation	endosome|integral to plasma membrane|membrane fraction	serotonin receptor activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Cisapride(DB00604)|Rizatriptan(DB00953)|Tegaserod(DB01079)|Zolmitriptan(DB00315)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	148449040	148449040	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148449040delA								SH3TC2 (6303 upstream) : ABLIM3 (72014 downstream)																																			---	---	---	---
CSNK1A1	1452	broad.mit.edu	37	5	148904917	148904917	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148904917delT	uc003lqx.1	-						CSNK1A1_uc011dcc.1_Intron|CSNK1A1_uc003lqv.1_Intron|CSNK1A1_uc003lqw.1_Intron|CSNK1A1_uc003lqy.1_Intron|CSNK1A1_uc010jha.1_Intron	NM_001892	NP_001883			casein kinase 1, alpha 1 isoform 2						cell division|mitosis|Wnt receptor signaling pathway	centrosome|condensed chromosome kinetochore|cytosol|nuclear speck	ATP binding|protein binding|protein binding|protein serine/threonine kinase activity			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.0407)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	149055790	149055790	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149055790delT								ARHGEF37 (41263 upstream) : PPARGC1B (54074 downstream)																																			---	---	---	---
PDE6A	5145	broad.mit.edu	37	5	149298355	149298355	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149298355delT	uc003lrg.3	-							NM_000440	NP_000431			phosphodiesterase 6A						cytosolic calcium ion homeostasis|GMP metabolic process|platelet activation|signal transduction|visual perception	cytosol|plasma membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding			ovary(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)															---	---	---	---
CSF1R	1436	broad.mit.edu	37	5	149446764	149446766	+	Intron	DEL	TTT	-	-	rs66517680		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149446764_149446766delTTT	uc003lrl.2	-						CSF1R_uc011dcd.1_Intron|CSF1R_uc010jhc.2_Intron|CSF1R_uc003lrm.2_Intron	NM_005211	NP_005202			colony stimulating factor 1 receptor precursor						cell proliferation|multicellular organismal development|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane|receptor complex	ATP binding|cytokine binding|macrophage colony-stimulating factor receptor activity|protein homodimerization activity			haematopoietic_and_lymphoid_tissue(38)|lung(6)|central_nervous_system(3)|liver(3)|breast(2)|endometrium(1)|ovary(1)	54			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Imatinib(DB00619)|Sunitinib(DB01268)													---	---	---	---
NDST1	3340	broad.mit.edu	37	5	149919109	149919109	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149919109delT	uc003lsk.3	+						NDST1_uc011dcj.1_Intron|NDST1_uc003lsl.2_3'UTR	NM_001543	NP_001534			N-deacetylase/N-sulfotransferase (heparan						heparan sulfate proteoglycan biosynthetic process|inflammatory response	Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			breast(1)|skin(1)	2		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	149958269	149958269	+	IGR	DEL	A	-	-	rs111391287		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149958269delA								NDST1 (20497 upstream) : SYNPO (22373 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	151412877	151412877	+	Intron	DEL	T	-	-	rs35738950		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151412877delT	uc003luu.1	+											Homo sapiens cDNA FLJ10720 fis, clone NT2RP3001116.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	151517680	151517681	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151517680_151517681delAA	uc003luu.1	+											Homo sapiens cDNA FLJ10720 fis, clone NT2RP3001116.																														---	---	---	---
Unknown	0	broad.mit.edu	37	5	151879962	151879962	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:151879962delC								NMUR2 (95122 upstream) : GRIA1 (989213 downstream)																																			---	---	---	---
GRIA1	2890	broad.mit.edu	37	5	152870806	152870806	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:152870806delA	uc003lva.3	+						GRIA1_uc003luy.3_Intron|GRIA1_uc003luz.3_Intron|GRIA1_uc011dcv.1_Intron|GRIA1_uc011dcw.1_Intron|GRIA1_uc011dcx.1_5'Flank|GRIA1_uc011dcy.1_5'Flank|GRIA1_uc011dcz.1_5'Flank|GRIA1_uc010jia.1_Intron	NM_001114183	NP_001107655			glutamate receptor, ionotropic, AMPA 1 isoform						synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|dendritic spine|endocytic vesicle membrane|endoplasmic reticulum membrane|neuronal cell body|postsynaptic density|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity|PDZ domain binding			ovary(4)|skin(2)	6		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|L-Glutamic Acid(DB00142)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)													---	---	---	---
GRIA1	2890	broad.mit.edu	37	5	153146709	153146709	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153146709delA	uc003lva.3	+						GRIA1_uc003luy.3_Intron|GRIA1_uc003luz.3_Intron|GRIA1_uc011dcv.1_Intron|GRIA1_uc011dcw.1_Intron|GRIA1_uc011dcx.1_Intron|GRIA1_uc011dcy.1_Intron|GRIA1_uc011dcz.1_Intron	NM_001114183	NP_001107655			glutamate receptor, ionotropic, AMPA 1 isoform						synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|dendritic spine|endocytic vesicle membrane|endoplasmic reticulum membrane|neuronal cell body|postsynaptic density|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity|PDZ domain binding			ovary(4)|skin(2)	6		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|L-Glutamic Acid(DB00142)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)													---	---	---	---
MFAP3	4238	broad.mit.edu	37	5	153432331	153432331	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153432331delT	uc003lvf.2	+						MFAP3_uc010jib.2_Intron|MFAP3_uc011ddb.1_Intron	NM_001135037	NP_001128509			microfibrillar-associated protein 3 isoform 2							integral to membrane|plasma membrane					0	Renal(175;0.00488)	Lung NSC(249;0.00145)|all_lung(500;0.00226)|all_neural(177;0.122)|Breast(839;0.14)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)	OV - Ovarian serous cystadenocarcinoma(192;9.69e-06)|GBM - Glioblastoma multiforme(465;0.0201)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	153562055	153562057	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153562055_153562057delTTT								MFAP3 (125041 upstream) : GALNT10 (8238 downstream)																																			---	---	---	---
GALNT10	55568	broad.mit.edu	37	5	153718077	153718077	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153718077delT	uc003lvh.2	+						GALNT10_uc003lvg.1_Intron|GALNT10_uc010jic.2_Intron|GALNT10_uc010jid.2_Intron	NM_198321	NP_938080			GalNAc transferase 10 isoform a							Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(2)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)|all_hematologic(541;0.21)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	153948887	153948888	+	IGR	DEL	AA	-	-	rs76771474		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153948887_153948888delAA								HAND1 (91063 upstream) : MIR1303 (116448 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	153949862	153949863	+	IGR	INS	-	AA	AA			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153949862_153949863insAA								HAND1 (92038 upstream) : MIR1303 (115473 downstream)																																			---	---	---	---
LARP1	23367	broad.mit.edu	37	5	154127424	154127424	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154127424delA	uc003lvo.2	+							NM_015315	NP_056130			la related protein isoform 1								protein binding|RNA binding			ovary(2)|pancreas(1)|skin(1)	4	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)															---	---	---	---
LARP1	23367	broad.mit.edu	37	5	154132493	154132494	+	5'Flank	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154132493_154132494delAA	uc003lvp.2	+						LARP1_uc003lvo.2_Intron	NM_033551	NP_291029			la related protein isoform 2								protein binding|RNA binding			ovary(2)|pancreas(1)|skin(1)	4	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)															---	---	---	---
GEMIN5	25929	broad.mit.edu	37	5	154293377	154293378	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154293377_154293378delAA	uc003lvx.3	-						GEMIN5_uc011ddk.1_Intron	NM_015465	NP_056280			gemin 5						ncRNA metabolic process|protein complex assembly|spliceosomal snRNP assembly	Cajal body|cytosol|spliceosomal complex	protein binding|snRNA binding			skin(2)|ovary(1)	3	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)															---	---	---	---
MRPL22	29093	broad.mit.edu	37	5	154335911	154335911	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154335911delT	uc003lvy.3	+						MRPL22_uc003lvz.3_Intron	NM_014180	NP_054899			mitochondrial ribosomal protein L22 isoform a						translation	large ribosomal subunit|mitochondrion	structural constituent of ribosome				0	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)															---	---	---	---
SGCD	6444	broad.mit.edu	37	5	155885629	155885630	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155885629_155885630insA	uc003lwd.3	+						SGCD_uc003lwa.1_Intron|SGCD_uc003lwb.2_Intron|SGCD_uc003lwc.3_Intron	NM_001128209	NP_001121681			delta-sarcoglycan isoform 3						cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
TIMD4	91937	broad.mit.edu	37	5	156381896	156381896	+	Intron	DEL	T	-	-	rs71922795		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156381896delT	uc003lwh.2	-						TIMD4_uc010jii.2_Intron	NM_138379	NP_612388			T-cell immunoglobulin and mucin domain							integral to membrane				ovary(2)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
HAVCR1	26762	broad.mit.edu	37	5	156484327	156484327	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156484327delA	uc010jij.1	-						HAVCR1_uc003lwi.2_Intron|HAVCR1_uc011ddm.1_Intron	NM_001099414	NP_001092884			hepatitis A virus cellular receptor 1						interspecies interaction between organisms	integral to membrane	receptor activity			ovary(1)|skin(1)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	156562104	156562104	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156562104delT								HAVCR2 (25966 upstream) : MED7 (3349 downstream)																																			---	---	---	---
ITK	3702	broad.mit.edu	37	5	156607744	156607744	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156607744delT	uc003lwo.1	+							NM_005546	NP_005537			IL2-inducible T-cell kinase						cellular defense response|intracellular signal transduction|T cell receptor signaling pathway	cytosol|plasma membrane	ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(12)|ovary(8)|skin(4)|stomach(1)|central_nervous_system(1)	26	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.1)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)					T	SYK	peripheral T-cell lymphoma								---	---	---	---
ADAM19	8728	broad.mit.edu	37	5	156833780	156833780	+	Intron	DEL	T	-	-	rs7705868	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156833780delT	uc003lww.1	-											SubName: Full=cDNA FLJ34145 fis, clone FCBBF3011867, highly similar to ADAM 19 (EC 3.4.24.-);						proteolysis	integral to membrane	metalloendopeptidase activity|SH3 domain binding|zinc ion binding			ovary(3)|large_intestine(2)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8	Renal(175;0.00488)	Medulloblastoma(196;0.0359)|all_neural(177;0.14)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	157147411	157147412	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157147411_157147412delTT								C5orf52 (40251 upstream) : THG1L (10911 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	157584163	157584163	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157584163delT								CLINT1 (297995 upstream) : EBF1 (538761 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	157769382	157769382	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157769382delA								CLINT1 (483214 upstream) : EBF1 (353542 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	157822645	157822645	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157822645delA								CLINT1 (536477 upstream) : EBF1 (300279 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	158090829	158090829	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158090829delA								CLINT1 (804661 upstream) : EBF1 (32095 downstream)																																			---	---	---	---
EBF1	1879	broad.mit.edu	37	5	158383471	158383472	+	Intron	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158383471_158383472delAC	uc010jip.2	-						EBF1_uc011ddw.1_Intron|EBF1_uc011ddx.1_Intron|EBF1_uc003lxl.3_Intron	NM_024007	NP_076870			early B-cell factor						multicellular organismal development	nucleus	DNA binding|metal ion binding		HMGA2/EBF1(2)	soft_tissue(2)|ovary(1)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Acute lymphoblastic leukemia(3;2.99e-06)|all_hematologic(3;0.000772)|Medulloblastoma(196;0.037)|all_neural(177;0.143)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)					T	HMGA2	lipoma								---	---	---	---
EBF1	1879	broad.mit.edu	37	5	158461113	158461113	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158461113delA	uc010jip.2	-						EBF1_uc011ddw.1_Intron|EBF1_uc011ddx.1_Intron|EBF1_uc003lxl.3_Intron	NM_024007	NP_076870			early B-cell factor						multicellular organismal development	nucleus	DNA binding|metal ion binding		HMGA2/EBF1(2)	soft_tissue(2)|ovary(1)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Acute lymphoblastic leukemia(3;2.99e-06)|all_hematologic(3;0.000772)|Medulloblastoma(196;0.037)|all_neural(177;0.143)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)					T	HMGA2	lipoma								---	---	---	---
RNF145	153830	broad.mit.edu	37	5	158596568	158596568	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158596568delA	uc003lxp.2	-						RNF145_uc011ddy.1_Intron|RNF145_uc003lxo.1_Intron|RNF145_uc011ddz.1_Intron|RNF145_uc010jiq.1_Intron	NM_144726	NP_653327			ring finger protein 145							integral to membrane	zinc ion binding			ovary(3)|lung(1)|skin(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	159073864	159073864	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159073864delA								LOC285627 (180580 upstream) : ADRA1B (269876 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	159113725	159113726	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159113725_159113726delTT								LOC285627 (220441 upstream) : ADRA1B (230014 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	159149794	159149795	+	IGR	DEL	AA	-	-	rs113836783		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159149794_159149795delAA								LOC285627 (256510 upstream) : ADRA1B (193945 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	159574211	159574211	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159574211delA								PWWP2A (27759 upstream) : FABP6 (40163 downstream)																																			---	---	---	---
CCNJL	79616	broad.mit.edu	37	5	159740553	159740553	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159740553delA	uc003lyb.1	-						CCNJL_uc011dee.1_5'Flank|CCNJL_uc003lyc.1_Intron|CCNJL_uc011def.1_5'Flank	NM_024565	NP_078841			cyclin J-like							nucleus					0	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	159883193	159883194	+	IGR	DEL	TT	-	-	rs67640435		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159883193_159883194delTT								PTTG1 (27448 upstream) : MIR146A (29165 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	160336304	160336305	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160336304_160336305insT								ATP10B (57085 upstream) : LOC285629 (22483 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	160401751	160401751	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160401751delT								LOC285629 (36118 upstream) : GABRB2 (313685 downstream)																																			---	---	---	---
GABRB2	2561	broad.mit.edu	37	5	160800595	160800595	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160800595delT	uc003lys.1	-						GABRB2_uc011deh.1_Intron|GABRB2_uc003lyr.1_Intron|GABRB2_uc003lyt.1_Intron|GABRB2_uc010jiu.1_Intron	NM_021911	NP_068711			gamma-aminobutyric acid (GABA) A receptor, beta						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|GABA-A receptor activity				0	Renal(175;0.00259)	Medulloblastoma(196;0.021)|all_neural(177;0.0463)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)													---	---	---	---
Unknown	0	broad.mit.edu	37	5	161348522	161348523	+	IGR	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161348522_161348523delTC								GABRA1 (21559 upstream) : GABRG2 (146125 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	161396822	161396822	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161396822delT								GABRA1 (69859 upstream) : GABRG2 (97826 downstream)																																			---	---	---	---
GABRG2	2566	broad.mit.edu	37	5	161578664	161578664	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161578664delT	uc003lyz.3	+						GABRG2_uc010jjc.2_Intron|GABRG2_uc003lyy.3_Intron|GABRG2_uc011dej.1_Intron	NM_000816	NP_000807			gamma-aminobutyric acid A receptor, gamma 2						gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity|protein binding			ovary(4)|skin(1)	5	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	161802234	161802235	+	IGR	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161802234_161802235delAC								GABRG2 (219690 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	162001038	162001038	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162001038delA								GABRG2 (418494 upstream) : CCNG1 (863539 downstream)																																			---	---	---	---
CCNG1	900	broad.mit.edu	37	5	162864167	162864168	+	5'Flank	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162864167_162864168delTT	uc003lzb.2	+						CCNG1_uc011dek.1_5'Flank|CCNG1_uc011del.1_5'Flank|CCNG1_uc003lzc.2_5'Flank	NM_199246	NP_954854			cyclin G1						cell division|mitosis|regulation of cyclin-dependent protein kinase activity	nucleus				lung(1)|kidney(1)	2	Renal(175;0.000281)	Medulloblastoma(196;0.00853)|all_neural(177;0.0408)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0597)|OV - Ovarian serous cystadenocarcinoma(192;0.107)|Epithelial(171;0.164)														---	---	---	---
HMMR	3161	broad.mit.edu	37	5	162898608	162898609	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162898608_162898609insT	uc003lzf.2	+						HMMR_uc003lzh.2_Intron|HMMR_uc003lzg.2_Intron|HMMR_uc011dem.1_Intron	NM_012484	NP_036616			hyaluronan-mediated motility receptor isoform b							cell surface|cytoplasm	hyaluronic acid binding				0	Renal(175;0.000281)	Medulloblastoma(196;0.00853)|all_neural(177;0.0408)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0296)|OV - Ovarian serous cystadenocarcinoma(192;0.0423)|Epithelial(171;0.0848)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	162956948	162956948	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162956948delA								MAT2B (10615 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	162962910	162962910	+	IGR	DEL	T	-	-	rs5872830		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162962910delT								MAT2B (16577 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	163111075	163111076	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:163111075_163111076delTT								MAT2B (164742 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	164378204	164378204	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:164378204delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	164384372	164384373	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:164384372_164384373insA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	165213823	165213823	+	IGR	DEL	A	-	-	rs34398428		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:165213823delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	165587236	165587236	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:165587236delG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	165775001	165775002	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:165775001_165775002insT								None (None upstream) : ODZ2 (936841 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	166132908	166132908	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166132908delA								None (None upstream) : ODZ2 (578935 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	166530851	166530851	+	IGR	DEL	A	-	-	rs112026301		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166530851delA								None (None upstream) : ODZ2 (180992 downstream)																																			---	---	---	---
ODZ2	57451	broad.mit.edu	37	5	166926815	166926816	+	Intron	DEL	GT	-	-	rs138346546	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166926815_166926816delGT	uc010jjd.2	+							NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)														---	---	---	---
ODZ2	57451	broad.mit.edu	37	5	167145069	167145069	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167145069delT	uc010jjd.2	+							NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)														---	---	---	---
ODZ2	57451	broad.mit.edu	37	5	167335309	167335310	+	Intron	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167335309_167335310insC	uc010jjd.2	+						ODZ2_uc003lzq.2_Intron|ODZ2_uc003lzr.3_Intron	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)														---	---	---	---
ODZ2	57451	broad.mit.edu	37	5	167346943	167346943	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167346943delT	uc010jjd.2	+						ODZ2_uc003lzq.2_Intron|ODZ2_uc003lzr.3_Intron	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)														---	---	---	---
ODZ2	57451	broad.mit.edu	37	5	167379581	167379581	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167379581delT	uc010jjd.2	+						ODZ2_uc003lzq.2_Intron|ODZ2_uc003lzr.3_Intron	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)														---	---	---	---
ODZ2	57451	broad.mit.edu	37	5	167669253	167669253	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167669253delG	uc010jjd.2	+						ODZ2_uc003lzr.3_Intron|ODZ2_uc003lzt.3_Intron|ODZ2_uc010jje.2_Intron	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)														---	---	---	---
ODZ2	57451	broad.mit.edu	37	5	167685506	167685506	+	Intron	DEL	A	-	-	rs78828202		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167685506delA	uc010jjd.2	+						ODZ2_uc003lzr.3_Intron|ODZ2_uc003lzt.3_Intron|ODZ2_uc010jje.2_Intron	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)														---	---	---	---
WWC1	23286	broad.mit.edu	37	5	167825035	167825036	+	Intron	DEL	AT	-	-	rs142942307		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167825035_167825036delAT	uc003lzu.2	+						WWC1_uc003lzv.2_Intron|WWC1_uc011den.1_Intron	NM_015238	NP_056053			WW and C2 domain containing 1 isoform 3						cell migration|positive regulation of MAPKKK cascade|regulation of hippo signaling cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|perinuclear region of cytoplasm|ruffle membrane	protein binding|transcription coactivator activity			ovary(2)|skin(2)|breast(1)	5	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)														---	---	---	---
WWC1	23286	broad.mit.edu	37	5	167889061	167889062	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167889061_167889062delAA	uc003lzu.2	+						WWC1_uc003lzv.2_Intron|WWC1_uc011den.1_Intron|WWC1_uc003lzw.2_Intron|WWC1_uc010jjf.1_Intron	NM_015238	NP_056053			WW and C2 domain containing 1 isoform 3						cell migration|positive regulation of MAPKKK cascade|regulation of hippo signaling cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|perinuclear region of cytoplasm|ruffle membrane	protein binding|transcription coactivator activity			ovary(2)|skin(2)|breast(1)	5	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)														---	---	---	---
SLIT3	6586	broad.mit.edu	37	5	168174576	168174576	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168174576delC	uc003mab.2	-						SLIT3_uc010jjg.2_Intron	NM_003062	NP_003053			slit homolog 3 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
SLIT3	6586	broad.mit.edu	37	5	168211102	168211103	+	Intron	DEL	CA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168211102_168211103delCA	uc003mab.2	-						SLIT3_uc010jjg.2_Intron|SLIT3_uc010jji.2_Intron|SLIT3_uc003mac.1_Intron	NM_003062	NP_003053			slit homolog 3 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
SLIT3	6586	broad.mit.edu	37	5	168691068	168691068	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168691068delA	uc003mab.2	-						SLIT3_uc010jjg.2_Intron|SLIT3_uc010jji.2_Intron|MIR585_hsa-mir-585|MI0003592_5'Flank	NM_003062	NP_003053			slit homolog 3 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
SLIT3	6586	broad.mit.edu	37	5	168713326	168713326	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168713326delT	uc003mab.2	-						SLIT3_uc010jjg.2_Intron|SLIT3_uc010jji.2_Intron	NM_003062	NP_003053			slit homolog 3 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
SLIT3	6586	broad.mit.edu	37	5	168724481	168724482	+	Intron	INS	-	AC	AC			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168724481_168724482insAC	uc003mab.2	-						SLIT3_uc010jjg.2_Intron|SLIT3_uc010jji.2_Intron	NM_003062	NP_003053			slit homolog 3 precursor						apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
DOCK2	1794	broad.mit.edu	37	5	169092682	169092682	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169092682delA	uc003maf.2	+						DOCK2_uc011der.1_Intron	NM_004946	NP_004937			dedicator of cytokinesis 2						actin cytoskeleton organization|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|endomembrane system|membrane	electron carrier activity|GTP binding|GTPase binding|heme binding|Rac guanyl-nucleotide exchange factor activity|T cell receptor binding			ovary(5)|pancreas(2)	7	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
DOCK2	1794	broad.mit.edu	37	5	169107728	169107728	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169107728delA	uc003maf.2	+						DOCK2_uc011der.1_Intron	NM_004946	NP_004937			dedicator of cytokinesis 2						actin cytoskeleton organization|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|endomembrane system|membrane	electron carrier activity|GTP binding|GTPase binding|heme binding|Rac guanyl-nucleotide exchange factor activity|T cell receptor binding			ovary(5)|pancreas(2)	7	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
DOCK2	1794	broad.mit.edu	37	5	169237976	169237979	+	Intron	DEL	CTCT	-	-	rs72104717		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169237976_169237979delCTCT	uc003maf.2	+						DOCK2_uc011der.1_Intron|DOCK2_uc010jjm.2_Intron	NM_004946	NP_004937			dedicator of cytokinesis 2						actin cytoskeleton organization|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|endomembrane system|membrane	electron carrier activity|GTP binding|GTPase binding|heme binding|Rac guanyl-nucleotide exchange factor activity|T cell receptor binding			ovary(5)|pancreas(2)	7	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
DOCK2	1794	broad.mit.edu	37	5	169365915	169365915	+	Intron	DEL	T	-	-	rs140964941		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169365915delT	uc003maf.2	+						DOCK2_uc011der.1_Intron|DOCK2_uc010jjm.2_Intron|FAM196B_uc003mag.2_Intron	NM_004946	NP_004937			dedicator of cytokinesis 2						actin cytoskeleton organization|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|endomembrane system|membrane	electron carrier activity|GTP binding|GTPase binding|heme binding|Rac guanyl-nucleotide exchange factor activity|T cell receptor binding			ovary(5)|pancreas(2)	7	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
DOCK2	1794	broad.mit.edu	37	5	169386378	169386378	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169386378delA	uc003maf.2	+						DOCK2_uc011der.1_Intron|DOCK2_uc010jjm.2_Intron|FAM196B_uc003mag.2_Intron	NM_004946	NP_004937			dedicator of cytokinesis 2						actin cytoskeleton organization|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|endomembrane system|membrane	electron carrier activity|GTP binding|GTPase binding|heme binding|Rac guanyl-nucleotide exchange factor activity|T cell receptor binding			ovary(5)|pancreas(2)	7	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
KCNIP1	30820	broad.mit.edu	37	5	170030924	170030924	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170030924delG	uc003mas.2	+						KCNIP1_uc003map.2_Intron|KCNIP1_uc003mat.2_Intron|KCNIP1_uc010jjp.2_Intron|KCNIP1_uc010jjq.2_Intron	NM_001034837	NP_001030009			Kv channel interacting protein 1 isoform 1						detection of calcium ion|signal transduction|synaptic transmission	plasma membrane	potassium channel activity|voltage-gated ion channel activity			skin(2)	2	Renal(175;0.000159)|Lung NSC(126;0.0191)|all_lung(126;0.0297)	Medulloblastoma(196;0.0109)|all_neural(177;0.0177)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)													OREG0017026	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	5	170187405	170187406	+	IGR	DEL	CA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170187405_170187406delCA								KCNIP1 (23771 upstream) : GABRP (23317 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	170195108	170195108	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170195108delA								KCNIP1 (31474 upstream) : GABRP (15615 downstream)																																			---	---	---	---
GABRP	2568	broad.mit.edu	37	5	170221219	170221219	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170221219delT	uc003mau.2	+						GABRP_uc011dev.1_Intron	NM_014211	NP_055026			gamma-aminobutyric acid (GABA) A receptor, pi							cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			breast(1)	1	Renal(175;0.000159)|Lung NSC(126;0.0122)|all_lung(126;0.0193)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)															---	---	---	---
RANBP17	64901	broad.mit.edu	37	5	170667800	170667800	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170667800delA	uc003mba.2	+						RANBP17_uc003mbb.2_Intron|RANBP17_uc003mbd.2_Intron|RANBP17_uc010jjs.2_Intron	NM_022897	NP_075048			RAN binding protein 17						mRNA transport|protein import into nucleus|transmembrane transport	cytoplasm|nuclear pore	GTP binding|protein transporter activity			ovary(2)|central_nervous_system(1)	3	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)					T	TRD@	ALL								---	---	---	---
RANBP17	64901	broad.mit.edu	37	5	170668308	170668309	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170668308_170668309insT	uc003mba.2	+						RANBP17_uc003mbb.2_Intron|RANBP17_uc003mbd.2_Intron|RANBP17_uc010jjs.2_Intron	NM_022897	NP_075048			RAN binding protein 17						mRNA transport|protein import into nucleus|transmembrane transport	cytoplasm|nuclear pore	GTP binding|protein transporter activity			ovary(2)|central_nervous_system(1)	3	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)					T	TRD@	ALL								---	---	---	---
Unknown	0	broad.mit.edu	37	5	170740996	170740996	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170740996delT								TLX3 (1859 upstream) : NPM1 (73124 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	170794721	170794725	+	IGR	DEL	TTTTT	-	-	rs79285065		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170794721_170794725delTTTTT								TLX3 (55584 upstream) : NPM1 (19395 downstream)																																			---	---	---	---
NPM1	4869	broad.mit.edu	37	5	170819655	170819655	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170819655delT	uc011dex.1	+						NPM1_uc003mbh.2_Intron|NPM1_uc003mbi.2_Intron|NPM1_uc003mbj.2_Intron	NM_002520	NP_002511			nucleophosmin 1 isoform 1						anti-apoptosis|cell aging|CenH3-containing nucleosome assembly at centromere|centrosome cycle|DNA repair|interspecies interaction between organisms|intracellular protein transport|negative regulation of cell proliferation|negative regulation of centrosome duplication|nucleocytoplasmic transport|positive regulation of NF-kappaB transcription factor activity|protein oligomerization|regulation of endodeoxyribonuclease activity|regulation of endoribonuclease activity|ribosome assembly|signal transduction	nucleolus|nucleoplasm|ribonucleoprotein complex|spindle pole centrosome	histone binding|NF-kappaB binding|protein binding|protein heterodimerization activity|protein homodimerization activity|ribosomal large subunit binding|ribosomal small subunit binding|RNA binding|Tat protein binding|transcription coactivator activity|unfolded protein binding		NPM1/ALK(632)	haematopoietic_and_lymphoid_tissue(3109)|skin(1)	3110	Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)					T|F 	ALK|RARA|MLF1	NHL|APL|AML								---	---	---	---
Unknown	0	broad.mit.edu	37	5	171224512	171224512	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171224512delA								FGF18 (340350 upstream) : FBXW11 (64044 downstream)																																			---	---	---	---
FBXW11	23291	broad.mit.edu	37	5	171291781	171291782	+	Intron	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171291781_171291782delAC	uc003mbm.1	-						FBXW11_uc011dey.1_Intron|FBXW11_uc003mbl.1_Intron|FBXW11_uc003mbn.1_Intron	NM_012300	NP_036432			F-box and WD repeat domain containing 11 isoform						cell cycle|negative regulation of transcription, DNA-dependent|positive regulation of circadian rhythm|positive regulation of proteolysis|positive regulation of transcription, DNA-dependent|protein dephosphorylation|protein destabilization|protein polyubiquitination|rhythmic process|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway	centrosome|cytosol|nucleus|SCF ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(1)|breast(1)	2	Renal(175;0.000159)|Lung NSC(126;0.00384)|all_lung(126;0.00659)	Medulloblastoma(196;0.00853)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)															---	---	---	---
FBXW11	23291	broad.mit.edu	37	5	171325896	171325897	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171325896_171325897insA	uc003mbm.1	-						FBXW11_uc011dey.1_Intron|FBXW11_uc003mbl.1_Intron|FBXW11_uc003mbn.1_Intron	NM_012300	NP_036432			F-box and WD repeat domain containing 11 isoform						cell cycle|negative regulation of transcription, DNA-dependent|positive regulation of circadian rhythm|positive regulation of proteolysis|positive regulation of transcription, DNA-dependent|protein dephosphorylation|protein destabilization|protein polyubiquitination|rhythmic process|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway	centrosome|cytosol|nucleus|SCF ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(1)|breast(1)	2	Renal(175;0.000159)|Lung NSC(126;0.00384)|all_lung(126;0.00659)	Medulloblastoma(196;0.00853)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)															---	---	---	---
STK10	6793	broad.mit.edu	37	5	171534189	171534189	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171534189delG	uc003mbo.1	-							NM_005990	NP_005981			serine/threonine kinase 10								ATP binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|testis(1)|breast(1)|pancreas(1)	8	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)													OREG0017039	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
UBTD2	92181	broad.mit.edu	37	5	171639834	171639834	+	Intron	DEL	A	-	-	rs150072593		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171639834delA	uc003mbp.1	-							NM_152277	NP_689490			dendritic cell-derived ubiquitin-like protein							cytoplasm					0	Renal(175;0.000159)|Lung NSC(126;0.00976)|all_lung(126;0.0156)	Medulloblastoma(196;0.00853)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	171719064	171719064	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171719064delT								UBTD2 (8269 upstream) : SH3PXD2B (41441 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	171733024	171733024	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171733024delA								UBTD2 (22229 upstream) : SH3PXD2B (27481 downstream)																																			---	---	---	---
SH3PXD2B	285590	broad.mit.edu	37	5	171784428	171784430	+	Intron	DEL	AAA	-	-	rs79666668		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171784428_171784430delAAA	uc003mbr.2	-							NM_001017995	NP_001017995			SH3 and PX domains 2B						adipose tissue development|bone development|cell communication|cell differentiation|eye development|heart development|podosome assembly	cell junction|cell projection|cytoplasm|podosome	phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-5-phosphate binding|SH2 domain binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	Medulloblastoma(196;0.0207)|all_neural(177;0.0625)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	171921492	171921492	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:171921492delA								SH3PXD2B (39965 upstream) : NEURL1B (146784 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	172030095	172030095	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172030095delG								SH3PXD2B (148568 upstream) : NEURL1B (38181 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	172166061	172166061	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172166061delA								NEURL1B (47530 upstream) : DUSP1 (29041 downstream)																																			---	---	---	---
C5orf41	153222	broad.mit.edu	37	5	172532229	172532232	+	Intron	DEL	TGTG	-	-	rs113596042		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172532229_172532232delTGTG	uc003mch.2	+						C5orf41_uc011dfd.1_Intron	NM_153607	NP_705835			luman-recruiting factor								protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	Renal(175;0.000159)|Lung NSC(126;0.00223)|all_lung(126;0.00391)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	173137430	173137430	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173137430delT								BOD1 (93764 upstream) : CPEB4 (177901 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	173184539	173184539	+	IGR	DEL	T	-	-	rs72326246		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173184539delT								BOD1 (140873 upstream) : CPEB4 (130792 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	173448020	173448020	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173448020delA								C5orf47 (14878 upstream) : HMP19 (24704 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	173950491	173950491	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173950491delA								HMP19 (414310 upstream) : MSX2 (201084 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	173966061	173966061	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173966061delA								HMP19 (429880 upstream) : MSX2 (185514 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	173969331	173969331	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173969331delA								HMP19 (433150 upstream) : MSX2 (182244 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	173972458	173972458	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:173972458delA								HMP19 (436277 upstream) : MSX2 (179117 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	174020204	174020206	+	IGR	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174020204_174020206delAAA								HMP19 (484023 upstream) : MSX2 (131369 downstream)																																			---	---	---	---
SFXN1	94081	broad.mit.edu	37	5	174949356	174949356	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174949356delT	uc003mda.2	+						SFXN1_uc003mdb.1_Intron	NM_022754	NP_073591			sideroflexin 1						iron ion homeostasis	integral to membrane	cation transmembrane transporter activity|protein binding			ovary(1)	1	all_cancers(89;0.00922)|Renal(175;0.000269)|Lung NSC(126;0.00515)|all_lung(126;0.00873)	Medulloblastoma(196;0.0399)|all_neural(177;0.0663)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)															---	---	---	---
CPLX2	10814	broad.mit.edu	37	5	175260160	175260160	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175260160delA	uc003mde.1	+							NM_006650	NP_006641			complexin 2						mast cell degranulation|positive regulation of synaptic plasticity|vesicle docking involved in exocytosis	cytosol				ovary(1)	1	all_cancers(89;0.004)|Renal(175;0.000269)|Lung NSC(126;0.00441)|all_lung(126;0.00747)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)															---	---	---	---
CPLX2	10814	broad.mit.edu	37	5	175309161	175309161	+	3'UTR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175309161delG	uc003mde.1	+	5					CPLX2_uc003mdf.1_3'UTR	NM_006650	NP_006641			complexin 2						mast cell degranulation|positive regulation of synaptic plasticity|vesicle docking involved in exocytosis	cytosol				ovary(1)	1	all_cancers(89;0.004)|Renal(175;0.000269)|Lung NSC(126;0.00441)|all_lung(126;0.00747)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)															---	---	---	---
FAF2	23197	broad.mit.edu	37	5	175906091	175906091	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175906091delT	uc003mej.3	+							NM_014613	NP_055428			UBX domain containing 8						response to unfolded protein	endoplasmic reticulum|lipid particle	protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	5	175973323	175973323	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:175973323delA								RNF44 (8297 upstream) : CDHR2 (3042 downstream)																																			---	---	---	---
ZNF346	23567	broad.mit.edu	37	5	176466457	176466457	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176466457delT	uc003mfi.2	+						ZNF346_uc011dfr.1_Intron|ZNF346_uc011dfs.1_Intron|ZNF346_uc003mfj.2_Intron|ZNF346_uc003mfk.1_Intron|ZNF346_uc011dft.1_Intron	NM_012279	NP_036411			zinc finger protein 346							cytoplasm|nucleolus	double-stranded RNA binding|zinc ion binding				0	all_cancers(89;6.3e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
ZNF346	23567	broad.mit.edu	37	5	176480013	176480014	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176480013_176480014delTT	uc003mfi.2	+						ZNF346_uc011dfr.1_Intron|ZNF346_uc011dfs.1_Intron|ZNF346_uc003mfj.2_Intron|ZNF346_uc003mfk.1_Intron|ZNF346_uc011dft.1_Intron	NM_012279	NP_036411			zinc finger protein 346							cytoplasm|nucleolus	double-stranded RNA binding|zinc ion binding				0	all_cancers(89;6.3e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
NSD1	64324	broad.mit.edu	37	5	176575121	176575123	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176575121_176575123delTTT	uc003mfr.3	+						NSD1_uc003mft.3_Intron|NSD1_uc003mfs.1_Intron|NSD1_uc011dfx.1_Intron|NSD1_uc003mfp.2_Intron	NM_022455	NP_071900			nuclear receptor binding SET domain protein 1						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding			ovary(2)|kidney(1)	3	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)				T	NUP98	AML		Sotos Syndrome		Beckwith-Wiedemann_syndrome|Sotos_syndrome|Weaver_syndrome	HNSCC(47;0.14)			---	---	---	---
NSD1	64324	broad.mit.edu	37	5	176682306	176682307	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176682306_176682307delAA	uc003mfr.3	+						NSD1_uc003mft.3_Intron|NSD1_uc003mfs.1_Intron|NSD1_uc011dfx.1_Intron	NM_022455	NP_071900			nuclear receptor binding SET domain protein 1						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding			ovary(2)|kidney(1)	3	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)				T	NUP98	AML		Sotos Syndrome		Beckwith-Wiedemann_syndrome|Sotos_syndrome|Weaver_syndrome	HNSCC(47;0.14)			---	---	---	---
NSD1	64324	broad.mit.edu	37	5	176722543	176722543	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176722543delA	uc003mfr.3	+	23					NSD1_uc003mft.3_3'UTR|NSD1_uc011dfx.1_3'UTR	NM_022455	NP_071900			nuclear receptor binding SET domain protein 1						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding			ovary(2)|kidney(1)	3	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)				T	NUP98	AML		Sotos Syndrome		Beckwith-Wiedemann_syndrome|Sotos_syndrome|Weaver_syndrome	HNSCC(47;0.14)			---	---	---	---
PDLIM7	9260	broad.mit.edu	37	5	176927020	176927024	+	5'Flank	DEL	AAAAT	-	-	rs74632868		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176927020_176927024delAAAAT	uc003mhc.1	-						PDLIM7_uc003mhb.1_5'Flank|PDLIM7_uc003mhd.1_5'Flank|PDLIM7_uc003mhe.1_5'Flank|PDLIM7_uc003mhf.2_5'Flank|PDLIM7_uc003mhg.1_5'Flank	NM_005451	NP_005442			PDZ and LIM domain 7 isoform 1						cell differentiation|multicellular organismal development|ossification|receptor-mediated endocytosis	cytoplasm|focal adhesion	protein binding|zinc ion binding			breast(1)	1	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	177110392	177110393	+	IGR	DEL	GT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177110392_177110393delGT								LOC202181 (11114 upstream) : FAM153A (27844 downstream)																																			---	---	---	---
FAM153A	285596	broad.mit.edu	37	5	177167589	177167589	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177167589delT	uc010jkp.1	-						FAM153A_uc011dgd.1_Intron|FAM153A_uc003mib.1_Intron|FAM153A_uc003mic.2_Intron	NM_173663	NP_775934			hypothetical protein LOC285596											skin(1)	1	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
COL23A1	91522	broad.mit.edu	37	5	177928576	177928576	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177928576delA	uc003mje.2	-							NM_173465	NP_775736			collagen, type XXIII, alpha 1							collagen|integral to membrane|plasma membrane	protein binding			central_nervous_system(1)|skin(1)	2	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	178161399	178161399	+	IGR	DEL	T	-	-	rs146504927		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178161399delT								ZNF354A (3696 upstream) : AACSL (30467 downstream)																																			---	---	---	---
AACSL	729522	broad.mit.edu	37	5	178223656	178223656	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178223656delC	uc011dgl.1	-						AACSL_uc003mjk.2_Intron					Homo sapiens acetoacetyl-CoA synthetase-like, mRNA (cDNA clone IMAGE:3945810), partial cds.												0																		---	---	---	---
ADAMTS2	9509	broad.mit.edu	37	5	178549809	178549809	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178549809delC	uc003mjw.2	-							NM_014244	NP_055059			ADAM metallopeptidase with thrombospondin type 1						collagen catabolic process	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)														---	---	---	---
Unknown	0	broad.mit.edu	37	5	178911483	178911484	+	IGR	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178911483_178911484delTC								ADAMTS2 (139154 upstream) : RUFY1 (66087 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	5	179066624	179066625	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179066624_179066625delAA								HNRNPH1 (14954 upstream) : C5orf60 (1935 downstream)																																			---	---	---	---
CANX	821	broad.mit.edu	37	5	179135170	179135170	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179135170delT	uc003mkk.2	+						CANX_uc011dgp.1_Intron|CANX_uc010jlb.1_Intron|CANX_uc003mkl.2_Intron|CANX_uc011dgq.1_Intron	NM_001746	NP_001737			calnexin precursor						post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|protein secretion	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane|melanosome	calcium ion binding|sugar binding|unfolded protein binding				0	all_cancers(89;0.000129)|all_epithelial(37;5.59e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0413)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
SQSTM1	8878	broad.mit.edu	37	5	179249568	179249568	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179249568delC	uc003mkw.3	+						SQSTM1_uc011dgr.1_Intron|SQSTM1_uc011dgs.1_Intron|SQSTM1_uc003mkv.3_Intron|SQSTM1_uc003mkx.2_5'UTR	NM_003900	NP_003891			sequestosome 1 isoform 1						anti-apoptosis|apoptosis|cell differentiation|endosome transport|induction of apoptosis by extracellular signals|intracellular signal transduction|macroautophagy|nerve growth factor receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|protein localization|regulation of I-kappaB kinase/NF-kappaB cascade|ubiquitin-dependent protein catabolic process	cytosol|late endosome|nucleoplasm	protein kinase C binding|receptor tyrosine kinase binding|SH2 domain binding|ubiquitin binding|zinc ion binding		SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(2)|ovary(1)	3	all_cancers(89;0.000205)|all_epithelial(37;7.15e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0395)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)											Paget_Disease_of_Bone				---	---	---	---
Unknown	0	broad.mit.edu	37	5	179367689	179367689	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179367689delT								TBC1D9B (32833 upstream) : RNF130 (14785 downstream)																																			---	---	---	---
GFPT2	9945	broad.mit.edu	37	5	179751635	179751635	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179751635delA	uc003mlw.1	-							NM_005110	NP_005101			glutamine-fructose-6-phosphate transaminase 2						dolichol-linked oligosaccharide biosynthetic process|energy reserve metabolic process|fructose 6-phosphate metabolic process|glutamine metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine|UDP-N-acetylglucosamine biosynthetic process	cytosol	glutamine-fructose-6-phosphate transaminase (isomerizing) activity|sugar binding			ovary(1)|skin(1)	2	all_cancers(89;4.97e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	Medulloblastoma(196;0.0392)|all_neural(177;0.0529)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		L-Glutamine(DB00130)													---	---	---	---
GFPT2	9945	broad.mit.edu	37	5	179765393	179765393	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179765393delA	uc003mlw.1	-							NM_005110	NP_005101			glutamine-fructose-6-phosphate transaminase 2						dolichol-linked oligosaccharide biosynthetic process|energy reserve metabolic process|fructose 6-phosphate metabolic process|glutamine metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine|UDP-N-acetylglucosamine biosynthetic process	cytosol	glutamine-fructose-6-phosphate transaminase (isomerizing) activity|sugar binding			ovary(1)|skin(1)	2	all_cancers(89;4.97e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	Medulloblastoma(196;0.0392)|all_neural(177;0.0529)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		L-Glutamine(DB00130)													---	---	---	---
CNOT6	57472	broad.mit.edu	37	5	179942724	179942724	+	Intron	DEL	A	-	-	rs112232424		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179942724delA	uc003mlx.2	+						CNOT6_uc010jld.2_Intron|CNOT6_uc010jle.2_Intron	NM_015455	NP_056270			CCR4-NOT transcription complex, subunit 6						nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	exonuclease activity|metal ion binding|protein binding|RNA binding				0	all_cancers(89;3.3e-05)|all_epithelial(37;7.38e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00543)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.023)														---	---	---	---
BTNL9	153579	broad.mit.edu	37	5	180482769	180482769	+	Intron	DEL	A	-	-	rs78636845		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180482769delA	uc003mmt.2	+							NM_152547	NP_689760			butyrophilin-like 9 precursor							integral to membrane				ovary(1)|central_nervous_system(1)	2	all_cancers(89;2.45e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
DUSP22	56940	broad.mit.edu	37	6	295621	295621	+	Intron	DEL	A	-	-	rs146633623		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:295621delA	uc003msx.2	+						DUSP22_uc011dhn.1_Intron	NM_020185	NP_064570			dual specificity phosphatase 22						apoptosis|cell proliferation|inactivation of MAPK activity|multicellular organismal development|positive regulation of JNK cascade|regulation of cell proliferation|transforming growth factor beta receptor signaling pathway	cytoplasm|nucleus	protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(1)|kidney(1)|central_nervous_system(1)	3	all_hematologic(77;0.228)	Breast(5;0.0249)|all_hematologic(90;0.0489)		OV - Ovarian serous cystadenocarcinoma(45;0.0277)|BRCA - Breast invasive adenocarcinoma(62;0.0669)														---	---	---	---
IRF4	3662	broad.mit.edu	37	6	403476	403476	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:403476delT	uc003msz.3	+						IRF4_uc003mta.3_Intron|IRF4_uc003mtb.3_Intron	NM_002460	NP_002451			interferon regulatory factor 4						interferon-gamma-mediated signaling pathway|positive regulation of interleukin-10 biosynthetic process|positive regulation of interleukin-13 biosynthetic process|positive regulation of interleukin-2 biosynthetic process|positive regulation of interleukin-4 biosynthetic process|positive regulation of transcription, DNA-dependent|regulation of T-helper cell differentiation|T cell activation|type I interferon-mediated signaling pathway	cytoplasm	DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			ovary(1)	1		Breast(5;0.0155)|all_lung(73;0.0691)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.03)|BRCA - Breast invasive adenocarcinoma(62;0.0702)				T	IGH@	MM 								---	---	---	---
LOC285768	285768	broad.mit.edu	37	6	1003502	1003503	+	Intron	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1003502_1003503insC	uc011dhp.1	-						LOC285768_uc010jnf.1_Intron|LOC285768_uc003mtj.2_Intron	NR_027115				Homo sapiens cDNA clone IMAGE:5272115.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	1135939	1135940	+	IGR	INS	-	A	A	rs1029047	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1135939_1135940insA								LOC285768 (34372 upstream) : FOXQ1 (176735 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	1140965	1140966	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1140965_1140966delAA								LOC285768 (39398 upstream) : FOXQ1 (171709 downstream)																																			---	---	---	---
GMDS	2762	broad.mit.edu	37	6	2081819	2081820	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2081819_2081820delAA	uc003mtq.2	-							NM_001500	NP_001491			GDP-mannose 4,6-dehydratase						'de novo' GDP-L-fucose biosynthetic process|GDP-mannose metabolic process|leukocyte cell-cell adhesion		coenzyme binding|GDP-mannose 4,6-dehydratase activity			central_nervous_system(1)	1	Ovarian(93;0.0733)	all_cancers(2;7.64e-19)|all_epithelial(2;3.05e-16)|Colorectal(2;0.00414)|all_hematologic(90;0.00997)|all_lung(73;0.0141)|Lung NSC(90;0.0802)		Epithelial(2;7.61e-06)|all cancers(2;0.000111)|STAD - Stomach adenocarcinoma(2;0.000231)|Colorectal(2;0.00445)|COAD - Colon adenocarcinoma(2;0.0125)|OV - Ovarian serous cystadenocarcinoma(45;0.0563)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	2413914	2413915	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2413914_2413915delTT	uc003mtu.1	+											Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 1572223.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	2798644	2798664	+	IGR	DEL	CTCCGGGGACATTTACTCTTC	-	-	rs11267932		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2798644_2798664delCTCCGGGGACATTTACTCTTC								WRNIP1 (12666 upstream) : SERPINB1 (35072 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	2938702	2938702	+	IGR	DEL	T	-	-	rs80093529	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2938702delT								SERPINB9 (35157 upstream) : SERPINB6 (9692 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	3214704	3214704	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3214704delT								TUBB2A (56921 upstream) : TUBB2B (9792 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	3651036	3651036	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3651036delC								SLC22A23 (194243 upstream) : C6orf145 (71800 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	4187010	4187010	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4187010delA								PECI (51179 upstream) : CDYL (519383 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	4311139	4311139	+	IGR	DEL	G	-	-	rs76753220	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4311139delG								PECI (175308 upstream) : CDYL (395254 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	4569867	4569867	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4569867delA								PECI (434036 upstream) : CDYL (136526 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	4671733	4671734	+	IGR	DEL	AA	-	-	rs66828875		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:4671733_4671734delAA								PECI (535902 upstream) : CDYL (34659 downstream)																																			---	---	---	---
LYRM4	57128	broad.mit.edu	37	6	5186355	5186355	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5186355delG	uc003mwp.2	-						LYRM4_uc010jnu.2_Intron|LYRM4_uc003mwq.2_Intron|uc003mwn.1_Intron	NM_020408	NP_065141			LYR motif containing 4 isoform 1							mitochondrion|nucleus					0	Ovarian(93;0.11)	all_hematologic(90;0.0901)																---	---	---	---
FARS2	10667	broad.mit.edu	37	6	5557384	5557385	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5557384_5557385insT	uc010jnv.1	+						FARS2_uc003mwr.2_Intron	NM_006567	NP_006558			phenylalanyl-tRNA synthetase 2 precursor						phenylalanyl-tRNA aminoacylation|tRNA processing	mitochondrial matrix|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|tRNA binding				0	Ovarian(93;0.11)	all_hematologic(90;0.0104)			L-Phenylalanine(DB00120)													---	---	---	---
FARS2	10667	broad.mit.edu	37	6	5568611	5568611	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5568611delA	uc010jnv.1	+						FARS2_uc003mwr.2_Intron	NM_006567	NP_006558			phenylalanyl-tRNA synthetase 2 precursor						phenylalanyl-tRNA aminoacylation|tRNA processing	mitochondrial matrix|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|tRNA binding				0	Ovarian(93;0.11)	all_hematologic(90;0.0104)			L-Phenylalanine(DB00120)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	5986002	5986002	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5986002delA								FARS2 (214186 upstream) : NRN1 (12233 downstream)																																			---	---	---	---
F13A1	2162	broad.mit.edu	37	6	6290864	6290864	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6290864delC	uc003mwv.2	-						F13A1_uc011dib.1_Intron	NM_000129	NP_000120			coagulation factor XIII A1 subunit precursor						peptide cross-linking|platelet activation|platelet degranulation	extracellular region|platelet alpha granule lumen	acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|pancreas(1)|skin(1)	6	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)													---	---	---	---
LOC285780	285780	broad.mit.edu	37	6	6469789	6469790	+	Intron	INS	-	CACAA	CACAA	rs142107587	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6469789_6469790insCACAA	uc003mww.3	-						LOC285780_uc003mwx.2_Intron	NR_026970				Homo sapiens cDNA FLJ33708 fis, clone BRAWH2007862.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	6876881	6876881	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6876881delA								LY86 (221665 upstream) : RREB1 (231307 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	7010648	7010648	+	IGR	DEL	A	-	-	rs57570152	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7010648delA								LY86 (355432 upstream) : RREB1 (97540 downstream)																																			---	---	---	---
RREB1	6239	broad.mit.edu	37	6	7130854	7130855	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7130854_7130855delTT	uc003mxc.2	+						RREB1_uc010jnw.2_Intron|RREB1_uc003mxb.2_Intron|RREB1_uc010jnx.2_Intron|RREB1_uc003mxd.2_Intron	NM_001003698	NP_001003698			ras responsive element binding protein 1 isoform						multicellular organismal development|positive regulation of transcription, DNA-dependent|Ras protein signal transduction|transcription from RNA polymerase II promoter	cytoplasm|nuclear speck	DNA binding|zinc ion binding			ovary(4)|large_intestine(2)|pancreas(2)|skin(2)|breast(1)	11	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)																---	---	---	---
RREB1	6239	broad.mit.edu	37	6	7178710	7178710	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7178710delT	uc003mxc.2	+						RREB1_uc010jnw.2_Intron|RREB1_uc003mxb.2_Intron|RREB1_uc010jnx.2_Intron|RREB1_uc003mxd.2_Intron	NM_001003698	NP_001003698			ras responsive element binding protein 1 isoform						multicellular organismal development|positive regulation of transcription, DNA-dependent|Ras protein signal transduction|transcription from RNA polymerase II promoter	cytoplasm|nuclear speck	DNA binding|zinc ion binding			ovary(4)|large_intestine(2)|pancreas(2)|skin(2)|breast(1)	11	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)																---	---	---	---
Unknown	0	broad.mit.edu	37	6	7266717	7266717	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7266717delC								RREB1 (15025 upstream) : SSR1 (14573 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	7506824	7506824	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7506824delA								RIOK1 (88556 upstream) : DSP (35046 downstream)																																			---	---	---	---
DSP	1832	broad.mit.edu	37	6	7542148	7542149	+	Translation_Start_Site	INS	-	A	A	rs151331814	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7542148_7542149insA	uc003mxp.1	+	1					DSP_uc003mxq.1_Translation_Start_Site	NM_004415	NP_004406			desmoplakin isoform I						cellular component disassembly involved in apoptosis|keratinocyte differentiation|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural constituent of cytoskeleton			central_nervous_system(6)|ovary(2)|skin(1)	9	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)														---	---	---	---
DSP	1832	broad.mit.edu	37	6	7565382	7565382	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7565382delA	uc003mxp.1	+						DSP_uc003mxq.1_Intron	NM_004415	NP_004406			desmoplakin isoform I						cellular component disassembly involved in apoptosis|keratinocyte differentiation|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural constituent of cytoskeleton			central_nervous_system(6)|ovary(2)|skin(1)	9	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	7630263	7630263	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7630263delC								SNRNP48 (18064 upstream) : BMP6 (96748 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	8221089	8221089	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8221089delT								EEF1E1 (118261 upstream) : SLC35B3 (190644 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	8495018	8495018	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:8495018delT	uc003mye.2	+											Homo sapiens, clone IMAGE:5539086, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	9063905	9063905	+	IGR	DEL	G	-	-	rs34025693		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9063905delG								HULC (409828 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	9251387	9251388	+	IGR	INS	-	CA	CA	rs5874207		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9251387_9251388insCA								HULC (597310 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	9421716	9421717	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:9421716_9421717insA								HULC (767639 upstream) : TFAP2A (975200 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	10061364	10061364	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10061364delA	uc003myn.2	-						uc010joj.1_Intron|uc003myp.1_Intron					RecName: Full=Orofacial cleft 1 candidate gene 1 protein; AltName: Full=Orofacial clefting chromosomal breakpoint region candidate 1 protein;																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	10099284	10099284	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10099284delT	uc010joj.1	-						uc003myp.1_Intron					Homo sapiens clone 958LR MRDS1 protein (MRDS1) mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	10323114	10323114	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10323114delT								None (None upstream) : TFAP2A (73803 downstream)																																			---	---	---	---
GCNT2	2651	broad.mit.edu	37	6	10534930	10534931	+	Intron	INS	-	A	A	rs55699454		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10534930_10534931insA	uc010joo.2	+						GCNT2_uc010jol.2_Intron|GCNT2_uc010jom.2_Intron|GCNT2_uc010jop.2_Intron|GCNT2_uc003mza.2_Intron|GCNT2_uc003mzc.3_Intron	NM_145649	NP_663624			glucosaminyl (N-acetyl) transferase 2,							Golgi membrane|integral to membrane	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity			ovary(2)	2	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)														---	---	---	---
MAK	4117	broad.mit.edu	37	6	10808864	10808864	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10808864delT	uc003mzl.2	-						SYCP2L_uc011dim.1_Intron|TMEM14B_uc010jos.1_Intron|MAK_uc010jot.2_Intron|MAK_uc010jou.2_Intron|MAK_uc003mzm.2_Intron|MAK_uc010jov.1_Intron	NM_005906	NP_005897			male germ cell-associated kinase						cell differentiation|multicellular organismal development|spermatogenesis		ATP binding|cyclin-dependent protein kinase activity			breast(2)|skin(1)	3	Breast(50;0.107)|Ovarian(93;0.107)	all_hematologic(90;0.117)																---	---	---	---
Unknown	0	broad.mit.edu	37	6	11458840	11458840	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11458840delT	uc003mzy.2	+											Homo sapiens cDNA clone IMAGE:4812340.																														---	---	---	---
C6orf105	84830	broad.mit.edu	37	6	11736202	11736202	+	Intron	DEL	G	-	-	rs75743169	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11736202delG	uc003nab.2	-						C6orf105_uc003naa.2_Intron|C6orf105_uc011dip.1_Intron	NM_032744	NP_116133			hypothetical protein LOC84830 isoform 2							integral to membrane					0	Ovarian(93;0.0848)|Breast(50;0.0871)	all_hematologic(90;0.135)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.193)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	11791691	11791691	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11791691delA								C6orf105 (12411 upstream) : HIVEP1 (221033 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	11944022	11944022	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11944022delA								C6orf105 (164742 upstream) : HIVEP1 (68702 downstream)																																			---	---	---	---
HIVEP1	3096	broad.mit.edu	37	6	12053458	12053459	+	Intron	INS	-	TG	TG	rs143330891	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12053458_12053459insTG	uc003nac.2	+							NM_002114	NP_002105			human immunodeficiency virus type I enhancer						transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)																---	---	---	---
Unknown	0	broad.mit.edu	37	6	12269956	12269956	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12269956delT								HIVEP1 (104725 upstream) : EDN1 (20573 downstream)																																			---	---	---	---
PHACTR1	221692	broad.mit.edu	37	6	13115610	13115611	+	Intron	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13115610_13115611delCT	uc010jpc.2	+						PHACTR1_uc011dir.1_Intron|PHACTR1_uc003nag.1_Intron|PHACTR1_uc003nah.1_Intron	NM_030948	NP_112210			phosphatase and actin regulator 1							cell junction|cytoplasm|synapse	actin binding|protein phosphatase inhibitor activity				0	Breast(50;0.0427)|Ovarian(93;0.12)	all_hematologic(90;0.122)|Lung SC(78;0.195)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239)															---	---	---	---
PHACTR1	221692	broad.mit.edu	37	6	13243824	13243824	+	Intron	DEL	A	-	-	rs71905479		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13243824delA	uc010jpc.2	+						PHACTR1_uc011dir.1_Intron|PHACTR1_uc003nag.1_Intron|PHACTR1_uc003nah.1_Intron	NM_030948	NP_112210			phosphatase and actin regulator 1							cell junction|cytoplasm|synapse	actin binding|protein phosphatase inhibitor activity				0	Breast(50;0.0427)|Ovarian(93;0.12)	all_hematologic(90;0.122)|Lung SC(78;0.195)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	13512565	13512566	+	IGR	DEL	CT	-	-	rs35331551		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13512565_13512566delCT								GFOD1 (24778 upstream) : SIRT5 (62226 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	13547592	13547592	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13547592delT								GFOD1 (59805 upstream) : SIRT5 (27200 downstream)																																			---	---	---	---
NOL7	51406	broad.mit.edu	37	6	13620381	13620381	+	Intron	DEL	A	-	-	rs79413126		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13620381delA	uc003naz.2	+							NM_016167	NP_057251			nucleolar protein 7, 27kDa							mitochondrion|nucleolus					0	Breast(50;0.00669)|Ovarian(93;0.0634)	all_hematologic(90;0.135)	Epithelial(50;0.176)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	14518271	14518271	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14518271delT								CD83 (381125 upstream) : JARID2 (727463 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	14537960	14537960	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14537960delT								CD83 (400814 upstream) : JARID2 (707774 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	15228745	15228745	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15228745delA								None (None upstream) : JARID2 (16989 downstream)																																			---	---	---	---
JARID2	3720	broad.mit.edu	37	6	15250514	15250516	+	Intron	DEL	AGT	-	-	rs3215722		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15250514_15250516delAGT	uc003nbj.2	+						JARID2_uc011diu.1_Intron|JARID2_uc011div.1_Intron|uc003nbk.2_5'Flank	NM_004973	NP_004964			jumonji, AT rich interactive domain 2 protein						central nervous system development|chromatin modification|negative regulation of histone methylation|positive regulation of histone H3-K9 methylation|stem cell differentiation|transcription, DNA-dependent		chromatin binding			ovary(2)|lung(1)|pancreas(1)	4	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)																---	---	---	---
Unknown	0	broad.mit.edu	37	6	15881023	15881023	+	IGR	DEL	T	-	-	rs113665285		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15881023delT								DTNBP1 (217752 upstream) : MYLIP (248294 downstream)																																			---	---	---	---
ATXN1	6310	broad.mit.edu	37	6	16381518	16381519	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:16381518_16381519delAA	uc003nbt.2	-						ATXN1_uc010jpi.2_Intron|ATXN1_uc010jpj.1_Intron	NM_000332	NP_000323			ataxin 1						cell death|negative regulation of transcription, DNA-dependent|nuclear export|RNA processing	cytoplasm|nuclear inclusion body|nuclear matrix|nucleoplasm	identical protein binding|poly(G) RNA binding|poly(U) RNA binding|protein binding|protein C-terminus binding|protein self-association			skin(3)|central_nervous_system(1)	4	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)																---	---	---	---
Unknown	0	broad.mit.edu	37	6	17122559	17122559	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17122559delA								ATXN1 (360838 upstream) : RBM24 (159250 downstream)																																			---	---	---	---
CAP2	10486	broad.mit.edu	37	6	17512628	17512629	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17512628_17512629delAA	uc003ncb.2	+						CAP2_uc010jpk.1_Intron|CAP2_uc011dja.1_Intron|CAP2_uc011djb.1_Intron|CAP2_uc011djc.1_Intron|CAP2_uc011djd.1_Intron	NM_006366	NP_006357			adenylyl cyclase-associated protein 2						activation of adenylate cyclase activity|axon guidance|cytoskeleton organization|establishment or maintenance of cell polarity|signal transduction	plasma membrane	actin binding			ovary(1)	1	Breast(50;0.0333)|Ovarian(93;0.0386)	all_hematologic(90;0.0466)	all cancers(50;0.194)|Epithelial(50;0.227)															---	---	---	---
FAM8A1	51439	broad.mit.edu	37	6	17603123	17603123	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17603123delA	uc003ncc.2	+							NM_016255	NP_057339			family with sequence similarity 8, member A1							integral to membrane					0	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.143)	all cancers(50;0.176)|Epithelial(50;0.204)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	17747649	17747650	+	IGR	INS	-	CTA	CTA			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17747649_17747650insCTA								NUP153 (40831 upstream) : KIF13A (12935 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	17997470	17997470	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17997470delT								KIF13A (9671 upstream) : NHLRC1 (123248 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	18480866	18480866	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18480866delA								RNF144B (12018 upstream) : MIR548A1 (91149 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	19374881	19374882	+	IGR	INS	-	G	G	rs139691723	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19374881_19374882insG								MIR548A1 (802770 upstream) : ID4 (462735 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	19930237	19930237	+	IGR	DEL	G	-	-	rs11327950		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:19930237delG								ID4 (89323 upstream) : MBOAT1 (170698 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	20276590	20276590	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20276590delA								MBOAT1 (63920 upstream) : E2F3 (125547 downstream)																																			---	---	---	---
CDKAL1	54901	broad.mit.edu	37	6	20770318	20770318	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20770318delT	uc003ndc.1	+						CDKAL1_uc003ndd.1_Intron|CDKAL1_uc003nde.1_Intron	NM_017774	NP_060244			CDK5 regulatory subunit associated protein						RNA modification	integral to membrane	4 iron, 4 sulfur cluster binding|metal ion binding|transferase activity			ovary(2)	2	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)															---	---	---	---
CDKAL1	54901	broad.mit.edu	37	6	20944012	20944013	+	Intron	DEL	TT	-	-	rs78778852		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:20944012_20944013delTT	uc003ndc.1	+						CDKAL1_uc003ndd.1_Intron|CDKAL1_uc003nde.1_Intron	NM_017774	NP_060244			CDK5 regulatory subunit associated protein						RNA modification	integral to membrane	4 iron, 4 sulfur cluster binding|metal ion binding|transferase activity			ovary(2)	2	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	21429331	21429332	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21429331_21429332delTT								CDKAL1 (196699 upstream) : SOX4 (164640 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	21606726	21606727	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21606726_21606727delAA								SOX4 (7879 upstream) : FLJ22536 (58276 downstream)																																			---	---	---	---
FLJ22536	401237	broad.mit.edu	37	6	21837753	21837753	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:21837753delT	uc010jpp.1	+						FLJ22536_uc003ndj.2_Intron|FLJ22536_uc011djk.1_Intron|FLJ22536_uc011djj.1_Intron					Homo sapiens cDNA FLJ12803 fis, clone NT2RP2002172.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	23082462	23082463	+	IGR	DEL	GT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:23082462_23082463delGT								HDGFL1 (511713 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	23341195	23341195	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:23341195delA								HDGFL1 (770446 upstream) : NRSN1 (785219 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	23612403	23612404	+	IGR	INS	-	T	T	rs144919364	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:23612403_23612404insT								None (None upstream) : NRSN1 (514010 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	24020430	24020431	+	IGR	DEL	CA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24020430_24020431delCA								None (None upstream) : NRSN1 (105983 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	24066017	24066017	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24066017delA								None (None upstream) : NRSN1 (60397 downstream)																																			---	---	---	---
NRSN1	140767	broad.mit.edu	37	6	24146992	24146992	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24146992delA	uc010jpq.1	+	4						NM_080723	NP_542454			neurensin 1						nervous system development	growth cone|integral to membrane|neuronal cell body|transport vesicle					0																		---	---	---	---
DCDC2	51473	broad.mit.edu	37	6	24356787	24356787	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24356787delA	uc003ndx.2	-						DCDC2_uc003ndy.2_Intron|KAAG1_uc003ndz.1_5'Flank	NM_016356	NP_057440			doublecortin domain containing 2						cellular defense response|intracellular signal transduction|neuron migration					ovary(1)	1		Ovarian(999;0.101)																---	---	---	---
MRS2	57380	broad.mit.edu	37	6	24423946	24423946	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24423946delT	uc003neb.2	+	11					MRS2_uc011djl.1_3'UTR|MRS2_uc011djm.1_RNA|MRS2_uc011djn.1_3'UTR|MRS2_uc003nec.2_3'UTR	NM_020662	NP_065713			MRS2-like, magnesium homeostasis factor						ion transport	integral to membrane|mitochondrial inner membrane					0																		---	---	---	---
KIAA0319	9856	broad.mit.edu	37	6	24576991	24576991	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24576991delA	uc011djo.1	-						KIAA0319_uc011djp.1_Intron|KIAA0319_uc003neh.1_Intron|KIAA0319_uc011djq.1_Intron|KIAA0319_uc011djr.1_Intron|KIAA0319_uc010jpt.1_Intron	NM_014809	NP_055624			KIAA0319 precursor						negative regulation of dendrite development|neuron migration	early endosome membrane|integral to membrane|plasma membrane	protein binding			ovary(1)|skin(1)	2																		---	---	---	---
KIAA0319	9856	broad.mit.edu	37	6	24587509	24587509	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24587509delT	uc011djo.1	-						KIAA0319_uc011djp.1_Intron|KIAA0319_uc003neh.1_Intron|KIAA0319_uc011djq.1_Intron|KIAA0319_uc011djr.1_Intron	NM_014809	NP_055624			KIAA0319 precursor						negative regulation of dendrite development|neuron migration	early endosome membrane|integral to membrane|plasma membrane	protein binding			ovary(1)|skin(1)	2																		---	---	---	---
FAM65B	9750	broad.mit.edu	37	6	24819748	24819748	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24819748delT	uc003neo.1	-						FAM65B_uc011djs.1_Intron	NM_014722	NP_055537			hypothetical protein LOC9750 isoform 1						cell differentiation|muscle organ development	cytoskeleton|filopodium|mitochondrion	binding			ovary(1)	1																		---	---	---	---
LRRC16A	55604	broad.mit.edu	37	6	25373444	25373444	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25373444delT	uc011djw.1	+						LRRC16A_uc010jpx.2_Intron|LRRC16A_uc010jpy.2_Intron	NM_017640	NP_060110			leucine rich repeat containing 16A						actin filament organization|blood coagulation|cell migration|lamellipodium assembly|ruffle organization|urate metabolic process	cytosol|lamellipodium|nucleus				ovary(1)|breast(1)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
LRRC16A	55604	broad.mit.edu	37	6	25469760	25469761	+	Intron	INS	-	TG	TG	rs35568793		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25469760_25469761insTG	uc011djw.1	+						LRRC16A_uc010jpx.2_Intron|LRRC16A_uc010jpy.2_Intron|LRRC16A_uc003nez.1_Intron	NM_017640	NP_060110			leucine rich repeat containing 16A						actin filament organization|blood coagulation|cell migration|lamellipodium assembly|ruffle organization|urate metabolic process	cytosol|lamellipodium|nucleus				ovary(1)|breast(1)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	25624439	25624440	+	IGR	INS	-	AGCTATGCAGTGTTTGCATC	AGCTATGCAGTGTTTGCATC	rs138656942	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25624439_25624440insAGCTATGCAGTGTTTGCATC								LRRC16A (3683 upstream) : SCGN (27989 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	26047966	26047967	+	IGR	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26047966_26047967delAG								HIST1H3C (1870 upstream) : HIST1H1C (8002 downstream)																																			---	---	---	---
BTN1A1	696	broad.mit.edu	37	6	26503420	26503420	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26503420delA	uc003nif.3	+							NM_001732	NP_001723			butyrophilin, subfamily 1, member A1 precursor							extracellular region|integral to plasma membrane	receptor activity			ovary(1)|skin(1)	2																		---	---	---	---
HMGN4	10473	broad.mit.edu	37	6	26540568	26540570	+	Intron	DEL	TTC	-	-	rs61577337		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26540568_26540570delTTC	uc003nig.2	+							NM_006353	NP_006344			high mobility group nucleosomal binding domain							chromatin|nucleus	DNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	26601356	26601356	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26601356delT	uc010jqm.1	+											Homo sapiens cDNA clone IMAGE:4830894.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	26745342	26745342	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26745342delC								ZNF322A (85379 upstream) : GUSBL1 (93924 downstream)																																			---	---	---	---
FKSG83	83954	broad.mit.edu	37	6	27289807	27289808	+	5'Flank	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27289807_27289808delAC	uc010jqt.2	+						FKSG83_uc010jqs.1_5'Flank	NM_032030	NP_114419			FKSG83							integral to membrane	pheromone receptor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	27694040	27694050	+	IGR	DEL	TGACTATATTC	-	-	rs67869107		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27694040_27694050delTGACTATATTC								ZNF184 (253143 upstream) : HIST1H2BL (81208 downstream)																																			---	---	---	---
HIST1H4K	8362	broad.mit.edu	37	6	27799470	27799470	+	5'Flank	DEL	A	-	-	rs71559051		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27799470delA	uc003njr.2	-							NM_003541	NP_003532			histone cluster 1, H4k						CenH3-containing nucleosome assembly at centromere|negative regulation of megakaryocyte differentiation|phosphatidylinositol-mediated signaling|telomere maintenance	nucleoplasm|nucleosome	DNA binding|protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	28011941	28011941	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28011941delA								OR2B6 (85983 upstream) : ZNF165 (34631 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	28334701	28334702	+	5'Flank	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28334701_28334702delTT	uc010jrd.2	+											Homo sapiens chromosome 15 open reading frame 40, mRNA (cDNA clone IMAGE:5141794), **** WARNING: chimeric clone ****.																														---	---	---	---
ZSCAN12	9753	broad.mit.edu	37	6	28358666	28358666	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28358666delT	uc011dlh.1	-	4	1580	c.1401delA	c.(1399-1401)AAAfs	p.K467fs	ZSCAN12_uc010jre.2_Frame_Shift_Del_p.K467fs	NM_001163391	NP_001156863			zinc finger and SCAN domain containing 12												0																		---	---	---	---
ZSCAN23	222696	broad.mit.edu	37	6	28403542	28403542	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28403542delA	uc003nli.3	-						ZSCAN23_uc003nlh.2_Intron|ZSCAN23_uc010jrf.1_Intron|ZSCAN23_uc011dli.1_Intron	NM_001012455	NP_001012458			zinc finger protein 390						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	29245853	29245853	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29245853delA								OR2J2 (103503 upstream) : OR14J1 (28614 downstream)																																			---	---	---	---
TRIM26	7726	broad.mit.edu	37	6	30157254	30157254	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30157254delT	uc003npr.2	-	7	1054	c.845delA	c.(844-846)AAGfs	p.K282fs	TRIM26_uc003nps.2_Frame_Shift_Del_p.K282fs|TRIM26_uc010jry.2_5'UTR|TRIM26_uc003npt.2_Frame_Shift_Del_p.K282fs	NM_003449	NP_003440	Q12899	TRI26_HUMAN	tripartite motif-containing 26	282							DNA binding|zinc ion binding			ovary(2)|lung(1)	3																		---	---	---	---
HCG18	414777	broad.mit.edu	37	6	30261975	30261976	+	Intron	INS	-	C	C	rs150055200	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30261975_30261976insC	uc003npw.2	-						HCG18_uc003npx.2_Intron|HCG18_uc003npy.2_Intron					Homo sapiens cDNA FLJ13272 fis, clone OVARC1001004.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	30444279	30444279	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30444279delA								TRIM39 (129647 upstream) : HLA-E (12992 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	30964398	30964398	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30964398delC								MUC21 (6723 upstream) : HCG22 (57586 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	31410118	31410118	+	IGR	DEL	G	-	-	rs112344639		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31410118delG								MICA (27028 upstream) : HCP5 (20839 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	31572571	31572571	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31572571delA								NCR3 (11809 upstream) : AIF1 (10423 downstream)																																			---	---	---	---
MSH5	4439	broad.mit.edu	37	6	31708750	31708750	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31708750delA	uc003nwv.1	+						MSH5_uc003nwt.1_Intron|MSH5_uc003nwu.1_Intron|MSH5_uc003nww.1_Intron|MSH5_uc003nwx.1_Intron	NM_172166	NP_751898			mutS homolog 5 isoform c						chiasma assembly|homologous chromosome segregation|meiotic prophase II|mismatch repair|reciprocal meiotic recombination	synaptonemal complex	ATP binding|DNA-dependent ATPase activity|mismatched DNA binding			ovary(2)|breast(1)	3													Direct_reversal_of_damage|MMR					---	---	---	---
MSH5	4439	broad.mit.edu	37	6	31709163	31709163	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31709163delT	uc003nwv.1	+						MSH5_uc003nwt.1_Intron|MSH5_uc003nwu.1_Intron|MSH5_uc003nww.1_Intron|MSH5_uc003nwx.1_Intron	NM_172166	NP_751898			mutS homolog 5 isoform c						chiasma assembly|homologous chromosome segregation|meiotic prophase II|mismatch repair|reciprocal meiotic recombination	synaptonemal complex	ATP binding|DNA-dependent ATPase activity|mismatched DNA binding			ovary(2)|breast(1)	3													Direct_reversal_of_damage|MMR					---	---	---	---
LSM2	57819	broad.mit.edu	37	6	31765402	31765402	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31765402delA	uc003nxg.2	-	5					VARS_uc003nxe.2_5'Flank|VARS_uc011doi.1_5'Flank	NM_021177	NP_067000			LSM2 homolog, U6 small nuclear RNA associated						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|cytosol|nucleoplasm	U6 snRNA binding				0																		---	---	---	---
EHMT2	10919	broad.mit.edu	37	6	31864887	31864887	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31864887delC	uc003nxz.1	-						EHMT2_uc003nxy.1_5'Flank|EHMT2_uc011don.1_Frame_Shift_Del_p.G31fs|EHMT2_uc003nya.1_Intron|EHMT2_uc003nyb.1_Intron|C2_uc003nyc.2_5'Flank|C2_uc011doo.1_5'Flank	NM_006709	NP_006700			euchromatic histone-lysine N-methyltransferase 2						DNA methylation|peptidyl-lysine dimethylation	chromosome|nucleus	histone methyltransferase activity (H3-K27 specific)|histone methyltransferase activity (H3-K9 specific)|p53 binding|zinc ion binding			ovary(1)	1																		---	---	---	---
STK19	8859	broad.mit.edu	37	6	31947410	31947411	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31947410_31947411insT	uc003nyv.2	+						STK19_uc003nyt.2_Intron|STK19_uc011dox.1_Intron|STK19_uc003nyw.2_Intron|STK19_uc010jtn.1_Intron|C4A_uc011doy.1_5'Flank|C4A_uc011doz.1_5'Flank	NM_032454	NP_115830			serine/threonine kinase 19 isoform 2							nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			skin(4)	4																		---	---	---	---
NOTCH4	4855	broad.mit.edu	37	6	32173814	32173814	+	Intron	DEL	A	-	-	rs148768186		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32173814delA	uc003obb.2	-						NOTCH4_uc003oba.2_5'Flank|NOTCH4_uc011dpu.1_Intron|NOTCH4_uc011dpv.1_Intron	NM_004557	NP_004548			notch4 preproprotein						cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|protein heterodimerization activity|receptor activity			lung(8)|ovary(5)|breast(4)|central_nervous_system(3)|upper_aerodigestive_tract(1)|skin(1)	22																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	32223856	32223856	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32223856delT	uc003obd.1	+											Homo sapiens cDNA FLJ40408 fis, clone TESTI2037673.																														---	---	---	---
HLA-DRB5	3127	broad.mit.edu	37	6	32497617	32497617	+	Intron	DEL	A	-	-	rs67587376		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32497617delA	uc003obj.2	-						HLA-DRB1_uc011dqa.1_Intron|HLA-DRB5_uc003obk.3_Intron	NM_002125	NP_002116			major histocompatibility complex, class II, DR						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex					0																		---	---	---	---
HLA-DRB5	3127	broad.mit.edu	37	6	32550372	32550372	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32550372delC	uc003obk.3	-						HLA-DRB1_uc011dqa.1_Intron|HLA-DRB6_uc003obo.1_Intron|HLA-DRB1_uc003obp.3_Intron|HLA-DRB1_uc011dqb.1_5'Flank|HLA-DRB1_uc011dqc.1_Intron	NM_002125	NP_002116			major histocompatibility complex, class II, DR						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex					0																		---	---	---	---
HLA-DQA1	3117	broad.mit.edu	37	6	32608936	32608937	+	Intron	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32608936_32608937insG	uc003obr.2	+						HLA-DQA1_uc003obs.2_Intron|HLA-DQA1_uc003obt.1_Intron|HLA-DQA1_uc003obu.2_5'Flank	NM_002122	NP_002113			major histocompatibility complex, class II, DQ						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway	endoplasmic reticulum membrane|endosome membrane|Golgi apparatus|integral to plasma membrane|lysosomal membrane|MHC class II protein complex	MHC class II receptor activity				0																		---	---	---	---
HLA-DQB1	3119	broad.mit.edu	37	6	32628605	32628605	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32628605delT	uc003obw.2	-						HLA-DQB1_uc010juc.1_Intron|HLA-DQB1_uc003obv.2_Intron|HLA-DQB1_uc011dqd.1_Intron	NM_002123	NP_002114			major histocompatibility complex, class II, DQ						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway	endoplasmic reticulum membrane|endosome membrane|Golgi apparatus|integral to membrane|lysosomal membrane|MHC class II protein complex	MHC class II receptor activity				0					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)									Melanoma_Familial_Clustering_of|ACTH-independent_macronodular_adrenal_hyperplasia|T-cell_Lymphoma_(Cutaneous)__Familial_Clustering_of|Sj_gren_syndrome				---	---	---	---
HLA-DQB2	3120	broad.mit.edu	37	6	32723961	32723961	+	3'UTR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32723961delG	uc003oby.3	-	5					HLA-DQB2_uc003obz.2_3'UTR	NR_003937				SubName: Full=Major histocompatibility complex, class II, DQ beta 2; SubName: Full=Putative uncharacterized protein ENSP00000372579;						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response	integral to membrane|MHC class II protein complex					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	32761083	32761083	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32761083delT								HLA-DQB2 (29753 upstream) : HLA-DOB (19458 downstream)																																			---	---	---	---
HLA-DOB	3112	broad.mit.edu	37	6	32784740	32784741	+	5'UTR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32784740_32784741insA	uc003oca.2	-	1					TAP2_uc011dqf.1_Intron|HLA-DOB_uc011dqg.1_5'UTR	NM_002120	NP_002111			major histocompatibility complex, class II, DO						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway	endosome membrane|integral to membrane|lysosomal membrane|MHC class II protein complex	MHC class II receptor activity			skin(1)	1																		---	---	---	---
TAP2	6891	broad.mit.edu	37	6	32790111	32790111	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32790111delA	uc011dqf.1	-						TAP2_uc003ocb.1_Intron	NM_018833	NP_061313			transporter 2, ATP-binding cassette, sub-family						antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent|cytosol to ER transport|intracellular transport of viral proteins in host cell|peptide antigen transport|positive regulation of antigen processing and presentation of peptide antigen via MHC class I|positive regulation of T cell mediated cytotoxicity	nucleus|plasma membrane|TAP complex	ATP binding|MHC class I protein binding|oligopeptide-transporting ATPase activity|peptide antigen binding|peptide antigen-transporting ATPase activity|TAP1 binding|TAP2 binding|tapasin binding				0																		---	---	---	---
TAP1	6890	broad.mit.edu	37	6	32814594	32814596	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32814594_32814596delAAA	uc003ocg.2	-						PSMB8_uc003oce.2_5'Flank|PSMB8_uc003ocf.2_5'Flank|PSMB8_uc011dqh.1_5'Flank|TAP1_uc011dqi.1_Intron	NM_000593	NP_000584			transporter 1, ATP-binding cassette, sub-family						antigen processing and presentation of endogenous peptide antigen via MHC class I|cytosol to ER transport|intracellular transport of viral proteins in host cell|positive regulation of T cell mediated cytotoxicity	cytosol|plasma membrane|TAP complex	ADP binding|ATP binding|MHC class I protein binding|oligopeptide-transporting ATPase activity|peptide antigen binding|protein homodimerization activity|TAP1 binding|TAP2 binding|tapasin binding			skin(1)	1																		---	---	---	---
HLA-DOA	3111	broad.mit.edu	37	6	32973986	32973986	+	3'UTR	DEL	A	-	-	rs34809248		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32973986delA	uc003ocr.2	-	5					HLA-DOA_uc010juj.2_3'UTR	NM_002119	NP_002110			major histocompatibility complex, class II, DO						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway	endosome membrane|integral to membrane|lysosomal membrane|MHC class II protein complex	MHC class II receptor activity				0																		---	---	---	---
SYNGAP1	8831	broad.mit.edu	37	6	33402719	33402720	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33402719_33402720delAA	uc011dri.1	+						SYNGAP1_uc003oeo.1_Intron|SYNGAP1_uc010juy.2_Intron|SYNGAP1_uc010juz.2_5'Flank	NM_006772	NP_006763			synaptic Ras GTPase activating protein 1						negative regulation of Ras protein signal transduction|signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	Ras GTPase activator activity|SH3 domain binding			ovary(4)	4																		---	---	---	---
IP6K3	117283	broad.mit.edu	37	6	33697423	33697423	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33697423delC	uc010jvf.2	-						IP6K3_uc003ofb.2_Intron	NM_001142883	NP_001136355			inositol hexakisphosphate kinase 3						inositol phosphate biosynthetic process|phosphatidylinositol metabolic process|protein phosphorylation	cytoplasm	ATP binding|inositol hexakisphosphate 5-kinase activity|inositol hexakisphosphate 6-kinase activity|inositol trisphosphate 3-kinase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	33880757	33880757	+	RNA	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33880757delA	uc003oin.2	+	1		c.1879delA								Homo sapiens mRNA; cDNA DKFZp434D1229 (from clone DKFZp434D1229).																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	33895108	33895108	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33895108delC								MLN (123315 upstream) : MIR1275 (72641 downstream)																																			---	---	---	---
GRM4	2914	broad.mit.edu	37	6	34110602	34110602	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34110602delG	uc010jvh.2	-						GRM4_uc010jvi.2_Intron	NM_000841	NP_000832			glutamate receptor, metabotropic 4 precursor						activation of MAPK activity|inhibition of adenylate cyclase activity by metabotropic glutamate receptor signaling pathway|neuroprotection|neurotransmitter secretion|positive regulation of MAPKKK cascade	cytoplasmic vesicle|integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(3)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	6					L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	34169156	34169156	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34169156delA								GRM4 (55287 upstream) : HMGA1 (35421 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	34194162	34194162	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34194162delA								GRM4 (80293 upstream) : HMGA1 (10415 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	34231770	34231770	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34231770delA								C6orf1 (14866 upstream) : NUDT3 (24232 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	34253086	34253087	+	IGR	INS	-	AC	AC	rs146090719	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34253086_34253087insAC								C6orf1 (36182 upstream) : NUDT3 (2915 downstream)																																			---	---	---	---
TCP11	6954	broad.mit.edu	37	6	35089680	35089680	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35089680delG	uc003okd.2	-						TCP11_uc003ojz.1_Intron|TCP11_uc003oka.2_Intron|TCP11_uc003okb.2_Intron|TCP11_uc003okc.2_Intron|TCP11_uc011dsu.1_Intron|TCP11_uc011dsv.1_Intron|TCP11_uc011dsw.1_Intron	NM_001093728	NP_001087197			t-complex 11 isoform 1						cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane				ovary(3)|skin(2)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	35135664	35135664	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35135664delT								TCP11 (26477 upstream) : SCUBE3 (46526 downstream)																																			---	---	---	---
SCUBE3	222663	broad.mit.edu	37	6	35188462	35188462	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35188462delC	uc003okf.1	+						SCUBE3_uc003okg.1_Intron	NM_152753	NP_689966			signal peptide, CUB domain, EGF-like 3						protein heterooligomerization|protein homooligomerization	cell surface|extracellular region	calcium ion binding|protein binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	35900324	35900324	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35900324delA								SRPK1 (11368 upstream) : SLC26A8 (10971 downstream)																																			---	---	---	---
SLC26A8	116369	broad.mit.edu	37	6	35957678	35957682	+	Intron	DEL	TTTTG	-	-	rs2395647		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35957678_35957682delTTTTG	uc003olm.2	-						SLC26A8_uc003oln.2_Intron|SLC26A8_uc003oll.2_Intron	NM_052961	NP_443193			solute carrier family 26, member 8 isoform a						cell differentiation|meiosis|multicellular organismal development|spermatogenesis	integral to membrane|plasma membrane	anion:anion antiporter activity|chloride channel activity|oxalate transmembrane transporter activity|protein binding|sulfate transmembrane transporter activity			ovary(2)	2																		---	---	---	---
BRPF3	27154	broad.mit.edu	37	6	36196481	36196481	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36196481delA	uc003olv.3	+						BRPF3_uc010jwb.2_Intron|BRPF3_uc011dtj.1_Intron|BRPF3_uc010jwc.2_Intron|BRPF3_uc011dtk.1_Intron|BRPF3_uc010jwd.2_Intron	NM_015695	NP_056510			bromodomain and PHD finger containing, 3						histone H3 acetylation|platelet activation|platelet degranulation	cytosol|extracellular region|MOZ/MORF histone acetyltransferase complex	protein binding|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	36392697	36392697	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36392697delA								PXT1 (24386 upstream) : KCTD20 (17847 downstream)																																			---	---	---	---
KCTD20	222658	broad.mit.edu	37	6	36428093	36428093	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36428093delT	uc003ome.2	+						KCTD20_uc011dtm.1_Intron|KCTD20_uc011dtn.1_Intron|KCTD20_uc010jwk.2_Intron|KCTD20_uc011dto.1_Intron	NM_173562	NP_775833			potassium channel tetramerisation domain							voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	36459252	36459252	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36459252delA								KCTD20 (939 upstream) : STK38 (2422 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	36692954	36692954	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36692954delT								CDKN1A (37846 upstream) : CPNE5 (15601 downstream)																																			---	---	---	---
CPNE5	57699	broad.mit.edu	37	6	36761982	36761983	+	Intron	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36761982_36761983insG	uc003omr.1	-						CPNE5_uc003oms.1_Intron	NM_020939	NP_065990			copine V											skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	36917671	36917672	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36917671_36917672delTT								C6orf89 (20933 upstream) : PI16 (4537 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	37014746	37014746	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37014746delT								FGD2 (17901 upstream) : PIM1 (123176 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	37040381	37040381	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37040381delA								FGD2 (43536 upstream) : PIM1 (97541 downstream)																																			---	---	---	---
PIM1	5292	broad.mit.edu	37	6	37140059	37140059	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37140059delT	uc003onk.2	+						PIM1_uc011dtw.1_5'Flank	NM_002648	NP_002639			non-specific serine/threonine protein kinase						cell cycle|cell proliferation|multicellular organismal development|negative regulation of apoptosis|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|protein autophosphorylation	cytoplasm|nucleus|plasma membrane	ATP binding|manganese ion binding|protein binding|protein binding|protein serine/threonine kinase activity|transcription factor binding			large_intestine(1)|central_nervous_system(1)	2			OV - Ovarian serous cystadenocarcinoma(102;0.241)		Adenosine monophosphate(DB00131)			T	BCL6	NHL						OREG0017397	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
RNF8	9025	broad.mit.edu	37	6	37319934	37319934	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37319934delT	uc003onq.3	+						RNF8_uc003onr.3_5'Flank|RNF8_uc011dtx.1_5'Flank	NM_003958	NP_003949			ring finger protein 8 isoform 1						cell division|double-strand break repair|histone H2A ubiquitination|histone H2B ubiquitination|mitosis|positive regulation of DNA repair|response to ionizing radiation	midbody|nucleus|ubiquitin ligase complex	chromatin binding|histone binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1																		---	---	---	---
RNF8	9025	broad.mit.edu	37	6	37320361	37320362	+	5'Flank	INS	-	AGAA	AGAA	rs72031950		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37320361_37320362insAGAA	uc003onq.3	+						RNF8_uc003onr.3_5'Flank|RNF8_uc011dtx.1_5'Flank	NM_003958	NP_003949			ring finger protein 8 isoform 1						cell division|double-strand break repair|histone H2A ubiquitination|histone H2B ubiquitination|mitosis|positive regulation of DNA repair|response to ionizing radiation	midbody|nucleus|ubiquitin ligase complex	chromatin binding|histone binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	37522566	37522566	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37522566delG								C6orf129 (54866 upstream) : MDGA1 (77718 downstream)																																			---	---	---	---
ZFAND3	60685	broad.mit.edu	37	6	37805283	37805286	+	Intron	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37805283_37805286delTTTT	uc003onx.2	+							NM_021943	NP_068762			zinc finger, AN1-type domain 3								DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	38130599	38130599	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38130599delT								ZFAND3 (8202 upstream) : BTBD9 (5629 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	38135841	38135841	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38135841delA								ZFAND3 (13444 upstream) : BTBD9 (387 downstream)																																			---	---	---	---
BTBD9	114781	broad.mit.edu	37	6	38435695	38435696	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38435695_38435696insT	uc003ooa.3	-						BTBD9_uc003ony.3_Intron|BTBD9_uc010jwv.2_Intron|BTBD9_uc010jww.2_Intron|BTBD9_uc010jwx.2_Intron	NM_052893	NP_443125			BTB (POZ) domain containing 9 isoform a						cell adhesion						0																		---	---	---	---
DNAH8	1769	broad.mit.edu	37	6	38703906	38703906	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38703906delA	uc003ooe.1	+							NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21																		---	---	---	---
DNAH8	1769	broad.mit.edu	37	6	38941356	38941356	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38941356delA	uc003ooe.1	+						DNAH8_uc003oog.1_Intron	NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21																		---	---	---	---
DNAH8	1769	broad.mit.edu	37	6	38947352	38947352	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38947352delT	uc003ooe.1	+						DNAH8_uc003oog.1_Intron	NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	39245377	39245378	+	IGR	DEL	GG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39245377_39245378delGG								KCNK5 (48126 upstream) : KCNK17 (21400 downstream)																																			---	---	---	---
KIF6	221458	broad.mit.edu	37	6	39422108	39422108	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39422108delC	uc003oot.2	-						KIF6_uc010jwz.1_Intron|KIF6_uc010jxa.1_Intron|KIF6_uc011dua.1_Intron|KIF6_uc010jxb.1_Intron	NM_145027	NP_659464			kinesin family member 6						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity|protein binding			breast(2)|central_nervous_system(1)	3																		---	---	---	---
KIF6	221458	broad.mit.edu	37	6	39602474	39602474	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39602474delA	uc003oot.2	-						KIF6_uc010jxa.1_Intron|KIF6_uc011dua.1_Intron|KIF6_uc010jxb.1_Intron	NM_145027	NP_659464			kinesin family member 6						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity|protein binding			breast(2)|central_nervous_system(1)	3																		---	---	---	---
DAAM2	23500	broad.mit.edu	37	6	39810609	39810609	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39810609delG	uc003oow.2	+						DAAM2_uc010jxc.2_Intron|DAAM2_uc003oox.2_Intron|DAAM2_uc003oov.3_Intron	NM_015345	NP_056160			dishevelled associated activator of						actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)|skin(1)	3	Ovarian(28;0.0355)|Colorectal(47;0.196)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	40350934	40350935	+	IGR	DEL	TT	-	-	rs16863	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40350934_40350935delTT								TDRG1 (3303 upstream) : LRFN2 (8438 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	40606421	40606423	+	IGR	DEL	GAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40606421_40606423delGAA								LRFN2 (51295 upstream) : UNC5CL (388349 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	40806493	40806493	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40806493delA								LRFN2 (251367 upstream) : UNC5CL (188279 downstream)																																			---	---	---	---
USP49	25862	broad.mit.edu	37	6	41823253	41823253	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41823253delA	uc003ori.2	-							NM_018561	NP_061031			ubiquitin thioesterase 49						ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Ovarian(28;0.0919)|Colorectal(47;0.121)		STAD - Stomach adenocarcinoma(11;0.000204)|Epithelial(12;0.000309)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)															---	---	---	---
USP49	25862	broad.mit.edu	37	6	41860001	41860001	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41860001delA	uc003ori.2	-							NM_018561	NP_061031			ubiquitin thioesterase 49						ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Ovarian(28;0.0919)|Colorectal(47;0.121)		STAD - Stomach adenocarcinoma(11;0.000204)|Epithelial(12;0.000309)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	42171360	42171361	+	IGR	DEL	AA	-	-	rs34442150		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42171360_42171361delAA								GUCA1B (8666 upstream) : MRPS10 (3179 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	42518615	42518615	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42518615delA								TRERF1 (98750 upstream) : UBR2 (13443 downstream)																																			---	---	---	---
PRPH2	5961	broad.mit.edu	37	6	42671818	42671819	+	Intron	DEL	AC	-	-	rs147103337		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42671818_42671819delAC	uc003osk.2	-							NM_000322	NP_000313			peripherin 2						cell adhesion|visual perception	integral to membrane				ovary(4)|central_nervous_system(1)	5	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.00178)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0904)															---	---	---	---
KIAA0240	23506	broad.mit.edu	37	6	42756630	42756630	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42756630delT	uc003osn.1	+						KIAA0240_uc003osm.1_Intron|KIAA0240_uc011duw.1_Intron	NM_015349	NP_056164			hypothetical protein LOC23506											ovary(1)	1	Colorectal(47;0.196)		Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|all cancers(41;0.00524)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.104)															---	---	---	---
PTK7	5754	broad.mit.edu	37	6	43126042	43126043	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43126042_43126043delAA	uc003oub.1	+						PTK7_uc003ouc.1_Intron|PTK7_uc003oud.1_Intron|PTK7_uc003oue.1_Intron|PTK7_uc003ouf.1_Intron|PTK7_uc003oug.1_Intron|PTK7_uc011dve.1_Intron|PTK7_uc010jyj.1_Intron|PTK7_uc003ouh.1_5'Flank	NM_002821	NP_002812			PTK7 protein tyrosine kinase 7 isoform a						actin cytoskeleton reorganization|canonical Wnt receptor signaling pathway|cell adhesion|cell migration	cell-cell junction|integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			ovary(2)|large_intestine(1)	3			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)															---	---	---	---
ZNF318	24149	broad.mit.edu	37	6	43310013	43310013	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43310013delT	uc003oux.2	-						ZNF318_uc003ouw.2_Intron	NM_014345	NP_055160			zinc finger protein 318						meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	nucleic acid binding|zinc ion binding			ovary(3)|breast(2)|central_nervous_system(1)|skin(1)	7			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)															---	---	---	---
TJAP1	93643	broad.mit.edu	37	6	43444924	43444924	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43444924delA	uc003ovd.2	+						TJAP1_uc003ovf.2_5'Flank|TJAP1_uc003ove.2_5'Flank|TJAP1_uc003ovc.2_5'Flank|TJAP1_uc010jyp.2_5'Flank|TJAP1_uc011dvh.1_5'Flank	NM_001146016	NP_001139488			tight junction associated protein 1 isoform a							Golgi apparatus|tight junction	protein binding				0	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0122)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)															---	---	---	---
TJAP1	93643	broad.mit.edu	37	6	43459037	43459038	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43459037_43459038insT	uc003ovd.2	+						TJAP1_uc003ovf.2_Intron|TJAP1_uc003ove.2_Intron|TJAP1_uc003ovc.2_Intron|TJAP1_uc010jyp.2_Intron|TJAP1_uc011dvh.1_Intron|TJAP1_uc003ovg.2_Intron|TJAP1_uc010jyq.2_Intron|TJAP1_uc011dvi.1_Intron	NM_001146016	NP_001139488			tight junction associated protein 1 isoform a							Golgi apparatus|tight junction	protein binding				0	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0122)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)															---	---	---	---
XPO5	57510	broad.mit.edu	37	6	43528049	43528049	+	Intron	DEL	A	-	-	rs74544728		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43528049delA	uc003ovp.2	-							NM_020750	NP_065801			exportin 5						gene silencing by RNA	cytosol|nucleoplasm	protein binding|tRNA binding			skin(2)|breast(1)|kidney(1)	4	all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243)		all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	43816824	43816825	+	Intron	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43816824_43816825delGA	uc003owl.1	-											Homo sapiens cDNA FLJ40534 fis, clone TESTI2047824.																														---	---	---	---
LOC100132354	100132354	broad.mit.edu	37	6	43858104	43858104	+	5'Flank	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43858104delG	uc011dvm.1	+							NR_024478				Homo sapiens cDNA FLJ38229 fis, clone FCBBF2004256.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	43940371	43940372	+	IGR	INS	-	G	G	rs145492668	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43940371_43940372insG								LOC100132354 (34428 upstream) : C6orf223 (27967 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	44455408	44455409	+	IGR	INS	-	T	T	rs148352915	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44455408_44455409insT								CDC5L (40629 upstream) : SUPT3H (321645 downstream)																																			---	---	---	---
SUPT3H	8464	broad.mit.edu	37	6	45235569	45235569	+	Intron	DEL	C	-	-	rs113477245		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45235569delC	uc003oxo.2	-						SUPT3H_uc003oxn.1_Intron|SUPT3H_uc011dvv.1_Intron|SUPT3H_uc003oxp.2_Intron	NM_181356	NP_852001			suppressor of Ty 3 homolog isoform 2						histone deubiquitination|histone H3 acetylation|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	STAGA complex|transcription factor TFTC complex	DNA binding|transcription coactivator activity			ovary(2)|breast(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	45765840	45765841	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45765840_45765841delAA								RUNX2 (247022 upstream) : CLIC5 (100349 downstream)																																			---	---	---	---
CLIC5	53405	broad.mit.edu	37	6	45931390	45931390	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45931390delA	uc003oxv.3	-						CLIC5_uc003oxu.3_Intron|CLIC5_uc003oxx.2_Intron	NM_001114086	NP_001107558			chloride intracellular channel 5 isoform a						female pregnancy	actin cytoskeleton|cell cortex|chloride channel complex|Golgi apparatus|Golgi apparatus|insoluble fraction|microtubule organizing center	protein binding|voltage-gated chloride channel activity			ovary(1)|skin(1)	2																		---	---	---	---
CLIC5	53405	broad.mit.edu	37	6	45974192	45974192	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:45974192delT	uc003oxv.3	-						CLIC5_uc003oxu.3_Intron|CLIC5_uc003oxx.2_Intron	NM_001114086	NP_001107558			chloride intracellular channel 5 isoform a						female pregnancy	actin cytoskeleton|cell cortex|chloride channel complex|Golgi apparatus|Golgi apparatus|insoluble fraction|microtubule organizing center	protein binding|voltage-gated chloride channel activity			ovary(1)|skin(1)	2																		---	---	---	---
PLA2G7	7941	broad.mit.edu	37	6	46682474	46682474	+	Intron	DEL	T	-	-	rs71984523		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46682474delT	uc010jzf.2	-						PLA2G7_uc010jzg.1_Intron|PLA2G7_uc011dwd.1_Intron|PLA2G7_uc011dwe.1_Intron	NM_005084	NP_005075			phospholipase A2, group VII						inflammatory response|lipid catabolic process	extracellular space	1-alkyl-2-acetylglycerophosphocholine esterase activity|phospholipid binding				0			Lung(136;0.192)															---	---	---	---
GPR110	266977	broad.mit.edu	37	6	46985429	46985430	+	Intron	DEL	AA	-	-	rs34535266		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46985429_46985430delAA	uc003oyt.2	-						GPR110_uc011dwl.1_Intron	NM_153840	NP_722582			G-protein coupled receptor 110 isoform 1						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
TNFRSF21	27242	broad.mit.edu	37	6	47219101	47219101	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47219101delA	uc003oyv.2	-							NM_014452	NP_055267			tumor necrosis factor receptor superfamily,						cellular lipid metabolic process	cytoplasm|integral to membrane	protein binding|receptor activity				0			Lung(136;0.189)															---	---	---	---
GPR115	221393	broad.mit.edu	37	6	47684723	47684723	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:47684723delA	uc003oza.1	+						GPR115_uc003oyz.1_Intron|GPR115_uc003ozb.1_Intron	NM_153838	NP_722580			G-protein coupled receptor 115 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(3)|skin(3)|upper_aerodigestive_tract(1)|breast(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	49241176	49241176	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49241176delT								None (None upstream) : MUT (157818 downstream)																																			---	---	---	---
CENPQ	55166	broad.mit.edu	37	6	49440769	49440769	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49440769delA	uc003ozh.1	+							NM_018132	NP_060602			centromere protein Q						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	chromosome, centromeric region|cytosol|nucleoplasm				ovary(2)	2	Lung NSC(77;0.0128)																	---	---	---	---
CRISP3	10321	broad.mit.edu	37	6	49701364	49701364	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49701364delT	uc003ozs.2	-							NM_006061	NP_006052			cysteine-rich secretory protein 3 precursor						innate immune response	proteinaceous extracellular matrix|specific granule				skin(2)	2	Lung NSC(77;0.0161)		KIRC - Kidney renal clear cell carcinoma(2;0.106)|Kidney(12;0.156)															---	---	---	---
CRISP1	167	broad.mit.edu	37	6	49808537	49808537	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49808537delA	uc003ozw.2	-						CRISP1_uc003ozx.2_Intron	NM_001131	NP_001122			acidic epididymal glycoprotein-like 1 isoform 1						fusion of sperm to egg plasma membrane	extracellular space					0	Lung NSC(77;0.0358)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	50245481	50245481	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50245481delT								DEFB112 (229117 upstream) : TFAP2D (435776 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	50421081	50421081	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50421081delA								DEFB112 (404717 upstream) : TFAP2D (260176 downstream)																																			---	---	---	---
TFAP2B	7021	broad.mit.edu	37	6	50798223	50798223	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50798223delC	uc003pag.2	+							NM_003221	NP_003212			transcription factor AP-2 beta						nervous system development|positive regulation of transcription from RNA polymerase II promoter		protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity				0	Lung NSC(77;0.156)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	51409661	51409662	+	IGR	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51409661_51409662insC								TFAP2B (594336 upstream) : PKHD1 (70483 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	51441144	51441144	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51441144delA								TFAP2B (625819 upstream) : PKHD1 (39001 downstream)																																			---	---	---	---
MCM3	4172	broad.mit.edu	37	6	52143962	52143962	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52143962delT	uc003pan.1	-						MCM3_uc011dwu.1_Intron	NM_002388	NP_002379			minichromosome maintenance complex component 3						cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	alpha DNA polymerase:primase complex|centrosome|MCM complex|perinuclear region of cytoplasm	ATP binding|DNA binding|helicase activity|protein binding			ovary(1)|lung(1)|skin(1)	3	Lung NSC(77;0.0931)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	52470331	52470331	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52470331delA								TRAM2 (28469 upstream) : LOC730101 (58868 downstream)																																			---	---	---	---
ICK	22858	broad.mit.edu	37	6	52876397	52876397	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52876397delA	uc003pbh.2	-						ICK_uc003pbi.2_Intron	NM_016513	NP_057597			intestinal cell kinase						intracellular protein kinase cascade|multicellular organismal development	cytosol|nucleus	ATP binding|cyclin-dependent protein kinase activity|magnesium ion binding			ovary(1)|large_intestine(1)|lung(1)|kidney(1)|central_nervous_system(1)	5	Lung NSC(77;0.103)																	---	---	---	---
ICK	22858	broad.mit.edu	37	6	52920213	52920213	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52920213delT	uc003pbh.2	-						ICK_uc003pbi.2_Intron|ICK_uc003pbj.2_Intron	NM_016513	NP_057597			intestinal cell kinase						intracellular protein kinase cascade|multicellular organismal development	cytosol|nucleus	ATP binding|cyclin-dependent protein kinase activity|magnesium ion binding			ovary(1)|large_intestine(1)|lung(1)|kidney(1)|central_nervous_system(1)	5	Lung NSC(77;0.103)																	---	---	---	---
FBXO9	26268	broad.mit.edu	37	6	52957766	52957767	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52957766_52957767delAA	uc003pbo.2	+						FBXO9_uc003pbk.2_Intron|FBXO9_uc003pbl.2_Intron|FBXO9_uc003pbm.2_Intron|FBXO9_uc003pbn.2_Intron	NM_012347	NP_036479			F-box only protein 9 isoform 1							ubiquitin ligase complex	ubiquitin-protein ligase activity			pancreas(1)	1	Lung NSC(77;0.103)																	---	---	---	---
GCM1	8521	broad.mit.edu	37	6	53009220	53009224	+	Intron	DEL	AAAAA	-	-	rs79285986		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53009220_53009224delAAAAA	uc003pbp.2	-						GCM1_uc010jzr.2_Intron	NM_003643	NP_003634			glial cells missing homolog a							transcription factor complex	DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			central_nervous_system(1)	1	Lung NSC(77;0.0755)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	53039748	53039748	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53039748delC								GCM1 (26124 upstream) : ELOVL5 (92448 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	53074139	53074139	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53074139delT								GCM1 (60515 upstream) : ELOVL5 (58057 downstream)																																			---	---	---	---
ELOVL5	60481	broad.mit.edu	37	6	53134248	53134249	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53134248_53134249insT	uc003pbq.1	-						ELOVL5_uc003pbr.1_Intron|ELOVL5_uc011dwx.1_Intron|ELOVL5_uc003pbs.1_Intron	NM_021814	NP_068586			elongation of very long chain fatty acids-like						fatty acid elongation, monounsaturated fatty acid|fatty acid elongation, polyunsaturated fatty acid|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process|very long-chain fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	fatty acid elongase activity|protein binding				0	Lung NSC(77;0.116)																	---	---	---	---
ELOVL5	60481	broad.mit.edu	37	6	53172616	53172616	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53172616delT	uc003pbq.1	-						ELOVL5_uc003pbr.1_Intron|ELOVL5_uc011dwx.1_Intron|ELOVL5_uc003pbs.1_Intron|ELOVL5_uc003pbu.2_Intron|ELOVL5_uc011dwy.1_Intron	NM_021814	NP_068586			elongation of very long chain fatty acids-like						fatty acid elongation, monounsaturated fatty acid|fatty acid elongation, polyunsaturated fatty acid|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process|very long-chain fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	fatty acid elongase activity|protein binding				0	Lung NSC(77;0.116)																	---	---	---	---
GCLC	2729	broad.mit.edu	37	6	53385958	53385958	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53385958delT	uc003pbw.1	-						GCLC_uc003pbx.2_Intron	NM_001498	NP_001489			glutamate-cysteine ligase, catalytic subunit						anti-apoptosis|cell redox homeostasis|cysteine metabolic process|glutamate metabolic process|glutathione biosynthetic process|negative regulation of transcription, DNA-dependent|regulation of blood vessel size|response to heat|response to hormone stimulus|response to oxidative stress|xenobiotic metabolic process	cytosol	ADP binding|ATP binding|coenzyme binding|glutamate binding|glutamate-cysteine ligase activity|magnesium ion binding			ovary(1)|central_nervous_system(1)	2	Lung NSC(77;0.0137)				L-Cysteine(DB00151)|L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	53502330	53502330	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53502330delT								GCLC (92499 upstream) : KLHL31 (10370 downstream)																																			---	---	---	---
C6orf142	90523	broad.mit.edu	37	6	54130887	54130887	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54130887delA	uc003pcg.3	+	13					C6orf142_uc003pch.3_3'UTR|C6orf142_uc011dxa.1_3'UTR	NM_138569	NP_612636			hypothetical protein LOC90523							nuclear envelope|PML body	protein binding				0	Lung NSC(77;0.0317)																	---	---	---	---
Unknown	0	broad.mit.edu	37	6	54348455	54348455	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54348455delT								TINAG (93505 upstream) : FAM83B (363114 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	54613007	54613008	+	IGR	DEL	AC	-	-	rs145797314	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54613007_54613008delAC								TINAG (358057 upstream) : FAM83B (98561 downstream)																																			---	---	---	---
FAM83B	222584	broad.mit.edu	37	6	54718439	54718440	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54718439_54718440insA	uc003pck.2	+							NM_001010872	NP_001010872			hypothetical protein LOC222584											ovary(6)	6	Lung NSC(77;0.0178)|Renal(3;0.122)																	---	---	---	---
HCRTR2	3062	broad.mit.edu	37	6	55128706	55128707	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55128706_55128707delTT	uc003pcl.2	+						HCRTR2_uc010jzv.2_Intron|HCRTR2_uc010jzw.1_Frame_Shift_Del_p.L218fs	NM_001526	NP_001517			orexin receptor 2						feeding behavior	integral to plasma membrane	neuropeptide receptor activity			ovary(2)|lung(2)|upper_aerodigestive_tract(1)|breast(1)	6	Lung NSC(77;0.107)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)															---	---	---	---
HMGCLL1	54511	broad.mit.edu	37	6	55439183	55439183	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55439183delA	uc003pcn.2	-						HMGCLL1_uc003pco.2_Intron|HMGCLL1_uc010jzx.2_Intron|HMGCLL1_uc011dxc.1_Intron|HMGCLL1_uc011dxd.1_Intron|HMGCLL1_uc011dxe.1_Intron|HMGCLL1_uc003pcp.2_Intron	NM_019036	NP_061909			3-hydroxymethyl-3-methylglutaryl-Coenzyme A								hydroxymethylglutaryl-CoA lyase activity|metal ion binding			skin(2)|ovary(1)|pancreas(1)	4	Lung NSC(77;0.0875)		LUSC - Lung squamous cell carcinoma(124;0.23)															---	---	---	---
Unknown	0	broad.mit.edu	37	6	55582166	55582167	+	IGR	INS	-	T	T	rs145497726	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55582166_55582167insT								HMGCLL1 (138154 upstream) : BMP5 (38073 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	55587306	55587307	+	IGR	DEL	AA	-	-	rs78173759		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:55587306_55587307delAA								HMGCLL1 (143294 upstream) : BMP5 (32933 downstream)																																			---	---	---	---
DST	667	broad.mit.edu	37	6	56642507	56642508	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56642507_56642508delTT	uc003pdf.2	-						DST_uc003pcz.3_Intron|DST_uc011dxj.1_Intron|DST_uc011dxk.1_Intron|DST_uc011dxl.1_Intron	NM_001144769	NP_001138241			dystonin isoform 2						cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)															---	---	---	---
BEND6	221336	broad.mit.edu	37	6	56883115	56883115	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56883115delA	uc010kab.2	+						BEND6_uc003pdi.3_Intron	NM_152731	NP_689944			BEN domain containing 6												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	57121767	57121767	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57121767delA								RAB23 (34666 upstream) : PRIM2 (60655 downstream)																																			---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57207700	57207701	+	Intron	DEL	TT	-	-	rs33966680		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57207700_57207701delTT	uc003pdx.2	+						PRIM2_uc003pdw.2_Intron	NM_000947	NP_000938			DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57218500	57218501	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57218500_57218501insT	uc003pdx.2	+						PRIM2_uc003pdw.2_Intron	NM_000947	NP_000938			DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57252823	57252824	+	Intron	DEL	TT	-	-	rs4492196	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57252823_57252824delTT	uc003pdx.2	+						hsa-mir-548u|MI0014168_5'Flank	NM_000947	NP_000938			DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57311088	57311090	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57311088_57311090delTTT	uc003pdx.2	+							NM_000947	NP_000938			DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57371285	57371285	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57371285delA	uc003pdx.2	+							NM_000947	NP_000938			DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57377539	57377540	+	Intron	INS	-	TCTG	TCTG	rs138307214		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57377539_57377540insTCTG	uc003pdx.2	+							NM_000947	NP_000938			DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57411988	57411988	+	Intron	DEL	A	-	-	rs67728115		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57411988delA	uc003pdx.2	+							NM_000947	NP_000938			DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57434024	57434024	+	Intron	DEL	T	-	-	rs11337337		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57434024delT	uc003pdx.2	+							NM_000947	NP_000938			DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57448117	57448117	+	Intron	DEL	T	-	-	rs67190200		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57448117delT	uc003pdx.2	+							NM_000947	NP_000938			DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57454042	57454042	+	Intron	DEL	G	-	-	rs67619850		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57454042delG	uc003pdx.2	+							NM_000947	NP_000938			DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57479500	57479504	+	Intron	DEL	TTTTA	-	-	rs67357032		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57479500_57479504delTTTTA	uc003pdx.2	+							NM_000947	NP_000938			DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)														---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57511867	57511868	+	Intron	INS	-	CTCA	CTCA			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57511867_57511868insCTCA	uc003pdx.2	+							NM_000947	NP_000938			DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	57528513	57528516	+	IGR	DEL	TTGC	-	-	rs142702882		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57528513_57528516delTTGC								PRIM2 (15138 upstream) : GUSBL2 (717643 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57540010	57540010	+	IGR	DEL	C	-	-	rs66493514		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57540010delC								PRIM2 (26635 upstream) : GUSBL2 (706149 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57557095	57557095	+	IGR	DEL	T	-	-	rs79478192		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57557095delT								PRIM2 (43720 upstream) : GUSBL2 (689064 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57563953	57563954	+	IGR	INS	-	T	T	rs78276649		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57563953_57563954insT								PRIM2 (50578 upstream) : GUSBL2 (682205 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57582258	57582259	+	IGR	INS	-	A	A	rs141383306	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57582258_57582259insA								PRIM2 (68883 upstream) : GUSBL2 (663900 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57605490	57605491	+	IGR	INS	-	AT	AT	rs149698270	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57605490_57605491insAT								PRIM2 (92115 upstream) : GUSBL2 (640668 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	57748883	57748884	+	IGR	DEL	GA	-	-	rs71729734		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57748883_57748884delGA								PRIM2 (235508 upstream) : GUSBL2 (497275 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	58188329	58188330	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:58188329_58188330delTG								PRIM2 (674954 upstream) : GUSBL2 (57829 downstream)																																			---	---	---	---
GUSBL2	375513	broad.mit.edu	37	6	58251803	58251804	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:58251803_58251804delAA	uc011dxq.1	-						GUSBL2_uc011dxp.1_Intron					SubName: Full=Putative uncharacterized protein ENSP00000348869; Flags: Fragment;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	62063072	62063073	+	IGR	DEL	AA	-	-	rs33983543		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:62063072_62063073delAA								None (None upstream) : KHDRBS2 (326792 downstream)																																			---	---	---	---
KHDRBS2	202559	broad.mit.edu	37	6	62495084	62495084	+	Intron	DEL	A	-	-	rs114883932	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:62495084delA	uc003peg.2	-							NM_152688	NP_689901			KH domain-containing, RNA-binding, signal						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	SH3 domain binding			skin(7)|ovary(3)|liver(1)	11				BRCA - Breast invasive adenocarcinoma(397;0.149)														---	---	---	---
KHDRBS2	202559	broad.mit.edu	37	6	62505384	62505385	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:62505384_62505385delAA	uc003peg.2	-							NM_152688	NP_689901			KH domain-containing, RNA-binding, signal						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	SH3 domain binding			skin(7)|ovary(3)|liver(1)	11				BRCA - Breast invasive adenocarcinoma(397;0.149)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	63097707	63097707	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:63097707delT								KHDRBS2 (101607 upstream) : LGSN (888150 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	63189784	63189784	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:63189784delG								KHDRBS2 (193684 upstream) : LGSN (796073 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	63951743	63951745	+	IGR	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:63951743_63951745delAAA								KHDRBS2 (955643 upstream) : LGSN (34112 downstream)																																			---	---	---	---
PTP4A1	7803	broad.mit.edu	37	6	64288317	64288317	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64288317delT	uc003pek.2	+						PTP4A1_uc003pel.2_Intron	NM_003463	NP_003454			protein tyrosine phosphatase type IVA, member 1						cell cycle|multicellular organismal development	early endosome|endoplasmic reticulum|internal side of plasma membrane|spindle	protein binding|protein tyrosine phosphatase activity				0	all_cancers(3;0.071)|all_epithelial(2;0.0146)|Lung NSC(77;0.175)		Epithelial(2;0.0365)|LUSC - Lung squamous cell carcinoma(74;0.0644)|all cancers(2;0.112)|Lung(124;0.13)															---	---	---	---
EYS	346007	broad.mit.edu	37	6	64555419	64555419	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64555419delA	uc011dxu.1	-						EYS_uc011dxt.1_Intron	NM_001142800	NP_001136272			eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6																		---	---	---	---
EYS	346007	broad.mit.edu	37	6	64758800	64758801	+	Intron	DEL	TC	-	-	rs70999133		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64758800_64758801delTC	uc011dxu.1	-						EYS_uc011dxt.1_Intron	NM_001142800	NP_001136272			eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6																		---	---	---	---
EYS	346007	broad.mit.edu	37	6	65297082	65297082	+	Intron	DEL	T	-	-	rs9353933	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:65297082delT	uc011dxu.1	-						EYS_uc011dxt.1_Intron	NM_001142800	NP_001136272			eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6																		---	---	---	---
EYS	346007	broad.mit.edu	37	6	66314735	66314743	+	Intron	DEL	CTTTTTTTT	-	-	rs35924341		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:66314735_66314743delCTTTTTTTT	uc011dxu.1	-						EYS_uc003peq.2_Intron	NM_001142800	NP_001136272			eyes shut homolog isoform 1						response to stimulus|visual perception	extracellular region	calcium ion binding			lung(4)|ovary(1)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	67013099	67013100	+	IGR	DEL	TT	-	-	rs72465304		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:67013099_67013100delTT								MCART3P (513724 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	67616024	67616024	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:67616024delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	67917794	67917795	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:67917794_67917795delAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	67982022	67982022	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:67982022delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	68438829	68438829	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:68438829delT								None (None upstream) : BAI3 (906803 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	68821139	68821139	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:68821139delA								None (None upstream) : BAI3 (524493 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	68837064	68837064	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:68837064delT								None (None upstream) : BAI3 (508568 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	69281177	69281178	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69281177_69281178insT								None (None upstream) : BAI3 (64454 downstream)																																			---	---	---	---
BAI3	577	broad.mit.edu	37	6	69450990	69450990	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69450990delA	uc003pev.3	+						BAI3_uc010kak.2_Intron	NM_001704	NP_001695			brain-specific angiogenesis inhibitor 3						negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1)	50		all_lung(197;0.212)																---	---	---	---
LMBRD1	55788	broad.mit.edu	37	6	70452859	70452859	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70452859delA	uc003pfa.2	-						LMBRD1_uc003pey.2_5'Flank|LMBRD1_uc003pez.2_Intron|LMBRD1_uc010kal.2_Intron|LMBRD1_uc003pfb.2_Intron	NM_018368	NP_060838			liver regeneration p-53 related protein						interspecies interaction between organisms|transport	integral to membrane|lysosomal membrane	cobalamin binding			ovary(1)	1																		---	---	---	---
LMBRD1	55788	broad.mit.edu	37	6	70456953	70456956	+	Intron	DEL	AAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70456953_70456956delAAAA	uc003pfa.2	-						LMBRD1_uc003pez.2_Intron|LMBRD1_uc010kal.2_Intron|LMBRD1_uc003pfb.2_Intron	NM_018368	NP_060838			liver regeneration p-53 related protein						interspecies interaction between organisms|transport	integral to membrane|lysosomal membrane	cobalamin binding			ovary(1)	1																		---	---	---	---
COL19A1	1310	broad.mit.edu	37	6	70627718	70627718	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70627718delA	uc003pfc.1	+							NM_001858	NP_001849			alpha 1 type XIX collagen precursor						cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4																		---	---	---	---
COL19A1	1310	broad.mit.edu	37	6	70679301	70679301	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70679301delT	uc003pfc.1	+						COL19A1_uc010kam.1_Intron	NM_001858	NP_001849			alpha 1 type XIX collagen precursor						cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4																		---	---	---	---
FAM135A	57579	broad.mit.edu	37	6	71125129	71125130	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71125129_71125130delAA	uc003pfi.2	+						FAM135A_uc003pfh.2_Intron	NM_001105531	NP_001099001			hypothetical protein LOC57579 isoform a											central_nervous_system(1)	1																		---	---	---	---
FAM135A	57579	broad.mit.edu	37	6	71145213	71145213	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71145213delT	uc003pfj.2	+						FAM135A_uc003pfi.2_Intron|FAM135A_uc003pfh.2_Intron|FAM135A_uc003pfk.2_Intron|FAM135A_uc003pfl.2_Intron	NM_001162529	NP_001156001			hypothetical protein LOC57579 isoform c											central_nervous_system(1)	1																		---	---	---	---
FAM135A	57579	broad.mit.edu	37	6	71231615	71231615	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71231615delT	uc003pfj.2	+						FAM135A_uc003pfi.2_Intron|FAM135A_uc003pfh.2_Intron|FAM135A_uc003pfk.2_Intron|FAM135A_uc003pfl.2_Intron|FAM135A_uc003pfn.2_5'Flank	NM_001162529	NP_001156001			hypothetical protein LOC57579 isoform c											central_nervous_system(1)	1																		---	---	---	---
SMAP1	60682	broad.mit.edu	37	6	71508304	71508304	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71508304delA	uc003pfr.2	+						SMAP1_uc011dxy.1_Intron|SMAP1_uc003pfs.2_Intron|SMAP1_uc010kao.2_Intron|SMAP1_uc010kap.2_Intron	NM_001044305	NP_001037770			stromal membrane-associated GTPase-activating						regulation of ARF GTPase activity	plasma membrane	ARF GTPase activator activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	71813115	71813115	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:71813115delT								B3GAT2 (146327 upstream) : OGFRL1 (185362 downstream)																																			---	---	---	---
RIMS1	22999	broad.mit.edu	37	6	72829363	72829363	+	Intron	DEL	T	-	-	rs78180788		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72829363delT	uc003pga.2	+							NM_014989	NP_055804			regulating synaptic membrane exocytosis 1						calcium ion-dependent exocytosis|cellular membrane fusion|glutamate secretion|intracellular protein transport|protein complex assembly|regulated secretory pathway|response to stimulus|synaptic vesicle exocytosis|visual perception	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(7)|pancreas(2)|breast(1)	10		all_epithelial(107;0.179)|all_hematologic(105;0.212)																---	---	---	---
Unknown	0	broad.mit.edu	37	6	73308513	73308513	+	IGR	DEL	T	-	-	rs1147570	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73308513delT								RIMS1 (196006 upstream) : KCNQ5 (23058 downstream)																																			---	---	---	---
KHDC1	80759	broad.mit.edu	37	6	73948915	73948917	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73948915_73948917delTTT	uc011dyl.1	-											Homo sapiens cDNA FLJ30329 fis, clone BRACE2007201.							integral to membrane	RNA binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	74054749	74054750	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74054749_74054750delAA								C6orf147 (34661 upstream) : DPPA5 (8037 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	74750726	74750726	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74750726delT								CD109 (212686 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	75192066	75192067	+	Intron	DEL	GT	-	-	rs112234299		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75192066_75192067delGT	uc003phr.2	+											Homo sapiens full length insert cDNA clone ZD50H02.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	75368415	75368415	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75368415delA	uc003phr.2	+											Homo sapiens full length insert cDNA clone ZD50H02.																														---	---	---	---
COL12A1	1303	broad.mit.edu	37	6	75798720	75798722	+	Intron	DEL	AAC	-	-	rs672648		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75798720_75798722delAAC	uc003phs.2	-						COL12A1_uc003pht.2_Intron	NM_004370	NP_004361			collagen, type XII, alpha 1 long isoform						cell adhesion|collagen fibril organization|skeletal system development	collagen type XII|extracellular space	extracellular matrix structural constituent conferring tensile strength			ovary(6)|large_intestine(1)|breast(1)|skin(1)	9																		---	---	---	---
COL12A1	1303	broad.mit.edu	37	6	75887218	75887218	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75887218delA	uc003phs.2	-						COL12A1_uc003pht.2_Intron	NM_004370	NP_004361			collagen, type XII, alpha 1 long isoform						cell adhesion|collagen fibril organization|skeletal system development	collagen type XII|extracellular space	extracellular matrix structural constituent conferring tensile strength			ovary(6)|large_intestine(1)|breast(1)|skin(1)	9																		---	---	---	---
TMEM30A	55754	broad.mit.edu	37	6	75965692	75965692	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75965692delT	uc003phw.2	-	7					TMEM30A_uc003phx.2_3'UTR	NM_018247	NP_060717			transmembrane protein 30A isoform 1							integral to membrane					0																		---	---	---	---
SENP6	26054	broad.mit.edu	37	6	76331349	76331349	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76331349delT	uc003pid.3	+						SENP6_uc003pie.3_Intron|SENP6_uc003pic.2_Intron	NM_015571	NP_056386			SUMO1/sentrin specific peptidase 6 isoform 1						proteolysis	cytoplasm|nucleus	cysteine-type peptidase activity			breast(2)|urinary_tract(1)|ovary(1)|lung(1)|skin(1)	6		all_hematologic(105;0.189)																---	---	---	---
SENP6	26054	broad.mit.edu	37	6	76385140	76385140	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76385140delT	uc003pid.3	+						SENP6_uc003pie.3_Intron|SENP6_uc010kbf.2_Intron|SENP6_uc003pic.2_Intron|SENP6_uc003pif.1_Intron	NM_015571	NP_056386			SUMO1/sentrin specific peptidase 6 isoform 1						proteolysis	cytoplasm|nucleus	cysteine-type peptidase activity			breast(2)|urinary_tract(1)|ovary(1)|lung(1)|skin(1)	6		all_hematologic(105;0.189)																---	---	---	---
SENP6	26054	broad.mit.edu	37	6	76421202	76421202	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76421202delT	uc003pid.3	+						SENP6_uc003pie.3_Intron|SENP6_uc010kbf.2_Intron	NM_015571	NP_056386			SUMO1/sentrin specific peptidase 6 isoform 1						proteolysis	cytoplasm|nucleus	cysteine-type peptidase activity			breast(2)|urinary_tract(1)|ovary(1)|lung(1)|skin(1)	6		all_hematologic(105;0.189)																---	---	---	---
SENP6	26054	broad.mit.edu	37	6	76423085	76423085	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76423085delT	uc003pid.3	+						SENP6_uc003pie.3_Intron|SENP6_uc010kbf.2_Intron	NM_015571	NP_056386			SUMO1/sentrin specific peptidase 6 isoform 1						proteolysis	cytoplasm|nucleus	cysteine-type peptidase activity			breast(2)|urinary_tract(1)|ovary(1)|lung(1)|skin(1)	6		all_hematologic(105;0.189)																---	---	---	---
Unknown	0	broad.mit.edu	37	6	76630320	76630320	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76630320delA								MYO6 (1066 upstream) : IMPG1 (742 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	76928259	76928260	+	IGR	DEL	CA	-	-	rs59427850	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76928259_76928260delCA								IMPG1 (145924 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	77282321	77282323	+	IGR	DEL	TTT	-	-	rs78704256	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:77282321_77282323delTTT								IMPG1 (499986 upstream) : HTR1B (889625 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	77947345	77947346	+	IGR	INS	-	TCC	TCC	rs141745608	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:77947345_77947346insTCC								None (None upstream) : HTR1B (224602 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	78045991	78045991	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:78045991delT								None (None upstream) : HTR1B (125957 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	78453672	78453672	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:78453672delA								HTR1B (280552 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	78730816	78730816	+	IGR	DEL	A	-	-	rs11330402		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:78730816delA								HTR1B (557696 upstream) : IRAK1BP1 (846373 downstream)																																			---	---	---	---
HMGN3	9324	broad.mit.edu	37	6	79911547	79911547	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79911547delT	uc003pit.2	-						HMGN3_uc003pis.2_Intron|HMGN3_uc003piu.1_3'UTR	NM_004242	NP_004233			high mobility group nucleosomal binding domain 3						chromatin modification	chromatin|cytoplasm|nucleus	DNA binding|thyroid hormone receptor binding				0		all_cancers(76;0.000116)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0393)		BRCA - Breast invasive adenocarcinoma(397;0.125)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	79969191	79969191	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79969191delA								HMGN3 (24736 upstream) : LCA5 (225518 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	79986134	79986134	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79986134delT								HMGN3 (41679 upstream) : LCA5 (208575 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	80070831	80070832	+	IGR	DEL	CT	-	-	rs139482946		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80070831_80070832delCT								HMGN3 (126376 upstream) : LCA5 (123877 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	80329874	80329874	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80329874delT								LCA5 (82727 upstream) : SH3BGRL2 (11126 downstream)																																			---	---	---	---
BCKDHB	594	broad.mit.edu	37	6	80872648	80872649	+	Intron	DEL	TT	-	-	rs75127848	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80872648_80872649delTT	uc003pjd.2	+						BCKDHB_uc003pje.2_Intron	NM_000056	NP_000047			branched chain keto acid dehydrogenase E1 beta						branched chain family amino acid catabolic process	mitochondrial alpha-ketoglutarate dehydrogenase complex	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity|carboxy-lyase activity|protein binding				0		all_cancers(76;1.38e-05)|Acute lymphoblastic leukemia(125;1.15e-05)|all_hematologic(105;0.00118)|all_epithelial(107;0.0149)		BRCA - Breast invasive adenocarcinoma(397;0.0291)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	81350192	81350192	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:81350192delT								BCKDHB (294205 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	82033534	82033534	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82033534delA								BCKDHB (977547 upstream) : FAM46A (421914 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	82041736	82041737	+	IGR	INS	-	TG	TG	rs149890506	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82041736_82041737insTG								BCKDHB (985749 upstream) : FAM46A (413711 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	82589575	82589577	+	IGR	DEL	AAA	-	-	rs75772618		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82589575_82589577delAAA								FAM46A (127147 upstream) : IBTK (290379 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	82699348	82699348	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82699348delA								FAM46A (236920 upstream) : IBTK (180608 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	82846558	82846558	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:82846558delT								FAM46A (384130 upstream) : IBTK (33398 downstream)																																			---	---	---	---
UBE2CBP	90025	broad.mit.edu	37	6	83656093	83656093	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83656093delA	uc003pjp.2	-						UBE2CBP_uc011dyx.1_Intron	NM_198920	NP_944602			ubiquitin-conjugating enzyme E2C binding							cytoplasm	ligase activity			ovary(1)	1		all_cancers(76;0.000374)|Acute lymphoblastic leukemia(125;3.85e-06)|all_hematologic(105;0.0017)|all_epithelial(107;0.0548)		BRCA - Breast invasive adenocarcinoma(397;0.0944)														---	---	---	---
ME1	4199	broad.mit.edu	37	6	84116690	84116691	+	Intron	INS	-	ACAC	ACAC	rs139710629	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84116690_84116691insACAC	uc003pjy.2	-						ME1_uc011dzb.1_Intron|ME1_uc011dzc.1_Intron	NM_002395	NP_002386			cytosolic malic enzyme 1						carbohydrate metabolic process|cellular lipid metabolic process|malate metabolic process|NADP biosynthetic process|response to carbohydrate stimulus|response to hormone stimulus	cytosol	ADP binding|electron carrier activity|malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) activity|manganese ion binding|NAD binding|NADP binding			upper_aerodigestive_tract(1)|ovary(1)	2		all_cancers(76;1.28e-06)|Acute lymphoblastic leukemia(125;5.03e-07)|all_hematologic(105;0.000238)|all_epithelial(107;0.00218)		BRCA - Breast invasive adenocarcinoma(397;0.0641)	NADH(DB00157)													---	---	---	---
CYB5R4	51167	broad.mit.edu	37	6	84588621	84588621	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84588621delT	uc003pkf.2	+							NM_016230	NP_057314			cytochrome b5 reductase 4						cell development|detection of oxygen|generation of precursor metabolites and energy|glucose homeostasis|insulin secretion|response to antibiotic|superoxide metabolic process	endoplasmic reticulum|perinuclear region of cytoplasm	cytochrome-b5 reductase activity|heme binding|NAD(P)H oxidase activity			breast(2)	2		all_cancers(76;7e-07)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00128)		BRCA - Breast invasive adenocarcinoma(397;0.0871)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	85139531	85139531	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85139531delT								KIAA1009 (202196 upstream) : TBX18 (257550 downstream)																																			---	---	---	---
TBX18	9096	broad.mit.edu	37	6	85454056	85454056	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85454056delA	uc003pkl.1	-						TBX18_uc010kbq.1_Intron	NM_001080508	NP_001073977			T-box 18						multicellular organismal development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|pancreas(2)|lung(1)	5		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	85501318	85501318	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85501318delT								TBX18 (27419 upstream) : NT5E (657984 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	85552073	85552073	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85552073delT								TBX18 (78174 upstream) : NT5E (607229 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	85729631	85729632	+	IGR	INS	-	AC	AC	rs145432442	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85729631_85729632insAC								TBX18 (255732 upstream) : NT5E (429670 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	85748406	85748407	+	IGR	DEL	TT	-	-	rs67044254		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:85748406_85748407delTT								TBX18 (274507 upstream) : NT5E (410895 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	86061233	86061233	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86061233delA								TBX18 (587334 upstream) : NT5E (98069 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	86370946	86370949	+	IGR	DEL	TTTT	-	-	rs71948899		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86370946_86370949delTTTT								SYNCRIP (17903 upstream) : SNHG5 (15777 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	86826642	86826643	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86826642_86826643delTG								SNHG5 (438191 upstream) : HTR1E (820381 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	87579591	87579592	+	IGR	DEL	AA	-	-	rs112233099		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87579591_87579592delAA								None (None upstream) : HTR1E (67432 downstream)																																			---	---	---	---
ZNF292	23036	broad.mit.edu	37	6	87955207	87955208	+	Intron	DEL	TT	-	-	rs72438234		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87955207_87955208delTT	uc003plm.3	+							NM_015021	NP_055836			zinc finger protein 292						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)	4		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)														---	---	---	---
GJB7	375519	broad.mit.edu	37	6	87993733	87993734	+	3'UTR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87993733_87993734insA	uc003plo.2	-	3						NM_198568	NP_940970			gap junction protein, beta 7, 25kDa						cell communication	connexon complex|integral to membrane					0		all_cancers(76;1.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;7.38e-10)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00323)		BRCA - Breast invasive adenocarcinoma(108;0.0167)														---	---	---	---
ORC3L	23595	broad.mit.edu	37	6	88313301	88313301	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88313301delT	uc003pmh.2	+						ORC3L_uc011dzl.1_Intron|ORC3L_uc011dzm.1_Intron|ORC3L_uc011dzn.1_Intron|ORC3L_uc003pmg.2_Intron|ORC3L_uc003pmi.2_Intron|ORC3L_uc011dzo.1_Intron|ORC3L_uc011dzp.1_Intron	NM_012381	NP_036513			origin recognition complex, subunit 3 isoform 2						cell cycle checkpoint|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	nuclear origin of replication recognition complex|nucleoplasm	DNA replication origin binding|protein binding				0		all_cancers(76;9.05e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;5.29e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.0469)														---	---	---	---
ORC3L	23595	broad.mit.edu	37	6	88331561	88331561	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88331561delA	uc003pmh.2	+						ORC3L_uc011dzl.1_Intron|ORC3L_uc011dzm.1_Intron|ORC3L_uc011dzn.1_Intron|ORC3L_uc003pmg.2_Intron|ORC3L_uc003pmi.2_Intron|ORC3L_uc011dzo.1_Intron|ORC3L_uc011dzp.1_Intron	NM_012381	NP_036513			origin recognition complex, subunit 3 isoform 2						cell cycle checkpoint|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	nuclear origin of replication recognition complex|nucleoplasm	DNA replication origin binding|protein binding				0		all_cancers(76;9.05e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;5.29e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.0469)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	88740443	88740443	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88740443delA								AKIRIN2 (328458 upstream) : SPACA1 (17064 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	88980915	88980916	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:88980915_88980916delAA								CNR1 (105148 upstream) : RNGTT (339073 downstream)																																			---	---	---	---
RNGTT	8732	broad.mit.edu	37	6	89608868	89608868	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89608868delT	uc003pmr.2	-						RNGTT_uc003pms.2_Intron|RNGTT_uc011dzu.1_Intron|RNGTT_uc003pmt.2_Intron	NM_003800	NP_003791			RNA guanylyltransferase and 5'-phosphatase						interspecies interaction between organisms|mRNA capping|transcription from RNA polymerase II promoter|viral reproduction	nucleoplasm	GTP binding|mRNA guanylyltransferase activity|polynucleotide 5'-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			upper_aerodigestive_tract(1)	1		all_cancers(76;4.07e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;6.86e-05)		BRCA - Breast invasive adenocarcinoma(108;0.151)														---	---	---	---
GABRR1	2569	broad.mit.edu	37	6	89927156	89927156	+	5'UTR	DEL	A	-	-	rs34012805		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89927156delA	uc003pna.2	-	1					GABRR1_uc011dzv.1_5'UTR|GABRR1_uc011dzw.1_RNA	NM_002042	NP_002033			gamma-aminobutyric acid (GABA) receptor, rho 1						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			pancreas(1)	1		all_cancers(76;9.49e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.46e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.00917)	Picrotoxin(DB00466)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	90072668	90072669	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90072668_90072669insA								UBE2J1 (10049 upstream) : RRAGD (1668 downstream)																																			---	---	---	---
ANKRD6	22881	broad.mit.edu	37	6	90274906	90274906	+	Intron	DEL	T	-	-	rs72412399		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90274906delT	uc003pni.3	+						ANKRD6_uc003pne.3_Intron|ANKRD6_uc003pnf.3_Intron|ANKRD6_uc011dzy.1_Intron|ANKRD6_uc010kcd.2_5'Flank	NM_014942	NP_055757			ankyrin repeat domain 6								protein binding			ovary(2)|pancreas(1)	3		all_cancers(76;1.22e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;1.83e-05)|Lung NSC(302;0.239)		BRCA - Breast invasive adenocarcinoma(108;0.0209)														---	---	---	---
MDN1	23195	broad.mit.edu	37	6	90409616	90409617	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90409616_90409617delAA	uc003pnn.1	-							NM_014611	NP_055426			MDN1, midasin homolog						protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)														---	---	---	---
MDN1	23195	broad.mit.edu	37	6	90511685	90511686	+	Intron	DEL	AA	-	-	rs149181191		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90511685_90511686delAA	uc003pnn.1	-						MDN1_uc003pnp.1_Intron	NM_014611	NP_055426			MDN1, midasin homolog						protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)														---	---	---	---
MDN1	23195	broad.mit.edu	37	6	90511989	90511989	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90511989delC	uc003pnn.1	-						MDN1_uc003pnp.1_Intron	NM_014611	NP_055426			MDN1, midasin homolog						protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)														---	---	---	---
CASP8AP2	9994	broad.mit.edu	37	6	90540315	90540315	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90540315delC	uc003pnr.2	+						CASP8AP2_uc003pns.2_Intron|CASP8AP2_uc003pnt.2_Intron|CASP8AP2_uc011dzz.1_Intron	NM_001137667	NP_001131139			caspase 8 associated protein 2						cell cycle|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	cytoplasm|nucleus	caspase activator activity|death receptor binding|transcription corepressor activity			ovary(2)	2		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)														---	---	---	---
CASP8AP2	9994	broad.mit.edu	37	6	90553396	90553396	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90553396delT	uc003pnr.2	+						CASP8AP2_uc003pns.2_Intron|CASP8AP2_uc003pnt.2_Intron|CASP8AP2_uc011dzz.1_Intron	NM_001137667	NP_001131139			caspase 8 associated protein 2						cell cycle|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	cytoplasm|nucleus	caspase activator activity|death receptor binding|transcription corepressor activity			ovary(2)	2		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)														---	---	---	---
CASP8AP2	9994	broad.mit.edu	37	6	90558601	90558601	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90558601delT	uc003pnr.2	+						CASP8AP2_uc003pns.2_Intron|CASP8AP2_uc003pnt.2_Intron|CASP8AP2_uc011dzz.1_Intron	NM_001137667	NP_001131139			caspase 8 associated protein 2						cell cycle|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	cytoplasm|nucleus	caspase activator activity|death receptor binding|transcription corepressor activity			ovary(2)	2		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)														---	---	---	---
CASP8AP2	9994	broad.mit.edu	37	6	90583372	90583372	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90583372delT	uc003pnr.2	+						CASP8AP2_uc003pnt.2_Intron|CASP8AP2_uc011dzz.1_Intron	NM_001137667	NP_001131139			caspase 8 associated protein 2						cell cycle|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	cytoplasm|nucleus	caspase activator activity|death receptor binding|transcription corepressor activity			ovary(2)	2		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	90597825	90597825	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90597825delG								CASP8AP2 (13671 upstream) : GJA10 (6363 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	91504844	91504846	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91504844_91504846delTTT								MAP3K7 (207937 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	91709113	91709113	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91709113delA								MAP3K7 (412206 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	91788831	91788831	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91788831delT								MAP3K7 (491924 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	91795952	91795952	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91795952delA								MAP3K7 (499045 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	91901961	91901961	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:91901961delA								MAP3K7 (605054 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	92491165	92491165	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:92491165delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	92651939	92651939	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:92651939delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	92706234	92706234	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:92706234delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	92897197	92897197	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:92897197delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	93382022	93382023	+	IGR	INS	-	G	G	rs13192490	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93382022_93382023insG								None (None upstream) : EPHA7 (567719 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	93661052	93661052	+	IGR	DEL	A	-	-	rs76291597		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93661052delA								None (None upstream) : EPHA7 (288690 downstream)																																			---	---	---	---
EPHA7	2045	broad.mit.edu	37	6	93954897	93954897	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93954897delT	uc003poe.2	-						EPHA7_uc003pof.2_Intron|EPHA7_uc011eac.1_Intron	NM_004440	NP_004431			ephrin receptor EphA7 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity			lung(8)|ovary(7)|upper_aerodigestive_tract(3)|central_nervous_system(3)|skin(3)|large_intestine(2)|stomach(1)|pancreas(1)	28		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	95197120	95197120	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:95197120delT								TSG1 (710921 upstream) : MANEA (828293 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	96920803	96920803	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:96920803delT								FUT9 (257316 upstream) : KIAA0776 (48899 downstream)																																			---	---	---	---
FHL5	9457	broad.mit.edu	37	6	97055283	97055284	+	Intron	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97055283_97055284delAC	uc003pos.1	+						FHL5_uc003pot.1_Intron	NM_020482	NP_065228			activator of cAMP-responsive element modulator							nucleus	zinc ion binding			ovary(2)	2		all_cancers(76;1.57e-07)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00266)|Colorectal(196;0.0341)|Lung NSC(302;0.204)		BRCA - Breast invasive adenocarcinoma(108;0.0948)														---	---	---	---
FHL5	9457	broad.mit.edu	37	6	97058329	97058329	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97058329delT	uc003pos.1	+						FHL5_uc003pot.1_Intron	NM_020482	NP_065228			activator of cAMP-responsive element modulator							nucleus	zinc ion binding			ovary(2)	2		all_cancers(76;1.57e-07)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00266)|Colorectal(196;0.0341)|Lung NSC(302;0.204)		BRCA - Breast invasive adenocarcinoma(108;0.0948)														---	---	---	---
KLHL32	114792	broad.mit.edu	37	6	97384930	97384930	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97384930delA	uc010kcm.1	+						KLHL32_uc003poy.2_Intron|KLHL32_uc011ead.1_Intron|KLHL32_uc003poz.2_Intron|KLHL32_uc011eae.1_Intron	NM_052904	NP_443136			kelch-like 32											ovary(3)|skin(1)	4		all_cancers(76;1.19e-06)|Acute lymphoblastic leukemia(125;5.83e-10)|all_hematologic(75;3.67e-07)|all_epithelial(107;0.00778)|Colorectal(196;0.122)		BRCA - Breast invasive adenocarcinoma(108;0.0558)														---	---	---	---
KLHL32	114792	broad.mit.edu	37	6	97532863	97532864	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97532863_97532864delTT	uc010kcm.1	+						KLHL32_uc003poy.2_Intron|KLHL32_uc011ead.1_Intron|KLHL32_uc003poz.2_Intron|KLHL32_uc011eae.1_Intron|KLHL32_uc003ppa.2_Intron	NM_052904	NP_443136			kelch-like 32											ovary(3)|skin(1)	4		all_cancers(76;1.19e-06)|Acute lymphoblastic leukemia(125;5.83e-10)|all_hematologic(75;3.67e-07)|all_epithelial(107;0.00778)|Colorectal(196;0.122)		BRCA - Breast invasive adenocarcinoma(108;0.0558)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	98088863	98088864	+	Intron	DEL	TC	-	-	rs142398091	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:98088863_98088864delTC	uc003ppd.1	+											Homo sapiens cDNA FLJ34046 fis, clone FCBBF2007610.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	98161665	98161666	+	IGR	DEL	TT	-	-	rs71712066		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:98161665_98161666delTT								C6orf167 (430604 upstream) : MIR2113 (310741 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	98173225	98173226	+	IGR	INS	-	AG	AG	rs139385309	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:98173225_98173226insAG								C6orf167 (442164 upstream) : MIR2113 (299181 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	98576417	98576417	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:98576417delT								MIR2113 (103920 upstream) : POU3F2 (706163 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	98985124	98985124	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:98985124delA								MIR2113 (512627 upstream) : POU3F2 (297456 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	99164294	99164294	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99164294delG								MIR2113 (691797 upstream) : POU3F2 (118286 downstream)																																			---	---	---	---
FBXL4	26235	broad.mit.edu	37	6	99346488	99346488	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99346488delA	uc003ppf.1	-						FBXL4_uc003ppg.1_Intron|FBXL4_uc003pph.1_Intron|FBXL4_uc010kcp.2_Intron	NM_012160	NP_036292			F-box and leucine-rich repeat protein 4						ubiquitin-dependent protein catabolic process	cytoplasm|nucleus|ubiquitin ligase complex				skin(2)	2		all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197)		BRCA - Breast invasive adenocarcinoma(108;0.0413)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	99706479	99706480	+	IGR	INS	-	A	A	rs34640166		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99706479_99706480insA								FBXL4 (310630 upstream) : C6orf168 (14314 downstream)																																			---	---	---	---
COQ3	51805	broad.mit.edu	37	6	99817819	99817820	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99817819_99817820insA	uc003ppk.2	-							NM_017421	NP_059117			hexaprenyldihydroxybenzoate methyltransferase						glycerol metabolic process|ubiquinone biosynthetic process	mitochondrial matrix	2-polyprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity|3-demethylubiquinone-9 3-O-methyltransferase activity|hexaprenyldihydroxybenzoate methyltransferase activity			upper_aerodigestive_tract(1)	1		all_cancers(76;1.24e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.00716)|Colorectal(196;0.0691)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.0625)														---	---	---	---
COQ3	51805	broad.mit.edu	37	6	99831704	99831704	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99831704delA	uc003ppk.2	-							NM_017421	NP_059117			hexaprenyldihydroxybenzoate methyltransferase						glycerol metabolic process|ubiquinone biosynthetic process	mitochondrial matrix	2-polyprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity|3-demethylubiquinone-9 3-O-methyltransferase activity|hexaprenyldihydroxybenzoate methyltransferase activity			upper_aerodigestive_tract(1)	1		all_cancers(76;1.24e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.00716)|Colorectal(196;0.0691)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.0625)														---	---	---	---
SFRS18	25957	broad.mit.edu	37	6	99852665	99852665	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99852665delT	uc003ppo.3	-						SFRS18_uc003ppp.3_Intron|SFRS18_uc011eag.1_Intron	NM_032870	NP_116259			splicing factor, arginine/serine-rich 130							nuclear speck					0		all_cancers(76;1.24e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.00716)|Colorectal(196;0.0691)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.0631)														---	---	---	---
USP45	85015	broad.mit.edu	37	6	99884442	99884442	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99884442delA	uc003ppx.2	-						USP45_uc003ppv.2_Intron|USP45_uc003ppw.2_Intron	NM_001080481	NP_001073950			ubiquitin specific peptidase 45						ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity|zinc ion binding			ovary(1)|breast(1)	2		all_cancers(76;0.000208)|Acute lymphoblastic leukemia(125;8.41e-11)|all_hematologic(75;2.56e-07)|all_epithelial(107;0.122)|Colorectal(196;0.133)		BRCA - Breast invasive adenocarcinoma(108;0.0718)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	100071089	100071089	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100071089delT								PRDM13 (7635 upstream) : MCHR2 (296697 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	100083549	100083549	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100083549delT								PRDM13 (20095 upstream) : MCHR2 (284237 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	100157092	100157092	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100157092delT								PRDM13 (93638 upstream) : MCHR2 (210694 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	100552048	100552048	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100552048delA								MCHR2 (109934 upstream) : SIM1 (284703 downstream)																																			---	---	---	---
ASCC3	10973	broad.mit.edu	37	6	101075980	101075980	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101075980delA	uc003pqk.2	-							NM_006828	NP_006819			activating signal cointegrator 1 complex subunit						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(5)|skin(1)	6		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	101664383	101664383	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101664383delT								ASCC3 (335159 upstream) : GRIK2 (182522 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	101671487	101671487	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101671487delT								ASCC3 (342263 upstream) : GRIK2 (175418 downstream)																																			---	---	---	---
GRIK2	2898	broad.mit.edu	37	6	102179974	102179975	+	Intron	DEL	CA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:102179974_102179975delCA	uc003pqp.3	+						GRIK2_uc003pqn.2_Intron|GRIK2_uc003pqo.3_Intron|GRIK2_uc010kcw.2_Intron	NM_021956	NP_068775			glutamate receptor, ionotropic, kainate 2						glutamate signaling pathway|induction of programmed cell death in response to chemical stimulus|neuron apoptosis|positive regulation of synaptic transmission|regulation of short-term neuronal synaptic plasticity	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|pancreas(1)|breast(1)|skin(1)	5		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	L-Glutamic Acid(DB00142)													---	---	---	---
GRIK2	2898	broad.mit.edu	37	6	102302688	102302690	+	Intron	DEL	ATA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:102302688_102302690delATA	uc003pqp.3	+						GRIK2_uc003pqn.2_Intron|GRIK2_uc003pqo.3_Intron|GRIK2_uc010kcw.2_Intron	NM_021956	NP_068775			glutamate receptor, ionotropic, kainate 2						glutamate signaling pathway|induction of programmed cell death in response to chemical stimulus|neuron apoptosis|positive regulation of synaptic transmission|regulation of short-term neuronal synaptic plasticity	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|pancreas(1)|breast(1)|skin(1)	5		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	L-Glutamic Acid(DB00142)													---	---	---	---
GRIK2	2898	broad.mit.edu	37	6	102503432	102503432	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:102503432delA	uc003pqp.3	+	15	2788	c.2539delA	c.(2539-2541)AAAfs	p.K847fs	GRIK2_uc003pqo.3_Frame_Shift_Del_p.K847fs|GRIK2_uc010kcw.2_Frame_Shift_Del_p.K847fs	NM_021956	NP_068775	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	847	Cytoplasmic (Potential).				glutamate signaling pathway|induction of programmed cell death in response to chemical stimulus|neuron apoptosis|positive regulation of synaptic transmission|regulation of short-term neuronal synaptic plasticity	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|pancreas(1)|breast(1)|skin(1)	5		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	103386435	103386435	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:103386435delT								GRIK2 (868478 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	103508102	103508103	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:103508102_103508103delAA								GRIK2 (990145 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	104054581	104054583	+	IGR	DEL	TTT	-	-	rs77393838		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:104054581_104054583delTTT								None (None upstream) : None (None downstream)																																			---	---	---	---
HACE1	57531	broad.mit.edu	37	6	105309276	105309277	+	5'Flank	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105309276_105309277insA	uc003pqu.1	-						HACE1_uc010kcy.1_5'Flank|HACE1_uc010kcz.1_5'Flank	NM_020771	NP_065822			HECT domain and ankyrin repeat containing, E3						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	endoplasmic reticulum	ubiquitin-protein ligase activity			ovary(5)|lung(2)	7		all_cancers(87;6.89e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0216)|Colorectal(196;0.202)		BRCA - Breast invasive adenocarcinoma(108;0.122)|Epithelial(106;0.204)														---	---	---	---
HACE1	57531	broad.mit.edu	37	6	105310636	105310636	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105310636delA	uc003pqu.1	-						HACE1_uc010kcy.1_5'Flank|HACE1_uc010kcz.1_5'Flank	NM_020771	NP_065822			HECT domain and ankyrin repeat containing, E3						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	endoplasmic reticulum	ubiquitin-protein ligase activity			ovary(5)|lung(2)	7		all_cancers(87;6.89e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0216)|Colorectal(196;0.202)		BRCA - Breast invasive adenocarcinoma(108;0.122)|Epithelial(106;0.204)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	105347410	105347410	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105347410delT								HACE1 (39616 upstream) : LIN28B (57513 downstream)																																			---	---	---	---
LIN28B	389421	broad.mit.edu	37	6	105429084	105429085	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105429084_105429085insT	uc003pqv.1	+						LIN28B_uc010kda.1_Intron	NM_001004317	NP_001004317			lin-28 homolog B						miRNA catabolic process|pre-miRNA processing|regulation of transcription, DNA-dependent|RNA 3'-end processing	cytoplasm|nucleus	DNA binding|protein binding|RNA binding|zinc ion binding				0		all_cancers(87;0.00346)|Acute lymphoblastic leukemia(125;2.26e-08)|all_hematologic(75;2.79e-06)|all_epithelial(87;0.204)																---	---	---	---
BVES	11149	broad.mit.edu	37	6	105564867	105564867	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105564867delA	uc003pqw.2	-						BVES_uc003pqx.2_Intron|BVES_uc003pqy.2_Intron	NM_147147	NP_671488			blood vessel epicardial substance isoform 5						epithelial cell-cell adhesion|muscle organ development|positive regulation of locomotion|positive regulation of receptor recycling|regulation of Cdc42 GTPase activity|regulation of cell shape|regulation of Rac GTPase activity|substrate adhesion-dependent cell spreading|vesicle-mediated transport	integral to membrane|lateral plasma membrane|tight junction	structural molecule activity				0		all_cancers(87;2.83e-05)|Acute lymphoblastic leukemia(125;1.95e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0101)|Colorectal(196;0.204)|Lung NSC(302;0.238)																---	---	---	---
Unknown	0	broad.mit.edu	37	6	105935834	105935834	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:105935834delA								PREP (84865 upstream) : PRDM1 (598361 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	106089808	106089808	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106089808delT								PREP (238839 upstream) : PRDM1 (444387 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	106305087	106305087	+	IGR	DEL	A	-	-	rs5878860		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106305087delA								PREP (454118 upstream) : PRDM1 (229108 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	106359794	106359794	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106359794delT								PREP (508825 upstream) : PRDM1 (174401 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	106370405	106370405	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106370405delA								PREP (519436 upstream) : PRDM1 (163790 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	106472017	106472018	+	IGR	DEL	AA	-	-	rs72450799		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106472017_106472018delAA								PREP (621048 upstream) : PRDM1 (62177 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	106610623	106610623	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106610623delA								PRDM1 (52809 upstream) : ATG5 (21731 downstream)																																			---	---	---	---
ATG5	9474	broad.mit.edu	37	6	106760686	106760686	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106760686delA	uc003prf.2	-						ATG5_uc010kdb.2_Intron|ATG5_uc003prg.2_Intron|ATG5_uc010kdc.2_Intron	NM_004849	NP_004840			APG5 autophagy 5-like						apoptosis|autophagic vacuole assembly|negative regulation of type I interferon production|post-translational protein modification	autophagic vacuole|pre-autophagosomal structure membrane	protein binding			large_intestine(1)	1	Breast(9;0.0296)	all_cancers(87;0.000301)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0612)|Lung NSC(302;0.216)	BRCA - Breast invasive adenocarcinoma(8;0.00802)	OV - Ovarian serous cystadenocarcinoma(136;0.128)|Epithelial(106;0.159)|all cancers(137;0.18)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	106779238	106779239	+	IGR	INS	-	T	T	rs150870950	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:106779238_106779239insT								ATG5 (5543 upstream) : AIM1 (180491 downstream)																																			---	---	---	---
AIM1	202	broad.mit.edu	37	6	107015558	107015558	+	Intron	DEL	A	-	-	rs34224051		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107015558delA	uc003prh.2	+						AIM1_uc003pri.2_Intron	NM_001624	NP_001615			absent in melanoma 1								sugar binding			breast(4)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)	9	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)														---	---	---	---
PDSS2	57107	broad.mit.edu	37	6	107527878	107527878	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107527878delA	uc003prt.2	-						PDSS2_uc011eak.1_Intron|PDSS2_uc011eal.1_Intron	NM_020381	NP_065114			prenyl diphosphate synthase, subunit 2						isoprenoid biosynthetic process|ubiquinone biosynthetic process	mitochondrion	protein heterodimerization activity			ovary(2)	2	Breast(9;0.0127)	all_cancers(87;3.63e-05)|Acute lymphoblastic leukemia(125;2.86e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.0108)|Colorectal(196;0.156)|Lung NSC(302;0.211)	BRCA - Breast invasive adenocarcinoma(8;0.0101)|all cancers(7;0.243)	BRCA - Breast invasive adenocarcinoma(108;0.112)|OV - Ovarian serous cystadenocarcinoma(136;0.173)|all cancers(137;0.191)														---	---	---	---
PDSS2	57107	broad.mit.edu	37	6	107638520	107638520	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107638520delA	uc003prt.2	-						PDSS2_uc011eak.1_Intron|PDSS2_uc011eal.1_Intron|PDSS2_uc003pru.2_Intron|PDSS2_uc003prv.2_Intron	NM_020381	NP_065114			prenyl diphosphate synthase, subunit 2						isoprenoid biosynthetic process|ubiquinone biosynthetic process	mitochondrion	protein heterodimerization activity			ovary(2)	2	Breast(9;0.0127)	all_cancers(87;3.63e-05)|Acute lymphoblastic leukemia(125;2.86e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.0108)|Colorectal(196;0.156)|Lung NSC(302;0.211)	BRCA - Breast invasive adenocarcinoma(8;0.0101)|all cancers(7;0.243)	BRCA - Breast invasive adenocarcinoma(108;0.112)|OV - Ovarian serous cystadenocarcinoma(136;0.173)|all cancers(137;0.191)														---	---	---	---
SOBP	55084	broad.mit.edu	37	6	107955840	107955840	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107955840delC	uc003prx.2	+	6	2296	c.1792delC	c.(1792-1794)CCCfs	p.P598fs		NM_018013	NP_060483	A7XYQ1	SOBP_HUMAN	sine oculis binding protein homolog	598							metal ion binding			ovary(1)	1		all_cancers(87;5.26e-06)|Acute lymphoblastic leukemia(125;2.87e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.00193)|Colorectal(196;0.156)		BRCA - Breast invasive adenocarcinoma(108;0.026)|all cancers(137;0.087)|Epithelial(106;0.104)|OV - Ovarian serous cystadenocarcinoma(136;0.154)														---	---	---	---
SEC63	11231	broad.mit.edu	37	6	108222728	108222730	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108222728_108222730delAAA	uc003psc.3	-						SEC63_uc003psb.3_Intron	NM_007214	NP_009145			SEC63-like protein						protein folding|protein targeting to membrane	endoplasmic reticulum membrane|integral to membrane	heat shock protein binding|receptor activity|unfolded protein binding			ovary(1)|skin(1)	2		all_cancers(87;5.35e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00225)|Colorectal(196;0.0294)		BRCA - Breast invasive adenocarcinoma(108;0.0079)|Epithelial(106;0.0356)|all cancers(137;0.0525)|OV - Ovarian serous cystadenocarcinoma(136;0.054)														---	---	---	---
OSTM1	28962	broad.mit.edu	37	6	108379982	108379985	+	Intron	DEL	AAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108379982_108379985delAAAA	uc003psd.2	-							NM_014028	NP_054747			osteopetrosis associated transmembrane protein 1							integral to membrane				central_nervous_system(1)	1		all_cancers(87;3.82e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000195)|Colorectal(196;0.0293)|all_lung(197;0.0938)		BRCA - Breast invasive adenocarcinoma(108;0.0131)|Epithelial(106;0.0438)|OV - Ovarian serous cystadenocarcinoma(136;0.0571)|all cancers(137;0.0581)														---	---	---	---
LACE1	246269	broad.mit.edu	37	6	108670957	108670957	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108670957delA	uc003psj.2	+							NM_145315	NP_660358			lactation elevated 1								ATP binding			central_nervous_system(1)	1		all_cancers(87;1.5e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;6.79e-05)|Colorectal(196;0.0294)|all_lung(197;0.0486)|Lung SC(18;0.152)		BRCA - Breast invasive adenocarcinoma(108;0.00179)|Epithelial(106;0.0024)|all cancers(137;0.00379)|OV - Ovarian serous cystadenocarcinoma(136;0.0118)														---	---	---	---
FOXO3	2309	broad.mit.edu	37	6	108977339	108977339	+	Intron	DEL	A	-	-	rs146161678		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108977339delA	uc003psk.2	+						FOXO3_uc003psn.2_Intron|FOXO3_uc003psm.2_Intron|FOXO3_uc011ean.1_Intron|FOXO3_uc010kdj.1_5'Flank	NM_201559	NP_963853			forkhead box O3A						antral ovarian follicle growth|apoptosis|embryo development|glucose homeostasis|induction of apoptosis|initiation of primordial ovarian follicle growth|insulin receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|oocyte maturation|ovulation from ovarian follicle|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of erythrocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|tissue development	cytosol|transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding			central_nervous_system(4)|lung(2)	6		all_cancers(87;1.78e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;3.88e-05)|Colorectal(196;0.0294)|all_lung(197;0.0487)|Lung SC(18;0.152)		Epithelial(106;0.000759)|all cancers(137;0.00121)|BRCA - Breast invasive adenocarcinoma(108;0.00163)|OV - Ovarian serous cystadenocarcinoma(136;0.00718)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	109636544	109636544	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109636544delT								C6orf182 (151431 upstream) : CD164 (51174 downstream)																																			---	---	---	---
CDC40	51362	broad.mit.edu	37	6	110528894	110528894	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110528894delT	uc003pua.2	+							NM_015891	NP_056975			cell division cycle 40 homolog						mRNA 3'-end processing|mRNA export from nucleus|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|nucleoplasm					0		all_cancers(87;6.23e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00159)|Colorectal(196;0.0488)		Epithelial(106;0.0221)|all cancers(137;0.0314)|OV - Ovarian serous cystadenocarcinoma(136;0.034)														---	---	---	---
CDC40	51362	broad.mit.edu	37	6	110551052	110551052	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:110551052delT	uc003pua.2	+							NM_015891	NP_056975			cell division cycle 40 homolog						mRNA 3'-end processing|mRNA export from nucleus|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|nucleoplasm					0		all_cancers(87;6.23e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00159)|Colorectal(196;0.0488)		Epithelial(106;0.0221)|all cancers(137;0.0314)|OV - Ovarian serous cystadenocarcinoma(136;0.034)														---	---	---	---
RPF2	84154	broad.mit.edu	37	6	111329614	111329614	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111329614delT	uc003pun.2	+						RPF2_uc003puo.2_Intron	NM_032194	NP_115570			brix domain containing 1							nucleolus	protein binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	111388802	111388802	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111388802delT								GSTM2P1 (20045 upstream) : SLC16A10 (19979 downstream)																																			---	---	---	---
REV3L	5980	broad.mit.edu	37	6	111693720	111693720	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111693720delT	uc003puy.3	-						REV3L_uc003pux.3_Intron|REV3L_uc003puz.3_Intron	NM_002912	NP_002903			DNA polymerase zeta						DNA-dependent DNA replication|translesion synthesis	nucleus|zeta DNA polymerase complex	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|nucleotide binding			large_intestine(2)|ovary(2)|skin(2)	6		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)									DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
FYN	2534	broad.mit.edu	37	6	112021117	112021125	+	Intron	DEL	TTTTTTTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112021117_112021125delTTTTTTTTT	uc003pvj.2	-						FYN_uc003pvi.2_Intron|FYN_uc003pvk.2_Intron|FYN_uc003pvh.2_Intron|FYN_uc010kdy.1_Intron	NM_002037	NP_002028			protein-tyrosine kinase fyn isoform a						axon guidance|calcium ion transport|feeding behavior|interspecies interaction between organisms|intracellular protein kinase cascade|learning|leukocyte migration|platelet activation|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|viral reproduction	cytosol|endosome|plasma membrane	ATP binding|glycoprotein binding|identical protein binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity			lung(5)|central_nervous_system(1)|skin(1)	7		all_cancers(87;1.37e-05)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00125)|Colorectal(196;0.0211)		all cancers(137;0.0451)|OV - Ovarian serous cystadenocarcinoma(136;0.0476)|Epithelial(106;0.102)	Dasatinib(DB01254)													---	---	---	---
LAMA4	3910	broad.mit.edu	37	6	112575076	112575077	+	Intron	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112575076_112575077delGA	uc003pvu.2	-						LAMA4_uc003pvv.2_Intron|LAMA4_uc003pvt.2_Intron|LAMA4_uc003pvw.2_Intron|LAMA4_uc010kdz.1_Frame_Shift_Del_p.S92fs|LAMA4_uc010kea.1_Frame_Shift_Del_p.S92fs	NM_001105206	NP_001098676			laminin, alpha 4 isoform 1 precursor						cell adhesion|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	extracellular matrix structural constituent|receptor binding			ovary(4)|breast(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	9		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	113221100	113221101	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:113221100_113221101delTT								RFPL4B (548602 upstream) : MARCKS (957426 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	113919561	113919561	+	IGR	DEL	A	-	-	rs112224098		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:113919561delA								None (None upstream) : MARCKS (258966 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	113993437	113993440	+	IGR	DEL	AAAG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:113993437_113993440delAAAG								None (None upstream) : MARCKS (185087 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	113997322	113997322	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:113997322delA								None (None upstream) : MARCKS (181205 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	114083194	114083194	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114083194delA								None (None upstream) : MARCKS (95333 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	114119192	114119193	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114119192_114119193delTT								None (None upstream) : MARCKS (59334 downstream)																																			---	---	---	---
HS3ST5	222537	broad.mit.edu	37	6	114486885	114486885	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114486885delT	uc003pwh.3	-						uc003pwf.2_Intron	NM_153612	NP_705840			heparan sulfate (glucosamine)						heparan sulfate proteoglycan biosynthetic process, enzymatic modification|negative regulation of coagulation|protein sulfation|regulation of virion penetration into host cell	Golgi membrane|integral to membrane	3'-phosphoadenosine 5'-phosphosulfate binding|[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity|protein binding			ovary(1)|pancreas(1)	2		all_cancers(87;0.0587)|Colorectal(196;0.0676)|all_epithelial(87;0.154)		OV - Ovarian serous cystadenocarcinoma(136;0.00937)|all cancers(137;0.0117)|Epithelial(106;0.0274)|GBM - Glioblastoma multiforme(226;0.143)														---	---	---	---
HS3ST5	222537	broad.mit.edu	37	6	114615386	114615386	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114615386delA	uc003pwh.3	-						uc003pwf.2_Intron	NM_153612	NP_705840			heparan sulfate (glucosamine)						heparan sulfate proteoglycan biosynthetic process, enzymatic modification|negative regulation of coagulation|protein sulfation|regulation of virion penetration into host cell	Golgi membrane|integral to membrane	3'-phosphoadenosine 5'-phosphosulfate binding|[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity|protein binding			ovary(1)|pancreas(1)	2		all_cancers(87;0.0587)|Colorectal(196;0.0676)|all_epithelial(87;0.154)		OV - Ovarian serous cystadenocarcinoma(136;0.00937)|all cancers(137;0.0117)|Epithelial(106;0.0274)|GBM - Glioblastoma multiforme(226;0.143)														---	---	---	---
HS3ST5	222537	broad.mit.edu	37	6	114662818	114662818	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114662818delG	uc003pwh.3	-							NM_153612	NP_705840			heparan sulfate (glucosamine)						heparan sulfate proteoglycan biosynthetic process, enzymatic modification|negative regulation of coagulation|protein sulfation|regulation of virion penetration into host cell	Golgi membrane|integral to membrane	3'-phosphoadenosine 5'-phosphosulfate binding|[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity|protein binding			ovary(1)|pancreas(1)	2		all_cancers(87;0.0587)|Colorectal(196;0.0676)|all_epithelial(87;0.154)		OV - Ovarian serous cystadenocarcinoma(136;0.00937)|all cancers(137;0.0117)|Epithelial(106;0.0274)|GBM - Glioblastoma multiforme(226;0.143)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	114669652	114669653	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114669652_114669653insT								HS3ST5 (6112 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	114745158	114745159	+	IGR	INS	-	A	A	rs150293684		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114745158_114745159insA								HS3ST5 (81618 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	115216242	115216242	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:115216242delT								HS3ST5 (552702 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	115916622	115916623	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:115916622_115916623delTT								None (None upstream) : FRK (346070 downstream)																																			---	---	---	---
FRK	2444	broad.mit.edu	37	6	116347786	116347786	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116347786delT	uc003pwi.1	-							NM_002031	NP_002022			fyn-related kinase						negative regulation of cell proliferation	cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding			ovary(3)|lung(3)	6		all_cancers(87;0.00559)|all_epithelial(87;0.00738)|Colorectal(196;0.0465)		all cancers(137;0.0128)|OV - Ovarian serous cystadenocarcinoma(136;0.0209)|GBM - Glioblastoma multiforme(226;0.0459)|Epithelial(106;0.0625)														---	---	---	---
DSE	29940	broad.mit.edu	37	6	116669609	116669609	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116669609delA	uc003pws.2	+						DSE_uc011ebf.1_Intron|DSE_uc003pwq.1_Intron|DSE_uc003pwr.2_Intron	NM_001080976	NP_001074445			dermatan sulfate epimerase precursor						dermatan sulfate biosynthetic process	endoplasmic reticulum|Golgi apparatus|integral to membrane	chondroitin-glucuronate 5-epimerase activity			ovary(1)	1		all_cancers(87;0.00019)|all_epithelial(87;0.000416)|Ovarian(999;0.133)|Colorectal(196;0.234)		Epithelial(106;0.00915)|OV - Ovarian serous cystadenocarcinoma(136;0.0149)|GBM - Glioblastoma multiforme(226;0.0189)|all cancers(137;0.0262)														---	---	---	---
DSE	29940	broad.mit.edu	37	6	116736710	116736710	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116736710delT	uc003pws.2	+						DSE_uc011ebf.1_Intron|DSE_uc011ebg.1_Intron|DSE_uc003pwt.2_Intron	NM_001080976	NP_001074445			dermatan sulfate epimerase precursor						dermatan sulfate biosynthetic process	endoplasmic reticulum|Golgi apparatus|integral to membrane	chondroitin-glucuronate 5-epimerase activity			ovary(1)	1		all_cancers(87;0.00019)|all_epithelial(87;0.000416)|Ovarian(999;0.133)|Colorectal(196;0.234)		Epithelial(106;0.00915)|OV - Ovarian serous cystadenocarcinoma(136;0.0149)|GBM - Glioblastoma multiforme(226;0.0189)|all cancers(137;0.0262)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	117102980	117102981	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117102980_117102981delTT								FAM162B (16094 upstream) : GPRC6A (10267 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	117286789	117286789	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117286789delT								RFX6 (33481 upstream) : VGLL2 (299932 downstream)																																			---	---	---	---
GOPC	57120	broad.mit.edu	37	6	117910789	117910790	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117910789_117910790delTT	uc003pxu.2	-						GOPC_uc003pxv.2_Intron	NM_020399	NP_065132			golgi associated PDZ and coiled-coil motif						apical protein localization|cytoplasmic sequestering of CFTR protein|ER to Golgi vesicle-mediated transport|Golgi to plasma membrane transport|protein homooligomerization|protein transport	cell junction|dendrite|Golgi membrane|postsynaptic density|postsynaptic membrane|trans-Golgi network transport vesicle	cystic fibrosis transmembrane conductance regulator binding			ovary(1)	1		all_cancers(87;0.00844)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0363)|OV - Ovarian serous cystadenocarcinoma(136;0.0821)|all cancers(137;0.0976)				O	ROS1	glioblastoma								---	---	---	---
Unknown	0	broad.mit.edu	37	6	118180542	118180542	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118180542delA								NUS1 (148658 upstream) : SLC35F1 (48147 downstream)																																			---	---	---	---
SLC35F1	222553	broad.mit.edu	37	6	118552530	118552530	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118552530delT	uc003pxx.3	+							NM_001029858	NP_001025029			solute carrier family 35, member F1						transport	integral to membrane				breast(1)	1				GBM - Glioblastoma multiforme(226;0.217)														---	---	---	---
SLC35F1	222553	broad.mit.edu	37	6	118598986	118598986	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118598986delA	uc003pxx.3	+						SLC35F1_uc003pxy.1_Intron	NM_001029858	NP_001025029			solute carrier family 35, member F1						transport	integral to membrane				breast(1)	1				GBM - Glioblastoma multiforme(226;0.217)														---	---	---	---
C6orf204	387119	broad.mit.edu	37	6	118861216	118861217	+	Intron	DEL	TT	-	-	rs72331980		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118861216_118861217delTT	uc003pxz.1	-						C6orf204_uc003pya.1_Intron|C6orf204_uc003pyb.2_Intron|C6orf204_uc011ebj.1_Intron|C6orf204_uc003pyc.2_Intron	NM_001042475	NP_001035940			chromosome 6 open reading frame 204 isoform a							centrosome				breast(1)	1		all_cancers(87;0.0814)|all_epithelial(87;0.115)		GBM - Glioblastoma multiforme(226;0.0114)|all cancers(137;0.035)|OV - Ovarian serous cystadenocarcinoma(136;0.0618)														---	---	---	---
C6orf204	387119	broad.mit.edu	37	6	118949796	118949797	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:118949796_118949797insA	uc003pxz.1	-						C6orf204_uc003pya.1_Intron|C6orf204_uc003pyb.2_Intron|C6orf204_uc011ebj.1_Intron|C6orf204_uc003pyc.2_Intron|C6orf204_uc011ebl.1_Intron	NM_001042475	NP_001035940			chromosome 6 open reading frame 204 isoform a							centrosome				breast(1)	1		all_cancers(87;0.0814)|all_epithelial(87;0.115)		GBM - Glioblastoma multiforme(226;0.0114)|all cancers(137;0.035)|OV - Ovarian serous cystadenocarcinoma(136;0.0618)														---	---	---	---
FAM184A	79632	broad.mit.edu	37	6	119469070	119469070	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119469070delT	uc003pyk.3	-						FAM184A_uc003pyl.3_Intron	NM_001100411	NP_001093881			hypothetical protein LOC79632 isoform 2											ovary(2)|central_nervous_system(2)|skin(2)|pancreas(1)	7																		---	---	---	---
MAN1A1	4121	broad.mit.edu	37	6	119562262	119562262	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119562262delT	uc003pym.1	-						MAN1A1_uc010kei.1_Intron	NM_005907	NP_005898			mannosidase, alpha, class 1A, member 1						post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum|ER-Golgi intermediate compartment|Golgi membrane|integral to membrane|membrane fraction	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			ovary(2)|central_nervous_system(1)|skin(1)	4		all_epithelial(87;0.173)		OV - Ovarian serous cystadenocarcinoma(136;0.0612)|GBM - Glioblastoma multiforme(226;0.0702)|all cancers(137;0.115)														---	---	---	---
MAN1A1	4121	broad.mit.edu	37	6	119589760	119589760	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:119589760delT	uc003pym.1	-						MAN1A1_uc010kei.1_Intron	NM_005907	NP_005898			mannosidase, alpha, class 1A, member 1						post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum|ER-Golgi intermediate compartment|Golgi membrane|integral to membrane|membrane fraction	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			ovary(2)|central_nervous_system(1)|skin(1)	4		all_epithelial(87;0.173)		OV - Ovarian serous cystadenocarcinoma(136;0.0612)|GBM - Glioblastoma multiforme(226;0.0702)|all cancers(137;0.115)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	120123370	120123371	+	IGR	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:120123370_120123371delAC								MAN1A1 (452444 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	120179218	120179218	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:120179218delA								MAN1A1 (508292 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	120203200	120203200	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:120203200delT								MAN1A1 (532274 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	120847320	120847320	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:120847320delT								None (None upstream) : C6orf170 (553307 downstream)																																			---	---	---	---
C6orf170	221322	broad.mit.edu	37	6	121435316	121435317	+	Intron	INS	-	CA	CA			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:121435316_121435317insCA	uc003pyo.1	-						C6orf170_uc003pyq.1_Intron|C6orf170_uc010kej.1_Intron|C6orf170_uc003pyp.1_Intron	NM_152730	NP_689943			hypothetical protein LOC221322						multicellular organismal development	cilium|cytoplasm	Rab GTPase activator activity			central_nervous_system(2)|ovary(1)	3				GBM - Glioblastoma multiforme(226;0.00521)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	121779313	121779313	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:121779313delT								GJA1 (8441 upstream) : HSF2 (941383 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	121899846	121899846	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:121899846delA								GJA1 (128974 upstream) : HSF2 (820850 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	122109256	122109256	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122109256delC								GJA1 (338384 upstream) : HSF2 (611440 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	122226204	122226204	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122226204delA								GJA1 (455332 upstream) : HSF2 (494492 downstream)																																			---	---	---	---
HSF2	3298	broad.mit.edu	37	6	122733681	122733681	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122733681delT	uc003pyu.2	+						HSF2_uc003pyt.3_Intron|HSF2_uc003pyv.2_Intron	NM_004506	NP_004497			heat shock transcription factor 2 isoform a						response to stress|transcription from RNA polymerase II promoter	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription coactivator activity				0				OV - Ovarian serous cystadenocarcinoma(136;0.00371)|all cancers(137;0.0299)|GBM - Glioblastoma multiforme(226;0.0586)														---	---	---	---
PKIB	5570	broad.mit.edu	37	6	122971115	122971115	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122971115delT	uc003pyz.2	+						PKIB_uc003pza.2_Intron|PKIB_uc003pzb.2_Intron|PKIB_uc003pzc.2_5'Flank	NM_181794	NP_861459			cAMP-dependent protein kinase inhibitor beta								cAMP-dependent protein kinase inhibitor activity				0				GBM - Glioblastoma multiforme(226;0.164)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	123069463	123069463	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123069463delA								PKIB (21946 upstream) : FABP7 (31183 downstream)																																			---	---	---	---
SMPDL3A	10924	broad.mit.edu	37	6	123117151	123117152	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123117151_123117152insA	uc003pzg.2	+						SMPDL3A_uc003pzh.2_Intron	NM_006714	NP_006705			acid sphingomyelinase-like phosphodiesterase 3A						sphingomyelin catabolic process	extracellular space	hydrolase activity, acting on glycosyl bonds|protein binding|sphingomyelin phosphodiesterase activity				0				GBM - Glioblastoma multiforme(226;0.236)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	123510914	123510915	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123510914_123510915insT								CLVS2 (125851 upstream) : TRDN (26568 downstream)																																			---	---	---	---
TRDN	10345	broad.mit.edu	37	6	123687281	123687281	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123687281delT	uc003pzj.1	-	20	1342	c.1320delA	c.(1318-1320)AAAfs	p.K440fs	TRDN_uc003pzk.1_Frame_Shift_Del_p.K441fs|TRDN_uc003pzl.1_Frame_Shift_Del_p.K441fs|TRDN_uc010kem.1_5'UTR	NM_006073	NP_006064	Q13061	TRDN_HUMAN	triadin	440	Lumenal.				muscle contraction	integral to membrane|plasma membrane|sarcoplasmic reticulum membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(226;0.184)														---	---	---	---
TRDN	10345	broad.mit.edu	37	6	123786155	123786155	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:123786155delA	uc003pzj.1	-						TRDN_uc003pzk.1_Intron|TRDN_uc003pzl.1_Intron|TRDN_uc010ken.2_Intron|uc003pzm.1_Intron	NM_006073	NP_006064			triadin						muscle contraction	integral to membrane|plasma membrane|sarcoplasmic reticulum membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(226;0.184)														---	---	---	---
NKAIN2	154215	broad.mit.edu	37	6	124237878	124237879	+	Intron	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:124237878_124237879delTG	uc003pzo.2	+						NKAIN2_uc003pzn.1_Intron|NKAIN2_uc003pzp.2_Intron|NKAIN2_uc010keq.2_Intron|NKAIN2_uc010kep.1_Intron	NM_001040214	NP_001035304			T-cell lymphoma breakpoint-associated target 1							integral to membrane|plasma membrane					0				GBM - Glioblastoma multiforme(226;0.104)														---	---	---	---
NKAIN2	154215	broad.mit.edu	37	6	124329650	124329651	+	Intron	INS	-	G	G	rs72551958	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:124329650_124329651insG	uc003pzo.2	+						NKAIN2_uc003pzn.1_Intron|NKAIN2_uc003pzp.2_Intron|NKAIN2_uc010keq.2_Intron|NKAIN2_uc010kep.1_Intron	NM_001040214	NP_001035304			T-cell lymphoma breakpoint-associated target 1							integral to membrane|plasma membrane					0				GBM - Glioblastoma multiforme(226;0.104)														---	---	---	---
NKAIN2	154215	broad.mit.edu	37	6	124495735	124495736	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:124495735_124495736insT	uc003pzo.2	+						NKAIN2_uc003pzn.1_Intron|NKAIN2_uc003pzp.2_Intron|NKAIN2_uc010keq.2_Intron|NKAIN2_uc010kep.1_Intron	NM_001040214	NP_001035304			T-cell lymphoma breakpoint-associated target 1							integral to membrane|plasma membrane					0				GBM - Glioblastoma multiforme(226;0.104)														---	---	---	---
NKAIN2	154215	broad.mit.edu	37	6	124678673	124678673	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:124678673delA	uc003pzo.2	+						NKAIN2_uc003pzn.1_Intron|NKAIN2_uc003pzp.2_Intron|NKAIN2_uc010keq.2_Intron|NKAIN2_uc010ker.2_Intron	NM_001040214	NP_001035304			T-cell lymphoma breakpoint-associated target 1							integral to membrane|plasma membrane					0				GBM - Glioblastoma multiforme(226;0.104)														---	---	---	---
NKAIN2	154215	broad.mit.edu	37	6	124979215	124979215	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:124979215delA	uc003pzo.2	+						NKAIN2_uc003pzn.1_Intron|NKAIN2_uc003pzp.2_Intron|NKAIN2_uc010keq.2_Intron|NKAIN2_uc010ker.2_Intron	NM_001040214	NP_001035304			T-cell lymphoma breakpoint-associated target 1							integral to membrane|plasma membrane					0				GBM - Glioblastoma multiforme(226;0.104)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	125423597	125423597	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:125423597delA								RNF217 (18940 upstream) : TPD52L1 (51282 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	125653008	125653008	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:125653008delT								HDDC2 (29726 upstream) : HEY2 (415772 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	127422956	127422957	+	Intron	DEL	AC	-	-	rs67586730		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127422956_127422957delAC	uc003qaq.1	-											Homo sapiens cDNA FLJ45564 fis, clone BRTHA3007469.																														---	---	---	---
ECHDC1	55862	broad.mit.edu	37	6	127622933	127622933	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127622933delT	uc003qax.2	-						ECHDC1_uc003qaz.3_Intron|ECHDC1_uc010key.2_Intron|ECHDC1_uc003qay.3_Intron|ECHDC1_uc010kez.2_Intron|ECHDC1_uc010kex.2_Intron	NM_001139510	NP_001132982			enoyl Coenzyme A hydratase domain containing 1								catalytic activity				0				GBM - Glioblastoma multiforme(226;0.0423)|all cancers(137;0.156)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	127678717	127678718	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127678717_127678718delAA								ECHDC1 (13963 upstream) : C6orf174 (80834 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	127683598	127683599	+	IGR	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127683598_127683599delAG								ECHDC1 (18844 upstream) : C6orf174 (75953 downstream)																																			---	---	---	---
PTPRK	5796	broad.mit.edu	37	6	128400152	128400152	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128400152delA	uc003qbk.2	-						PTPRK_uc003qbj.2_Intron|PTPRK_uc010kfc.2_Intron|PTPRK_uc011ebu.1_Intron|PTPRK_uc003qbl.1_Intron|PTPRK_uc011ebv.1_Intron	NM_002844	NP_002835			protein tyrosine phosphatase, receptor type, K						cell migration|cellular response to reactive oxygen species|cellular response to UV|focal adhesion assembly|negative regulation of cell cycle|negative regulation of cell migration|negative regulation of keratinocyte proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transforming growth factor beta receptor signaling pathway	adherens junction|cell surface|cell-cell junction|integral to plasma membrane|leading edge membrane	beta-catenin binding|gamma-catenin binding|protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|skin(2)|pancreas(1)|kidney(1)|central_nervous_system(1)	8				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)														---	---	---	---
PTPRK	5796	broad.mit.edu	37	6	128531845	128531845	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128531845delT	uc003qbk.2	-						PTPRK_uc003qbj.2_Intron|PTPRK_uc010kfc.2_Intron|PTPRK_uc011ebu.1_Intron|PTPRK_uc003qbl.1_Intron|PTPRK_uc011ebv.1_Intron	NM_002844	NP_002835			protein tyrosine phosphatase, receptor type, K						cell migration|cellular response to reactive oxygen species|cellular response to UV|focal adhesion assembly|negative regulation of cell cycle|negative regulation of cell migration|negative regulation of keratinocyte proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transforming growth factor beta receptor signaling pathway	adherens junction|cell surface|cell-cell junction|integral to plasma membrane|leading edge membrane	beta-catenin binding|gamma-catenin binding|protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|skin(2)|pancreas(1)|kidney(1)|central_nervous_system(1)	8				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)														---	---	---	---
PTPRK	5796	broad.mit.edu	37	6	128580174	128580176	+	Intron	DEL	GAG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:128580174_128580176delGAG	uc003qbk.2	-						PTPRK_uc003qbj.2_Intron|PTPRK_uc010kfc.2_Intron|PTPRK_uc011ebu.1_Intron|PTPRK_uc003qbl.1_Intron|PTPRK_uc011ebv.1_Intron	NM_002844	NP_002835			protein tyrosine phosphatase, receptor type, K						cell migration|cellular response to reactive oxygen species|cellular response to UV|focal adhesion assembly|negative regulation of cell cycle|negative regulation of cell migration|negative regulation of keratinocyte proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transforming growth factor beta receptor signaling pathway	adherens junction|cell surface|cell-cell junction|integral to plasma membrane|leading edge membrane	beta-catenin binding|gamma-catenin binding|protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|skin(2)|pancreas(1)|kidney(1)|central_nervous_system(1)	8				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	129140945	129140946	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129140945_129140946delTT								PTPRK (299075 upstream) : LAMA2 (63340 downstream)																																			---	---	---	---
LAMA2	3908	broad.mit.edu	37	6	129316264	129316264	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129316264delT	uc003qbn.2	+						LAMA2_uc003qbo.2_Intron	NM_000426	NP_000417			laminin alpha 2 subunit isoform a precursor						cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)														---	---	---	---
ARHGAP18	93663	broad.mit.edu	37	6	129936186	129936186	+	Intron	DEL	A	-	-	rs76778866		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129936186delA	uc003qbr.2	-						ARHGAP18_uc011ebw.1_Intron	NM_033515	NP_277050			Rho GTPase activating protein 18						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding			ovary(2)|skin(1)	3				OV - Ovarian serous cystadenocarcinoma(136;0.0621)|GBM - Glioblastoma multiforme(226;0.0638)|all cancers(137;0.074)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	130106550	130106551	+	IGR	INS	-	G	G	rs138293746	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130106550_130106551insG								ARHGAP18 (75180 upstream) : C6orf191 (45840 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	130294063	130294063	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130294063delT								C6orf191 (111647 upstream) : L3MBTL3 (45671 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	130311404	130311405	+	IGR	INS	-	A	A	rs150087999	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130311404_130311405insA								C6orf191 (128988 upstream) : L3MBTL3 (28329 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	130314387	130314387	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130314387delT								C6orf191 (131971 upstream) : L3MBTL3 (25347 downstream)																																			---	---	---	---
L3MBTL3	84456	broad.mit.edu	37	6	130377374	130377374	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130377374delT	uc003qbt.2	+						L3MBTL3_uc003qbu.2_Intron	NM_032438	NP_115814			l(3)mbt-like 3 isoform a						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(5)|skin(1)	6				GBM - Glioblastoma multiforme(226;0.0266)|OV - Ovarian serous cystadenocarcinoma(155;0.154)														---	---	---	---
SAMD3	154075	broad.mit.edu	37	6	130503581	130503581	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130503581delA	uc003qbv.2	-						SAMD3_uc003qbx.2_Intron|SAMD3_uc003qbw.2_Intron|SAMD3_uc010kfg.1_Intron	NM_001017373	NP_001017373			sterile alpha motif domain containing 3 isoform											ovary(1)	1				GBM - Glioblastoma multiforme(226;0.00594)|OV - Ovarian serous cystadenocarcinoma(155;0.128)														---	---	---	---
SAMD3	154075	broad.mit.edu	37	6	130552958	130552958	+	Intron	DEL	T	-	-	rs6569670	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130552958delT	uc003qbx.2	-							NM_001017373	NP_001017373			sterile alpha motif domain containing 3 isoform											ovary(1)	1				GBM - Glioblastoma multiforme(226;0.00594)|OV - Ovarian serous cystadenocarcinoma(155;0.128)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	131016066	131016066	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131016066delA								TMEM200A (251858 upstream) : LOC285733 (132258 downstream)																																			---	---	---	---
EPB41L2	2037	broad.mit.edu	37	6	131199492	131199492	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131199492delA	uc003qch.2	-						EPB41L2_uc003qce.1_Intron|EPB41L2_uc003qcf.1_Intron|EPB41L2_uc003qcg.1_Intron|EPB41L2_uc011eby.1_Intron|EPB41L2_uc003qci.2_Intron|EPB41L2_uc010kfk.2_Intron|EPB41L2_uc010kfl.1_Intron|EPB41L2_uc003qcj.1_5'Flank	NM_001431	NP_001422			erythrocyte membrane protein band 4.1-like 2						cortical actin cytoskeleton organization	extrinsic to membrane|plasma membrane|spectrin	actin binding|structural molecule activity			central_nervous_system(1)|skin(1)	2	Breast(56;0.0639)			OV - Ovarian serous cystadenocarcinoma(155;0.0271)|GBM - Glioblastoma multiforme(226;0.0355)														---	---	---	---
EPB41L2	2037	broad.mit.edu	37	6	131300633	131300640	+	Intron	DEL	AAAAAAAA	-	-	rs148627738		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131300633_131300640delAAAAAAAA	uc003qch.2	-						EPB41L2_uc003qcg.1_Intron|EPB41L2_uc011eby.1_Intron|EPB41L2_uc003qci.2_Intron|EPB41L2_uc010kfk.2_Intron	NM_001431	NP_001422			erythrocyte membrane protein band 4.1-like 2						cortical actin cytoskeleton organization	extrinsic to membrane|plasma membrane|spectrin	actin binding|structural molecule activity			central_nervous_system(1)|skin(1)	2	Breast(56;0.0639)			OV - Ovarian serous cystadenocarcinoma(155;0.0271)|GBM - Glioblastoma multiforme(226;0.0355)														---	---	---	---
EPB41L2	2037	broad.mit.edu	37	6	131346191	131346192	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131346191_131346192delTT	uc003qch.2	-						EPB41L2_uc011eby.1_Intron|EPB41L2_uc003qci.2_Intron|EPB41L2_uc010kfk.2_Intron	NM_001431	NP_001422			erythrocyte membrane protein band 4.1-like 2						cortical actin cytoskeleton organization	extrinsic to membrane|plasma membrane|spectrin	actin binding|structural molecule activity			central_nervous_system(1)|skin(1)	2	Breast(56;0.0639)			OV - Ovarian serous cystadenocarcinoma(155;0.0271)|GBM - Glioblastoma multiforme(226;0.0355)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	131403319	131403319	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131403319delA								EPB41L2 (18857 upstream) : AKAP7 (53552 downstream)																																			---	---	---	---
AKAP7	9465	broad.mit.edu	37	6	131481276	131481276	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131481276delA	uc003qck.2	+	3	262	c.229delA	c.(229-231)AAAfs	p.K77fs	AKAP7_uc011ebz.1_Frame_Shift_Del_p.K55fs	NM_016377	NP_057461	O43687	AKA7A_HUMAN	A-kinase anchor protein 7 isoform gamma	Error:Variant_position_missing_in_O43687_after_alignment					intracellular signal transduction|ion transport	apical plasma membrane|intracellular|lateral plasma membrane	protein kinase A binding			ovary(2)	2	Breast(56;0.152)			GBM - Glioblastoma multiforme(226;0.0184)|OV - Ovarian serous cystadenocarcinoma(155;0.0345)														---	---	---	---
AKAP7	9465	broad.mit.edu	37	6	131498778	131498778	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131498778delA	uc003qck.2	+						AKAP7_uc011ebz.1_Intron|AKAP7_uc003qcl.1_Intron	NM_016377	NP_057461			A-kinase anchor protein 7 isoform gamma						intracellular signal transduction|ion transport	apical plasma membrane|intracellular|lateral plasma membrane	protein kinase A binding			ovary(2)	2	Breast(56;0.152)			GBM - Glioblastoma multiforme(226;0.0184)|OV - Ovarian serous cystadenocarcinoma(155;0.0345)														---	---	---	---
ARG1	383	broad.mit.edu	37	6	131894346	131894346	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131894346delA	uc003qcp.1	+						ARG1_uc003qco.1_5'Flank|ARG1_uc010kfm.1_5'Flank	NM_000045	NP_000036			arginase 1						arginine catabolic process|urea cycle	cytosol	arginase activity			ovary(1)	1	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0106)|OV - Ovarian serous cystadenocarcinoma(155;0.0713)	L-Ornithine(DB00129)													---	---	---	---
MED23	9439	broad.mit.edu	37	6	131936265	131936265	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131936265delA	uc003qcs.1	-						MED23_uc003qcq.2_Intron|MED23_uc003qct.1_Intron|MED23_uc011ecb.1_Intron	NM_004830	NP_004821			mediator complex subunit 23 isoform a						regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	transcription factor complex	protein binding|transcription coactivator activity			ovary(1)|kidney(1)|central_nervous_system(1)	3	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0115)|OV - Ovarian serous cystadenocarcinoma(155;0.0608)														---	---	---	---
ENPP1	5167	broad.mit.edu	37	6	132199544	132199544	+	Intron	DEL	A	-	-	rs75833731		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132199544delA	uc011ecf.1	+							NM_006208	NP_006199			ectonucleotide pyrophosphatase/phosphodiesterase						3'-phosphoadenosine 5'-phosphosulfate metabolic process|biomineral tissue development|cellular phosphate ion homeostasis|cellular response to insulin stimulus|generation of precursor metabolites and energy|immune response|inorganic diphosphate transport|negative regulation of cell growth|negative regulation of fat cell differentiation|negative regulation of glucose import|negative regulation of glycogen biosynthetic process|negative regulation of insulin receptor signaling pathway|negative regulation of protein autophosphorylation|nucleoside triphosphate catabolic process|phosphate metabolic process|sequestering of triglyceride|water-soluble vitamin metabolic process	basolateral plasma membrane|cell surface|extracellular space|integral to membrane	ATP binding|insulin receptor binding|metal ion binding|nucleic acid binding|nucleoside-triphosphate diphosphatase activity|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|protein homodimerization activity|scavenger receptor activity			upper_aerodigestive_tract(2)|ovary(2)	4	Breast(56;0.0505)			GBM - Glioblastoma multiforme(226;0.0216)|OV - Ovarian serous cystadenocarcinoma(155;0.022)	Amifostine(DB01143)|Ribavirin(DB00811)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	132349248	132349248	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132349248delT								CTGF (76730 upstream) : MOXD1 (267947 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	132474464	132474465	+	Intron	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132474464_132474465delTG	uc003qdd.2	+											Homo sapiens full length insert cDNA clone ZC30H06.																														---	---	---	---
MOXD1	26002	broad.mit.edu	37	6	132652636	132652637	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132652636_132652637delTT	uc003qdf.2	-						MOXD1_uc003qde.2_Intron	NM_015529	NP_056344			monooxygenase, DBH-like 1 isoform 2						catecholamine metabolic process	endoplasmic reticulum membrane|integral to membrane	copper ion binding|dopamine beta-monooxygenase activity			ovary(1)	1	Breast(56;0.0495)			OV - Ovarian serous cystadenocarcinoma(155;0.0132)|GBM - Glioblastoma multiforme(226;0.0191)														---	---	---	---
MOXD1	26002	broad.mit.edu	37	6	132705598	132705598	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132705598delG	uc003qdf.2	-							NM_015529	NP_056344			monooxygenase, DBH-like 1 isoform 2						catecholamine metabolic process	endoplasmic reticulum membrane|integral to membrane	copper ion binding|dopamine beta-monooxygenase activity			ovary(1)	1	Breast(56;0.0495)			OV - Ovarian serous cystadenocarcinoma(155;0.0132)|GBM - Glioblastoma multiforme(226;0.0191)														---	---	---	---
VNN3	55350	broad.mit.edu	37	6	133055258	133055258	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133055258delA	uc003qdp.2	-						VNN3_uc010kfs.2_Intron|VNN3_uc011ecl.1_Intron|VNN3_uc011ecm.1_Intron|VNN3_uc011ecn.1_Intron|VNN3_uc010kfu.2_Intron|VNN3_uc010kfv.2_Intron|VNN3_uc010kfw.2_Intron|VNN3_uc010kfx.2_Intron|VNN3_uc010kfy.2_Intron|VNN3_uc010kfz.2_Intron	NM_078625	NP_523239			SubName: Full=PAGEL-beta;												0	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00242)|GBM - Glioblastoma multiforme(226;0.0168)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	133356228	133356229	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133356228_133356229insT								RPS12 (217526 upstream) : LOC285735 (52990 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	133926676	133926676	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:133926676delT	uc003qeg.1	-											Homo sapiens cDNA FLJ36194 fis, clone TESTI2027615.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	134925853	134925853	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:134925853delC	uc003qev.1	-											AJ606331																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	135030676	135030676	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135030676delA								SGK1 (391480 upstream) : ALDH8A1 (207853 downstream)																																			---	---	---	---
HBS1L	10767	broad.mit.edu	37	6	135289383	135289385	+	Intron	DEL	TTT	-	-	rs67893469		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135289383_135289385delTTT	uc003qez.2	-						HBS1L_uc003qey.2_Intron|HBS1L_uc011ecy.1_Intron|HBS1L_uc011ecz.1_Intron|HBS1L_uc011eda.1_Intron	NM_006620	NP_006611			Hsp70 subfamily B suppressor 1-like protein						signal transduction		GTP binding|GTPase activity|translation elongation factor activity			skin(2)	2	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	135600045	135600045	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135600045delA								MIR548A2 (39651 upstream) : AHI1 (5067 downstream)																																			---	---	---	---
AHI1	54806	broad.mit.edu	37	6	135751150	135751150	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135751150delA	uc003qgi.2	-						AHI1_uc003qgf.2_Intron|AHI1_uc003qgg.2_Intron|AHI1_uc003qgh.2_Intron|AHI1_uc003qgj.2_Intron|AHI1_uc003qgk.3_Intron|AHI1_uc003qgl.3_Intron	NM_001134831	NP_001128303			Abelson helper integration site 1 isoform a							adherens junction|cilium|microtubule basal body				ovary(1)|kidney(1)|central_nervous_system(1)	3	Breast(56;0.239)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00904)|OV - Ovarian serous cystadenocarcinoma(155;0.00991)														---	---	---	---
PDE7B	27115	broad.mit.edu	37	6	136359108	136359108	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136359108delA	uc003qgp.2	+						uc003qgq.1_Intron|PDE7B_uc003qgr.2_5'Flank	NM_018945	NP_061818			phosphodiesterase 7B						signal transduction|synaptic transmission	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			ovary(1)	1	Colorectal(23;0.24)			OV - Ovarian serous cystadenocarcinoma(155;0.0136)|GBM - Glioblastoma multiforme(68;0.0147)	Dyphylline(DB00651)|Ketotifen(DB00920)													---	---	---	---
BCLAF1	9774	broad.mit.edu	37	6	136590359	136590359	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136590359delT	uc003qgx.1	-						BCLAF1_uc011edb.1_5'Flank|BCLAF1_uc003qgw.1_Intron|BCLAF1_uc003qgy.1_Intron|BCLAF1_uc011edc.1_RNA|BCLAF1_uc011edd.1_RNA|BCLAF1_uc011ede.1_Intron	NM_014739	NP_055554			BCL2-associated transcription factor 1 isoform						induction of apoptosis|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding			ovary(1)	1	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)														---	---	---	---
BCLAF1	9774	broad.mit.edu	37	6	136606374	136606374	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136606374delA	uc003qgx.1	-						BCLAF1_uc003qgw.1_Intron|BCLAF1_uc003qgy.1_Intron|BCLAF1_uc011edc.1_Intron|BCLAF1_uc011edd.1_Intron|BCLAF1_uc011ede.1_Intron	NM_014739	NP_055554			BCL2-associated transcription factor 1 isoform						induction of apoptosis|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding			ovary(1)	1	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	136619561	136619562	+	IGR	DEL	TG	-	-	rs145189210		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136619561_136619562delTG								BCLAF1 (8572 upstream) : MAP7 (44311 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	136648859	136648859	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136648859delT								BCLAF1 (37870 upstream) : MAP7 (15014 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	136656421	136656426	+	IGR	DEL	TGTCTC	-	-	rs55923771		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:136656421_136656426delTGTCTC								BCLAF1 (45432 upstream) : MAP7 (7447 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	137125265	137125265	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137125265delT								MAP3K5 (11609 upstream) : PEX7 (18437 downstream)																																			---	---	---	---
PEX7	5191	broad.mit.edu	37	6	137209320	137209320	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137209320delA	uc003qhd.2	+						PEX7_uc010kgx.2_Intron	NM_000288	NP_000279			peroxisomal biogenesis factor 7						ether lipid biosynthetic process|protein import into peroxisome matrix	peroxisome	peroxisome matrix targeting signal-2 binding				0	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000257)|OV - Ovarian serous cystadenocarcinoma(155;0.00492)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	138289742	138289742	+	IGR	DEL	A	-	-	rs56725144		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138289742delA								TNFAIP3 (85297 upstream) : PERP (119900 downstream)																																			---	---	---	---
KIAA1244	57221	broad.mit.edu	37	6	138531618	138531618	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138531618delT	uc003qhu.2	+							NM_020340	NP_065073			brefeldin A-inhibited guanine						regulation of ARF protein signal transduction	cytoplasm|integral to membrane	ARF guanyl-nucleotide exchange factor activity			ovary(1)|skin(1)	2	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	138942879	138942879	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:138942879delA								NHSL1 (49211 upstream) : CCDC28A (151778 downstream)																																			---	---	---	---
ECT2L	345930	broad.mit.edu	37	6	139220577	139220578	+	Intron	DEL	TG	-	-	rs60379586		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139220577_139220578delTG	uc003qif.1	+						ECT2L_uc011edq.1_Intron	NM_001077706	NP_001071174			epithelial cell transforming sequence 2						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity				0																		---	---	---	---
REPS1	85021	broad.mit.edu	37	6	139285346	139285346	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139285346delT	uc003qii.2	-						REPS1_uc003qig.3_Intron|REPS1_uc011edr.1_Intron|REPS1_uc003qij.2_Intron|REPS1_uc003qik.2_Intron	NM_031922	NP_114128			RALBP1 associated Eps domain containing 1							coated pit|plasma membrane	calcium ion binding|SH3 domain binding			lung(1)|breast(1)	2				GBM - Glioblastoma multiforme(68;0.000434)|OV - Ovarian serous cystadenocarcinoma(155;0.000548)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	139340224	139340224	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139340224delA								REPS1 (30826 upstream) : C6orf115 (9595 downstream)																																			---	---	---	---
HECA	51696	broad.mit.edu	37	6	139492369	139492369	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139492369delA	uc003qin.2	+							NM_016217	NP_057301			headcase						respiratory tube development						0				GBM - Glioblastoma multiforme(68;0.000252)|OV - Ovarian serous cystadenocarcinoma(155;0.000387)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	140177387	140177388	+	Intron	DEL	TT	-	-	rs66718828		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:140177387_140177388delTT	uc003qir.2	+											Homo sapiens, clone IMAGE:5557975, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	140409577	140409577	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:140409577delT	uc003qis.2	+											Homo sapiens, clone IMAGE:3451765, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	140548220	140548220	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:140548220delA								CITED2 (852435 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	141177143	141177143	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:141177143delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	141177906	141177906	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:141177906delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	141184703	141184703	+	IGR	DEL	T	-	-	rs111408851		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:141184703delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	141681256	141681256	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:141681256delT								None (None upstream) : NMBR (715490 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	141777533	141777533	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:141777533delA								None (None upstream) : NMBR (619213 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	141806520	141806520	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:141806520delT								None (None upstream) : NMBR (590226 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	141975928	141975928	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:141975928delA	uc003qit.1	-											SubName: Full=ORF2-like protein; Flags: Fragment;																														---	---	---	---
GPR126	57211	broad.mit.edu	37	6	142623668	142623669	+	Intron	INS	-	TG	TG			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142623668_142623669insTG	uc010khc.2	+						GPR126_uc010khd.2_Intron|GPR126_uc010khe.2_Intron|GPR126_uc010khf.2_Intron|GPR126_uc003qix.2_Intron	NM_020455	NP_065188			G protein-coupled receptor 126 alpha 1						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)	1	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)														---	---	---	---
GPR126	57211	broad.mit.edu	37	6	142730714	142730714	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142730714delT	uc010khc.2	+						GPR126_uc010khd.2_Intron|GPR126_uc010khe.2_Intron|GPR126_uc010khf.2_Intron	NM_020455	NP_065188			G protein-coupled receptor 126 alpha 1						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)	1	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)														---	---	---	---
HIVEP2	3097	broad.mit.edu	37	6	143202127	143202127	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143202127delT	uc003qjd.2	-							NM_006734	NP_006725			human immunodeficiency virus type I enhancer						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|skin(2)|central_nervous_system(1)	6				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)														---	---	---	---
AIG1	51390	broad.mit.edu	37	6	143409404	143409404	+	Intron	DEL	T	-	-	rs68022476		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143409404delT	uc003qjh.2	+						AIG1_uc003qjf.2_Intron|AIG1_uc003qji.2_Intron|AIG1_uc011edw.1_Intron|AIG1_uc003qjg.2_Intron	NM_016108	NP_057192			androgen-induced 1							integral to membrane					0				OV - Ovarian serous cystadenocarcinoma(155;2.34e-05)|GBM - Glioblastoma multiforme(68;0.0246)														---	---	---	---
PLAGL1	5325	broad.mit.edu	37	6	144266898	144266898	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144266898delT	uc003qjv.2	-						PLAGL1_uc003qjx.2_Intron|PLAGL1_uc003qjy.2_Intron|PLAGL1_uc010khl.2_Intron|PLAGL1_uc010khm.2_Intron|PLAGL1_uc003qjz.2_Intron|PLAGL1_uc003qka.2_Intron|PLAGL1_uc003qkb.2_Intron|PLAGL1_uc003qkc.2_Intron|PLAGL1_uc003qkd.2_Intron|PLAGL1_uc003qke.2_Intron|PLAGL1_uc003qkf.2_Intron|PLAGL1_uc003qkg.2_Intron|PLAGL1_uc003qkh.2_Intron|PLAGL1_uc003qki.2_Intron|PLAGL1_uc003qkj.2_Intron|PLAGL1_uc003qkk.2_Intron|PLAGL1_uc003qkl.2_Intron|PLAGL1_uc003qkm.2_Intron|PLAGL1_uc010khn.2_Intron|PLAGL1_uc003qkn.2_Intron|PLAGL1_uc003qko.2_Intron|PLAGL1_uc003qkp.2_Intron|PLAGL1_uc003qjw.2_Intron	NM_002656	NP_002647			pleiomorphic adenoma gene-like 1 isoform 1						cell cycle arrest|induction of apoptosis|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(155;5.74e-07)|GBM - Glioblastoma multiforme(68;0.0885)														---	---	---	---
PLAGL1	5325	broad.mit.edu	37	6	144335580	144335580	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144335580delA	uc003qkj.2	-						PLAGL1_uc003qki.2_Intron|PLAGL1_uc003qkk.2_Intron|PLAGL1_uc003qkl.2_Intron|PLAGL1_uc003qkm.2_Intron|PLAGL1_uc010khn.2_Intron|PLAGL1_uc003qkn.2_Intron|PLAGL1_uc003qko.2_Intron|PLAGL1_uc003qkp.2_Intron	NM_002656	NP_002647			pleiomorphic adenoma gene-like 1 isoform 1						cell cycle arrest|induction of apoptosis|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(155;5.74e-07)|GBM - Glioblastoma multiforme(68;0.0885)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	144410591	144410591	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144410591delT								PLAGL1 (24856 upstream) : SF3B5 (5427 downstream)																																			---	---	---	---
UTRN	7402	broad.mit.edu	37	6	144685029	144685029	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144685029delT	uc003qkt.2	+						UTRN_uc010khq.1_Intron	NM_007124	NP_009055			utrophin						muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)														---	---	---	---
UTRN	7402	broad.mit.edu	37	6	144772824	144772825	+	Intron	DEL	TT	-	-	rs113888539	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144772824_144772825delTT	uc003qkt.2	+						UTRN_uc010khq.1_Intron	NM_007124	NP_009055			utrophin						muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)														---	---	---	---
UTRN	7402	broad.mit.edu	37	6	144796037	144796037	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144796037delA	uc003qkt.2	+						UTRN_uc010khq.1_Intron	NM_007124	NP_009055			utrophin						muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)														---	---	---	---
UTRN	7402	broad.mit.edu	37	6	144960819	144960819	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144960819delT	uc003qkt.2	+							NM_007124	NP_009055			utrophin						muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)														---	---	---	---
UTRN	7402	broad.mit.edu	37	6	145029206	145029206	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145029206delT	uc003qkt.2	+							NM_007124	NP_009055			utrophin						muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)														---	---	---	---
UTRN	7402	broad.mit.edu	37	6	145103327	145103327	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145103327delT	uc003qkt.2	+							NM_007124	NP_009055			utrophin						muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	145502743	145502743	+	IGR	DEL	A	-	-	rs144345441		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145502743delA								UTRN (328575 upstream) : EPM2A (443703 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	145705237	145705237	+	IGR	DEL	A	-	-	rs67348781		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145705237delA								UTRN (531069 upstream) : EPM2A (241209 downstream)																																			---	---	---	---
GRM1	2911	broad.mit.edu	37	6	146477628	146477628	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146477628delT	uc010khw.1	+						GRM1_uc010khu.1_Intron|GRM1_uc010khv.1_Intron|GRM1_uc003qll.2_Intron|GRM1_uc011edz.1_Intron|GRM1_uc011eea.1_Intron	NM_000838	NP_000829			glutamate receptor, metabotropic 1 isoform alpha						synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(8)|ovary(4)|central_nervous_system(3)|large_intestine(2)|breast(2)	19		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)	Acamprosate(DB00659)|L-Glutamic Acid(DB00142)													---	---	---	---
GRM1	2911	broad.mit.edu	37	6	146515087	146515088	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146515087_146515088delTT	uc010khw.1	+						GRM1_uc010khv.1_Intron|GRM1_uc003qll.2_Intron|GRM1_uc011edz.1_Intron|GRM1_uc011eea.1_Intron	NM_000838	NP_000829			glutamate receptor, metabotropic 1 isoform alpha						synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(8)|ovary(4)|central_nervous_system(3)|large_intestine(2)|breast(2)	19		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)	Acamprosate(DB00659)|L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	147461349	147461349	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147461349delA	uc003qlt.1	-						uc003qlu.1_Intron					Homo sapiens cDNA FLJ34275 fis, clone FEBRA2003454.																														---	---	---	---
STXBP5	134957	broad.mit.edu	37	6	147576274	147576274	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147576274delA	uc003qlz.2	+						STXBP5_uc010khz.1_Intron|STXBP5_uc003qlx.2_Intron|STXBP5_uc003qly.2_Intron	NM_001127715	NP_001121187			syntaxin binding protein 5 (tomosyn) isoform b						exocytosis|positive regulation of exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|nicotinic acetylcholine-gated receptor-channel complex|synaptic vesicle	syntaxin-1 binding				0		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.77e-09)|GBM - Glioblastoma multiforme(68;0.0694)														---	---	---	---
STXBP5	134957	broad.mit.edu	37	6	147695068	147695068	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147695068delT	uc003qlz.2	+						STXBP5_uc010khz.1_Intron|STXBP5_uc003qlx.2_Intron|STXBP5_uc003qly.2_Intron	NM_001127715	NP_001121187			syntaxin binding protein 5 (tomosyn) isoform b						exocytosis|positive regulation of exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|nicotinic acetylcholine-gated receptor-channel complex|synaptic vesicle	syntaxin-1 binding				0		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.77e-09)|GBM - Glioblastoma multiforme(68;0.0694)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	148013110	148013111	+	IGR	INS	-	AC	AC	rs141475823	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148013110_148013111insAC								SAMD5 (121953 upstream) : SASH1 (650618 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	148652995	148652995	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148652995delT								SAMD5 (761838 upstream) : SASH1 (10734 downstream)																																			---	---	---	---
SASH1	23328	broad.mit.edu	37	6	148673145	148673145	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:148673145delA	uc003qme.1	+							NM_015278	NP_056093			SAM and SH3 domain containing 1								protein binding			central_nervous_system(1)	1		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)														---	---	---	---
UST	10090	broad.mit.edu	37	6	149103026	149103026	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149103026delA	uc003qmg.2	+							NM_005715	NP_005706			uronyl-2-sulfotransferase						protein sulfation	Golgi membrane|integral to membrane	sulfotransferase activity			ovary(2)	2		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;1.78e-10)|GBM - Glioblastoma multiforme(68;0.138)														---	---	---	---
UST	10090	broad.mit.edu	37	6	149114802	149114802	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149114802delT	uc003qmg.2	+							NM_005715	NP_005706			uronyl-2-sulfotransferase						protein sulfation	Golgi membrane|integral to membrane	sulfotransferase activity			ovary(2)	2		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;1.78e-10)|GBM - Glioblastoma multiforme(68;0.138)														---	---	---	---
TAB2	23118	broad.mit.edu	37	6	149602068	149602072	+	Intron	DEL	AAAAA	-	-	rs67384567		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149602068_149602072delAAAAA	uc011eec.1	+							NM_015093	NP_055908			mitogen-activated protein kinase kinase kinase 7						activation of MAPK activity|heart development|I-kappaB kinase/NF-kappaB cascade|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane|plasma membrane	K63-linked polyubiquitin binding|zinc ion binding				0																		---	---	---	---
PPIL4	85313	broad.mit.edu	37	6	149849393	149849393	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149849393delA	uc003qmo.1	-						PPIL4_uc010kic.2_Intron|PPIL4_uc003qmp.1_Intron	NM_139126	NP_624311			peptidylprolyl isomerase-like 4						protein folding	nucleus	nucleotide binding|peptidyl-prolyl cis-trans isomerase activity|RNA binding				0		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.11e-11)|GBM - Glioblastoma multiforme(68;0.0885)														---	---	---	---
PCMT1	5110	broad.mit.edu	37	6	150072943	150072943	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150072943delT	uc003qne.2	+						PCMT1_uc003qna.2_Intron|PCMT1_uc003qnb.2_Intron|PCMT1_uc011eeg.1_Intron|PCMT1_uc003qnc.2_Intron|PCMT1_uc003qnd.2_Intron|PCMT1_uc003qnf.2_Intron	NM_005389	NP_005380			protein-L-isoaspartate (D-aspartate)											ovary(1)	1		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.221)	OV - Ovarian serous cystadenocarcinoma(155;5.63e-13)|GBM - Glioblastoma multiforme(68;0.207)														---	---	---	---
PCMT1	5110	broad.mit.edu	37	6	150104831	150104831	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150104831delT	uc003qne.2	+						PCMT1_uc003qna.2_Intron|PCMT1_uc003qnb.2_Intron|PCMT1_uc011eeg.1_Intron|PCMT1_uc003qnc.2_Intron|PCMT1_uc003qnd.2_Intron|PCMT1_uc003qnf.2_Intron	NM_005389	NP_005380			protein-L-isoaspartate (D-aspartate)											ovary(1)	1		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.221)	OV - Ovarian serous cystadenocarcinoma(155;5.63e-13)|GBM - Glioblastoma multiforme(68;0.207)														---	---	---	---
RAET1K	646024	broad.mit.edu	37	6	150328288	150328288	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150328288delT	uc003qnq.2	-							NR_024045				Homo sapiens RAET1K mRNA, partial sequence.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	150604906	150604906	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150604906delT								PPP1R14C (33380 upstream) : IYD (85122 downstream)																																			---	---	---	---
MTHFD1L	25902	broad.mit.edu	37	6	151336482	151336482	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151336482delT	uc003qob.2	+						MTHFD1L_uc011een.1_Intron|MTHFD1L_uc011eeo.1_Intron|MTHFD1L_uc003qoc.2_Intron	NM_015440	NP_056255			methylenetetrahydrofolate dehydrogenase (NADP+						folic acid-containing compound biosynthetic process|formate metabolic process|one-carbon metabolic process|tetrahydrofolate metabolic process	mitochondrion	ATP binding|formate-tetrahydrofolate ligase activity|protein homodimerization activity			ovary(3)|large_intestine(1)	4		Ovarian(120;0.128)		OV - Ovarian serous cystadenocarcinoma(155;8.7e-12)														---	---	---	---
ESR1	2099	broad.mit.edu	37	6	152084643	152084643	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152084643delT	uc003qom.3	+							NM_001122742	NP_001116214			estrogen receptor alpha isoform 4						positive regulation of retinoic acid receptor signaling pathway|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to estradiol stimulus	chromatin remodeling complex|cytoplasm|nucleoplasm	beta-catenin binding|enzyme binding|estrogen receptor activity|estrogen response element binding|nitric-oxide synthase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|zinc ion binding			central_nervous_system(2)|ovary(1)|lung(1)|breast(1)	5		Ovarian(120;0.0448)	BRCA - Breast invasive adenocarcinoma(37;0.0841)	OV - Ovarian serous cystadenocarcinoma(155;4.55e-10)	Chlorotrianisene(DB00269)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Dromostanolone(DB00858)|Drospirenone(DB01395)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Ethynodiol Diacetate(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Letrozole(DB01006)|Levonorgestrel(DB00367)|Medroxyprogesterone(DB00603)|Megestrol(DB00351)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Norgestrel(DB00506)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539)													---	---	---	---
ESR1	2099	broad.mit.edu	37	6	152089798	152089798	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152089798delA	uc003qom.3	+							NM_001122742	NP_001116214			estrogen receptor alpha isoform 4						positive regulation of retinoic acid receptor signaling pathway|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to estradiol stimulus	chromatin remodeling complex|cytoplasm|nucleoplasm	beta-catenin binding|enzyme binding|estrogen receptor activity|estrogen response element binding|nitric-oxide synthase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|zinc ion binding			central_nervous_system(2)|ovary(1)|lung(1)|breast(1)	5		Ovarian(120;0.0448)	BRCA - Breast invasive adenocarcinoma(37;0.0841)	OV - Ovarian serous cystadenocarcinoma(155;4.55e-10)	Chlorotrianisene(DB00269)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Dromostanolone(DB00858)|Drospirenone(DB01395)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Ethynodiol Diacetate(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Letrozole(DB01006)|Levonorgestrel(DB00367)|Medroxyprogesterone(DB00603)|Megestrol(DB00351)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Norgestrel(DB00506)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539)													---	---	---	---
ESR1	2099	broad.mit.edu	37	6	152245971	152245971	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152245971delT	uc003qom.3	+						ESR1_uc010kin.2_Intron|ESR1_uc010kio.2_Intron|ESR1_uc010kip.2_Intron|ESR1_uc003qon.3_Intron|ESR1_uc003qoo.3_Intron|ESR1_uc010kiq.2_Intron|ESR1_uc010kir.2_Intron|ESR1_uc011eet.1_Intron|ESR1_uc011eeu.1_Intron|ESR1_uc011eev.1_Intron|ESR1_uc011eew.1_Intron|ESR1_uc010kis.2_Intron|ESR1_uc011eex.1_Intron	NM_001122742	NP_001116214			estrogen receptor alpha isoform 4						positive regulation of retinoic acid receptor signaling pathway|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to estradiol stimulus	chromatin remodeling complex|cytoplasm|nucleoplasm	beta-catenin binding|enzyme binding|estrogen receptor activity|estrogen response element binding|nitric-oxide synthase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|zinc ion binding			central_nervous_system(2)|ovary(1)|lung(1)|breast(1)	5		Ovarian(120;0.0448)	BRCA - Breast invasive adenocarcinoma(37;0.0841)	OV - Ovarian serous cystadenocarcinoma(155;4.55e-10)	Chlorotrianisene(DB00269)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Dromostanolone(DB00858)|Drospirenone(DB01395)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Ethynodiol Diacetate(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Letrozole(DB01006)|Levonorgestrel(DB00367)|Medroxyprogesterone(DB00603)|Megestrol(DB00351)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Norgestrel(DB00506)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539)													---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152480098	152480098	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152480098delT	uc010kiw.2	-						SYNE1_uc010kiv.2_Intron|SYNE1_uc003qos.3_Intron|SYNE1_uc003qot.3_Intron|SYNE1_uc003qou.3_Intron|SYNE1_uc003qop.3_Intron|SYNE1_uc011eez.1_Intron|SYNE1_uc003qoq.3_Intron|SYNE1_uc003qor.3_Intron	NM_182961	NP_892006			spectrin repeat containing, nuclear envelope 1						cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)											HNSCC(10;0.0054)			---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152642258	152642258	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152642258delT	uc010kiw.2	-						SYNE1_uc010kiv.2_5'Flank|SYNE1_uc003qos.3_5'Flank|SYNE1_uc003qot.3_Intron|SYNE1_uc003qou.3_Intron|SYNE1_uc010kiz.2_Intron	NM_182961	NP_892006			spectrin repeat containing, nuclear envelope 1						cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)											HNSCC(10;0.0054)			---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152793344	152793344	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152793344delA	uc010kiw.2	-						SYNE1_uc003qot.3_Intron|SYNE1_uc003qou.3_Intron|SYNE1_uc010kjb.1_Intron|SYNE1_uc003qpa.1_Intron|SYNE1_uc003qox.1_Intron|SYNE1_uc003qoz.2_Intron|SYNE1_uc003qoy.2_Intron	NM_182961	NP_892006			spectrin repeat containing, nuclear envelope 1						cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)											HNSCC(10;0.0054)			---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152866102	152866102	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152866102delA	uc010kiw.2	-						SYNE1_uc003qot.3_Intron|SYNE1_uc003qou.3_Intron|SYNE1_uc010kjb.1_Intron|SYNE1_uc003qpa.1_Intron	NM_182961	NP_892006			spectrin repeat containing, nuclear envelope 1						cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)											HNSCC(10;0.0054)			---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152889605	152889605	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152889605delT	uc010kiw.2	-						SYNE1_uc003qot.3_Intron|SYNE1_uc003qou.3_Intron|SYNE1_uc010kjb.1_Intron|SYNE1_uc003qpa.1_Intron	NM_182961	NP_892006			spectrin repeat containing, nuclear envelope 1						cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)											HNSCC(10;0.0054)			---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152917406	152917407	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152917406_152917407delTT	uc010kiw.2	-						SYNE1_uc003qot.3_Intron|SYNE1_uc003qou.3_Intron|SYNE1_uc010kjb.1_Intron|SYNE1_uc003qpa.1_Intron	NM_182961	NP_892006			spectrin repeat containing, nuclear envelope 1						cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)											HNSCC(10;0.0054)			---	---	---	---
Unknown	0	broad.mit.edu	37	6	153182465	153182466	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153182465_153182466insA								VIP (101567 upstream) : FBXO5 (109194 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	153603371	153603373	+	IGR	DEL	TTT	-	-	rs113533278	by1000genomes;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153603371_153603373delTTT								RGS17 (150982 upstream) : OPRM1 (728263 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	153936041	153936041	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:153936041delC								RGS17 (483652 upstream) : OPRM1 (395595 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	154037518	154037518	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154037518delT								RGS17 (585129 upstream) : OPRM1 (294118 downstream)																																			---	---	---	---
TIAM2	26230	broad.mit.edu	37	6	155323998	155323998	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155323998delT	uc003qqb.2	+							NM_012454	NP_036586			T-cell lymphoma invasion and metastasis 2						apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			ovary(3)|breast(1)	4		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)														---	---	---	---
NOX3	50508	broad.mit.edu	37	6	155740035	155740035	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155740035delA	uc003qqm.2	-							NM_015718	NP_056533			NADPH oxidase 3								electron carrier activity|flavin adenine dinucleotide binding|iron ion binding			ovary(1)	1		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)														---	---	---	---
NOX3	50508	broad.mit.edu	37	6	155761308	155761308	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155761308delA	uc003qqm.2	-							NM_015718	NP_056533			NADPH oxidase 3								electron carrier activity|flavin adenine dinucleotide binding|iron ion binding			ovary(1)	1		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	155800269	155800270	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155800269_155800270delAA								NOX3 (23232 upstream) : MIR1202 (467661 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	155870101	155870101	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155870101delT								NOX3 (93064 upstream) : MIR1202 (397830 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	156061546	156061546	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:156061546delT								NOX3 (284509 upstream) : MIR1202 (206385 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	156297112	156297112	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:156297112delT								MIR1202 (29099 upstream) : ARID1B (801974 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	156427419	156427419	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:156427419delA								MIR1202 (159406 upstream) : ARID1B (671667 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	156695541	156695541	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:156695541delA								MIR1202 (427528 upstream) : ARID1B (403545 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	157022579	157022579	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157022579delA								MIR1202 (754566 upstream) : ARID1B (76507 downstream)																																			---	---	---	---
ARID1B	57492	broad.mit.edu	37	6	157529244	157529244	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157529244delT	uc003qqn.2	+	20					ARID1B_uc003qqo.2_3'UTR|ARID1B_uc003qqp.2_3'UTR	NM_017519	NP_059989			AT rich interactive domain 1B (SWI1-like)						chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent	SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			ovary(1)|breast(1)	2		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	158213184	158213184	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158213184delT								ZDHHC14 (118208 upstream) : SNX9 (31110 downstream)																																			---	---	---	---
SNX9	51429	broad.mit.edu	37	6	158317948	158317948	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158317948delG	uc003qqv.1	+	5	563	c.390delG	c.(388-390)GAGfs	p.E130fs		NM_016224	NP_057308	Q9Y5X1	SNX9_HUMAN	sorting nexin 9	130					cell communication|intracellular protein transport|lipid tube assembly|positive regulation of GTPase activity|positive regulation of protein oligomerization|receptor-mediated endocytosis	clathrin-coated vesicle|cytoplasmic vesicle membrane|extrinsic to internal side of plasma membrane|ruffle|trans-Golgi network	1-phosphatidylinositol binding|protein homodimerization activity|ubiquitin protein ligase binding				0		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.167)		OV - Ovarian serous cystadenocarcinoma(65;8.06e-18)|BRCA - Breast invasive adenocarcinoma(81;4.48e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	158372430	158372431	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158372430_158372431insA								SNX9 (6321 upstream) : SYNJ2 (30488 downstream)																																			---	---	---	---
SYNJ2	8871	broad.mit.edu	37	6	158418795	158418795	+	Intron	DEL	A	-	-	rs66812044		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158418795delA	uc003qqx.1	+						SYNJ2_uc011efm.1_Intron|SYNJ2_uc003qqw.1_Intron	NM_003898	NP_003889			synaptojanin 2								nucleotide binding|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|RNA binding			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05)														---	---	---	---
SYNJ2	8871	broad.mit.edu	37	6	158496672	158496672	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158496672delA	uc003qqx.1	+						SYNJ2_uc003qqw.1_Intron|SYNJ2_uc003qqy.1_Intron|SYNJ2_uc003qqz.1_Intron|SYNJ2_uc003qra.1_Intron	NM_003898	NP_003889			synaptojanin 2								nucleotide binding|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|RNA binding			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05)														---	---	---	---
SERAC1	84947	broad.mit.edu	37	6	158554885	158554885	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158554885delA	uc003qrc.2	-						SERAC1_uc003qrb.2_Intron	NM_032861	NP_116250			serine active site containing 1						GPI anchor metabolic process|intracellular protein transport	integral to membrane|intrinsic to endoplasmic reticulum membrane	binding|hydrolase activity, acting on ester bonds				0		Breast(66;0.00519)|Ovarian(120;0.123)|Prostate(117;0.178)		OV - Ovarian serous cystadenocarcinoma(65;1.37e-18)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	158671190	158671190	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158671190delT								GTF2H5 (50824 upstream) : TULP4 (62502 downstream)																																			---	---	---	---
TULP4	56995	broad.mit.edu	37	6	158899342	158899342	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158899342delG	uc003qrf.2	+						TULP4_uc011efo.1_Intron|TULP4_uc003qrg.2_Intron	NM_020245	NP_064630			tubby like protein 4 isoform 1						intracellular signal transduction|response to nutrient	cytoplasm	protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)														---	---	---	---
TMEM181	57583	broad.mit.edu	37	6	158959487	158959488	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158959487_158959488delTT	uc003qrm.3	+						TMEM181_uc010kjr.1_Intron	NM_020823	NP_065874			G protein-coupled receptor 178						pathogenesis	integral to membrane	toxin binding			ovary(2)|central_nervous_system(1)	3		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;8.15e-18)|BRCA - Breast invasive adenocarcinoma(81;1.38e-05)														---	---	---	---
EZR	7430	broad.mit.edu	37	6	159215009	159215009	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159215009delA	uc003qrt.3	-						EZR_uc011efs.1_Intron|EZR_uc003qru.3_Intron	NM_003379	NP_003370			ezrin						actin filament bundle assembly|axon guidance|cytoskeletal anchoring at plasma membrane|leukocyte cell-cell adhesion|membrane to membrane docking|regulation of cell shape	actin filament|apical plasma membrane|basolateral plasma membrane|cortical cytoskeleton|cytosol|extrinsic to membrane|filopodium|microvillus membrane|nucleolus|ruffle membrane	actin filament binding|cell adhesion molecule binding			ovary(1)	1		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.16e-17)|BRCA - Breast invasive adenocarcinoma(81;6.58e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	159245976	159245976	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:159245976delT								EZR (5520 upstream) : OSTCL (16184 downstream)																																			---	---	---	---
SOD2	6648	broad.mit.edu	37	6	160103796	160103796	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160103796delT	uc003qsg.2	-						SOD2_uc003qsf.3_5'Flank|SOD2_uc003qsh.2_Intron|SOD2_uc003qsi.1_Intron|SOD2_uc011efu.1_Intron|SOD2_uc011efv.1_Intron	NM_001024465	NP_001019636			manganese superoxide dismutase isoform A						age-dependent response to reactive oxygen species|negative regulation of neuron apoptosis|oxygen homeostasis|protein homotetramerization|regulation of transcription from RNA polymerase II promoter|release of cytochrome c from mitochondria|removal of superoxide radicals|vasodilation by acetylcholine involved in regulation of systemic arterial blood pressure		manganese ion binding|superoxide dismutase activity				0		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.103)		OV - Ovarian serous cystadenocarcinoma(65;1.4e-18)|BRCA - Breast invasive adenocarcinoma(81;5.77e-06)														---	---	---	---
WTAP	9589	broad.mit.edu	37	6	160145892	160145892	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160145892delA	uc003qsl.2	+						WTAP_uc010kjx.2_5'Flank|WTAP_uc003qsk.2_5'Flank|WTAP_uc003qsm.1_5'Flank|WTAP_uc003qsn.2_5'Flank	NM_004906	NP_004897			Wilms' tumour 1-associating protein isoform 1						cell cycle|mRNA processing|RNA splicing	nuclear membrane|nucleolus					0		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.75e-18)|BRCA - Breast invasive adenocarcinoma(81;5.93e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	160265505	160265505	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160265505delG								PNLDC1 (23770 upstream) : MAS1 (62469 downstream)																																			---	---	---	---
IGF2R	3482	broad.mit.edu	37	6	160483802	160483802	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160483802delT	uc003qta.2	+							NM_000876	NP_000867			insulin-like growth factor 2 receptor precursor						receptor-mediated endocytosis	cell surface|endocytic vesicle|endosome|integral to plasma membrane|lysosomal membrane|trans-Golgi network transport vesicle	glycoprotein binding|insulin-like growth factor receptor activity|phosphoprotein binding|transporter activity			ovary(3)	3		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	160877767	160877767	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160877767delT								SLC22A3 (1754 upstream) : LPAL2 (9820 downstream)																																			---	---	---	---
LPA	4018	broad.mit.edu	37	6	161017426	161017428	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161017426_161017428delTTT	uc003qtl.2	-							NM_005577	NP_005568			lipoprotein Lp(a) precursor						blood circulation|lipid metabolic process|lipid transport|lipoprotein metabolic process|proteolysis|receptor-mediated endocytosis	plasma lipoprotein particle	apolipoprotein binding|endopeptidase inhibitor activity|fibronectin binding|heparin binding|serine-type endopeptidase activity			ovary(3)|skin(2)|pancreas(1)	6		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	161211638	161211638	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161211638delA								PLG (37293 upstream) : MAP3K4 (201184 downstream)																																			---	---	---	---
AGPAT4	56895	broad.mit.edu	37	6	161600389	161600390	+	Intron	INS	-	G	G	rs74853816	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161600389_161600390insG	uc003qtr.1	-						AGPAT4_uc003qts.1_Intron|AGPAT4_uc011egb.1_Intron|AGPAT4_uc003qtt.1_Intron|AGPAT4_uc011egc.1_Intron|AGPAT4_uc011egd.1_Intron|AGPAT4_uc011ege.1_Intron	NM_020133	NP_064518			1-acylglycerol-3-phosphate O-acyltransferase 4						phospholipid biosynthetic process	integral to membrane	1-acylglycerol-3-phosphate O-acyltransferase activity|protein binding				0		Breast(66;0.000289)|Ovarian(120;0.0266)|Prostate(117;0.0285)		OV - Ovarian serous cystadenocarcinoma(65;2.23e-17)|BRCA - Breast invasive adenocarcinoma(81;3.58e-05)														---	---	---	---
PARK2	5071	broad.mit.edu	37	6	161889332	161889333	+	Intron	DEL	AA	-	-	rs34739701		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161889332_161889333delAA	uc003qtx.3	-						PARK2_uc003qtv.3_Intron|PARK2_uc010kkd.2_Intron|PARK2_uc003qtw.3_Intron|PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc011egf.1_Intron	NM_004562	NP_004553			parkin isoform 1						aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)														---	---	---	---
PARK2	5071	broad.mit.edu	37	6	162017336	162017336	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162017336delA	uc003qtx.3	-						PARK2_uc003qtv.3_Intron|PARK2_uc010kkd.2_Intron|PARK2_uc003qtw.3_Intron|PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc010kke.1_Intron|PARK2_uc011egf.1_Intron	NM_004562	NP_004553			parkin isoform 1						aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)														---	---	---	---
PARK2	5071	broad.mit.edu	37	6	162131888	162131889	+	Intron	INS	-	TTT	TTT	rs57835841		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162131888_162131889insTTT	uc003qtx.3	-						PARK2_uc003qtv.3_Intron|PARK2_uc010kkd.2_Intron|PARK2_uc003qtw.3_Intron|PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc010kke.1_Intron|PARK2_uc011egf.1_Intron	NM_004562	NP_004553			parkin isoform 1						aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)														---	---	---	---
PARK2	5071	broad.mit.edu	37	6	162252835	162252836	+	Intron	INS	-	G	G	rs139559362	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162252835_162252836insG	uc003qtx.3	-						PARK2_uc003qtv.3_Intron|PARK2_uc010kkd.2_Intron|PARK2_uc003qtw.3_Intron|PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc010kke.1_Intron|PARK2_uc011egf.1_Intron	NM_004562	NP_004553			parkin isoform 1						aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)														---	---	---	---
PARK2	5071	broad.mit.edu	37	6	162656676	162656676	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:162656676delA	uc003qtx.3	-						PARK2_uc003qtv.3_Intron|PARK2_uc010kkd.2_Intron|PARK2_uc003qtw.3_Intron|PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc010kke.1_Intron	NM_004562	NP_004553			parkin isoform 1						aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)														---	---	---	---
PARK2	5071	broad.mit.edu	37	6	163049404	163049404	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163049404delA	uc003qtx.3	-						PARK2_uc003qty.3_Intron|PARK2_uc003qtz.3_Intron|PARK2_uc010kke.1_Intron	NM_004562	NP_004553			parkin isoform 1						aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein monoubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of autophagy|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			upper_aerodigestive_tract(1)	1		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)														---	---	---	---
PACRG	135138	broad.mit.edu	37	6	163186427	163186428	+	Intron	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163186427_163186428insC	uc003qua.2	+						PACRG_uc003qub.2_Intron|PACRG_uc003quc.2_Intron	NM_152410	NP_689623			parkin co-regulated gene protein isoform 1												0		Breast(66;2.41e-05)|Ovarian(120;0.0245)|Prostate(117;0.0273)|all_neural(5;0.0416)|Glioma(2;0.203)		OV - Ovarian serous cystadenocarcinoma(33;4.31e-19)|GBM - Glioblastoma multiforme(2;7.42e-11)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)|KIRC - Kidney renal clear cell carcinoma(3;0.205)|Kidney(3;0.242)														---	---	---	---
PACRG	135138	broad.mit.edu	37	6	163648034	163648034	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163648034delA	uc003qua.2	+						PACRG_uc003qub.2_Intron|PACRG_uc003quc.2_Intron	NM_152410	NP_689623			parkin co-regulated gene protein isoform 1												0		Breast(66;2.41e-05)|Ovarian(120;0.0245)|Prostate(117;0.0273)|all_neural(5;0.0416)|Glioma(2;0.203)		OV - Ovarian serous cystadenocarcinoma(33;4.31e-19)|GBM - Glioblastoma multiforme(2;7.42e-11)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)|KIRC - Kidney renal clear cell carcinoma(3;0.205)|Kidney(3;0.242)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	163778747	163778747	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163778747delG								LOC285796 (33253 upstream) : QKI (56928 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	163791601	163791601	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163791601delT								LOC285796 (46107 upstream) : QKI (44074 downstream)																																			---	---	---	---
QKI	9444	broad.mit.edu	37	6	163834006	163834006	+	5'Flank	DEL	A	-	-	rs73244749	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163834006delA	uc003qui.2	+						QKI_uc003que.2_5'Flank|QKI_uc003quf.2_5'Flank|QKI_uc003qug.2_5'Flank|QKI_uc003quh.2_5'Flank|QKI_uc003quj.2_5'Flank	NM_006775	NP_006766			quaking homolog, KH domain RNA binding isoform						mRNA processing|mRNA transport|regulation of translation|RNA splicing	cytoplasm|nucleus|plasma membrane	RNA binding|SH3 domain binding			large_intestine(1)|ovary(1)	2		Breast(66;5e-05)|Prostate(117;0.0235)|all_neural(5;0.0416)|Ovarian(120;0.0448)|Glioma(2;0.203)		all cancers(1;4.4e-46)|OV - Ovarian serous cystadenocarcinoma(33;6.91e-23)|GBM - Glioblastoma multiforme(1;2.94e-19)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|Kidney(3;0.000199)|KIRC - Kidney renal clear cell carcinoma(3;0.000234)														---	---	---	---
QKI	9444	broad.mit.edu	37	6	163842103	163842103	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163842103delA	uc003qui.2	+						QKI_uc003que.2_Intron|QKI_uc003quf.2_Intron|QKI_uc003qug.2_Intron|QKI_uc003quh.2_Intron|QKI_uc003quj.2_Intron	NM_006775	NP_006766			quaking homolog, KH domain RNA binding isoform						mRNA processing|mRNA transport|regulation of translation|RNA splicing	cytoplasm|nucleus|plasma membrane	RNA binding|SH3 domain binding			large_intestine(1)|ovary(1)	2		Breast(66;5e-05)|Prostate(117;0.0235)|all_neural(5;0.0416)|Ovarian(120;0.0448)|Glioma(2;0.203)		all cancers(1;4.4e-46)|OV - Ovarian serous cystadenocarcinoma(33;6.91e-23)|GBM - Glioblastoma multiforme(1;2.94e-19)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|Kidney(3;0.000199)|KIRC - Kidney renal clear cell carcinoma(3;0.000234)														---	---	---	---
QKI	9444	broad.mit.edu	37	6	163987932	163987933	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:163987932_163987933insT	uc003qui.2	+						QKI_uc003que.2_3'UTR|QKI_uc003quf.2_3'UTR|QKI_uc003qug.2_3'UTR|QKI_uc003quh.2_3'UTR|QKI_uc003quj.2_Intron	NM_006775	NP_006766			quaking homolog, KH domain RNA binding isoform						mRNA processing|mRNA transport|regulation of translation|RNA splicing	cytoplasm|nucleus|plasma membrane	RNA binding|SH3 domain binding			large_intestine(1)|ovary(1)	2		Breast(66;5e-05)|Prostate(117;0.0235)|all_neural(5;0.0416)|Ovarian(120;0.0448)|Glioma(2;0.203)		all cancers(1;4.4e-46)|OV - Ovarian serous cystadenocarcinoma(33;6.91e-23)|GBM - Glioblastoma multiforme(1;2.94e-19)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|Kidney(3;0.000199)|KIRC - Kidney renal clear cell carcinoma(3;0.000234)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	164042519	164042519	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164042519delA								QKI (47627 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	164287051	164287052	+	IGR	INS	-	A	A	rs147851731	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164287051_164287052insA								QKI (292159 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	164369854	164369854	+	IGR	DEL	T	-	-	rs66934921		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164369854delT								QKI (374962 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	164437104	164437107	+	IGR	DEL	TGTG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:164437104_164437107delTGTG								QKI (442212 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	165128485	165128486	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165128485_165128486insT								None (None upstream) : C6orf118 (564669 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	165260198	165260200	+	IGR	DEL	TTG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165260198_165260200delTTG								None (None upstream) : C6orf118 (432955 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	165646174	165646174	+	IGR	DEL	T	-	-	rs74726924		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165646174delT								None (None upstream) : C6orf118 (46981 downstream)																																			---	---	---	---
PDE10A	10846	broad.mit.edu	37	6	165827478	165827478	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165827478delA	uc003qun.2	-						PDE10A_uc011egj.1_Intron|PDE10A_uc011egk.1_Intron|PDE10A_uc003quo.2_Intron	NM_006661	NP_006652			phosphodiesterase 10A isoform 2						platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cAMP binding|cGMP binding|metal ion binding			ovary(3)|skin(2)	5		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Dipyridamole(DB00975)													---	---	---	---
PDE10A	10846	broad.mit.edu	37	6	165957360	165957361	+	Intron	DEL	GT	-	-	rs72310587		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:165957360_165957361delGT	uc003qun.2	-						PDE10A_uc011egj.1_Intron|PDE10A_uc011egk.1_Intron|PDE10A_uc003quo.2_Intron	NM_006661	NP_006652			phosphodiesterase 10A isoform 2						platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cAMP binding|cGMP binding|metal ion binding			ovary(3)|skin(2)	5		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Dipyridamole(DB00975)													---	---	---	---
Unknown	0	broad.mit.edu	37	6	166153071	166153071	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166153071delT								PDE10A (77487 upstream) : C6orf176 (184465 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	166259565	166259565	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166259565delT	uc003qup.1	-											Homo sapiens cDNA FLJ33369 fis, clone BRACE2005904.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	166325710	166325711	+	Intron	INS	-	AC	AC			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166325710_166325711insAC	uc003qup.1	-											Homo sapiens cDNA FLJ33369 fis, clone BRACE2005904.																														---	---	---	---
C6orf176	90632	broad.mit.edu	37	6	166352856	166352856	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166352856delT	uc011egl.1	-						uc003qup.1_Intron	NR_026861				Homo sapiens cDNA FLJ76352 complete cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	166822308	166822308	+	IGR	DEL	A	-	-	rs111304849		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166822308delA								BRP44L (25822 upstream) : RPS6KA2 (546 downstream)																																			---	---	---	---
RPS6KA2	6196	broad.mit.edu	37	6	166843613	166843613	+	Intron	DEL	T	-	-	rs111475748		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166843613delT	uc003qvb.1	-						RPS6KA2_uc011ego.1_Intron|RPS6KA2_uc010kkl.1_Intron|RPS6KA2_uc003qvc.1_Intron|RPS6KA2_uc003qvd.1_Intron	NM_021135	NP_066958			ribosomal protein S6 kinase, 90kDa, polypeptide						axon guidance|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|skin(2)|large_intestine(1)|central_nervous_system(1)	8		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)														---	---	---	---
RPS6KA2	6196	broad.mit.edu	37	6	166901903	166901903	+	Intron	DEL	G	-	-	rs9366022	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166901903delG	uc003qvb.1	-						RPS6KA2_uc011ego.1_Intron|RPS6KA2_uc010kkl.1_Intron|RPS6KA2_uc003qvc.1_Intron|RPS6KA2_uc003qvd.1_Intron	NM_021135	NP_066958			ribosomal protein S6 kinase, 90kDa, polypeptide						axon guidance|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|skin(2)|large_intestine(1)|central_nervous_system(1)	8		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)														---	---	---	---
RPS6KA2	6196	broad.mit.edu	37	6	166975049	166975049	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166975049delG	uc003qvb.1	-						RPS6KA2_uc003qvc.1_Intron|RPS6KA2_uc003qvd.1_Intron	NM_021135	NP_066958			ribosomal protein S6 kinase, 90kDa, polypeptide						axon guidance|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|skin(2)|large_intestine(1)|central_nervous_system(1)	8		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)														---	---	---	---
RPS6KA2	6196	broad.mit.edu	37	6	167087908	167087908	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167087908delT	uc003qvd.1	-						RPS6KA2_uc003qvc.1_Intron	NM_021135	NP_066958			ribosomal protein S6 kinase, 90kDa, polypeptide						axon guidance|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|skin(2)|large_intestine(1)|central_nervous_system(1)	8		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)														---	---	---	---
RPS6KA2	6196	broad.mit.edu	37	6	167268880	167268882	+	Intron	DEL	AGA	-	-	rs13198675		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167268880_167268882delAGA	uc003qvd.1	-						RPS6KA2_uc003qvc.1_Intron	NM_021135	NP_066958			ribosomal protein S6 kinase, 90kDa, polypeptide						axon guidance|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|skin(2)|large_intestine(1)|central_nervous_system(1)	8		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)														---	---	---	---
RNASET2	8635	broad.mit.edu	37	6	167343955	167343956	+	Intron	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167343955_167343956delAC	uc003qve.2	-						RNASET2_uc003qvh.2_Intron|RNASET2_uc003qvf.2_Intron|RNASET2_uc003qvg.2_Intron	NM_003730	NP_003721			ribonuclease T2 precursor						RNA catabolic process	extracellular region	ribonuclease T2 activity|RNA binding				0		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;1.53e-19)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00665)														---	---	---	---
RNASET2	8635	broad.mit.edu	37	6	167377923	167377923	+	Intron	DEL	T	-	-	rs145188497		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167377923delT	uc003qvh.2	-											Homo sapiens mRNA for extra-cellular ribonuclease (RNASE6PL gene).						RNA catabolic process	extracellular region	ribonuclease T2 activity|RNA binding				0		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;1.53e-19)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00665)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	167818411	167818411	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167818411delC								TCP10 (20413 upstream) : C6orf123 (366810 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	167898565	167898565	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167898565delA								TCP10 (100567 upstream) : C6orf123 (286656 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	168201288	168201288	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168201288delA								C6orf123 (3749 upstream) : C6orf124 (23282 downstream)																																			---	---	---	---
MLLT4	4301	broad.mit.edu	37	6	168355084	168355084	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168355084delT	uc003qwd.2	+						MLLT4_uc003qwc.1_Intron|MLLT4_uc003qwg.1_Intron	NM_001040001	NP_001035090			myeloid/lymphoid or mixed-lineage leukemia						adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction	adherens junction|cell-cell junction|cytosol|nucleus	protein C-terminus binding			ovary(2)|lung(1)|kidney(1)|central_nervous_system(1)	5		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)				T	MLL	AL								---	---	---	---
Unknown	0	broad.mit.edu	37	6	168394852	168394853	+	Intron	DEL	TT	-	-	rs139829733		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168394852_168394853delTT	uc003qwi.2	-											Homo sapiens HGC6.1.1 mRNA, complete cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	6	168603376	168603376	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168603376delT								FRMD1 (123537 upstream) : DACT2 (104210 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	6	168785545	168785545	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168785545delC								DACT2 (65143 upstream) : SMOC2 (56486 downstream)																																			---	---	---	---
SMOC2	64094	broad.mit.edu	37	6	168932321	168932321	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168932321delC	uc003qws.1	+						SMOC2_uc003qwr.1_Intron	NM_022138	NP_071421			SPARC related modular calcium binding 2						signal transduction	basement membrane	calcium ion binding			ovary(1)	1		Breast(66;0.000141)|Esophageal squamous(34;0.222)|Ovarian(120;0.231)		OV - Ovarian serous cystadenocarcinoma(33;1.31e-19)|BRCA - Breast invasive adenocarcinoma(81;3.06e-06)|GBM - Glioblastoma multiforme(31;0.00109)														---	---	---	---
SMOC2	64094	broad.mit.edu	37	6	168959611	168959612	+	Intron	DEL	GT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168959611_168959612delGT	uc003qws.1	+						SMOC2_uc003qwr.1_Intron	NM_022138	NP_071421			SPARC related modular calcium binding 2						signal transduction	basement membrane	calcium ion binding			ovary(1)	1		Breast(66;0.000141)|Esophageal squamous(34;0.222)|Ovarian(120;0.231)		OV - Ovarian serous cystadenocarcinoma(33;1.31e-19)|BRCA - Breast invasive adenocarcinoma(81;3.06e-06)|GBM - Glioblastoma multiforme(31;0.00109)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	169224203	169224203	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169224203delT								SMOC2 (155532 upstream) : THBS2 (391673 downstream)																																			---	---	---	---
THBS2	7058	broad.mit.edu	37	6	169644409	169644410	+	Intron	DEL	AC	-	-	rs35075375		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169644409_169644410delAC	uc003qwt.2	-							NM_003247	NP_003238			thrombospondin 2 precursor						cell adhesion	extracellular region	calcium ion binding|heparin binding|protein binding|structural molecule activity			ovary(5)	5		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)														---	---	---	---
Unknown	0	broad.mit.edu	37	6	169763293	169763294	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169763293_169763294delTG								THBS2 (109156 upstream) : WDR27 (94013 downstream)																																			---	---	---	---
C6orf70	55780	broad.mit.edu	37	6	170181412	170181412	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170181412delT	uc003qxg.1	+						C6orf70_uc011ehb.1_Intron|C6orf70_uc003qxh.1_Intron|C6orf70_uc010kky.1_Intron|C6orf70_uc003qxi.1_Intron	NM_018341	NP_060811			hypothetical protein LOC55780							integral to membrane				ovary(1)	1		Breast(66;5.08e-05)|Ovarian(120;0.208)		OV - Ovarian serous cystadenocarcinoma(33;1.2e-22)|BRCA - Breast invasive adenocarcinoma(81;1.49e-07)|GBM - Glioblastoma multiforme(31;0.00191)														---	---	---	---
PSMB1	5689	broad.mit.edu	37	6	170846946	170846949	+	Intron	DEL	CAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170846946_170846949delCAAA	uc011ehe.1	-						PSMB1_uc003qxq.2_Intron|PSMB1_uc003qxr.2_Intron	NM_002793	NP_002784			proteasome beta 1 subunit precursor						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cell junction|cytoplasm|nucleus|proteasome core complex	protein binding|threonine-type endopeptidase activity			ovary(1)	1		Breast(66;5.08e-05)|Ovarian(120;0.0563)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;7.5e-23)|BRCA - Breast invasive adenocarcinoma(81;4.88e-06)|GBM - Glioblastoma multiforme(31;0.00643)	Bortezomib(DB00188)													---	---	---	---
PSMB1	5689	broad.mit.edu	37	6	170862211	170862211	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170862211delT	uc011ehe.1	-						PSMB1_uc003qxq.2_Intron|PSMB1_uc003qxr.2_5'Flank|TBP_uc003qxt.2_5'Flank|TBP_uc003qxu.2_5'Flank|TBP_uc011ehf.1_5'Flank	NM_002793	NP_002784			proteasome beta 1 subunit precursor						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cell junction|cytoplasm|nucleus|proteasome core complex	protein binding|threonine-type endopeptidase activity			ovary(1)	1		Breast(66;5.08e-05)|Ovarian(120;0.0563)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;7.5e-23)|BRCA - Breast invasive adenocarcinoma(81;4.88e-06)|GBM - Glioblastoma multiforme(31;0.00643)	Bortezomib(DB00188)													---	---	---	---
FAM20C	56975	broad.mit.edu	37	7	215238	215238	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:215238delA	uc003sip.2	+							NM_020223	NP_064608			family with sequence similarity 20, member C							extracellular region					0		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.57e-17)|Epithelial(4;1.26e-16)|all cancers(6;4.79e-14)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	414095	414098	+	IGR	DEL	AGGG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:414095_414098delAGGG								FAM20C (113384 upstream) : PDGFA (122801 downstream)																																			---	---	---	---
C7orf50	84310	broad.mit.edu	37	7	1054835	1054835	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1054835delG	uc003sju.2	-						C7orf50_uc003sjs.2_Intron|C7orf50_uc011jvt.1_Intron|C7orf50_uc011jvu.1_Intron	NM_032350	NP_115726			hypothetical protein LOC84310								protein binding				0		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0216)|OV - Ovarian serous cystadenocarcinoma(56;1.3e-15)														---	---	---	---
C7orf50	84310	broad.mit.edu	37	7	1167118	1167118	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1167118delA	uc003sju.2	-						C7orf50_uc011jvt.1_Intron|C7orf50_uc011jvu.1_Intron	NM_032350	NP_115726			hypothetical protein LOC84310								protein binding				0		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0216)|OV - Ovarian serous cystadenocarcinoma(56;1.3e-15)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	1284622	1284622	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1284622delA								UNCX (8010 upstream) : MICALL2 (189374 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	1439549	1439550	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1439549_1439550delTT								UNCX (162937 upstream) : MICALL2 (34446 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	1464604	1464604	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1464604delT								UNCX (187992 upstream) : MICALL2 (9392 downstream)																																			---	---	---	---
INTS1	26173	broad.mit.edu	37	7	1527075	1527075	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1527075delG	uc003skn.2	-	20	2628	c.2527delC	c.(2527-2529)CGGfs	p.R843fs	INTS1_uc003skp.1_Frame_Shift_Del_p.R190fs	NM_001080453	NP_001073922	Q8N201	INT1_HUMAN	integrator complex subunit 1	843					snRNA processing	integral to membrane|integrator complex|nuclear membrane					0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	1641593	1641593	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1641593delC								KIAA1908 (12334 upstream) : TFAMP1 (12513 downstream)																																			---	---	---	---
MAD1L1	8379	broad.mit.edu	37	7	2027201	2027201	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2027201delG	uc003slh.1	-						MAD1L1_uc003sle.1_Intron|MAD1L1_uc003slf.1_Intron|MAD1L1_uc003slg.1_Intron|MAD1L1_uc010ksh.1_Intron|MAD1L1_uc003sli.1_Intron|MAD1L1_uc010ksi.1_Intron|MAD1L1_uc010ksj.2_Intron	NM_001013836	NP_001013858			MAD1-like 1 protein						cell division|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase|mitotic prometaphase|mitotic telophase	actin cytoskeleton|centrosome|condensed chromosome kinetochore|cytosol|mitochondrion|nucleus|spindle	protein binding			lung(1)|central_nervous_system(1)	2		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)														---	---	---	---
SNX8	29886	broad.mit.edu	37	7	2330933	2330933	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2330933delA	uc003slw.2	-							NM_013321	NP_037453			sorting nexin 8						cell communication|early endosome to Golgi transport|intracellular protein transport	early endosome membrane	phosphatidylinositol binding|protein binding			large_intestine(1)|ovary(1)	2		Ovarian(82;0.11)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0853)|OV - Ovarian serous cystadenocarcinoma(56;3.79e-14)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	2422826	2422826	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2422826delA								EIF3B (2451 upstream) : CHST12 (20397 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	2509315	2509318	+	IGR	DEL	AAGA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2509315_2509318delAAGA								CHST12 (35101 upstream) : LFNG (50161 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	2523521	2523522	+	IGR	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2523521_2523522insG								CHST12 (49307 upstream) : LFNG (35957 downstream)																																			---	---	---	---
IQCE	23288	broad.mit.edu	37	7	2619335	2619336	+	Intron	DEL	GT	-	-	rs68086038		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2619335_2619336delGT	uc003smo.3	+						IQCE_uc010ksm.1_Intron|IQCE_uc003sml.1_Intron|IQCE_uc011jvy.1_Intron|IQCE_uc011jvz.1_Intron|IQCE_uc003smk.3_Intron|IQCE_uc003smn.3_Intron	NM_152558	NP_689771			IQ motif containing E isoform 1												0		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;1.23e-13)														---	---	---	---
TTYH3	80727	broad.mit.edu	37	7	2688391	2688392	+	Intron	DEL	GG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2688391_2688392delGG	uc003smp.2	+						TTYH3_uc010ksn.2_Intron|TTYH3_uc003smq.2_Intron	NM_025250	NP_079526			tweety 3							chloride channel complex|plasma membrane	chloride channel activity				0		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.04e-14)														---	---	---	---
TTYH3	80727	broad.mit.edu	37	7	2694778	2694778	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2694778delT	uc003smp.2	+						TTYH3_uc010ksn.2_Intron|TTYH3_uc003smq.2_Intron	NM_025250	NP_079526			tweety 3							chloride channel complex|plasma membrane	chloride channel activity				0		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.04e-14)														---	---	---	---
TTYH3	80727	broad.mit.edu	37	7	2697032	2697043	+	Intron	DEL	GTGGTGGTGGTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2697032_2697043delGTGGTGGTGGTT	uc003smp.2	+						TTYH3_uc010ksn.2_Intron|TTYH3_uc003smq.2_Intron	NM_025250	NP_079526			tweety 3							chloride channel complex|plasma membrane	chloride channel activity				0		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.04e-14)														---	---	---	---
AMZ1	155185	broad.mit.edu	37	7	2753549	2753549	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2753549delT	uc003smr.1	+	7					AMZ1_uc003sms.1_3'UTR|AMZ1_uc011jwa.1_3'UTR	NM_133463	NP_597720			archaelysin family metallopeptidase 1								metallopeptidase activity|zinc ion binding				0		Ovarian(82;0.0779)		OV - Ovarian serous cystadenocarcinoma(56;5.03e-14)														---	---	---	---
GNA12	2768	broad.mit.edu	37	7	2877776	2877776	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2877776delA	uc003smu.2	-						GNA12_uc011jwb.1_Intron	NM_007353	NP_031379			guanine nucleotide binding protein (G protein)						G-protein signaling, coupled to cAMP nucleotide second messenger|platelet activation|Rho protein signal transduction	brush border membrane|heterotrimeric G-protein complex	D5 dopamine receptor binding|G-protein beta/gamma-subunit complex binding|GTP binding|GTPase activity|signal transducer activity			ovary(1)	1		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;1.02e-13)														---	---	---	---
CARD11	84433	broad.mit.edu	37	7	2952625	2952627	+	Intron	DEL	GGA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2952625_2952627delGGA	uc003smv.2	-							NM_032415	NP_115791			caspase recruitment domain family, member 11						positive regulation of cytokine production|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis|T cell costimulation|T cell receptor signaling pathway	cytosol|membrane raft|plasma membrane	CARD domain binding|guanylate kinase activity			haematopoietic_and_lymphoid_tissue(43)|ovary(2)|kidney(2)|skin(2)|central_nervous_system(1)	50		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)				Mis		DLBCL								---	---	---	---
CARD11	84433	broad.mit.edu	37	7	2968323	2968323	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2968323delG	uc003smv.2	-	13	2067	c.1663delC	c.(1663-1665)CGGfs	p.R555fs		NM_032415	NP_115791	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	555					positive regulation of cytokine production|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis|T cell costimulation|T cell receptor signaling pathway	cytosol|membrane raft|plasma membrane	CARD domain binding|guanylate kinase activity			haematopoietic_and_lymphoid_tissue(43)|ovary(2)|kidney(2)|skin(2)|central_nervous_system(1)	50		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)				Mis		DLBCL								---	---	---	---
CARD11	84433	broad.mit.edu	37	7	3075548	3075548	+	Intron	DEL	T	-	-	rs112443832		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3075548delT	uc003smv.2	-							NM_032415	NP_115791			caspase recruitment domain family, member 11						positive regulation of cytokine production|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis|T cell costimulation|T cell receptor signaling pathway	cytosol|membrane raft|plasma membrane	CARD domain binding|guanylate kinase activity			haematopoietic_and_lymphoid_tissue(43)|ovary(2)|kidney(2)|skin(2)|central_nervous_system(1)	50		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)				Mis		DLBCL								---	---	---	---
Unknown	0	broad.mit.edu	37	7	3222216	3222216	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3222216delC								CARD11 (138637 upstream) : SDK1 (118864 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	3332740	3332741	+	IGR	INS	-	GA	GA			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3332740_3332741insGA								CARD11 (249161 upstream) : SDK1 (8339 downstream)																																			---	---	---	---
SDK1	221935	broad.mit.edu	37	7	3454462	3454462	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3454462delT	uc003smx.2	+							NM_152744	NP_689957			sidekick 1 precursor						cell adhesion	integral to membrane				large_intestine(3)|ovary(2)|skin(1)	6		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)														---	---	---	---
SDK1	221935	broad.mit.edu	37	7	3524355	3524355	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3524355delT	uc003smx.2	+							NM_152744	NP_689957			sidekick 1 precursor						cell adhesion	integral to membrane				large_intestine(3)|ovary(2)|skin(1)	6		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)														---	---	---	---
SDK1	221935	broad.mit.edu	37	7	4240414	4240414	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4240414delC	uc003smx.2	+						SDK1_uc010kso.2_Intron|SDK1_uc003smy.2_Intron	NM_152744	NP_689957			sidekick 1 precursor						cell adhesion	integral to membrane				large_intestine(3)|ovary(2)|skin(1)	6		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	4380520	4380520	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4380520delT								SDK1 (71891 upstream) : FOXK1 (302868 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	4401502	4401503	+	IGR	DEL	AG	-	-	rs11767003	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4401502_4401503delAG								SDK1 (92873 upstream) : FOXK1 (281885 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	4552537	4552537	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4552537delA								SDK1 (243908 upstream) : FOXK1 (130851 downstream)																																			---	---	---	---
RADIL	55698	broad.mit.edu	37	7	4896707	4896707	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4896707delT	uc003snj.1	-						RADIL_uc003sng.1_Intron|RADIL_uc011jwd.1_Intron	NM_018059	NP_060529			Rap GTPase interactor						cell adhesion|multicellular organismal development|signal transduction		protein binding			lung(2)|central_nervous_system(2)|pancreas(2)|breast(1)	7		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)														---	---	---	---
MMD2	221938	broad.mit.edu	37	7	4945527	4945528	+	Intron	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4945527_4945528delAC	uc003snl.1	-											Homo sapiens cDNA FLJ37205 fis, clone BRALZ2007376, moderately similar to MONOCYTE TO MACROPHAGE DIFFERENTIATION PROTEIN.							integral to membrane	receptor activity			central_nervous_system(1)	1		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.097)|OV - Ovarian serous cystadenocarcinoma(56;3.4e-14)														---	---	---	---
MMD2	221938	broad.mit.edu	37	7	4969164	4969164	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4969164delT	uc003sno.3	-						MMD2_uc003snl.1_Intron|MMD2_uc003snn.3_Intron|MMD2_uc010ksq.2_Intron	NM_001100600	NP_001094070			monocyte to macrophage							integral to membrane	receptor activity			central_nervous_system(1)	1		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.097)|OV - Ovarian serous cystadenocarcinoma(56;3.4e-14)														---	---	---	---
MMD2	221938	broad.mit.edu	37	7	4989151	4989153	+	Intron	DEL	TTT	-	-	rs80318250		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4989151_4989153delTTT	uc003sno.3	-						MMD2_uc003snl.1_Intron|MMD2_uc003snn.3_Intron|MMD2_uc010ksq.2_Intron	NM_001100600	NP_001094070			monocyte to macrophage							integral to membrane	receptor activity			central_nervous_system(1)	1		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.097)|OV - Ovarian serous cystadenocarcinoma(56;3.4e-14)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	5171709	5171712	+	Intron	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5171709_5171712delTTTT	uc003snu.1	-						uc010ksu.1_Intron|uc011jwf.1_Intron					SubName: Full=cDNA FLJ60262, weakly similar to Zinc finger protein 81;																														---	---	---	---
WIPI2	26100	broad.mit.edu	37	7	5232565	5232565	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5232565delT	uc003snv.2	+						WIPI2_uc003snw.2_Intron|WIPI2_uc003snx.2_Intron|WIPI2_uc003sny.2_Intron|WIPI2_uc010ksv.2_Intron	NM_015610	NP_056425			WD repeat domain, phosphoinositide interacting 2						autophagic vacuole assembly	cytosol|PAS complex|pre-autophagosomal structure membrane	phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding			ovary(2)	2		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0925)|OV - Ovarian serous cystadenocarcinoma(56;2.59e-14)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	5281192	5281192	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5281192delT								WIPI2 (7707 upstream) : SLC29A4 (41369 downstream)																																			---	---	---	---
TNRC18	84629	broad.mit.edu	37	7	5419032	5419035	+	Intron	DEL	AAAA	-	-	rs34098204		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5419032_5419035delAAAA	uc003soi.3	-							NM_001080495	NP_001073964			trinucleotide repeat containing 18								DNA binding				0		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	5495395	5495396	+	IGR	DEL	AC	-	-	rs36071919		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5495395_5495396delAC								TNRC18 (30350 upstream) : FBXL18 (20033 downstream)																																			---	---	---	---
FBXL18	80028	broad.mit.edu	37	7	5522669	5522669	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5522669delA	uc003son.3	-							NM_024963	NP_079239			F-box and leucine-rich repeat protein 18											central_nervous_system(2)|ovary(1)	3		Ovarian(82;0.0607)		UCEC - Uterine corpus endometrioid carcinoma (126;0.181)|OV - Ovarian serous cystadenocarcinoma(56;3.64e-13)														---	---	---	---
RNF216	54476	broad.mit.edu	37	7	5686031	5686031	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5686031delA	uc003soy.1	-						RNF216_uc010ksz.1_Intron|RNF216_uc010kta.1_Intron|RNF216_uc011jwj.1_Intron|RNF216_uc003sox.1_Intron	NM_207116	NP_996999			ring finger protein 216 isoform b						apoptosis|interspecies interaction between organisms|proteasomal ubiquitin-dependent protein catabolic process|protein K48-linked ubiquitination|regulation of defense response to virus by host|regulation of interferon-beta production	cytoplasm|nucleus|nucleus	ligase activity|protein binding|protein binding|zinc ion binding			ovary(3)|breast(2)	5		Ovarian(82;0.07)		UCEC - Uterine corpus endometrioid carcinoma (126;0.135)|OV - Ovarian serous cystadenocarcinoma(56;2.69e-13)														---	---	---	---
RNF216	54476	broad.mit.edu	37	7	5714099	5714100	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5714099_5714100delAA	uc003soy.1	-						RNF216_uc010ksz.1_Intron|RNF216_uc010kta.1_Intron|RNF216_uc011jwj.1_Intron|RNF216_uc003sox.1_Intron|RNF216_uc003spa.1_Intron	NM_207116	NP_996999			ring finger protein 216 isoform b						apoptosis|interspecies interaction between organisms|proteasomal ubiquitin-dependent protein catabolic process|protein K48-linked ubiquitination|regulation of defense response to virus by host|regulation of interferon-beta production	cytoplasm|nucleus|nucleus	ligase activity|protein binding|protein binding|zinc ion binding			ovary(3)|breast(2)	5		Ovarian(82;0.07)		UCEC - Uterine corpus endometrioid carcinoma (126;0.135)|OV - Ovarian serous cystadenocarcinoma(56;2.69e-13)														---	---	---	---
USP42	84132	broad.mit.edu	37	7	6148428	6148428	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6148428delT	uc011jwo.1	+						USP42_uc011jwn.1_Intron|USP42_uc010kth.1_Intron|USP42_uc011jwp.1_Intron|USP42_uc011jwq.1_5'Flank	NM_032172	NP_115548			ubiquitin specific peptidase 42						cell differentiation|protein deubiquitination|spermatogenesis|ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			skin(2)|ovary(1)|pancreas(1)|breast(1)	5		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)														---	---	---	---
CYTH3	9265	broad.mit.edu	37	7	6259339	6259339	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6259339delT	uc003spt.2	-							NM_004227	NP_004218			cytohesin 3						regulation of ARF protein signal transduction|regulation of cell adhesion|vesicle-mediated transport	cytoplasm|membrane fraction|plasma membrane	1-phosphatidylinositol binding|ARF guanyl-nucleotide exchange factor activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity				0																		---	---	---	---
CYTH3	9265	broad.mit.edu	37	7	6266393	6266393	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6266393delT	uc003spt.2	-							NM_004227	NP_004218			cytohesin 3						regulation of ARF protein signal transduction|regulation of cell adhesion|vesicle-mediated transport	cytoplasm|membrane fraction|plasma membrane	1-phosphatidylinositol binding|ARF guanyl-nucleotide exchange factor activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	6400994	6400994	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6400994delT								C7orf70 (12404 upstream) : RAC1 (13132 downstream)																																			---	---	---	---
DAGLB	221955	broad.mit.edu	37	7	6458302	6458302	+	Intron	DEL	T	-	-	rs112615158		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6458302delT	uc003sqa.2	-						DAGLB_uc003spy.2_5'Flank|DAGLB_uc003spz.2_Intron|DAGLB_uc011jwt.1_Intron|DAGLB_uc011jwu.1_Intron|DAGLB_uc003sqb.2_Intron|DAGLB_uc003sqc.2_Intron|DAGLB_uc011jwv.1_Intron|DAGLB_uc003sqd.3_Intron|DAGLB_uc011jww.1_Intron	NM_139179	NP_631918			diacylglycerol lipase, beta isoform 1						lipid catabolic process|platelet activation	integral to membrane|plasma membrane	acylglycerol lipase activity|metal ion binding|triglyceride lipase activity			ovary(2)|central_nervous_system(1)	3		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.102)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	6608087	6608087	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6608087delA								GRID2IP (17020 upstream) : ZDHHC4 (8978 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	6723576	6723576	+	IGR	DEL	T	-	-	rs71539968		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6723576delT								ZNF853 (59657 upstream) : ZNF12 (4488 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	6933560	6933560	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6933560delT								C7orf28B (67699 upstream) : C1GALT1 (288686 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	7098085	7098085	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7098085delC								C7orf28B (232224 upstream) : C1GALT1 (124161 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	7131527	7131527	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7131527delA								C7orf28B (265666 upstream) : C1GALT1 (90719 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	7922643	7922646	+	IGR	DEL	AGGA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7922643_7922646delAGGA								RPA3 (164405 upstream) : GLCCI1 (85777 downstream)																																			---	---	---	---
NXPH1	30010	broad.mit.edu	37	7	8487427	8487427	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8487427delC	uc003srv.2	+						NXPH1_uc011jxh.1_Intron	NM_152745	NP_689958			neurexophilin 1 precursor							extracellular region				ovary(1)|central_nervous_system(1)	2		Ovarian(82;0.0628)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	8871154	8871155	+	IGR	DEL	TT	-	-	rs4725132	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8871154_8871155delTT								NXPH1 (78562 upstream) : PER4 (802745 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	8948354	8948354	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8948354delA								NXPH1 (155762 upstream) : PER4 (725546 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	9099594	9099596	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:9099594_9099596delTTT								NXPH1 (307002 upstream) : PER4 (574304 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	9132668	9132668	+	IGR	DEL	A	-	-	rs112240204		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:9132668delA								NXPH1 (340076 upstream) : PER4 (541232 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	9348335	9348335	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:9348335delA								NXPH1 (555743 upstream) : PER4 (325565 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	9410676	9410676	+	IGR	DEL	A	-	-	rs35807979		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:9410676delA								NXPH1 (618084 upstream) : PER4 (263224 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	10264435	10264438	+	IGR	DEL	CGCA	-	-	rs71023824		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10264435_10264438delCGCA								PER4 (588988 upstream) : NDUFA4 (708377 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	10602998	10602998	+	IGR	DEL	T	-	-	rs142159582		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10602998delT								PER4 (927551 upstream) : NDUFA4 (369817 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	10634465	10634465	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10634465delA								PER4 (959018 upstream) : NDUFA4 (338350 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	10992643	10992643	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:10992643delT								NDUFA4 (12830 upstream) : PHF14 (20873 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	11238302	11238305	+	IGR	DEL	TCCT	-	-	rs71023898		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11238302_11238305delTCCT								PHF14 (29061 upstream) : THSD7A (175868 downstream)																																			---	---	---	---
THSD7A	221981	broad.mit.edu	37	7	11452108	11452109	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11452108_11452109delAA	uc003ssf.3	-							NM_015204	NP_056019			thrombospondin, type I, domain containing 7A							integral to membrane				ovary(3)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)											HNSCC(18;0.044)			---	---	---	---
THSD7A	221981	broad.mit.edu	37	7	11460238	11460238	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11460238delC	uc003ssf.3	-							NM_015204	NP_056019			thrombospondin, type I, domain containing 7A							integral to membrane				ovary(3)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)											HNSCC(18;0.044)			---	---	---	---
THSD7A	221981	broad.mit.edu	37	7	11796222	11796222	+	Intron	DEL	A	-	-	rs77446346		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11796222delA	uc003ssf.3	-							NM_015204	NP_056019			thrombospondin, type I, domain containing 7A							integral to membrane				ovary(3)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)											HNSCC(18;0.044)			---	---	---	---
Unknown	0	broad.mit.edu	37	7	12451549	12451549	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12451549delA								VWDE (7697 upstream) : SCIN (144638 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	13120049	13120049	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:13120049delT								ARL4A (389493 upstream) : ETV1 (810809 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	13138371	13138372	+	IGR	INS	-	A	A	rs142770011	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:13138371_13138372insA								ARL4A (407815 upstream) : ETV1 (792486 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	14058969	14058969	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:14058969delT								ETV1 (27919 upstream) : DGKB (125706 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	14105298	14105298	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:14105298delT								ETV1 (74248 upstream) : DGKB (79377 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	14109097	14109097	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:14109097delA								ETV1 (78047 upstream) : DGKB (75578 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	14119983	14119983	+	IGR	DEL	T	-	-	rs113470652		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:14119983delT								ETV1 (88933 upstream) : DGKB (64692 downstream)																																			---	---	---	---
DGKB	1607	broad.mit.edu	37	7	14647156	14647156	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:14647156delA	uc003ssz.2	-						DGKB_uc011jxt.1_Intron|DGKB_uc003sta.2_Intron|DGKB_uc011jxu.1_Intron	NM_004080	NP_004071			diacylglycerol kinase, beta isoform 1						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity|protein binding			lung(5)|ovary(4)|breast(2)|skin(1)	12					Phosphatidylserine(DB00144)													---	---	---	---
TMEM195	392636	broad.mit.edu	37	7	15421042	15421042	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15421042delA	uc003stb.1	-							NM_001004320	NP_001004320			transmembrane protein 195						ether lipid metabolic process|fatty acid biosynthetic process|membrane lipid metabolic process	endoplasmic reticulum membrane|integral to membrane	glyceryl-ether monooxygenase activity|iron ion binding				0																		---	---	---	---
TMEM195	392636	broad.mit.edu	37	7	15576658	15576659	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15576658_15576659insT	uc003stb.1	-							NM_001004320	NP_001004320			transmembrane protein 195						ether lipid metabolic process|fatty acid biosynthetic process|membrane lipid metabolic process	endoplasmic reticulum membrane|integral to membrane	glyceryl-ether monooxygenase activity|iron ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	15635941	15635941	+	IGR	DEL	C	-	-	rs2057742	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15635941delC								TMEM195 (34301 upstream) : MEOX2 (14898 downstream)																																			---	---	---	---
ISPD	729920	broad.mit.edu	37	7	16337476	16337476	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16337476delG	uc010ktx.2	-						ISPD_uc010kty.2_Intron	NM_001101426	NP_001094896			notch1-induced protein isoform a						isoprenoid biosynthetic process		nucleotidyltransferase activity			ovary(1)	1															Multiple Myeloma(15;0.18)			---	---	---	---
SOSTDC1	25928	broad.mit.edu	37	7	16504277	16504278	+	Intron	INS	-	TC	TC	rs148918243	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16504277_16504278insTC	uc003stg.2	-						SOSTDC1_uc003sth.2_Intron	NM_015464	NP_056279			sclerostin domain containing 1 precursor						Wnt receptor signaling pathway					ovary(2)|central_nervous_system(1)	3	Lung NSC(10;0.185)			UCEC - Uterine corpus endometrioid carcinoma (126;0.177)														---	---	---	---
SOSTDC1	25928	broad.mit.edu	37	7	16519062	16519062	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16519062delT	uc003sth.2	-							NM_015464	NP_056279			sclerostin domain containing 1 precursor						Wnt receptor signaling pathway					ovary(2)|central_nervous_system(1)	3	Lung NSC(10;0.185)			UCEC - Uterine corpus endometrioid carcinoma (126;0.177)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	16620936	16620936	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16620936delT								SOSTDC1 (50731 upstream) : ANKMY2 (18477 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	16867435	16867438	+	IGR	DEL	AAGG	-	-	rs35745061		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16867435_16867438delAAGG								AGR2 (22697 upstream) : AGR3 (31593 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	17047336	17047336	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17047336delA								AGR3 (125723 upstream) : AHR (290940 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	17317628	17317629	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17317628_17317629insT								AGR3 (396015 upstream) : AHR (20647 downstream)																																			---	---	---	---
AHR	196	broad.mit.edu	37	7	17370261	17370262	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17370261_17370262insT	uc011jxz.1	+						AHR_uc003stt.3_Intron	NM_001621	NP_001612			aryl hydrocarbon receptor precursor						apoptosis|blood vessel development|cell cycle|regulation of B cell proliferation|response to stress|transcription from RNA polymerase II promoter|xenobiotic metabolic process	cytosolic aryl hydrocarbon receptor complex|transcription factor complex	Hsp90 protein binding|ligand-dependent nuclear receptor activity|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			urinary_tract(1)|kidney(1)|pancreas(1)	3	Lung NSC(10;0.0392)|all_lung(11;0.0754)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	17760063	17760063	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17760063delA								AHR (374288 upstream) : SNX13 (70323 downstream)																																			---	---	---	---
SNX13	23161	broad.mit.edu	37	7	17920219	17920219	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:17920219delC	uc003stw.1	-						SNX13_uc003stv.2_Intron|SNX13_uc010kuc.2_Intron|SNX13_uc003stx.1_Intron|SNX13_uc003sty.2_3'UTR					SubName: Full=Putative uncharacterized protein SNX13; SubName: Full=Sorting nexin 13, isoform CRA_g;						cell communication|intracellular protein transport|negative regulation of signal transduction|positive regulation of GTPase activity	early endosome membrane	phosphatidylinositol binding|signal transducer activity			central_nervous_system(2)|kidney(1)	3	Lung NSC(10;0.0261)|all_lung(11;0.0521)																	---	---	---	---
HDAC9	9734	broad.mit.edu	37	7	18491053	18491054	+	Intron	DEL	TG	-	-	rs28700993		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18491053_18491054delTG	uc003sua.1	+						HDAC9_uc011jya.1_Intron	NM_014707	NP_055522			histone deacetylase 9 isoform 3						B cell differentiation|cellular response to insulin stimulus|heart development|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|positive regulation of cell migration involved in sprouting angiogenesis|regulation of skeletal muscle fiber development|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|transcription factor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein binding|protein kinase C binding|repressing transcription factor binding|transcription corepressor activity			lung(2)|central_nervous_system(2)|kidney(1)	5	all_lung(11;0.187)				Valproic Acid(DB00313)													---	---	---	---
HDAC9	9734	broad.mit.edu	37	7	18724985	18724985	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:18724985delT	uc003suh.2	+						HDAC9_uc003sue.2_Intron|HDAC9_uc011jyd.1_Intron|HDAC9_uc003sui.2_Intron|HDAC9_uc003suj.2_Intron|HDAC9_uc003sua.1_Intron|HDAC9_uc010kue.1_Intron	NM_058176	NP_478056			histone deacetylase 9 isoform 1						B cell differentiation|cellular response to insulin stimulus|heart development|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|positive regulation of cell migration involved in sprouting angiogenesis|regulation of skeletal muscle fiber development|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|transcription factor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein binding|protein kinase C binding|repressing transcription factor binding|transcription corepressor activity			lung(2)|central_nervous_system(2)|kidney(1)	5	all_lung(11;0.187)				Valproic Acid(DB00313)													---	---	---	---
TMEM196	256130	broad.mit.edu	37	7	19797182	19797182	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:19797182delT	uc011jyg.1	-						TMEM196_uc003sur.2_Intron	NM_152774	NP_689987			transmembrane protein 196							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	20321820	20321821	+	IGR	INS	-	TG	TG	rs145574996	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20321820_20321821insTG								MACC1 (64807 upstream) : ITGB8 (48504 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	20511198	20511198	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20511198delC								ITGB8 (55820 upstream) : ABCB5 (144047 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	20583065	20583067	+	IGR	DEL	TTT	-	-	rs72240425		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20583065_20583067delTTT								ITGB8 (127687 upstream) : ABCB5 (72178 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	21242349	21242349	+	IGR	DEL	A	-	-	rs71768469		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21242349delA								RPL23P8 (374910 upstream) : SP4 (225340 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	21351252	21351252	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21351252delA								RPL23P8 (483813 upstream) : SP4 (116437 downstream)																																			---	---	---	---
SP4	6671	broad.mit.edu	37	7	21516676	21516677	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21516676_21516677insT	uc003sva.2	+						SP4_uc003svb.2_Intron	NM_003112	NP_003103			Sp4 transcription factor						regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|transcription coactivator activity|zinc ion binding			ovary(3)|skin(2)	5																		---	---	---	---
DNAH11	8701	broad.mit.edu	37	7	21934928	21934930	+	Intron	DEL	GTT	-	-	rs137883598		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21934928_21934930delGTT	uc003svc.2	+							NM_003777	NP_003768			dynein, axonemal, heavy chain 11						microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15														Kartagener_syndrome				---	---	---	---
CDCA7L	55536	broad.mit.edu	37	7	21944618	21944618	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21944618delT	uc010kuk.2	-						CDCA7L_uc003sve.3_Intron|CDCA7L_uc010kul.2_Intron|CDCA7L_uc003svf.3_Intron	NM_018719	NP_061189			cell division cycle associated 7-like isoform 1						positive regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus					0																		---	---	---	---
RAPGEF5	9771	broad.mit.edu	37	7	22190201	22190201	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22190201delA	uc003svg.2	-						RAPGEF5_uc011jyl.1_Intron	NM_012294	NP_036426			Rap guanine nucleotide exchange factor (GEF) 5						nervous system development|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	nucleus	GTP-dependent protein binding|Rap guanyl-nucleotide exchange factor activity			ovary(1)	1																		---	---	---	---
RAPGEF5	9771	broad.mit.edu	37	7	22194363	22194364	+	Intron	INS	-	T	T	rs150777301	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22194363_22194364insT	uc003svg.2	-						RAPGEF5_uc011jyl.1_Intron	NM_012294	NP_036426			Rap guanine nucleotide exchange factor (GEF) 5						nervous system development|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	nucleus	GTP-dependent protein binding|Rap guanyl-nucleotide exchange factor activity			ovary(1)	1																		---	---	---	---
RAPGEF5	9771	broad.mit.edu	37	7	22357672	22357672	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22357672delA	uc003svg.2	-							NM_012294	NP_036426			Rap guanine nucleotide exchange factor (GEF) 5						nervous system development|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	nucleus	GTP-dependent protein binding|Rap guanyl-nucleotide exchange factor activity			ovary(1)	1																		---	---	---	---
IL6	3569	broad.mit.edu	37	7	22770846	22770847	+	Intron	DEL	AA	-	-	rs78229116	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22770846_22770847delAA	uc011jyn.1	+						IL6_uc003svj.3_Intron	NM_000600	NP_000591			interleukin 6 precursor						acute-phase response|cellular response to hydrogen peroxide|defense response to Gram-negative bacterium|defense response to Gram-positive bacterium|defense response to virus|endocrine pancreas development|glucagon secretion|hepatic immune response|interleukin-6-mediated signaling pathway|negative regulation of apoptosis|negative regulation of cell proliferation|negative regulation of chemokine biosynthetic process|negative regulation of collagen biosynthetic process|negative regulation of fat cell differentiation|negative regulation of lipid storage|neuron projection development|neutrophil apoptosis|platelet activation|positive regulation of acute inflammatory response|positive regulation of anti-apoptosis|positive regulation of B cell activation|positive regulation of chemokine production|positive regulation of immunoglobulin secretion|positive regulation of interleukin-6 production|positive regulation of osteoblast differentiation|positive regulation of peptidyl-serine phosphorylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of smooth muscle cell proliferation|positive regulation of T cell proliferation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of translation|positive regulation of tyrosine phosphorylation of Stat3 protein|regulation of vascular endothelial growth factor production|response to glucocorticoid stimulus|response to peptidoglycan	extracellular space|interleukin-6 receptor complex	cytokine activity|growth factor activity|interleukin-6 receptor binding				0					Arsenic trioxide(DB01169)|Bicalutamide(DB01128)|Ginseng(DB01404)|Simvastatin(DB00641)													---	---	---	---
KLHL7	55975	broad.mit.edu	37	7	23183456	23183456	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23183456delT	uc003svs.3	+						KLHL7_uc003svr.3_Intron|KLHL7_uc011jys.1_Intron|KLHL7_uc011jyt.1_Intron|KLHL7_uc003svt.2_Intron|KLHL7_uc011jyv.1_Intron	NM_001031710	NP_001026880			kelch-like 7 isoform 1							Golgi apparatus|nucleolus|plasma membrane					0																		---	---	---	---
C7orf30	115416	broad.mit.edu	37	7	23347411	23347411	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23347411delA	uc003swd.1	+						C7orf30_uc003swe.2_5'Flank	NM_138446	NP_612455			hypothetical protein LOC115416							mitochondrion					0			GBM - Glioblastoma multiforme(13;0.154)															---	---	---	---
TRA2A	29896	broad.mit.edu	37	7	23552393	23552395	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23552393_23552395delAAA	uc003swi.2	-						TRA2A_uc011jzb.1_Intron|TRA2A_uc011jzc.1_Intron|TRA2A_uc011jzd.1_Intron	NM_013293	NP_037425			transformer-2 alpha						nuclear mRNA splicing, via spliceosome	nucleus	nucleotide binding|RNA binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	23687651	23687652	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23687651_23687652insT								CCDC126 (3325 upstream) : C7orf46 (32097 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	24455255	24455255	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24455255delA								NPY (123778 upstream) : MPP6 (157830 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	24489163	24489163	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24489163delT								NPY (157686 upstream) : MPP6 (123922 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	24530793	24530793	+	IGR	DEL	A	-	-	rs57952494	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24530793delA								NPY (199316 upstream) : MPP6 (82292 downstream)																																			---	---	---	---
C7orf31	136895	broad.mit.edu	37	7	25192368	25192370	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25192368_25192370delTTT	uc003sxn.1	-						C7orf31_uc003sxm.1_Intron	NM_138811	NP_620166			hypothetical protein LOC136895												0																		---	---	---	---
C7orf31	136895	broad.mit.edu	37	7	25200833	25200833	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25200833delT	uc003sxn.1	-	4	919	c.358delA	c.(358-360)AGTfs	p.S120fs	C7orf31_uc003sxm.1_5'Flank	NM_138811	NP_620166	Q8N865	CG031_HUMAN	hypothetical protein LOC136895	120											0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	25336360	25336360	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25336360delC								NPVF (68255 upstream) : MIR148A (653179 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	25588273	25588274	+	IGR	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25588273_25588274delTC								NPVF (320168 upstream) : MIR148A (401265 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	25899924	25899924	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25899924delA								NPVF (631819 upstream) : MIR148A (89615 downstream)																																			---	---	---	---
HNRNPA2B1	3181	broad.mit.edu	37	7	26237495	26237495	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26237495delA	uc003sxr.3	-						HNRNPA2B1_uc003sxs.3_Intron	NM_031243	NP_112533			heterogeneous nuclear ribonucleoprotein A2/B1						RNA transport	catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleolus|nucleoplasm	nucleotide binding|protein binding|protein binding|RNA binding|single-stranded telomeric DNA binding			ovary(1)|central_nervous_system(1)|skin(1)	3								T	ETV1	prostate								---	---	---	---
Unknown	0	broad.mit.edu	37	7	26316251	26316251	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26316251delA								CBX3 (63277 upstream) : SNX10 (15264 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	26417290	26417290	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26417290delT								SNX10 (3353 upstream) : LOC441204 (21049 downstream)																																			---	---	---	---
LOC441204	441204	broad.mit.edu	37	7	26452141	26452141	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26452141delT	uc003sxy.1	+						LOC441204_uc003sxz.2_Intron					Homo sapiens cDNA FLJ31922 fis, clone NT2RP7005219.												0																		---	---	---	---
LOC441204	441204	broad.mit.edu	37	7	26485559	26485559	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26485559delA	uc003sxy.1	+						LOC441204_uc003sxz.2_Intron					Homo sapiens cDNA FLJ31922 fis, clone NT2RP7005219.												0																		---	---	---	---
SKAP2	8935	broad.mit.edu	37	7	26900852	26900852	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26900852delA	uc003syc.2	-						SKAP2_uc011jzj.1_Intron	NM_003930	NP_003921			src kinase associated phosphoprotein 2						B cell activation|cell junction assembly|protein complex assembly|signal transduction	cytosol|plasma membrane	SH3/SH2 adaptor activity			pancreas(1)	1																		---	---	---	---
HOXA2	3199	broad.mit.edu	37	7	27142248	27142248	+	5'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27142248delT	uc003syh.2	-	1						NM_006735	NP_006726			homeobox A2							nucleus	sequence-specific DNA binding transcription factor activity			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	27289439	27289439	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27289439delT								EVX1 (3247 upstream) : HIBADH (275624 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	27549503	27549504	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27549503_27549504delTT								EVX1 (263311 upstream) : HIBADH (15559 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	27706898	27706898	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27706898delA								HIBADH (4296 upstream) : TAX1BP1 (72094 downstream)																																			---	---	---	---
JAZF1	221895	broad.mit.edu	37	7	27877628	27877631	+	Intron	DEL	TTTT	-	-	rs77704087		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27877628_27877631delTTTT	uc003szn.2	-						JAZF1_uc003szm.2_Intron	NM_175061	NP_778231			JAZF zinc finger 1						negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	transcriptional repressor complex	nucleic acid binding|transcription corepressor activity|zinc ion binding		JAZF1/SUZ12(131)	soft_tissue(98)|endometrium(33)	131								T	SUZ12	endometrial stromal tumours								---	---	---	---
JAZF1	221895	broad.mit.edu	37	7	27888710	27888710	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27888710delA	uc003szn.2	-						JAZF1_uc003szm.2_Intron	NM_175061	NP_778231			JAZF zinc finger 1						negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	transcriptional repressor complex	nucleic acid binding|transcription corepressor activity|zinc ion binding		JAZF1/SUZ12(131)	soft_tissue(98)|endometrium(33)	131								T	SUZ12	endometrial stromal tumours								---	---	---	---
JAZF1	221895	broad.mit.edu	37	7	27936104	27936104	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27936104delC	uc003szn.2	-						JAZF1_uc003szm.2_Intron	NM_175061	NP_778231			JAZF zinc finger 1						negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	transcriptional repressor complex	nucleic acid binding|transcription corepressor activity|zinc ion binding		JAZF1/SUZ12(131)	soft_tissue(98)|endometrium(33)	131								T	SUZ12	endometrial stromal tumours								---	---	---	---
CREB5	9586	broad.mit.edu	37	7	28500660	28500661	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28500660_28500661insA	uc003szq.2	+						CREB5_uc003szo.2_Intron|CREB5_uc003szr.2_Intron	NM_182898	NP_878901			cAMP responsive element binding protein 5						positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter		protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)	2																		---	---	---	---
CPVL	54504	broad.mit.edu	37	7	29035303	29035303	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29035303delT	uc003szv.2	-	13					CPVL_uc003szw.2_3'UTR|CPVL_uc003szx.2_3'UTR	NM_031311	NP_112601			serine carboxypeptidase vitellogenic-like						proteolysis		protein binding|serine-type carboxypeptidase activity			ovary(2)	2																		---	---	---	---
CPVL	54504	broad.mit.edu	37	7	29090419	29090419	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29090419delA	uc003szv.2	-						CPVL_uc003szw.2_Intron|CPVL_uc003szx.2_Intron	NM_031311	NP_112601			serine carboxypeptidase vitellogenic-like						proteolysis		protein binding|serine-type carboxypeptidase activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	29956919	29956920	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:29956919_29956920insT								WIPF3 (11128 upstream) : SCRN1 (2800 downstream)																																			---	---	---	---
ZNRF2	223082	broad.mit.edu	37	7	30323798	30323798	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30323798delT	uc003tat.2	+							NM_147128	NP_667339			zinc finger/RING finger 2							cell junction|endosome membrane|lysosomal membrane|presynaptic membrane	ligase activity|zinc ion binding				0																		---	---	---	---
ZNRF2	223082	broad.mit.edu	37	7	30360750	30360750	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30360750delT	uc003tat.2	+							NM_147128	NP_667339			zinc finger/RING finger 2							cell junction|endosome membrane|lysosomal membrane|presynaptic membrane	ligase activity|zinc ion binding				0																		---	---	---	---
ZNRF2	223082	broad.mit.edu	37	7	30384943	30384943	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30384943delT	uc003tat.2	+							NM_147128	NP_667339			zinc finger/RING finger 2							cell junction|endosome membrane|lysosomal membrane|presynaptic membrane	ligase activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	30588862	30588862	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30588862delA	uc003tbd.2	-						uc003tbe.1_RNA|uc003tbf.1_RNA					Homo sapiens full length insert cDNA clone ZC66C07.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	30623163	30623164	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30623163_30623164delAA	uc003tbj.2	-						uc003tbk.3_Intron|uc003tbl.3_Intron|uc010kvv.2_Intron					Homo sapiens cDNA FLJ39368 fis, clone PEBLM2007188.																														---	---	---	---
GARS	2617	broad.mit.edu	37	7	30636103	30636104	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30636103_30636104delAA	uc003tbm.2	+						uc003tbj.2_5'Flank|uc003tbl.3_5'Flank|uc010kvv.2_5'Flank	NM_002047	NP_002038			glycyl-tRNA synthetase						cell death|diadenosine tetraphosphate biosynthetic process|glycyl-tRNA aminoacylation	cytosol|mitochondrial matrix|soluble fraction	ATP binding|glycine-tRNA ligase activity|protein dimerization activity			ovary(1)	1					Glycine(DB00145)													---	---	---	---
GARS	2617	broad.mit.edu	37	7	30662267	30662267	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30662267delT	uc003tbm.2	+							NM_002047	NP_002038			glycyl-tRNA synthetase						cell death|diadenosine tetraphosphate biosynthetic process|glycyl-tRNA aminoacylation	cytosol|mitochondrial matrix|soluble fraction	ATP binding|glycine-tRNA ligase activity|protein dimerization activity			ovary(1)	1					Glycine(DB00145)													---	---	---	---
CRHR2	1395	broad.mit.edu	37	7	30694783	30694783	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30694783delG	uc003tbn.2	-						CRHR2_uc010kvw.1_Intron|CRHR2_uc010kvx.1_Intron|CRHR2_uc010kvy.1_Intron|CRHR2_uc003tbo.2_Intron|CRHR2_uc003tbp.2_Intron	NM_001883	NP_001874			corticotropin releasing hormone receptor 2						G-protein signaling, coupled to cAMP nucleotide second messenger	integral to plasma membrane	corticotrophin-releasing factor receptor activity|protein binding			lung(2)|ovary(1)|skin(1)	4																		---	---	---	---
ADCYAP1R1	117	broad.mit.edu	37	7	31132571	31132572	+	Intron	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31132571_31132572delAG	uc003tca.1	+						ADCYAP1R1_uc003tcb.1_Intron|ADCYAP1R1_uc003tcc.1_Intron|ADCYAP1R1_uc003tcd.1_Intron|ADCYAP1R1_uc003tce.1_Intron|ADCYAP1R1_uc003tcf.1_Intron	NM_001118	NP_001109			adenylate cyclase activating polypeptide 1						activation of adenylate cyclase activity|cell differentiation|nerve growth factor receptor signaling pathway|spermatogenesis	integral to plasma membrane	vasoactive intestinal polypeptide receptor activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	31443838	31443838	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31443838delT								NEUROD6 (63300 upstream) : CCDC129 (109847 downstream)																																			---	---	---	---
CCDC129	223075	broad.mit.edu	37	7	31685781	31685781	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31685781delA	uc003tcj.1	+						CCDC129_uc011kad.1_Intron|CCDC129_uc003tci.1_Intron|CCDC129_uc011kae.1_Intron|CCDC129_uc003tck.1_Intron	NM_194300	NP_919276			coiled-coil domain containing 129												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	31702852	31702852	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31702852delA								CCDC129 (4519 upstream) : C7orf16 (23947 downstream)																																			---	---	---	---
C7orf16	10842	broad.mit.edu	37	7	31736760	31736760	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31736760delG	uc003tcl.2	+						C7orf16_uc011kaf.1_Intron	NM_006658	NP_006649			G-substrate isoform 1						behavior|central nervous system development|intracellular protein kinase cascade|protein phosphorylation	soluble fraction				ovary(2)|central_nervous_system(1)	3			GBM - Glioblastoma multiforme(11;0.216)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	31770969	31770980	+	IGR	DEL	CATTAAGTACAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31770969_31770980delCATTAAGTACAA								C7orf16 (22901 upstream) : PDE1C (21652 downstream)																																			---	---	---	---
PDE1C	5137	broad.mit.edu	37	7	32275030	32275030	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32275030delA	uc003tco.1	-							NM_005020	NP_005011			phosphodiesterase 1C						activation of phospholipase C activity|nerve growth factor receptor signaling pathway	cytosol	calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			skin(3)|central_nervous_system(1)	4			GBM - Glioblastoma multiforme(11;0.216)															---	---	---	---
AVL9	23080	broad.mit.edu	37	7	32582583	32582583	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32582583delT	uc003tcv.1	+						AVL9_uc011kai.1_Intron|AVL9_uc010kwj.1_5'Flank	NM_015060	NP_055875			AVL9 homolog (S. cerevisiase)							integral to membrane					0																		---	---	---	---
AVL9	23080	broad.mit.edu	37	7	32867251	32867251	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32867251delT	uc011kai.1	+						uc003tda.1_Intron	NM_015060	NP_055875			AVL9 homolog (S. cerevisiase)							integral to membrane					0																		---	---	---	---
FKBP9	11328	broad.mit.edu	37	7	33020351	33020351	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33020351delT	uc003tdh.2	+						AVL9_uc011kai.1_Intron|FKBP9_uc011kak.1_Intron|FKBP9_uc011kal.1_Intron|FKBP9_uc011kam.1_Intron|FKBP9_uc003tdg.2_Intron	NM_007270	NP_009201			FK506 binding protein 9 precursor						protein folding	endoplasmic reticulum|membrane	calcium ion binding|FK506 binding|peptidyl-prolyl cis-trans isomerase activity			central_nervous_system(13)|ovary(1)	14			GBM - Glioblastoma multiforme(11;0.0156)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	33108969	33108969	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33108969delT								NT5C3 (6560 upstream) : RP9 (25443 downstream)																																			---	---	---	---
BBS9	27241	broad.mit.edu	37	7	33221761	33221761	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33221761delA	uc003tdn.1	+						BBS9_uc003tdo.1_Intron|BBS9_uc003tdp.1_Intron|BBS9_uc003tdq.1_Intron|BBS9_uc010kwn.1_Intron|BBS9_uc011kan.1_Intron|BBS9_uc011kao.1_Intron	NM_198428	NP_940820			parathyroid hormone-responsive B1 isoform 2						fat cell differentiation|response to stimulus|visual perception	BBSome|cilium membrane|microtubule organizing center|nucleus	protein binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			GBM - Glioblastoma multiforme(11;0.0894)											Bardet-Biedl_syndrome				---	---	---	---
BBS9	27241	broad.mit.edu	37	7	33320034	33320034	+	Intron	DEL	T	-	-	rs11368362		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33320034delT	uc003tdn.1	+						BBS9_uc003tdo.1_Intron|BBS9_uc003tdp.1_Intron|BBS9_uc003tdq.1_Intron|BBS9_uc010kwn.1_Intron|BBS9_uc011kan.1_Intron|BBS9_uc011kao.1_Intron	NM_198428	NP_940820			parathyroid hormone-responsive B1 isoform 2						fat cell differentiation|response to stimulus|visual perception	BBSome|cilium membrane|microtubule organizing center|nucleus	protein binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			GBM - Glioblastoma multiforme(11;0.0894)											Bardet-Biedl_syndrome				---	---	---	---
BBS9	27241	broad.mit.edu	37	7	33365455	33365456	+	Intron	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33365455_33365456delTC	uc003tdn.1	+						BBS9_uc003tdo.1_Intron|BBS9_uc003tdp.1_Intron|BBS9_uc003tdq.1_Intron|BBS9_uc010kwn.1_Intron|BBS9_uc011kao.1_Intron	NM_198428	NP_940820			parathyroid hormone-responsive B1 isoform 2						fat cell differentiation|response to stimulus|visual perception	BBSome|cilium membrane|microtubule organizing center|nucleus	protein binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			GBM - Glioblastoma multiforme(11;0.0894)											Bardet-Biedl_syndrome				---	---	---	---
BBS9	27241	broad.mit.edu	37	7	33380412	33380412	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33380412delT	uc003tdn.1	+						BBS9_uc003tdo.1_Intron|BBS9_uc003tdp.1_Intron|BBS9_uc003tdq.1_Intron|BBS9_uc010kwn.1_Intron|BBS9_uc011kao.1_Intron	NM_198428	NP_940820			parathyroid hormone-responsive B1 isoform 2						fat cell differentiation|response to stimulus|visual perception	BBSome|cilium membrane|microtubule organizing center|nucleus	protein binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			GBM - Glioblastoma multiforme(11;0.0894)											Bardet-Biedl_syndrome				---	---	---	---
BBS9	27241	broad.mit.edu	37	7	33620708	33620709	+	Intron	DEL	GA	-	-	rs71554105		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33620708_33620709delGA	uc003tdn.1	+						BBS9_uc003tdo.1_Intron|BBS9_uc003tdp.1_Intron|BBS9_uc003tdq.1_Intron|BBS9_uc010kwn.1_Intron|BBS9_uc003tdr.1_Intron|BBS9_uc003tds.1_Intron|BBS9_uc003tdt.2_Intron	NM_198428	NP_940820			parathyroid hormone-responsive B1 isoform 2						fat cell differentiation|response to stimulus|visual perception	BBSome|cilium membrane|microtubule organizing center|nucleus	protein binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			GBM - Glioblastoma multiforme(11;0.0894)											Bardet-Biedl_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	7	34253520	34253521	+	IGR	DEL	GT	-	-	rs34564349		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34253520_34253521delGT								BMPER (59409 upstream) : AAA1 (136514 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	34274175	34274176	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34274175_34274176insT								BMPER (80064 upstream) : AAA1 (115859 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	34937969	34937969	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:34937969delT								NPSR1 (20025 upstream) : DPY19L1 (23112 downstream)																																			---	---	---	---
SEPT7	989	broad.mit.edu	37	7	35870939	35870939	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35870939delT	uc010kxc.2	+						SEPT7_uc011kat.1_Intron|SEPT7_uc011kau.1_Intron|SEPT7_uc011kav.1_5'Flank	NM_001788	NP_001779			cell division cycle 10 isoform 1						cilium morphogenesis|cytokinesis|mitosis|protein heterooligomerization|regulation of embryonic cell shape	cilium axoneme|cleavage furrow|condensed chromosome kinetochore|midbody|nucleus|septin complex|spindle|stress fiber	GTP binding|protein binding|structural molecule activity				0																		---	---	---	---
EEPD1	80820	broad.mit.edu	37	7	36200279	36200280	+	Intron	INS	-	GGT	GGT			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36200279_36200280insGGT	uc003tfa.2	+							NM_030636	NP_085139			endonuclease/exonuclease/phosphatase family						DNA repair		DNA binding				0																		---	---	---	---
EEPD1	80820	broad.mit.edu	37	7	36215146	36215147	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36215146_36215147delTT	uc003tfa.2	+							NM_030636	NP_085139			endonuclease/exonuclease/phosphatase family						DNA repair		DNA binding				0																		---	---	---	---
ELMO1	9844	broad.mit.edu	37	7	37359473	37359473	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37359473delT	uc003tfk.1	-						ELMO1_uc010kxg.1_Intron	NM_014800	NP_055615			engulfment and cell motility 1 isoform 1						actin cytoskeleton organization|apoptosis|cellular component movement|phagocytosis, engulfment|Rac protein signal transduction|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|plasma membrane	SH3 domain binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)	6																		---	---	---	---
ELMO1	9844	broad.mit.edu	37	7	37398320	37398320	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37398320delA	uc003tfk.1	-						ELMO1_uc010kxg.1_Intron	NM_014800	NP_055615			engulfment and cell motility 1 isoform 1						actin cytoskeleton organization|apoptosis|cellular component movement|phagocytosis, engulfment|Rac protein signal transduction|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|plasma membrane	SH3 domain binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	37497132	37497132	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:37497132delA								ELMO1 (8602 upstream) : GPR141 (282864 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	38295922	38295922	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38295922delA	uc003tfu.3	-						uc003tfv.2_Intron|uc003tfw.2_Intron|uc003tfx.1_Intron|uc003tfz.1_Intron|uc003tga.1_5'Flank					SubName: Full=TARP protein;																														---	---	---	---
TARP	445347	broad.mit.edu	37	7	38303245	38303245	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38303245delA	uc003tge.1	-						uc003tfz.1_Intron|TARP_uc003tgb.2_Intron|TARP_uc003tgc.1_Intron|TARP_uc003tgd.1_Intron					Homo sapiens TCRgamma alternate reading frame protein (TCRg) mRNA, complete cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	38415495	38415495	+	RNA	DEL	C	-	-	rs3832481		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38415495delC	uc003tgp.1	+	4		c.735delC								Homo sapiens cDNA FLJ43658 fis, clone SYNOV4004184.																														---	---	---	---
POU6F2	11281	broad.mit.edu	37	7	39287701	39287701	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39287701delA	uc003thb.1	+						POU6F2_uc010kxo.2_Intron	NM_007252	NP_009183			POU class 6 homeobox 2 isoform 1						central nervous system development|ganglion mother cell fate determination|transcription from RNA polymerase II promoter|visual perception		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1																		---	---	---	---
RALA	5898	broad.mit.edu	37	7	39722245	39722245	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39722245delT	uc003thd.2	+							NM_005402	NP_005393			ras related v-ral simian leukemia viral oncogene						actin cytoskeleton reorganization|cell cycle|chemotaxis|cytokinesis|exocytosis|interspecies interaction between organisms|membrane raft localization|nerve growth factor receptor signaling pathway|positive regulation of filopodium assembly|Ras protein signal transduction|regulation of exocytosis	cell surface|cleavage furrow|cytosol|midbody|plasma membrane	Edg-2 lysophosphatidic acid receptor binding|GTP binding|GTPase activity			lung(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	39841952	39841952	+	IGR	DEL	A	-	-	rs66718562		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39841952delA								LOC349114 (7731 upstream) : CDK13 (148007 downstream)																																			---	---	---	---
CDK13	8621	broad.mit.edu	37	7	40134735	40134735	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40134735delA	uc003thh.3	+	14					CDK13_uc003thi.3_3'UTR|CDK13_uc003thj.2_3'UTR|CDK13_uc003thk.2_3'UTR	NM_003718	NP_003709			cell division cycle 2-like 5 isoform 1						alternative nuclear mRNA splicing, via spliceosome|hemopoiesis|interspecies interaction between organisms|phosphorylation of RNA polymerase II C-terminal domain|positive regulation of cell proliferation|regulation of mitosis	nuclear cyclin-dependent protein kinase holoenzyme complex|nuclear speck	ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity			lung(2)|skin(2)|ovary(1)	5																		---	---	---	---
C7orf10	79783	broad.mit.edu	37	7	40276438	40276438	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40276438delT	uc003thn.1	+						C7orf10_uc003thm.1_Intron|C7orf10_uc003tho.1_Intron	NM_024728	NP_079004			dermal papilla derived protein 13								transferase activity			ovary(2)	2																		---	---	---	---
C7orf10	79783	broad.mit.edu	37	7	40654182	40654182	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40654182delT	uc003thn.1	+						C7orf10_uc003thm.1_Intron|C7orf10_uc003tho.1_Intron	NM_024728	NP_079004			dermal papilla derived protein 13								transferase activity			ovary(2)	2																		---	---	---	---
C7orf10	79783	broad.mit.edu	37	7	40883108	40883108	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40883108delA	uc003thn.1	+						C7orf10_uc003thm.1_Intron|C7orf10_uc003tho.1_Intron|C7orf10_uc003thp.1_Intron	NM_024728	NP_079004			dermal papilla derived protein 13								transferase activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	40957742	40957742	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40957742delC								C7orf10 (57385 upstream) : INHBA (770861 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	41181335	41181335	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41181335delT								C7orf10 (280978 upstream) : INHBA (547268 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	41913036	41913036	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41913036delA								LOC285954 (94062 upstream) : GLI3 (87514 downstream)																																			---	---	---	---
GLI3	2737	broad.mit.edu	37	7	42032619	42032619	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42032619delA	uc011kbh.1	-						GLI3_uc011kbg.1_Intron	NM_000168	NP_000159			GLI-Kruppel family member GLI3						negative regulation of alpha-beta T cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of smoothened signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative thymic T cell selection|positive regulation of alpha-beta T cell differentiation|positive regulation of transcription from RNA polymerase II promoter|thymocyte apoptosis	cilium|cytosol|nucleolus	beta-catenin binding|histone acetyltransferase binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(11)|ovary(3)|large_intestine(2)|central_nervous_system(1)|kidney(1)|pancreas(1)	19														Greig_Cephalopolysyndactyly|Pallister-Hall_syndrome				---	---	---	---
GLI3	2737	broad.mit.edu	37	7	42134333	42134333	+	Intron	DEL	A	-	-	rs113517945		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42134333delA	uc011kbh.1	-						GLI3_uc011kbg.1_Intron	NM_000168	NP_000159			GLI-Kruppel family member GLI3						negative regulation of alpha-beta T cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of smoothened signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative thymic T cell selection|positive regulation of alpha-beta T cell differentiation|positive regulation of transcription from RNA polymerase II promoter|thymocyte apoptosis	cilium|cytosol|nucleolus	beta-catenin binding|histone acetyltransferase binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(11)|ovary(3)|large_intestine(2)|central_nervous_system(1)|kidney(1)|pancreas(1)	19														Greig_Cephalopolysyndactyly|Pallister-Hall_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	7	42302551	42302552	+	IGR	DEL	TT	-	-	rs112354454		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42302551_42302552delTT								GLI3 (25933 upstream) : C7orf25 (646322 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	42527045	42527045	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42527045delT								GLI3 (250427 upstream) : C7orf25 (421829 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	43015737	43015737	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43015737delA								MRPL32 (38286 upstream) : HECW1 (136461 downstream)																																			---	---	---	---
HECW1	23072	broad.mit.edu	37	7	43506036	43506036	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43506036delT	uc003tid.1	+						HECW1_uc011kbi.1_Intron	NM_015052	NP_055867			NEDD4-like ubiquitin-protein ligase 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1)	23																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	43613601	43613602	+	IGR	INS	-	A	A	rs78231130		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43613601_43613602insA								HECW1 (10663 upstream) : STK17A (9090 downstream)																																			---	---	---	---
C7orf44	55744	broad.mit.edu	37	7	43699584	43699584	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43699584delA	uc003tin.1	-						C7orf44_uc003til.2_Intron|C7orf44_uc003tii.2_Intron|C7orf44_uc003tij.2_Intron|C7orf44_uc010kxu.1_Intron|C7orf44_uc003tik.2_Intron|C7orf44_uc003tim.1_Intron|C7orf44_uc003tio.1_Intron|C7orf44_uc003tiq.1_Intron|C7orf44_uc003tip.1_Intron	NM_018224	NP_060694			hypothetical protein LOC55744							integral to membrane				ovary(1)	1																		---	---	---	---
C7orf44	55744	broad.mit.edu	37	7	43712372	43712373	+	Intron	INS	-	A	A	rs34219718		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43712372_43712373insA	uc003tin.1	-						C7orf44_uc003til.2_Intron|C7orf44_uc003tii.2_Intron|C7orf44_uc003tij.2_Intron|C7orf44_uc010kxu.1_Intron|C7orf44_uc003tik.2_Intron|C7orf44_uc003tim.1_Intron|C7orf44_uc003tio.1_Intron|C7orf44_uc003tiq.1_Intron|C7orf44_uc003tip.1_Intron	NM_018224	NP_060694			hypothetical protein LOC55744							integral to membrane				ovary(1)	1																		---	---	---	---
RASA4P	401331	broad.mit.edu	37	7	44073272	44073273	+	Intron	INS	-	AC	AC			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44073272_44073273insAC	uc011kbk.1	-						RASA4P_uc003tji.2_RNA|RASA4P_uc010kxx.2_Intron	NM_006989	NP_008920			RAS p21 protein activator 4 isoform 1												0																		---	---	---	---
POLM	27434	broad.mit.edu	37	7	44124391	44124391	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44124391delT	uc003tjt.2	-						POLM_uc003tju.2_5'Flank|POLM_uc003tjx.2_5'Flank|POLM_uc003tjv.2_5'Flank|POLM_uc011kbt.1_5'Flank|POLM_uc003tjz.3_5'Flank|POLM_uc011kbu.1_5'Flank|POLM_uc010kxy.2_5'Flank	NM_013284	NP_037416			DNA-directed DNA polymerase mu						DNA recombination|DNA repair	nucleus	DNA binding|DNA nucleotidylexotransferase activity|DNA-directed DNA polymerase activity|metal ion binding			ovary(2)|central_nervous_system(1)	3													DNA_polymerases_(catalytic_subunits)					---	---	---	---
Unknown	0	broad.mit.edu	37	7	44174768	44174769	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44174768_44174769delTT								POLD2 (11621 upstream) : MYL7 (3696 downstream)																																			---	---	---	---
CAMK2B	816	broad.mit.edu	37	7	44268675	44268676	+	Intron	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44268675_44268676insC	uc003tkq.2	-						CAMK2B_uc003tkp.2_Intron|CAMK2B_uc003tkx.2_Intron|CAMK2B_uc010kyd.2_Intron|CAMK2B_uc003tkr.2_Intron|CAMK2B_uc003tks.2_Intron|CAMK2B_uc003tku.2_Intron|CAMK2B_uc003tkv.2_Intron|CAMK2B_uc003tkt.2_Intron|CAMK2B_uc003tkw.2_Intron|CAMK2B_uc010kyc.2_Intron|CAMK2B_uc003tkn.2_Frame_Shift_Ins_p.G29fs	NM_001220	NP_001211			calcium/calmodulin-dependent protein kinase II						interferon-gamma-mediated signaling pathway|synaptic transmission	cytosol|endocytic vesicle membrane|nucleoplasm|plasma membrane	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			large_intestine(1)|ovary(1)	2																		---	---	---	---
CAMK2B	816	broad.mit.edu	37	7	44300276	44300276	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44300276delC	uc003tkq.2	-						CAMK2B_uc003tkp.2_Intron|CAMK2B_uc003tkx.2_Intron|CAMK2B_uc010kyd.2_Intron|CAMK2B_uc003tkr.2_Intron|CAMK2B_uc003tks.2_Intron|CAMK2B_uc003tku.2_Intron|CAMK2B_uc003tkv.2_Intron|CAMK2B_uc003tkt.2_Intron|CAMK2B_uc003tkw.2_Intron|CAMK2B_uc010kyc.2_Intron	NM_001220	NP_001211			calcium/calmodulin-dependent protein kinase II						interferon-gamma-mediated signaling pathway|synaptic transmission	cytosol|endocytic vesicle membrane|nucleoplasm|plasma membrane	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			large_intestine(1)|ovary(1)	2																		---	---	---	---
NUDCD3	23386	broad.mit.edu	37	7	44454146	44454146	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44454146delA	uc003tkz.2	-						NUDCD3_uc010kye.2_Intron	NM_015332	NP_056147			NudC domain containing 3												0																		---	---	---	---
NUDCD3	23386	broad.mit.edu	37	7	44468042	44468042	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44468042delA	uc003tkz.2	-						NUDCD3_uc010kye.2_Intron	NM_015332	NP_056147			NudC domain containing 3												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	44550790	44550791	+	IGR	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44550790_44550791insC								NUDCD3 (20405 upstream) : NPC1L1 (1345 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	45571617	45571618	+	IGR	DEL	TA	-	-	rs141885711	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45571617_45571618delTA								RAMP3 (347770 upstream) : ADCY1 (42121 downstream)																																			---	---	---	---
ADCY1	107	broad.mit.edu	37	7	45650487	45650489	+	Intron	DEL	TGG	-	-	rs72117112		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45650487_45650489delTGG	uc003tne.3	+						ADCY1_uc003tnd.2_Intron	NM_021116	NP_066939			adenylate cyclase 1						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|calmodulin binding|metal ion binding			ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	6					Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)													---	---	---	---
Unknown	0	broad.mit.edu	37	7	45897543	45897555	+	IGR	DEL	AAGGAAGGAAGGG	-	-	rs140295102		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45897543_45897555delAAGGAAGGAAGGG								SEPT7P2 (88926 upstream) : IGFBP1 (30404 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	46051689	46051689	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46051689delA								IGFBP3 (90818 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	46132682	46132682	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46132682delT								IGFBP3 (171811 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	46136310	46136310	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46136310delT								IGFBP3 (175439 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	46155836	46155837	+	IGR	DEL	CA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46155836_46155837delCA								IGFBP3 (194965 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	46299698	46299698	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46299698delT								IGFBP3 (338827 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	46361312	46361313	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:46361312_46361313delAA								IGFBP3 (400441 upstream) : TNS3 (953440 downstream)																																			---	---	---	---
TNS3	64759	broad.mit.edu	37	7	47365452	47365452	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47365452delT	uc003tnv.2	-						TNS3_uc003tnw.2_Intron	NM_022748	NP_073585			tensin 3							focal adhesion	protein binding			ovary(4)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	47649594	47649595	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47649594_47649595delAA								TNS3 (27852 upstream) : C7orf65 (45247 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	47725512	47725512	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47725512delG								C7orf65 (24266 upstream) : PKD1L1 (88778 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	47767132	47767132	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47767132delT								C7orf65 (65886 upstream) : PKD1L1 (47158 downstream)																																			---	---	---	---
PKD1L1	168507	broad.mit.edu	37	7	47868832	47868832	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47868832delA	uc003tny.1	-						C7orf69_uc003toa.1_Intron|PKD1L1_uc003tob.2_5'Flank	NM_138295	NP_612152			polycystin-1L1						cell-cell adhesion	integral to membrane				ovary(8)|upper_aerodigestive_tract(2)|breast(1)	11																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	48156381	48156381	+	IGR	DEL	C	-	-	rs112282342		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48156381delC								UPP1 (8052 upstream) : ABCA13 (54676 downstream)																																			---	---	---	---
ABCA13	154664	broad.mit.edu	37	7	48441341	48441342	+	Intron	INS	-	AC	AC	rs146576513	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48441341_48441342insAC	uc003toq.2	+						ABCA13_uc010kys.1_Intron|ABCA13_uc003tos.1_Intron|ABCA13_uc010kyt.1_Intron	NM_152701	NP_689914			ATP binding cassette, sub-family A (ABC1),						transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10																		---	---	---	---
ABCA13	154664	broad.mit.edu	37	7	48597849	48597849	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48597849delT	uc003toq.2	+						ABCA13_uc010kys.1_Intron|ABCA13_uc010kyt.1_Intron|ABCA13_uc010kyu.1_Intron	NM_152701	NP_689914			ATP binding cassette, sub-family A (ABC1),						transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10																		---	---	---	---
ABCA13	154664	broad.mit.edu	37	7	48683029	48683029	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48683029delA	uc003toq.2	+						ABCA13_uc010kys.1_Intron|ABCA13_uc010kyt.1_Intron|ABCA13_uc010kyu.1_Intron	NM_152701	NP_689914			ATP binding cassette, sub-family A (ABC1),						transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	48933910	48933911	+	IGR	INS	-	A	A	rs144179148	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48933910_48933911insA								ABCA13 (246819 upstream) : CDC14C (30246 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	49026182	49026183	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:49026182_49026183insT								CDC14C (59133 upstream) : VWC2 (787074 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	49750499	49750499	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:49750499delA								CDC14C (783450 upstream) : VWC2 (62758 downstream)																																			---	---	---	---
ZPBP	11055	broad.mit.edu	37	7	50118581	50118581	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50118581delA	uc003tou.2	-						ZPBP_uc011kci.1_Intron|ZPBP_uc010kyw.2_Intron	NM_007009	NP_008940			zona pellucida binding protein isoform 1						binding of sperm to zona pellucida	extracellular region					0	Glioma(55;0.08)|all_neural(89;0.245)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	50476393	50476393	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50476393delA								IKZF1 (3597 upstream) : FIGNL1 (35441 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	50911078	50911078	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:50911078delT								GRB10 (49919 upstream) : COBL (172832 downstream)																																			---	---	---	---
COBL	23242	broad.mit.edu	37	7	51167423	51167424	+	Intron	INS	-	T	T	rs146905953	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51167423_51167424insT	uc003tpr.3	-						COBL_uc003tps.2_Intron|COBL_uc011kcl.1_Intron|COBL_uc010kzc.2_Intron|COBL_uc003tpt.2_Intron|COBL_uc003tpp.3_Intron|COBL_uc003tpq.3_Intron	NM_015198	NP_056013			cordon-bleu homolog											skin(3)|ovary(2)	5	Glioma(55;0.08)																	---	---	---	---
COBL	23242	broad.mit.edu	37	7	51251754	51251754	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51251754delT	uc003tpr.3	-						COBL_uc003tps.2_Intron|COBL_uc011kcl.1_Intron|COBL_uc010kzc.2_Intron|COBL_uc003tpt.2_Intron|COBL_uc003tpp.3_Intron|COBL_uc003tpq.3_Intron	NM_015198	NP_056013			cordon-bleu homolog											skin(3)|ovary(2)	5	Glioma(55;0.08)																	---	---	---	---
COBL	23242	broad.mit.edu	37	7	51362341	51362347	+	Intron	DEL	AAAAAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51362341_51362347delAAAAAAA	uc003tpr.3	-						COBL_uc003tps.2_Intron|COBL_uc011kcl.1_Intron|COBL_uc010kzc.2_Intron|COBL_uc003tpt.2_Intron	NM_015198	NP_056013			cordon-bleu homolog											skin(3)|ovary(2)	5	Glioma(55;0.08)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	51669370	51669370	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51669370delA								COBL (284855 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	52528758	52528759	+	IGR	DEL	AA	-	-	rs67354874	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:52528758_52528759delAA								None (None upstream) : POM121L12 (574590 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	52614145	52614145	+	IGR	DEL	T	-	-	rs112930407		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:52614145delT								None (None upstream) : POM121L12 (489204 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	52658368	52658368	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:52658368delA								None (None upstream) : POM121L12 (444981 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	52761942	52761943	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:52761942_52761943delTG								None (None upstream) : POM121L12 (341406 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	52786990	52786991	+	IGR	DEL	GT	-	-	rs145095614	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:52786990_52786991delGT								None (None upstream) : POM121L12 (316358 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	53016595	53016596	+	IGR	INS	-	C	C	rs112460359		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53016595_53016596insC								None (None upstream) : POM121L12 (86753 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	53372456	53372456	+	IGR	DEL	T	-	-	rs76020977		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53372456delT								POM121L12 (267839 upstream) : HPVC1 (896461 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	53374090	53374091	+	IGR	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53374090_53374091delTC								POM121L12 (269473 upstream) : HPVC1 (894826 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	53552094	53552094	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53552094delA								POM121L12 (447477 upstream) : HPVC1 (716823 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	53634180	53634180	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53634180delT								POM121L12 (529563 upstream) : HPVC1 (634737 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	53682780	53682780	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53682780delT								POM121L12 (578163 upstream) : HPVC1 (586137 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	53999071	53999071	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:53999071delA								POM121L12 (894454 upstream) : HPVC1 (269846 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	54470175	54470175	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:54470175delT								HPVC1 (200061 upstream) : VSTM2A (139844 downstream)																																			---	---	---	---
EGFR	1956	broad.mit.edu	37	7	55164651	55164651	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55164651delC	uc003tqk.2	+						EGFR_uc003tqh.2_Intron|EGFR_uc003tqi.2_Intron|EGFR_uc003tqj.2_Intron|EGFR_uc010kzg.1_Intron	NM_005228	NP_005219			epidermal growth factor receptor isoform a						activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity			lung(9213)|central_nervous_system(103)|stomach(41)|upper_aerodigestive_tract(39)|prostate(32)|ovary(31)|thyroid(24)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|kidney(8)|urinary_tract(6)|skin(5)|adrenal_gland(5)|soft_tissue(4)|bone(3)|NS(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)	9571	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)		8	A|O|Mis		glioma|NSCLC	NSCLC			Lung_Cancer_Familial_Clustering_of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			---	---	---	---
VOPP1	81552	broad.mit.edu	37	7	55627915	55627915	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55627915delT	uc003tqs.2	-						VOPP1_uc011kcr.1_Intron	NM_030796	NP_110423			EGFR-coamplified and overexpressed protein						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic vesicle membrane|endosome|integral to organelle membrane	signal transducer activity				0																		---	---	---	---
FKBP9L	360132	broad.mit.edu	37	7	55773456	55773456	+	5'Flank	DEL	T	-	-	rs113066121		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55773456delT	uc010kzl.2	-							NR_003949				SubName: Full=cDNA, FLJ79189, highly similar to FK506-binding protein 9 (EC 5.2.1.8);												0																		---	---	---	---
SEPT14	346288	broad.mit.edu	37	7	55910824	55910824	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55910824delA	uc003tqz.2	-							NM_207366	NP_997249			septin 14						cell cycle|cell division	septin complex	GTP binding|protein binding				0	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)															---	---	---	---
GBAS	2631	broad.mit.edu	37	7	56048840	56048840	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56048840delT	uc003tre.1	+						GBAS_uc003trf.1_Intron	NM_001483	NP_001474			nipsnap homolog 2							integral to plasma membrane|membrane fraction|mitochondrion	protein binding			central_nervous_system(1)	1	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)															---	---	---	---
GBAS	2631	broad.mit.edu	37	7	56063672	56063672	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56063672delA	uc003tre.1	+						GBAS_uc003trf.1_Intron	NM_001483	NP_001474			nipsnap homolog 2							integral to plasma membrane|membrane fraction|mitochondrion	protein binding			central_nervous_system(1)	1	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)															---	---	---	---
CCT6A	908	broad.mit.edu	37	7	56127164	56127164	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56127164delA	uc003trl.1	+						PSPH_uc003trj.2_Intron|CCT6A_uc003trm.1_Intron|CCT6A_uc011kcu.1_Intron|SNORA15_uc003trn.1_5'Flank	NM_001762	NP_001753			chaperonin containing TCP1, subunit 6A isoform						'de novo' posttranslational protein folding	cytosol	ATP binding|unfolded protein binding			upper_aerodigestive_tract(1)	1	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)															---	---	---	---
PHKG1	5260	broad.mit.edu	37	7	56149761	56149762	+	Intron	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56149761_56149762insC	uc003trz.1	-						PSPH_uc003trj.2_Intron|PHKG1_uc003try.1_Intron|PHKG1_uc011kdb.1_Intron|PHKG1_uc011kdc.1_Intron|PHKG1_uc011kdd.1_Intron	NM_006213	NP_006204			phosphorylase kinase gamma subunit 1						glucose metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol	ATP binding|calmodulin binding|phosphorylase kinase activity			large_intestine(1)	1	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	56231403	56231403	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56231403delA								PSPH (47313 upstream) : DKFZp434L192 (332513 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	56336119	56336134	+	IGR	DEL	TCCCTCCTTTCCTCCT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56336119_56336134delTCCCTCCTTTCCTCCT								PSPH (152029 upstream) : DKFZp434L192 (227782 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	56339244	56339244	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56339244delT								PSPH (155154 upstream) : DKFZp434L192 (224672 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	56450411	56450412	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56450411_56450412insT								PSPH (266321 upstream) : DKFZp434L192 (113504 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	56524750	56524750	+	IGR	DEL	T	-	-	rs113955675		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56524750delT								PSPH (340660 upstream) : DKFZp434L192 (39166 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	56586754	56586754	+	IGR	DEL	T	-	-	rs34625858		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56586754delT								DKFZp434L192 (21777 upstream) : ZNF479 (600574 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	56805397	56805397	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56805397delG								DKFZp434L192 (240420 upstream) : ZNF479 (381931 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57437092	57437097	+	IGR	DEL	TTTTTT	-	-	rs150771162		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57437092_57437097delTTTTTT								ZNF479 (229521 upstream) : ZNF716 (72786 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57626666	57626667	+	IGR	INS	-	CT	CT	rs148667050	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57626666_57626667insCT								ZNF716 (93401 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57647342	57647343	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57647342_57647343insT								ZNF716 (114077 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57651750	57651751	+	IGR	INS	-	T	T	rs148924254		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57651750_57651751insT								ZNF716 (118485 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57676858	57676859	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57676858_57676859delTG								ZNF716 (143593 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57714427	57714428	+	IGR	INS	-	G	G	rs140210527	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57714427_57714428insG								ZNF716 (181162 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57882290	57882291	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57882290_57882291delTG								ZNF716 (349025 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	57929339	57929342	+	IGR	DEL	TTTG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:57929339_57929342delTTTG								ZNF716 (396074 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61096393	61096393	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61096393delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61886967	61886968	+	IGR	INS	-	T	T	rs145530532	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61886967_61886968insT								None (None upstream) : LOC643955 (864704 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61913959	61913959	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61913959delT								None (None upstream) : LOC643955 (837713 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	61986100	61986100	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:61986100delT								None (None upstream) : LOC643955 (765572 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	62673404	62673404	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62673404delT								None (None upstream) : LOC643955 (78268 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	62984752	62984752	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:62984752delA								LOC100287704 (172601 upstream) : ZNF727 (521069 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	63762752	63762752	+	IGR	DEL	A	-	-	rs34069180		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63762752delA								ZNF679 (35452 upstream) : ZNF680 (217503 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	63809719	63809719	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63809719delT	uc011kdo.1	+	4										SubName: Full=cDNA FLJ57041, moderately similar to Zinc finger protein 92;																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	63836552	63836552	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63836552delG								ZNF679 (109252 upstream) : ZNF680 (143703 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	63869160	63869160	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63869160delA								ZNF679 (141860 upstream) : ZNF680 (111095 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	64036501	64036502	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64036501_64036502delTT	uc003ttc.1	+											Homo sapiens cDNA FLJ43440 fis, clone OCBBF2030517.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	64513332	64513332	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64513332delT	uc003ttt.1	+						uc010kzt.1_Intron					Homo sapiens cDNA clone IMAGE:4215179, partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	64728451	64728451	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64728451delA								INTS4L1 (33852 upstream) : ZNF92 (110317 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	64917365	64917365	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64917365delA								ZNF92 (51368 upstream) : INTS4L2 (195412 downstream)																																			---	---	---	---
VKORC1L1	154807	broad.mit.edu	37	7	65365030	65365037	+	Intron	DEL	GTGTGTGT	-	-	rs112479964		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65365030_65365037delGTGTGTGT	uc003tul.2	+						VKORC1L1_uc011kds.1_Intron	NM_173517	NP_775788			vitamin K epoxide reductase complex, subunit							integral to membrane					0		Lung NSC(55;0.197)			Menadione(DB00170)|Warfarin(DB00682)													---	---	---	---
GUSB	2990	broad.mit.edu	37	7	65431416	65431416	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65431416delA	uc003tun.2	-						GUSB_uc011kdt.1_Intron	NM_000181	NP_000172			glucuronidase, beta precursor						glycosaminoglycan catabolic process	lysosome	beta-glucuronidase activity|cation binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	65518345	65518346	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65518345_65518346insT								GUSB (71099 upstream) : ASL (22430 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	65658733	65658736	+	IGR	DEL	CCTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65658733_65658736delCCTT								CRCP (39182 upstream) : TPST1 (11523 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	65899617	65899617	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65899617delA								NCRNA00174 (34222 upstream) : LOC493754 (93829 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	65917420	65917421	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65917420_65917421insA								NCRNA00174 (52025 upstream) : LOC493754 (76025 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	65961993	65961994	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65961993_65961994delAA								NCRNA00174 (96598 upstream) : LOC493754 (31452 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	65963247	65963248	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65963247_65963248delTT								NCRNA00174 (97852 upstream) : LOC493754 (30198 downstream)																																			---	---	---	---
LOC493754	493754	broad.mit.edu	37	7	65996239	65996240	+	RNA	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65996239_65996240delAA	uc010lac.1	-	6		c.1471_1472delTT								Homo sapiens cDNA FLJ14309 fis, clone PLACE3000221.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	66063215	66063215	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66063215delT								LOC493754 (5852 upstream) : RABGEF1 (30675 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	66071681	66071681	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66071681delT								LOC493754 (14318 upstream) : RABGEF1 (22209 downstream)																																			---	---	---	---
LOC729156	729156	broad.mit.edu	37	7	66295937	66295937	+	Intron	DEL	A	-	-	rs75178156		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66295937delA	uc003tvj.1	-							NR_003934				Homo sapiens cDNA FLJ36054 fis, clone TESTI2018290.												0																		---	---	---	---
TYW1	55253	broad.mit.edu	37	7	66546141	66546141	+	Intron	DEL	G	-	-	rs7795081	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66546141delG	uc003tvn.2	+						TYW1_uc010lai.2_Intron|TYW1_uc011kef.1_Intron	NM_018264	NP_060734			radical S-adenosyl methionine and flavodoxin						tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity			skin(1)	1		Lung NSC(55;0.0846)|all_lung(88;0.183)																---	---	---	---
TYW1	55253	broad.mit.edu	37	7	66669482	66669482	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66669482delC	uc003tvn.2	+						TYW1_uc010lai.2_Intron|TYW1_uc011kef.1_Intron|PMS2L4_uc003tvo.2_Intron	NM_018264	NP_060734			radical S-adenosyl methionine and flavodoxin						tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity			skin(1)	1		Lung NSC(55;0.0846)|all_lung(88;0.183)																---	---	---	---
PMS2L4	5382	broad.mit.edu	37	7	66746635	66746635	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66746635delA	uc003tvo.2	-											Homo sapiens cDNA clone IMAGE:4081618.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	66909159	66909161	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66909159_66909161delTTT								STAG3L4 (122647 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	67259396	67259396	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67259396delT								STAG3L4 (472884 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	67370814	67370814	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67370814delC								STAG3L4 (584302 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	67458810	67458810	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67458810delT								STAG3L4 (672298 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	67518238	67518238	+	IGR	DEL	T	-	-	rs80009336		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67518238delT								STAG3L4 (731726 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	67917206	67917206	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67917206delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	67983029	67983029	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67983029delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68010665	68010667	+	IGR	DEL	AGA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68010665_68010667delAGA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68010776	68010781	+	IGR	DEL	CTCCTT	-	-	rs10537591		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68010776_68010781delCTCCTT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68191735	68191735	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68191735delA								None (None upstream) : AUTS2 (872170 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68914942	68914946	+	IGR	DEL	CAAAA	-	-	rs146626927		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68914942_68914946delCAAAA								None (None upstream) : AUTS2 (148959 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68952382	68952383	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68952382_68952383delTT								None (None upstream) : AUTS2 (111522 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	68958459	68958460	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:68958459_68958460insT								None (None upstream) : AUTS2 (105445 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	69017864	69017864	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69017864delT								None (None upstream) : AUTS2 (46041 downstream)																																			---	---	---	---
AUTS2	26053	broad.mit.edu	37	7	69235890	69235890	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69235890delA	uc003tvw.3	+						AUTS2_uc003tvv.3_Intron|AUTS2_uc003tvx.3_Intron	NM_015570	NP_056385			autism susceptibility candidate 2 isoform 1											ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)														---	---	---	---
AUTS2	26053	broad.mit.edu	37	7	69445582	69445584	+	Intron	DEL	AAA	-	-	rs111555232		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69445582_69445584delAAA	uc003tvw.3	+						AUTS2_uc003tvv.3_Intron|AUTS2_uc003tvx.3_Intron	NM_015570	NP_056385			autism susceptibility candidate 2 isoform 1											ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)														---	---	---	---
AUTS2	26053	broad.mit.edu	37	7	69801924	69801924	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:69801924delT	uc003tvw.3	+						AUTS2_uc003tvx.3_Intron	NM_015570	NP_056385			autism susceptibility candidate 2 isoform 1											ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)														---	---	---	---
AUTS2	26053	broad.mit.edu	37	7	70007659	70007659	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70007659delC	uc003tvw.3	+						AUTS2_uc003tvx.3_Intron	NM_015570	NP_056385			autism susceptibility candidate 2 isoform 1											ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)														---	---	---	---
AUTS2	26053	broad.mit.edu	37	7	70080523	70080523	+	Intron	DEL	A	-	-	rs34820489		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70080523delA	uc003tvw.3	+						AUTS2_uc003tvx.3_Intron	NM_015570	NP_056385			autism susceptibility candidate 2 isoform 1											ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)														---	---	---	---
WBSCR17	64409	broad.mit.edu	37	7	70786853	70786853	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70786853delT	uc003tvy.2	+						WBSCR17_uc003tvz.2_Intron	NM_022479	NP_071924			UDP-GalNAc:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|central_nervous_system(1)	7		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)																---	---	---	---
WBSCR17	64409	broad.mit.edu	37	7	70877362	70877365	+	Intron	DEL	TTTT	-	-	rs79669363		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70877362_70877365delTTTT	uc003tvy.2	+						WBSCR17_uc003tvz.2_Intron	NM_022479	NP_071924			UDP-GalNAc:polypeptide							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|central_nervous_system(1)	7		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)																---	---	---	---
TYW1B	441250	broad.mit.edu	37	7	72061974	72061974	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72061974delA	uc011kej.1	-						TYW1B_uc011keh.1_Intron|TYW1B_uc011kei.1_Intron	NM_001145440	NP_001138912			tRNA-yW synthesizing protein 1 homolog B isoform						tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity				0																		---	---	---	---
TYW1B	441250	broad.mit.edu	37	7	72080333	72080334	+	Intron	INS	-	GA	GA	rs144937533	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72080333_72080334insGA	uc011kej.1	-						TYW1B_uc011keh.1_Intron|TYW1B_uc011kei.1_Intron	NM_001145440	NP_001138912			tRNA-yW synthesizing protein 1 homolog B isoform						tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity				0																		---	---	---	---
TYW1B	441250	broad.mit.edu	37	7	72181590	72181592	+	Intron	DEL	TGT	-	-	rs72250945		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72181590_72181592delTGT	uc011kej.1	-						TYW1B_uc011keh.1_Intron|TYW1B_uc011kei.1_Intron	NM_001145440	NP_001138912			tRNA-yW synthesizing protein 1 homolog B isoform						tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity				0																		---	---	---	---
TYW1B	441250	broad.mit.edu	37	7	72286071	72286071	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72286071delA	uc011kej.1	-						TYW1B_uc011keh.1_Intron|TYW1B_uc011kek.1_Intron	NM_001145440	NP_001138912			tRNA-yW synthesizing protein 1 homolog B isoform						tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity				0																		---	---	---	---
SBDSP1	155370	broad.mit.edu	37	7	72301571	72301572	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72301571_72301572delTT	uc003twf.2	+						TYW1B_uc011keh.1_5'Flank|TYW1B_uc011kej.1_5'Flank|TYW1B_uc011kek.1_5'Flank|SBDSP1_uc011kel.1_Intron|SBDSP1_uc003twg.2_Intron|SBDSP1_uc003twh.2_Intron|SBDSP1_uc003twe.2_Intron	NR_001588				Homo sapiens Shwachman-Bodian-Diamond syndrome pseudogene, mRNA (cDNA clone IMAGE:4329436).												0																		---	---	---	---
GTF2IP1	2970	broad.mit.edu	37	7	72614315	72614316	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72614315_72614316insA	uc003txo.3	+						FKBP6_uc003twz.2_Intron|GTF2IP1_uc011keq.1_Intron	NR_003580				SubName: Full=cDNA FLJ61347, highly similar to General transcription factor II-I;												0																		---	---	---	---
FKBP6	8468	broad.mit.edu	37	7	72695720	72695720	+	Intron	DEL	A	-	-	rs78555983		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72695720delA	uc003twz.2	+						uc003txt.2_Intron	NM_001135211	NP_001128683			FK506 binding protein 6 isoform b						protein folding	membrane	FK506 binding|peptidyl-prolyl cis-trans isomerase activity				0		Lung NSC(55;0.0908)|all_lung(88;0.198)																---	---	---	---
FKBP6	8468	broad.mit.edu	37	7	72747282	72747285	+	Intron	DEL	AAAC	-	-	rs139382378	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72747282_72747285delAAAC	uc003tya.2	+						FKBP6_uc003twz.2_Intron|FKBP6_uc011kew.1_Intron|FKBP6_uc010lbe.1_Intron	NM_003602	NP_003593			FK506 binding protein 6 isoform a						protein folding	membrane	FK506 binding|peptidyl-prolyl cis-trans isomerase activity				0		Lung NSC(55;0.0908)|all_lung(88;0.198)																---	---	---	---
Unknown	0	broad.mit.edu	37	7	72791128	72791129	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72791128_72791129insA								FKBP6 (18487 upstream) : FZD9 (56980 downstream)																																			---	---	---	---
STX1A	6804	broad.mit.edu	37	7	73136623	73136626	+	5'Flank	DEL	AAAA	-	-	rs146526023		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73136623_73136626delAAAA	uc003tyx.2	-						STX1A_uc003tyy.2_5'Flank|STX1A_uc010lbj.1_5'Flank	NM_004603	NP_004594			syntaxin 1A isoform 1						energy reserve metabolic process|glutamate secretion|intracellular protein transport|regulation of insulin secretion	cell junction|extracellular region|integral to membrane|neuron projection|synaptic vesicle membrane|synaptosome	SNAP receptor activity				0		Lung NSC(55;0.0908)|all_lung(88;0.198)																---	---	---	---
RFC2	5982	broad.mit.edu	37	7	73303685	73303688	+	Intron	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73303685_73303688delTTTT	uc011kfa.1	-							NM_181471				replication factor C 2 isoform 1						cell cycle checkpoint|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|protein binding			liver(1)|central_nervous_system(1)	2																		---	---	---	---
RFC2	5982	broad.mit.edu	37	7	73493381	73493381	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73493381delA	uc011kfa.1	-							NM_181471				replication factor C 2 isoform 1						cell cycle checkpoint|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|protein binding			liver(1)|central_nervous_system(1)	2																		---	---	---	---
LIMK1	3984	broad.mit.edu	37	7	73525771	73525773	+	Intron	DEL	AAA	-	-	rs76335411		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73525771_73525773delAAA	uc003uaa.1	+						RFC2_uc011kfa.1_Intron|LIMK1_uc010lbl.1_Intron|LIMK1_uc003uab.2_Intron	NM_002314	NP_002305			LIM domain kinase 1						actin cytoskeleton organization|axon guidance|negative regulation of ubiquitin-protein ligase activity|positive regulation of actin filament bundle assembly|positive regulation of axon extension|Rho protein signal transduction	cytosol|growth cone|nucleus	ATP binding|heat shock protein binding|protein serine/threonine kinase activity|zinc ion binding			stomach(2)|ovary(1)	3		Lung NSC(55;0.137)																---	---	---	---
RFC2	5982	broad.mit.edu	37	7	73661209	73661209	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73661209delT	uc003uaj.2	-						RFC2_uc011kfa.1_Intron|RFC2_uc003uak.2_Intron|RFC2_uc010lbp.2_Intron|RFC2_uc003ual.2_Intron	NM_181471	NP_852136			replication factor C 2 isoform 1						cell cycle checkpoint|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|protein binding			liver(1)|central_nervous_system(1)	2																		---	---	---	---
CLIP2	7461	broad.mit.edu	37	7	73781526	73781526	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73781526delT	uc003uam.2	+						CLIP2_uc003uan.2_Intron	NM_003388	NP_003379			CAP-GLY domain containing linker protein 2							microtubule associated complex				skin(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	73838629	73838630	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73838629_73838630insA								CLIP2 (18357 upstream) : GTF2IRD1 (29490 downstream)																																			---	---	---	---
GTF2IRD1	9569	broad.mit.edu	37	7	73938055	73938055	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73938055delA	uc003uaq.2	+						GTF2IRD1_uc010lbq.2_Intron|GTF2IRD1_uc003uap.2_Intron|GTF2IRD1_uc003uar.1_Intron	NM_016328	NP_057412			GTF2I repeat domain containing 1 isoform 1							nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(4)	4																		---	---	---	---
GTF2IRD1	9569	broad.mit.edu	37	7	73940128	73940128	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73940128delA	uc003uaq.2	+						GTF2IRD1_uc010lbq.2_Intron|GTF2IRD1_uc003uap.2_Intron|GTF2IRD1_uc003uar.1_Intron	NM_016328	NP_057412			GTF2I repeat domain containing 1 isoform 1							nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(4)	4																		---	---	---	---
GTF2IRD1	9569	broad.mit.edu	37	7	73956505	73956505	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73956505delC	uc003uaq.2	+						GTF2IRD1_uc010lbq.2_Intron|GTF2IRD1_uc003uap.2_Intron|GTF2IRD1_uc003uar.1_Intron	NM_016328	NP_057412			GTF2I repeat domain containing 1 isoform 1							nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(4)	4																		---	---	---	---
GTF2IRD1	9569	broad.mit.edu	37	7	73963244	73963244	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73963244delA	uc003uaq.2	+						GTF2IRD1_uc010lbq.2_Intron|GTF2IRD1_uc003uap.2_Intron|GTF2IRD1_uc003uar.1_Intron	NM_016328	NP_057412			GTF2I repeat domain containing 1 isoform 1							nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(4)	4																		---	---	---	---
GTF2IRD1	9569	broad.mit.edu	37	7	73984986	73984986	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73984986delA	uc003uaq.2	+						GTF2IRD1_uc010lbq.2_Intron|GTF2IRD1_uc003uap.2_Intron|GTF2IRD1_uc003uar.1_Intron	NM_016328	NP_057412			GTF2I repeat domain containing 1 isoform 1							nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(4)	4																		---	---	---	---
GTF2IRD1	9569	broad.mit.edu	37	7	74004418	74004418	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74004418delT	uc003uaq.2	+						GTF2IRD1_uc010lbq.2_Intron|GTF2IRD1_uc003uap.2_Intron|GTF2IRD1_uc003uar.1_Intron	NM_016328	NP_057412			GTF2I repeat domain containing 1 isoform 1							nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(4)	4																		---	---	---	---
GTF2IRD1	9569	broad.mit.edu	37	7	74006739	74006739	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74006739delT	uc003uaq.2	+						GTF2IRD1_uc010lbq.2_Intron|GTF2IRD1_uc003uap.2_Intron|GTF2IRD1_uc003uar.1_Intron	NM_016328	NP_057412			GTF2I repeat domain containing 1 isoform 1							nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(4)	4																		---	---	---	---
GTF2IRD1	9569	broad.mit.edu	37	7	74012781	74012781	+	Intron	DEL	A	-	-	rs76034441		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74012781delA	uc003uaq.2	+						GTF2IRD1_uc010lbq.2_Intron|GTF2IRD1_uc003uap.2_Intron|GTF2IRD1_uc003uar.1_Intron	NM_016328	NP_057412			GTF2I repeat domain containing 1 isoform 1							nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(4)	4																		---	---	---	---
PMS2L5	5383	broad.mit.edu	37	7	74328495	74328495	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74328495delT	uc003ubm.3	+							NR_027777				Homo sapiens cDNA, FLJ99701.												0																		---	---	---	---
POM121C	100101267	broad.mit.edu	37	7	75114786	75114787	+	Intron	INS	-	G	G	rs11301130		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75114786_75114787insG	uc003udk.3	-						POM121C_uc003udl.1_5'Flank	NM_001099415	NP_001092885			POM121 membrane glycoprotein (rat)-like						mRNA transport|protein transport|transmembrane transport	endoplasmic reticulum membrane|nuclear membrane|nuclear pore	protein binding				0																		---	---	---	---
HIP1	3092	broad.mit.edu	37	7	75182913	75182913	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75182913delT	uc003uds.1	-						HIP1_uc011kfz.1_Intron	NM_005338	NP_005329			huntingtin interacting protein 1						activation of caspase activity|cell differentiation|clathrin coat assembly|endocytosis|induction of apoptosis|positive regulation of receptor-mediated endocytosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	clathrin coated vesicle membrane|cytoskeleton|Golgi apparatus|membrane fraction|nucleus	actin binding|clathrin binding|phosphatidylinositol binding|structural constituent of cytoskeleton			lung(3)|pancreas(2)|ovary(1)|breast(1)|central_nervous_system(1)	8								T	PDGFRB	CMML								---	---	---	---
HIP1	3092	broad.mit.edu	37	7	75189545	75189545	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75189545delT	uc003uds.1	-						HIP1_uc011kfz.1_Intron	NM_005338	NP_005329			huntingtin interacting protein 1						activation of caspase activity|cell differentiation|clathrin coat assembly|endocytosis|induction of apoptosis|positive regulation of receptor-mediated endocytosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	clathrin coated vesicle membrane|cytoskeleton|Golgi apparatus|membrane fraction|nucleus	actin binding|clathrin binding|phosphatidylinositol binding|structural constituent of cytoskeleton			lung(3)|pancreas(2)|ovary(1)|breast(1)|central_nervous_system(1)	8								T	PDGFRB	CMML								---	---	---	---
HIP1	3092	broad.mit.edu	37	7	75242404	75242405	+	Intron	DEL	CA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75242404_75242405delCA	uc003uds.1	-							NM_005338	NP_005329			huntingtin interacting protein 1						activation of caspase activity|cell differentiation|clathrin coat assembly|endocytosis|induction of apoptosis|positive regulation of receptor-mediated endocytosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	clathrin coated vesicle membrane|cytoskeleton|Golgi apparatus|membrane fraction|nucleus	actin binding|clathrin binding|phosphatidylinositol binding|structural constituent of cytoskeleton			lung(3)|pancreas(2)|ovary(1)|breast(1)|central_nervous_system(1)	8								T	PDGFRB	CMML								---	---	---	---
HIP1	3092	broad.mit.edu	37	7	75255303	75255304	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75255303_75255304insT	uc003uds.1	-							NM_005338	NP_005329			huntingtin interacting protein 1						activation of caspase activity|cell differentiation|clathrin coat assembly|endocytosis|induction of apoptosis|positive regulation of receptor-mediated endocytosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	clathrin coated vesicle membrane|cytoskeleton|Golgi apparatus|membrane fraction|nucleus	actin binding|clathrin binding|phosphatidylinositol binding|structural constituent of cytoskeleton			lung(3)|pancreas(2)|ovary(1)|breast(1)|central_nervous_system(1)	8								T	PDGFRB	CMML								---	---	---	---
CCL26	10344	broad.mit.edu	37	7	75420258	75420259	+	5'Flank	DEL	AA	-	-	rs80106601		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75420258_75420259delAA	uc003udt.1	-							NM_006072	NP_006063			chemokine (C-C motif) ligand 26 precursor						cell-cell signaling|chemotaxis|immune response|inflammatory response|positive regulation of actin filament polymerization|positive regulation of cell migration|positive regulation of endothelial cell proliferation|positive regulation of Rac GTPase activity|signal transduction	extracellular space	chemokine activity				0																		---	---	---	---
RHBDD2	57414	broad.mit.edu	37	7	75512837	75512837	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75512837delA	uc003udw.1	+						RHBDD2_uc003udv.1_Intron	NM_001040456	NP_001035546			rhomboid domain containing 2 isoform a							integral to membrane	serine-type endopeptidase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	75530740	75530741	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75530740_75530741delAA								RHBDD2 (12496 upstream) : POR (13679 downstream)																																			---	---	---	---
SRCRB4D	136853	broad.mit.edu	37	7	76037742	76037742	+	Intron	DEL	G	-	-	rs76141960	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76037742delG	uc003ufb.2	-						ZP3_uc003ufc.3_Intron	NM_080744	NP_542782			scavenger receptor cysteine rich domain							extracellular region|membrane	scavenger receptor activity			pancreas(1)	1																		---	---	---	---
ZP3	7784	broad.mit.edu	37	7	76040325	76040326	+	Intron	INS	-	AG	AG	rs71879406		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76040325_76040326insAG	uc003ufc.3	+						SRCRB4D_uc003ufb.2_5'Flank	NM_007155	NP_009086			zona pellucida glycoprotein 3 isoform 2						binding of sperm to zona pellucida|blastocyst formation|egg coat formation|humoral immune response mediated by circulating immunoglobulin|intracellular protein transport|negative regulation of binding of sperm to zona pellucida|negative regulation of transcription, DNA-dependent|oocyte development|phosphatidylinositol-mediated signaling|positive regulation of acrosomal vesicle exocytosis|positive regulation of acrosome reaction|positive regulation of antral ovarian follicle growth|positive regulation of calcium ion import|positive regulation of calcium ion transport via store-operated calcium channel activity|positive regulation of humoral immune response|positive regulation of interferon-gamma production|positive regulation of interleukin-4 production|positive regulation of leukocyte migration|positive regulation of ovarian follicle development|positive regulation of phosphatidylinositol biosynthetic process|positive regulation of protein kinase activity|positive regulation of protein kinase B signaling cascade|positive regulation of T cell proliferation|positive regulation of transcription, DNA-dependent|positive regulation of type IV hypersensitivity|protein kinase C signaling cascade	endoplasmic reticulum|extracellular space|Golgi apparatus|integral to membrane|multivesicular body|outer acrosomal membrane|perinuclear region of cytoplasm|plasma membrane|proteinaceous extracellular matrix	acrosin binding|manganese ion transmembrane transporter activity|receptor activity|sugar binding				0																		---	---	---	---
ZP3	7784	broad.mit.edu	37	7	76041505	76041506	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76041505_76041506delAA	uc003ufc.3	+						SRCRB4D_uc003ufb.2_5'Flank	NM_007155	NP_009086			zona pellucida glycoprotein 3 isoform 2						binding of sperm to zona pellucida|blastocyst formation|egg coat formation|humoral immune response mediated by circulating immunoglobulin|intracellular protein transport|negative regulation of binding of sperm to zona pellucida|negative regulation of transcription, DNA-dependent|oocyte development|phosphatidylinositol-mediated signaling|positive regulation of acrosomal vesicle exocytosis|positive regulation of acrosome reaction|positive regulation of antral ovarian follicle growth|positive regulation of calcium ion import|positive regulation of calcium ion transport via store-operated calcium channel activity|positive regulation of humoral immune response|positive regulation of interferon-gamma production|positive regulation of interleukin-4 production|positive regulation of leukocyte migration|positive regulation of ovarian follicle development|positive regulation of phosphatidylinositol biosynthetic process|positive regulation of protein kinase activity|positive regulation of protein kinase B signaling cascade|positive regulation of T cell proliferation|positive regulation of transcription, DNA-dependent|positive regulation of type IV hypersensitivity|protein kinase C signaling cascade	endoplasmic reticulum|extracellular space|Golgi apparatus|integral to membrane|multivesicular body|outer acrosomal membrane|perinuclear region of cytoplasm|plasma membrane|proteinaceous extracellular matrix	acrosin binding|manganese ion transmembrane transporter activity|receptor activity|sugar binding				0																		---	---	---	---
ZP3	7784	broad.mit.edu	37	7	76054010	76054010	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76054010delA	uc003ufd.3	+						ZP3_uc003ufc.3_Intron	NM_001110354	NP_001103824			zona pellucida glycoprotein 3 isoform 1						binding of sperm to zona pellucida|blastocyst formation|egg coat formation|humoral immune response mediated by circulating immunoglobulin|intracellular protein transport|negative regulation of binding of sperm to zona pellucida|negative regulation of transcription, DNA-dependent|oocyte development|phosphatidylinositol-mediated signaling|positive regulation of acrosomal vesicle exocytosis|positive regulation of acrosome reaction|positive regulation of antral ovarian follicle growth|positive regulation of calcium ion import|positive regulation of calcium ion transport via store-operated calcium channel activity|positive regulation of humoral immune response|positive regulation of interferon-gamma production|positive regulation of interleukin-4 production|positive regulation of leukocyte migration|positive regulation of ovarian follicle development|positive regulation of phosphatidylinositol biosynthetic process|positive regulation of protein kinase activity|positive regulation of protein kinase B signaling cascade|positive regulation of T cell proliferation|positive regulation of transcription, DNA-dependent|positive regulation of type IV hypersensitivity|protein kinase C signaling cascade	endoplasmic reticulum|extracellular space|Golgi apparatus|integral to membrane|multivesicular body|outer acrosomal membrane|perinuclear region of cytoplasm|plasma membrane|proteinaceous extracellular matrix	acrosin binding|manganese ion transmembrane transporter activity|receptor activity|sugar binding				0																		---	---	---	---
PMS2L11	441263	broad.mit.edu	37	7	76620660	76620660	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76620660delT	uc003ufw.3	+						PMS2L11_uc011kgn.1_Intron	NR_023383				Homo sapiens cDNA FLJ59034 complete cds, moderately similar to Protein deltex-2.												0																		---	---	---	---
PMS2L11	441263	broad.mit.edu	37	7	76627942	76627944	+	Intron	DEL	GTG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76627942_76627944delGTG	uc003ufw.3	+						PMS2L11_uc011kgn.1_Intron	NR_023383				Homo sapiens cDNA FLJ59034 complete cds, moderately similar to Protein deltex-2.												0																		---	---	---	---
PION	54103	broad.mit.edu	37	7	76957078	76957078	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76957078delT	uc003ugf.2	-						PION_uc011kgo.1_5'Flank|PION_uc003ugd.2_5'Flank	NM_017439	NP_059135			pigeon homolog						beta-amyloid formation|regulation of proteolysis	trans-Golgi network	beta-amyloid binding			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	77076131	77076131	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77076131delT								PION (30414 upstream) : PTPN12 (90642 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	77409757	77409757	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77409757delT								RSBN1L (637 upstream) : TMEM60 (13289 downstream)																																			---	---	---	---
MAGI2	9863	broad.mit.edu	37	7	77807188	77807188	+	Intron	DEL	A	-	-	rs113984102		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77807188delA	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron|MAGI2_uc010ldx.1_Intron	NM_012301	NP_036433			membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)																---	---	---	---
MAGI2	9863	broad.mit.edu	37	7	78447031	78447032	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78447031_78447032delTT	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron	NM_012301	NP_036433			membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)																---	---	---	---
MAGI2	9863	broad.mit.edu	37	7	78500882	78500882	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:78500882delA	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron	NM_012301	NP_036433			membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)																---	---	---	---
MAGI2	9863	broad.mit.edu	37	7	79045706	79045707	+	Intron	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79045706_79045707insG	uc003ugx.2	-						MAGI2_uc003ugy.2_Intron	NM_012301	NP_036433			membrane associated guanylate kinase, WW and PDZ							cell junction|synapse|synaptosome	phosphatase binding			ovary(5)|lung(4)|breast(1)|skin(1)	11		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)																---	---	---	---
Unknown	0	broad.mit.edu	37	7	79313520	79313520	+	IGR	DEL	T	-	-	rs145361412		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79313520delT								MAGI2 (230630 upstream) : GNAI1 (450620 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	79392670	79392670	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79392670delT								MAGI2 (309780 upstream) : GNAI1 (371470 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	79426089	79426090	+	IGR	INS	-	A	A	rs76950965		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79426089_79426090insA								MAGI2 (343199 upstream) : GNAI1 (338050 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	79444646	79444646	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79444646delG								MAGI2 (361756 upstream) : GNAI1 (319494 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	79717793	79717793	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79717793delT								MAGI2 (634903 upstream) : GNAI1 (46347 downstream)																																			---	---	---	---
GNAI1	2770	broad.mit.edu	37	7	79782582	79782582	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:79782582delT	uc003uhb.1	+						GNAI1_uc011kgt.1_Intron	NM_002069	NP_002060			guanine nucleotide binding protein (G protein),						cell cycle|cell division|inhibition of adenylate cyclase activity by G-protein signaling pathway|platelet activation|synaptic transmission	centrosome|heterotrimeric G-protein complex|midbody|nucleus	G-protein beta/gamma-subunit complex binding|GTP binding|metabotropic serotonin receptor binding|signal transducer activity			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
CD36	948	broad.mit.edu	37	7	80247746	80247746	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:80247746delA	uc003uhc.2	+						CD36_uc003uhd.3_Intron|CD36_uc011kgv.1_Intron	NM_001127444	NP_001120916			CD36 antigen						cell adhesion|cGMP-mediated signaling|cholesterol transport|lipid metabolic process|lipid storage|lipoprotein transport|low-density lipoprotein particle clearance|nitric oxide mediated signal transduction|plasma membrane long-chain fatty acid transport|platelet activation|platelet degranulation|positive regulation of cell-matrix adhesion|positive regulation of macrophage derived foam cell differentiation	integral to plasma membrane|membrane fraction|platelet alpha granule membrane	lipid binding|low-density lipoprotein receptor activity|thrombospondin receptor activity|transforming growth factor beta binding			ovary(1)	1																		---	---	---	---
CD36	948	broad.mit.edu	37	7	80290537	80290537	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:80290537delA	uc003uhc.2	+						CD36_uc003uhd.3_Intron|CD36_uc011kgv.1_Intron|CD36_uc003uhe.3_Intron|CD36_uc003uhf.3_Intron|CD36_uc003uhg.3_Intron|CD36_uc003uhh.3_Intron	NM_001127444	NP_001120916			CD36 antigen						cell adhesion|cGMP-mediated signaling|cholesterol transport|lipid metabolic process|lipid storage|lipoprotein transport|low-density lipoprotein particle clearance|nitric oxide mediated signal transduction|plasma membrane long-chain fatty acid transport|platelet activation|platelet degranulation|positive regulation of cell-matrix adhesion|positive regulation of macrophage derived foam cell differentiation	integral to plasma membrane|membrane fraction|platelet alpha granule membrane	lipid binding|low-density lipoprotein receptor activity|thrombospondin receptor activity|transforming growth factor beta binding			ovary(1)	1																		---	---	---	---
SEMA3C	10512	broad.mit.edu	37	7	80410269	80410269	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:80410269delA	uc003uhj.2	-						SEMA3C_uc011kgw.1_Intron	NM_006379	NP_006370			semaphorin 3C precursor						immune response|response to drug	membrane	receptor activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	81269213	81269213	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81269213delT	uc003uhk.1	-											Homo sapiens mRNA sequence.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	81272468	81272468	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81272468delA	uc003uhk.1	-											Homo sapiens mRNA sequence.																														---	---	---	---
HGF	3082	broad.mit.edu	37	7	81381622	81381622	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81381622delT	uc003uhl.2	-						HGF_uc003uhm.2_Intron|HGF_uc003uhn.1_Intron|HGF_uc003uho.1_Intron|HGF_uc003uhp.2_Intron	NM_000601	NP_000592			hepatocyte growth factor isoform 1						epithelial to mesenchymal transition|mitosis|platelet activation|platelet degranulation|proteolysis|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling	platelet alpha granule lumen	growth factor activity|serine-type endopeptidase activity			ovary(2)|central_nervous_system(2)	4																		---	---	---	---
CACNA2D1	781	broad.mit.edu	37	7	81779296	81779297	+	Intron	DEL	GT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:81779296_81779297delGT	uc003uhr.1	-							NM_000722	NP_000713			calcium channel, voltage-dependent, alpha							voltage-gated calcium channel complex	metal ion binding			ovary(5)|pancreas(1)	6					Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)													---	---	---	---
PCLO	27445	broad.mit.edu	37	7	82407476	82407476	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82407476delA	uc003uhx.2	-							NM_033026	NP_149015			piccolo isoform 1						cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	83472489	83472489	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:83472489delT								SEMA3E (194165 upstream) : SEMA3A (115176 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	84424831	84424831	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:84424831delT								SEMA3A (600614 upstream) : SEMA3D (200043 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	85017001	85017001	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:85017001delT								SEMA3D (200830 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	85042838	85042838	+	IGR	DEL	A	-	-	rs144692129		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:85042838delA								SEMA3D (226667 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	85425864	85425864	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:85425864delA								SEMA3D (609693 upstream) : GRM3 (847366 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	85932284	85932285	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:85932284_85932285delTT								None (None upstream) : GRM3 (340945 downstream)																																			---	---	---	---
ABCB4	5244	broad.mit.edu	37	7	87101981	87101981	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87101981delT	uc003uiv.1	-	3	167	c.91delA	c.(91-93)AGGfs	p.R31fs	ABCB4_uc003uiw.1_Frame_Shift_Del_p.R31fs|ABCB4_uc003uix.1_Frame_Shift_Del_p.R31fs|ABCB4_uc003uiy.2_Frame_Shift_Del_p.R31fs	NM_018849	NP_061337	P21439	MDR3_HUMAN	ATP-binding cassette, subfamily B, member 4	31	Cytoplasmic (By similarity).				cellular lipid metabolic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|xenobiotic-transporting ATPase activity			ovary(4)|skin(1)|pancreas(1)	6	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)																	---	---	---	---
ABCB1	5243	broad.mit.edu	37	7	87155481	87155484	+	Intron	DEL	TTTT	-	-	rs111465883		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87155481_87155484delTTTT	uc003uiz.1	-						ABCB1_uc011khc.1_Intron	NM_000927	NP_000918			ATP-binding cassette, subfamily B, member 1						G2/M transition of mitotic cell cycle|stem cell proliferation	apical plasma membrane|cell surface|Golgi membrane|integral to membrane|intercellular canaliculus|membrane fraction	ATP binding|protein binding|xenobiotic-transporting ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	Esophageal squamous(14;0.00164)				Adenosine triphosphate(DB00171)|Alfentanil(DB00802)|Arsenic trioxide(DB01169)|Atazanavir(DB01072)|Carvedilol(DB01136)|Colchicine(DB01394)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dipyridamole(DB00975)|Estramustine(DB01196)|Flupenthixol(DB00875)|Imatinib(DB00619)|Itraconazole(DB01167)|Nicardipine(DB00622)|Propafenone(DB01182)|Quinacrine(DB01103)|Quinidine(DB00908)|Ranolazine(DB00243)|Rifampin(DB01045)|Roxithromycin(DB00778)|Saquinavir(DB01232)|Tamoxifen(DB00675)|Vinblastine(DB00570)													---	---	---	---
ABCB1	5243	broad.mit.edu	37	7	87250325	87250325	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87250325delA	uc003uiz.1	-						ABCB1_uc003uja.1_Intron|ABCB1_uc010lei.1_Intron	NM_000927	NP_000918			ATP-binding cassette, subfamily B, member 1						G2/M transition of mitotic cell cycle|stem cell proliferation	apical plasma membrane|cell surface|Golgi membrane|integral to membrane|intercellular canaliculus|membrane fraction	ATP binding|protein binding|xenobiotic-transporting ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	Esophageal squamous(14;0.00164)				Adenosine triphosphate(DB00171)|Alfentanil(DB00802)|Arsenic trioxide(DB01169)|Atazanavir(DB01072)|Carvedilol(DB01136)|Colchicine(DB01394)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dipyridamole(DB00975)|Estramustine(DB01196)|Flupenthixol(DB00875)|Imatinib(DB00619)|Itraconazole(DB01167)|Nicardipine(DB00622)|Propafenone(DB01182)|Quinacrine(DB01103)|Quinidine(DB00908)|Ranolazine(DB00243)|Rifampin(DB01045)|Roxithromycin(DB00778)|Saquinavir(DB01232)|Tamoxifen(DB00675)|Vinblastine(DB00570)													---	---	---	---
ADAM22	53616	broad.mit.edu	37	7	87778496	87778496	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87778496delT	uc003ujn.2	+						ADAM22_uc003ujk.1_Intron|ADAM22_uc003ujl.1_Intron|ADAM22_uc003ujm.2_Intron|ADAM22_uc003ujo.2_Intron|ADAM22_uc003ujp.1_Intron	NM_021723	NP_068369			ADAM metallopeptidase domain 22 isoform 1						cell adhesion|central nervous system development|negative regulation of cell adhesion|proteolysis	integral to membrane	integrin binding|metalloendopeptidase activity|protein binding|receptor activity|zinc ion binding			ovary(4)|skin(2)|lung(1)|kidney(1)	8	Esophageal squamous(14;0.00202)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	88285246	88285246	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88285246delT								STEAP4 (349037 upstream) : ZNF804B (103507 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	88294501	88294501	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88294501delA								STEAP4 (358292 upstream) : ZNF804B (94252 downstream)																																			---	---	---	---
ZNF804B	219578	broad.mit.edu	37	7	88501118	88501118	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88501118delA	uc011khi.1	+							NM_181646	NP_857597			zinc finger protein 804B							intracellular	zinc ion binding			ovary(5)|skin(3)|pancreas(2)|upper_aerodigestive_tract(1)	11	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)												HNSCC(36;0.09)			---	---	---	---
ZNF804B	219578	broad.mit.edu	37	7	88784014	88784014	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88784014delT	uc011khi.1	+							NM_181646	NP_857597			zinc finger protein 804B							intracellular	zinc ion binding			ovary(5)|skin(3)|pancreas(2)|upper_aerodigestive_tract(1)	11	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)												HNSCC(36;0.09)			---	---	---	---
ZNF804B	219578	broad.mit.edu	37	7	88818579	88818579	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88818579delA	uc011khi.1	+							NM_181646	NP_857597			zinc finger protein 804B							intracellular	zinc ion binding			ovary(5)|skin(3)|pancreas(2)|upper_aerodigestive_tract(1)	11	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)												HNSCC(36;0.09)			---	---	---	---
Unknown	0	broad.mit.edu	37	7	88983732	88983733	+	IGR	INS	-	CA	CA	rs142063221	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88983732_88983733insCA								ZNF804B (17388 upstream) : DPY19L2P4 (764981 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	89733593	89733595	+	IGR	DEL	TAC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89733593_89733595delTAC								ZNF804B (767249 upstream) : DPY19L2P4 (15119 downstream)																																			---	---	---	---
GTPBP10	85865	broad.mit.edu	37	7	89982117	89982117	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89982117delT	uc003ukm.1	+						GTPBP10_uc003uki.1_Intron|GTPBP10_uc003ukj.1_Intron|GTPBP10_uc003ukk.1_Intron|GTPBP10_uc003ukl.1_Intron|GTPBP10_uc003ukn.1_Intron|GTPBP10_uc003uko.1_Intron	NM_033107	NP_149098			GTP-binding protein 10 isoform 2						ribosome biogenesis	chromosome|nucleolus	GTP binding|GTPase activity|magnesium ion binding				0																OREG0003797	type=REGULATORY REGION|Gene=BC021573|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	---	---	---	---
CDK14	5218	broad.mit.edu	37	7	90376819	90376819	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90376819delT	uc003uky.2	+						CDK14_uc003ukt.1_Intron|CDK14_uc003ukv.1_Intron|CDK14_uc003uku.1_Intron|CDK14_uc003ukx.1_Intron|CDK14_uc003ukz.1_Intron|CDK14_uc010les.1_Intron|CDK14_uc011khl.1_Intron	NM_012395	NP_036527			PFTAIRE protein kinase 1						cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4																		---	---	---	---
CDK14	5218	broad.mit.edu	37	7	90378463	90378463	+	Intron	DEL	A	-	-	rs36081296		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90378463delA	uc003uky.2	+						CDK14_uc003ukt.1_Intron|CDK14_uc003ukv.1_Intron|CDK14_uc003uku.1_Intron|CDK14_uc003ukx.1_Intron|CDK14_uc003ukz.1_Intron|CDK14_uc010les.1_Intron|CDK14_uc011khl.1_Intron	NM_012395	NP_036527			PFTAIRE protein kinase 1						cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4																		---	---	---	---
CDK14	5218	broad.mit.edu	37	7	90407127	90407128	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90407127_90407128insA	uc003uky.2	+						CDK14_uc003ukt.1_Intron|CDK14_uc003ukv.1_Intron|CDK14_uc003uku.1_Intron|CDK14_uc003ukx.1_Intron|CDK14_uc003ukz.1_Intron|CDK14_uc010les.1_Intron|CDK14_uc011khl.1_Intron	NM_012395	NP_036527			PFTAIRE protein kinase 1						cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4																		---	---	---	---
CDK14	5218	broad.mit.edu	37	7	90747307	90747308	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90747307_90747308insT	uc003uky.2	+						CDK14_uc003ukz.1_Intron|CDK14_uc010les.1_Intron|CDK14_uc011khl.1_Intron	NM_012395	NP_036527			PFTAIRE protein kinase 1						cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4																		---	---	---	---
CDK14	5218	broad.mit.edu	37	7	90764575	90764575	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90764575delA	uc003uky.2	+						CDK14_uc003ukz.1_Intron|CDK14_uc010les.1_Intron|CDK14_uc011khl.1_Intron	NM_012395	NP_036527			PFTAIRE protein kinase 1						cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4																		---	---	---	---
CDK14	5218	broad.mit.edu	37	7	90834261	90834263	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90834261_90834263delAAA	uc003uky.2	+						CDK14_uc003ukz.1_Intron|CDK14_uc010les.1_Intron|CDK14_uc011khl.1_Intron	NM_012395	NP_036527			PFTAIRE protein kinase 1						cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4																		---	---	---	---
MTERF	7978	broad.mit.edu	37	7	91504571	91504571	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91504571delT	uc003ulb.1	-						MTERF_uc010let.1_Intron|MTERF_uc003ulc.1_Intron|MTERF_uc011khm.1_Intron|MTERF_uc010leu.1_Intron	NM_006980	NP_008911			mitochondrial transcription termination factor						DNA geometric change|regulation of transcription, DNA-dependent|termination of mitochondrial transcription	mitochondrial nucleoid	double-stranded DNA binding				0	all_cancers(62;2.28e-09)|all_epithelial(64;1.07e-07)|Breast(17;0.00371)|all_hematologic(106;0.091)|all_lung(186;0.178)|Lung NSC(181;0.235)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.0993)|Kidney(17;0.118)|Epithelial(20;0.136)|LUSC - Lung squamous cell carcinoma(200;0.176)															---	---	---	---
AKAP9	10142	broad.mit.edu	37	7	91630147	91630147	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91630147delT	uc003ulg.2	+						AKAP9_uc003ule.2_Intron|AKAP9_uc003ulf.2_Intron|AKAP9_uc003uli.2_5'Flank	NM_005751	NP_005742			A-kinase anchor protein 9 isoform 2						G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1)	26	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)					T	BRAF	papillary thyroid								---	---	---	---
AKAP9	10142	broad.mit.edu	37	7	91662564	91662564	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91662564delA	uc003ulg.2	+						AKAP9_uc003ule.2_Intron|AKAP9_uc003ulf.2_Intron|AKAP9_uc003uli.2_Intron	NM_005751	NP_005742			A-kinase anchor protein 9 isoform 2						G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1)	26	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)					T	BRAF	papillary thyroid								---	---	---	---
CDK6	1021	broad.mit.edu	37	7	92427512	92427512	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92427512delA	uc011khw.1	-						CDK6_uc010lez.2_Intron	NM_001259	NP_001250			cyclin-dependent kinase 6						cell dedifferentiation|cell division|G1 phase of mitotic cell cycle|gliogenesis|negative regulation of cell cycle|negative regulation of epithelial cell proliferation|negative regulation of osteoblast differentiation|positive regulation of cell-matrix adhesion|positive regulation of fibroblast proliferation|regulation of erythrocyte differentiation|regulation of gene expression|response to virus	cyclin-dependent protein kinase holoenzyme complex|cytosol|nucleus|ruffle	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			central_nervous_system(1)|skin(1)	2	all_cancers(62;8.72e-12)|all_epithelial(64;3.65e-10)|Breast(17;0.000675)|all_lung(186;0.0392)|Lung NSC(181;0.053)|all_neural(327;0.219)|all_hematologic(106;0.237)		STAD - Stomach adenocarcinoma(4;6.16e-07)|GBM - Glioblastoma multiforme(5;1.2e-06)|all cancers(6;3.1e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)					T	MLLT10	ALL								---	---	---	---
Unknown	0	broad.mit.edu	37	7	92509411	92509414	+	IGR	DEL	AGAG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92509411_92509414delAGAG								CDK6 (43470 upstream) : SAMD9 (219418 downstream)																																			---	---	---	---
CCDC132	55610	broad.mit.edu	37	7	92926367	92926367	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92926367delT	uc003umo.2	+						CCDC132_uc003umq.2_Intron|CCDC132_uc003ump.2_Intron|CCDC132_uc003umr.2_Intron|CCDC132_uc011khz.1_Intron	NM_017667	NP_060137			coiled-coil domain containing 132 isoform a												0	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	92996638	92996639	+	IGR	DEL	CA	-	-	rs141273557	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92996638_92996639delCA								CCDC132 (8301 upstream) : CALCR (57160 downstream)																																			---	---	---	---
CASD1	64921	broad.mit.edu	37	7	94182609	94182609	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94182609delA	uc003uni.3	+						CASD1_uc003unj.3_Intron	NM_022900	NP_075051			CAS1 domain containing 1 precursor							integral to membrane				ovary(2)	2	all_cancers(62;6.71e-10)|all_epithelial(64;5e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	94190914	94190914	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94190914delT								CASD1 (4588 upstream) : SGCE (23622 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	94209858	94209858	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94209858delA								CASD1 (23532 upstream) : SGCE (4678 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	94481232	94481232	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94481232delA								PEG10 (182228 upstream) : PPP1R9A (55717 downstream)																																			---	---	---	---
PPP1R9A	55607	broad.mit.edu	37	7	94912030	94912030	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94912030delC	uc003unp.2	+						PPP1R9A_uc010lfj.2_Intron|PPP1R9A_uc011kif.1_Intron|PPP1R9A_uc003unq.2_Intron|PPP1R9A_uc011kig.1_Intron|PPP1R9A_uc003unr.2_Intron	NM_017650	NP_060120			protein phosphatase 1, regulatory (inhibitor)							cell junction|synapse|synaptosome	actin binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4	all_cancers(62;9.12e-11)|all_epithelial(64;4.34e-09)		STAD - Stomach adenocarcinoma(171;0.0031)												HNSCC(28;0.073)			---	---	---	---
ASB4	51666	broad.mit.edu	37	7	95146914	95146914	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95146914delA	uc011kij.1	+						ASB4_uc003unx.2_Intron	NM_016116	NP_057200			ankyrin repeat and SOCS box-containing protein 4						intracellular signal transduction					central_nervous_system(1)	1	all_cancers(62;2.27e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.218)|all_lung(186;0.246)		STAD - Stomach adenocarcinoma(171;0.0151)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	95736346	95736347	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95736346_95736347delTT								DYNC1I1 (8611 upstream) : SLC25A13 (13186 downstream)																																			---	---	---	---
ACN9	57001	broad.mit.edu	37	7	96768109	96768109	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96768109delT	uc003uoo.3	+							NM_020186	NP_064571			ACN9 homolog precursor						regulation of gluconeogenesis	mitochondrial intermembrane space					0	all_cancers(62;2.54e-08)|all_epithelial(64;2.24e-08)|Esophageal squamous(72;0.00507)|all_lung(186;0.154)|Lung NSC(181;0.159)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	96869261	96869261	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96869261delA								ACN9 (58188 upstream) : TAC1 (492010 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	96907682	96907682	+	IGR	DEL	A	-	-	rs78707787		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96907682delA								ACN9 (96609 upstream) : TAC1 (453589 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	97190530	97190530	+	IGR	DEL	A	-	-	rs140931375		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97190530delA								ACN9 (379457 upstream) : TAC1 (170741 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	97252823	97252823	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97252823delA								ACN9 (441750 upstream) : TAC1 (108448 downstream)																																			---	---	---	---
OCM2	4951	broad.mit.edu	37	7	97616714	97616715	+	Intron	DEL	GT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97616714_97616715delGT	uc003upc.2	-							NM_006188	NP_006179			oncomodulin-like								calcium ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	97646966	97646967	+	IGR	INS	-	GT	GT	rs148273559	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97646966_97646967insGT								OCM2 (27550 upstream) : LMTK2 (89230 downstream)																																			---	---	---	---
LMTK2	22853	broad.mit.edu	37	7	97766852	97766852	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97766852delT	uc003upd.1	+							NM_014916	NP_055731			lemur tyrosine kinase 2 precursor						early endosome to late endosome transport|endocytic recycling|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|protein autophosphorylation|receptor recycling|transferrin transport	early endosome|Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|recycling endosome	ATP binding|myosin VI binding|protein phosphatase inhibitor activity|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(9)|stomach(3)|pancreas(2)|large_intestine(1)|breast(1)	16	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)																	---	---	---	---
LMTK2	22853	broad.mit.edu	37	7	97776542	97776542	+	Intron	DEL	T	-	-	rs111286597		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97776542delT	uc003upd.1	+							NM_014916	NP_055731			lemur tyrosine kinase 2 precursor						early endosome to late endosome transport|endocytic recycling|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|protein autophosphorylation|receptor recycling|transferrin transport	early endosome|Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|recycling endosome	ATP binding|myosin VI binding|protein phosphatase inhibitor activity|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(9)|stomach(3)|pancreas(2)|large_intestine(1)|breast(1)	16	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)																	---	---	---	---
LMTK2	22853	broad.mit.edu	37	7	97783020	97783020	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97783020delA	uc003upd.1	+							NM_014916	NP_055731			lemur tyrosine kinase 2 precursor						early endosome to late endosome transport|endocytic recycling|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|protein autophosphorylation|receptor recycling|transferrin transport	early endosome|Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|recycling endosome	ATP binding|myosin VI binding|protein phosphatase inhibitor activity|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(9)|stomach(3)|pancreas(2)|large_intestine(1)|breast(1)	16	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)																	---	---	---	---
LMTK2	22853	broad.mit.edu	37	7	97831431	97831431	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97831431delT	uc003upd.1	+							NM_014916	NP_055731			lemur tyrosine kinase 2 precursor						early endosome to late endosome transport|endocytic recycling|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|protein autophosphorylation|receptor recycling|transferrin transport	early endosome|Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|recycling endosome	ATP binding|myosin VI binding|protein phosphatase inhibitor activity|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(9)|stomach(3)|pancreas(2)|large_intestine(1)|breast(1)	16	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	98107786	98107786	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98107786delT								BAIAP2L1 (77359 upstream) : NPTX2 (138811 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	98131128	98131128	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98131128delT								BAIAP2L1 (100701 upstream) : NPTX2 (115469 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	98395700	98395700	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98395700delA								NPTX2 (136519 upstream) : TMEM130 (48412 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	98472990	98472990	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98472990delT								TMEM130 (5317 upstream) : TRRAP (3123 downstream)																																			---	---	---	---
TRRAP	8295	broad.mit.edu	37	7	98482212	98482213	+	Intron	INS	-	TG	TG			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98482212_98482213insTG	uc003upp.2	+						TRRAP_uc011kis.1_Intron	NM_003496	NP_003487			transformation/transcription domain-associated						histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
TRRAP	8295	broad.mit.edu	37	7	98484720	98484720	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98484720delT	uc003upp.2	+						TRRAP_uc011kis.1_Intron	NM_003496	NP_003487			transformation/transcription domain-associated						histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
TRRAP	8295	broad.mit.edu	37	7	98490582	98490582	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98490582delT	uc003upp.2	+						TRRAP_uc011kis.1_Intron	NM_003496	NP_003487			transformation/transcription domain-associated						histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
TRRAP	8295	broad.mit.edu	37	7	98581179	98581180	+	Intron	DEL	TT	-	-	rs57779646		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98581179_98581180delTT	uc003upp.2	+						TRRAP_uc011kis.1_Intron|TRRAP_uc003upr.2_Intron	NM_003496	NP_003487			transformation/transcription domain-associated						histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	98758498	98758498	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98758498delT								SMURF1 (16775 upstream) : KPNA7 (12699 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	98825055	98825056	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98825055_98825056delAA								KPNA7 (19966 upstream) : MYH16 (45868 downstream)																																			---	---	---	---
ARPC1A	10552	broad.mit.edu	37	7	98933584	98933585	+	Intron	DEL	AA	-	-	rs11764622		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98933584_98933585delAA	uc003upx.1	+						ARPC1A_uc010lfu.1_Intron|ARPC1A_uc003upy.1_Intron|ARPC1A_uc011kit.1_Intron	NM_006409	NP_006400			actin related protein 2/3 complex subunit 1A						actin cytoskeleton organization|regulation of actin filament polymerization	actin cytoskeleton|cytoplasm	actin binding			ovary(1)	1	all_cancers(62;4.46e-09)|all_epithelial(64;3.44e-10)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0258)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
BUD31	8896	broad.mit.edu	37	7	99008673	99008673	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99008673delT	uc003uqf.2	+						PDAP1_uc003uqe.2_5'Flank|BUD31_uc011kiu.1_Intron|BUD31_uc011kiv.1_Intron|BUD31_uc003uqg.3_Intron	NM_003910	NP_003901			G10 protein						regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding transcription factor activity			ovary(1)	1	all_cancers(62;1.76e-08)|all_epithelial(64;1.63e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
BUD31	8896	broad.mit.edu	37	7	99014689	99014689	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99014689delT	uc003uqf.2	+						BUD31_uc011kiu.1_Intron|BUD31_uc011kiv.1_Intron|BUD31_uc003uqg.3_Intron	NM_003910	NP_003901			G10 protein						regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding transcription factor activity			ovary(1)	1	all_cancers(62;1.76e-08)|all_epithelial(64;1.63e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
PTCD1	26024	broad.mit.edu	37	7	99042081	99042082	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99042081_99042082delAA	uc011kiw.1	-						CPSF4_uc003uqi.2_Intron|CPSF4_uc003uqj.2_Intron|CPSF4_uc003uqk.2_Intron|CPSF4_uc011kix.1_Intron	NM_015545	NP_056360			pentatricopeptide repeat domain 1											ovary(1)	1	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	99178594	99178594	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99178594delT								ZNF655 (4520 upstream) : ZNF498 (35977 downstream)																																			---	---	---	---
CYP3A43	64816	broad.mit.edu	37	7	99463417	99463417	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99463417delT	uc003urx.1	+						CYP3A43_uc003ury.1_Intron|CYP3A43_uc003urz.1_Intron|CYP3A43_uc003usa.1_Intron|CYP3A43_uc010lgi.1_Intron|CYP3A43_uc003usb.1_Intron	NM_057095	NP_476436			cytochrome P450, family 3, subfamily A,						xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding			ovary(1)|skin(1)	2	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)				Cetirizine(DB00341)|Doxycycline(DB00254)													---	---	---	---
COPS6	10980	broad.mit.edu	37	7	99687409	99687409	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99687409delA	uc003usu.2	+						COPS6_uc011kjf.1_Frame_Shift_Del_p.*125fs	NM_006833	NP_006824			COP9 signalosome subunit 6						cullin deneddylation|interspecies interaction between organisms	cytoplasm|signalosome	protein binding				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)															---	---	---	---
C7orf59	389541	broad.mit.edu	37	7	99748621	99748622	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99748621_99748622delAA	uc003utq.2	+							NM_001008395	NP_001008396			hypothetical protein LOC389541												0																		---	---	---	---
STAG3	10734	broad.mit.edu	37	7	99784960	99784960	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99784960delT	uc003utx.1	+						STAG3_uc010lgs.1_Intron|STAG3_uc011kjk.1_Intron	NM_012447	NP_036579			stromal antigen 3						chromosome segregation|synaptonemal complex assembly	chromosome, centromeric region|meiotic cohesin complex|synaptonemal complex	binding			ovary(4)|skin(2)|lung(1)|kidney(1)	8	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
GATS	352954	broad.mit.edu	37	7	99856501	99856501	+	Intron	DEL	T	-	-	rs57999130	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99856501delT	uc003uua.3	-						GATS_uc003uty.3_Intron|GATS_uc003utz.3_Intron|GATS_uc010lgt.2_Intron|GATS_uc010lgu.2_Intron	NM_178831	NP_849153			GATS, stromal antigen 3 opposite strand												0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
ZCWPW1	55063	broad.mit.edu	37	7	100004130	100004130	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100004130delA	uc003uut.2	-						ZCWPW1_uc011kjq.1_Intron|ZCWPW1_uc003uur.2_Intron|ZCWPW1_uc003uus.2_Intron|ZCWPW1_uc011kjr.1_Intron|ZCWPW1_uc003uuu.1_Intron|ZCWPW1_uc011kjp.1_Intron	NM_017984	NP_060454			zinc finger, CW type with PWWP domain 1								zinc ion binding				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
ZCWPW1	55063	broad.mit.edu	37	7	100017105	100017105	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100017105delA	uc003uut.2	-						ZCWPW1_uc011kjq.1_5'Flank|ZCWPW1_uc003uur.2_5'Flank|ZCWPW1_uc003uus.2_Intron|ZCWPW1_uc011kjr.1_Intron|ZCWPW1_uc003uuu.1_Intron|ZCWPW1_uc011kjs.1_5'Flank|ZCWPW1_uc011kjt.1_Intron|ZCWPW1_uc011kju.1_Intron	NM_017984	NP_060454			zinc finger, CW type with PWWP domain 1								zinc ion binding				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
C7orf61	402573	broad.mit.edu	37	7	100060733	100060736	+	Intron	DEL	AAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100060733_100060736delAAAA	uc003uuz.1	-							NM_001004323	NP_001004323			hypothetical protein LOC402573												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	100171592	100171593	+	5'Flank	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100171592_100171593insC	uc003uvh.2	-											RecName: Full=Histone deacetylase complex subunit SAP25; AltName: Full=Sin3-associated polypeptide, 25 kDa; AltName: Full=Sin3 corepressor complex subunit SAP25;																														---	---	---	---
ACTL6B	51412	broad.mit.edu	37	7	100248297	100248297	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100248297delA	uc003uvy.2	-						ACTL6B_uc003uvx.1_5'Flank|ACTL6B_uc003uvz.2_Intron	NM_016188	NP_057272			actin-like 6B						chromatin modification|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nBAF complex|SWI/SNF complex	ATP binding|protein binding|structural constituent of cytoskeleton			ovary(1)	1	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	100314670	100314671	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100314670_100314671delTT								POP7 (9548 upstream) : EPO (3752 downstream)																																			---	---	---	---
ZAN	7455	broad.mit.edu	37	7	100343683	100343684	+	Intron	INS	-	A	A	rs111812152		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100343683_100343684insA	uc003uwj.2	+						ZAN_uc003uwk.2_Intron|ZAN_uc003uwl.2_Intron|ZAN_uc010lhh.2_Intron|ZAN_uc010lhi.2_Intron	NM_003386	NP_003377			zonadhesin isoform 3						binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)|large_intestine(3)|central_nervous_system(2)|pancreas(2)	11	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)															---	---	---	---
EPHB4	2050	broad.mit.edu	37	7	100405271	100405271	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100405271delT	uc003uwn.1	-						EPHB4_uc003uwm.1_Intron|EPHB4_uc010lhj.1_Intron	NM_004444	NP_004435			EPH receptor B4 precursor						cell proliferation|organ morphogenesis|regulation of angiogenesis	cell surface|integral to plasma membrane	ATP binding|ephrin receptor activity			lung(4)|stomach(3)|skin(3)|central_nervous_system(2)|ovary(2)|breast(1)	15	Lung NSC(181;0.041)|all_lung(186;0.0581)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	100429830	100429830	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100429830delA								EPHB4 (4687 upstream) : SLC12A9 (20528 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	100761168	100761169	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100761168_100761169delTT								TRIM56 (26160 upstream) : SERPINE1 (9210 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	100783562	100783563	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100783562_100783563delAA								SERPINE1 (1020 upstream) : AP1S1 (14123 downstream)																																			---	---	---	---
VGF	7425	broad.mit.edu	37	7	100810622	100810622	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100810622delA	uc003uxx.3	-							NM_003378	NP_003369			VGF nerve growth factor inducible precursor						response to cAMP	extracellular space|transport vesicle	growth factor activity				0	Lung NSC(181;0.168)|all_lung(186;0.215)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	100868767	100868767	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100868767delT								ZNHIT1 (1298 upstream) : CLDN15 (6607 downstream)																																			---	---	---	---
EMID2	136227	broad.mit.edu	37	7	101192401	101192401	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101192401delG	uc010lhy.1	+						EMID2_uc003uyo.1_Intron	NM_133457	NP_597714			EMI domain containing 2							collagen				ovary(1)	1	Lung NSC(181;0.215)																	---	---	---	---
CUX1	1523	broad.mit.edu	37	7	101839857	101839857	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101839857delT	uc003uyx.3	+						CUX1_uc003uys.3_Intron|CUX1_uc003uyt.2_Intron|CUX1_uc011kkn.1_Intron|CUX1_uc003uyw.2_Intron|CUX1_uc003uyv.2_Intron|CUX1_uc003uyu.2_Intron	NM_181552	NP_853530			cut-like homeobox 1 isoform a						negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	101967964	101967965	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101967964_101967965delAA								SH2B2 (5787 upstream) : SPDYE6 (18228 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	101973365	101973365	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101973365delA								SH2B2 (11188 upstream) : SPDYE6 (12828 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	102024785	102024787	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102024785_102024787delAAA	uc003uzd.1	+						uc003uze.1_Intron|PRKRIP1_uc003uzf.2_Intron|PRKRIP1_uc003uzg.2_Intron|PRKRIP1_uc011kkq.1_Intron	NM_001003686	NP_001003686			SubName: Full=Putative uncharacterized protein PMS2L3;																														---	---	---	---
RASA4	10156	broad.mit.edu	37	7	102243412	102243412	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102243412delT	uc003vae.2	-						UPK3BL_uc003uzy.2_Intron|RASA4_uc011kla.1_Intron|RASA4_uc010lig.2_Intron|RASA4_uc003vaf.2_Intron|RASA4_uc011klb.1_Intron|RASA4_uc010lih.2_Intron|RASA4_uc011kld.1_Intron|uc003vag.1_Intron	NM_006989	NP_008920			RAS p21 protein activator 4 isoform 1						intracellular signal transduction|negative regulation of Ras protein signal transduction	cytosol|intrinsic to internal side of plasma membrane	metal ion binding|Ras GTPase activator activity				0																		---	---	---	---
FBXL13	222235	broad.mit.edu	37	7	102534215	102534217	+	Intron	DEL	AAA	-	-	rs72305289		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102534215_102534217delAAA	uc003vaq.2	-						FBXL13_uc010liq.1_Intron|FBXL13_uc010lir.1_Intron|FBXL13_uc003var.2_Intron|FBXL13_uc003vas.2_Intron	NM_145032	NP_659469			F-box and leucine-rich repeat protein 13 isoform												0																		---	---	---	---
FBXL13	222235	broad.mit.edu	37	7	102668057	102668058	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102668057_102668058insA	uc003vaq.2	-						FBXL13_uc010liq.1_5'Flank|FBXL13_uc010lir.1_Intron|FBXL13_uc003var.2_Intron|FBXL13_uc003vas.2_Intron|FBXL13_uc003vav.2_Intron	NM_145032	NP_659469			F-box and leucine-rich repeat protein 13 isoform												0																		---	---	---	---
DPY19L2P2	349152	broad.mit.edu	37	7	102902926	102902926	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102902926delA	uc003vbh.3	-						DPY19L2P2_uc003vbg.3_Intron|DPY19L2P2_uc010lit.2_Intron	NR_003561				RecName: Full=Protein dpy-19 homolog 2-like 2; AltName: Full=Dpy-19-like protein 2 pseudogene 2;												0																		---	---	---	---
DNAJC2	27000	broad.mit.edu	37	7	102983769	102983770	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102983769_102983770insA	uc003vbo.2	-						DNAJC2_uc003vbn.2_5'Flank|DNAJC2_uc010lix.2_Intron|DNAJC2_uc003vbp.2_Intron|DNAJC2_uc003vbq.1_Intron|DNAJC2_uc003vbr.1_Intron	NM_014377	NP_055192			DnaJ (Hsp40) homolog, subfamily C, member 2						'de novo' cotranslational protein folding|chromatin modification|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nuclear membrane	chromatin binding|DNA binding|histone binding|Hsp70 protein binding|ubiquitin binding			kidney(1)	1																		---	---	---	---
SLC26A5	375611	broad.mit.edu	37	7	103048080	103048081	+	Intron	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103048080_103048081delAG	uc003vbz.2	-						SLC26A5_uc003vbt.1_Intron|SLC26A5_uc003vbu.1_Intron|SLC26A5_uc003vbv.1_Intron|SLC26A5_uc003vbw.2_Intron|SLC26A5_uc003vbx.2_Intron|SLC26A5_uc003vby.2_Intron|SLC26A5_uc010liy.2_Intron	NM_198999	NP_945350			prestin isoform a						regulation of cell shape|sensory perception of sound	integral to membrane	secondary active sulfate transmembrane transporter activity			ovary(1)	1																		---	---	---	---
RELN	5649	broad.mit.edu	37	7	103314199	103314199	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103314199delA	uc003vca.2	-						RELN_uc010liz.2_Intron	NM_005045	NP_005036			reelin isoform a						axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|upper_aerodigestive_tract(5)|large_intestine(2)|central_nervous_system(2)|skin(1)|pancreas(1)	19				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	104608915	104608915	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104608915delT								LOC723809 (41823 upstream) : LOC100216545 (42074 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	105044957	105044958	+	IGR	DEL	AA	-	-	rs79687065		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105044957_105044958delAA								SRPK2 (5159 upstream) : PUS7 (52004 downstream)																																			---	---	---	---
PUS7	54517	broad.mit.edu	37	7	105146874	105146875	+	Intron	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105146874_105146875delTC	uc003vcx.2	-						PUS7_uc010lji.2_Intron|PUS7_uc003vcy.2_Intron|PUS7_uc003vcz.1_Intron	NM_019042	NP_061915			pseudouridylate synthase 7 homolog						pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding			breast(1)	1																		---	---	---	---
ATXN7L1	222255	broad.mit.edu	37	7	105366030	105366032	+	Intron	DEL	TTT	-	-	rs140417663		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105366030_105366032delTTT	uc003vde.2	-							NM_020725	NP_065776			ataxin 7-like 1 isoform 1												0																		---	---	---	---
ATXN7L1	222255	broad.mit.edu	37	7	105424403	105424404	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105424403_105424404insT	uc003vde.2	-						ATXN7L1_uc003vdi.2_Intron	NM_020725	NP_065776			ataxin 7-like 1 isoform 1												0																		---	---	---	---
CDHR3	222256	broad.mit.edu	37	7	105536665	105536666	+	Intron	INS	-	GA	GA	rs142328638	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105536665_105536666insGA	uc003vdk.2	+											RecName: Full=Cadherin-like protein 28; Flags: Precursor;						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1																		---	---	---	---
CDHR3	222256	broad.mit.edu	37	7	105672824	105672824	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105672824delT	uc003vdl.3	+						CDHR3_uc003vdk.2_Intron|CDHR3_uc003vdm.3_Intron|CDHR3_uc011klt.1_Intron|CDHR3_uc003vdn.2_Intron	NM_152750	NP_689963			hypothetical protein LOC222256 precursor						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	105825488	105825488	+	IGR	DEL	T	-	-	rs113116353		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105825488delT								SYPL1 (72431 upstream) : NAMPT (63246 downstream)																																			---	---	---	---
NAMPT	10135	broad.mit.edu	37	7	105912418	105912418	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105912418delA	uc003vdq.2	-						NAMPT_uc003vdr.1_Intron|NAMPT_uc011klu.1_Intron	NM_005746	NP_005737			nicotinamide phosphoribosyltransferase						cell-cell signaling|NAD biosynthetic process|nicotinamide metabolic process|positive regulation of cell proliferation|positive regulation of nitric-oxide synthase biosynthetic process|signal transduction|water-soluble vitamin metabolic process	cytosol	cytokine activity|nicotinamide phosphoribosyltransferase activity|nicotinate phosphoribosyltransferase activity|nicotinate-nucleotide diphosphorylase (carboxylating) activity			large_intestine(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	106166522	106166540	+	Intron	DEL	TTTTTTTTTTTTTTTTTTG	-	-	rs113303626		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106166522_106166540delTTTTTTTTTTTTTTTTTTG	uc003vds.2	-											Homo sapiens full length insert cDNA clone ZC44D09.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	106552480	106552480	+	IGR	DEL	A	-	-	rs75868597		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106552480delA								PIK3CG (4895 upstream) : PRKAR2B (132698 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	106555759	106555759	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:106555759delA								PIK3CG (8174 upstream) : PRKAR2B (129419 downstream)																																			---	---	---	---
CBLL1	79872	broad.mit.edu	37	7	107392891	107392892	+	Intron	INS	-	TCTG	TCTG	rs138759049	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107392891_107392892insTCTG	uc003veq.2	+						CBLL1_uc011kme.1_Intron|CBLL1_uc011kmf.1_Intron	NM_024814	NP_079090			Cas-Br-M (murine) ecotropic retroviral						cell-cell adhesion|negative regulation of cell adhesion|positive regulation of cell migration|positive regulation of endocytosis		protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)|skin(2)|lung(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	107562158	107562158	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107562158delT								DLD (516 upstream) : LAMB1 (2088 downstream)																																			---	---	---	---
LAMB1	3912	broad.mit.edu	37	7	107574432	107574432	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107574432delT	uc003vew.2	-						LAMB1_uc003vev.2_Intron	NM_002291	NP_002282			laminin, beta 1 precursor						axon guidance|odontogenesis|positive regulation of cell migration|positive regulation of epithelial cell proliferation|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-2 complex|laminin-8 complex|perinuclear region of cytoplasm	extracellular matrix structural constituent			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	8					Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
LAMB1	3912	broad.mit.edu	37	7	107636396	107636396	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107636396delG	uc003vew.2	-						LAMB1_uc003vev.2_Intron|LAMB1_uc003vex.2_Intron|LAMB1_uc010ljn.1_Intron	NM_002291	NP_002282			laminin, beta 1 precursor						axon guidance|odontogenesis|positive regulation of cell migration|positive regulation of epithelial cell proliferation|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-2 complex|laminin-8 complex|perinuclear region of cytoplasm	extracellular matrix structural constituent			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	8					Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
NRCAM	4897	broad.mit.edu	37	7	107962384	107962384	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107962384delA	uc003vfb.2	-						NRCAM_uc003vfc.2_Intron|NRCAM_uc011kmk.1_Intron|NRCAM_uc003vfd.2_Intron|NRCAM_uc003vfe.2_Intron	NM_001037132	NP_001032209			neuronal cell adhesion molecule isoform A						angiogenesis|axon guidance|axonal fasciculation|cell-cell adhesion|central nervous system development|clustering of voltage-gated sodium channels|neuron migration|positive regulation of neuron differentiation|regulation of axon extension|synapse assembly	external side of plasma membrane|integral to plasma membrane	ankyrin binding			ovary(3)|breast(2)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	108439024	108439024	+	IGR	DEL	A	-	-	rs139608352		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108439024delA								DNAJB9 (223732 upstream) : C7orf66 (85016 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	108629715	108629716	+	IGR	DEL	TT	-	-	rs113067143		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108629715_108629716delTT								C7orf66 (105078 upstream) : EIF3IP1 (969568 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	108963140	108963140	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108963140delT								C7orf66 (438503 upstream) : EIF3IP1 (636144 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	110215493	110215493	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110215493delT								EIF3IP1 (615223 upstream) : IMMP2L (87617 downstream)																																			---	---	---	---
IMMP2L	83943	broad.mit.edu	37	7	110634071	110634071	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110634071delA	uc003vfq.1	-						IMMP2L_uc010ljr.1_Intron|IMMP2L_uc003vfr.2_Intron	NM_032549	NP_115938			IMP2 inner mitochondrial membrane protease-like						protein processing involved in protein targeting to mitochondrion|proteolysis	integral to membrane|mitochondrial inner membrane peptidase complex|nucleus	serine-type peptidase activity				0				UCEC - Uterine corpus endometrioid carcinoma (4;0.053)|Epithelial(3;2.27e-07)|all cancers(3;1.36e-05)|STAD - Stomach adenocarcinoma(3;0.00148)|KIRC - Kidney renal clear cell carcinoma(11;0.0339)|Lung(3;0.0375)|Kidney(11;0.0415)|LUSC - Lung squamous cell carcinoma(290;0.173)														---	---	---	---
IMMP2L	83943	broad.mit.edu	37	7	111085314	111085314	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111085314delA	uc003vfq.1	-						IMMP2L_uc010ljr.1_Intron|IMMP2L_uc003vfr.2_Intron	NM_032549	NP_115938			IMP2 inner mitochondrial membrane protease-like						protein processing involved in protein targeting to mitochondrion|proteolysis	integral to membrane|mitochondrial inner membrane peptidase complex|nucleus	serine-type peptidase activity				0				UCEC - Uterine corpus endometrioid carcinoma (4;0.053)|Epithelial(3;2.27e-07)|all cancers(3;1.36e-05)|STAD - Stomach adenocarcinoma(3;0.00148)|KIRC - Kidney renal clear cell carcinoma(11;0.0339)|Lung(3;0.0375)|Kidney(11;0.0415)|LUSC - Lung squamous cell carcinoma(290;0.173)														---	---	---	---
DOCK4	9732	broad.mit.edu	37	7	111679520	111679520	+	Intron	DEL	T	-	-	rs67482182		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111679520delT	uc003vfx.2	-						DOCK4_uc003vfy.2_Intron|DOCK4_uc003vga.1_Intron|DOCK4_uc010ljt.1_Intron	NM_014705	NP_055520			dedicator of cytokinesis 4						cell chemotaxis	cytosol|endomembrane system|membrane|stereocilium	GTP binding|guanyl-nucleotide exchange factor activity|PDZ domain binding|Rac GTPase activator activity|Rac GTPase binding|receptor tyrosine kinase binding|SH3 domain binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)	4		Acute lymphoblastic leukemia(1;0.0441)																---	---	---	---
IFRD1	3475	broad.mit.edu	37	7	112097284	112097284	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112097284delA	uc003vgh.2	+						IFRD1_uc011kmn.1_Intron|IFRD1_uc003vgi.2_3'UTR|IFRD1_uc003vgj.2_Intron|IFRD1_uc011kmo.1_Intron|IFRD1_uc011kmp.1_Intron	NM_001007245	NP_001007246			interferon-related developmental regulator 1						multicellular organismal development|myoblast cell fate determination		binding			kidney(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	112221858	112221860	+	IGR	DEL	AGT	-	-	rs80001117		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112221858_112221860delAGT								C7orf53 (90923 upstream) : TMEM168 (183929 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	112970072	112970072	+	IGR	DEL	A	-	-	rs113374748		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:112970072delA								LOC401397 (211435 upstream) : PPP1R3A (546810 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	113661639	113661641	+	IGR	DEL	AAA	-	-	rs111596013		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:113661639_113661641delAAA								PPP1R3A (102557 upstream) : FOXP2 (64741 downstream)																																			---	---	---	---
MDFIC	29969	broad.mit.edu	37	7	114611516	114611516	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114611516delG	uc003vhf.2	+							NM_199072	NP_951038			MyoD family inhibitor domain containing protein						activation of JUN kinase activity|interspecies interaction between organisms|negative regulation of protein import into nucleus|negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|positive regulation of viral transcription|regulation of Wnt receptor signaling pathway|transcription, DNA-dependent	cytoplasm|cytoplasm|nucleolus|nucleolus|nucleus	cyclin binding|Tat protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	114824123	114824124	+	IGR	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:114824123_114824124delGA								MDFIC (164860 upstream) : TFEC (751078 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	115113203	115113203	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:115113203delT								MDFIC (453940 upstream) : TFEC (461999 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	115427087	115427087	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:115427087delT								MDFIC (767824 upstream) : TFEC (148115 downstream)																																			---	---	---	---
TFEC	22797	broad.mit.edu	37	7	115644843	115644845	+	Intron	DEL	AAA	-	-	rs112030961		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:115644843_115644845delAAA	uc003vhj.1	-						TFEC_uc003vhk.1_Intron|TFEC_uc003vhl.3_Intron|TFEC_uc011kmw.1_Intron	NM_012252	NP_036384			transcription factor EC isoform a							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity			large_intestine(1)	1			STAD - Stomach adenocarcinoma(10;0.00878)															---	---	---	---
MET	4233	broad.mit.edu	37	7	116398987	116398987	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116398987delT	uc003vij.2	+						MET_uc010lkh.2_Intron|MET_uc011kng.1_Intron|MET_uc011knh.1_Intron|MET_uc011kni.1_Intron|MET_uc011knj.1_Intron	NM_000245	NP_000236			met proto-oncogene isoform b precursor						axon guidance|cell proliferation	basal plasma membrane|integral to plasma membrane	ATP binding|hepatocyte growth factor receptor activity|protein binding			upper_aerodigestive_tract(63)|lung(41)|kidney(18)|NS(10)|ovary(5)|thyroid(4)|central_nervous_system(4)|stomach(3)|liver(3)|pleura(2)|large_intestine(2)|breast(2)|testis(1)|skin(1)	159	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)					Mis		papillary renal|head-neck squamous cell 	papillary renal			Hereditary_Papillary_Renal_Carcinoma_(type_1)				---	---	---	---
CAPZA2	830	broad.mit.edu	37	7	116552344	116552344	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116552344delT	uc003vil.2	+						CAPZA2_uc011knk.1_Intron	NM_006136	NP_006127			capping protein (actin filament) muscle Z-line,						actin cytoskeleton organization|actin filament capping|blood coagulation|cellular component movement|innate immune response|protein complex assembly	cytosol|extracellular region|F-actin capping protein complex	actin binding				0	all_cancers(3;8.53e-08)|all_epithelial(6;7.79e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)		GBM - Glioblastoma multiforme(2;5.01e-06)|STAD - Stomach adenocarcinoma(10;0.000512)|all cancers(2;0.00326)															---	---	---	---
CAPZA2	830	broad.mit.edu	37	7	116556988	116556988	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116556988delT	uc003vil.2	+						CAPZA2_uc011knk.1_Intron	NM_006136	NP_006127			capping protein (actin filament) muscle Z-line,						actin cytoskeleton organization|actin filament capping|blood coagulation|cellular component movement|innate immune response|protein complex assembly	cytosol|extracellular region|F-actin capping protein complex	actin binding				0	all_cancers(3;8.53e-08)|all_epithelial(6;7.79e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)		GBM - Glioblastoma multiforme(2;5.01e-06)|STAD - Stomach adenocarcinoma(10;0.000512)|all cancers(2;0.00326)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	116578226	116578227	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116578226_116578227delTT								CAPZA2 (18914 upstream) : ST7OT1 (14276 downstream)																																			---	---	---	---
CFTR	1080	broad.mit.edu	37	7	117171398	117171399	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117171398_117171399insT	uc003vjd.2	+						CFTR_uc011knq.1_Intron	NM_000492	NP_000483			cystic fibrosis transmembrane conductance						respiratory gaseous exchange	apical plasma membrane|basolateral plasma membrane|chloride channel complex|early endosome membrane	ATP binding|ATP-binding and phosphorylation-dependent chloride channel activity|channel-conductance-controlling ATPase activity|chloride channel regulator activity|enzyme binding|PDZ domain binding			central_nervous_system(2)|skin(2)|ovary(1)	5	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Glibenclamide(DB01016)									Cystic_Fibrosis				---	---	---	---
CFTR	1080	broad.mit.edu	37	7	117188929	117188929	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117188929delT	uc003vjd.2	+						CFTR_uc011knq.1_Intron	NM_000492	NP_000483			cystic fibrosis transmembrane conductance						respiratory gaseous exchange	apical plasma membrane|basolateral plasma membrane|chloride channel complex|early endosome membrane	ATP binding|ATP-binding and phosphorylation-dependent chloride channel activity|channel-conductance-controlling ATPase activity|chloride channel regulator activity|enzyme binding|PDZ domain binding			central_nervous_system(2)|skin(2)|ovary(1)	5	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Glibenclamide(DB01016)									Cystic_Fibrosis				---	---	---	---
CTTNBP2	83992	broad.mit.edu	37	7	117387297	117387298	+	Intron	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117387297_117387298delTG	uc003vjf.2	-							NM_033427	NP_219499			cortactin binding protein 2											ovary(4)|central_nervous_system(1)	5	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	117944521	117944521	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117944521delA								ANKRD7 (61739 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	118168007	118168008	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:118168007_118168008insA								ANKRD7 (285225 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	118517115	118517115	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:118517115delA								ANKRD7 (634333 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	119667323	119667323	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:119667323delT								None (None upstream) : KCND2 (246399 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	119872298	119872299	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:119872298_119872299delAA								None (None upstream) : KCND2 (41423 downstream)																																			---	---	---	---
KCND2	3751	broad.mit.edu	37	7	119987096	119987096	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:119987096delT	uc003vjj.1	+							NM_012281	NP_036413			potassium voltage-gated channel, Shal-related						regulation of action potential|synaptic transmission	cell surface|dendritic spine	metal ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5	all_neural(327;0.117)																	---	---	---	---
KCND2	3751	broad.mit.edu	37	7	120043685	120043685	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120043685delT	uc003vjj.1	+							NM_012281	NP_036413			potassium voltage-gated channel, Shal-related						regulation of action potential|synaptic transmission	cell surface|dendritic spine	metal ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5	all_neural(327;0.117)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	120511788	120511789	+	IGR	DEL	AC	-	-	rs35159851		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120511788_120511789delAC								TSPAN12 (13611 upstream) : ING3 (79028 downstream)																																			---	---	---	---
C7orf58	79974	broad.mit.edu	37	7	120702746	120702746	+	Intron	DEL	C	-	-	rs36113801		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120702746delC	uc003vjq.3	+						C7orf58_uc003vjr.1_Intron|C7orf58_uc003vjs.3_Intron|C7orf58_uc003vjt.3_5'Flank	NM_024913	NP_079189			hypothetical protein LOC79974 isoform 1							endoplasmic reticulum				ovary(4)|large_intestine(2)|skin(2)|pancreas(1)	9	all_neural(327;0.117)																	---	---	---	---
PTPRZ1	5803	broad.mit.edu	37	7	121693766	121693766	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121693766delA	uc003vjy.2	+						PTPRZ1_uc003vjz.2_Intron|PTPRZ1_uc011knt.1_Intron	NM_002851	NP_002842			protein tyrosine phosphatase, receptor-type,						central nervous system development	integral to plasma membrane	protein binding|protein tyrosine/threonine phosphatase activity|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|large_intestine(2)|lung(2)|central_nervous_system(1)|kidney(1)	9																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	121864758	121864759	+	IGR	INS	-	A	A	rs146787711	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121864758_121864759insA								AASS (80414 upstream) : FEZF1 (76690 downstream)																																			---	---	---	---
CADPS2	93664	broad.mit.edu	37	7	122111296	122111299	+	Intron	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122111296_122111299delTTTT	uc010lkp.2	-						CADPS2_uc011knx.1_Intron|CADPS2_uc003vkg.3_Intron|CADPS2_uc010lkq.2_Intron	NM_017954	NP_060424			Ca2+-dependent activator protein for secretion 2						exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|synapse	lipid binding|metal ion binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
CADPS2	93664	broad.mit.edu	37	7	122194752	122194752	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122194752delA	uc010lkp.2	-						CADPS2_uc003vkg.3_Intron|CADPS2_uc010lkq.2_Intron	NM_017954	NP_060424			Ca2+-dependent activator protein for secretion 2						exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|synapse	lipid binding|metal ion binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	123530382	123530382	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123530382delT								HYAL4 (12853 upstream) : SPAM1 (34947 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	123679891	123679892	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123679891_123679892insA	uc011koc.1	+											Homo sapiens disrupted in Rett 1 mRNA sequence.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	124162510	124162510	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124162510delT								TMEM229A (488987 upstream) : GPR37 (223606 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	124315844	124315844	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124315844delA								TMEM229A (642321 upstream) : GPR37 (70272 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	124412919	124412919	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124412919delT								GPR37 (7238 upstream) : POT1 (49522 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	124686462	124686462	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124686462delT	uc010lkx.1	+						uc003vlp.2_Intron|uc003vlq.1_Intron					Homo sapiens cDNA FLJ33356 fis, clone BRACE2005160.																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	125258976	125258976	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:125258976delA								POT1 (688939 upstream) : GRM8 (819676 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	126007762	126007762	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126007762delA								None (None upstream) : GRM8 (70890 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	126992442	126992443	+	IGR	INS	-	T	T	rs143719809	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126992442_126992443insT								GRM8 (99295 upstream) : ZNF800 (17911 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	127150188	127150189	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127150188_127150189delAA								ZNF800 (117421 upstream) : GCC1 (70494 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	127214375	127214375	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127214375delT								ZNF800 (181608 upstream) : GCC1 (6308 downstream)																																			---	---	---	---
LEP	3952	broad.mit.edu	37	7	127896185	127896185	+	3'UTR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127896185delG	uc003vml.2	+	3						NM_000230	NP_000221			leptin precursor						adult feeding behavior|energy reserve metabolic process|negative regulation of appetite|placenta development|positive regulation of developmental growth	extracellular space					0																		---	---	---	---
KCP	375616	broad.mit.edu	37	7	128545438	128545438	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128545438delC	uc011kor.1	-						KCP_uc011kos.1_Intron	NM_001135914	NP_001129386			cysteine rich BMP regulator 2 isoform 1							extracellular region				central_nervous_system(1)	1																OREG0018302	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	7	128701709	128701710	+	IGR	DEL	TT	-	-	rs35947320		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128701709_128701710delTT								TPI1P2 (4416 upstream) : LOC407835 (64615 downstream)																																			---	---	---	---
TSPAN33	340348	broad.mit.edu	37	7	128783684	128783684	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128783684delT	uc003vop.1	+							NM_178562	NP_848657			tetraspanin 33							integral to membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	128816462	128816462	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128816462delT								TSPAN33 (7791 upstream) : SMO (12251 downstream)																																			---	---	---	---
AHCYL2	23382	broad.mit.edu	37	7	128950947	128950948	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128950947_128950948delAA	uc011kov.1	+						AHCYL2_uc003vot.2_Intron	NM_015328	NP_056143			S-adenosylhomocysteine hydrolase-like 2 isoform						one-carbon metabolic process		adenosylhomocysteinase activity			ovary(2)	2																		---	---	---	---
AHCYL2	23382	broad.mit.edu	37	7	129013441	129013441	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129013441delA	uc011kov.1	+						AHCYL2_uc003vot.2_Intron|AHCYL2_uc003vov.2_Intron|AHCYL2_uc011kow.1_Intron|AHCYL2_uc011kox.1_5'Flank	NM_015328	NP_056143			S-adenosylhomocysteine hydrolase-like 2 isoform						one-carbon metabolic process		adenosylhomocysteinase activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	129248167	129248168	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129248167_129248168insA								FAM40B (119930 upstream) : NRF1 (3387 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	129404945	129404946	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129404945_129404946delTT								NRF1 (8025 upstream) : MIR182 (5277 downstream)																																			---	---	---	---
ZC3HC1	51530	broad.mit.edu	37	7	129663647	129663647	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129663647delT	uc003vpi.2	-						ZC3HC1_uc003vph.2_Intron|ZC3HC1_uc010lma.2_Intron	NM_016478	NP_057562			zinc finger, C3HC type 1						cell division|mitosis	nucleus	protein kinase binding|zinc ion binding				0	Melanoma(18;0.0435)																	---	---	---	---
ZC3HC1	51530	broad.mit.edu	37	7	129680483	129680483	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129680483delA	uc003vpi.2	-						ZC3HC1_uc003vph.2_Intron|ZC3HC1_uc010lma.2_Intron	NM_016478	NP_057562			zinc finger, C3HC type 1						cell division|mitosis	nucleus	protein kinase binding|zinc ion binding				0	Melanoma(18;0.0435)																	---	---	---	---
KLHDC10	23008	broad.mit.edu	37	7	129707426	129707427	+	5'Flank	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129707426_129707427delGA	uc003vpj.1	+						KLHDC10_uc003vpk.1_5'Flank|KLHDC10_uc010lmb.1_5'Flank	NM_014997	NP_055812			kelch domain containing 10												0																		---	---	---	---
KLHDC10	23008	broad.mit.edu	37	7	129760950	129760950	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129760950delT	uc003vpj.1	+						KLHDC10_uc003vpk.1_Intron|KLHDC10_uc010lmb.1_Intron	NM_014997	NP_055812			kelch domain containing 10												0																		---	---	---	---
FLJ43663	378805	broad.mit.edu	37	7	130693715	130693715	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130693715delG	uc011kpk.1	-						FLJ43663_uc003vqo.1_Intron|FLJ43663_uc003vqp.2_Intron|FLJ43663_uc003vqq.2_Intron	NR_024153				Homo sapiens cDNA FLJ43663 fis, clone SYNOV4005989.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	131567132	131567133	+	IGR	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131567132_131567133delGA								PODXL (325756 upstream) : PLXNA4 (240959 downstream)																																			---	---	---	---
PLXNA4	91584	broad.mit.edu	37	7	131810166	131810166	+	3'UTR	DEL	T	-	-	rs113584906		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131810166delT	uc003vra.3	-	32					PLXNA4_uc003vqz.3_3'UTR	NM_020911	NP_065962			plexin A4 isoform 1							integral to membrane|intracellular|plasma membrane				ovary(1)	1																		---	---	---	---
PLXNA4	91584	broad.mit.edu	37	7	132028674	132028674	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132028674delA	uc003vra.3	-							NM_020911	NP_065962			plexin A4 isoform 1							integral to membrane|intracellular|plasma membrane				ovary(1)	1																		---	---	---	---
PLXNA4	91584	broad.mit.edu	37	7	132104676	132104676	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132104676delT	uc003vra.3	-						PLXNA4_uc003vrc.2_Intron	NM_020911	NP_065962			plexin A4 isoform 1							integral to membrane|intracellular|plasma membrane				ovary(1)	1																		---	---	---	---
PLXNA4	91584	broad.mit.edu	37	7	132153494	132153495	+	Intron	DEL	CA	-	-	rs113442670		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:132153494_132153495delCA	uc003vra.3	-						PLXNA4_uc003vrc.2_Intron	NM_020911	NP_065962			plexin A4 isoform 1							integral to membrane|intracellular|plasma membrane				ovary(1)	1																		---	---	---	---
EXOC4	60412	broad.mit.edu	37	7	133120046	133120046	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133120046delA	uc003vrk.2	+						EXOC4_uc011kpo.1_Intron|EXOC4_uc003vri.2_Intron|EXOC4_uc003vrj.2_Intron	NM_021807	NP_068579			SEC8 protein isoform a						vesicle docking involved in exocytosis	exocyst	protein N-terminus binding			ovary(4)|large_intestine(3)|upper_aerodigestive_tract(1)|skin(1)	9		Esophageal squamous(399;0.129)																---	---	---	---
EXOC4	60412	broad.mit.edu	37	7	133465241	133465241	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133465241delT	uc003vrk.2	+						EXOC4_uc011kpo.1_Intron|EXOC4_uc003vrl.2_Intron|EXOC4_uc011kpp.1_Intron	NM_021807	NP_068579			SEC8 protein isoform a						vesicle docking involved in exocytosis	exocyst	protein N-terminus binding			ovary(4)|large_intestine(3)|upper_aerodigestive_tract(1)|skin(1)	9		Esophageal squamous(399;0.129)																---	---	---	---
EXOC4	60412	broad.mit.edu	37	7	133509938	133509939	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133509938_133509939delAA	uc003vrk.2	+						EXOC4_uc011kpo.1_Intron|EXOC4_uc003vrl.2_Intron|EXOC4_uc011kpp.1_Intron	NM_021807	NP_068579			SEC8 protein isoform a						vesicle docking involved in exocytosis	exocyst	protein N-terminus binding			ovary(4)|large_intestine(3)|upper_aerodigestive_tract(1)|skin(1)	9		Esophageal squamous(399;0.129)																---	---	---	---
Unknown	0	broad.mit.edu	37	7	133792643	133792643	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133792643delA								EXOC4 (42132 upstream) : LRGUK (19462 downstream)																																			---	---	---	---
LRGUK	136332	broad.mit.edu	37	7	133906514	133906515	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133906514_133906515delTT	uc003vrm.1	+							NM_144648	NP_653249			leucine-rich repeats and guanylate kinase domain								ATP binding|kinase activity			lung(2)|skin(2)|kidney(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	134450067	134450069	+	IGR	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134450067_134450069delAAA								BPGM (85502 upstream) : CALD1 (14102 downstream)																																			---	---	---	---
CALD1	800	broad.mit.edu	37	7	134632612	134632612	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134632612delT	uc003vrz.2	+						CALD1_uc003vry.2_Intron|CALD1_uc003vsa.2_Intron|CALD1_uc003vsb.2_Intron|CALD1_uc010lmm.2_Intron|CALD1_uc011kpt.1_Intron|CALD1_uc003vsc.2_Intron|CALD1_uc003vsd.2_Intron|CALD1_uc011kpu.1_Intron|CALD1_uc011kpv.1_Intron|CALD1_uc003vse.2_Intron	NM_033138	NP_149129			caldesmon 1 isoform 1						cellular component movement|muscle contraction	cytosol|focal adhesion|myofibril	actin binding|calmodulin binding|myosin binding|tropomyosin binding				0																		---	---	---	---
CALD1	800	broad.mit.edu	37	7	134635269	134635269	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134635269delT	uc003vrz.2	+						CALD1_uc003vry.2_Intron|CALD1_uc003vsa.2_Intron|CALD1_uc003vsb.2_Intron|CALD1_uc010lmm.2_Intron|CALD1_uc011kpt.1_Intron|CALD1_uc003vsc.2_Intron|CALD1_uc003vsd.2_Intron|CALD1_uc011kpu.1_Intron|CALD1_uc011kpv.1_Intron|CALD1_uc003vse.2_Intron	NM_033138	NP_149129			caldesmon 1 isoform 1						cellular component movement|muscle contraction	cytosol|focal adhesion|myofibril	actin binding|calmodulin binding|myosin binding|tropomyosin binding				0																		---	---	---	---
WDR91	29062	broad.mit.edu	37	7	134870852	134870852	+	3'UTR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134870852delC	uc003vsp.2	-	15					WDR91_uc010lmq.2_3'UTR|WDR91_uc010lmr.2_RNA	NM_014149	NP_054868			WD repeat domain 91											breast(2)|ovary(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	134980685	134980685	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134980685delA								STRA8 (37443 upstream) : CNOT4 (65868 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	135013710	135013711	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135013710_135013711delTT								STRA8 (70468 upstream) : CNOT4 (32842 downstream)																																			---	---	---	---
CNOT4	4850	broad.mit.edu	37	7	135127505	135127505	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135127505delA	uc003vsv.1	-						CNOT4_uc003vss.2_Intron|CNOT4_uc011kpz.1_Intron|CNOT4_uc003vst.2_Intron|CNOT4_uc003vsu.1_Intron	NM_001008225	NP_001008226			CCR4-NOT transcription complex, subunit 4						nuclear-transcribed mRNA poly(A) tail shortening|protein autoubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	nucleotide binding|protein binding|RNA binding|ubiquitin-protein ligase activity|zinc ion binding				0																		---	---	---	---
NUP205	23165	broad.mit.edu	37	7	135296882	135296882	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135296882delA	uc003vsw.2	+							NM_015135	NP_055950			nucleoporin 205kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
NUP205	23165	broad.mit.edu	37	7	135327103	135327103	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135327103delT	uc003vsw.2	+						NUP205_uc003vsx.2_Intron	NM_015135	NP_055950			nucleoporin 205kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	135504442	135504442	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135504442delT								FAM180A (70848 upstream) : LUZP6 (107063 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	135851624	135851624	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135851624delT								LUZP6 (189420 upstream) : CHRM2 (701775 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	136121264	136121264	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136121264delT								LUZP6 (459060 upstream) : CHRM2 (432135 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	136368491	136368491	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136368491delA								LUZP6 (706287 upstream) : CHRM2 (184908 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	136447155	136447155	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136447155delT								LUZP6 (784951 upstream) : CHRM2 (106244 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	136874875	136874876	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136874875_136874876insA								CHRM2 (173104 upstream) : PTN (37216 downstream)																																			---	---	---	---
DGKI	9162	broad.mit.edu	37	7	137307350	137307350	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137307350delA	uc003vtt.2	-						DGKI_uc003vtu.2_Intron	NM_004717	NP_004708			diacylglycerol kinase, iota						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	nucleus|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(1)|kidney(1)|skin(1)	3																		---	---	---	---
AKR1D1	6718	broad.mit.edu	37	7	137791279	137791279	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137791279delT	uc003vtz.2	+						AKR1D1_uc011kqe.1_Intron|AKR1D1_uc011kqf.1_Intron|AKR1D1_uc010lmy.1_Intron	NM_005989	NP_005980			aldo-keto reductase family 1, member D1						androgen metabolic process|bile acid biosynthetic process|bile acid catabolic process|C21-steroid hormone metabolic process|cholesterol catabolic process|digestion	cytosol	aldo-keto reductase (NADP) activity|delta4-3-oxosteroid 5beta-reductase activity|steroid binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	138139451	138139452	+	IGR	INS	-	TTG	TTG	rs150860209	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138139451_138139452insTTG								AKR1D1 (336401 upstream) : TRIM24 (5627 downstream)																																			---	---	---	---
TTC26	79989	broad.mit.edu	37	7	138869948	138869949	+	Intron	DEL	AA	-	-	rs113917082		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138869948_138869949delAA	uc003vus.2	+						TTC26_uc011kqn.1_Intron|TTC26_uc011kqo.1_Intron|TTC26_uc011kqp.1_Intron|TTC26_uc003vut.2_Intron|TTC26_uc011kqq.1_Intron	NM_024926	NP_079202			tetratricopeptide repeat domain 26 isoform 1								binding			ovary(1)	1																		---	---	---	---
UBN2	254048	broad.mit.edu	37	7	138989575	138989575	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138989575delT	uc011kqr.1	+	18						NM_173569	NP_775840			ubinuclein 2											ovary(1)|skin(1)	2																		---	---	---	---
CLEC2L	154790	broad.mit.edu	37	7	139226075	139226075	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139226075delA	uc010lnd.2	+							NM_001080511	NP_001073980			C-type lectin domain family 2, member L							integral to membrane	sugar binding				0	Melanoma(164;0.233)																	---	---	---	---
HIPK2	28996	broad.mit.edu	37	7	139256694	139256694	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139256694delT	uc003vvf.3	-	15					HIPK2_uc003vvd.3_3'UTR	NM_022740	NP_073577			homeodomain interacting protein kinase 2 isoform						apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|negative regulation of BMP signaling pathway|positive regulation of JNK cascade|positive regulation of transforming growth factor beta receptor signaling pathway|SMAD protein signal transduction|transcription, DNA-dependent|virus-host interaction	centrosome|nuclear membrane|PML body	ATP binding|protein serine/threonine kinase activity|SMAD binding|transcription corepressor activity|virion binding			ovary(3)|central_nervous_system(3)|skin(1)	7	Melanoma(164;0.205)																	---	---	---	---
TBXAS1	6916	broad.mit.edu	37	7	139714709	139714709	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139714709delA	uc011kqv.1	+						TBXAS1_uc003vvh.2_Intron|TBXAS1_uc010lne.2_Intron|TBXAS1_uc011kqu.1_Intron|TBXAS1_uc003vvi.2_Intron|TBXAS1_uc003vvj.2_Intron|TBXAS1_uc011kqw.1_Intron	NM_001130966	NP_001124438			thromboxane A synthase 1, platelet isoform						hormone biosynthetic process|prostaglandin biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|thromboxane-A synthase activity			ovary(2)|breast(1)	3	Melanoma(164;0.0142)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	139930883	139930883	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139930883delG								LOC100134229 (51444 upstream) : SLC37A3 (102671 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	140018734	140018735	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140018734_140018735insT								LOC100134229 (139295 upstream) : SLC37A3 (14819 downstream)																																			---	---	---	---
SLC37A3	84255	broad.mit.edu	37	7	140092892	140092892	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140092892delA	uc003vvo.2	-						SLC37A3_uc003vvp.2_Intron|SLC37A3_uc010lnh.2_Intron|SLC37A3_uc011kqz.1_Intron|SLC37A3_uc011kra.1_Intron|SLC37A3_uc011krb.1_Intron	NM_207113	NP_996996			solute carrier family 37 (glycerol-3-phosphate						carbohydrate transport|transmembrane transport	integral to membrane				ovary(3)	3	Melanoma(164;0.0142)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	140205757	140205757	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140205757delT								MKRN1 (26388 upstream) : DENND2A (12470 downstream)																																			---	---	---	---
DENND2A	27147	broad.mit.edu	37	7	140242922	140242922	+	Intron	DEL	T	-	-	rs35896324		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140242922delT	uc010lnj.2	-						DENND2A_uc011kre.1_Intron|DENND2A_uc010lnk.2_Intron|DENND2A_uc003vvw.2_Intron	NM_015689	NP_056504			DENN/MADD domain containing 2A											ovary(3)|breast(1)	4	Melanoma(164;0.00956)																	---	---	---	---
DENND2A	27147	broad.mit.edu	37	7	140284301	140284301	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140284301delT	uc010lnj.2	-						DENND2A_uc011kre.1_Intron|DENND2A_uc010lnk.2_Intron|DENND2A_uc003vvw.2_Intron|DENND2A_uc003vvx.2_Intron	NM_015689	NP_056504			DENN/MADD domain containing 2A											ovary(3)|breast(1)	4	Melanoma(164;0.00956)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	140344470	140344471	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140344470_140344471delTT								DENND2A (3184 upstream) : ADCK2 (28482 downstream)																																			---	---	---	---
ADCK2	90956	broad.mit.edu	37	7	140370192	140370192	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140370192delT	uc003vvy.1	+						ADCK2_uc003vvz.2_5'Flank	NM_052853	NP_443085			aarF domain containing kinase 2							integral to membrane	ATP binding|protein serine/threonine kinase activity				0	Melanoma(164;0.00956)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	140427429	140427429	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140427429delT								NDUFB2 (20985 upstream) : BRAF (6386 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	141046458	141046458	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141046458delT								MRPS33 (331677 upstream) : AGK (204620 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	141109881	141109881	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141109881delT								MRPS33 (395100 upstream) : AGK (141197 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	141218617	141218617	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141218617delT								MRPS33 (503836 upstream) : AGK (32461 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	141236114	141236117	+	IGR	DEL	AAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141236114_141236117delAAAA								MRPS33 (521333 upstream) : AGK (14961 downstream)																																			---	---	---	---
KIAA1147	57189	broad.mit.edu	37	7	141397549	141397549	+	Intron	DEL	A	-	-	rs115467541	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141397549delA	uc003vwk.2	-							NM_001080392	NP_001073861			hypothetical protein LOC57189											ovary(1)	1	Melanoma(164;0.0171)																	---	---	---	---
MGAM	8972	broad.mit.edu	37	7	141735206	141735206	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141735206delA	uc003vwy.2	+							NM_004668	NP_004659			maltase-glucoamylase						polysaccharide digestion|starch catabolic process	apical plasma membrane|integral to membrane	carbohydrate binding|glucan 1,4-alpha-glucosidase activity|maltose alpha-glucosidase activity			ovary(2)	2	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)													---	---	---	---
MGAM	8972	broad.mit.edu	37	7	141792115	141792115	+	Intron	DEL	T	-	-	rs80104641	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141792115delT	uc003vwy.2	+							NM_004668	NP_004659			maltase-glucoamylase						polysaccharide digestion|starch catabolic process	apical plasma membrane|integral to membrane	carbohydrate binding|glucan 1,4-alpha-glucosidase activity|maltose alpha-glucosidase activity			ovary(2)	2	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)													---	---	---	---
TAS2R39	259285	broad.mit.edu	37	7	142879666	142879667	+	5'Flank	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142879666_142879667delTG	uc011ksw.1	+							NM_176881	NP_795362			taste receptor, type 2, member 39						sensory perception of taste	integral to membrane	G-protein coupled receptor activity			skin(1)	1	Melanoma(164;0.059)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	143118198	143118198	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143118198delT	uc003wda.2	+											Homo sapiens mRNA; cDNA DKFZp686O0656 (from clone DKFZp686O0656).																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	143540727	143540727	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143540727delT								LOC154761 (6917 upstream) : FAM115A (9322 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	143613067	143613067	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143613067delT								FAM115A (13848 upstream) : OR2F2 (19259 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	143709911	143709911	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143709911delT								OR6B1 (7886 upstream) : OR2A5 (37584 downstream)																																			---	---	---	---
OR2A25	392138	broad.mit.edu	37	7	143771619	143771619	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143771619delT	uc011ktx.1	+	1	307	c.307delT	c.(307-309)TTTfs	p.F103fs		NM_001004488	NP_001004488	A4D2G3	O2A25_HUMAN	olfactory receptor, family 2, subfamily A,	103	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	Melanoma(164;0.0783)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	144737016	144737016	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144737016delT								TPK1 (203870 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	145080381	145080381	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:145080381delT								TPK1 (547235 upstream) : CNTNAP2 (733072 downstream)																																			---	---	---	---
CNTNAP2	26047	broad.mit.edu	37	7	145933075	145933076	+	Intron	INS	-	GT	GT	rs2110372	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:145933075_145933076insGT	uc003weu.1	+							NM_014141	NP_054860			cell recognition molecule Caspr2 precursor						behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)												HNSCC(39;0.1)			---	---	---	---
CNTNAP2	26047	broad.mit.edu	37	7	146020333	146020333	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146020333delT	uc003weu.1	+							NM_014141	NP_054860			cell recognition molecule Caspr2 precursor						behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)												HNSCC(39;0.1)			---	---	---	---
CNTNAP2	26047	broad.mit.edu	37	7	146746859	146746860	+	Intron	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146746859_146746860delAG	uc003weu.1	+							NM_014141	NP_054860			cell recognition molecule Caspr2 precursor						behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)												HNSCC(39;0.1)			---	---	---	---
CNTNAP2	26047	broad.mit.edu	37	7	146991752	146991752	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:146991752delT	uc003weu.1	+							NM_014141	NP_054860			cell recognition molecule Caspr2 precursor						behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)												HNSCC(39;0.1)			---	---	---	---
CUL1	8454	broad.mit.edu	37	7	148430950	148430950	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148430950delT	uc010lpg.2	+						CUL1_uc003wey.2_Intron|CUL1_uc003wez.2_Intron	NM_003592	NP_003583			cullin 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell cycle arrest|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein ubiquitination|S phase of mitotic cell cycle|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	cytosol|nucleoplasm|SCF ubiquitin ligase complex	ubiquitin protein ligase binding			lung(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)															---	---	---	---
CUL1	8454	broad.mit.edu	37	7	148457382	148457382	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148457382delA	uc010lpg.2	+						CUL1_uc003wey.2_Intron|CUL1_uc003wez.2_Intron	NM_003592	NP_003583			cullin 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell cycle arrest|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein ubiquitination|S phase of mitotic cell cycle|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	cytosol|nucleoplasm|SCF ubiquitin ligase complex	ubiquitin protein ligase binding			lung(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	148794800	148794800	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148794800delT								ZNF786 (6931 upstream) : ZNF425 (5080 downstream)																																			---	---	---	---
ZNF425	155054	broad.mit.edu	37	7	148811876	148811878	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148811876_148811878delAAA	uc003wfj.2	-							NM_001001661	NP_001001661			zinc finger protein 425						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			breast(2)|ovary(1)	3	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)															---	---	---	---
ZNF398	57541	broad.mit.edu	37	7	148855272	148855272	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148855272delA	uc003wfl.2	+						ZNF398_uc011kul.1_Intron|ZNF398_uc011kum.1_Intron	NM_170686	NP_733787			zinc finger 398 isoform a						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00143)															---	---	---	---
ZNF212	7988	broad.mit.edu	37	7	148947139	148947139	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148947139delT	uc003wfp.2	+							NM_012256	NP_036388			zinc finger protein 212						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|identical protein binding|zinc ion binding			ovary(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00171)															---	---	---	---
Unknown	0	broad.mit.edu	37	7	149459544	149459544	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149459544delT								KRBA1 (27882 upstream) : ZNF467 (1729 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	149596849	149596849	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149596849delA								ATP6V0E2 (19063 upstream) : ACTR3C (347453 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	149624824	149624824	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149624824delA								ATP6V0E2 (47038 upstream) : ACTR3C (319478 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	149842139	149842139	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149842139delA								ATP6V0E2 (264353 upstream) : ACTR3C (102163 downstream)																																			---	---	---	---
ACTR3C	653857	broad.mit.edu	37	7	149988520	149988520	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149988520delA	uc003wgu.1	-							NM_001040135	NP_001035225			actin-related protein 3-beta isoform 2						regulation of actin filament polymerization	cytoskeleton	actin binding|ATP binding				0																		---	---	---	---
LOC100128542	100128542	broad.mit.edu	37	7	150467104	150467104	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150467104delA	uc011kuw.1	+							NM_001162367	NP_001155839			hypothetical protein LOC100128542												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	7	150684566	150684566	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150684566delG								KCNH2 (9552 upstream) : NOS3 (3578 downstream)																																			---	---	---	---
AGAP3	116988	broad.mit.edu	37	7	150827450	150827450	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150827450delG	uc003wjg.1	+						AGAP3_uc003wje.1_Intron	NM_031946	NP_114152			centaurin, gamma 3 isoform a						regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm|membrane	ARF GTPase activator activity|GTP binding|GTPase activity|zinc ion binding			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
ABCF2	10061	broad.mit.edu	37	7	150914878	150914878	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150914878delA	uc003wjp.2	-						ABCF2_uc003wjo.1_Intron	NM_007189	NP_009120			ATP-binding cassette, sub-family F, member 2							ATP-binding cassette (ABC) transporter complex|mitochondrial envelope	ATP binding|ATPase activity|transporter activity			central_nervous_system(1)	1			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)														---	---	---	---
WDR86	349136	broad.mit.edu	37	7	151098002	151098002	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151098002delT	uc003wkb.2	-						WDR86_uc003wka.2_Intron|WDR86_uc011kvk.1_Intron|WDR86_uc003wkc.2_Intron	NM_198285	NP_938026			WD repeat domain 86												0			OV - Ovarian serous cystadenocarcinoma(82;0.00419)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)														---	---	---	---
RHEB	6009	broad.mit.edu	37	7	151177479	151177480	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151177479_151177480insA	uc003wkh.1	-							NM_005614	NP_005605			Ras homolog enriched in brain precursor						cell cycle arrest|insulin receptor signaling pathway|positive regulation of TOR signaling cascade|small GTPase mediated signal transduction	cytosol|plasma membrane	GTP binding|GTPase activity|metal ion binding|protein binding			large_intestine(1)|lung(1)	2			OV - Ovarian serous cystadenocarcinoma(82;0.00306)	UCEC - Uterine corpus endometrioid carcinoma (81;0.174)														---	---	---	---
PRKAG2	51422	broad.mit.edu	37	7	151272916	151272917	+	Intron	INS	-	CAA	CAA	rs142531527	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151272916_151272917insCAA	uc003wkk.2	-						PRKAG2_uc003wki.2_Intron|PRKAG2_uc011kvl.1_Intron|PRKAG2_uc003wkj.2_Intron|PRKAG2_uc003wkl.2_Intron|PRKAG2_uc010lqe.1_Intron	NM_016203	NP_057287			AMP-activated protein kinase gamma2 subunit						ATP biosynthetic process|carnitine shuttle|cell cycle arrest|fatty acid biosynthetic process|glycogen metabolic process|insulin receptor signaling pathway|intracellular protein kinase cascade|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein kinase activity|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation|regulation of glucose import|regulation of glycolysis|sterol biosynthetic process	AMP-activated protein kinase complex|cytosol|nucleoplasm	ADP binding|ATP binding|cAMP-dependent protein kinase inhibitor activity|cAMP-dependent protein kinase regulator activity|phosphorylase kinase regulator activity|protein kinase activator activity|protein kinase binding			breast(1)|kidney(1)	2	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)														---	---	---	---
PRKAG2	51422	broad.mit.edu	37	7	151460298	151460298	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151460298delA	uc003wkk.2	-						PRKAG2_uc003wkj.2_Intron|PRKAG2_uc010lqe.1_Intron|PRKAG2_uc003wkm.1_Intron	NM_016203	NP_057287			AMP-activated protein kinase gamma2 subunit						ATP biosynthetic process|carnitine shuttle|cell cycle arrest|fatty acid biosynthetic process|glycogen metabolic process|insulin receptor signaling pathway|intracellular protein kinase cascade|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein kinase activity|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation|regulation of glucose import|regulation of glycolysis|sterol biosynthetic process	AMP-activated protein kinase complex|cytosol|nucleoplasm	ADP binding|ATP binding|cAMP-dependent protein kinase inhibitor activity|cAMP-dependent protein kinase regulator activity|phosphorylase kinase regulator activity|protein kinase activator activity|protein kinase binding			breast(1)|kidney(1)	2	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)														---	---	---	---
PRKAG2	51422	broad.mit.edu	37	7	151504031	151504031	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151504031delA	uc003wkj.2	-						PRKAG2_uc003wkk.2_Intron|PRKAG2_uc010lqe.1_Intron|PRKAG2_uc003wkm.1_Intron|uc003wkn.2_Frame_Shift_Del_p.E17fs	NM_001040633	NP_001035723			AMP-activated protein kinase gamma2 subunit						ATP biosynthetic process|carnitine shuttle|cell cycle arrest|fatty acid biosynthetic process|glycogen metabolic process|insulin receptor signaling pathway|intracellular protein kinase cascade|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein kinase activity|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation|regulation of glucose import|regulation of glycolysis|sterol biosynthetic process	AMP-activated protein kinase complex|cytosol|nucleoplasm	ADP binding|ATP binding|cAMP-dependent protein kinase inhibitor activity|cAMP-dependent protein kinase regulator activity|phosphorylase kinase regulator activity|protein kinase activator activity|protein kinase binding			breast(1)|kidney(1)	2	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	151642716	151642717	+	IGR	INS	-	T	T	rs142418620		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151642716_151642717insT								PRKAG2 (68400 upstream) : GALNTL5 (10794 downstream)																																			---	---	---	---
GALNT11	63917	broad.mit.edu	37	7	151755244	151755244	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151755244delA	uc010lqg.1	+						GALNT11_uc011kvm.1_Intron	NM_022087	NP_071370			N-acetylgalactosaminyltransferase 11							Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.214)	OV - Ovarian serous cystadenocarcinoma(82;0.00168)	UCEC - Uterine corpus endometrioid carcinoma (81;0.177)|BRCA - Breast invasive adenocarcinoma(188;0.0932)														---	---	---	---
MLL3	58508	broad.mit.edu	37	7	151921038	151921038	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151921038delT	uc003wla.2	-						MLL3_uc003wkz.2_Intron	NM_170606	NP_733751			myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)				N		medulloblastoma								---	---	---	---
MLL3	58508	broad.mit.edu	37	7	151948814	151948814	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151948814delA	uc003wla.2	-							NM_170606	NP_733751			myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)				N		medulloblastoma								---	---	---	---
DPP6	1804	broad.mit.edu	37	7	153702128	153702128	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153702128delA	uc003wli.2	+							NM_001039350	NP_001034439			dipeptidyl-peptidase 6 isoform 3						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)															---	---	---	---
DPP6	1804	broad.mit.edu	37	7	153827185	153827185	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153827185delA	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlj.2_Intron	NM_130797	NP_570629			dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)															---	---	---	---
DPP6	1804	broad.mit.edu	37	7	153974245	153974245	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:153974245delT	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlj.2_Intron	NM_130797	NP_570629			dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)															---	---	---	---
DPP6	1804	broad.mit.edu	37	7	154218453	154218455	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154218453_154218455delTTT	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlj.2_Intron|DPP6_uc003wlm.2_Intron|DPP6_uc011kvq.1_Intron	NM_130797	NP_570629			dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)															---	---	---	---
DPP6	1804	broad.mit.edu	37	7	154442145	154442145	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154442145delA	uc003wlk.2	+						DPP6_uc003wli.2_Intron|DPP6_uc003wlm.2_Intron|DPP6_uc011kvq.1_Intron	NM_130797	NP_570629			dipeptidyl-peptidase 6 isoform 1						cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)															---	---	---	---
PAXIP1	22976	broad.mit.edu	37	7	154753158	154753158	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154753158delA	uc003wlp.2	-						PAXIP1_uc003wlq.1_Intron|PAXIP1_uc011kvs.1_Intron	NM_007349	NP_031375			PAX interacting protein 1						DNA damage response, signal transduction by p53 class mediator|DNA recombination|DNA repair|histone H3-K4 methylation|positive regulation of histone acetylation|positive regulation of histone H3-K36 methylation|positive regulation of histone H3-K4 methylation|positive regulation of isotype switching|positive regulation of protein ubiquitination|positive regulation of transcription initiation from RNA polymerase II promoter|response to ionizing radiation|transcription, DNA-dependent	histone methyltransferase complex|nuclear matrix				lung(2)|ovary(1)|breast(1)|pancreas(1)	5	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0296)	UCEC - Uterine corpus endometrioid carcinoma (81;0.178)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	155157835	155157835	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155157835delT								INSIG1 (55893 upstream) : EN2 (92989 downstream)																																			---	---	---	---
RBM33	155435	broad.mit.edu	37	7	155539066	155539068	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155539066_155539068delAAA	uc010lqk.1	+						RBM33_uc011kvv.1_Intron|RBM33_uc003wmg.2_5'Flank	NM_053043	NP_444271			RNA binding motif protein 33								nucleotide binding|RNA binding			ovary(1)	1	all_neural(206;0.101)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	155584767	155584768	+	IGR	INS	-	T	T	rs147360748		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155584767_155584768insT								RBM33 (10588 upstream) : SHH (7968 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	7	155742582	155742582	+	IGR	DEL	T	-	-	rs35232478		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155742582delT								SHH (137615 upstream) : C7orf4 (590603 downstream)																																			---	---	---	---
LMBR1	64327	broad.mit.edu	37	7	156476636	156476636	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156476636delA	uc003wmw.3	-	17					LMBR1_uc003wmv.3_3'UTR|LMBR1_uc003wmx.3_3'UTR|LMBR1_uc010lqn.2_3'UTR|LMBR1_uc011kvx.1_3'UTR	NM_022458	NP_071903			limb region 1 protein							integral to membrane	receptor activity				0	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.208)														---	---	---	---
LMBR1	64327	broad.mit.edu	37	7	156631411	156631411	+	Intron	DEL	C	-	-	rs74825186		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:156631411delC	uc003wmw.3	-						LMBR1_uc003wmx.3_Intron|LMBR1_uc010lqn.2_Intron|LMBR1_uc011kvx.1_Intron|LMBR1_uc010lqo.2_Intron	NM_022458	NP_071903			limb region 1 protein							integral to membrane	receptor activity				0	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.208)														---	---	---	---
UBE3C	9690	broad.mit.edu	37	7	157029424	157029424	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157029424delT	uc010lqs.2	+						UBE3C_uc003wni.3_Intron	NM_014671	NP_055486			ubiquitin protein ligase E3C						protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus|proteasome complex	protein binding|ubiquitin-protein ligase activity			ovary(2)|lung(2)|large_intestine(1)	5		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)														---	---	---	---
DNAJB6	10049	broad.mit.edu	37	7	157160555	157160557	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157160555_157160557delAAA	uc003wnk.2	+						DNAJB6_uc003wnj.2_Intron|DNAJB6_uc003wnl.2_Intron|DNAJB6_uc011kvy.1_Intron|DNAJB6_uc011kvz.1_Intron|DNAJB6_uc010lqt.2_Intron	NM_058246	NP_490647			DnaJ (Hsp40) homolog, subfamily B, member 6						intermediate filament organization|negative regulation of caspase activity|protein folding|response to unfolded protein	nucleus|perinuclear region of cytoplasm	ATPase activator activity|chaperone binding|heat shock protein binding|unfolded protein binding			ovary(2)	2	all_neural(206;0.181)	all_epithelial(9;0.000606)|all_hematologic(28;0.00287)|Acute lymphoblastic leukemia(9;0.0647)|Ovarian(593;0.196)	OV - Ovarian serous cystadenocarcinoma(82;0.00399)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)														---	---	---	---
PTPRN2	5799	broad.mit.edu	37	7	157505920	157505921	+	Intron	INS	-	CTG	CTG	rs79142764		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157505920_157505921insCTG	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838			protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)														---	---	---	---
PTPRN2	5799	broad.mit.edu	37	7	157582997	157582998	+	Intron	DEL	GT	-	-	rs113620681		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157582997_157582998delGT	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838			protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)														---	---	---	---
PTPRN2	5799	broad.mit.edu	37	7	157659174	157659175	+	Intron	INS	-	AC	AC			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157659174_157659175insAC	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838			protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)														---	---	---	---
PTPRN2	5799	broad.mit.edu	37	7	157875438	157875439	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:157875438_157875439delTT	uc003wno.2	-						PTPRN2_uc003wnp.2_Intron|PTPRN2_uc003wnq.2_Intron|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Intron	NM_002847	NP_002838			protein tyrosine phosphatase, receptor type, N							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)														---	---	---	---
WDR60	55112	broad.mit.edu	37	7	158708404	158708405	+	Intron	DEL	TG	-	-	rs67244090		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158708404_158708405delTG	uc003woe.3	+						WDR60_uc010lqv.2_Intron|WDR60_uc010lqw.2_Intron	NM_018051	NP_060521			WD repeat domain 60											ovary(2)|breast(1)|central_nervous_system(1)	4	Ovarian(565;0.152)	all_cancers(7;1.25e-09)|all_epithelial(9;0.000894)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)|STAD - Stomach adenocarcinoma(7;0.18)														---	---	---	---
FBXO25	26260	broad.mit.edu	37	8	363407	363407	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:363407delT	uc003wox.2	+						FBXO25_uc003woy.2_Intron|FBXO25_uc003woz.2_Intron	NM_183421	NP_904357			F-box only protein 25 isoform 1							nucleus|SCF ubiquitin ligase complex	actin binding|ubiquitin-protein ligase activity			lung(1)	1		Ovarian(12;0.00965)|Colorectal(14;0.0815)|Myeloproliferative disorder(644;0.116)|all_neural(12;0.122)		Epithelial(5;3.14e-14)|OV - Ovarian serous cystadenocarcinoma(5;1.56e-07)|BRCA - Breast invasive adenocarcinoma(11;1.88e-06)														---	---	---	---
FBXO25	26260	broad.mit.edu	37	8	414364	414364	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:414364delA	uc003wox.2	+						FBXO25_uc003woy.2_Intron|FBXO25_uc003woz.2_Intron|FBXO25_uc003wpa.2_Intron	NM_183421	NP_904357			F-box only protein 25 isoform 1							nucleus|SCF ubiquitin ligase complex	actin binding|ubiquitin-protein ligase activity			lung(1)	1		Ovarian(12;0.00965)|Colorectal(14;0.0815)|Myeloproliferative disorder(644;0.116)|all_neural(12;0.122)		Epithelial(5;3.14e-14)|OV - Ovarian serous cystadenocarcinoma(5;1.56e-07)|BRCA - Breast invasive adenocarcinoma(11;1.88e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	1115301	1115302	+	IGR	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1115301_1115302delGA								ERICH1 (434075 upstream) : DLGAP2 (334267 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	1160925	1160937	+	IGR	DEL	CCAGCAATCAATG	-	-	rs149924440		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1160925_1160937delCCAGCAATCAATG								ERICH1 (479699 upstream) : DLGAP2 (288632 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	1429032	1429032	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1429032delA								ERICH1 (747806 upstream) : DLGAP2 (20537 downstream)																																			---	---	---	---
ARHGEF10	9639	broad.mit.edu	37	8	1817227	1817227	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:1817227delA	uc003wpr.2	+						ARHGEF10_uc003wpq.1_Intron|ARHGEF10_uc003wps.2_Intron|ARHGEF10_uc003wpt.2_Intron|ARHGEF10_uc010lrd.1_Intron|ARHGEF10_uc003wpu.2_Intron	NM_014629	NP_055444			Rho guanine nucleotide exchange factor 10						centrosome duplication|myelination in peripheral nervous system|positive regulation of GTP catabolic process|positive regulation of stress fiber assembly|regulation of Rho protein signal transduction|spindle assembly involved in mitosis	centrosome|cytosol|soluble fraction	kinesin binding|Rho guanyl-nucleotide exchange factor activity			large_intestine(1)	1		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	2211263	2211263	+	IGR	DEL	G	-	-	rs111316181		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2211263delG								MYOM2 (117884 upstream) : CSMD1 (581613 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	2227373	2227374	+	IGR	INS	-	TG	TG	rs144758496		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2227373_2227374insTG								MYOM2 (133994 upstream) : CSMD1 (565502 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	2563086	2563087	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2563086_2563087insT	uc003wqb.1	-											Homo sapiens cDNA FLJ46912 fis, clone SKNMC2000583.																														---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	3027003	3027004	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3027003_3027004delAA	uc011kwk.1	-						CSMD1_uc011kwj.1_Intron|CSMD1_uc003wqe.2_Intron|CSMD1_uc010lrg.2_Intron	NM_033225	NP_150094			CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)														---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	3300164	3300164	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3300164delG	uc011kwk.1	-							NM_033225	NP_150094			CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)														---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	3410647	3410647	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3410647delA	uc011kwk.1	-							NM_033225	NP_150094			CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)														---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	3415845	3415847	+	Intron	DEL	ATG	-	-	rs150387740		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3415845_3415847delATG	uc011kwk.1	-							NM_033225	NP_150094			CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)														---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	3889408	3889408	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3889408delC	uc011kwk.1	-							NM_033225	NP_150094			CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)														---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	3910276	3910276	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3910276delA	uc011kwk.1	-							NM_033225	NP_150094			CUB and Sushi multiple domains 1 precursor							integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	5277252	5277252	+	IGR	DEL	T	-	-	rs34987868		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5277252delT								CSMD1 (424924 upstream) : MCPH1 (986869 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	5309004	5309004	+	IGR	DEL	A	-	-	rs146687307		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5309004delA								CSMD1 (456676 upstream) : MCPH1 (955117 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	5414444	5414444	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5414444delT								CSMD1 (562116 upstream) : MCPH1 (849677 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	5459891	5459891	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5459891delA								CSMD1 (607563 upstream) : MCPH1 (804230 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	5477317	5477317	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5477317delG								CSMD1 (624989 upstream) : MCPH1 (786804 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	5907642	5907643	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:5907642_5907643delAA								None (None upstream) : MCPH1 (356478 downstream)																																			---	---	---	---
MCPH1	79648	broad.mit.edu	37	8	6380518	6380518	+	Intron	DEL	T	-	-	rs73199051	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6380518delT	uc003wqi.2	+						ANGPT2_uc003wqj.3_Intron|ANGPT2_uc003wqk.3_Intron|ANGPT2_uc010lri.2_Intron|ANGPT2_uc003wql.3_Intron	NM_024596	NP_078872			microcephalin							microtubule organizing center				central_nervous_system(1)|skin(1)	2		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)														---	---	---	---
MCPH1	79648	broad.mit.edu	37	8	6400121	6400122	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6400121_6400122delAA	uc003wqi.2	+						ANGPT2_uc003wqj.3_Intron|ANGPT2_uc003wqk.3_Intron|ANGPT2_uc010lri.2_Intron|ANGPT2_uc003wql.3_Intron	NM_024596	NP_078872			microcephalin							microtubule organizing center				central_nervous_system(1)|skin(1)	2		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	7005181	7005181	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:7005181delT								DEFA5 (90922 upstream) : LOC349196 (112961 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	7275973	7275974	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:7275973_7275974delAA								LOC349196 (63099 upstream) : DEFB103B (10517 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	8616499	8616500	+	IGR	DEL	TT	-	-	rs72475515		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8616499_8616500delTT								CLDN23 (54883 upstream) : MFHAS1 (25499 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	8784817	8784817	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8784817delA								MFHAS1 (33686 upstream) : ERI1 (75497 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	9355223	9355224	+	IGR	DEL	GT	-	-	rs61460170		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9355223_9355224delGT								PPP1R3B (346139 upstream) : TNKS (58221 downstream)																																			---	---	---	---
TNKS	8658	broad.mit.edu	37	8	9609110	9609110	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9609110delT	uc003wss.2	+						TNKS_uc011kww.1_Intron|TNKS_uc010lrt.1_Intron	NM_003747	NP_003738			tankyrase, TRF1-interacting ankyrin-related						mitotic spindle organization|mRNA transport|negative regulation of DNA binding|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of telomere maintenance via telomerase|protein auto-ADP-ribosylation|protein localization to chromosome, telomeric region|protein poly-ADP-ribosylation|protein polyubiquitination|protein transport|spindle assembly|transmembrane transport|Wnt receptor signaling pathway	chromosome, centromeric region|Golgi membrane|microsome|nuclear chromosome, telomeric region|nuclear membrane|nuclear pore|pericentriolar material	NAD+ ADP-ribosyltransferase activity|protein binding|zinc ion binding			lung(4)|ovary(2)|kidney(1)	7				COAD - Colon adenocarcinoma(149;0.0467)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	9786348	9786348	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:9786348delA								MIR124-1 (25366 upstream) : MSRA (125482 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	10289539	10289539	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10289539delA								MSRA (3140 upstream) : PRSS55 (93542 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	10371645	10371645	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10371645delA	uc010lru.2	-											Homo sapiens cDNA, FLJ97155.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	10400224	10400224	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10400224delA	uc010lru.2	-						PRSS55_uc003wtb.2_Intron					Homo sapiens cDNA, FLJ97155.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	10568449	10568449	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10568449delG								C8orf74 (10346 upstream) : SOX7 (12830 downstream)																																			---	---	---	---
SOX7	83595	broad.mit.edu	37	8	10661008	10661008	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10661008delT	uc011kwz.1	-						PINX1_uc003wth.2_Intron|PINX1_uc003wti.2_Intron	NM_031439	NP_113627			SRY-box 7						endoderm formation|negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|positive regulation of caspase activity|regulation of canonical Wnt receptor signaling pathway	cytoplasm|nucleus	transcription regulatory region DNA binding			breast(1)	1				COAD - Colon adenocarcinoma(149;0.0732)														---	---	---	---
XKR6	286046	broad.mit.edu	37	8	10773018	10773019	+	Intron	DEL	TT	-	-	rs113163728		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10773018_10773019delTT	uc003wtk.1	-							NM_173683	NP_775954			XK, Kell blood group complex subunit-related							integral to membrane				ovary(1)|skin(1)	2				Lung(29;0.0407)|COAD - Colon adenocarcinoma(149;0.0555)														---	---	---	---
XKR6	286046	broad.mit.edu	37	8	10979669	10979669	+	Intron	DEL	A	-	-	rs74673974	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10979669delA	uc003wtk.1	-							NM_173683	NP_775954			XK, Kell blood group complex subunit-related							integral to membrane				ovary(1)|skin(1)	2				Lung(29;0.0407)|COAD - Colon adenocarcinoma(149;0.0555)														---	---	---	---
MTMR9	66036	broad.mit.edu	37	8	11155041	11155043	+	Intron	DEL	TTT	-	-	rs113523374		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11155041_11155043delTTT	uc003wtm.2	+						MTMR9_uc010lrx.2_Intron|MTMR9_uc011kxa.1_Intron	NM_015458	NP_056273			myotubularin related protein 9							cytoplasm	phosphatase activity|protein binding				0			STAD - Stomach adenocarcinoma(15;0.215)	COAD - Colon adenocarcinoma(149;0.0678)														---	---	---	---
FAM167A	83648	broad.mit.edu	37	8	11316295	11316296	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11316295_11316296delAA	uc003wtw.2	-							NM_053279	NP_444509			hypothetical protein LOC83648												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	11331391	11331391	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11331391delT								FAM167A (7115 upstream) : BLK (20130 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	11646446	11646446	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11646446delA								NEIL2 (1592 upstream) : FDFT1 (6636 downstream)																																			---	---	---	---
FAM66D	100132923	broad.mit.edu	37	8	12397242	12397242	+	Intron	DEL	A	-	-	rs111282922		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12397242delA	uc011kxp.1	+						uc003wvm.1_Intron|uc003wvv.2_Intron|uc003wvw.1_Intron|uc003wvx.1_Intron|uc003wvy.3_Intron					Homo sapiens cDNA FLJ37098 fis, clone BRACE2019004.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	12515590	12515591	+	Intron	DEL	GT	-	-	rs142279011		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12515590_12515591delGT	uc003wvy.3	-						uc003wwc.3_Intron					Homo sapiens cDNA FLJ42906 fis, clone BRHIP3016213.																														---	---	---	---
LONRF1	91694	broad.mit.edu	37	8	12589221	12589221	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12589221delT	uc003wwd.1	-						LONRF1_uc011kxv.1_Intron|LONRF1_uc010lsp.1_Intron	NM_152271	NP_689484			LON peptidase N-terminal domain and ring finger						proteolysis		ATP-dependent peptidase activity|zinc ion binding			ovary(1)	1				READ - Rectum adenocarcinoma(644;0.236)														---	---	---	---
LOC340357	340357	broad.mit.edu	37	8	12625881	12625882	+	Intron	INS	-	AG	AG			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12625881_12625882insAG	uc003wwf.3	-						LOC340357_uc003wwe.3_Intron	NR_015383				Homo sapiens cDNA clone IMAGE:3922201.												0																		---	---	---	---
C8orf79	57604	broad.mit.edu	37	8	12810251	12810251	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12810251delT	uc010lsq.2	+						C8orf79_uc011kxw.1_Intron	NM_020844	NP_065895			hypothetical protein LOC57604 isoform 1								methyltransferase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	12928368	12928368	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12928368delT								C8orf79 (39357 upstream) : DLC1 (12504 downstream)																																			---	---	---	---
DLC1	10395	broad.mit.edu	37	8	12948489	12948489	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12948489delT	uc003wwm.2	-						DLC1_uc003wwk.1_Intron|DLC1_uc003wwl.1_Intron|DLC1_uc011kxx.1_Intron	NM_182643	NP_872584			deleted in liver cancer 1 isoform 1						actin cytoskeleton organization|activation of caspase activity|focal adhesion assembly|forebrain development|heart morphogenesis|hindbrain morphogenesis|induction of apoptosis|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of stress fiber assembly|neural tube closure|positive regulation of protein dephosphorylation|regulation of cell shape|small GTPase mediated signal transduction	caveola|cytosol|focal adhesion|nucleus	Rho GTPase activator activity|SH2 domain binding			ovary(3)|pancreas(2)|lung(1)|kidney(1)	7																		---	---	---	---
SGCZ	137868	broad.mit.edu	37	8	14066933	14066933	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14066933delA	uc003wwq.2	-						SGCZ_uc010lss.2_Intron	NM_139167	NP_631906			sarcoglycan zeta						cytoskeleton organization	cytoplasm|cytoskeleton|integral to membrane|sarcolemma				ovary(2)|central_nervous_system(1)	3				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)														---	---	---	---
SGCZ	137868	broad.mit.edu	37	8	14422823	14422823	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14422823delT	uc003wwq.2	-							NM_139167	NP_631906			sarcoglycan zeta						cytoskeleton organization	cytoplasm|cytoskeleton|integral to membrane|sarcolemma				ovary(2)|central_nervous_system(1)	3				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	15210013	15210013	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15210013delT								SGCZ (114221 upstream) : TUSC3 (187717 downstream)																																			---	---	---	---
MSR1	4481	broad.mit.edu	37	8	16007838	16007838	+	Intron	DEL	A	-	-	rs10614948		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16007838delA	uc003wwz.2	-						MSR1_uc010lsu.2_Intron|MSR1_uc003wxa.2_Intron|MSR1_uc003wxb.2_Intron|MSR1_uc011kxz.1_Intron	NM_138715	NP_619729			macrophage scavenger receptor 1 isoform type 1						cholesterol transport|plasma lipoprotein particle clearance|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis	collagen|integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|protein binding|scavenger receptor activity			ovary(1)	1				Colorectal(111;0.00475)|COAD - Colon adenocarcinoma(73;0.0164)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	16390687	16390687	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16390687delA								MSR1 (340387 upstream) : FGF20 (459647 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	16511051	16511051	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16511051delT								MSR1 (460751 upstream) : FGF20 (339283 downstream)																																			---	---	---	---
EFHA2	286097	broad.mit.edu	37	8	16899103	16899104	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16899103_16899104delTT	uc003wxd.2	+							NM_181723	NP_859074			EF-hand domain family, member A2							integral to membrane	calcium ion binding			skin(1)	1				Colorectal(111;0.0686)|COAD - Colon adenocarcinoma(73;0.239)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	17006999	17006999	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17006999delT								EFHA2 (26851 upstream) : ZDHHC2 (6837 downstream)																																			---	---	---	---
VPS37A	137492	broad.mit.edu	37	8	17145187	17145189	+	Intron	DEL	AAA	-	-	rs74353301		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17145187_17145189delAAA	uc003wxj.2	+						VPS37A_uc003wxk.2_Intron|VPS37A_uc003wxl.2_Intron	NM_152415	NP_689628			hepatocellular carcinoma related protein 1						cellular membrane organization|endosome transport|protein transport	centrosome|late endosome membrane|nucleus					0				Colorectal(111;0.0553)|COAD - Colon adenocarcinoma(73;0.212)														---	---	---	---
MTUS1	57509	broad.mit.edu	37	8	17504627	17504628	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17504627_17504628delAA	uc003wxv.2	-						MTUS1_uc003wxt.2_Intron|MTUS1_uc011kyg.1_Intron|MTUS1_uc010lsy.2_Intron|MTUS1_uc003wxw.2_Intron|MTUS1_uc003wxs.2_Intron	NM_001001924	NP_001001924			mitochondrial tumor suppressor 1 isoform 1							Golgi apparatus|microtubule|microtubule organizing center|mitochondrion|nucleus|plasma membrane|spindle				ovary(1)|skin(1)	2				Colorectal(111;0.0778)														---	---	---	---
PCM1	5108	broad.mit.edu	37	8	17826953	17826953	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17826953delT	uc003wyi.3	+						PCM1_uc011kyh.1_Intron|PCM1_uc003wyj.3_Intron|PCM1_uc011kyi.1_5'Flank|PCM1_uc011kyj.1_5'Flank|PCM1_uc003wyk.3_5'Flank	NM_006197	NP_006188			pericentriolar material 1						centrosome organization|cilium assembly|G2/M transition of mitotic cell cycle|interkinetic nuclear migration|microtubule anchoring|negative regulation of neurogenesis|protein localization to centrosome	centriolar satellite|cytosol|nuclear membrane|pericentriolar material	identical protein binding		PCM1/JAK2(30)	haematopoietic_and_lymphoid_tissue(30)|breast(4)|ovary(2)	36				Colorectal(111;0.0789)				T	RET|JAK2	papillary thyroid|CML|MPD								---	---	---	---
Unknown	0	broad.mit.edu	37	8	18120945	18120945	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18120945delA								NAT1 (39748 upstream) : NAT2 (127810 downstream)																																			---	---	---	---
PSD3	23362	broad.mit.edu	37	8	18481435	18481435	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18481435delT	uc003wza.2	-						PSD3_uc003wyx.3_Intron|PSD3_uc003wyy.2_Intron|PSD3_uc003wyz.2_Intron	NM_015310	NP_056125			ADP-ribosylation factor guanine nucleotide						regulation of ARF protein signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	ARF guanyl-nucleotide exchange factor activity			ovary(3)	3				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)														---	---	---	---
PSD3	23362	broad.mit.edu	37	8	18629906	18629906	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18629906delT	uc003wza.2	-						PSD3_uc003wyy.2_Intron|PSD3_uc003wyz.2_Intron	NM_015310	NP_056125			ADP-ribosylation factor guanine nucleotide						regulation of ARF protein signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	ARF guanyl-nucleotide exchange factor activity			ovary(3)	3				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	18893267	18893268	+	IGR	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18893267_18893268insG								PSD3 (22071 upstream) : SH2D4A (277939 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	18991452	18991453	+	IGR	INS	-	AC	AC			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:18991452_18991453insAC								PSD3 (120256 upstream) : SH2D4A (179754 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	19116267	19116267	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19116267delA								PSD3 (245071 upstream) : SH2D4A (54940 downstream)																																			---	---	---	---
CSGALNACT1	55790	broad.mit.edu	37	8	19477942	19477942	+	Intron	DEL	T	-	-	rs72391387		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19477942delT	uc011kyo.1	-						CSGALNACT1_uc003wzg.2_Intron|CSGALNACT1_uc011kyp.1_Intron	NM_018371	NP_060841			chondroitin sulfate						anatomical structure morphogenesis|cell proliferation|cell recognition|chondroitin sulfate biosynthetic process|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|dermatan sulfate proteoglycan biosynthetic process|extracellular matrix organization|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|heparin biosynthetic process|nervous system development|UDP-glucuronate metabolic process|UDP-N-acetylgalactosamine metabolic process	Golgi cisterna membrane|integral to Golgi membrane|soluble fraction	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|glucuronosyltransferase activity|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|peptidoglycan glycosyltransferase activity			central_nervous_system(2)|ovary(1)	3				Colorectal(111;0.182)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	19619674	19619674	+	IGR	DEL	A	-	-	rs75960671		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19619674delA								CSGALNACT1 (4292 upstream) : INTS10 (55244 downstream)																																			---	---	---	---
INTS10	55174	broad.mit.edu	37	8	19680155	19680155	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19680155delT	uc003wzj.2	+							NM_018142	NP_060612			integrator complex subunit 10						snRNA processing	integrator complex	protein binding			ovary(1)	1				Colorectal(111;0.057)|COAD - Colon adenocarcinoma(73;0.215)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	20309259	20309259	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20309259delT								LZTS1 (196456 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	20772443	20772443	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20772443delT								LZTS1 (659640 upstream) : GFRA2 (777087 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	20997265	20997266	+	IGR	INS	-	TGAC	TGAC	rs112486650		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:20997265_20997266insTGAC								LZTS1 (884462 upstream) : GFRA2 (552264 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	21376206	21376206	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21376206delA								None (None upstream) : GFRA2 (173324 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	21448484	21448484	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21448484delC								None (None upstream) : GFRA2 (101046 downstream)																																			---	---	---	---
DOK2	9046	broad.mit.edu	37	8	21708921	21708921	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21708921delA	uc003wzx.1	-							NM_003974	NP_003965			docking protein 2						blood coagulation|leukocyte migration	cytosol	identical protein binding|insulin receptor binding				0				Colorectal(74;0.0145)|COAD - Colon adenocarcinoma(73;0.0608)														---	---	---	---
DOK2	9046	broad.mit.edu	37	8	21755266	21755266	+	Intron	DEL	A	-	-	rs34798682		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21755266delA	uc003wzx.1	-							NM_003974	NP_003965			docking protein 2						blood coagulation|leukocyte migration	cytosol	identical protein binding|insulin receptor binding				0				Colorectal(74;0.0145)|COAD - Colon adenocarcinoma(73;0.0608)														---	---	---	---
XPO7	23039	broad.mit.edu	37	8	21815391	21815391	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21815391delT	uc003xaa.3	+						XPO7_uc010lti.2_Intron|XPO7_uc010ltj.1_Intron	NM_015024	NP_055839			exportin 7 isoform b						mRNA transport|protein export from nucleus|transmembrane transport	cytoplasm|nuclear pore	nuclear export signal receptor activity|protein transporter activity			ovary(1)|kidney(1)|breast(1)|central_nervous_system(1)|pancreas(1)	5				Colorectal(74;0.0187)|COAD - Colon adenocarcinoma(73;0.0724)														---	---	---	---
XPO7	23039	broad.mit.edu	37	8	21829688	21829688	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21829688delT	uc003xaa.3	+						XPO7_uc010lti.2_Intron|XPO7_uc010ltj.1_Intron|XPO7_uc010ltk.2_Intron	NM_015024	NP_055839			exportin 7 isoform b						mRNA transport|protein export from nucleus|transmembrane transport	cytoplasm|nuclear pore	nuclear export signal receptor activity|protein transporter activity			ovary(1)|kidney(1)|breast(1)|central_nervous_system(1)|pancreas(1)	5				Colorectal(74;0.0187)|COAD - Colon adenocarcinoma(73;0.0724)														---	---	---	---
FGF17	8822	broad.mit.edu	37	8	21900408	21900408	+	5'Flank	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21900408delG	uc003xag.2	+						FGF17_uc003xah.2_5'Flank|FGF17_uc003xai.2_5'Flank	NM_003867	NP_003858			fibroblast growth factor 17 precursor						cell-cell signaling|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|nervous system development	extracellular space	growth factor activity|type 1 fibroblast growth factor receptor binding|type 2 fibroblast growth factor receptor binding				0				Colorectal(74;8.48e-05)|READ - Rectum adenocarcinoma(5;0.0276)|COAD - Colon adenocarcinoma(73;0.0618)														---	---	---	---
EPB49	2039	broad.mit.edu	37	8	21939823	21939823	+	3'UTR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21939823delC	uc011kyt.1	+	15					EPB49_uc010ltl.2_3'UTR|EPB49_uc010ltn.2_3'UTR|EPB49_uc011kyu.1_3'UTR|EPB49_uc011kyv.1_3'UTR|EPB49_uc010ltq.2_3'UTR	NM_001114136	NP_001107608			erythrocyte membrane protein band 4.9 isoform 1						actin filament bundle assembly|actin filament capping	actin cytoskeleton|nucleus	actin binding			central_nervous_system(1)	1				Colorectal(74;9.05e-05)|READ - Rectum adenocarcinoma(5;0.0276)|COAD - Colon adenocarcinoma(73;0.0631)														---	---	---	---
HR	55806	broad.mit.edu	37	8	21979015	21979016	+	Intron	INS	-	G	G	rs148117748	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21979015_21979016insG	uc003xas.2	-						HR_uc003xat.2_Intron	NM_005144	NP_005135			hairless protein isoform a								DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity			large_intestine(1)|ovary(1)	2		Breast(100;0.000162)|Acute lymphoblastic leukemia(644;0.0775)|Prostate(55;0.116)		KIRC - Kidney renal clear cell carcinoma(542;1.19e-05)|BRCA - Breast invasive adenocarcinoma(99;3.56e-05)|Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)														---	---	---	---
PIWIL2	55124	broad.mit.edu	37	8	22173618	22173618	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22173618delT	uc003xbn.2	+						PIWIL2_uc011kzf.1_Intron|PIWIL2_uc010ltv.2_Intron	NM_018068	NP_060538			piwi-like 2						DNA methylation involved in gamete generation|gene silencing by RNA|germ-line stem cell maintenance|multicellular organismal development|oogenesis|piRNA metabolic process|positive regulation of translation|RNA 5'-end processing|spermatogenesis	chromatoid body|pi-body	piRNA binding			skin(1)	1				Colorectal(74;0.018)|COAD - Colon adenocarcinoma(73;0.0707)														---	---	---	---
KIAA1967	57805	broad.mit.edu	37	8	22470145	22470146	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22470145_22470146insT	uc003xch.2	+						KIAA1967_uc003xci.2_Intron|KIAA1967_uc003xcj.1_Intron	NM_199205	NP_954675			p30 DBC protein						apoptosis|positive regulation of apoptosis	mitochondrial matrix|nucleus	enzyme binding|enzyme inhibitor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Prostate(55;0.0421)|Breast(100;0.102)|all_epithelial(46;0.142)		BRCA - Breast invasive adenocarcinoma(99;0.00593)|Colorectal(74;0.0157)|COAD - Colon adenocarcinoma(73;0.064)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	22810419	22810419	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22810419delA								PEBP4 (24998 upstream) : RHOBTB2 (34511 downstream)																																			---	---	---	---
CHMP7	91782	broad.mit.edu	37	8	23117526	23117526	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23117526delT	uc003xdc.2	+						CHMP7_uc003xdd.2_Intron|CHMP7_uc003xde.2_Intron	NM_152272	NP_689485			CHMP family, member 7						cellular membrane organization|late endosome to vacuole transport	cytosol|ESCRT III complex	protein transporter activity				0		Prostate(55;0.0513)		Colorectal(74;0.0155)|COAD - Colon adenocarcinoma(73;0.0632)														---	---	---	---
SLC25A37	51312	broad.mit.edu	37	8	23414373	23414373	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23414373delT	uc003xdo.2	+						SLC25A37_uc003xdn.1_Intron|SLC25A37_uc003xdp.2_Intron|SLC25A37_uc010ltz.2_Intron	NM_016612	NP_057696			solute carrier family 25, member 37						ion transport|iron ion homeostasis	integral to membrane|mitochondrial inner membrane					0		Prostate(55;0.114)		Colorectal(74;0.0198)|COAD - Colon adenocarcinoma(73;0.0751)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	23797126	23797126	+	IGR	DEL	T	-	-	rs73214861	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23797126delT								STC1 (84806 upstream) : ADAM28 (354454 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	23827628	23827628	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:23827628delA								STC1 (115308 upstream) : ADAM28 (323952 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	24492336	24492337	+	IGR	INS	-	AG	AG	rs149821843	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24492336_24492337insAG								ADAM7 (107855 upstream) : NEFM (278937 downstream)																																			---	---	---	---
DOCK5	80005	broad.mit.edu	37	8	25156677	25156677	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25156677delC	uc003xeg.2	+						DOCK5_uc010luf.1_Intron|DOCK5_uc003xeh.1_Intron|DOCK5_uc003xef.2_Intron	NM_024940	NP_079216			dedicator of cytokinesis 5							cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)	3		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)														---	---	---	---
DOCK5	80005	broad.mit.edu	37	8	25257417	25257417	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25257417delT	uc003xeg.2	+						PPP2R2A_uc003xek.2_Intron|DOCK5_uc003xej.2_Intron	NM_024940	NP_079216			dedicator of cytokinesis 5							cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)	3		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)														---	---	---	---
PPP2R2A	5520	broad.mit.edu	37	8	25424746	25424746	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25424746delA	uc003xek.2	+							NM_002717	NP_002708			alpha isoform of regulatory subunit B55, protein						protein dephosphorylation|signal transduction	protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity|protein serine/threonine phosphatase activity			ovary(1)|kidney(1)	2		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155)														---	---	---	---
EBF2	64641	broad.mit.edu	37	8	25842198	25842198	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25842198delA	uc003xes.1	-						PPP2R2A_uc003xek.2_Intron	NM_022659	NP_073150			early B-cell factor 2						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|metal ion binding			ovary(3)|skin(1)	4		all_cancers(63;0.0989)|Ovarian(32;2.74e-05)|all_epithelial(46;0.0608)|Prostate(55;0.0845)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0277)|Epithelial(17;3.29e-10)|Colorectal(74;0.00383)|COAD - Colon adenocarcinoma(73;0.00738)														---	---	---	---
BNIP3L	665	broad.mit.edu	37	8	26245707	26245708	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26245707_26245708insT	uc003xex.1	+						BNIP3L_uc010luh.1_Intron|BNIP3L_uc010lui.1_Intron|BNIP3L_uc003xey.2_5'Flank	NM_004331	NP_004322			BCL2/adenovirus E1B 19kD-interacting protein						apoptosis|defense response to virus|induction of apoptosis|interspecies interaction between organisms|mitochondrial protein catabolic process|negative regulation of survival gene product expression	endoplasmic reticulum|integral to membrane|mitochondrial outer membrane|nuclear envelope	lamin binding|protein heterodimerization activity|protein homodimerization activity				0		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0019)|Epithelial(17;1.59e-12)|all cancers(2;3.75e-11)|OV - Ovarian serous cystadenocarcinoma(2;2.57e-08)|Colorectal(74;0.135)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	26279263	26279263	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26279263delT								BNIP3L (8619 upstream) : PNMA2 (82933 downstream)																																			---	---	---	---
DPYSL2	1808	broad.mit.edu	37	8	26453073	26453073	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26453073delG	uc003xfb.1	+						DPYSL2_uc003xfa.2_Intron|DPYSL2_uc011lag.1_Intron|DPYSL2_uc010luk.1_Intron|DPYSL2_uc011lah.1_Intron	NM_001386	NP_001377			dihydropyrimidinase-like 2						axon guidance|pyrimidine base catabolic process|signal transduction	cytosol	dihydropyrimidinase activity|protein binding			large_intestine(1)	1		all_cancers(63;0.121)|Ovarian(32;2.68e-05)|all_epithelial(46;0.116)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;3.33e-10)|Colorectal(74;0.183)														---	---	---	---
DPYSL2	1808	broad.mit.edu	37	8	26474307	26474308	+	Intron	INS	-	GAGGGCTCTCCA	GAGGGCTCTCCA			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:26474307_26474308insGAGGGCTCTCCA	uc003xfb.1	+						DPYSL2_uc003xfa.2_Intron|DPYSL2_uc011lag.1_Intron|DPYSL2_uc010luk.1_Intron|DPYSL2_uc011lah.1_Intron	NM_001386	NP_001377			dihydropyrimidinase-like 2						axon guidance|pyrimidine base catabolic process|signal transduction	cytosol	dihydropyrimidinase activity|protein binding			large_intestine(1)	1		all_cancers(63;0.121)|Ovarian(32;2.68e-05)|all_epithelial(46;0.116)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;3.33e-10)|Colorectal(74;0.183)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	27015319	27015319	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27015319delT								MIR548H-4 (108839 upstream) : STMN4 (78497 downstream)																																			---	---	---	---
STMN4	81551	broad.mit.edu	37	8	27117572	27117572	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27117572delT	uc003xfk.2	-						STMN4_uc003xfj.2_5'Flank|STMN4_uc011lai.1_5'Flank|STMN4_uc011laj.1_5'Flank|STMN4_uc011lak.1_5'Flank|STMN4_uc010luo.2_5'Flank					RecName: Full=Stathmin-4; AltName: Full=Stathmin-like protein B3;          Short=RB3;						intracellular signal transduction					large_intestine(1)|pancreas(1)	2		Ovarian(32;0.00167)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0214)|Epithelial(17;9.82e-10)|Colorectal(74;0.142)														---	---	---	---
EPHX2	2053	broad.mit.edu	37	8	27399371	27399371	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27399371delG	uc003xfu.2	+						EPHX2_uc010luu.2_Intron|EPHX2_uc010luv.2_Intron|EPHX2_uc003xfv.2_Intron|EPHX2_uc010luw.2_Intron	NM_001979	NP_001970			epoxide hydrolase 2, cytoplasmic						aromatic compound catabolic process|cellular calcium ion homeostasis|drug metabolic process|inflammatory response|positive regulation of vasodilation|reactive oxygen species metabolic process|regulation of blood pressure|response to toxin|xenobiotic metabolic process	cytosol|focal adhesion|Golgi apparatus|nucleolus|peroxisome|soluble fraction	epoxide hydrolase activity|metal ion binding|protein homodimerization activity			ovary(1)	1		Ovarian(32;2.61e-05)|all_epithelial(46;0.207)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0226)|Epithelial(17;1.12e-09)|Colorectal(74;0.157)	Tamoxifen(DB00675)													---	---	---	---
Unknown	0	broad.mit.edu	37	8	27446317	27446318	+	IGR	INS	-	TG	TG			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27446317_27446318insTG								EPHX2 (43833 upstream) : CLU (8133 downstream)																																			---	---	---	---
SCARA3	51435	broad.mit.edu	37	8	27531062	27531063	+	Intron	INS	-	T	T	rs34847340	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27531062_27531063insT	uc003xgb.1	+							NM_182826	NP_878185			scavenger receptor class A, member 3 isoform 2						response to oxidative stress|UV protection	collagen|endoplasmic reticulum membrane|Golgi membrane|integral to membrane	scavenger receptor activity			skin(2)|ovary(1)|breast(1)	4		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0219)|Colorectal(74;0.148)														---	---	---	---
PBK	55872	broad.mit.edu	37	8	27682534	27682534	+	Intron	DEL	T	-	-	rs111963987		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27682534delT	uc003xgi.2	-						PBK_uc011lap.1_Intron	NM_018492	NP_060962			PDZ binding kinase						mitosis		ATP binding|protein binding|protein serine/threonine kinase activity				0		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0213)|KIRC - Kidney renal clear cell carcinoma(542;0.101)|Kidney(114;0.121)|Colorectal(74;0.141)														---	---	---	---
SCARA5	286133	broad.mit.edu	37	8	27768763	27768764	+	Intron	INS	-	C	C	rs147535465	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27768763_27768764insC	uc003xgj.2	-						SCARA5_uc010luz.2_Intron|SCARA5_uc003xgk.2_Intron|SCARA5_uc003xgl.2_Intron	NM_173833	NP_776194			scavenger receptor class A, member 5						cellular iron ion homeostasis|endocytosis|iron ion transmembrane transport|protein homotrimerization	integral to plasma membrane	ferritin receptor activity|scavenger receptor activity			central_nervous_system(1)|skin(1)	2		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)|Colorectal(74;0.228)														---	---	---	---
C8orf80	389643	broad.mit.edu	37	8	27942597	27942597	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27942597delT	uc003xgm.3	-							NM_001010906	NP_001010906			speckled-like pattern in the germinal center							nucleus	GTP binding|GTPase activity			ovary(1)|central_nervous_system(1)	2		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|KIRC - Kidney renal clear cell carcinoma(542;0.126)|Kidney(114;0.15)|Colorectal(74;0.181)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	28097164	28097164	+	IGR	DEL	A	-	-	rs71549641		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28097164delA								ELP3 (48497 upstream) : PNOC (77485 downstream)																																			---	---	---	---
ZNF395	55893	broad.mit.edu	37	8	28306742	28306742	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28306742delA	uc003xgt.2	-						FBXO16_uc003xgu.2_Intron|FBXO16_uc003xgv.2_Intron|FBXO16_uc003xgw.2_Intron	NM_018660	NP_061130			zinc finger protein 395						transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding				0		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.102)|Kidney(114;0.123)|Colorectal(74;0.142)														---	---	---	---
FZD3	7976	broad.mit.edu	37	8	28365584	28365584	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28365584delT	uc003xgx.2	+						FZD3_uc010lvb.2_Intron|hsa-mir-4288|MI0015896_5'Flank	NM_017412	NP_059108			frizzled 3 precursor						canonical Wnt receptor signaling pathway|cell proliferation in midbrain|commissural neuron axon guidance|establishment of planar polarity|facial nucleus development|G-protein signaling, coupled to cGMP nucleotide second messenger|gonad development|inner ear morphogenesis|neural tube closure|vasculature development	apical part of cell|axon|cytoplasm|dendrite|integral to membrane|neuron projection membrane|neuronal cell body|presynaptic active zone	G-protein coupled receptor activity|PDZ domain binding|Wnt-protein binding			ovary(1)|central_nervous_system(1)	2		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.109)|Kidney(114;0.13)|Colorectal(74;0.23)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	28488660	28488661	+	IGR	INS	-	T	T	rs71549680		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28488660_28488661insT								FZD3 (66701 upstream) : EXTL3 (70492 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	29393224	29393225	+	IGR	INS	-	TC	TC			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29393224_29393225insTC								DUSP4 (185039 upstream) : C8orf75 (185553 downstream)																																			---	---	---	---
C8orf75	619351	broad.mit.edu	37	8	29581562	29581562	+	Intron	DEL	A	-	-	rs33974115		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29581562delA	uc003xhn.2	-							NR_026765				Homo sapiens chromosome 8 open reading frame 75, mRNA (cDNA clone IMAGE:3607242), partial cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	30225319	30225320	+	IGR	DEL	TT	-	-	rs34443000	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30225319_30225320delTT								DCTN6 (184260 upstream) : RBPMS (16624 downstream)																																			---	---	---	---
RBPMS	11030	broad.mit.edu	37	8	30369970	30369970	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30369970delT	uc003xic.1	+						RBPMS_uc003xid.1_Intron|RBPMS_uc003xie.1_Intron|RBPMS_uc003xif.1_Intron|RBPMS_uc011lba.1_Intron|RBPMS_uc003xib.2_Intron|RBPMS_uc010lvh.1_Intron	NM_006867	NP_006858			RNA-binding protein with multiple splicing						positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|regulation of transcription, DNA-dependent|RNA processing|transcription, DNA-dependent	cytoplasm|nucleus	nucleotide binding|poly(A) RNA binding|protein binding|transcription coactivator activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(542;0.144)|Kidney(114;0.172)														---	---	---	---
GSR	2936	broad.mit.edu	37	8	30539225	30539225	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30539225delA	uc003xih.1	-							NM_000637	NP_000628			glutathione reductase precursor						cell redox homeostasis|nucleobase, nucleoside and nucleotide interconversion	cytosol|mitochondrion	electron carrier activity|glutathione-disulfide reductase activity			ovary(2)|pancreas(2)|central_nervous_system(1)	5				KIRC - Kidney renal clear cell carcinoma(542;0.105)|Kidney(114;0.125)	Carmustine(DB00262)|Glutathione(DB00143)|NADH(DB00157)													---	---	---	---
GSR	2936	broad.mit.edu	37	8	30573524	30573524	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30573524delT	uc003xih.1	-							NM_000637	NP_000628			glutathione reductase precursor						cell redox homeostasis|nucleobase, nucleoside and nucleotide interconversion	cytosol|mitochondrion	electron carrier activity|glutathione-disulfide reductase activity			ovary(2)|pancreas(2)|central_nervous_system(1)	5				KIRC - Kidney renal clear cell carcinoma(542;0.105)|Kidney(114;0.125)	Carmustine(DB00262)|Glutathione(DB00143)|NADH(DB00157)													---	---	---	---
PPP2CB	5516	broad.mit.edu	37	8	30665627	30665627	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30665627delT	uc003xik.2	-							NM_004156	NP_004147			protein phosphatase 2, catalytic subunit, beta						protein dephosphorylation	chromosome, centromeric region|cytoplasm|nucleus|protein phosphatase type 2A complex|spindle pole	metal ion binding				0				KIRC - Kidney renal clear cell carcinoma(542;0.095)|Kidney(114;0.114)	Vitamin E(DB00163)													---	---	---	---
WRN	7486	broad.mit.edu	37	8	30926007	30926007	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30926007delT	uc003xio.3	+							NM_000553	NP_000544			Werner syndrome protein						base-excision repair|cellular response to starvation|DNA recombination|DNA synthesis involved in DNA repair|multicellular organismal aging|nucleolus to nucleoplasm transport|positive regulation of hydrolase activity|regulation of apoptosis|replication fork processing|response to oxidative stress|response to UV-C|telomere maintenance	centrosome|nucleolus|nucleoplasm	3'-5' exonuclease activity|ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|four-way junction helicase activity|G-quadruplex DNA binding|magnesium ion binding|manganese ion binding|protein complex binding|protein homodimerization activity|Y-form DNA binding			ovary(2)|kidney(2)|large_intestine(1)|lung(1)|skin(1)	7		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)				Mis|N|F|S			osteosarcoma|meningioma|others		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Werner_syndrome				---	---	---	---
WRN	7486	broad.mit.edu	37	8	30945667	30945667	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30945667delT	uc003xio.3	+						WRN_uc011lbe.1_Intron|WRN_uc010lvk.2_Intron	NM_000553	NP_000544			Werner syndrome protein						base-excision repair|cellular response to starvation|DNA recombination|DNA synthesis involved in DNA repair|multicellular organismal aging|nucleolus to nucleoplasm transport|positive regulation of hydrolase activity|regulation of apoptosis|replication fork processing|response to oxidative stress|response to UV-C|telomere maintenance	centrosome|nucleolus|nucleoplasm	3'-5' exonuclease activity|ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|four-way junction helicase activity|G-quadruplex DNA binding|magnesium ion binding|manganese ion binding|protein complex binding|protein homodimerization activity|Y-form DNA binding			ovary(2)|kidney(2)|large_intestine(1)|lung(1)|skin(1)	7		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)				Mis|N|F|S			osteosarcoma|meningioma|others		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Werner_syndrome				---	---	---	---
WRN	7486	broad.mit.edu	37	8	30977943	30977943	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30977943delA	uc003xio.3	+						WRN_uc010lvk.2_Intron	NM_000553	NP_000544			Werner syndrome protein						base-excision repair|cellular response to starvation|DNA recombination|DNA synthesis involved in DNA repair|multicellular organismal aging|nucleolus to nucleoplasm transport|positive regulation of hydrolase activity|regulation of apoptosis|replication fork processing|response to oxidative stress|response to UV-C|telomere maintenance	centrosome|nucleolus|nucleoplasm	3'-5' exonuclease activity|ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|four-way junction helicase activity|G-quadruplex DNA binding|magnesium ion binding|manganese ion binding|protein complex binding|protein homodimerization activity|Y-form DNA binding			ovary(2)|kidney(2)|large_intestine(1)|lung(1)|skin(1)	7		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)				Mis|N|F|S			osteosarcoma|meningioma|others		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Werner_syndrome				---	---	---	---
NRG1	3084	broad.mit.edu	37	8	31513661	31513661	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31513661delA	uc003xip.2	+							NM_013962	NP_039256			neuregulin 1 isoform GGF2						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)														---	---	---	---
NRG1	3084	broad.mit.edu	37	8	32253704	32253704	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32253704delT	uc003xip.2	+							NM_013962	NP_039256			neuregulin 1 isoform GGF2						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)														---	---	---	---
NRG1	3084	broad.mit.edu	37	8	32397069	32397069	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32397069delT	uc003xip.2	+							NM_013962	NP_039256			neuregulin 1 isoform GGF2						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)														---	---	---	---
NRG1	3084	broad.mit.edu	37	8	32571086	32571086	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32571086delT	uc003xiv.2	+						NRG1_uc003xip.2_Intron|NRG1_uc003xir.2_Intron|NRG1_uc010lvl.2_Intron|NRG1_uc010lvm.2_Intron|NRG1_uc010lvn.2_Intron|NRG1_uc003xis.2_Intron|NRG1_uc011lbf.1_Intron|NRG1_uc010lvo.2_Intron|NRG1_uc003xiu.2_Intron|NRG1_uc003xiw.2_Intron|NRG1_uc003xit.2_Intron|NRG1_uc010lvr.2_Intron|NRG1_uc010lvs.2_Intron|NRG1_uc010lvp.2_Intron|NRG1_uc010lvq.2_Intron|NRG1_uc003xix.2_Intron|NRG1_uc003xiy.2_Intron|NRG1_uc010lvt.2_Intron	NM_013964	NP_039258			neuregulin 1 isoform HRG-alpha						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)														---	---	---	---
NRG1	3084	broad.mit.edu	37	8	32604980	32604980	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32604980delA	uc003xiv.2	+						NRG1_uc011lbf.1_Intron|NRG1_uc010lvo.2_Intron|NRG1_uc003xiu.2_Intron|NRG1_uc003xiw.2_Intron|NRG1_uc003xit.2_Intron|NRG1_uc010lvr.2_Intron|NRG1_uc010lvs.2_Intron|NRG1_uc010lvp.2_Intron|NRG1_uc010lvq.2_Intron|NRG1_uc011lbg.1_Intron|NRG1_uc011lbh.1_Intron|NRG1_uc003xiz.1_Intron|NRG1_uc003xja.2_Intron	NM_013964	NP_039258			neuregulin 1 isoform HRG-alpha						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	32715332	32715332	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32715332delT								NRG1 (92774 upstream) : FUT10 (513014 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	32902546	32902546	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32902546delT								NRG1 (279988 upstream) : FUT10 (325800 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	33205927	33205927	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33205927delA								NRG1 (583369 upstream) : FUT10 (22419 downstream)																																			---	---	---	---
C8orf41	80185	broad.mit.edu	37	8	33333263	33333263	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33333263delA	uc010lvu.1	-						FUT10_uc003xje.2_5'Flank|FUT10_uc011lbi.1_5'Flank|FUT10_uc003xjh.2_5'Flank|FUT10_uc003xji.1_5'Flank					Homo sapiens cDNA: FLJ23263 fis, clone COL06129.								binding				0				KIRC - Kidney renal clear cell carcinoma(67;0.0923)|Kidney(114;0.111)														---	---	---	---
C8orf41	80185	broad.mit.edu	37	8	33367554	33367554	+	Intron	DEL	A	-	-	rs79956819		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33367554delA	uc003xjl.3	-						C8orf41_uc003xjk.3_Intron|C8orf41_uc010lvv.2_Intron|C8orf41_uc003xjm.3_Intron|C8orf41_uc003xjn.1_Intron	NM_025115	NP_079391			hypothetical protein LOC80185								binding				0				KIRC - Kidney renal clear cell carcinoma(67;0.0923)|Kidney(114;0.111)														---	---	---	---
RNF122	79845	broad.mit.edu	37	8	33406740	33406740	+	Intron	DEL	A	-	-	rs71899502		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33406740delA	uc003xjo.1	-							NM_024787	NP_079063			ring finger protein 122							endoplasmic reticulum|Golgi apparatus|integral to membrane	zinc ion binding				0				KIRC - Kidney renal clear cell carcinoma(67;0.0966)|Kidney(114;0.116)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	33516778	33516779	+	IGR	DEL	TT	-	-	rs35851314		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:33516778_33516779delTT								DUSP26 (59339 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34436909	34436909	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34436909delT								DUSP26 (979470 upstream) : UNC5D (656066 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34540726	34540726	+	IGR	DEL	T	-	-	rs113252009		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34540726delT								None (None upstream) : UNC5D (552249 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34610507	34610507	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34610507delT								None (None upstream) : UNC5D (482468 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	34925125	34925125	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:34925125delA								None (None upstream) : UNC5D (167850 downstream)																																			---	---	---	---
UNC5D	137970	broad.mit.edu	37	8	35251560	35251560	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35251560delT	uc003xjr.1	+							NM_080872	NP_543148			unc-5 homolog D precursor						apoptosis|axon guidance	integral to membrane	receptor activity			upper_aerodigestive_tract(2)|ovary(2)|pancreas(1)|skin(1)	6				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	35666920	35666920	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35666920delC								UNC5D (14740 upstream) : KCNU1 (974922 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	35932346	35932346	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35932346delA								UNC5D (280166 upstream) : KCNU1 (709496 downstream)																																			---	---	---	---
KCNU1	157855	broad.mit.edu	37	8	36773498	36773498	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36773498delA	uc010lvw.2	+						KCNU1_uc003xjw.2_Intron	NM_001031836	NP_001027006			potassium channel, subfamily U, member 1							voltage-gated potassium channel complex	binding|large conductance calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)														---	---	---	---
Unknown	0	broad.mit.edu	37	8	37406442	37406442	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37406442delA								KCNU1 (612801 upstream) : ZNF703 (146859 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37430870	37430871	+	IGR	INS	-	T	T	rs142392410	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37430870_37430871insT								KCNU1 (637229 upstream) : ZNF703 (122430 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	37450716	37450717	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37450716_37450717delAA								KCNU1 (657075 upstream) : ZNF703 (102584 downstream)																																			---	---	---	---
RAB11FIP1	80223	broad.mit.edu	37	8	37725231	37725231	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37725231delA	uc003xkm.1	-						RAB11FIP1_uc010lvz.1_Intron|RAB11FIP1_uc003xkn.1_Intron|RAB11FIP1_uc003xkl.1_Intron|RAB11FIP1_uc003xko.1_3'UTR|RAB11FIP1_uc003xkp.1_3'UTR	NM_001002814	NP_001002814			RAB11 family interacting protein 1 isoform 3						protein transport	centrosome|phagocytic vesicle membrane|recycling endosome	protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;3.62e-11)															---	---	---	---
RAB11FIP1	80223	broad.mit.edu	37	8	37757059	37757059	+	5'Flank	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:37757059delC	uc003xkm.1	-						RAB11FIP1_uc010lvz.1_5'Flank|RAB11FIP1_uc003xkn.1_5'Flank	NM_001002814	NP_001002814			RAB11 family interacting protein 1 isoform 3						protein transport	centrosome|phagocytic vesicle membrane|recycling endosome	protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;3.62e-11)															---	---	---	---
DDHD2	23259	broad.mit.edu	37	8	38109887	38109887	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38109887delT	uc003xlb.2	+						DDHD2_uc003xlc.2_Intron|DDHD2_uc003xld.2_Intron	NM_015214	NP_056029			DDHD domain containing 2 isoform 1						lipid catabolic process	centrosome	hydrolase activity|metal ion binding			large_intestine(1)|ovary(1)	2	Colorectal(12;0.000442)	all_lung(54;0.0657)|Lung NSC(58;0.175)	BRCA - Breast invasive adenocarcinoma(5;3.76e-25)|COAD - Colon adenocarcinoma(9;0.0977)															---	---	---	---
PPAPDC1B	84513	broad.mit.edu	37	8	38126013	38126013	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38126013delA	uc003xlf.3	-						PPAPDC1B_uc003xle.3_Intron|PPAPDC1B_uc003xlg.3_Intron|PPAPDC1B_uc010lwd.2_Intron	NM_001102559	NP_001096029			phosphatidic acid phosphatase type 2 domain						phospholipid dephosphorylation	cytoplasm|integral to membrane|plasma membrane	phosphatidate phosphatase activity				0	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.121)	BRCA - Breast invasive adenocarcinoma(5;3.04e-26)|COAD - Colon adenocarcinoma(9;0.188)															---	---	---	---
WHSC1L1	54904	broad.mit.edu	37	8	38176095	38176095	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38176095delA	uc003xli.2	-						WHSC1L1_uc011lbm.1_Intron|WHSC1L1_uc010lwe.2_Intron|WHSC1L1_uc003xlj.2_Intron	NM_023034	NP_075447			WHSC1L1 protein isoform long						cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome	histone-lysine N-methyltransferase activity|zinc ion binding			breast(1)	1	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)					T	NUP98	AML								---	---	---	---
Unknown	0	broad.mit.edu	37	8	38466738	38466739	+	IGR	DEL	CA	-	-	rs72633407	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38466738_38466739delCA								RNF5P1 (7963 upstream) : TACC1 (118965 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	38501101	38501101	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38501101delA								RNF5P1 (42326 upstream) : TACC1 (84603 downstream)																																			---	---	---	---
TACC1	6867	broad.mit.edu	37	8	38590822	38590822	+	Intron	DEL	T	-	-	rs113616267		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38590822delT	uc011lbz.1	+						TACC1_uc011lby.1_Intron|TACC1_uc003xma.2_Intron|TACC1_uc003xlz.2_Intron|TACC1_uc003xmc.3_Intron|TACC1_uc003xmb.3_Intron	NM_006283	NP_006274			transforming, acidic coiled-coil containing						cell cycle|cell division	intermediate filament cytoskeleton|microtubule organizing center|nucleus	protein binding			ovary(1)	1		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.065)	LUSC - Lung squamous cell carcinoma(45;1.7e-09)|COAD - Colon adenocarcinoma(9;0.235)															---	---	---	---
PLEKHA2	59339	broad.mit.edu	37	8	38808024	38808024	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38808024delT	uc003xmi.3	+						PLEKHA2_uc011lce.1_Intron	NM_021623	NP_067636			pleckstrin homology domain containing, family A						positive regulation of cell-matrix adhesion	cytoplasm|nucleus|plasma membrane|protein complex	fibronectin binding|laminin binding				0		all_lung(54;0.0413)|Lung NSC(58;0.115)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;4.68e-08)|COAD - Colon adenocarcinoma(9;0.235)															---	---	---	---
ADAM2	2515	broad.mit.edu	37	8	39613729	39613729	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39613729delT	uc003xnj.2	-						ADAM2_uc003xnk.2_Intron|ADAM2_uc011lck.1_Intron|ADAM2_uc003xnl.2_Intron	NM_001464	NP_001455			ADAM metallopeptidase domain 2 proprotein						cell adhesion|fusion of sperm to egg plasma membrane|proteolysis	integral to plasma membrane	integrin binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)	2		all_cancers(7;2.38e-28)|all_epithelial(6;8.85e-21)|all_lung(54;1.24e-07)|Lung NSC(58;1.94e-07)|Hepatocellular(245;0.00745)|Breast(189;0.00908)|Renal(179;0.0183)|Colorectal(162;0.246)	LUSC - Lung squamous cell carcinoma(45;0.000149)	READ - Rectum adenocarcinoma(644;0.0689)|Kidney(114;0.162)														---	---	---	---
ADAM2	2515	broad.mit.edu	37	8	39661028	39661028	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39661028delT	uc003xnj.2	-						ADAM2_uc003xnk.2_Intron|ADAM2_uc011lck.1_Intron|ADAM2_uc003xnl.2_Intron	NM_001464	NP_001455			ADAM metallopeptidase domain 2 proprotein						cell adhesion|fusion of sperm to egg plasma membrane|proteolysis	integral to plasma membrane	integrin binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)	2		all_cancers(7;2.38e-28)|all_epithelial(6;8.85e-21)|all_lung(54;1.24e-07)|Lung NSC(58;1.94e-07)|Hepatocellular(245;0.00745)|Breast(189;0.00908)|Renal(179;0.0183)|Colorectal(162;0.246)	LUSC - Lung squamous cell carcinoma(45;0.000149)	READ - Rectum adenocarcinoma(644;0.0689)|Kidney(114;0.162)														---	---	---	---
IDO1	3620	broad.mit.edu	37	8	39769645	39769647	+	5'Flank	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39769645_39769647delTTT	uc003xnm.2	+						IDO1_uc003xnn.2_5'Flank	NM_002164	NP_002155			indoleamine 2,3-dioxygenase 1						female pregnancy|tryptophan catabolic process	cytosol	electron carrier activity|heme binding|indoleamine 2,3-dioxygenase activity|tryptophan 2,3-dioxygenase activity			central_nervous_system(2)	2					L-Tryptophan(DB00150)													---	---	---	---
IDO2	169355	broad.mit.edu	37	8	39840349	39840349	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39840349delT	uc010lwy.1	+						IDO2_uc003xno.1_Intron|IDO2_uc010lwz.1_Intron	NM_194294	NP_919270			indoleamine-pyrrole 2,3 dioxygenase-like 1						tryptophan catabolic process to kynurenine	cytosol	heme binding|indoleamine 2,3-dioxygenase activity|tryptophan 2,3-dioxygenase activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	40812682	40812683	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40812682_40812683insA								ZMAT4 (57339 upstream) : SFRP1 (306796 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	40835164	40835164	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40835164delA								ZMAT4 (79821 upstream) : SFRP1 (284315 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	41089367	41089367	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41089367delT								ZMAT4 (334024 upstream) : SFRP1 (30112 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	41183824	41183824	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41183824delT								SFRP1 (16844 upstream) : GOLGA7 (164257 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	41778812	41778812	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41778812delA								ANK1 (24532 upstream) : MYST3 (8186 downstream)																																			---	---	---	---
MYST3	7994	broad.mit.edu	37	8	41801617	41801617	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41801617delA	uc010lxb.2	-						MYST3_uc010lxc.2_Intron|MYST3_uc003xon.3_Intron|MYST3_uc010lxd.2_Intron	NM_001099412	NP_001092882			MYST histone acetyltransferase (monocytic						histone H3 acetylation|myeloid cell differentiation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription coactivator activity|transcription factor binding|zinc ion binding			ovary(4)|pancreas(1)|central_nervous_system(1)|skin(1)	7	all_epithelial(6;1.12e-27)|all_lung(13;3.94e-12)|Lung NSC(13;6.54e-11)|Ovarian(28;0.00744)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211)	all_lung(54;0.000294)|Lung NSC(58;0.00105)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983)	Epithelial(1;2.82e-19)|all cancers(1;1.15e-16)|BRCA - Breast invasive adenocarcinoma(8;9.17e-11)|OV - Ovarian serous cystadenocarcinoma(14;9.4e-05)|Colorectal(10;0.000728)|Lung(22;0.00153)|LUSC - Lung squamous cell carcinoma(45;0.00741)|COAD - Colon adenocarcinoma(11;0.0171)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	41975205	41975205	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41975205delT								MYST3 (65700 upstream) : AP3M2 (35259 downstream)																																			---	---	---	---
AP3M2	10947	broad.mit.edu	37	8	42010655	42010656	+	Intron	INS	-	G	G	rs142450582	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42010655_42010656insG	uc003xop.2	+						AP3M2_uc003xoo.2_Intron|AP3M2_uc010lxe.2_Intron|AP3M2_uc003xoq.1_5'Flank|AP3M2_uc003xor.1_5'Flank	NM_001134296	NP_001127768			adaptor-related protein complex 3, mu 2 subunit						intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|Golgi apparatus					0	all_cancers(6;8.14e-25)|all_epithelial(6;2.41e-27)|all_lung(13;5.09e-13)|Lung NSC(13;8.38e-12)|Ovarian(28;0.00438)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983)	BRCA - Breast invasive adenocarcinoma(8;5.23e-10)|Colorectal(10;0.00165)|OV - Ovarian serous cystadenocarcinoma(14;0.00346)|Lung(22;0.00467)|COAD - Colon adenocarcinoma(11;0.0171)|LUSC - Lung squamous cell carcinoma(45;0.024)															---	---	---	---
IKBKB	3551	broad.mit.edu	37	8	42155413	42155413	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42155413delA	uc003xow.1	+						IKBKB_uc003xov.2_Intron|IKBKB_uc010lxh.1_Intron|IKBKB_uc011lco.1_Intron|IKBKB_uc010lxj.1_Intron|IKBKB_uc003xox.1_Intron|IKBKB_uc011lcp.1_Intron|IKBKB_uc011lcq.1_Intron|IKBKB_uc010lxi.1_Intron|IKBKB_uc011lcr.1_Intron	NM_001556	NP_001547			inhibitor of nuclear factor kappa B kinase beta						anti-apoptosis|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription, DNA-dependent|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	CD40 receptor complex|cytosol|internal side of plasma membrane|membrane raft	ATP binding|identical protein binding|IkappaB kinase activity			breast(3)|ovary(2)|lung(1)|skin(1)	7	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;6.21e-12)|Lung NSC(13;1.04e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;1.37e-10)|Colorectal(10;0.00102)|OV - Ovarian serous cystadenocarcinoma(14;0.00168)|Lung(22;0.00467)|LUSC - Lung squamous cell carcinoma(45;0.024)|COAD - Colon adenocarcinoma(11;0.0264)		Arsenic trioxide(DB01169)|Auranofin(DB00995)													---	---	---	---
VDAC3	7419	broad.mit.edu	37	8	42257067	42257068	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42257067_42257068insT	uc011lct.1	+						VDAC3_uc010lxk.2_Intron|VDAC3_uc003xpc.2_Intron	NM_005662	NP_005653			voltage-dependent anion channel 3 isoform b						adenine transport	mitochondrial outer membrane|pore complex	nucleotide binding|porin activity|protein binding|voltage-gated anion channel activity			upper_aerodigestive_tract(1)	1	all_cancers(6;3.86e-23)|all_lung(13;6.47e-12)|Lung NSC(13;1.08e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;3.48e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00266)|Lung(22;0.00849)|LUSC - Lung squamous cell carcinoma(45;0.024)		Dihydroxyaluminium(DB01375)													---	---	---	---
SLC20A2	6575	broad.mit.edu	37	8	42287889	42287890	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42287889_42287890insT	uc010lxl.2	-						SLC20A2_uc010lxm.2_Intron|SLC20A2_uc003xpe.2_Intron|SLC20A2_uc011lcu.1_Intron	NM_006749	NP_006740			solute carrier family 20, member 2						interspecies interaction between organisms	integral to plasma membrane|membrane fraction	inorganic phosphate transmembrane transporter activity|receptor activity|sodium-dependent phosphate transmembrane transporter activity|sodium:phosphate symporter activity			ovary(2)	2	all_lung(13;8.33e-12)|Lung NSC(13;1.41e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;5.73e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00419)|Lung(22;0.0302)|LUSC - Lung squamous cell carcinoma(45;0.0869)															---	---	---	---
SLC20A2	6575	broad.mit.edu	37	8	42293634	42293634	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42293634delA	uc010lxl.2	-						SLC20A2_uc010lxm.2_Intron|SLC20A2_uc003xpe.2_Intron|SLC20A2_uc011lcu.1_Intron	NM_006749	NP_006740			solute carrier family 20, member 2						interspecies interaction between organisms	integral to plasma membrane|membrane fraction	inorganic phosphate transmembrane transporter activity|receptor activity|sodium-dependent phosphate transmembrane transporter activity|sodium:phosphate symporter activity			ovary(2)	2	all_lung(13;8.33e-12)|Lung NSC(13;1.41e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;5.73e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00419)|Lung(22;0.0302)|LUSC - Lung squamous cell carcinoma(45;0.0869)															---	---	---	---
SLC20A2	6575	broad.mit.edu	37	8	42297283	42297283	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42297283delA	uc010lxl.2	-						SLC20A2_uc010lxm.2_Intron|SLC20A2_uc003xpe.2_Intron|SLC20A2_uc011lcu.1_Intron	NM_006749	NP_006740			solute carrier family 20, member 2						interspecies interaction between organisms	integral to plasma membrane|membrane fraction	inorganic phosphate transmembrane transporter activity|receptor activity|sodium-dependent phosphate transmembrane transporter activity|sodium:phosphate symporter activity			ovary(2)	2	all_lung(13;8.33e-12)|Lung NSC(13;1.41e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;5.73e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00419)|Lung(22;0.0302)|LUSC - Lung squamous cell carcinoma(45;0.0869)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	42538738	42538738	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42538738delG								C8orf40 (130599 upstream) : CHRNB3 (13824 downstream)																																			---	---	---	---
HOOK3	84376	broad.mit.edu	37	8	42765500	42765500	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42765500delT	uc003xpr.2	+						HOOK3_uc010lxq.1_Intron	NM_032410	NP_115786			golgi-associated microtubule-binding protein						cytoplasmic microtubule organization|early endosome to late endosome transport|endosome organization|endosome to lysosome transport|Golgi localization|interkinetic nuclear migration|lysosome organization|microtubule anchoring|negative regulation of neurogenesis|protein localization to centrosome|protein transport	cis-Golgi network|FHF complex|microtubule|pericentriolar material	identical protein binding|microtubule binding			ovary(1)|breast(1)	2	Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.000105)|Lung NSC(58;0.000419)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)					T	RET	papillary thyroid								---	---	---	---
SGK196	84197	broad.mit.edu	37	8	42978201	42978202	+	3'UTR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42978201_42978202delTT	uc003xpw.2	+	5						NM_032237	NP_115613			protein kinase-like protein SgK196							integral to membrane	ATP binding|protein kinase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	43482048	43482050	+	IGR	DEL	TTT	-	-	rs111934907		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43482048_43482050delTTT								POTEA (263720 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	47134685	47134685	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47134685delA								None (None upstream) : BEYLA (617823 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	47677002	47677002	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:47677002delT								None (None upstream) : BEYLA (75506 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	48156025	48156026	+	IGR	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48156025_48156026insC								BEYLA (388618 upstream) : KIAA0146 (17516 downstream)																																			---	---	---	---
KIAA0146	23514	broad.mit.edu	37	8	48297334	48297334	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48297334delA	uc003xqd.2	+						KIAA0146_uc011lcz.1_Intron|KIAA0146_uc011lda.1_Intron|KIAA0146_uc011ldb.1_Intron|KIAA0146_uc010lxs.2_Intron|KIAA0146_uc011ldc.1_Intron|KIAA0146_uc011ldd.1_Intron|KIAA0146_uc003xqe.2_Intron|KIAA0146_uc003xqf.2_Intron|KIAA0146_uc011lde.1_Intron	NM_001080394	NP_001073863			hypothetical protein LOC23514												0		Lung NSC(58;0.175)																---	---	---	---
KIAA0146	23514	broad.mit.edu	37	8	48428377	48428377	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48428377delT	uc003xqd.2	+						KIAA0146_uc011lcz.1_Intron|KIAA0146_uc011lda.1_Intron|KIAA0146_uc011ldb.1_Intron|KIAA0146_uc010lxs.2_Intron|KIAA0146_uc011ldc.1_Intron|KIAA0146_uc011ldd.1_Intron|KIAA0146_uc003xqe.2_Intron|KIAA0146_uc003xqf.2_Intron|KIAA0146_uc011lde.1_Intron|KIAA0146_uc010lxt.2_Intron	NM_001080394	NP_001073863			hypothetical protein LOC23514												0		Lung NSC(58;0.175)																---	---	---	---
PRKDC	5591	broad.mit.edu	37	8	48685754	48685756	+	3'UTR	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48685754_48685756delAAA	uc003xqi.2	-	87					PRKDC_uc003xqj.2_3'UTR|PRKDC_uc011ldh.1_3'UTR	NM_006904	NP_008835			protein kinase, DNA-activated, catalytic						cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter	DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex	ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding			lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3)	34		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)											NHEJ					---	---	---	---
PRKDC	5591	broad.mit.edu	37	8	48689477	48689477	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48689477delT	uc003xqi.2	-	86	12167	c.12110delA	c.(12109-12111)AATfs	p.N4037fs	PRKDC_uc003xqj.2_Frame_Shift_Del_p.N4006fs|PRKDC_uc011ldh.1_Intron	NM_006904	NP_008835	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic	4037					cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter	DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex	ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding			lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3)	34		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)											NHEJ					---	---	---	---
PRKDC	5591	broad.mit.edu	37	8	48704284	48704285	+	Intron	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48704284_48704285delAG	uc003xqi.2	-						PRKDC_uc003xqj.2_Intron|PRKDC_uc011ldh.1_Intron	NM_006904	NP_008835			protein kinase, DNA-activated, catalytic						cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter	DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex	ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding			lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3)	34		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)											NHEJ					---	---	---	---
Unknown	0	broad.mit.edu	37	8	49020461	49020461	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49020461delT								UBE2V2 (46009 upstream) : EFCAB1 (602890 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	49025455	49025457	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49025455_49025457delTTT								UBE2V2 (51003 upstream) : EFCAB1 (597894 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	49259397	49259397	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49259397delG								UBE2V2 (284945 upstream) : EFCAB1 (363954 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	49297743	49297744	+	IGR	DEL	AA	-	-	rs140564135		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49297743_49297744delAA								UBE2V2 (323291 upstream) : EFCAB1 (325607 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	49324431	49324431	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49324431delA								UBE2V2 (349979 upstream) : EFCAB1 (298920 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	49453850	49453851	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49453850_49453851delTT								UBE2V2 (479398 upstream) : EFCAB1 (169500 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	49475867	49475867	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49475867delT								UBE2V2 (501415 upstream) : EFCAB1 (147484 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	49536950	49536951	+	IGR	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49536950_49536951delCT								UBE2V2 (562498 upstream) : EFCAB1 (86400 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	49906228	49906228	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:49906228delT								SNAI2 (72240 upstream) : C8orf22 (78675 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	50732895	50732895	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:50732895delT								C8orf22 (744254 upstream) : SNTG1 (89454 downstream)																																			---	---	---	---
SNTG1	54212	broad.mit.edu	37	8	51636349	51636350	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51636349_51636350delAA	uc010lxy.1	+						SNTG1_uc003xqs.1_Intron|SNTG1_uc010lxz.1_Intron|SNTG1_uc011ldl.1_Intron	NM_018967	NP_061840			syntrophin, gamma 1						cell communication	cytoplasm|cytoskeleton|nucleus|ruffle membrane|syntrophin complex	actin binding|protein C-terminus binding			ovary(5)	5		all_cancers(86;0.00754)|all_epithelial(80;9.76e-05)|Lung NSC(129;0.000865)|all_lung(136;0.00249)|Colorectal(162;0.22)																---	---	---	---
Unknown	0	broad.mit.edu	37	8	51710642	51710642	+	IGR	DEL	T	-	-	rs11296846		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51710642delT								SNTG1 (5215 upstream) : PXDNL (521502 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	51968721	51968722	+	IGR	INS	-	TG	TG	rs146427485	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:51968721_51968722insTG								SNTG1 (263294 upstream) : PXDNL (263422 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	52225421	52225421	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52225421delA								SNTG1 (519994 upstream) : PXDNL (6723 downstream)																																			---	---	---	---
PXDNL	137902	broad.mit.edu	37	8	52336760	52336760	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52336760delA	uc003xqu.3	-							NM_144651	NP_653252			peroxidasin homolog-like precursor						hydrogen peroxide catabolic process	extracellular space	heme binding|peroxidase activity			ovary(1)|pancreas(1)	2		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)																---	---	---	---
PXDNL	137902	broad.mit.edu	37	8	52351789	52351789	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52351789delA	uc003xqu.3	-							NM_144651	NP_653252			peroxidasin homolog-like precursor						hydrogen peroxide catabolic process	extracellular space	heme binding|peroxidase activity			ovary(1)|pancreas(1)	2		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)																---	---	---	---
PXDNL	137902	broad.mit.edu	37	8	52453510	52453510	+	Intron	DEL	T	-	-	rs113417763		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52453510delT	uc003xqu.3	-							NM_144651	NP_653252			peroxidasin homolog-like precursor						hydrogen peroxide catabolic process	extracellular space	heme binding|peroxidase activity			ovary(1)|pancreas(1)	2		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)																---	---	---	---
ST18	9705	broad.mit.edu	37	8	53075042	53075042	+	Intron	DEL	T	-	-	rs140414148	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53075042delT	uc003xqz.2	-						ST18_uc011ldq.1_Intron|ST18_uc011ldr.1_Intron|ST18_uc011lds.1_Intron|ST18_uc003xra.2_Intron|ST18_uc003xrb.2_Intron	NM_014682	NP_055497			suppression of tumorigenicity 18							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|skin(1)	5		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)																---	---	---	---
ST18	9705	broad.mit.edu	37	8	53084293	53084293	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53084293delT	uc003xqz.2	-						ST18_uc011ldq.1_Intron|ST18_uc011ldr.1_Intron|ST18_uc011lds.1_Intron|ST18_uc003xra.2_Intron|ST18_uc003xrb.2_Intron	NM_014682	NP_055497			suppression of tumorigenicity 18							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|skin(1)	5		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)																---	---	---	---
ST18	9705	broad.mit.edu	37	8	53136246	53136246	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53136246delT	uc003xra.2	-						ST18_uc003xrb.2_Intron|ST18_uc010lyb.2_Intron	NM_014682	NP_055497			suppression of tumorigenicity 18							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|skin(1)	5		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)																---	---	---	---
Unknown	0	broad.mit.edu	37	8	53434906	53434906	+	IGR	DEL	T	-	-	rs76409231		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53434906delT								ST18 (112467 upstream) : FAM150A (11692 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	53502697	53502697	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53502697delA								FAM150A (24676 upstream) : RB1CC1 (32322 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	53872722	53872723	+	IGR	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53872722_53872723delGA								NPBWR1 (19269 upstream) : OPRK1 (265553 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	54103477	54103477	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54103477delT								NPBWR1 (250024 upstream) : OPRK1 (34799 downstream)																																			---	---	---	---
TCEA1	6917	broad.mit.edu	37	8	54922859	54922859	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54922859delA	uc003xru.2	-						TCEA1_uc003xrv.2_Intron|TCEA1_uc011ldw.1_Intron|TCEA1_uc003xrw.1_Intron	NM_006756	NP_006747			transcription elongation factor A 1 isoform 1						positive regulation of viral transcription|regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription elongation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	nucleoplasm	DNA binding|translation elongation factor activity|zinc ion binding				0		Lung NSC(129;0.109)|all_epithelial(80;0.11)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;9.1e-07)|Epithelial(17;9.44e-05)|all cancers(17;0.000699)					T	PLAG1	salivary adenoma								---	---	---	---
Unknown	0	broad.mit.edu	37	8	55173833	55173833	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55173833delT								MRPL15 (112759 upstream) : SOX17 (196662 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	55884651	55884653	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55884651_55884653delTTT								RP1 (202120 upstream) : XKR4 (130364 downstream)																																			---	---	---	---
XKR4	114786	broad.mit.edu	37	8	56282627	56282628	+	Intron	INS	-	AAC	AAC			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56282627_56282628insAAC	uc003xsf.2	+							NM_052898	NP_443130			XK, Kell blood group complex subunit-related							integral to membrane				pancreas(2)	2			Epithelial(17;0.000117)|all cancers(17;0.000836)															---	---	---	---
XKR4	114786	broad.mit.edu	37	8	56322126	56322127	+	Intron	DEL	TT	-	-	rs66632860		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56322126_56322127delTT	uc003xsf.2	+							NM_052898	NP_443130			XK, Kell blood group complex subunit-related							integral to membrane				pancreas(2)	2			Epithelial(17;0.000117)|all cancers(17;0.000836)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	56587313	56587314	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56587313_56587314insT								XKR4 (148605 upstream) : TMEM68 (64006 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	56617140	56617141	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56617140_56617141delTT								XKR4 (178432 upstream) : TMEM68 (34179 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	56635244	56635244	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56635244delG								XKR4 (196536 upstream) : TMEM68 (16076 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	57532684	57532684	+	IGR	DEL	A	-	-	rs34872658		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57532684delA								PENK (173402 upstream) : IMPAD1 (337807 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	57948057	57948057	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57948057delT								IMPAD1 (41630 upstream) : C8orf71 (244045 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	57958868	57958868	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:57958868delA								IMPAD1 (52441 upstream) : C8orf71 (233234 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	58440252	58440252	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58440252delT								C8orf71 (242964 upstream) : FAM110B (466861 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	58821665	58821665	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:58821665delA								C8orf71 (624377 upstream) : FAM110B (85448 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	59090023	59090023	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59090023delT								FAM110B (27746 upstream) : UBXN2B (233800 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	59160300	59160301	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59160300_59160301delAA								FAM110B (98023 upstream) : UBXN2B (163522 downstream)																																			---	---	---	---
NSMAF	8439	broad.mit.edu	37	8	59500894	59500895	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59500894_59500895delTT	uc003xtt.2	-						NSMAF_uc011lee.1_Intron	NM_003580	NP_003571			neutral sphingomyelinase (N-SMase) activation						ceramide metabolic process	cytoplasm|soluble fraction	protein binding|receptor signaling protein activity			ovary(1)	1		all_lung(136;0.174)|Lung NSC(129;0.2)																---	---	---	---
NSMAF	8439	broad.mit.edu	37	8	59520477	59520477	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59520477delA	uc003xtt.2	-						NSMAF_uc011lee.1_Intron|NSMAF_uc003xtu.2_Intron	NM_003580	NP_003571			neutral sphingomyelinase (N-SMase) activation						ceramide metabolic process	cytoplasm|soluble fraction	protein binding|receptor signaling protein activity			ovary(1)	1		all_lung(136;0.174)|Lung NSC(129;0.2)																---	---	---	---
Unknown	0	broad.mit.edu	37	8	59598866	59598866	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59598866delA								NSMAF (26462 upstream) : TOX (119111 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	60127078	60127078	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60127078delT								TOX (95311 upstream) : CA8 (974345 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	60278429	60278429	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:60278429delT								TOX (246662 upstream) : CA8 (822994 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	61024229	61024230	+	IGR	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61024229_61024230delTC								TOX (992462 upstream) : CA8 (77193 downstream)																																			---	---	---	---
CA8	767	broad.mit.edu	37	8	61119503	61119503	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61119503delA	uc003xtz.1	-							NM_004056	NP_004047			carbonic anhydrase VIII						one-carbon metabolic process		carbonate dehydratase activity|zinc ion binding				0		all_cancers(86;0.172)|all_epithelial(80;0.0383)|all_lung(136;0.0413)|Lung NSC(129;0.0474)																---	---	---	---
CA8	767	broad.mit.edu	37	8	61189919	61189920	+	Intron	DEL	TT	-	-	rs113659462		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61189919_61189920delTT	uc003xtz.1	-						CA8_uc003xua.1_Intron|CA8_uc003xub.2_Intron	NM_004056	NP_004047			carbonic anhydrase VIII						one-carbon metabolic process		carbonate dehydratase activity|zinc ion binding				0		all_cancers(86;0.172)|all_epithelial(80;0.0383)|all_lung(136;0.0413)|Lung NSC(129;0.0474)																---	---	---	---
Unknown	0	broad.mit.edu	37	8	61586035	61586036	+	IGR	DEL	TT	-	-	rs35995813		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61586035_61586036delTT								RAB2A (52406 upstream) : CHD7 (5303 downstream)																																			---	---	---	---
CHD7	55636	broad.mit.edu	37	8	61593259	61593259	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61593259delT	uc003xue.2	+							NM_017780	NP_060250			chromodomain helicase DNA binding protein 7						central nervous system development|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	nucleus	ATP binding|chromatin binding|DNA binding|helicase activity			ovary(4)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|pancreas(1)	9		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)															---	---	---	---
CHD7	55636	broad.mit.edu	37	8	61735360	61735360	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61735360delA	uc003xue.2	+						CHD7_uc003xuf.2_Intron	NM_017780	NP_060250			chromodomain helicase DNA binding protein 7						central nervous system development|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	nucleus	ATP binding|chromatin binding|DNA binding|helicase activity			ovary(4)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|pancreas(1)	9		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	61945613	61945620	+	IGR	DEL	AGAAAGAT	-	-	rs60907426		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61945613_61945620delAGAAAGAT								CHD7 (166150 upstream) : CLVS1 (254905 downstream)																																			---	---	---	---
ASPH	444	broad.mit.edu	37	8	62583320	62583320	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62583320delA	uc003xuj.2	-						ASPH_uc011leg.1_Intron|ASPH_uc003xuo.2_Intron|ASPH_uc011leh.1_Intron|ASPH_uc003xul.2_Intron|ASPH_uc011lei.1_Intron|ASPH_uc011lej.1_Intron|ASPH_uc003xun.2_Intron|ASPH_uc011lek.1_Intron|ASPH_uc003xum.2_Intron|ASPH_uc011lel.1_Intron|ASPH_uc011lem.1_Intron	NM_004318	NP_004309			aspartate beta-hydroxylase isoform a						muscle contraction	integral to endoplasmic reticulum membrane	calcium ion binding|electron carrier activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity|structural constituent of muscle			ovary(3)	3	Lung SC(2;0.153)	Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101)			L-Aspartic Acid(DB00128)|Succinic acid(DB00139)													---	---	---	---
Unknown	0	broad.mit.edu	37	8	62726023	62726023	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62726023delA								ASPH (98824 upstream) : NKAIN3 (435478 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	62797317	62797317	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:62797317delT								ASPH (170118 upstream) : NKAIN3 (364184 downstream)																																			---	---	---	---
NKAIN3	286183	broad.mit.edu	37	8	63165169	63165169	+	Intron	DEL	T	-	-	rs34899376		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63165169delT	uc010lyq.1	+							NM_173688	NP_775959			Na+/K+ transporting ATPase interacting 3							integral to membrane|plasma membrane					0	Breast(64;0.127)	Lung NSC(129;0.187)																---	---	---	---
NKAIN3	286183	broad.mit.edu	37	8	63243283	63243283	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63243283delT	uc010lyq.1	+							NM_173688	NP_775959			Na+/K+ transporting ATPase interacting 3							integral to membrane|plasma membrane					0	Breast(64;0.127)	Lung NSC(129;0.187)																---	---	---	---
Unknown	0	broad.mit.edu	37	8	64035866	64035866	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64035866delA								TTPA (37254 upstream) : YTHDF3 (45255 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	64522320	64522320	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:64522320delT								YTHDF3 (396975 upstream) : MIR124-2 (769386 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	65107028	65107028	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65107028delT								YTHDF3 (981683 upstream) : MIR124-2 (184678 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	65372270	65372270	+	IGR	DEL	T	-	-	rs11302353		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65372270delT								MIR124-2 (80456 upstream) : LOC401463 (114598 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	65775920	65775920	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65775920delA								CYP7B1 (64572 upstream) : ARMC1 (739152 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	66402108	66402109	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66402108_66402109delAA								CYP7B1 (690760 upstream) : ARMC1 (112963 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	66441941	66441941	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66441941delT	uc003xvk.1	-											Homo sapiens cDNA FLJ37641 fis, clone BRHIP2000087.																														---	---	---	---
MTFR1	9650	broad.mit.edu	37	8	66563901	66563901	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66563901delT	uc003xvm.2	+						MTFR1_uc011lep.1_Intron	NM_014637	NP_055452			mitochondrial fission regulator 1 isoform 1							mitochondrion|plasma membrane				pancreas(1)	1			Epithelial(68;0.0526)|BRCA - Breast invasive adenocarcinoma(89;0.156)|all cancers(69;0.171)|OV - Ovarian serous cystadenocarcinoma(28;0.194)															---	---	---	---
MTFR1	9650	broad.mit.edu	37	8	66607583	66607583	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66607583delT	uc003xvm.2	+						MTFR1_uc011lep.1_Intron|MTFR1_uc003xvn.2_Intron|MTFR1_uc003xvo.1_Intron	NM_014637	NP_055452			mitochondrial fission regulator 1 isoform 1							mitochondrion|plasma membrane				pancreas(1)	1			Epithelial(68;0.0526)|BRCA - Breast invasive adenocarcinoma(89;0.156)|all cancers(69;0.171)|OV - Ovarian serous cystadenocarcinoma(28;0.194)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	67202810	67202810	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67202810delT								CRH (112112 upstream) : RRS1 (138453 downstream)																																			---	---	---	---
CSPP1	79848	broad.mit.edu	37	8	68044403	68044403	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68044403delA	uc003xxi.2	+						CSPP1_uc003xxg.1_Intron|CSPP1_uc003xxh.1_Intron|CSPP1_uc003xxj.2_Intron|CSPP1_uc003xxk.2_Intron	NM_001077204	NP_001070672			centrosome spindle pole associated protein 1							centrosome|microtubule|spindle				ovary(3)|breast(2)	5	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153)															---	---	---	---
CSPP1	79848	broad.mit.edu	37	8	68066152	68066152	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68066152delT	uc003xxi.2	+						CSPP1_uc003xxg.1_Intron|CSPP1_uc003xxh.1_Intron|CSPP1_uc003xxj.2_Intron|CSPP1_uc003xxk.2_Intron	NM_001077204	NP_001070672			centrosome spindle pole associated protein 1							centrosome|microtubule|spindle				ovary(3)|breast(2)	5	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153)															---	---	---	---
CSPP1	79848	broad.mit.edu	37	8	68078870	68078870	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68078870delT	uc003xxi.2	+						CSPP1_uc003xxj.2_Intron|CSPP1_uc003xxk.2_Intron|CSPP1_uc010lyw.2_Intron	NM_001077204	NP_001070672			centrosome spindle pole associated protein 1							centrosome|microtubule|spindle				ovary(3)|breast(2)	5	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153)															---	---	---	---
ARFGEF1	10565	broad.mit.edu	37	8	68192227	68192227	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68192227delA	uc003xxo.1	-							NM_006421	NP_006412			brefeldin A-inhibited guanine						exocytosis|regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity|myosin binding			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|kidney(1)	8	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)															---	---	---	---
ARFGEF1	10565	broad.mit.edu	37	8	68193765	68193765	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68193765delA	uc003xxo.1	-							NM_006421	NP_006412			brefeldin A-inhibited guanine						exocytosis|regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity|myosin binding			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|kidney(1)	8	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)															---	---	---	---
CPA6	57094	broad.mit.edu	37	8	68351825	68351825	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68351825delA	uc003xxq.3	-						CPA6_uc003xxr.3_Intron	NM_020361	NP_065094			carboxypeptidase A6 isoform 1 precursor						proteolysis	proteinaceous extracellular matrix	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2			Epithelial(68;0.04)|OV - Ovarian serous cystadenocarcinoma(28;0.0593)|all cancers(69;0.136)															---	---	---	---
CPA6	57094	broad.mit.edu	37	8	68453324	68453324	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68453324delA	uc003xxq.3	-						CPA6_uc003xxr.3_Intron|CPA6_uc003xxs.2_Intron	NM_020361	NP_065094			carboxypeptidase A6 isoform 1 precursor						proteolysis	proteinaceous extracellular matrix	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2			Epithelial(68;0.04)|OV - Ovarian serous cystadenocarcinoma(28;0.0593)|all cancers(69;0.136)															---	---	---	---
CPA6	57094	broad.mit.edu	37	8	68480978	68480978	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68480978delT	uc003xxq.3	-						CPA6_uc003xxr.3_Intron|CPA6_uc003xxs.2_Intron	NM_020361	NP_065094			carboxypeptidase A6 isoform 1 precursor						proteolysis	proteinaceous extracellular matrix	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2			Epithelial(68;0.04)|OV - Ovarian serous cystadenocarcinoma(28;0.0593)|all cancers(69;0.136)															---	---	---	---
CPA6	57094	broad.mit.edu	37	8	68486434	68486434	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68486434delA	uc003xxq.3	-						CPA6_uc003xxr.3_Intron|CPA6_uc003xxs.2_Intron	NM_020361	NP_065094			carboxypeptidase A6 isoform 1 precursor						proteolysis	proteinaceous extracellular matrix	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2			Epithelial(68;0.04)|OV - Ovarian serous cystadenocarcinoma(28;0.0593)|all cancers(69;0.136)															---	---	---	---
C8orf34	116328	broad.mit.edu	37	8	69684016	69684016	+	Intron	DEL	A	-	-	rs114790396	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69684016delA	uc010lyz.2	+						C8orf34_uc003xyb.2_Intron	NM_052958	NP_443190			hypothetical protein LOC116328						signal transduction		cAMP-dependent protein kinase regulator activity			large_intestine(1)	1			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)															---	---	---	---
C8orf34	116328	broad.mit.edu	37	8	69699867	69699868	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69699867_69699868delAA	uc010lyz.2	+						C8orf34_uc003xyb.2_Intron	NM_052958	NP_443190			hypothetical protein LOC116328						signal transduction		cAMP-dependent protein kinase regulator activity			large_intestine(1)	1			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	69912070	69912071	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69912070_69912071insA	uc003xyc.1	-											Homo sapiens cDNA FLJ30952 fis, clone HCASM1000130.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	69987742	69987742	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69987742delA	uc003xyc.1	-											Homo sapiens cDNA FLJ30952 fis, clone HCASM1000130.																														---	---	---	---
XKR9	389668	broad.mit.edu	37	8	71593234	71593234	+	5'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71593234delT	uc003xyq.2	+	3					XKR9_uc010lze.2_5'UTR|XKR9_uc010lzd.2_5'UTR	NM_001011720	NP_001011720			XK, Kell blood group complex subunit-related							integral to membrane				ovary(1)|skin(1)	2	Breast(64;0.0716)		Epithelial(68;0.00301)|all cancers(69;0.0165)|OV - Ovarian serous cystadenocarcinoma(28;0.0524)|BRCA - Breast invasive adenocarcinoma(89;0.166)															---	---	---	---
XKR9	389668	broad.mit.edu	37	8	71606343	71606343	+	Intron	DEL	C	-	-	rs75548454		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:71606343delC	uc003xyq.2	+						XKR9_uc010lze.2_Intron|XKR9_uc010lzd.2_Intron	NM_001011720	NP_001011720			XK, Kell blood group complex subunit-related							integral to membrane				ovary(1)|skin(1)	2	Breast(64;0.0716)		Epithelial(68;0.00301)|all cancers(69;0.0165)|OV - Ovarian serous cystadenocarcinoma(28;0.0524)|BRCA - Breast invasive adenocarcinoma(89;0.166)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	72410890	72410890	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72410890delC	uc003xyw.2	-											Homo sapiens cDNA clone IMAGE:5264099.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	72494408	72494408	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72494408delG								EYA1 (219941 upstream) : MSC (259369 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	72596267	72596267	+	IGR	DEL	A	-	-	rs77075098		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72596267delA								EYA1 (321800 upstream) : MSC (157510 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	72890286	72890287	+	Intron	INS	-	TACT	TACT			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:72890286_72890287insTACT	uc011lff.1	+						uc003xyy.2_Intron					Homo sapiens cDNA FLJ41321 fis, clone BRAMY2045299.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	73025129	73025129	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73025129delT								TRPA1 (37310 upstream) : KCNB2 (424497 downstream)																																			---	---	---	---
KCNB2	9312	broad.mit.edu	37	8	73557378	73557379	+	Intron	DEL	CA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73557378_73557379delCA	uc003xzb.2	+							NM_004770	NP_004761			potassium voltage-gated channel, Shab-related						regulation of smooth muscle contraction	voltage-gated potassium channel complex	delayed rectifier potassium channel activity|protein binding			skin(3)|large_intestine(1)|pancreas(1)|ovary(1)|central_nervous_system(1)	7	Breast(64;0.137)		Epithelial(68;0.105)															---	---	---	---
RDH10	157506	broad.mit.edu	37	8	74210536	74210536	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74210536delT	uc003xzi.2	+						RDH10_uc003xzj.2_Intron	NM_172037	NP_742034			retinol dehydrogenase 10						retinal metabolic process|retinol metabolic process|visual perception	endoplasmic reticulum membrane|integral to membrane|microsome	binding|NADP-retinol dehydrogenase activity|retinol dehydrogenase activity				0	Breast(64;0.0954)		Epithelial(68;0.0105)|all cancers(69;0.0465)|BRCA - Breast invasive adenocarcinoma(89;0.0608)															---	---	---	---
RDH10	157506	broad.mit.edu	37	8	74221321	74221322	+	Intron	INS	-	T	T	rs145466922	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74221321_74221322insT	uc003xzi.2	+						RDH10_uc003xzj.2_Intron	NM_172037	NP_742034			retinol dehydrogenase 10						retinal metabolic process|retinol metabolic process|visual perception	endoplasmic reticulum membrane|integral to membrane|microsome	binding|NADP-retinol dehydrogenase activity|retinol dehydrogenase activity				0	Breast(64;0.0954)		Epithelial(68;0.0105)|all cancers(69;0.0465)|BRCA - Breast invasive adenocarcinoma(89;0.0608)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	74307570	74307571	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74307570_74307571delAA								RDH10 (70056 upstream) : STAU2 (25035 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	74805128	74805128	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74805128delA								UBE2W (14018 upstream) : TCEB1 (53506 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	74805912	74805912	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74805912delA								UBE2W (14802 upstream) : TCEB1 (52722 downstream)																																			---	---	---	---
TCEB1	6921	broad.mit.edu	37	8	74865896	74865896	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74865896delA	uc003xzx.1	-						TCEB1_uc003xzy.1_Intron|TCEB1_uc003xzz.1_Intron|TCEB1_uc003yaa.1_Intron	NM_005648	NP_005639			elongin C						interspecies interaction between organisms|positive regulation of viral transcription|regulation of transcription from RNA polymerase II promoter|transcription elongation from RNA polymerase II promoter|ubiquitin-dependent protein catabolic process|viral reproduction	cytosol|nucleoplasm	protein binding				0	Breast(64;0.0311)		Epithelial(68;0.0136)|all cancers(69;0.0431)|BRCA - Breast invasive adenocarcinoma(89;0.0499)															---	---	---	---
TCEB1	6921	broad.mit.edu	37	8	74878724	74878727	+	Intron	DEL	TTTT	-	-	rs66903607		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74878724_74878727delTTTT	uc003xzx.1	-						TCEB1_uc003xzy.1_Intron|TCEB1_uc003xzz.1_Intron|TCEB1_uc003yaa.1_Intron	NM_005648	NP_005639			elongin C						interspecies interaction between organisms|positive regulation of viral transcription|regulation of transcription from RNA polymerase II promoter|transcription elongation from RNA polymerase II promoter|ubiquitin-dependent protein catabolic process|viral reproduction	cytosol|nucleoplasm	protein binding				0	Breast(64;0.0311)		Epithelial(68;0.0136)|all cancers(69;0.0431)|BRCA - Breast invasive adenocarcinoma(89;0.0499)															---	---	---	---
TCEB1	6921	broad.mit.edu	37	8	74881542	74881542	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74881542delT	uc003xzx.1	-						TCEB1_uc003xzy.1_Intron|TCEB1_uc003xzz.1_Intron|TCEB1_uc003yaa.1_Intron	NM_005648	NP_005639			elongin C						interspecies interaction between organisms|positive regulation of viral transcription|regulation of transcription from RNA polymerase II promoter|transcription elongation from RNA polymerase II promoter|ubiquitin-dependent protein catabolic process|viral reproduction	cytosol|nucleoplasm	protein binding				0	Breast(64;0.0311)		Epithelial(68;0.0136)|all cancers(69;0.0431)|BRCA - Breast invasive adenocarcinoma(89;0.0499)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	74996094	74996094	+	IGR	DEL	T	-	-	rs113368652		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74996094delT								LY96 (54789 upstream) : JPH1 (150847 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	75597001	75597001	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75597001delT	uc003yaj.1	+											Homo sapiens cDNA FLJ39080 fis, clone NT2RP7018197.																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	76298169	76298169	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76298169delT								CRISPLD1 (351378 upstream) : HNF4G (22014 downstream)																																			---	---	---	---
HNF4G	3174	broad.mit.edu	37	8	76373333	76373333	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76373333delT	uc003yaq.2	+						HNF4G_uc003yap.1_Intron	NM_004133	NP_004124			hepatocyte nuclear factor 4, gamma						endocrine pancreas development|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)	1	Breast(64;0.0448)		BRCA - Breast invasive adenocarcinoma(89;0.161)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	76710612	76710613	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:76710612_76710613insA								HNF4G (231553 upstream) : LOC100192378 (812502 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	77279204	77279205	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77279204_77279205delTT								HNF4G (800145 upstream) : LOC100192378 (243910 downstream)																																			---	---	---	---
LOC100192378	100192378	broad.mit.edu	37	8	77531833	77531833	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77531833delT	uc003yas.3	-							NR_024360				Homo sapiens cDNA clone IMAGE:4811567.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	77779765	77779765	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77779765delT								ZFHX4 (245 upstream) : PEX2 (112731 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	78153996	78153996	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:78153996delA								PEX2 (241472 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	79262505	79262505	+	IGR	DEL	A	-	-	rs75937155		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79262505delA								None (None upstream) : PKIA (165831 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	79302710	79302710	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:79302710delT								None (None upstream) : PKIA (125626 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	80326317	80326318	+	IGR	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80326317_80326318insG								IL7 (608559 upstream) : STMN2 (197062 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	80809972	80809972	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:80809972delA								HEY1 (129874 upstream) : MRPS28 (21124 downstream)																																			---	---	---	---
TPD52	7163	broad.mit.edu	37	8	81024817	81024817	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81024817delA	uc003ybs.1	-						TPD52_uc010lzs.1_Intron|TPD52_uc003ybt.1_Intron	NM_001025253	NP_001020424			tumor protein D52 isoform 2						anatomical structure morphogenesis|B cell differentiation|secretion	endoplasmic reticulum|perinuclear region of cytoplasm	calcium ion binding|protein heterodimerization activity|protein homodimerization activity			ovary(1)	1	all_epithelial(4;1.13e-09)|Lung NSC(7;9.71e-07)|all_lung(9;3.75e-06)	Lung NSC(129;3.55e-06)|all_lung(136;1.53e-05)|Acute lymphoblastic leukemia(644;0.158)	BRCA - Breast invasive adenocarcinoma(6;0.00181)|Epithelial(68;0.0149)|all cancers(69;0.0612)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	81304865	81304866	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81304865_81304866delAA								TPD52 (221029 upstream) : ZBTB10 (92988 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	81319365	81319365	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81319365delA								TPD52 (235529 upstream) : ZBTB10 (78489 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	81350240	81350240	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81350240delA								TPD52 (266404 upstream) : ZBTB10 (47614 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	81472059	81472060	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81472059_81472060delAA								ZBTB10 (37451 upstream) : ZNF704 (78709 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	82144640	82144641	+	IGR	INS	-	TG	TG			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82144640_82144641insTG								PAG1 (120337 upstream) : FABP5 (48144 downstream)																																			---	---	---	---
FABP5	2171	broad.mit.edu	37	8	82196888	82196888	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82196888delT	uc003yca.1	+	4						NM_001444	NP_001435			fatty acid binding protein 5						epidermis development	cytoplasm	fatty acid binding|protein binding|transporter activity				0	Lung NSC(7;3.57e-05)|all_lung(9;0.00011)		Epithelial(68;0.102)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	82487160	82487160	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82487160delT								FABP12 (43610 upstream) : IMPA1 (81991 downstream)																																			---	---	---	---
RALYL	138046	broad.mit.edu	37	8	85159087	85159087	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85159087delA	uc003ycq.3	+						RALYL_uc003ycr.3_Intron|RALYL_uc003ycs.3_Intron|RALYL_uc010lzy.2_Intron|RALYL_uc003yct.3_Intron	NM_001100392	NP_001093862			RALY RNA binding protein-like isoform 2								identical protein binding|nucleotide binding|RNA binding			ovary(1)	1																		---	---	---	---
RALYL	138046	broad.mit.edu	37	8	85199868	85199868	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85199868delA	uc003ycq.3	+						RALYL_uc003ycr.3_Intron|RALYL_uc003ycs.3_Intron|RALYL_uc010lzy.2_Intron|RALYL_uc003yct.3_Intron	NM_001100392	NP_001093862			RALY RNA binding protein-like isoform 2								identical protein binding|nucleotide binding|RNA binding			ovary(1)	1																		---	---	---	---
RALYL	138046	broad.mit.edu	37	8	85766073	85766073	+	Intron	DEL	C	-	-	rs2042763	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:85766073delC	uc003ycq.3	+						RALYL_uc003ycr.3_Intron|RALYL_uc003ycs.3_Intron|RALYL_uc010lzy.2_Intron|RALYL_uc003yct.3_Intron|RALYL_uc003ycu.3_Intron|RALYL_uc003ycv.3_Intron	NM_001100392	NP_001093862			RALY RNA binding protein-like isoform 2								identical protein binding|nucleotide binding|RNA binding			ovary(1)	1																		---	---	---	---
C8orf59	401466	broad.mit.edu	37	8	86129455	86129456	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86129455_86129456delTT	uc010mac.1	-						C8orf59_uc003ydd.2_Intron|C8orf59_uc010mad.1_Intron|C8orf59_uc003yde.2_Intron|C8orf59_uc011lfu.1_Intron	NM_001099670	NP_001093140			hypothetical protein LOC401466												0																		---	---	---	---
CA13	377677	broad.mit.edu	37	8	86195147	86195147	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86195147delT	uc003ydg.2	+	7					CA13_uc003ydf.1_Intron	NM_198584	NP_940986			carbonic anhydrase XIII						one-carbon metabolic process		carbonate dehydratase activity|zinc ion binding				0																		---	---	---	---
CA13	377677	broad.mit.edu	37	8	86196369	86196369	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86196369delT	uc003ydf.1	+											Homo sapiens cDNA FLJ36434 fis, clone THYMU2012002.						one-carbon metabolic process		carbonate dehydratase activity|zinc ion binding				0																		---	---	---	---
CA2	760	broad.mit.edu	37	8	86389131	86389134	+	Intron	DEL	TTTT	-	-	rs111230295		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86389131_86389134delTTTT	uc003ydk.2	+							NM_000067	NP_000058			carbonic anhydrase II						one-carbon metabolic process	apical part of cell	carbonate dehydratase activity|zinc ion binding			central_nervous_system(1)	1					Acetazolamide(DB00819)|Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Brinzolamide(DB01194)|Chlorothiazide(DB00880)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Dorzolamide(DB00869)|Ethinamate(DB01031)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Topiramate(DB00273)|Trichlormethiazide(DB01021)													---	---	---	---
Unknown	0	broad.mit.edu	37	8	86516936	86516936	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86516936delA								CA2 (123215 upstream) : REXO1L1 (51628 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	86521562	86521562	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86521562delT								CA2 (127841 upstream) : REXO1L1 (47002 downstream)																																			---	---	---	---
CNBD1	168975	broad.mit.edu	37	8	88003621	88003622	+	Intron	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88003621_88003622delTC	uc003ydy.2	+							NM_173538	NP_775809			cyclic nucleotide binding domain containing 1											ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	88522197	88522198	+	IGR	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88522197_88522198delAC								CNBD1 (127242 upstream) : DCAF4L2 (360775 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	88529934	88529935	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:88529934_88529935delTT								CNBD1 (134979 upstream) : DCAF4L2 (353038 downstream)																																			---	---	---	---
MMP16	4325	broad.mit.edu	37	8	89190565	89190565	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89190565delA	uc003yeb.3	-						MMP16_uc003yec.2_Intron	NM_005941	NP_005932			matrix metalloproteinase 16 isoform 1						collagen catabolic process|proteolysis	cell surface|integral to plasma membrane|proteinaceous extracellular matrix	calcium ion binding|enzyme activator activity|metalloendopeptidase activity|zinc ion binding			upper_aerodigestive_tract(2)|ovary(2)|central_nervous_system(1)|urinary_tract(1)|skin(1)|kidney(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	89866514	89866514	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89866514delT								MMP16 (526797 upstream) : RIPK2 (903461 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	90380105	90380106	+	IGR	DEL	AA	-	-	rs75480132		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90380105_90380106delAA								None (None upstream) : RIPK2 (389869 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	90737910	90737915	+	Intron	DEL	AGAACA	-	-	rs34790922		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90737910_90737915delAGAACA	uc003yed.2	-											full-length cDNA clone CS0DL001YK24 of B cells (Ramos cell line) Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	8	91359725	91359725	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91359725delT								CALB1 (252038 upstream) : TMEM64 (274498 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	91560378	91560378	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91560378delT								CALB1 (452691 upstream) : TMEM64 (73845 downstream)																																			---	---	---	---
TMEM64	169200	broad.mit.edu	37	8	91637754	91637754	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91637754delA	uc003yen.2	-	3					TMEM64_uc003yeo.2_3'UTR|TMEM64_uc011lgf.1_3'UTR	NM_001008495	NP_001008495			transmembrane protein 64 isoform 1							integral to membrane					0			BRCA - Breast invasive adenocarcinoma(11;0.0598)															---	---	---	---
OTUD6B	51633	broad.mit.edu	37	8	92086233	92086233	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92086233delA	uc003yeu.3	+						OTUD6B_uc011lgh.1_Intron	NM_016023	NP_057107			OTU domain containing 6B											ovary(2)|lung(1)	3			BRCA - Breast invasive adenocarcinoma(11;0.0187)															---	---	---	---
RUNX1T1	862	broad.mit.edu	37	8	92987997	92987997	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92987997delT	uc003yfd.2	-						RUNX1T1_uc003yfc.1_Intron|RUNX1T1_uc003yfe.1_Intron|RUNX1T1_uc010mao.2_Intron|RUNX1T1_uc011lgi.1_Intron|RUNX1T1_uc010man.1_Intron|RUNX1T1_uc003yfb.1_Intron	NM_175634	NP_783552			acute myelogenous leukemia 1 translocation 1						generation of precursor metabolites and energy	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(9)|large_intestine(3)|breast(2)|central_nervous_system(1)|pancreas(1)	16			BRCA - Breast invasive adenocarcinoma(11;0.0141)															---	---	---	---
RUNX1T1	862	broad.mit.edu	37	8	92998987	92998987	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:92998987delT	uc003yfd.2	-						RUNX1T1_uc003yfc.1_Intron|RUNX1T1_uc003yfe.1_Intron|RUNX1T1_uc010mao.2_Intron|RUNX1T1_uc011lgi.1_Intron|RUNX1T1_uc010man.1_Intron|RUNX1T1_uc003yfb.1_Intron	NM_175634	NP_783552			acute myelogenous leukemia 1 translocation 1						generation of precursor metabolites and energy	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(9)|large_intestine(3)|breast(2)|central_nervous_system(1)|pancreas(1)	16			BRCA - Breast invasive adenocarcinoma(11;0.0141)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	93244925	93244926	+	IGR	DEL	TG	-	-	rs71920194		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93244925_93244926delTG								RUNX1T1 (137219 upstream) : C8orf83 (650939 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	93367890	93367890	+	IGR	DEL	T	-	-	rs73315719	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93367890delT								RUNX1T1 (260184 upstream) : C8orf83 (527975 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	93760651	93760651	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93760651delT	uc003yfj.1	-											Homo sapiens cDNA FLJ46284 fis, clone TESTI4031818.																														---	---	---	---
C8orf83	286144	broad.mit.edu	37	8	93898972	93898972	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93898972delA	uc003yfk.3	-						C8orf83_uc003yfr.3_Intron|C8orf83_uc010map.2_Intron|C8orf83_uc003yfo.3_Intron|C8orf83_uc003yfn.3_Intron|C8orf83_uc003yfq.3_Intron|C8orf83_uc003yfl.3_Intron|C8orf83_uc003yfm.3_Intron	NR_015339				RecName: Full=UPF0599 protein C8orf83;							endoplasmic reticulum membrane|integral to membrane					0																		---	---	---	---
C8orf83	286144	broad.mit.edu	37	8	93931004	93931004	+	Intron	DEL	C	-	-	rs139658932		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93931004delC	uc003yfk.3	-						C8orf83_uc003yfr.3_Intron|C8orf83_uc010map.2_Intron|C8orf83_uc003yfo.3_Intron|C8orf83_uc003yfn.3_Intron|C8orf83_uc003yfq.3_Intron|C8orf83_uc003yfl.3_Intron|C8orf83_uc003yfm.3_Intron	NR_015339				RecName: Full=UPF0599 protein C8orf83;							endoplasmic reticulum membrane|integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	94664993	94664994	+	IGR	INS	-	TAAG	TAAG	rs143797009	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94664993_94664994insTAAG								C8orf83 (635092 upstream) : FAM92A1 (47779 downstream)																																			---	---	---	---
RBM12B	389677	broad.mit.edu	37	8	94745548	94745548	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94745548delA	uc003yfz.2	-	3						NM_203390	NP_976324			RNA binding motif protein 12B								nucleotide binding|RNA binding				0	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	94893231	94893231	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94893231delA								TMEM67 (62885 upstream) : PDP1 (35852 downstream)																																			---	---	---	---
RAD54B	25788	broad.mit.edu	37	8	95440559	95440559	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95440559delA	uc003ygk.2	-						RAD54B_uc010may.1_Intron|RAD54B_uc003ygl.1_Intron	NM_012415	NP_036547			RAD54 homolog B						double-strand break repair via homologous recombination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA translocase activity|protein binding			kidney(2)|lung(1)|skin(1)	4	Breast(36;4.5e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00217)										Direct_reversal_of_damage|Homologous_recombination					---	---	---	---
INTS8	55656	broad.mit.edu	37	8	95848640	95848640	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95848640delT	uc003yhb.2	+						INTS8_uc003yha.1_Intron|INTS8_uc011lgq.1_Intron|INTS8_uc011lgr.1_Intron|INTS8_uc010mba.2_Intron	NM_017864	NP_060334			integrator complex subunit 8						snRNA processing	integrator complex	protein binding				0	Breast(36;1.05e-06)																	---	---	---	---
Unknown	0	broad.mit.edu	37	8	96832461	96832461	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96832461delC								C8orf37 (551024 upstream) : GDF6 (322099 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	97208909	97208909	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97208909delA								GDF6 (35889 upstream) : UQCRB (30401 downstream)																																			---	---	---	---
PTDSS1	9791	broad.mit.edu	37	8	97324255	97324255	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97324255delT	uc003yht.1	+						PTDSS1_uc003yhu.1_Intron	NM_014754	NP_055569			phosphatidylserine synthase 1						phosphatidylserine biosynthetic process	integral to membrane	transferase activity			ovary(1)	1	Breast(36;6.18e-05)				Phosphatidylserine(DB00144)													---	---	---	---
MTDH	92140	broad.mit.edu	37	8	98735626	98735627	+	Intron	DEL	AA	-	-	rs76844933		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98735626_98735627delAA	uc003yhz.2	+						MTDH_uc010mbf.2_Intron	NM_178812	NP_848927			metadherin						lipopolysaccharide-mediated signaling pathway|negative regulation of apoptosis|negative regulation of transcription from RNA polymerase II promoter|positive regulation of angiogenesis|positive regulation of autophagy|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of protein kinase B signaling cascade	apical plasma membrane|endoplasmic reticulum membrane|integral to membrane|intercellular canaliculus|nuclear body|nuclear membrane|nucleolus|perinuclear region of cytoplasm|tight junction	NF-kappaB binding|RNA polymerase II transcription factor binding|transcription coactivator activity			liver(1)|central_nervous_system(1)	2	Breast(36;2.56e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.178)															---	---	---	---
LAPTM4B	55353	broad.mit.edu	37	8	98858556	98858556	+	Intron	DEL	T	-	-	rs113961837		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98858556delT	uc003yia.2	+						LAPTM4B_uc010mbg.2_Intron	NM_018407	NP_060877			lysosomal associated transmembrane protein 4						transport	endomembrane system|integral to membrane	protein binding			skin(1)	1	Breast(36;1.59e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.149)															---	---	---	---
MATN2	4147	broad.mit.edu	37	8	98890238	98890239	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98890238_98890239insA	uc003yic.2	+						MATN2_uc003yib.1_Intron|MATN2_uc010mbh.1_Intron|MATN2_uc003yid.2_Intron	NM_002380	NP_002371			matrilin 2 isoform a precursor							proteinaceous extracellular matrix	calcium ion binding			ovary(2)	2	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)															---	---	---	---
MATN2	4147	broad.mit.edu	37	8	98921175	98921175	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:98921175delT	uc003yic.2	+						MATN2_uc003yib.1_Intron|MATN2_uc010mbh.1_Intron|MATN2_uc003yid.2_Intron|MATN2_uc003yie.1_Intron	NM_002380	NP_002371			matrilin 2 isoform a precursor							proteinaceous extracellular matrix	calcium ion binding			ovary(2)	2	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)															---	---	---	---
MATN2	4147	broad.mit.edu	37	8	99007613	99007613	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99007613delT	uc003yic.2	+						MATN2_uc003yib.1_Intron|MATN2_uc010mbh.1_Intron|MATN2_uc003yid.2_Intron|MATN2_uc003yie.1_Intron|MATN2_uc010mbi.1_Intron	NM_002380	NP_002371			matrilin 2 isoform a precursor							proteinaceous extracellular matrix	calcium ion binding			ovary(2)	2	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)															---	---	---	---
STK3	6788	broad.mit.edu	37	8	99510366	99510367	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99510366_99510367delTT	uc003yip.2	-						STK3_uc003yio.2_Intron	NM_006281	NP_006272			serine/threonine kinase 3						apoptosis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of apoptosis	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein dimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity			lung(3)|ovary(1)	4	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)														---	---	---	---
STK3	6788	broad.mit.edu	37	8	99582854	99582854	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99582854delA	uc003yip.2	-						STK3_uc003yio.2_Intron|STK3_uc010mbm.1_Intron	NM_006281	NP_006272			serine/threonine kinase 3						apoptosis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of apoptosis	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein dimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity			lung(3)|ovary(1)	4	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)														---	---	---	---
STK3	6788	broad.mit.edu	37	8	99611675	99611675	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99611675delT	uc003yip.2	-						STK3_uc003yio.2_Intron|STK3_uc010mbm.1_Intron	NM_006281	NP_006272			serine/threonine kinase 3						apoptosis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of apoptosis	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein dimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity			lung(3)|ovary(1)	4	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)														---	---	---	---
STK3	6788	broad.mit.edu	37	8	99643888	99643889	+	Intron	INS	-	T	T	rs139111936	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99643888_99643889insT	uc003yip.2	-						STK3_uc003yio.2_Intron|STK3_uc010mbm.1_Intron	NM_006281	NP_006272			serine/threonine kinase 3						apoptosis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of apoptosis	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein dimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity			lung(3)|ovary(1)	4	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)														---	---	---	---
VPS13B	157680	broad.mit.edu	37	8	100447192	100447192	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100447192delA	uc003yiv.2	+						VPS13B_uc003yiw.2_Intron|VPS13B_uc003yiu.1_Intron|VPS13B_uc003yix.1_Intron	NM_017890	NP_060360			vacuolar protein sorting 13B isoform 5						protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)															---	---	---	---
VPS13B	157680	broad.mit.edu	37	8	100833879	100833879	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100833879delT	uc003yiv.2	+						VPS13B_uc003yiw.2_Intron	NM_017890	NP_060360			vacuolar protein sorting 13B isoform 5						protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)															---	---	---	---
VPS13B	157680	broad.mit.edu	37	8	100882406	100882406	+	Intron	DEL	T	-	-	rs113637410		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100882406delT	uc003yiv.2	+						VPS13B_uc003yiw.2_Intron	NM_017890	NP_060360			vacuolar protein sorting 13B isoform 5						protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	100917547	100917548	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100917547_100917548delAA								COX6C (11652 upstream) : RGS22 (55728 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	101688796	101688797	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101688796_101688797insT								SNX31 (26903 upstream) : PABPC1 (26347 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	101810071	101810071	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:101810071delT								PABPC1 (75756 upstream) : YWHAZ (120733 downstream)																																			---	---	---	---
ZNF706	51123	broad.mit.edu	37	8	102219198	102219199	+	5'Flank	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102219198_102219199delAA	uc003yka.2	-						ZNF706_uc003ykb.2_5'Flank	NM_001042510	NP_001035975			HSPC038 protein							intracellular	zinc ion binding			ovary(2)	2	all_cancers(14;3.3e-07)|all_epithelial(15;3.47e-09)|Lung NSC(17;3.44e-05)|all_lung(17;0.000117)		Epithelial(11;8.57e-11)|all cancers(13;1.43e-08)|OV - Ovarian serous cystadenocarcinoma(57;1.43e-05)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	102232335	102232335	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102232335delA								ZNF706 (14375 upstream) : NACAP1 (141687 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	102350083	102350083	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102350083delA								ZNF706 (132123 upstream) : NACAP1 (23939 downstream)																																			---	---	---	---
GRHL2	79977	broad.mit.edu	37	8	102678028	102678029	+	Intron	INS	-	TGAT	TGAT	rs141258646	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:102678028_102678029insTGAT	uc010mbu.2	+							NM_024915	NP_079191			transcription factor CP2-like 3							cytoplasm|nucleus	DNA binding			ovary(2)|skin(1)	3	all_cancers(14;4.39e-08)|all_epithelial(15;4.09e-10)|Lung NSC(17;7.11e-06)|all_lung(17;1.44e-05)		Epithelial(11;5.81e-09)|all cancers(13;3.81e-07)|OV - Ovarian serous cystadenocarcinoma(57;0.000213)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	103160823	103160823	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103160823delA								NCALD (23688 upstream) : RRM2B (55909 downstream)																																			---	---	---	---
UBR5	51366	broad.mit.edu	37	8	103275947	103275947	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103275947delT	uc003ykr.1	-						UBR5_uc003yks.1_Intron|UBR5_uc003ykq.2_Intron	NM_015902	NP_056986			ubiquitin protein ligase E3 component n-recognin						cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			lung(16)|ovary(4)|large_intestine(3)|breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	28	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	103488699	103488700	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103488699_103488700delTT								UBR5 (64204 upstream) : ODF1 (75148 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	103530298	103530298	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103530298delC								UBR5 (105803 upstream) : ODF1 (33550 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	103652548	103652548	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103652548delA								ODF1 (79303 upstream) : KLF10 (8457 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	103704852	103704853	+	IGR	INS	-	C	C	rs144902898	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103704852_103704853insC								KLF10 (36869 upstream) : AZIN1 (133684 downstream)																																			---	---	---	---
AZIN1	51582	broad.mit.edu	37	8	103846502	103846502	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103846502delA	uc003ykx.2	-						AZIN1_uc003yky.2_Intron	NM_015878	NP_056962			ornithine decarboxylase antizyme inhibitor						polyamine biosynthetic process|regulation of cellular amino acid metabolic process	cytosol	catalytic activity|protein binding				0	Lung NSC(17;0.000143)|all_lung(17;0.000294)		OV - Ovarian serous cystadenocarcinoma(57;0.000196)|STAD - Stomach adenocarcinoma(118;0.0414)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	104012449	104012449	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104012449delA								AZIN1 (136052 upstream) : ATP6V1C1 (20799 downstream)																																			---	---	---	---
RIMS2	9699	broad.mit.edu	37	8	104772172	104772172	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:104772172delA	uc003ylp.2	+							NM_001100117	NP_001093587			regulating synaptic membrane exocytosis 2						intracellular protein transport	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	15			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)												HNSCC(12;0.0054)			---	---	---	---
DPYS	1807	broad.mit.edu	37	8	105396273	105396274	+	Intron	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105396273_105396274delCT	uc003yly.3	-						DPYS_uc010mcf.1_Intron	NM_001385	NP_001376			dihydropyrimidinase						protein homotetramerization|pyrimidine nucleoside catabolic process|thymine catabolic process|uracil catabolic process	cytosol	dihydropyrimidinase activity|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2			OV - Ovarian serous cystadenocarcinoma(57;1.61e-06)|STAD - Stomach adenocarcinoma(118;0.229)															---	---	---	---
LRP12	29967	broad.mit.edu	37	8	105570985	105570986	+	Intron	DEL	AA	-	-	rs78839326		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105570985_105570986delAA	uc003yma.2	-						LRP12_uc003ymb.2_Intron|LRP12_uc003ymc.3_Intron	NM_013437	NP_038465			low density lipoprotein-related protein 12						endocytosis|regulation of growth	coated pit|integral to plasma membrane	low-density lipoprotein receptor activity|protein binding				0			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)															---	---	---	---
LRP12	29967	broad.mit.edu	37	8	105593972	105593972	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105593972delA	uc003yma.2	-						LRP12_uc003ymb.2_Intron|LRP12_uc003ymc.3_Intron	NM_013437	NP_038465			low density lipoprotein-related protein 12						endocytosis|regulation of growth	coated pit|integral to plasma membrane	low-density lipoprotein receptor activity|protein binding				0			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	105861723	105861724	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105861723_105861724delTG								LRP12 (260503 upstream) : ZFPM2 (469423 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	106833139	106833139	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:106833139delT								ZFPM2 (16374 upstream) : OXR1 (449334 downstream)																																			---	---	---	---
OXR1	55074	broad.mit.edu	37	8	107444518	107444518	+	Intron	DEL	C	-	-	rs76363699	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107444518delC	uc003ymf.2	+							NM_018002	NP_060472			oxidation resistance 1 isoform 1						cell wall macromolecule catabolic process|response to oxidative stress	mitochondrion					0			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)															---	---	---	---
OXR1	55074	broad.mit.edu	37	8	107510016	107510017	+	Intron	INS	-	TG	TG	rs139204547	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107510016_107510017insTG	uc011lht.1	+						OXR1_uc003ymf.2_Intron	NM_018002	NP_060472			oxidation resistance 1 isoform 1						cell wall macromolecule catabolic process|response to oxidative stress	mitochondrion					0			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	108071638	108071638	+	IGR	DEL	A	-	-	rs56347811		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108071638delA								ABRA (289166 upstream) : ANGPT1 (190073 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	108513589	108513589	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108513589delT								ANGPT1 (3335 upstream) : RSPO2 (397956 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	108534255	108534255	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108534255delT								ANGPT1 (24001 upstream) : RSPO2 (377290 downstream)																																			---	---	---	---
RSPO2	340419	broad.mit.edu	37	8	108966757	108966757	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108966757delT	uc003yms.2	-						RSPO2_uc003ymq.2_Intron|RSPO2_uc003ymr.2_Intron	NM_178565	NP_848660			R-spondin family, member 2 precursor						Wnt receptor signaling pathway	extracellular region	heparin binding			skin(3)|ovary(2)|pancreas(1)|lung(1)	7			OV - Ovarian serous cystadenocarcinoma(57;1.55e-09)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	109164806	109164806	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109164806delA								RSPO2 (68893 upstream) : EIF3E (49167 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	109410028	109410029	+	IGR	DEL	AA	-	-	rs36110124		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109410028_109410029delAA								EIF3E (149069 upstream) : TTC35 (45824 downstream)																																			---	---	---	---
TTC35	9694	broad.mit.edu	37	8	109462630	109462630	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:109462630delT	uc003ymw.1	+							NM_014673	NP_055488			tetratricopeptide repeat domain 35							endoplasmic reticulum|nucleus	binding			ovary(1)|central_nervous_system(1)	2			OV - Ovarian serous cystadenocarcinoma(57;2.34e-10)															---	---	---	---
PKHD1L1	93035	broad.mit.edu	37	8	110453445	110453445	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110453445delA	uc003yne.2	+							NM_177531	NP_803875			fibrocystin L precursor						immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)												HNSCC(38;0.096)			---	---	---	---
SYBU	55638	broad.mit.edu	37	8	110591951	110591951	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110591951delT	uc003ynj.3	-						SYBU_uc003yni.3_Intron|SYBU_uc003ynk.3_Intron|SYBU_uc010mco.2_Intron|SYBU_uc003ynl.3_Intron|SYBU_uc010mcp.2_Intron|SYBU_uc010mcq.2_Intron|SYBU_uc003yno.3_Intron|SYBU_uc010mcr.2_Intron|SYBU_uc003ynm.3_Intron|SYBU_uc003ynn.3_Intron|SYBU_uc010mcs.2_Intron|SYBU_uc010mct.2_Intron|SYBU_uc010mcu.2_Intron|SYBU_uc003ynp.3_Intron|SYBU_uc010mcv.2_Intron|SYBU_uc003ynh.3_Intron|SYBU_uc011lhw.1_Intron	NM_001099754	NP_001093224			Golgi-localized syntaphilin-related protein							cytoplasmic membrane-bounded vesicle|cytoskeleton|Golgi membrane|integral to membrane				ovary(1)	1																		---	---	---	---
SYBU	55638	broad.mit.edu	37	8	110644160	110644160	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110644160delT	uc003ynj.3	-						SYBU_uc003yni.3_Intron|SYBU_uc003ynk.3_Intron|SYBU_uc010mco.2_Intron|SYBU_uc003ynl.3_Intron|SYBU_uc010mcp.2_Intron|SYBU_uc010mcq.2_Intron|SYBU_uc003yno.3_Intron|SYBU_uc010mcr.2_Intron|SYBU_uc003ynm.3_Intron|SYBU_uc003ynn.3_Intron|SYBU_uc010mcs.2_Intron|SYBU_uc010mct.2_Intron|SYBU_uc010mcu.2_Intron|SYBU_uc003ynp.3_Intron|SYBU_uc010mcv.2_Intron	NM_001099754	NP_001093224			Golgi-localized syntaphilin-related protein							cytoplasmic membrane-bounded vesicle|cytoskeleton|Golgi membrane|integral to membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	111119443	111119444	+	IGR	INS	-	A	A	rs145119598	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111119443_111119444insA								KCNV1 (131367 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	111207697	111207697	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111207697delT								KCNV1 (219621 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	111397947	111397948	+	IGR	INS	-	TC	TC			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111397947_111397948insTC								KCNV1 (409871 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	111478381	111478381	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:111478381delT								KCNV1 (490305 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	112707981	112707982	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112707981_112707982delAA								None (None upstream) : CSMD3 (527179 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	112766390	112766391	+	IGR	DEL	TT	-	-	rs72103857		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:112766390_112766391delTT								None (None upstream) : CSMD3 (468770 downstream)																																			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	114217218	114217219	+	Intron	DEL	TT	-	-	rs77978749		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:114217218_114217219delTT	uc003ynu.2	-						CSMD3_uc003ynt.2_Intron|CSMD3_uc011lhx.1_Intron|CSMD3_uc010mcx.1_Intron	NM_198123	NP_937756			CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
Unknown	0	broad.mit.edu	37	8	115759183	115759183	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:115759183delT								None (None upstream) : TRPS1 (661542 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	115995117	115995118	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:115995117_115995118insT								None (None upstream) : TRPS1 (425607 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116170034	116170034	+	IGR	DEL	A	-	-	rs72102065		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116170034delA								None (None upstream) : TRPS1 (250691 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116246562	116246562	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116246562delA								None (None upstream) : TRPS1 (174163 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116252988	116252988	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116252988delA								None (None upstream) : TRPS1 (167737 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	116355697	116355697	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116355697delA								None (None upstream) : TRPS1 (65028 downstream)																																			---	---	---	---
TRPS1	7227	broad.mit.edu	37	8	116463552	116463552	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116463552delT	uc003ynz.2	-						TRPS1_uc011lhy.1_Intron|TRPS1_uc003yny.2_Intron|TRPS1_uc010mcy.2_Intron	NM_014112	NP_054831			zinc finger transcription factor TRPS1						negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)											Langer-Giedion_syndrome				---	---	---	---
TRPS1	7227	broad.mit.edu	37	8	116574062	116574063	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116574062_116574063delAA	uc003ynz.2	-						TRPS1_uc011lhy.1_Intron|TRPS1_uc003yny.2_Intron|TRPS1_uc010mcy.2_Intron	NM_014112	NP_054831			zinc finger transcription factor TRPS1						negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)											Langer-Giedion_syndrome				---	---	---	---
TRPS1	7227	broad.mit.edu	37	8	116625229	116625229	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:116625229delA	uc003ynz.2	-						TRPS1_uc011lhy.1_Intron|TRPS1_uc003yny.2_Intron|TRPS1_uc010mcy.2_Intron	NM_014112	NP_054831			zinc finger transcription factor TRPS1						negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)											Langer-Giedion_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	8	117099691	117099691	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117099691delT								TRPS1 (418463 upstream) : EIF3H (557365 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	117294653	117294653	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117294653delA								TRPS1 (613425 upstream) : EIF3H (362403 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	117420732	117420733	+	IGR	DEL	TT	-	-	rs75747612	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117420732_117420733delTT								TRPS1 (739504 upstream) : EIF3H (236323 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	117499017	117499017	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117499017delA								TRPS1 (817789 upstream) : EIF3H (158039 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	117500475	117500476	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117500475_117500476insA								TRPS1 (819247 upstream) : EIF3H (156580 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	117593870	117593870	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117593870delA								TRPS1 (912642 upstream) : EIF3H (63186 downstream)																																			---	---	---	---
EIF3H	8667	broad.mit.edu	37	8	117668365	117668366	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117668365_117668366delAA	uc003yoa.2	-						EIF3H_uc003yob.2_Intron	NM_003756	NP_003747			eukaryotic translation initiation factor 3,						regulation of translational initiation	cytosol|eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			lung(3)	3	all_cancers(13;3.98e-22)|Lung NSC(37;0.000183)|Ovarian(258;0.0172)																	---	---	---	---
Unknown	0	broad.mit.edu	37	8	117846285	117846285	+	IGR	DEL	T	-	-	rs71305446		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117846285delT								UTP23 (59366 upstream) : RAD21 (11889 downstream)																																			---	---	---	---
RAD21	5885	broad.mit.edu	37	8	117869182	117869182	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117869182delA	uc003yod.2	-							NM_006265	NP_006256			RAD21 homolog						apoptosis|cell division|chromosome segregation|double-strand break repair|mitotic metaphase/anaphase transition|mitotic prometaphase|protein localization to chromatin|reciprocal meiotic recombination|regulation of transcription from RNA polymerase II promoter	chromosome, centromeric region|cohesin complex|nuclear chromosome|nucleoplasm	protein binding			lung(1)|skin(1)	2	all_cancers(13;1.21e-21)|Lung NSC(37;0.000134)|Ovarian(258;0.0172)																	---	---	---	---
Unknown	0	broad.mit.edu	37	8	117918698	117918698	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117918698delT								RAD21 (31593 upstream) : C8orf85 (31766 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	117939621	117939621	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117939621delG								RAD21 (52516 upstream) : C8orf85 (10843 downstream)																																			---	---	---	---
SLC30A8	169026	broad.mit.edu	37	8	117994499	117994499	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:117994499delT	uc010mcz.2	+						SLC30A8_uc011lia.1_Intron|SLC30A8_uc003yog.2_Intron	NM_173851	NP_776250			solute carrier family 30 member 8						insulin secretion|positive regulation of insulin secretion|regulation of sequestering of zinc ion|regulation of vesicle-mediated transport|response to glucose stimulus|sequestering of zinc ion	integral to membrane|plasma membrane|secretory granule membrane|transport vesicle membrane	protein homodimerization activity|zinc ion transmembrane transporter activity			ovary(2)|skin(2)	4	all_cancers(13;2.11e-22)|Lung NSC(37;6.08e-05)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.203)															---	---	---	---
EXT1	2131	broad.mit.edu	37	8	119002411	119002411	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119002411delA	uc003yok.1	-							NM_000127	NP_000118			exostosin 1						glycosaminoglycan biosynthetic process|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|ossification|signal transduction|skeletal system development	Golgi membrane|integral to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|heparan sulfate N-acetylglucosaminyltransferase activity|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity			ovary(2)|lung(2)	4	all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.012)					Mis|N|F|S			exostoses|osteosarcoma			Hereditary_Multiple_Exostoses|Langer-Giedion_syndrome				---	---	---	---
SAMD12	401474	broad.mit.edu	37	8	119229253	119229254	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119229253_119229254delTT	uc010mda.1	-						SAMD12_uc010mdb.1_Intron	NM_001101676	NP_001095146			sterile alpha motif domain containing 12 isoform											ovary(1)	1	all_cancers(13;3.91e-25)|Lung NSC(37;1.13e-07)|Ovarian(258;0.0249)		STAD - Stomach adenocarcinoma(47;0.00391)															---	---	---	---
SAMD12	401474	broad.mit.edu	37	8	119264169	119264169	+	Intron	DEL	A	-	-	rs78669004		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119264169delA	uc010mda.1	-						SAMD12_uc010mdb.1_Intron	NM_001101676	NP_001095146			sterile alpha motif domain containing 12 isoform											ovary(1)	1	all_cancers(13;3.91e-25)|Lung NSC(37;1.13e-07)|Ovarian(258;0.0249)		STAD - Stomach adenocarcinoma(47;0.00391)															---	---	---	---
SAMD12	401474	broad.mit.edu	37	8	119380815	119380815	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119380815delA	uc010mda.1	-						SAMD12_uc010mdb.1_Intron	NM_001101676	NP_001095146			sterile alpha motif domain containing 12 isoform											ovary(1)	1	all_cancers(13;3.91e-25)|Lung NSC(37;1.13e-07)|Ovarian(258;0.0249)		STAD - Stomach adenocarcinoma(47;0.00391)															---	---	---	---
SAMD12	401474	broad.mit.edu	37	8	119506939	119506942	+	Intron	DEL	AGTC	-	-	rs72330976		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119506939_119506942delAGTC	uc003yom.2	-						SAMD12_uc010mda.1_Intron|SAMD12_uc010mdb.1_Intron	NM_207506	NP_997389			sterile alpha motif domain containing 12 isoform											ovary(1)	1	all_cancers(13;3.91e-25)|Lung NSC(37;1.13e-07)|Ovarian(258;0.0249)		STAD - Stomach adenocarcinoma(47;0.00391)															---	---	---	---
TAF2	6873	broad.mit.edu	37	8	120803702	120803702	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120803702delA	uc003you.2	-							NM_003184	NP_003175			TBP-associated factor 2						G2/M transition of mitotic cell cycle|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	transcription factor TFIID complex|transcription factor TFTC complex	metallopeptidase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			large_intestine(2)|ovary(2)|kidney(1)|skin(1)	6	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)															---	---	---	---
DEPDC6	64798	broad.mit.edu	37	8	120979329	120979330	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:120979329_120979330insT	uc003yow.3	+						DEPDC6_uc011lid.1_Intron	NM_022783	NP_073620			DEP domain containing 6						intracellular signal transduction|negative regulation of cell size|negative regulation of protein kinase activity|negative regulation of TOR signaling cascade|regulation of apoptosis	intracellular	protein binding				0	Lung NSC(37;9.35e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)															---	---	---	---
COL14A1	7373	broad.mit.edu	37	8	121173910	121173910	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121173910delT	uc003yox.2	+							NM_021110	NP_066933			collagen, type XIV, alpha 1 precursor						cell-cell adhesion|collagen fibril organization	collagen type XIV|extracellular space	collagen binding|extracellular matrix structural constituent|protein binding, bridging			ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1)	12	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)															---	---	---	---
COL14A1	7373	broad.mit.edu	37	8	121368967	121368967	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121368967delA	uc003yox.2	+						COL14A1_uc003yoz.2_Intron	NM_021110	NP_066933			collagen, type XIV, alpha 1 precursor						cell-cell adhesion|collagen fibril organization	collagen type XIV|extracellular space	collagen binding|extracellular matrix structural constituent|protein binding, bridging			ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1)	12	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)															---	---	---	---
MRPL13	28998	broad.mit.edu	37	8	121438747	121438747	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121438747delT	uc003ypa.2	-						MRPL13_uc010mdf.2_Intron	NM_014078	NP_054797			mitochondrial ribosomal protein L13						translation	mitochondrial large ribosomal subunit	protein binding|structural constituent of ribosome			central_nervous_system(1)	1	Lung NSC(37;1.69e-07)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)															---	---	---	---
MTBP	27085	broad.mit.edu	37	8	121512423	121512423	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121512423delT	uc003ypc.1	+							NM_022045	NP_071328			Mdm2, transformed 3T3 cell double minute 2, p53						cell cycle arrest					skin(2)|ovary(1)	3	Lung NSC(37;5.68e-08)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)															---	---	---	---
SNTB1	6641	broad.mit.edu	37	8	121622387	121622387	+	Intron	DEL	T	-	-	rs72455629		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121622387delT	uc010mdg.2	-						SNTB1_uc003ype.2_Intron	NM_021021	NP_066301			basic beta 1 syntrophin						muscle contraction	cell junction|cytoplasm|cytoskeleton|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|calmodulin binding			skin(5)	5	Lung NSC(37;4.46e-09)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)		STAD - Stomach adenocarcinoma(47;0.00503)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	121923693	121923693	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:121923693delT								SNTB1 (99384 upstream) : HAS2 (701578 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	122077351	122077353	+	IGR	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122077351_122077353delAAA								SNTB1 (253042 upstream) : HAS2 (547918 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	122619481	122619494	+	IGR	DEL	TCTGATATCTTATT	-	-	rs72155959		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122619481_122619494delTCTGATATCTTATT								SNTB1 (795172 upstream) : HAS2 (5777 downstream)																																			---	---	---	---
HAS2	3037	broad.mit.edu	37	8	122648929	122648929	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122648929delA	uc003yph.2	-						HAS2AS_uc003ypi.1_5'Flank	NM_005328	NP_005319			hyaluronan synthase 2							integral to plasma membrane	hyaluronan synthase activity		HAS2/PLAG1(10)	soft_tissue(10)|ovary(5)	15	Lung NSC(37;3.12e-08)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)|all_neural(195;0.142)		STAD - Stomach adenocarcinoma(47;0.00503)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	122658249	122658249	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122658249delA								HAS2AS (1316 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	122881520	122881520	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122881520delC								HAS2AS (224587 upstream) : ZHX2 (912381 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	123707465	123707465	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123707465delA								None (None upstream) : ZHX2 (86436 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	123782555	123782555	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123782555delT								None (None upstream) : ZHX2 (11346 downstream)																																			---	---	---	---
FAM83A	84985	broad.mit.edu	37	8	124192526	124192526	+	Intron	DEL	A	-	-	rs72388487		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124192526delA	uc003ypv.2	+						FAM83A_uc003ypw.2_Intron|FAM83A_uc003ypy.2_5'Flank|FAM83A_uc003ypx.2_5'Flank|FAM83A_uc003ypz.2_5'Flank	NM_032899	NP_116288			hypothetical protein LOC84985 isoform a											ovary(3)|skin(1)	4	Lung NSC(37;1.55e-09)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)															---	---	---	---
C8orf76	84933	broad.mit.edu	37	8	124239725	124239725	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124239725delA	uc003yqc.1	-						C8orf76_uc003yqd.2_Intron	NM_032847	NP_116236			hypothetical protein LOC84933								binding			ovary(2)	2	Lung NSC(37;1.25e-09)|Ovarian(258;0.0154)		STAD - Stomach adenocarcinoma(47;0.00527)															---	---	---	---
TATDN1	83940	broad.mit.edu	37	8	125520941	125520941	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125520941delA	uc003yrd.2	-						TATDN1_uc003yre.2_Intron|TATDN1_uc010mdm.2_Intron|TATDN1_uc003yrf.2_Intron	NM_032026	NP_114415			TatD DNase domain containing 1 isoform a							nucleus	endodeoxyribonuclease activity, producing 5'-phosphomonoesters|metal ion binding				0	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	125850164	125850164	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:125850164delT								MTSS1 (109434 upstream) : LOC157381 (101720 downstream)																																			---	---	---	---
NSMCE2	286053	broad.mit.edu	37	8	126181974	126181974	+	Intron	DEL	T	-	-	rs33933127		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126181974delT	uc003yrw.2	+						NSMCE2_uc003yrv.2_Intron	NM_173685	NP_775956			non-SMC element 2, MMS21 homolog						DNA recombination|DNA repair	nucleus	ligase activity|zinc ion binding			breast(1)	1	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)															---	---	---	---
NSMCE2	286053	broad.mit.edu	37	8	126246435	126246436	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126246435_126246436delAA	uc003yrw.2	+							NM_173685	NP_775956			non-SMC element 2, MMS21 homolog						DNA recombination|DNA repair	nucleus	ligase activity|zinc ion binding			breast(1)	1	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)															---	---	---	---
NSMCE2	286053	broad.mit.edu	37	8	126329202	126329202	+	Intron	DEL	T	-	-	rs112763782		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126329202delT	uc003yrw.2	+							NM_173685	NP_775956			non-SMC element 2, MMS21 homolog						DNA recombination|DNA repair	nucleus	ligase activity|zinc ion binding			breast(1)	1	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	126481704	126481704	+	IGR	DEL	T	-	-	rs35030529		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126481704delT								TRIB1 (31062 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	126509413	126509418	+	IGR	DEL	TTTTTT	-	-	rs78170168		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:126509413_126509418delTTTTTT								TRIB1 (58771 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	127424932	127424932	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127424932delC								TRIB1 (974290 upstream) : FAM84B (139755 downstream)																																			---	---	---	---
FAM84B	157638	broad.mit.edu	37	8	127570050	127570050	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127570050delC	uc003yrz.1	-							NM_174911	NP_777571			family with sequence similarity 84, member B							cytoplasm|plasma membrane	protein binding				0	Ovarian(5;9.43e-05)|Esophageal squamous(12;0.0012)|Hepatocellular(40;0.128)|Myeloproliferative disorder(2;0.135)		STAD - Stomach adenocarcinoma(47;0.000556)|Colorectal(2;0.0102)|Lung(2;0.0136)|READ - Rectum adenocarcinoma(2;0.0723)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	127921651	127921663	+	IGR	DEL	TTCCTTCCTTCCT	-	-	rs58044433		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:127921651_127921663delTTCCTTCCTTCCT								FAM84B (351185 upstream) : LOC727677 (380399 downstream)																																			---	---	---	---
PVT1	5820	broad.mit.edu	37	8	128858940	128858940	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:128858940delT	uc003ysj.2	+						PVT1_uc010mdq.2_Intron|PVT1_uc010mdp.1_Intron					Human proto-oncogene myc mRNA, 5' end, clone DMmyc.												0																		---	---	---	---
PVT1	5820	broad.mit.edu	37	8	129038198	129038200	+	Intron	DEL	TTT	-	-	rs72027467		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129038198_129038200delTTT	uc010mdq.2	+						PVT1_uc003ysl.2_Intron	NR_003367				Homo sapiens Pvt1 oncogene (non-protein coding), mRNA (cDNA clone IMAGE:5517530), with apparent retained intron.												0																		---	---	---	---
PVT1	5820	broad.mit.edu	37	8	129110369	129110369	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129110369delC	uc010mdq.2	+						PVT1_uc003ysl.2_Intron	NR_003367				Homo sapiens Pvt1 oncogene (non-protein coding), mRNA (cDNA clone IMAGE:5517530), with apparent retained intron.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	129149706	129149706	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129149706delT								PVT1 (36208 upstream) : MIR1208 (12656 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	129558604	129558604	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:129558604delA								MIR1208 (396170 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	130537648	130537648	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130537648delA								None (None upstream) : GSDMC (222795 downstream)																																			---	---	---	---
GSDMC	56169	broad.mit.edu	37	8	130780975	130780975	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130780975delA	uc003ysr.2	-							NM_031415	NP_113603			melanoma-derived leucine zipper, extra-nuclear							mitochondrion				ovary(2)|skin(1)	3																		---	---	---	---
FAM49B	51571	broad.mit.edu	37	8	130963952	130963952	+	Intron	DEL	A	-	-	rs35141996		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130963952delA	uc003ysw.2	-						FAM49B_uc003ysx.2_Intron|FAM49B_uc003ysy.1_Intron	NM_016623	NP_057707			hypothetical protein LOC51571												0	Ovarian(5;0.000567)|Esophageal squamous(12;0.00693)|Acute lymphoblastic leukemia(118;0.155)		LUAD - Lung adenocarcinoma(14;0.0989)															---	---	---	---
ASAP1	50807	broad.mit.edu	37	8	131391316	131391316	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131391316delA	uc003yta.1	-						ASAP1_uc011liw.1_Intron	NM_018482	NP_060952			development and differentiation enhancing factor						cilium morphogenesis|filopodium assembly|regulation of ARF GTPase activity|signal transduction	cytoplasm|membrane	ARF GTPase activator activity|cytoskeletal adaptor activity|SH3 domain binding|zinc ion binding			ovary(4)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	131519115	131519115	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131519115delA								ASAP1 (104899 upstream) : ADCY8 (273433 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	131530629	131530629	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:131530629delA								ASAP1 (116413 upstream) : ADCY8 (261919 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	132176839	132176839	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132176839delT								ADCY8 (124004 upstream) : EFR3A (739520 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	132353595	132353595	+	IGR	DEL	A	-	-	rs5895088		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132353595delA								ADCY8 (300760 upstream) : EFR3A (562764 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	132475419	132475420	+	IGR	INS	-	C	C	rs149494083	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132475419_132475420insC								ADCY8 (422584 upstream) : EFR3A (440939 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	132740371	132740371	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132740371delT								ADCY8 (687536 upstream) : EFR3A (175988 downstream)																																			---	---	---	---
KCNQ3	3786	broad.mit.edu	37	8	133144356	133144356	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133144356delA	uc003ytj.2	-						KCNQ3_uc010mdt.2_Intron	NM_004519	NP_004510			potassium voltage-gated channel KQT-like protein						axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	133503171	133503171	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133503171delT								KCNQ3 (10167 upstream) : HPYR1 (69574 downstream)																																			---	---	---	---
TG	7038	broad.mit.edu	37	8	134053944	134053944	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134053944delC	uc003ytw.2	+						TG_uc010mdw.2_Intron|TG_uc011ljb.1_Intron|TG_uc011ljc.1_Intron|SLA_uc003ytz.2_Intron|SLA_uc011lje.1_Intron|SLA_uc011ljf.1_Intron|SLA_uc011ljg.1_Intron|SLA_uc011ljd.1_Intron	NM_003235	NP_003226			thyroglobulin precursor						hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)														---	---	---	---
NDRG1	10397	broad.mit.edu	37	8	134256230	134256231	+	Intron	DEL	CA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134256230_134256231delCA	uc003yuh.2	-						NDRG1_uc003yue.1_Intron|NDRG1_uc003yuf.1_Intron|NDRG1_uc003yug.2_Intron|NDRG1_uc010mee.2_Intron|NDRG1_uc010mef.2_Intron|NDRG1_uc011ljh.1_Intron|NDRG1_uc011lji.1_Intron|NDRG1_uc003yui.1_5'Flank	NM_001135242	NP_001128714			N-myc downstream regulated 1						cellular response to hypoxia|response to metal ion	cytoplasm|microtubule cytoskeleton|nucleus|plasma membrane	protein binding			ovary(4)	4	all_epithelial(106;4.26e-24)|Lung NSC(106;7.26e-07)|all_lung(105;2.77e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0107)															---	---	---	---
ST3GAL1	6482	broad.mit.edu	37	8	134542390	134542390	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134542390delG	uc003yuk.2	-						ST3GAL1_uc003yum.2_Intron	NM_173344	NP_775479			ST3 beta-galactoside alpha-2,3-sialyltransferase						protein glycosylation	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,3-sialyltransferase activity				0	all_epithelial(106;1.53e-23)|Lung NSC(106;3.15e-07)|all_lung(105;1.26e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.00721)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	134607376	134607377	+	IGR	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134607376_134607377delGA								ST3GAL1 (23193 upstream) : ZFAT (882656 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	135185112	135185112	+	IGR	DEL	T	-	-	rs72069712		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135185112delT								ST3GAL1 (600929 upstream) : ZFAT (304921 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	135368371	135368372	+	IGR	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135368371_135368372delAC								ST3GAL1 (784188 upstream) : ZFAT (121661 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	135452490	135452491	+	IGR	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135452490_135452491delCT								ST3GAL1 (868307 upstream) : ZFAT (37542 downstream)																																			---	---	---	---
ZFAT	57623	broad.mit.edu	37	8	135564491	135564492	+	Intron	DEL	AA	-	-	rs75507471		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135564491_135564492delAA	uc003yup.2	-						ZFAT_uc011ljj.1_Intron|ZFAT_uc003yun.2_Intron|ZFAT_uc003yuo.2_Intron|ZFAT_uc010meh.2_Intron|ZFAT_uc010mei.2_Intron|ZFAT_uc003yuq.2_Intron|ZFAT_uc010mej.2_Intron	NM_020863	NP_065914			zinc finger protein 406 isoform ZFAT-1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	136203668	136203668	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136203668delC								MIR30D (386480 upstream) : LOC286094 (42706 downstream)																																			---	---	---	---
KHDRBS3	10656	broad.mit.edu	37	8	136527702	136527702	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:136527702delT	uc003yuv.2	+						KHDRBS3_uc003yuw.2_Intron	NM_006558	NP_006549			KH domain containing, RNA binding, signal						regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	nucleus	SH3 domain binding			ovary(2)	2	all_epithelial(106;2.85e-16)|all_neural(2;2.72e-06)|Lung NSC(106;3.95e-06)|all_lung(105;1.11e-05)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.247)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	137426207	137426208	+	IGR	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137426207_137426208delTC								KHDRBS3 (766361 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	137990481	137990481	+	IGR	DEL	A	-	-	rs111947836		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:137990481delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138176087	138176087	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138176087delT								None (None upstream) : FAM135B (966181 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	138291623	138291623	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:138291623delT								None (None upstream) : FAM135B (850645 downstream)																																			---	---	---	---
FAM135B	51059	broad.mit.edu	37	8	139313732	139313733	+	Intron	INS	-	T	T	rs139984160	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139313732_139313733insT	uc003yuy.2	-						FAM135B_uc003yux.2_Intron|FAM135B_uc003yuz.2_Intron	NM_015912	NP_056996			hypothetical protein LOC51059											ovary(7)|skin(2)	9	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)												HNSCC(54;0.14)			---	---	---	---
COL22A1	169044	broad.mit.edu	37	8	139614399	139614399	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139614399delC	uc003yvd.2	-	60	4591	c.4144delG	c.(4144-4146)GTCfs	p.V1382fs	COL22A1_uc011ljo.1_Frame_Shift_Del_p.V662fs	NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	1382	Pro-rich.|Gly-rich.				cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)												HNSCC(7;0.00092)			---	---	---	---
COL22A1	169044	broad.mit.edu	37	8	139787089	139787090	+	Intron	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139787089_139787090delCT	uc003yvd.2	-							NM_152888	NP_690848			collagen, type XXII, alpha 1						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)												HNSCC(7;0.00092)			---	---	---	---
COL22A1	169044	broad.mit.edu	37	8	139850914	139850914	+	Intron	DEL	A	-	-	rs147858722		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139850914delA	uc003yvd.2	-							NM_152888	NP_690848			collagen, type XXII, alpha 1						cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)												HNSCC(7;0.00092)			---	---	---	---
Unknown	0	broad.mit.edu	37	8	140227840	140227840	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140227840delA								COL22A1 (301604 upstream) : KCNK9 (385242 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	140611310	140611310	+	IGR	DEL	A	-	-	rs10706758		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140611310delA								COL22A1 (685074 upstream) : KCNK9 (1772 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	141505440	141505441	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141505440_141505441insT								TRAPPC9 (36762 upstream) : CHRAC1 (15960 downstream)																																			---	---	---	---
PTK2	5747	broad.mit.edu	37	8	141980989	141980989	+	Intron	DEL	A	-	-	rs111788818		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141980989delA	uc003yvu.2	-						PTK2_uc003yvt.2_Intron|PTK2_uc003yvv.2_Intron|PTK2_uc011ljr.1_Intron	NM_153831	NP_722560			PTK2 protein tyrosine kinase 2 isoform a						axon guidance|blood coagulation|cellular component disassembly involved in apoptosis|ephrin receptor signaling pathway|growth hormone receptor signaling pathway|integrin-mediated signaling pathway|peptidyl-tyrosine phosphorylation|protein autophosphorylation|regulation of cell adhesion mediated by integrin|signal complex assembly	cytoskeleton|cytosol|focal adhesion	ATP binding|JUN kinase binding|non-membrane spanning protein tyrosine kinase activity|SH2 domain binding|signal transducer activity			ovary(2)|lung(2)|central_nervous_system(1)|skin(1)	6	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	142086480	142086480	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142086480delG								PTK2 (75148 upstream) : DENND3 (52240 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	142092873	142092873	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142092873delT								PTK2 (81541 upstream) : DENND3 (45847 downstream)																																			---	---	---	---
DENND3	22898	broad.mit.edu	37	8	142151514	142151514	+	Intron	DEL	G	-	-	rs147664697	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142151514delG	uc003yvy.2	+						DENND3_uc003yvw.1_3'UTR|DENND3_uc003yvx.2_Intron|DENND3_uc010mep.2_Intron	NM_014957	NP_055772			DENN/MADD domain containing 3											ovary(1)	1	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)															---	---	---	---
FLJ43860	389690	broad.mit.edu	37	8	142453020	142453020	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142453020delA	uc003ywi.2	-						FLJ43860_uc011ljs.1_Intron|FLJ43860_uc010meu.1_Intron	NM_207414	NP_997297			hypothetical protein LOC389690								binding				0	all_cancers(97;7.79e-15)|all_epithelial(106;4.52e-13)|Lung NSC(106;2.07e-05)|all_lung(105;2.89e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)															---	---	---	---
FLJ43860	389690	broad.mit.edu	37	8	142468194	142468197	+	Intron	DEL	AAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142468194_142468197delAAAA	uc003ywi.2	-						FLJ43860_uc011ljs.1_Intron|FLJ43860_uc010meu.1_Intron	NM_207414	NP_997297			hypothetical protein LOC389690								binding				0	all_cancers(97;7.79e-15)|all_epithelial(106;4.52e-13)|Lung NSC(106;2.07e-05)|all_lung(105;2.89e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)															---	---	---	---
Unknown	0	broad.mit.edu	37	8	142733367	142733367	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142733367delT								FLJ43860 (216037 upstream) : MIR1302-7 (134236 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	143158856	143158856	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143158856delA								MIR1302-7 (291182 upstream) : NCRNA00051 (120861 downstream)																																			---	---	---	---
TSNARE1	203062	broad.mit.edu	37	8	143345362	143345362	+	Intron	DEL	A	-	-	rs116531951	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143345362delA	uc003ywk.2	-						TSNARE1_uc011lju.1_Intron|TSNARE1_uc003ywj.2_Intron	NM_145003	NP_659440			t-SNARE domain containing 1						vesicle-mediated transport	integral to membrane					0	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)																	---	---	---	---
JRK	8629	broad.mit.edu	37	8	143740520	143740520	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143740520delA	uc003ywo.2	-						JRK_uc003ywp.2_3'UTR	NM_001077527	NP_001070995			jerky isoform b												0	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;2.31e-05)																---	---	---	---
Unknown	0	broad.mit.edu	37	8	144466709	144466710	+	IGR	DEL	CC	-	-	rs35470357		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144466709_144466710delCC								RHPN1 (320 upstream) : MAFA (44805 downstream)																																			---	---	---	---
ZC3H3	23144	broad.mit.edu	37	8	144530476	144530477	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144530476_144530477delAA	uc003yyd.2	-							NM_015117	NP_055932			zinc finger CCCH-type containing 3						mRNA polyadenylation|poly(A)+ mRNA export from nucleus|regulation of mRNA export from nucleus	nucleus	nucleic acid binding|zinc ion binding			skin(1)	1	all_cancers(97;8.64e-11)|all_epithelial(106;6.43e-09)|Lung NSC(106;0.000202)|all_lung(105;0.000548)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.107)															---	---	---	---
EPPK1	83481	broad.mit.edu	37	8	144941378	144941378	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144941378delC	uc003zaa.1	-	1	6057	c.6044delG	c.(6043-6045)GGTfs	p.G2015fs		NM_031308	NP_112598	P58107	EPIPL_HUMAN	epiplakin 1	2015	Plectin 34.					cytoplasm|cytoskeleton	protein binding|structural molecule activity			pancreas(1)|skin(1)	2	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)															---	---	---	---
PLEC	5339	broad.mit.edu	37	8	145027421	145027421	+	5'Flank	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145027421delC	uc003zaf.1	-						PLEC_uc003zag.1_Intron|PLEC_uc003zah.2_Intron|PLEC_uc003zaj.2_Intron	NM_201380	NP_958782			plectin isoform 1						cellular component disassembly involved in apoptosis|hemidesmosome assembly	cytosol|focal adhesion|hemidesmosome|intermediate filament cytoskeleton|sarcolemma	actin binding|structural constituent of muscle|structural constituent of muscle			large_intestine(2)|ovary(2)|pancreas(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	9																		---	---	---	---
SPATC1	375686	broad.mit.edu	37	8	145095437	145095437	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145095437delT	uc011lkw.1	+						SPATC1_uc011lkx.1_Intron	NM_198572	NP_940974			spermatogenesis and centriole associated 1											ovary(1)|central_nervous_system(1)	2	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;3.67e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)															---	---	---	---
CPSF1	29894	broad.mit.edu	37	8	145627692	145627692	+	Intron	DEL	T	-	-	rs148011256	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145627692delT	uc003zcj.2	-						CPSF1_uc003zck.1_Intron|CPSF1_uc011lle.1_Intron|MIR1234_hsa-mir-1234|MI0006324_5'Flank|CPSF1_uc011llf.1_Intron	NM_013291	NP_037423			cleavage and polyadenylation specific factor 1,						mRNA cleavage|mRNA export from nucleus|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex	mRNA 3'-UTR binding|protein binding			skin(1)	1	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)															---	---	---	---
ARHGAP39	80728	broad.mit.edu	37	8	145869314	145869314	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145869314delA	uc011llk.1	-							NM_025251	NP_079527			KIAA1688 protein						axon guidance|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytoskeleton|cytosol|nucleus	GTPase activator activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	146236943	146236944	+	IGR	DEL	TT	-	-	rs72050183		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:146236943_146236944delTT								C8orf77 (5512 upstream) : C8orf33 (40880 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	53893	53893	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:53893delA								WASH5P (24154 upstream) : FOXD4 (62342 downstream)																																			---	---	---	---
CBWD1	55871	broad.mit.edu	37	9	159448	159448	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:159448delA	uc003zga.3	-						CBWD1_uc010mgs.2_Intron|CBWD1_uc003zgb.3_Intron|CBWD1_uc003zgc.3_Intron|CBWD1_uc011llr.1_Intron	NM_018491	NP_060961			COBW domain containing 1 isoform 1								ATP binding|protein binding			ovary(1)	1	all_lung(41;0.218)	all_cancers(5;3.04e-16)|all_epithelial(5;4.68e-12)|all_lung(10;1.94e-10)|Lung NSC(10;3.61e-10)|Acute lymphoblastic leukemia(5;0.00439)|Breast(48;0.0148)|all_hematologic(5;0.024)|Prostate(43;0.122)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)														---	---	---	---
DOCK8	81704	broad.mit.edu	37	9	277838	277838	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:277838delA	uc003zgf.2	+						DOCK8_uc011lls.1_Intron|DOCK8_uc010mgu.2_Intron|DOCK8_uc010mgv.2_Intron|DOCK8_uc010mgt.2_Intron|DOCK8_uc003zgg.2_Intron|DOCK8_uc003zgh.2_Intron	NM_203447	NP_982272			dedicator of cytokinesis 8						blood coagulation	cytosol	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)	6		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)														---	---	---	---
DOCK8	81704	broad.mit.edu	37	9	293740	293740	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:293740delT	uc003zgf.2	+						DOCK8_uc011lls.1_Intron|DOCK8_uc010mgu.2_Intron|DOCK8_uc010mgv.2_Intron|DOCK8_uc010mgt.2_Intron|DOCK8_uc003zgg.2_Intron|DOCK8_uc003zgh.2_Intron	NM_203447	NP_982272			dedicator of cytokinesis 8						blood coagulation	cytosol	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)	6		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	776616	776617	+	IGR	DEL	CA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:776616_776617delCA								KANK1 (30512 upstream) : DMRT1 (65073 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	1007157	1007157	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1007157delT								DMRT3 (15425 upstream) : DMRT2 (42701 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	1011401	1011402	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1011401_1011402insT								DMRT3 (19669 upstream) : DMRT2 (38456 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	1313062	1313062	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1313062delG								DMRT2 (255509 upstream) : SMARCA2 (702280 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	1529267	1529268	+	IGR	INS	-	C	C	rs143209239	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1529267_1529268insC								DMRT2 (471714 upstream) : SMARCA2 (486074 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	1648709	1648709	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1648709delT								DMRT2 (591156 upstream) : SMARCA2 (366633 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	1790022	1790023	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1790022_1790023insA								DMRT2 (732469 upstream) : SMARCA2 (225319 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	1965791	1965791	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:1965791delC								DMRT2 (908238 upstream) : SMARCA2 (49551 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	2198863	2198863	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2198863delT								SMARCA2 (5242 upstream) : FLJ35024 (223839 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	2274475	2274475	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2274475delA								SMARCA2 (80854 upstream) : FLJ35024 (148227 downstream)																																			---	---	---	---
FLJ35024	401491	broad.mit.edu	37	9	2552347	2552347	+	Intron	DEL	A	-	-	rs35560492		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2552347delA	uc003zhh.1	-						FLJ35024_uc003zhi.2_Intron|FLJ35024_uc003zhj.3_Intron					Homo sapiens cDNA FLJ35024 fis, clone OCBBF2015233.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	3183795	3183796	+	IGR	DEL	TC	-	-	rs76809162		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:3183795_3183796delTC								KIAA0020 (339665 upstream) : RFX3 (40853 downstream)																																			---	---	---	---
RFX3	5991	broad.mit.edu	37	9	3405964	3405964	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:3405964delT	uc003zhr.2	-						RFX3_uc010mhd.2_Intron|RFX3_uc003zhs.1_Intron|RFX3_uc003zht.1_Intron|RFX3_uc010mhe.1_Intron	NM_134428	NP_602304			regulatory factor X3 isoform b						cell maturation|ciliary cell motility|cilium assembly|cilium movement involved in determination of left/right asymmetry|endocrine pancreas development|negative regulation of transcription, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|positive regulation of type B pancreatic cell development|regulation of insulin secretion	nuclear chromatin	protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4				GBM - Glioblastoma multiforme(50;0.00124)|Lung(2;0.0337)														---	---	---	---
RCL1	10171	broad.mit.edu	37	9	4859802	4859802	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4859802delA	uc003zis.2	+						RCL1_uc003zit.2_Intron|RCL1_uc010mhk.1_Intron|RCL1_uc010mhl.1_Intron|RCL1_uc003ziv.1_5'Flank	NM_005772	NP_005763			RNA terminal phosphate cyclase-like 1						ribosome biogenesis|RNA processing	nucleolus	RNA-3'-phosphate cyclase activity				0	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0206)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0244)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	4952700	4952704	+	IGR	DEL	CTCAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:4952700_4952704delCTCAA								RCL1 (66783 upstream) : JAK2 (32382 downstream)																																			---	---	---	---
JAK2	3717	broad.mit.edu	37	9	5010331	5010332	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5010331_5010332delTT	uc010mhm.2	+						JAK2_uc003ziw.2_Intron	NM_004972	NP_004963			Janus kinase 2						actin filament polymerization|activation of caspase activity by protein phosphorylation|activation of JAK2 kinase activity|blood coagulation|cellular component movement|erythrocyte differentiation|interferon-gamma-mediated signaling pathway|interleukin-12-mediated signaling pathway|JAK-STAT cascade involved in growth hormone signaling pathway|mammary gland epithelium development|mesoderm development|negative regulation of cell proliferation|negative regulation of DNA binding|positive regulation of apoptosis|positive regulation of cell-substrate adhesion|positive regulation of growth hormone receptor signaling pathway|positive regulation of nitric-oxide synthase 2 biosynthetic process|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of tumor necrosis factor production|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of tyrosine phosphorylation of Stat5 protein|protein autophosphorylation|regulation of inflammatory response|regulation of interferon-gamma-mediated signaling pathway|response to antibiotic|response to lipopolysaccharide|STAT protein import into nucleus|tumor necrosis factor-mediated signaling pathway|tyrosine phosphorylation of STAT protein	caveola|cytoskeleton|cytosol|endomembrane system|nucleus	ATP binding|growth hormone receptor binding|heme binding|histone binding|histone kinase activity (H3-Y41 specific)|interleukin-12 receptor binding|non-membrane spanning protein tyrosine kinase activity|protein kinase binding|SH2 domain binding		PCM1/JAK2(30)|PAX5/JAK2(18)|ETV6/JAK2(11)|BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)	haematopoietic_and_lymphoid_tissue(28629)|lung(5)|breast(5)|ovary(1)|liver(1)	28641	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)			1	T|Mis|O	ETV6|PCM1|BCR	ALL|AML|MPD| CML				Polycythemia_Vera_Familial				---	---	---	---
C9orf46	55848	broad.mit.edu	37	9	5385688	5385689	+	Intron	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5385688_5385689delAG	uc003zjc.2	-						C9orf46_uc003zjd.2_Intron	NM_018465	NP_060935			hypothetical protein LOC55848							integral to membrane				ovary(1)	1	all_hematologic(13;0.158)	Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.00106)|Lung(218;0.125)														---	---	---	---
C9orf46	55848	broad.mit.edu	37	9	5432077	5432077	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5432077delA	uc003zjc.2	-						C9orf46_uc003zjd.2_Intron	NM_018465	NP_060935			hypothetical protein LOC55848							integral to membrane				ovary(1)	1	all_hematologic(13;0.158)	Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.00106)|Lung(218;0.125)														---	---	---	---
CD274	29126	broad.mit.edu	37	9	5463852	5463852	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5463852delT	uc003zje.2	+						C9orf46_uc003zjd.2_Intron|CD274_uc011lmb.1_Intron|CD274_uc010mhn.2_Intron|CD274_uc003zjf.2_Intron	NM_014143	NP_054862			CD274 molecule precursor						cell proliferation|cell surface receptor linked signaling pathway|immune response|T cell costimulation	endomembrane system|integral to membrane	receptor activity			lung(1)|central_nervous_system(1)	2	all_hematologic(13;0.158)	Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000742)|Lung(218;0.111)				T	CIITA	PMBL|Hodgkin Lymphona|								---	---	---	---
CD274	29126	broad.mit.edu	37	9	5464318	5464318	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5464318delT	uc003zje.2	+						C9orf46_uc003zjd.2_Intron|CD274_uc011lmb.1_Intron|CD274_uc010mhn.2_Intron|CD274_uc003zjf.2_Intron	NM_014143	NP_054862			CD274 molecule precursor						cell proliferation|cell surface receptor linked signaling pathway|immune response|T cell costimulation	endomembrane system|integral to membrane	receptor activity			lung(1)|central_nervous_system(1)	2	all_hematologic(13;0.158)	Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000742)|Lung(218;0.111)				T	CIITA	PMBL|Hodgkin Lymphona|								---	---	---	---
KIAA1432	57589	broad.mit.edu	37	9	5649740	5649741	+	Intron	DEL	TT	-	-	rs141623320		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:5649740_5649741delTT	uc003zjh.2	+							NM_001135920	NP_001129392			connexin 43-interacting protein 150 isoform b							integral to membrane					0		Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000525)|Lung(218;0.122)														---	---	---	---
GLDC	2731	broad.mit.edu	37	9	6559815	6559816	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6559815_6559816delAA	uc003zkc.2	-							NM_000170	NP_000161			glycine dehydrogenase (decarboxylating)						glycine catabolic process	mitochondrion	electron carrier activity|glycine dehydrogenase (decarboxylating) activity|lyase activity|pyridoxal phosphate binding			ovary(2)	2		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)|Pyridoxal Phosphate(DB00114)													---	---	---	---
Unknown	0	broad.mit.edu	37	9	7749724	7749724	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7749724delA								KDM4C (574077 upstream) : C9orf123 (46769 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	7780720	7780720	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7780720delA								KDM4C (605073 upstream) : C9orf123 (15773 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	7912747	7912747	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:7912747delC								C9orf123 (112948 upstream) : PTPRD (401500 downstream)																																			---	---	---	---
PTPRD	5789	broad.mit.edu	37	9	9467255	9467255	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:9467255delT	uc003zkk.2	-						PTPRD_uc003zkl.2_Intron|PTPRD_uc003zkm.2_Intron|PTPRD_uc003zkn.2_Intron|PTPRD_uc003zko.2_Intron|PTPRD_uc003zkt.1_Intron	NM_002839	NP_002830			protein tyrosine phosphatase, receptor type, D						transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)											TSP Lung(15;0.13)			---	---	---	---
PTPRD	5789	broad.mit.edu	37	9	10260409	10260409	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:10260409delT	uc003zkk.2	-						PTPRD_uc003zkl.2_Intron|PTPRD_uc003zkm.2_Intron|PTPRD_uc003zkn.2_Intron|PTPRD_uc003zko.2_Intron|PTPRD_uc003zkt.1_Intron	NM_002839	NP_002830			protein tyrosine phosphatase, receptor type, D						transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)											TSP Lung(15;0.13)			---	---	---	---
Unknown	0	broad.mit.edu	37	9	11702445	11702446	+	IGR	INS	-	ATA	ATA	rs140970956	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:11702445_11702446insATA								None (None upstream) : TYRP1 (990940 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	11721833	11721833	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:11721833delT								None (None upstream) : TYRP1 (971553 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	11738892	11738894	+	IGR	DEL	CTC	-	-	rs148144770		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:11738892_11738894delCTC								None (None upstream) : TYRP1 (954492 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	11905604	11905604	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:11905604delT								None (None upstream) : TYRP1 (787782 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	12117758	12117759	+	IGR	DEL	CA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:12117758_12117759delCA								None (None upstream) : TYRP1 (575627 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	12901892	12901892	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:12901892delC								C9orf150 (78834 upstream) : MPDZ (203817 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	12991075	12991075	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:12991075delA								C9orf150 (168017 upstream) : MPDZ (114634 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	13624311	13624312	+	IGR	INS	-	AA	AA			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:13624311_13624312insAA								MPDZ (344748 upstream) : NFIB (457536 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	14539025	14539025	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14539025delA								NFIB (225080 upstream) : ZDHHC21 (16456 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	15001532	15001532	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15001532delA	uc003zln.1	-						LOC389705_uc010mid.1_Intron					Homo sapiens cDNA FLJ46077 fis, clone TESTI2003768, weakly  similar to Chloride channel protein 3.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	15330413	15330413	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15330413delA								TTC39B (23169 upstream) : SNAPC3 (92369 downstream)																																			---	---	---	---
SNAPC3	6619	broad.mit.edu	37	9	15443396	15443396	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15443396delT	uc003zlt.2	+						SNAPC3_uc011lmt.1_Intron|SNAPC3_uc003zlu.2_Intron	NM_001039697	NP_001034786			small nuclear RNA activating complex,						regulation of transcription, DNA-dependent|snRNA transcription|transcription from RNA polymerase II promoter|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding|protein binding				0				GBM - Glioblastoma multiforme(50;2.15e-06)														---	---	---	---
C9orf93	203238	broad.mit.edu	37	9	15657002	15657002	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15657002delA	uc003zmd.2	+						C9orf93_uc010mih.1_Intron|C9orf93_uc003zme.2_Intron|C9orf93_uc011lmu.1_Intron|C9orf93_uc003zmc.2_Intron	NM_173550	NP_775821			hypothetical protein LOC203238												0				GBM - Glioblastoma multiforme(50;4.84e-07)														---	---	---	---
BNC2	54796	broad.mit.edu	37	9	16698693	16698694	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16698693_16698694delAA	uc003zml.2	-						BNC2_uc011lmw.1_Intron|BNC2_uc003zmm.2_Intron|BNC2_uc003zmq.1_Intron|BNC2_uc003zmr.1_Intron|BNC2_uc003zmp.1_Intron|BNC2_uc010mij.1_Intron|BNC2_uc003zmu.1_Intron|BNC2_uc010mim.1_Intron|BNC2_uc010min.1_Intron|BNC2_uc003zmo.1_Intron|BNC2_uc003zms.1_Intron|BNC2_uc010mik.1_Intron|BNC2_uc010mil.1_Intron|BNC2_uc003zmt.1_Intron	NM_017637	NP_060107			basonuclin 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	zinc ion binding			ovary(2)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(50;9.01e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	16893900	16893900	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:16893900delT								BNC2 (23114 upstream) : CNTLN (241138 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	17099720	17099721	+	IGR	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17099720_17099721delAG								BNC2 (228934 upstream) : CNTLN (35317 downstream)																																			---	---	---	---
SH3GL2	6456	broad.mit.edu	37	9	17581242	17581243	+	Intron	INS	-	TA	TA	rs144325674	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17581242_17581243insTA	uc003zna.2	+							NM_003026	NP_003017			SH3-domain GRB2-like 2						axon guidance|central nervous system development|endocytosis|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport	cytosol|Golgi membrane|plasma membrane	identical protein binding|lipid binding			skin(1)	1				GBM - Glioblastoma multiforme(50;2.71e-10)|Lung(42;0.203)														---	---	---	---
SH3GL2	6456	broad.mit.edu	37	9	17743568	17743569	+	Intron	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17743568_17743569delAC	uc003zna.2	+						SH3GL2_uc011lmx.1_Intron|SH3GL2_uc011lmy.1_Intron	NM_003026	NP_003017			SH3-domain GRB2-like 2						axon guidance|central nervous system development|endocytosis|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport	cytosol|Golgi membrane|plasma membrane	identical protein binding|lipid binding			skin(1)	1				GBM - Glioblastoma multiforme(50;2.71e-10)|Lung(42;0.203)														---	---	---	---
SH3GL2	6456	broad.mit.edu	37	9	17780107	17780107	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17780107delA	uc003zna.2	+						SH3GL2_uc011lmx.1_Intron|SH3GL2_uc011lmy.1_Intron	NM_003026	NP_003017			SH3-domain GRB2-like 2						axon guidance|central nervous system development|endocytosis|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport	cytosol|Golgi membrane|plasma membrane	identical protein binding|lipid binding			skin(1)	1				GBM - Glioblastoma multiforme(50;2.71e-10)|Lung(42;0.203)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	17867989	17867990	+	IGR	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17867989_17867990delTC								SH3GL2 (70869 upstream) : ADAMTSL1 (606114 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	18150903	18150903	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18150903delT								SH3GL2 (353783 upstream) : ADAMTSL1 (323201 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	18217852	18217852	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18217852delT								SH3GL2 (420732 upstream) : ADAMTSL1 (256252 downstream)																																			---	---	---	---
ADAMTSL1	92949	broad.mit.edu	37	9	18622069	18622069	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18622069delT	uc003zne.3	+						ADAMTSL1_uc003znb.2_Intron|ADAMTSL1_uc003znc.3_Intron	NM_001040272	NP_001035362			ADAMTS-like 1 isoform 4 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)	5				GBM - Glioblastoma multiforme(50;1.29e-17)														---	---	---	---
ADAMTSL1	92949	broad.mit.edu	37	9	18681696	18681698	+	Intron	DEL	GGG	-	-	rs66675938		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18681696_18681698delGGG	uc003zne.3	+						ADAMTSL1_uc003znc.3_Intron	NM_001040272	NP_001035362			ADAMTS-like 1 isoform 4 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)	5				GBM - Glioblastoma multiforme(50;1.29e-17)														---	---	---	---
ADAMTSL1	92949	broad.mit.edu	37	9	18861828	18861829	+	Intron	INS	-	CTC	CTC			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18861828_18861829insCTC	uc003zne.3	+						ADAMTSL1_uc003znf.3_Intron	NM_001040272	NP_001035362			ADAMTS-like 1 isoform 4 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)	5				GBM - Glioblastoma multiforme(50;1.29e-17)														---	---	---	---
ADAMTSL1	92949	broad.mit.edu	37	9	18870667	18870667	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18870667delA	uc003zne.3	+						ADAMTSL1_uc003znf.3_Intron	NM_001040272	NP_001035362			ADAMTS-like 1 isoform 4 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)	5				GBM - Glioblastoma multiforme(50;1.29e-17)														---	---	---	---
FAM154A	158297	broad.mit.edu	37	9	18965573	18965573	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18965573delT	uc003zni.1	-						FAM154A_uc010mip.1_Intron	NM_153707	NP_714918			hypothetical protein LOC158297											pancreas(1)	1				GBM - Glioblastoma multiforme(50;6.53e-16)														---	---	---	---
HAUS6	54801	broad.mit.edu	37	9	19065934	19065937	+	Intron	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19065934_19065937delTTTT	uc003znk.2	-						HAUS6_uc011lmz.1_Intron|HAUS6_uc003znl.1_Intron|HAUS6_uc003znm.1_Intron|SCARNA8_uc003znn.1_5'Flank	NM_017645	NP_060115			HAUS augmin-like complex, subunit 6						cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|nucleus|spindle				ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	19184300	19184300	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19184300delA								PLIN2 (56727 upstream) : DENND4C (106402 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	19879095	19879095	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19879095delT								SLC24A2 (90287 upstream) : MLLT3 (465873 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	19990850	19990851	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19990850_19990851delAA								SLC24A2 (202042 upstream) : MLLT3 (354117 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	20312323	20312323	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20312323delA								SLC24A2 (523515 upstream) : MLLT3 (32645 downstream)																																			---	---	---	---
KIAA1797	54914	broad.mit.edu	37	9	20784930	20784930	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20784930delT	uc003zog.1	+							NM_017794	NP_060264			hypothetical protein LOC54914							integral to membrane	binding			ovary(8)|breast(1)|kidney(1)	10				GBM - Glioblastoma multiforme(3;2.1e-125)|Lung(42;2.76e-14)|LUSC - Lung squamous cell carcinoma(42;1.99e-11)														---	---	---	---
KIAA1797	54914	broad.mit.edu	37	9	20974160	20974160	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20974160delT	uc003zog.1	+						KIAA1797_uc003zoh.1_Intron	NM_017794	NP_060264			hypothetical protein LOC54914							integral to membrane	binding			ovary(8)|breast(1)|kidney(1)	10				GBM - Glioblastoma multiforme(3;2.1e-125)|Lung(42;2.76e-14)|LUSC - Lung squamous cell carcinoma(42;1.99e-11)														---	---	---	---
IFNA14	3448	broad.mit.edu	37	9	21231020	21231020	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21231020delA	uc003zoo.1	-						IFNA17_uc003zos.1_5'Flank	NM_002172				interferon, alpha 14 precursor						blood coagulation|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	extracellular space	cytokine activity|cytokine receptor binding				0				Lung(24;2.12e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	22462943	22462944	+	IGR	DEL	GT	-	-	rs35779009		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22462943_22462944delGT								DMRTA1 (10471 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	22803209	22803209	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:22803209delC	uc003zpq.1	+											Homo sapiens cDNA FLJ35282 fis, clone PROST2007328.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	23638299	23638299	+	Intron	DEL	T	-	-	rs76458477	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23638299delT	uc003zpr.2	-											Homo sapiens mRNA; cDNA DKFZp781D1719 (from clone DKFZp781D1719).																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	23934822	23934822	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:23934822delT								ELAVL2 (108759 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	24039330	24039330	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:24039330delT								ELAVL2 (213267 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	24116747	24116748	+	IGR	DEL	TG	-	-	rs72172285		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:24116747_24116748delTG								ELAVL2 (290684 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	24216960	24216961	+	IGR	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:24216960_24216961delGA								ELAVL2 (390897 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	25358617	25358617	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:25358617delT								None (None upstream) : TUSC1 (317777 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	25954929	25954929	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:25954929delA								TUSC1 (276073 upstream) : C9orf82 (885755 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	26119403	26119403	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26119403delT								TUSC1 (440547 upstream) : C9orf82 (721281 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	26178879	26178879	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26178879delT								TUSC1 (500023 upstream) : C9orf82 (661805 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	26786185	26786185	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26786185delT								None (None upstream) : C9orf82 (54499 downstream)																																			---	---	---	---
PLAA	9373	broad.mit.edu	37	9	26920087	26920087	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26920087delA	uc003zqd.2	-						PLAA_uc003zqe.2_Intron	NM_001031689	NP_001026859			phospholipase A2-activating protein						phospholipid metabolic process|signal transduction		phospholipase A2 activator activity				0		all_neural(3;3.53e-10)|Glioma(3;2.71e-09)		Lung(218;1.32e-05)|LUSC - Lung squamous cell carcinoma(38;0.00011)														---	---	---	---
TEK	7010	broad.mit.edu	37	9	27211992	27211992	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27211992delA	uc003zqi.3	+						TEK_uc011lno.1_Intron|TEK_uc011lnp.1_Intron	NM_000459	NP_000450			TEK tyrosine kinase, endothelial precursor						angiogenesis|blood coagulation|cell-cell signaling|leukocyte migration|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein kinase B signaling cascade|protein oligomerization|transmembrane receptor protein tyrosine kinase signaling pathway	apical plasma membrane|basolateral plasma membrane|cell surface|integral to plasma membrane|membrane raft|microvillus	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity			ovary(3)|central_nervous_system(3)|breast(3)|lung(2)|kidney(1)	12		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)														---	---	---	---
MOBKL2B	79817	broad.mit.edu	37	9	27384260	27384261	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27384260_27384261insT	uc003zqn.2	-							NM_024761	NP_079037			MOB1, Mps One Binder kinase activator-like 2B								metal ion binding|protein binding			ovary(1)|pleura(1)	2		all_neural(11;9.12e-11)		Lung(218;6.54e-05)|LUSC - Lung squamous cell carcinoma(38;0.000397)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	27700202	27700202	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27700202delA								C9orf72 (126360 upstream) : LINGO2 (248326 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	27801871	27801872	+	IGR	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:27801871_27801872delAG								C9orf72 (228029 upstream) : LINGO2 (146656 downstream)																																			---	---	---	---
LINGO2	158038	broad.mit.edu	37	9	28535701	28535702	+	Intron	DEL	CA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:28535701_28535702delCA	uc003zqv.1	-							NM_152570	NP_689783			leucine rich repeat and Ig domain containing 2							integral to membrane				upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	Melanoma(11;0.242)	all_neural(11;2.78e-09)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0818)|GBM - Glioblastoma multiforme(2;1.31e-34)|all cancers(2;2.37e-25)|Lung(2;7.48e-08)|LUSC - Lung squamous cell carcinoma(38;5.09e-07)|KIRC - Kidney renal clear cell carcinoma(2;0.0465)|Kidney(2;0.0604)														---	---	---	---
LINGO2	158038	broad.mit.edu	37	9	28687748	28687748	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:28687748delT	uc003zqv.1	-							NM_152570	NP_689783			leucine rich repeat and Ig domain containing 2							integral to membrane				upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	Melanoma(11;0.242)	all_neural(11;2.78e-09)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0818)|GBM - Glioblastoma multiforme(2;1.31e-34)|all cancers(2;2.37e-25)|Lung(2;7.48e-08)|LUSC - Lung squamous cell carcinoma(38;5.09e-07)|KIRC - Kidney renal clear cell carcinoma(2;0.0465)|Kidney(2;0.0604)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	29014063	29014063	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:29014063delT								MIR873 (125110 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	29025162	29025162	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:29025162delA								MIR873 (136209 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	29315553	29315553	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:29315553delA								MIR873 (426600 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	31445431	31445432	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:31445431_31445432delAA								None (None upstream) : ACO1 (939169 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	32708766	32708766	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32708766delA								TAF1L (73099 upstream) : TMEM215 (74731 downstream)																																			---	---	---	---
APTX	54840	broad.mit.edu	37	9	33023220	33023221	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33023220_33023221delTT	uc003zrz.2	-						DNAJA1_uc003zsd.1_5'Flank|DNAJA1_uc011lnt.1_5'Flank	NM_175071	NP_778241			aprataxin isoform d						cell death|double-strand break repair|regulation of protein stability|response to hydrogen peroxide|single strand break repair	chromatin|nucleolus|nucleoplasm	chromatin binding|damaged DNA binding|DNA 5'-adenosine monophosphate hydrolase activity|double-stranded DNA binding|double-stranded RNA binding|phosphoglycolate phosphatase activity|phosphoprotein binding|polynucleotide 3'-phosphatase activity|protein N-terminus binding|zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(29;0.0302)	GBM - Glioblastoma multiforme(74;0.105)									Direct_reversal_of_damage|Editing_and_processing_nucleases					---	---	---	---
B4GALT1	2683	broad.mit.edu	37	9	33128419	33128419	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33128419delA	uc003zsg.2	-							NM_001497	NP_001488			UDP-Gal:betaGlcNAc beta 1,4-						oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	basolateral plasma membrane|brush border membrane|desmosome|external side of plasma membrane|extracellular region|glycocalyx|Golgi cisterna membrane|Golgi trans cisterna|integral to membrane	alpha-tubulin binding|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity|beta-tubulin binding|lactose synthase activity|metal ion binding|N-acetyllactosamine synthase activity|protein binding|protein homodimerization activity				0			LUSC - Lung squamous cell carcinoma(29;0.0084)	GBM - Glioblastoma multiforme(74;0.121)	N-Acetyl-D-glucosamine(DB00141)													---	---	---	---
Unknown	0	broad.mit.edu	37	9	33203813	33203814	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33203813_33203814insT								B4GALT1 (36457 upstream) : SUGT1P1 (15256 downstream)																																			---	---	---	---
SUGT1P1	441394	broad.mit.edu	37	9	33225556	33225557	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33225556_33225557insA	uc010mjq.1	-							NR_003667				Homo sapiens suppressor of G2 allele of SKP1 pseudogene (S. cerevisiae) (SUGT1P), non-coding RNA.												0																		---	---	---	---
CHMP5	51510	broad.mit.edu	37	9	33270523	33270523	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33270523delT	uc003zsl.3	+						SUGT1P1_uc010mjq.1_Intron|CHMP5_uc003zsm.3_Intron|CHMP5_uc011lnv.1_Intron|CHMP5_uc003zsn.2_5'Flank	NM_016410	NP_057494			chromatin modifying protein 5						cellular membrane organization|protein transport	cytosol|endosome membrane	protein binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(29;0.00506)															---	---	---	---
SUGT1P1	441394	broad.mit.edu	37	9	33409528	33409529	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33409528_33409529delTT	uc010mjq.1	-							NR_003667				Homo sapiens suppressor of G2 allele of SKP1 pseudogene (S. cerevisiae) (SUGT1P), non-coding RNA.												0																		---	---	---	---
SUGT1P1	441394	broad.mit.edu	37	9	33501758	33501759	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33501758_33501759insA	uc010mjq.1	-							NR_003667				Homo sapiens suppressor of G2 allele of SKP1 pseudogene (S. cerevisiae) (SUGT1P), non-coding RNA.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	33646718	33646718	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33646718delT								ANXA2P2 (21188 upstream) : PTENP1 (26789 downstream)																																			---	---	---	---
PRSS3	5646	broad.mit.edu	37	9	33796502	33796502	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33796502delG	uc003ztj.3	+						uc003ztk.1_Intron|PRSS3_uc003zti.3_Intron|PRSS3_uc003ztl.3_Intron	NM_007343	NP_031369			mesotrypsin isoform 1 preproprotein						digestion|endothelial cell migration|zymogen activation	extracellular space	calcium ion binding|protein binding|serine-type endopeptidase activity|serine-type peptidase activity				0			LUSC - Lung squamous cell carcinoma(29;0.0176)															---	---	---	---
UBAP2	55833	broad.mit.edu	37	9	33960612	33960612	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33960612delA	uc003ztq.1	-						UBAP2_uc011loc.1_Intron|UBAP2_uc011lod.1_Intron|UBAP2_uc011loe.1_Intron|UBAP2_uc011lof.1_Intron|UBAP2_uc011log.1_Intron|UBAP2_uc003ztr.2_Intron	NM_018449	NP_060919			ubiquitin associated protein 2											ovary(3)	3			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)														---	---	---	---
UBAP2	55833	broad.mit.edu	37	9	33966292	33966294	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33966292_33966294delAAA	uc003ztq.1	-						UBAP2_uc011loc.1_Intron|UBAP2_uc011lod.1_Intron|UBAP2_uc011loe.1_Intron|UBAP2_uc011lof.1_Intron|UBAP2_uc011log.1_Intron|UBAP2_uc003ztr.2_Intron	NM_018449	NP_060919			ubiquitin associated protein 2											ovary(3)	3			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)														---	---	---	---
DCAF12	25853	broad.mit.edu	37	9	34088274	34088274	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34088274delA	uc003ztt.2	-	9						NM_015397	NP_056212			DDB1 and CUL4 associated factor 12							centrosome|CUL4 RING ubiquitin ligase complex					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	34165939	34165940	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34165939_34165940insT								DCAF12 (39168 upstream) : UBAP1 (13071 downstream)																																			---	---	---	---
DNAI1	27019	broad.mit.edu	37	9	34459449	34459449	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34459449delT	uc003zum.2	+						DNAI1_uc011lom.1_Intron|C9orf25_uc003zuj.2_5'Flank|C9orf25_uc011lok.1_5'Flank|C9orf25_uc003zuk.2_5'Flank|C9orf25_uc011lol.1_5'Flank|C9orf25_uc003zul.2_5'Flank	NM_012144	NP_036276			dynein, axonemal, intermediate chain 1						cell projection organization	cilium axoneme|cytoplasm|dynein complex|microtubule	motor activity				0	all_epithelial(49;0.244)		LUSC - Lung squamous cell carcinoma(29;0.0107)|STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.0222)										Kartagener_syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	9	34607924	34607924	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34607924delA								CNTFR (18202 upstream) : C9orf23 (2569 downstream)																																			---	---	---	---
IL11RA	3590	broad.mit.edu	37	9	34658929	34658930	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34658929_34658930delTT	uc003zvi.2	+						IL11RA_uc011loq.1_Intron|IL11RA_uc003zvj.2_Intron|IL11RA_uc003zvk.2_Intron|IL11RA_uc010mke.2_Intron|IL11RA_uc003zvl.2_Intron	NM_004512	NP_004503			interleukin 11 receptor, alpha isoform 1							integral to plasma membrane	cytokine receptor activity			skin(1)	1	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.174)	Oprelvekin(DB00038)													---	---	---	---
CCL27	10850	broad.mit.edu	37	9	34662981	34662981	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34662981delA	uc003zvm.1	-							NM_006664	NP_006655			small inducible cytokine A27 precursor						cell-cell signaling|chemotaxis|immune response	extracellular space	chemokine activity				0	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.173)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	34697324	34697324	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34697324delT								CCL19 (6050 upstream) : CCL21 (11680 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	35000336	35000336	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35000336delT								DNAJB5 (1908 upstream) : C9orf131 (40766 downstream)																																			---	---	---	---
UNC13B	10497	broad.mit.edu	37	9	35371347	35371347	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35371347delT	uc003zwq.2	+						UNC13B_uc003zwr.2_Intron	NM_006377	NP_006368			UNC13 (C. elegans)-like						excretion|induction of apoptosis|intracellular signal transduction	cell junction|Golgi apparatus|synapse	metal ion binding|receptor activity			ovary(3)|large_intestine(1)|skin(1)	5	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)															---	---	---	---
ATP8B5P	158381	broad.mit.edu	37	9	35450411	35450411	+	RNA	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35450411delT	uc010mkn.1	+	10		c.3261delT			ATP8B5P_uc010mko.2_RNA|ATP8B5P_uc010mkp.2_RNA|ATP8B5P_uc003zwu.2_Intron					Homo sapiens cDNA, FLJ17320.												0																		---	---	---	---
CA9	768	broad.mit.edu	37	9	35677613	35677613	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35677613delA	uc003zxo.3	+						C9orf100_uc003zxl.2_5'Flank|CA9_uc003zxp.3_Intron	NM_001216	NP_001207			carbonic anhydrase IX precursor						one-carbon metabolic process	integral to membrane|microvillus membrane|nucleolus	carbonate dehydratase activity|zinc ion binding			ovary(4)|skin(1)	5	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)															---	---	---	---
RECK	8434	broad.mit.edu	37	9	36040810	36040810	+	Intron	DEL	T	-	-	rs67810399		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36040810delT	uc003zyv.2	+						RECK_uc010mld.2_Intron|RECK_uc003zyu.3_Intron|RECK_uc003zyw.2_Intron	NM_021111	NP_066934			RECK protein precursor							anchored to membrane|peripheral to membrane of membrane fraction|plasma membrane	metalloendopeptidase inhibitor activity|serine-type endopeptidase inhibitor activity			skin(2)|ovary(1)	3			LUSC - Lung squamous cell carcinoma(32;0.112)|STAD - Stomach adenocarcinoma(86;0.228)															---	---	---	---
CLTA	1211	broad.mit.edu	37	9	36197220	36197221	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36197220_36197221delTT	uc003zzc.2	+						CLTA_uc003zzd.2_Intron|CLTA_uc003zze.2_Intron|CLTA_uc011lpk.1_Intron|CLTA_uc003zzf.1_Intron	NM_007096	NP_009027			clathrin, light polypeptide A isoform b						axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|cytosol	structural molecule activity			central_nervous_system(1)	1			STAD - Stomach adenocarcinoma(86;0.228)															---	---	---	---
MELK	9833	broad.mit.edu	37	9	36610590	36610590	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:36610590delT	uc003zzn.2	+						MELK_uc011lpm.1_Intron|MELK_uc011lpn.1_Intron|MELK_uc011lpo.1_Intron|MELK_uc010mll.2_Intron|MELK_uc011lpp.1_Intron|MELK_uc010mlm.2_Intron|MELK_uc011lpq.1_Intron|MELK_uc011lpr.1_Intron|MELK_uc011lps.1_Intron	NM_014791	NP_055606			maternal embryonic leucine zipper kinase							cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	6		Acute lymphoblastic leukemia(2;1.09e-08)|all_hematologic(2;8.15e-06)	STAD - Stomach adenocarcinoma(86;0.228)															---	---	---	---
Unknown	0	broad.mit.edu	37	9	37394193	37394193	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37394193delT								ZCCHC7 (36050 upstream) : GRHPR (28488 downstream)																																			---	---	---	---
FRMPD1	22844	broad.mit.edu	37	9	37667059	37667060	+	Intron	INS	-	T	T	rs5897695		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37667059_37667060insT	uc004aag.1	+						FRMPD1_uc004aah.1_5'Flank	NM_014907	NP_055722			FERM and PDZ domain containing 1							cytoskeleton|cytosol|plasma membrane				ovary(4)|central_nervous_system(2)|skin(2)|breast(1)	9				GBM - Glioblastoma multiforme(29;0.00655)														---	---	---	---
FRMPD1	22844	broad.mit.edu	37	9	37674959	37674959	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37674959delA	uc004aag.1	+						FRMPD1_uc004aah.1_Intron	NM_014907	NP_055722			FERM and PDZ domain containing 1							cytoskeleton|cytosol|plasma membrane				ovary(4)|central_nervous_system(2)|skin(2)|breast(1)	9				GBM - Glioblastoma multiforme(29;0.00655)														---	---	---	---
EXOSC3	51010	broad.mit.edu	37	9	37780659	37780659	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37780659delA	uc004aal.2	-	4					EXOSC3_uc010mly.1_3'UTR|EXOSC3_uc004aam.2_3'UTR	NM_016042	NP_057126			exosome component 3 isoform 1						CUT catabolic process|DNA deamination|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|isotype switching|rRNA processing	cytoplasmic exosome (RNase complex)|cytosol|nuclear exosome (RNase complex)|nucleolus|transcriptionally active chromatin	3'-5'-exoribonuclease activity|protein binding|RNA binding			breast(2)	2				GBM - Glioblastoma multiforme(29;0.00771)|Lung(182;0.221)														---	---	---	---
DCAF10	79269	broad.mit.edu	37	9	37836770	37836770	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37836770delT	uc004aao.2	+						DCAF10_uc010mlz.2_Intron	NM_024345	NP_077321			WD repeat domain 32							CUL4 RING ubiquitin ligase complex				central_nervous_system(1)	1																		---	---	---	---
SHB	6461	broad.mit.edu	37	9	37979618	37979619	+	Intron	DEL	AA	-	-	rs111982445		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37979618_37979619delAA	uc004aax.2	-							NM_003028	NP_003019			Src homology 2 domain containing adaptor protein						angiogenesis|apoptosis|cell differentiation|signal transduction	cytoplasm|plasma membrane	SH3/SH2 adaptor activity			central_nervous_system(2)|skin(1)	3		all_epithelial(88;0.122)		GBM - Glioblastoma multiforme(29;3.27e-05)|Lung(182;0.0658)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	38643838	38643838	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:38643838delA								C9orf122 (20563 upstream) : CNTNAP3 (428928 downstream)																																			---	---	---	---
CNTNAP3	79937	broad.mit.edu	37	9	39117880	39117880	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:39117880delA	uc004abi.2	-						CNTNAP3_uc004abj.2_Intron|CNTNAP3_uc011lqr.1_Intron|CNTNAP3_uc004abk.1_Intron	NM_033655	NP_387504			cell recognition molecule CASPR3 precursor						cell adhesion|cell recognition|signal transduction	extracellular region|integral to membrane|plasma membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	40384118	40384118	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:40384118delA								FAM74A1 (476878 upstream) : FAM75A3 (316173 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	45436157	45436158	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:45436157_45436158delTT								FAM27C (444666 upstream) : FAM27A (290871 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	46874241	46874242	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:46874241_46874242delTG								KGFLP1 (125856 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	47202619	47202619	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:47202619delA								KGFLP1 (454234 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	65917354	65917355	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:65917354_65917355delAA								FAM74A4 (422968 upstream) : LOC442421 (579115 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	66532439	66532440	+	Intron	DEL	TC	-	-	rs67597739		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66532439_66532440delTC	uc010mnh.1	-						uc004aef.2_Intron					Homo sapiens cDNA FLJ20444 fis, clone KAT05128.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	68367122	68367122	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68367122delA								FAM27B (572933 upstream) : MIR1299 (635117 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	68375419	68375420	+	IGR	INS	-	C	C	rs138387266	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68375419_68375420insC								FAM27B (581230 upstream) : MIR1299 (626819 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	68411745	68411746	+	Intron	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68411745_68411746delCT	uc004aew.1	+						uc004aex.2_5'Flank					Homo sapiens cDNA, FLJ98602.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	68473056	68473056	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68473056delT								FAM27B (678867 upstream) : MIR1299 (529183 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	68480277	68480277	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68480277delA								FAM27B (686088 upstream) : MIR1299 (521962 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	68491533	68491534	+	IGR	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68491533_68491534delTC								FAM27B (697344 upstream) : MIR1299 (510705 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	68989452	68989452	+	IGR	DEL	G	-	-	rs71498602		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68989452delG								None (None upstream) : MIR1299 (12787 downstream)																																			---	---	---	---
LOC440896	440896	broad.mit.edu	37	9	69187177	69187177	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69187177delG	uc004afh.2	-											Homo sapiens cDNA FLJ30529 fis, clone BRAWH2001052.												0																		---	---	---	---
CBWD6	644019	broad.mit.edu	37	9	69260359	69260360	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69260359_69260360delAA	uc004afj.3	-						CBWD6_uc004afk.3_Intron|CBWD6_uc011lrf.1_Intron|CBWD6_uc004afl.3_Intron	NM_001085457	NP_001078926			COBW domain containing 6								ATP binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	69818103	69818104	+	IGR	INS	-	CTG	CTG			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69818103_69818104insCTG								LOC100133920 (153154 upstream) : FOXD4L5 (357605 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	69823054	69823057	+	IGR	DEL	CCTG	-	-	rs142790503	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69823054_69823057delCCTG								LOC100133920 (158105 upstream) : FOXD4L5 (352652 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	69829540	69829541	+	IGR	DEL	TC	-	-	rs112099364		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:69829540_69829541delTC								LOC100133920 (164591 upstream) : FOXD4L5 (346168 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	70653055	70653056	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:70653055_70653056delAA								CBWD3 (152992 upstream) : FOXD4L3 (264727 downstream)																																			---	---	---	---
PGM5	5239	broad.mit.edu	37	9	71100685	71100685	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71100685delT	uc004agr.2	+							NM_021965	NP_068800			phosphoglucomutase 5						cell adhesion|cellular calcium ion homeostasis|glucose metabolic process	costamere|dystrophin-associated glycoprotein complex|focal adhesion|intercalated disc|internal side of plasma membrane|sarcolemma|spot adherens junction|stress fiber|Z disc	intramolecular transferase activity, phosphotransferases|magnesium ion binding|structural molecule activity			ovary(1)|pancreas(1)	2																		---	---	---	---
PIP5K1B	8395	broad.mit.edu	37	9	71344848	71344848	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71344848delA	uc004agu.2	+						PIP5K1B_uc011lrq.1_Intron	NM_003558	NP_003549			phosphatidylinositol-4-phosphate 5-kinase, type							endomembrane system|membrane|uropod	1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|protein binding			stomach(1)	1				Lung(182;0.133)														---	---	---	---
PIP5K1B	8395	broad.mit.edu	37	9	71555419	71555419	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71555419delA	uc004agu.2	+						PIP5K1B_uc011lrq.1_Intron|PIP5K1B_uc004agv.2_Intron	NM_003558	NP_003549			phosphatidylinositol-4-phosphate 5-kinase, type							endomembrane system|membrane|uropod	1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|protein binding			stomach(1)	1				Lung(182;0.133)														---	---	---	---
PIP5K1B	8395	broad.mit.edu	37	9	71577124	71577124	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71577124delA	uc004agu.2	+						PIP5K1B_uc011lrq.1_Intron|PIP5K1B_uc004agv.2_Intron|uc004agx.1_Intron	NM_003558	NP_003549			phosphatidylinositol-4-phosphate 5-kinase, type							endomembrane system|membrane|uropod	1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|protein binding			stomach(1)	1				Lung(182;0.133)														---	---	---	---
PIP5K1B	8395	broad.mit.edu	37	9	71606877	71606877	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71606877delA	uc004agu.2	+						PIP5K1B_uc011lrq.1_Intron|PIP5K1B_uc004agv.2_Intron	NM_003558	NP_003549			phosphatidylinositol-4-phosphate 5-kinase, type							endomembrane system|membrane|uropod	1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|protein binding			stomach(1)	1				Lung(182;0.133)														---	---	---	---
PTAR1	375743	broad.mit.edu	37	9	72353279	72353279	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72353279delT	uc004ahj.3	-						PTAR1_uc004ahi.2_Intron	NM_001099666	NP_001093136			protein prenyltransferase alpha subunit repeat						protein prenylation		protein prenyltransferase activity			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	72569700	72569700	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72569700delA								C9orf135 (48553 upstream) : MAMDC2 (88797 downstream)																																			---	---	---	---
MAMDC2	256691	broad.mit.edu	37	9	72753579	72753579	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72753579delT	uc004ahm.2	+						MAMDC2_uc004ahn.2_Intron	NM_153267	NP_694999			MAM domain containing 2 precursor							endoplasmic reticulum|membrane				central_nervous_system(1)|pancreas(1)	2																		---	---	---	---
SMC5	23137	broad.mit.edu	37	9	72933303	72933304	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72933303_72933304delAA	uc004ahr.2	+						uc004ahs.1_5'Flank	NM_015110	NP_055925			SMC5 protein						DNA recombination|DNA repair	chromosome|nucleus	ATP binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
TRPM3	80036	broad.mit.edu	37	9	73625845	73625848	+	Intron	DEL	ACAT	-	-	rs59803868		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73625845_73625848delACAT	uc004aid.2	-						TRPM3_uc004aic.2_Intron|TRPM3_uc010mor.2_Intron|TRPM3_uc004aii.2_Intron	NM_001007471	NP_001007472			transient receptor potential cation channel,							integral to membrane	calcium channel activity			ovary(3)|pancreas(2)|central_nervous_system(2)|skin(2)	9																		---	---	---	---
TRPM3	80036	broad.mit.edu	37	9	74020004	74020004	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74020004delT	uc004aii.2	-							NM_206948	NP_996831			transient receptor potential cation channel,							integral to membrane	calcium channel activity			ovary(3)|pancreas(2)|central_nervous_system(2)|skin(2)	9																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	74406958	74406959	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74406958_74406959delAA								TMEM2 (23158 upstream) : FAM108B1 (70411 downstream)																																			---	---	---	---
C9orf85	138241	broad.mit.edu	37	9	74581541	74581541	+	Intron	DEL	A	-	-	rs113434939		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74581541delA	uc004ain.2	+						C9orf85_uc004aio.2_Intron|C9orf85_uc010mou.2_Intron|C9orf85_uc010mov.2_Intron	NM_182505	NP_872311			hypothetical protein LOC138241												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	74622336	74622336	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74622336delT								C9orf85 (22946 upstream) : C9orf57 (43962 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	74627078	74627078	+	IGR	DEL	T	-	-	rs113085964		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74627078delT								C9orf85 (27688 upstream) : C9orf57 (39220 downstream)																																			---	---	---	---
C9orf57	138240	broad.mit.edu	37	9	74685468	74685469	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:74685468_74685469insA	uc011lsd.1	-							NM_001128618	NP_001122090			hypothetical protein LOC138240							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	75486041	75486046	+	IGR	DEL	GGGCAA	-	-	rs145879053		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75486041_75486046delGGGCAA								TMC1 (34774 upstream) : ALDH1A1 (29542 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	75861549	75861549	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:75861549delA								ANXA1 (76242 upstream) : None (None downstream)																																			---	---	---	---
RORB	6096	broad.mit.edu	37	9	77214231	77214231	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77214231delA	uc004ajh.2	+							NM_006914	NP_008845			RAR-related orphan receptor B						eye photoreceptor cell development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|visual perception	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(2)|lung(1)|skin(1)	4																		---	---	---	---
RORB	6096	broad.mit.edu	37	9	77300186	77300186	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77300186delG	uc004aji.2	+						RORB_uc004ajh.2_Intron	NM_006914	NP_008845			RAR-related orphan receptor B						eye photoreceptor cell development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|visual perception	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(2)|lung(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	77314233	77314233	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77314233delA								RORB (12118 upstream) : TRPM6 (23178 downstream)																																			---	---	---	---
TRPM6	140803	broad.mit.edu	37	9	77424605	77424605	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77424605delA	uc004ajl.1	-						TRPM6_uc004ajk.1_Intron|TRPM6_uc010mpb.1_Intron|TRPM6_uc010mpc.1_Intron|TRPM6_uc010mpd.1_Intron|TRPM6_uc010mpe.1_Intron	NM_017662	NP_060132			transient receptor potential cation channel,						response to toxin	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|stomach(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	77668709	77668709	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77668709delA								C9orf41 (25399 upstream) : C9orf95 (7409 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	77998270	77998271	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77998270_77998271delAA								OSTF1 (236157 upstream) : PCSK5 (507289 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	78269696	78269696	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78269696delC								OSTF1 (507583 upstream) : PCSK5 (235864 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	78373941	78373942	+	IGR	INS	-	A	A	rs112432235		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78373941_78373942insA								OSTF1 (611828 upstream) : PCSK5 (131618 downstream)																																			---	---	---	---
PCSK5	5125	broad.mit.edu	37	9	78678053	78678053	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78678053delT	uc004ajz.2	+						PCSK5_uc004ajy.2_Intron|PCSK5_uc004aka.2_Intron	NM_006200	NP_006191			proprotein convertase subtilisin/kexin type 5						anterior/posterior pattern formation|cell-cell signaling|cytokine biosynthetic process|embryo implantation|embryonic digestive tract development|embryonic skeletal system development|heart development|kidney development|limb morphogenesis|nerve growth factor processing|nerve growth factor receptor signaling pathway|peptide biosynthetic process|renin secretion into blood stream|respiratory tube development|signal peptide processing|viral assembly, maturation, egress, and release	extracellular space|Golgi lumen|stored secretory granule	peptide binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3																		---	---	---	---
PCSK5	5125	broad.mit.edu	37	9	78709527	78709528	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78709527_78709528delTT	uc004ajz.2	+						PCSK5_uc004ajy.2_Intron|PCSK5_uc004aka.2_Intron	NM_006200	NP_006191			proprotein convertase subtilisin/kexin type 5						anterior/posterior pattern formation|cell-cell signaling|cytokine biosynthetic process|embryo implantation|embryonic digestive tract development|embryonic skeletal system development|heart development|kidney development|limb morphogenesis|nerve growth factor processing|nerve growth factor receptor signaling pathway|peptide biosynthetic process|renin secretion into blood stream|respiratory tube development|signal peptide processing|viral assembly, maturation, egress, and release	extracellular space|Golgi lumen|stored secretory granule	peptide binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3																		---	---	---	---
PCSK5	5125	broad.mit.edu	37	9	78794417	78794417	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78794417delA	uc004ajz.2	+						PCSK5_uc004aka.2_Intron|PCSK5_uc004akb.2_5'Flank	NM_006200	NP_006191			proprotein convertase subtilisin/kexin type 5						anterior/posterior pattern formation|cell-cell signaling|cytokine biosynthetic process|embryo implantation|embryonic digestive tract development|embryonic skeletal system development|heart development|kidney development|limb morphogenesis|nerve growth factor processing|nerve growth factor receptor signaling pathway|peptide biosynthetic process|renin secretion into blood stream|respiratory tube development|signal peptide processing|viral assembly, maturation, egress, and release	extracellular space|Golgi lumen|stored secretory granule	peptide binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3																		---	---	---	---
VPS13A	23230	broad.mit.edu	37	9	79802618	79802618	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79802618delT	uc004akr.2	+						VPS13A_uc004akp.3_Intron|VPS13A_uc004akq.3_Intron|VPS13A_uc004aks.2_Intron	NM_033305	NP_150648			vacuolar protein sorting 13A isoform A						Golgi to endosome transport|protein transport	intracellular	protein binding			pancreas(3)|skin(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)	10																		---	---	---	---
VPS13A	23230	broad.mit.edu	37	9	79811592	79811593	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79811592_79811593delTT	uc004akr.2	+						VPS13A_uc004akp.3_Intron|VPS13A_uc004akq.3_Intron|VPS13A_uc004aks.2_Intron	NM_033305	NP_150648			vacuolar protein sorting 13A isoform A						Golgi to endosome transport|protein transport	intracellular	protein binding			pancreas(3)|skin(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)	10																		---	---	---	---
GNA14	9630	broad.mit.edu	37	9	80194112	80194112	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80194112delA	uc004aku.2	-							NM_004297	NP_004288			G alpha 14						activation of phospholipase C activity by dopamine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|platelet activation|protein ADP-ribosylation	heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			ovary(2)	2																		---	---	---	---
GNA14	9630	broad.mit.edu	37	9	80203273	80203273	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80203273delT	uc004aku.2	-							NM_004297	NP_004288			G alpha 14						activation of phospholipase C activity by dopamine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|platelet activation|protein ADP-ribosylation	heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	80286844	80286845	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80286844_80286845delAA								GNA14 (23612 upstream) : GNAQ (44794 downstream)																																			---	---	---	---
GNAQ	2776	broad.mit.edu	37	9	80575691	80575691	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80575691delA	uc004akw.2	-							NM_002072	NP_002063			guanine nucleotide binding protein (G protein),						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|glutamate signaling pathway|negative regulation of protein kinase activity|platelet activation|protein ADP-ribosylation|protein stabilization|regulation of action potential|regulation of catenin import into nucleus	cytoplasm|heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activator activity|GTPase activity|signal transducer activity			eye(136)|skin(44)|meninges(11)|ovary(1)|kidney(1)	193								Mis		uveal melanoma								---	---	---	---
Unknown	0	broad.mit.edu	37	9	80828495	80828495	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80828495delC								GNAQ (182303 upstream) : CEP78 (22496 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	80902011	80902011	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:80902011delA								CEP78 (15212 upstream) : PSAT1 (10048 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	81923479	81923479	+	IGR	DEL	C	-	-	rs273434	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:81923479delC								PSAT1 (978472 upstream) : TLE4 (263399 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	82439464	82439464	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82439464delA								TLE4 (97807 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	82517708	82517708	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82517708delA								TLE4 (176051 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	82629942	82629943	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82629942_82629943delTT								TLE4 (288285 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	83109556	83109557	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:83109556_83109557delTT								TLE4 (767899 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	83871925	83871925	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:83871925delA								None (None upstream) : TLE1 (326675 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	84078698	84078698	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84078698delT								None (None upstream) : TLE1 (119902 downstream)																																			---	---	---	---
TLE1	7088	broad.mit.edu	37	9	84237357	84237357	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84237357delT	uc004aly.2	-						TLE1_uc004alz.2_Intron|TLE1_uc011lsr.1_Intron|TLE1_uc004ama.1_Intron|TLE1_uc011lss.1_Intron	NM_005077	NP_005068			transducin-like enhancer protein 1						negative regulation of Wnt receptor signaling pathway|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway		transcription factor binding			ovary(1)|skin(1)	2																		---	---	---	---
TLE1	7088	broad.mit.edu	37	9	84247006	84247006	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84247006delA	uc004aly.2	-						TLE1_uc004alz.2_Intron|TLE1_uc011lsr.1_Intron|TLE1_uc004ama.1_Intron|TLE1_uc011lss.1_Intron	NM_005077	NP_005068			transducin-like enhancer protein 1						negative regulation of Wnt receptor signaling pathway|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway		transcription factor binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	84441825	84441825	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84441825delT								TLE1 (138229 upstream) : FLJ43950 (86527 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	84518013	84518013	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84518013delA								TLE1 (214417 upstream) : FLJ43950 (10339 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	84780074	84780075	+	IGR	INS	-	TAAAC	TAAAC	rs145432543		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84780074_84780075insTAAAC								FLJ46321 (169904 upstream) : RASEF (817242 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	85551279	85551279	+	IGR	DEL	T	-	-	rs74458854		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85551279delT								FLJ46321 (941109 upstream) : RASEF (46038 downstream)																																			---	---	---	---
FRMD3	257019	broad.mit.edu	37	9	85906483	85906484	+	Intron	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:85906483_85906484delTC	uc004ams.1	-						FRMD3_uc004amr.1_Intron	NM_174938	NP_777598			FERM domain containing 3							cytoplasm|cytoskeleton|extrinsic to membrane|integral to membrane	cytoskeletal protein binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	86207927	86207929	+	IGR	DEL	TTT	-	-	rs141519195		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86207927_86207929delTTT								FRMD3 (54579 upstream) : C9orf103 (30037 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	86210769	86210769	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86210769delA								FRMD3 (57421 upstream) : C9orf103 (27197 downstream)																																			---	---	---	---
UBQLN1	29979	broad.mit.edu	37	9	86278507	86278507	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86278507delA	uc004amv.2	-						UBQLN1_uc004amw.2_Intron	NM_013438	NP_038466			ubiquilin 1 isoform 1						apoptosis|regulation of protein ubiquitination|response to hypoxia	endoplasmic reticulum|nucleus|perinuclear region of cytoplasm|proteasome complex	kinase binding				0																		---	---	---	---
KIF27	55582	broad.mit.edu	37	9	86503511	86503511	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86503511delA	uc004ana.2	-						KIF27_uc010mpw.2_Intron|KIF27_uc010mpx.2_Intron	NM_017576	NP_060046			kinesin family member 27						cilium assembly|microtubule-based movement	cilium|cytoplasm|microtubule	ATP binding|microtubule motor activity			lung(4)|skin(1)	5																		---	---	---	---
KIF27	55582	broad.mit.edu	37	9	86504825	86504826	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86504825_86504826insA	uc004ana.2	-						KIF27_uc010mpw.2_Intron|KIF27_uc010mpx.2_Intron	NM_017576	NP_060046			kinesin family member 27						cilium assembly|microtubule-based movement	cilium|cytoplasm|microtubule	ATP binding|microtubule motor activity			lung(4)|skin(1)	5																		---	---	---	---
KIF27	55582	broad.mit.edu	37	9	86506111	86506112	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86506111_86506112insA	uc004ana.2	-						KIF27_uc010mpw.2_Intron|KIF27_uc010mpx.2_Intron	NM_017576	NP_060046			kinesin family member 27						cilium assembly|microtubule-based movement	cilium|cytoplasm|microtubule	ATP binding|microtubule motor activity			lung(4)|skin(1)	5																		---	---	---	---
KIF27	55582	broad.mit.edu	37	9	86535299	86535299	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86535299delA	uc004ana.2	-						KIF27_uc010mpw.2_Intron|KIF27_uc010mpx.2_Intron	NM_017576	NP_060046			kinesin family member 27						cilium assembly|microtubule-based movement	cilium|cytoplasm|microtubule	ATP binding|microtubule motor activity			lung(4)|skin(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	86645745	86645747	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:86645745_86645747delTTT								RMI1 (26763 upstream) : SLC28A3 (247345 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	87180188	87180188	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87180188delA								SLC28A3 (196775 upstream) : NTRK2 (103278 downstream)																																			---	---	---	---
NTRK2	4915	broad.mit.edu	37	9	87632933	87632934	+	Intron	DEL	TT	-	-	rs75919039		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87632933_87632934delTT	uc004aoa.1	+						NTRK2_uc004anz.1_Intron	NM_001018064	NP_001018074			neurotrophic tyrosine kinase, receptor, type 2						activation of adenylate cyclase activity|cell differentiation|nerve growth factor receptor signaling pathway|nervous system development	integral to plasma membrane	ATP binding|neurotrophin receptor activity|transmembrane receptor protein tyrosine kinase activity			lung(11)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|liver(1)	16															TSP Lung(25;0.17)			---	---	---	---
Unknown	0	broad.mit.edu	37	9	87706802	87706802	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:87706802delT								NTRK2 (68297 upstream) : AGTPBP1 (454653 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	88368144	88368144	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88368144delA								AGTPBP1 (11200 upstream) : NAA35 (187913 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	88470607	88470607	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88470607delA								AGTPBP1 (113663 upstream) : NAA35 (85450 downstream)																																			---	---	---	---
NAA35	60560	broad.mit.edu	37	9	88571356	88571356	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88571356delT	uc004aoi.3	+						NAA35_uc004aoj.3_Intron|NAA35_uc004aok.1_Intron	NM_024635	NP_078911			corneal wound healing-related protein						smooth muscle cell proliferation	cytoplasm|nucleus|plasma membrane				skin(2)|central_nervous_system(1)	3																		---	---	---	---
NAA35	60560	broad.mit.edu	37	9	88618680	88618680	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88618680delT	uc004aoi.3	+						NAA35_uc004aoj.3_Intron	NM_024635	NP_078911			corneal wound healing-related protein						smooth muscle cell proliferation	cytoplasm|nucleus|plasma membrane				skin(2)|central_nervous_system(1)	3																		---	---	---	---
ZCCHC6	79670	broad.mit.edu	37	9	88919729	88919729	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:88919729delT	uc004aoq.2	-						ZCCHC6_uc010mqe.2_Intron|ZCCHC6_uc011ltf.1_Intron|ZCCHC6_uc004aor.2_Intron|ZCCHC6_uc004aos.2_Intron|ZCCHC6_uc004aot.2_Intron|ZCCHC6_uc004aou.2_Intron	NM_024617	NP_078893			zinc finger, CCHC domain containing 6						RNA 3'-end processing		nucleic acid binding|RNA uridylyltransferase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	89290808	89290809	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:89290808_89290809delTT								ZCCHC6 (321430 upstream) : GAS1 (268470 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	89858597	89858598	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:89858597_89858598insA	uc004apb.1	-											Homo sapiens cDNA clone IMAGE:30346008.																														---	---	---	---
DAPK1	1612	broad.mit.edu	37	9	90122561	90122561	+	Intron	DEL	T	-	-	rs111451985		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90122561delT	uc004apc.2	+						DAPK1_uc004ape.2_Intron|DAPK1_uc004apd.2_Intron|DAPK1_uc011ltg.1_Intron|DAPK1_uc011lth.1_Intron	NM_004938	NP_004929			death-associated protein kinase 1						apoptosis|induction of apoptosis by extracellular signals|intracellular protein kinase cascade	actin cytoskeleton|cytoplasm	ATP binding|calmodulin binding|protein serine/threonine kinase activity			ovary(1)|breast(1)	2														Chronic_Lymphocytic_Leukemia_Familial_Clustering_of				---	---	---	---
DAPK1	1612	broad.mit.edu	37	9	90197050	90197050	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90197050delT	uc004apc.2	+						DAPK1_uc004ape.2_Intron|DAPK1_uc004apd.2_Intron|DAPK1_uc011ltg.1_Intron|DAPK1_uc011lth.1_Intron	NM_004938	NP_004929			death-associated protein kinase 1						apoptosis|induction of apoptosis by extracellular signals|intracellular protein kinase cascade	actin cytoskeleton|cytoplasm	ATP binding|calmodulin binding|protein serine/threonine kinase activity			ovary(1)|breast(1)	2														Chronic_Lymphocytic_Leukemia_Familial_Clustering_of				---	---	---	---
DAPK1	1612	broad.mit.edu	37	9	90235697	90235697	+	Intron	DEL	A	-	-	rs13289919		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90235697delA	uc004apc.2	+						DAPK1_uc004ape.2_Intron|DAPK1_uc004apd.2_Intron|DAPK1_uc011ltg.1_Intron|DAPK1_uc011lth.1_Intron	NM_004938	NP_004929			death-associated protein kinase 1						apoptosis|induction of apoptosis by extracellular signals|intracellular protein kinase cascade	actin cytoskeleton|cytoplasm	ATP binding|calmodulin binding|protein serine/threonine kinase activity			ovary(1)|breast(1)	2														Chronic_Lymphocytic_Leukemia_Familial_Clustering_of				---	---	---	---
DAPK1	1612	broad.mit.edu	37	9	90312868	90312868	+	Intron	DEL	A	-	-	rs78217135		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90312868delA	uc004apc.2	+						DAPK1_uc004apd.2_Intron|DAPK1_uc011ltg.1_Intron|DAPK1_uc011lth.1_Intron	NM_004938	NP_004929			death-associated protein kinase 1						apoptosis|induction of apoptosis by extracellular signals|intracellular protein kinase cascade	actin cytoskeleton|cytoplasm	ATP binding|calmodulin binding|protein serine/threonine kinase activity			ovary(1)|breast(1)	2														Chronic_Lymphocytic_Leukemia_Familial_Clustering_of				---	---	---	---
Unknown	0	broad.mit.edu	37	9	90673891	90673891	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90673891delA	uc004apv.1	-											full-length cDNA clone CS0DI004YC05 of Placenta Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
SPIN1	10927	broad.mit.edu	37	9	91006252	91006252	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91006252delA	uc010mqj.2	+						SPIN1_uc004apy.2_Intron|SPIN1_uc004apz.2_Intron|SPIN1_uc010mqk.2_Intron	NM_006717	NP_006708			spindlin						cell cycle|gamete generation|multicellular organismal development	nucleus	methylated histone residue binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	91410367	91410368	+	IGR	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91410367_91410368delAC								LOC286238 (143292 upstream) : C9orf47 (195410 downstream)																																			---	---	---	---
SEMA4D	10507	broad.mit.edu	37	9	92007239	92007239	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92007239delG	uc004aqo.1	-						SEMA4D_uc011ltm.1_Intron|SEMA4D_uc011ltn.1_Intron|SEMA4D_uc011lto.1_Intron|SEMA4D_uc004aqp.1_Intron	NM_006378	NP_006369			semaphorin 4D isoform 1						anti-apoptosis|axon guidance|cell adhesion|immune response	integral to membrane|plasma membrane	receptor activity|receptor binding			ovary(1)|pancreas(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	92730379	92730379	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:92730379delT								LOC100129066 (395705 upstream) : DIRAS2 (641735 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	93291961	93291962	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93291961_93291962delTT	uc004aqt.1	-											Homo sapiens cDNA FLJ46333 fis, clone TESTI4045701.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	93868193	93868193	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:93868193delT								SYK (207360 upstream) : AUH (107906 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	94274119	94274119	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94274119delT								NFIL3 (87975 upstream) : ROR2 (51254 downstream)																																			---	---	---	---
ROR2	4920	broad.mit.edu	37	9	94337565	94337565	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94337565delA	uc004ari.1	-							NM_004560	NP_004551			receptor tyrosine kinase-like orphan receptor 2						negative regulation of cell proliferation|positive regulation of cell migration|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			lung(8)|central_nervous_system(5)|ovary(3)|large_intestine(2)|stomach(1)|breast(1)	20																		---	---	---	---
ROR2	4920	broad.mit.edu	37	9	94562625	94562627	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94562625_94562627delAAA	uc004arj.1	-						ROR2_uc004ari.1_Intron|ROR2_uc004ark.2_Intron	NM_004560	NP_004551			receptor tyrosine kinase-like orphan receptor 2						negative regulation of cell proliferation|positive regulation of cell migration|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			lung(8)|central_nervous_system(5)|ovary(3)|large_intestine(2)|stomach(1)|breast(1)	20																		---	---	---	---
ROR2	4920	broad.mit.edu	37	9	94636515	94636515	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94636515delA	uc004arj.1	-						ROR2_uc004ari.1_Intron|ROR2_uc004ark.2_Intron	NM_004560	NP_004551			receptor tyrosine kinase-like orphan receptor 2						negative regulation of cell proliferation|positive regulation of cell migration|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			lung(8)|central_nervous_system(5)|ovary(3)|large_intestine(2)|stomach(1)|breast(1)	20																		---	---	---	---
ROR2	4920	broad.mit.edu	37	9	94654815	94654815	+	Intron	DEL	T	-	-	rs145553027	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94654815delT	uc004arj.1	-						ROR2_uc004ari.1_Intron|ROR2_uc004ark.2_Intron	NM_004560	NP_004551			receptor tyrosine kinase-like orphan receptor 2						negative regulation of cell proliferation|positive regulation of cell migration|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			lung(8)|central_nervous_system(5)|ovary(3)|large_intestine(2)|stomach(1)|breast(1)	20																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	94774317	94774317	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94774317delA								ROR2 (61873 upstream) : SPTLC1 (19103 downstream)																																			---	---	---	---
SPTLC1	10558	broad.mit.edu	37	9	94802682	94802683	+	Intron	INS	-	A	A	rs112216789		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:94802682_94802683insA	uc004arl.1	-						SPTLC1_uc011ltv.1_Intron	NM_006415	NP_006406			serine palmitoyltransferase subunit 1 isoform a							integral to membrane|SPOTS complex	protein binding|pyridoxal phosphate binding|serine C-palmitoyltransferase activity|transferase activity, transferring nitrogenous groups			ovary(1)|breast(1)	2					L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)													---	---	---	---
IARS	3376	broad.mit.edu	37	9	95020882	95020884	+	Intron	DEL	AAC	-	-	rs3837251		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95020882_95020884delAAC	uc004art.1	-						IARS_uc004ars.1_Intron|IARS_uc004aru.3_Intron|IARS_uc010mqr.2_Intron|IARS_uc010mqt.2_Intron	NM_013417	NP_038203			isoleucine tRNA synthetase						isoleucyl-tRNA aminoacylation	cytosol|nucleus|soluble fraction	ATP binding|isoleucine-tRNA ligase activity|protein binding			ovary(1)|skin(1)	2					L-Isoleucine(DB00167)													---	---	---	---
IARS	3376	broad.mit.edu	37	9	95025341	95025341	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95025341delA	uc004art.1	-						IARS_uc004ars.1_Intron|IARS_uc004aru.3_Intron|IARS_uc010mqr.2_Intron|IARS_uc010mqt.2_Intron	NM_013417	NP_038203			isoleucine tRNA synthetase						isoleucyl-tRNA aminoacylation	cytosol|nucleus|soluble fraction	ATP binding|isoleucine-tRNA ligase activity|protein binding			ovary(1)|skin(1)	2					L-Isoleucine(DB00167)													---	---	---	---
NOL8	55035	broad.mit.edu	37	9	95085870	95085870	+	Intron	DEL	A	-	-	rs75489638		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95085870delA	uc004arv.2	-						CENPP_uc004arz.2_5'Flank|CENPP_uc010mqx.2_5'Flank|NOL8_uc004arw.2_Intron|NOL8_uc011ltw.1_Intron|NOL8_uc004arx.2_Intron|CENPP_uc004ary.1_5'Flank	NM_017948	NP_060418			nucleolar protein 8						DNA replication|positive regulation of cell growth	nucleolus	nucleotide binding|protein binding|RNA binding			ovary(1)	1																		---	---	---	---
CENPP	401541	broad.mit.edu	37	9	95173260	95173260	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95173260delT	uc004arz.2	+						CENPP_uc010mqx.2_Intron	NM_001012267	NP_001012267			centromere protein P						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	chromosome, centromeric region|cytosol|nucleoplasm				ovary(2)	2																		---	---	---	---
ASPN	54829	broad.mit.edu	37	9	95233140	95233140	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95233140delT	uc004ase.1	-						CENPP_uc004arz.2_Intron|CENPP_uc010mqx.2_Intron|ASPN_uc010mqy.1_Intron	NM_017680	NP_060150			asporin precursor						bone mineralization|negative regulation of tooth mineralization|negative regulation of transforming growth factor beta receptor signaling pathway	proteinaceous extracellular matrix	calcium ion binding				0																		---	---	---	---
FAM120A	23196	broad.mit.edu	37	9	96217951	96217951	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96217951delT	uc004atw.2	+						FAM120AOS_uc004ats.3_5'Flank|FAM120AOS_uc004att.3_5'Flank|FAM120AOS_uc004atu.3_5'Flank|FAM120A_uc004atv.2_Intron	NM_014612	NP_055427			oxidative stress-associated Src activator							cytoplasm|plasma membrane	RNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	96729098	96729099	+	IGR	DEL	AA	-	-	rs75045968		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96729098_96729099delAA								BARX1 (11490 upstream) : PTPDC1 (63977 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	97097144	97097144	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97097144delT	uc004auq.1	+											Homo sapiens cDNA FLJ37869 fis, clone BRSSN2017422.																														---	---	---	---
FANCC	2176	broad.mit.edu	37	9	97934766	97934766	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97934766delT	uc004avh.2	-						FANCC_uc004avi.3_Intron|FANCC_uc010mrm.1_Intron|FANCC_uc011lul.1_Intron	NM_000136	NP_000127			Fanconi anemia, complementation group C						protein complex assembly	cytosol|nucleoplasm	protein binding			kidney(1)	1		Acute lymphoblastic leukemia(62;0.138)						D|Mis|N|F|S			AML|leukemia		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
Unknown	0	broad.mit.edu	37	9	98114626	98114627	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98114626_98114627delAA								FANCC (34635 upstream) : PTCH1 (90639 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	98120158	98120158	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98120158delT								FANCC (40167 upstream) : PTCH1 (85108 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	98171327	98171327	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98171327delT								FANCC (91336 upstream) : PTCH1 (33939 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	98203649	98203649	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98203649delA								FANCC (123658 upstream) : PTCH1 (1617 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	98352054	98352054	+	IGR	DEL	A	-	-	rs115174885	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98352054delA								PTCH1 (72807 upstream) : C9orf130 (216318 downstream)																																			---	---	---	---
C9orf130	100128782	broad.mit.edu	37	9	98579474	98579474	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98579474delT	uc004avp.3	-							NR_023390				Homo sapiens cDNA FLJ34818 fis, clone NT2NE2008077.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	98890940	98890941	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98890940_98890941insT								NCRNA00092 (106903 upstream) : HSD17B3 (106648 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	98955317	98955317	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98955317delT								NCRNA00092 (171280 upstream) : HSD17B3 (42272 downstream)																																			---	---	---	---
SLC35D2	11046	broad.mit.edu	37	9	99111815	99111815	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99111815delT	uc004awc.2	-						SLC35D2_uc010msd.2_Intron|SLC35D2_uc010mse.2_Intron|SLC35D2_uc010msf.2_Intron|SLC35D2_uc004awd.2_Intron	NM_007001	NP_008932			solute carrier family 35, member D2							Golgi membrane|integral to membrane	nucleotide-sugar transmembrane transporter activity				0		Acute lymphoblastic leukemia(62;0.0167)																---	---	---	---
CDC14B	8555	broad.mit.edu	37	9	99348463	99348463	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99348463delG	uc004awj.2	-						CDC14B_uc004awk.2_Intron|CDC14B_uc004awl.2_Intron	NM_033331	NP_201588			CDC14 homolog B isoform 2						activation of anaphase-promoting complex activity|DNA repair|G2/M transition DNA damage checkpoint	nucleolus|nucleoplasm	protein binding|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(1)	1		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
TDRD7	23424	broad.mit.edu	37	9	100173155	100173155	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100173155delT	uc004axj.2	+						TDRD7_uc011lux.1_5'Flank	NM_014290	NP_055105			tudor domain containing 7						lens fiber cell differentiation|lens morphogenesis in camera-type eye|posttranscriptional regulation of gene expression|spermatogenesis	chromatoid body	mRNA binding			ovary(2)|pancreas(1)	3		Acute lymphoblastic leukemia(62;0.158)																---	---	---	---
TDRD7	23424	broad.mit.edu	37	9	100258231	100258231	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100258231delA	uc004axj.2	+	17					TDRD7_uc011lux.1_3'UTR|TDRD7_uc011luy.1_3'UTR	NM_014290	NP_055105			tudor domain containing 7						lens fiber cell differentiation|lens morphogenesis in camera-type eye|posttranscriptional regulation of gene expression|spermatogenesis	chromatoid body	mRNA binding			ovary(2)|pancreas(1)	3		Acute lymphoblastic leukemia(62;0.158)																---	---	---	---
TSTD2	158427	broad.mit.edu	37	9	100365282	100365282	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100365282delT	uc004axn.2	-						TSTD2_uc004axo.2_Intron	NM_139246	NP_640339			thiosulfate sulfurtransferase (rhodanese)-like											ovary(2)	2																		---	---	---	---
NCBP1	4686	broad.mit.edu	37	9	100420786	100420786	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100420786delT	uc004axq.2	+							NM_002486	NP_002477			nuclear cap binding protein subunit 1, 80kDa						gene silencing by RNA|histone mRNA metabolic process|mRNA 3'-end processing|mRNA capping|mRNA cleavage|mRNA export from nucleus|ncRNA metabolic process|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of mRNA 3'-end processing|positive regulation of viral transcription|regulation of translational initiation|spliceosomal snRNP assembly|termination of RNA polymerase II transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	cytosol|mRNA cap binding complex|nucleoplasm|ribonucleoprotein complex	protein binding|RNA cap binding			central_nervous_system(1)	1		Acute lymphoblastic leukemia(62;0.158)																---	---	---	---
ANP32B	10541	broad.mit.edu	37	9	100777785	100777788	+	3'UTR	DEL	AAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100777785_100777788delAAAA	uc004aya.2	+	7						NM_006401	NP_006392			acidic (leucine-rich) nuclear phosphoprotein 32							cytoplasm|nucleus					0		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
Unknown	0	broad.mit.edu	37	9	100788318	100788321	+	IGR	DEL	AAAA	-	-	rs36000914		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100788318_100788321delAAAA								ANP32B (10096 upstream) : NANS (19568 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	101047317	101047318	+	IGR	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101047317_101047318delAG								TBC1D2 (29314 upstream) : GABBR2 (3048 downstream)																																			---	---	---	---
GABBR2	9568	broad.mit.edu	37	9	101162639	101162639	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101162639delA	uc004ays.2	-							NM_005458	NP_005449			G protein-coupled receptor 51 precursor						negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(2)|skin(2)	4		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)													---	---	---	---
GABBR2	9568	broad.mit.edu	37	9	101322185	101322185	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101322185delA	uc004ays.2	-							NM_005458	NP_005449			G protein-coupled receptor 51 precursor						negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(2)|skin(2)	4		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)													---	---	---	---
GABBR2	9568	broad.mit.edu	37	9	101455664	101455664	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101455664delG	uc004ays.2	-							NM_005458	NP_005449			G protein-coupled receptor 51 precursor						negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(2)|skin(2)	4		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)													---	---	---	---
ANKS6	203286	broad.mit.edu	37	9	101536043	101536043	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101536043delA	uc004ayu.2	-						ANKS6_uc004ayt.2_Intron|ANKS6_uc004ayv.1_Intron|ANKS6_uc004ayw.1_Intron|ANKS6_uc004ayx.1_Intron|ANKS6_uc004ayy.1_Intron	NM_173551	NP_775822			ankyrin repeat and sterile alpha motif domain											ovary(2)	2		Acute lymphoblastic leukemia(62;0.0527)																---	---	---	---
Unknown	0	broad.mit.edu	37	9	101562211	101562213	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101562211_101562213delTTT								ANKS6 (3417 upstream) : GALNT12 (7768 downstream)																																			---	---	---	---
COL15A1	1306	broad.mit.edu	37	9	101771255	101771255	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101771255delA	uc004azb.1	+							NM_001855	NP_001846			alpha 1 type XV collagen precursor						angiogenesis|cell differentiation|signal transduction	collagen type XV|extracellular space|integral to membrane	binding			ovary(6)	6		Acute lymphoblastic leukemia(62;0.0562)																---	---	---	---
COL15A1	1306	broad.mit.edu	37	9	101777389	101777389	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101777389delT	uc004azb.1	+							NM_001855	NP_001846			alpha 1 type XV collagen precursor						angiogenesis|cell differentiation|signal transduction	collagen type XV|extracellular space|integral to membrane	binding			ovary(6)	6		Acute lymphoblastic leukemia(62;0.0562)																---	---	---	---
COL15A1	1306	broad.mit.edu	37	9	101803788	101803788	+	Intron	DEL	G	-	-	rs114738247	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101803788delG	uc004azb.1	+							NM_001855	NP_001846			alpha 1 type XV collagen precursor						angiogenesis|cell differentiation|signal transduction	collagen type XV|extracellular space|integral to membrane	binding			ovary(6)	6		Acute lymphoblastic leukemia(62;0.0562)																---	---	---	---
Unknown	0	broad.mit.edu	37	9	102562989	102562989	+	Intron	DEL	A	-	-	rs35003152		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102562989delA	uc004bad.1	-											Homo sapiens cDNA FLJ32889 fis, clone TESTI2004560.																														---	---	---	---
GRIN3A	116443	broad.mit.edu	37	9	104401626	104401627	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104401626_104401627delAA	uc004bbp.1	-						GRIN3A_uc004bbq.1_Intron	NM_133445	NP_597702			glutamate receptor, ionotropic,						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|neuron projection|neuronal cell body|outer membrane-bounded periplasmic space|postsynaptic density|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|glycine binding|identical protein binding|N-methyl-D-aspartate selective glutamate receptor activity|protein phosphatase 2A binding			ovary(4)|pancreas(1)|central_nervous_system(1)|skin(1)	7		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Ketamine(DB01221)|L-Glutamic Acid(DB00142)|Memantine(DB01043)|Meperidine(DB00454)|Methadone(DB00333)|Orphenadrine(DB01173)|Procaine(DB00721)|Riluzole(DB00740)													---	---	---	---
GRIN3A	116443	broad.mit.edu	37	9	104471380	104471380	+	Intron	DEL	T	-	-	rs76490063		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104471380delT	uc004bbp.1	-						GRIN3A_uc004bbq.1_Intron	NM_133445	NP_597702			glutamate receptor, ionotropic,						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|neuron projection|neuronal cell body|outer membrane-bounded periplasmic space|postsynaptic density|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|glycine binding|identical protein binding|N-methyl-D-aspartate selective glutamate receptor activity|protein phosphatase 2A binding			ovary(4)|pancreas(1)|central_nervous_system(1)|skin(1)	7		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Ketamine(DB01221)|L-Glutamic Acid(DB00142)|Memantine(DB01043)|Meperidine(DB00454)|Methadone(DB00333)|Orphenadrine(DB01173)|Procaine(DB00721)|Riluzole(DB00740)													---	---	---	---
Unknown	0	broad.mit.edu	37	9	104594989	104594989	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104594989delT								GRIN3A (94127 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	105210586	105210586	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:105210586delA								GRIN3A (709724 upstream) : CYLC2 (547007 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	105265749	105265749	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:105265749delA								GRIN3A (764887 upstream) : CYLC2 (491844 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	105467961	105467961	+	IGR	DEL	A	-	-	rs72063323		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:105467961delA								GRIN3A (967099 upstream) : CYLC2 (289632 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	105501141	105501141	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:105501141delT								None (None upstream) : CYLC2 (256452 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	106266833	106266833	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:106266833delA								CYLC2 (486063 upstream) : SMC2 (589708 downstream)																																			---	---	---	---
SMC2	10592	broad.mit.edu	37	9	106888729	106888730	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:106888729_106888730delTT	uc004bbv.2	+						SMC2_uc004bbw.2_Intron|SMC2_uc011lvl.1_Intron|SMC2_uc004bbx.2_Intron|SMC2_uc004bby.2_5'Flank	NM_001042551	NP_001036016			structural maintenance of chromosomes 2						cell division|mitotic chromosome condensation|symbiosis, encompassing mutualism through parasitism	condensin complex|cytoplasm|nuclear chromosome	ATP binding|protein heterodimerization activity			ovary(4)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|breast(1)	9																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	107137226	107137227	+	IGR	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107137226_107137227delTC								SMC2 (233533 upstream) : OR13F1 (129317 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	107352803	107352804	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107352803_107352804insA								OR13C8 (20393 upstream) : OR13C5 (7936 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	107400573	107400575	+	IGR	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107400573_107400575delAAA								OR13C9 (20088 upstream) : OR13D1 (56128 downstream)																																			---	---	---	---
NIPSNAP3A	25934	broad.mit.edu	37	9	107515428	107515430	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107515428_107515430delAAA	uc004bch.1	+						NIPSNAP3A_uc011lvt.1_Intron|NIPSNAP3A_uc011lvu.1_Intron	NM_015469	NP_056284			nipsnap homolog 3A							cytosol					0																		---	---	---	---
ABCA1	19	broad.mit.edu	37	9	107605382	107605382	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107605382delA	uc004bcl.2	-							NM_005502	NP_005493			ATP-binding cassette, sub-family A member 1						Cdc42 protein signal transduction|cellular lipid metabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|endosome transport|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|interleukin-1 beta secretion|intracellular cholesterol transport|lysosome organization|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|platelet dense granule organization|positive regulation of cAMP biosynthetic process|reverse cholesterol transport	integral to plasma membrane|membrane fraction|membrane raft|phagocytic vesicle	anion transmembrane transporter activity|apolipoprotein A-I receptor activity|ATP binding|ATPase activity|cholesterol transporter activity|phospholipid transporter activity|small GTPase binding|syntaxin-13 binding			large_intestine(4)|lung(4)|ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	17				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)													---	---	---	---
ABCA1	19	broad.mit.edu	37	9	107691416	107691416	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107691416delA	uc004bcl.2	-						ABCA1_uc004bcm.2_5'Flank|uc010mtj.1_Intron	NM_005502	NP_005493			ATP-binding cassette, sub-family A member 1						Cdc42 protein signal transduction|cellular lipid metabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|endosome transport|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|interleukin-1 beta secretion|intracellular cholesterol transport|lysosome organization|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|platelet dense granule organization|positive regulation of cAMP biosynthetic process|reverse cholesterol transport	integral to plasma membrane|membrane fraction|membrane raft|phagocytic vesicle	anion transmembrane transporter activity|apolipoprotein A-I receptor activity|ATP binding|ATPase activity|cholesterol transporter activity|phospholipid transporter activity|small GTPase binding|syntaxin-13 binding			large_intestine(4)|lung(4)|ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	17				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)													---	---	---	---
Unknown	0	broad.mit.edu	37	9	107723323	107723326	+	IGR	DEL	GGAG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107723323_107723326delGGAG								ABCA1 (32887 upstream) : SLC44A1 (283603 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	107743516	107743517	+	IGR	DEL	AA	-	-	rs71872387		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107743516_107743517delAA								ABCA1 (53080 upstream) : SLC44A1 (263412 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	107867777	107867777	+	IGR	DEL	A	-	-	rs72027701		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107867777delA								ABCA1 (177341 upstream) : SLC44A1 (139152 downstream)																																			---	---	---	---
SLC44A1	23446	broad.mit.edu	37	9	108022614	108022615	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108022614_108022615insT	uc004bcn.2	+						SLC44A1_uc010mtk.1_Intron	NM_080546	NP_536856			CDW92 antigen							integral to membrane|mitochondrial outer membrane|plasma membrane	choline transmembrane transporter activity			breast(3)|ovary(1)	4					Choline(DB00122)													---	---	---	---
FSD1L	83856	broad.mit.edu	37	9	108300871	108300871	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108300871delT	uc011lvv.1	+						FSD1L_uc011lvw.1_Intron|FSD1L_uc004bcq.2_Intron	NM_001145313	NP_001138785			fibronectin type III and SPRY domain containing												0																		---	---	---	---
FKTN	2218	broad.mit.edu	37	9	108382270	108382270	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108382270delT	uc004bcr.2	+	10	1316	c.1100delT	c.(1099-1101)GTTfs	p.V367fs	FKTN_uc011lvx.1_Frame_Shift_Del_p.V367fs|FKTN_uc004bcs.2_Frame_Shift_Del_p.V367fs|FKTN_uc011lvy.1_Intron|FKTN_uc010mtm.2_Frame_Shift_Del_p.V235fs	NM_001079802	NP_001073270	O75072	FKTN_HUMAN	fukutin	367	Lumenal (Potential).				muscle organ development|negative regulation of cell proliferation|negative regulation of JNK cascade|nervous system development|regulation of protein glycosylation	cis-Golgi network|endoplasmic reticulum|extracellular space|Golgi membrane|integral to membrane|nucleus	transferase activity			breast(2)|ovary(1)	3																		---	---	---	---
FKTN	2218	broad.mit.edu	37	9	108396420	108396420	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108396420delT	uc004bcr.2	+						FKTN_uc011lvx.1_Intron|FKTN_uc004bcs.2_Intron|FKTN_uc011lvy.1_Intron|FKTN_uc010mtm.2_Intron	NM_001079802	NP_001073270			fukutin						muscle organ development|negative regulation of cell proliferation|negative regulation of JNK cascade|nervous system development|regulation of protein glycosylation	cis-Golgi network|endoplasmic reticulum|extracellular space|Golgi membrane|integral to membrane|nucleus	transferase activity			breast(2)|ovary(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	108776652	108776652	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108776652delA								TMEM38B (239208 upstream) : ZNF462 (848726 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	108778786	108778787	+	IGR	INS	-	GTGTGT	GTGTGT	rs151018670	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108778786_108778787insGTGTGT								TMEM38B (241342 upstream) : ZNF462 (846591 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	108786698	108786698	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108786698delT								TMEM38B (249254 upstream) : ZNF462 (838680 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	109215488	109215490	+	Intron	DEL	TTG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109215488_109215490delTTG	uc004bcx.2	+											Homo sapiens, clone IMAGE:4246712, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	109385370	109385370	+	Intron	DEL	T	-	-	rs66601268		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109385370delT	uc004bcy.1	+											Homo sapiens cDNA FLJ36044 fis, clone TESTI2017584.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	109428850	109428850	+	RNA	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109428850delA	uc004bcy.1	+	5		c.589delA								Homo sapiens cDNA FLJ36044 fis, clone TESTI2017584.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	109567749	109567749	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109567749delA								None (None upstream) : ZNF462 (57629 downstream)																																			---	---	---	---
ZNF462	58499	broad.mit.edu	37	9	109635180	109635181	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109635180_109635181insT	uc004bcz.2	+							NM_021224	NP_067047			zinc finger protein 462						transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(5)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	109987101	109987101	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109987101delT								ZNF462 (213312 upstream) : RAD23B (58443 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	110401282	110401285	+	IGR	DEL	ACAC	-	-	rs113729134		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110401282_110401285delACAC								KLF4 (149235 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	110659954	110659955	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110659954_110659955insA								KLF4 (407907 upstream) : ACTL7B (956916 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	110678394	110678394	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110678394delT								KLF4 (426347 upstream) : ACTL7B (938477 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	110976535	110976536	+	IGR	DEL	TT	-	-	rs74829616		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110976535_110976536delTT								KLF4 (724488 upstream) : ACTL7B (640335 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	111254480	111254483	+	IGR	DEL	CCTC	-	-	rs34771019		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111254480_111254483delCCTC								None (None upstream) : ACTL7B (362388 downstream)																																			---	---	---	---
CTNNAL1	8727	broad.mit.edu	37	9	111767544	111767544	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111767544delA	uc004bdo.1	-						CTNNAL1_uc010mtt.1_Intron|CTNNAL1_uc004bdp.1_Intron	NM_003798	NP_003789			catenin, alpha-like 1						cell adhesion|Rho protein signal transduction	actin cytoskeleton|cytosol|plasma membrane	cadherin binding|structural molecule activity			ovary(1)	1				STAD - Stomach adenocarcinoma(157;0.0768)														---	---	---	---
C9orf5	23731	broad.mit.edu	37	9	111812735	111812735	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111812735delA	uc004bdt.3	-						C9orf5_uc004bds.3_Intron|C9orf5_uc004bdr.3_Intron	NM_032012	NP_114401			hypothetical protein LOC23731							integral to membrane				central_nervous_system(1)	1		Myeloproliferative disorder(63;0.204)		OV - Ovarian serous cystadenocarcinoma(323;3.08e-05)|STAD - Stomach adenocarcinoma(157;0.0823)														---	---	---	---
C9orf4	23732	broad.mit.edu	37	9	111902997	111902997	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111902997delT	uc004bdw.1	-							NM_014334	NP_055149			hypothetical protein LOC23732							integral to membrane					0																		---	---	---	---
C9orf4	23732	broad.mit.edu	37	9	111907999	111908000	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111907999_111908000insA	uc004bdw.1	-							NM_014334	NP_055149			hypothetical protein LOC23732							integral to membrane					0																		---	---	---	---
EPB41L4B	54566	broad.mit.edu	37	9	112043086	112043087	+	Intron	DEL	AA	-	-	rs112970575		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112043086_112043087delAA	uc004bdz.1	-						EPB41L4B_uc004bea.2_Intron	NM_019114	NP_061987			erythrocyte membrane protein band 4.1 like 4B							cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|structural constituent of cytoskeleton			ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	112114228	112114228	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112114228delT								EPB41L4B (31207 upstream) : PTPN3 (23746 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	112363538	112363539	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112363538_112363539delTG								PTPN3 (102945 upstream) : PALM2 (39533 downstream)																																			---	---	---	---
PALM2	114299	broad.mit.edu	37	9	112468586	112468586	+	Intron	DEL	A	-	-	rs7035307	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112468586delA	uc004beg.2	+						PALM2_uc004bef.2_Intron	NM_001037293	NP_001032370			paralemmin 2 isoform b						regulation of cell shape	plasma membrane				ovary(2)	2																		---	---	---	---
PALM2-AKAP2	445815	broad.mit.edu	37	9	112917091	112917092	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112917091_112917092insA	uc004bej.3	+						PALM2-AKAP2_uc004bek.3_Intron|AKAP2_uc011lwi.1_Intron|AKAP2_uc004bem.2_Intron|AKAP2_uc011lwj.1_Intron|PALM2-AKAP2_uc004ben.2_Intron	NM_007203	NP_009134			PALM2-AKAP2 protein isoform 1								enzyme binding			ovary(3)|central_nervous_system(2)|skin(1)	6																		---	---	---	---
SVEP1	79987	broad.mit.edu	37	9	113206130	113206130	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113206130delT	uc010mtz.2	-						SVEP1_uc010mua.1_Intron	NM_153366	NP_699197			polydom						cell adhesion	cytoplasm|extracellular region|membrane	calcium ion binding			ovary(7)	7																		---	---	---	---
MUSK	4593	broad.mit.edu	37	9	113543534	113543534	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:113543534delT	uc004bey.2	+						MUSK_uc004bez.1_Intron	NM_005592	NP_005583			skeletal muscle receptor tyrosine kinase						transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(3)|ovary(2)|central_nervous_system(1)	6																		---	---	---	---
KIAA0368	23392	broad.mit.edu	37	9	114199530	114199530	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114199530delA	uc004bfe.1	-						KIAA0368_uc010muc.1_Intron	NM_001080398	NP_001073867			KIAA0368 protein												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	114573703	114573703	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114573703delT								C9orf84 (16480 upstream) : UGCG (85503 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	114646556	114646557	+	IGR	INS	-	C	C	rs151112231	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114646556_114646557insC								C9orf84 (89333 upstream) : UGCG (12649 downstream)																																			---	---	---	---
UGCG	7357	broad.mit.edu	37	9	114672215	114672215	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114672215delT	uc004bft.2	+							NM_003358	NP_003349			ceramide glucosyltransferase						epidermis development|glucosylceramide biosynthetic process	Golgi membrane|integral to membrane|membrane fraction	ceramide glucosyltransferase activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(323;0.0433)	Miglustat(DB00419)													---	---	---	---
Unknown	0	broad.mit.edu	37	9	114752064	114752065	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114752064_114752065delTT								UGCG (56633 upstream) : SUSD1 (50997 downstream)																																			---	---	---	---
SUSD1	64420	broad.mit.edu	37	9	114874938	114874938	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114874938delA	uc004bfu.2	-						SUSD1_uc010mui.2_Intron|SUSD1_uc010muj.2_Intron	NM_022486	NP_071931			sushi domain containing 1 precursor							integral to membrane	calcium ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	114968648	114968649	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114968648_114968649delAA								SUSD1 (31092 upstream) : ROD1 (12066 downstream)																																			---	---	---	---
HSDL2	84263	broad.mit.edu	37	9	115179055	115179055	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115179055delA	uc004bga.1	+						HSDL2_uc011lwv.1_Intron|HSDL2_uc004bgb.1_Intron|HSDL2_uc004bgc.1_Intron|HSDL2_uc011lww.1_Intron|HSDL2_uc004bgd.2_RNA	NM_032303	NP_115679			hydroxysteroid dehydrogenase like 2							peroxisome	oxidoreductase activity|sterol binding				0																		---	---	---	---
C9orf80	58493	broad.mit.edu	37	9	115451407	115451407	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115451407delA	uc004bgg.2	-						C9orf80_uc010muk.2_Intron	NM_021218	NP_067041			SOSSC protein						DNA repair|response to ionizing radiation	SOSS complex	protein binding				0																		---	---	---	---
SNX30	401548	broad.mit.edu	37	9	115581025	115581025	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115581025delT	uc004bgj.3	+							NM_001012994	NP_001013012			sorting nexin family member 30						cell communication|protein transport	cytoplasm	phosphatidylinositol binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	115721053	115721053	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115721053delT								SLC46A2 (67860 upstream) : ZNF883 (38349 downstream)																																			---	---	---	---
ZFP37	7539	broad.mit.edu	37	9	115806416	115806416	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115806416delT	uc004bgm.1	-	4	510	c.482delA	c.(481-483)AATfs	p.N161fs	ZFP37_uc011lwz.1_Frame_Shift_Del_p.N176fs|ZFP37_uc011lxa.1_Frame_Shift_Del_p.N162fs	NM_003408	NP_003399	Q9Y6Q3	ZFP37_HUMAN	zinc finger protein 37 homolog	161						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	116464878	116464878	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116464878delG								RGS3 (104861 upstream) : ZNF618 (173684 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	116510662	116510662	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116510662delA								RGS3 (150645 upstream) : ZNF618 (127900 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	116579713	116579713	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116579713delA								RGS3 (219696 upstream) : ZNF618 (58849 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	116612943	116612943	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116612943delT								RGS3 (252926 upstream) : ZNF618 (25619 downstream)																																			---	---	---	---
ZNF618	114991	broad.mit.edu	37	9	116700623	116700624	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116700623_116700624delAA	uc004bid.2	+						ZNF618_uc004bib.1_Intron|ZNF618_uc004bic.2_Intron|ZNF618_uc011lxi.1_Intron|ZNF618_uc011lxj.1_Intron	NM_133374	NP_588615			zinc finger protein 618						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
AKNA	80709	broad.mit.edu	37	9	117130569	117130569	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117130569delT	uc004biq.3	-						AKNA_uc004bio.3_Intron|AKNA_uc004bip.3_Intron|AKNA_uc004bir.3_Intron|AKNA_uc004bis.3_Intron|AKNA_uc010mve.2_Intron|AKNA_uc004biu.1_Intron|AKNA_uc004biv.1_Intron	NM_030767	NP_110394			AT-hook transcription factor						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(4)|central_nervous_system(2)	6																		---	---	---	---
TNFSF15	9966	broad.mit.edu	37	9	117560653	117560654	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117560653_117560654delTT	uc004bjh.2	-							NM_005118	NP_005109			tumor necrosis factor (ligand) superfamily,						activation of caspase activity|activation of NF-kappaB-inducing kinase activity|cytokine metabolic process|immune response	extracellular space|integral to plasma membrane	cytokine activity|tumor necrosis factor receptor binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	117654036	117654037	+	IGR	INS	-	A	A	rs144933443	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117654036_117654037insA								TNFSF15 (85628 upstream) : TNFSF8 (11087 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	118187018	118187018	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118187018delT								DEC1 (22095 upstream) : C9orf27 (463528 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	118195552	118195552	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118195552delT								DEC1 (30629 upstream) : C9orf27 (454994 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	118487040	118487040	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118487040delA								DEC1 (322117 upstream) : C9orf27 (163506 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	118751237	118751237	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118751237delT								C9orf27 (63860 upstream) : PAPPA (164834 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	118908913	118908914	+	IGR	DEL	AA	-	-	rs111445315		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118908913_118908914delAA								C9orf27 (221536 upstream) : PAPPA (7157 downstream)																																			---	---	---	---
PAPPA	5069	broad.mit.edu	37	9	118961197	118961197	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118961197delT	uc004bjn.2	+						PAPPA_uc011lxp.1_Intron|PAPPA_uc011lxq.1_Intron	NM_002581	NP_002572			pregnancy-associated plasma protein A						cell differentiation|female pregnancy	cytoplasm|extracellular region|membrane	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(4)|pancreas(1)	9																		---	---	---	---
PAPPA	5069	broad.mit.edu	37	9	119071364	119071364	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119071364delT	uc004bjn.2	+						PAPPA_uc011lxp.1_Intron|PAPPA_uc011lxq.1_Intron	NM_002581	NP_002572			pregnancy-associated plasma protein A						cell differentiation|female pregnancy	cytoplasm|extracellular region|membrane	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(4)|pancreas(1)	9																		---	---	---	---
ASTN2	23245	broad.mit.edu	37	9	119529432	119529433	+	Intron	INS	-	AC	AC	rs143276372	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119529432_119529433insAC	uc004bjs.1	-						ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjt.1_Intron	NM_198187	NP_937830			astrotactin 2 isoform c							integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9																		---	---	---	---
ASTN2	23245	broad.mit.edu	37	9	119571641	119571642	+	Intron	DEL	TT	-	-	rs34810817		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119571641_119571642delTT	uc004bjs.1	-						ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjt.1_Intron	NM_198187	NP_937830			astrotactin 2 isoform c							integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9																		---	---	---	---
ASTN2	23245	broad.mit.edu	37	9	119651812	119651812	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119651812delT	uc004bjs.1	-						ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjt.1_Intron	NM_198187	NP_937830			astrotactin 2 isoform c							integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9																		---	---	---	---
ASTN2	23245	broad.mit.edu	37	9	120012931	120012931	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120012931delA	uc004bjs.1	-						ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjt.1_Intron	NM_198187	NP_937830			astrotactin 2 isoform c							integral to membrane				skin(4)|ovary(3)|breast(1)|kidney(1)	9																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	120536281	120536281	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120536281delT								TLR4 (56517 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	120622830	120622830	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120622830delT								TLR4 (143066 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	120626617	120626617	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120626617delA								TLR4 (146853 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	120720123	120720123	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120720123delT								TLR4 (240359 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	120876770	120876770	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:120876770delA								TLR4 (397006 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	121027162	121027163	+	IGR	INS	-	TG	TG	rs111729110		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:121027162_121027163insTG								TLR4 (547398 upstream) : DBC1 (901745 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	121288181	121288182	+	IGR	INS	-	A	A	rs144737367	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:121288181_121288182insA								TLR4 (808417 upstream) : DBC1 (640726 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	121477862	121477863	+	IGR	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:121477862_121477863insC								TLR4 (998098 upstream) : DBC1 (451045 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	121578930	121578930	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:121578930delG								None (None upstream) : DBC1 (349978 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	122418554	122418554	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122418554delT								DBC1 (286815 upstream) : MIR147 (588703 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	122629861	122629862	+	IGR	DEL	AA	-	-	rs111500243		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122629861_122629862delAA								DBC1 (498122 upstream) : MIR147 (377395 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	122781641	122781641	+	IGR	DEL	A	-	-	rs66807069		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122781641delA								DBC1 (649902 upstream) : MIR147 (225616 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	122926126	122926126	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122926126delT								DBC1 (794387 upstream) : MIR147 (81131 downstream)																																			---	---	---	---
CDK5RAP2	55755	broad.mit.edu	37	9	123318337	123318337	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123318337delA	uc004bkf.2	-						CDK5RAP2_uc004bkg.2_Intron|CDK5RAP2_uc011lxw.1_Intron|CDK5RAP2_uc011lxx.1_Intron|CDK5RAP2_uc011lxy.1_Intron|CDK5RAP2_uc011lxz.1_Intron|CDK5RAP2_uc011lya.1_Intron|CDK5RAP2_uc004bkh.1_Intron	NM_018249	NP_060719			CDK5 regulatory subunit associated protein 2						brain development|centrosome organization|chromosome segregation|G2/M transition of mitotic cell cycle|microtubule bundle formation|negative regulation of centriole replication|positive regulation of transcription, DNA-dependent|regulation of neuron differentiation|regulation of spindle checkpoint	cytosol|Golgi apparatus|microtubule|pericentriolar material|perinuclear region of cytoplasm|spindle pole	calmodulin binding|microtubule binding|neuronal Cdc2-like kinase binding|transcription regulatory region DNA binding			ovary(2)|lung(1)|skin(1)	4																		---	---	---	---
MEGF9	1955	broad.mit.edu	37	9	123374631	123374631	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123374631delT	uc004bkj.1	-						MEGF9_uc011lyb.1_Intron	NM_001080497	NP_001073966			multiple EGF-like-domains 9							integral to membrane	calcium ion binding				0																		---	---	---	---
MEGF9	1955	broad.mit.edu	37	9	123421596	123421596	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123421596delT	uc004bkj.1	-						MEGF9_uc011lyb.1_Intron|MEGF9_uc004bkk.3_3'UTR	NM_001080497	NP_001073966			multiple EGF-like-domains 9							integral to membrane	calcium ion binding				0																		---	---	---	---
FBXW2	26190	broad.mit.edu	37	9	123542471	123542471	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123542471delA	uc004bkl.1	-						FBXW2_uc011lyc.1_Intron|FBXW2_uc004bkn.2_Intron|FBXW2_uc004bkm.1_Intron|FBXW2_uc010mvj.1_Intron	NM_012164	NP_036296			F-box and WD repeat domain containing 2						proteolysis		protein binding|ubiquitin-protein ligase activity			urinary_tract(1)|ovary(1)|pancreas(1)|skin(1)	4																		---	---	---	---
FBXW2	26190	broad.mit.edu	37	9	123544743	123544743	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123544743delA	uc004bkl.1	-						FBXW2_uc011lyc.1_Intron|FBXW2_uc004bkn.2_Intron|FBXW2_uc004bkm.1_Intron|FBXW2_uc010mvj.1_Intron	NM_012164	NP_036296			F-box and WD repeat domain containing 2						proteolysis		protein binding|ubiquitin-protein ligase activity			urinary_tract(1)|ovary(1)|pancreas(1)|skin(1)	4																		---	---	---	---
C5	727	broad.mit.edu	37	9	123751833	123751833	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123751833delT	uc004bkv.2	-							NM_001735	NP_001726			complement component 5 preproprotein						activation of MAPK activity|chemotaxis|complement activation, alternative pathway|complement activation, classical pathway|cytolysis|G-protein coupled receptor protein signaling pathway|inflammatory response|negative regulation of macrophage chemotaxis|positive regulation of chemokine secretion|positive regulation vascular endothelial growth factor production	extracellular space|membrane attack complex	chemokine activity|endopeptidase inhibitor activity			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)													---	---	---	---
C5	727	broad.mit.edu	37	9	123805814	123805814	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123805814delT	uc004bkv.2	-						C5_uc010mvm.1_Intron|C5_uc010mvn.1_Intron	NM_001735	NP_001726			complement component 5 preproprotein						activation of MAPK activity|chemotaxis|complement activation, alternative pathway|complement activation, classical pathway|cytolysis|G-protein coupled receptor protein signaling pathway|inflammatory response|negative regulation of macrophage chemotaxis|positive regulation of chemokine secretion|positive regulation vascular endothelial growth factor production	extracellular space|membrane attack complex	chemokine activity|endopeptidase inhibitor activity			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)													---	---	---	---
GSN	2934	broad.mit.edu	37	9	124074857	124074857	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124074857delA	uc004blf.1	+						GSN_uc004bld.1_Intron|GSN_uc010mvq.1_Intron|GSN_uc010mvr.1_Intron|GSN_uc010mvu.1_Intron|GSN_uc010mvt.1_Intron|GSN_uc010mvs.1_Intron|GSN_uc004ble.1_Intron|GSN_uc010mvv.1_Intron|GSN_uc011lyh.1_Intron|GSN_uc011lyi.1_Intron|GSN_uc011lyj.1_Intron|GSN_uc004blg.1_Intron	NM_000177	NP_000168			gelsolin isoform a precursor						actin filament polymerization|actin filament severing|barbed-end actin filament capping|cellular component disassembly involved in apoptosis|cilium morphogenesis	actin cytoskeleton|cytosol	actin binding|calcium ion binding|protein binding			breast(2)|ovary(1)	3																		---	---	---	---
GSN	2934	broad.mit.edu	37	9	124089775	124089775	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124089775delG	uc004blf.1	+						GSN_uc004bld.1_Intron|GSN_uc010mvq.1_Intron|GSN_uc010mvr.1_Intron|GSN_uc010mvu.1_Intron|GSN_uc010mvt.1_Intron|GSN_uc010mvs.1_Intron|GSN_uc004ble.1_Intron|GSN_uc010mvv.1_Intron|GSN_uc011lyh.1_Intron|GSN_uc011lyi.1_Intron|GSN_uc011lyj.1_Intron|GSN_uc004blg.1_Intron	NM_000177	NP_000168			gelsolin isoform a precursor						actin filament polymerization|actin filament severing|barbed-end actin filament capping|cellular component disassembly involved in apoptosis|cilium morphogenesis	actin cytoskeleton|cytosol	actin binding|calcium ion binding|protein binding			breast(2)|ovary(1)	3																		---	---	---	---
DAB2IP	153090	broad.mit.edu	37	9	124328564	124328565	+	5'Flank	INS	-	G	G	rs146387526	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124328564_124328565insG	uc004bln.2	+							NM_032552	NP_115941			disabled homolog 2 interacting protein isoform						activation of JUN kinase activity|apoptosis in response to endoplasmic reticulum stress|cellular response to epidermal growth factor stimulus|cellular response to tumor necrosis factor|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|negative regulation of epithelial to mesenchymal transition|negative regulation of fibroblast proliferation|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of MAP kinase activity|negative regulation of NF-kappaB transcription factor activity|negative regulation of Ras GTPase activity|negative regulation of transcription from RNA polymerase II promoter|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|intrinsic to internal side of plasma membrane	14-3-3 protein binding|death receptor binding|mitogen-activated protein kinase kinase kinase binding|protein homodimerization activity|protein phosphatase 2A binding|Ras GTPase activator activity|signaling adaptor activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
DAB2IP	153090	broad.mit.edu	37	9	124424261	124424261	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124424261delA	uc004bln.2	+							NM_032552	NP_115941			disabled homolog 2 interacting protein isoform						activation of JUN kinase activity|apoptosis in response to endoplasmic reticulum stress|cellular response to epidermal growth factor stimulus|cellular response to tumor necrosis factor|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|negative regulation of epithelial to mesenchymal transition|negative regulation of fibroblast proliferation|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of MAP kinase activity|negative regulation of NF-kappaB transcription factor activity|negative regulation of Ras GTPase activity|negative regulation of transcription from RNA polymerase II promoter|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|intrinsic to internal side of plasma membrane	14-3-3 protein binding|death receptor binding|mitogen-activated protein kinase kinase kinase binding|protein homodimerization activity|protein phosphatase 2A binding|Ras GTPase activator activity|signaling adaptor activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
TTLL11	158135	broad.mit.edu	37	9	124660202	124660203	+	Intron	INS	-	T	T	rs113818323		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124660202_124660203insT	uc011lyl.1	-						TTLL11_uc004blr.2_Intron|uc004bls.1_Intron	NM_001139442	NP_001132914			tubulin tyrosine ligase-like family, member 11						protein modification process	cilium|microtubule basal body	tubulin-tyrosine ligase activity				0																		---	---	---	---
NDUFA8	4702	broad.mit.edu	37	9	124910619	124910619	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124910619delA	uc004blv.2	-							NM_014222	NP_055037			NADH dehydrogenase (ubiquinone) 1 alpha						mitochondrial electron transport, NADH to ubiquinone|transport	mitochondrial intermembrane space|mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity			breast(1)	1					NADH(DB00157)													---	---	---	---
OR1J2	26740	broad.mit.edu	37	9	125237342	125237342	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125237342delT	uc004bmj.1	+							NM_054107	NP_473448			olfactory receptor, family 1, subfamily J,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(3)|pancreas(1)|breast(1)	5																		---	---	---	---
PDCL	5082	broad.mit.edu	37	9	125592449	125592449	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125592449delT	uc004bmz.1	-						PDCL_uc004bna.2_5'Flank	NM_005388	NP_005379			phosducin-like						signal transduction|visual perception						0																		---	---	---	---
RC3H2	54542	broad.mit.edu	37	9	125618164	125618164	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125618164delA	uc010mwc.1	-						RC3H2_uc004bnc.2_Intron|RC3H2_uc004bnd.1_Intron|RC3H2_uc004bne.3_Intron	NM_001100588	NP_001094058			ring finger and CCCH-type zinc finger domains 2							cell surface|endomembrane system|membrane|membrane fraction|perinuclear region of cytoplasm	DNA binding|zinc ion binding			ovary(2)|lung(2)	4																		---	---	---	---
RABGAP1	23637	broad.mit.edu	37	9	125719135	125719135	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125719135delA	uc011lzh.1	+						RABGAP1_uc004bnl.3_Intron|RABGAP1_uc004bnm.1_Intron	NM_012197	NP_036329			RAB GTPase activating protein 1						cell cycle	centrosome|cytosol|microtubule associated complex	Rab GTPase activator activity|tubulin binding			ovary(3)|kidney(2)	5																		---	---	---	---
STRBP	55342	broad.mit.edu	37	9	126029775	126029775	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126029775delC	uc004bns.2	-						STRBP_uc004bnt.2_Intron|STRBP_uc004bnu.2_Intron|STRBP_uc004bnv.2_Intron	NM_018387	NP_060857			spermatid perinuclear RNA binding protein						multicellular organismal development	cytoplasm|nucleus	DNA binding			breast(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	126034849	126034849	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126034849delT								STRBP (4006 upstream) : CRB2 (83599 downstream)																																			---	---	---	---
DENND1A	57706	broad.mit.edu	37	9	126168350	126168350	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126168350delC	uc004bnz.1	-						DENND1A_uc011lzl.1_Intron|DENND1A_uc004bny.1_Intron|DENND1A_uc011lzm.1_Intron|DENND1A_uc004boa.1_Intron|DENND1A_uc004bob.1_Intron|DENND1A_uc010mwh.1_Intron	NM_020946	NP_065997			DENN/MADD domain containing 1A isoform 1							cell junction|clathrin coated vesicle membrane|presynaptic membrane	guanyl-nucleotide exchange factor activity			ovary(2)	2																		---	---	---	---
DENND1A	57706	broad.mit.edu	37	9	126213202	126213202	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126213202delA	uc004bnz.1	-						DENND1A_uc011lzl.1_Intron|DENND1A_uc004bny.1_Intron|DENND1A_uc011lzm.1_Intron|DENND1A_uc004boa.1_Intron|DENND1A_uc004bob.1_Intron|DENND1A_uc004boc.2_Intron	NM_020946	NP_065997			DENN/MADD domain containing 1A isoform 1							cell junction|clathrin coated vesicle membrane|presynaptic membrane	guanyl-nucleotide exchange factor activity			ovary(2)	2																		---	---	---	---
DENND1A	57706	broad.mit.edu	37	9	126297177	126297177	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126297177delT	uc004bnz.1	-						DENND1A_uc011lzl.1_Intron|DENND1A_uc004bny.1_Intron|DENND1A_uc011lzm.1_Intron|DENND1A_uc004boa.1_Intron|DENND1A_uc004bob.1_Intron|DENND1A_uc004boc.2_Intron	NM_020946	NP_065997			DENN/MADD domain containing 1A isoform 1							cell junction|clathrin coated vesicle membrane|presynaptic membrane	guanyl-nucleotide exchange factor activity			ovary(2)	2																		---	---	---	---
DENND1A	57706	broad.mit.edu	37	9	126495950	126495952	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126495950_126495952delTTT	uc004bnz.1	-						DENND1A_uc004bny.1_Intron|DENND1A_uc011lzm.1_Intron|DENND1A_uc004boa.1_Intron|DENND1A_uc004bob.1_Intron|DENND1A_uc004boc.2_Intron	NM_020946	NP_065997			DENN/MADD domain containing 1A isoform 1							cell junction|clathrin coated vesicle membrane|presynaptic membrane	guanyl-nucleotide exchange factor activity			ovary(2)	2																		---	---	---	---
DENND1A	57706	broad.mit.edu	37	9	126537809	126537810	+	Intron	DEL	AA	-	-	rs74572932	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126537809_126537810delAA	uc004bnz.1	-						DENND1A_uc004bny.1_Intron|DENND1A_uc011lzm.1_Intron|DENND1A_uc004boa.1_Intron|DENND1A_uc004bob.1_Intron|DENND1A_uc004boc.2_Intron	NM_020946	NP_065997			DENN/MADD domain containing 1A isoform 1							cell junction|clathrin coated vesicle membrane|presynaptic membrane	guanyl-nucleotide exchange factor activity			ovary(2)	2																		---	---	---	---
DENND1A	57706	broad.mit.edu	37	9	126634450	126634450	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126634450delA	uc004bnz.1	-						DENND1A_uc011lzm.1_Intron|DENND1A_uc004boa.1_Intron|DENND1A_uc004bob.1_Intron|DENND1A_uc004boc.2_Intron	NM_020946	NP_065997			DENN/MADD domain containing 1A isoform 1							cell junction|clathrin coated vesicle membrane|presynaptic membrane	guanyl-nucleotide exchange factor activity			ovary(2)	2																		---	---	---	---
LHX2	9355	broad.mit.edu	37	9	126776091	126776091	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126776091delG	uc004boe.1	+						LHX2_uc010mwi.1_Intron	NM_004789	NP_004780			LIM homeobox protein 2							nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding				0																		---	---	---	---
GOLGA1	2800	broad.mit.edu	37	9	127653923	127653924	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127653923_127653924delTT	uc004bpc.2	-						GOLGA1_uc010mws.2_Intron	NM_002077	NP_002068			golgin 97							Golgi cisterna membrane				ovary(1)	1																		---	---	---	---
GOLGA1	2800	broad.mit.edu	37	9	127689148	127689148	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127689148delA	uc004bpc.2	-						GOLGA1_uc010mws.2_Intron|GOLGA1_uc010mwt.1_Intron	NM_002077	NP_002068			golgin 97							Golgi cisterna membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	128151830	128151830	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128151830delT								GAPVD1 (24541 upstream) : MAPKAP1 (47844 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	128175573	128175573	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128175573delT								GAPVD1 (48284 upstream) : MAPKAP1 (24101 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	128497919	128497919	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128497919delT								MAPKAP1 (28406 upstream) : PBX3 (11698 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	129555042	129555042	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129555042delA								LMX1B (91731 upstream) : ZBTB43 (12243 downstream)																																			---	---	---	---
ZBTB43	23099	broad.mit.edu	37	9	129596298	129596298	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129596298delA	uc004bql.2	+	3					ZBTB43_uc010mxf.2_3'UTR	NM_014007	NP_054726			zinc finger and BTB domain containing 43						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
RALGPS1	9649	broad.mit.edu	37	9	129784797	129784797	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:129784797delA	uc004bqo.1	+						RALGPS1_uc011mab.1_Intron|RALGPS1_uc011mac.1_Intron|RALGPS1_uc004bqq.3_Intron	NM_014636	NP_055451			Ral GEF with PH domain and SH3 binding motif 1						small GTPase mediated signal transduction	cytoplasm|plasma membrane	guanyl-nucleotide exchange factor activity			ovary(1)	1																		---	---	---	---
GARNL3	84253	broad.mit.edu	37	9	130097346	130097346	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130097346delG	uc011mae.1	+						GARNL3_uc011mad.1_Intron|GARNL3_uc004bqt.1_Intron	NM_032293	NP_115669			GTPase activating Rap/RanGAP domain-like 3						regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity|small GTPase regulator activity			ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
LRSAM1	90678	broad.mit.edu	37	9	130247868	130247868	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130247868delT	uc004brb.1	+						LRSAM1_uc010mxk.1_Intron|LRSAM1_uc004brc.1_Intron|LRSAM1_uc004brd.1_Intron|LRSAM1_uc004bre.1_Intron	NM_001005373	NP_001005373			leucine rich repeat and sterile alpha motif						negative regulation of endocytosis|non-lytic virus budding|protein autoubiquitination|protein catabolic process|protein polyubiquitination|protein transport|ubiquitin-dependent endocytosis	cytoplasm|extracellular region|membrane part	hormone activity|ubiquitin-protein ligase activity|zinc ion binding				0																		---	---	---	---
LRSAM1	90678	broad.mit.edu	37	9	130253463	130253463	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130253463delA	uc004brb.1	+						LRSAM1_uc010mxk.1_Intron|LRSAM1_uc004brc.1_Intron|LRSAM1_uc004brd.1_Intron|LRSAM1_uc004bre.1_Intron	NM_001005373	NP_001005373			leucine rich repeat and sterile alpha motif						negative regulation of endocytosis|non-lytic virus budding|protein autoubiquitination|protein catabolic process|protein polyubiquitination|protein transport|ubiquitin-dependent endocytosis	cytoplasm|extracellular region|membrane part	hormone activity|ubiquitin-protein ligase activity|zinc ion binding				0																		---	---	---	---
STXBP1	6812	broad.mit.edu	37	9	130421912	130421912	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130421912delT	uc004brl.2	+						STXBP1_uc004brk.2_Intron	NM_001032221	NP_001027392			syntaxin binding protein 1 isoform b						axon target recognition|energy reserve metabolic process|glutamate secretion|negative regulation of synaptic transmission, GABAergic|neurotransmitter secretion|platelet aggregation|platelet degranulation|protein transport|regulation of insulin secretion|regulation of synaptic vesicle priming|synaptic vesicle maturation|vesicle docking involved in exocytosis	cytosol|mitochondrion|plasma membrane|platelet alpha granule|protein complex	identical protein binding|syntaxin-1 binding|syntaxin-2 binding			skin(1)	1																		---	---	---	---
STXBP1	6812	broad.mit.edu	37	9	130437001	130437001	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130437001delA	uc004brl.2	+						STXBP1_uc004brk.2_Intron	NM_001032221	NP_001027392			syntaxin binding protein 1 isoform b						axon target recognition|energy reserve metabolic process|glutamate secretion|negative regulation of synaptic transmission, GABAergic|neurotransmitter secretion|platelet aggregation|platelet degranulation|protein transport|regulation of insulin secretion|regulation of synaptic vesicle priming|synaptic vesicle maturation|vesicle docking involved in exocytosis	cytosol|mitochondrion|plasma membrane|platelet alpha granule|protein complex	identical protein binding|syntaxin-1 binding|syntaxin-2 binding			skin(1)	1																		---	---	---	---
STXBP1	6812	broad.mit.edu	37	9	130449024	130449024	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130449024delA	uc004brl.2	+						STXBP1_uc004brk.2_Intron	NM_001032221	NP_001027392			syntaxin binding protein 1 isoform b						axon target recognition|energy reserve metabolic process|glutamate secretion|negative regulation of synaptic transmission, GABAergic|neurotransmitter secretion|platelet aggregation|platelet degranulation|protein transport|regulation of insulin secretion|regulation of synaptic vesicle priming|synaptic vesicle maturation|vesicle docking involved in exocytosis	cytosol|mitochondrion|plasma membrane|platelet alpha granule|protein complex	identical protein binding|syntaxin-1 binding|syntaxin-2 binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	130801591	130801591	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130801591delA								FAM102A (59096 upstream) : NAIF1 (21922 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	130818807	130818808	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130818807_130818808delTT								FAM102A (76312 upstream) : NAIF1 (4705 downstream)																																			---	---	---	---
DNM1	1759	broad.mit.edu	37	9	130986745	130986745	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130986745delC	uc011mau.1	+						DNM1_uc010mxr.2_Intron|DNM1_uc011mat.1_Intron	NM_004408	NP_004399			dynamin 1 isoform 1						receptor-mediated endocytosis	microtubule	GTP binding|GTPase activity			ovary(2)	2																		---	---	---	---
GLE1	2733	broad.mit.edu	37	9	131302336	131302336	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131302336delA	uc004bvj.2	+						GLE1_uc010myd.2_Intron	NM_001003722	NP_001003722			GLE1 RNA export mediator homolog isoform 1						poly(A)+ mRNA export from nucleus|protein transport|transmembrane transport	cytoplasm|nuclear pore	protein binding				0																		---	---	---	---
ZDHHC12	84885	broad.mit.edu	37	9	131485718	131485718	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131485718delG	uc004bvy.2	-						ZDHHC12_uc004bvz.2_Intron	NM_032799	NP_116188			zinc finger, DHHC domain containing 12							integral to membrane	acyltransferase activity|zinc ion binding				0																		---	---	---	---
NUP188	23511	broad.mit.edu	37	9	131707778	131707778	+	5'Flank	DEL	A	-	-	rs112403860		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131707778delA	uc004bws.1	+						NUP188_uc004bwq.1_Intron	NM_015354	NP_056169			nucleoporin 188kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|kidney(1)|breast(1)	7																		---	---	---	---
NUP188	23511	broad.mit.edu	37	9	131719458	131719458	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131719458delA	uc004bws.1	+							NM_015354	NP_056169			nucleoporin 188kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|kidney(1)|breast(1)	7																		---	---	---	---
FAM73B	84895	broad.mit.edu	37	9	131811597	131811597	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131811597delG	uc004bxa.2	+						FAM73B_uc004bwy.2_Intron|FAM73B_uc004bwz.2_Intron|FAM73B_uc011mbn.1_Intron	NM_032809	NP_116198			hypothetical protein LOC84895							integral to membrane				skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	9	131972121	131972121	+	RNA	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131972121delT	uc010myu.1	+	2		c.1215delT								Homo sapiens cDNA FLJ41803 fis, clone NHNPC2002749.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	132122834	132122835	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132122834_132122835insA								C9orf106 (37952 upstream) : C9orf50 (251671 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	132140961	132140961	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132140961delG								C9orf106 (56079 upstream) : C9orf50 (233545 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	9	132156476	132156476	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132156476delG								C9orf106 (71594 upstream) : C9orf50 (218030 downstream)																																			---	---	---	---
C9orf78	51759	broad.mit.edu	37	9	132597186	132597186	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132597186delT	uc004byp.2	-						C9orf78_uc004byo.2_5'Flank|C9orf78_uc004byq.1_5'Flank|USP20_uc004bys.2_5'Flank|USP20_uc004byr.2_5'Flank|USP20_uc004byt.1_5'Flank	NM_016520	NP_057604			chromosome 9 open reading frame 78												0		Ovarian(14;0.00556)																---	---	---	---
USP20	10868	broad.mit.edu	37	9	132623004	132623004	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132623004delA	uc004bys.2	+						USP20_uc004byr.2_Intron|USP20_uc004byt.1_Intron	NM_001110303	NP_001103773			ubiquitin specific protease 20						endocytosis|protein K48-linked deubiquitination|protein K63-linked deubiquitination|regulation of G-protein coupled receptor protein signaling pathway|ubiquitin-dependent protein catabolic process	perinuclear region of cytoplasm	cysteine-type endopeptidase activity|G-protein-coupled receptor binding|ubiquitin thiolesterase activity|zinc ion binding			lung(1)|breast(1)	2		Ovarian(14;0.00556)																---	---	---	---
FNBP1	23048	broad.mit.edu	37	9	132660778	132660778	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132660778delT	uc004byw.1	-						FNBP1_uc011mbv.1_Intron|FNBP1_uc011mbw.1_Intron|FNBP1_uc004bza.2_Intron|FNBP1_uc004byz.1_Intron|FNBP1_uc011mbu.1_Intron|FNBP1_uc004byx.1_Intron|FNBP1_uc004byy.1_Intron	NM_015033	NP_055848			formin binding protein 1						endocytosis	cell cortex|cytoplasmic membrane-bounded vesicle|cytoskeleton|lysosome|plasma membrane	identical protein binding|lipid binding				0		Ovarian(14;0.000536)		GBM - Glioblastoma multiforme(294;0.0378)				T	MLL	AML								---	---	---	---
FNBP1	23048	broad.mit.edu	37	9	132719836	132719836	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132719836delT	uc004byw.1	-						FNBP1_uc011mbv.1_Intron|FNBP1_uc011mbw.1_Intron|FNBP1_uc004bza.2_Intron|FNBP1_uc004byz.1_Intron|FNBP1_uc004byx.1_Intron|FNBP1_uc004byy.1_Intron	NM_015033	NP_055848			formin binding protein 1						endocytosis	cell cortex|cytoplasmic membrane-bounded vesicle|cytoskeleton|lysosome|plasma membrane	identical protein binding|lipid binding				0		Ovarian(14;0.000536)		GBM - Glioblastoma multiforme(294;0.0378)				T	MLL	AML								---	---	---	---
FNBP1	23048	broad.mit.edu	37	9	132737138	132737139	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132737138_132737139delAA	uc004byw.1	-						FNBP1_uc011mbv.1_Intron|FNBP1_uc011mbw.1_Intron|FNBP1_uc004bza.2_Intron|FNBP1_uc004byz.1_Intron|FNBP1_uc004byx.1_Intron|FNBP1_uc004byy.1_Intron	NM_015033	NP_055848			formin binding protein 1						endocytosis	cell cortex|cytoplasmic membrane-bounded vesicle|cytoskeleton|lysosome|plasma membrane	identical protein binding|lipid binding				0		Ovarian(14;0.000536)		GBM - Glioblastoma multiforme(294;0.0378)				T	MLL	AML								---	---	---	---
FNBP1	23048	broad.mit.edu	37	9	132764148	132764148	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132764148delA	uc004byw.1	-						FNBP1_uc011mbv.1_Intron|FNBP1_uc011mbw.1_Intron|FNBP1_uc004bza.2_Intron|FNBP1_uc004byz.1_Intron	NM_015033	NP_055848			formin binding protein 1						endocytosis	cell cortex|cytoplasmic membrane-bounded vesicle|cytoskeleton|lysosome|plasma membrane	identical protein binding|lipid binding				0		Ovarian(14;0.000536)		GBM - Glioblastoma multiforme(294;0.0378)				T	MLL	AML								---	---	---	---
NCS1	23413	broad.mit.edu	37	9	132985258	132985259	+	Intron	DEL	GC	-	-	rs145828712	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132985258_132985259delGC	uc004bzi.2	+						NCS1_uc010myz.1_Intron	NM_014286	NP_055101			frequenin homolog isoform 1						negative regulation of calcium ion transport via voltage-gated calcium channel activity|regulation of neuron projection development	cell junction|Golgi cisterna membrane|perinuclear region of cytoplasm|postsynaptic density|postsynaptic membrane	calcium ion binding|protein binding				0																		---	---	---	---
ASS1	445	broad.mit.edu	37	9	133331851	133331851	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133331851delA	uc004bzm.2	+						ASS1_uc004bzn.2_Intron|ASS1_uc010mza.2_Intron|ASS1_uc004bzo.2_Intron|ASS1_uc010mzb.2_Intron|ASS1_uc004bzp.2_Intron|ASS1_uc010mzc.2_Intron	NM_000050	NP_000041			argininosuccinate synthetase 1						arginine biosynthetic process|urea cycle	cytosol	argininosuccinate synthase activity|ATP binding|protein binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(145;0.000514)	Adenosine triphosphate(DB00171)|L-Arginine(DB00125)|L-Aspartic Acid(DB00128)|L-Citrulline(DB00155)													---	---	---	---
PRDM12	59335	broad.mit.edu	37	9	133541886	133541886	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133541886delG	uc004bzt.1	+							NM_021619	NP_067632			PR domain containing 12						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_hematologic(13;0.0433)|Acute lymphoblastic leukemia(5;0.0534)		OV - Ovarian serous cystadenocarcinoma(145;0.000344)														---	---	---	---
ABL1	25	broad.mit.edu	37	9	133655712	133655712	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133655712delA	uc004bzv.2	+							NM_007313	NP_009297			c-abl oncogene 1, receptor tyrosine kinase						actin cytoskeleton organization|axon guidance|blood coagulation|cell adhesion|DNA damage induced protein phosphorylation|DNA damage response, signal transduction resulting in induction of apoptosis|mismatch repair|muscle cell differentiation|negative regulation of protein serine/threonine kinase activity|peptidyl-tyrosine phosphorylation|positive regulation of muscle cell differentiation|positive regulation of oxidoreductase activity|regulation of transcription involved in S phase of mitotic cell cycle	cytoskeleton|cytosol|nuclear membrane|nucleolus|perinuclear region of cytoplasm	ATP binding|DNA binding|magnesium ion binding|manganese ion binding|mitogen-activated protein kinase binding|non-membrane spanning protein tyrosine kinase activity|proline-rich region binding|protein C-terminus binding|SH3 domain binding			haematopoietic_and_lymphoid_tissue(807)|lung(5)|stomach(2)|central_nervous_system(1)|breast(1)|skin(1)	817		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Dasatinib(DB01254)|Imatinib(DB00619)			T|Mis	BCR|ETV6|NUP214	CML|ALL|T-ALL								---	---	---	---
ABL1	25	broad.mit.edu	37	9	133717423	133717423	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133717423delA	uc004bzw.2	+						ABL1_uc004bzv.2_Intron	NM_005157	NP_005148			c-abl oncogene 1, receptor tyrosine kinase						actin cytoskeleton organization|axon guidance|blood coagulation|cell adhesion|DNA damage induced protein phosphorylation|DNA damage response, signal transduction resulting in induction of apoptosis|mismatch repair|muscle cell differentiation|negative regulation of protein serine/threonine kinase activity|peptidyl-tyrosine phosphorylation|positive regulation of muscle cell differentiation|positive regulation of oxidoreductase activity|regulation of transcription involved in S phase of mitotic cell cycle	cytoskeleton|cytosol|nuclear membrane|nucleolus|perinuclear region of cytoplasm	ATP binding|DNA binding|magnesium ion binding|manganese ion binding|mitogen-activated protein kinase binding|non-membrane spanning protein tyrosine kinase activity|proline-rich region binding|protein C-terminus binding|SH3 domain binding			haematopoietic_and_lymphoid_tissue(807)|lung(5)|stomach(2)|central_nervous_system(1)|breast(1)|skin(1)	817		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Dasatinib(DB01254)|Imatinib(DB00619)			T|Mis	BCR|ETV6|NUP214	CML|ALL|T-ALL								---	---	---	---
NUP214	8021	broad.mit.edu	37	9	134026946	134026946	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134026946delA	uc004cag.2	+						NUP214_uc004cah.2_Intron|NUP214_uc004cai.2_Intron|NUP214_uc004caf.1_Intron|NUP214_uc010mzf.2_Intron	NM_005085	NP_005076			nucleoporin 214kDa						carbohydrate metabolic process|glucose transport|mRNA metabolic process|protein export from nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore|nucleoplasm	protein binding			breast(7)|lung(3)|skin(3)|ovary(2)|central_nervous_system(1)	16	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)				T	DEK|SET|ABL1	AML|T-ALL								---	---	---	---
NUP214	8021	broad.mit.edu	37	9	134100636	134100637	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134100636_134100637insA	uc004cag.2	+						NUP214_uc004cah.2_Intron|NUP214_uc004cai.2_Intron|NUP214_uc010mzg.2_Intron|NUP214_uc011mcg.1_Intron	NM_005085	NP_005076			nucleoporin 214kDa						carbohydrate metabolic process|glucose transport|mRNA metabolic process|protein export from nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore|nucleoplasm	protein binding			breast(7)|lung(3)|skin(3)|ovary(2)|central_nervous_system(1)	16	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)				T	DEK|SET|ABL1	AML|T-ALL								---	---	---	---
PPAPDC3	84814	broad.mit.edu	37	9	134168634	134168634	+	Intron	DEL	C	-	-	rs11330905		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134168634delC	uc004cal.2	+							NM_032728	NP_116117			phosphatidic acid phosphatase type 2 domain							endoplasmic reticulum membrane|integral to membrane|nuclear envelope	hydrolase activity			breast(1)	1	all_hematologic(7;0.0119)			OV - Ovarian serous cystadenocarcinoma(145;1.22e-05)|Epithelial(140;0.000173)														---	---	---	---
BAT2L1	84726	broad.mit.edu	37	9	134305448	134305450	+	5'Flank	DEL	TTT	-	-	rs112930686		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134305448_134305450delTTT	uc004can.3	+						BAT2L1_uc004cam.1_Intron	NM_013318	NP_037450			HLA-B associated transcript 2-like								protein binding				0																		---	---	---	---
RAPGEF1	2889	broad.mit.edu	37	9	134599984	134599984	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134599984delA	uc004cbc.2	-						RAPGEF1_uc010mzn.2_Intron|RAPGEF1_uc004cbd.2_Intron	NM_005312	NP_005303			guanine nucleotide-releasing factor 2 isoform a						activation of MAPKK activity|nerve growth factor receptor signaling pathway|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|endosome	guanyl-nucleotide exchange factor activity|SH3 domain binding			lung(3)|ovary(2)|breast(1)|skin(1)	7		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.19e-05)|Epithelial(140;0.000364)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	134676930	134676931	+	IGR	INS	-	TG	TG			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134676930_134676931insTG								RAPGEF1 (61713 upstream) : MED27 (58568 downstream)																																			---	---	---	---
C9orf171	389799	broad.mit.edu	37	9	135295070	135295070	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135295070delT	uc004cbn.2	+						C9orf171_uc004cbo.2_Intron	NM_207417	NP_997300			hypothetical protein LOC389799											ovary(4)|large_intestine(1)	5																		---	---	---	---
C9orf171	389799	broad.mit.edu	37	9	135391254	135391255	+	Intron	INS	-	C	C	rs141894664	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135391254_135391255insC	uc004cbn.2	+						C9orf171_uc004cbo.2_Intron	NM_207417	NP_997300			hypothetical protein LOC389799											ovary(4)|large_intestine(1)	5																		---	---	---	---
SURF6	6838	broad.mit.edu	37	9	136201139	136201139	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136201139delT	uc004cdb.3	-							NM_006753	NP_006744			surfeit 6							granular component	DNA binding|RNA binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(145;1.16e-06)|Epithelial(140;8.34e-06)|all cancers(34;7.08e-05)														---	---	---	---
MED22	6837	broad.mit.edu	37	9	136213056	136213056	+	Intron	DEL	A	-	-	rs604402	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136213056delA	uc004cdc.2	-						MED22_uc004cdd.2_Intron|RPL7A_uc004cde.1_5'Flank	NM_133640	NP_598395			mediator complex subunit 22 isoform b						regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|mediator complex|soluble fraction	protein binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(145;1.14e-06)|Epithelial(140;8.2e-06)|all cancers(34;6.94e-05)														---	---	---	---
SURF4	6836	broad.mit.edu	37	9	136240480	136240480	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136240480delA	uc004cdj.2	-						SURF4_uc011mda.1_5'Flank|SURF4_uc010nal.2_Intron|SURF4_uc011mdb.1_Intron|SURF4_uc011mdc.1_Intron|SURF4_uc011mdd.1_Intron|C9orf96_uc004cdk.2_5'Flank|C9orf96_uc004cdl.2_5'Flank	NM_033161	NP_149351			surfeit 4							endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane	protein binding				0				OV - Ovarian serous cystadenocarcinoma(145;5.32e-07)|Epithelial(140;4.56e-06)|all cancers(34;4.25e-05)														---	---	---	---
ADAMTS13	11093	broad.mit.edu	37	9	136318560	136318560	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136318560delC	uc004cdv.3	+						ADAMTS13_uc004cdp.3_Intron|ADAMTS13_uc004cdt.1_Intron|ADAMTS13_uc004cdu.1_Intron|ADAMTS13_uc004cdw.3_Intron|ADAMTS13_uc004cdx.3_Intron|ADAMTS13_uc004cdz.3_Intron|ADAMTS13_uc004cea.1_5'Flank|ADAMTS13_uc004ceb.3_5'Flank	NM_139025	NP_620594			ADAM metallopeptidase with thrombospondin type 1						cell-matrix adhesion|glycoprotein metabolic process|integrin-mediated signaling pathway|peptide catabolic process|platelet activation|protein processing|proteolysis	cell surface|proteinaceous extracellular matrix	calcium ion binding|integrin binding|metalloendopeptidase activity|zinc ion binding			central_nervous_system(2)|skin(2)|ovary(1)|kidney(1)	6				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)														---	---	---	---
VAV2	7410	broad.mit.edu	37	9	136710542	136710542	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136710542delG	uc004ces.2	-						VAV2_uc004cer.2_Intron	NM_001134398	NP_001127870			vav 2 guanine nucleotide exchange factor isoform						angiogenesis|apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	metal ion binding|Rho guanyl-nucleotide exchange factor activity			central_nervous_system(3)|ovary(2)|lung(2)|breast(1)	8				OV - Ovarian serous cystadenocarcinoma(145;3.9e-07)|Epithelial(140;2.07e-06)|all cancers(34;9.39e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	136882714	136882714	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136882714delT								VAV2 (25268 upstream) : NCRNA00094 (7847 downstream)																																			---	---	---	---
COL5A1	1289	broad.mit.edu	37	9	137683140	137683140	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137683140delG	uc004cfe.2	+							NM_000093	NP_000084			alpha 1 type V collagen preproprotein						axon guidance|cell adhesion|collagen biosynthetic process|collagen fibril organization|eye morphogenesis|fibril organization|integrin biosynthetic process|skin development|wound healing, spreading of epidermal cells	collagen type V	heparin binding|integrin binding|platelet-derived growth factor binding|proteoglycan binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|kidney(1)	11		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)														---	---	---	---
Unknown	0	broad.mit.edu	37	9	137752456	137752456	+	Intron	DEL	A	-	-	rs34441602		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137752456delA	uc004cff.2	-											Homo sapiens cDNA clone IMAGE:5468304, partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	9	138158620	138158620	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138158620delC								OLFM1 (145589 upstream) : KIAA0649 (213028 downstream)																																			---	---	---	---
LCN1	3933	broad.mit.edu	37	9	138418176	138418176	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138418176delC	uc004cfz.1	+						LCN1_uc004cga.1_Intron	NM_002297	NP_002288			lipocalin 1 precursor						proteolysis|response to stimulus|sensory perception of taste	extracellular region	cysteine-type endopeptidase inhibitor activity|transporter activity				0		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.54e-08)|Epithelial(140;5.25e-08)|all cancers(34;9.27e-07)|READ - Rectum adenocarcinoma(205;0.155)														---	---	---	---
SEC16A	9919	broad.mit.edu	37	9	139339692	139339692	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139339692delA	uc004chx.2	-						SEC16A_uc004chp.2_Intron|SEC16A_uc004chq.2_Intron|SEC16A_uc011mea.1_Intron|SEC16A_uc004chr.2_Intron|SEC16A_uc004chs.2_Intron|SEC16A_uc004cht.2_Intron|SEC16A_uc004chu.2_Intron|SEC16A_uc004chv.3_Intron|SEC16A_uc004chw.2_Intron|SEC16A_uc010nbn.2_Intron	NM_014866	NP_055681			SEC16 homolog A						protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|Golgi membrane					0		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)														---	---	---	---
EGFL7	51162	broad.mit.edu	37	9	139560939	139560940	+	Intron	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139560939_139560940insC	uc004cid.2	+						EGFL7_uc004cif.2_Intron|EGFL7_uc004cig.2_Intron|EGFL7_uc010nbp.2_Intron|EGFL7_uc004cie.2_Intron|EGFL7_uc004cih.2_Intron	NM_201446	NP_958854			EGF-like-domain, multiple 7						angiogenesis|vasculogenesis		calcium ion binding			ovary(1)	1	all_cancers(76;0.109)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.87e-06)|Epithelial(140;0.000123)														---	---	---	---
C8G	733	broad.mit.edu	37	9	139839920	139839920	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139839920delG	uc004cka.2	+						FBXW5_uc010nbx.2_5'Flank|FBXW5_uc004cjx.2_5'Flank|FBXW5_uc004cjy.2_5'Flank|FBXW5_uc004cjz.2_5'Flank	NM_000606	NP_000597			complement component 8, gamma polypeptide						complement activation, alternative pathway|complement activation, classical pathway|cytolysis	extracellular region|membrane attack complex	retinol binding|transporter activity				0	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.19)	OV - Ovarian serous cystadenocarcinoma(145;7.88e-06)|Epithelial(140;0.000107)												OREG0019623	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	9	139856251	139856251	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139856251delC								LCN12 (6303 upstream) : PTGDS (13295 downstream)																																			---	---	---	---
COBRA1	25920	broad.mit.edu	37	9	140167078	140167078	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140167078delG	uc004cmm.3	+							NM_015456	NP_056271			cofactor of BRCA1						negative regulation of transcription, DNA-dependent|positive regulation of viral transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	cytoplasm|nucleoplasm	protein binding				0	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.137)	OV - Ovarian serous cystadenocarcinoma(145;9.42e-05)|Epithelial(140;0.000766)														---	---	---	---
EXD3	54932	broad.mit.edu	37	9	140229535	140229535	+	Intron	DEL	A	-	-	rs79120496		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140229535delA	uc004cmp.2	-						C9orf167_uc011mew.1_Intron|EXD3_uc010ncf.1_Intron	NM_017820	NP_060290			exonuclease 3'-5' domain containing 3						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	intracellular	3'-5' exonuclease activity|nucleic acid binding				0																		---	---	---	---
EXD3	54932	broad.mit.edu	37	9	140259069	140259069	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140259069delA	uc004cmp.2	-						C9orf167_uc011mew.1_Intron|EXD3_uc010ncf.1_Intron|EXD3_uc004cmq.1_Intron|EXD3_uc010ncg.1_Intron	NM_017820	NP_060290			exonuclease 3'-5' domain containing 3						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	intracellular	3'-5' exonuclease activity|nucleic acid binding				0																		---	---	---	---
EHMT1	79813	broad.mit.edu	37	9	140632091	140632092	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140632091_140632092delAA	uc011mfc.1	+						EHMT1_uc004coa.2_Intron|EHMT1_uc004cob.1_Intron|EHMT1_uc010ncn.1_5'Flank	NM_024757	NP_079033			euchromatic histone-lysine N-methyltransferase 1						DNA methylation|embryo development|peptidyl-lysine dimethylation|peptidyl-lysine monomethylation	chromosome|nucleus	histone methyltransferase activity (H3-K27 specific)|histone methyltransferase activity (H3-K9 specific)|p53 binding|zinc ion binding			breast(2)|pancreas(1)	3	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)														---	---	---	---
CACNA1B	774	broad.mit.edu	37	9	140772488	140772488	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140772488delG	uc004cog.2	+	1	248	c.103delG	c.(103-105)GGGfs	p.G35fs	uc004cof.1_Intron	NM_000718	NP_000709	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type,	35	Cytoplasmic (Potential).				membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	ATP binding|protein C-terminus binding|voltage-gated calcium channel activity			breast(3)|large_intestine(2)|ovary(1)	6	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)													---	---	---	---
CACNA1B	774	broad.mit.edu	37	9	140919750	140919751	+	Intron	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140919750_140919751delGA	uc004cog.2	+						CACNA1B_uc011mfd.1_Intron|CACNA1B_uc004coi.2_Intron	NM_000718	NP_000709			calcium channel, voltage-dependent, N type,						membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	ATP binding|protein C-terminus binding|voltage-gated calcium channel activity			breast(3)|large_intestine(2)|ovary(1)	6	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)													---	---	---	---
DIP2C	22982	broad.mit.edu	37	10	441036	441037	+	Intron	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:441036_441037insG	uc001ifp.2	-						DIP2C_uc009xhj.1_Intron	NM_014974	NP_055789			DIP2 disco-interacting protein 2 homolog C							nucleus	catalytic activity|transcription factor binding			breast(4)|ovary(2)|large_intestine(1)	7		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)														---	---	---	---
GTPBP4	23560	broad.mit.edu	37	10	1052579	1052579	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1052579delA	uc001ift.2	+						GTPBP4_uc010qac.1_Intron|GTPBP4_uc001ifu.2_Intron|GTPBP4_uc010qad.1_Intron|GTPBP4_uc010qae.1_Intron	NM_012341	NP_036473			G protein-binding protein CRFG						negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of collagen binding|negative regulation of DNA replication|negative regulation of protein ubiquitination|protein stabilization|regulation of cyclin-dependent protein kinase activity|ribosome biogenesis	nucleolus|perinuclear region of cytoplasm	GTP binding|GTPase activity|protein binding			ovary(1)|skin(1)	2		all_epithelial(10;0.107)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.0814)	Epithelial(11;0.0513)|all cancers(11;0.135)|OV - Ovarian serous cystadenocarcinoma(14;0.173)														---	---	---	---
GTPBP4	23560	broad.mit.edu	37	10	1056344	1056344	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1056344delT	uc001ift.2	+						GTPBP4_uc010qac.1_Intron|GTPBP4_uc001ifu.2_Intron|GTPBP4_uc010qad.1_Intron|GTPBP4_uc010qae.1_Intron	NM_012341	NP_036473			G protein-binding protein CRFG						negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of collagen binding|negative regulation of DNA replication|negative regulation of protein ubiquitination|protein stabilization|regulation of cyclin-dependent protein kinase activity|ribosome biogenesis	nucleolus|perinuclear region of cytoplasm	GTP binding|GTPase activity|protein binding			ovary(1)|skin(1)	2		all_epithelial(10;0.107)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.0814)	Epithelial(11;0.0513)|all cancers(11;0.135)|OV - Ovarian serous cystadenocarcinoma(14;0.173)														---	---	---	---
GTPBP4	23560	broad.mit.edu	37	10	1056665	1056665	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1056665delC	uc001ift.2	+						GTPBP4_uc001ifu.2_Intron|GTPBP4_uc010qad.1_Intron|GTPBP4_uc010qae.1_Intron	NM_012341	NP_036473			G protein-binding protein CRFG						negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of collagen binding|negative regulation of DNA replication|negative regulation of protein ubiquitination|protein stabilization|regulation of cyclin-dependent protein kinase activity|ribosome biogenesis	nucleolus|perinuclear region of cytoplasm	GTP binding|GTPase activity|protein binding			ovary(1)|skin(1)	2		all_epithelial(10;0.107)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.0814)	Epithelial(11;0.0513)|all cancers(11;0.135)|OV - Ovarian serous cystadenocarcinoma(14;0.173)														---	---	---	---
WDR37	22884	broad.mit.edu	37	10	1151734	1151734	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1151734delT	uc001igf.1	+						WDR37_uc009xhm.1_Intron|WDR37_uc009xhn.1_Intron|WDR37_uc001igg.1_Intron	NM_014023	NP_054742			WD repeat domain 37												0		all_epithelial(10;0.0449)|Colorectal(49;0.142)		Epithelial(11;0.134)														---	---	---	---
NCRNA00200	399706	broad.mit.edu	37	10	1206472	1206472	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1206472delT	uc010qag.1	+							NR_015376				Homo sapiens cDNA FLJ40354 fis, clone TESTI2033641.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	1221250	1221250	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1221250delA								NCRNA00200 (10638 upstream) : ADARB2 (6824 downstream)																																			---	---	---	---
ADARB2	105	broad.mit.edu	37	10	1600857	1600857	+	Intron	DEL	A	-	-	rs2676740	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1600857delA	uc009xhq.2	-							NM_018702	NP_061172			adenosine deaminase, RNA-specific, B2						mRNA processing	mitochondrion|nucleus	adenosine deaminase activity|double-stranded RNA binding|metal ion binding|single-stranded RNA binding			large_intestine(2)|central_nervous_system(1)	3		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)														---	---	---	---
ADARB2	105	broad.mit.edu	37	10	1778279	1778280	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1778279_1778280insA	uc009xhq.2	-							NM_018702	NP_061172			adenosine deaminase, RNA-specific, B2						mRNA processing	mitochondrion|nucleus	adenosine deaminase activity|double-stranded RNA binding|metal ion binding|single-stranded RNA binding			large_intestine(2)|central_nervous_system(1)	3		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	1828889	1828890	+	IGR	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1828889_1828890delAC								ADARB2 (49171 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	2015846	2015846	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:2015846delA								ADARB2 (236128 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	2202054	2202055	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:2202054_2202055insA								ADARB2 (422336 upstream) : PFKP (907697 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	2566226	2566226	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:2566226delC								ADARB2 (786508 upstream) : PFKP (543526 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	2728062	2728062	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:2728062delT								ADARB2 (948344 upstream) : PFKP (381690 downstream)																																			---	---	---	---
PITRM1	10531	broad.mit.edu	37	10	3192595	3192596	+	Intron	DEL	CA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3192595_3192596delCA	uc010qah.1	-						PITRM1_uc001igr.1_Intron|PITRM1_uc001igt.1_Intron|PITRM1_uc009xhv.1_Intron|PITRM1_uc001igu.1_Intron|PITRM1_uc010qai.1_Intron					SubName: Full=cDNA FLJ54065, moderately similar to Mus musculus pitrilysin metallepetidase 1 (Pitrm1), mRNA;						proteolysis		metalloendopeptidase activity|zinc ion binding			pancreas(1)	1																		---	---	---	---
PITRM1	10531	broad.mit.edu	37	10	3193572	3193572	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3193572delA	uc010qah.1	-						PITRM1_uc001igr.1_Intron|PITRM1_uc001igt.1_Intron|PITRM1_uc009xhv.1_Intron|PITRM1_uc001igu.1_Intron|PITRM1_uc010qai.1_Intron|PITRM1_uc001igw.1_Intron					SubName: Full=cDNA FLJ54065, moderately similar to Mus musculus pitrilysin metallepetidase 1 (Pitrm1), mRNA;						proteolysis		metalloendopeptidase activity|zinc ion binding			pancreas(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	3357105	3357106	+	IGR	INS	-	A	A	rs140602943		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:3357105_3357106insA								PITRM1 (142102 upstream) : KLF6 (461083 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	4347950	4347950	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4347950delG								KLF6 (520477 upstream) : LOC100216001 (273494 downstream)																																			---	---	---	---
LOC100216001	100216001	broad.mit.edu	37	10	4666593	4666593	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4666593delC	uc001ihe.3	-											Homo sapiens, clone IMAGE:4450067, mRNA.												0																		---	---	---	---
LOC100216001	100216001	broad.mit.edu	37	10	4666972	4666972	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4666972delC	uc001ihe.3	-											Homo sapiens, clone IMAGE:4450067, mRNA.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	5866808	5866808	+	IGR	DEL	A	-	-	rs78438106		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5866808delA								GDI2 (11296 upstream) : ANKRD16 (36883 downstream)																																			---	---	---	---
ANKRD16	54522	broad.mit.edu	37	10	5922598	5922599	+	Intron	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5922598_5922599insG	uc010qat.1	-						ANKRD16_uc009xie.2_Intron|ANKRD16_uc009xif.2_Intron|ANKRD16_uc001iiq.2_Intron	NM_019046	NP_061919			ankyrin repeat domain 16 isoform a												0																		---	---	---	---
ANKRD16	54522	broad.mit.edu	37	10	5925286	5925286	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5925286delT	uc010qat.1	-						ANKRD16_uc009xie.2_Intron|ANKRD16_uc009xif.2_Intron|ANKRD16_uc001iiq.2_Intron	NM_019046	NP_061919			ankyrin repeat domain 16 isoform a												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	5988781	5988781	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5988781delA								FBXO18 (9226 upstream) : IL15RA (2078 downstream)																																			---	---	---	---
PFKFB3	5209	broad.mit.edu	37	10	6262371	6262371	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6262371delT	uc001ije.2	+						PFKFB3_uc001ijd.2_Intron|PFKFB3_uc009xii.2_Intron|PFKFB3_uc010qaw.1_Intron|PFKFB3_uc001ijf.2_Intron	NM_004566	NP_004557			6-phosphofructo-2-kinase/fructose-2,						fructose 2,6-bisphosphate metabolic process|glycolysis	cytosol	6-phosphofructo-2-kinase activity|ATP binding|fructose-2,6-bisphosphate 2-phosphatase activity|identical protein binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
PRKCQ	5588	broad.mit.edu	37	10	6616075	6616075	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6616075delA	uc001ijj.1	-						PRKCQ_uc009xin.1_Intron|PRKCQ_uc010qax.1_Intron	NM_006257	NP_006248			protein kinase C, theta						axon guidance|cellular component disassembly involved in apoptosis|intracellular signal transduction|membrane protein ectodomain proteolysis|platelet activation|regulation of cell growth|T cell receptor signaling pathway	cytosol	ATP binding|metal ion binding|protein binding|protein kinase C activity			ovary(3)|lung(2)|large_intestine(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	6638676	6638676	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6638676delT								PRKCQ (16438 upstream) : SFMBT2 (565573 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	6890787	6890787	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6890787delT								PRKCQ (268549 upstream) : SFMBT2 (313462 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	7085496	7085497	+	IGR	DEL	TT	-	-	rs149000515		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7085496_7085497delTT								PRKCQ (463258 upstream) : SFMBT2 (118752 downstream)																																			---	---	---	---
SFMBT2	57713	broad.mit.edu	37	10	7211564	7211564	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7211564delT	uc009xio.1	-						SFMBT2_uc001ijn.1_Intron|SFMBT2_uc010qay.1_Intron	NM_001029880	NP_001025051			Scm-like with four mbt domains 2						regulation of transcription, DNA-dependent	nucleus				ovary(4)|upper_aerodigestive_tract(2)|large_intestine(1)|central_nervous_system(1)	8																		---	---	---	---
SFMBT2	57713	broad.mit.edu	37	10	7271690	7271690	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7271690delT	uc009xio.1	-						SFMBT2_uc001ijn.1_Intron|SFMBT2_uc010qay.1_Intron	NM_001029880	NP_001025051			Scm-like with four mbt domains 2						regulation of transcription, DNA-dependent	nucleus				ovary(4)|upper_aerodigestive_tract(2)|large_intestine(1)|central_nervous_system(1)	8																		---	---	---	---
SFMBT2	57713	broad.mit.edu	37	10	7321068	7321068	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7321068delA	uc009xio.1	-						SFMBT2_uc001ijn.1_Intron|SFMBT2_uc010qay.1_Intron	NM_001029880	NP_001025051			Scm-like with four mbt domains 2						regulation of transcription, DNA-dependent	nucleus				ovary(4)|upper_aerodigestive_tract(2)|large_intestine(1)|central_nervous_system(1)	8																		---	---	---	---
SFMBT2	57713	broad.mit.edu	37	10	7375683	7375684	+	Intron	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7375683_7375684delTC	uc009xio.1	-						SFMBT2_uc001ijn.1_Intron|SFMBT2_uc010qay.1_Intron|SFMBT2_uc001ijo.1_Intron	NM_001029880	NP_001025051			Scm-like with four mbt domains 2						regulation of transcription, DNA-dependent	nucleus				ovary(4)|upper_aerodigestive_tract(2)|large_intestine(1)|central_nervous_system(1)	8																		---	---	---	---
ATP5C1	509	broad.mit.edu	37	10	7840376	7840377	+	Intron	DEL	TT	-	-	rs78930463		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7840376_7840377delTT	uc001iju.2	+						ATP5C1_uc010qbb.1_Intron|ATP5C1_uc009xiq.1_Intron|ATP5C1_uc010qbc.1_Intron|ATP5C1_uc001ijv.2_Intron	NM_001001973	NP_001001973			ATP synthase, H+ transporting, mitochondrial F1						oxidative phosphorylation|respiratory electron transport chain	mitochondrial matrix|mitochondrial proton-transporting ATP synthase complex, catalytic core F(1)	hydrogen ion transporting ATP synthase activity, rotational mechanism|proton-transporting ATPase activity, rotational mechanism				0																		---	---	---	---
TAF3	83860	broad.mit.edu	37	10	7979793	7979793	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7979793delT	uc010qbd.1	+							NM_031923	NP_114129			RNA polymerase II transcription factor TAFII140						maintenance of protein location in nucleus|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	transcription factor TFIID complex	protein binding|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	8255345	8255345	+	IGR	DEL	T	-	-	rs1538510	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8255345delT								GATA3 (138183 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	8291790	8291790	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8291790delT								GATA3 (174628 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	8369902	8369902	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8369902delA								GATA3 (252740 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	8573412	8573412	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8573412delA								GATA3 (456250 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	9203540	9203541	+	IGR	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:9203540_9203541insC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	9298920	9298920	+	IGR	DEL	G	-	-	rs140284873	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:9298920delG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	9312088	9312089	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:9312088_9312089insA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	9941820	9941820	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:9941820delT								None (None upstream) : SFTA1P (884582 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	10183592	10183592	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10183592delT								None (None upstream) : SFTA1P (642810 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	10183981	10183982	+	IGR	INS	-	AA	AA	rs150014792	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10183981_10183982insAA								None (None upstream) : SFTA1P (642420 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	10292236	10292236	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10292236delA								None (None upstream) : SFTA1P (534166 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	10329532	10329532	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10329532delA								None (None upstream) : SFTA1P (496870 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	10477012	10477012	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10477012delA								None (None upstream) : SFTA1P (349390 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	10534869	10534869	+	IGR	DEL	T	-	-	rs142511675		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10534869delT								None (None upstream) : SFTA1P (291533 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	10604889	10604889	+	IGR	DEL	T	-	-	rs113628740		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10604889delT								None (None upstream) : SFTA1P (221513 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	10936646	10936646	+	IGR	DEL	A	-	-	rs10708773		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:10936646delA								SFTA1P (99769 upstream) : LOC254312 (40258 downstream)																																			---	---	---	---
CELF2	10659	broad.mit.edu	37	10	11136367	11136368	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11136367_11136368insT	uc001iki.3	+						CELF2_uc010qbi.1_Intron|CELF2_uc010qbj.1_Intron|CELF2_uc001ikk.2_Intron|CELF2_uc001ikl.3_Intron|uc001ikn.1_Intron	NM_001025077	NP_001020248			CUG triplet repeat, RNA binding protein 2						mRNA processing|regulation of heart contraction	cytoplasm|nucleus	nucleotide binding|protein binding|RNA binding				0																		---	---	---	---
USP6NL	9712	broad.mit.edu	37	10	11567482	11567482	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11567482delA	uc001ikt.3	-						USP6NL_uc001iks.1_Intron	NM_014688	NP_055503			USP6 N-terminal like isoform 1							intracellular	Rab GTPase activator activity				0																		---	---	---	---
USP6NL	9712	broad.mit.edu	37	10	11567611	11567611	+	Intron	DEL	T	-	-	rs77058930		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11567611delT	uc001ikt.3	-						USP6NL_uc001iks.1_Intron	NM_014688	NP_055503			USP6 N-terminal like isoform 1							intracellular	Rab GTPase activator activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	11661156	11661156	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11661156delT								USP6NL (7477 upstream) : ECHDC3 (123200 downstream)																																			---	---	---	---
DHTKD1	55526	broad.mit.edu	37	10	12134810	12134810	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12134810delA	uc001ild.3	+							NM_018706	NP_061176			dehydrogenase E1 and transketolase domain						glycolysis	mitochondrion	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding			ovary(1)|central_nervous_system(1)	2		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)															---	---	---	---
SEC61A2	55176	broad.mit.edu	37	10	12186145	12186145	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12186145delT	uc001ile.2	+						SEC61A2_uc010qbq.1_Intron|SEC61A2_uc001ilf.3_Intron|SEC61A2_uc001ilh.3_Intron|SEC61A2_uc001ilg.3_Intron	NM_018144	NP_060614			Sec61 alpha form 2 isoform a							endoplasmic reticulum membrane|integral to membrane	P-P-bond-hydrolysis-driven protein transmembrane transporter activity			ovary(1)	1		Renal(717;0.228)																---	---	---	---
CDC123	8872	broad.mit.edu	37	10	12289504	12289505	+	Intron	INS	-	CT	CT			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12289504_12289505insCT	uc001ill.2	+						CDC123_uc001ilm.2_Intron	NM_006023	NP_006014			cell division cycle 123						cell cycle arrest|cell division|positive regulation of cell proliferation|regulation of mitotic cell cycle	cytoplasm				central_nervous_system(1)	1																		---	---	---	---
CAMK1D	57118	broad.mit.edu	37	10	12500879	12500880	+	Intron	INS	-	T	T	rs150219433		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12500879_12500880insT	uc001ilo.2	+						CAMK1D_uc001iln.2_Intron	NM_153498	NP_705718			calcium/calmodulin-dependent protein kinase ID							calcium- and calmodulin-dependent protein kinase complex|cytoplasm|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)|stomach(1)	2				GBM - Glioblastoma multiforme(1;3.16e-05)														---	---	---	---
CAMK1D	57118	broad.mit.edu	37	10	12720783	12720784	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12720783_12720784insT	uc001ilo.2	+						CAMK1D_uc001iln.2_Intron	NM_153498	NP_705718			calcium/calmodulin-dependent protein kinase ID							calcium- and calmodulin-dependent protein kinase complex|cytoplasm|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)|stomach(1)	2				GBM - Glioblastoma multiforme(1;3.16e-05)														---	---	---	---
CAMK1D	57118	broad.mit.edu	37	10	12855367	12855367	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12855367delA	uc001ilo.2	+						CAMK1D_uc001iln.2_Intron	NM_153498	NP_705718			calcium/calmodulin-dependent protein kinase ID							calcium- and calmodulin-dependent protein kinase complex|cytoplasm|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)|stomach(1)	2				GBM - Glioblastoma multiforme(1;3.16e-05)														---	---	---	---
CCDC3	83643	broad.mit.edu	37	10	13099529	13099529	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13099529delT	uc001ilr.2	-						CCDC3_uc009xjc.1_Intron|uc009xjd.1_Intron					Homo sapiens MSTP151 (MST151) mRNA, complete cds.							endoplasmic reticulum|extracellular region				ovary(1)	1		Ovarian(717;0.0822)	BRCA - Breast invasive adenocarcinoma(52;0.163)															---	---	---	---
PHYH	5264	broad.mit.edu	37	10	13326338	13326338	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13326338delA	uc001imf.2	-						PHYH_uc001ime.2_Intron|PHYH_uc001img.2_Intron	NM_006214	NP_006205			phytanoyl-CoA 2-hydroxylase isoform a precursor						fatty acid alpha-oxidation|nervous system development	peroxisomal matrix	electron carrier activity|L-ascorbic acid binding|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|phytanoyl-CoA dioxygenase activity|protein binding				0		Ovarian(717;0.0448)			Antihemophilic Factor(DB00025)|Vitamin C(DB00126)													---	---	---	---
BEND7	222389	broad.mit.edu	37	10	13512551	13512551	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13512551delA	uc001imm.2	-						BEND7_uc001imn.2_Intron|BEND7_uc001imo.3_Intron	NM_152751	NP_689964			BEN domain containing 7 isoform 1								protein binding			ovary(1)|breast(1)	2																		---	---	---	---
FRMD4A	55691	broad.mit.edu	37	10	13899198	13899198	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13899198delT	uc001ims.2	-						FRMD4A_uc009xjf.1_Intron|FRMD4A_uc001imt.1_Intron|FRMD4A_uc001imu.1_Intron	NM_018027	NP_060497			FERM domain containing 4A							cytoplasm|cytoskeleton	binding			ovary(1)|skin(1)|pancreas(1)	3																		---	---	---	---
FAM107B	83641	broad.mit.edu	37	10	14572299	14572299	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14572299delA	uc001imx.1	-						FAM107B_uc001ina.1_Intron|FAM107B_uc010qbu.1_Intron|FAM107B_uc009xjg.1_Intron|FAM107B_uc001imy.1_Intron|FAM107B_uc001imz.1_Intron	NM_031453	NP_113641			hypothetical protein LOC83641											breast(4)	4																		---	---	---	---
FAM107B	83641	broad.mit.edu	37	10	14677105	14677105	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14677105delA	uc001ina.1	-						FAM107B_uc010qbu.1_Intron	NM_031453	NP_113641			hypothetical protein LOC83641											breast(4)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	16190852	16190853	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16190852_16190853insA								FAM188A (288333 upstream) : PTER (288114 downstream)																																			---	---	---	---
CUBN	8029	broad.mit.edu	37	10	16947996	16947997	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16947996_16947997insA	uc001ioo.2	-						CUBN_uc009xjq.1_Intron|CUBN_uc009xjr.1_Intron	NM_001081	NP_001072			cubilin precursor						cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1)	19					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)													---	---	---	---
CUBN	8029	broad.mit.edu	37	10	17064400	17064401	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17064400_17064401insT	uc001ioo.2	-							NM_001081	NP_001072			cubilin precursor						cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1)	19					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)													---	---	---	---
CUBN	8029	broad.mit.edu	37	10	17132237	17132237	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17132237delA	uc001ioo.2	-							NM_001081	NP_001072			cubilin precursor						cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|kidney(1)	19					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)													---	---	---	---
ST8SIA6	338596	broad.mit.edu	37	10	17425125	17425125	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17425125delT	uc001ipd.2	-						ST8SIA6_uc010qce.1_Intron	NM_001004470	NP_001004470			ST8 alpha-N-acetyl-neuraminide						post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	17570336	17570337	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17570336_17570337delAA								ST8SIA6 (74082 upstream) : PTPLA (61623 downstream)																																			---	---	---	---
STAM	8027	broad.mit.edu	37	10	17756959	17756959	+	3'UTR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17756959delC	uc001ipj.1	+	14					STAM_uc009xjw.1_3'UTR	NM_003473	NP_003464			signal transducing adaptor molecule 1						cellular membrane organization|endosome transport|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway	cytosol|early endosome membrane	SH3/SH2 adaptor activity			large_intestine(1)|ovary(1)	2																		---	---	---	---
MRC1	4360	broad.mit.edu	37	10	17891551	17891552	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:17891551_17891552insT	uc001ipk.2	+							NM_002438	NP_002429			mannose receptor C type 1 precursor						receptor-mediated endocytosis	endosome membrane|integral to plasma membrane	mannose binding|receptor activity				0																		---	---	---	---
CACNB2	783	broad.mit.edu	37	10	18563157	18563157	+	Intron	DEL	A	-	-	rs11288271		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18563157delA	uc001ipr.2	+						CACNB2_uc009xjz.1_Intron|CACNB2_uc001ips.2_Intron|CACNB2_uc001ipt.2_Intron|CACNB2_uc010qcl.1_Intron|CACNB2_uc001ipu.2_Intron|CACNB2_uc001ipv.2_Intron|CACNB2_uc009xka.1_Intron|CACNB2_uc001ipw.2_Intron|CACNB2_uc001ipx.2_Intron	NM_201596	NP_963890			calcium channel, voltage-dependent, beta 2						axon guidance|neuromuscular junction development	integral to plasma membrane|sarcolemma|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			large_intestine(1)|central_nervous_system(1)|skin(1)	3					Magnesium Sulfate(DB00653)|Verapamil(DB00661)													---	---	---	---
ARL5B	221079	broad.mit.edu	37	10	18964316	18964316	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18964316delT	uc001iqd.1	+	6					uc001iqe.2_5'Flank	NM_178815	NP_848930			ADP-ribosylation factor-like 8						small GTPase mediated signal transduction	intracellular	GTP binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	18987930	18987930	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:18987930delT								ARL5B (20990 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	19027631	19027631	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19027631delT								ARL5B (60691 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	19206377	19206378	+	IGR	DEL	TC	-	-	rs67905360		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:19206377_19206378delTC								ARL5B (239437 upstream) : PLXDC2 (898994 downstream)																																			---	---	---	---
PLXDC2	84898	broad.mit.edu	37	10	20218970	20218970	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20218970delT	uc001iqg.1	+						PLXDC2_uc001iqh.1_Intron	NM_032812	NP_116201			plexin domain containing 2 precursor							integral to membrane				ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	20746920	20746920	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20746920delA								PLXDC2 (177805 upstream) : NEBL (321985 downstream)																																			---	---	---	---
NEBL	10529	broad.mit.edu	37	10	21426852	21426852	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21426852delA	uc001iqk.2	-						C10orf113_uc001iqm.2_Intron	NM_213569	NP_998734			nebulette non-muscle isoform						regulation of actin filament length		actin binding|structural constituent of muscle			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	21488147	21488147	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21488147delG								NEBL (25031 upstream) : C10orf114 (295275 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	21597279	21597279	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21597279delT								NEBL (134163 upstream) : C10orf114 (186143 downstream)																																			---	---	---	---
MLLT10	8028	broad.mit.edu	37	10	21827397	21827397	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21827397delA	uc001iqs.2	+						MLLT10_uc001iqt.2_Intron|MLLT10_uc001iqv.2_Intron|MLLT10_uc001iqy.2_Intron|MLLT10_uc001iqr.1_Intron|MLLT10_uc001iqq.1_Intron|MLLT10_uc001iqu.1_Intron|MLLT10_uc009xke.1_Intron|MLLT10_uc001iqw.1_Intron|MLLT10_uc001iqx.1_Intron|MLLT10_uc009xkf.1_Intron	NM_004641	NP_004632			myeloid/lymphoid or mixed-lineage leukemia						positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(1)|skin(1)	2								T	MLL|PICALM|CDK6	AL								---	---	---	---
MLLT10	8028	broad.mit.edu	37	10	21853386	21853386	+	Intron	DEL	T	-	-	rs77475297		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21853386delT	uc001iqs.2	+						MLLT10_uc001iqt.2_Intron|MLLT10_uc001iqv.2_Intron|MLLT10_uc001iqy.2_Intron|MLLT10_uc009xke.1_Intron|MLLT10_uc001iqw.1_Intron|MLLT10_uc001iqx.1_Intron|MLLT10_uc009xkf.1_Intron	NM_004641	NP_004632			myeloid/lymphoid or mixed-lineage leukemia						positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(1)|skin(1)	2								T	MLL|PICALM|CDK6	AL								---	---	---	---
MLLT10	8028	broad.mit.edu	37	10	21861546	21861546	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21861546delT	uc001iqs.2	+						MLLT10_uc001iqt.2_Intron|MLLT10_uc001iqv.2_Intron|MLLT10_uc001iqy.2_Intron|MLLT10_uc009xke.1_Intron|MLLT10_uc001iqw.1_Intron|MLLT10_uc001iqx.1_Intron|MLLT10_uc009xkf.1_Intron	NM_004641	NP_004632			myeloid/lymphoid or mixed-lineage leukemia						positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(1)|skin(1)	2								T	MLL|PICALM|CDK6	AL								---	---	---	---
MLLT10	8028	broad.mit.edu	37	10	21906186	21906186	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21906186delT	uc001iqs.2	+						MLLT10_uc001iqt.2_Intron|MLLT10_uc001iqv.2_Intron|MLLT10_uc001iqy.2_Intron|MLLT10_uc001ira.2_Intron|MLLT10_uc001iqz.2_Intron	NM_004641	NP_004632			myeloid/lymphoid or mixed-lineage leukemia						positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(1)|skin(1)	2								T	MLL|PICALM|CDK6	AL								---	---	---	---
MLLT10	8028	broad.mit.edu	37	10	21990139	21990139	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21990139delT	uc001iqs.2	+						MLLT10_uc001iqt.2_Intron|MLLT10_uc001iqv.2_Intron|MLLT10_uc001iqy.2_Intron|MLLT10_uc001ira.2_Intron|MLLT10_uc001irb.2_Intron	NM_004641	NP_004632			myeloid/lymphoid or mixed-lineage leukemia						positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(1)|skin(1)	2								T	MLL|PICALM|CDK6	AL								---	---	---	---
Unknown	0	broad.mit.edu	37	10	22424202	22424202	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22424202delA								DNAJC1 (131552 upstream) : COMMD3 (181097 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	22425651	22425651	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22425651delA								DNAJC1 (133001 upstream) : COMMD3 (179648 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	22511921	22511922	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22511921_22511922insT								DNAJC1 (219271 upstream) : COMMD3 (93377 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	22630923	22630924	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22630923_22630924insA								BMI1 (10506 upstream) : SPAG6 (3475 downstream)																																			---	---	---	---
PIP4K2A	5305	broad.mit.edu	37	10	22859013	22859014	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22859013_22859014delAA	uc001irl.3	-						PIP4K2A_uc010qcu.1_Intron	NM_005028	NP_005019			phosphatidylinositol-5-phosphate 4-kinase, type								1-phosphatidylinositol-4-phosphate 5-kinase activity|1-phosphatidylinositol-5-phosphate 4-kinase activity|ATP binding			ovary(1)|skin(1)	2																		---	---	---	---
PIP4K2A	5305	broad.mit.edu	37	10	22993224	22993224	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22993224delA	uc001irl.3	-							NM_005028	NP_005019			phosphatidylinositol-5-phosphate 4-kinase, type								1-phosphatidylinositol-4-phosphate 5-kinase activity|1-phosphatidylinositol-5-phosphate 4-kinase activity|ATP binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	23703436	23703436	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:23703436delA								C10orf67 (69664 upstream) : OTUD1 (24762 downstream)																																			---	---	---	---
KIAA1217	56243	broad.mit.edu	37	10	24292353	24292353	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24292353delT	uc001irs.2	+							NM_001098500	NP_001091970			sickle tail isoform 2						embryonic skeletal system development	cytoplasm				ovary(5)|skin(2)	7																		---	---	---	---
KIAA1217	56243	broad.mit.edu	37	10	24476820	24476820	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24476820delA	uc001irs.2	+							NM_001098500	NP_001091970			sickle tail isoform 2						embryonic skeletal system development	cytoplasm				ovary(5)|skin(2)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	24870209	24870209	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24870209delA								KIAA1217 (33438 upstream) : ARHGAP21 (2329 downstream)																																			---	---	---	---
PRTFDC1	56952	broad.mit.edu	37	10	25192637	25192637	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25192637delT	uc001ise.1	-						PRTFDC1_uc010qdd.1_Intron|PRTFDC1_uc001isf.1_Intron|PRTFDC1_uc009xkm.1_Intron	NM_020200	NP_064585			phosphoribosyl transferase domain containing 1						adenine salvage|central nervous system neuron development|cerebral cortex neuron differentiation|cytolysis|dendrite morphogenesis|GMP salvage|grooming behavior|hypoxanthine metabolic process|IMP salvage|lymphocyte proliferation|positive regulation of dopamine metabolic process|purine ribonucleoside salvage|response to amphetamine|striatum development	cytosol	hypoxanthine phosphoribosyltransferase activity|magnesium ion binding|nucleotide binding|protein homodimerization activity			ovary(1)	1																		---	---	---	---
GPR158	57512	broad.mit.edu	37	10	25595946	25595947	+	Intron	DEL	AG	-	-	rs67926384		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25595946_25595947delAG	uc001isj.2	+							NM_020752	NP_065803			G protein-coupled receptor 158 precursor							integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(4)|large_intestine(2)|pancreas(1)|skin(1)	8																		---	---	---	---
MYO3A	53904	broad.mit.edu	37	10	26481548	26481551	+	Intron	DEL	TTCC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26481548_26481551delTTCC	uc001isn.2	+						MYO3A_uc009xkp.1_Intron|MYO3A_uc009xkq.1_Intron	NM_017433	NP_059129			myosin IIIA						protein autophosphorylation|response to stimulus|sensory perception of sound|visual perception	cytoplasm|filamentous actin|filopodium|myosin complex	actin binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|plus-end directed microfilament motor activity|protein serine/threonine kinase activity			ovary(6)|stomach(3)|lung(3)|central_nervous_system(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	18																		---	---	---	---
GAD2	2572	broad.mit.edu	37	10	26519355	26519362	+	Intron	DEL	TTTGTTTG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26519355_26519362delTTTGTTTG	uc001isp.2	+						GAD2_uc001isq.2_Intron	NM_001134366	NP_001127838			glutamate decarboxylase 2						glutamate decarboxylation to succinate|neurotransmitter biosynthetic process|neurotransmitter secretion	cell junction|clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|cytosol|Golgi membrane|presynaptic membrane	glutamate decarboxylase activity|protein binding|pyridoxal phosphate binding			central_nervous_system(1)|skin(1)	2					L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	26673222	26673222	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26673222delA								GAD2 (79731 upstream) : APBB1IP (54044 downstream)																																			---	---	---	---
ABI1	10006	broad.mit.edu	37	10	27132700	27132701	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27132700_27132701insA	uc001isx.2	-						ABI1_uc001ite.2_Intron|ABI1_uc010qdh.1_Intron|ABI1_uc010qdi.1_Intron|ABI1_uc001isy.2_Intron|ABI1_uc001ita.2_Intron|ABI1_uc001isz.2_Intron|ABI1_uc001itb.2_Intron|ABI1_uc001itc.2_Intron|ABI1_uc010qdj.1_Intron|ABI1_uc001itd.2_Intron|ABI1_uc010qdk.1_Intron	NM_005470	NP_005461			abl-interactor 1 isoform a						actin polymerization or depolymerization|cellular component movement|negative regulation of cell proliferation|peptidyl-tyrosine phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	cell junction|cytoskeleton|cytosol|endoplasmic reticulum|filopodium|growth cone|lamellipodium|nucleus|soluble fraction|synapse|synaptosome	cytoskeletal protein binding			central_nervous_system(1)	1																		---	---	---	---
YME1L1	10730	broad.mit.edu	37	10	27410387	27410387	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27410387delA	uc001iti.2	-						YME1L1_uc001itj.2_Intron|YME1L1_uc010qdl.1_Intron|YME1L1_uc009xkv.2_Intron	NM_139312	NP_647473			YME1-like 1 isoform 1						protein catabolic process|proteolysis	membrane|mitochondrion	ATP binding|metal ion binding|metalloendopeptidase activity|nucleoside-triphosphatase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	27606914	27606915	+	IGR	INS	-	T	T	rs140134629	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27606914_27606915insT								LOC387646 (65679 upstream) : PTCHD3 (80202 downstream)																																			---	---	---	---
ARMC4	55130	broad.mit.edu	37	10	28270269	28270269	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28270269delA	uc009xky.2	-						ARMC4_uc010qds.1_Intron|ARMC4_uc010qdt.1_Intron|ARMC4_uc001itz.2_Intron|ARMC4_uc010qdu.1_Intron	NM_018076	NP_060546			armadillo repeat containing 4								binding			ovary(4)|skin(2)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	28668597	28668597	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28668597delT								MPP7 (76602 upstream) : WAC (152830 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	28785709	28785709	+	IGR	DEL	G	-	-	rs113128663		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28785709delG								MPP7 (193714 upstream) : WAC (35718 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	30059667	30059667	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30059667delT								SVIL (33803 upstream) : KIAA1462 (242062 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	30094954	30094954	+	IGR	DEL	A	-	-	rs67807454		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30094954delA								SVIL (69090 upstream) : KIAA1462 (206775 downstream)																																			---	---	---	---
KIAA1462	57608	broad.mit.edu	37	10	30305328	30305331	+	3'UTR	DEL	AGGG	-	-	rs11292871	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30305328_30305331delAGGG	uc001iux.2	-	3					KIAA1462_uc001iuw.1_5'Flank|KIAA1462_uc001iuy.2_3'UTR|KIAA1462_uc001iuz.2_3'UTR	NM_020848	NP_065899			hypothetical protein LOC57608											ovary(4)	4																		---	---	---	---
MTPAP	55149	broad.mit.edu	37	10	30615017	30615017	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30615017delT	uc001iva.3	-						MTPAP_uc001ivb.3_Intron	NM_018109	NP_060579			PAP associated domain containing 1 precursor						cell death|histone mRNA catabolic process|mRNA polyadenylation|transcription, DNA-dependent	mitochondrion	ATP binding|magnesium ion binding|manganese ion binding|polynucleotide adenylyltransferase activity|protein homodimerization activity|RNA binding|UTP binding			ovary(1)	1																		---	---	---	---
MTPAP	55149	broad.mit.edu	37	10	30665113	30665113	+	5'Flank	DEL	T	-	-	rs112439610		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30665113delT	uc001ivb.3	-						LOC729668_uc001ivd.2_5'Flank	NM_018109	NP_060579			PAP associated domain containing 1 precursor						cell death|histone mRNA catabolic process|mRNA polyadenylation|transcription, DNA-dependent	mitochondrion	ATP binding|magnesium ion binding|manganese ion binding|polynucleotide adenylyltransferase activity|protein homodimerization activity|RNA binding|UTP binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	30678371	30678371	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30678371delA								MTPAP (14994 upstream) : MAP3K8 (44495 downstream)																																			---	---	---	---
MAP3K8	1326	broad.mit.edu	37	10	30728362	30728362	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30728362delA	uc001ivi.1	+						MAP3K8_uc009xlf.1_Intron|MAP3K8_uc001ivj.1_Intron	NM_005204	NP_005195			mitogen-activated protein kinase kinase kinase						cell cycle|T cell costimulation	cytosol	ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein binding			breast(3)|central_nervous_system(1)	4		Prostate(175;0.151)																---	---	---	---
LYZL2	119180	broad.mit.edu	37	10	30901429	30901429	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30901429delT	uc001ivk.2	-							NM_183058	NP_898881			lysozyme-like 2						cell wall macromolecule catabolic process	extracellular region	lysozyme activity				0		Prostate(175;0.151)																---	---	---	---
ZNF438	220929	broad.mit.edu	37	10	31217579	31217579	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31217579delT	uc010qdz.1	-						ZNF438_uc001ivn.2_Intron|ZNF438_uc010qdy.1_Intron|ZNF438_uc001ivo.3_Intron|ZNF438_uc009xlg.2_Intron|ZNF438_uc001ivp.3_Intron|ZNF438_uc010qea.1_Intron|ZNF438_uc010qeb.1_Intron|ZNF438_uc010qec.1_Intron	NM_182755	NP_877432			zinc finger protein 438 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|breast(1)	2		Prostate(175;0.0587)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	31490482	31490482	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31490482delC								ZNF438 (169616 upstream) : LOC220930 (114976 downstream)																																			---	---	---	---
KIF5B	3799	broad.mit.edu	37	10	32316904	32316904	+	Intron	DEL	T	-	-	rs75133731		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32316904delT	uc001iwe.3	-							NM_004521	NP_004512			kinesin family member 5B						stress granule disassembly|vesicle transport along microtubule	kinesin complex|microtubule|perinuclear region of cytoplasm|vesicle	ATP binding|microtubule binding|microtubule motor activity		KIF5B/ALK(4)	lung(4)|ovary(1)	5		Prostate(175;0.0137)																---	---	---	---
KIF5B	3799	broad.mit.edu	37	10	32321427	32321427	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32321427delA	uc001iwe.3	-							NM_004521	NP_004512			kinesin family member 5B						stress granule disassembly|vesicle transport along microtubule	kinesin complex|microtubule|perinuclear region of cytoplasm|vesicle	ATP binding|microtubule binding|microtubule motor activity		KIF5B/ALK(4)	lung(4)|ovary(1)	5		Prostate(175;0.0137)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	32543689	32543689	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32543689delT								KIF5B (198318 upstream) : EPC1 (14170 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	32711918	32711918	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32711918delT								EPC1 (44251 upstream) : CCDC7 (23123 downstream)																																			---	---	---	---
CCDC7	221016	broad.mit.edu	37	10	32766481	32766482	+	Intron	DEL	TT	-	-	rs112895821		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32766481_32766482delTT	uc001iwj.2	+						CCDC7_uc009xlu.1_Intron|CCDC7_uc001iwk.2_Intron|CCDC7_uc009xlv.2_Intron|CCDC7_uc009xlw.1_Intron|CCDC7_uc009xlx.1_Intron|CCDC7_uc009xly.1_Intron	NM_145023	NP_659460			coiled-coil domain containing 7												0		Breast(68;0.000207)|Prostate(175;0.0107)																---	---	---	---
C10orf68	79741	broad.mit.edu	37	10	32908839	32908853	+	Intron	DEL	TTTTTTTTTTTTTTT	-	-	rs72262498		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32908839_32908853delTTTTTTTTTTTTTTT	uc001iwn.3	+						C10orf68_uc001iwl.1_Intron|C10orf68_uc001iwm.1_Intron	NM_024688	NP_078964			chromosome 10 open reading frame 68											skin(2)|ovary(1)	3																		---	---	---	---
C10orf68	79741	broad.mit.edu	37	10	32975916	32975916	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:32975916delT	uc001iwn.3	+						C10orf68_uc001iwl.1_Intron|C10orf68_uc001iwm.1_Intron|C10orf68_uc010qei.1_Intron	NM_024688	NP_078964			chromosome 10 open reading frame 68											skin(2)|ovary(1)	3																		---	---	---	---
NRP1	8829	broad.mit.edu	37	10	33518779	33518780	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33518779_33518780insT	uc001iwx.3	-						NRP1_uc001iwv.3_Intron|NRP1_uc009xlz.2_Intron|NRP1_uc001iww.3_Intron|NRP1_uc001iwy.3_Intron|NRP1_uc001iwz.2_Intron|NRP1_uc001ixa.2_Intron|NRP1_uc001ixb.1_Intron|NRP1_uc001ixc.1_Intron	NM_003873	NP_003864			neuropilin 1 isoform a						axon guidance|cell adhesion|cell-cell signaling|organ morphogenesis|positive regulation of cell proliferation	extracellular region|integral to membrane|plasma membrane	growth factor binding|heparin binding|metal ion binding|vascular endothelial growth factor receptor activity			central_nervous_system(2)|ovary(1)|skin(1)	4					Palifermin(DB00039)|Pegaptanib(DB04895)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	33700068	33700068	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33700068delT								NRP1 (76062 upstream) : PARD3 (700030 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	33965553	33965553	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:33965553delA								NRP1 (341547 upstream) : PARD3 (434545 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	34084176	34084176	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34084176delT								NRP1 (460170 upstream) : PARD3 (315922 downstream)																																			---	---	---	---
PARD3	56288	broad.mit.edu	37	10	34708445	34708445	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:34708445delA	uc010qej.1	-						PARD3_uc010qek.1_Intron|PARD3_uc010qel.1_Intron|PARD3_uc010qem.1_Intron|PARD3_uc010qen.1_Intron|PARD3_uc010qeo.1_Intron|PARD3_uc010qep.1_Intron|PARD3_uc010qeq.1_Intron|PARD3_uc001ixo.1_Intron|PARD3_uc001ixp.1_Intron|PARD3_uc001ixq.1_Intron|PARD3_uc001ixr.1_Intron|PARD3_uc001ixt.1_Intron|PARD3_uc001ixu.1_Intron	NM_019619	NP_062565			partitioning-defective protein 3 homolog						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|asymmetric cell division|axonogenesis|cell cycle|establishment of epithelial cell polarity|protein complex assembly|protein targeting to membrane|tight junction assembly	cell cortex|cytoskeleton|cytosol|endomembrane system|tight junction	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|protein binding			ovary(1)	1		Breast(68;0.0707)																---	---	---	---
PARD3	56288	broad.mit.edu	37	10	35100611	35100611	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35100611delT	uc010qej.1	-						PARD3_uc010qek.1_Intron|PARD3_uc010qel.1_Intron|PARD3_uc010qem.1_Intron|PARD3_uc010qen.1_Intron|PARD3_uc010qeo.1_Intron|PARD3_uc010qep.1_Intron|PARD3_uc010qeq.1_Intron|PARD3_uc001ixq.1_Intron|PARD3_uc001ixr.1_Intron|PARD3_uc001ixu.1_Intron	NM_019619	NP_062565			partitioning-defective protein 3 homolog						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|asymmetric cell division|axonogenesis|cell cycle|establishment of epithelial cell polarity|protein complex assembly|protein targeting to membrane|tight junction assembly	cell cortex|cytoskeleton|cytosol|endomembrane system|tight junction	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|protein binding			ovary(1)	1		Breast(68;0.0707)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	35126104	35126104	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35126104delT								PARD3 (22181 upstream) : CUL2 (172704 downstream)																																			---	---	---	---
CUL2	8453	broad.mit.edu	37	10	35336834	35336835	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35336834_35336835delAA	uc001ixv.2	-						CUL2_uc009xma.2_Intron|CUL2_uc010qer.1_Intron|CUL2_uc001ixw.2_Intron|CUL2_uc010qes.1_Intron	NM_003591	NP_003582			cullin 2						cell cycle arrest|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|ubiquitin-dependent protein catabolic process	cullin-RING ubiquitin ligase complex	ubiquitin protein ligase binding			ovary(3)	3																		---	---	---	---
CUL2	8453	broad.mit.edu	37	10	35344670	35344670	+	Intron	DEL	T	-	-	rs144478245		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35344670delT	uc001ixv.2	-						CUL2_uc009xma.2_Intron|CUL2_uc010qer.1_Intron|CUL2_uc001ixw.2_Intron|CUL2_uc010qes.1_Intron	NM_003591	NP_003582			cullin 2						cell cycle arrest|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|ubiquitin-dependent protein catabolic process	cullin-RING ubiquitin ligase complex	ubiquitin protein ligase binding			ovary(3)	3																		---	---	---	---
CUL2	8453	broad.mit.edu	37	10	35371063	35371063	+	Intron	DEL	A	-	-	rs112516169		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35371063delA	uc001ixv.2	-						CUL2_uc001ixw.2_Intron|CUL2_uc010qes.1_Intron	NM_003591	NP_003582			cullin 2						cell cycle arrest|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|ubiquitin-dependent protein catabolic process	cullin-RING ubiquitin ligase complex	ubiquitin protein ligase binding			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	35511319	35511319	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35511319delA								CREM (9434 upstream) : CCNY (24634 downstream)																																			---	---	---	---
CCNY	219771	broad.mit.edu	37	10	35551854	35551855	+	Intron	DEL	AA	-	-	rs72046776		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35551854_35551855delAA	uc001iyu.3	+						CCNY_uc001iyv.3_Intron	NM_181698	NP_859049			cyclin Y isoform 2						cell division|G2/M transition of mitotic cell cycle|positive regulation of cyclin-dependent protein kinase activity|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	cyclin-dependent protein kinase regulator activity|protein kinase binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	35909519	35909522	+	IGR	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35909519_35909522delTTTT								GJD4 (11656 upstream) : FZD8 (17655 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	36054603	36054603	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:36054603delT								FZD8 (124241 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	36788682	36788684	+	IGR	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:36788682_36788684delAAA								FZD8 (858320 upstream) : ANKRD30A (626101 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	37022378	37022378	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:37022378delA								None (None upstream) : ANKRD30A (392407 downstream)																																			---	---	---	---
ZNF248	57209	broad.mit.edu	37	10	38137043	38137043	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38137043delA	uc001izd.1	-						ZNF248_uc009xmc.2_Intron|ZNF248_uc001izb.2_Intron|ZNF248_uc001izc.2_Intron|ZNF248_uc010qeu.1_Intron	NM_021045	NP_066383			zinc finger protein 248						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
ZNF37A	7587	broad.mit.edu	37	10	38385093	38385093	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38385093delA	uc001izk.2	+						ZNF37A_uc001izl.2_Intron|ZNF37A_uc001izm.2_Intron	NM_001007094	NP_001007095			zinc finger protein 37a							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			breast(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	38808309	38808309	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38808309delT								LOC399744 (67229 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	38981874	38981875	+	IGR	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:38981874_38981875delAC								LOC399744 (240794 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	39042250	39042250	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:39042250delT								LOC399744 (301170 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	39097099	39097103	+	IGR	DEL	TTCCG	-	-	rs10870419		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:39097099_39097103delTTCCG								LOC399744 (356019 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42370638	42370639	+	IGR	INS	-	C	C	rs142905507		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42370638_42370639insC								None (None upstream) : LOC441666 (456676 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42640990	42640990	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42640990delG								None (None upstream) : LOC441666 (186325 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42700107	42700108	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42700107_42700108insT								None (None upstream) : LOC441666 (127207 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42723722	42723723	+	IGR	INS	-	TT	TT			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42723722_42723723insTT								None (None upstream) : LOC441666 (103592 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	42800222	42800226	+	IGR	DEL	TTGGG	-	-	rs147989481		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42800222_42800226delTTGGG								None (None upstream) : LOC441666 (27089 downstream)																																			---	---	---	---
LOC441666	441666	broad.mit.edu	37	10	42860000	42860001	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42860000_42860001delAA	uc010qey.1	-							NR_024380				Homo sapiens noncoding mRNA sequence.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	43465232	43465233	+	IGR	INS	-	C	C	rs143021042	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43465232_43465233insC								BMS1 (134849 upstream) : RET (107284 downstream)																																			---	---	---	---
CSGALNACT2	55454	broad.mit.edu	37	10	43653973	43653973	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43653973delT	uc001jan.2	+						CSGALNACT2_uc001jam.1_Intron	NM_018590	NP_061060			chondroitin sulfate						chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|dermatan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process	Golgi cisterna membrane|integral to Golgi membrane	glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	43817730	43817730	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43817730delA								RASGEF1A (55363 upstream) : FXYD4 (49362 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	43837362	43837364	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43837362_43837364delTTT								RASGEF1A (74995 upstream) : FXYD4 (29728 downstream)																																			---	---	---	---
HNRNPF	3185	broad.mit.edu	37	10	43899287	43899287	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43899287delA	uc001jas.2	-						HNRNPF_uc001jat.2_Intron|HNRNPF_uc001jav.2_Intron|HNRNPF_uc001jau.2_Intron	NM_001098206	NP_001091676			heterogeneous nuclear ribonucleoprotein F						regulation of RNA splicing	catalytic step 2 spliceosome|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|single-stranded RNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	44040110	44040110	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44040110delA								ZNF487 (62103 upstream) : ZNF239 (11685 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	44179335	44179335	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44179335delT								ZNF32 (35009 upstream) : HNRNPA3P1 (103525 downstream)																																	OREG0020144	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	10	44313785	44313786	+	IGR	DEL	GC	-	-	rs142661294	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44313785_44313786delGC								HNRNPA3P1 (27920 upstream) : CXCL12 (551821 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	44437293	44437293	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44437293delC	uc001jbe.1	+											Homo sapiens cDNA FLJ35823 fis, clone TESTI2006333.																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	44527665	44527667	+	IGR	DEL	AAA	-	-	rs5784622		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44527665_44527667delAAA								HNRNPA3P1 (241800 upstream) : CXCL12 (337940 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	44825981	44825982	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44825981_44825982insA								HNRNPA3P1 (540116 upstream) : CXCL12 (39625 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	44890295	44890295	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:44890295delG								CXCL12 (9753 upstream) : TMEM72 (516469 downstream)																																			---	---	---	---
ZNF22	7570	broad.mit.edu	37	10	45499501	45499501	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45499501delT	uc001jbw.2	+	2					uc001jbx.1_RNA	NM_006963	NP_008894			zinc finger protein 22 (KOX 15)						odontogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus|plasma membrane	DNA binding|zinc ion binding			breast(1)|kidney(1)	2		Prostate(175;0.0352)|all_neural(218;0.202)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	45568536	45568538	+	5'Flank	DEL	ATT	-	-	rs35080476		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45568536_45568538delATT	uc001jbx.1	-											Homo sapiens zinc finger protein 22 (KOX 15), mRNA (cDNA clone IMAGE:4826621).																														---	---	---	---
LOC100133308	100133308	broad.mit.edu	37	10	45630911	45630911	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45630911delG	uc001jbz.2	-						LOC100133308_uc009xmq.1_Intron					Homo sapiens cDNA FLJ32851 fis, clone TESTI2003432.												0																		---	---	---	---
ALOX5	240	broad.mit.edu	37	10	45911031	45911032	+	Intron	INS	-	T	T	rs151251355	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45911031_45911032insT	uc001jce.2	+						ALOX5_uc009xmt.2_Intron|ALOX5_uc010qfg.1_Intron	NM_000698	NP_000689			arachidonate 5-lipoxygenase						hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process	cytosol|nuclear envelope lumen|nuclear matrix|nuclear membrane	arachidonate 5-lipoxygenase activity|iron ion binding|lipoxygenase activity|protein binding			ovary(1)|pancreas(1)	2		Lung SC(717;0.0257)			Diethylcarbamazine(DB00711)|Hydrocortisone(DB00741)|Leflunomide(DB01097)|Masoprocol(DB00179)|Meclofenamic acid(DB00939)|Minocycline(DB01017)|Montelukast(DB00471)|Quinacrine(DB01103)|Vitamin E(DB00163)|Zileuton(DB00744)													---	---	---	---
MARCH8	220972	broad.mit.edu	37	10	45970853	45970854	+	Intron	INS	-	G	G	rs139616642	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45970853_45970854insG	uc001jci.1	-						MARCH8_uc001jch.2_Intron|MARCH8_uc001jcj.1_Intron|MARCH8_uc001jck.1_Intron	NM_001002266	NP_001002266			cellular modulator of immune recognition isoform							cytoplasmic vesicle membrane|early endosome membrane|integral to membrane|lysosomal membrane	ubiquitin-protein ligase activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	46218822	46218822	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46218822delA								ANUBL1 (50571 upstream) : FAM21C (3845 downstream)																																			---	---	---	---
ANXA8	653145	broad.mit.edu	37	10	47067979	47067979	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47067979delT	uc001jed.3	-											Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3																		---	---	---	---
ANXA8	653145	broad.mit.edu	37	10	47083051	47083052	+	Intron	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47083051_47083052delAG	uc001jed.3	-						PPYR1_uc001jee.2_5'Flank|PPYR1_uc009xna.2_5'Flank					Homo sapiens cDNA FLJ58071 complete cds, highly similar to Annexin A8.						blood coagulation		calcium ion binding|calcium-dependent phospholipid binding			central_nervous_system(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	47357923	47357923	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47357923delT								LOC642826 (114421 upstream) : FAM35B2 (21797 downstream)																																			---	---	---	---
FAM35B2	439965	broad.mit.edu	37	10	47416689	47416689	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47416689delA	uc010qga.1	+						FAM35B2_uc010qfz.1_Intron					SubName: Full=cDNA FLJ59018, highly similar to Protein FAM35A;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	48592131	48592131	+	IGR	DEL	T	-	-	rs150518189		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:48592131delT								GDF10 (152965 upstream) : FRMPD2L1 (251912 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	49334338	49334341	+	Intron	DEL	AAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49334338_49334341delAAAA	uc009xny.1	-											Homo sapiens cDNA, FLJ99963.																														---	---	---	---
FRMPD2	143162	broad.mit.edu	37	10	49382781	49382781	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49382781delA	uc001jgi.2	-						FRMPD2_uc001jgh.2_Intron|FRMPD2_uc001jgj.2_Intron|FRMPD2L1_uc001jgf.2_Intron|FRMPD2_uc001jgg.2_Intron|FRMPD2_uc001jgk.2_Intron	NM_001018071	NP_001018081			FERM and PDZ domain containing 2 isoform 3						tight junction assembly	basolateral plasma membrane|cytoplasm|cytoskeleton|tight junction	1-phosphatidylinositol binding|protein binding			large_intestine(1)	1				Kidney(211;0.201)														---	---	---	---
MAPK8	5599	broad.mit.edu	37	10	49632499	49632499	+	Intron	DEL	T	-	-	rs78072348		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49632499delT	uc009xnz.2	+						MAPK8_uc001jgl.2_Intron|MAPK8_uc001jgm.2_Intron|MAPK8_uc001jgo.2_Intron|MAPK8_uc009xoa.2_Intron|MAPK8_uc001jgn.2_Intron|MAPK8_uc010qgk.1_Intron|MAPK8_uc001jgp.2_Intron|MAPK8_uc001jgq.2_Intron	NM_139047	NP_620635			mitogen-activated protein kinase 8 isoform JNK1						activation of pro-apoptotic gene products|cellular response to mechanical stimulus|induction of apoptosis by intracellular signals|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of apoptosis|negative regulation of protein binding|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of deacetylase activity|regulation of protein localization|regulation of sequence-specific DNA binding transcription factor activity|response to UV|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|histone deacetylase binding|histone deacetylase regulator activity|JUN kinase activity|protein binding			central_nervous_system(3)|lung(2)|stomach(1)|ovary(1)|kidney(1)	8		Ovarian(717;0.0221)|Lung SC(717;0.113)|all_neural(218;0.116)		Epithelial(53;3.46e-65)|Lung(62;0.125)														---	---	---	---
WDFY4	57705	broad.mit.edu	37	10	50166650	50166651	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50166650_50166651delTT	uc001jha.3	+						WDFY4_uc009xob.2_Intron|WDFY4_uc010qgn.1_Intron	NM_020945	NP_065996			WDFY family member 4							integral to membrane	binding				0																		---	---	---	---
C10orf72	196740	broad.mit.edu	37	10	50256688	50256688	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50256688delA	uc001jhf.2	-							NM_001031746	NP_001026916			hypothetical protein LOC196740 isoform 1							integral to membrane|plasma membrane					0																		---	---	---	---
C10orf72	196740	broad.mit.edu	37	10	50317171	50317171	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50317171delC	uc001jhf.2	-						C10orf72_uc001jhh.2_Intron	NM_001031746	NP_001026916			hypothetical protein LOC196740 isoform 1							integral to membrane|plasma membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	52063869	52063869	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52063869delG								ASAH2 (55499 upstream) : SGMS1 (1477 downstream)																																			---	---	---	---
SGMS1	259230	broad.mit.edu	37	10	52122942	52122942	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52122942delA	uc001jje.2	-						SGMS1_uc010qhk.1_Intron|SGMS1_uc009xot.1_Intron|SGMS1_uc009xou.1_Intron	NM_147156	NP_671512			sphingomyelin synthase 1						apoptosis|cell growth|sphingomyelin biosynthetic process	endoplasmic reticulum|Golgi trans cisterna|integral to Golgi membrane|nucleus|plasma membrane	ceramide cholinephosphotransferase activity|kinase activity|sphingomyelin synthase activity			ovary(1)|kidney(1)	2																		---	---	---	---
SGMS1	259230	broad.mit.edu	37	10	52290412	52290413	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52290412_52290413delTT	uc001jje.2	-						SGMS1_uc010qhk.1_Intron|SGMS1_uc009xot.1_Intron|SGMS1_uc009xou.1_Intron	NM_147156	NP_671512			sphingomyelin synthase 1						apoptosis|cell growth|sphingomyelin biosynthetic process	endoplasmic reticulum|Golgi trans cisterna|integral to Golgi membrane|nucleus|plasma membrane	ceramide cholinephosphotransferase activity|kinase activity|sphingomyelin synthase activity			ovary(1)|kidney(1)	2																		---	---	---	---
SGMS1	259230	broad.mit.edu	37	10	52296113	52296113	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52296113delA	uc001jje.2	-						SGMS1_uc010qhk.1_Intron|SGMS1_uc009xot.1_Intron|SGMS1_uc009xou.1_Intron	NM_147156	NP_671512			sphingomyelin synthase 1						apoptosis|cell growth|sphingomyelin biosynthetic process	endoplasmic reticulum|Golgi trans cisterna|integral to Golgi membrane|nucleus|plasma membrane	ceramide cholinephosphotransferase activity|kinase activity|sphingomyelin synthase activity			ovary(1)|kidney(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	52467957	52467958	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52467957_52467958delTT								SGMS1 (83034 upstream) : ASAH2B (31738 downstream)																																			---	---	---	---
PRKG1	5592	broad.mit.edu	37	10	53508979	53508979	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53508979delT	uc001jjm.2	+						PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron	NM_001098512	NP_001091982			protein kinase, cGMP-dependent, type I isoform						actin cytoskeleton organization|platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			lung(2)|stomach(1)|ovary(1)|central_nervous_system(1)|skin(1)	6		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)														---	---	---	---
PRKG1	5592	broad.mit.edu	37	10	53582223	53582223	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:53582223delA	uc001jjm.2	+						PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron	NM_001098512	NP_001091982			protein kinase, cGMP-dependent, type I isoform						actin cytoskeleton organization|platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			lung(2)|stomach(1)|ovary(1)|central_nervous_system(1)|skin(1)	6		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	54119002	54119002	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:54119002delT								DKK1 (41586 upstream) : MBL2 (406139 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	54226276	54226276	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:54226276delA								DKK1 (148860 upstream) : MBL2 (298865 downstream)																																			---	---	---	---
MBL2	4153	broad.mit.edu	37	10	54529167	54529167	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:54529167delA	uc001jjt.2	-							NM_000242	NP_000233			soluble mannose-binding lectin precursor						acute-phase response|complement activation, classical pathway|complement activation, lectin pathway|defense response to Gram-positive bacterium|negative regulation of growth of symbiont in host|opsonization|response to oxidative stress	collagen|extracellular space	bacterial cell surface binding|calcium-dependent protein binding|eukaryotic cell surface binding|mannose binding|receptor binding			ovary(1)	1																		---	---	---	---
PCDH15	65217	broad.mit.edu	37	10	56658841	56658841	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:56658841delA	uc001jjv.1	-							NM_001142770	NP_001136242			protocadherin 15 isoform CD2-2 precursor						equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)													HNSCC(58;0.16)			---	---	---	---
PCDH15	65217	broad.mit.edu	37	10	57187761	57187761	+	Intron	DEL	A	-	-	rs146100779		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:57187761delA	uc001jjv.1	-							NM_001142770	NP_001136242			protocadherin 15 isoform CD2-2 precursor						equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)													HNSCC(58;0.16)			---	---	---	---
Unknown	0	broad.mit.edu	37	10	57562205	57562206	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:57562205_57562206delTT								PCDH15 (174503 upstream) : ZWINT (554993 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	57607234	57607234	+	IGR	DEL	A	-	-	rs112717674		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:57607234delA								PCDH15 (219532 upstream) : ZWINT (509965 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	57932055	57932055	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:57932055delT								PCDH15 (544353 upstream) : ZWINT (185144 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	58298334	58298334	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:58298334delT								ZWINT (177300 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	58419326	58419327	+	IGR	INS	-	TC	TC	rs149483596	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:58419326_58419327insTC								ZWINT (298292 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	58584475	58584475	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:58584475delA								ZWINT (463441 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	59147041	59147041	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:59147041delC								None (None upstream) : IPMK (808577 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	59356286	59356286	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:59356286delT								None (None upstream) : IPMK (599332 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	59743800	59743801	+	IGR	INS	-	T	T	rs139817182	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:59743800_59743801insT								None (None upstream) : IPMK (211817 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	59848678	59848678	+	IGR	DEL	A	-	-	rs34144310		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:59848678delA								None (None upstream) : IPMK (106940 downstream)																																			---	---	---	---
UBE2D1	7321	broad.mit.edu	37	10	60091844	60091848	+	5'Flank	DEL	TTTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:60091844_60091848delTTTTT	uc001jke.1	+							NM_003338	NP_003329			ubiquitin-conjugating enzyme E2D 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|BMP signaling pathway|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K48-linked ubiquitination|transforming growth factor beta receptor signaling pathway	cytosol|nucleoplasm	ATP binding|protein binding|ubiquitin-protein ligase activity			skin(2)	2																		---	---	---	---
BICC1	80114	broad.mit.edu	37	10	60554698	60554698	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:60554698delA	uc001jki.1	+						BICC1_uc001jkj.1_Intron	NM_001080512	NP_001073981			bicaudal C homolog 1						multicellular organismal development		RNA binding			ovary(2)|lung(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	62525138	62525140	+	IGR	DEL	AAG	-	-	rs72200584		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:62525138_62525140delAAG								ANK3 (31983 upstream) : CDK1 (12983 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	62921170	62921170	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:62921170delA								RHOBTB1 (159972 upstream) : TMEM26 (245231 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	63008442	63008442	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63008442delA								RHOBTB1 (247244 upstream) : TMEM26 (157959 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	63257287	63257287	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63257287delA								TMEM26 (44079 upstream) : C10orf107 (165432 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	63590890	63590890	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63590890delA								C10orf107 (64801 upstream) : ARID5B (70553 downstream)																																			---	---	---	---
ARID5B	84159	broad.mit.edu	37	10	63745224	63745224	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63745224delT	uc001jlt.1	+						ARID5B_uc010qil.1_Intron	NM_032199	NP_115575			AT rich interactive domain 5B (MRF1-like)						liver development|negative regulation of transcription, DNA-dependent|positive regulation of sequence-specific DNA binding transcription factor activity|transcription, DNA-dependent		protein binding|transcription regulatory region DNA binding			ovary(2)|upper_aerodigestive_tract(1)|kidney(1)	4	Prostate(12;0.016)|all_hematologic(501;0.215)																	---	---	---	---
Unknown	0	broad.mit.edu	37	10	63871689	63871689	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63871689delA								ARID5B (14986 upstream) : RTKN2 (71105 downstream)																																			---	---	---	---
RTKN2	219790	broad.mit.edu	37	10	63955208	63955208	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63955208delT	uc001jlw.2	-	12					RTKN2_uc009xpf.1_Intron|RTKN2_uc001jlv.2_3'UTR	NM_145307	NP_660350			rhotekin 2						signal transduction	intracellular					0	Prostate(12;0.0297)|all_hematologic(501;0.215)																	---	---	---	---
ZNF365	22891	broad.mit.edu	37	10	64093031	64093031	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64093031delT	uc001jly.3	+							NM_014951	NP_055766			zinc finger protein 365 isoform A											ovary(1)|skin(1)	2	Prostate(12;0.0297)|all_hematologic(501;0.228)																	---	---	---	---
Unknown	0	broad.mit.edu	37	10	64662653	64662656	+	IGR	DEL	CACA	-	-	rs72270043		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64662653_64662656delCACA								EGR2 (83726 upstream) : NRBF2 (230351 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	64755324	64755324	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64755324delT								EGR2 (176397 upstream) : NRBF2 (137683 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	64831809	64831809	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64831809delC								EGR2 (252882 upstream) : NRBF2 (61198 downstream)																																			---	---	---	---
JMJD1C	221037	broad.mit.edu	37	10	64949228	64949228	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64949228delA	uc001jmn.2	-						JMJD1C_uc001jml.2_Intron|JMJD1C_uc001jmm.2_Intron|JMJD1C_uc010qiq.1_Intron|JMJD1C_uc009xpi.2_Intron|JMJD1C_uc009xpj.1_Intron|JMJD1C_uc001jmo.2_Intron	NM_032776	NP_116165			jumonji domain containing 1C isoform a						blood coagulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	histone demethylase activity (H3-K9 specific)|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|thyroid hormone receptor binding			ovary(4)|breast(1)|central_nervous_system(1)	6	Prostate(12;0.0119)|all_hematologic(501;0.191)																	---	---	---	---
JMJD1C	221037	broad.mit.edu	37	10	64957048	64957048	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64957048delA	uc001jmn.2	-						JMJD1C_uc001jml.2_Intron|JMJD1C_uc001jmm.2_Intron|JMJD1C_uc010qiq.1_Intron|JMJD1C_uc009xpi.2_Intron|JMJD1C_uc009xpj.1_Intron|JMJD1C_uc009xpk.1_Intron	NM_032776	NP_116165			jumonji domain containing 1C isoform a						blood coagulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	histone demethylase activity (H3-K9 specific)|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|thyroid hormone receptor binding			ovary(4)|breast(1)|central_nervous_system(1)	6	Prostate(12;0.0119)|all_hematologic(501;0.191)																	---	---	---	---
JMJD1C	221037	broad.mit.edu	37	10	64985746	64985746	+	Intron	DEL	C	-	-	rs72048401		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64985746delC	uc001jmn.2	-						JMJD1C_uc001jml.2_Intron|JMJD1C_uc001jmm.2_Intron|JMJD1C_uc010qiq.1_Intron|JMJD1C_uc009xpi.2_Intron|JMJD1C_uc009xpj.1_Intron|JMJD1C_uc001jmp.1_Intron	NM_032776	NP_116165			jumonji domain containing 1C isoform a						blood coagulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	histone demethylase activity (H3-K9 specific)|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|thyroid hormone receptor binding			ovary(4)|breast(1)|central_nervous_system(1)	6	Prostate(12;0.0119)|all_hematologic(501;0.191)																	---	---	---	---
REEP3	221035	broad.mit.edu	37	10	65337579	65337579	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65337579delC	uc001jmt.2	+						REEP3_uc009xpl.1_Intron	NM_001001330	NP_001001330			receptor accessory protein 3							integral to membrane					0	Prostate(12;0.0119)|all_hematologic(501;0.191)																	---	---	---	---
Unknown	0	broad.mit.edu	37	10	65424903	65424903	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65424903delG								REEP3 (42932 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	65810295	65810295	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65810295delT								REEP3 (428324 upstream) : ANXA2P3 (774990 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	65890408	65890408	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65890408delT								REEP3 (508437 upstream) : ANXA2P3 (694877 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	65978111	65978112	+	IGR	INS	-	TG	TG	rs150224710	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:65978111_65978112insTG								REEP3 (596140 upstream) : ANXA2P3 (607173 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	66474167	66474167	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:66474167delT								None (None upstream) : ANXA2P3 (111118 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	66492527	66492527	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:66492527delA								None (None upstream) : ANXA2P3 (92758 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	66513635	66513635	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:66513635delA								None (None upstream) : ANXA2P3 (71650 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	66564919	66564919	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:66564919delT								None (None upstream) : ANXA2P3 (20366 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	66710311	66710311	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:66710311delT								ANXA2P3 (123677 upstream) : CTNNA3 (969414 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	66967398	66967398	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:66967398delT								ANXA2P3 (380764 upstream) : CTNNA3 (712327 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	67050049	67050049	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:67050049delT								ANXA2P3 (463415 upstream) : CTNNA3 (629676 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	67592263	67592263	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:67592263delA								None (None upstream) : CTNNA3 (87462 downstream)																																			---	---	---	---
CTNNA3	29119	broad.mit.edu	37	10	67702289	67702291	+	Intron	DEL	AAC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:67702289_67702291delAAC	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron	NM_001127384	NP_001120856			catenin, alpha 3						cell-cell adhesion	actin cytoskeleton|cytoplasm|fascia adherens	cadherin binding|structural molecule activity			skin(3)|ovary(2)|pancreas(1)|lung(1)|central_nervous_system(1)	8																		---	---	---	---
CTNNA3	29119	broad.mit.edu	37	10	68000455	68000455	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:68000455delA	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron	NM_001127384	NP_001120856			catenin, alpha 3						cell-cell adhesion	actin cytoskeleton|cytoplasm|fascia adherens	cadherin binding|structural molecule activity			skin(3)|ovary(2)|pancreas(1)|lung(1)|central_nervous_system(1)	8																		---	---	---	---
CTNNA3	29119	broad.mit.edu	37	10	68246577	68246578	+	Intron	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:68246577_68246578delAC	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron	NM_001127384	NP_001120856			catenin, alpha 3						cell-cell adhesion	actin cytoskeleton|cytoplasm|fascia adherens	cadherin binding|structural molecule activity			skin(3)|ovary(2)|pancreas(1)|lung(1)|central_nervous_system(1)	8																		---	---	---	---
CTNNA3	29119	broad.mit.edu	37	10	69377194	69377195	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69377194_69377195insT	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron|CTNNA3_uc001jmx.3_Intron|CTNNA3_uc009xpo.1_Intron|CTNNA3_uc001jna.2_Intron	NM_001127384	NP_001120856			catenin, alpha 3						cell-cell adhesion	actin cytoskeleton|cytoplasm|fascia adherens	cadherin binding|structural molecule activity			skin(3)|ovary(2)|pancreas(1)|lung(1)|central_nervous_system(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	69630031	69630031	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69630031delA								DNAJC12 (32094 upstream) : SIRT1 (14396 downstream)																																			---	---	---	---
SIRT1	23411	broad.mit.edu	37	10	69666107	69666107	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69666107delA	uc001jnd.2	+						SIRT1_uc010qis.1_Intron|SIRT1_uc009xpp.2_Intron|SIRT1_uc001jne.2_Intron	NM_012238	NP_036370			sirtuin 1 isoform a						apoptosis|cell aging|cellular response to hydrogen peroxide|cellular response to starvation|chromatin silencing at rDNA|DNA repair|DNA replication|establishment of chromatin silencing|histone H3 deacetylation|interspecies interaction between organisms|maintenance of chromatin silencing|muscle organ development|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of DNA damage response, signal transduction by p53 class mediator|negative regulation of fat cell differentiation|negative regulation of helicase activity|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|peptidyl-lysine acetylation|peptidyl-lysine deacetylation|positive regulation of anti-apoptosis|positive regulation of chromatin silencing|positive regulation of DNA repair|regulation of apoptosis|regulation of cell proliferation|regulation of endodeoxyribonuclease activity|regulation of protein import into nucleus, translocation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|rRNA processing|transcription, DNA-dependent|triglyceride mobilization|white fat cell differentiation	chromatin silencing complex|cytoplasm|nuclear euchromatin|nuclear heterochromatin|nuclear inner membrane|nucleolus|PML body|rDNA heterochromatin	bHLH transcription factor binding|histone binding|HLH domain binding|identical protein binding|mitogen-activated protein kinase binding|NAD+ binding|NAD-dependent histone deacetylase activity (H3-K9 specific)|p53 binding|protein C-terminus binding|transcription corepressor activity|zinc ion binding				0																		---	---	---	---
MYPN	84665	broad.mit.edu	37	10	69875657	69875657	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69875657delT	uc001jnm.3	+						MYPN_uc001jnl.1_Intron|MYPN_uc001jnn.3_Intron|MYPN_uc001jno.3_Intron|MYPN_uc001jnp.1_Intron|MYPN_uc009xps.2_Intron|MYPN_uc009xpt.2_Intron|MYPN_uc010qit.1_Intron|MYPN_uc010qiu.1_Intron	NM_032578	NP_115967			myopalladin							nucleus|sarcomere	actin binding			ovary(3)|skin(2)	5																		---	---	---	---
MYPN	84665	broad.mit.edu	37	10	69957375	69957375	+	Intron	DEL	C	-	-	rs7095492	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:69957375delC	uc001jnm.3	+						MYPN_uc001jnn.3_Intron|MYPN_uc001jno.3_Intron|MYPN_uc009xpt.2_Intron|MYPN_uc010qit.1_Intron|MYPN_uc010qiu.1_Intron	NM_032578	NP_115967			myopalladin							nucleus|sarcomere	actin binding			ovary(3)|skin(2)	5																		---	---	---	---
RUFY2	55680	broad.mit.edu	37	10	70131417	70131417	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70131417delA	uc001job.2	-						RUFY2_uc001jnz.1_Intron|RUFY2_uc001joa.2_Intron	NM_017987	NP_060457			RUN and FYVE domain-containing 2 isoform a							nucleus	metal ion binding			ovary(1)	1																		---	---	---	---
SLC25A16	8034	broad.mit.edu	37	10	70277732	70277732	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70277732delA	uc001joi.2	-						SLC25A16_uc010qix.1_5'Flank|SLC25A16_uc010qiy.1_Intron|SLC25A16_uc001joj.2_Intron	NM_152707	NP_689920			solute carrier family 25, member 16						coenzyme biosynthetic process|pantothenate metabolic process	integral to membrane|mitochondrial inner membrane	binding|solute:solute antiporter activity				0																		---	---	---	---
TET1	80312	broad.mit.edu	37	10	70317145	70317146	+	5'Flank	INS	-	A	A	rs141143885		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70317145_70317146insA	uc001jok.3	+							NM_030625	NP_085128			CXXC finger 6						DNA demethylation|inner cell mass cell differentiation|negative regulation of methylation-dependent chromatin silencing|stem cell maintenance		iron ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|structure-specific DNA binding|zinc ion binding			ovary(5)|lung(2)|prostate(1)|breast(1)	9																		---	---	---	---
TET1	80312	broad.mit.edu	37	10	70360945	70360946	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70360945_70360946insT	uc001jok.3	+							NM_030625	NP_085128			CXXC finger 6						DNA demethylation|inner cell mass cell differentiation|negative regulation of methylation-dependent chromatin silencing|stem cell maintenance		iron ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|structure-specific DNA binding|zinc ion binding			ovary(5)|lung(2)|prostate(1)|breast(1)	9																		---	---	---	---
TET1	80312	broad.mit.edu	37	10	70392079	70392079	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70392079delA	uc001jok.3	+							NM_030625	NP_085128			CXXC finger 6						DNA demethylation|inner cell mass cell differentiation|negative regulation of methylation-dependent chromatin silencing|stem cell maintenance		iron ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|structure-specific DNA binding|zinc ion binding			ovary(5)|lung(2)|prostate(1)|breast(1)	9																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	70475457	70475457	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70475457delT								TET1 (21219 upstream) : CCAR1 (5514 downstream)																																			---	---	---	---
CCAR1	55749	broad.mit.edu	37	10	70542180	70542182	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70542180_70542182delAAA	uc001joo.2	+						CCAR1_uc010qiz.1_Intron|CCAR1_uc010qjb.1_Intron	NM_018237	NP_060707			cell-cycle and apoptosis regulatory protein 1						apoptosis|cell cycle|nuclear mRNA splicing, via spliceosome|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm|perinuclear region of cytoplasm	calcium ion binding|nucleic acid binding|protein binding			ovary(6)|large_intestine(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	70559581	70559581	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70559581delA								CCAR1 (8274 upstream) : STOX1 (27713 downstream)																																			---	---	---	---
DDX50	79009	broad.mit.edu	37	10	70665960	70665960	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70665960delA	uc001jou.2	+						DDX50_uc001jot.2_Intron|DDX50_uc010qjc.1_Intron	NM_024045	NP_076950			nucleolar protein GU2							nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1																		---	---	---	---
DDX50	79009	broad.mit.edu	37	10	70669411	70669411	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70669411delT	uc001jou.2	+						DDX50_uc001jot.2_Intron|DDX50_uc010qjc.1_Intron	NM_024045	NP_076950			nucleolar protein GU2							nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1																		---	---	---	---
DDX50	79009	broad.mit.edu	37	10	70673882	70673882	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70673882delA	uc001jou.2	+	7	1118	c.1011delA	c.(1009-1011)GCAfs	p.A337fs	DDX50_uc001jot.2_Frame_Shift_Del_p.A337fs|DDX50_uc010qjc.1_Frame_Shift_Del_p.A337fs	NM_024045	NP_076950	Q9BQ39	DDX50_HUMAN	nucleolar protein GU2	337	Helicase ATP-binding.					nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1																		---	---	---	---
DDX50	79009	broad.mit.edu	37	10	70680240	70680240	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70680240delT	uc001jou.2	+						DDX50_uc010qjc.1_Intron	NM_024045	NP_076950			nucleolar protein GU2							nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1																		---	---	---	---
DDX21	9188	broad.mit.edu	37	10	70741207	70741207	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70741207delT	uc001jov.1	+						DDX21_uc001jow.1_Intron	NM_004728	NP_004719			DEAD (Asp-Glu-Ala-Asp) box polypeptide 21							nucleolus	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(2)|kidney(1)	3																		---	---	---	---
VPS26A	9559	broad.mit.edu	37	10	70922690	70922691	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70922690_70922691insA	uc001jpb.2	+						VPS26A_uc001jpc.2_Intron|VPS26A_uc009xqa.2_Intron|VPS26A_uc001jpd.2_Intron	NM_004896	NP_004887			vacuolar protein sorting 26 A isoform 1						retrograde transport, endosome to Golgi|vacuolar transport	cytosol|endosome membrane|retromer complex|vesicle	protein binding|protein transporter activity				0																		---	---	---	---
HKDC1	80201	broad.mit.edu	37	10	70980320	70980320	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70980320delA	uc001jpf.3	+							NM_025130	NP_079406			hexokinase domain containing 1						glycolysis	mitochondrion|nucleus	ATP binding|hexokinase activity			ovary(4)|skin(1)	5																		---	---	---	---
HK1	3098	broad.mit.edu	37	10	71028805	71028805	+	5'Flank	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71028805delG	uc001jpj.3	+						HK1_uc009xqc.1_5'Flank|HK1_uc001jpg.3_5'Flank|HK1_uc001jph.3_5'Flank|HK1_uc001jpi.3_5'Flank	NM_033500	NP_277035			hexokinase 1 isoform HKI-td						glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane|nucleus	ATP binding|glucokinase activity			ovary(1)	1																		---	---	---	---
HK1	3098	broad.mit.edu	37	10	71065308	71065308	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71065308delA	uc001jpj.3	+						HK1_uc009xqc.1_Intron|HK1_uc001jpg.3_Intron|HK1_uc001jph.3_Intron|HK1_uc001jpi.3_Intron	NM_033500	NP_277035			hexokinase 1 isoform HKI-td						glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane|nucleus	ATP binding|glucokinase activity			ovary(1)	1																		---	---	---	---
HK1	3098	broad.mit.edu	37	10	71120795	71120796	+	Intron	INS	-	CTC	CTC	rs139562651	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71120795_71120796insCTC	uc001jpl.3	+						HK1_uc001jpg.3_Intron|HK1_uc001jph.3_Intron|HK1_uc001jpi.3_Intron|HK1_uc001jpj.3_Intron|HK1_uc001jpk.3_Intron|HK1_uc009xqd.2_Intron	NM_000188	NP_000179			hexokinase 1 isoform HKI						glucose transport|glycolysis|transmembrane transport	cytosol|mitochondrial outer membrane|nucleus	ATP binding|glucokinase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	71184176	71184183	+	IGR	DEL	ACACACAC	-	-	rs150672022		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71184176_71184183delACACACAC								TACR2 (7502 upstream) : TSPAN15 (27043 downstream)																																			---	---	---	---
TSPAN15	23555	broad.mit.edu	37	10	71228275	71228276	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71228275_71228276delTT	uc001jpo.1	+							NM_012339	NP_036471			transmembrane 4 superfamily member 15							integral to plasma membrane|membrane fraction					0																		---	---	---	---
TSPAN15	23555	broad.mit.edu	37	10	71246095	71246096	+	Intron	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71246095_71246096insC	uc001jpo.1	+							NM_012339	NP_036471			transmembrane 4 superfamily member 15							integral to plasma membrane|membrane fraction					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	71300265	71300265	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71300265delT								TSPAN15 (32842 upstream) : NEUROG3 (31527 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	71383119	71383119	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71383119delT								NEUROG3 (49997 upstream) : C10orf35 (6884 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	71386877	71386878	+	IGR	INS	-	ACT	ACT	rs72512108		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71386877_71386878insACT								NEUROG3 (53755 upstream) : C10orf35 (3125 downstream)																																			---	---	---	---
COL13A1	1305	broad.mit.edu	37	10	71624943	71624944	+	Intron	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71624943_71624944delCT	uc001jpr.1	+						COL13A1_uc001jqj.1_Intron|COL13A1_uc001jps.1_Intron|COL13A1_uc001jpt.1_Intron|COL13A1_uc001jpu.1_Intron|COL13A1_uc001jpv.1_Intron|COL13A1_uc001jpx.1_Intron|COL13A1_uc001jpw.1_Intron|COL13A1_uc001jpy.1_Intron|COL13A1_uc001jpz.1_Intron|COL13A1_uc001jqa.1_Intron|COL13A1_uc001jqc.1_Intron|COL13A1_uc001jqb.1_Intron|COL13A1_uc001jql.2_Intron|COL13A1_uc001jqd.1_Intron|COL13A1_uc001jqe.1_Intron|COL13A1_uc001jqf.1_Intron|COL13A1_uc001jqg.1_Intron|COL13A1_uc001jqh.1_Intron|COL13A1_uc001jqi.1_Intron|COL13A1_uc010qjf.1_Intron|COL13A1_uc001jqk.1_Intron	NM_005203	NP_005194			alpha 1 type XIII collagen isoform 1						cell differentiation|cell-cell adhesion|cell-matrix adhesion|endochondral ossification|morphogenesis of a branching structure	collagen type XIII|integral to membrane	extracellular matrix structural constituent|heparin binding|protein binding			ovary(1)	1					Atorvastatin(DB01076)|Simvastatin(DB00641)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	71743093	71743093	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71743093delA								COL13A1 (24190 upstream) : H2AFY2 (69264 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	71937469	71937469	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71937469delT								SAR1A (7184 upstream) : PPA1 (25117 downstream)																																			---	---	---	---
KIAA1274	27143	broad.mit.edu	37	10	72281952	72281952	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72281952delT	uc001jrd.3	+							NM_014431	NP_055246			KIAA1274											ovary(2)|central_nervous_system(1)	3																		---	---	---	---
KIAA1274	27143	broad.mit.edu	37	10	72288965	72288973	+	Intron	DEL	CCCCCCCCC	-	-	rs72290492		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72288965_72288973delCCCCCCCCC	uc001jrd.3	+							NM_014431	NP_055246			KIAA1274											ovary(2)|central_nervous_system(1)	3																		---	---	---	---
KIAA1274	27143	broad.mit.edu	37	10	72326507	72326507	+	3'UTR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72326507delC	uc001jrd.3	+	20					KIAA1274_uc001jre.3_3'UTR	NM_014431	NP_055246			KIAA1274											ovary(2)|central_nervous_system(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	72418240	72418240	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72418240delA								PRF1 (55709 upstream) : ADAMTS14 (14319 downstream)																																			---	---	---	---
SGPL1	8879	broad.mit.edu	37	10	72584008	72584008	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72584008delA	uc001jrm.2	+							NM_003901	NP_003892			sphingosine-1-phosphate lyase 1						apoptosis|carboxylic acid metabolic process|ceramide metabolic process|sphingolipid catabolic process	integral to endoplasmic reticulum membrane	carboxy-lyase activity|pyridoxal phosphate binding|sphinganine-1-phosphate aldolase activity				0					Pyridoxal Phosphate(DB00114)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	72729650	72729650	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72729650delA								PCBD1 (81109 upstream) : UNC5B (242648 downstream)																																			---	---	---	---
UNC5B	219699	broad.mit.edu	37	10	73006149	73006149	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73006149delG	uc001jro.2	+						UNC5B_uc001jrp.2_Intron	NM_170744	NP_734465			unc-5 homolog B precursor						apoptosis|axon guidance|regulation of apoptosis	integral to membrane				ovary(2)|lung(1)	3																		---	---	---	---
CDH23	64072	broad.mit.edu	37	10	73251454	73251454	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73251454delG	uc001jrx.3	+						CDH23_uc001jrw.3_Intron|CDH23_uc001jrv.2_Intron|CDH23_uc009xql.2_Intron	NM_022124	NP_071407			cadherin-like 23 isoform 1 precursor						calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11																		---	---	---	---
CDH23	64072	broad.mit.edu	37	10	73420454	73420454	+	Intron	DEL	A	-	-	rs113874947		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73420454delA	uc001jrx.3	+						CDH23_uc001jry.2_Intron|CDH23_uc001jrz.2_Intron	NM_022124	NP_071407			cadherin-like 23 isoform 1 precursor						calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11																		---	---	---	---
C10orf54	64115	broad.mit.edu	37	10	73511467	73511467	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73511467delG	uc001jsd.2	-	6	997	c.856delC	c.(856-858)CTGfs	p.L286fs	CDH23_uc001jrx.3_Intron|C10orf54_uc001jse.2_Frame_Shift_Del_p.L154fs|C10orf54_uc009xqm.2_Frame_Shift_Del_p.L124fs	NM_022153	NP_071436	Q9H7M9	GI24_HUMAN	platelet receptor Gi24 precursor	286	Cytoplasmic (Potential).					integral to membrane	receptor activity			ovary(1)|breast(1)|central_nervous_system(1)	3																		---	---	---	---
CHST3	9469	broad.mit.edu	37	10	73751694	73751694	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73751694delA	uc001jsn.2	+							NM_004273	NP_004264			chondroitin 6-sulfotransferase 3						chondroitin sulfate biosynthetic process	Golgi membrane|integral to membrane	chondroitin 6-sulfotransferase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	73780375	73780375	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73780375delT								CHST3 (7054 upstream) : SPOCK2 (38418 downstream)																																			---	---	---	---
ASCC1	51008	broad.mit.edu	37	10	73931866	73931866	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73931866delT	uc001jst.1	-						ASCC1_uc001jsr.1_Intron|ASCC1_uc001jss.1_Intron|ASCC1_uc001jsu.1_Intron|ASCC1_uc010qju.1_Intron					RecName: Full=Activating signal cointegrator 1 complex subunit 1; AltName: Full=ASC-1 complex subunit p50; AltName: Full=Trip4 complex subunit p50;						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|transcription factor complex	RNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	74015387	74015387	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74015387delA								ANAPC16 (19771 upstream) : DDIT4 (18290 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	74054985	74054985	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74054985delA								DDIT4 (19188 upstream) : DNAJB12 (37603 downstream)																																			---	---	---	---
CCDC109A	90550	broad.mit.edu	37	10	74555003	74555008	+	Intron	DEL	TTTCCT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74555003_74555008delTTTCCT	uc001jtc.2	+						CCDC109A_uc009xqp.1_Intron|CCDC109A_uc009xqq.1_Intron|CCDC109A_uc010qjy.1_Intron|CCDC109A_uc009xqr.2_Intron|CCDC109A_uc001jtd.2_Intron	NM_138357	NP_612366			coiled-coil domain containing 109A						elevation of mitochondrial calcium ion concentration|mitochondrial calcium ion transport|protein complex oligomerization	integral to membrane|mitochondrial inner membrane	protein binding				0	Prostate(51;0.0198)																	---	---	---	---
CCDC109A	90550	broad.mit.edu	37	10	74645668	74645668	+	3'UTR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74645668delG	uc001jtc.2	+	8					CCDC109A_uc009xqr.2_3'UTR|CCDC109A_uc001jtd.2_3'UTR	NM_138357	NP_612366			coiled-coil domain containing 109A						elevation of mitochondrial calcium ion concentration|mitochondrial calcium ion transport|protein complex oligomerization	integral to membrane|mitochondrial inner membrane	protein binding				0	Prostate(51;0.0198)																	---	---	---	---
OIT3	170392	broad.mit.edu	37	10	74653469	74653470	+	5'UTR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74653469_74653470delAA	uc001jte.1	+	1					OIT3_uc009xqs.1_RNA	NM_152635	NP_689848			oncoprotein-induced transcript 3 precursor							nuclear envelope	calcium ion binding			ovary(2)	2	Prostate(51;0.0198)																	---	---	---	---
OIT3	170392	broad.mit.edu	37	10	74682272	74682273	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74682272_74682273insT	uc001jte.1	+						OIT3_uc009xqs.1_Intron	NM_152635	NP_689848			oncoprotein-induced transcript 3 precursor							nuclear envelope	calcium ion binding			ovary(2)	2	Prostate(51;0.0198)																	---	---	---	---
FAM149B1	317662	broad.mit.edu	37	10	74941387	74941387	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74941387delT	uc009xqz.2	+						FAM149B1_uc010qkf.1_Intron|FAM149B1_uc001jtq.2_Intron	NM_173348	NP_775483			hypothetical protein LOC317662												0																		---	---	---	---
FAM149B1	317662	broad.mit.edu	37	10	74958955	74958956	+	Intron	INS	-	TTG	TTG	rs145739809	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74958955_74958956insTTG	uc009xqz.2	+						FAM149B1_uc010qkf.1_Intron|FAM149B1_uc001jtq.2_Intron	NM_173348	NP_775483			hypothetical protein LOC317662												0																		---	---	---	---
TTC18	118491	broad.mit.edu	37	10	75039687	75039688	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75039687_75039688delAA	uc009xrc.2	-						TTC18_uc001jty.2_Intron|TTC18_uc001jtv.3_Intron|TTC18_uc001jtw.3_Intron|TTC18_uc001jtx.2_Intron	NM_145170	NP_660153			tetratricopeptide repeat domain 18								binding			ovary(2)|central_nervous_system(1)	3	Prostate(51;0.0119)																	---	---	---	---
PPP3CB	5532	broad.mit.edu	37	10	75208423	75208423	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75208423delT	uc001jue.2	-						PPP3CB_uc001juf.2_Intron|PPP3CB_uc001jug.2_Intron|PPP3CB_uc001jui.2_Intron|PPP3CB_uc001juh.2_Intron|PPP3CB_uc010qkj.1_Intron	NM_021132	NP_066955			protein phosphatase 3, catalytic subunit, beta											skin(1)	1	Prostate(51;0.0119)																	---	---	---	---
Unknown	0	broad.mit.edu	37	10	75537315	75537317	+	IGR	DEL	TTT	-	-	rs111899472		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75537315_75537317delTTT								FUT11 (1341 upstream) : CHCHD1 (4491 downstream)																																			---	---	---	---
ADK	132	broad.mit.edu	37	10	75921459	75921460	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75921459_75921460delTT	uc001jwi.2	+						ADK_uc010qlb.1_Intron	NM_006721	NP_006712			adenosine kinase isoform b						purine base metabolic process|purine ribonucleoside salvage	cytosol	adenosine kinase activity|ATP binding|metal ion binding|phosphotransferase activity, alcohol group as acceptor			ovary(1)|skin(1)	2	Prostate(51;0.0112)|Ovarian(15;0.148)				Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Pegademase bovine(DB00061)|Ribavirin(DB00811)													---	---	---	---
ADK	132	broad.mit.edu	37	10	75922735	75922735	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75922735delT	uc001jwi.2	+						ADK_uc010qlb.1_Intron	NM_006721	NP_006712			adenosine kinase isoform b						purine base metabolic process|purine ribonucleoside salvage	cytosol	adenosine kinase activity|ATP binding|metal ion binding|phosphotransferase activity, alcohol group as acceptor			ovary(1)|skin(1)	2	Prostate(51;0.0112)|Ovarian(15;0.148)				Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Pegademase bovine(DB00061)|Ribavirin(DB00811)													---	---	---	---
ADK	132	broad.mit.edu	37	10	75949626	75949626	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75949626delT	uc001jwi.2	+						ADK_uc010qlb.1_Intron|ADK_uc001jwj.2_Intron|ADK_uc010qlc.1_Intron	NM_006721	NP_006712			adenosine kinase isoform b						purine base metabolic process|purine ribonucleoside salvage	cytosol	adenosine kinase activity|ATP binding|metal ion binding|phosphotransferase activity, alcohol group as acceptor			ovary(1)|skin(1)	2	Prostate(51;0.0112)|Ovarian(15;0.148)				Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Pegademase bovine(DB00061)|Ribavirin(DB00811)													---	---	---	---
ADK	132	broad.mit.edu	37	10	76019813	76019814	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76019813_76019814delAA	uc001jwi.2	+						ADK_uc010qlb.1_Intron|ADK_uc001jwj.2_Intron|ADK_uc010qlc.1_Intron	NM_006721	NP_006712			adenosine kinase isoform b						purine base metabolic process|purine ribonucleoside salvage	cytosol	adenosine kinase activity|ATP binding|metal ion binding|phosphotransferase activity, alcohol group as acceptor			ovary(1)|skin(1)	2	Prostate(51;0.0112)|Ovarian(15;0.148)				Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Pegademase bovine(DB00061)|Ribavirin(DB00811)													---	---	---	---
ADK	132	broad.mit.edu	37	10	76356310	76356311	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76356310_76356311delTT	uc001jwi.2	+						ADK_uc010qlb.1_Intron|ADK_uc001jwj.2_Intron|ADK_uc010qlc.1_Intron|ADK_uc001jwl.2_Intron	NM_006721	NP_006712			adenosine kinase isoform b						purine base metabolic process|purine ribonucleoside salvage	cytosol	adenosine kinase activity|ATP binding|metal ion binding|phosphotransferase activity, alcohol group as acceptor			ovary(1)|skin(1)	2	Prostate(51;0.0112)|Ovarian(15;0.148)				Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Pegademase bovine(DB00061)|Ribavirin(DB00811)													---	---	---	---
ADK	132	broad.mit.edu	37	10	76388800	76388800	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76388800delT	uc001jwi.2	+						ADK_uc010qlb.1_Intron|ADK_uc001jwj.2_Intron|ADK_uc010qlc.1_Intron|ADK_uc001jwl.2_Intron	NM_006721	NP_006712			adenosine kinase isoform b						purine base metabolic process|purine ribonucleoside salvage	cytosol	adenosine kinase activity|ATP binding|metal ion binding|phosphotransferase activity, alcohol group as acceptor			ovary(1)|skin(1)	2	Prostate(51;0.0112)|Ovarian(15;0.148)				Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Pegademase bovine(DB00061)|Ribavirin(DB00811)													---	---	---	---
ADK	132	broad.mit.edu	37	10	76409383	76409385	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76409383_76409385delAAA	uc001jwi.2	+						ADK_uc010qlb.1_Intron|ADK_uc001jwj.2_Intron|ADK_uc010qlc.1_Intron|ADK_uc001jwl.2_Intron	NM_006721	NP_006712			adenosine kinase isoform b						purine base metabolic process|purine ribonucleoside salvage	cytosol	adenosine kinase activity|ATP binding|metal ion binding|phosphotransferase activity, alcohol group as acceptor			ovary(1)|skin(1)	2	Prostate(51;0.0112)|Ovarian(15;0.148)				Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Pegademase bovine(DB00061)|Ribavirin(DB00811)													---	---	---	---
ADK	132	broad.mit.edu	37	10	76414781	76414781	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76414781delC	uc001jwi.2	+						ADK_uc010qlb.1_Intron|ADK_uc001jwj.2_Intron|ADK_uc010qlc.1_Intron|ADK_uc001jwl.2_Intron	NM_006721	NP_006712			adenosine kinase isoform b						purine base metabolic process|purine ribonucleoside salvage	cytosol	adenosine kinase activity|ATP binding|metal ion binding|phosphotransferase activity, alcohol group as acceptor			ovary(1)|skin(1)	2	Prostate(51;0.0112)|Ovarian(15;0.148)				Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Pegademase bovine(DB00061)|Ribavirin(DB00811)													---	---	---	---
Unknown	0	broad.mit.edu	37	10	76514201	76514201	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76514201delG								ADK (45142 upstream) : MYST4 (72178 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	76545101	76545101	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76545101delC								ADK (76042 upstream) : MYST4 (41278 downstream)																																			---	---	---	---
MYST4	23522	broad.mit.edu	37	10	76593961	76593963	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76593961_76593963delTTT	uc001jwn.1	+						MYST4_uc001jwm.1_Intron	NM_012330	NP_036462			MYST histone acetyltransferase (monocytic						histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1)	16	all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964)							T	CREBBP	AML								---	---	---	---
MYST4	23522	broad.mit.edu	37	10	76621066	76621066	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76621066delA	uc001jwn.1	+						MYST4_uc001jwm.1_Intron|MYST4_uc001jwo.1_Intron|MYST4_uc001jwp.1_Intron	NM_012330	NP_036462			MYST histone acetyltransferase (monocytic						histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1)	16	all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964)							T	CREBBP	AML								---	---	---	---
MYST4	23522	broad.mit.edu	37	10	76640689	76640689	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76640689delT	uc001jwn.1	+						MYST4_uc001jwm.1_Intron|MYST4_uc001jwo.1_Intron|MYST4_uc001jwp.1_Intron	NM_012330	NP_036462			MYST histone acetyltransferase (monocytic						histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1)	16	all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964)							T	CREBBP	AML								---	---	---	---
MYST4	23522	broad.mit.edu	37	10	76787932	76787932	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76787932delT	uc001jwn.1	+						MYST4_uc001jwo.1_Intron|MYST4_uc001jwp.1_Intron	NM_012330	NP_036462			MYST histone acetyltransferase (monocytic						histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1)	16	all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964)							T	CREBBP	AML								---	---	---	---
DUPD1	338599	broad.mit.edu	37	10	76808157	76808158	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76808157_76808158delTT	uc001jwq.1	-							NM_001003892	NP_001003892			dual specificity phosphatase and pro isomerase							cytoplasm	protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)	2	all_cancers(46;0.0207)|all_epithelial(25;0.00126)|Prostate(51;0.0112)|Ovarian(15;0.0348)																	---	---	---	---
SAMD8	142891	broad.mit.edu	37	10	76932563	76932563	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76932563delT	uc001jwx.1	+						SAMD8_uc001jwy.1_Intron	NM_144660	NP_653261			sterile alpha motif domain containing 8						sphingomyelin biosynthetic process	integral to membrane					0	all_cancers(46;0.0207)|all_epithelial(25;0.00126)|Prostate(51;0.0112)|Ovarian(15;0.0348)																	---	---	---	---
VDAC2	7417	broad.mit.edu	37	10	76981855	76981855	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76981855delA	uc001jwz.2	+						VDAC2_uc010qld.1_Intron|VDAC2_uc001jxa.2_Intron|VDAC2_uc010qle.1_Intron	NM_003375	NP_003366			voltage-dependent anion channel 2							mitochondrial nucleoid|mitochondrial outer membrane|pore complex	nucleotide binding|porin activity|protein binding|voltage-gated anion channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.0642)|all_epithelial(25;0.00604)|Prostate(51;0.0112)|Ovarian(15;0.183)				Dihydroxyaluminium(DB01375)													---	---	---	---
VDAC2	7417	broad.mit.edu	37	10	76989625	76989626	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76989625_76989626delTT	uc001jwz.2	+						VDAC2_uc010qld.1_Intron|VDAC2_uc001jxa.2_Intron|VDAC2_uc010qle.1_Intron	NM_003375	NP_003366			voltage-dependent anion channel 2							mitochondrial nucleoid|mitochondrial outer membrane|pore complex	nucleotide binding|porin activity|protein binding|voltage-gated anion channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.0642)|all_epithelial(25;0.00604)|Prostate(51;0.0112)|Ovarian(15;0.183)				Dihydroxyaluminium(DB01375)													---	---	---	---
COMTD1	118881	broad.mit.edu	37	10	76995106	76995106	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76995106delC	uc001jxb.2	-	3	331	c.247delG	c.(247-249)GATfs	p.D83fs	COMTD1_uc001jxc.1_Frame_Shift_Del_p.G46fs	NM_144589	NP_653190	Q86VU5	CMTD1_HUMAN	catechol-O-methyltransferase domain containing	83						integral to membrane	O-methyltransferase activity				0	all_cancers(46;0.0642)|all_epithelial(25;0.00604)|Prostate(51;0.0112)|Ovarian(15;0.183)																	---	---	---	---
Unknown	0	broad.mit.edu	37	10	77002680	77002680	+	IGR	DEL	C	-	-	rs36066831		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77002680delC								COMTD1 (6910 upstream) : ZNF503 (154925 downstream)																																			---	---	---	---
C10orf41	100131213	broad.mit.edu	37	10	77164477	77164477	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77164477delG	uc010qlf.1	+						ZNF503_uc001jxg.2_5'Flank|C10orf41_uc010qlg.1_Intron	NR_024421				Homo sapiens, clone IMAGE:4696119, mRNA.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	77274074	77274075	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77274074_77274075delTT								C10orf41 (105335 upstream) : MIR606 (38141 downstream)																																			---	---	---	---
C10orf11	83938	broad.mit.edu	37	10	77561787	77561788	+	Intron	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77561787_77561788delAC	uc001jxi.2	+							NM_032024	NP_114413			chromosome 10 open reading frame 11												0	Prostate(51;0.0095)|all_epithelial(25;0.0221)																	---	---	---	---
C10orf11	83938	broad.mit.edu	37	10	77599826	77599826	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77599826delT	uc001jxi.2	+							NM_032024	NP_114413			chromosome 10 open reading frame 11												0	Prostate(51;0.0095)|all_epithelial(25;0.0221)																	---	---	---	---
C10orf11	83938	broad.mit.edu	37	10	77714106	77714106	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77714106delC	uc001jxi.2	+							NM_032024	NP_114413			chromosome 10 open reading frame 11												0	Prostate(51;0.0095)|all_epithelial(25;0.0221)																	---	---	---	---
C10orf11	83938	broad.mit.edu	37	10	77746827	77746827	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77746827delT	uc001jxi.2	+							NM_032024	NP_114413			chromosome 10 open reading frame 11												0	Prostate(51;0.0095)|all_epithelial(25;0.0221)																	---	---	---	---
C10orf11	83938	broad.mit.edu	37	10	77802880	77802880	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:77802880delA	uc001jxi.2	+							NM_032024	NP_114413			chromosome 10 open reading frame 11												0	Prostate(51;0.0095)|all_epithelial(25;0.0221)																	---	---	---	---
C10orf11	83938	broad.mit.edu	37	10	78121896	78121896	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78121896delA	uc001jxi.2	+							NM_032024	NP_114413			chromosome 10 open reading frame 11												0	Prostate(51;0.0095)|all_epithelial(25;0.0221)																	---	---	---	---
C10orf11	83938	broad.mit.edu	37	10	78163824	78163824	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78163824delA	uc001jxi.2	+							NM_032024	NP_114413			chromosome 10 open reading frame 11												0	Prostate(51;0.0095)|all_epithelial(25;0.0221)																	---	---	---	---
Unknown	0	broad.mit.edu	37	10	78319957	78319958	+	IGR	DEL	TG	-	-	rs71898861		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78319957_78319958delTG								C10orf11 (2833 upstream) : KCNMA1 (309401 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	78532419	78532419	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78532419delC								C10orf11 (215295 upstream) : KCNMA1 (96940 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	78627310	78627310	+	IGR	DEL	A	-	-	rs35075849		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78627310delA								C10orf11 (310186 upstream) : KCNMA1 (2049 downstream)																																			---	---	---	---
KCNMA1	3778	broad.mit.edu	37	10	78763067	78763067	+	Intron	DEL	A	-	-	rs34473997		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78763067delA	uc001jxn.2	-						KCNMA1_uc001jxj.2_Intron|KCNMA1_uc001jxk.1_Intron|KCNMA1_uc009xrt.1_Intron|KCNMA1_uc001jxl.1_Intron|KCNMA1_uc001jxo.2_Intron|KCNMA1_uc001jxm.2_Intron|KCNMA1_uc001jxq.2_Intron	NM_001161352	NP_001154824			large conductance calcium-activated potassium						cellular potassium ion homeostasis|negative regulation of cell volume|platelet activation|positive regulation of apoptosis|regulation of membrane potential|response to calcium ion|response to carbon monoxide|response to hypoxia|response to osmotic stress|smooth muscle contraction involved in micturition	apical plasma membrane|caveola|integral to membrane|voltage-gated potassium channel complex	actin binding|calcium-activated potassium channel activity|large conductance calcium-activated potassium channel activity|metal ion binding|voltage-gated potassium channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Chlorzoxazone(DB00356)|Cromoglicate(DB01003)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Enflurane(DB00228)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)													---	---	---	---
KCNMA1	3778	broad.mit.edu	37	10	78882315	78882315	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78882315delA	uc001jxn.2	-						KCNMA1_uc001jxj.2_Intron|KCNMA1_uc001jxk.1_Intron|KCNMA1_uc009xrt.1_Intron|KCNMA1_uc001jxo.2_Intron|KCNMA1_uc001jxm.2_Intron|KCNMA1_uc001jxq.2_Intron	NM_001161352	NP_001154824			large conductance calcium-activated potassium						cellular potassium ion homeostasis|negative regulation of cell volume|platelet activation|positive regulation of apoptosis|regulation of membrane potential|response to calcium ion|response to carbon monoxide|response to hypoxia|response to osmotic stress|smooth muscle contraction involved in micturition	apical plasma membrane|caveola|integral to membrane|voltage-gated potassium channel complex	actin binding|calcium-activated potassium channel activity|large conductance calcium-activated potassium channel activity|metal ion binding|voltage-gated potassium channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Chlorzoxazone(DB00356)|Cromoglicate(DB01003)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Enflurane(DB00228)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)													---	---	---	---
KCNMA1	3778	broad.mit.edu	37	10	78901477	78901478	+	Intron	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78901477_78901478delAG	uc001jxn.2	-						KCNMA1_uc001jxj.2_Intron|KCNMA1_uc001jxk.1_Intron|KCNMA1_uc009xrt.1_Intron|KCNMA1_uc001jxo.2_Intron|KCNMA1_uc001jxm.2_Intron|KCNMA1_uc001jxq.2_Intron	NM_001161352	NP_001154824			large conductance calcium-activated potassium						cellular potassium ion homeostasis|negative regulation of cell volume|platelet activation|positive regulation of apoptosis|regulation of membrane potential|response to calcium ion|response to carbon monoxide|response to hypoxia|response to osmotic stress|smooth muscle contraction involved in micturition	apical plasma membrane|caveola|integral to membrane|voltage-gated potassium channel complex	actin binding|calcium-activated potassium channel activity|large conductance calcium-activated potassium channel activity|metal ion binding|voltage-gated potassium channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Chlorzoxazone(DB00356)|Cromoglicate(DB01003)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Enflurane(DB00228)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)													---	---	---	---
KCNMA1	3778	broad.mit.edu	37	10	79015359	79015359	+	Intron	DEL	A	-	-	rs138839780		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79015359delA	uc001jxn.2	-						KCNMA1_uc001jxj.2_Intron|KCNMA1_uc009xrt.1_Intron|KCNMA1_uc001jxo.2_Intron|KCNMA1_uc001jxm.2_Intron|KCNMA1_uc001jxq.2_Intron	NM_001161352	NP_001154824			large conductance calcium-activated potassium						cellular potassium ion homeostasis|negative regulation of cell volume|platelet activation|positive regulation of apoptosis|regulation of membrane potential|response to calcium ion|response to carbon monoxide|response to hypoxia|response to osmotic stress|smooth muscle contraction involved in micturition	apical plasma membrane|caveola|integral to membrane|voltage-gated potassium channel complex	actin binding|calcium-activated potassium channel activity|large conductance calcium-activated potassium channel activity|metal ion binding|voltage-gated potassium channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Chlorzoxazone(DB00356)|Cromoglicate(DB01003)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Enflurane(DB00228)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)													---	---	---	---
KCNMA1	3778	broad.mit.edu	37	10	79065599	79065599	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79065599delC	uc001jxn.2	-						KCNMA1_uc001jxj.2_Intron|KCNMA1_uc009xrt.1_Intron|KCNMA1_uc001jxo.2_Intron|KCNMA1_uc001jxm.2_Intron|KCNMA1_uc001jxq.2_Intron	NM_001161352	NP_001154824			large conductance calcium-activated potassium						cellular potassium ion homeostasis|negative regulation of cell volume|platelet activation|positive regulation of apoptosis|regulation of membrane potential|response to calcium ion|response to carbon monoxide|response to hypoxia|response to osmotic stress|smooth muscle contraction involved in micturition	apical plasma membrane|caveola|integral to membrane|voltage-gated potassium channel complex	actin binding|calcium-activated potassium channel activity|large conductance calcium-activated potassium channel activity|metal ion binding|voltage-gated potassium channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Chlorzoxazone(DB00356)|Cromoglicate(DB01003)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Enflurane(DB00228)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)													---	---	---	---
KCNMA1	3778	broad.mit.edu	37	10	79194491	79194491	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79194491delT	uc001jxn.2	-						KCNMA1_uc001jxj.2_Intron|KCNMA1_uc001jxo.2_Intron|KCNMA1_uc001jxm.2_Intron|KCNMA1_uc001jxq.2_Intron	NM_001161352	NP_001154824			large conductance calcium-activated potassium						cellular potassium ion homeostasis|negative regulation of cell volume|platelet activation|positive regulation of apoptosis|regulation of membrane potential|response to calcium ion|response to carbon monoxide|response to hypoxia|response to osmotic stress|smooth muscle contraction involved in micturition	apical plasma membrane|caveola|integral to membrane|voltage-gated potassium channel complex	actin binding|calcium-activated potassium channel activity|large conductance calcium-activated potassium channel activity|metal ion binding|voltage-gated potassium channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Chlorzoxazone(DB00356)|Cromoglicate(DB01003)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Enflurane(DB00228)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)													---	---	---	---
KCNMA1	3778	broad.mit.edu	37	10	79361597	79361597	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79361597delT	uc001jxn.2	-						KCNMA1_uc001jxj.2_Intron|KCNMA1_uc001jxo.2_Intron|KCNMA1_uc001jxm.2_Intron|KCNMA1_uc001jxq.2_Intron	NM_001161352	NP_001154824			large conductance calcium-activated potassium						cellular potassium ion homeostasis|negative regulation of cell volume|platelet activation|positive regulation of apoptosis|regulation of membrane potential|response to calcium ion|response to carbon monoxide|response to hypoxia|response to osmotic stress|smooth muscle contraction involved in micturition	apical plasma membrane|caveola|integral to membrane|voltage-gated potassium channel complex	actin binding|calcium-activated potassium channel activity|large conductance calcium-activated potassium channel activity|metal ion binding|voltage-gated potassium channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Chlorzoxazone(DB00356)|Cromoglicate(DB01003)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Enflurane(DB00228)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)													---	---	---	---
POLR3A	11128	broad.mit.edu	37	10	79770063	79770064	+	Intron	DEL	AA	-	-	rs3832673		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79770063_79770064delAA	uc001jzn.2	-							NM_007055	NP_008986			polymerase (RNA) III (DNA directed) polypeptide						innate immune response|positive regulation of interferon-beta production|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	DNA-directed RNA polymerase III complex	DNA binding|DNA-directed RNA polymerase activity|ribonucleoside binding|zinc ion binding				0	all_cancers(46;0.0356)|all_epithelial(25;0.00102)|Breast(12;0.00124)|Prostate(51;0.0095)		Epithelial(14;0.00161)|OV - Ovarian serous cystadenocarcinoma(4;0.00323)|all cancers(16;0.00646)															---	---	---	---
POLR3A	11128	broad.mit.edu	37	10	79788277	79788277	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79788277delT	uc001jzn.2	-							NM_007055	NP_008986			polymerase (RNA) III (DNA directed) polypeptide						innate immune response|positive regulation of interferon-beta production|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	DNA-directed RNA polymerase III complex	DNA binding|DNA-directed RNA polymerase activity|ribonucleoside binding|zinc ion binding				0	all_cancers(46;0.0356)|all_epithelial(25;0.00102)|Breast(12;0.00124)|Prostate(51;0.0095)		Epithelial(14;0.00161)|OV - Ovarian serous cystadenocarcinoma(4;0.00323)|all cancers(16;0.00646)															---	---	---	---
Unknown	0	broad.mit.edu	37	10	80062398	80062399	+	Intron	INS	-	G	G	rs72515558	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80062398_80062399insG	uc010qlp.1	+						uc001jzw.1_Intron					SubName: Full=cDNA FLJ57363;																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	80595351	80595351	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80595351delT								RPS24 (778781 upstream) : LOC283050 (107733 downstream)																																			---	---	---	---
ZMIZ1	57178	broad.mit.edu	37	10	80976224	80976224	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:80976224delG	uc001kaf.2	+						ZMIZ1_uc001kae.2_3'UTR	NM_020338	NP_065071			retinoic acid induced 17						transcription, DNA-dependent	cytoplasm|nuclear speck	zinc ion binding			ovary(2)|breast(1)|skin(1)	4	all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985)		Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229)															---	---	---	---
ZMIZ1	57178	broad.mit.edu	37	10	81060045	81060045	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81060045delG	uc001kaf.2	+						ZMIZ1_uc001kag.2_Intron	NM_020338	NP_065071			retinoic acid induced 17						transcription, DNA-dependent	cytoplasm|nuclear speck	zinc ion binding			ovary(2)|breast(1)|skin(1)	4	all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985)		Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229)															---	---	---	---
ZCCHC24	219654	broad.mit.edu	37	10	81159939	81159939	+	Intron	DEL	A	-	-	rs147819323	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81159939delA	uc001kak.2	-						ZCCHC24_uc010qlr.1_Intron|ZCCHC24_uc009xrw.2_Intron	NM_153367	NP_699198			zinc finger, CCHC domain containing 24								nucleic acid binding|zinc ion binding			breast(1)	1																		---	---	---	---
ZCCHC24	219654	broad.mit.edu	37	10	81203935	81203935	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81203935delA	uc001kak.2	-						ZCCHC24_uc010qlr.1_5'Flank|ZCCHC24_uc009xrw.2_Intron	NM_153367	NP_699198			zinc finger, CCHC domain containing 24								nucleic acid binding|zinc ion binding			breast(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	81485540	81485540	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81485540delT	uc001kat.2	-											full-length cDNA clone CS0DC003YI17 of Neuroblastoma Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
MBL1P	8512	broad.mit.edu	37	10	81682865	81682865	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81682865delG	uc001kbf.2	+						MBL1P_uc001kbg.1_RNA					Homo sapiens mannose-binding protein-A pseudogene (MBL1P1) mRNA sequence.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	81777995	81777996	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81777995_81777996insT								MBL1P (67212 upstream) : LOC219347 (27995 downstream)																																			---	---	---	---
LOC219347	219347	broad.mit.edu	37	10	81813402	81813402	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81813402delG	uc001kbk.2	-						LOC219347_uc001kbi.3_Intron|LOC219347_uc009xsk.2_Intron|LOC219347_uc009xsl.2_Intron|LOC219347_uc009xsm.2_Intron|LOC219347_uc001kbj.3_Intron					Homo sapiens cDNA FLJ11611 fis, clone HEMBA1003987.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	82286358	82286358	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82286358delT								TSPAN14 (3968 upstream) : SH2D4B (11300 downstream)																																			---	---	---	---
SH2D4B	387694	broad.mit.edu	37	10	82337733	82337733	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82337733delT	uc001kck.1	+						SH2D4B_uc001kcl.1_Intron	NM_207372	NP_997255			SH2 domain containing 4B isoform 1												0			Colorectal(32;0.229)															---	---	---	---
Unknown	0	broad.mit.edu	37	10	82433919	82433919	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82433919delC								SH2D4B (27603 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	82563364	82563365	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82563364_82563365delTT								SH2D4B (157048 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	82948444	82948444	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82948444delT								SH2D4B (542128 upstream) : NRG3 (686626 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	83155490	83155490	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:83155490delT								SH2D4B (749174 upstream) : NRG3 (479580 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	83572575	83572575	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:83572575delA								None (None upstream) : NRG3 (62495 downstream)																																			---	---	---	---
NRG3	10718	broad.mit.edu	37	10	84110653	84110654	+	Intron	DEL	TT	-	-	rs71745611		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:84110653_84110654delTT	uc001kco.2	+						NRG3_uc010qlz.1_Intron|NRG3_uc001kcp.2_Intron|NRG3_uc001kcq.2_Intron	NM_001010848	NP_001010848			neuregulin 3 isoform 1						regulation of cell growth	extracellular region|integral to plasma membrane	growth factor activity|receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity			lung(5)|breast(1)	6				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)														---	---	---	---
NRG3	10718	broad.mit.edu	37	10	84503150	84503150	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:84503150delA	uc001kco.2	+						NRG3_uc010qlz.1_Intron|NRG3_uc001kcp.2_Intron|NRG3_uc001kcq.2_Intron	NM_001010848	NP_001010848			neuregulin 3 isoform 1						regulation of cell growth	extracellular region|integral to plasma membrane	growth factor activity|receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity			lung(5)|breast(1)	6				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)														---	---	---	---
NRG3	10718	broad.mit.edu	37	10	84632489	84632490	+	Intron	DEL	AA	-	-	rs113038442		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:84632489_84632490delAA	uc001kco.2	+						NRG3_uc010qlz.1_Intron|NRG3_uc001kcp.2_Intron|NRG3_uc001kcq.2_Intron|NRG3_uc001kcr.2_Intron	NM_001010848	NP_001010848			neuregulin 3 isoform 1						regulation of cell growth	extracellular region|integral to plasma membrane	growth factor activity|receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity			lung(5)|breast(1)	6				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)														---	---	---	---
NRG3	10718	broad.mit.edu	37	10	84646032	84646039	+	Intron	DEL	GCCCTCAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:84646032_84646039delGCCCTCAA	uc001kco.2	+						NRG3_uc010qlz.1_Intron|NRG3_uc001kcp.2_Intron|NRG3_uc001kcq.2_Intron|NRG3_uc001kcr.2_Intron	NM_001010848	NP_001010848			neuregulin 3 isoform 1						regulation of cell growth	extracellular region|integral to plasma membrane	growth factor activity|receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity			lung(5)|breast(1)	6				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	84757859	84757859	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:84757859delT								NRG3 (10924 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	84922481	84922482	+	IGR	INS	-	G	G	rs139171390	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:84922481_84922482insG								NRG3 (175546 upstream) : GHITM (976703 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	85540135	85540136	+	IGR	DEL	TT	-	-	rs112860821		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85540135_85540136delTT								NRG3 (793200 upstream) : GHITM (359049 downstream)																																			---	---	---	---
FAM190B	54462	broad.mit.edu	37	10	86114919	86114919	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86114919delT	uc001kdh.1	+						FAM190B_uc001kdg.1_Intron|FAM190B_uc010qmd.1_Intron	NM_018999	NP_061872			granule cell antiserum positive 14											ovary(3)|skin(1)	4																		---	---	---	---
FAM190B	54462	broad.mit.edu	37	10	86228265	86228265	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86228265delA	uc001kdh.1	+						FAM190B_uc010qmd.1_Intron|FAM190B_uc001kdi.1_Intron|FAM190B_uc010qme.1_Intron	NM_018999	NP_061872			granule cell antiserum positive 14											ovary(3)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	86526993	86526993	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86526993delT								FAM190B (248717 upstream) : GRID1 (832319 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	87085837	87085837	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87085837delT								FAM190B (807561 upstream) : GRID1 (273475 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	87158363	87158363	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87158363delA								FAM190B (880087 upstream) : GRID1 (200949 downstream)																																			---	---	---	---
GRID1	2894	broad.mit.edu	37	10	87394671	87394671	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87394671delG	uc001kdl.1	-						GRID1_uc009xsu.1_Intron|GRID1_uc010qmf.1_Intron	NM_017551	NP_060021			glutamate receptor, ionotropic, delta 1							cell junction|integral to membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(5)|upper_aerodigestive_tract(2)|large_intestine(2)|central_nervous_system(1)	10					L-Glutamic Acid(DB00142)										Multiple Myeloma(13;0.14)			---	---	---	---
GRID1	2894	broad.mit.edu	37	10	87752373	87752373	+	Intron	DEL	G	-	-	rs34589755		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87752373delG	uc001kdl.1	-						GRID1_uc009xsu.1_Intron	NM_017551	NP_060021			glutamate receptor, ionotropic, delta 1							cell junction|integral to membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(5)|upper_aerodigestive_tract(2)|large_intestine(2)|central_nervous_system(1)	10					L-Glutamic Acid(DB00142)										Multiple Myeloma(13;0.14)			---	---	---	---
WAPAL	23063	broad.mit.edu	37	10	88277854	88277854	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88277854delA	uc001kdo.2	-						WAPAL_uc001kdn.2_Intron|WAPAL_uc009xsw.2_Intron|WAPAL_uc010qmh.1_Intron|WAPAL_uc010qmi.1_Intron|WAPAL_uc010qmj.1_Intron	NM_015045	NP_055860			wings apart-like homolog						cell division|interspecies interaction between organisms|mitosis|negative regulation of chromatin binding|negative regulation of DNA replication|negative regulation of sister chromatid cohesion|protein localization to chromatin|regulation of cohesin localization to chromatin	chromatin|cohesin complex|cytoplasm	protein binding			ovary(1)	1																		---	---	---	---
BMPR1A	657	broad.mit.edu	37	10	88676750	88676751	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88676750_88676751delAA	uc001kdy.2	+							NM_004329	NP_004320			bone morphogenetic protein receptor, type IA						BMP signaling pathway|immune response|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|transforming growth factor beta receptor signaling pathway	integral to membrane|plasma membrane	ATP binding|metal ion binding|protein homodimerization activity|SMAD binding|transforming growth factor beta receptor activity			lung(3)|large_intestine(1)|stomach(1)|central_nervous_system(1)|breast(1)|kidney(1)	8								Mis|N|F			gastrointestinal polyps			Hereditary_Mixed_Polyposis_syndrome_type_2|Juvenile_Polyposis				---	---	---	---
AGAP11	119385	broad.mit.edu	37	10	88760457	88760457	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88760457delT	uc001kee.2	+						AGAP11_uc001kef.2_Intron	NM_133447	NP_597704			ankyrin repeat and GTPase domain Arf GTPase						regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	88805871	88805871	+	IGR	DEL	T	-	-	rs75464240		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88805871delT								AGAP11 (21385 upstream) : GLUD1 (4375 downstream)																																			---	---	---	---
GLUD1	2746	broad.mit.edu	37	10	88836428	88836428	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88836428delA	uc001keh.2	-						GLUD1_uc001keg.2_Intron|GLUD1_uc010qmp.1_Intron	NM_005271	NP_005262			glutamate dehydrogenase 1 precursor						glutamate biosynthetic process|glutamate catabolic process|positive regulation of insulin secretion	mitochondrial matrix	ADP binding|ATP binding|glutamate dehydrogenase|glutamate dehydrogenase activity|GTP binding|identical protein binding|leucine binding|NAD+ binding				0					L-Glutamic Acid(DB00142)|NADH(DB00157)													---	---	---	---
MINPP1	9562	broad.mit.edu	37	10	89296700	89296700	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89296700delT	uc001keu.2	+						MINPP1_uc009xtf.1_Intron|MINPP1_uc001kev.2_Intron	NM_004897	NP_004888			multiple inositol polyphosphate histidine						bone mineralization|polyphosphate metabolic process	endoplasmic reticulum lumen	acid phosphatase activity|bisphosphoglycerate 3-phosphatase activity|multiple inositol-polyphosphate phosphatase activity|phosphohistidine phosphatase activity			urinary_tract(1)	1		Colorectal(252;0.122)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00123)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	89332104	89332104	+	IGR	DEL	A	-	-	rs77340838		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89332104delA								MINPP1 (18936 upstream) : PAPSS2 (87372 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	89780355	89780356	+	IGR	INS	-	A	A	rs143088440	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89780355_89780356insA								PTEN (51824 upstream) : RNLS (111701 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	89791194	89791194	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:89791194delT								PTEN (62663 upstream) : RNLS (100863 downstream)																																			---	---	---	---
LIPF	8513	broad.mit.edu	37	10	90426449	90426449	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90426449delA	uc001kfg.1	+						LIPF_uc009xtk.2_Intron|LIPF_uc001kfh.1_Intron|LIPF_uc010qmt.1_Intron|LIPF_uc010qmu.1_Intron	NM_004190	NP_004181			lipase, gastric precursor						lipid catabolic process|triglyceride metabolic process	extracellular region	lipid binding|triglyceride lipase activity				0		Colorectal(252;0.0161)		Colorectal(12;3.91e-05)|COAD - Colon adenocarcinoma(12;5.43e-05)														---	---	---	---
ACTA2	59	broad.mit.edu	37	10	90739368	90739368	+	Intron	DEL	A	-	-	rs1571014	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90739368delA	uc001kfq.2	-						FAS_uc010qna.1_Intron	NM_001141945	NP_001135417			alpha 2 actin						response to virus	cytosol	ATP binding				0		Colorectal(252;0.0161)		Colorectal(12;0.000123)|COAD - Colon adenocarcinoma(12;0.00018)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	90838447	90838447	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90838447delT								FAS (62906 upstream) : CH25H (127249 downstream)																																			---	---	---	---
LIPA	3988	broad.mit.edu	37	10	91104925	91104925	+	Intron	DEL	A	-	-	rs112470457		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91104925delA	uc001kgc.3	-						LIPA_uc001kgb.3_Intron|uc001kgd.2_5'Flank	NM_001127605	NP_001121077			lipase A precursor						lipid catabolic process	lysosome	lipase activity|sterol esterase activity				0		Colorectal(252;0.0162)		GBM - Glioblastoma multiforme(2;0.00406)														---	---	---	---
SLC16A12	387700	broad.mit.edu	37	10	91266655	91266656	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91266655_91266656insA	uc001kgm.2	-							NM_213606	NP_998771			solute carrier family 16 (monocarboxylic acid							integral to membrane|plasma membrane	symporter activity			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	91306905	91306905	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91306905delT								SLC16A12 (11592 upstream) : PANK1 (35844 downstream)																																			---	---	---	---
PANK1	53354	broad.mit.edu	37	10	91343951	91343951	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91343951delA	uc001kgp.1	-	7					PANK1_uc001kgn.1_3'UTR|PANK1_uc001kgo.1_3'UTR|PANK1_uc009xtu.1_3'UTR	NM_148977	NP_683878			pantothenate kinase 1 isoform alpha						coenzyme A biosynthetic process|pantothenate metabolic process	cytosol|nucleus	ATP binding|pantothenate kinase activity				0					Bezafibrate(DB01393)													---	---	---	---
KIF20B	9585	broad.mit.edu	37	10	91477314	91477314	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91477314delT	uc001kgs.1	+						KIF20B_uc001kgr.1_Intron	NM_016195	NP_057279			M-phase phosphoprotein 1						cell cycle arrest|cell division|microtubule-based movement|mitosis|regulation of mitosis	centrosome|microtubule|nucleolus|nucleoplasm|spindle	ATP binding|ATPase activity|microtubule motor activity|WW domain binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	92063731	92063731	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92063731delC								KIF20B (529031 upstream) : HTR7 (436847 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	92295365	92295366	+	IGR	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92295365_92295366delAG								KIF20B (760665 upstream) : HTR7 (205212 downstream)																																			---	---	---	---
RPP30	10556	broad.mit.edu	37	10	92638255	92638255	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92638255delT	uc009xtx.2	+						RPP30_uc001khd.2_Intron|RPP30_uc010qnj.1_Intron	NM_006413	NP_006404			ribonuclease P/MRP 30kDa subunit isoform b						tRNA processing	nucleolar ribonuclease P complex	protein binding|ribonuclease P activity				0																		---	---	---	---
RPP30	10556	broad.mit.edu	37	10	92666683	92666683	+	3'UTR	DEL	T	-	-	rs4522081	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92666683delT	uc001khd.2	+	14						NM_001104546	NP_001098016			ribonuclease P/MRP 30kDa subunit isoform a						tRNA processing	nucleolar ribonuclease P complex	protein binding|ribonuclease P activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	92751903	92751903	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92751903delA								ANKRD1 (70871 upstream) : NUDT9P1 (159858 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	93048284	93048285	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93048284_93048285insT								PCGF5 (4264 upstream) : LOC100188947 (18435 downstream)																																			---	---	---	---
BTAF1	9044	broad.mit.edu	37	10	93747240	93747240	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93747240delA	uc001khr.2	+						BTAF1_uc001khs.1_Intron|BTAF1_uc001kht.1_Intron	NM_003972	NP_003963			BTAF1 RNA polymerase II, B-TFIID transcription						negative regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.0846)																---	---	---	---
CPEB3	22849	broad.mit.edu	37	10	93889859	93889859	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93889859delT	uc001khw.1	-						CPEB3_uc001khu.1_Intron|CPEB3_uc001khv.1_Intron|CPEB3_uc010qnn.1_Intron	NM_014912	NP_055727			cytoplasmic polyadenylation element binding								nucleotide binding|RNA binding				0		Colorectal(252;0.0869)																---	---	---	---
CPEB3	22849	broad.mit.edu	37	10	94020850	94020850	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94020850delA	uc001khw.1	-						CPEB3_uc010qnn.1_Intron	NM_014912	NP_055727			cytoplasmic polyadenylation element binding								nucleotide binding|RNA binding				0		Colorectal(252;0.0869)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	94148484	94148484	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94148484delC								MARCH5 (34763 upstream) : IDE (65116 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	94512439	94512439	+	IGR	DEL	A	-	-	rs12780532		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94512439delA								HHEX (57033 upstream) : EXOC6 (78496 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	94862909	94862910	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94862909_94862910delTG								CYP26A1 (25268 upstream) : MYOF (203277 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	94923715	94923716	+	IGR	INS	-	T	T	rs79369251		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94923715_94923716insT								CYP26A1 (86074 upstream) : MYOF (142471 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	95046064	95046064	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95046064delA								CYP26A1 (208423 upstream) : MYOF (20123 downstream)																																			---	---	---	---
PIPSL	266971	broad.mit.edu	37	10	95718422	95718423	+	3'UTR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95718422_95718423delTT	uc009xuj.2	-	1						NR_002319				RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha;          Short=PtdIns(4)P-5-kinase alpha;          Short=PIP5KIalpha;          EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha;												0																		---	---	---	---
PLCE1	51196	broad.mit.edu	37	10	95795506	95795507	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95795506_95795507insT	uc001kjk.2	+						PLCE1_uc010qnx.1_Intron	NM_016341	NP_057425			phospholipase C, epsilon 1 isoform 1						activation of MAPK activity|activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|calcium-mediated signaling|cell proliferation|cytoskeleton organization|diacylglycerol biosynthetic process|elevation of cytosolic calcium ion concentration|epidermal growth factor receptor signaling pathway|glomerulus development|heart development|lipid catabolic process|Ras protein signal transduction|regulation of cell growth|regulation of G-protein coupled receptor protein signaling pathway|regulation of Ras protein signal transduction|regulation of smooth muscle contraction	cytosol|Golgi membrane|membrane fraction|plasma membrane	calcium ion binding|guanyl-nucleotide exchange factor activity|phosphatidylinositol phospholipase C activity|Ras GTPase binding|receptor signaling protein activity			ovary(2)|skin(1)	3		Colorectal(252;0.0458)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	96146133	96146133	+	IGR	DEL	G	-	-	rs9420637	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96146133delG								NOC3L (23450 upstream) : TBC1D12 (16053 downstream)																																			---	---	---	---
TBC1D12	23232	broad.mit.edu	37	10	96287776	96287776	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96287776delT	uc001kjr.2	+							NM_015188	NP_056003			TBC1 domain family, member 12							intracellular	Rab GTPase activator activity				0		Colorectal(252;0.0429)																---	---	---	---
HELLS	3070	broad.mit.edu	37	10	96313824	96313824	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96313824delA	uc001kjt.2	+						HELLS_uc001kjs.2_Intron|HELLS_uc009xul.2_Intron|HELLS_uc009xum.2_Intron|HELLS_uc009xun.2_Intron|HELLS_uc009xuo.2_Intron|HELLS_uc001kju.2_Intron|HELLS_uc009xup.2_Intron|HELLS_uc009xuq.2_Intron|HELLS_uc009xur.2_Intron	NM_018063	NP_060533			helicase, lymphoid-specific						cell division|centromeric heterochromatin formation|lymphocyte proliferation|maintenance of DNA methylation|methylation-dependent chromatin silencing|mitosis|transcription, DNA-dependent	centromeric heterochromatin|nucleus	ATP binding|DNA binding|helicase activity			ovary(1)|kidney(1)	2		Colorectal(252;0.0429)		all cancers(201;2.13e-05)														---	---	---	---
HELLS	3070	broad.mit.edu	37	10	96322556	96322557	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96322556_96322557delTT	uc001kjt.2	+						HELLS_uc001kjs.2_Intron|HELLS_uc009xul.2_Intron|HELLS_uc009xum.2_Intron|HELLS_uc009xun.2_Intron|HELLS_uc009xuo.2_Intron|HELLS_uc001kju.2_Intron|HELLS_uc009xup.2_Intron|HELLS_uc009xuq.2_Intron|HELLS_uc009xur.2_Intron	NM_018063	NP_060533			helicase, lymphoid-specific						cell division|centromeric heterochromatin formation|lymphocyte proliferation|maintenance of DNA methylation|methylation-dependent chromatin silencing|mitosis|transcription, DNA-dependent	centromeric heterochromatin|nucleus	ATP binding|DNA binding|helicase activity			ovary(1)|kidney(1)	2		Colorectal(252;0.0429)		all cancers(201;2.13e-05)														---	---	---	---
HELLS	3070	broad.mit.edu	37	10	96331305	96331305	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96331305delA	uc001kjt.2	+						HELLS_uc001kjs.2_Intron|HELLS_uc009xul.2_Intron|HELLS_uc009xum.2_Intron|HELLS_uc009xun.2_Intron|HELLS_uc009xuo.2_Intron|HELLS_uc001kju.2_Intron|HELLS_uc009xup.2_Intron|HELLS_uc009xuq.2_Intron|HELLS_uc009xur.2_Intron	NM_018063	NP_060533			helicase, lymphoid-specific						cell division|centromeric heterochromatin formation|lymphocyte proliferation|maintenance of DNA methylation|methylation-dependent chromatin silencing|mitosis|transcription, DNA-dependent	centromeric heterochromatin|nucleus	ATP binding|DNA binding|helicase activity			ovary(1)|kidney(1)	2		Colorectal(252;0.0429)		all cancers(201;2.13e-05)														---	---	---	---
HELLS	3070	broad.mit.edu	37	10	96336228	96336229	+	Intron	INS	-	TT	TT			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96336228_96336229insTT	uc001kjt.2	+						HELLS_uc001kjs.2_Intron|HELLS_uc009xul.2_Intron|HELLS_uc009xum.2_Intron|HELLS_uc009xun.2_Intron|HELLS_uc009xuo.2_Intron|HELLS_uc001kju.2_Intron|HELLS_uc009xup.2_Intron|HELLS_uc009xuq.2_Intron|HELLS_uc009xur.2_Intron	NM_018063	NP_060533			helicase, lymphoid-specific						cell division|centromeric heterochromatin formation|lymphocyte proliferation|maintenance of DNA methylation|methylation-dependent chromatin silencing|mitosis|transcription, DNA-dependent	centromeric heterochromatin|nucleus	ATP binding|DNA binding|helicase activity			ovary(1)|kidney(1)	2		Colorectal(252;0.0429)		all cancers(201;2.13e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	96620041	96620041	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96620041delA								CYP2C19 (7371 upstream) : CYP2C9 (78374 downstream)																																			---	---	---	---
SORBS1	10580	broad.mit.edu	37	10	97128619	97128621	+	Intron	DEL	CTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97128619_97128621delCTT	uc001kkp.2	-						SORBS1_uc001kkk.2_Intron|SORBS1_uc001kkl.2_Intron|SORBS1_uc001kkn.2_Intron|SORBS1_uc001kkm.2_Intron|SORBS1_uc001kko.2_Intron|SORBS1_uc001kkq.2_Intron|SORBS1_uc001kkr.2_Intron|SORBS1_uc001kks.2_Intron|SORBS1_uc001kkt.2_Intron|SORBS1_uc001kku.2_Intron|SORBS1_uc001kkv.2_Intron|SORBS1_uc001kkw.2_Intron|SORBS1_uc010qoe.1_Intron|SORBS1_uc010qof.1_Intron	NM_001034954	NP_001030126			sorbin and SH3 domain containing 1 isoform 3						focal adhesion assembly|glucose transport|insulin receptor signaling pathway|muscle contraction|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of lipid biosynthetic process|stress fiber assembly	centrosome|cytosol|focal adhesion|membrane raft|nucleus|stress fiber|zonula adherens	actin binding|insulin receptor binding|SH3/SH2 adaptor activity			breast(1)	1		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)														---	---	---	---
SORBS1	10580	broad.mit.edu	37	10	97131604	97131605	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97131604_97131605delAA	uc001kkp.2	-						SORBS1_uc001kkk.2_Intron|SORBS1_uc001kkl.2_Intron|SORBS1_uc001kkn.2_Intron|SORBS1_uc001kkm.2_Intron|SORBS1_uc001kko.2_Intron|SORBS1_uc001kkq.2_Intron|SORBS1_uc001kkr.2_Intron|SORBS1_uc001kks.2_Intron|SORBS1_uc001kkt.2_Intron|SORBS1_uc001kku.2_Intron|SORBS1_uc001kkv.2_Intron|SORBS1_uc001kkw.2_Intron|SORBS1_uc010qoe.1_Intron|SORBS1_uc010qof.1_Intron	NM_001034954	NP_001030126			sorbin and SH3 domain containing 1 isoform 3						focal adhesion assembly|glucose transport|insulin receptor signaling pathway|muscle contraction|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of lipid biosynthetic process|stress fiber assembly	centrosome|cytosol|focal adhesion|membrane raft|nucleus|stress fiber|zonula adherens	actin binding|insulin receptor binding|SH3/SH2 adaptor activity			breast(1)	1		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)														---	---	---	---
SORBS1	10580	broad.mit.edu	37	10	97305453	97305455	+	Intron	DEL	AAG	-	-	rs139781417		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97305453_97305455delAAG	uc001kkw.2	-						SORBS1_uc001kku.2_Intron|SORBS1_uc001kkv.2_Intron|SORBS1_uc010qoe.1_Intron|SORBS1_uc010qof.1_Intron|SORBS1_uc001kkx.1_Intron	NM_001034954	NP_001030126			sorbin and SH3 domain containing 1 isoform 3						focal adhesion assembly|glucose transport|insulin receptor signaling pathway|muscle contraction|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of lipid biosynthetic process|stress fiber assembly	centrosome|cytosol|focal adhesion|membrane raft|nucleus|stress fiber|zonula adherens	actin binding|insulin receptor binding|SH3/SH2 adaptor activity			breast(1)	1		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)														---	---	---	---
CC2D2B	387707	broad.mit.edu	37	10	97778863	97778864	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97778863_97778864insA	uc001kll.2	+						uc001klg.1_Intron|uc001klj.1_Intron|CC2D2B_uc001klk.2_Intron|CC2D2B_uc010qop.1_Intron|uc009xvb.1_RNA	NM_001001732	NP_001001732			coiled-coil and C2 domain containing 2B isoform											ovary(1)	1		Colorectal(252;0.158)		Epithelial(162;7.08e-08)|all cancers(201;2.71e-06)														---	---	---	---
CC2D2B	387707	broad.mit.edu	37	10	97780851	97780851	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97780851delA	uc001kll.2	+						uc001klg.1_Intron|uc001klj.1_Intron|CC2D2B_uc001klk.2_Intron|CC2D2B_uc010qop.1_Intron|uc009xvb.1_RNA	NM_001001732	NP_001001732			coiled-coil and C2 domain containing 2B isoform											ovary(1)	1		Colorectal(252;0.158)		Epithelial(162;7.08e-08)|all cancers(201;2.71e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	97822712	97822712	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97822712delT	uc001klg.1	-						uc001klj.1_Intron|uc009xvb.1_Intron					Homo sapiens cDNA FLJ34077 fis, clone FCBBF3003481, weakly similar to ZINC FINGER PROTEIN 195.																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	97946164	97946165	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97946164_97946165insT								ZNF518A (22654 upstream) : BLNK (5298 downstream)																																			---	---	---	---
TM9SF3	56889	broad.mit.edu	37	10	98287259	98287259	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98287259delG	uc001kmm.3	-						TM9SF3_uc010qot.1_Intron	NM_020123	NP_064508			transmembrane 9 superfamily member 3 precursor							integral to membrane	binding				0		Colorectal(252;0.158)		Epithelial(162;1.84e-09)|all cancers(201;2.84e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	98570132	98570132	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98570132delA								PIK3AP1 (89853 upstream) : MIR607 (18294 downstream)																																			---	---	---	---
ARHGAP19	84986	broad.mit.edu	37	10	98993624	98993624	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98993624delA	uc001knb.2	-						ARHGAP19_uc001kmy.2_Intron|ARHGAP19_uc001kna.2_Intron|ARHGAP19_uc009xvi.2_Intron|ARHGAP19_uc009xvj.2_Intron|ARHGAP19_uc009xvk.2_Intron	NM_032900	NP_116289			Rho GTPase activating protein 19						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|nucleus	GTPase activator activity				0		Colorectal(252;0.0854)		Epithelial(162;7.65e-09)|all cancers(201;4.49e-07)														---	---	---	---
ARHGAP19	84986	broad.mit.edu	37	10	99011400	99011401	+	Intron	INS	-	AGG	AGG	rs143718626	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99011400_99011401insAGG	uc001knb.2	-						ARHGAP19_uc001kmy.2_Intron|ARHGAP19_uc001kna.2_Intron|ARHGAP19_uc009xvi.2_Intron|ARHGAP19_uc009xvj.2_Intron|ARHGAP19_uc009xvk.2_Intron	NM_032900	NP_116289			Rho GTPase activating protein 19						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|nucleus	GTPase activator activity				0		Colorectal(252;0.0854)		Epithelial(162;7.65e-09)|all cancers(201;4.49e-07)														---	---	---	---
ARHGAP19	84986	broad.mit.edu	37	10	99032522	99032522	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99032522delT	uc001knb.2	-						ARHGAP19_uc001kmy.2_Intron|ARHGAP19_uc001kna.2_5'Flank|ARHGAP19_uc009xvi.2_Intron|ARHGAP19_uc009xvj.2_Intron|ARHGAP19_uc009xvk.2_Intron	NM_032900	NP_116289			Rho GTPase activating protein 19						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|nucleus	GTPase activator activity				0		Colorectal(252;0.0854)		Epithelial(162;7.65e-09)|all cancers(201;4.49e-07)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	99071297	99071297	+	IGR	DEL	G	-	-	rs7914834	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99071297delG								ARHGAP19 (18884 upstream) : FRAT1 (7725 downstream)																																			---	---	---	---
FRAT1	10023	broad.mit.edu	37	10	99077737	99077738	+	5'Flank	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99077737_99077738insT	uc001knc.1	+							NM_005479	NP_005470			GSK-3 binding protein FRAT1						Wnt receptor signaling pathway	cytoplasm					0		Colorectal(252;0.0846)		Epithelial(162;2.76e-09)|all cancers(201;1.57e-07)														---	---	---	---
MMS19	64210	broad.mit.edu	37	10	99221731	99221731	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99221731delA	uc001kns.3	-						MMS19_uc001knq.2_5'Flank|MMS19_uc009xvs.2_Intron|MMS19_uc009xvt.2_Intron|MMS19_uc001knr.2_Intron|MMS19_uc010qox.1_Intron|MMS19_uc001knt.2_Intron|MMS19_uc001knu.1_Intron	NM_022362	NP_071757			MMS19 nucleotide excision repair homolog						chromosome segregation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|response to hormone stimulus|transcription, DNA-dependent|two-component signal transduction system (phosphorelay)	cytoplasm|holo TFIIH complex|MMXD complex	estrogen receptor binding|protein binding, bridging|receptor signaling complex scaffold activity|transcription coactivator activity				0		Colorectal(252;0.0846)		Epithelial(162;3.33e-10)|all cancers(201;2.74e-08)									Direct_reversal_of_damage|NER					---	---	---	---
UBTD1	80019	broad.mit.edu	37	10	99274805	99274805	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99274805delG	uc001knv.1	+							NM_024954	NP_079230			ubiquitin domain containing 1												0		Colorectal(252;0.162)		Epithelial(162;3.04e-10)|all cancers(201;2.86e-08)														---	---	---	---
UBTD1	80019	broad.mit.edu	37	10	99306658	99306659	+	Intron	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99306658_99306659delCT	uc001knv.1	+							NM_024954	NP_079230			ubiquitin domain containing 1												0		Colorectal(252;0.162)		Epithelial(162;3.04e-10)|all cancers(201;2.86e-08)														---	---	---	---
SFRP5	6425	broad.mit.edu	37	10	99530968	99530968	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99530968delG	uc001kor.3	-							NM_003015	NP_003006			secreted frizzled-related protein 5 precursor						apoptosis|brain development|cell differentiation|embryo development|establishment or maintenance of cell polarity|gonad development|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of cell proliferation|negative regulation of protein kinase B signaling cascade|negative regulation of sequence-specific DNA binding transcription factor activity|vasculature development|visual perception	cytoplasm|extracellular space|plasma membrane	PDZ domain binding|Wnt receptor activity|Wnt-protein binding			lung(1)	1		Colorectal(252;0.234)		Epithelial(162;4.98e-10)|all cancers(201;3.58e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	99577197	99577198	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99577197_99577198delTT								SFRP5 (45441 upstream) : GOLGA7B (32798 downstream)																																			---	---	---	---
HPSE2	60495	broad.mit.edu	37	10	100401358	100401359	+	Intron	INS	-	AA	AA	rs149789116	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100401358_100401359insAA	uc001kpn.1	-						HPSE2_uc009xwc.1_Intron|HPSE2_uc001kpo.1_Intron|HPSE2_uc009xwd.1_Intron	NM_021828	NP_068600			heparanase 2						carbohydrate metabolic process	intracellular|membrane	cation binding|heparanase activity			ovary(1)	1				Epithelial(162;1.8e-09)|all cancers(201;4.72e-07)														---	---	---	---
HPSE2	60495	broad.mit.edu	37	10	100522917	100522917	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100522917delT	uc001kpn.1	-						HPSE2_uc009xwc.1_Intron|HPSE2_uc001kpo.1_Intron|HPSE2_uc009xwd.1_Intron	NM_021828	NP_068600			heparanase 2						carbohydrate metabolic process	intracellular|membrane	cation binding|heparanase activity			ovary(1)	1				Epithelial(162;1.8e-09)|all cancers(201;4.72e-07)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	101224071	101224075	+	IGR	DEL	TTTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101224071_101224075delTTTTT								GOT1 (33541 upstream) : NKX2-3 (68615 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	101306692	101306693	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101306692_101306693delTT								NKX2-3 (10414 upstream) : SLC25A28 (63582 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	101633943	101633944	+	IGR	INS	-	T	T	rs149834824	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101633943_101633944insT								ABCC2 (22281 upstream) : DNMBP (1390 downstream)																																			---	---	---	---
ERLIN1	10613	broad.mit.edu	37	10	101916789	101916790	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101916789_101916790insA	uc001kqn.3	-						ERLIN1_uc001kqm.3_5'Flank|ERLIN1_uc001kqo.3_Intron|ERLIN1_uc010qpm.1_Intron	NM_006459	NP_006450			ER lipid raft associated 1						ER-associated protein catabolic process	endoplasmic reticulum membrane|integral to membrane	protein binding				0		Colorectal(252;0.234)		Epithelial(162;3.85e-10)|all cancers(201;3.25e-08)														---	---	---	---
SCD	6319	broad.mit.edu	37	10	102116733	102116733	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102116733delA	uc001kqy.2	+							NM_005063	NP_005054			stearoyl-CoA desaturase 1						fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	iron ion binding|stearoyl-CoA 9-desaturase activity				0		Colorectal(252;0.0323)		Epithelial(162;1.97e-10)|all cancers(201;1.73e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	102471287	102471287	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102471287delG								HIF1AN (157607 upstream) : PAX2 (34181 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	102597000	102597000	+	IGR	DEL	T	-	-	rs113959996		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102597000delT								PAX2 (7303 upstream) : FAM178A (75326 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	102628452	102628453	+	IGR	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102628452_102628453insC								PAX2 (38755 upstream) : FAM178A (43873 downstream)																																			---	---	---	---
FAM178A	55719	broad.mit.edu	37	10	102692450	102692457	+	Intron	DEL	GTGTGTGT	-	-	rs111530755		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102692450_102692457delGTGTGTGT	uc001krt.3	+						FAM178A_uc001krs.2_Intron	NM_018121	NP_060591			hypothetical protein LOC55719 isoform 1												0																		---	---	---	---
PDZD7	79955	broad.mit.edu	37	10	102777649	102777649	+	Intron	DEL	A	-	-	rs66819144		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102777649delA	uc001kso.1	-						PDZD7_uc001ksn.2_Intron	NM_024895	NP_079171			PDZ domain containing 7							cilium|nucleus	protein binding			ovary(1)|breast(1)|central_nervous_system(1)	3				Epithelial(162;6.98e-09)|all cancers(201;3.55e-07)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	102830390	102830390	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102830390delT								KAZALD1 (2504 upstream) : TLX1NB (18689 downstream)																																			---	---	---	---
LDB1	8861	broad.mit.edu	37	10	103875564	103875564	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103875564delT	uc009xwz.2	-						LDB1_uc001kuk.3_5'Flank|LDB1_uc001kul.3_5'Flank	NM_001113407	NP_001106878			LIM domain binding 1 isoform 1						histone H3-K4 acetylation|negative regulation of erythrocyte differentiation|negative regulation of transcription, DNA-dependent|positive regulation of hemoglobin biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription elongation, DNA-dependent|transcription, DNA-dependent|transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery	nuclear chromatin|protein complex	LIM domain binding|protein homodimerization activity|transcription corepressor activity			large_intestine(1)	1		Colorectal(252;0.122)		Epithelial(162;1.11e-07)|all cancers(201;1.82e-06)														---	---	---	---
GBF1	8729	broad.mit.edu	37	10	104016795	104016795	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104016795delA	uc001kux.1	+						GBF1_uc001kuw.2_Intron|GBF1_uc001kuy.1_Intron|GBF1_uc001kuz.1_Intron	NM_004193	NP_004184			golgi-specific brefeldin A resistant guanine						COPI coating of Golgi vesicle|post-Golgi vesicle-mediated transport|regulation of ARF protein signal transduction|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane	ARF guanyl-nucleotide exchange factor activity|protein binding			ovary(1)|central_nervous_system(1)	2		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)														---	---	---	---
ACTR1A	10121	broad.mit.edu	37	10	104245714	104245714	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104245714delC	uc001kvv.2	-						ACTR1A_uc010qqn.1_Intron|ACTR1A_uc010qqo.1_Intron	NM_005736	NP_005727			ARP1 actin-related protein 1 homolog A,						G2/M transition of mitotic cell cycle|vesicle-mediated transport	centrosome|cytosol|dynactin complex	ATP binding			central_nervous_system(1)	1		Colorectal(252;0.122)		Epithelial(162;5.34e-09)|all cancers(201;1.43e-07)|BRCA - Breast invasive adenocarcinoma(275;0.222)														---	---	---	---
SUFU	51684	broad.mit.edu	37	10	104300780	104300780	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104300780delA	uc001kvy.1	+						SUFU_uc001kvw.1_Intron|SUFU_uc001kvx.2_Intron	NM_016169	NP_057253			suppressor of fused						negative regulation of transcription from RNA polymerase II promoter|proteolysis|skeletal system development	cytoplasm|nucleus	identical protein binding|protein binding|signal transducer activity|transcription corepressor activity|transcription factor binding			central_nervous_system(4)|skin(2)|breast(1)	7		Colorectal(252;0.207)		Epithelial(162;1.36e-08)|all cancers(201;3.81e-07)|BRCA - Breast invasive adenocarcinoma(275;0.242)				D|F|S		medulloblastoma	medulloblastoma			Medulloblastoma_associated_with_Germline_SUFU_Mutation				---	---	---	---
SUFU	51684	broad.mit.edu	37	10	104312326	104312327	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104312326_104312327insA	uc001kvy.1	+						SUFU_uc001kvw.1_Intron|SUFU_uc001kvx.2_Intron	NM_016169	NP_057253			suppressor of fused						negative regulation of transcription from RNA polymerase II promoter|proteolysis|skeletal system development	cytoplasm|nucleus	identical protein binding|protein binding|signal transducer activity|transcription corepressor activity|transcription factor binding			central_nervous_system(4)|skin(2)|breast(1)	7		Colorectal(252;0.207)		Epithelial(162;1.36e-08)|all cancers(201;3.81e-07)|BRCA - Breast invasive adenocarcinoma(275;0.242)				D|F|S		medulloblastoma	medulloblastoma			Medulloblastoma_associated_with_Germline_SUFU_Mutation				---	---	---	---
SUFU	51684	broad.mit.edu	37	10	104376500	104376500	+	Intron	DEL	T	-	-	rs74931282		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104376500delT	uc001kvy.1	+						SUFU_uc001kvw.1_Intron|SUFU_uc001kvx.2_Intron|SUFU_uc009xxe.1_Intron|SUFU_uc009xxf.1_Intron	NM_016169	NP_057253			suppressor of fused						negative regulation of transcription from RNA polymerase II promoter|proteolysis|skeletal system development	cytoplasm|nucleus	identical protein binding|protein binding|signal transducer activity|transcription corepressor activity|transcription factor binding			central_nervous_system(4)|skin(2)|breast(1)	7		Colorectal(252;0.207)		Epithelial(162;1.36e-08)|all cancers(201;3.81e-07)|BRCA - Breast invasive adenocarcinoma(275;0.242)				D|F|S		medulloblastoma	medulloblastoma			Medulloblastoma_associated_with_Germline_SUFU_Mutation				---	---	---	---
C10orf26	54838	broad.mit.edu	37	10	104565804	104565805	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104565804_104565805delAA	uc001kwe.3	+						C10orf26_uc001kwf.3_Intron|C10orf26_uc009xxg.1_Intron	NM_017787	NP_060257			hypothetical protein LOC54838 isoform 2							integral to membrane				central_nervous_system(1)	1		Colorectal(252;0.122)|all_hematologic(284;0.152)		Epithelial(162;6.14e-09)|all cancers(201;1.66e-07)|BRCA - Breast invasive adenocarcinoma(275;0.224)														---	---	---	---
AS3MT	57412	broad.mit.edu	37	10	104636524	104636524	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104636524delA	uc001kwk.2	+						AS3MT_uc001kwj.2_Intron|AS3MT_uc009xxh.2_Intron	NM_020682	NP_065733			arsenic (+3 oxidation state) methyltransferase						arsonoacetate metabolic process|toxin metabolic process	cytosol	arsenite methyltransferase activity|methylarsonite methyltransferase activity				0		Colorectal(252;0.122)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;5.87e-09)|all cancers(201;1.58e-07)|BRCA - Breast invasive adenocarcinoma(275;0.223)														---	---	---	---
CNNM2	54805	broad.mit.edu	37	10	104691967	104691967	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104691967delT	uc001kwm.2	+						CNNM2_uc001kwn.2_Intron	NM_017649	NP_060119			cyclin M2 isoform 1						ion transport	integral to membrane				ovary(1)|central_nervous_system(1)	2		Colorectal(252;0.103)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;7.89e-09)|all cancers(201;1.82e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)														---	---	---	---
NT5C2	22978	broad.mit.edu	37	10	104867429	104867430	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104867429_104867430delAA	uc001kwo.2	-						NT5C2_uc010qqp.1_Intron|NT5C2_uc001kwq.2_Intron|NT5C2_uc001kwp.2_Intron	NM_012229	NP_036361			5'-nucleotidase, cytosolic II						purine base metabolic process|purine nucleotide catabolic process	cytosol	5'-nucleotidase activity|metal ion binding|nucleotide binding|protein binding				0		all_hematologic(284;0.176)|Colorectal(252;0.178)		Epithelial(162;1.33e-08)|all cancers(201;1.04e-07)|BRCA - Breast invasive adenocarcinoma(275;0.159)	Adenosine triphosphate(DB00171)|Ribavirin(DB00811)													---	---	---	---
NT5C2	22978	broad.mit.edu	37	10	104940481	104940481	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104940481delA	uc001kwo.2	-						NT5C2_uc001kwq.2_Intron|NT5C2_uc001kwp.2_Intron	NM_012229	NP_036361			5'-nucleotidase, cytosolic II						purine base metabolic process|purine nucleotide catabolic process	cytosol	5'-nucleotidase activity|metal ion binding|nucleotide binding|protein binding				0		all_hematologic(284;0.176)|Colorectal(252;0.178)		Epithelial(162;1.33e-08)|all cancers(201;1.04e-07)|BRCA - Breast invasive adenocarcinoma(275;0.159)	Adenosine triphosphate(DB00171)|Ribavirin(DB00811)													---	---	---	---
CALHM2	51063	broad.mit.edu	37	10	105208932	105208934	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105208932_105208934delAAA	uc001kwz.2	-						CALHM2_uc001kxa.2_Intron|CALHM2_uc001kxc.2_Intron|CALHM2_uc001kxb.2_Intron|CALHM2_uc001kxd.1_3'UTR	NM_015916	NP_057000			calcium homeostasis modulator 2							integral to membrane				skin(1)	1																		---	---	---	---
CALHM2	51063	broad.mit.edu	37	10	105211400	105211402	+	5'Flank	DEL	AGG	-	-	rs3837347		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105211400_105211402delAGG	uc001kwz.2	-						CALHM2_uc001kxa.2_Intron|CALHM2_uc001kxc.2_Intron|CALHM2_uc001kxb.2_Intron|CALHM2_uc001kxd.1_Intron	NM_015916	NP_057000			calcium homeostasis modulator 2							integral to membrane				skin(1)	1																		---	---	---	---
C10orf79	80217	broad.mit.edu	37	10	105915375	105915375	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105915375delA	uc001kxw.2	-						C10orf79_uc009xxq.2_Intron	NM_025145	NP_079421			hypothetical protein LOC80217												0		Colorectal(252;0.178)		Epithelial(162;4.83e-10)|all cancers(201;2.26e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0194)														---	---	---	---
GSTO1	9446	broad.mit.edu	37	10	106020762	106020762	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106020762delA	uc001kya.2	+							NM_004832	NP_004823			glutathione-S-transferase omega 1						xenobiotic metabolic process	cytosol	glutathione transferase activity|monodehydroascorbate reductase (NADH) activity				0		Colorectal(252;0.102)|Breast(234;0.122)		Epithelial(162;8.07e-10)|all cancers(201;2.72e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0147)	Glutathione(DB00143)													---	---	---	---
CCDC147	159686	broad.mit.edu	37	10	106166264	106166264	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106166264delT	uc001kyh.2	+							NM_001008723	NP_001008723			coiled-coil domain containing 147											ovary(2)|central_nervous_system(2)|skin(1)	5		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;7.55e-10)|all cancers(201;3.37e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0189)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	106375807	106375807	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106375807delT								CCDC147 (160968 upstream) : SORCS3 (25052 downstream)																																			---	---	---	---
SORCS3	22986	broad.mit.edu	37	10	106614633	106614634	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106614633_106614634insT	uc001kyi.1	+							NM_014978	NP_055793			VPS10 domain receptor protein SORCS 3 precursor							integral to membrane	neuropeptide receptor activity			ovary(6)|skin(3)|central_nervous_system(1)	10		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)														---	---	---	---
SORCS3	22986	broad.mit.edu	37	10	106845752	106845752	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106845752delT	uc001kyi.1	+							NM_014978	NP_055793			VPS10 domain receptor protein SORCS 3 precursor							integral to membrane	neuropeptide receptor activity			ovary(6)|skin(3)|central_nervous_system(1)	10		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	107085694	107085694	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107085694delG								SORCS3 (60701 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	107363968	107363969	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107363968_107363969insA								SORCS3 (338975 upstream) : SORCS1 (969453 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	107662862	107662862	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107662862delT								SORCS3 (637869 upstream) : SORCS1 (670560 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	107675187	107675187	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107675187delT								SORCS3 (650194 upstream) : SORCS1 (658235 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	107757618	107757619	+	IGR	DEL	TG	-	-	rs61875571		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:107757618_107757619delTG								SORCS3 (732625 upstream) : SORCS1 (575803 downstream)																																			---	---	---	---
SORCS1	114815	broad.mit.edu	37	10	108359126	108359127	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108359126_108359127delAA	uc001kym.2	-						SORCS1_uc001kyl.2_Intron|SORCS1_uc009xxs.2_Intron|SORCS1_uc001kyn.1_Intron|SORCS1_uc001kyo.2_Intron	NM_052918	NP_443150			SORCS receptor 1 isoform a							integral to membrane	neuropeptide receptor activity|protein binding			breast(1)|central_nervous_system(1)	2		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)														---	---	---	---
SORCS1	114815	broad.mit.edu	37	10	108434955	108434955	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108434955delA	uc001kym.2	-						SORCS1_uc001kyl.2_Intron|SORCS1_uc009xxs.2_Intron|SORCS1_uc001kyn.1_Intron|SORCS1_uc001kyo.2_Intron	NM_052918	NP_443150			SORCS receptor 1 isoform a							integral to membrane	neuropeptide receptor activity|protein binding			breast(1)|central_nervous_system(1)	2		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)														---	---	---	---
SORCS1	114815	broad.mit.edu	37	10	108697095	108697097	+	Intron	DEL	TTT	-	-	rs111634393		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108697095_108697097delTTT	uc001kym.2	-						SORCS1_uc001kyl.2_Intron|SORCS1_uc009xxs.2_Intron|SORCS1_uc001kyn.1_Intron|SORCS1_uc001kyo.2_Intron	NM_052918	NP_443150			SORCS receptor 1 isoform a							integral to membrane	neuropeptide receptor activity|protein binding			breast(1)|central_nervous_system(1)	2		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)														---	---	---	---
SORCS1	114815	broad.mit.edu	37	10	108867796	108867796	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108867796delG	uc001kym.2	-						SORCS1_uc001kyl.2_Intron|SORCS1_uc009xxs.2_Intron|SORCS1_uc001kyn.1_Intron|SORCS1_uc001kyo.2_Intron	NM_052918	NP_443150			SORCS receptor 1 isoform a							integral to membrane	neuropeptide receptor activity|protein binding			breast(1)|central_nervous_system(1)	2		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	108950360	108950360	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108950360delA								SORCS1 (26068 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	109142533	109142533	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:109142533delT								SORCS1 (218241 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	109395577	109395577	+	IGR	DEL	C	-	-	rs7917678	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:109395577delC								SORCS1 (471285 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	109663907	109663907	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:109663907delA								SORCS1 (739615 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	109813948	109813949	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:109813948_109813949delAA								SORCS1 (889656 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	110139468	110139468	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:110139468delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	110776457	110776457	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:110776457delT								None (None upstream) : XPNPEP1 (848067 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	111088311	111088312	+	IGR	DEL	TT	-	-	rs74374455		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111088311_111088312delTT								None (None upstream) : XPNPEP1 (536212 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	111221065	111221065	+	IGR	DEL	T	-	-	rs77293495		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111221065delT								None (None upstream) : XPNPEP1 (403459 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	111236575	111236575	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111236575delT								None (None upstream) : XPNPEP1 (387949 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	111266630	111266631	+	IGR	INS	-	AC	AC	rs34175167		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111266630_111266631insAC								None (None upstream) : XPNPEP1 (357893 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	111694120	111694144	+	IGR	DEL	CAGGCCAACAGATCCTGTTGGATCC	-	-	rs6144086		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111694120_111694144delCAGGCCAACAGATCCTGTTGGATCC								XPNPEP1 (10918 upstream) : ADD3 (61964 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	111747526	111747526	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111747526delA	uc001kyr.1	-											Homo sapiens mRNA; cDNA DKFZp686J1229 (from clone DKFZp686J1229).																														---	---	---	---
ADD3	120	broad.mit.edu	37	10	111837053	111837053	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111837053delT	uc001kyt.3	+						ADD3_uc001kys.3_Intron|ADD3_uc001kyu.2_Intron|ADD3_uc001kyv.2_Intron|ADD3_uc001kyw.2_Intron	NM_016824	NP_058432			adducin 3 (gamma) isoform a							cytoskeleton	actin binding|calmodulin binding|metal ion binding|structural constituent of cytoskeleton			ovary(2)|skin(2)|large_intestine(1)	5		Breast(234;0.052)|Lung NSC(174;0.223)		Epithelial(162;4.15e-05)|all cancers(201;0.000587)|BRCA - Breast invasive adenocarcinoma(275;0.0742)														---	---	---	---
ADD3	120	broad.mit.edu	37	10	111874461	111874462	+	Intron	DEL	GT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111874461_111874462delGT	uc001kyt.3	+						ADD3_uc001kys.3_Intron|ADD3_uc001kyu.2_Intron|ADD3_uc001kyv.2_Intron|ADD3_uc001kyw.2_Intron	NM_016824	NP_058432			adducin 3 (gamma) isoform a							cytoskeleton	actin binding|calmodulin binding|metal ion binding|structural constituent of cytoskeleton			ovary(2)|skin(2)|large_intestine(1)	5		Breast(234;0.052)|Lung NSC(174;0.223)		Epithelial(162;4.15e-05)|all cancers(201;0.000587)|BRCA - Breast invasive adenocarcinoma(275;0.0742)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	111917345	111917345	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:111917345delA								ADD3 (22025 upstream) : MXI1 (50018 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	112163770	112163771	+	IGR	INS	-	C	C	rs113622346	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112163770_112163771insC								SMNDC1 (99063 upstream) : DUSP5 (93854 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	112242175	112242175	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112242175delT								SMNDC1 (177468 upstream) : DUSP5 (15450 downstream)																																			---	---	---	---
SMC3	9126	broad.mit.edu	37	10	112337260	112337260	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112337260delT	uc001kze.2	+							NM_005445	NP_005436			structural maintenance of chromosomes 3						cell division|DNA mediated transformation|DNA repair|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|mitotic spindle organization|negative regulation of DNA endoreduplication|signal transduction|sister chromatid cohesion	basement membrane|chromatin|chromosome, centromeric region|cytoplasm|meiotic cohesin complex|nuclear matrix|nucleoplasm|spindle pole	ATP binding|dynein binding|microtubule motor activity|protein heterodimerization activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.00206)|all cancers(201;0.0227)|BRCA - Breast invasive adenocarcinoma(275;0.127)														---	---	---	---
SMC3	9126	broad.mit.edu	37	10	112343399	112343399	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112343399delT	uc001kze.2	+							NM_005445	NP_005436			structural maintenance of chromosomes 3						cell division|DNA mediated transformation|DNA repair|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|mitotic spindle organization|negative regulation of DNA endoreduplication|signal transduction|sister chromatid cohesion	basement membrane|chromatin|chromosome, centromeric region|cytoplasm|meiotic cohesin complex|nuclear matrix|nucleoplasm|spindle pole	ATP binding|dynein binding|microtubule motor activity|protein heterodimerization activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.00206)|all cancers(201;0.0227)|BRCA - Breast invasive adenocarcinoma(275;0.127)														---	---	---	---
RBM20	282996	broad.mit.edu	37	10	112445558	112445558	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112445558delT	uc001kzf.2	+							NM_001134363	NP_001127835			RNA binding motif protein 20							nucleus	nucleotide binding|RNA binding|zinc ion binding				0																		---	---	---	---
RBM20	282996	broad.mit.edu	37	10	112540475	112540475	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112540475delG	uc001kzf.2	+							NM_001134363	NP_001127835			RNA binding motif protein 20							nucleus	nucleotide binding|RNA binding|zinc ion binding				0																		---	---	---	---
PDCD4	27250	broad.mit.edu	37	10	112657654	112657655	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112657654_112657655delTT	uc001kzh.2	+						PDCD4_uc001kzg.2_Intron|PDCD4_uc010qre.1_Intron	NM_014456	NP_055271			programmed cell death 4 isoform 1						apoptosis|cell aging|negative regulation of cell cycle|negative regulation of JUN kinase activity|negative regulation of transcription, DNA-dependent	cytosol|nucleus	protein binding|RNA binding			ovary(1)|breast(1)|skin(1)	3		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.000526)|all cancers(201;0.00794)|BRCA - Breast invasive adenocarcinoma(275;0.125)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	113030433	113030433	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113030433delT								ADRA2A (189773 upstream) : GPAM (879189 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	113649662	113649662	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113649662delA								ADRA2A (809002 upstream) : GPAM (259960 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	113686838	113686839	+	IGR	DEL	AA	-	-	rs113482022		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113686838_113686839delAA								ADRA2A (846178 upstream) : GPAM (222783 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	113887231	113887232	+	IGR	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:113887231_113887232delTC								None (None upstream) : GPAM (22390 downstream)																																			---	---	---	---
GUCY2GP	390003	broad.mit.edu	37	10	114095987	114095987	+	Intron	DEL	A	-	-	rs117871930	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114095987delA	uc010qri.1	-							NR_028134				Homo sapiens guanylate cyclase 2G homolog (mouse) pseudogene (GUCY2G), non-coding RNA, 611.												0																		---	---	---	---
VTI1A	143187	broad.mit.edu	37	10	114436150	114436150	+	Intron	DEL	G	-	-	rs117161620	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114436150delG	uc001kzy.2	+						VTI1A_uc001kzz.2_Intron	NM_145206	NP_660207			SNARE Vti1a-beta protein						intracellular protein transport|retrograde transport, endosome to Golgi	SNARE complex	protein transporter activity|SNAP receptor activity			ovary(1)	1		Colorectal(252;0.0314)|Breast(234;0.183)		Epithelial(162;0.0126)|all cancers(201;0.0487)														---	---	---	---
VTI1A	143187	broad.mit.edu	37	10	114547046	114547046	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114547046delT	uc001kzz.2	+							NM_145206	NP_660207			SNARE Vti1a-beta protein						intracellular protein transport|retrograde transport, endosome to Golgi	SNARE complex	protein transporter activity|SNAP receptor activity			ovary(1)	1		Colorectal(252;0.0314)|Breast(234;0.183)		Epithelial(162;0.0126)|all cancers(201;0.0487)														---	---	---	---
TCF7L2	6934	broad.mit.edu	37	10	114744074	114744074	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114744074delT	uc001lae.3	+						TCF7L2_uc001lac.3_Intron|TCF7L2_uc010qrk.1_Intron|TCF7L2_uc010qrl.1_Intron|TCF7L2_uc010qrm.1_Intron|TCF7L2_uc010qrn.1_Intron|TCF7L2_uc001lad.3_Intron|TCF7L2_uc001lag.3_Intron|TCF7L2_uc001laf.3_Intron|TCF7L2_uc010qro.1_Intron|TCF7L2_uc001lah.2_Intron|TCF7L2_uc010qrp.1_Intron|TCF7L2_uc010qrq.1_Intron|TCF7L2_uc010qrr.1_Intron|TCF7L2_uc010qrs.1_Intron|TCF7L2_uc010qrt.1_Intron	NM_001146274	NP_001139746			transcription factor 7-like 2 isoform 1						anti-apoptosis|blood vessel development|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell cycle arrest|cell proliferation|fat cell differentiation|glucose homeostasis|maintenance of DNA repeat elements|myoblast cell fate commitment|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|pancreas development|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of insulin secretion|positive regulation of protein binding|positive regulation of protein export from nucleus|positive regulation of protein kinase B signaling cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of hormone metabolic process|regulation of smooth muscle cell proliferation|response to glucose stimulus	beta-catenin-TCF7L2 complex|PML body|protein-DNA complex	armadillo repeat domain binding|beta-catenin binding|gamma-catenin binding|nuclear hormone receptor binding|protein kinase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			large_intestine(3)|ovary(1)	4		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)														---	---	---	---
TCF7L2	6934	broad.mit.edu	37	10	114918647	114918647	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114918647delT	uc001lae.3	+						TCF7L2_uc001lac.3_Intron|TCF7L2_uc010qrk.1_Intron|TCF7L2_uc010qrl.1_Intron|TCF7L2_uc010qrm.1_Intron|TCF7L2_uc010qrn.1_Intron|TCF7L2_uc001lad.3_Intron|TCF7L2_uc001lag.3_Intron|TCF7L2_uc001laf.3_Intron|TCF7L2_uc010qro.1_Intron|TCF7L2_uc001lah.2_Intron|TCF7L2_uc010qrp.1_Intron|TCF7L2_uc010qrq.1_Intron|TCF7L2_uc010qrr.1_Intron|TCF7L2_uc010qrs.1_Intron|TCF7L2_uc010qrt.1_Intron|TCF7L2_uc010qru.1_Intron|TCF7L2_uc010qrv.1_Intron|TCF7L2_uc010qrw.1_Intron|TCF7L2_uc010qrx.1_Intron	NM_001146274	NP_001139746			transcription factor 7-like 2 isoform 1						anti-apoptosis|blood vessel development|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell cycle arrest|cell proliferation|fat cell differentiation|glucose homeostasis|maintenance of DNA repeat elements|myoblast cell fate commitment|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|pancreas development|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of insulin secretion|positive regulation of protein binding|positive regulation of protein export from nucleus|positive regulation of protein kinase B signaling cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of hormone metabolic process|regulation of smooth muscle cell proliferation|response to glucose stimulus	beta-catenin-TCF7L2 complex|PML body|protein-DNA complex	armadillo repeat domain binding|beta-catenin binding|gamma-catenin binding|nuclear hormone receptor binding|protein kinase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			large_intestine(3)|ovary(1)	4		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	115033146	115033146	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115033146delC								TCF7L2 (105712 upstream) : HABP2 (279632 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	115175706	115175707	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115175706_115175707insA								TCF7L2 (248272 upstream) : HABP2 (137071 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	115232273	115232273	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115232273delT								TCF7L2 (304839 upstream) : HABP2 (80505 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	115283376	115283376	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115283376delT								TCF7L2 (355942 upstream) : HABP2 (29402 downstream)																																			---	---	---	---
NRAP	4892	broad.mit.edu	37	10	115351797	115351797	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115351797delT	uc001laj.2	-						NRAP_uc009xyb.2_Intron|NRAP_uc001lak.2_Intron|NRAP_uc001lal.3_Intron	NM_198060	NP_932326			nebulin-related anchoring protein isoform S							fascia adherens|muscle tendon junction	actin binding|muscle alpha-actinin binding|zinc ion binding			ovary(6)|central_nervous_system(3)|upper_aerodigestive_tract(1)	10		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)														---	---	---	---
DCLRE1A	9937	broad.mit.edu	37	10	115597121	115597121	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115597121delA	uc001law.2	-							NM_014881	NP_055696			DNA cross-link repair 1A						cell division|mitosis	nucleus	hydrolase activity			skin(2)	2				Epithelial(162;0.0157)|all cancers(201;0.0171)									Direct_reversal_of_damage|Other_identified_genes_with_known_or_suspected_DNA_repair_function					---	---	---	---
NHLRC2	374354	broad.mit.edu	37	10	115639931	115639931	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115639931delA	uc001lax.1	+							NM_198514	NP_940916			NHL repeat containing 2						cell redox homeostasis					ovary(1)	1				Epithelial(162;0.017)|all cancers(201;0.0187)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	115788394	115788395	+	IGR	INS	-	GT	GT	rs143519191	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115788394_115788395insGT								NHLRC2 (119942 upstream) : ADRB1 (15411 downstream)																																			---	---	---	---
ADRB1	153	broad.mit.edu	37	10	115802574	115802574	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115802574delT	uc001lba.2	+							NM_000684	NP_000675			beta-1-adrenergic receptor						positive regulation of cAMP biosynthetic process	integral to plasma membrane	alpha-2A adrenergic receptor binding|beta1-adrenergic receptor activity|protein heterodimerization activity				0		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0124)|all cancers(201;0.0298)	Acebutolol(DB01193)|Alprenolol(DB00866)|Amiodarone(DB01118)|Arbutamine(DB01102)|Atenolol(DB00335)|Betaxolol(DB00195)|Bevantolol(DB01295)|Bisoprolol(DB00612)|Bretylium(DB01158)|Carteolol(DB00521)|Carvedilol(DB01136)|Desipramine(DB01151)|Dobutamine(DB00841)|Dopamine(DB00988)|Epinephrine(DB00668)|Esmolol(DB00187)|Isoetharine(DB00221)|Isoproterenol(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Metipranolol(DB01214)|Metoprolol(DB00264)|Nadolol(DB01203)|Norepinephrine(DB00368)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Pindolol(DB00960)|Practolol(DB01297)|Propranolol(DB00571)|Risperidone(DB00734)|Timolol(DB00373)|Ziprasidone(DB00246)													---	---	---	---
TDRD1	56165	broad.mit.edu	37	10	115947355	115947355	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115947355delT	uc001lbg.1	+						TDRD1_uc001lbf.2_Intron|TDRD1_uc001lbh.1_Intron|TDRD1_uc001lbi.1_Intron	NM_198795	NP_942090			tudor domain containing 1						DNA methylation involved in gamete generation|gene silencing by RNA|germ cell development|meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	pi-body	nucleic acid binding|protein binding|zinc ion binding				0		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0343)|all cancers(201;0.0754)														---	---	---	---
VWA2	340706	broad.mit.edu	37	10	116007423	116007423	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116007423delA	uc001lbl.1	+						VWA2_uc001lbk.1_Intron|VWA2_uc009xyf.1_Intron	NM_198496	NP_940898			von Willebrand factor A domain containing 2							extracellular region				ovary(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5				Epithelial(162;0.036)|all cancers(201;0.0793)														---	---	---	---
VWA2	340706	broad.mit.edu	37	10	116026060	116026060	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116026060delA	uc001lbl.1	+						VWA2_uc001lbk.1_Intron|VWA2_uc009xyf.1_Intron	NM_198496	NP_940898			von Willebrand factor A domain containing 2							extracellular region				ovary(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5				Epithelial(162;0.036)|all cancers(201;0.0793)														---	---	---	---
AFAP1L2	84632	broad.mit.edu	37	10	116134433	116134433	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116134433delA	uc001lbn.2	-						AFAP1L2_uc001lbo.2_Intron|AFAP1L2_uc010qse.1_Intron|AFAP1L2_uc001lbp.2_Intron|AFAP1L2_uc001lbr.1_Intron	NM_001001936	NP_001001936			KIAA1914 protein isoform 1						inflammatory response|positive regulation of epidermal growth factor receptor signaling pathway|positive regulation of interleukin-8 production|positive regulation of transcription, DNA-dependent|regulation of interleukin-6 production|regulation of mitotic cell cycle	cytoplasm	protein tyrosine kinase activator activity|SH2 domain binding|SH3 domain binding			ovary(1)|breast(1)	2		Colorectal(252;0.175)|Breast(234;0.231)		Epithelial(162;0.0219)|all cancers(201;0.0561)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	116172189	116172189	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116172189delC								AFAP1L2 (7674 upstream) : ABLIM1 (18681 downstream)																																			---	---	---	---
ATRNL1	26033	broad.mit.edu	37	10	117024646	117024647	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:117024646_117024647insT	uc001lcg.2	+							NM_207303	NP_997186			attractin-like 1 precursor							integral to membrane	sugar binding			ovary(5)|lung(1)|central_nervous_system(1)	7		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)														---	---	---	---
GFRA1	2674	broad.mit.edu	37	10	117845201	117845201	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:117845201delC	uc001lcj.2	-						GFRA1_uc001lci.2_Intron|GFRA1_uc009xyr.2_Intron	NM_005264	NP_005255			GDNF family receptor alpha 1 isoform a						axon guidance	anchored to membrane|extrinsic to membrane|plasma membrane	glial cell-derived neurotrophic factor receptor activity			ovary(1)|pancreas(1)	2		Lung NSC(174;0.21)		all cancers(201;0.0337)														---	---	---	---
GFRA1	2674	broad.mit.edu	37	10	117922319	117922319	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:117922319delA	uc001lcj.2	-						GFRA1_uc001lci.2_Intron|GFRA1_uc009xyr.2_Intron	NM_005264	NP_005255			GDNF family receptor alpha 1 isoform a						axon guidance	anchored to membrane|extrinsic to membrane|plasma membrane	glial cell-derived neurotrophic factor receptor activity			ovary(1)|pancreas(1)	2		Lung NSC(174;0.21)		all cancers(201;0.0337)														---	---	---	---
GFRA1	2674	broad.mit.edu	37	10	118012469	118012469	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118012469delC	uc001lcj.2	-						GFRA1_uc001lci.2_Intron|GFRA1_uc009xyr.2_Intron	NM_005264	NP_005255			GDNF family receptor alpha 1 isoform a						axon guidance	anchored to membrane|extrinsic to membrane|plasma membrane	glial cell-derived neurotrophic factor receptor activity			ovary(1)|pancreas(1)	2		Lung NSC(174;0.21)		all cancers(201;0.0337)														---	---	---	---
C10orf96	374355	broad.mit.edu	37	10	118115869	118115869	+	Intron	DEL	G	-	-	rs79499888		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118115869delG	uc001lck.2	+							NM_198515	NP_940917			hypothetical protein LOC374355											ovary(2)	2		Lung NSC(174;0.204)|all_lung(145;0.248)		all cancers(201;0.014)														---	---	---	---
KIAA1598	57698	broad.mit.edu	37	10	118667519	118667519	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118667519delA	uc009xyw.2	-						KIAA1598_uc001lcz.3_Intron|KIAA1598_uc010qso.1_Intron|KIAA1598_uc010qsp.1_Intron|KIAA1598_uc010qsq.1_Intron|KIAA1598_uc001lcy.3_Intron	NM_001127211	NP_001120683			shootin1 isoform a						axon guidance	axon					0				all cancers(201;0.00494)														---	---	---	---
KIAA1598	57698	broad.mit.edu	37	10	118719752	118719752	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118719752delG	uc009xyw.2	-						KIAA1598_uc001lcz.3_Intron|KIAA1598_uc010qso.1_Intron|KIAA1598_uc010qsp.1_Intron|KIAA1598_uc010qsq.1_Intron|KIAA1598_uc001lcy.3_Intron	NM_001127211	NP_001120683			shootin1 isoform a						axon guidance	axon					0				all cancers(201;0.00494)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	118914950	118914950	+	IGR	DEL	A	-	-	rs77268158		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118914950delA								VAX1 (17138 upstream) : KCNK18 (42050 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	118930283	118930283	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118930283delT								VAX1 (32471 upstream) : KCNK18 (26717 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	119153812	119153812	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119153812delT								PDZD8 (18875 upstream) : EMX2OS (89993 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	119422191	119422191	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119422191delT								EMX2 (113135 upstream) : RAB11FIP2 (342238 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	119450791	119450791	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:119450791delT								EMX2 (141735 upstream) : RAB11FIP2 (313638 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	120207687	120207687	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120207687delT								C10orf84 (105848 upstream) : PRLHR (145229 downstream)																																			---	---	---	---
C10orf46	143384	broad.mit.edu	37	10	120445798	120445798	+	Intron	DEL	A	-	-	rs34771788		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120445798delA	uc001lds.1	-						C10orf46_uc010qst.1_Intron	NM_153810	NP_722517			chromosome 10 open reading frame 46						ubiquitin-dependent protein catabolic process	cullin-RING ubiquitin ligase complex	ubiquitin protein ligase binding				0		Lung NSC(174;0.142)|all_lung(145;0.175)		all cancers(201;0.0131)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	120615058	120615058	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120615058delT								C10orf46 (100300 upstream) : NANOS1 (174170 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	120629248	120629248	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120629248delA								C10orf46 (114490 upstream) : NANOS1 (159980 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	120755902	120755902	+	IGR	DEL	T	-	-	rs149830140		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120755902delT								C10orf46 (241144 upstream) : NANOS1 (33326 downstream)																																			---	---	---	---
EIF3A	8661	broad.mit.edu	37	10	120842995	120842995	+	5'Flank	DEL	A	-	-	rs76210818		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120842995delA	uc001ldu.2	-						EIF3A_uc010qsu.1_5'Flank	NM_003750	NP_003741			eukaryotic translation initiation factor 3,						formation of translation initiation complex	cytosol|eukaryotic translation initiation factor 3 complex	protein binding|structural molecule activity|translation initiation factor activity				0		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0236)														---	---	---	---
SFXN4	119559	broad.mit.edu	37	10	120920633	120920633	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120920633delT	uc001leb.2	-						SFXN4_uc001ldy.2_5'UTR|SFXN4_uc001ldz.2_Intron|SFXN4_uc001lea.2_Intron	NM_213649	NP_998814			sideroflexin 4						iron ion homeostasis	integral to membrane|mitochondrial membrane	cation transmembrane transporter activity			ovary(1)	1		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0261)														---	---	---	---
TIAL1	7073	broad.mit.edu	37	10	121347864	121347864	+	Intron	DEL	T	-	-	rs58919083		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121347864delT	uc001lei.1	-						TIAL1_uc001leh.1_Intron|TIAL1_uc001lej.1_Intron|TIAL1_uc001lek.1_Intron|TIAL1_uc009xzi.1_Intron|TIAL1_uc010qtb.1_Intron	NM_003252	NP_003243			TIA-1 related protein isoform 1						apoptosis|defense response|induction of apoptosis|regulation of transcription from RNA polymerase II promoter	lysosome|nucleus|stress granule	nucleotide binding|RNA binding			ovary(1)	1		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.00239)|BRCA - Breast invasive adenocarcinoma(275;0.0932)														---	---	---	---
INPP5F	22876	broad.mit.edu	37	10	121502775	121502775	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121502775delC	uc001leo.2	+						INPP5F_uc001len.3_Intron	NM_014937	NP_055752			inositol polyphosphate-5-phosphatase F								phosphoric ester hydrolase activity			ovary(2)	2		Lung NSC(174;0.109)|all_lung(145;0.142)		all cancers(201;0.00205)|BRCA - Breast invasive adenocarcinoma(275;0.158)														---	---	---	---
WDR11	55717	broad.mit.edu	37	10	122640428	122640428	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122640428delA	uc010qtf.1	+						WDR11_uc010qte.1_Intron|WDR11_uc001lfd.1_Intron	NM_018117	NP_060587			bromodomain and WD repeat domain containing 2							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	122872188	122872188	+	IGR	DEL	T	-	-	rs71959509		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:122872188delT								WDR11 (203153 upstream) : FGFR2 (365657 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	123698422	123698423	+	IGR	INS	-	T	T	rs150894967	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123698422_123698423insT								ATE1 (10205 upstream) : NSMCE4A (18186 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	124121697	124121698	+	IGR	INS	-	G	G	rs144076775	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124121697_124121698insG								BTBD16 (24021 upstream) : PLEKHA1 (12522 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	124561845	124561845	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124561845delC								FLJ46361 (4684 upstream) : CUZD1 (29830 downstream)																																			---	---	---	---
CUZD1	50624	broad.mit.edu	37	10	124625428	124625430	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124625428_124625430delTTT	uc010qtz.1	-						FAM24B_uc001lgt.2_Intron|LOC399815_uc001lgu.3_Intron	NM_022034	NP_071317			CUB and zona pellucida-like domains 1 precursor						cell cycle|cell division|cell proliferation|substrate-dependent cell migration, cell attachment to substrate|trypsinogen activation	integral to membrane|transport vesicle membrane|zymogen granule membrane				ovary(1)|skin(1)	2		all_neural(114;0.169)|Glioma(114;0.222)		Colorectal(40;0.126)|COAD - Colon adenocarcinoma(40;0.141)														---	---	---	---
BUB3	9184	broad.mit.edu	37	10	124917510	124917510	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124917510delA	uc001lhe.2	+						BUB3_uc009yah.2_Intron|BUB3_uc001lhf.3_Intron|BUB3_uc001lhd.2_Intron|BUB3_uc010qud.1_Intron	NM_004725	NP_004716			budding uninhibited by benzimidazoles 3 isoform						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|attachment of spindle microtubules to kinetochore|cell division|meiosis|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle	condensed chromosome kinetochore|cytosol|nucleus	protein binding			ovary(1)	1		all_neural(114;0.0765)|Colorectal(57;0.102)|all_lung(145;0.11)|Lung NSC(174;0.163)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	125061204	125061204	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125061204delA								BUB3 (136318 upstream) : GPR26 (364667 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	125218488	125218488	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125218488delG	uc001lhg.1	+											full-length cDNA clone CS0DD008YJ14 of Neuroblastoma Cot 50-normalized of Homo sapiens (human).																														---	---	---	---
CPXM2	119587	broad.mit.edu	37	10	125519891	125519891	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125519891delT	uc001lhk.1	-						CPXM2_uc001lhj.2_Intron	NM_198148	NP_937791			carboxypeptidase X (M14 family), member 2						cell adhesion|proteolysis	extracellular space	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.212)|Colorectal(40;0.237)														---	---	---	---
LHPP	64077	broad.mit.edu	37	10	126293892	126293892	+	Intron	DEL	G	-	-	rs3832702		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126293892delG	uc001lhs.1	+						LHPP_uc001lht.1_Intron|LHPP_uc009yai.1_Intron|LHPP_uc009yaj.1_RNA	NM_022126	NP_071409			phospholysine phosphohistidine inorganic						protein dephosphorylation	cytosol|nucleus	inorganic diphosphatase activity|magnesium ion binding|phosphohistidine phosphatase activity|protein homodimerization activity				0		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.163)|Colorectal(40;0.187)														---	---	---	---
FAM53B	9679	broad.mit.edu	37	10	126390418	126390418	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126390418delT	uc001lhv.1	-						FAM53B_uc001lhu.1_Intron|FAM53B_uc001lhw.2_Intron|uc001lhx.2_5'Flank	NM_014661	NP_055476			hypothetical protein LOC9679											ovary(1)|pancreas(1)	2		all_lung(145;0.0191)|Lung NSC(174;0.0301)|Colorectal(57;0.106)|all_neural(114;0.117)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.15)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	126595945	126595946	+	IGR	INS	-	TG	TG	rs112130778		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126595945_126595946insTG								FAM175B (70707 upstream) : ZRANB1 (33026 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	126597775	126597775	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126597775delA								FAM175B (72537 upstream) : ZRANB1 (31197 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	126863278	126863278	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126863278delT								CTBP2 (13654 upstream) : LOC100169752 (399662 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	127174531	127174531	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127174531delA								CTBP2 (324907 upstream) : LOC100169752 (88409 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	127234701	127234701	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127234701delG								CTBP2 (385077 upstream) : LOC100169752 (28239 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	127393799	127393799	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127393799delA	uc001lil.2	+											Homo sapiens hypothetical protein LOC283038, mRNA (cDNA clone IMAGE:4825614).																														---	---	---	---
FANK1	92565	broad.mit.edu	37	10	127606656	127606656	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127606656delA	uc001ljh.3	+						FANK1_uc010quk.1_Intron|FANK1_uc009yan.2_Intron	NM_145235	NP_660278			fibronectin type III and ankyrin repeat domains							cytoplasm|nucleus				ovary(1)	1		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)																---	---	---	---
ADAM12	8038	broad.mit.edu	37	10	128013006	128013006	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128013006delC	uc001ljk.2	-						ADAM12_uc010qul.1_Intron|ADAM12_uc001ljm.2_Intron|ADAM12_uc001ljn.2_Intron|ADAM12_uc001ljl.3_Intron	NM_003474	NP_003465			ADAM metallopeptidase domain 12 isoform 1						cell adhesion|epidermal growth factor receptor signaling pathway|myoblast fusion|proteolysis	extracellular region|integral to membrane|plasma membrane	metalloendopeptidase activity|protein binding|SH3 domain binding|zinc ion binding			breast(4)|ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	9		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)														---	---	---	---
DOCK1	1793	broad.mit.edu	37	10	129016936	129016936	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129016936delT	uc001ljt.2	+						DOCK1_uc010qun.1_Intron	NM_001380	NP_001371			dedicator of cytokinesis 1						apoptosis|axon guidance|blood coagulation|integrin-mediated signaling pathway|phagocytosis, engulfment|small GTPase mediated signal transduction	cytosol|membrane	GTP binding|GTPase activator activity|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding			central_nervous_system(4)|ovary(2)|lung(1)|breast(1)|kidney(1)	9		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)														---	---	---	---
DOCK1	1793	broad.mit.edu	37	10	129080513	129080514	+	Intron	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129080513_129080514delTC	uc001ljt.2	+						DOCK1_uc010qun.1_Intron	NM_001380	NP_001371			dedicator of cytokinesis 1						apoptosis|axon guidance|blood coagulation|integrin-mediated signaling pathway|phagocytosis, engulfment|small GTPase mediated signal transduction	cytosol|membrane	GTP binding|GTPase activator activity|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding			central_nervous_system(4)|ovary(2)|lung(1)|breast(1)|kidney(1)	9		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	129548187	129548187	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129548187delC								FOXI2 (8737 upstream) : CLRN3 (127927 downstream)																																			---	---	---	---
PTPRE	5791	broad.mit.edu	37	10	129709348	129709348	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129709348delA	uc001lkb.2	+						PTPRE_uc009yat.2_Intron	NM_006504	NP_006495			protein tyrosine phosphatase, receptor type, E						negative regulation of insulin receptor signaling pathway|protein phosphorylation	cytoplasm|integral to membrane|intermediate filament cytoskeleton|nucleus|plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			ovary(1)	1		all_epithelial(44;1.66e-05)|all_lung(145;0.00456)|Lung NSC(174;0.0066)|all_neural(114;0.0936)|Colorectal(57;0.141)|Breast(234;0.166)|Melanoma(40;0.203)																---	---	---	---
PTPRE	5791	broad.mit.edu	37	10	129808314	129808317	+	Intron	DEL	CATT	-	-	rs68122724		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129808314_129808317delCATT	uc001lkb.2	+						PTPRE_uc009yat.2_Intron|PTPRE_uc010qup.1_Intron|PTPRE_uc009yau.2_Intron|PTPRE_uc001lkc.1_Intron	NM_006504	NP_006495			protein tyrosine phosphatase, receptor type, E						negative regulation of insulin receptor signaling pathway|protein phosphorylation	cytoplasm|integral to membrane|intermediate filament cytoskeleton|nucleus|plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			ovary(1)	1		all_epithelial(44;1.66e-05)|all_lung(145;0.00456)|Lung NSC(174;0.0066)|all_neural(114;0.0936)|Colorectal(57;0.141)|Breast(234;0.166)|Melanoma(40;0.203)																---	---	---	---
MKI67	4288	broad.mit.edu	37	10	129895892	129895892	+	3'UTR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129895892delG	uc001lke.2	-	15					MKI67_uc001lkf.2_3'UTR	NM_002417	NP_002408			antigen identified by monoclonal antibody Ki-67						cell proliferation	nucleolus	ATP binding|protein C-terminus binding			ovary(4)|central_nervous_system(2)|skin(1)	7		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)																---	---	---	---
MKI67	4288	broad.mit.edu	37	10	129897532	129897532	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129897532delA	uc001lke.2	-						MKI67_uc001lkf.2_Intron	NM_002417	NP_002408			antigen identified by monoclonal antibody Ki-67						cell proliferation	nucleolus	ATP binding|protein C-terminus binding			ovary(4)|central_nervous_system(2)|skin(1)	7		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)																---	---	---	---
Unknown	0	broad.mit.edu	37	10	130050188	130050189	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130050188_130050189delAA	uc001lkg.1	+											Homo sapiens cDNA FLJ42232 fis, clone THYMU3000224.																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	130254920	130254920	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130254920delA								MKI67 (330452 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	130512306	130512319	+	IGR	DEL	GCAAAGCTCATTCT	-	-	rs149374883		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130512306_130512319delGCAAAGCTCATTCT								MKI67 (587838 upstream) : MGMT (753135 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	130533543	130533544	+	IGR	INS	-	GA	GA	rs149956346	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130533543_130533544insGA								MKI67 (609075 upstream) : MGMT (731910 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	130646766	130646766	+	IGR	DEL	A	-	-	rs112413932		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130646766delA								MKI67 (722298 upstream) : MGMT (618688 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	130978913	130978913	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:130978913delA								None (None upstream) : MGMT (286541 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	131074117	131074117	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131074117delC								None (None upstream) : MGMT (191337 downstream)																																			---	---	---	---
EBF3	253738	broad.mit.edu	37	10	131760659	131760659	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131760659delT	uc001lki.1	-						EBF3_uc010qur.1_3'UTR	NM_001005463	NP_001005463			early B-cell factor 3						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|metal ion binding|protein binding			central_nervous_system(1)|pancreas(1)	2		all_cancers(35;1.8e-08)|all_epithelial(44;8.26e-08)|Lung NSC(174;0.0091)|all_lung(145;0.0123)|Breast(234;0.039)|all_neural(114;0.0722)|Colorectal(57;0.0764)		OV - Ovarian serous cystadenocarcinoma(35;0.00513)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	131891009	131891009	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131891009delA	uc010qus.1	-											Homo sapiens cDNA FLJ36799 fis, clone ADRGL2007357.																														---	---	---	---
Unknown	0	broad.mit.edu	37	10	131994586	131994587	+	IGR	DEL	TG	-	-	rs113782668		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131994586_131994587delTG								GLRX3 (11802 upstream) : TCERG1L (896069 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	132010560	132010560	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132010560delG								GLRX3 (27776 upstream) : TCERG1L (880096 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	132052810	132052810	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132052810delC								GLRX3 (70026 upstream) : TCERG1L (837846 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	132203855	132203855	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132203855delG								GLRX3 (221071 upstream) : TCERG1L (686801 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	132509817	132509817	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132509817delC								GLRX3 (527033 upstream) : TCERG1L (380839 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	132768916	132768916	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132768916delG								GLRX3 (786132 upstream) : TCERG1L (121740 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	10	132881030	132881030	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132881030delT								GLRX3 (898246 upstream) : TCERG1L (9626 downstream)																																			---	---	---	---
TCERG1L	256536	broad.mit.edu	37	10	132891411	132891412	+	3'UTR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132891411_132891412insT	uc001lkp.2	-	12						NM_174937	NP_777597			transcription elongation regulator 1-like											large_intestine(2)|ovary(2)	4		all_cancers(35;1.22e-10)|all_epithelial(44;2.65e-09)|Lung NSC(174;0.00188)|all_lung(145;0.00307)|Melanoma(40;0.0179)|all_neural(114;0.0424)|Breast(234;0.0743)|Colorectal(57;0.09)		all cancers(32;0.000899)|OV - Ovarian serous cystadenocarcinoma(35;0.0021)|Epithelial(32;0.00276)														---	---	---	---
TCERG1L	256536	broad.mit.edu	37	10	132907422	132907423	+	Intron	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:132907422_132907423delTC	uc001lkp.2	-						TCERG1L_uc009yax.1_Intron	NM_174937	NP_777597			transcription elongation regulator 1-like											large_intestine(2)|ovary(2)	4		all_cancers(35;1.22e-10)|all_epithelial(44;2.65e-09)|Lung NSC(174;0.00188)|all_lung(145;0.00307)|Melanoma(40;0.0179)|all_neural(114;0.0424)|Breast(234;0.0743)|Colorectal(57;0.09)		all cancers(32;0.000899)|OV - Ovarian serous cystadenocarcinoma(35;0.0021)|Epithelial(32;0.00276)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	133358983	133358983	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133358983delG								TCERG1L (248999 upstream) : PPP2R2D (388977 downstream)																																			---	---	---	---
STK32C	282974	broad.mit.edu	37	10	134082300	134082301	+	Intron	INS	-	AT	AT	rs34032641		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134082300_134082301insAT	uc001lle.1	-						STK32C_uc001lld.1_Intron|STK32C_uc010quu.1_Intron|STK32C_uc009ybc.1_Intron|STK32C_uc009ybd.1_Intron	NM_173575	NP_775846			serine/threonine kinase 32C								ATP binding|metal ion binding|protein serine/threonine kinase activity			large_intestine(2)|lung(2)|breast(1)	5		all_cancers(35;2.72e-11)|all_epithelial(44;2.33e-08)|Lung NSC(174;0.000855)|all_lung(145;0.00146)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.112)|Melanoma(40;0.124)|Glioma(114;0.203)		Epithelial(32;3.99e-05)|all cancers(32;5.58e-05)|OV - Ovarian serous cystadenocarcinoma(35;9.96e-05)|BRCA - Breast invasive adenocarcinoma(275;0.222)														---	---	---	---
Unknown	0	broad.mit.edu	37	10	134328284	134328285	+	Intron	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134328284_134328285delTG	uc001lln.2	-											Homo sapiens full length insert cDNA clone ZB55F04.																														---	---	---	---
INPP5A	3632	broad.mit.edu	37	10	134463290	134463291	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134463290_134463291insT	uc001llp.2	+						INPP5A_uc001llo.1_Intron|INPP5A_uc001llq.2_Intron	NM_005539	NP_005530			inositol polyphosphate-5-phosphatase A						cell communication	membrane	inositol 1,3,4,5-tetrakisphosphate 5-phosphatase activity|inositol-1,4,5-trisphosphate 5-phosphatase activity|inositol-polyphosphate 5-phosphatase activity|PH domain binding			skin(1)	1		all_cancers(35;8.59e-13)|all_epithelial(44;5.49e-09)|Lung NSC(174;0.000854)|all_lung(145;0.00146)|all_neural(114;0.0299)|Colorectal(31;0.0599)|Breast(234;0.0849)|Melanoma(40;0.124)|all_hematologic(284;0.196)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;0.000102)|Epithelial(32;0.00023)|all cancers(32;0.000326)														---	---	---	---
INPP5A	3632	broad.mit.edu	37	10	134569670	134569670	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134569670delG	uc001llp.2	+						INPP5A_uc001llo.1_Intron|INPP5A_uc001llq.2_Intron	NM_005539	NP_005530			inositol polyphosphate-5-phosphatase A						cell communication	membrane	inositol 1,3,4,5-tetrakisphosphate 5-phosphatase activity|inositol-1,4,5-trisphosphate 5-phosphatase activity|inositol-polyphosphate 5-phosphatase activity|PH domain binding			skin(1)	1		all_cancers(35;8.59e-13)|all_epithelial(44;5.49e-09)|Lung NSC(174;0.000854)|all_lung(145;0.00146)|all_neural(114;0.0299)|Colorectal(31;0.0599)|Breast(234;0.0849)|Melanoma(40;0.124)|all_hematologic(284;0.196)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;0.000102)|Epithelial(32;0.00023)|all cancers(32;0.000326)														---	---	---	---
KNDC1	85442	broad.mit.edu	37	10	134980253	134980253	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134980253delG	uc001llz.1	+						KNDC1_uc001lma.1_5'Flank	NM_152643	NP_689856			kinase non-catalytic C-lobe domain (KIND)						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction					upper_aerodigestive_tract(1)|ovary(1)	2		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)														---	---	---	---
TUBGCP2	10844	broad.mit.edu	37	10	135113670	135113670	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135113670delA	uc001lmg.1	-						TUBGCP2_uc010qvc.1_Intron|TUBGCP2_uc009ybk.1_Intron|TUBGCP2_uc010qvd.1_Intron|TUBGCP2_uc001lmh.1_Intron	NM_006659	NP_006650			tubulin, gamma complex associated protein 2						G2/M transition of mitotic cell cycle|microtubule nucleation|protein complex assembly	centrosome|cytoplasmic microtubule|cytosol|spindle pole	protein binding				0		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.87e-06)|all cancers(32;8.98e-06)|Epithelial(32;1.15e-05)														---	---	---	---
LOC619207	619207	broad.mit.edu	37	10	135275085	135275085	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135275085delC	uc001lnh.1	+						LOC619207_uc001lng.2_Intron					Homo sapiens cDNA FLJ45320 fis, clone BRHIP3005944, weakly  similar to Antigen WC1.1 precursor.												0																		---	---	---	---
LOC619207	619207	broad.mit.edu	37	10	135285076	135285077	+	Intron	INS	-	G	G	rs34455488		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135285076_135285077insG	uc001lni.1	+											Homo sapiens cDNA FLJ41380 fis, clone BRCAN2011254.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	10	135499780	135499780	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135499780delG								LOC653544 (4587 upstream) : None (None downstream)																																			---	---	---	---
SIRT3	23410	broad.mit.edu	37	11	230293	230293	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:230293delT	uc001lok.3	-						SIRT3_uc001loj.3_Intron|SIRT3_uc010qvm.1_Intron|SIRT3_uc010qvn.1_Intron|SIRT3_uc010qvo.1_Intron|SIRT3_uc010qvp.1_Intron|SIRT3_uc010qvq.1_Intron|SIRT3_uc009ybt.1_Intron	NM_012239	NP_036371			sirtuin 3 isoform a						chromatin silencing|protein ADP-ribosylation|protein deacetylation	mitochondrial matrix	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides|NAD+ ADP-ribosyltransferase activity|NAD+ binding|protein binding|zinc ion binding			urinary_tract(1)	1		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;3.66e-27)|Epithelial(43;2.02e-26)|OV - Ovarian serous cystadenocarcinoma(40;2.9e-21)|BRCA - Breast invasive adenocarcinoma(625;3.88e-05)|Lung(200;0.111)|LUSC - Lung squamous cell carcinoma(625;0.129)														---	---	---	---
PTDSS2	81490	broad.mit.edu	37	11	486854	486855	+	Intron	DEL	AT	-	-	rs55961417	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:486854_486855delAT	uc001lpj.2	+							NM_030783	NP_110410			phosphatidylserine synthase 2							integral to membrane					0		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;2.76e-26)|Epithelial(43;2.56e-25)|OV - Ovarian serous cystadenocarcinoma(40;7.54e-20)|BRCA - Breast invasive adenocarcinoma(625;8.76e-05)|Lung(200;0.0407)|LUSC - Lung squamous cell carcinoma(625;0.0735)	Phosphatidylserine(DB00144)													---	---	---	---
CEND1	51286	broad.mit.edu	37	11	788204	788204	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:788204delG	uc001lrh.1	-	2	552	c.373delC	c.(373-375)CTGfs	p.L125fs		NM_016564	NP_057648	Q8N111	CEND_HUMAN	cell cycle exit and neuronal differentiation 1	125	Cytoplasmic (Potential).					integral to membrane					0		all_cancers(49;1.13e-08)|all_epithelial(84;2.95e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.159)|all_lung(207;0.198)		all cancers(45;6.27e-26)|Epithelial(43;4.84e-25)|OV - Ovarian serous cystadenocarcinoma(40;2.72e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	1066466	1066466	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1066466delA								MUC6 (29760 upstream) : MUC2 (8409 downstream)																																			---	---	---	---
MUC2	4583	broad.mit.edu	37	11	1090144	1090144	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1090144delT	uc001lsx.1	+							NM_002457	NP_002448			mucin 2 precursor							inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)													---	---	---	---
MUC5B	727897	broad.mit.edu	37	11	1270160	1270160	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1270160delC	uc009ycr.1	+	51	13595	c.13469delC	c.(13468-13470)TCCfs	p.S4490fs	MUC5B_uc001ltb.2_Frame_Shift_Del_p.S4020fs	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;	4017	7 X Cys-rich subdomain repeats.|Thr-rich.				cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	1693816	1693817	+	IGR	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1693816_1693817delTC								FAM99A (4731 upstream) : FAM99B (10683 downstream)																																			---	---	---	---
LSP1	4046	broad.mit.edu	37	11	1894138	1894138	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1894138delG	uc001lui.2	+						LSP1_uc001luj.2_Intron|LSP1_uc001luk.2_Intron|LSP1_uc001lul.2_Intron|LSP1_uc001lum.2_Intron	NM_002339	NP_002330			lymphocyte-specific protein 1 isoform 1						cellular component movement|cellular defense response	actin cytoskeleton|Golgi apparatus|plasma membrane	actin binding|signal transducer activity			large_intestine(1)	1		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|Lung(200;0.0729)|LUSC - Lung squamous cell carcinoma(625;0.0856)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	2014529	2014530	+	IGR	INS	-	T	T	rs143048734	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2014529_2014530insT								LOC100133545 (3379 upstream) : H19 (1876 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	2214045	2214045	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2214045delC								TH (21010 upstream) : ASCL2 (75684 downstream)																																			---	---	---	---
CD81	975	broad.mit.edu	37	11	2408638	2408638	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2408638delT	uc001lwf.1	+						CD81_uc001lwg.1_Intron	NM_004356	NP_004347			CD81 antigen						activation of MAPK activity|cell proliferation|phosphatidylinositol biosynthetic process|positive regulation of 1-phosphatidylinositol 4-kinase activity|positive regulation of cell proliferation|positive regulation of peptidyl-tyrosine phosphorylation|protein localization|regulation of immune response|virion attachment, binding of host cell surface receptor	integral to plasma membrane	protein binding				0		all_epithelial(84;0.000161)|Breast(177;0.000962)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|all_neural(188;0.0137)|Lung NSC(207;0.209)		BRCA - Breast invasive adenocarcinoma(625;0.000338)|LUSC - Lung squamous cell carcinoma(625;0.191)														---	---	---	---
KCNQ1	3784	broad.mit.edu	37	11	2609933	2609933	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2609933delT	uc001lwn.2	+						KCNQ1_uc009ydp.1_Intron|KCNQ1_uc001lwo.2_Intron	NM_000218	NP_000209			potassium voltage-gated channel, KQT-like						blood circulation|membrane depolarization|muscle contraction|sensory perception of sound		delayed rectifier potassium channel activity|protein binding			ovary(1)	1		all_epithelial(84;3.26e-05)|Breast(177;0.001)|Medulloblastoma(188;0.00111)|Ovarian(85;0.00158)|all_neural(188;0.00725)|all_lung(207;0.11)|Lung NSC(207;0.159)		BRCA - Breast invasive adenocarcinoma(625;0.00251)|Lung(200;0.131)	Bepridil(DB01244)|Indapamide(DB00808)													---	---	---	---
KCNQ1DN	55539	broad.mit.edu	37	11	2888895	2888895	+	5'Flank	DEL	A	-	-	rs79648318		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2888895delA	uc009ydq.2	+							NR_024627				Homo sapiens KCNQ1DN mRNA, imprinted gene.												0																		---	---	---	---
SLC22A18AS	5003	broad.mit.edu	37	11	2910315	2910316	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2910315_2910316delAA	uc001lwv.3	-						SLC22A18AS_uc001lww.3_Intron	NM_007105	NP_009036			solute carrier family 22 (organic cation												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	2960610	2960610	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2960610delA								PHLDA2 (9960 upstream) : NAP1L4 (5051 downstream)																																			---	---	---	---
CARS	833	broad.mit.edu	37	11	3045128	3045128	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3045128delT	uc001lxh.2	-						CARS_uc001lxe.2_Intron|CARS_uc001lxf.2_Intron|CARS_uc001lxg.2_Intron|CARS_uc010qxo.1_Intron|CARS_uc010qxp.1_Intron	NM_001751	NP_001742			cysteinyl-tRNA synthetase isoform b						cysteinyl-tRNA aminoacylation	cytoplasm|cytosol	ATP binding|cysteine-tRNA ligase activity|metal ion binding|protein homodimerization activity|protein homodimerization activity|tRNA binding|tRNA binding		CARS/ALK(5)	soft_tissue(5)|ovary(2)	7		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00317)|LUSC - Lung squamous cell carcinoma(625;0.218)	L-Cysteine(DB00151)			T	ALK	ALCL								---	---	---	---
Unknown	0	broad.mit.edu	37	11	3374659	3374662	+	IGR	DEL	TTTT	-	-	rs112941612		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3374659_3374662delTTTT								MRGPRE (121043 upstream) : ZNF195 (5349 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	3536641	3536641	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3536641delT								LOC650368 (106263 upstream) : TRPC2 (101821 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	3566243	3566244	+	IGR	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3566243_3566244delAG								LOC650368 (135865 upstream) : TRPC2 (72218 downstream)																																			---	---	---	---
NUP98	4928	broad.mit.edu	37	11	3766014	3766017	+	Intron	DEL	GTAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3766014_3766017delGTAA	uc001lyh.2	-						NUP98_uc001lyi.2_Intron|NUP98_uc001lyj.1_Intron|NUP98_uc001lyk.1_Intron	NM_016320	NP_057404			nucleoporin 98kD isoform 1						carbohydrate metabolic process|DNA replication|glucose transport|interspecies interaction between organisms|mitotic prometaphase|mRNA transport|nuclear pore organization|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear membrane|nucleoplasm|Nup107-160 complex	protein binding|structural constituent of nuclear pore|transporter activity			breast(4)|skin(3)|ovary(2)|central_nervous_system(1)|lung(1)|kidney(1)	12		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)				T	HOXA9|NSD1|WHSC1L1|DDX10|TOP1|HOXD13|PMX1|HOXA13|HOXD11|HOXA11|RAP1GDS1|HOXC11	AML								---	---	---	---
STIM1	6786	broad.mit.edu	37	11	3944023	3944023	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3944023delA	uc001lyv.2	+						STIM1_uc009yef.2_Intron	NM_003156	NP_003147			stromal interaction molecule 1 precursor						activation of store-operated calcium channel activity|calcium ion transport|detection of calcium ion|platelet activation	integral to endoplasmic reticulum membrane|integral to plasma membrane|microtubule	calcium ion binding|microtubule plus-end binding			pancreas(1)	1		Breast(177;0.00159)|Medulloblastoma(188;0.00258)|all_neural(188;0.0233)		BRCA - Breast invasive adenocarcinoma(625;0.114)|LUSC - Lung squamous cell carcinoma(625;0.141)														---	---	---	---
STIM1	6786	broad.mit.edu	37	11	4041994	4041994	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4041994delT	uc001lyv.2	+						STIM1_uc009yef.2_Intron	NM_003156	NP_003147			stromal interaction molecule 1 precursor						activation of store-operated calcium channel activity|calcium ion transport|detection of calcium ion|platelet activation	integral to endoplasmic reticulum membrane|integral to plasma membrane|microtubule	calcium ion binding|microtubule plus-end binding			pancreas(1)	1		Breast(177;0.00159)|Medulloblastoma(188;0.00258)|all_neural(188;0.0233)		BRCA - Breast invasive adenocarcinoma(625;0.114)|LUSC - Lung squamous cell carcinoma(625;0.141)														---	---	---	---
RRM1	6240	broad.mit.edu	37	11	4127094	4127094	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4127094delT	uc001lyw.3	+						RRM1_uc009yeh.1_Intron|RRM1_uc009yei.2_Intron|RRM1_uc010qyc.1_Intron	NM_001033	NP_001024			ribonucleoside-diphosphate reductase M1 chain						deoxyribonucleotide biosynthetic process|DNA replication|nucleobase, nucleoside and nucleotide interconversion	cytosol|nucleoplasm|ribonucleoside-diphosphate reductase complex	ATP binding|ribonucleoside-diphosphate reductase activity			skin(1)	1		Medulloblastoma(188;0.0025)|Breast(177;0.00502)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0848)|LUSC - Lung squamous cell carcinoma(625;0.205)	Clofarabine(DB00631)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Hydroxyurea(DB01005)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	5237238	5237238	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5237238delT								OR51V1 (15308 upstream) : HBB (9458 downstream)																																			---	---	---	---
HBG2	3048	broad.mit.edu	37	11	5569759	5569760	+	Intron	INS	-	AA	AA	rs140460952	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5569759_5569760insAA	uc001mak.1	-											Homo sapiens hemoglobin gamma-G (HBG2) mRNA, partial cds.						blood coagulation	hemoglobin complex	heme binding|oxygen binding|oxygen transporter activity			skin(1)	1		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.76e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
OR56A3	390083	broad.mit.edu	37	11	5968291	5968291	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5968291delA	uc010qzt.1	+							NM_001003443	NP_001003443			olfactory receptor, family 56, subfamily A,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;9.41e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
CCKBR	887	broad.mit.edu	37	11	6287103	6287105	+	Intron	DEL	AAG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6287103_6287105delAAG	uc001mcp.2	+						CCKBR_uc001mcq.2_Intron|CCKBR_uc001mcr.2_Intron|CCKBR_uc001mcs.2_Intron	NM_176875	NP_795344			cholecystokinin B receptor						activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|cell proliferation|digestion|elevation of cytosolic calcium ion concentration|feeding behavior|positive regulation of cell proliferation|sensory perception		1-phosphatidylinositol-3-kinase regulator activity|gastrin receptor activity|phosphatidylinositol phospholipase C activity|type B gastrin/cholecystokinin receptor binding			lung(5)|ovary(2)|breast(1)	8		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.139)	Pentagastrin(DB00183)													---	---	---	---
APBB1	322	broad.mit.edu	37	11	6419453	6419453	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6419453delT	uc001mdb.1	-						APBB1_uc001mcz.1_Intron|APBB1_uc001mdd.3_Intron|APBB1_uc001mda.2_Intron|APBB1_uc001mdc.1_Intron|APBB1_uc010rab.1_Intron|APBB1_uc001mcy.1_5'Flank	NM_001164	NP_001155			amyloid beta A4 precursor protein-binding,						apoptosis|axonogenesis|cell cycle arrest|histone H4 acetylation|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of thymidylate synthase biosynthetic process|positive regulation of apoptosis|positive regulation of transcription, DNA-dependent|response to DNA damage stimulus|signal transduction|transcription, DNA-dependent	cytoplasm|growth cone|lamellipodium|nucleus|plasma membrane|synapse	beta-amyloid binding|chromatin binding|histone binding|proline-rich region binding|transcription factor binding			breast(2)	2		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;6.49e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)														---	---	---	---
APBB1	322	broad.mit.edu	37	11	6423779	6423779	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6423779delC	uc001mdb.1	-						APBB1_uc001mcz.1_Intron|APBB1_uc001mdd.3_Intron|APBB1_uc001mda.2_Intron|APBB1_uc001mdc.1_Intron|APBB1_uc010rab.1_5'Flank|APBB1_uc010rac.1_5'Flank|APBB1_uc010rad.1_Intron|APBB1_uc010rae.1_Intron|APBB1_uc010raf.1_3'UTR|APBB1_uc009yfa.2_Intron|APBB1_uc009yey.2_Intron|APBB1_uc010rag.1_Intron|APBB1_uc009yfb.2_Intron|APBB1_uc001mde.2_Intron|APBB1_uc010rah.1_Intron	NM_001164	NP_001155			amyloid beta A4 precursor protein-binding,						apoptosis|axonogenesis|cell cycle arrest|histone H4 acetylation|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of thymidylate synthase biosynthetic process|positive regulation of apoptosis|positive regulation of transcription, DNA-dependent|response to DNA damage stimulus|signal transduction|transcription, DNA-dependent	cytoplasm|growth cone|lamellipodium|nucleus|plasma membrane|synapse	beta-amyloid binding|chromatin binding|histone binding|proline-rich region binding|transcription factor binding			breast(2)	2		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;6.49e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)														---	---	---	---
ILK	3611	broad.mit.edu	37	11	6629056	6629056	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6629056delT	uc001mee.2	+						ILK_uc001mef.2_Intron|ILK_uc010rap.1_Intron|ILK_uc010raq.1_Intron|ILK_uc001meg.2_Intron|ILK_uc001meh.2_Intron|ILK_uc001mei.2_5'Flank	NM_001014794	NP_001014794			integrin-linked kinase						cell junction assembly|cell proliferation|cell-matrix adhesion|integrin-mediated signaling pathway|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of phosphorylation|positive regulation of transcription, DNA-dependent	cytosol|focal adhesion	ATP binding|protein serine/threonine kinase activity			central_nervous_system(1)	1		Breast(177;7.61e-05)|Medulloblastoma(188;0.00263)|all_neural(188;0.026)|all_lung(207;0.152)		Epithelial(150;5.49e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00012)|Lung(200;0.00942)|LUSC - Lung squamous cell carcinoma(625;0.0163)														---	---	---	---
MRPL17	63875	broad.mit.edu	37	11	6707066	6707066	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6707066delT	uc001men.2	-							NM_022061	NP_071344			mitochondrial ribosomal protein L17 precursor						translation	ribosome	protein domain specific binding|structural constituent of ribosome				0		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;4.68e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	6730533	6730533	+	IGR	DEL	C	-	-	rs74825517		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6730533delC								MRPL17 (25901 upstream) : GVIN1 (3850 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	7097918	7097919	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7097918_7097919delTT								NLRP14 (5161 upstream) : RBMXL2 (12246 downstream)																																			---	---	---	---
RBMXL2	27288	broad.mit.edu	37	11	7108268	7108272	+	5'Flank	DEL	AGATA	-	-	rs151068894		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7108268_7108272delAGATA	uc001mfc.2	+							NM_014469	NP_055284			testes-specific heterogenous nuclear							nucleus|ribonucleoprotein complex	nucleotide binding|RNA binding				0				Epithelial(150;5.14e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	7127443	7127444	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7127443_7127444delTT								RBMXL2 (15064 upstream) : MIR302E (128553 downstream)																																			---	---	---	---
NLRP10	338322	broad.mit.edu	37	11	7981609	7981609	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7981609delA	uc001mfv.1	-	2	1567	c.1550delT	c.(1549-1551)TTAfs	p.L517fs		NM_176821	NP_789791	Q86W26	NAL10_HUMAN	NLR family, pyrin domain containing 10	517							ATP binding			lung(4)|ovary(2)|pancreas(1)|kidney(1)|skin(1)	9				Epithelial(150;1.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)														---	---	---	---
TUB	7275	broad.mit.edu	37	11	8127285	8127285	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8127285delT	uc001mga.2	+	12					TUB_uc010rbk.1_3'UTR|TUB_uc001mfy.2_3'UTR	NM_177972	NP_813977			tubby isoform b						phagocytosis|positive regulation of phagocytosis|response to stimulus	cytoplasm|extracellular region|nucleus|plasma membrane				ovary(1)	1		all_lung(207;6.91e-20)|Lung NSC(207;3.36e-17)		Epithelial(150;1.69e-62)|BRCA - Breast invasive adenocarcinoma(625;8.54e-06)|LUSC - Lung squamous cell carcinoma(625;0.000184)														---	---	---	---
RIC3	79608	broad.mit.edu	37	11	8157689	8157689	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8157689delC	uc001mgd.2	-						RIC3_uc001mgb.2_Intron|RIC3_uc001mgc.2_Intron|RIC3_uc001mge.2_Intron|RIC3_uc010rbl.1_Intron|RIC3_uc010rbm.1_Intron|RIC3_uc009yfm.2_Intron|RIC3_uc009yfn.2_Intron	NM_024557	NP_078833			resistance to inhibitors of cholinesterase 3							endoplasmic reticulum membrane|Golgi membrane|integral to membrane				large_intestine(1)|ovary(1)|pancreas(1)	3				Epithelial(150;2.89e-07)|BRCA - Breast invasive adenocarcinoma(625;0.204)														---	---	---	---
RIC3	79608	broad.mit.edu	37	11	8159967	8159967	+	Intron	DEL	A	-	-	rs78612783		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8159967delA	uc001mgd.2	-						RIC3_uc001mgb.2_5'UTR|RIC3_uc001mgc.2_Intron|RIC3_uc001mge.2_Intron|RIC3_uc010rbl.1_Intron|RIC3_uc010rbm.1_Intron|RIC3_uc009yfm.2_Intron|RIC3_uc009yfn.2_Intron	NM_024557	NP_078833			resistance to inhibitors of cholinesterase 3							endoplasmic reticulum membrane|Golgi membrane|integral to membrane				large_intestine(1)|ovary(1)|pancreas(1)	3				Epithelial(150;2.89e-07)|BRCA - Breast invasive adenocarcinoma(625;0.204)														---	---	---	---
RIC3	79608	broad.mit.edu	37	11	8160039	8160040	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8160039_8160040delAA	uc001mgd.2	-						RIC3_uc001mgb.2_5'UTR|RIC3_uc001mgc.2_Intron|RIC3_uc001mge.2_Intron|RIC3_uc010rbl.1_Intron|RIC3_uc010rbm.1_Intron|RIC3_uc009yfm.2_Intron|RIC3_uc009yfn.2_Intron	NM_024557	NP_078833			resistance to inhibitors of cholinesterase 3							endoplasmic reticulum membrane|Golgi membrane|integral to membrane				large_intestine(1)|ovary(1)|pancreas(1)	3				Epithelial(150;2.89e-07)|BRCA - Breast invasive adenocarcinoma(625;0.204)														---	---	---	---
STK33	65975	broad.mit.edu	37	11	8426689	8426689	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8426689delA	uc001mgi.1	-						STK33_uc001mgj.1_Intron|STK33_uc001mgk.1_Intron|STK33_uc010rbn.1_Intron|STK33_uc001mgl.3_Intron	NM_030906	NP_112168			serine/threonine kinase 33							Golgi apparatus|nucleus|perinuclear region of cytoplasm	ATP binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|pancreas(1)|central_nervous_system(1)|skin(1)	7				Epithelial(150;2.13e-06)|BRCA - Breast invasive adenocarcinoma(625;0.239)														---	---	---	---
STK33	65975	broad.mit.edu	37	11	8551268	8551268	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8551268delA	uc001mgj.1	-						STK33_uc001mgk.1_Intron|STK33_uc010rbn.1_Intron|STK33_uc001mgl.3_Intron|STK33_uc009yfp.2_Intron	NM_030906	NP_112168			serine/threonine kinase 33							Golgi apparatus|nucleus|perinuclear region of cytoplasm	ATP binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|pancreas(1)|central_nervous_system(1)|skin(1)	7				Epithelial(150;2.13e-06)|BRCA - Breast invasive adenocarcinoma(625;0.239)														---	---	---	---
STK33	65975	broad.mit.edu	37	11	8592435	8592436	+	Intron	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8592435_8592436delAC	uc001mgj.1	-						STK33_uc001mgk.1_Intron|STK33_uc010rbn.1_Intron|STK33_uc001mgl.3_Intron|STK33_uc009yfp.2_Intron	NM_030906	NP_112168			serine/threonine kinase 33							Golgi apparatus|nucleus|perinuclear region of cytoplasm	ATP binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|pancreas(1)|central_nervous_system(1)|skin(1)	7				Epithelial(150;2.13e-06)|BRCA - Breast invasive adenocarcinoma(625;0.239)														---	---	---	---
TRIM66	9866	broad.mit.edu	37	11	8635431	8635431	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8635431delA	uc010rbo.1	-	20						NM_014818	NP_055633			tripartite motif-containing 66							aggresome|nucleus	zinc ion binding				0																		---	---	---	---
ST5	6764	broad.mit.edu	37	11	8787641	8787641	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8787641delA	uc001mgt.2	-						ST5_uc009yfr.2_Intron|ST5_uc001mgu.2_Intron|ST5_uc001mgv.2_Intron|ST5_uc010rbq.1_Intron|ST5_uc001mgw.1_Intron	NM_213618	NP_998783			suppression of tumorigenicity 5 isoform 1						positive regulation of ERK1 and ERK2 cascade		protein binding			upper_aerodigestive_tract(1)	1				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)														---	---	---	---
ST5	6764	broad.mit.edu	37	11	8870440	8870440	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8870440delA	uc001mgv.2	-						ST5_uc001mgw.1_Intron	NM_005418	NP_005409			suppression of tumorigenicity 5 isoform 1						positive regulation of ERK1 and ERK2 cascade		protein binding			upper_aerodigestive_tract(1)	1				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)														---	---	---	---
TMEM9B	56674	broad.mit.edu	37	11	8969710	8969711	+	3'UTR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8969710_8969711insA	uc001mhe.1	-	5					TMEM9B_uc001mhf.1_3'UTR|TMEM9B_uc010rbt.1_3'UTR	NM_020644	NP_065695			TMEM9 domain family, member B precursor						positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to membrane	signal transducer activity				0				Epithelial(150;4.39e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0237)														---	---	---	---
NRIP3	56675	broad.mit.edu	37	11	9004002	9004002	+	3'UTR	DEL	C	-	-	rs2742470	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9004002delC	uc001mhg.2	-	7						NM_020645	NP_065696			nuclear receptor interacting protein 3						proteolysis		aspartic-type endopeptidase activity				0				Epithelial(150;4.77e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0241)														---	---	---	---
DENND5A	23258	broad.mit.edu	37	11	9200048	9200050	+	Intron	DEL	AAA	-	-	rs76387081		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9200048_9200050delAAA	uc001mhl.2	-						DENND5A_uc010rbw.1_Intron|DENND5A_uc010rbx.1_Intron	NM_015213	NP_056028			RAB6 interacting protein 1											liver(1)	1																		---	---	---	---
IPO7	10527	broad.mit.edu	37	11	9431457	9431457	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9431457delT	uc001mho.2	+							NM_006391	NP_006382			importin 7						interspecies interaction between organisms|signal transduction	Golgi apparatus|nuclear pore|soluble fraction	protein transporter activity|Ran GTPase binding|small GTPase regulator activity			lung(1)|breast(1)	2				all cancers(16;8.29e-09)|Epithelial(150;4.76e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0217)														---	---	---	---
SWAP70	23075	broad.mit.edu	37	11	9746451	9746451	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9746451delT	uc001mhw.2	+						SWAP70_uc001mhv.2_Intron|SWAP70_uc001mhx.2_Intron	NM_015055	NP_055870			SWAP-70 protein							cytoplasm|lamellipodium|nucleus|plasma membrane	calcium ion binding|DNA binding			ovary(2)|central_nervous_system(1)	3				all cancers(16;1.21e-10)|Epithelial(150;2.81e-09)|BRCA - Breast invasive adenocarcinoma(625;0.00649)														---	---	---	---
SBF2	81846	broad.mit.edu	37	11	10110601	10110601	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10110601delA	uc001mib.2	-						SBF2_uc001mif.3_Intron	NM_030962	NP_112224			SET binding factor 2						myelination	cytoplasm|membrane	phosphatase activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)														---	---	---	---
AMPD3	272	broad.mit.edu	37	11	10488937	10488937	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10488937delA	uc001mio.1	+						AMPD3_uc010rbz.1_Intron|AMPD3_uc001min.1_Intron|AMPD3_uc009yfw.1_Intron|AMPD3_uc009yfx.1_Intron|AMPD3_uc009yfz.2_Intron|AMPD3_uc001mip.1_Intron|AMPD3_uc009yfy.2_Intron	NM_001025389	NP_001020560			adenosine monophosphate deaminase 3 isoform 1B						AMP catabolic process|purine base metabolic process|purine ribonucleoside monophosphate biosynthetic process|purine-containing compound salvage	cytosol	AMP deaminase activity|metal ion binding			large_intestine(1)|ovary(1)	2				all cancers(16;1.14e-08)|Epithelial(150;2.83e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0291)														---	---	---	---
MRVI1	10335	broad.mit.edu	37	11	10698930	10698930	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10698930delT	uc010rcc.1	-						MRVI1_uc009ygb.1_Intron|MRVI1_uc001mix.2_Intron|MRVI1_uc001miz.2_Intron|MRVI1_uc009ygc.1_Intron|MRVI1_uc010rcd.1_Intron|MRVI1_uc009ygd.1_Intron	NM_001100167	NP_001093637			JAW1-related protein isoform c						platelet activation	endoplasmic reticulum membrane|integral to membrane|perinuclear region of cytoplasm|platelet dense tubular network membrane|sarcoplasmic reticulum				ovary(2)|central_nervous_system(1)	3				all cancers(16;2.68e-07)|Epithelial(150;3.04e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0723)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	11137676	11137676	+	IGR	DEL	T	-	-	rs77586175		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11137676delT								ZBED5 (258056 upstream) : GALNTL4 (154745 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	11287267	11287270	+	IGR	DEL	CAGC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11287267_11287270delCAGC								ZBED5 (407647 upstream) : GALNTL4 (5151 downstream)																																			---	---	---	---
USP47	55031	broad.mit.edu	37	11	11877760	11877761	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11877760_11877761delTT	uc001mjq.1	+						USP47_uc001mjr.2_Intron|USP47_uc001mjs.2_Intron	NM_017944	NP_060414			ubiquitin specific protease 47						base-excision repair|cellular response to UV|monoubiquitinated protein deubiquitination|negative regulation of apoptosis|negative regulation of caspase activity|negative regulation of G2/M transition of mitotic cell cycle|negative regulation of transcription, DNA-dependent|positive regulation of cell growth|response to drug|ubiquitin-dependent protein catabolic process	cytoplasm|SCF ubiquitin ligase complex	ubiquitin thiolesterase activity|ubiquitin-specific protease activity|WD40-repeat domain binding			ovary(1)|skin(1)	2				Epithelial(150;0.000339)														---	---	---	---
USP47	55031	broad.mit.edu	37	11	11969772	11969772	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:11969772delT	uc001mjs.2	+						USP47_uc001mjr.2_Intron|USP47_uc009ygi.2_5'Flank	NM_017944	NP_060414			ubiquitin specific protease 47						base-excision repair|cellular response to UV|monoubiquitinated protein deubiquitination|negative regulation of apoptosis|negative regulation of caspase activity|negative regulation of G2/M transition of mitotic cell cycle|negative regulation of transcription, DNA-dependent|positive regulation of cell growth|response to drug|ubiquitin-dependent protein catabolic process	cytoplasm|SCF ubiquitin ligase complex	ubiquitin thiolesterase activity|ubiquitin-specific protease activity|WD40-repeat domain binding			ovary(1)|skin(1)	2				Epithelial(150;0.000339)														---	---	---	---
MICAL2	9645	broad.mit.edu	37	11	12171973	12171974	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12171973_12171974insA	uc001mjz.2	+						MICAL2_uc010rch.1_Intron|MICAL2_uc001mjy.2_Intron|MICAL2_uc001mka.2_Intron|MICAL2_uc010rci.1_Intron	NM_014632	NP_055447			microtubule associated monoxygenase, calponin							cytoplasm|cytoskeleton	monooxygenase activity|zinc ion binding			upper_aerodigestive_tract(2)	2				Epithelial(150;0.00552)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	12686657	12686657	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12686657delA								PARVA (135247 upstream) : TEAD1 (9312 downstream)																																			---	---	---	---
TEAD1	7003	broad.mit.edu	37	11	12768316	12768316	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12768316delC	uc001mkj.3	+							NM_021961	NP_068780			TEA domain family member 1						hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0				Epithelial(150;0.00223)|BRCA - Breast invasive adenocarcinoma(625;0.236)														---	---	---	---
TEAD1	7003	broad.mit.edu	37	11	12807439	12807439	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:12807439delT	uc001mkj.3	+							NM_021961	NP_068780			TEA domain family member 1						hippo signaling cascade		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0				Epithelial(150;0.00223)|BRCA - Breast invasive adenocarcinoma(625;0.236)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	13612784	13612784	+	IGR	DEL	A	-	-	rs113532355		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13612784delA								PTH (95217 upstream) : FAR1 (77422 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	13672065	13672065	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13672065delT								PTH (154498 upstream) : FAR1 (18141 downstream)																																			---	---	---	---
SPON1	10418	broad.mit.edu	37	11	14165239	14165239	+	Intron	DEL	A	-	-	rs35865034		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14165239delA	uc001mle.2	+							NM_006108	NP_006099			spondin 1, extracellular matrix protein						cell adhesion	extracellular space|proteinaceous extracellular matrix	protein binding				0				Epithelial(150;0.00898)														---	---	---	---
RRAS2	22800	broad.mit.edu	37	11	14361509	14361510	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:14361509_14361510insA	uc001mlf.3	-						RRAS2_uc009ygq.2_Intron|RRAS2_uc010rco.1_Intron	NM_012250	NP_036382			related RAS viral (r-ras) oncogene homolog 2							endoplasmic reticulum|plasma membrane	GTP binding|GTPase activity|protein binding			breast(1)	1				Epithelial(150;0.203)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	15009167	15009167	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15009167delG								CALCA (15335 upstream) : CALCB (85979 downstream)																																			---	---	---	---
INSC	387755	broad.mit.edu	37	11	15155140	15155141	+	Intron	DEL	CT	-	-	rs145493466		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15155140_15155141delCT	uc001mly.2	+						INSC_uc001mlz.2_Intron	NM_001031853	NP_001027024			inscuteable isoform a						cell differentiation|nervous system development	cytoplasm	binding			upper_aerodigestive_tract(2)|ovary(2)|central_nervous_system(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	15281557	15281557	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15281557delA								INSC (12805 upstream) : SOX6 (706439 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	15590019	15590019	+	IGR	DEL	A	-	-	rs111738672		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15590019delA								INSC (321267 upstream) : SOX6 (397977 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	15710143	15710143	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15710143delT								INSC (441391 upstream) : SOX6 (277853 downstream)																																			---	---	---	---
SOX6	55553	broad.mit.edu	37	11	16001444	16001447	+	Intron	DEL	TTTG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16001444_16001447delTTTG	uc001mme.2	-						SOX6_uc001mmd.2_Intron|SOX6_uc001mmf.2_Intron|SOX6_uc001mmg.2_Intron	NM_001145819	NP_001139291			SRY (sex determining region Y)-box 6 isoform 4						muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3																		---	---	---	---
SOX6	55553	broad.mit.edu	37	11	16170404	16170404	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16170404delA	uc001mme.2	-						SOX6_uc001mmd.2_Intron|SOX6_uc001mmf.2_Intron|SOX6_uc001mmg.2_Intron	NM_001145819	NP_001139291			SRY (sex determining region Y)-box 6 isoform 4						muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3																		---	---	---	---
SOX6	55553	broad.mit.edu	37	11	16343556	16343556	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16343556delT	uc001mme.2	-						SOX6_uc001mmd.2_Intron|SOX6_uc001mmf.2_Intron|SOX6_uc001mmg.2_Intron|SOX6_uc001mmh.1_Intron|SOX6_uc009ygs.2_Intron|SOX6_uc001mmi.3_Intron|SOX6_uc001mmj.2_Intron	NM_001145819	NP_001139291			SRY (sex determining region Y)-box 6 isoform 4						muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3																		---	---	---	---
SOX6	55553	broad.mit.edu	37	11	16355941	16355941	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16355941delA	uc001mme.2	-						SOX6_uc001mmd.2_Intron|SOX6_uc001mmf.2_Intron|SOX6_uc001mmg.2_Intron|SOX6_uc001mmh.1_Intron|SOX6_uc009ygs.2_Intron|SOX6_uc001mmi.3_Intron|SOX6_uc001mmj.2_Intron	NM_001145819	NP_001139291			SRY (sex determining region Y)-box 6 isoform 4						muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3																		---	---	---	---
SOX6	55553	broad.mit.edu	37	11	16372377	16372377	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16372377delC	uc001mme.2	-						SOX6_uc001mmd.2_Intron|SOX6_uc001mmf.2_Intron|SOX6_uc001mmg.2_Intron|SOX6_uc001mmh.1_Intron|SOX6_uc009ygs.2_Intron|SOX6_uc001mmi.3_Intron|SOX6_uc001mmj.2_Intron	NM_001145819	NP_001139291			SRY (sex determining region Y)-box 6 isoform 4						muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3																		---	---	---	---
SOX6	55553	broad.mit.edu	37	11	16569836	16569836	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16569836delA	uc001mmi.3	-						SOX6_uc001mmh.1_Intron|SOX6_uc001mmj.2_Intron					Synthetic construct DNA, clone: pF1KB8405, Homo sapiens SOX6 gene for SRY (sex determining region Y)-box 6, without stop codon, in Flexi system.						muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3																		---	---	---	---
SOX6	55553	broad.mit.edu	37	11	16683418	16683418	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16683418delA	uc001mmh.1	-											Synthetic construct DNA, clone: pF1KB8405, Homo sapiens SOX6 gene for SRY (sex determining region Y)-box 6, without stop codon, in Flexi system.						muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3																		---	---	---	---
PIK3C2A	5286	broad.mit.edu	37	11	17147070	17147070	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17147070delT	uc001mmq.3	-						PIK3C2A_uc009ygu.1_Intron|PIK3C2A_uc010rcw.1_Intron|PIK3C2A_uc001mmr.3_Intron	NM_002645	NP_002636			phosphoinositide-3-kinase, class 2 alpha						cell communication|phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling	clathrin-coated vesicle|Golgi apparatus|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity			lung(4)|central_nervous_system(4)|stomach(1)|ovary(1)	10					Phosphatidylserine(DB00144)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	17250736	17250736	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17250736delA								PIK3C2A (21206 upstream) : NUCB2 (31151 downstream)																																			---	---	---	---
NUCB2	4925	broad.mit.edu	37	11	17370332	17370332	+	Intron	DEL	T	-	-	rs72132781		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17370332delT	uc001mmx.3	+						uc001mmy.1_Intron|DKFZp686O24166_uc001mmz.3_5'Flank					Homo sapiens mRNA for Nucb2 splice variant, complete cds.							cytosol|ER-Golgi intermediate compartment|extracellular space|Golgi apparatus|plasma membrane	calcium ion binding|DNA binding				0																		---	---	---	---
ABCC8	6833	broad.mit.edu	37	11	17461173	17461173	+	Intron	DEL	A	-	-	rs4148616		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17461173delA	uc001mnc.2	-						ABCC8_uc010rcy.1_Intron	NM_000352	NP_000343			ATP-binding cassette, sub-family C, member 8						carbohydrate metabolic process|energy reserve metabolic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium ion transmembrane transporter activity|sulfonylurea receptor activity			ovary(1)	1				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)|Gliclazide(DB01120)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)													---	---	---	---
TPH1	7166	broad.mit.edu	37	11	18042322	18042322	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18042322delA	uc001mnp.2	-	10					TPH1_uc009yhe.2_RNA	NM_004179	NP_004170			tryptophan hydroxylase 1						aromatic amino acid family metabolic process|hormone biosynthetic process|serotonin biosynthetic process	cytosol	amino acid binding|iron ion binding|tryptophan 5-monooxygenase activity				0					L-Tryptophan(DB00150)|Tetrahydrobiopterin(DB00360)													---	---	---	---
TPH1	7166	broad.mit.edu	37	11	18062087	18062087	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18062087delT	uc001mnp.2	-						TPH1_uc009yhe.2_Intron	NM_004179	NP_004170			tryptophan hydroxylase 1						aromatic amino acid family metabolic process|hormone biosynthetic process|serotonin biosynthetic process	cytosol	amino acid binding|iron ion binding|tryptophan 5-monooxygenase activity				0					L-Tryptophan(DB00150)|Tetrahydrobiopterin(DB00360)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	18225717	18225718	+	IGR	DEL	CA	-	-	rs150319448		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18225717_18225718delCA								MRGPRX4 (29890 upstream) : LOC494141 (4967 downstream)																																			---	---	---	---
GTF2H1	2965	broad.mit.edu	37	11	18355921	18355921	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18355921delA	uc001moi.2	+						GTF2H1_uc001moh.2_Intron|GTF2H1_uc009yhm.2_Intron	NM_001142307	NP_001135779			general transcription factor IIH, polypeptide 1,						mRNA capping|nucleotide-excision repair, DNA damage removal|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|protein phosphorylation|regulation of cyclin-dependent protein kinase activity|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	holo TFIIH complex	protein binding				0													NER					---	---	---	---
LDHC	3948	broad.mit.edu	37	11	18464120	18464120	+	Intron	DEL	C	-	-	rs73440606	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18464120delC	uc001mon.3	+						LDHC_uc001mom.3_Intron|LDHC_uc009yhp.2_Intron|LDHC_uc001moo.3_Intron|LDHC_uc009yhq.2_Intron|LDHC_uc009yhr.2_Intron	NM_017448	NP_059144			L-lactate dehydrogenase C						glycolysis	cytoplasm	binding|L-lactate dehydrogenase activity				0					NADH(DB00157)													---	---	---	---
LDHC	3948	broad.mit.edu	37	11	18468020	18468020	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18468020delA	uc001mon.3	+						LDHC_uc001mom.3_Intron|LDHC_uc009yhp.2_Intron|LDHC_uc001moo.3_Intron|LDHC_uc009yhq.2_Intron|LDHC_uc009yhr.2_Intron	NM_017448	NP_059144			L-lactate dehydrogenase C						glycolysis	cytoplasm	binding|L-lactate dehydrogenase activity				0					NADH(DB00157)													---	---	---	---
TSG101	7251	broad.mit.edu	37	11	18537903	18537904	+	Intron	INS	-	T	T	rs146216750	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18537903_18537904insT	uc001mor.2	-						TSG101_uc001mos.1_Intron|TSG101_uc009yhs.1_Intron	NM_006292	NP_006283			tumor susceptibility gene 101						cell division|cellular membrane organization|endosome transport|interspecies interaction between organisms|non-lytic virus budding|protein transport|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	early endosome|late endosome membrane|multivesicular body|nucleolus|plasma membrane	calcium-dependent protein binding|DNA binding|transcription corepressor activity|ubiquitin binding|ubiquitin protein ligase binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	18894389	18894389	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18894389delT								PTPN5 (81000 upstream) : MRGPRX1 (60972 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	19336937	19336937	+	IGR	DEL	T	-	-	rs68037122		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19336937delT								E2F8 (73770 upstream) : NAV2 (35334 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	19364212	19364213	+	IGR	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19364212_19364213delGA								E2F8 (101045 upstream) : NAV2 (8058 downstream)																																			---	---	---	---
NAV2	89797	broad.mit.edu	37	11	19812447	19812450	+	Intron	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19812447_19812450delTTTT	uc010rdm.1	+						NAV2_uc001mpp.2_Intron|NAV2_uc001mpr.3_Intron	NM_145117	NP_660093			neuron navigator 2 isoform 2							nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6																		---	---	---	---
NAV2	89797	broad.mit.edu	37	11	19814459	19814459	+	Intron	DEL	A	-	-	rs71816549		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19814459delA	uc010rdm.1	+						NAV2_uc001mpp.2_Intron|NAV2_uc001mpr.3_Intron	NM_145117	NP_660093			neuron navigator 2 isoform 2							nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6																		---	---	---	---
NAV2	89797	broad.mit.edu	37	11	19962968	19962968	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19962968delA	uc010rdm.1	+						NAV2_uc001mpp.2_Intron|NAV2_uc001mpr.3_Intron	NM_145117	NP_660093			neuron navigator 2 isoform 2							nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6																		---	---	---	---
HTATIP2	10553	broad.mit.edu	37	11	20404503	20404503	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20404503delT	uc009yia.1	+						HTATIP2_uc009yib.1_Intron|HTATIP2_uc001mpx.2_Intron|HTATIP2_uc001mpz.2_Intron	NM_006410	NP_006401			HIV-1 Tat interactive protein 2, 30kDa isoform						angiogenesis|anti-apoptosis|apoptosis|cell differentiation|cellular amino acid metabolic process|induction of apoptosis|interspecies interaction between organisms|nuclear import|regulation of angiogenesis|regulation of transcription from RNA polymerase II promoter	cytoplasm|nuclear envelope	NAD binding|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor|protein binding|transcription coactivator activity				0																		---	---	---	---
NELL1	4745	broad.mit.edu	37	11	20772569	20772570	+	Intron	INS	-	AC	AC	rs150624420	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20772569_20772570insAC	uc001mqe.2	+						NELL1_uc001mqf.2_Intron|NELL1_uc009yid.2_Intron|NELL1_uc010rdo.1_Intron|NELL1_uc010rdp.1_Intron	NM_006157	NP_006148			nel-like 1 isoform 1 precursor						cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3																		---	---	---	---
NELL1	4745	broad.mit.edu	37	11	20806967	20806967	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20806967delT	uc001mqe.2	+						NELL1_uc001mqf.2_Intron|NELL1_uc009yid.2_Intron|NELL1_uc010rdo.1_Intron|NELL1_uc010rdp.1_Intron	NM_006157	NP_006148			nel-like 1 isoform 1 precursor						cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3																		---	---	---	---
NELL1	4745	broad.mit.edu	37	11	20935220	20935220	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20935220delA	uc001mqe.2	+						NELL1_uc001mqf.2_Intron|NELL1_uc009yid.2_Intron|NELL1_uc010rdo.1_Intron|NELL1_uc010rdp.1_Intron	NM_006157	NP_006148			nel-like 1 isoform 1 precursor						cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3																		---	---	---	---
NELL1	4745	broad.mit.edu	37	11	21228280	21228280	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:21228280delT	uc001mqe.2	+						NELL1_uc001mqf.2_Intron|NELL1_uc009yid.2_Intron|NELL1_uc010rdo.1_Intron|NELL1_uc010rdp.1_Intron	NM_006157	NP_006148			nel-like 1 isoform 1 precursor						cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3																		---	---	---	---
SLC17A6	57084	broad.mit.edu	37	11	22395955	22395956	+	Intron	INS	-	CT	CT	rs146775795	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22395955_22395956insCT	uc001mqk.2	+							NM_020346	NP_065079			solute carrier family 17 (sodium-dependent						sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)|breast(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	22633741	22633741	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22633741delT								SLC17A6 (232697 upstream) : FANCF (10338 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	22873468	22873468	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22873468delT	uc001mqq.1	+											full-length cDNA clone CS0DJ011YO21 of T cells (Jurkat cell line) Cot 10-normalized of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	23154141	23154141	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:23154141delT								SVIP (302759 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	23785305	23785306	+	IGR	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:23785305_23785306insG								SVIP (933923 upstream) : LUZP2 (733250 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	24029867	24029868	+	IGR	DEL	AA	-	-	rs34775256		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:24029867_24029868delAA								None (None upstream) : LUZP2 (488688 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	24079772	24079773	+	IGR	DEL	TT	-	-	rs75541453		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:24079772_24079773delTT								None (None upstream) : LUZP2 (438783 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	25469488	25469489	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:25469488_25469489insA								LUZP2 (365306 upstream) : ANO3 (741340 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	25950207	25950207	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:25950207delA								LUZP2 (846025 upstream) : ANO3 (260622 downstream)																																			---	---	---	---
CCDC34	91057	broad.mit.edu	37	11	27367942	27367942	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27367942delA	uc001mrh.1	-							NM_030771	NP_110398			coiled-coil domain containing 34 isoform 1												0																		---	---	---	---
LGR4	55366	broad.mit.edu	37	11	27390693	27390693	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27390693delA	uc001mrj.3	-						LGR4_uc001mrk.3_Intron	NM_018490	NP_060960			leucine-rich repeat-containing G protein-coupled							integral to membrane|plasma membrane	protein-hormone receptor activity			ovary(1)	1																		---	---	---	---
LGR4	55366	broad.mit.edu	37	11	27393950	27393950	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27393950delA	uc001mrj.3	-						LGR4_uc001mrk.3_Intron	NM_018490	NP_060960			leucine-rich repeat-containing G protein-coupled							integral to membrane|plasma membrane	protein-hormone receptor activity			ovary(1)	1																		---	---	---	---
LGR4	55366	broad.mit.edu	37	11	27457462	27457463	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27457462_27457463insT	uc001mrj.3	-						LGR4_uc001mrk.3_Intron	NM_018490	NP_060960			leucine-rich repeat-containing G protein-coupled							integral to membrane|plasma membrane	protein-hormone receptor activity			ovary(1)	1																		---	---	---	---
LGR4	55366	broad.mit.edu	37	11	27483179	27483180	+	Intron	INS	-	T	T	rs35154112		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27483179_27483180insT	uc001mrj.3	-						LGR4_uc001mrk.3_Intron	NM_018490	NP_060960			leucine-rich repeat-containing G protein-coupled							integral to membrane|plasma membrane	protein-hormone receptor activity			ovary(1)	1																		---	---	---	---
LGR4	55366	broad.mit.edu	37	11	27491106	27491106	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27491106delC	uc001mrj.3	-						LGR4_uc001mrk.3_Intron	NM_018490	NP_060960			leucine-rich repeat-containing G protein-coupled							integral to membrane|plasma membrane	protein-hormone receptor activity			ovary(1)	1																		---	---	---	---
LIN7C	55327	broad.mit.edu	37	11	27520359	27520359	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27520359delA	uc001mrl.2	-						LIN7C_uc009yii.2_Intron	NM_018362	NP_060832			lin-7 homolog C						exocytosis|protein transport	basolateral plasma membrane|postsynaptic density|postsynaptic membrane|synaptosome|tight junction					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	27829878	27829878	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27829878delT								BDNF (86273 upstream) : KIF18A (212285 downstream)																																			---	---	---	---
METT5D1	196074	broad.mit.edu	37	11	28190015	28190015	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:28190015delT	uc001msh.2	+						METT5D1_uc001msg.2_Intron|METT5D1_uc001mse.2_Intron	NM_001113528	NP_001107000			methyltransferase 5 domain containing 1 isoform								methyltransferase activity				0																		---	---	---	---
METT5D1	196074	broad.mit.edu	37	11	28229411	28229411	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:28229411delC	uc001msh.2	+						METT5D1_uc001msg.2_Intron|METT5D1_uc001mse.2_Intron	NM_001113528	NP_001107000			methyltransferase 5 domain containing 1 isoform								methyltransferase activity				0																		---	---	---	---
METT5D1	196074	broad.mit.edu	37	11	28260508	28260509	+	Intron	DEL	TT	-	-	rs76357742		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:28260508_28260509delTT	uc001msh.2	+						METT5D1_uc001msg.2_Intron|METT5D1_uc001mse.2_Intron	NM_001113528	NP_001107000			methyltransferase 5 domain containing 1 isoform								methyltransferase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	28403464	28403465	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:28403464_28403465delTT								METT5D1 (48410 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	28608939	28608939	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:28608939delT								METT5D1 (253885 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	28673639	28673639	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:28673639delT								METT5D1 (318585 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	29520726	29520730	+	IGR	DEL	CAAAT	-	-	rs72051173		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:29520726_29520730delCAAAT								None (None upstream) : KCNA4 (511036 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	30279224	30279224	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30279224delG								FSHB (22401 upstream) : C11orf46 (65425 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	30646151	30646151	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30646151delT								MPPED2 (38221 upstream) : DCDC1 (318598 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	30682915	30682916	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30682915_30682916insT								MPPED2 (74985 upstream) : DCDC1 (281833 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	30925317	30925317	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:30925317delA	uc001mss.1	-						uc009yjk.1_Intron|uc009yjj.1_Intron					Homo sapiens mRNA for KIAA1493 protein, partial cds.																														---	---	---	---
DNAJC24	120526	broad.mit.edu	37	11	31408948	31408949	+	Intron	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31408948_31408949delAG	uc001msx.2	+						DNAJC24_uc001msw.1_Intron|DNAJC24_uc009yjm.2_Intron	NM_181706	NP_859057			zinc finger, CSL domain containing 3						protein folding		heat shock protein binding|metal ion binding|unfolded protein binding			breast(2)	2																		---	---	---	---
ELP4	26610	broad.mit.edu	37	11	31539173	31539173	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31539173delT	uc001mtb.2	+						ELP4_uc001mta.1_Intron|ELP4_uc001mtc.2_Intron|ELP4_uc010rdz.1_Intron	NM_019040	NP_061913			elongation protein 4 homolog						histone acetylation|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|DNA-directed RNA polymerase II, holoenzyme|Elongator holoenzyme complex|transcription elongation factor complex	phosphorylase kinase regulator activity|protein binding			upper_aerodigestive_tract(1)|ovary(1)|prostate(1)	3	Lung SC(675;0.225)																	---	---	---	---
Unknown	0	broad.mit.edu	37	11	32335864	32335864	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32335864delA								RCN1 (208593 upstream) : WT1 (73461 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	32504255	32504255	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32504255delA								WIT1 (35994 upstream) : EIF3M (101136 downstream)																																			---	---	---	---
CCDC73	493860	broad.mit.edu	37	11	32759340	32759340	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32759340delT	uc001mtv.2	-						CCDC73_uc001mtw.1_Intron|CCDC73_uc009yjt.2_Intron	NM_001008391	NP_001008392			sarcoma antigen NY-SAR-79											ovary(1)|central_nervous_system(1)	2	Breast(20;0.112)																	---	---	---	---
Unknown	0	broad.mit.edu	37	11	33031610	33031610	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33031610delA								QSER1 (16748 upstream) : DEPDC7 (5800 downstream)																																			---	---	---	---
CSTF3	1479	broad.mit.edu	37	11	33127404	33127404	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33127404delA	uc001muh.2	-						TCP11L1_uc001muf.1_RNA	NM_001326	NP_001317			cleavage stimulation factor subunit 3 isoform 1						mRNA cleavage|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	nucleoplasm	protein binding|RNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	33541979	33541980	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33541979_33541980delAA								HIPK3 (166040 upstream) : C11orf41 (21897 downstream)																																			---	---	---	---
FBXO3	26273	broad.mit.edu	37	11	33792523	33792523	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33792523delA	uc001muz.2	-						FBXO3_uc001muy.2_5'UTR|FBXO3_uc009ykb.2_Intron|FBXO3_uc001mva.1_Intron|FBXO3_uc001mvb.1_Intron|FBXO3_uc010rek.1_Intron	NM_012175	NP_036307			F-box only protein 3 isoform 1						proteolysis	nucleus	ubiquitin-protein ligase activity			pancreas(1)	1		Lung NSC(402;0.0804)		BRCA - Breast invasive adenocarcinoma(625;0.00315)|Lung(977;0.00488)|LUSC - Lung squamous cell carcinoma(625;0.008)														---	---	---	---
ABTB2	25841	broad.mit.edu	37	11	34218100	34218100	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34218100delA	uc001mvl.1	-							NM_145804	NP_665803			ankyrin repeat and BTB (POZ) domain containing								DNA binding			central_nervous_system(1)|skin(1)	2		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(20;0.0691)																---	---	---	---
ABTB2	25841	broad.mit.edu	37	11	34322287	34322288	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34322287_34322288insT	uc001mvl.1	-							NM_145804	NP_665803			ankyrin repeat and BTB (POZ) domain containing								DNA binding			central_nervous_system(1)|skin(1)	2		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(20;0.0691)																---	---	---	---
PDHX	8050	broad.mit.edu	37	11	34979161	34979161	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34979161delA	uc001mvt.2	+						PDHX_uc010rep.1_Intron|PDHX_uc010req.1_Intron	NM_003477	NP_003468			pyruvate dehydrogenase complex, component X						pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	acyltransferase activity			kidney(1)	1	all_epithelial(35;0.115)|Lung NSC(22;0.218)|all_lung(20;0.242)	all_hematologic(20;0.124)	STAD - Stomach adenocarcinoma(6;0.00113)															---	---	---	---
Unknown	0	broad.mit.edu	37	11	35102071	35102071	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35102071delT								PDHX (84397 upstream) : CD44 (58346 downstream)																																			---	---	---	---
PAMR1	25891	broad.mit.edu	37	11	35460747	35460747	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35460747delT	uc001mwg.2	-						PAMR1_uc001mwf.2_Intron|PAMR1_uc010rew.1_Intron|PAMR1_uc010rex.1_Intron	NM_001001991	NP_001001991			regeneration associated muscle protease isoform						proteolysis	extracellular region	serine-type endopeptidase activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	35911427	35911427	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35911427delA								TRIM44 (80497 upstream) : LDLRAD3 (54185 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	36488383	36488383	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36488383delC								PRR5L (1630 upstream) : TRAF6 (22340 downstream)																																			---	---	---	---
RAG1	5896	broad.mit.edu	37	11	36588076	36588076	+	5'Flank	DEL	G	-	-	rs144896778	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36588076delG	uc001mwu.3	+						RAG1_uc001mwt.2_RNA	NM_000448	NP_000439			recombination activating gene 1						histone monoubiquitination|immune response|pre-B cell allelic exclusion|protein autoubiquitination|T cell differentiation in thymus|V(D)J recombination	nucleus	endonuclease activity|histone binding|protein homodimerization activity|sequence-specific DNA binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|pancreas(1)|lung(1)|kidney(1)|skin(1)	5	all_lung(20;0.226)	all_hematologic(20;0.107)												Familial_Hemophagocytic_Lymphohistiocytosis				---	---	---	---
Unknown	0	broad.mit.edu	37	11	37307487	37307487	+	IGR	DEL	T	-	-	rs10717002		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:37307487delT								C11orf74 (611097 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	37331159	37331159	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:37331159delT								C11orf74 (634769 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	37439158	37439158	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:37439158delT								C11orf74 (742768 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	37538592	37538592	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:37538592delA								C11orf74 (842202 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	38386305	38386305	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:38386305delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	38803881	38803881	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:38803881delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	39032697	39032697	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:39032697delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	39731409	39731409	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:39731409delA								None (None upstream) : LRRC4C (404344 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	39865886	39865886	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:39865886delA								None (None upstream) : LRRC4C (269867 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	39926147	39926147	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:39926147delA								None (None upstream) : LRRC4C (209606 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	39931863	39931864	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:39931863_39931864delAA								None (None upstream) : LRRC4C (203889 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	40135669	40135670	+	IGR	INS	-	CAAT	CAAT	rs140476773	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:40135669_40135670insCAAT								None (None upstream) : LRRC4C (83 downstream)																																			---	---	---	---
LRRC4C	57689	broad.mit.edu	37	11	41143483	41143484	+	Intron	DEL	AA	-	-	rs5791421		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:41143483_41143484delAA	uc001mxc.1	-						LRRC4C_uc001mxd.1_Intron	NM_020929	NP_065980			netrin-G1 ligand precursor						regulation of axonogenesis	integral to membrane	protein binding			ovary(4)|skin(3)|central_nervous_system(1)	8		all_lung(304;0.0575)|Lung NSC(402;0.138)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	41816649	41816650	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:41816649_41816650insT								LRRC4C (335326 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	42248281	42248281	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:42248281delA								LRRC4C (766958 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	42357540	42357541	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:42357540_42357541insA								LRRC4C (876217 upstream) : API5 (975964 downstream)																																			---	---	---	---
TTC17	55761	broad.mit.edu	37	11	43401028	43401030	+	Intron	DEL	GTG	-	-	rs35337370		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43401028_43401030delGTG	uc001mxi.2	+						TTC17_uc001mxh.2_Intron|TTC17_uc010rfj.1_Intron	NM_018259	NP_060729			tetratricopeptide repeat domain 17								binding			ovary(5)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	43523382	43523382	+	IGR	DEL	A	-	-	rs75886377		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43523382delA								TTC17 (7889 upstream) : MIR670 (57824 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	43602272	43602272	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43602272delT	uc001mxo.1	+						MIR129-2_hsa-mir-129-2|MI0000473_5'Flank					DM004400																														---	---	---	---
HSD17B12	51144	broad.mit.edu	37	11	43704943	43704943	+	Intron	DEL	T	-	-	rs113122839	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43704943delT	uc001mxq.3	+						HSD17B12_uc001mxp.2_Intron	NM_016142	NP_057226			hydroxysteroid (17-beta) dehydrogenase 12						long-chain fatty-acyl-CoA biosynthetic process|steroid biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane	estradiol 17-beta-dehydrogenase activity|long-chain-3-hydroxyacyl-CoA dehydrogenase activity				0																		---	---	---	---
EXT2	2132	broad.mit.edu	37	11	44111865	44111865	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44111865delT	uc010rfo.1	+							NM_207122	NP_997005			exostosin 2 isoform 2						glycosaminoglycan biosynthetic process|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|ossification|signal transduction	Golgi membrane|integral to membrane|intrinsic to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|heparan sulfate N-acetylglucosaminyltransferase activity|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity|protein heterodimerization activity			lung(2)|breast(2)|skin(1)	5								Mis|N|F|S			exostoses|osteosarcoma			Hereditary_Multiple_Exostoses				---	---	---	---
EXT2	2132	broad.mit.edu	37	11	44219934	44219935	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44219934_44219935delAA	uc001mxz.2	+						EXT2_uc010rfo.1_Intron|EXT2_uc001mxy.2_Intron|EXT2_uc009ykt.2_Intron|EXT2_uc001mya.2_Intron	NM_207122	NP_997005			exostosin 2 isoform 2						glycosaminoglycan biosynthetic process|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|ossification|signal transduction	Golgi membrane|integral to membrane|intrinsic to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|heparan sulfate N-acetylglucosaminyltransferase activity|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity|protein heterodimerization activity			lung(2)|breast(2)|skin(1)	5								Mis|N|F|S			exostoses|osteosarcoma			Hereditary_Multiple_Exostoses				---	---	---	---
EXT2	2132	broad.mit.edu	37	11	44264781	44264781	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44264781delT	uc001mxz.2	+						EXT2_uc010rfo.1_Intron|EXT2_uc001mxy.2_Intron|EXT2_uc009ykt.2_Intron|EXT2_uc001mya.2_Intron	NM_207122	NP_997005			exostosin 2 isoform 2						glycosaminoglycan biosynthetic process|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|ossification|signal transduction	Golgi membrane|integral to membrane|intrinsic to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|heparan sulfate N-acetylglucosaminyltransferase activity|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity|protein heterodimerization activity			lung(2)|breast(2)|skin(1)	5								Mis|N|F|S			exostoses|osteosarcoma			Hereditary_Multiple_Exostoses				---	---	---	---
Unknown	0	broad.mit.edu	37	11	44345446	44345446	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44345446delA								ALX4 (13730 upstream) : CD82 (241695 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	44360634	44360634	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44360634delG								ALX4 (28918 upstream) : CD82 (226507 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	44442668	44442668	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44442668delG								ALX4 (110952 upstream) : CD82 (144473 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	44727097	44727097	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44727097delC								CD82 (85784 upstream) : TSPAN18 (154782 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	45603620	45603620	+	IGR	DEL	G	-	-	rs149804190	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45603620delG								SYT13 (295736 upstream) : CHST1 (66807 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	45714330	45714330	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45714330delT	uc010rfy.1	-						uc001mzg.2_5'Flank|uc001mzh.2_5'Flank					DQ577288																														---	---	---	---
PEX16	9409	broad.mit.edu	37	11	45934370	45934370	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45934370delT	uc001nbu.2	-						PEX16_uc001nbt.2_Intron	NM_004813	NP_004804			peroxisomal biogenesis factor 16 isoform 1						ER-dependent peroxisome organization|peroxisome membrane biogenesis|protein import into peroxisome matrix|protein import into peroxisome membrane	endoplasmic reticulum membrane|integral to peroxisomal membrane	protein C-terminus binding			ovary(2)|skin(1)	3				GBM - Glioblastoma multiforme(35;0.223)														---	---	---	---
PHF21A	51317	broad.mit.edu	37	11	46004856	46004857	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46004856_46004857delAA	uc001ncc.3	-						PHF21A_uc001ncb.3_Intron|PHF21A_uc009ykx.2_Intron|PHF21A_uc001nce.2_Intron	NM_001101802	NP_001095272			BRAF35/HDAC2 complex isoform a						blood coagulation|chromatin modification|negative regulation of transcription from RNA polymerase II promoter|regulation of transcription, DNA-dependent|transcription, DNA-dependent	histone deacetylase complex	DNA binding|zinc ion binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	46226175	46226175	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46226175delA								PHF21A (83190 upstream) : CREB3L1 (73053 downstream)																																			---	---	---	---
AMBRA1	55626	broad.mit.edu	37	11	46450142	46450142	+	Intron	DEL	C	-	-	rs2864834	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46450142delC	uc010rgu.1	-						AMBRA1_uc010rgt.1_Intron|AMBRA1_uc009ylc.1_Intron|AMBRA1_uc001ncu.1_Intron|AMBRA1_uc001ncv.2_Intron|AMBRA1_uc001ncw.2_Intron|AMBRA1_uc001ncx.2_Intron	NM_017749	NP_060219			activating molecule in beclin-1-regulated						autophagy|cell differentiation|nervous system development	autophagic vacuole|cytoplasmic vesicle				large_intestine(1)|ovary(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)														---	---	---	---
AMBRA1	55626	broad.mit.edu	37	11	46610813	46610813	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46610813delA	uc010rgu.1	-						AMBRA1_uc001ncu.1_Intron|AMBRA1_uc001ncv.2_Intron|AMBRA1_uc001ncw.2_Intron|AMBRA1_uc001ncx.2_Intron	NM_017749	NP_060219			activating molecule in beclin-1-regulated						autophagy|cell differentiation|nervous system development	autophagic vacuole|cytoplasmic vesicle				large_intestine(1)|ovary(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)														---	---	---	---
CKAP5	9793	broad.mit.edu	37	11	46775145	46775145	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46775145delT	uc001ndi.1	-						CKAP5_uc009ylg.1_Intron|CKAP5_uc001ndj.1_Intron|CKAP5_uc001ndh.1_Intron	NM_001008938	NP_001008938			colonic and hepatic tumor over-expressed protein						cell division|centrosome organization|establishment or maintenance of microtubule cytoskeleton polarity|G2/M transition of mitotic cell cycle|mitotic prometaphase|RNA transport|spindle organization	centrosome|cytosol	protein binding|protein binding			ovary(1)|skin(1)	2																		---	---	---	---
SLC39A13	91252	broad.mit.edu	37	11	47378911	47378912	+	Intron	INS	-	ACAC	ACAC	rs150309481		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47378911_47378912insACAC	uc001nfd.2	+						SPI1_uc001nfb.1_Intron|SPI1_uc001nfc.1_Intron					RecName: Full=Zinc transporter ZIP13; AltName: Full=Zrt- and Irt-like protein 13;          Short=ZIP-13; AltName: Full=Solute carrier family 39 member 13; AltName: Full=LIV-1 subfamily of ZIP zinc transporter 9; AltName: Full=LZT-Hs9;						zinc ion transport	integral to membrane	metal ion transmembrane transporter activity				0				Lung(87;0.0936)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	47438428	47438428	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47438428delT								SLC39A13 (382 upstream) : PSMC3 (1892 downstream)																																			---	---	---	---
AGBL2	79841	broad.mit.edu	37	11	47706980	47706980	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47706980delT	uc001ngg.2	-						AGBL2_uc001ngf.2_Intron|AGBL2_uc010rhq.1_Intron|AGBL2_uc001ngh.1_Intron	NM_024783	NP_079059			carboxypeptidase 2, cytosolic						proteolysis	cytosol	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
PTPRJ	5795	broad.mit.edu	37	11	48016679	48016679	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48016679delT	uc001ngp.3	+						PTPRJ_uc001ngo.3_Intron	NM_002843	NP_002834			protein tyrosine phosphatase, receptor type, J						contact inhibition|negative regulation of cell growth|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of MAP kinase activity|negative regulation of platelet-derived growth factor receptor signaling pathway|negative regulation of protein kinase B signaling cascade|negative regulation of T cell receptor signaling pathway|negative regulation of vascular permeability|platelet-derived growth factor receptor signaling pathway|positive chemotaxis|positive regulation of focal adhesion assembly|positive regulation of protein kinase B signaling cascade|positive regulation of survival gene product expression	cell surface|cell-cell junction|immunological synapse|integral to plasma membrane|ruffle membrane	beta-catenin binding|delta-catenin binding|gamma-catenin binding|mitogen-activated protein kinase binding|platelet-derived growth factor receptor binding|protein tyrosine phosphatase activity			breast(3)|kidney(3)|ovary(1)|skin(1)	8																		---	---	---	---
PTPRJ	5795	broad.mit.edu	37	11	48027840	48027841	+	Intron	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48027840_48027841delGA	uc001ngp.3	+						PTPRJ_uc001ngo.3_Intron	NM_002843	NP_002834			protein tyrosine phosphatase, receptor type, J						contact inhibition|negative regulation of cell growth|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of MAP kinase activity|negative regulation of platelet-derived growth factor receptor signaling pathway|negative regulation of protein kinase B signaling cascade|negative regulation of T cell receptor signaling pathway|negative regulation of vascular permeability|platelet-derived growth factor receptor signaling pathway|positive chemotaxis|positive regulation of focal adhesion assembly|positive regulation of protein kinase B signaling cascade|positive regulation of survival gene product expression	cell surface|cell-cell junction|immunological synapse|integral to plasma membrane|ruffle membrane	beta-catenin binding|delta-catenin binding|gamma-catenin binding|mitogen-activated protein kinase binding|platelet-derived growth factor receptor binding|protein tyrosine phosphatase activity			breast(3)|kidney(3)|ovary(1)|skin(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	48313154	48313154	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48313154delA								OR4X1 (26825 upstream) : OR4S1 (14621 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	48347622	48347623	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48347622_48347623delTT								OR4C3 (142 upstream) : OR4C45 (19279 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	48364859	48364860	+	IGR	INS	-	C	C	rs147261683	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48364859_48364860insC								OR4C3 (17379 upstream) : OR4C45 (2042 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	48765500	48765501	+	IGR	INS	-	G	G	rs61930777		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48765500_48765501insG								OR4A47 (254228 upstream) : FOLH1 (402687 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	48821856	48821857	+	IGR	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48821856_48821857delGA								OR4A47 (310584 upstream) : FOLH1 (346331 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	49573285	49573285	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:49573285delA								FOLH1 (343063 upstream) : LOC440040 (6795 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	50261100	50261100	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:50261100delT								LOC441601 (3477 upstream) : LOC646813 (107218 downstream)																																			---	---	---	---
LOC646813	646813	broad.mit.edu	37	11	50368965	50368965	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:50368965delT	uc001nhe.2	+						LOC646813_uc001nhf.1_Intron|LOC646813_uc001nhg.1_Intron	NR_024504				Homo sapiens mRNA for hypothetical protein, partial sequence, clone:Hsa11-digit09-11-09-R.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	50391793	50391793	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:50391793delT								LOC646813 (11990 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	55498899	55498899	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55498899delT								OR4C6 (64741 upstream) : OR5D13 (42015 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	55900444	55900444	+	IGR	DEL	C	-	-	rs2512790	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55900444delC								OR8H3 (9657 upstream) : OR8J3 (3805 downstream)																																			---	---	---	---
OR5T3	390154	broad.mit.edu	37	11	56017746	56017746	+	5'Flank	DEL	T	-	-	rs78441299		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56017746delT	uc010rjd.1	+							NM_001004747	NP_001004747			olfactory receptor, family 5, subfamily T,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	Esophageal squamous(21;0.00448)																	---	---	---	---
Unknown	0	broad.mit.edu	37	11	56222088	56222088	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56222088delT								OR5R1 (36380 upstream) : OR5M9 (7859 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	56439359	56439359	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56439359delA								OR5AR1 (7267 upstream) : OR9G9 (28505 downstream)																																			---	---	---	---
OR5AK2	390181	broad.mit.edu	37	11	56755774	56755774	+	5'Flank	DEL	A	-	-	rs71830792		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56755774delA	uc010rjp.1	+							NM_001005323	NP_001005323			olfactory receptor, family 5, subfamily AK,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	56770731	56770732	+	IGR	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56770731_56770732delTC								OR5AK2 (13415 upstream) : LRRC55 (178489 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	56940590	56940590	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56940590delG								OR5AK2 (183274 upstream) : LRRC55 (8631 downstream)																																			---	---	---	---
CTNND1	1500	broad.mit.edu	37	11	57500681	57500682	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57500681_57500682delTT	uc001nlf.1	+						TMX2_uc001nlc.1_Intron|TMX2_uc001nld.1_Intron|TMX2_uc001nle.1_Intron	NM_001085462	NP_001078931			catenin, delta 1 isoform 1A						adherens junction organization|cell junction assembly|negative regulation of canonical Wnt receptor signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent|Wnt receptor signaling pathway	cytosol|midbody|nucleus	cadherin binding|protein binding|receptor binding			breast(4)|ovary(1)|kidney(1)	6		all_epithelial(135;0.155)																---	---	---	---
CTNND1	1500	broad.mit.edu	37	11	57502689	57502690	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57502689_57502690delTT	uc001nlf.1	+						TMX2_uc001nlc.1_Intron|TMX2_uc001nld.1_Intron|TMX2_uc001nle.1_Intron	NM_001085462	NP_001078931			catenin, delta 1 isoform 1A						adherens junction organization|cell junction assembly|negative regulation of canonical Wnt receptor signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent|Wnt receptor signaling pathway	cytosol|midbody|nucleus	cadherin binding|protein binding|receptor binding			breast(4)|ovary(1)|kidney(1)	6		all_epithelial(135;0.155)																---	---	---	---
CTNND1	1500	broad.mit.edu	37	11	57506409	57506409	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57506409delT	uc001nlf.1	+						TMX2_uc001nlc.1_Intron|TMX2_uc001nld.1_Intron|TMX2_uc001nle.1_Intron|C11orf31_uc010rjx.1_5'Flank	NM_001085462	NP_001078931			catenin, delta 1 isoform 1A						adherens junction organization|cell junction assembly|negative regulation of canonical Wnt receptor signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent|Wnt receptor signaling pathway	cytosol|midbody|nucleus	cadherin binding|protein binding|receptor binding			breast(4)|ovary(1)|kidney(1)	6		all_epithelial(135;0.155)																---	---	---	---
CTNND1	1500	broad.mit.edu	37	11	57559270	57559270	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57559270delT	uc001nmc.3	+						CTNND1_uc001nlf.1_Intron|CTNND1_uc001nlh.1_Intron|CTNND1_uc001nlu.3_Intron|CTNND1_uc001nlt.3_Intron|CTNND1_uc001nls.3_Intron|CTNND1_uc001nlw.3_Intron|CTNND1_uc001nmf.3_Intron|CTNND1_uc001nmd.3_Intron|CTNND1_uc001nlk.3_Intron|CTNND1_uc001nme.3_Intron|CTNND1_uc001nll.3_Intron|CTNND1_uc001nmg.3_Intron|CTNND1_uc001nlj.3_Intron|CTNND1_uc001nlr.3_Intron|CTNND1_uc001nlp.3_Intron|CTNND1_uc001nlx.3_Intron|CTNND1_uc001nlz.3_Intron|CTNND1_uc009ymn.2_Intron|CTNND1_uc001nlm.3_Intron|CTNND1_uc001nly.3_Intron|CTNND1_uc001nmb.3_Intron|CTNND1_uc001nma.3_Intron|CTNND1_uc001nmi.3_Intron|CTNND1_uc001nmh.3_Intron|CTNND1_uc001nlq.3_Intron|CTNND1_uc001nln.3_Intron|CTNND1_uc001nli.3_Intron|CTNND1_uc001nlo.3_Intron|CTNND1_uc001nlv.3_Intron	NM_001085458	NP_001078927			catenin, delta 1 isoform 1ABC						adherens junction organization|cell junction assembly|negative regulation of canonical Wnt receptor signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent|Wnt receptor signaling pathway	cytosol|midbody|nucleus	cadherin binding|protein binding|receptor binding			breast(4)|ovary(1)|kidney(1)	6		all_epithelial(135;0.155)																---	---	---	---
CTNND1	1500	broad.mit.edu	37	11	57571337	57571340	+	Intron	DEL	AAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57571337_57571340delAAAA	uc001nmc.3	+						CTNND1_uc001nlh.1_Intron|CTNND1_uc001nlu.3_Intron|CTNND1_uc001nlt.3_Intron|CTNND1_uc001nls.3_Intron|CTNND1_uc001nlw.3_Intron|CTNND1_uc001nmf.3_Intron|CTNND1_uc001nmd.3_Intron|CTNND1_uc001nlk.3_Intron|CTNND1_uc001nme.3_Intron|CTNND1_uc001nll.3_Intron|CTNND1_uc001nmg.3_Intron|CTNND1_uc001nlj.3_Intron|CTNND1_uc001nlr.3_Intron|CTNND1_uc001nlp.3_Intron|CTNND1_uc001nlx.3_Intron|CTNND1_uc001nlz.3_Intron|CTNND1_uc009ymn.2_Intron|CTNND1_uc001nlm.3_Intron|CTNND1_uc001nly.3_Intron|CTNND1_uc001nmb.3_Intron|CTNND1_uc001nma.3_Intron|CTNND1_uc001nmi.3_Intron|CTNND1_uc001nmh.3_Intron|CTNND1_uc001nlq.3_Intron|CTNND1_uc001nln.3_Intron|CTNND1_uc001nli.3_Intron|CTNND1_uc001nlo.3_Intron|CTNND1_uc001nlv.3_Intron	NM_001085458	NP_001078927			catenin, delta 1 isoform 1ABC						adherens junction organization|cell junction assembly|negative regulation of canonical Wnt receptor signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent|Wnt receptor signaling pathway	cytosol|midbody|nucleus	cadherin binding|protein binding|receptor binding			breast(4)|ovary(1)|kidney(1)	6		all_epithelial(135;0.155)																---	---	---	---
OR1S2	219958	broad.mit.edu	37	11	57972785	57972785	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57972785delA	uc010rkb.1	-							NM_001004459	NP_001004459			olfactory receptor, family 1, subfamily S,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(21;0.0589)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	58019258	58019259	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58019258_58019259insT								OR10Q1 (22911 upstream) : OR10W1 (15005 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	58599816	58599816	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58599816delA								GLYAT (100369 upstream) : GLYATL2 (1726 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	59016686	59016686	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59016686delA								MPEG1 (36192 upstream) : OR5AN1 (115246 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	59186519	59186519	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59186519delA								OR5AN1 (53653 upstream) : OR5A2 (2935 downstream)																																			---	---	---	---
OSBP	5007	broad.mit.edu	37	11	59348340	59348340	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59348340delT	uc001noc.1	-						OSBP_uc009ymr.1_Intron	NM_002556	NP_002547			oxysterol binding protein						lipid transport	Golgi membrane	oxysterol binding			large_intestine(1)	1		all_epithelial(135;0.000236)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)														---	---	---	---
OSBP	5007	broad.mit.edu	37	11	59360787	59360787	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59360787delT	uc001noc.1	-						OSBP_uc009ymr.1_Intron	NM_002556	NP_002547			oxysterol binding protein						lipid transport	Golgi membrane	oxysterol binding			large_intestine(1)	1		all_epithelial(135;0.000236)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	59472527	59472527	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59472527delT								PATL1 (36016 upstream) : OR10V1 (7862 downstream)																																			---	---	---	---
GIF	2694	broad.mit.edu	37	11	59611620	59611620	+	Intron	DEL	T	-	-	rs72085643		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59611620delT	uc001noi.2	-						GIF_uc010rkz.1_Intron	NM_005142	NP_005133			gastric intrinsic factor (vitamin B synthesis)						cobalamin metabolic process|cobalamin transport|cobalt ion transport	apical plasma membrane|endosome|extracellular space|microvillus	cobalamin binding			ovary(1)|liver(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	59723674	59723674	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59723674delT	uc001nok.1	+											Homo sapiens mRNA for hypothetical protein, partial sequence, clone:Hsa11-digit01-13-09-F.																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	59818474	59818474	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59818474delA								PLAC1L (2960 upstream) : MS4A3 (5627 downstream)																																			---	---	---	---
MS4A3	932	broad.mit.edu	37	11	59834686	59834689	+	Intron	DEL	TTTT	-	-	rs146138976		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59834686_59834689delTTTT	uc001nom.2	+						MS4A3_uc001non.2_Intron|MS4A3_uc001noo.2_Intron	NM_006138	NP_006129			membrane-spanning 4-domains, subfamily A, member							endomembrane system|integral to membrane|perinuclear region of cytoplasm	protein binding|receptor activity			ovary(2)|skin(1)	3		all_epithelial(135;0.245)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	60114947	60114947	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60114947delT								MS4A6E (6507 upstream) : MS4A7 (31011 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	60514935	60514936	+	IGR	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60514935_60514936delCT								MS4A8B (31653 upstream) : MS4A15 (9404 downstream)																																			---	---	---	---
VWCE	220001	broad.mit.edu	37	11	61048947	61048947	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61048947delA	uc001nra.2	-						VWCE_uc001nrb.2_Intron	NM_152718	NP_689931			von Willebrand factor C and EGF domains							extracellular region	calcium ion binding			ovary(1)	1																		---	---	---	---
VWCE	220001	broad.mit.edu	37	11	61051594	61051594	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61051594delG	uc001nra.2	-						VWCE_uc001nrb.2_Intron	NM_152718	NP_689931			von Willebrand factor C and EGF domains							extracellular region	calcium ion binding			ovary(1)	1																		---	---	---	---
CYBASC3	220002	broad.mit.edu	37	11	61124341	61124341	+	5'UTR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61124341delC	uc001nrf.3	-	1					CYBASC3_uc010rlh.1_Intron|CYBASC3_uc001nrg.2_Intron|CYBASC3_uc009ynn.2_Intron|CYBASC3_uc001nrh.2_Intron|CYBASC3_uc001nri.2_Intron|CYBASC3_uc009yno.2_5'UTR	NM_001161452	NP_001154924			cytochrome b, ascorbate dependent 3 isoform 2						electron transport chain|transport	integral to membrane|late endosome membrane|lysosomal membrane	metal ion binding|oxidoreductase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	61359816	61359817	+	Intron	INS	-	GT	GT	rs150576049	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61359816_61359817insGT	uc001nry.2	+											Homo sapiens, clone IMAGE:5742657, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	61377268	61377269	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61377268_61377269delAA								SYT7 (28970 upstream) : RPLP0P2 (5239 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	61829600	61829600	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61829600delA								FTH1 (94468 upstream) : INCENP (61845 downstream)																																			---	---	---	---
SCGB2A1	4246	broad.mit.edu	37	11	61980400	61980401	+	Intron	DEL	AT	-	-	rs61893721	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61980400_61980401delAT	uc001nta.2	+							NM_002407	NP_002398			secretoglobin, family 2A, member 1 precursor							extracellular region	androgen binding				0																		---	---	---	---
AHNAK	79026	broad.mit.edu	37	11	62233802	62233802	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62233802delT	uc001ntk.1	-							NM_024060	NP_076965			AHNAK nucleoprotein isoform 2						nervous system development	nucleus	protein binding			ovary(10)|pancreas(4)|skin(4)|upper_aerodigestive_tract(1)	19		Melanoma(852;0.155)																---	---	---	---
AHNAK	79026	broad.mit.edu	37	11	62303120	62303122	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62303120_62303122delAAA	uc001ntl.2	-						AHNAK_uc001ntk.1_Intron	NM_001620	NP_001611			AHNAK nucleoprotein isoform 1						nervous system development	nucleus	protein binding			ovary(10)|pancreas(4)|skin(4)|upper_aerodigestive_tract(1)	19		Melanoma(852;0.155)																---	---	---	---
TUT1	64852	broad.mit.edu	37	11	62351085	62351085	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62351085delA	uc001nto.2	-							NM_022830	NP_073741			terminal uridylyl transferase 1, U6						mRNA cleavage|mRNA polyadenylation|snRNA processing	nuclear speck|nucleolus	ATP binding|enzyme binding|mRNA 3'-UTR binding|polynucleotide adenylyltransferase activity|RNA uridylyltransferase activity|zinc ion binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
GANAB	23193	broad.mit.edu	37	11	62402662	62402663	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62402662_62402663delTT	uc001nub.2	-						GANAB_uc001nua.2_Intron|GANAB_uc001nuc.2_Intron|GANAB_uc010rma.1_Intron|GANAB_uc010rmb.1_Intron	NM_198334	NP_938148			neutral alpha-glucosidase AB isoform 2						post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|Golgi apparatus|melanosome	carbohydrate binding|glucan 1,3-alpha-glucosidase activity|protein binding			ovary(3)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
INTS5	80789	broad.mit.edu	37	11	62423550	62423553	+	5'Flank	DEL	AAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62423550_62423553delAAAA	uc001nud.2	-							NM_030628	NP_085131			integrator complex subunit 5						snRNA processing	integral to membrane|integrator complex	protein binding			ovary(2)	2																		---	---	---	---
HNRNPUL2	221092	broad.mit.edu	37	11	62495238	62495238	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62495238delA	uc001nuw.2	-						HNRNPUL2_uc001nuu.1_5'Flank|TTC9C_uc001nux.2_5'Flank|TTC9C_uc001nuy.2_5'Flank	NM_001079559	NP_001073027			heterogeneous nuclear ribonucleoprotein U-like						cell killing	nucleus	ATP binding|nucleic acid binding				0																		---	---	---	---
TTC9C	283237	broad.mit.edu	37	11	62504326	62504327	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62504326_62504327delAA	uc001nuy.2	+						TTC9C_uc001nux.2_Intron	NM_173810	NP_776171			tetratricopeptide repeat domain 9C								binding			ovary(1)|pancreas(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	62508387	62508389	+	IGR	DEL	AAA	-	-	rs112259195		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62508387_62508389delAAA								TTC9C (2282 upstream) : ZBTB3 (10048 downstream)																																			---	---	---	---
TAF6L	10629	broad.mit.edu	37	11	62544804	62544804	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62544804delA	uc001nvc.2	+						TAF6L_uc010rmg.1_Intron|TAF6L_uc009yof.2_Intron	NM_006473	NP_006464			TAF6-like RNA polymerase II						chromatin remodeling|histone H3 acetylation|regulation of sequence-specific DNA binding transcription factor activity|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	histone deacetylase complex|STAGA complex	DNA binding|protein binding|transcription coactivator activity			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	62784711	62784716	+	IGR	DEL	AAAAAA	-	-	rs71973700		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62784711_62784716delAAAAAA								SLC22A8 (1400 upstream) : SLC22A24 (62698 downstream)																																			---	---	---	---
RTN3	10313	broad.mit.edu	37	11	63450315	63450315	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63450315delA	uc001nxq.2	+						RTN3_uc001nxo.2_Intron|RTN3_uc001nxm.2_Intron|RTN3_uc001nxn.2_Intron|RTN3_uc001nxp.2_Intron|RTN3_uc009yov.2_Intron|RTN3_uc010rmt.1_Intron|RTN3_uc010rmu.1_Intron	NM_201428	NP_958831			reticulon 3 isoform b						apoptosis|endoplasmic reticulum tubular network organization|interspecies interaction between organisms|response to stress|vesicle-mediated transport	endoplasmic reticulum membrane|extracellular space|Golgi membrane|integral to membrane				ovary(1)	1																		---	---	---	---
FLRT1	23769	broad.mit.edu	37	11	63881484	63881491	+	Intron	DEL	ATGGATGG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63881484_63881491delATGGATGG	uc001nyi.1	+						MACROD1_uc001nyh.2_Intron	NM_013280	NP_037412			fibronectin leucine rich transmembrane protein						cell adhesion	integral to plasma membrane|proteinaceous extracellular matrix	protein binding, bridging|receptor signaling protein activity				0																		---	---	---	---
MACROD1	28992	broad.mit.edu	37	11	63898833	63898834	+	Intron	DEL	TC	-	-	rs148139544		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63898833_63898834delTC	uc001nyh.2	-							NM_014067	NP_054786			MACRO domain containing 1												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	64259836	64259837	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64259836_64259837delTT								RPS6KA4 (120150 upstream) : SLC22A11 (63261 downstream)																																			---	---	---	---
NRXN2	9379	broad.mit.edu	37	11	64461662	64461662	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64461662delC	uc001oar.2	-						NRXN2_uc001oas.2_Intron	NM_015080	NP_055895			neurexin 2 isoform alpha-1 precursor						cell adhesion	integral to membrane				upper_aerodigestive_tract(2)|central_nervous_system(2)|skin(2)|ovary(2)|kidney(1)|pancreas(1)	10																		---	---	---	---
MEN1	4221	broad.mit.edu	37	11	64573491	64573491	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64573491delA	uc001obj.2	-						MAP4K2_uc001obh.2_5'Flank|MAP4K2_uc001obi.2_5'Flank|MAP4K2_uc010rnp.1_5'Flank|MEN1_uc001obk.2_Intron|MEN1_uc001obl.2_Intron|MEN1_uc001obm.2_Intron|MEN1_uc001obn.2_Intron|MEN1_uc001obo.2_Intron|MEN1_uc001obp.2_Intron|MEN1_uc001obq.2_Intron|MEN1_uc001obr.2_Intron	NM_130800	NP_570712			menin isoform 1						DNA repair|histone lysine methylation|MAPKKK cascade|negative regulation of cell proliferation|negative regulation of cyclin-dependent protein kinase activity|negative regulation of JNK cascade|negative regulation of osteoblast differentiation|negative regulation of protein phosphorylation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of telomerase activity|negative regulation of transcription from RNA polymerase II promoter|osteoblast development|positive regulation of protein binding|positive regulation of transforming growth factor beta receptor signaling pathway|response to gamma radiation|response to UV|transcription, DNA-dependent	chromatin|cleavage furrow|cytosol|histone methyltransferase complex|nuclear matrix|soluble fraction	double-stranded DNA binding|four-way junction DNA binding|protein binding, bridging|protein N-terminus binding|R-SMAD binding|transcription regulatory region DNA binding|Y-form DNA binding			parathyroid(105)|pancreas(64)|gastrointestinal_tract_(site_indeterminate)(15)|small_intestine(13)|lung(9)|pituitary(7)|NS(7)|adrenal_gland(5)|soft_tissue(4)|central_nervous_system(4)|thymus(2)|stomach(1)|retroperitoneum(1)|skin(1)	238								D|Mis|N|F|S		parathyroid tumors|Pancreatic neuroendocrine tumors	parathyroid adenoma|pituitary adenoma|pancreatic islet cell|carcinoid			Hyperparathyroidism_Familial_Isolated|Multiple_Endocrine_Neoplasia_type_1				---	---	---	---
GPHA2	170589	broad.mit.edu	37	11	64702106	64702106	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64702106delT	uc001oca.2	-	4						NM_130769	NP_570125			glycoprotein hormone alpha 2 precursor							extracellular region	hormone activity				0																		---	---	---	---
SNX15	29907	broad.mit.edu	37	11	64790411	64790412	+	Intron	DEL	AA	-	-	rs76658335		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64790411_64790412delAA	uc001oci.3	+							NM_013306	NP_037438			sorting nexin 15 isoform A						cell communication|intracellular protein transport	cytoplasmic vesicle membrane|cytosol	phosphatidylinositol binding|protein transporter activity			ovary(1)	1																		---	---	---	---
PCNXL3	399909	broad.mit.edu	37	11	65401943	65401943	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65401943delC	uc001oey.2	+						PCNXL3_uc001oez.2_Intron	NM_032223	NP_115599			pecanex-like 3							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	65499270	65499270	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65499270delA								RNASEH2C (10861 upstream) : DKFZp761E198 (44110 downstream)																																			---	---	---	---
SNX32	254122	broad.mit.edu	37	11	65613209	65613209	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65613209delA	uc001ofr.2	+						SNX32_uc009yqt.2_Intron|SNX32_uc010rop.1_Intron	NM_152760	NP_689973			sorting nexin 6B						cell communication|protein transport		phosphatidylinositol binding				0				READ - Rectum adenocarcinoma(159;0.171)														---	---	---	---
TSGA10IP	254187	broad.mit.edu	37	11	65723084	65723084	+	Intron	DEL	A	-	-	rs112447996		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65723084delA	uc001ogk.1	+						TSGA10IP_uc009yqw.1_Intron|TSGA10IP_uc009yqx.1_Intron	NM_152762	NP_689975			testis specific, 10 interacting protein												0																		---	---	---	---
BANF1	8815	broad.mit.edu	37	11	65770687	65770687	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65770687delT	uc001ogo.2	+						EIF1AD_uc001ogm.1_5'Flank|EIF1AD_uc001ogn.1_5'Flank|BANF1_uc001ogp.2_Intron	NM_003860	NP_003851			barrier to autointegration factor 1						initiation of viral infection|interspecies interaction between organisms|provirus integration|response to virus	chromosome|cytosol|nucleoplasm	DNA binding				0																		---	---	---	---
SF3B2	10992	broad.mit.edu	37	11	65820709	65820709	+	Intron	DEL	A	-	-	rs139893240		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65820709delA	uc001ogy.1	+						SF3B2_uc001ogx.1_Intron	NM_006842	NP_006833			splicing factor 3B subunit 2						interspecies interaction between organisms	catalytic step 2 spliceosome|nucleoplasm|U12-type spliceosomal complex	nucleic acid binding|protein binding			ovary(2)|breast(1)	3																		---	---	---	---
RAB1B	81876	broad.mit.edu	37	11	66039143	66039143	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66039143delA	uc001ohf.2	+						uc001ohg.1_RNA	NM_030981	NP_112243			RAB1B, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	Golgi apparatus|membrane	GTP binding|protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	66222215	66222215	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66222215delA								MRPL11 (15905 upstream) : PELI3 (12121 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	66225961	66225961	+	IGR	DEL	A	-	-	rs75702483		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66225961delA								MRPL11 (19651 upstream) : PELI3 (8375 downstream)																																			---	---	---	---
DPP3	10072	broad.mit.edu	37	11	66248961	66248961	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66248961delA	uc001oig.1	+						DPP3_uc001oif.1_Intron|DPP3_uc010rpe.1_Intron	NM_005700	NP_005691			dipeptidyl peptidase III						proteolysis	cytoplasm	aminopeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metallopeptidase activity			ovary(1)|skin(1)	2																		---	---	---	---
DPP3	10072	broad.mit.edu	37	11	66266835	66266836	+	Intron	DEL	AA	-	-	rs80248990		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66266835_66266836delAA	uc001oig.1	+						DPP3_uc001oif.1_Intron|DPP3_uc010rpe.1_Intron|DPP3_uc001oih.1_Intron	NM_005700	NP_005691			dipeptidyl peptidase III						proteolysis	cytoplasm	aminopeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metallopeptidase activity			ovary(1)|skin(1)	2																		---	---	---	---
RBM14	10432	broad.mit.edu	37	11	66384898	66384898	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66384898delG	uc001oit.2	+						RBM14_uc009yrh.2_Intron|RBM14_uc009yri.2_Intron|RBM4_uc009yrj.2_Intron|RBM4_uc009yrk.2_Intron	NM_006328	NP_006319			RNA binding motif protein 14						DNA recombination|DNA repair|DNA replication|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|histone deacetylation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus	mediator complex|ribonucleoprotein complex|transcription factor complex	ligand-dependent nuclear receptor transcription coactivator activity|nucleotide binding|protein binding, bridging|RNA binding|RNA polymerase II transcription cofactor activity			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
RBM4B	83759	broad.mit.edu	37	11	66436924	66436924	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66436924delT	uc001oja.2	-						RBM4B_uc001ojb.2_Intron	NM_031492	NP_113680			RNA binding motif protein 4B						circadian regulation of gene expression|entrainment of circadian clock by photoperiod|mRNA processing|RNA splicing	nucleolus	nucleotide binding|RNA binding|zinc ion binding				0																		---	---	---	---
SPTBN2	6712	broad.mit.edu	37	11	66453445	66453445	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66453445delG	uc001ojd.2	-	37	7142	c.7070delC	c.(7069-7071)CCAfs	p.P2357fs	SPTBN2_uc001ojc.1_3'UTR	NM_006946	NP_008877	O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	2357					actin filament capping|axon guidance|cell death|vesicle-mediated transport	cytosol|spectrin	actin binding|structural constituent of cytoskeleton			large_intestine(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
RHOD	29984	broad.mit.edu	37	11	66829457	66829457	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66829457delA	uc001ojv.2	+							NM_014578	NP_055393			ras homolog D precursor						regulation of small GTPase mediated signal transduction|Rho protein signal transduction	cytosol|plasma membrane	GTP binding|GTPase activity				0																		---	---	---	---
KDM2A	22992	broad.mit.edu	37	11	66932098	66932099	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66932098_66932099delTT	uc001ojw.2	+						KDM2A_uc001ojx.2_Intron	NM_012308	NP_036440			F-box and leucine-rich repeat protein 11						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	DNA binding|histone demethylase activity (H3-K36 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			ovary(4)|lung(3)|breast(1)|skin(1)	9																		---	---	---	---
SSH3	54961	broad.mit.edu	37	11	67079236	67079241	+	In_Frame_Del	DEL	CAGGAG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67079236_67079241delCAGGAG	uc001okj.2	+	14	2036_2041	c.1858_1863delCAGGAG	c.(1858-1863)CAGGAGdel	p.QE622del	SSH3_uc001okk.2_RNA|SSH3_uc001okl.2_In_Frame_Del_p.QE476del	NM_017857	NP_060327	Q8TE77	SSH3_HUMAN	slingshot homolog 3	622_623					regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of lamellipodium assembly	cytoplasm|cytoskeleton|nucleus	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)															---	---	---	---
PPP1CA	5499	broad.mit.edu	37	11	67168728	67168729	+	Intron	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67168728_67168729insG	uc001okw.1	-						PPP1CA_uc009yro.1_Intron|PPP1CA_uc001okt.1_Frame_Shift_Ins_p.P4fs|PPP1CA_uc001oku.1_Intron|PPP1CA_uc001okv.1_Intron|PPP1CA_uc001okx.1_Intron|PPP1CA_uc001oky.2_Intron|TBC1D10C_uc001okz.2_5'Flank|TBC1D10C_uc001ola.2_5'Flank|TBC1D10C_uc001olb.2_5'Flank	NM_002708	NP_002699			protein phosphatase 1, catalytic subunit, alpha						cell cycle|cell division|glycogen metabolic process|protein dephosphorylation|triglyceride catabolic process	cytosol|MLL5-L complex|nucleolus|PTW/PP1 phosphatase complex	metal ion binding|protein binding|protein phosphatase type 1 regulator activity|protein serine/threonine phosphatase activity			breast(1)|pancreas(1)	2			BRCA - Breast invasive adenocarcinoma(15;8.53e-07)															---	---	---	---
CABP4	57010	broad.mit.edu	37	11	67221698	67221698	+	5'Flank	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67221698delC	uc001olo.2	+						GPR152_uc001olm.2_5'Flank|CABP4_uc001oln.2_Intron	NM_145200	NP_660201			calcium binding protein 4						visual perception	cytoplasm|extracellular region|terminal button	calcium ion binding				0			BRCA - Breast invasive adenocarcinoma(15;8.18e-06)															---	---	---	---
AIP	9049	broad.mit.edu	37	11	67254767	67254768	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67254767_67254768delTT	uc001olv.2	+							NM_003977	NP_003968			aryl hydrocarbon receptor interacting protein						protein maturation by protein folding|protein targeting to mitochondrion	nucleus	signal transducer activity|transcription coactivator activity|transcription factor binding|unfolded protein binding				0														Familial_Isolated_Pituitary_Adenoma_				---	---	---	---
PITPNM1	9600	broad.mit.edu	37	11	67259794	67259794	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67259794delG	uc001olx.2	-						PITPNM1_uc001olw.2_Intron|PITPNM1_uc001oly.2_Intron|PITPNM1_uc001olz.2_Intron	NM_004910	NP_004901			phosphatidylinositol transfer protein,						brain development|lipid metabolic process|phototransduction|protein transport	cleavage furrow|endoplasmic reticulum membrane|Golgi cisterna membrane|lipid particle|membrane fraction|midbody	metal ion binding|phosphatidylinositol transporter activity			lung(2)|central_nervous_system(1)	3																		---	---	---	---
CABP2	51475	broad.mit.edu	37	11	67289709	67289709	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67289709delG	uc001omc.1	-						CABP2_uc001omd.1_Intron|CABP2_uc001ome.1_Intron	NM_016366	NP_057450			calcium binding protein 2 isoform 1						signal transduction	Golgi apparatus|perinuclear region of cytoplasm|plasma membrane	calcium ion binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	67359436	67359436	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67359436delA								GSTP1 (5313 upstream) : NDUFV1 (14887 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	67628604	67628607	+	IGR	DEL	TTTT	-	-	rs79678399		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67628604_67628607delTTTT								LOC645332 (55797 upstream) : UNC93B1 (129968 downstream)																																			---	---	---	---
LRP5	4041	broad.mit.edu	37	11	68185870	68185870	+	Intron	DEL	A	-	-	rs77498779		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68185870delA	uc001ont.2	+						LRP5_uc009ysg.2_Intron	NM_002335	NP_002326			low density lipoprotein receptor-related protein						adipose tissue development|bone marrow development|bone morphogenesis|canonical Wnt receptor signaling pathway|cholesterol homeostasis|endocytosis|glucose catabolic process|negative regulation of osteoblast differentiation|negative regulation of protein serine/threonine kinase activity|positive regulation of fat cell differentiation|positive regulation of mesenchymal cell proliferation|positive regulation of mitosis|positive regulation of transcription from RNA polymerase II promoter|regulation of blood pressure|regulation of canonical Wnt receptor signaling pathway|retina morphogenesis in camera-type eye|retinal blood vessel morphogenesis|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	endoplasmic reticulum|integral to membrane|plasma membrane|receptor complex	protein binding|receptor activity			lung(2)|skin(2)|ovary(1)|pancreas(1)|breast(1)	7																		---	---	---	---
GAL	51083	broad.mit.edu	37	11	68449323	68449324	+	5'Flank	DEL	TC	-	-	rs111597537		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68449323_68449324delTC	uc001oob.2	+							NM_015973	NP_057057			galanin preproprotein						growth hormone secretion|insulin secretion|neuropeptide signaling pathway|smooth muscle contraction	extracellular region	neuropeptide hormone activity				0	Esophageal squamous(3;7.33e-10)	Melanoma(852;0.0749)	LUAD - Lung adenocarcinoma(13;0.0514)	Kidney(183;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(183;3.23e-08)|Lung(977;0.000152)|LUSC - Lung squamous cell carcinoma(976;0.00154)														---	---	---	---
MTL5	9633	broad.mit.edu	37	11	68480623	68480623	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68480623delA	uc001ooc.2	-							NM_004923	NP_004914			metallothionein-like 5, testis-specific isoform						cell differentiation|cellular metal ion homeostasis|multicellular organismal development|response to metal ion|spermatogenesis	cytoplasm|nucleus|soluble fraction	metal ion binding			ovary(2)|breast(1)	3	Esophageal squamous(3;4.37e-12)		LUAD - Lung adenocarcinoma(13;0.0676)|STAD - Stomach adenocarcinoma(18;0.185)															---	---	---	---
MTL5	9633	broad.mit.edu	37	11	68506343	68506343	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68506343delT	uc001ooc.2	-						MTL5_uc001ood.1_Intron|MTL5_uc009ysi.1_Intron	NM_004923	NP_004914			metallothionein-like 5, testis-specific isoform						cell differentiation|cellular metal ion homeostasis|multicellular organismal development|response to metal ion|spermatogenesis	cytoplasm|nucleus|soluble fraction	metal ion binding			ovary(2)|breast(1)	3	Esophageal squamous(3;4.37e-12)		LUAD - Lung adenocarcinoma(13;0.0676)|STAD - Stomach adenocarcinoma(18;0.185)															---	---	---	---
MYEOV	26579	broad.mit.edu	37	11	69146854	69146854	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69146854delT	uc001oox.2	+											Homo sapiens mRNA for OCIM (Oncogene in Multiple Myeloma) protein.												0	all_lung(4;2.21e-19)|Lung NSC(4;6.13e-19)|Melanoma(5;0.00128)		LUSC - Lung squamous cell carcinoma(11;3.33e-11)|STAD - Stomach adenocarcinoma(18;0.00654)|LUAD - Lung adenocarcinoma(13;0.0713)	Kidney(183;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(183;3.23e-08)|Lung(977;0.00361)|LUSC - Lung squamous cell carcinoma(976;0.0153)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	69421540	69421553	+	IGR	DEL	TGTGTGTGTGTGTG	-	-	rs10524715		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69421540_69421553delTGTGTGTGTGTGTG								MYEOV (265091 upstream) : CCND1 (34320 downstream)																																			---	---	---	---
FGF3	2248	broad.mit.edu	37	11	69628677	69628688	+	Intron	DEL	TGGATTGCTGGA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69628677_69628688delTGGATTGCTGGA	uc001oph.2	-							NM_005247	NP_005238			fibroblast growth factor 3 precursor						fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|negative regulation of cardiac muscle tissue development|positive regulation of cell division|positive regulation of cell proliferation	extracellular region	growth factor activity			ovary(1)|lung(1)	2			LUSC - Lung squamous cell carcinoma(11;5.05e-15)|STAD - Stomach adenocarcinoma(18;0.0278)															---	---	---	---
Unknown	0	broad.mit.edu	37	11	69812172	69812172	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69812172delA								FGF3 (177980 upstream) : ANO1 (112236 downstream)																																			---	---	---	---
CTTN	2017	broad.mit.edu	37	11	70262923	70262924	+	Intron	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70262923_70262924insC	uc001opv.3	+						CTTN_uc001opu.2_Intron|CTTN_uc001opw.3_Intron	NM_005231	NP_005222			cortactin isoform a							cell cortex|cytoskeleton|lamellipodium|ruffle|soluble fraction	protein binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(2;4.34e-41)|LUSC - Lung squamous cell carcinoma(11;1.51e-13)|STAD - Stomach adenocarcinoma(18;0.0513)	Lung(977;0.0234)|LUSC - Lung squamous cell carcinoma(976;0.133)														---	---	---	---
SHANK2	22941	broad.mit.edu	37	11	70631567	70631567	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70631567delT	uc001oqc.2	-							NM_012309	NP_036441			SH3 and multiple ankyrin repeat domains 2						intracellular signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	GKAP/Homer scaffold activity|ionotropic glutamate receptor binding|SH3 domain binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)															---	---	---	---
RNF121	55298	broad.mit.edu	37	11	71674665	71674665	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71674665delA	uc001ora.2	+						RNF121_uc001ord.2_Intron|RNF121_uc001orb.2_Intron|RNF121_uc009yst.2_Intron	NM_018320	NP_060790			ring finger protein 121							integral to membrane	zinc ion binding				0																		---	---	---	---
NUMA1	4926	broad.mit.edu	37	11	71758370	71758371	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71758370_71758371insA	uc001orl.1	-						NUMA1_uc001ork.1_Intron|NUMA1_uc001orm.1_Intron|NUMA1_uc001oro.1_Intron|NUMA1_uc001orp.2_Intron|NUMA1_uc001orq.2_Intron	NM_006185	NP_006176			nuclear mitotic apparatus protein 1						G2/M transition of mitotic cell cycle|mitotic anaphase|nucleus organization	chromosome|cytosol|nucleoplasm|spindle microtubule|spindle pole	protein binding|structural molecule activity			ovary(3)|lung(2)|skin(2)|central_nervous_system(1)	8								T	RARA	APL								---	---	---	---
FOLR3	2352	broad.mit.edu	37	11	71843792	71843792	+	5'Flank	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71843792delG	uc001ory.1	+						FOLR3_uc001orx.1_5'Flank					SubName: Full=FOLR3 protein; Flags: Fragment;						folic acid transport	extracellular region|extrinsic to membrane|membrane fraction	folic acid binding|receptor activity				0					Folic Acid(DB00158)													---	---	---	---
CLPB	81570	broad.mit.edu	37	11	72089299	72089299	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72089299delT	uc001osj.2	-						CLPB_uc010rqx.1_Intron|CLPB_uc010rqy.1_Intron|CLPB_uc001osk.2_Intron|CLPB_uc009ytg.2_Intron|CLPB_uc010rqz.1_Intron	NM_030813	NP_110440			caseinolytic peptidase B						cellular response to heat		ATP binding|nucleoside-triphosphatase activity|protein binding			pancreas(1)	1																		---	---	---	---
PDE2A	5138	broad.mit.edu	37	11	72369721	72369721	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72369721delT	uc010rrc.1	-						PDE2A_uc010rrb.1_Intron|PDE2A_uc010rrd.1_Intron|PDE2A_uc001osq.2_Intron	NM_002599	NP_002590			phosphodiesterase 2A isoform 1						platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity|metal ion binding			ovary(2)|breast(1)|skin(1)	4			BRCA - Breast invasive adenocarcinoma(5;3.55e-05)		Sildenafil(DB00203)|Sulindac(DB00605)													---	---	---	---
ARAP1	116985	broad.mit.edu	37	11	72421120	72421120	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72421120delG	uc001osu.2	-						ARAP1_uc001osv.2_Intron|ARAP1_uc001osr.2_Intron|ARAP1_uc001oss.2_Intron|ARAP1_uc009yth.2_Intron|ARAP1_uc010rre.1_Intron	NM_001040118	NP_001035207			ArfGAP with RhoGAP domain, ankyrin repeat and PH						actin filament reorganization involved in cell cycle|negative regulation of stress fiber assembly|positive regulation of Cdc42 GTPase activity|positive regulation of filopodium assembly|regulation of ARF GTPase activity|regulation of cell shape|regulation of cellular component movement|small GTPase mediated signal transduction	cytosol|Golgi cisterna membrane|plasma membrane	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|protein binding|Rho GTPase activator activity|zinc ion binding			skin(1)	1																		---	---	---	---
FCHSD2	9873	broad.mit.edu	37	11	72743773	72743773	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72743773delA	uc009ytl.2	-						FCHSD2_uc010rrg.1_Intron|FCHSD2_uc001oth.3_Intron|FCHSD2_uc001oti.2_Intron	NM_014824	NP_055639			FCH and double SH3 domains 2								protein binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(5;3.3e-05)															---	---	---	---
Unknown	0	broad.mit.edu	37	11	72887582	72887582	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:72887582delT								FCHSD2 (34439 upstream) : P2RY2 (41762 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	73082348	73082350	+	IGR	DEL	AAA	-	-	rs113092988		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73082348_73082350delAAA								ARHGEF17 (1924 upstream) : RELT (5055 downstream)																																			---	---	---	---
FAM168A	23201	broad.mit.edu	37	11	73127991	73127991	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73127991delA	uc001otz.1	-						FAM168A_uc001oty.1_Intron|FAM168A_uc009ytp.1_Intron	NM_015159	NP_055974			hypothetical protein LOC23201												0																		---	---	---	---
RAB6A	5870	broad.mit.edu	37	11	73403021	73403021	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73403021delA	uc001oue.2	-						RAB6A_uc001ouf.2_Intron|RAB6A_uc009yts.2_Intron	NM_002869	NP_002860			RAB6A, member RAS oncogene family isoform a						minus-end-directed organelle transport along microtubule|peptidyl-cysteine methylation|protein targeting to Golgi|retrograde vesicle-mediated transport, Golgi to ER|small GTPase mediated signal transduction	cytoplasmic vesicle|cytosol|Golgi membrane|trans-Golgi network	GTP binding|GTPase activity|protein domain specific binding				0																		---	---	---	---
MRPL48	51642	broad.mit.edu	37	11	73546186	73546194	+	Intron	DEL	TTTTTTTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73546186_73546194delTTTTTTTTT	uc001ouh.3	+						MRPL48_uc009ytt.2_Intron|MRPL48_uc010rri.1_Intron|MRPL48_uc009ytu.2_Intron	NM_016055	NP_057139			mitochondrial ribosomal protein L48 precursor						translation	mitochondrial ribosome	protein binding|structural constituent of ribosome				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	74154767	74154767	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74154767delA								PGM2L1 (45265 upstream) : KCNE3 (11121 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	74449506	74449506	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74449506delA								CHRDL2 (7320 upstream) : RNF169 (10407 downstream)																																			---	---	---	---
RNF169	254225	broad.mit.edu	37	11	74457267	74457267	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74457267delT	uc001ovl.3	+							NM_001098638	NP_001092108			ring finger protein 169								zinc ion binding			ovary(1)	1																		---	---	---	---
ARRB1	408	broad.mit.edu	37	11	74980343	74980343	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:74980343delC	uc001owe.1	-						ARRB1_uc001owf.1_Intron	NM_004041	NP_004032			arrestin beta 1 isoform A						G-protein coupled receptor internalization|histone H4 acetylation|negative regulation of interleukin-6 production|negative regulation of interleukin-8 production|negative regulation of NF-kappaB transcription factor activity|negative regulation of protein ubiquitination|platelet activation|positive regulation of ERK1 and ERK2 cascade|positive regulation of histone acetylation|positive regulation of Rho protein signal transduction|positive regulation of transcription from RNA polymerase II promoter|post-Golgi vesicle-mediated transport|proteasomal ubiquitin-dependent protein catabolic process|protein transport|protein ubiquitination|signal transduction|stress fiber assembly|transcription from RNA polymerase II promoter	chromatin|coated pit|cytoplasmic vesicle membrane|cytosol|Golgi membrane|lysosomal membrane|membrane fraction|nucleus|plasma membrane|pseudopodium|soluble fraction	angiotensin receptor binding|enzyme inhibitor activity|GTPase activator activity|insulin-like growth factor receptor binding|transcription factor binding|transcription regulatory region DNA binding|ubiquitin protein ligase binding			breast(2)	2																		---	---	---	---
GDPD5	81544	broad.mit.edu	37	11	75208000	75208001	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75208000_75208001insT	uc001owp.3	-						GDPD5_uc001owq.3_Intron	NM_030792	NP_110419			glycerophosphodiester phosphodiesterase domain						glycerol metabolic process|lipid metabolic process|nervous system development	endomembrane system|growth cone|integral to membrane|perinuclear region of cytoplasm	glycerophosphodiester phosphodiesterase activity			ovary(1)	1																		---	---	---	---
GDPD5	81544	broad.mit.edu	37	11	75228500	75228501	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75228500_75228501delAA	uc001owp.3	-						GDPD5_uc001owq.3_Intron	NM_030792	NP_110419			glycerophosphodiester phosphodiesterase domain						glycerol metabolic process|lipid metabolic process|nervous system development	endomembrane system|growth cone|integral to membrane|perinuclear region of cytoplasm	glycerophosphodiester phosphodiesterase activity			ovary(1)	1																		---	---	---	---
SERPINH1	871	broad.mit.edu	37	11	75283797	75283797	+	3'UTR	DEL	T	-	-	rs35662648		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75283797delT	uc001owr.2	+	5					SERPINH1_uc009yug.2_3'UTR|SERPINH1_uc001ows.2_3'UTR|SERPINH1_uc001owt.2_3'UTR	NM_001235	NP_001226			serine (or cysteine) proteinase inhibitor, clade						regulation of proteolysis|response to unfolded protein	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	collagen binding|serine-type endopeptidase inhibitor activity			ovary(2)	2	Ovarian(111;0.11)																	---	---	---	---
UVRAG	7405	broad.mit.edu	37	11	75542549	75542550	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75542549_75542550delAA	uc001oxc.2	+							NM_003369	NP_003360			UV radiation resistance associated						DNA repair|positive regulation of autophagy	early endosome|late endosome|lysosome	protein binding			skin(4)|lung(2)	6																		---	---	---	---
UVRAG	7405	broad.mit.edu	37	11	75843596	75843596	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75843596delA	uc001oxc.2	+						UVRAG_uc010rrw.1_Intron|UVRAG_uc001oxd.2_Intron|UVRAG_uc010rrx.1_Intron|UVRAG_uc010rry.1_Intron	NM_003369	NP_003360			UV radiation resistance associated						DNA repair|positive regulation of autophagy	early endosome|late endosome|lysosome	protein binding			skin(4)|lung(2)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	75952388	75952388	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75952388delC								WNT11 (30585 upstream) : PRKRIR (108616 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	76026070	76026070	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76026070delA								WNT11 (104267 upstream) : PRKRIR (34934 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	76030473	76030473	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76030473delT								WNT11 (108670 upstream) : PRKRIR (30531 downstream)																																			---	---	---	---
C11orf30	56946	broad.mit.edu	37	11	76174674	76174677	+	Intron	DEL	AAAA	-	-	rs10557758		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76174674_76174677delAAAA	uc001oxl.2	+						C11orf30_uc009yuj.1_Intron|C11orf30_uc010rsa.1_Intron|C11orf30_uc001oxm.2_Intron|C11orf30_uc010rsb.1_Intron|C11orf30_uc010rsc.1_Intron|C11orf30_uc001oxn.2_Intron|C11orf30_uc010rsd.1_Intron	NM_020193	NP_064578			EMSY protein						chromatin modification|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(5)|skin(1)	6																		---	---	---	---
C11orf30	56946	broad.mit.edu	37	11	76246875	76246878	+	Intron	DEL	TTTT	-	-	rs145631372	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76246875_76246878delTTTT	uc001oxl.2	+						C11orf30_uc001oxm.2_Intron|C11orf30_uc010rsb.1_Intron|C11orf30_uc010rsc.1_Intron|C11orf30_uc001oxn.2_Intron|C11orf30_uc010rsd.1_Intron|C11orf30_uc001oxo.1_Intron|C11orf30_uc010rse.1_Intron	NM_020193	NP_064578			EMSY protein						chromatin modification|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(5)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	76322191	76322192	+	IGR	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76322191_76322192delAG								C11orf30 (59603 upstream) : LRRC32 (46377 downstream)																																			---	---	---	---
CAPN5	726	broad.mit.edu	37	11	76813797	76813797	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76813797delG	uc001oxx.2	+						CAPN5_uc009yup.2_Intron|CAPN5_uc009yuq.2_Intron|CAPN5_uc001oxy.2_Intron|OMP_uc010rsk.1_5'Flank	NM_004055	NP_004046			calpain 5						proteolysis|signal transduction	intracellular	calcium-dependent cysteine-type endopeptidase activity				0																		---	---	---	---
MYO7A	4647	broad.mit.edu	37	11	76901241	76901242	+	Intron	DEL	GT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76901241_76901242delGT	uc001oyb.2	+						MYO7A_uc010rsm.1_Intron|MYO7A_uc001oyc.2_Intron|MYO7A_uc009yus.1_Intron|MYO7A_uc009yut.1_Intron	NM_000260	NP_000251			myosin VIIA isoform 1						actin filament-based movement|equilibrioception|lysosome organization|sensory perception of sound|visual perception	cytosol|lysosomal membrane|myosin complex|photoreceptor inner segment|photoreceptor outer segment|synapse	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|breast(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	77023872	77023873	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77023872_77023873delAA								GDPD4 (25409 upstream) : PAK1 (9188 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	77197383	77197383	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77197383delA								PAK1 (12275 upstream) : AQP11 (103053 downstream)																																			---	---	---	---
RSF1	51773	broad.mit.edu	37	11	77394602	77394602	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77394602delA	uc001oyn.2	-						RSF1_uc001oym.2_Intron	NM_016578	NP_057662			remodeling and spacing factor 1						CenH3-containing nucleosome assembly at centromere|negative regulation of DNA binding|negative regulation of transcription, DNA-dependent|nucleosome positioning|positive regulation of transcription, DNA-dependent|positive regulation of viral transcription|transcription initiation, DNA-dependent	RSF complex	histone binding|protein binding|zinc ion binding			ovary(2)|central_nervous_system(2)	4	all_cancers(14;1.54e-17)|all_epithelial(13;4.06e-20)|Ovarian(111;0.152)		Epithelial(5;3e-50)|all cancers(3;6.37e-47)|BRCA - Breast invasive adenocarcinoma(5;9.82e-31)															---	---	---	---
RSF1	51773	broad.mit.edu	37	11	77406628	77406628	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77406628delT	uc001oyn.2	-						RSF1_uc001oym.2_Intron	NM_016578	NP_057662			remodeling and spacing factor 1						CenH3-containing nucleosome assembly at centromere|negative regulation of DNA binding|negative regulation of transcription, DNA-dependent|nucleosome positioning|positive regulation of transcription, DNA-dependent|positive regulation of viral transcription|transcription initiation, DNA-dependent	RSF complex	histone binding|protein binding|zinc ion binding			ovary(2)|central_nervous_system(2)	4	all_cancers(14;1.54e-17)|all_epithelial(13;4.06e-20)|Ovarian(111;0.152)		Epithelial(5;3e-50)|all cancers(3;6.37e-47)|BRCA - Breast invasive adenocarcinoma(5;9.82e-31)															---	---	---	---
Unknown	0	broad.mit.edu	37	11	77710869	77710869	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77710869delT								INTS4 (5152 upstream) : KCTD14 (15893 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	77807757	77807757	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77807757delT								NDUFC2 (16492 upstream) : ALG8 (4231 downstream)																																			---	---	---	---
GAB2	9846	broad.mit.edu	37	11	78092721	78092722	+	Intron	DEL	AA	-	-	rs72194282		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78092721_78092722delAA	uc001ozh.2	-							NM_080491	NP_536739			GRB2-associated binding protein 2 isoform a						osteoclast differentiation|phosphatidylinositol-mediated signaling|positive regulation of cell proliferation|positive regulation of mast cell degranulation	cytosol|plasma membrane	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|transmembrane receptor protein tyrosine kinase adaptor activity			ovary(5)|lung(1)	6	all_cancers(14;3.31e-18)|all_epithelial(13;5.3e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.58e-23)															---	---	---	---
GAB2	9846	broad.mit.edu	37	11	78117152	78117152	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78117152delA	uc001ozh.2	-							NM_080491	NP_536739			GRB2-associated binding protein 2 isoform a						osteoclast differentiation|phosphatidylinositol-mediated signaling|positive regulation of cell proliferation|positive regulation of mast cell degranulation	cytosol|plasma membrane	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|transmembrane receptor protein tyrosine kinase adaptor activity			ovary(5)|lung(1)	6	all_cancers(14;3.31e-18)|all_epithelial(13;5.3e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.58e-23)															---	---	---	---
ODZ4	26011	broad.mit.edu	37	11	78367063	78367064	+	3'UTR	DEL	TT	-	-	rs77841734	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78367063_78367064delTT	uc001ozl.3	-	34					ODZ4_uc001ozk.3_3'UTR	NM_001098816	NP_001092286			odz, odd Oz/ten-m homolog 4						signal transduction	integral to membrane				ovary(2)|pancreas(2)	4																		---	---	---	---
ODZ4	26011	broad.mit.edu	37	11	78379238	78379238	+	Intron	DEL	T	-	-	rs5792812		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78379238delT	uc001ozl.3	-						ODZ4_uc001ozk.3_Intron|ODZ4_uc009yvb.1_Intron	NM_001098816	NP_001092286			odz, odd Oz/ten-m homolog 4						signal transduction	integral to membrane				ovary(2)|pancreas(2)	4																		---	---	---	---
ODZ4	26011	broad.mit.edu	37	11	78710022	78710022	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78710022delA	uc001ozl.3	-							NM_001098816	NP_001092286			odz, odd Oz/ten-m homolog 4						signal transduction	integral to membrane				ovary(2)|pancreas(2)	4																		---	---	---	---
ODZ4	26011	broad.mit.edu	37	11	78713144	78713144	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78713144delC	uc001ozl.3	-							NM_001098816	NP_001092286			odz, odd Oz/ten-m homolog 4						signal transduction	integral to membrane				ovary(2)|pancreas(2)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	79436102	79436102	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79436102delT								ODZ4 (284407 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	79684794	79684795	+	IGR	INS	-	AT	AT			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79684794_79684795insAT								ODZ4 (533099 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	79996169	79996169	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:79996169delT								ODZ4 (844474 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	80824318	80824318	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:80824318delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	80893131	80893131	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:80893131delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	81070178	81070179	+	IGR	DEL	AA	-	-	rs55946098		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:81070178_81070179delAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	81711273	81711273	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:81711273delC	uc001ozo.1	-											Homo sapiens cDNA clone IMAGE:5298883.																														---	---	---	---
PRCP	5547	broad.mit.edu	37	11	82546781	82546781	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82546781delA	uc001ozs.2	-						PRCP_uc001ozr.2_Intron	NM_005040	NP_005031			prolylcarboxypeptidase isoform 1 preproprotein						blood coagulation, intrinsic pathway|proteolysis	lysosome|plasma membrane	protein binding|serine-type carboxypeptidase activity			skin(1)	1																		---	---	---	---
PRCP	5547	broad.mit.edu	37	11	82551830	82551830	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82551830delA	uc001ozs.2	-						PRCP_uc001ozr.2_Intron	NM_005040	NP_005031			prolylcarboxypeptidase isoform 1 preproprotein						blood coagulation, intrinsic pathway|proteolysis	lysosome|plasma membrane	protein binding|serine-type carboxypeptidase activity			skin(1)	1																		---	---	---	---
ANKRD42	338699	broad.mit.edu	37	11	82935877	82935877	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82935877delT	uc001ozz.1	+						ANKRD42_uc010rsv.1_Intron|ANKRD42_uc001paa.2_Intron|ANKRD42_uc001pab.1_Intron	NM_182603	NP_872409			ankyrin repeat domain 42											skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	83121971	83121971	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83121971delT	uc001pag.2	+											Homo sapiens cDNA clone IMAGE:5296561.																														---	---	---	---
DLG2	1740	broad.mit.edu	37	11	83419802	83419802	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83419802delT	uc001paj.2	-						DLG2_uc001pai.2_Intron|DLG2_uc010rsy.1_Intron|DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc010rtb.1_Intron|DLG2_uc001pal.1_Intron	NM_001364	NP_001355			chapsyn-110 isoform 2							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)																---	---	---	---
DLG2	1740	broad.mit.edu	37	11	83820159	83820159	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83820159delA	uc001paj.2	-						DLG2_uc001pai.2_Intron|DLG2_uc010rsy.1_Intron|DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc010rtb.1_Intron|DLG2_uc001pal.1_Intron|DLG2_uc001pam.1_Intron	NM_001364	NP_001355			chapsyn-110 isoform 2							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)																---	---	---	---
DLG2	1740	broad.mit.edu	37	11	83863435	83863437	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83863435_83863437delTTT	uc001paj.2	-						DLG2_uc001pai.2_Intron|DLG2_uc010rsy.1_Intron|DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc010rtb.1_Intron|DLG2_uc001pal.1_Intron|DLG2_uc001pam.1_Intron	NM_001364	NP_001355			chapsyn-110 isoform 2							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)																---	---	---	---
DLG2	1740	broad.mit.edu	37	11	84024608	84024609	+	Intron	DEL	GA	-	-	rs57295435	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:84024608_84024609delGA	uc001paj.2	-						DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc001pal.1_Intron|DLG2_uc001pam.1_Intron	NM_001364	NP_001355			chapsyn-110 isoform 2							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)																---	---	---	---
DLG2	1740	broad.mit.edu	37	11	84613961	84613962	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:84613961_84613962insT	uc001paj.2	-						DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc001pal.1_Intron	NM_001364	NP_001355			chapsyn-110 isoform 2							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)																---	---	---	---
PICALM	8301	broad.mit.edu	37	11	85704926	85704926	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85704926delT	uc001pbm.2	-						PICALM_uc001pbl.2_Intron|PICALM_uc001pbn.2_Intron|PICALM_uc010rtl.1_Intron|PICALM_uc010rtk.1_Intron|PICALM_uc001pbo.1_Intron	NM_007166	NP_009097			phosphatidylinositol-binding clathrin assembly						clathrin coat assembly|endosome transport|negative regulation of receptor-mediated endocytosis|positive regulation of transcription, DNA-dependent|receptor internalization|regulation of protein localization	clathrin coat|clathrin-coated vesicle|coated pit|Golgi apparatus|nucleus|postsynaptic membrane|presynaptic membrane	1-phosphatidylinositol binding|clathrin heavy chain binding			urinary_tract(1)|ovary(1)	2		Acute lymphoblastic leukemia(157;7.42e-07)|all_hematologic(158;0.00092)						T	MLLT10|MLL	TALL|AML|								---	---	---	---
PICALM	8301	broad.mit.edu	37	11	85779118	85779118	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85779118delA	uc001pbm.2	-						PICALM_uc001pbl.2_Intron|PICALM_uc001pbn.2_Intron|PICALM_uc010rtl.1_Intron	NM_007166	NP_009097			phosphatidylinositol-binding clathrin assembly						clathrin coat assembly|endosome transport|negative regulation of receptor-mediated endocytosis|positive regulation of transcription, DNA-dependent|receptor internalization|regulation of protein localization	clathrin coat|clathrin-coated vesicle|coated pit|Golgi apparatus|nucleus|postsynaptic membrane|presynaptic membrane	1-phosphatidylinositol binding|clathrin heavy chain binding			urinary_tract(1)|ovary(1)	2		Acute lymphoblastic leukemia(157;7.42e-07)|all_hematologic(158;0.00092)						T	MLLT10|MLL	TALL|AML|								---	---	---	---
Unknown	0	broad.mit.edu	37	11	85877048	85877048	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85877048delA								PICALM (96148 upstream) : EED (78767 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	85945535	85945535	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85945535delA								PICALM (164635 upstream) : EED (10280 downstream)																																			---	---	---	---
CCDC81	60494	broad.mit.edu	37	11	86108902	86108902	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86108902delT	uc001pbx.1	+						CCDC81_uc001pbw.1_Intron|CCDC81_uc010rtq.1_Intron|CCDC81_uc001pby.1_Intron	NM_001156474	NP_001149946			coiled-coil domain containing 81 isoform 1											skin(1)	1		Acute lymphoblastic leukemia(157;5.51e-06)|all_hematologic(158;0.00535)																---	---	---	---
ME3	10873	broad.mit.edu	37	11	86159492	86159493	+	Intron	DEL	GT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86159492_86159493delGT	uc001pbz.2	-						ME3_uc001pca.2_Intron|ME3_uc009yvk.2_Intron	NM_001014811	NP_001014811			mitochondrial malic enzyme 3 precursor						aerobic respiration|malate metabolic process|oxygen metabolic process|pyruvate metabolic process	mitochondrial matrix	malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) activity|metal ion binding|NAD binding			ovary(1)	1		Acute lymphoblastic leukemia(157;4.34e-06)|all_hematologic(158;0.00252)			NADH(DB00157)													---	---	---	---
FZD4	8322	broad.mit.edu	37	11	86664665	86664666	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86664665_86664666delTT	uc001pce.2	-						uc001pcf.2_5'Flank	NM_012193	NP_036325			frizzled 4 precursor						canonical Wnt receptor signaling pathway|cellular response to retinoic acid|embryo development|negative regulation of cell-substrate adhesion|neuron differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|progesterone secretion|regulation of vascular endothelial growth factor receptor signaling pathway|substrate adhesion-dependent cell spreading|vasculogenesis|Wnt receptor signaling pathway, calcium modulating pathway	cell projection|cell surface|cytoplasm	cytokine binding|G-protein coupled receptor activity|PDZ domain binding|protein heterodimerization activity|protein homodimerization activity|Wnt receptor activity|Wnt-protein binding			large_intestine(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	87130298	87130299	+	IGR	INS	-	AA	AA	rs143110173	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:87130298_87130299insAA								TMEM135 (95730 upstream) : RAB38 (716132 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	87221879	87221879	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:87221879delT								TMEM135 (187311 upstream) : RAB38 (624552 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	87926051	87926051	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:87926051delC								RAB38 (17452 upstream) : CTSC (100710 downstream)																																			---	---	---	---
GRM5	2915	broad.mit.edu	37	11	88482435	88482435	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:88482435delA	uc001pcq.2	-						GRM5_uc009yvm.2_Intron	NM_001143831	NP_001137303			glutamate receptor, metabotropic 5 isoform a						activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway|synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			central_nervous_system(4)|ovary(2)|lung(2)|breast(1)	9		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)													---	---	---	---
GRM5	2915	broad.mit.edu	37	11	88800648	88800648	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:88800648delA	uc009yvn.1	-											SubName: Full=Putative uncharacterized protein GRM5;						activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway|synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			central_nervous_system(4)|ovary(2)|lung(2)|breast(1)	9		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)													---	---	---	---
NOX4	50507	broad.mit.edu	37	11	89213411	89213411	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89213411delT	uc001pct.2	-						NOX4_uc009yvr.2_Intron|NOX4_uc001pcu.2_Intron|NOX4_uc001pcw.2_Intron|NOX4_uc001pcx.2_Intron|NOX4_uc001pcv.2_Intron|NOX4_uc009yvo.2_Intron|NOX4_uc010rtu.1_Intron|NOX4_uc009yvp.2_Intron|NOX4_uc010rtv.1_Intron|NOX4_uc009yvq.2_Intron|NOX4_uc009yvs.1_Intron	NM_016931	NP_058627			NADPH oxidase 4 isoform a						cell aging|cell morphogenesis|inflammatory response|negative regulation of cell proliferation|superoxide anion generation	endoplasmic reticulum membrane|focal adhesion|integral to membrane|nucleus	electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|nucleotide binding|oxygen sensor activity			ovary(1)|central_nervous_system(1)	2		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	89503872	89503872	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89503872delA								TRIM77 (52834 upstream) : TRIM49 (26952 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	89804293	89804294	+	IGR	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89804293_89804294delTC								TRIM64 (97055 upstream) : UBTFL1 (14824 downstream)																																			---	---	---	---
CHORDC1	26973	broad.mit.edu	37	11	89936343	89936343	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89936343delT	uc001pdg.2	-						CHORDC1_uc009yvz.2_Intron	NM_012124	NP_036256			cysteine and histidine-rich domain-containing						chaperone-mediated protein folding|regulation of response to stress|response to stress		Hsp90 protein binding|identical protein binding				0		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.00915)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	90922286	90922286	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:90922286delT								MIR1261 (319916 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	90971780	90971780	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:90971780delT								MIR1261 (369410 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	91360218	91360218	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:91360218delT								MIR1261 (757848 upstream) : FAT3 (725044 downstream)																																			---	---	---	---
FAT3	120114	broad.mit.edu	37	11	92446264	92446264	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92446264delA	uc001pdj.3	+							NM_001008781	NP_001008781			FAT tumor suppressor homolog 3						homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)													TCGA Ovarian(4;0.039)			---	---	---	---
FAT3	120114	broad.mit.edu	37	11	92550141	92550142	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92550141_92550142insA	uc001pdj.3	+							NM_001008781	NP_001008781			FAT tumor suppressor homolog 3						homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)													TCGA Ovarian(4;0.039)			---	---	---	---
Unknown	0	broad.mit.edu	37	11	92691539	92691539	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92691539delA								FAT3 (61906 upstream) : MTNR1B (11250 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	92716687	92716689	+	IGR	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92716687_92716689delAAA								MTNR1B (739 upstream) : SLC36A4 (164163 downstream)																																			---	---	---	---
CCDC67	159989	broad.mit.edu	37	11	93103134	93103134	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93103134delT	uc001pdq.2	+						CCDC67_uc001pdo.1_Intron|CCDC67_uc001pdp.2_Intron	NM_181645	NP_857596			coiled-coil domain containing 67											ovary(1)	1		Acute lymphoblastic leukemia(157;2.35e-05)|all_hematologic(158;0.00824)																---	---	---	---
CCDC67	159989	broad.mit.edu	37	11	93122460	93122461	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93122460_93122461insA	uc001pdq.2	+						CCDC67_uc001pdo.1_Intron|CCDC67_uc001pdp.2_Intron	NM_181645	NP_857596			coiled-coil domain containing 67											ovary(1)	1		Acute lymphoblastic leukemia(157;2.35e-05)|all_hematologic(158;0.00824)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	93306781	93306781	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93306781delA								C11orf75 (30235 upstream) : KIAA1731 (88035 downstream)																																			---	---	---	---
KIAA1731	85459	broad.mit.edu	37	11	93439896	93439896	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93439896delT	uc009ywb.1	+						KIAA1731_uc001pdu.1_Intron	NM_033395	NP_203753			hypothetical protein LOC85459							centrosome					0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)																---	---	---	---
Unknown	0	broad.mit.edu	37	11	93508359	93508359	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93508359delT								C11orf54 (12113 upstream) : MED17 (9046 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	93510646	93510648	+	IGR	DEL	TTC	-	-	rs623017	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93510646_93510648delTTC								C11orf54 (14400 upstream) : MED17 (6757 downstream)																																			---	---	---	---
MRE11A	4361	broad.mit.edu	37	11	94181589	94181589	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94181589delA	uc001peu.2	-						MRE11A_uc001pev.2_Intron|MRE11A_uc009ywj.2_Intron	NM_005591	NP_005582			meiotic recombination 11 homolog A isoform 1						DNA duplex unwinding|double-strand break repair via homologous recombination|double-strand break repair via nonhomologous end joining|negative regulation of DNA endoreduplication|positive regulation of kinase activity|positive regulation of protein autophosphorylation|reciprocal meiotic recombination|regulation of mitotic recombination|sister chromatid cohesion|telomere maintenance via telomerase	Mre11 complex|nucleoplasm	3'-5' exonuclease activity|double-stranded DNA binding|manganese ion binding|protein C-terminus binding|single-stranded DNA specific endodeoxyribonuclease activity			breast(4)|lung(1)	5		Acute lymphoblastic leukemia(157;2.37e-05)|all_hematologic(158;0.00824)											Homologous_recombination	Ataxia-Telangiectasia-Like_Disorder				---	---	---	---
Unknown	0	broad.mit.edu	37	11	94248763	94248763	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94248763delT								ANKRD49 (16023 upstream) : PIWIL4 (28243 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	94629450	94629450	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94629450delT								AMOTL1 (19533 upstream) : CWC15 (66339 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	95479432	95479432	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95479432delT								SESN3 (513727 upstream) : FAM76B (22674 downstream)																																			---	---	---	---
CEP57	9702	broad.mit.edu	37	11	95559765	95559765	+	Intron	DEL	A	-	-	rs111590430		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95559765delA	uc001pfp.1	+						CEP57_uc010ruh.1_Intron|CEP57_uc010rui.1_Intron|CEP57_uc009ywn.1_Intron|CEP57_uc001pfq.1_Intron|CEP57_uc001pfr.1_Intron	NM_014679	NP_055494			translokin						fibroblast growth factor receptor signaling pathway|G2/M transition of mitotic cell cycle|protein import into nucleus, translocation|spermatid development	centrosome|cytosol|Golgi apparatus|microtubule|nucleus	fibroblast growth factor binding|protein homodimerization activity			ovary(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)												Mosaic_Variegated_Aneuploidy_Syndrome				---	---	---	---
MTMR2	8898	broad.mit.edu	37	11	95625565	95625566	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95625565_95625566delTT	uc001pfu.2	-						MTMR2_uc001pfv.2_Intron|MTMR2_uc001pfs.2_Intron|MTMR2_uc001pft.2_Intron|MTMR2_uc010ruj.1_Intron	NM_016156	NP_057240			myotubularin-related protein 2 isoform 1							nucleus	inositol or phosphatidylinositol phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			pancreas(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)																---	---	---	---
MTMR2	8898	broad.mit.edu	37	11	95652008	95652008	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95652008delT	uc001pfu.2	-						MTMR2_uc001pfv.2_Intron|MTMR2_uc001pfs.2_Intron|MTMR2_uc001pft.2_Intron|MTMR2_uc010ruj.1_Intron	NM_016156	NP_057240			myotubularin-related protein 2 isoform 1							nucleus	inositol or phosphatidylinositol phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			pancreas(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)																---	---	---	---
MAML2	84441	broad.mit.edu	37	11	95720059	95720059	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95720059delA	uc001pfw.1	-							NM_032427	NP_115803			mastermind-like 2						Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity		CRTC1/MAML2(516)|CRTC3/MAML2(26)	salivary_gland(500)|lung(36)|thyroid(4)|breast(3)|skin(2)|ovary(1)	546		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)						T	MECT1|CRTC3	salivary gland mucoepidermoid								---	---	---	---
Unknown	0	broad.mit.edu	37	11	97214980	97214980	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:97214980delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	97457997	97457997	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:97457997delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	98150725	98150725	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:98150725delT								None (None upstream) : CNTN5 (741146 downstream)																																			---	---	---	---
CNTN5	53942	broad.mit.edu	37	11	99056292	99056292	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99056292delT	uc001pga.2	+						CNTN5_uc009ywv.1_Intron|CNTN5_uc001pfz.2_Intron|CNTN5_uc001pgb.2_Intron	NM_014361	NP_055176			contactin 5 isoform long						cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)														---	---	---	---
CNTN5	53942	broad.mit.edu	37	11	99146804	99146804	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99146804delA	uc001pga.2	+						CNTN5_uc009ywv.1_Intron|CNTN5_uc001pfz.2_Intron|CNTN5_uc001pgb.2_Intron	NM_014361	NP_055176			contactin 5 isoform long						cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)														---	---	---	---
CNTN5	53942	broad.mit.edu	37	11	99931925	99931925	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99931925delT	uc001pga.2	+						CNTN5_uc009ywv.1_Intron|CNTN5_uc001pfz.2_Intron|CNTN5_uc001pgb.2_Intron	NM_014361	NP_055176			contactin 5 isoform long						cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)														---	---	---	---
CNTN5	53942	broad.mit.edu	37	11	100168171	100168171	+	Intron	DEL	A	-	-	rs34145321		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100168171delA	uc001pga.2	+						CNTN5_uc001pfz.2_Intron|CNTN5_uc001pgb.2_Intron|CNTN5_uc010ruk.1_Intron	NM_014361	NP_055176			contactin 5 isoform long						cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)														---	---	---	---
ARHGAP42	143872	broad.mit.edu	37	11	100740137	100740139	+	Intron	DEL	TTT	-	-	rs67729705		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:100740137_100740139delTTT	uc001pge.2	+							NM_152432	NP_689645			Rho-type GTPase-activating protein FLJ32810						filopodium assembly|signal transduction	intracellular	cytoskeletal adaptor activity|GTPase activator activity|SH3 domain binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	101232437	101232437	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101232437delA								PGR (231893 upstream) : TRPC6 (89859 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	101266253	101266253	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101266253delA								PGR (265709 upstream) : TRPC6 (56043 downstream)																																			---	---	---	---
TRPC6	7225	broad.mit.edu	37	11	101444653	101444654	+	Intron	DEL	GT	-	-	rs72085412		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:101444653_101444654delGT	uc001pgk.3	-						TRPC6_uc009ywy.2_Intron|TRPC6_uc009ywz.1_Intron	NM_004621	NP_004612			transient receptor potential cation channel,						axon guidance|platelet activation|positive regulation of calcium ion transport via store-operated calcium channel activity	integral to membrane|plasma membrane	protein binding			skin(2)|ovary(1)|central_nervous_system(1)	4		Acute lymphoblastic leukemia(157;0.000918)|all_hematologic(158;0.0162)		BRCA - Breast invasive adenocarcinoma(274;0.0442)														---	---	---	---
BIRC2	329	broad.mit.edu	37	11	102248668	102248668	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102248668delT	uc001pgy.2	+						BIRC2_uc010ruq.1_Intron|BIRC2_uc010rur.1_Intron	NM_001166	NP_001157			baculoviral IAP repeat-containing protein 2						cell surface receptor linked signaling pathway|cellular component disassembly involved in apoptosis|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteasomal ubiquitin-dependent protein catabolic process|protein polyubiquitination	CD40 receptor complex|cytosol|internal side of plasma membrane	protein N-terminus binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|lung(1)|breast(1)	3	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|Epithelial(9;0.11)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0144)														---	---	---	---
DCUN1D5	84259	broad.mit.edu	37	11	102946117	102946118	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102946117_102946118delTT	uc001phm.2	-						DCUN1D5_uc010ruw.1_Intron	NM_032299	NP_115675			DCN1, defective in cullin neddylation 1, domain												0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.00032)|Epithelial(105;0.0689)|all cancers(92;0.186)														---	---	---	---
DYNC2H1	79659	broad.mit.edu	37	11	103123999	103123999	+	Intron	DEL	G	-	-	rs648387	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103123999delG	uc001pho.2	+						DYNC2H1_uc001phn.1_Intron|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932			dynein, cytoplasmic 2, heavy chain 1						cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)														---	---	---	---
DYNC2H1	79659	broad.mit.edu	37	11	103123999	103124000	+	Intron	INS	-	T	T	rs648387	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103123999_103124000insT	uc001pho.2	+						DYNC2H1_uc001phn.1_Intron|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932			dynein, cytoplasmic 2, heavy chain 1						cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)														---	---	---	---
DYNC2H1	79659	broad.mit.edu	37	11	103144852	103144853	+	Intron	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103144852_103144853delTG	uc001pho.2	+						DYNC2H1_uc001phn.1_Intron|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932			dynein, cytoplasmic 2, heavy chain 1						cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	103705187	103705187	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103705187delA								DYNC2H1 (354596 upstream) : PDGFD (72728 downstream)																																			---	---	---	---
PDGFD	80310	broad.mit.edu	37	11	103790588	103790588	+	Intron	DEL	A	-	-	rs71975942		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103790588delA	uc001phq.2	-						PDGFD_uc001php.2_Intron	NM_025208	NP_079484			platelet derived growth factor D isoform 1						positive regulation of cell division	endoplasmic reticulum lumen|extracellular region|Golgi membrane	growth factor activity			upper_aerodigestive_tract(1)|large_intestine(1)	2		Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Melanoma(852;0.0563)|all_neural(303;0.165)		BRCA - Breast invasive adenocarcinoma(274;0.00136)|Epithelial(105;0.111)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	104130040	104130040	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104130040delT								PDGFD (95013 upstream) : CASP12 (626402 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	104502271	104502272	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104502271_104502272delTG								PDGFD (467244 upstream) : CASP12 (254170 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	104588632	104588643	+	IGR	DEL	AAAACAAACAAA	-	-	rs150339148	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104588632_104588643delAAAACAAACAAA								PDGFD (553605 upstream) : CASP12 (167799 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	105424308	105424308	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105424308delT								CARD18 (414502 upstream) : GRIA4 (56492 downstream)																																			---	---	---	---
GRIA4	2893	broad.mit.edu	37	11	105737170	105737171	+	Intron	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105737170_105737171delTG	uc001pix.2	+						GRIA4_uc001piu.1_Intron|GRIA4_uc001piw.2_Intron|GRIA4_uc009yxk.1_Intron	NM_000829	NP_000820			glutamate receptor, ionotrophic, AMPA 4 isoform						glutamate signaling pathway|synaptic transmission	cell junction|endocytic vesicle membrane|integral to membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)	L-Glutamic Acid(DB00142)													---	---	---	---
GRIA4	2893	broad.mit.edu	37	11	105792033	105792036	+	Intron	DEL	GTGT	-	-	rs116122813	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105792033_105792036delGTGT	uc001pix.2	+						GRIA4_uc001piw.2_Intron	NM_000829	NP_000820			glutamate receptor, ionotrophic, AMPA 4 isoform						glutamate signaling pathway|synaptic transmission	cell junction|endocytic vesicle membrane|integral to membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)	L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	106233341	106233342	+	IGR	DEL	TT	-	-	rs66672165		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106233341_106233342delTT								AASDHPPT (263922 upstream) : GUCY1A2 (324568 downstream)																																			---	---	---	---
GUCY1A2	2977	broad.mit.edu	37	11	106683196	106683196	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106683196delT	uc001pjg.1	-						GUCY1A2_uc010rvo.1_Intron|GUCY1A2_uc009yxn.1_Intron	NM_000855	NP_000846			guanylate cyclase 1, soluble, alpha 2						intracellular signal transduction|platelet activation	cytoplasm	GTP binding|guanylate cyclase activity|heme binding			large_intestine(3)|lung(2)|pancreas(2)|ovary(1)	8		all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068)		BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	106916386	106916386	+	IGR	DEL	A	-	-	rs74338479		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106916386delA								GUCY1A2 (27215 upstream) : CWF19L2 (280688 downstream)																																			---	---	---	---
CWF19L2	143884	broad.mit.edu	37	11	107257779	107257780	+	Intron	DEL	AA	-	-	rs663652		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107257779_107257780delAA	uc010rvp.1	-						CWF19L2_uc001pjh.3_Intron|CWF19L2_uc009yxo.2_Intron	NM_152434	NP_689647			CWF19-like 2, cell cycle control								catalytic activity				0		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)														---	---	---	---
ELMOD1	55531	broad.mit.edu	37	11	107499288	107499288	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107499288delT	uc010rvs.1	+						ELMOD1_uc001pjm.2_Intron|ELMOD1_uc010rvt.1_Intron	NM_018712	NP_061182			ELMO/CED-12 domain containing 1 isoform 1						phagocytosis	cytoskeleton	GTPase activator activity				0		Melanoma(852;0.000288)|Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00301)|all_epithelial(67;0.00304)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)|Epithelial(105;0.00027)|all cancers(92;0.00481)														---	---	---	---
SLC35F2	54733	broad.mit.edu	37	11	107686332	107686334	+	Intron	DEL	ACT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107686332_107686334delACT	uc001pjq.2	-						SLC35F2_uc010rvu.1_Intron|SLC35F2_uc001pjs.2_Intron	NM_017515	NP_059985			solute carrier family 35, member F2						transport	integral to membrane				central_nervous_system(1)	1		all_cancers(61;9.46e-06)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;0.000111)|all_hematologic(158;0.000315)|all_epithelial(67;0.00197)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)|Epithelial(105;0.000105)|all cancers(92;0.00217)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	107780157	107780158	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107780157_107780158delTT								SLC35F2 (50243 upstream) : RAB39 (19119 downstream)																																			---	---	---	---
CUL5	8065	broad.mit.edu	37	11	107883939	107883939	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107883939delT	uc001pjv.2	+						CUL5_uc001pju.2_Intron	NM_003478	NP_003469			Vasopressin-activated calcium-mobilizing						cell cycle arrest|cell proliferation|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|ubiquitin-dependent protein catabolic process|viral reproduction	cullin-RING ubiquitin ligase complex|cytosol	calcium channel activity|receptor activity|ubiquitin protein ligase binding			ovary(1)	1		all_cancers(61;7.09e-10)|all_epithelial(67;2.97e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|Melanoma(852;4.48e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;3.58e-05)|Epithelial(105;4.68e-05)|all cancers(92;0.00122)|OV - Ovarian serous cystadenocarcinoma(223;0.217)														---	---	---	---
CUL5	8065	broad.mit.edu	37	11	107940724	107940724	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107940724delT	uc001pjv.2	+						CUL5_uc001pju.2_Intron	NM_003478	NP_003469			Vasopressin-activated calcium-mobilizing						cell cycle arrest|cell proliferation|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|ubiquitin-dependent protein catabolic process|viral reproduction	cullin-RING ubiquitin ligase complex|cytosol	calcium channel activity|receptor activity|ubiquitin protein ligase binding			ovary(1)	1		all_cancers(61;7.09e-10)|all_epithelial(67;2.97e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|Melanoma(852;4.48e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;3.58e-05)|Epithelial(105;4.68e-05)|all cancers(92;0.00122)|OV - Ovarian serous cystadenocarcinoma(223;0.217)														---	---	---	---
ACAT1	38	broad.mit.edu	37	11	107993965	107993965	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107993965delA	uc001pjy.2	+						ACAT1_uc001pjw.1_Intron|ACAT1_uc001pjx.2_Intron	NM_000019	NP_000010			acetyl-Coenzyme A acetyltransferase 1 precursor						acetoacetic acid biosynthetic process|branched chain family amino acid catabolic process|ketone body biosynthetic process|ketone body catabolic process	mitochondrial matrix	acetyl-CoA C-acetyltransferase activity|metal ion binding			ovary(3)	3		all_cancers(61;6.41e-10)|all_epithelial(67;2.83e-06)|Melanoma(852;1.46e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;2.96e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.00108)|OV - Ovarian serous cystadenocarcinoma(223;0.192)	Sulfasalazine(DB00795)													---	---	---	---
NPAT	4863	broad.mit.edu	37	11	108031565	108031565	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108031565delA	uc001pjz.3	-						NPAT_uc010rvv.1_Intron	NM_002519	NP_002510			nuclear protein,  ataxia-telangiectasia locus						positive regulation of transcription, DNA-dependent|regulation of transcription involved in G1/S phase of mitotic cell cycle	Cajal body	protein C-terminus binding|protein N-terminus binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity			ovary(2)	2		all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116)														---	---	---	---
ATM	472	broad.mit.edu	37	11	108103594	108103596	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108103594_108103596delTTT	uc001pkb.1	+						ATM_uc009yxr.1_Intron	NM_000051	NP_000042			ataxia telangiectasia mutated isoform 1						cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding			haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	240		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)				D|Mis|N|F|S		T-PLL	leukemia|lymphoma|medulloblastoma|glioma		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Ataxia_Telangiectasia	TSP Lung(14;0.12)			---	---	---	---
DDX10	1662	broad.mit.edu	37	11	108745524	108745524	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108745524delT	uc001pkm.2	+						DDX10_uc001pkl.1_Intron	NM_004398	NP_004389			DEAD (Asp-Glu-Ala-Asp) box polypeptide 10								ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity			breast(2)|lung(1)|prostate(1)	4		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)				T	NUP98	AML*								---	---	---	---
DDX10	1662	broad.mit.edu	37	11	108788854	108788854	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108788854delT	uc001pkm.2	+						DDX10_uc001pkl.1_3'UTR	NM_004398	NP_004389			DEAD (Asp-Glu-Ala-Asp) box polypeptide 10								ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity			breast(2)|lung(1)|prostate(1)	4		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)				T	NUP98	AML*								---	---	---	---
Unknown	0	broad.mit.edu	37	11	108877218	108877218	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108877218delA								DDX10 (65572 upstream) : C11orf87 (415657 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	108901191	108901191	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108901191delC								DDX10 (89545 upstream) : C11orf87 (391684 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	108912339	108912340	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108912339_108912340insA								DDX10 (100693 upstream) : C11orf87 (380535 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	109572519	109572519	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:109572519delA								C11orf87 (272681 upstream) : ZC3H12C (391407 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	109689104	109689104	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:109689104delA								C11orf87 (389266 upstream) : ZC3H12C (274822 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	109920192	109920192	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:109920192delA								C11orf87 (620354 upstream) : ZC3H12C (43734 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	109957216	109957217	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:109957216_109957217insT								C11orf87 (657378 upstream) : ZC3H12C (6709 downstream)																																			---	---	---	---
RDX	5962	broad.mit.edu	37	11	110060809	110060809	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110060809delA	uc009yxx.1	-							NM_002906				radixin						actin filament capping	cleavage furrow|cytoskeleton|extrinsic to membrane|Golgi apparatus|nucleolus|plasma membrane	actin binding				0		all_cancers(61;7.18e-13)|all_epithelial(67;2.61e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.13e-06)|BRCA - Breast invasive adenocarcinoma(274;9.75e-06)|all cancers(92;5.9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0248)														---	---	---	---
FDX1	2230	broad.mit.edu	37	11	110298819	110298819	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110298819delA	uc001pkx.2	+							NM_004109	NP_004100			ferredoxin 1 precursor						electron transport chain|transport	mitochondrial matrix	2 iron, 2 sulfur cluster binding|electron carrier activity|iron ion binding				0		all_cancers(61;1.59e-12)|all_epithelial(67;8.38e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.01e-06)|BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|all cancers(92;5.27e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0384)|Colorectal(284;0.228)	Mitotane(DB00648)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	110383829	110383829	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110383829delC								FDX1 (48225 upstream) : ARHGAP20 (63937 downstream)																																			---	---	---	---
ARHGAP20	57569	broad.mit.edu	37	11	110482117	110482117	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110482117delA	uc001pkz.1	-						ARHGAP20_uc001pky.1_Intron|ARHGAP20_uc009yyb.1_Intron|ARHGAP20_uc001pla.1_Intron	NM_020809	NP_065860			Rho GTPase activating protein 20						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(3)|kidney(2)	5		all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;3.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|all cancers(92;0.000147)|OV - Ovarian serous cystadenocarcinoma(223;0.0475)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	110607112	110607112	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110607112delA								ARHGAP20 (23200 upstream) : C11orf53 (519595 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	111463696	111463696	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111463696delT								LAYN (31908 upstream) : SIK2 (9474 downstream)																																			---	---	---	---
PPP2R1B	5519	broad.mit.edu	37	11	111625493	111625493	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111625493delT	uc001plx.1	-						PPP2R1B_uc001plw.1_Intron|PPP2R1B_uc010rwi.1_Intron|PPP2R1B_uc010rwj.1_Intron|PPP2R1B_uc010rwk.1_Intron|PPP2R1B_uc010rwl.1_Intron	NM_002716	NP_002707			beta isoform of regulatory subunit A, protein								protein binding				0		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|Epithelial(105;2.36e-06)|all cancers(92;3.78e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0761)														---	---	---	---
FDXACB1	91893	broad.mit.edu	37	11	111747600	111747600	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111747600delC	uc001pmc.3	-	3	762	c.465delG	c.(463-465)GGGfs	p.G155fs	ALG9_uc010rwo.1_5'UTR|FDXACB1_uc009yyi.2_Frame_Shift_Del_p.G6fs|C11orf1_uc001pmd.2_5'Flank	NM_138378	NP_612387	Q9BRP7	FDXA1_HUMAN	ferredoxin-fold anticodon binding domain	155					phenylalanyl-tRNA aminoacylation|tRNA processing		ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|tRNA binding				0																		---	---	---	---
DLAT	1737	broad.mit.edu	37	11	111896977	111896977	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111896977delA	uc001pmo.2	+	2	994	c.335delA	c.(334-336)GAAfs	p.E112fs	DLAT_uc009yyk.1_Frame_Shift_Del_p.E112fs|DLAT_uc010rwr.1_Frame_Shift_Del_p.E112fs	NM_001931	NP_001922	P10515	ODP2_HUMAN	dihydrolipoamide S-acetyltransferase precursor	112	Lipoyl-binding 1.			E -> K (in Ref. 4; CAA68787).	glycolysis|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial pyruvate dehydrogenase complex	dihydrolipoyllysine-residue acetyltransferase activity|protein binding				0		all_cancers(61;4.53e-11)|all_epithelial(67;2.76e-06)|Melanoma(852;9.42e-06)|all_hematologic(158;0.000885)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0512)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)		Epithelial(105;4.87e-07)|BRCA - Breast invasive adenocarcinoma(274;6.83e-07)|all cancers(92;9.63e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0557)	NADH(DB00157)													---	---	---	---
DLAT	1737	broad.mit.edu	37	11	111910356	111910356	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111910356delT	uc001pmo.2	+						DLAT_uc009yyk.1_Intron|DLAT_uc010rwr.1_Intron	NM_001931	NP_001922			dihydrolipoamide S-acetyltransferase precursor						glycolysis|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial pyruvate dehydrogenase complex	dihydrolipoyllysine-residue acetyltransferase activity|protein binding				0		all_cancers(61;4.53e-11)|all_epithelial(67;2.76e-06)|Melanoma(852;9.42e-06)|all_hematologic(158;0.000885)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0512)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)		Epithelial(105;4.87e-07)|BRCA - Breast invasive adenocarcinoma(274;6.83e-07)|all cancers(92;9.63e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0557)	NADH(DB00157)													---	---	---	---
IL18	3606	broad.mit.edu	37	11	112024223	112024223	+	Intron	DEL	T	-	-	rs78854082		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112024223delT	uc001pnb.1	-						IL18_uc001pna.1_5'Flank|IL18_uc009yym.1_Intron	NM_001562	NP_001553			interleukin 18 proprotein						angiogenesis|cell-cell signaling|chemokine biosynthetic process|granulocyte macrophage colony-stimulating factor biosynthetic process|interferon-gamma biosynthetic process|interleukin-13 biosynthetic process|interleukin-2 biosynthetic process|positive regulation of activated T cell proliferation|positive regulation of granulocyte macrophage colony-stimulating factor production|positive regulation of interferon-gamma production|positive regulation of interleukin-17 production|positive regulation of natural killer cell proliferation|positive regulation of NK T cell proliferation|regulation of cell adhesion|sleep|T-helper 1 type immune response|type 2 immune response	cytosol|extracellular space	cytokine activity|signal transducer activity				0		all_cancers(61;5.7e-14)|all_epithelial(67;3.4e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;6.72e-07)|Epithelial(105;8.15e-07)|all cancers(92;1.43e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.055)														---	---	---	---
C11orf34	349633	broad.mit.edu	37	11	112125862	112125863	+	Intron	INS	-	TG	TG			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112125862_112125863insTG	uc009yyp.2	-						PTS_uc009yyo.2_Intron	NM_001145024	NP_001138496			hypothetical protein LOC349633 precursor							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	112158623	112158623	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112158623delA	uc001pnm.1	+											full-length cDNA clone CS0DF020YJ04 of Fetal brain of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	112433496	112433504	+	IGR	DEL	TTTTTTTTT	-	-	rs71789147		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112433496_112433504delTTTTTTTTT								PTS (292819 upstream) : NCAM1 (398491 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	112735624	112735624	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112735624delC								PTS (594947 upstream) : NCAM1 (96371 downstream)																																			---	---	---	---
NCAM1	4684	broad.mit.edu	37	11	112904998	112904998	+	Intron	DEL	T	-	-	rs148642032		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112904998delT	uc009yyq.1	+						NCAM1_uc001pno.2_Intron	NM_001076682	NP_001070150			neural cell adhesion molecule 1 isoform 3						axon guidance|interferon-gamma-mediated signaling pathway	anchored to membrane|extracellular region|Golgi membrane|integral to membrane				ovary(1)	1		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)														---	---	---	---
NCAM1	4684	broad.mit.edu	37	11	113066402	113066402	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113066402delT	uc009yyq.1	+						NCAM1_uc001pno.2_Intron	NM_001076682	NP_001070150			neural cell adhesion molecule 1 isoform 3						axon guidance|interferon-gamma-mediated signaling pathway	anchored to membrane|extracellular region|Golgi membrane|integral to membrane				ovary(1)	1		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	113176052	113176053	+	IGR	INS	-	G	G	rs35940990		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113176052_113176053insG								NCAM1 (26895 upstream) : TTC12 (9198 downstream)																																			---	---	---	---
TTC12	54970	broad.mit.edu	37	11	113184621	113184621	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113184621delA	uc001pnu.2	+						TTC12_uc001pnv.2_5'Flank|TTC12_uc001pnw.2_5'Flank|TTC12_uc001pnx.2_5'Flank	NM_017868	NP_060338			tetratricopeptide repeat domain 12								binding			pancreas(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	4		all_cancers(61;2.73e-16)|all_epithelial(67;8.64e-10)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.183)|Renal(330;0.187)		BRCA - Breast invasive adenocarcinoma(274;5.3e-06)|Epithelial(105;8.37e-05)|all cancers(92;0.000694)														---	---	---	---
TTC12	54970	broad.mit.edu	37	11	113211952	113211952	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113211952delA	uc001pnu.2	+						TTC12_uc001pnv.2_Intron|TTC12_uc001pnw.2_Intron|TTC12_uc001pnx.2_Intron	NM_017868	NP_060338			tetratricopeptide repeat domain 12								binding			pancreas(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	4		all_cancers(61;2.73e-16)|all_epithelial(67;8.64e-10)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.183)|Renal(330;0.187)		BRCA - Breast invasive adenocarcinoma(274;5.3e-06)|Epithelial(105;8.37e-05)|all cancers(92;0.000694)														---	---	---	---
USP28	57646	broad.mit.edu	37	11	113737994	113737995	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113737994_113737995delTT	uc001poh.2	-						USP28_uc010rwy.1_Intron|USP28_uc001poi.2_Intron|USP28_uc001poj.3_Intron|USP28_uc010rwz.1_Intron	NM_020886	NP_065937			ubiquitin specific protease 28						cell proliferation|DNA damage checkpoint|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA repair|protein deubiquitination|response to ionizing radiation|ubiquitin-dependent protein catabolic process	nucleolus|nucleoplasm	protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			lung(2)|breast(2)|ovary(1)|large_intestine(1)|kidney(1)	7		all_cancers(61;3.74e-18)|all_epithelial(67;3.75e-11)|Melanoma(852;1.46e-05)|all_hematologic(158;4.65e-05)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|Prostate(24;0.0153)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|Epithelial(105;0.000122)|all cancers(92;0.00104)														---	---	---	---
NNMT	4837	broad.mit.edu	37	11	114162844	114162844	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114162844delT	uc001por.1	+							NM_006169	NP_006160			nicotinamide N-methyltransferase						xenobiotic metabolic process	cytosol	nicotinamide N-methyltransferase activity|pyridine N-methyltransferase activity			ovary(1)	1		all_cancers(61;4.83e-16)|all_epithelial(67;7.28e-09)|all_hematologic(158;0.000135)|Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0906)		BRCA - Breast invasive adenocarcinoma(274;2.79e-06)|Epithelial(105;1.32e-05)|all cancers(92;0.000144)|OV - Ovarian serous cystadenocarcinoma(223;0.128)	Niacin(DB00627)													---	---	---	---
Unknown	0	broad.mit.edu	37	11	114237734	114237734	+	IGR	DEL	A	-	-	rs138461625	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114237734delA								NNMT (54496 upstream) : C11orf71 (24436 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	114383759	114383759	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114383759delC								REXO2 (62761 upstream) : FAM55A (8679 downstream)																																			---	---	---	---
FAM55A	120400	broad.mit.edu	37	11	114425832	114425832	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114425832delT	uc001ppa.2	-						FAM55A_uc001ppb.1_5'Flank	NM_152315	NP_689528			hypothetical protein LOC120400							extracellular region					0		all_cancers(61;8.53e-16)|all_epithelial(67;1.71e-08)|all_hematologic(158;3.05e-05)|Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0194)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0906)		BRCA - Breast invasive adenocarcinoma(274;3.02e-06)|Epithelial(105;0.000144)|all cancers(92;0.00106)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	114751608	114751609	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114751608_114751609insA								FAM55B (173956 upstream) : CADM1 (288344 downstream)																																			---	---	---	---
CADM1	23705	broad.mit.edu	37	11	115090572	115090573	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115090572_115090573insA	uc001ppi.3	-						CADM1_uc001ppf.3_Intron|CADM1_uc001ppk.3_Intron|CADM1_uc001ppj.3_Intron|CADM1_uc001ppl.2_Intron|CADM1_uc001pph.3_5'Flank	NM_014333	NP_055148			immunoglobulin superfamily, member 4D isoform 1						adherens junction organization|apoptosis|cell differentiation|cell junction assembly|cell recognition|detection of stimulus|heterophilic cell-cell adhesion|homophilic cell adhesion|multicellular organismal development|positive regulation of cytokine secretion|spermatogenesis|susceptibility to natural killer cell mediated cytotoxicity	basolateral plasma membrane|cell-cell junction|integral to membrane	PDZ domain binding|protein C-terminus binding|protein homodimerization activity|receptor binding			ovary(2)	2	all_hematologic(175;0.0628)	all_cancers(61;2.98e-14)|all_epithelial(67;2.64e-08)|all_hematologic(158;0.000154)|Melanoma(852;0.000952)|Acute lymphoblastic leukemia(157;0.00101)|Breast(348;0.0102)|Medulloblastoma(222;0.0429)|Prostate(24;0.145)|all_neural(223;0.237)		BRCA - Breast invasive adenocarcinoma(274;5.01e-06)|Epithelial(105;0.000305)|all cancers(92;0.00303)														---	---	---	---
CADM1	23705	broad.mit.edu	37	11	115267568	115267569	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115267568_115267569insT	uc001ppi.3	-						CADM1_uc001ppf.3_Intron|CADM1_uc001ppk.3_Intron|CADM1_uc001ppj.3_Intron|CADM1_uc001ppl.2_Intron	NM_014333	NP_055148			immunoglobulin superfamily, member 4D isoform 1						adherens junction organization|apoptosis|cell differentiation|cell junction assembly|cell recognition|detection of stimulus|heterophilic cell-cell adhesion|homophilic cell adhesion|multicellular organismal development|positive regulation of cytokine secretion|spermatogenesis|susceptibility to natural killer cell mediated cytotoxicity	basolateral plasma membrane|cell-cell junction|integral to membrane	PDZ domain binding|protein C-terminus binding|protein homodimerization activity|receptor binding			ovary(2)	2	all_hematologic(175;0.0628)	all_cancers(61;2.98e-14)|all_epithelial(67;2.64e-08)|all_hematologic(158;0.000154)|Melanoma(852;0.000952)|Acute lymphoblastic leukemia(157;0.00101)|Breast(348;0.0102)|Medulloblastoma(222;0.0429)|Prostate(24;0.145)|all_neural(223;0.237)		BRCA - Breast invasive adenocarcinoma(274;5.01e-06)|Epithelial(105;0.000305)|all cancers(92;0.00303)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	115933486	115933486	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115933486delA								CADM1 (558245 upstream) : BUD13 (685402 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	115949118	115949118	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:115949118delC								CADM1 (573877 upstream) : BUD13 (669770 downstream)																																	OREG0021358	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	11	116100622	116100623	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116100622_116100623delAA								CADM1 (725381 upstream) : BUD13 (518265 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	116164561	116164562	+	IGR	DEL	TG	-	-	rs34036286		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116164561_116164562delTG								CADM1 (789320 upstream) : BUD13 (454326 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	116175214	116175215	+	IGR	INS	-	AC	AC	rs140423953	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116175214_116175215insAC								CADM1 (799973 upstream) : BUD13 (443673 downstream)																																			---	---	---	---
BUD13	84811	broad.mit.edu	37	11	116631787	116631787	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116631787delT	uc001ppn.2	-						BUD13_uc001ppo.2_Intron|BUD13_uc009yzc.2_Intron	NM_032725	NP_116114			BUD13 homolog isoform 1											large_intestine(1)|pancreas(1)	2	all_hematologic(175;0.0487)	all_cancers(61;1.72e-06)|all_epithelial(67;0.000735)|Melanoma(852;0.022)|Acute lymphoblastic leukemia(157;0.0255)|Medulloblastoma(222;0.0523)|Breast(348;0.056)|all_hematologic(158;0.0588)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|Epithelial(105;5.81e-06)|all cancers(92;0.000144)|OV - Ovarian serous cystadenocarcinoma(223;0.154)														---	---	---	---
APOC3	345	broad.mit.edu	37	11	116698848	116698849	+	5'Flank	INS	-	TC	TC	rs142122586		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116698848_116698849insTC	uc001ppt.1	+							NM_000040	NP_000031			apolipoprotein C-III precursor						Cdc42 protein signal transduction|cholesterol efflux|cholesterol homeostasis|chylomicron remnant clearance|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle remodeling|lipoprotein metabolic process|negative regulation of cholesterol import|negative regulation of fatty acid biosynthetic process|negative regulation of high-density lipoprotein particle clearance|negative regulation of lipoprotein lipase activity|negative regulation of low-density lipoprotein particle clearance|negative regulation of receptor-mediated endocytosis|negative regulation of triglyceride catabolic process|negative regulation of very-low-density lipoprotein particle clearance|negative regulation of very-low-density lipoprotein particle remodeling|phospholipid efflux|triglyceride catabolic process|triglyceride homeostasis|very-low-density lipoprotein particle assembly	chylomicron|intermediate-density lipoprotein particle|spherical high-density lipoprotein particle|very-low-density lipoprotein particle	high-density lipoprotein particle receptor binding|lipase inhibitor activity|phospholipid binding				0	all_hematologic(175;0.0487)	Breast(348;0.0126)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|Epithelial(105;1.62e-05)|all cancers(92;0.000165)|OV - Ovarian serous cystadenocarcinoma(223;0.148)														---	---	---	---
SIK3	23387	broad.mit.edu	37	11	116780035	116780036	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116780035_116780036delAA	uc001ppy.2	-						SIK3_uc001ppz.2_Intron|SIK3_uc001pqa.2_Intron	NM_025164	NP_079440			serine/threonine-protein kinase QSK							cytoplasm	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|breast(3)|stomach(2)|lung(1)|skin(1)|kidney(1)	12																		---	---	---	---
SIK3	23387	broad.mit.edu	37	11	116783172	116783172	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:116783172delT	uc001ppy.2	-						SIK3_uc001ppz.2_Intron|SIK3_uc001pqa.2_Intron	NM_025164	NP_079440			serine/threonine-protein kinase QSK							cytoplasm	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|breast(3)|stomach(2)|lung(1)|skin(1)|kidney(1)	12																		---	---	---	---
SIDT2	51092	broad.mit.edu	37	11	117061431	117061431	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117061431delC	uc001pqh.1	+	18	1751	c.1710delC	c.(1708-1710)TGCfs	p.C570fs	SIDT2_uc010rxe.1_Frame_Shift_Del_p.C570fs|SIDT2_uc001pqg.2_Frame_Shift_Del_p.C591fs|SIDT2_uc001pqi.1_Frame_Shift_Del_p.C567fs|SIDT2_uc001pqj.1_5'Flank	NM_001040455	NP_001035545	Q8NBJ9	SIDT2_HUMAN	SID1 transmembrane family, member 2 precursor	570	Extracellular (Potential).					integral to membrane|lysosomal membrane					0	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.69e-05)|Epithelial(105;0.000219)|all cancers(92;0.00144)														---	---	---	---
RNF214	257160	broad.mit.edu	37	11	117154090	117154091	+	Intron	DEL	TG	-	-	rs595297	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117154090_117154091delTG	uc001pqt.2	+						RNF214_uc001pqu.2_Intron|RNF214_uc010rxf.1_Intron	NM_207343	NP_997226			ring finger protein 214								zinc ion binding				0	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.88e-05)|Epithelial(105;0.000397)|all cancers(92;0.00258)														---	---	---	---
DSCAML1	57453	broad.mit.edu	37	11	117307231	117307232	+	Intron	DEL	TG	-	-	rs146622587		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117307231_117307232delTG	uc001prh.1	-							NM_020693	NP_065744			Down syndrome cell adhesion molecule like 1						axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)|skin(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)														---	---	---	---
DSCAML1	57453	broad.mit.edu	37	11	117374908	117374909	+	Intron	INS	-	CC	CC			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117374908_117374909insCC	uc001prh.1	-							NM_020693	NP_065744			Down syndrome cell adhesion molecule like 1						axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)|skin(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)														---	---	---	---
DSCAML1	57453	broad.mit.edu	37	11	117502406	117502407	+	Intron	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117502406_117502407delTG	uc001prh.1	-						DSCAML1_uc001pri.1_Intron	NM_020693	NP_065744			Down syndrome cell adhesion molecule like 1						axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)|skin(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)														---	---	---	---
DSCAML1	57453	broad.mit.edu	37	11	117613718	117613719	+	Intron	INS	-	CATC	CATC	rs143696830	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117613718_117613719insCATC	uc001prh.1	-						DSCAML1_uc001pri.1_Intron	NM_020693	NP_065744			Down syndrome cell adhesion molecule like 1						axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)|skin(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)														---	---	---	---
TMPRSS13	84000	broad.mit.edu	37	11	117790989	117790989	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117790989delA	uc001prs.1	-						TMPRSS13_uc009yzr.1_5'Flank|TMPRSS13_uc001prt.1_5'Flank|TMPRSS13_uc001pru.1_Intron	NM_001077263	NP_001070731			transmembrane protease, serine 13						proteolysis	integral to membrane	scavenger receptor activity|serine-type endopeptidase activity			pancreas(1)	1	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.00106)														---	---	---	---
IL10RA	3587	broad.mit.edu	37	11	117854466	117854466	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117854466delA	uc001prv.2	+						IL10RA_uc010rxl.1_5'Flank|IL10RA_uc010rxm.1_5'Flank|IL10RA_uc010rxn.1_5'Flank|IL10RA_uc001prw.2_5'Flank	NM_001558	NP_001549			interleukin 10 receptor, alpha precursor							integral to membrane|plasma membrane	interleukin-10 receptor activity			ovary(1)	1	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.07e-05)|Epithelial(105;0.00108)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	117919427	117919427	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117919427delG	uc001prx.1	-						uc001pry.1_Intron|uc001prz.1_Intron|uc009yzs.1_Intron|uc001psa.1_Intron					Homo sapiens mRNA for hypothetical protein, partial sequence, clone:Hsa11-digit26-03-15-R.																														---	---	---	---
MPZL3	196264	broad.mit.edu	37	11	118117150	118117151	+	Intron	DEL	TT	-	-	rs68003563		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118117150_118117151delTT	uc001psm.2	-						MPZL3_uc010rxy.1_Intron|MPZL3_uc010rxz.1_Intron|MPZL3_uc009yzy.2_Intron	NM_198275	NP_938016			myelin protein zero-like 3 precursor						cell adhesion	integral to membrane					0	all_hematologic(175;0.046)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)														---	---	---	---
CD3E	916	broad.mit.edu	37	11	118177978	118177978	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118177978delT	uc001psq.3	+						CD3E_uc009yzz.1_Intron|CD3E_uc010rya.1_Intron	NM_000733	NP_000724			CD3E antigen, epsilon polypeptide precursor						G-protein coupled receptor protein signaling pathway|signal complex assembly|T cell costimulation|T cell receptor signaling pathway|transmembrane receptor protein tyrosine kinase signaling pathway	external side of plasma membrane|integral to plasma membrane	protein heterodimerization activity|protein kinase binding|receptor signaling complex scaffold activity|receptor signaling protein activity|SH3 domain binding|T cell receptor binding|transmembrane receptor activity			ovary(2)	2	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.09e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0251)	Muromonab(DB00075)													---	---	---	---
CD3G	917	broad.mit.edu	37	11	118222931	118222932	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118222931_118222932delAA	uc001psu.2	+						CD3G_uc009zaa.1_Intron	NM_000073	NP_000064			CD3G antigen, gamma polypeptide precursor						establishment or maintenance of cell polarity|protein complex assembly|protein transport|regulation of apoptosis|T cell activation|T cell costimulation|T cell receptor signaling pathway	integral to plasma membrane|T cell receptor complex	protein heterodimerization activity|receptor signaling complex scaffold activity|T cell receptor binding|transmembrane receptor activity				0	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.04e-05)														---	---	---	---
UBE4A	9354	broad.mit.edu	37	11	118252002	118252002	+	Intron	DEL	T	-	-	rs139803253	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118252002delT	uc001psw.2	+						UBE4A_uc001psv.2_Intron	NM_004788	NP_004779			ubiquitination factor E4A						ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding			ovary(2)|upper_aerodigestive_tract(1)|breast(1)|kidney(1)	5	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)														---	---	---	---
MLL	4297	broad.mit.edu	37	11	118308391	118308391	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118308391delC	uc001pta.2	+						MLL_uc001ptb.2_Intron|uc001psy.2_5'Flank|MLL_uc001psz.1_Intron	NM_005933	NP_005924			myeloid/lymphoid or mixed-lineage leukemia						apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter	MLL1 complex	AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding			lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1)	25	all_hematologic(175;0.046)	all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244)		OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144)				T|O	MLL|MLLT1|MLLT2|MLLT3|MLLT4|MLLT7|MLLT10|MLLT6|ELL|EPS15|AF1Q|CREBBP|SH3GL1|FNBP1|PNUTL1|MSF|GPHN|GMPS|SSH3BP1|ARHGEF12|GAS7|FOXO3A|LAF4|LCX|SEPT6|LPP|CBFA2T1|GRAF|EP300|PICALM|HEAB	AML|ALL								---	---	---	---
MLL	4297	broad.mit.edu	37	11	118351036	118351036	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118351036delT	uc001pta.2	+						MLL_uc001ptb.2_Intron|MLL_uc001pte.1_5'Flank|MLL_uc009zab.1_5'Flank	NM_005933	NP_005924			myeloid/lymphoid or mixed-lineage leukemia						apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter	MLL1 complex	AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding			lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1)	25	all_hematologic(175;0.046)	all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244)		OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144)				T|O	MLL|MLLT1|MLLT2|MLLT3|MLLT4|MLLT7|MLLT10|MLLT6|ELL|EPS15|AF1Q|CREBBP|SH3GL1|FNBP1|PNUTL1|MSF|GPHN|GMPS|SSH3BP1|ARHGEF12|GAS7|FOXO3A|LAF4|LCX|SEPT6|LPP|CBFA2T1|GRAF|EP300|PICALM|HEAB	AML|ALL								---	---	---	---
MLL	4297	broad.mit.edu	37	11	118377629	118377629	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118377629delT	uc001pta.2	+						MLL_uc001ptb.2_Intron	NM_005933	NP_005924			myeloid/lymphoid or mixed-lineage leukemia						apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter	MLL1 complex	AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding			lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1)	25	all_hematologic(175;0.046)	all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244)		OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144)				T|O	MLL|MLLT1|MLLT2|MLLT3|MLLT4|MLLT7|MLLT10|MLLT6|ELL|EPS15|AF1Q|CREBBP|SH3GL1|FNBP1|PNUTL1|MSF|GPHN|GMPS|SSH3BP1|ARHGEF12|GAS7|FOXO3A|LAF4|LCX|SEPT6|LPP|CBFA2T1|GRAF|EP300|PICALM|HEAB	AML|ALL								---	---	---	---
IFT46	56912	broad.mit.edu	37	11	118432351	118432351	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118432351delA	uc001ptp.1	-						IFT46_uc001pto.1_Intron|IFT46_uc009zaf.1_Intron	NM_020153	NP_064538			IFT46						flagellum assembly|intraflagellar transport|protein stabilization	microtubule basal body|microtubule-based flagellum|nucleus	protein C-terminus binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	118737919	118737919	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118737919delA								DDX6 (75947 upstream) : CXCR5 (16622 downstream)																																			---	---	---	---
CBL	867	broad.mit.edu	37	11	119149127	119149127	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119149127delT	uc001pwe.2	+							NM_005188	NP_005179			Cas-Br-M (murine) ecotropic retroviral						epidermal growth factor receptor signaling pathway|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of receptor-mediated endocytosis	cytosol|nucleus	calcium ion binding|sequence-specific DNA binding transcription factor activity|SH3 domain binding|signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding	p.G397_I429del(1)|p.E366_K477del(1)		haematopoietic_and_lymphoid_tissue(135)|lung(10)|central_nervous_system(2)|ovary(1)|breast(1)	149		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)										CBL_gene-associated_Juvenile_Myelomonocytic_Leukemia_and_Developmental_Anomalies|Noonan_syndrome				---	---	---	---
MFRP	83552	broad.mit.edu	37	11	119215807	119215807	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119215807delC	uc001pwj.2	-						MFRP_uc010rzf.1_Intron|MFRP_uc010rzg.1_Intron	NM_031433	NP_113621			membrane frizzled-related protein							collagen					0		Medulloblastoma(222;0.0523)|Breast(348;0.174)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.84e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	119465295	119465295	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119465295delA								THY1 (171049 upstream) : PVRL1 (43513 downstream)																																			---	---	---	---
ARHGEF12	23365	broad.mit.edu	37	11	120241541	120241542	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120241541_120241542delTT	uc001pxl.1	+						ARHGEF12_uc009zat.2_Intron	NM_015313	NP_056128			Rho guanine nucleotide exchange factor (GEF) 12						apoptosis|axon guidance|G-protein coupled receptor protein signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane	G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(2)|breast(2)|skin(2)|ovary(1)	7		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)				T	MLL	AML								---	---	---	---
ARHGEF12	23365	broad.mit.edu	37	11	120317937	120317937	+	Intron	DEL	T	-	-	rs79430904		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120317937delT	uc001pxl.1	+						ARHGEF12_uc009zat.2_Intron|ARHGEF12_uc010rzn.1_Intron|ARHGEF12_uc009zau.1_Intron	NM_015313	NP_056128			Rho guanine nucleotide exchange factor (GEF) 12						apoptosis|axon guidance|G-protein coupled receptor protein signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane	G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(2)|breast(2)|skin(2)|ovary(1)	7		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)				T	MLL	AML								---	---	---	---
GRIK4	2900	broad.mit.edu	37	11	120467442	120467442	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120467442delT	uc001pxn.2	+						GRIK4_uc009zav.1_Intron|GRIK4_uc009zaw.1_Intron	NM_014619	NP_055434			glutamate receptor KA1 precursor						glutamate signaling pathway|synaptic transmission	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|central_nervous_system(1)	3		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)	L-Glutamic Acid(DB00142)													---	---	---	---
GRIK4	2900	broad.mit.edu	37	11	120613131	120613131	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120613131delA	uc001pxn.2	+						GRIK4_uc009zav.1_Intron|GRIK4_uc009zaw.1_Intron|GRIK4_uc009zax.1_Intron	NM_014619	NP_055434			glutamate receptor KA1 precursor						glutamate signaling pathway|synaptic transmission	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|central_nervous_system(1)	3		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)	L-Glutamic Acid(DB00142)													---	---	---	---
GRIK4	2900	broad.mit.edu	37	11	120614468	120614469	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120614468_120614469insT	uc001pxn.2	+						GRIK4_uc009zav.1_Intron|GRIK4_uc009zaw.1_Intron|GRIK4_uc009zax.1_Intron	NM_014619	NP_055434			glutamate receptor KA1 precursor						glutamate signaling pathway|synaptic transmission	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|central_nervous_system(1)	3		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)	L-Glutamic Acid(DB00142)													---	---	---	---
GRIK4	2900	broad.mit.edu	37	11	120652782	120652783	+	Intron	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120652782_120652783insC	uc001pxn.2	+						GRIK4_uc009zav.1_Intron|GRIK4_uc009zaw.1_Intron|GRIK4_uc009zax.1_Intron	NM_014619	NP_055434			glutamate receptor KA1 precursor						glutamate signaling pathway|synaptic transmission	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|central_nervous_system(1)	3		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)	L-Glutamic Acid(DB00142)													---	---	---	---
TBCEL	219899	broad.mit.edu	37	11	120926114	120926114	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120926114delT	uc009zay.2	+						TBCEL_uc001pxo.2_Intron|TBCEL_uc001pxp.2_Intron|TBCEL_uc001pxq.2_Intron	NM_001130047	NP_001123519			tubulin folding cofactor E-like							cytoplasm|cytoskeleton				skin(1)	1		Breast(109;0.00526)|Medulloblastoma(222;0.0523)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;5.89e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.121)														---	---	---	---
SORL1	6653	broad.mit.edu	37	11	121336242	121336245	+	Intron	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121336242_121336245delTTTT	uc001pxx.2	+							NM_003105	NP_003096			sortilin-related receptor containing LDLR class						cholesterol metabolic process|lipid transport|receptor-mediated endocytosis	integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|transmembrane receptor activity			ovary(5)|breast(4)|large_intestine(2)|skin(2)|central_nervous_system(1)|pancreas(1)	15		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)														---	---	---	---
SORL1	6653	broad.mit.edu	37	11	121378450	121378450	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121378450delT	uc001pxx.2	+							NM_003105	NP_003096			sortilin-related receptor containing LDLR class						cholesterol metabolic process|lipid transport|receptor-mediated endocytosis	integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|transmembrane receptor activity			ovary(5)|breast(4)|large_intestine(2)|skin(2)|central_nervous_system(1)|pancreas(1)	15		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	121661046	121661046	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121661046delT								SORL1 (156575 upstream) : LOC399959 (298765 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	121766361	121766361	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121766361delA								SORL1 (261890 upstream) : LOC399959 (193450 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	121842748	121842748	+	IGR	DEL	A	-	-	rs35796383		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121842748delA								SORL1 (338277 upstream) : LOC399959 (117063 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	122454980	122454980	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122454980delA								LOC399959 (216513 upstream) : UBASH3B (71418 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	123117075	123117075	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123117075delT								ASAM (51068 upstream) : GRAMD1B (279453 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	123314280	123314281	+	IGR	DEL	TT	-	-	rs35979038		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123314280_123314281delTT								ASAM (248273 upstream) : GRAMD1B (82247 downstream)																																			---	---	---	---
GRAMD1B	57476	broad.mit.edu	37	11	123410149	123410150	+	Intron	DEL	AT	-	-	rs142579508		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123410149_123410150delAT	uc001pyx.2	+						GRAMD1B_uc001pyw.2_Intron	NM_020716	NP_065767			GRAM domain containing 1B							integral to membrane				ovary(1)	1		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394)														---	---	---	---
GRAMD1B	57476	broad.mit.edu	37	11	123489375	123489375	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123489375delT	uc001pyx.2	+						GRAMD1B_uc001pyw.2_Intron|GRAMD1B_uc010rzw.1_Intron|GRAMD1B_uc010rzx.1_Intron|GRAMD1B_uc001pyy.2_Intron	NM_020716	NP_065767			GRAM domain containing 1B							integral to membrane				ovary(1)	1		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	123651883	123651883	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123651883delT								OR6X1 (26657 upstream) : OR6M1 (24234 downstream)																																			---	---	---	---
VWA5A	4013	broad.mit.edu	37	11	123994642	123994642	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123994642delA	uc001pzu.2	+						VWA5A_uc001pzr.2_Intron|VWA5A_uc001pzs.2_Intron|VWA5A_uc010sae.1_Intron|VWA5A_uc001pzt.2_Intron	NM_001130142	NP_001123614			BCSC-1 isoform 1											upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	124144175	124144177	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124144175_124144177delTTT								OR8G2 (47865 upstream) : OR8D1 (35560 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	124580682	124580683	+	IGR	INS	-	G	G	rs146038213	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124580682_124580683insG								SPA17 (15997 upstream) : NRGN (29146 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	124701958	124701959	+	Intron	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124701958_124701959delTC	uc001qbb.2	+											Homo sapiens mRNA; cDNA DKFZp667N1814 (from clone DKFZp667N1814).																														---	---	---	---
ROBO4	54538	broad.mit.edu	37	11	124765955	124765955	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124765955delG	uc001qbg.2	-						ROBO4_uc010sas.1_Intron|ROBO4_uc001qbh.2_Intron|ROBO4_uc001qbi.2_5'Flank|ROBO4_uc010sat.1_5'Flank	NM_019055	NP_061928			roundabout homolog 4, magic roundabout						angiogenesis|cell differentiation	integral to membrane	receptor activity			ovary(1)|skin(1)	2	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)														---	---	---	---
SLC37A2	219855	broad.mit.edu	37	11	124933386	124933386	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124933386delG	uc001qbn.2	+						SLC37A2_uc010sau.1_Intron	NM_001145290	NP_001138762			solute carrier family 37 (glycerol-3-phosphate						carbohydrate transport|transmembrane transport	integral to membrane				ovary(2)	2	all_hematologic(175;0.215)	Breast(109;0.012)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.152)|all_lung(97;0.159)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0384)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	125423488	125423488	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125423488delC								FEZ1 (57365 upstream) : EI24 (15810 downstream)																																			---	---	---	---
CHEK1	1111	broad.mit.edu	37	11	125496889	125496889	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125496889delA	uc009zbo.2	+						CHEK1_uc010sbh.1_Intron|CHEK1_uc010sbi.1_Intron|CHEK1_uc001qcf.3_Intron|CHEK1_uc009zbp.2_Intron|CHEK1_uc001qcg.3_Intron|CHEK1_uc009zbq.2_Intron|CHEK1_uc001qci.1_Intron	NM_001114122	NP_001107594			checkpoint kinase 1						cellular response to mechanical stimulus|DNA repair|DNA replication|gamete generation|negative regulation of cell proliferation|reciprocal meiotic recombination|regulation of cyclin-dependent protein kinase activity|replicative senescence	condensed nuclear chromosome|microtubule organizing center|nucleoplasm	ATP binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(3)|lung(2)|skin(1)	6	all_hematologic(175;0.228)	Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0748)									Other_conserved_DNA_damage_response_genes					---	---	---	---
CHEK1	1111	broad.mit.edu	37	11	125544036	125544036	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125544036delA	uc001qcf.3	+						ACRV1_uc001qck.2_Intron|ACRV1_uc001qcl.2_Intron|ACRV1_uc001qcm.2_Intron|ACRV1_uc001qcn.2_Intron|ACRV1_uc001qco.2_Intron|ACRV1_uc001qcp.2_Intron|ACRV1_uc001qcq.2_Intron|ACRV1_uc001qcr.2_Intron|ACRV1_uc001qcs.2_Intron	NM_001114121	NP_001107593			checkpoint kinase 1						cellular response to mechanical stimulus|DNA repair|DNA replication|gamete generation|negative regulation of cell proliferation|reciprocal meiotic recombination|regulation of cyclin-dependent protein kinase activity|replicative senescence	condensed nuclear chromosome|microtubule organizing center|nucleoplasm	ATP binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(3)|lung(2)|skin(1)	6	all_hematologic(175;0.228)	Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0748)									Other_conserved_DNA_damage_response_genes					---	---	---	---
CDON	50937	broad.mit.edu	37	11	125935215	125935215	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125935215delA	uc009zbw.2	-						CDON_uc001qdc.3_5'Flank	NM_016952	NP_058648			surface glycoprotein, Ig superfamily member						cell adhesion|muscle cell differentiation|positive regulation of muscle cell differentiation	integral to membrane|plasma membrane	protein binding			ovary(3)|skin(2)|breast(1)	6	all_hematologic(175;0.177)	Breast(109;0.00157)|Lung NSC(97;0.0127)|all_lung(97;0.0133)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.51e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0604)														---	---	---	---
FAM118B	79607	broad.mit.edu	37	11	126090264	126090264	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126090264delT	uc001qdf.2	+						FAM118B_uc009zca.2_Intron|FAM118B_uc001qdg.2_Intron	NM_024556	NP_078832			hypothetical protein LOC79607												0	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00948)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0784)														---	---	---	---
ST3GAL4	6484	broad.mit.edu	37	11	126272563	126272563	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126272563delC	uc001qds.2	+						ST3GAL4_uc001qdt.2_Intron|ST3GAL4_uc009zcc.2_Intron|ST3GAL4_uc009zcd.2_Intron|ST3GAL4_uc001qdu.2_Intron|ST3GAL4_uc001qdv.2_Intron	NM_006278	NP_006269			ST3 beta-galactoside alpha-2,3-sialyltransferase						post-translational protein modification|protein N-linked glycosylation via asparagine	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,3-sialyltransferase activity				0	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0739)|all_lung(97;0.0798)|all_neural(223;0.138)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0767)														---	---	---	---
ST3GAL4	6484	broad.mit.edu	37	11	126281048	126281048	+	Intron	DEL	T	-	-	rs72328982		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126281048delT	uc001qds.2	+						ST3GAL4_uc001qdt.2_Intron|ST3GAL4_uc009zcc.2_Intron|ST3GAL4_uc009zcd.2_Intron|ST3GAL4_uc001qdu.2_Intron|ST3GAL4_uc001qdv.2_Intron|ST3GAL4_uc009zce.2_Intron|ST3GAL4_uc001qdw.2_Intron|ST3GAL4_uc001qdx.1_Intron|ST3GAL4_uc001qdy.2_Intron|ST3GAL4_uc001qdz.2_Intron	NM_006278	NP_006269			ST3 beta-galactoside alpha-2,3-sialyltransferase						post-translational protein modification|protein N-linked glycosylation via asparagine	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,3-sialyltransferase activity				0	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0739)|all_lung(97;0.0798)|all_neural(223;0.138)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0767)														---	---	---	---
KIRREL3	84623	broad.mit.edu	37	11	126695703	126695703	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126695703delA	uc001qea.2	-						KIRREL3_uc001qeb.2_Intron|KIRREL3_uc001qec.1_Intron|KIRREL3_uc001qed.3_Intron	NM_032531	NP_115920			kin of IRRE like 3 isoform 1						hemopoiesis	extracellular region|integral to membrane|plasma membrane	protein binding			ovary(3)	3	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	126968018	126968019	+	Intron	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126968018_126968019delTG	uc001qeg.1	+											Homo sapiens cDNA FLJ37868 fis, clone BRSSN2017297.																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	127278956	127278956	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127278956delT								KIRREL3 (405601 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	127291530	127291531	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127291530_127291531insT								KIRREL3 (418175 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	127429268	127429269	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127429268_127429269delAA								KIRREL3 (555913 upstream) : ETS1 (899387 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	127480512	127480512	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:127480512delT								KIRREL3 (607157 upstream) : ETS1 (848144 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	128255985	128255985	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128255985delA								None (None upstream) : ETS1 (72671 downstream)																																			---	---	---	---
ETS1	2113	broad.mit.edu	37	11	128402553	128402554	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128402553_128402554delTT	uc001qej.2	-							NM_001143820	NP_001137292			v-ets erythroblastosis virus E26 oncogene						cell motility|immune response|induction of apoptosis|negative regulation of cell cycle|negative regulation of cell cycle|negative regulation of cell proliferation|PML body organization|positive regulation of cellular component movement|positive regulation of erythrocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|response to antibiotic|transcription from RNA polymerase II promoter	nucleus|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			lung(4)|central_nervous_system(1)|pleura(1)	6	all_hematologic(175;0.0537)	Lung NSC(97;0.000542)|all_lung(97;0.000665)|Breast(109;0.00765)|all_neural(223;0.0351)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.47e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0174)|LUSC - Lung squamous cell carcinoma(976;0.0815)|Lung(307;0.0833)														---	---	---	---
TP53AIP1	63970	broad.mit.edu	37	11	128805814	128805814	+	Intron	DEL	C	-	-	rs6590359	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128805814delC	uc001qey.2	-						TP53AIP1_uc001qex.2_3'UTR					RecName: Full=p53-regulated apoptosis-inducing protein 1;          Short=p53AIP1;						apoptosis	mitochondrion				lung(1)	1																		---	---	---	---
ARHGAP32	9743	broad.mit.edu	37	11	128933225	128933225	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128933225delT	uc009zcp.2	-						ARHGAP32_uc009zcq.1_Intron|ARHGAP32_uc001qfb.2_Intron	NM_001142685	NP_001136157			Rho GTPase-activating protein isoform 1						cell communication|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell cortex|cell junction|cytosol|dendritic spine|endoplasmic reticulum membrane|endosome membrane|Golgi membrane|postsynaptic density|postsynaptic membrane	GTPase activator activity|phosphatidylinositol binding			lung(3)|ovary(2)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	11	129140391	129140392	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129140391_129140392delTT								ARHGAP32 (78298 upstream) : BARX2 (105489 downstream)																																			---	---	---	---
BARX2	8538	broad.mit.edu	37	11	129310355	129310355	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129310355delC	uc001qfc.3	+							NM_003658	NP_003649			BarH-like homeobox 2												0	all_hematologic(175;0.0749)	Lung NSC(97;0.000383)|all_lung(97;0.000824)|Breast(109;0.000962)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.00929)|Lung(977;0.0245)|LUSC - Lung squamous cell carcinoma(976;0.0253)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	129482010	129482011	+	IGR	INS	-	T	T	rs145911149	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129482010_129482011insT								BARX2 (159837 upstream) : TMEM45B (203730 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	129604014	129604015	+	IGR	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129604014_129604015insG								BARX2 (281841 upstream) : TMEM45B (81726 downstream)																																			---	---	---	---
APLP2	334	broad.mit.edu	37	11	129987343	129987344	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129987343_129987344delTT	uc010sby.1	+						APLP2_uc001qfp.2_Intron|APLP2_uc001qfq.2_Intron|APLP2_uc010sbz.1_Intron|APLP2_uc001qfr.2_Intron|APLP2_uc001qfs.2_Intron|APLP2_uc001qfv.2_Intron	NM_001642	NP_001633			amyloid beta (A4) precursor-like protein 2						G-protein coupled receptor protein signaling pathway	integral to membrane|nucleus|plasma membrane	DNA binding|identical protein binding|serine-type endopeptidase inhibitor activity			ovary(3)	3	all_hematologic(175;0.0429)	Breast(109;0.00586)|Lung NSC(97;0.00785)|all_lung(97;0.0154)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0197)|Lung(977;0.24)														---	---	---	---
ST14	6768	broad.mit.edu	37	11	130052856	130052857	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130052856_130052857delTT	uc001qfw.2	+							NM_021978	NP_068813			matriptase						proteolysis	integral to plasma membrane	serine-type endopeptidase activity			ovary(2)|skin(2)|central_nervous_system(1)	5	all_hematologic(175;0.0429)	Lung NSC(97;0.000602)|Breast(109;0.000962)|all_lung(97;0.00126)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0183)|Lung(977;0.228)	Urokinase(DB00013)													---	---	---	---
ADAMTS8	11095	broad.mit.edu	37	11	130285207	130285208	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130285207_130285208delTT	uc001qgg.3	-							NM_007037	NP_008968			ADAM metallopeptidase with thrombospondin type 1						negative regulation of cell proliferation|proteolysis	proteinaceous extracellular matrix	heparin binding|integrin binding|low affinity phosphate transmembrane transporter activity|metalloendopeptidase activity|zinc ion binding			central_nervous_system(1)	1	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.039)|Lung(977;0.213)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	130687580	130687580	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130687580delA								ADAMTS15 (343865 upstream) : SNX19 (58187 downstream)																																			---	---	---	---
NTM	50863	broad.mit.edu	37	11	131394798	131394798	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131394798delG	uc010sci.1	+						NTM_uc001qgm.2_Intron|NTM_uc010sch.1_Intron	NM_001144058	NP_001137530			neurotrimin isoform 3						cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
NTM	50863	broad.mit.edu	37	11	131680331	131680331	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:131680331delC	uc010sci.1	+						NTM_uc001qgm.2_Intron|NTM_uc010sch.1_Intron	NM_001144058	NP_001137530			neurotrimin isoform 3						cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
OPCML	4978	broad.mit.edu	37	11	132522244	132522245	+	Intron	INS	-	ACAC	ACAC	rs5795793		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132522244_132522245insACAC	uc001qgs.2	-						OPCML_uc001qgu.2_Intron|OPCML_uc010sck.1_Intron|OPCML_uc001qgt.2_Intron|OPCML_uc010scl.1_Intron	NM_002545	NP_002536			opioid binding protein/cell adhesion						cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)														---	---	---	---
OPCML	4978	broad.mit.edu	37	11	132616349	132616350	+	Intron	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:132616349_132616350insC	uc001qgs.2	-						OPCML_uc001qgu.2_Intron|OPCML_uc010sck.1_Intron|OPCML_uc001qgt.2_Intron|OPCML_uc010scl.1_Intron	NM_002545	NP_002536			opioid binding protein/cell adhesion						cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)														---	---	---	---
OPCML	4978	broad.mit.edu	37	11	133107171	133107171	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133107171delG	uc001qgu.2	-							NM_001012393	NP_001012393			opioid binding protein/cell adhesion						cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)														---	---	---	---
OPCML	4978	broad.mit.edu	37	11	133173680	133173680	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133173680delA	uc001qgu.2	-							NM_001012393	NP_001012393			opioid binding protein/cell adhesion						cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)														---	---	---	---
OPCML	4978	broad.mit.edu	37	11	133196187	133196204	+	Intron	DEL	TGTGTGGGGGTGTGGGTA	-	-	rs79773383	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133196187_133196204delTGTGTGGGGGTGTGGGTA	uc001qgu.2	-							NM_001012393	NP_001012393			opioid binding protein/cell adhesion						cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)														---	---	---	---
OPCML	4978	broad.mit.edu	37	11	133203779	133203779	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133203779delA	uc001qgu.2	-							NM_001012393	NP_001012393			opioid binding protein/cell adhesion						cell adhesion|neuron recognition	anchored to membrane|integral to plasma membrane	opioid receptor activity			ovary(2)|skin(1)	3	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	133454731	133454732	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133454731_133454732delTT								OPCML (52328 upstream) : SPATA19 (255785 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	133457120	133457122	+	IGR	DEL	TGA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133457120_133457122delTGA								OPCML (54717 upstream) : SPATA19 (253395 downstream)																																			---	---	---	---
SPATA19	219938	broad.mit.edu	37	11	133717130	133717131	+	5'Flank	DEL	AC	-	-	rs72211641		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133717130_133717131delAC	uc001qgv.1	-							NM_174927	NP_777587			spermatogenesis associated 19 precursor						cell differentiation|multicellular organismal development|spermatogenesis	mitochondrial outer membrane					0	all_hematologic(175;0.127)	all_cancers(12;5.59e-17)|all_epithelial(12;2.65e-12)|all_lung(97;0.00045)|Lung NSC(97;0.000861)|Breast(109;0.000873)|Medulloblastoma(222;0.0425)|Esophageal squamous(93;0.0844)|all_neural(223;0.117)		Epithelial(10;4.36e-10)|all cancers(11;7.1e-09)|BRCA - Breast invasive adenocarcinoma(10;8.45e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00286)|Lung(977;0.207)														---	---	---	---
IGSF9B	22997	broad.mit.edu	37	11	133820890	133820891	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133820890_133820891insA	uc001qgx.3	-							NM_014987	NP_055802			immunoglobulin superfamily, member 9B							integral to membrane|plasma membrane					0	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)														---	---	---	---
NCAPD3	23310	broad.mit.edu	37	11	134030843	134030843	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134030843delT	uc001qhd.1	-						NCAPD3_uc010scm.1_Intron|NCAPD3_uc009zda.1_Intron|NCAPD3_uc001qhc.1_Intron	NM_015261	NP_056076			non-SMC condensin II complex, subunit D3						cell division|mitotic chromosome condensation	nuclear centromeric heterochromatin|nuclear condensin complex	methylated histone residue binding			ovary(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	5	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)														---	---	---	---
NCAPD3	23310	broad.mit.edu	37	11	134063809	134063809	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134063809delT	uc001qhd.1	-						NCAPD3_uc010scm.1_Intron|NCAPD3_uc009zda.1_Intron	NM_015261	NP_056076			non-SMC condensin II complex, subunit D3						cell division|mitotic chromosome condensation	nuclear centromeric heterochromatin|nuclear condensin complex	methylated histone residue binding			ovary(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	5	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)														---	---	---	---
VPS26B	112936	broad.mit.edu	37	11	134105639	134105639	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134105639delT	uc001qhe.2	+							NM_052875	NP_443107			vacuolar protein sorting 26 homolog B						protein transport|vacuolar transport	cytosol|retromer complex					0	all_hematologic(175;0.127)	all_cancers(12;1.1e-21)|all_epithelial(12;3.77e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;2.43e-10)|all cancers(11;2.94e-09)|BRCA - Breast invasive adenocarcinoma(10;9.57e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00164)|Lung(977;0.216)														---	---	---	---
GLB1L3	112937	broad.mit.edu	37	11	134178719	134178720	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134178719_134178720insA	uc009zdf.2	+						GLB1L3_uc010scu.1_Intron|GLB1L3_uc001qho.3_Intron	NM_001080407	NP_001073876			galactosidase, beta 1 like 3						carbohydrate metabolic process		cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			pancreas(1)	1	all_hematologic(175;0.127)	all_cancers(12;5.52e-23)|all_epithelial(12;2.15e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|all_neural(223;0.0182)|Medulloblastoma(222;0.0208)|Esophageal squamous(93;0.0559)		Epithelial(10;1.3e-11)|all cancers(11;2.07e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000873)|Lung(977;0.222)														---	---	---	---
B3GAT1	27087	broad.mit.edu	37	11	134281270	134281270	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134281270delG	uc001qhq.2	-						B3GAT1_uc001qhr.2_Intron	NM_018644	NP_061114			beta-1,3-glucuronyltransferase 1						carbohydrate metabolic process	Golgi membrane|integral to membrane	galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity|metal ion binding			ovary(1)	1	all_hematologic(175;0.127)	all_cancers(12;1.39e-23)|all_epithelial(12;7.17e-17)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|Medulloblastoma(222;0.0125)|all_neural(223;0.0137)|Esophageal squamous(93;0.0559)		Epithelial(10;2.58e-11)|all cancers(11;5.75e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.000879)|Lung(977;0.0864)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	134313837	134313838	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134313837_134313838insT	uc001qhs.2	+											Homo sapiens cDNA FLJ37762 fis, clone BRHIP2024347, weakly similar to GALECTIN-3.																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	134358230	134358230	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134358230delA	uc001qhs.2	+											Homo sapiens cDNA FLJ37762 fis, clone BRHIP2024347, weakly similar to GALECTIN-3.																														---	---	---	---
Unknown	0	broad.mit.edu	37	11	134403444	134403445	+	IGR	INS	-	TTTCAAAACCTG	TTTCAAAACCTG			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134403444_134403445insTTTCAAAACCTG								B3GAT1 (121632 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	134408686	134408686	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134408686delG								B3GAT1 (126874 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	134643387	134643389	+	IGR	DEL	AAG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134643387_134643389delAAG								B3GAT1 (361575 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	134671646	134671646	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134671646delA								B3GAT1 (389834 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	11	134924644	134924645	+	IGR	DEL	GT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134924644_134924645delGT								B3GAT1 (642832 upstream) : None (None downstream)																																			---	---	---	---
IQSEC3	440073	broad.mit.edu	37	12	281391	281391	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:281391delC	uc001qhw.1	+							NM_015232	NP_056047			IQ motif and Sec7 domain 3						regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity			central_nervous_system(2)|large_intestine(1)|skin(1)	4	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)														---	---	---	---
CCDC77	84318	broad.mit.edu	37	12	522112	522112	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:522112delT	uc001qig.2	+						CCDC77_uc009zdk.2_Intron|CCDC77_uc010sdp.1_Intron|CCDC77_uc010sdq.1_Intron	NM_032358	NP_115734			coiled-coil domain containing 77 isoform a							centrosome				ovary(1)	1	all_cancers(10;0.0149)|all_epithelial(11;0.035)|all_lung(10;0.111)|Ovarian(42;0.142)|Lung NSC(10;0.156)		OV - Ovarian serous cystadenocarcinoma(31;0.00123)|BRCA - Breast invasive adenocarcinoma(9;0.033)															---	---	---	---
B4GALNT3	283358	broad.mit.edu	37	12	664364	664364	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:664364delA	uc001qii.1	+						B4GALNT3_uc001qij.1_Intron|B4GALNT3_uc001qik.1_Intron	NM_173593	NP_775864			beta							Golgi cisterna membrane|integral to membrane	N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity			ovary(1)|skin(1)	2	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)															---	---	---	---
NINJ2	4815	broad.mit.edu	37	12	749967	749967	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:749967delT	uc001qil.2	-						NINJ2_uc010sdr.1_Intron|NINJ2_uc010sds.1_Intron|uc001qim.1_Intron|uc009zdl.1_5'Flank	NM_016533	NP_057617			ninjurin 2						nervous system development|neuron cell-cell adhesion|tissue regeneration	integral to plasma membrane				ovary(2)	2	all_cancers(10;0.0101)|all_epithelial(11;0.0174)|Ovarian(42;0.0512)|all_lung(10;0.103)|Lung NSC(10;0.185)		OV - Ovarian serous cystadenocarcinoma(31;3.26e-05)|BRCA - Breast invasive adenocarcinoma(9;0.0508)															---	---	---	---
WNK1	65125	broad.mit.edu	37	12	991052	991052	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:991052delT	uc001qio.3	+						WNK1_uc001qip.3_Intron|WNK1_uc001qir.3_Intron	NM_018979	NP_061852			WNK lysine deficient protein kinase 1						intracellular protein kinase cascade|ion transport|neuron development	cytoplasm	ATP binding|protein binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			stomach(6)|breast(6)|ovary(5)|lung(4)|large_intestine(1)|central_nervous_system(1)	23	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)															---	---	---	---
RAD52	5893	broad.mit.edu	37	12	1053380	1053380	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1053380delA	uc001qis.1	-						RAD52_uc001qit.1_Intron|RAD52_uc010sdt.1_Intron|RAD52_uc001qiu.1_Intron|RAD52_uc001qiv.1_Intron|RAD52_uc001qiw.1_Intron|RAD52_uc010sdu.1_Intron	NM_134424	NP_602296			RAD52 homolog						DNA recombinase assembly|mitotic recombination|reciprocal meiotic recombination	nucleoplasm	DNA binding|protein binding			central_nervous_system(1)	1	all_cancers(10;0.0119)|all_epithelial(11;0.0171)|all_lung(10;0.0521)|Ovarian(42;0.0816)|Lung NSC(10;0.0987)		OV - Ovarian serous cystadenocarcinoma(31;0.00123)|BRCA - Breast invasive adenocarcinoma(9;0.0323)										Homologous_recombination					---	---	---	---
ERC1	23085	broad.mit.edu	37	12	1142637	1142637	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1142637delT	uc001qjb.2	+						ERC1_uc001qiz.2_Intron|ERC1_uc001qjc.2_Intron|ERC1_uc001qja.2_Intron|ERC1_uc001qjd.2_Intron|ERC1_uc001qjf.2_Intron	NM_178040	NP_829884			RAB6-interacting protein 2 isoform epsilon						I-kappaB phosphorylation|multicellular organismal development|positive regulation of anti-apoptosis|positive regulation of NF-kappaB transcription factor activity|protein transport	Golgi membrane|IkappaB kinase complex|presynaptic membrane	leucine zipper domain binding			ovary(2)|lung(2)|breast(1)	5	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)															---	---	---	---
ERC1	23085	broad.mit.edu	37	12	1274475	1274476	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1274475_1274476delTT	uc001qjb.2	+						ERC1_uc001qiz.2_Intron|ERC1_uc001qjc.2_Intron|ERC1_uc001qja.2_Intron|ERC1_uc001qjd.2_Intron|ERC1_uc001qjf.2_Intron|ERC1_uc010sdv.1_Intron|ERC1_uc009zdp.2_Intron	NM_178040	NP_829884			RAB6-interacting protein 2 isoform epsilon						I-kappaB phosphorylation|multicellular organismal development|positive regulation of anti-apoptosis|positive regulation of NF-kappaB transcription factor activity|protein transport	Golgi membrane|IkappaB kinase complex|presynaptic membrane	leucine zipper domain binding			ovary(2)|lung(2)|breast(1)	5	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)															---	---	---	---
ERC1	23085	broad.mit.edu	37	12	1309730	1309730	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1309730delT	uc001qjb.2	+						ERC1_uc001qiz.2_Intron|ERC1_uc001qjc.2_Intron|ERC1_uc001qja.2_Intron|ERC1_uc001qjd.2_Intron|ERC1_uc001qjf.2_Intron|ERC1_uc010sdv.1_Intron|ERC1_uc009zdp.2_Intron|ERC1_uc001qje.2_Intron	NM_178040	NP_829884			RAB6-interacting protein 2 isoform epsilon						I-kappaB phosphorylation|multicellular organismal development|positive regulation of anti-apoptosis|positive regulation of NF-kappaB transcription factor activity|protein transport	Golgi membrane|IkappaB kinase complex|presynaptic membrane	leucine zipper domain binding			ovary(2)|lung(2)|breast(1)	5	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)															---	---	---	---
ADIPOR2	79602	broad.mit.edu	37	12	1823830	1823830	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1823830delG	uc001qjm.2	+						ADIPOR2_uc001qjn.2_Intron	NM_024551	NP_078827			adiponectin receptor 2						fatty acid oxidation|hormone-mediated signaling pathway	integral to membrane	hormone binding|receptor activity				0	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.000382)															---	---	---	---
CACNA1C	775	broad.mit.edu	37	12	2362031	2362033	+	Intron	DEL	TTT	-	-	rs112265708		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2362031_2362033delTTT	uc009zdu.1	+						CACNA1C_uc009zdv.1_Intron|CACNA1C_uc001qkb.2_Intron|CACNA1C_uc001qkc.2_Intron|CACNA1C_uc001qke.2_Intron|CACNA1C_uc001qkf.2_Intron|CACNA1C_uc001qjz.2_Intron|CACNA1C_uc001qkd.2_Intron|CACNA1C_uc001qkg.2_Intron|CACNA1C_uc009zdw.1_Intron|CACNA1C_uc001qkh.2_Intron|CACNA1C_uc001qkl.2_Intron|CACNA1C_uc001qkn.2_Intron|CACNA1C_uc001qko.2_Intron|CACNA1C_uc001qkp.2_Intron|CACNA1C_uc001qkr.2_Intron|CACNA1C_uc001qku.2_Intron|CACNA1C_uc001qkq.2_Intron|CACNA1C_uc001qks.2_Intron|CACNA1C_uc001qkt.2_Intron|CACNA1C_uc001qka.1_Intron|CACNA1C_uc001qki.1_Intron|CACNA1C_uc001qkj.1_Intron|CACNA1C_uc001qkk.1_Intron|CACNA1C_uc001qkm.1_Intron	NM_199460	NP_955630			calcium channel, voltage-dependent, L type,						axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)													---	---	---	---
CACNA1C	775	broad.mit.edu	37	12	2700807	2700808	+	Intron	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2700807_2700808delAG	uc009zdu.1	+						CACNA1C_uc009zdv.1_Intron|CACNA1C_uc001qkb.2_Intron|CACNA1C_uc001qkc.2_Intron|CACNA1C_uc001qke.2_Intron|CACNA1C_uc001qkf.2_Intron|CACNA1C_uc001qjz.2_Intron|CACNA1C_uc001qkd.2_Intron|CACNA1C_uc001qkg.2_Intron|CACNA1C_uc009zdw.1_Intron|CACNA1C_uc001qkh.2_Intron|CACNA1C_uc001qkl.2_Intron|CACNA1C_uc001qkn.2_Intron|CACNA1C_uc001qko.2_Intron|CACNA1C_uc001qkp.2_Intron|CACNA1C_uc001qkr.2_Intron|CACNA1C_uc001qku.2_Intron|CACNA1C_uc001qkq.2_Intron|CACNA1C_uc001qks.2_Intron|CACNA1C_uc001qkt.2_Intron|CACNA1C_uc001qka.1_Intron|CACNA1C_uc001qki.1_Intron|CACNA1C_uc001qkj.1_Intron|CACNA1C_uc001qkk.1_Intron|CACNA1C_uc001qkm.1_Intron|CACNA1C_uc001qkw.2_Intron	NM_199460	NP_955630			calcium channel, voltage-dependent, L type,						axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)													---	---	---	---
ITFG2	55846	broad.mit.edu	37	12	2931084	2931085	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2931084_2931085delTT	uc001qlb.1	+						ITFG2_uc010seb.1_Intron|ITFG2_uc010sec.1_Intron	NM_018463	NP_060933			integrin alpha FG-GAP repeat containing 2												0			OV - Ovarian serous cystadenocarcinoma(31;0.000818)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	2961536	2961536	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2961536delT	uc009zdz.1	+											Homo sapiens cDNA clone IMAGE:40132675.																														---	---	---	---
TULP3	7289	broad.mit.edu	37	12	3017106	3017106	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3017106delT	uc010seh.1	+						TULP3_uc010sef.1_Intron|TULP3_uc009zec.1_Intron|TULP3_uc010seg.1_Intron|TULP3_uc001qlj.2_Intron|TULP3_uc010sei.1_Intron	NM_003324	NP_003315			tubby like protein 3 isoform 1						G-protein coupled receptor protein signaling pathway|regulation of transcription, DNA-dependent	cytoplasm|extracellular region|nucleus|plasma membrane	phosphatidylinositol-4,5-bisphosphate binding				0			OV - Ovarian serous cystadenocarcinoma(31;0.000818)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	3397836	3397836	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3397836delG								TSPAN9 (2107 upstream) : PRMT8 (92679 downstream)																																			---	---	---	---
PRMT8	56341	broad.mit.edu	37	12	3628486	3628486	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3628486delA	uc001qmf.2	+						PRMT8_uc009zed.2_Intron	NM_019854	NP_062828			HMT1 hnRNP methyltransferase-like 4						regulation of protein binding	cytoplasm|plasma membrane	histone-arginine N-methyltransferase activity|protein heterodimerization activity|protein homodimerization activity|protein-arginine omega-N asymmetric methyltransferase activity|protein-arginine omega-N monomethyltransferase activity			ovary(3)|central_nervous_system(1)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(31;0.0109)|COAD - Colon adenocarcinoma(12;0.0264)															---	---	---	---
PRMT8	56341	broad.mit.edu	37	12	3702245	3702246	+	Intron	INS	-	CT	CT			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3702245_3702246insCT	uc001qmf.2	+						PRMT8_uc009zed.2_Intron|PRMT8_uc001qmg.2_Intron|PRMT8_uc001qmh.2_Intron	NM_019854	NP_062828			HMT1 hnRNP methyltransferase-like 4						regulation of protein binding	cytoplasm|plasma membrane	histone-arginine N-methyltransferase activity|protein heterodimerization activity|protein homodimerization activity|protein-arginine omega-N asymmetric methyltransferase activity|protein-arginine omega-N monomethyltransferase activity			ovary(3)|central_nervous_system(1)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(31;0.0109)|COAD - Colon adenocarcinoma(12;0.0264)															---	---	---	---
EFCAB4B	84766	broad.mit.edu	37	12	3759034	3759035	+	Intron	INS	-	A	A	rs145165843	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3759034_3759035insA	uc001qmj.2	-						EFCAB4B_uc010sen.1_Intron|EFCAB4B_uc010seo.1_Intron|EFCAB4B_uc001qmi.1_Intron	NM_032680	NP_116069			EF-hand calcium binding domain 4B isoform c						activation of store-operated calcium channel activity|store-operated calcium entry	cytoplasm	calcium ion binding|protein binding			ovary(1)|pancreas(1)	2			OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264)															---	---	---	---
EFCAB4B	84766	broad.mit.edu	37	12	3787865	3787865	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3787865delA	uc001qmj.2	-						EFCAB4B_uc010sen.1_Intron|EFCAB4B_uc010seo.1_Intron	NM_032680	NP_116069			EF-hand calcium binding domain 4B isoform c						activation of store-operated calcium channel activity|store-operated calcium entry	cytoplasm	calcium ion binding|protein binding			ovary(1)|pancreas(1)	2			OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	3992265	3992266	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3992265_3992266delAA								PARP11 (9657 upstream) : CCND2 (390636 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	4051757	4051758	+	IGR	DEL	CA	-	-	rs2907512	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4051757_4051758delCA								PARP11 (69149 upstream) : CCND2 (331144 downstream)																																			---	---	---	---
CCND2	894	broad.mit.edu	37	12	4409271	4409271	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4409271delA	uc001qmo.2	+	5						NM_001759	NP_001750			cyclin D2						cell division|positive regulation of cyclin-dependent protein kinase activity|positive regulation of protein phosphorylation	cyclin-dependent protein kinase holoenzyme complex|cytoplasm|membrane|nucleus	protein kinase binding			haematopoietic_and_lymphoid_tissue(1)|breast(1)|kidney(1)	3			all cancers(3;4.15e-10)|GBM - Glioblastoma multiforme(3;6.34e-05)|Colorectal(7;0.00245)|OV - Ovarian serous cystadenocarcinoma(31;0.00301)|COAD - Colon adenocarcinoma(12;0.0264)|STAD - Stomach adenocarcinoma(119;0.206)					T	IGL@	NHL,CLL								---	---	---	---
Unknown	0	broad.mit.edu	37	12	4470170	4470171	+	IGR	DEL	TG	-	-	rs11830066		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4470170_4470171delTG								C12orf5 (982 upstream) : FGF23 (7222 downstream)																																			---	---	---	---
RAD51AP1	10635	broad.mit.edu	37	12	4652237	4652237	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4652237delT	uc001qmw.2	+						RAD51AP1_uc001qmu.2_Intron|RAD51AP1_uc001qmv.2_Intron|RAD51AP1_uc010sep.1_Intron|RAD51AP1_uc010seq.1_Intron	NM_001130862	NP_001124334			RAD51 associated protein 1 isoform a						double-strand break repair via homologous recombination		double-stranded DNA binding|protein binding|protein binding|RNA binding|single-stranded DNA binding				0			Colorectal(7;0.00306)|COAD - Colon adenocarcinoma(12;0.0389)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	4896342	4896343	+	IGR	INS	-	TG	TG	rs140410268	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4896342_4896343insTG								GALNT8 (14450 upstream) : KCNA6 (21999 downstream)																																			---	---	---	---
ANO2	57101	broad.mit.edu	37	12	5941834	5941834	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5941834delA	uc001qnm.2	-							NM_020373	NP_065106			anoctamin 2							chloride channel complex|plasma membrane	intracellular calcium activated chloride channel activity			ovary(4)|large_intestine(2)|central_nervous_system(1)	7																		---	---	---	---
ANO2	57101	broad.mit.edu	37	12	6046627	6046629	+	Intron	DEL	CTT	-	-	rs71689845		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6046627_6046629delCTT	uc001qnm.2	-							NM_020373	NP_065106			anoctamin 2							chloride channel complex|plasma membrane	intracellular calcium activated chloride channel activity			ovary(4)|large_intestine(2)|central_nervous_system(1)	7																		---	---	---	---
VWF	7450	broad.mit.edu	37	12	6218825	6218825	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6218825delT	uc001qnn.1	-						VWF_uc010set.1_Intron|VWF_uc001qno.1_Intron	NM_000552	NP_000543			von Willebrand factor preproprotein						blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)	12					Antihemophilic Factor(DB00025)													---	---	---	---
VWF	7450	broad.mit.edu	37	12	6231704	6231704	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6231704delT	uc001qnn.1	-						VWF_uc010set.1_Intron|VWF_uc001qno.1_Intron	NM_000552	NP_000543			von Willebrand factor preproprotein						blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)	12					Antihemophilic Factor(DB00025)													---	---	---	---
Unknown	0	broad.mit.edu	37	12	6244943	6244946	+	IGR	DEL	AAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6244943_6244946delAAAA								VWF (11107 upstream) : CD9 (63927 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	6348342	6348343	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6348342_6348343insT								CD9 (915 upstream) : PLEKHG6 (71259 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	6414885	6414885	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6414885delA								CD9 (67458 upstream) : PLEKHG6 (4717 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	6454602	6454603	+	IGR	DEL	CA	-	-	rs72657512		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6454602_6454603delCA								TNFRSF1A (3341 upstream) : SCNN1A (1408 downstream)																																			---	---	---	---
LPCAT3	10162	broad.mit.edu	37	12	7092803	7092803	+	Intron	DEL	A	-	-	rs75408212		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7092803delA	uc001qsi.2	-						EMG1_uc010sfv.1_Intron|LPCAT3_uc010sfw.1_Intron|LPCAT3_uc009zfp.2_Intron|LPCAT3_uc010sfx.1_Intron|LPCAT3_uc009zfq.1_Intron	NM_005768	NP_005759			lysophosphatidylcholine acyltransferase 3						phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	1-acylglycerophosphocholine O-acyltransferase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	7182597	7182597	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7182597delT								C1S (4264 upstream) : C1R (4920 downstream)																																			---	---	---	---
CLSTN3	9746	broad.mit.edu	37	12	7310851	7310851	+	3'UTR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7310851delC	uc001qsr.2	+	18					CLSTN3_uc001qss.2_3'UTR|CLSTN3_uc001qst.2_3'UTR	NM_014718	NP_055533			calsyntenin 3 precursor						homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			large_intestine(1)	1																		---	---	---	---
CD163L1	283316	broad.mit.edu	37	12	7556021	7556021	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7556021delT	uc001qsy.2	-						CD163L1_uc010sge.1_Intron	NM_174941	NP_777601			scavenger receptor cysteine-rich type 1							extracellular region|integral to membrane|plasma membrane	scavenger receptor activity			ovary(8)|skin(2)|central_nervous_system(1)	11																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	7837695	7837695	+	IGR	DEL	T	-	-	rs113716228		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7837695delT								APOBEC1 (12907 upstream) : GDF3 (4687 downstream)																																			---	---	---	---
SLC2A14	144195	broad.mit.edu	37	12	7982151	7982153	+	Intron	DEL	AAA	-	-	rs36068117		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7982151_7982153delAAA	uc001qtk.2	-						SLC2A14_uc001qtl.2_Intron|SLC2A14_uc001qtm.2_Intron|SLC2A14_uc010sgg.1_Intron|SLC2A14_uc001qtn.2_Intron|SLC2A14_uc001qto.2_Intron|SLC2A14_uc010sgh.1_Intron	NM_153449	NP_703150			glucose transporter 14						cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane	glucose transmembrane transporter activity			ovary(1)	1				Kidney(36;0.0883)														---	---	---	---
SLC2A3	6515	broad.mit.edu	37	12	8076980	8076980	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8076980delT	uc001qtr.2	-							NM_006931	NP_008862			solute carrier family 2 (facilitated glucose						carbohydrate metabolic process|water-soluble vitamin metabolic process	integral to membrane|plasma membrane	D-glucose transmembrane transporter activity|dehydroascorbic acid transporter activity			ovary(3)|pancreas(1)	4				Kidney(36;0.0866)														---	---	---	---
FOXJ2	55810	broad.mit.edu	37	12	8196882	8196882	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8196882delA	uc001qtu.2	+						FOXJ2_uc001qtt.1_Intron	NM_018416	NP_060886			forkhead box J2						embryo development|organ development|pattern specification process|positive regulation of transcription, DNA-dependent|regulation of sequence-specific DNA binding transcription factor activity|tissue development	nucleolus|transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding			upper_aerodigestive_tract(2)|ovary(2)|skin(1)	5				Kidney(36;0.0944)														---	---	---	---
FOXJ2	55810	broad.mit.edu	37	12	8203079	8203079	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8203079delC	uc001qtu.2	+							NM_018416	NP_060886			forkhead box J2						embryo development|organ development|pattern specification process|positive regulation of transcription, DNA-dependent|regulation of sequence-specific DNA binding transcription factor activity|tissue development	nucleolus|transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding			upper_aerodigestive_tract(2)|ovary(2)|skin(1)	5				Kidney(36;0.0944)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	8398687	8398687	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8398687delT								LOC653113 (3145 upstream) : LOC389634 (110875 downstream)																																			---	---	---	---
CLEC4E	26253	broad.mit.edu	37	12	8692981	8692981	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8692981delT	uc001quo.1	-							NM_014358	NP_055173			C-type lectin domain family 4, member E							integral to membrane	sugar binding			central_nervous_system(1)	1	Lung SC(5;0.184)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	9207906	9207906	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9207906delA								KLRG1 (44568 upstream) : LOC144571 (9867 downstream)																																			---	---	---	---
DDX12	440081	broad.mit.edu	37	12	9595962	9595963	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9595962_9595963insA	uc010sgs.1	-							NM_004400	NP_004391			DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 12												0																		---	---	---	---
CLECL1	160365	broad.mit.edu	37	12	9870957	9870958	+	Intron	DEL	TT	-	-	rs139758574		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9870957_9870958delTT	uc001qwi.2	-											Homo sapiens, clone IMAGE:4536737, mRNA.							integral to membrane|plasma membrane	sugar binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	9917642	9917644	+	IGR	DEL	TTT	-	-	rs77757771		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9917642_9917644delTTT								CD69 (4145 upstream) : KLRF1 (62433 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	10262652	10262652	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10262652delA								CLEC1A (11047 upstream) : CLEC7A (6724 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	10392081	10392082	+	IGR	INS	-	TTA	TTA	rs143361134		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10392081_10392082insTTA								GABARAPL1 (16359 upstream) : KLRD1 (64968 downstream)																																			---	---	---	---
KLRD1	3824	broad.mit.edu	37	12	10467143	10467143	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10467143delA	uc001qxw.3	+						KLRD1_uc001qxx.3_Intron|KLRD1_uc001qxy.3_Intron|KLRD1_uc009zhh.2_Intron|KLRD1_uc009zhi.2_Intron|KLRD1_uc001qxz.3_Intron	NM_001114396	NP_001107868			killer cell lectin-like receptor subfamily D,						cell surface receptor linked signaling pathway|regulation of immune response	integral to membrane|plasma membrane	sugar binding|transmembrane receptor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	10720883	10720884	+	IGR	DEL	TC	-	-	rs35687852		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10720883_10720884delTC								KLRC1 (113899 upstream) : KLRA1 (20194 downstream)																																			---	---	---	---
ETV6	2120	broad.mit.edu	37	12	12032029	12032029	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12032029delT	uc001qzz.2	+						ETV6_uc001raa.1_Intron	NM_001987	NP_001978			ets variant 6							cytoplasm|nucleolus	protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		ETV6/NTRK3(234)|ETV6/JAK2(11)	soft_tissue(85)|kidney(66)|breast(55)|salivary_gland(26)|haematopoietic_and_lymphoid_tissue(13)|ovary(2)|upper_aerodigestive_tract(1)|skin(1)|pancreas(1)	250		all_cancers(2;1.88e-12)|Acute lymphoblastic leukemia(2;6.91e-39)|all_hematologic(2;2.7e-36)						T	NTRK3|RUNX1|PDGFRB|ABL1|MN1|ABL2|FACL6|CHIC2|ARNT|JAK2|EVI1|CDX2|STL|HLXB9|MDS2|PER1|SYK|TTL|FGFR3|PAX5	congenital fibrosarcoma|multiple leukemia and lymphoma| secretory breast|MDS|ALL								---	---	---	---
ETV6	2120	broad.mit.edu	37	12	12128809	12128809	+	Intron	DEL	G	-	-	rs11352755		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12128809delG	uc001raa.1	+							NM_001987	NP_001978			ets variant 6							cytoplasm|nucleolus	protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		ETV6/NTRK3(234)|ETV6/JAK2(11)	soft_tissue(85)|kidney(66)|breast(55)|salivary_gland(26)|haematopoietic_and_lymphoid_tissue(13)|ovary(2)|upper_aerodigestive_tract(1)|skin(1)|pancreas(1)	250		all_cancers(2;1.88e-12)|Acute lymphoblastic leukemia(2;6.91e-39)|all_hematologic(2;2.7e-36)						T	NTRK3|RUNX1|PDGFRB|ABL1|MN1|ABL2|FACL6|CHIC2|ARNT|JAK2|EVI1|CDX2|STL|HLXB9|MDS2|PER1|SYK|TTL|FGFR3|PAX5	congenital fibrosarcoma|multiple leukemia and lymphoma| secretory breast|MDS|ALL								---	---	---	---
ETV6	2120	broad.mit.edu	37	12	12267244	12267245	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12267244_12267245delTT	uc001raa.1	+						BCL2L14_uc001raf.1_Intron	NM_001987	NP_001978			ets variant 6							cytoplasm|nucleolus	protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		ETV6/NTRK3(234)|ETV6/JAK2(11)	soft_tissue(85)|kidney(66)|breast(55)|salivary_gland(26)|haematopoietic_and_lymphoid_tissue(13)|ovary(2)|upper_aerodigestive_tract(1)|skin(1)|pancreas(1)	250		all_cancers(2;1.88e-12)|Acute lymphoblastic leukemia(2;6.91e-39)|all_hematologic(2;2.7e-36)						T	NTRK3|RUNX1|PDGFRB|ABL1|MN1|ABL2|FACL6|CHIC2|ARNT|JAK2|EVI1|CDX2|STL|HLXB9|MDS2|PER1|SYK|TTL|FGFR3|PAX5	congenital fibrosarcoma|multiple leukemia and lymphoma| secretory breast|MDS|ALL								---	---	---	---
LRP6	4040	broad.mit.edu	37	12	12302229	12302229	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12302229delT	uc001rah.3	-						BCL2L14_uc001raf.1_Intron|LRP6_uc010shl.1_Intron	NM_002336	NP_002327			low density lipoprotein receptor-related protein						cellular response to cholesterol|negative regulation of protein phosphorylation|negative regulation of protein serine/threonine kinase activity|negative regulation of smooth muscle cell apoptosis|neural crest formation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell cycle|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	cell surface|cytoplasmic vesicle|endoplasmic reticulum|integral to membrane|plasma membrane	coreceptor activity|frizzled binding|kinase inhibitor activity|low-density lipoprotein receptor activity|protein homodimerization activity|toxin transporter activity|Wnt-protein binding			lung(4)|skin(4)|ovary(2)|kidney(1)|central_nervous_system(1)	12		Prostate(47;0.0865)																---	---	---	---
LRP6	4040	broad.mit.edu	37	12	12333851	12333854	+	Intron	DEL	AGAC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12333851_12333854delAGAC	uc001rah.3	-						BCL2L14_uc001raf.1_Intron|LRP6_uc010shl.1_Intron	NM_002336	NP_002327			low density lipoprotein receptor-related protein						cellular response to cholesterol|negative regulation of protein phosphorylation|negative regulation of protein serine/threonine kinase activity|negative regulation of smooth muscle cell apoptosis|neural crest formation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell cycle|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	cell surface|cytoplasmic vesicle|endoplasmic reticulum|integral to membrane|plasma membrane	coreceptor activity|frizzled binding|kinase inhibitor activity|low-density lipoprotein receptor activity|protein homodimerization activity|toxin transporter activity|Wnt-protein binding			lung(4)|skin(4)|ovary(2)|kidney(1)|central_nervous_system(1)	12		Prostate(47;0.0865)																---	---	---	---
Unknown	0	broad.mit.edu	37	12	12471644	12471644	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12471644delA								LRP6 (51833 upstream) : MANSC1 (10574 downstream)																																			---	---	---	---
LOH12CR1	118426	broad.mit.edu	37	12	12510571	12510571	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12510571delA	uc001ral.2	+						LOH12CR1_uc009zhu.2_Intron|LOH12CR2_uc001rak.2_5'Flank	NM_058169	NP_477517			LOH1CR12											ovary(1)	1		Prostate(47;0.0802)		BRCA - Breast invasive adenocarcinoma(232;0.0205)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	12757484	12757485	+	IGR	INS	-	A	A	rs34950665		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12757484_12757485insA								DUSP16 (42167 upstream) : CREBL2 (7346 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	12798822	12798822	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12798822delA								CREBL2 (781 upstream) : GPR19 (15173 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	12862307	12862307	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12862307delT								GPR19 (13186 upstream) : CDKN1B (7995 downstream)																																			---	---	---	---
RPL13AP20	387841	broad.mit.edu	37	12	13026142	13026142	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13026142delT	uc010sho.1	+							NR_003932				SubName: Full=Ribosomal protein L13a variant; Flags: Fragment;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	13403900	13403900	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13403900delT								EMP1 (34193 upstream) : C12orf36 (120123 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	13662732	13662732	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13662732delG								C12orf36 (133087 upstream) : GRIN2B (51678 downstream)																																			---	---	---	---
GRIN2B	2904	broad.mit.edu	37	12	13731827	13731828	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13731827_13731828insA	uc001rbt.2	-							NM_000834	NP_000825			N-methyl-D-aspartate receptor subunit 2B						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			central_nervous_system(4)|ovary(3)|skin(3)|lung(2)	12					Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)													---	---	---	---
Unknown	0	broad.mit.edu	37	12	14271188	14271188	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14271188delA								GRIN2B (138166 upstream) : ATF7IP (247423 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	14912863	14912863	+	IGR	DEL	A	-	-	rs74824908		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14912863delA								GUCY2C (63344 upstream) : HIST4H4 (8071 downstream)																																			---	---	---	---
ART4	420	broad.mit.edu	37	12	14998424	14998424	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14998424delT	uc001rcl.1	-						ART4_uc009zid.1_5'Flank|ART4_uc009zie.1_5'Flank|ART4_uc001rcm.1_5'Flank	NM_021071	NP_066549			ADP-ribosyltransferase 4 precursor						arginine metabolic process|protein ADP-ribosylation	anchored to membrane|plasma membrane	NAD(P)+-protein-arginine ADP-ribosyltransferase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	15120251	15120251	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15120251delT								ARHGDIB (5689 upstream) : PDE6H (5727 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	15147884	15147884	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15147884delT								PDE6H (13087 upstream) : RERG (112834 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	15421002	15421003	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15421002_15421003delTT								RERG (46698 upstream) : PTPRO (54484 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	15454165	15454165	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15454165delA								RERG (79861 upstream) : PTPRO (21322 downstream)																																			---	---	---	---
PTPRO	5800	broad.mit.edu	37	12	15489557	15489557	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15489557delA	uc001rcv.1	+						PTPRO_uc001rcw.1_Intron|PTPRO_uc001rcu.1_Intron	NM_030667	NP_109592			receptor-type protein tyrosine phosphatase O							integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	9		Hepatocellular(102;0.244)																---	---	---	---
Unknown	0	broad.mit.edu	37	12	16555113	16555113	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16555113delT								MGST1 (31771 upstream) : LMO3 (146194 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	16626468	16626468	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16626468delT								MGST1 (103126 upstream) : LMO3 (74839 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	16875667	16875667	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16875667delC								LMO3 (112909 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	17296530	17296530	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:17296530delT								LMO3 (533772 upstream) : RERGL (937274 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	17627368	17627369	+	IGR	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:17627368_17627369delCT								LMO3 (864610 upstream) : RERGL (606435 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	18134573	18134573	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18134573delA								None (None upstream) : RERGL (99231 downstream)																																			---	---	---	---
PLEKHA5	54477	broad.mit.edu	37	12	19475665	19475665	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19475665delT	uc001reb.2	+						PLEKHA5_uc010sie.1_Intron|PLEKHA5_uc001rea.2_Intron|PLEKHA5_uc009zin.2_Intron|PLEKHA5_uc010sif.1_Intron|PLEKHA5_uc010sig.1_Intron|PLEKHA5_uc010sih.1_Intron|PLEKHA5_uc001rec.1_Intron|PLEKHA5_uc009zio.2_Intron	NM_019012	NP_061885			pleckstrin homology domain containing, family A								1-phosphatidylinositol binding|protein binding			ovary(1)|kidney(1)|skin(1)	3	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)																	---	---	---	---
AEBP2	121536	broad.mit.edu	37	12	19626888	19626889	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19626888_19626889insT	uc001ref.2	+						AEBP2_uc001ree.2_Intron|AEBP2_uc001reg.1_Intron	NM_001114176	NP_001107648			AE binding protein 2 isoform b						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex	DNA binding|zinc ion binding			ovary(1)	1	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)|Esophageal squamous(101;0.143)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	19680400	19680400	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19680400delT								AEBP2 (5227 upstream) : PDE3A (841797 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	19752146	19752146	+	IGR	DEL	C	-	-	rs7489070	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:19752146delC								AEBP2 (76973 upstream) : PDE3A (770051 downstream)																																			---	---	---	---
SLCO1C1	53919	broad.mit.edu	37	12	20864580	20864580	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20864580delA	uc001rej.3	+						SLCO1C1_uc010sii.1_Intron|SLCO1C1_uc010sij.1_Intron|SLCO1C1_uc009zip.2_Intron|SLCO1C1_uc001rei.2_Intron|SLCO1C1_uc010sik.1_Intron	NM_017435	NP_059131			solute carrier organic anion transporter family,						sodium-independent organic anion transport	integral to membrane|plasma membrane	thyroid hormone transmembrane transporter activity			ovary(5)|pancreas(1)|skin(1)	7	Esophageal squamous(101;0.149)																	---	---	---	---
SLCO1B3	28234	broad.mit.edu	37	12	21011114	21011114	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21011114delA	uc001rek.2	+						SLCO1B3_uc001rel.2_Intron|SLCO1B3_uc010sil.1_Intron|LST-3TM12_uc010sim.1_Intron	NM_019844	NP_062818			solute carrier organic anion transporter family,						bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|cytoplasm|integral to plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(2)|ovary(1)|skin(1)	4	Esophageal squamous(101;0.149)																	---	---	---	---
SLCO1B3	28234	broad.mit.edu	37	12	21242746	21242746	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21242746delT	uc010sil.1	+						LST-3TM12_uc010sim.1_Intron|LST-3TM12_uc010sin.1_Intron					SubName: Full=Liver-specific organic anion transporter 3TM13; SubName: Full=Organic anion transporter LST-3c;						bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|cytoplasm|integral to plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(2)|ovary(1)|skin(1)	4	Esophageal squamous(101;0.149)																	---	---	---	---
RECQL	5965	broad.mit.edu	37	12	21633453	21633453	+	Intron	DEL	T	-	-	rs78229960		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21633453delT	uc001rex.2	-						RECQL_uc001rey.2_Intron	NM_032941	NP_116559			RecQ protein-like						DNA recombination|DNA repair|DNA replication	nucleus	ATP binding|ATP-dependent 3'-5' DNA helicase activity|DNA strand annealing activity|protein binding			ovary(1)|lung(1)	2													Direct_reversal_of_damage|Other_identified_genes_with_known_or_suspected_DNA_repair_function					---	---	---	---
GYS2	2998	broad.mit.edu	37	12	21727271	21727271	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21727271delA	uc001rfb.2	-							NM_021957	NP_068776			glycogen synthase 2						glucose metabolic process|glycogen biosynthetic process|response to glucose stimulus	cortical actin cytoskeleton|cytosol|ectoplasm|insoluble fraction|soluble fraction	glycogen (starch) synthase activity|protein homodimerization activity			lung(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	21865367	21865367	+	IGR	DEL	T	-	-	rs35432964		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21865367delT								LDHB (54591 upstream) : KCNJ8 (52523 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	22193961	22193961	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22193961delA								ABCC9 (99625 upstream) : CMAS (5198 downstream)																																			---	---	---	---
ST8SIA1	6489	broad.mit.edu	37	12	22356024	22356024	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22356024delA	uc001rfo.3	-						ST8SIA1_uc009zix.2_Intron	NM_003034	NP_003025			alpha-2,8-sialyltransferase 1						glycosphingolipid biosynthetic process|protein glycosylation	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			ovary(3)	3																		---	---	---	---
ETNK1	55500	broad.mit.edu	37	12	22790796	22790797	+	Intron	INS	-	GA	GA	rs142902265	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22790796_22790797insGA	uc001rft.2	+						ETNK1_uc009ziz.2_Intron|ETNK1_uc001rfs.2_Intron	NM_018638	NP_061108			ethanolamine kinase 1 isoform A						phosphatidylethanolamine biosynthetic process	cytoplasm	ATP binding|ethanolamine kinase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	23035939	23035939	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:23035939delT								ETNK1 (192332 upstream) : SOX5 (649293 downstream)																																			---	---	---	---
SOX5	6660	broad.mit.edu	37	12	23982052	23982052	+	Intron	DEL	A	-	-	rs34363532		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:23982052delA	uc001rfw.2	-						SOX5_uc001rfx.2_Intron|SOX5_uc001rfy.2_Intron|SOX5_uc010siv.1_Intron|SOX5_uc010siw.1_Intron|SOX5_uc001rfz.1_Intron|SOX5_uc001rga.2_Intron	NM_006940	NP_008871			SRY (sex determining region Y)-box 5 isoform a						transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(5)|lung(1)	6																		---	---	---	---
SOX5	6660	broad.mit.edu	37	12	24130257	24130257	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:24130257delA	uc001rfx.2	-						SOX5_uc001rfy.2_Intron	NM_152989	NP_694534			SRY (sex determining region Y)-box 5 isoform b						transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(5)|lung(1)	6																		---	---	---	---
SOX5	6660	broad.mit.edu	37	12	24401629	24401629	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:24401629delT	uc001rfx.2	-						SOX5_uc001rfy.2_Intron	NM_152989	NP_694534			SRY (sex determining region Y)-box 5 isoform b						transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(5)|lung(1)	6																		---	---	---	---
SOX5	6660	broad.mit.edu	37	12	24568357	24568357	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:24568357delT	uc001rfx.2	-						SOX5_uc001rfy.2_Intron	NM_152989	NP_694534			SRY (sex determining region Y)-box 5 isoform b						transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(5)|lung(1)	6																		---	---	---	---
SOX5	6660	broad.mit.edu	37	12	24585742	24585742	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:24585742delA	uc001rfx.2	-						SOX5_uc001rfy.2_Intron	NM_152989	NP_694534			SRY (sex determining region Y)-box 5 isoform b						transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(5)|lung(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	25598496	25598497	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25598496_25598497delTT								KRAS (194633 upstream) : IFLTD1 (30519 downstream)																																			---	---	---	---
IFLTD1	160492	broad.mit.edu	37	12	25689621	25689621	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25689621delA	uc001rgs.2	-						IFLTD1_uc001rgt.1_Intron|IFLTD1_uc010sji.1_Intron|IFLTD1_uc010sjj.1_Intron|IFLTD1_uc009zjc.2_Intron	NM_152590	NP_689803			intermediate filament tail domain containing 1							intermediate filament	structural molecule activity			ovary(2)|central_nervous_system(1)	3	all_lung(3;2.75e-22)|Lung NSC(3;1.77e-21)|all_hematologic(7;0.00656)|Colorectal(261;0.0847)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	25821340	25821340	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25821340delT								IFLTD1 (19852 upstream) : RASSF8 (290629 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	26021935	26021936	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26021935_26021936delAA								IFLTD1 (220447 upstream) : RASSF8 (90033 downstream)																																			---	---	---	---
RASSF8	11228	broad.mit.edu	37	12	26175129	26175129	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26175129delA	uc001rgx.2	+						RASSF8_uc001rgy.2_Intron|RASSF8_uc001rgz.2_Intron|RASSF8_uc009zjd.1_Intron|RASSF8_uc001rgw.1_Intron	NM_007211	NP_009142			Ras association (RalGDS/AF-6) domain family						signal transduction						0	Colorectal(261;0.0847)																	---	---	---	---
ITPR2	3709	broad.mit.edu	37	12	26576137	26576138	+	Intron	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26576137_26576138delGA	uc001rhg.2	-						ITPR2_uc009zjg.1_Intron	NM_002223	NP_002214			inositol 1,4,5-triphosphate receptor, type 2						activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)																	---	---	---	---
ITPR2	3709	broad.mit.edu	37	12	26596595	26596595	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26596595delA	uc001rhg.2	-						ITPR2_uc009zjg.1_Intron	NM_002223	NP_002214			inositol 1,4,5-triphosphate receptor, type 2						activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)																	---	---	---	---
ITPR2	3709	broad.mit.edu	37	12	26752812	26752812	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26752812delA	uc001rhg.2	-							NM_002223	NP_002214			inositol 1,4,5-triphosphate receptor, type 2						activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)																	---	---	---	---
ITPR2	3709	broad.mit.edu	37	12	26799210	26799210	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26799210delT	uc001rhg.2	-							NM_002223	NP_002214			inositol 1,4,5-triphosphate receptor, type 2						activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)																	---	---	---	---
ITPR2	3709	broad.mit.edu	37	12	26939950	26939950	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26939950delA	uc001rhg.2	-						ITPR2_uc001rhh.1_Intron|ITPR2_uc001rhi.1_Intron	NM_002223	NP_002214			inositol 1,4,5-triphosphate receptor, type 2						activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	26995888	26995888	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26995888delT								ITPR2 (9757 upstream) : C12orf11 (62227 downstream)																																			---	---	---	---
TM7SF3	51768	broad.mit.edu	37	12	27128989	27128989	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27128989delA	uc010sjl.1	-							NM_016551	NP_057635			transmembrane 7 superfamily member 3 precursor							integral to membrane|plasma membrane				upper_aerodigestive_tract(2)	2	Colorectal(261;0.0847)																	---	---	---	---
ARNTL2	56938	broad.mit.edu	37	12	27506609	27506609	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27506609delA	uc001rht.1	+						ARNTL2_uc001rhw.2_Intron|ARNTL2_uc010sjp.1_Intron|ARNTL2_uc001rhu.1_Intron|ARNTL2_uc009zji.1_Intron|ARNTL2_uc001rhv.1_Intron	NM_020183	NP_064568			aryl hydrocarbon receptor nuclear						circadian rhythm|entrainment of circadian clock|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(1)|skin(1)	2	Colorectal(261;0.0847)|Lung SC(9;0.184)																	---	---	---	---
ARNTL2	56938	broad.mit.edu	37	12	27533131	27533131	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27533131delG	uc001rht.1	+						ARNTL2_uc001rhw.2_Intron|ARNTL2_uc010sjp.1_Intron|ARNTL2_uc001rhu.1_Intron|ARNTL2_uc009zji.1_Intron|ARNTL2_uc001rhv.1_Intron	NM_020183	NP_064568			aryl hydrocarbon receptor nuclear						circadian rhythm|entrainment of circadian clock|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(1)|skin(1)	2	Colorectal(261;0.0847)|Lung SC(9;0.184)																	---	---	---	---
PPFIBP1	8496	broad.mit.edu	37	12	27716715	27716716	+	Intron	INS	-	T	T	rs146673448	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27716715_27716716insT	uc001ric.1	+						PPFIBP1_uc001rhy.1_Intron|PPFIBP1_uc001rhz.1_Intron|PPFIBP1_uc010sjr.1_Intron|PPFIBP1_uc001rib.1_Intron|PPFIBP1_uc001ria.2_Intron|PPFIBP1_uc001rid.1_Intron	NM_003622	NP_003613			PTPRF interacting protein binding protein 1						cell adhesion	plasma membrane	protein binding		PPFIBP1/ALK(3)	soft_tissue(3)|kidney(1)|skin(1)	5	Lung SC(9;0.0873)																	---	---	---	---
PPFIBP1	8496	broad.mit.edu	37	12	27724408	27724408	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27724408delT	uc001ric.1	+						PPFIBP1_uc001rhy.1_Intron|PPFIBP1_uc001rhz.1_Intron|PPFIBP1_uc010sjr.1_Intron|PPFIBP1_uc001rib.1_Intron|PPFIBP1_uc001ria.2_Intron|PPFIBP1_uc001rid.1_Intron	NM_003622	NP_003613			PTPRF interacting protein binding protein 1						cell adhesion	plasma membrane	protein binding		PPFIBP1/ALK(3)	soft_tissue(3)|kidney(1)|skin(1)	5	Lung SC(9;0.0873)																	---	---	---	---
MRPS35	60488	broad.mit.edu	37	12	27883878	27883878	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27883878delA	uc001rih.2	+						MRPS35_uc001rii.2_Intron	NM_021821	NP_068593			mitochondrial ribosomal protein S35 precursor						DNA damage response, detection of DNA damage	mitochondrial small ribosomal subunit					0	Lung SC(9;0.0873)																	---	---	---	---
KLHDC5	57542	broad.mit.edu	37	12	27952483	27952483	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27952483delA	uc001rij.2	+	3					KLHDC5_uc009zjj.2_RNA	NM_020782	NP_065833			kelch domain containing 5											ovary(1)|central_nervous_system(1)	2	Lung SC(9;0.0873)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	28178252	28178252	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28178252delT								PTHLH (53336 upstream) : CCDC91 (153958 downstream)																																			---	---	---	---
CCDC91	55297	broad.mit.edu	37	12	28334640	28334640	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28334640delA	uc001rio.2	+											RecName: Full=Coiled-coil domain-containing protein 91; AltName: Full=GGA-binding partner; AltName: Full=p56 accessory protein;						protein transport	Golgi apparatus|membrane				central_nervous_system(1)	1	Acute lymphoblastic leukemia(23;0.00718)|all_hematologic(23;0.0113)|Lung SC(9;0.184)																	---	---	---	---
CCDC91	55297	broad.mit.edu	37	12	28523756	28523757	+	Intron	DEL	GA	-	-	rs143361204		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28523756_28523757delGA	uc001riq.2	+						CCDC91_uc001rio.2_Intron|CCDC91_uc009zjk.2_Intron|CCDC91_uc001rip.1_Intron|CCDC91_uc001rir.2_Intron|CCDC91_uc009zjl.2_Intron	NM_018318	NP_060788			GGA binding partner						protein transport	Golgi apparatus|membrane				central_nervous_system(1)	1	Acute lymphoblastic leukemia(23;0.00718)|all_hematologic(23;0.0113)|Lung SC(9;0.184)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	28720580	28720581	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28720580_28720581delAA								CCDC91 (17482 upstream) : FAR2 (581651 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	28986272	28986272	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:28986272delC								CCDC91 (283174 upstream) : FAR2 (315960 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	29078694	29078694	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29078694delT								CCDC91 (375596 upstream) : FAR2 (223538 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	29491579	29491579	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29491579delA								FAR2 (4574 upstream) : ERGIC2 (2001 downstream)																																			---	---	---	---
TMTC1	83857	broad.mit.edu	37	12	29759800	29759800	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29759800delT	uc001rjb.2	-						TMTC1_uc001riz.2_Intron|TMTC1_uc001rja.2_Intron|TMTC1_uc001rjc.1_Intron	NM_175861	NP_787057			transmembrane and tetratricopeptide repeat							integral to membrane	binding				0	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	30627283	30627284	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30627283_30627284delAA								TMTC1 (689591 upstream) : IPO8 (154639 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	31006190	31006191	+	IGR	INS	-	T	T	rs147106787	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31006190_31006191insT								CAPRIN2 (98742 upstream) : TSPAN11 (73171 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	31195625	31195625	+	Intron	DEL	G	-	-	rs10711716		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31195625delG	uc001rjq.1	-											Homo sapiens cDNA FLJ39041 fis, clone NT2RP7010109.																														---	---	---	---
DENND5B	160518	broad.mit.edu	37	12	31630952	31630952	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31630952delT	uc001rki.1	-						DENND5B_uc001rkh.1_Intron|DENND5B_uc009zjq.1_Intron|DENND5B_uc001rkj.2_Intron|DENND5B_uc001rkk.1_Intron	NM_144973	NP_659410			DENN/MADD domain containing 5B							integral to membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
DENND5B	160518	broad.mit.edu	37	12	31633203	31633203	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31633203delA	uc001rki.1	-						DENND5B_uc001rkh.1_Intron|DENND5B_uc009zjq.1_5'Flank|DENND5B_uc001rkj.2_Intron|DENND5B_uc001rkk.1_Intron	NM_144973	NP_659410			DENN/MADD domain containing 5B							integral to membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	31928641	31928641	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31928641delC								AMN1 (46533 upstream) : H3F3C (15480 downstream)																																			---	---	---	---
C12orf35	55196	broad.mit.edu	37	12	32140362	32140363	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32140362_32140363delTT	uc001rks.2	+						C12orf35_uc001rkt.2_Intron	NM_018169	NP_060639			hypothetical protein LOC55196											ovary(1)|skin(1)	2	all_cancers(9;3.36e-11)|all_epithelial(9;2.56e-11)|all_lung(12;5.67e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0336)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0114)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	32545450	32545450	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32545450delT								BICD1 (14310 upstream) : FGD4 (93456 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	32594978	32594979	+	IGR	DEL	TT	-	-	rs138553349		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32594978_32594979delTT								BICD1 (63838 upstream) : FGD4 (43927 downstream)																																			---	---	---	---
FGD4	121512	broad.mit.edu	37	12	32755049	32755049	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32755049delA	uc001rkz.2	+						FGD4_uc001rlc.2_Intron|FGD4_uc001rky.2_Intron|FGD4_uc001rla.2_Intron|FGD4_uc010ske.1_Intron|FGD4_uc001rlb.1_Intron	NM_139241	NP_640334			FYVE, RhoGEF and PH domain containing 4						actin cytoskeleton organization|apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Cdc42 GTPase activity|regulation of cell shape|small GTPase mediated signal transduction	cytoskeleton|cytosol|filopodium|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(2)|central_nervous_system(1)	3	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	33272760	33272761	+	IGR	INS	-	A	A	rs76976671		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:33272760_33272761insA								PKP2 (222980 upstream) : SYT10 (255587 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	33667241	33667241	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:33667241delT								SYT10 (74487 upstream) : ALG10 (507975 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	34466517	34466518	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34466517_34466518delTT								ALG10 (285283 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	34758828	34758828	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34758828delA								ALG10 (577594 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	34816737	34816738	+	IGR	INS	-	T	T	rs144354914	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34816737_34816738insT								ALG10 (635503 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	38583788	38583788	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:38583788delA								None (None upstream) : ALG10B (126769 downstream)																																			---	---	---	---
SLC2A13	114134	broad.mit.edu	37	12	40247410	40247410	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40247410delT	uc010skm.1	-						C12orf40_uc009zjv.1_Intron|SLC2A13_uc001rme.1_Intron	NM_052885	NP_443117			solute carrier family 2 (facilitated glucose							integral to membrane|plasma membrane	myo-inositol:hydrogen symporter activity			ovary(1)	1		Lung NSC(34;0.105)|all_lung(34;0.123)													HNSCC(50;0.14)			---	---	---	---
SLC2A13	114134	broad.mit.edu	37	12	40421120	40421120	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40421120delA	uc010skm.1	-						SLC2A13_uc001rmf.2_Intron	NM_052885	NP_443117			solute carrier family 2 (facilitated glucose							integral to membrane|plasma membrane	myo-inositol:hydrogen symporter activity			ovary(1)	1		Lung NSC(34;0.105)|all_lung(34;0.123)													HNSCC(50;0.14)			---	---	---	---
LRRK2	120892	broad.mit.edu	37	12	40699570	40699570	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40699570delT	uc001rmg.3	+						LRRK2_uc009zjw.2_Intron|LRRK2_uc001rmi.2_Intron	NM_198578	NP_940980			leucine-rich repeat kinase 2						activation of MAPKK activity|determination of adult lifespan|exploration behavior|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of dopamine receptor signaling pathway|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb	external side of mitochondrial outer membrane	ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding			ovary(12)|stomach(5)|upper_aerodigestive_tract(2)|lung(2)|large_intestine(1)|urinary_tract(1)|pancreas(1)	24	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)																---	---	---	---
LRRK2	120892	broad.mit.edu	37	12	40725251	40725251	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40725251delT	uc001rmg.3	+						LRRK2_uc009zjw.2_Intron|LRRK2_uc001rmi.2_Intron	NM_198578	NP_940980			leucine-rich repeat kinase 2						activation of MAPKK activity|determination of adult lifespan|exploration behavior|intracellular distribution of mitochondria|negative regulation of branching morphogenesis of a nerve|negative regulation of dendritic spine morphogenesis|negative regulation of neuroblast proliferation|negative regulation of neuron maturation|neuromuscular junction development|neuron death|peptidyl-serine phosphorylation|positive regulation of autophagy|positive regulation of dopamine receptor signaling pathway|positive regulation of programmed cell death|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of protein ubiquitination|protein autophosphorylation|regulation of kidney size|regulation of locomotion|regulation of membrane potential|response to oxidative stress|small GTPase mediated signal transduction|tangential migration from the subventricular zone to the olfactory bulb	external side of mitochondrial outer membrane	ATP binding|GTP binding|GTP-dependent protein kinase activity|GTPase activator activity|MAP kinase kinase activity|protein homodimerization activity|tubulin binding			ovary(12)|stomach(5)|upper_aerodigestive_tract(2)|lung(2)|large_intestine(1)|urinary_tract(1)|pancreas(1)	24	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)																---	---	---	---
Unknown	0	broad.mit.edu	37	12	41015621	41015621	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41015621delT								LRRK2 (252537 upstream) : CNTN1 (70737 downstream)																																			---	---	---	---
CNTN1	1272	broad.mit.edu	37	12	41154561	41154561	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41154561delT	uc001rmm.1	+						CNTN1_uc009zjy.1_Intron|CNTN1_uc001rmn.1_Intron	NM_001843	NP_001834			contactin 1 isoform 1 precursor						axon guidance|cell adhesion|Notch signaling pathway	anchored to membrane|membrane fraction|plasma membrane				lung(4)|ovary(3)|large_intestine(1)|skin(1)	9	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)																---	---	---	---
PDZRN4	29951	broad.mit.edu	37	12	41911591	41911591	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41911591delT	uc010skn.1	+						PDZRN4_uc001rmq.3_Intron|PDZRN4_uc009zjz.2_Intron|PDZRN4_uc001rmr.2_Intron	NM_013377	NP_037509			PDZ domain containing RING finger 4 isoform 2								ubiquitin-protein ligase activity|zinc ion binding			lung(3)|skin(3)|ovary(2)|large_intestine(1)|kidney(1)|pancreas(1)	11	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)																---	---	---	---
Unknown	0	broad.mit.edu	37	12	42047608	42047608	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42047608delA								PDZRN4 (79224 upstream) : GXYLT1 (428042 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	42080169	42080170	+	IGR	DEL	AA	-	-	rs72072766		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42080169_42080170delAA								PDZRN4 (111785 upstream) : GXYLT1 (395480 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	42150980	42150980	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42150980delT								PDZRN4 (182596 upstream) : GXYLT1 (324670 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	42181503	42181503	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42181503delC								PDZRN4 (213119 upstream) : GXYLT1 (294147 downstream)																																			---	---	---	---
GXYLT1	283464	broad.mit.edu	37	12	42491076	42491076	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42491076delA	uc001rms.3	-						GXYLT1_uc001rmt.3_Intron	NM_173601	NP_775872			glycosyltransferase 8 domain containing 3						O-glycan processing	integral to membrane	UDP-xylosyltransferase activity				0																		---	---	---	---
YAF2	10138	broad.mit.edu	37	12	42566307	42566307	+	Intron	DEL	T	-	-	rs75075777		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42566307delT	uc001rmv.2	-						YAF2_uc001rmw.2_Intron|YAF2_uc010sko.1_Intron|YAF2_uc010skp.1_Intron	NM_005748	NP_005739			YY1 associated factor 2						negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	protein binding|transcription coactivator activity|transcription corepressor activity|zinc ion binding				0	all_cancers(12;0.000425)	Lung NSC(34;0.0402)|all_lung(34;0.057)		GBM - Glioblastoma multiforme(48;0.0514)														---	---	---	---
YAF2	10138	broad.mit.edu	37	12	42586144	42586145	+	Intron	DEL	CA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42586144_42586145delCA	uc001rmv.2	-						YAF2_uc001rmw.2_Intron|YAF2_uc010sko.1_Intron|YAF2_uc010skp.1_Intron	NM_005748	NP_005739			YY1 associated factor 2						negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	protein binding|transcription coactivator activity|transcription corepressor activity|zinc ion binding				0	all_cancers(12;0.000425)	Lung NSC(34;0.0402)|all_lung(34;0.057)		GBM - Glioblastoma multiforme(48;0.0514)														---	---	---	---
PPHLN1	51535	broad.mit.edu	37	12	42703035	42703035	+	Intron	DEL	A	-	-	rs35480990		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42703035delA	uc001rmy.2	+							NM_201439	NP_958847			periphilin 1 isoform 3						keratinization	cytoplasm|nucleus				ovary(1)|breast(1)	2	all_cancers(12;0.00049)|Breast(8;0.165)	Lung NSC(34;0.123)		GBM - Glioblastoma multiforme(48;0.0875)														---	---	---	---
PRICKLE1	144165	broad.mit.edu	37	12	42935807	42935807	+	Intron	DEL	C	-	-	rs11295718		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42935807delC	uc001rnm.2	-						PRICKLE1_uc009zka.2_Intron	NM_153026	NP_694571			prickle homolog 1						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cardiac muscle cell myoblast differentiation|negative regulation of transcription, DNA-dependent|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein import into nucleus	cytosol|nuclear membrane	zinc ion binding			ovary(3)|skin(1)	4	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	43108077	43108078	+	IGR	DEL	AT	-	-	rs141494515		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43108077_43108078delAT								PRICKLE1 (124505 upstream) : ADAMTS20 (639935 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	43279483	43279483	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43279483delT								PRICKLE1 (295911 upstream) : ADAMTS20 (468530 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	43430386	43430386	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43430386delT								PRICKLE1 (446814 upstream) : ADAMTS20 (317627 downstream)																																			---	---	---	---
ADAMTS20	80070	broad.mit.edu	37	12	43756633	43756634	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43756633_43756634insA	uc010skx.1	-							NM_025003	NP_079279			a disintegrin-like and metalloprotease with							proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)														---	---	---	---
TMEM117	84216	broad.mit.edu	37	12	44338306	44338306	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44338306delT	uc001rod.2	+						TMEM117_uc001roe.2_Intron|TMEM117_uc009zkc.2_Intron	NM_032256	NP_115632			transmembrane protein 117							endoplasmic reticulum|integral to membrane					0	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.124)														---	---	---	---
TMEM117	84216	broad.mit.edu	37	12	44364703	44364703	+	Intron	DEL	T	-	-	rs111467716		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44364703delT	uc001rod.2	+						TMEM117_uc001roe.2_Intron|TMEM117_uc009zkc.2_Intron	NM_032256	NP_115632			transmembrane protein 117							endoplasmic reticulum|integral to membrane					0	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.124)														---	---	---	---
TMEM117	84216	broad.mit.edu	37	12	44674348	44674348	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44674348delT	uc001rod.2	+						TMEM117_uc001roe.2_Intron|TMEM117_uc009zkc.2_Intron	NM_032256	NP_115632			transmembrane protein 117							endoplasmic reticulum|integral to membrane					0	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.124)														---	---	---	---
ANO6	196527	broad.mit.edu	37	12	45743874	45743874	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45743874delA	uc001roo.2	+						ANO6_uc010sld.1_Intron|ANO6_uc010sle.1_Intron|ANO6_uc010slf.1_Intron|ANO6_uc010slg.1_Intron	NM_001025356	NP_001020527			anoctamin 6 isoform a						activation of blood coagulation via clotting cascade|phosphatidylserine exposure on blood platelet	chloride channel complex|plasma membrane	chloride channel activity			ovary(1)|kidney(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	45867817	45867817	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45867817delG								ANO6 (33630 upstream) : LOC400027 (251993 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	46087339	46087339	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46087339delG								ANO6 (253152 upstream) : LOC400027 (32471 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	46398968	46398968	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46398968delT								SFRS2IP (13065 upstream) : SLC38A1 (177875 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	46462452	46462452	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46462452delA								SFRS2IP (76549 upstream) : SLC38A1 (114391 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	46916293	46916294	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46916293_46916294delAA								SLC38A2 (149648 upstream) : SLC38A4 (242250 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	46952350	46952351	+	IGR	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:46952350_46952351delGA								SLC38A2 (185705 upstream) : SLC38A4 (206193 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	47142874	47142874	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47142874delA								SLC38A2 (376229 upstream) : SLC38A4 (15670 downstream)																																			---	---	---	---
FAM113B	91523	broad.mit.edu	37	12	47621636	47621636	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47621636delA	uc001rpn.2	+						FAM113B_uc010slj.1_Intron|FAM113B_uc001rpq.2_Intron	NM_138371	NP_612380			hypothetical protein LOC91523								hydrolase activity			skin(3)|ovary(2)	5	Renal(347;0.138)|Lung SC(27;0.192)																	---	---	---	---
VDR	7421	broad.mit.edu	37	12	48287248	48287248	+	Intron	DEL	A	-	-	rs36108348		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48287248delA	uc001rqm.2	-						VDR_uc001rql.2_Intron|VDR_uc001rqn.2_Intron|VDR_uc010slq.1_Intron	NM_001017535	NP_001017535			vitamin D (1,25-dihydroxyvitamin D3) receptor						decidualization|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of vitamin D 24-hydroxylase activity|regulation of calcidiol 1-monooxygenase activity|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	retinoid X receptor binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|vitamin D3 receptor activity|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Acute lymphoblastic leukemia(13;0.109)|all_hematologic(14;0.214)		GBM - Glioblastoma multiforme(48;0.17)	Calcidiol(DB00146)|Calcipotriol(DB02300)|Calcitriol(DB00136)|Dihydrotachysterol(DB01070)|Ergocalciferol(DB00153)|Paricalcitol(DB00910)													---	---	---	---
PFKM	5213	broad.mit.edu	37	12	48539184	48539184	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48539184delT	uc001rrc.2	+						PFKM_uc001rra.1_Intron|PFKM_uc001rrb.1_Intron|PFKM_uc001rrd.2_Intron|PFKM_uc001rre.1_Intron|PFKM_uc001rrg.1_Intron	NM_000289	NP_000280			phosphofructokinase, muscle						fructose 6-phosphate metabolic process|glycolysis|muscle cell homeostasis	6-phosphofructokinase complex|apical plasma membrane	6-phosphofructokinase activity|ATP binding|identical protein binding|kinase binding|metal ion binding|protein C-terminus binding			ovary(2)|upper_aerodigestive_tract(1)|kidney(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	48640096	48640096	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48640096delA								OR10AD1 (43021 upstream) : H1FNT (82667 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	48967280	48967280	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48967280delA								LALBA (3451 upstream) : C12orf41 (79715 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	49041997	49041997	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49041997delA								LALBA (78168 upstream) : C12orf41 (4998 downstream)																																			---	---	---	---
DDX23	9416	broad.mit.edu	37	12	49245256	49245256	+	Intron	DEL	A	-	-	rs74917035		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49245256delA	uc001rsm.2	-							NM_004818	NP_004809			DEAD (Asp-Glu-Ala-Asp) box polypeptide 23							catalytic step 2 spliceosome|nucleoplasm|U5 snRNP	ATP binding|ATP-dependent RNA helicase activity|nucleic acid binding|protein binding			kidney(3)|ovary(1)|lung(1)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	49286116	49286116	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49286116delT								RND1 (26463 upstream) : CCDC65 (11777 downstream)																																			---	---	---	---
TROAP	10024	broad.mit.edu	37	12	49722647	49722648	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49722647_49722648delAA	uc001rtx.3	+						TROAP_uc009zlh.2_Intron|TROAP_uc001rty.2_Intron	NM_005480	NP_005471			tastin isoform 1						cell adhesion	cytoplasm				ovary(1)	1																		---	---	---	---
SPATS2	65244	broad.mit.edu	37	12	49766503	49766503	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49766503delA	uc001rud.2	+						SPATS2_uc001ruc.2_Intron|SPATS2_uc001rue.2_Intron|SPATS2_uc009zli.1_Intron|SPATS2_uc001ruf.2_Intron	NM_023071	NP_075559			spermatogenesis associated, serine-rich 2							cytoplasm				breast(1)	1																		---	---	---	---
FMNL3	91010	broad.mit.edu	37	12	50056426	50056426	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50056426delA	uc001ruv.1	-						FMNL3_uc001ruw.1_Intron|FMNL3_uc001ruu.1_5'Flank	NM_175736	NP_783863			formin-like 3 isoform 1						actin cytoskeleton organization		actin binding|Rho GTPase binding			breast(2)|pancreas(2)	4																		---	---	---	---
TMBIM6	7009	broad.mit.edu	37	12	50140573	50140573	+	Intron	DEL	G	-	-	rs73306897	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50140573delG	uc001rux.2	+						TMBIM6_uc010sml.1_Intron|TMBIM6_uc001ruy.2_Intron|TMBIM6_uc001ruz.2_Intron	NM_003217	NP_003208			testis enhanced gene transcript (BAX inhibitor						apoptosis|negative regulation of apoptosis	endoplasmic reticulum|insoluble fraction|integral to plasma membrane|nucleus					0																		---	---	---	---
ACCN2	41	broad.mit.edu	37	12	50456393	50456393	+	Intron	DEL	A	-	-	rs11345352		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50456393delA	uc001rvw.2	+						ACCN2_uc001rvv.2_Intron|ACCN2_uc009zln.2_Intron|ACCN2_uc009zlo.2_Intron	NM_001095	NP_001086			amiloride-sensitive cation channel 2, neuronal						calcium ion transport|response to pH|signal transduction	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(1)	1					Amiloride(DB00594)													---	---	---	---
SMARCD1	6602	broad.mit.edu	37	12	50479778	50479778	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50479778delT	uc001rvx.3	+						SMARCD1_uc010smo.1_Intron|SMARCD1_uc001rvy.3_Intron|SMARCD1_uc009zlp.2_Intron	NM_003076	NP_003067			SWI/SNF-related matrix-associated						chromatin-mediated maintenance of transcription|nervous system development|regulation of transcription from RNA polymerase II promoter	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex	protein complex scaffold|transcription coactivator activity			ovary(1)	1																		---	---	---	---
LIMA1	51474	broad.mit.edu	37	12	50594689	50594689	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50594689delA	uc001rwj.3	-						LIMA1_uc001rwg.3_5'UTR|LIMA1_uc001rwh.3_Intron|LIMA1_uc001rwi.3_Intron|LIMA1_uc001rwk.3_Intron|LIMA1_uc010smr.1_Intron|LIMA1_uc010sms.1_Intron	NM_016357	NP_057441			LIM domain and actin binding 1 isoform b						actin filament bundle assembly|negative regulation of actin filament depolymerization|ruffle organization	cytoplasm|focal adhesion|stress fiber	actin filament binding|actin monomer binding|zinc ion binding			ovary(1)	1																		---	---	---	---
FAM186A	121006	broad.mit.edu	37	12	50725034	50725034	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50725034delT	uc001rwl.2	-						FAM186A_uc010smt.1_Intron	NM_001145475	NP_001138947			family with sequence similarity 186, member A												0																		---	---	---	---
FAM186A	121006	broad.mit.edu	37	12	50732805	50732805	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50732805delT	uc001rwl.2	-						FAM186A_uc010smt.1_Intron	NM_001145475	NP_001138947			family with sequence similarity 186, member A												0																		---	---	---	---
FAM186A	121006	broad.mit.edu	37	12	50752893	50752893	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50752893delA	uc001rwl.2	-						FAM186A_uc010smt.1_5'Flank	NM_001145475	NP_001138947			family with sequence similarity 186, member A												0																		---	---	---	---
LARP4	113251	broad.mit.edu	37	12	50867693	50867693	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50867693delA	uc001rwp.1	+						LARP4_uc001rwo.1_Intron|LARP4_uc001rwq.1_Intron|LARP4_uc001rwr.1_Intron|LARP4_uc001rws.1_Intron|LARP4_uc009zlr.1_Intron|LARP4_uc001rwt.1_Intron	NM_052879	NP_443111			c-Mpl binding protein isoform a								nucleotide binding|RNA binding			ovary(1)	1																		---	---	---	---
DIP2B	57609	broad.mit.edu	37	12	50901698	50901698	+	Intron	DEL	T	-	-	rs5798141		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50901698delT	uc001rwv.2	+						DIP2B_uc001rwu.2_Intron	NM_173602	NP_775873			DIP2 disco-interacting protein 2 homolog B							nucleus	catalytic activity|transcription factor binding			ovary(4)|breast(1)|pancreas(1)	6																		---	---	---	---
DIP2B	57609	broad.mit.edu	37	12	50911612	50911613	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50911612_50911613insT	uc001rwv.2	+						DIP2B_uc001rwu.2_Intron	NM_173602	NP_775873			DIP2 disco-interacting protein 2 homolog B							nucleus	catalytic activity|transcription factor binding			ovary(4)|breast(1)|pancreas(1)	6																		---	---	---	---
HIGD1C	613227	broad.mit.edu	37	12	51350774	51350774	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51350774delT	uc010smw.1	+							NM_001109619	NP_001103089			HIG1 domain family, member 1C							integral to membrane					0																		---	---	---	---
TFCP2	7024	broad.mit.edu	37	12	51503117	51503117	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51503117delT	uc001rxw.2	-						TFCP2_uc001rxv.1_Intron|TFCP2_uc009zlx.1_Intron|TFCP2_uc001rxx.2_Intron|TFCP2_uc009zly.1_Intron	NM_005653	NP_005644			transcription factor CP2						regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1																		---	---	---	---
DAZAP2	9802	broad.mit.edu	37	12	51629961	51629961	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51629961delT	uc010snd.1	+						DAZAP2_uc001ryb.2_5'Flank|DAZAP2_uc010snc.1_5'Flank|DAZAP2_uc010sne.1_5'Flank|DAZAP2_uc010snf.1_5'Flank	NM_001136266	NP_001129738			DAZ associated protein 2 isoform c								WW domain binding				0																		---	---	---	---
SMAGP	57228	broad.mit.edu	37	12	51644296	51644296	+	Intron	DEL	T	-	-	rs11169783		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51644296delT	uc001ryc.1	-						SMAGP_uc001ryd.1_Intron|SMAGP_uc001rye.1_Intron|SMAGP_uc001ryf.1_Intron	NM_001033873	NP_001029045			small trans-membrane and glycosylated protein							cytoplasmic vesicle membrane|integral to membrane|plasma membrane					0																		---	---	---	---
SLC4A8	9498	broad.mit.edu	37	12	51804245	51804248	+	Intron	DEL	TTTT	-	-	rs12582245		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51804245_51804248delTTTT	uc010snj.1	+						SLC4A8_uc010sni.1_Intron|SLC4A8_uc001rym.2_Intron|SLC4A8_uc001ryn.2_Intron|SLC4A8_uc001ryo.2_Intron|SLC4A8_uc001ryp.1_Intron	NM_004858	NP_004849			solute carrier family 4, sodium bicarbonate						bicarbonate transport|sodium ion transport	integral to membrane|plasma membrane	inorganic anion exchanger activity			ovary(3)|pancreas(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.15)														---	---	---	---
SLC4A8	9498	broad.mit.edu	37	12	51845570	51845572	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51845570_51845572delAAA	uc001rys.1	+						SLC4A8_uc010sni.1_Intron|SLC4A8_uc001rym.2_Intron|SLC4A8_uc001ryn.2_Intron|SLC4A8_uc001ryo.2_Intron|SLC4A8_uc001ryp.1_Intron|SLC4A8_uc010snj.1_Intron|SLC4A8_uc001ryq.3_Intron|SLC4A8_uc001ryr.2_Intron|SLC4A8_uc010snk.1_Intron	NM_001039960	NP_001035049			solute carrier family 4, sodium bicarbonate						bicarbonate transport|sodium ion transport	integral to membrane|plasma membrane	inorganic anion exchanger activity			ovary(3)|pancreas(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.15)														---	---	---	---
SLC4A8	9498	broad.mit.edu	37	12	51888945	51888945	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51888945delT	uc001rys.1	+						SLC4A8_uc001rym.2_Intron|SLC4A8_uc001ryn.2_Intron|SLC4A8_uc001ryo.2_Intron|SLC4A8_uc010snj.1_Intron|SLC4A8_uc001ryr.2_Intron	NM_001039960	NP_001035049			solute carrier family 4, sodium bicarbonate						bicarbonate transport|sodium ion transport	integral to membrane|plasma membrane	inorganic anion exchanger activity			ovary(3)|pancreas(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.15)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	52484231	52484231	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52484231delG	uc009zme.1	+											Homo sapiens olfactory receptor, family 7, subfamily E, member 47 pseudogene, mRNA (cDNA clone IMAGE:5590288).																														---	---	---	---
KRT72	140807	broad.mit.edu	37	12	52982321	52982321	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52982321delA	uc001sar.2	-						KRT72_uc001saq.2_Intron|KRT72_uc010sns.1_Intron|KRT72_uc010snt.1_Intron	NM_001146225	NP_001139697			keratin 72 isoform 1							keratin filament	structural molecule activity			ovary(5)|pancreas(1)	6				BRCA - Breast invasive adenocarcinoma(357;0.195)														---	---	---	---
KRT8	3856	broad.mit.edu	37	12	53300033	53300033	+	5'Flank	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53300033delG	uc001sbd.2	-						KRT8_uc009zmj.2_5'Flank|KRT8_uc009zmk.1_Intron|KRT8_uc009zml.1_Intron|KRT8_uc009zmm.1_Intron	NM_002273	NP_002264			keratin 8						cytoskeleton organization|interspecies interaction between organisms	cytoplasm|keratin filament|nuclear matrix|nucleoplasm	protein binding|structural molecule activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(357;0.108)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
KRT8	3856	broad.mit.edu	37	12	53328020	53328021	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53328020_53328021insA	uc009zml.1	-						KRT8_uc009zmm.1_Intron	NM_002273	NP_002264			keratin 8						cytoskeleton organization|interspecies interaction between organisms	cytoplasm|keratin filament|nuclear matrix|nucleoplasm	protein binding|structural molecule activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(357;0.108)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
ESPL1	9700	broad.mit.edu	37	12	53672382	53672382	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53672382delT	uc001sck.2	+						ESPL1_uc001scj.2_Intron|ESPL1_uc010soe.1_5'Flank	NM_012291	NP_036423			separase						apoptosis|cytokinesis|establishment of mitotic spindle localization|mitotic sister chromatid segregation|negative regulation of sister chromatid cohesion|positive regulation of mitotic metaphase/anaphase transition|proteolysis	centrosome|nucleus	cysteine-type peptidase activity|protein binding			lung(1)|kidney(1)|skin(1)	3																		---	---	---	---
AAAS	8086	broad.mit.edu	37	12	53711526	53711526	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53711526delA	uc001scr.3	-						AAAS_uc001scs.3_Intron	NM_015665	NP_056480			achalasia, adrenocortical insufficiency,						carbohydrate metabolic process|glucose transport|nucleocytoplasmic transport|regulation of glucose transport|regulation of nucleocytoplasmic transport|transmembrane transport|viral reproduction	nuclear pore				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	53747834	53747834	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53747834delA								SP7 (17668 upstream) : SP1 (26145 downstream)																																			---	---	---	---
HOTAIR	100124700	broad.mit.edu	37	12	54357757	54357757	+	RNA	DEL	G	-	-	rs111434707		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54357757delG	uc009zne.2	-	6		c.672delC				NR_003716				Homo sapiens cDNA FLJ41747 fis, clone HSYRA2006873.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	54593803	54593803	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54593803delA								SMUG1 (11046 upstream) : CBX5 (30929 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	54608507	54608507	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54608507delG								SMUG1 (25750 upstream) : CBX5 (16225 downstream)																																	OREG0021888	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
COPZ1	22818	broad.mit.edu	37	12	54728203	54728203	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54728203delA	uc001sfs.1	+						COPZ1_uc001sft.2_Intron|COPZ1_uc009znm.1_Intron|COPZ1_uc010sot.1_Intron|uc010sou.1_5'Flank|MIR148B_hsa-mir-148b|MI0000811_5'Flank	NM_016057	NP_057141			coatomer protein complex, subunit zeta 1						COPI coating of Golgi vesicle|intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol					0																		---	---	---	---
COPZ1	22818	broad.mit.edu	37	12	54739315	54739315	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54739315delT	uc001sfs.1	+						COPZ1_uc001sft.2_Intron|COPZ1_uc009znm.1_Intron|COPZ1_uc010sot.1_Intron	NM_016057	NP_057141			coatomer protein complex, subunit zeta 1						COPI coating of Golgi vesicle|intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol					0																		---	---	---	---
ZNF385A	25946	broad.mit.edu	37	12	54779572	54779573	+	5'Flank	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54779572_54779573insC	uc001sfw.1	-						ZNF385A_uc009zno.1_5'Flank|ZNF385A_uc010sov.1_5'Flank|ZNF385A_uc001sfx.1_5'Flank|ZNF385A_uc001sfy.3_Intron|ZNF385A_uc001sfz.3_Intron	NM_015481	NP_056296			zinc finger protein 385A isoform c						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding|zinc ion binding			ovary(1)	1																		---	---	---	---
PPP1R1A	5502	broad.mit.edu	37	12	54979746	54979747	+	Intron	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54979746_54979747delGA	uc001sgg.2	-							NM_006741	NP_006732			protein phosphatase 1, regulatory (inhibitor)						glycogen metabolic process|signal transduction		protein binding|protein serine/threonine phosphatase inhibitor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	55331416	55331416	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55331416delA								MUCL1 (79244 upstream) : KIAA0748 (12449 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	55967729	55967729	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55967729delA								OR6C4 (21791 upstream) : OR10P1 (62947 downstream)																																			---	---	---	---
ITGA7	3679	broad.mit.edu	37	12	56082835	56082837	+	Intron	DEL	CCT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56082835_56082837delCCT	uc001shh.2	-						ITGA7_uc001shg.2_Intron|ITGA7_uc010sps.1_Intron|ITGA7_uc001shf.2_5'Flank|ITGA7_uc009znw.2_Intron|ITGA7_uc009znx.2_Intron	NM_001144996	NP_001138468			integrin alpha 7 isoform 1 precursor						cell-matrix adhesion|integrin-mediated signaling pathway|muscle organ development|regulation of cell shape	integrin complex	receptor activity			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
DNAJC14	85406	broad.mit.edu	37	12	56197268	56197268	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56197268delA	uc001shu.1	-						SARNP_uc009zoa.2_Intron|SARNP_uc001shs.3_Intron|SARNP_uc001sht.2_Intron|SARNP_uc001shv.3_Intron	NM_032364	NP_115740			dopamine receptor interacting protein						protein folding|protein transport	endoplasmic reticulum membrane|integral to membrane	heat shock protein binding|unfolded protein binding			ovary(3)|large_intestine(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	56294484	56294484	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56294484delA								MMP19 (57749 upstream) : WIBG (713 downstream)																																			---	---	---	---
WIBG	84305	broad.mit.edu	37	12	56296283	56296284	+	Intron	DEL	AT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56296283_56296284delAT	uc001sif.1	-						WIBG_uc001sie.1_Intron	NM_032345	NP_115721			within bgcn homolog isoform 1						nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of translation	cytoplasm|exon-exon junction complex|nucleolus|nucleoplasm	protein binding|ribosome binding|RNA binding				0																		---	---	---	---
RAB5B	5869	broad.mit.edu	37	12	56367703	56367703	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56367703delA	uc001siv.2	+						RAB5B_uc001siw.2_5'Flank|RAB5B_uc009zog.2_5'Flank|RAB5B_uc010spz.1_5'Flank	NM_002868	NP_002859			RAB5B, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	early endosome membrane|melanosome|membrane fraction|plasma membrane	GTP binding|GTP-dependent protein binding|GTPase activity				0			UCEC - Uterine corpus endometrioid carcinoma (6;0.0471)|OV - Ovarian serous cystadenocarcinoma(18;0.235)															---	---	---	---
ERBB3	2065	broad.mit.edu	37	12	56487854	56487854	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56487854delC	uc001sjh.2	+						ERBB3_uc009zoj.2_Intron|ERBB3_uc010sqb.1_Intron|ERBB3_uc010sqc.1_Intron|ERBB3_uc009zok.2_Intron|ERBB3_uc001sjk.2_5'Flank	NM_001982	NP_001973			erbB-3 isoform 1 precursor						cranial nerve development|heart development|negative regulation of cell adhesion|negative regulation of neuron apoptosis|negative regulation of secretion|negative regulation of signal transduction|neuron apoptosis|phosphatidylinositol 3-kinase cascade|positive regulation of phosphatidylinositol 3-kinase cascade|regulation of cell proliferation|Schwann cell differentiation|transmembrane receptor protein tyrosine kinase signaling pathway|wound healing	basolateral plasma membrane|extracellular space|integral to plasma membrane|receptor complex	ATP binding|growth factor binding|protein heterodimerization activity|protein homodimerization activity|protein tyrosine kinase activator activity|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(3)|central_nervous_system(2)|stomach(1)|ovary(1)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	56517119	56517120	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56517119_56517120delAA								ZC3H10 (841 upstream) : ESYT1 (4934 downstream)																																			---	---	---	---
BAZ2A	11176	broad.mit.edu	37	12	57006416	57006416	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57006416delT	uc001slq.1	-						BAZ2A_uc001slp.1_Intron|BAZ2A_uc009zow.1_Intron	NM_013449	NP_038477			bromodomain adjacent to zinc finger domain, 2A						chromatin silencing at rDNA|DNA methylation|transcription, DNA-dependent	chromatin silencing complex|nucleolus|rDNA heterochromatin	DNA binding|histone acetyl-lysine binding|ligand-dependent nuclear receptor binding|RNA binding|zinc ion binding				0																		---	---	---	---
NACA	4666	broad.mit.edu	37	12	57120070	57120077	+	5'Flank	DEL	TTTTTTTT	-	-	rs63502261		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57120070_57120077delTTTTTTTT	uc001slz.2	-						NACA_uc001sly.2_5'Flank|NACA_uc009zoy.1_5'Flank|NACA_uc001smc.2_5'Flank|NACA_uc001sma.2_5'Flank|NACA_uc001smb.2_5'Flank|NACA_uc010squ.1_5'Flank	NM_001113201	NP_001106672			nascent polypeptide-associated complex alpha						interspecies interaction between organisms|protein transport|transcription, DNA-dependent|translation	nascent polypeptide-associated complex|nucleus	DNA binding			ovary(1)	1								T	BCL6	NHL								---	---	---	---
PRIM1	5557	broad.mit.edu	37	12	57142411	57142415	+	Intron	DEL	AAAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57142411_57142415delAAAAA	uc001smd.2	-						PRIM1_uc001sme.1_Intron|PRIM1_uc009zoz.1_Intron|PRIM1_uc001smf.2_Intron	NM_000946	NP_000937			DNA primase polypeptide 1						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	DNA primase activity|metal ion binding				0																		---	---	---	---
PRIM1	5557	broad.mit.edu	37	12	57144805	57144805	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57144805delA	uc001smd.2	-						PRIM1_uc001sme.1_Intron|PRIM1_uc009zoz.1_Intron|PRIM1_uc001smf.2_Intron	NM_000946	NP_000937			DNA primase polypeptide 1						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	DNA primase activity|metal ion binding				0																		---	---	---	---
HSD17B6	8630	broad.mit.edu	37	12	57175586	57175586	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57175586delA	uc001smg.1	+							NM_003725	NP_003716			hydroxysteroid (17-beta) dehydrogenase 6						androgen biosynthetic process|androgen catabolic process	early endosome membrane|endoplasmic reticulum|microsome	binding|electron carrier activity|estradiol 17-beta-dehydrogenase activity|retinol dehydrogenase activity|testosterone 17-beta-dehydrogenase (NAD+) activity			upper_aerodigestive_tract(1)|pancreas(1)	2					Succinic acid(DB00139)													---	---	---	---
Unknown	0	broad.mit.edu	37	12	57191144	57191145	+	IGR	DEL	AA	-	-	rs72241514		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57191144_57191145delAA								HSD17B6 (9570 upstream) : SDR9C7 (126474 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	57191892	57191892	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57191892delA								HSD17B6 (10318 upstream) : SDR9C7 (125727 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	57244350	57244350	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57244350delT								HSD17B6 (62776 upstream) : SDR9C7 (73269 downstream)																																			---	---	---	---
TMEM194A	23306	broad.mit.edu	37	12	57456741	57456744	+	Intron	DEL	AAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57456741_57456744delAAAA	uc001smy.2	-						TMEM194A_uc001smx.2_Intron|TMEM194A_uc010sra.1_Intron	NM_001130963	NP_001124435			transmembrane protein 194A isoform a							integral to membrane					0																		---	---	---	---
NXPH4	11247	broad.mit.edu	37	12	57608495	57608495	+	5'Flank	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57608495delC	uc010srf.1	+						NXPH4_uc009zpj.2_5'Flank	NM_007224	NP_009155			neurexophilin 4 precursor						neuropeptide signaling pathway	extracellular region					0																OREG0021939	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
NXPH4	11247	broad.mit.edu	37	12	57609692	57609693	+	5'Flank	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57609692_57609693delGA	uc010srf.1	+						NXPH4_uc009zpj.2_5'Flank	NM_007224	NP_009155			neurexophilin 4 precursor						neuropeptide signaling pathway	extracellular region					0																		---	---	---	---
SHMT2	6472	broad.mit.edu	37	12	57625248	57625248	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57625248delC	uc001snf.1	+						SHMT2_uc001sng.1_Intron|SHMT2_uc001snh.1_Intron|SHMT2_uc009zpk.1_Intron|SHMT2_uc001sni.1_Intron|SHMT2_uc010srg.1_Intron|SHMT2_uc001snj.1_Intron|SHMT2_uc010srh.1_Intron|SHMT2_uc001snk.1_Intron|SHMT2_uc010sri.1_Intron|SHMT2_uc001snl.2_Intron|SHMT2_uc010srj.1_5'Flank	NM_005412	NP_005403			serine hydroxymethyltransferase 2							microtubule cytoskeleton|mitochondrial nucleoid	glycine hydroxymethyltransferase activity|methyltransferase activity			ovary(1)|central_nervous_system(1)	2					Glycine(DB00145)|Pyridoxal Phosphate(DB00114)|Tetrahydrofolic acid(DB00116)													---	---	---	---
CTDSP2	10106	broad.mit.edu	37	12	58230426	58230427	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58230426_58230427delAA	uc001sqm.2	-						CTDSP2_uc009zqf.2_Intron|CTDSP2_uc009zqg.2_Intron	NM_005730	NP_005721			nuclear LIM interactor-interacting factor 2						protein dephosphorylation	nucleus|soluble fraction	CTD phosphatase activity|metal ion binding			central_nervous_system(1)	1	all_neural(12;0.00559)|Glioma(12;0.0143)|Melanoma(17;0.122)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	59107064	59107065	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:59107064_59107065insT	uc001sqq.1	-											Homo sapiens cDNA FLJ35805 fis, clone TESTI2005982.																														---	---	---	---
Unknown	0	broad.mit.edu	37	12	59196996	59196996	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:59196996delT								XRCC6BP1 (845945 upstream) : LRIG3 (68942 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	60447833	60447833	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:60447833delA								SLC16A7 (272426 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	60665523	60665523	+	IGR	DEL	T	-	-	rs11303461		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:60665523delT								SLC16A7 (490116 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	61356874	61356877	+	IGR	DEL	AAGC	-	-	rs146207055		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:61356874_61356877delAAGC								None (None upstream) : FAM19A2 (745166 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	61421760	61421760	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:61421760delT								None (None upstream) : FAM19A2 (680283 downstream)																																			---	---	---	---
FAM19A2	338811	broad.mit.edu	37	12	62104373	62104373	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62104373delT	uc001sqw.2	-						FAM19A2_uc001sqv.2_Intron|FAM19A2_uc001sqx.2_Intron|FAM19A2_uc001sqy.2_Intron	NM_178539	NP_848634			family with sequence similarity 19 (chemokine							cytoplasm				ovary(1)	1			GBM - Glioblastoma multiforme(1;0.00484)	GBM - Glioblastoma multiforme(3;0.02)														---	---	---	---
FAM19A2	338811	broad.mit.edu	37	12	62135068	62135068	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62135068delT	uc001sqw.2	-						FAM19A2_uc001sqv.2_Intron|FAM19A2_uc001sqx.2_Intron|FAM19A2_uc001sqy.2_Intron	NM_178539	NP_848634			family with sequence similarity 19 (chemokine							cytoplasm				ovary(1)	1			GBM - Glioblastoma multiforme(1;0.00484)	GBM - Glioblastoma multiforme(3;0.02)														---	---	---	---
FAM19A2	338811	broad.mit.edu	37	12	62291210	62291211	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62291210_62291211insA	uc001sqw.2	-						FAM19A2_uc001sqx.2_Intron|FAM19A2_uc001sqy.2_Intron	NM_178539	NP_848634			family with sequence similarity 19 (chemokine							cytoplasm				ovary(1)	1			GBM - Glioblastoma multiforme(1;0.00484)	GBM - Glioblastoma multiforme(3;0.02)														---	---	---	---
FAM19A2	338811	broad.mit.edu	37	12	62482092	62482092	+	Intron	DEL	A	-	-	rs141981598		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62482092delA	uc001sqw.2	-						FAM19A2_uc001sqx.2_Intron|FAM19A2_uc001sqy.2_Intron	NM_178539	NP_848634			family with sequence similarity 19 (chemokine							cytoplasm				ovary(1)	1			GBM - Glioblastoma multiforme(1;0.00484)	GBM - Glioblastoma multiforme(3;0.02)														---	---	---	---
FAM19A2	338811	broad.mit.edu	37	12	62607502	62607503	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62607502_62607503delTT	uc001sqx.2	-						FAM19A2_uc001sqy.2_Intron	NM_178539	NP_848634			family with sequence similarity 19 (chemokine							cytoplasm				ovary(1)	1			GBM - Glioblastoma multiforme(1;0.00484)	GBM - Glioblastoma multiforme(3;0.02)														---	---	---	---
USP15	9958	broad.mit.edu	37	12	62691341	62691341	+	Intron	DEL	A	-	-	rs112083123		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62691341delA	uc001src.1	+						USP15_uc001srb.1_Intron|USP15_uc010ssj.1_Intron|USP15_uc010ssk.1_Intron|USP15_uc001sra.2_Intron	NM_006313	NP_006304			ubiquitin specific peptidase 15						protein deubiquitination|ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(2)|lung(1)	3			GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)														---	---	---	---
MON2	23041	broad.mit.edu	37	12	62889227	62889227	+	Intron	DEL	A	-	-	rs80114155		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62889227delA	uc001sre.2	+						MON2_uc009zqj.2_Intron|MON2_uc010ssl.1_Intron|MON2_uc010ssm.1_Intron|MON2_uc010ssn.1_Intron|MON2_uc001srd.1_Intron	NM_015026	NP_055841			MON2 homolog						Golgi to endosome transport|protein transport	cytoplasm	ARF guanyl-nucleotide exchange factor activity|binding			central_nervous_system(2)	2			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)														---	---	---	---
MON2	23041	broad.mit.edu	37	12	62902369	62902369	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62902369delT	uc001sre.2	+						MON2_uc009zqj.2_Intron|MON2_uc010ssl.1_Intron|MON2_uc010ssm.1_Intron|MON2_uc010ssn.1_Intron|MON2_uc001srf.2_Intron|MON2_uc001srd.1_3'UTR	NM_015026	NP_055841			MON2 homolog						Golgi to endosome transport|protein transport	cytoplasm	ARF guanyl-nucleotide exchange factor activity|binding			central_nervous_system(2)	2			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)														---	---	---	---
C12orf61	283416	broad.mit.edu	37	12	62996043	62996043	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:62996043delA	uc001sri.1	-	1					MIRLET7I_hsa-let-7i|MI0000434_5'Flank|uc001srj.1_5'Flank	NM_175895	NP_787091			hypothetical protein LOC283416												0			BRCA - Breast invasive adenocarcinoma(9;0.0399)	GBM - Glioblastoma multiforme(28;0.134)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	63002324	63002325	+	IGR	DEL	TT	-	-	rs72269418		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63002324_63002325delTT								MIRLET7I (4775 upstream) : PPM1H (35438 downstream)																																			---	---	---	---
PPM1H	57460	broad.mit.edu	37	12	63041688	63041689	+	3'UTR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63041688_63041689insA	uc001srk.3	-	10						NM_020700	NP_065751			protein phosphatase 1H (PP2C domain containing)								phosphoprotein phosphatase activity			lung(3)|ovary(1)	4			GBM - Glioblastoma multiforme(1;0.000443)|BRCA - Breast invasive adenocarcinoma(9;0.209)	GBM - Glioblastoma multiforme(28;0.0126)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	63738726	63738726	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63738726delA								AVPR1A (192136 upstream) : DPY19L2 (213967 downstream)																																			---	---	---	---
SRGAP1	57522	broad.mit.edu	37	12	64265418	64265418	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64265418delT	uc010ssp.1	+						SRGAP1_uc001srt.2_Intron	NM_020762	NP_065813			SLIT-ROBO Rho GTPase activating protein 1						axon guidance	cytosol				ovary(2)|central_nervous_system(2)	4			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)														---	---	---	---
SRGAP1	57522	broad.mit.edu	37	12	64380208	64380210	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64380208_64380210delTTT	uc010ssp.1	+						SRGAP1_uc001srt.2_Intron|SRGAP1_uc001srv.2_Intron	NM_020762	NP_065813			SLIT-ROBO Rho GTPase activating protein 1						axon guidance	cytosol				ovary(2)|central_nervous_system(2)	4			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)														---	---	---	---
SRGAP1	57522	broad.mit.edu	37	12	64426159	64426159	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64426159delT	uc010ssp.1	+						SRGAP1_uc001srt.2_Intron|SRGAP1_uc001srv.2_Intron	NM_020762	NP_065813			SLIT-ROBO Rho GTPase activating protein 1						axon guidance	cytosol				ovary(2)|central_nervous_system(2)	4			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)														---	---	---	---
SRGAP1	57522	broad.mit.edu	37	12	64508440	64508440	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64508440delT	uc010ssp.1	+						SRGAP1_uc001srv.2_Intron	NM_020762	NP_065813			SLIT-ROBO Rho GTPase activating protein 1						axon guidance	cytosol				ovary(2)|central_nervous_system(2)	4			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	64647658	64647658	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64647658delT	uc001srx.2	+											Homo sapiens mRNA; cDNA DKFZp434A0326 (from clone DKFZp434A0326).																														---	---	---	---
C12orf56	115749	broad.mit.edu	37	12	64729042	64729042	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64729042delA	uc001ssa.3	-						uc001srx.2_Intron	NM_001099676	NP_001093146			hypothetical protein LOC115749												0			GBM - Glioblastoma multiforme(3;0.000582)	GBM - Glioblastoma multiforme(28;0.0259)														---	---	---	---
XPOT	11260	broad.mit.edu	37	12	64799866	64799866	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64799866delT	uc001ssb.2	+						XPOT_uc009zqm.1_Intron	NM_007235	NP_009166			tRNA exportin						intracellular protein transport|tRNA export from nucleus	cytoplasm|nucleoplasm	protein transporter activity|tRNA binding			ovary(2)	2				GBM - Glioblastoma multiforme(28;0.0404)														---	---	---	---
XPOT	11260	broad.mit.edu	37	12	64815401	64815401	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64815401delA	uc001ssb.2	+							NM_007235	NP_009166			tRNA exportin						intracellular protein transport|tRNA export from nucleus	cytoplasm|nucleoplasm	protein transporter activity|tRNA binding			ovary(2)	2				GBM - Glioblastoma multiforme(28;0.0404)														---	---	---	---
XPOT	11260	broad.mit.edu	37	12	64828782	64828782	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64828782delT	uc001ssb.2	+							NM_007235	NP_009166			tRNA exportin						intracellular protein transport|tRNA export from nucleus	cytoplasm|nucleoplasm	protein transporter activity|tRNA binding			ovary(2)	2				GBM - Glioblastoma multiforme(28;0.0404)														---	---	---	---
GNS	2799	broad.mit.edu	37	12	65133419	65133421	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65133419_65133421delAAA	uc001ssg.3	-						GNS_uc001ssf.2_Intron|GNS_uc010ssq.1_Intron|GNS_uc010ssr.1_Intron	NM_002076	NP_002067			glucosamine (N-acetyl)-6-sulfatase precursor							lysosome	metal ion binding|N-acetylglucosamine-6-sulfatase activity|protein binding			central_nervous_system(1)	1	Lung NSC(1;7.25e-14)|all_lung(1;1.25e-12)		LUAD - Lung adenocarcinoma(6;0.115)	GBM - Glioblastoma multiforme(28;0.0435)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	65296652	65296652	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65296652delT	uc001ssj.1	+											Homo sapiens cDNA FLJ41278 fis, clone BRAMY2037147.																														---	---	---	---
WIF1	11197	broad.mit.edu	37	12	65482577	65482577	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65482577delA	uc001ssk.2	-							NM_007191	NP_009122			WNT inhibitory factor 1 precursor						multicellular organismal development|Wnt receptor signaling pathway	extracellular region	protein tyrosine kinase activity			ovary(2)|lung(1)|skin(1)	4			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0231)				T	HMGA2	pleomorphic salivary gland adenoma								---	---	---	---
LEMD3	23592	broad.mit.edu	37	12	65604874	65604874	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65604874delA	uc001ssl.1	+						LEMD3_uc009zqo.1_Intron	NM_014319	NP_055134			LEM domain containing 3						negative regulation of activin receptor signaling pathway|negative regulation of BMP signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway	integral to nuclear inner membrane|membrane fraction	DNA binding|nucleotide binding|protein binding			central_nervous_system(3)|ovary(1)	4			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0104)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	65652736	65652736	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65652736delT								LEMD3 (10629 upstream) : MSRB3 (19752 downstream)																																			---	---	---	---
MSRB3	253827	broad.mit.edu	37	12	65839182	65839182	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65839182delC	uc001ssn.2	+						MSRB3_uc001ssm.2_Intron|MSRB3_uc009zqp.2_Intron	NM_198080	NP_932346			methionine sulfoxide reductase B3 isoform 1						protein repair	endoplasmic reticulum|mitochondrion	peptide-methionine-(S)-S-oxide reductase activity|protein-methionine-R-oxide reductase activity|zinc ion binding			central_nervous_system(1)|skin(1)	2			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.131)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	65957467	65957469	+	IGR	DEL	GAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65957467_65957469delGAA								MSRB3 (96787 upstream) : RPSAP52 (194334 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	66425608	66425608	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66425608delT								HMGA2 (65540 upstream) : LLPH (91242 downstream)																																			---	---	---	---
TMBIM4	51643	broad.mit.edu	37	12	66545940	66545941	+	Intron	INS	-	A	A	rs150814684	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66545940_66545941insA	uc001stc.2	-						LLPH_uc010ssx.1_Intron|TMBIM4_uc001std.2_Intron|TMBIM4_uc009zqr.2_Intron|TMBIM4_uc001ste.2_Intron|TMBIM4_uc001stf.2_Intron|TMBIM4_uc009zqs.2_Intron	NM_016056	NP_057140			transmembrane BAX inhibitor motif containing 4							integral to membrane	protein binding			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(28;0.0745)														---	---	---	---
GRIP1	23426	broad.mit.edu	37	12	66787492	66787492	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66787492delA	uc001stk.2	-						GRIP1_uc010sta.1_Intron|GRIP1_uc001stj.2_Intron|GRIP1_uc001stl.1_Intron|GRIP1_uc001stm.2_Intron	NM_021150	NP_066973			glutamate receptor interacting protein 1						androgen receptor signaling pathway|intracellular signal transduction|positive regulation of transcription, DNA-dependent|synaptic transmission	cell junction|cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|postsynaptic membrane	androgen receptor binding|beta-catenin binding|protein C-terminus binding|receptor signaling complex scaffold activity|transcription coactivator activity			ovary(2)	2			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)														---	---	---	---
GRIP1	23426	broad.mit.edu	37	12	67027760	67027760	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67027760delT	uc001stk.2	-						GRIP1_uc010sta.1_Intron|GRIP1_uc001stm.2_Intron	NM_021150	NP_066973			glutamate receptor interacting protein 1						androgen receptor signaling pathway|intracellular signal transduction|positive regulation of transcription, DNA-dependent|synaptic transmission	cell junction|cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|postsynaptic membrane	androgen receptor binding|beta-catenin binding|protein C-terminus binding|receptor signaling complex scaffold activity|transcription coactivator activity			ovary(2)	2			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	67730555	67730555	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67730555delT								CAND1 (22167 upstream) : DYRK2 (311957 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	68112003	68112003	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68112003delA	uc001stu.2	-											Homo sapiens cDNA clone IMAGE:4822681.																														---	---	---	---
Unknown	0	broad.mit.edu	37	12	68376828	68376828	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68376828delT								DYRK2 (320385 upstream) : IFNG (171722 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	68864437	68864437	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68864437delA								MDM1 (138276 upstream) : RAP1B (140215 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	68967584	68967584	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68967584delT								MDM1 (241423 upstream) : RAP1B (37068 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	69070608	69070609	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69070608_69070609insA	uc001sud.1	-						uc001sue.1_Intron					Homo sapiens cDNA clone IMAGE:5268292.																														---	---	---	---
Unknown	0	broad.mit.edu	37	12	69512573	69512573	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69512573delA								CPM (155553 upstream) : CPSF6 (120744 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	69607273	69607273	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69607273delA								CPM (250253 upstream) : CPSF6 (26044 downstream)																																			---	---	---	---
BEST3	144453	broad.mit.edu	37	12	70070528	70070535	+	Intron	DEL	TGAATCTC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70070528_70070535delTGAATCTC	uc001svg.2	-						BEST3_uc001svd.1_Intron|BEST3_uc001sve.1_Intron|BEST3_uc001svf.2_Intron|BEST3_uc010stm.1_Intron|BEST3_uc001svh.2_Intron	NM_032735	NP_116124			vitelliform macular dystrophy 2-like 3 isoform							chloride channel complex|plasma membrane	chloride channel activity				0	Breast(13;2.31e-06)|Esophageal squamous(21;0.187)		Lung(24;0.000278)|OV - Ovarian serous cystadenocarcinoma(12;0.0019)|STAD - Stomach adenocarcinoma(21;0.00694)															---	---	---	---
BEST3	144453	broad.mit.edu	37	12	70094353	70094354	+	5'Flank	INS	-	T	T	rs111635433		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70094353_70094354insT	uc001svg.2	-						BEST3_uc001svd.1_5'Flank|BEST3_uc001sve.1_5'Flank|BEST3_uc010stm.1_5'Flank|BEST3_uc001svh.2_5'Flank|BEST3_uc001svi.1_5'Flank	NM_032735	NP_116124			vitelliform macular dystrophy 2-like 3 isoform							chloride channel complex|plasma membrane	chloride channel activity				0	Breast(13;2.31e-06)|Esophageal squamous(21;0.187)		Lung(24;0.000278)|OV - Ovarian serous cystadenocarcinoma(12;0.0019)|STAD - Stomach adenocarcinoma(21;0.00694)															---	---	---	---
Unknown	0	broad.mit.edu	37	12	70117204	70117204	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70117204delA	uc001svj.1	-						uc001svk.2_Intron					Homo sapiens cDNA clone IMAGE:4829132.																														---	---	---	---
KCNMB4	27345	broad.mit.edu	37	12	70821781	70821781	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70821781delT	uc001svx.2	+							NM_014505	NP_055320			calcium-activated potassium channel beta 4						detection of calcium ion|platelet activation|regulation of action potential in neuron|regulation of neurotransmitter secretion|regulation of vasoconstriction|synaptic transmission	voltage-gated potassium channel complex	calcium-activated potassium channel activity|protein binding				0	Renal(347;0.236)		Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00243)|STAD - Stomach adenocarcinoma(21;0.0118)															---	---	---	---
PTPRR	5801	broad.mit.edu	37	12	71200046	71200047	+	Intron	INS	-	AG	AG			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71200046_71200047insAG	uc001swi.1	-							NM_002849	NP_002840			protein tyrosine phosphatase, receptor type, R						in utero embryonic development	cell surface|Golgi apparatus|integral to membrane|nucleus|perinuclear region of cytoplasm|plasma membrane	protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			skin(2)|ovary(1)	3			GBM - Glioblastoma multiforme(2;5.67e-07)|Lung(24;0.00283)|OV - Ovarian serous cystadenocarcinoma(12;0.00578)|LUSC - Lung squamous cell carcinoma(43;0.132)	COAD - Colon adenocarcinoma(1;0.136)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	71430866	71430866	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71430866delT								PTPRR (116282 upstream) : TSPAN8 (88011 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	71469525	71469525	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71469525delG								PTPRR (154941 upstream) : TSPAN8 (49352 downstream)																																			---	---	---	---
TSPAN8	7103	broad.mit.edu	37	12	71628009	71628009	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71628009delT	uc001swk.1	-							NM_004616	NP_004607			transmembrane 4 superfamily member 3						protein glycosylation	integral to membrane|lysosome	signal transducer activity			skin(2)|lung(1)|central_nervous_system(1)	4			LUSC - Lung squamous cell carcinoma(43;0.24)|OV - Ovarian serous cystadenocarcinoma(12;0.244)															---	---	---	---
LGR5	8549	broad.mit.edu	37	12	71848623	71848623	+	Intron	DEL	A	-	-	rs112152816		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71848623delA	uc001swl.2	+						LGR5_uc001swm.2_Intron|LGR5_uc001swn.1_Intron	NM_003667	NP_003658			leucine-rich repeat-containing G protein-coupled							integral to plasma membrane	protein-hormone receptor activity			lung(4)|skin(3)|ovary(1)|pancreas(1)	9																		---	---	---	---
ZFC3H1	196441	broad.mit.edu	37	12	72038598	72038599	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72038598_72038599insA	uc001swo.2	-							NM_144982	NP_659419			proline/serine-rich coiled-coil 2						RNA processing	intracellular	metal ion binding			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
TPH2	121278	broad.mit.edu	37	12	72374283	72374283	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72374283delT	uc009zrw.1	+						TPH2_uc001swy.2_Intron	NM_173353	NP_775489			tryptophan hydroxylase 2						aromatic amino acid family metabolic process|hormone biosynthetic process|serotonin biosynthetic process	cytosol	amino acid binding|iron ion binding|tryptophan 5-monooxygenase activity			ovary(2)|central_nervous_system(1)|skin(1)	4					L-Tryptophan(DB00150)													---	---	---	---
Unknown	0	broad.mit.edu	37	12	72560099	72560100	+	IGR	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72560099_72560100delAC								TPH2 (133878 upstream) : LOC283392 (96228 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	73327193	73327193	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:73327193delC								TRHDE (267772 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	73347643	73347643	+	IGR	DEL	A	-	-	rs112348341		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:73347643delA								TRHDE (288222 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	73506979	73506979	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:73506979delT								TRHDE (447558 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	73700004	73700004	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:73700004delA								TRHDE (640583 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	74139544	74139545	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:74139544_74139545insT								None (None upstream) : ATXN7L3B (792006 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	74355507	74355509	+	IGR	DEL	TAG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:74355507_74355509delTAG								None (None upstream) : ATXN7L3B (576042 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	75625025	75625026	+	IGR	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75625025_75625026delTC								KCNC2 (21514 upstream) : CAPS2 (44734 downstream)																																			---	---	---	---
CAPS2	84698	broad.mit.edu	37	12	75692575	75692575	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75692575delA	uc001sxk.3	-						CAPS2_uc001sxm.3_Intron|CAPS2_uc009zsa.2_Intron|CAPS2_uc001sxi.3_Intron|CAPS2_uc001sxj.3_Intron|CAPS2_uc001sxl.3_Intron	NM_032606	NP_115995			calcyphosine 2								calcium ion binding			ovary(2)	2																		---	---	---	---
GLIPR1	11010	broad.mit.edu	37	12	75874927	75874927	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75874927delT	uc001sxs.2	+						GLIPR1_uc009zsb.1_Intron	NM_006851	NP_006842			GLI pathogenesis-related 1 precursor						cellular lipid metabolic process	extracellular region|integral to membrane				large_intestine(1)|ovary(1)|skin(1)	3																		---	---	---	---
GLIPR1	11010	broad.mit.edu	37	12	75884348	75884348	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75884348delA	uc001sxs.2	+						GLIPR1_uc009zsb.1_Intron	NM_006851	NP_006842			GLI pathogenesis-related 1 precursor						cellular lipid metabolic process	extracellular region|integral to membrane				large_intestine(1)|ovary(1)|skin(1)	3																		---	---	---	---
GLIPR1	11010	broad.mit.edu	37	12	75894905	75894905	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75894905delA	uc001sxs.2	+	6					KRR1_uc001sxt.2_Intron|KRR1_uc009zsc.2_Intron	NM_006851	NP_006842			GLI pathogenesis-related 1 precursor						cellular lipid metabolic process	extracellular region|integral to membrane				large_intestine(1)|ovary(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	75953858	75953858	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75953858delT								KRR1 (48440 upstream) : PHLDA1 (465370 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	76353879	76353880	+	IGR	INS	-	A	A	rs113836825		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76353879_76353880insA								KRR1 (448461 upstream) : PHLDA1 (65348 downstream)																																			---	---	---	---
NAP1L1	4673	broad.mit.edu	37	12	76468043	76468043	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76468043delA	uc001sxw.2	-						NAP1L1_uc001sxz.2_Intron|NAP1L1_uc001sxx.2_Intron|NAP1L1_uc001sxy.2_Intron|NAP1L1_uc010sty.1_Intron|NAP1L1_uc010stz.1_Intron|NAP1L1_uc010sua.1_Intron|NAP1L1_uc001syb.2_Intron|NAP1L1_uc001sya.2_Intron|NAP1L1_uc001syc.2_Intron	NM_139207	NP_631946			nucleosome assembly protein 1-like 1						DNA replication|nucleosome assembly|positive regulation of cell proliferation	chromatin assembly complex|melanosome	protein binding			ovary(1)|skin(1)	2		Colorectal(145;0.09)																---	---	---	---
OSBPL8	114882	broad.mit.edu	37	12	76772555	76772555	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76772555delT	uc001sye.1	-						OSBPL8_uc001syf.1_Intron|OSBPL8_uc001syg.1_Intron|OSBPL8_uc001syh.1_Intron	NM_020841	NP_065892			oxysterol-binding protein-like protein 8 isoform						lipid transport		lipid binding			ovary(1)	1																		---	---	---	---
E2F7	144455	broad.mit.edu	37	12	77453008	77453008	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:77453008delA	uc001sym.3	-						E2F7_uc001syn.2_Intron	NM_203394	NP_976328			E2F transcription factor 7						cell cycle	transcription factor complex	DNA binding|identical protein binding			upper_aerodigestive_tract(1)|ovary(1)|kidney(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	78119415	78119415	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78119415delA								E2F7 (660055 upstream) : NAV3 (105654 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	78156389	78156389	+	IGR	DEL	A	-	-	rs71903380		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78156389delA								E2F7 (697029 upstream) : NAV3 (68680 downstream)																																			---	---	---	---
NAV3	89795	broad.mit.edu	37	12	78439082	78439082	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78439082delT	uc001syp.2	+						NAV3_uc001syo.2_Intron|NAV3_uc010sub.1_Intron	NM_014903	NP_055718			neuron navigator 3							nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	17															HNSCC(70;0.22)			---	---	---	---
NAV3	89795	broad.mit.edu	37	12	78502266	78502266	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78502266delA	uc001syp.2	+						NAV3_uc001syo.2_Intron|NAV3_uc010sub.1_Intron	NM_014903	NP_055718			neuron navigator 3							nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	17															HNSCC(70;0.22)			---	---	---	---
NAV3	89795	broad.mit.edu	37	12	78550803	78550803	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78550803delA	uc001syp.2	+						NAV3_uc001syo.2_Intron|NAV3_uc010sub.1_Intron|NAV3_uc009zsf.2_Intron	NM_014903	NP_055718			neuron navigator 3							nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	17															HNSCC(70;0.22)			---	---	---	---
Unknown	0	broad.mit.edu	37	12	79862147	79862147	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:79862147delT								SYT1 (16360 upstream) : PAWR (123600 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	79945705	79945705	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:79945705delA								SYT1 (99918 upstream) : PAWR (40042 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	79982951	79982951	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:79982951delA								SYT1 (137164 upstream) : PAWR (2796 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	80356074	80356074	+	IGR	DEL	T	-	-	rs76738517		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80356074delT								PPP1R12A (26839 upstream) : PTPRQ (482052 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	80496628	80496628	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80496628delT								PPP1R12A (167393 upstream) : PTPRQ (341498 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	80632597	80632598	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:80632597_80632598delTG								PPP1R12A (303362 upstream) : PTPRQ (205528 downstream)																																			---	---	---	---
LIN7A	8825	broad.mit.edu	37	12	81220312	81220312	+	Intron	DEL	T	-	-	rs12308574		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81220312delT	uc001szj.1	-						LIN7A_uc001szk.1_Intron	NM_004664	NP_004655			lin-7 homolog A						exocytosis|protein complex assembly|protein transport	basolateral plasma membrane|postsynaptic density|postsynaptic membrane|synaptosome|tight junction	L27 domain binding			ovary(1)|skin(1)	2																		---	---	---	---
LIN7A	8825	broad.mit.edu	37	12	81283066	81283066	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81283066delT	uc001szj.1	-	2	358	c.165delA	c.(163-165)AAAfs	p.K55fs	LIN7A_uc001szk.1_RNA	NM_004664	NP_004655	O14910	LIN7A_HUMAN	lin-7 homolog A	55	L27.				exocytosis|protein complex assembly|protein transport	basolateral plasma membrane|postsynaptic density|postsynaptic membrane|synaptosome|tight junction	L27 domain binding			ovary(1)|skin(1)	2																		---	---	---	---
PPFIA2	8499	broad.mit.edu	37	12	81660978	81660982	+	Intron	DEL	TTTTT	-	-	rs71822940		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81660978_81660982delTTTTT	uc001szo.1	-						PPFIA2_uc010sue.1_Intron|PPFIA2_uc010sug.1_Intron|PPFIA2_uc010suh.1_Intron|PPFIA2_uc010sui.1_Intron|PPFIA2_uc010suj.1_Intron|PPFIA2_uc009zsi.1_Intron|PPFIA2_uc010suf.1_Intron|PPFIA2_uc009zsh.2_Intron	NM_003625	NP_003616			PTPRF interacting protein alpha 2											ovary(3)|lung(2)|pancreas(1)	6																		---	---	---	---
TMTC2	160335	broad.mit.edu	37	12	83256938	83256938	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:83256938delC	uc001szt.2	+						TMTC2_uc001szr.1_Intron|TMTC2_uc001szs.1_Intron|TMTC2_uc010suk.1_Intron	NM_152588	NP_689801			transmembrane and tetratricopeptide repeat							endoplasmic reticulum|integral to membrane	binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	83797368	83797368	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:83797368delT								TMTC2 (269305 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	84218382	84218384	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:84218382_84218384delTTT								TMTC2 (690319 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	84785951	84785951	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:84785951delT								None (None upstream) : SLC6A15 (467318 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	85215274	85215277	+	IGR	DEL	AAAT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85215274_85215277delAAAT								None (None upstream) : SLC6A15 (37992 downstream)																																			---	---	---	---
LRRIQ1	84125	broad.mit.edu	37	12	85529968	85529969	+	Intron	INS	-	CA	CA	rs142662115	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85529968_85529969insCA	uc001tac.2	+							NM_001079910	NP_001073379			leucine-rich repeats and IQ motif containing 1											ovary(4)|central_nervous_system(1)|skin(1)	6				GBM - Glioblastoma multiforme(134;0.212)														---	---	---	---
LRRIQ1	84125	broad.mit.edu	37	12	85554294	85554294	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85554294delT	uc001tac.2	+							NM_001079910	NP_001073379			leucine-rich repeats and IQ motif containing 1											ovary(4)|central_nervous_system(1)|skin(1)	6				GBM - Glioblastoma multiforme(134;0.212)														---	---	---	---
LRRIQ1	84125	broad.mit.edu	37	12	85594771	85594771	+	Intron	DEL	T	-	-	rs112924533		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85594771delT	uc001tac.2	+							NM_001079910	NP_001073379			leucine-rich repeats and IQ motif containing 1											ovary(4)|central_nervous_system(1)|skin(1)	6				GBM - Glioblastoma multiforme(134;0.212)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	86253597	86253597	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:86253597delA								RASSF9 (23279 upstream) : NTS (14478 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	87601784	87601784	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:87601784delA								MGAT4C (369103 upstream) : C12orf50 (772032 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	88343990	88343990	+	IGR	DEL	A	-	-	rs34094092		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88343990delA								None (None upstream) : C12orf50 (29826 downstream)																																			---	---	---	---
CEP290	80184	broad.mit.edu	37	12	88448067	88448067	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88448067delT	uc001tar.2	-						CEP290_uc001taq.2_Intron|uc001tas.2_5'Flank	NM_025114	NP_079390			centrosomal protein 290kDa						cilium assembly|eye photoreceptor cell development|G2/M transition of mitotic cell cycle|hindbrain development|otic vesicle formation|positive regulation of transcription, DNA-dependent|pronephros development|protein transport	cell surface|centrosome|cytosol|nucleus|photoreceptor connecting cilium	protein binding			ovary(5)|breast(1)|pancreas(1)	7																		---	---	---	---
TMTC3	160418	broad.mit.edu	37	12	88547371	88547371	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88547371delA	uc001tau.2	+						TMTC3_uc009zsm.2_Intron	NM_181783	NP_861448			transmembrane and tetratricopeptide repeat							integral to membrane	binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	88677316	88677316	+	IGR	DEL	A	-	-	rs141934463	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88677316delA								TMTC3 (83653 upstream) : KITLG (209253 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	88853312	88853312	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88853312delG								TMTC3 (259649 upstream) : KITLG (33257 downstream)																																			---	---	---	---
KITLG	4254	broad.mit.edu	37	12	88928152	88928152	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88928152delT	uc001tav.2	-						KITLG_uc001taw.2_Intron|KITLG_uc009zso.1_5'Flank	NM_000899	NP_000890			KIT ligand isoform b precursor						cell adhesion|cell proliferation|hemopoiesis|male gonad development|positive regulation of DNA replication|signal transduction	cytoplasm|cytoskeleton|integral to membrane|plasma membrane	growth factor activity|identical protein binding|stem cell factor receptor binding			ovary(1)	1														Testicular_Cancer_Familial_Clustering_of				---	---	---	---
Unknown	0	broad.mit.edu	37	12	89072963	89072963	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89072963delT								KITLG (98725 upstream) : DUSP6 (668876 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	89389918	89389920	+	IGR	DEL	AGA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89389918_89389920delAGA								KITLG (415680 upstream) : DUSP6 (351919 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	89563197	89563197	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89563197delA								KITLG (588959 upstream) : DUSP6 (178642 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	89786596	89786596	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89786596delT								DUSP6 (40300 upstream) : POC1B (26905 downstream)																																			---	---	---	---
POC1B	282809	broad.mit.edu	37	12	89853510	89853510	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89853510delA	uc001tbc.2	-						POC1B_uc001tba.2_Intron|POC1B_uc001tbb.2_Intron|POC1B_uc010sun.1_Intron|POC1B_uc009zsp.2_Intron|POC1B_uc009zsq.2_Intron	NM_172240	NP_758440			WD repeat domain 51B						cell projection organization	centriole|microtubule basal body				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	89969539	89969539	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89969539delT								POC1B (49762 upstream) : ATP2B1 (12289 downstream)																																			---	---	---	---
ATP2B1	490	broad.mit.edu	37	12	89984602	89984603	+	3'UTR	DEL	TT	-	-	rs78076751		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89984602_89984603delTT	uc001tbh.2	-	20					ATP2B1_uc001tbg.2_3'UTR|ATP2B1_uc009zsr.2_RNA|ATP2B1_uc001tbf.2_3'UTR	NM_001682	NP_001673			plasma membrane calcium ATPase 1 isoform 1b						ATP biosynthetic process|platelet activation	integral to plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
ATP2B1	490	broad.mit.edu	37	12	89985022	89985022	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89985022delT	uc001tbh.2	-	20	3583	c.3402delA	c.(3400-3402)AAAfs	p.K1134fs	ATP2B1_uc001tbg.2_3'UTR|ATP2B1_uc009zsr.2_RNA|ATP2B1_uc001tbf.2_Frame_Shift_Del_p.K768fs	NM_001682	NP_001673	P20020	AT2B1_HUMAN	plasma membrane calcium ATPase 1 isoform 1b	1172	Cytoplasmic (Potential).				ATP biosynthetic process|platelet activation	integral to plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
ATP2B1	490	broad.mit.edu	37	12	90029925	90029925	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:90029925delA	uc001tbh.2	-						ATP2B1_uc001tbg.2_Intron	NM_001682	NP_001673			plasma membrane calcium ATPase 1 isoform 1b						ATP biosynthetic process|platelet activation	integral to plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	90165382	90165383	+	IGR	DEL	TT	-	-	rs78204538		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:90165382_90165383delTT								LOC338758 (59654 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	91195865	91195866	+	IGR	DEL	TT	-	-	rs146912005	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91195865_91195866delTT								None (None upstream) : C12orf12 (150127 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	91231482	91231482	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91231482delA								None (None upstream) : C12orf12 (114511 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	91515280	91515281	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91515280_91515281delTT								LUM (9738 upstream) : DCN (23755 downstream)																																			---	---	---	---
DCN	1634	broad.mit.edu	37	12	91541640	91541640	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91541640delT	uc001tbs.2	-						DCN_uc001tbo.2_Intron|DCN_uc001tbp.2_Intron|DCN_uc001tbq.2_Intron|DCN_uc001tbr.2_Intron|DCN_uc001tbt.2_Intron|DCN_uc001tbu.2_Intron	NM_133503	NP_598010			decorin isoform a preproprotein						organ morphogenesis	extracellular space				central_nervous_system(2)|ovary(1)|lung(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	91863720	91863720	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:91863720delG								DCN (286914 upstream) : BTG1 (515146 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	92907931	92907931	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:92907931delA								CLLU1 (30475 upstream) : C12orf74 (188909 downstream)																																			---	---	---	---
EEA1	8411	broad.mit.edu	37	12	93195481	93195481	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93195481delA	uc001tck.2	-							NM_003566	NP_003557			early endosome antigen 1, 162kD						early endosome to late endosome transport|synaptic vesicle to endosome fusion|vesicle fusion	cytosol|early endosome membrane|extrinsic to plasma membrane|membrane fraction	1-phosphatidylinositol binding|calmodulin binding|GTP-dependent protein binding|protein homodimerization activity|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
EEA1	8411	broad.mit.edu	37	12	93284124	93284124	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93284124delT	uc001tck.2	-							NM_003566	NP_003557			early endosome antigen 1, 162kD						early endosome to late endosome transport|synaptic vesicle to endosome fusion|vesicle fusion	cytosol|early endosome membrane|extrinsic to plasma membrane|membrane fraction	1-phosphatidylinositol binding|calmodulin binding|GTP-dependent protein binding|protein homodimerization activity|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	93567653	93567653	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93567653delA								EEA1 (244546 upstream) : NUDT4 (204048 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	93753814	93753814	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93753814delA								EEA1 (430707 upstream) : NUDT4 (17887 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	93767864	93767864	+	IGR	DEL	A	-	-	rs71947924		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93767864delA								EEA1 (444757 upstream) : NUDT4 (3837 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	93843563	93843563	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93843563delT								UBE2N (7537 upstream) : MRPL42 (17707 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	93844941	93844942	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93844941_93844942insT								UBE2N (8915 upstream) : MRPL42 (16328 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	94006139	94006139	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94006139delT								SOCS2 (36161 upstream) : CRADD (65012 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	94014199	94014199	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94014199delT								SOCS2 (44221 upstream) : CRADD (56952 downstream)																																			---	---	---	---
CRADD	8738	broad.mit.edu	37	12	94095735	94095735	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94095735delT	uc001tda.2	+						CRADD_uc010sur.1_Intron|CRADD_uc010sus.1_Intron	NM_003805	NP_003796			CASP2 and RIPK1 domain containing adaptor with						apoptosis|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|signal transduction	intracellular	death domain binding|protease binding|protein binding, bridging			ovary(1)	1																		---	---	---	---
CRADD	8738	broad.mit.edu	37	12	94277445	94277445	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94277445delA	uc010sur.1	+						CRADD_uc010sus.1_Intron	NM_003805	NP_003796			CASP2 and RIPK1 domain containing adaptor with						apoptosis|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|signal transduction	intracellular	death domain binding|protease binding|protein binding, bridging			ovary(1)	1																		---	---	---	---
PLXNC1	10154	broad.mit.edu	37	12	94652073	94652073	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94652073delT	uc001tdc.2	+						PLXNC1_uc010sut.1_Intron	NM_005761	NP_005752			plexin C1 precursor						axon guidance|cell adhesion	integral to membrane|intracellular|plasma membrane	receptor activity|receptor binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
NR2C1	7181	broad.mit.edu	37	12	95453642	95453643	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95453642_95453643delTT	uc001tdm.3	-						NR2C1_uc010suu.1_Intron|NR2C1_uc001tdo.3_Intron|NR2C1_uc001tdn.3_Intron	NM_003297	NP_003288			nuclear receptor subfamily 2, group C, member 1						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	PML body	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)	1																		---	---	---	---
FGD6	55785	broad.mit.edu	37	12	95592214	95592215	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95592214_95592215insT	uc001tdp.3	-						FGD6_uc009zsx.2_Intron	NM_018351	NP_060821			FYVE, RhoGEF and PH domain containing 6						actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(2)|breast(1)	3																		---	---	---	---
VEZT	55591	broad.mit.edu	37	12	95689727	95689727	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95689727delT	uc001tdz.2	+						VEZT_uc009ztb.1_Intron|VEZT_uc009ztc.1_Intron|VEZT_uc001tdy.2_Intron	NM_017599	NP_060069			vezatin, adherens junctions transmembrane							acrosomal vesicle|adherens junction|integral to membrane|nucleus				ovary(1)	1																		---	---	---	---
USP44	84101	broad.mit.edu	37	12	95928451	95928451	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95928451delC	uc001teg.2	-						USP44_uc001teh.2_Intron|USP44_uc009zte.2_Intron	NM_001042403	NP_001035862			ubiquitin thiolesterase 44						anaphase|cell division|mitosis|negative regulation of mitotic anaphase-promoting complex activity|protein deubiquitination|regulation of spindle checkpoint|ubiquitin-dependent protein catabolic process	nucleus	protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(1)|breast(1)|central_nervous_system(1)	3																		---	---	---	---
ELK3	2004	broad.mit.edu	37	12	96588323	96588323	+	5'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96588323delA	uc001teo.1	+	1						NM_005230	NP_005221			ELK3 protein						negative regulation of transcription, DNA-dependent|signal transduction	mitochondrion	protein binding|purine-rich negative regulatory element binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(1)	1	all_cancers(2;0.00173)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	96858261	96858261	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96858261delA								CDK17 (64038 upstream) : C12orf63 (183492 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	96926916	96926916	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96926916delT	uc009ztl.1	+						uc001teq.2_Intron					RecName: Full=Uncharacterized protein C12orf55;																														---	---	---	---
Unknown	0	broad.mit.edu	37	12	96974605	96974605	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96974605delT	uc001ter.1	+											Homo sapiens cDNA FLJ31514 fis, clone NT2RI1000164.																														---	---	---	---
C12orf63	374467	broad.mit.edu	37	12	97100861	97100862	+	Intron	INS	-	AGA	AGA	rs138063267	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97100861_97100862insAGA	uc001tet.1	+							NM_198520	NP_940922			hypothetical protein LOC374467											skin(6)|ovary(1)	7																		---	---	---	---
C12orf63	374467	broad.mit.edu	37	12	97137786	97137786	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97137786delT	uc001tet.1	+							NM_198520	NP_940922			hypothetical protein LOC374467											skin(6)|ovary(1)	7																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	97359804	97359805	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97359804_97359805insA								NEDD1 (12343 upstream) : RMST (498994 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	97629204	97629205	+	IGR	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:97629204_97629205delTC								NEDD1 (281743 upstream) : RMST (229594 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	98836903	98836905	+	IGR	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98836903_98836905delAAA								RMST (878110 upstream) : LOC100128191 (69848 downstream)																																			---	---	---	---
SLC25A3	5250	broad.mit.edu	37	12	98993271	98993272	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98993271_98993272delTT	uc001tfo.2	+						SLC25A3_uc001tfm.2_Intron|SLC25A3_uc001tfn.2_Intron|SLC25A3_uc001tfp.2_Intron|SLC25A3_uc001tfq.2_Intron|SLC25A3_uc001tfr.2_Intron|SLC25A3_uc001tfs.2_Intron|SLC25A3_uc009ztn.2_Intron|SLC25A3_uc001tft.2_Intron|SNORA53_uc001tfu.1_5'Flank	NM_005888	NP_005879			solute carrier family 25 member 3 isoform a						generation of precursor metabolites and energy	integral to plasma membrane|mitochondrial inner membrane	phosphate carrier activity|symporter activity				0		Lung NSC(355;4.08e-05)|Breast(359;0.00191)|Colorectal(145;0.00205)|Myeloproliferative disorder(1001;0.0255)		GBM - Glioblastoma multiforme(134;1.36e-23)|BRCA - Breast invasive adenocarcinoma(302;0.000115)														---	---	---	---
ANKS1B	56899	broad.mit.edu	37	12	99740092	99740093	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99740092_99740093insT	uc001tge.1	-						ANKS1B_uc001tgf.1_Intron|ANKS1B_uc009ztt.1_Intron	NM_152788	NP_690001			cajalin 2 isoform a							Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)														---	---	---	---
ANKS1B	56899	broad.mit.edu	37	12	100036787	100036787	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100036787delC	uc001tge.1	-						ANKS1B_uc001tgf.1_Intron|ANKS1B_uc009ztt.1_Intron	NM_152788	NP_690001			cajalin 2 isoform a							Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)														---	---	---	---
SCYL2	55681	broad.mit.edu	37	12	100723184	100723184	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100723184delA	uc001thn.2	+						SCYL2_uc001thm.1_Intron	NM_017988	NP_060458			SCY1-like 2 protein						endosome to lysosome transport|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of clathrin-mediated endocytosis|positive regulation of receptor internalization	clathrin-coated vesicle|endosome membrane|Golgi apparatus|perinuclear region of cytoplasm	ATP binding|protein kinase activity|receptor binding			lung(3)|ovary(2)|skin(1)	6																		---	---	---	---
SLC17A8	246213	broad.mit.edu	37	12	100789403	100789405	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100789403_100789405delTTT	uc010svi.1	+						SLC17A8_uc009ztx.2_Intron	NM_139319	NP_647480			solute carrier family 17 (sodium-dependent						neurotransmitter transport|sensory perception of sound|sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)	3																		---	---	---	---
GAS2L3	283431	broad.mit.edu	37	12	101012976	101012976	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101012976delT	uc001thu.2	+						GAS2L3_uc009zty.2_Intron|GAS2L3_uc001thv.2_Intron	NM_174942	NP_777602			growth arrest-specific 2 like 3						cell cycle arrest					skin(1)	1																		---	---	---	---
ANO4	121601	broad.mit.edu	37	12	101299187	101299187	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101299187delA	uc010svm.1	+						ANO4_uc010svl.1_Intron|ANO4_uc001thw.2_Intron|ANO4_uc001thx.2_Intron	NM_178826	NP_849148			anoctamin 4							chloride channel complex	chloride channel activity			ovary(4)|skin(2)	6															HNSCC(74;0.22)			---	---	---	---
UTP20	27340	broad.mit.edu	37	12	101700374	101700374	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101700374delT	uc001tia.1	+							NM_014503	NP_055318			down-regulated in metastasis						endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|negative regulation of cell proliferation	90S preribosome|cytoplasm|nucleolus|nucleoplasm|preribosome, small subunit precursor|small-subunit processome	protein binding			ovary(2)|breast(2)	4																		---	---	---	---
UTP20	27340	broad.mit.edu	37	12	101738703	101738703	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101738703delT	uc001tia.1	+							NM_014503	NP_055318			down-regulated in metastasis						endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|negative regulation of cell proliferation	90S preribosome|cytoplasm|nucleolus|nucleoplasm|preribosome, small subunit precursor|small-subunit processome	protein binding			ovary(2)|breast(2)	4																		---	---	---	---
MYBPC1	4604	broad.mit.edu	37	12	102040417	102040417	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102040417delA	uc001tii.2	+						MYBPC1_uc001tif.1_Intron|MYBPC1_uc001tig.2_Intron|MYBPC1_uc010svq.1_Intron|MYBPC1_uc001tih.2_Intron|MYBPC1_uc001tij.2_Intron|MYBPC1_uc010svr.1_Intron|MYBPC1_uc010svs.1_Intron|MYBPC1_uc010svt.1_Intron|MYBPC1_uc010svu.1_Intron|MYBPC1_uc001tik.2_Intron	NM_206820	NP_996556			myosin binding protein C, slow type isoform 3						cell adhesion|muscle filament sliding	cytosol|myofibril|myosin filament	actin binding|structural constituent of muscle|titin binding			ovary(2)|liver(1)|skin(1)	4																		---	---	---	---
MYBPC1	4604	broad.mit.edu	37	12	102054878	102054878	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102054878delT	uc001tii.2	+						MYBPC1_uc001tig.2_Intron|MYBPC1_uc010svq.1_Intron|MYBPC1_uc001tih.2_Intron|MYBPC1_uc001tij.2_Intron|MYBPC1_uc010svr.1_Intron|MYBPC1_uc010svs.1_Intron|MYBPC1_uc010svt.1_Intron|MYBPC1_uc010svu.1_Intron|MYBPC1_uc001tik.2_Intron	NM_206820	NP_996556			myosin binding protein C, slow type isoform 3						cell adhesion|muscle filament sliding	cytosol|myofibril|myosin filament	actin binding|structural constituent of muscle|titin binding			ovary(2)|liver(1)|skin(1)	4																		---	---	---	---
DRAM1	55332	broad.mit.edu	37	12	102301163	102301163	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102301163delT	uc001tix.2	+						DRAM1_uc010svv.1_Intron	NM_018370	NP_060840			DNA-damage regulated autophagy modulator 1						apoptosis|autophagy	integral to membrane|lysosomal membrane				ovary(1)	1																		---	---	---	---
CCDC53	51019	broad.mit.edu	37	12	102409069	102409070	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102409069_102409070delAA	uc010svw.1	-						CCDC53_uc010svx.1_Intron|CCDC53_uc010svy.1_Intron|CCDC53_uc010svz.1_Intron	NM_016053	NP_057137			coiled-coil domain containing 53							WASH complex	protein binding				0																		---	---	---	---
NUP37	79023	broad.mit.edu	37	12	102468961	102468961	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102468961delT	uc001tjc.2	-							NM_024057	NP_076962			nucleoporin 37kDa						carbohydrate metabolic process|cell division|chromosome segregation|glucose transport|mitotic prometaphase|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	protein binding			ovary(1)	1																		---	---	---	---
NUP37	79023	broad.mit.edu	37	12	102501216	102501216	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102501216delA	uc001tjc.2	-						NUP37_uc009zub.1_Intron	NM_024057	NP_076962			nucleoporin 37kDa						carbohydrate metabolic process|cell division|chromosome segregation|glucose transport|mitotic prometaphase|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	102742647	102742647	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102742647delT								PMCH (151033 upstream) : IGF1 (46998 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	103075568	103075569	+	IGR	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103075568_103075569delTC								IGF1 (201190 upstream) : PAH (156535 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	103202553	103202554	+	IGR	DEL	TC	-	-	rs7969194	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103202553_103202554delTC								IGF1 (328175 upstream) : PAH (29550 downstream)																																			---	---	---	---
C12orf42	374470	broad.mit.edu	37	12	103754782	103754782	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103754782delA	uc001tjt.2	-						C12orf42_uc001tjs.2_Intron|C12orf42_uc009zuf.1_Intron|C12orf42_uc001tju.2_Intron	NM_198521	NP_940923			hypothetical protein LOC374470											ovary(1)|central_nervous_system(1)	2																		---	---	---	---
STAB2	55576	broad.mit.edu	37	12	103995053	103995053	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103995053delA	uc001tjw.2	+							NM_017564	NP_060034			stabilin 2 precursor						angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			ovary(9)|skin(5)	14																		---	---	---	---
GLT8D2	83468	broad.mit.edu	37	12	104396751	104396752	+	Intron	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104396751_104396752delAG	uc001tkh.1	-						GLT8D2_uc001tki.1_Intron	NM_031302	NP_112592			glycosyltransferase 8 domain containing 2							integral to membrane	transferase activity, transferring glycosyl groups			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	104591680	104591680	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104591680delT								NFYB (59640 upstream) : TXNRD1 (14808 downstream)																																			---	---	---	---
TXNRD1	7296	broad.mit.edu	37	12	104725255	104725255	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104725255delT	uc010swk.1	+						TXNRD1_uc010swl.1_Intron|TXNRD1_uc010swm.1_Intron|TXNRD1_uc010swn.1_Intron|TXNRD1_uc010swo.1_Intron|TXNRD1_uc010swp.1_Intron|TXNRD1_uc010swq.1_Intron|TXNRD1_uc001tku.2_Intron|TXNRD1_uc009zun.2_Intron	NM_001093771	NP_001087240			thioredoxin reductase 1 isoform 3						cell redox homeostasis|cellular lipid metabolic process|electron transport chain|nucleobase, nucleoside and nucleotide interconversion|signal transduction|transport	cytosol|nucleolus	electron carrier activity|flavin adenine dinucleotide binding|NADP binding|protein disulfide oxidoreductase activity|thioredoxin-disulfide reductase activity				0																		---	---	---	---
CHST11	50515	broad.mit.edu	37	12	104984976	104984977	+	Intron	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104984976_104984977insG	uc001tkx.1	+						CHST11_uc001tky.2_Intron	NM_018413	NP_060883			carbohydrate sulfotransferase 11						chondroitin sulfate biosynthetic process	Golgi membrane|integral to membrane	chondroitin 4-sulfotransferase activity|N-acetylgalactosamine 4-O-sulfotransferase activity				0																		---	---	---	---
SLC41A2	84102	broad.mit.edu	37	12	105265886	105265888	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105265886_105265888delAAA	uc001tla.2	-							NM_032148	NP_115524			solute carrier family 41, member 2							integral to membrane|plasma membrane	magnesium ion transmembrane transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	105362050	105362051	+	IGR	DEL	TT	-	-	rs34118653		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105362050_105362051delTT								SLC41A2 (39578 upstream) : C12orf45 (18047 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	105803746	105803746	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105803746delT								C12orf75 (38451 upstream) : NUAK1 (653379 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	106092113	106092114	+	IGR	INS	-	G	G	rs141242046	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106092113_106092114insG								C12orf75 (326818 upstream) : NUAK1 (365011 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	106253772	106253772	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106253772delG								C12orf75 (488477 upstream) : NUAK1 (203353 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	106382151	106382152	+	IGR	INS	-	T	T	rs143267538	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106382151_106382152insT								C12orf75 (616856 upstream) : NUAK1 (74973 downstream)																																			---	---	---	---
NUAK1	9891	broad.mit.edu	37	12	106459322	106459322	+	3'UTR	DEL	A	-	-	rs3839981		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106459322delA	uc001tlj.1	-	7						NM_014840	NP_055655			AMPK-related protein kinase 5								ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	107158466	107158466	+	IGR	DEL	G	-	-	rs111762235	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107158466delG								RFX4 (1886 upstream) : RIC8B (9933 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	107323405	107323406	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107323405_107323406delTT								RIC8B (40313 upstream) : C12orf23 (26138 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	107328245	107328245	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107328245delA								RIC8B (45153 upstream) : C12orf23 (21299 downstream)																																			---	---	---	---
CRY1	1407	broad.mit.edu	37	12	107393932	107393932	+	Intron	DEL	T	-	-	rs80347092		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107393932delT	uc001tmi.3	-							NM_004075	NP_004066			cryptochrome 1 (photolyase-like)						DNA repair|protein-chromophore linkage|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	blue light photoreceptor activity|DNA photolyase activity|double-stranded DNA binding|nucleotide binding|protein binding			ovary(3)	3																		---	---	---	---
BTBD11	121551	broad.mit.edu	37	12	107827245	107827257	+	Intron	DEL	AGCTTGACAAGCA	-	-	rs11267161		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107827245_107827257delAGCTTGACAAGCA	uc001tmk.1	+						BTBD11_uc009zut.1_Intron|BTBD11_uc001tmj.2_Intron	NM_001018072	NP_001018082			BTB (POZ) domain containing 11 isoform a							integral to membrane	DNA binding			skin(2)|ovary(1)	3																		---	---	---	---
BTBD11	121551	broad.mit.edu	37	12	107849214	107849214	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107849214delT	uc001tmk.1	+						BTBD11_uc009zut.1_Intron|BTBD11_uc001tmj.2_Intron	NM_001018072	NP_001018082			BTB (POZ) domain containing 11 isoform a							integral to membrane	DNA binding			skin(2)|ovary(1)	3																		---	---	---	---
BTBD11	121551	broad.mit.edu	37	12	107950789	107950789	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107950789delA	uc001tmk.1	+						BTBD11_uc009zut.1_Intron|BTBD11_uc001tmj.2_Intron	NM_001018072	NP_001018082			BTB (POZ) domain containing 11 isoform a							integral to membrane	DNA binding			skin(2)|ovary(1)	3																		---	---	---	---
BTBD11	121551	broad.mit.edu	37	12	107957418	107957419	+	Intron	DEL	AA	-	-	rs113037302		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107957418_107957419delAA	uc001tmk.1	+						BTBD11_uc009zut.1_Intron|BTBD11_uc001tmj.2_Intron	NM_001018072	NP_001018082			BTB (POZ) domain containing 11 isoform a							integral to membrane	DNA binding			skin(2)|ovary(1)	3																		---	---	---	---
BTBD11	121551	broad.mit.edu	37	12	107959076	107959076	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:107959076delT	uc001tmk.1	+						BTBD11_uc009zut.1_Intron|BTBD11_uc001tmj.2_Intron	NM_001018072	NP_001018082			BTB (POZ) domain containing 11 isoform a							integral to membrane	DNA binding			skin(2)|ovary(1)	3																		---	---	---	---
BTBD11	121551	broad.mit.edu	37	12	108006718	108006718	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108006718delT	uc001tmk.1	+						BTBD11_uc009zut.1_Intron|BTBD11_uc001tmj.2_Intron|BTBD11_uc001tml.1_Intron	NM_001018072	NP_001018082			BTB (POZ) domain containing 11 isoform a							integral to membrane	DNA binding			skin(2)|ovary(1)	3																		---	---	---	---
PWP1	11137	broad.mit.edu	37	12	108092139	108092139	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108092139delA	uc001tmo.1	+						PWP1_uc009zuu.1_Intron	NM_007062	NP_008993			periodic tryptophan protein 1						transcription, DNA-dependent	nucleus					0																		---	---	---	---
PRDM4	11108	broad.mit.edu	37	12	108141580	108141581	+	Intron	DEL	TT	-	-	rs77969916		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108141580_108141581delTT	uc001tmp.2	-						PRDM4_uc001tmq.2_Intron	NM_012406	NP_036538			PR domain containing 4						cell proliferation|negative regulation of cell cycle|nerve growth factor receptor signaling pathway|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding			breast(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	108247730	108247730	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108247730delA								ASCL4 (77310 upstream) : WSCD2 (275781 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	108272709	108272709	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108272709delT								ASCL4 (102289 upstream) : WSCD2 (250802 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	108345900	108345900	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108345900delA								ASCL4 (175480 upstream) : WSCD2 (177611 downstream)																																			---	---	---	---
WSCD2	9671	broad.mit.edu	37	12	108612238	108612238	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108612238delG	uc001tms.2	+						WSCD2_uc001tmt.2_Intron	NM_014653	NP_055468			WSC domain containing 2							integral to membrane				ovary(1)|large_intestine(1)|breast(1)	3																		---	---	---	---
UNG	7374	broad.mit.edu	37	12	109532768	109532769	+	5'Flank	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109532768_109532769insC	uc001tnz.1	+						ALKBH2_uc001tnx.2_5'Flank|ALKBH2_uc001tny.2_5'Flank|ALKBH2_uc010sxj.1_5'Flank|ALKBH2_uc009zvd.2_5'Flank|ALKBH2_uc010sxk.1_5'Flank	NM_080911	NP_550433			uracil-DNA glycosylase isoform UNG2						base-excision repair|interspecies interaction between organisms	mitochondrion|nucleus	protein binding|uracil DNA N-glycosylase activity			lung(1)|central_nervous_system(1)	2													BER_DNA_glycosylases	Immune_Deficiency_with_Hyper-IgM				---	---	---	---
ACACB	32	broad.mit.edu	37	12	109692587	109692590	+	Intron	DEL	TTTT	-	-	rs111235224		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109692587_109692590delTTTT	uc001tob.2	+						ACACB_uc001toc.2_Intron|ACACB_uc010sxl.1_Intron|ACACB_uc001tod.2_Intron|ACACB_uc010sxm.1_Intron	NM_001093	NP_001084			acetyl-Coenzyme A carboxylase beta						acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation	cytosol|endomembrane system|Golgi apparatus|membrane	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8					Biotin(DB00121)													---	---	---	---
Unknown	0	broad.mit.edu	37	12	109751065	109751065	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109751065delA								FOXN4 (4040 upstream) : MYO1H (75459 downstream)																																			---	---	---	---
MYO1H	283446	broad.mit.edu	37	12	109839544	109839545	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109839544_109839545delTT	uc010sxn.1	+							NM_001101421	NP_001094891			myosin 1H							myosin complex	motor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	110286590	110286591	+	IGR	DEL	AA	-	-	rs112542802		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110286590_110286591delAA								TRPV4 (15378 upstream) : GLTP (2158 downstream)																																			---	---	---	---
GLTP	51228	broad.mit.edu	37	12	110289400	110289400	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110289400delT	uc001tpm.2	-	5						NM_016433	NP_057517			glycolipid transfer protein							cytoplasm	glycolipid binding|glycolipid transporter activity				0		Lung NSC(355;2.38e-06)|Breast(359;0.00354)|Myeloproliferative disorder(1001;0.0122)		BRCA - Breast invasive adenocarcinoma(302;0.0025)														---	---	---	---
TCHP	84260	broad.mit.edu	37	12	110366568	110366568	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110366568delC	uc001tpo.1	+							NM_032300				trichoplein						apoptosis|negative regulation of cell growth	apical cortex|centrosome|keratin filament|mitochondrion|plasma membrane	protein binding			skin(1)	1																		---	---	---	---
ANKRD13A	88455	broad.mit.edu	37	12	110465449	110465449	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110465449delT	uc001tpx.2	+						ANKRD13A_uc009zvl.1_Intron|ANKRD13A_uc010sxw.1_Intron|ANKRD13A_uc001tpy.2_Intron|ANKRD13A_uc001tpz.2_5'Flank|ANKRD13A_uc001tqa.2_5'Flank	NM_033121	NP_149112			ankyrin repeat domain 13												0																		---	---	---	---
C12orf76	400073	broad.mit.edu	37	12	110480480	110480480	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110480480delA	uc001tqd.1	-						C12orf76_uc001tqe.1_Intron|C12orf76_uc010sxx.1_Intron|C12orf76_uc001tqb.1_Intron|C12orf76_uc001tqc.1_Intron	NM_207435	NP_997318			hypothetical protein LOC400073											large_intestine(1)	1																		---	---	---	---
C12orf76	400073	broad.mit.edu	37	12	110480873	110480873	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110480873delA	uc001tqd.1	-						C12orf76_uc001tqe.1_Intron|C12orf76_uc010sxx.1_Intron|C12orf76_uc001tqb.1_Intron|C12orf76_uc001tqc.1_Intron	NM_207435	NP_997318			hypothetical protein LOC400073											large_intestine(1)	1																		---	---	---	---
IFT81	28981	broad.mit.edu	37	12	110584651	110584651	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110584651delA	uc001tqi.2	+						IFT81_uc001tqh.2_Intron|IFT81_uc001tqj.2_Intron|IFT81_uc001tqg.2_Intron	NM_001143779	NP_001137251			intraflagellar transport 81-like isoform 1						cell differentiation|multicellular organismal development|spermatogenesis	intraflagellar transport particle B|microtubule-based flagellum				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	110675582	110675582	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110675582delA								IFT81 (18983 upstream) : ATP2A2 (43450 downstream)																																			---	---	---	---
RAD9B	144715	broad.mit.edu	37	12	110967395	110967397	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110967395_110967397delAAA	uc001trf.3	+						RAD9B_uc001trg.3_Intron|RAD9B_uc010sya.1_Intron|RAD9B_uc001tre.3_Intron|RAD9B_uc001trd.3_Intron	NM_152442	NP_689655			RAD9 homolog B						cell cycle checkpoint|DNA repair|DNA replication	nucleoplasm	protein binding			pancreas(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	111048521	111048521	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111048521delT								PPTC7 (27457 upstream) : TCTN1 (3359 downstream)																																			---	---	---	---
HVCN1	84329	broad.mit.edu	37	12	111093511	111093514	+	Intron	DEL	TTTT	-	-	rs150136698		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111093511_111093514delTTTT	uc001trs.1	-						HVCN1_uc001trq.1_Intron|HVCN1_uc001trt.1_Intron|HVCN1_uc010syd.1_Intron	NM_032369	NP_115745			hydrogen voltage-gated channel 1						response to pH|response to zinc ion	integral to membrane	voltage-gated proton channel activity			skin(1)	1																		---	---	---	---
CCDC63	160762	broad.mit.edu	37	12	111329155	111329156	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111329155_111329156insA	uc001trv.1	+						CCDC63_uc010sye.1_Intron|CCDC63_uc001trw.1_Intron	NM_152591	NP_689804			coiled-coil domain containing 63											skin(6)|ovary(1)|pancreas(1)	8																		---	---	---	---
CUX2	23316	broad.mit.edu	37	12	111531299	111531300	+	Intron	DEL	AA	-	-	rs112495995		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111531299_111531300delAA	uc001tsa.1	+							NM_015267	NP_056082			cut-like 2							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|skin(2)|breast(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	111839403	111839404	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111839403_111839404delTT								FAM109A (32478 upstream) : SH2B3 (4348 downstream)																																			---	---	---	---
SH2B3	10019	broad.mit.edu	37	12	111887736	111887736	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111887736delT	uc001tse.2	+	8					SH2B3_uc010syf.1_3'UTR|SH2B3_uc001tsf.2_3'UTR|SH2B3_uc010syg.1_3'UTR	NM_005475	NP_005466			SH2B adaptor protein 3						blood coagulation	cytosol	signal transducer activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	112052789	112052789	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112052789delT								ATXN2 (15309 upstream) : BRAP (27162 downstream)																																			---	---	---	---
BRAP	8315	broad.mit.edu	37	12	112083193	112083193	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112083193delT	uc001tsn.3	-						BRAP_uc010syh.1_Intron|BRAP_uc009zvv.2_Intron	NM_006768	NP_006759			BRCA1 associated protein						MAPKKK cascade|negative regulation of signal transduction|Ras protein signal transduction	cytoplasm|ubiquitin ligase complex	identical protein binding|nuclear localization sequence binding|nucleotide binding|ubiquitin-protein ligase activity|zinc ion binding			lung(1)	1																		---	---	---	---
ALDH2	217	broad.mit.edu	37	12	112220688	112220688	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112220688delA	uc001tst.2	+						ALDH2_uc010syi.1_Intron|ALDH2_uc009zvy.2_Intron	NM_000690	NP_000681			mitochondrial aldehyde dehydrogenase 2						carbohydrate metabolic process|ethanol oxidation|neurotransmitter biosynthetic process|xenobiotic metabolic process	mitochondrial matrix	aldehyde dehydrogenase (NAD) activity|aldehyde dehydrogenase|electron carrier activity			skin(2)|ovary(1)|central_nervous_system(1)	4					Disulfiram(DB00822)|Guanidine(DB00536)|NADH(DB00157)|Nitroglycerin(DB00727)			T	HMGA2	leiomyoma								---	---	---	---
NAA25	80018	broad.mit.edu	37	12	112492461	112492462	+	Intron	INS	-	C	C	rs143230855	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112492461_112492462insC	uc001ttm.2	-						NAA25_uc001ttn.3_Intron|NAA25_uc009zvz.1_Intron|NAA25_uc009zwa.1_Intron	NM_024953	NP_079229			mitochondrial distribution and morphology 20							cytoplasm	protein binding			ovary(1)|breast(1)|pancreas(1)	3																		---	---	---	---
NAA25	80018	broad.mit.edu	37	12	112545186	112545186	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112545186delT	uc001ttm.2	-						NAA25_uc001ttn.3_Intron|NAA25_uc009zvz.1_Intron|NAA25_uc009zwa.1_Intron	NM_024953	NP_079229			mitochondrial distribution and morphology 20							cytoplasm	protein binding			ovary(1)|breast(1)|pancreas(1)	3																		---	---	---	---
PTPN11	5781	broad.mit.edu	37	12	112915337	112915337	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112915337delT	uc001ttx.2	+						PTPN11_uc001ttw.1_Intron	NM_002834	NP_002825			protein tyrosine phosphatase, non-receptor type						axon guidance|cell junction assembly|ephrin receptor signaling pathway|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|interferon-gamma-mediated signaling pathway|leukocyte migration|platelet activation|regulation of cell adhesion mediated by integrin|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|T cell costimulation|type I interferon-mediated signaling pathway	cytosol	non-membrane spanning protein tyrosine phosphatase activity|protein binding			haematopoietic_and_lymphoid_tissue(375)|lung(6)|autonomic_ganglia(2)|soft_tissue(2)|central_nervous_system(2)|large_intestine(1)|skin(1)|ovary(1)|NS(1)|kidney(1)	392								Mis		JMML|AML|MDS		Noonan Syndrome		Noonan_syndrome				---	---	---	---
PTPN11	5781	broad.mit.edu	37	12	112919306	112919306	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112919306delT	uc001ttx.2	+						PTPN11_uc001ttw.1_Intron	NM_002834	NP_002825			protein tyrosine phosphatase, non-receptor type						axon guidance|cell junction assembly|ephrin receptor signaling pathway|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|interferon-gamma-mediated signaling pathway|leukocyte migration|platelet activation|regulation of cell adhesion mediated by integrin|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|T cell costimulation|type I interferon-mediated signaling pathway	cytosol	non-membrane spanning protein tyrosine phosphatase activity|protein binding			haematopoietic_and_lymphoid_tissue(375)|lung(6)|autonomic_ganglia(2)|soft_tissue(2)|central_nervous_system(2)|large_intestine(1)|skin(1)|ovary(1)|NS(1)|kidney(1)	392								Mis		JMML|AML|MDS		Noonan Syndrome		Noonan_syndrome				---	---	---	---
DTX1	1840	broad.mit.edu	37	12	113513767	113513768	+	Intron	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113513767_113513768insG	uc001tuk.1	+							NM_004416	NP_004407			deltex homolog 1						negative regulation of neuron differentiation|Notch signaling pathway|regulation of Notch signaling pathway|transcription from RNA polymerase II promoter	cytoplasm|nucleus	Notch binding|SH3 domain binding|transcription coactivator activity|ubiquitin protein ligase binding|zinc ion binding			lung(2)|ovary(1)|central_nervous_system(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	113789876	113789876	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113789876delG								SLC24A6 (16951 upstream) : PLBD2 (6495 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	114154848	114154848	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114154848delC								LHX5 (244971 upstream) : RBM19 (99695 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	114211756	114211756	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114211756delA	uc001tvk.1	-						uc001tvl.3_5'Flank					Homo sapiens cDNA FLJ39613 fis, clone SKNSH2009357.																														---	---	---	---
Unknown	0	broad.mit.edu	37	12	114222070	114222071	+	IGR	DEL	CA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114222070_114222071delCA								LHX5 (312193 upstream) : RBM19 (32472 downstream)																																			---	---	---	---
RBM19	9904	broad.mit.edu	37	12	114296154	114296154	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114296154delA	uc009zwi.2	-						RBM19_uc001tvn.3_Intron|RBM19_uc001tvm.2_Intron	NM_001146699	NP_001140171			RNA binding motif protein 19						multicellular organismal development|positive regulation of embryonic development	chromosome|cytoplasm|nucleolus|nucleoplasm	nucleotide binding|RNA binding			skin(3)|ovary(1)|liver(1)|central_nervous_system(1)	6	Medulloblastoma(191;0.163)|all_neural(191;0.178)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	114639829	114639830	+	IGR	DEL	CT	-	-	rs34780461		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114639829_114639830delCT								RBM19 (235653 upstream) : TBX5 (151906 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	114772772	114772774	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114772772_114772774delTTT								RBM19 (368596 upstream) : TBX5 (18962 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	115179574	115179574	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115179574delA	uc001tvv.1	+											full-length cDNA clone CS0DI031YB14 of Placenta Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	12	116131615	116131616	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116131615_116131616delTG								None (None upstream) : MED13L (264767 downstream)																																			---	---	---	---
MAP1LC3B2	643246	broad.mit.edu	37	12	117006046	117006046	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117006046delA	uc009zwk.1	+							NM_001085481	NP_001078950			microtubule-associated protein 1 light chain 3						autophagy	autophagic vacuole membrane|cytoplasmic vesicle|endomembrane system|microtubule					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	117109695	117109696	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117109695_117109696insT								MAP1LC3B2 (95270 upstream) : C12orf49 (43900 downstream)																																			---	---	---	---
FBXW8	26259	broad.mit.edu	37	12	117445067	117445067	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117445067delA	uc001twg.1	+						FBXW8_uc001twf.1_Intron|FBXW8_uc009zwp.1_Intron	NM_153348	NP_699179			F-box and WD repeat domain containing 8 isoform								protein binding			ovary(2)|pancreas(1)	3	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0353)														---	---	---	---
NOS1	4842	broad.mit.edu	37	12	117696833	117696833	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117696833delC	uc001twm.1	-	15	3156	c.2470delG	c.(2470-2472)GAGfs	p.E824fs	NOS1_uc001twn.1_5'Flank	NM_000620	NP_000611	P29475	NOS1_HUMAN	nitric oxide synthase 1, neuronal	824	Flavodoxin-like.				multicellular organismal response to stress|myoblast fusion|negative regulation of calcium ion transport into cytosol|neurotransmitter biosynthetic process|nitric oxide biosynthetic process|platelet activation|positive regulation of vasodilation|regulation of cardiac muscle contraction|response to heat|response to hypoxia	cytoskeleton|cytosol|dendritic spine|perinuclear region of cytoplasm|photoreceptor inner segment|sarcolemma|sarcoplasmic reticulum	arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding			ovary(3)|skin(3)|pancreas(1)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)	L-Citrulline(DB00155)													---	---	---	---
KSR2	283455	broad.mit.edu	37	12	117968845	117968845	+	Intron	DEL	A	-	-	rs79395177		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:117968845delA	uc001two.2	-							NM_173598	NP_775869			kinase suppressor of ras 2						intracellular signal transduction	cytoplasm|membrane	ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(10)|central_nervous_system(2)|stomach(1)|large_intestine(1)|breast(1)	15	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
KSR2	283455	broad.mit.edu	37	12	118061038	118061038	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118061038delT	uc001two.2	-							NM_173598	NP_775869			kinase suppressor of ras 2						intracellular signal transduction	cytoplasm|membrane	ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(10)|central_nervous_system(2)|stomach(1)|large_intestine(1)|breast(1)	15	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
RFC5	5985	broad.mit.edu	37	12	118458889	118458889	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118458889delA	uc001twq.2	+						RFC5_uc010syx.1_Intron|RFC5_uc010syy.1_Intron|RFC5_uc010syz.1_Intron|RFC5_uc009zwr.2_Intron	NM_007370	NP_031396			replication factor C 5 isoform 1						cell cycle checkpoint|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|enzyme binding				0	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
WSB2	55884	broad.mit.edu	37	12	118473286	118473286	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118473286delA	uc001twr.2	-						WSB2_uc010sza.1_Intron|WSB2_uc010szb.1_Intron|WSB2_uc009zws.1_Intron	NM_018639	NP_061109			WD SOCS-box protein 2						intracellular signal transduction					ovary(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)															OREG0022175	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	12	119395729	119395729	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119395729delC								SUDS3 (539890 upstream) : SRRM4 (23667 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	119637596	119637596	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119637596delT								HSPB8 (5046 upstream) : LOC144742 (84034 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	119671965	119671966	+	IGR	INS	-	CT	CT			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119671965_119671966insCT								HSPB8 (39415 upstream) : LOC144742 (49664 downstream)																																			---	---	---	---
CIT	11113	broad.mit.edu	37	12	120181036	120181038	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120181036_120181038delAAA	uc001txi.1	-						CIT_uc001txh.1_Intron|CIT_uc001txj.1_Intron	NM_007174	NP_009105			citron						intracellular signal transduction		ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity			ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1)	10	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	120338815	120338815	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120338815delT								CIT (23723 upstream) : CCDC64 (88833 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	120396653	120396653	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120396653delA								CIT (81561 upstream) : CCDC64 (30995 downstream)																																			---	---	---	---
CCDC64	92558	broad.mit.edu	37	12	120428948	120428948	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120428948delA	uc001txl.1	+						CCDC64_uc001txk.2_Intron|CCDC64_uc009zwv.1_Intron	NM_207311	NP_997194			coiled-coil domain containing 64						Golgi to secretory granule transport|neuron projection development	centrosome	dynactin binding|Rab GTPase binding			ovary(2)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
CCDC64	92558	broad.mit.edu	37	12	120521806	120521806	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120521806delT	uc001txl.1	+						CCDC64_uc009zwv.1_Intron|CCDC64_uc010sze.1_Intron|CCDC64_uc010szf.1_Intron	NM_207311	NP_997194			coiled-coil domain containing 64						Golgi to secretory granule transport|neuron projection development	centrosome	dynactin binding|Rab GTPase binding			ovary(2)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
GCN1L1	10985	broad.mit.edu	37	12	120593703	120593703	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120593703delT	uc001txo.2	-							NM_006836	NP_006827			GCN1 general control of amino-acid synthesis						regulation of translation	ribosome	protein binding|translation factor activity, nucleic acid binding			ovary(4)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
PXN	5829	broad.mit.edu	37	12	120671119	120671119	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120671119delT	uc001txt.2	-						PXN_uc001txx.2_Intron|PXN_uc001txy.2_Intron|PXN_uc001txz.2_Intron	NM_001080855	NP_001074324			paxillin isoform 1						cell junction assembly|cell-matrix adhesion|cellular response to reactive oxygen species|epidermal growth factor receptor signaling pathway|growth hormone receptor signaling pathway|muscle contraction|signal complex assembly	cytoplasm|focal adhesion|lamellipodium|microtubule associated complex	beta-catenin binding|vinculin binding|zinc ion binding			ovary(1)|breast(1)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
MSI1	4440	broad.mit.edu	37	12	120801286	120801286	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120801286delC	uc001tye.1	-							NM_002442	NP_002433			musashi 1						nervous system development	cytoplasm|nucleus	nucleotide binding			central_nervous_system(2)|breast(1)	3	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	121071237	121071237	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121071237delA								POP5 (52036 upstream) : CABP1 (7185 downstream)																																			---	---	---	---
UNC119B	84747	broad.mit.edu	37	12	121156294	121156294	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121156294delT	uc001tyz.2	+							NM_001080533	NP_001074002			unc-119 homolog B											haematopoietic_and_lymphoid_tissue(1)	1	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)																	---	---	---	---
SPPL3	121665	broad.mit.edu	37	12	121204347	121204347	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121204347delA	uc001tzd.2	-						SPPL3_uc009zwz.2_Intron|SPPL3_uc001tzc.2_Intron	NM_139015	NP_620584			signal peptide peptidase 3							integral to membrane	aspartic-type endopeptidase activity				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)																	---	---	---	---
Unknown	0	broad.mit.edu	37	12	121401947	121401947	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121401947delT								SPPL3 (59796 upstream) : C12orf27 (5694 downstream)																																			---	---	---	---
HNF1A	6927	broad.mit.edu	37	12	121416195	121416195	+	5'Flank	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121416195delC	uc001tzg.2	+						HNF1A_uc001tze.1_5'Flank|HNF1A_uc001tzf.2_5'Flank|HNF1A_uc010szn.1_5'Flank	NM_000545	NP_000536			hepatic nuclear factor-1-alpha						glucose homeostasis|glucose import|insulin secretion|positive regulation of transcription initiation from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|renal glucose absorption	cytoplasm|nucleus|protein complex	DNA binding|protein dimerization activity|protein heterodimerization activity|protein homodimerization activity|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			liver(92)|large_intestine(15)|endometrium(6)|breast(2)|lung(1)	116	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)													Hepatic_Adenoma_Familial_Clustering_of				---	---	---	---
Unknown	0	broad.mit.edu	37	12	121799191	121799191	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121799191delA								ANAPC5 (7179 upstream) : RNF34 (38711 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	122122172	122122172	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122122172delA								MORN3 (11635 upstream) : TMEM120B (28486 downstream)																																			---	---	---	---
TMEM120B	144404	broad.mit.edu	37	12	122191250	122191250	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122191250delT	uc001ubc.3	+						TMEM120B_uc009zxh.2_Intron	NM_001080825	NP_001074294			transmembrane protein 120B							integral to membrane					0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;5.75e-05)|Epithelial(86;0.000128)|BRCA - Breast invasive adenocarcinoma(302;0.238)														---	---	---	---
PSMD9	5715	broad.mit.edu	37	12	122343132	122343133	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122343132_122343133delTT	uc001ubl.2	+						PSMD9_uc009zxj.2_Intron|PSMD9_uc001ubm.2_Intron	NM_002813	NP_002804			proteasome 26S non-ATPase subunit 9						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of insulin secretion|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of insulin secretion|positive regulation of transcription, DNA-dependent|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|proteasome regulatory particle assembly|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	nucleus|proteasome regulatory particle	bHLH transcription factor binding|transcription coactivator activity				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000117)|Epithelial(86;0.000415)|BRCA - Breast invasive adenocarcinoma(302;0.231)														---	---	---	---
CLIP1	6249	broad.mit.edu	37	12	122867057	122867057	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122867057delA	uc001ucg.1	-						CLIP1_uc001uch.1_Intron|CLIP1_uc001uci.1_Intron|CLIP1_uc010tae.1_Intron	NM_002956	NP_002947			restin isoform a						mitotic prometaphase|positive regulation of microtubule polymerization	centrosome|cytosol|endosome|intermediate filament|kinetochore	nucleic acid binding|protein homodimerization activity|zinc ion binding			ovary(2)|breast(1)	3	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)														---	---	---	---
ZCCHC8	55596	broad.mit.edu	37	12	122962860	122962860	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122962860delA	uc001ucn.2	-						ZCCHC8_uc001ucl.2_5'UTR|ZCCHC8_uc001ucm.2_Intron|ZCCHC8_uc009zxp.2_Intron|ZCCHC8_uc009zxq.2_Intron	NM_017612	NP_060082			zinc finger, CCHC domain containing 8							catalytic step 2 spliceosome	nucleic acid binding|protein binding|zinc ion binding				0	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.25e-05)|Epithelial(86;0.000113)|BRCA - Breast invasive adenocarcinoma(302;0.202)														---	---	---	---
RSRC2	65117	broad.mit.edu	37	12	122991552	122991552	+	Intron	DEL	A	-	-	rs144251671		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122991552delA	uc001ucr.2	-						RSRC2_uc001uco.2_Intron|RSRC2_uc001ucp.2_Intron|RSRC2_uc001ucq.2_Intron|RSRC2_uc001ucs.2_Intron|RSRC2_uc001uct.2_Intron|RSRC2_uc001ucu.2_Intron	NM_023012	NP_075388			arginine/serine-rich coiled-coil 2 isoform a											ovary(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.14e-05)|Epithelial(86;0.000183)|BRCA - Breast invasive adenocarcinoma(302;0.201)														---	---	---	---
RSRC2	65117	broad.mit.edu	37	12	123011179	123011179	+	Intron	DEL	A	-	-	rs114012333	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123011179delA	uc001ucr.2	-						KNTC1_uc001ucv.2_5'Flank|KNTC1_uc010taf.1_5'Flank|RSRC2_uc001ucp.2_Intron|RSRC2_uc001ucq.2_Intron|RSRC2_uc001ucs.2_Intron|RSRC2_uc001uct.2_Intron|RSRC2_uc001ucu.2_Intron	NM_023012	NP_075388			arginine/serine-rich coiled-coil 2 isoform a											ovary(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.14e-05)|Epithelial(86;0.000183)|BRCA - Breast invasive adenocarcinoma(302;0.201)														---	---	---	---
KNTC1	9735	broad.mit.edu	37	12	123025897	123025898	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123025897_123025898delTT	uc001ucv.2	+						KNTC1_uc010taf.1_Intron	NM_014708	NP_055523			Rough Deal homolog, centromere/kinetochore						cell division|mitotic cell cycle checkpoint|mitotic prometaphase|protein complex assembly|regulation of exit from mitosis	condensed chromosome kinetochore|cytosol|kinetochore microtubule|nucleus|spindle pole	protein binding			ovary(5)|kidney(3)|lung(1)|central_nervous_system(1)	10	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)														---	---	---	---
KNTC1	9735	broad.mit.edu	37	12	123056785	123056785	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123056785delA	uc001ucv.2	+						KNTC1_uc010taf.1_Intron	NM_014708	NP_055523			Rough Deal homolog, centromere/kinetochore						cell division|mitotic cell cycle checkpoint|mitotic prometaphase|protein complex assembly|regulation of exit from mitosis	condensed chromosome kinetochore|cytosol|kinetochore microtubule|nucleus|spindle pole	protein binding			ovary(5)|kidney(3)|lung(1)|central_nervous_system(1)	10	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)														---	---	---	---
KNTC1	9735	broad.mit.edu	37	12	123073397	123073397	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123073397delT	uc001ucv.2	+						KNTC1_uc010taf.1_Intron	NM_014708	NP_055523			Rough Deal homolog, centromere/kinetochore						cell division|mitotic cell cycle checkpoint|mitotic prometaphase|protein complex assembly|regulation of exit from mitosis	condensed chromosome kinetochore|cytosol|kinetochore microtubule|nucleus|spindle pole	protein binding			ovary(5)|kidney(3)|lung(1)|central_nervous_system(1)	10	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)														---	---	---	---
GPR81	27198	broad.mit.edu	37	12	123159042	123159043	+	Intron	DEL	TT	-	-	rs79489238		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123159042_123159043delTT	uc001ucw.1	-							NM_032554				G protein-coupled receptor 81						response to estradiol stimulus	integral to membrane|plasma membrane	G-protein coupled receptor activity				0	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.14e-05)|Epithelial(86;3.25e-05)|BRCA - Breast invasive adenocarcinoma(302;0.197)														---	---	---	---
GPR81	27198	broad.mit.edu	37	12	123164208	123164209	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123164208_123164209insT	uc001ucw.1	-							NM_032554				G protein-coupled receptor 81						response to estradiol stimulus	integral to membrane|plasma membrane	G-protein coupled receptor activity				0	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.14e-05)|Epithelial(86;3.25e-05)|BRCA - Breast invasive adenocarcinoma(302;0.197)														---	---	---	---
PITPNM2	57605	broad.mit.edu	37	12	123541596	123541596	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123541596delA	uc001uej.1	-						PITPNM2_uc001uek.1_Intron|PITPNM2_uc009zxu.1_Intron	NM_020845	NP_065896			phosphatidylinositol transfer protein,						metabolic process|transport	endomembrane system|integral to membrane|intracellular membrane-bounded organelle	calcium ion binding|lipid binding			ovary(1)|central_nervous_system(1)|skin(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.55e-05)|Epithelial(86;8.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.123)														---	---	---	---
CDK2AP1	8099	broad.mit.edu	37	12	123746060	123746060	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123746060delA	uc001ueq.2	-	4					CDK2AP1_uc001uep.2_RNA	NM_004642	NP_004633			CDK2-associated protein  1						DNA-dependent DNA replication|protein phosphorylation|S phase of mitotic cell cycle	cytoplasm|nucleus	DNA binding|protein binding				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000554)|Epithelial(86;0.00178)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	123855569	123855570	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123855569_123855570delAA								SBNO1 (6181 upstream) : SETD8 (13134 downstream)																																			---	---	---	---
RILPL2	196383	broad.mit.edu	37	12	123900176	123900176	+	3'UTR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123900176delC	uc001uey.1	-	4						NM_145058	NP_659495			Rab interacting lysosomal protein-like 2							cytosol|plasma membrane	identical protein binding				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000546)|Epithelial(86;0.00179)|all cancers(50;0.0168)														---	---	---	---
RILPL2	196383	broad.mit.edu	37	12	123902885	123902885	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123902885delT	uc001uey.1	-							NM_145058	NP_659495			Rab interacting lysosomal protein-like 2							cytosol|plasma membrane	identical protein binding				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000546)|Epithelial(86;0.00179)|all cancers(50;0.0168)														---	---	---	---
RILPL1	353116	broad.mit.edu	37	12	123970739	123970739	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123970739delT	uc001ufe.2	-						RILPL1_uc001ufd.2_Intron|RILPL1_uc010tas.1_Intron	NM_178314	NP_847884			Rab interacting lysosomal protein-like 1						neuroprotection	cytosol					0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.00067)|all cancers(50;0.00836)|BRCA - Breast invasive adenocarcinoma(302;0.197)														---	---	---	---
RILPL1	353116	broad.mit.edu	37	12	124005798	124005798	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124005798delT	uc001ufe.2	-						RILPL1_uc001ufd.2_5'Flank|RILPL1_uc010tas.1_Intron	NM_178314	NP_847884			Rab interacting lysosomal protein-like 1						neuroprotection	cytosol					0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.00067)|all cancers(50;0.00836)|BRCA - Breast invasive adenocarcinoma(302;0.197)														---	---	---	---
DDX55	57696	broad.mit.edu	37	12	124085169	124085169	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124085169delT	uc001ufi.2	+						DDX55_uc001ufh.2_5'Flank	NM_020936	NP_065987			DEAD (Asp-Glu-Ala-Asp) box polypeptide 55								ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000142)|Epithelial(86;0.000637)|all cancers(50;0.00772)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	124148890	124148890	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124148890delT								GTF2H3 (3556 upstream) : TCTN2 (6770 downstream)																																			---	---	---	---
TCTN2	79867	broad.mit.edu	37	12	124162346	124162346	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124162346delT	uc001ufp.2	+						TCTN2_uc009zya.2_Intron	NM_024809	NP_079085			tectonic family member 2 isoform 1						cilium assembly|smoothened signaling pathway	integral to membrane				ovary(1)	1	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000163)|Epithelial(86;0.000502)|all cancers(50;0.00451)														---	---	---	---
ATP6V0A2	23545	broad.mit.edu	37	12	124224024	124224024	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124224024delT	uc001ufr.2	+							NM_012463	NP_036595			ATPase, H+ transporting, lysosomal V0 subunit						ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|immune response|insulin receptor signaling pathway|transferrin transport	endosome membrane|integral to membrane|plasma membrane|proton-transporting two-sector ATPase complex, proton-transporting domain	hydrogen ion transmembrane transporter activity|protein binding			ovary(2)	2	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.000625)|all cancers(50;0.00775)														---	---	---	---
DNAH10	196385	broad.mit.edu	37	12	124252690	124252690	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124252690delT	uc001uft.3	+							NM_207437	NP_997320			dynein, axonemal, heavy chain 10						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(3)|skin(2)|central_nervous_system(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)														---	---	---	---
DNAH10	196385	broad.mit.edu	37	12	124265628	124265628	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124265628delT	uc001uft.3	+	6	465	c.440delT	c.(439-441)GTTfs	p.V147fs		NM_207437	NP_997320	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	147	Stem (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(3)|skin(2)|central_nervous_system(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)														---	---	---	---
DNAH10	196385	broad.mit.edu	37	12	124337720	124337720	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124337720delT	uc001uft.3	+							NM_207437	NP_997320			dynein, axonemal, heavy chain 10						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(3)|skin(2)|central_nervous_system(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)														---	---	---	---
DNAH10	196385	broad.mit.edu	37	12	124401600	124401600	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124401600delT	uc001uft.3	+							NM_207437	NP_997320			dynein, axonemal, heavy chain 10						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(3)|skin(2)|central_nervous_system(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)														---	---	---	---
NCOR2	9612	broad.mit.edu	37	12	124864254	124864254	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124864254delC	uc010tba.1	-						NCOR2_uc010tay.1_Intron|NCOR2_uc010taz.1_Intron|NCOR2_uc010tbb.1_Intron|NCOR2_uc010tbc.1_Intron|NCOR2_uc001ugj.1_Intron	NM_001077261	NP_001070729			nuclear receptor co-repressor 2 isoform 2						cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity			skin(3)|ovary(1)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	125116127	125116127	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125116127delA								NCOR2 (64117 upstream) : SCARB1 (146048 downstream)																																			---	---	---	---
BRI3BP	140707	broad.mit.edu	37	12	125486275	125486276	+	Intron	DEL	TT	-	-	rs72198379		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125486275_125486276delTT	uc001uha.1	+							NM_080626	NP_542193			BRI3-binding protein							integral to membrane|mitochondrial outer membrane				ovary(1)	1	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.35e-05)|Epithelial(86;0.000426)|all cancers(50;0.00576)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	125658283	125658283	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125658283delA								AACS (30411 upstream) : TMEM132B (152879 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	125738845	125738845	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125738845delG								AACS (110973 upstream) : TMEM132B (72317 downstream)																																			---	---	---	---
TMEM132B	114795	broad.mit.edu	37	12	126003279	126003279	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126003279delC	uc001uhe.1	+							NM_052907	NP_443139			transmembrane protein 132B							integral to membrane				skin(11)|ovary(5)|large_intestine(1)|pancreas(1)|breast(1)	19	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	126246919	126246920	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126246919_126246920delTT								TMEM132B (103330 upstream) : LOC100128554 (680107 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	126498321	126498321	+	IGR	DEL	A	-	-	rs7310050	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126498321delA								TMEM132B (354732 upstream) : LOC100128554 (428706 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	126837168	126837168	+	IGR	DEL	T	-	-	rs11334588		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:126837168delT								TMEM132B (693579 upstream) : LOC100128554 (89859 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	127307219	127307219	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:127307219delG								LOC100128554 (349889 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	128626510	128626510	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128626510delT								None (None upstream) : TMEM132C (272781 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	128657931	128657931	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128657931delT								None (None upstream) : TMEM132C (241360 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	128826555	128826556	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:128826555_128826556delTT								None (None upstream) : TMEM132C (72735 downstream)																																			---	---	---	---
GLT1D1	144423	broad.mit.edu	37	12	129339945	129339945	+	Intron	DEL	A	-	-	rs113168444		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129339945delA	uc001uhx.1	+						GLT1D1_uc001uhy.1_Intron	NM_144669	NP_653270			glycosyltransferase 1 domain containing 1						biosynthetic process	extracellular region	transferase activity, transferring glycosyl groups				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.97e-06)|Epithelial(86;3.97e-05)|all cancers(50;0.00019)														---	---	---	---
GLT1D1	144423	broad.mit.edu	37	12	129350387	129350388	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129350387_129350388insA	uc010tbh.1	+						GLT1D1_uc001uhx.1_Intron|GLT1D1_uc001uhy.1_Intron	NM_144669	NP_653270			glycosyltransferase 1 domain containing 1						biosynthetic process	extracellular region	transferase activity, transferring glycosyl groups				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.97e-06)|Epithelial(86;3.97e-05)|all cancers(50;0.00019)														---	---	---	---
GLT1D1	144423	broad.mit.edu	37	12	129380004	129380006	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129380004_129380006delTTT	uc010tbh.1	+						GLT1D1_uc001uhx.1_Intron|GLT1D1_uc001uhy.1_Intron	NM_144669	NP_653270			glycosyltransferase 1 domain containing 1						biosynthetic process	extracellular region	transferase activity, transferring glycosyl groups				0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.97e-06)|Epithelial(86;3.97e-05)|all cancers(50;0.00019)														---	---	---	---
TMEM132D	121256	broad.mit.edu	37	12	129760802	129760802	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129760802delA	uc009zyl.1	-							NM_133448	NP_597705			transmembrane protein 132D precursor							integral to membrane				ovary(10)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)														---	---	---	---
TMEM132D	121256	broad.mit.edu	37	12	130379292	130379292	+	Intron	DEL	T	-	-	rs71749162		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130379292delT	uc009zyl.1	-							NM_133448	NP_597705			transmembrane protein 132D precursor							integral to membrane				ovary(10)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	130589707	130589707	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130589707delT								LOC100190940 (62820 upstream) : FZD10 (57325 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	130733961	130733961	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130733961delA								FZD10 (83677 upstream) : PIWIL1 (88653 downstream)																																			---	---	---	---
RIMBP2	23504	broad.mit.edu	37	12	131050721	131050722	+	Intron	DEL	CA	-	-	rs34362003		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131050721_131050722delCA	uc001uim.2	-											RecName: Full=RIMS-binding protein 2;          Short=RIM-BP2;							cell junction|synapse				upper_aerodigestive_tract(3)|ovary(3)|large_intestine(2)|central_nervous_system(2)|pancreas(1)	11	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)														---	---	---	---
RIMBP2	23504	broad.mit.edu	37	12	131115501	131115502	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131115501_131115502delAA	uc001uim.2	-											RecName: Full=RIMS-binding protein 2;          Short=RIM-BP2;							cell junction|synapse				upper_aerodigestive_tract(3)|ovary(3)|large_intestine(2)|central_nervous_system(2)|pancreas(1)	11	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)														---	---	---	---
RIMBP2	23504	broad.mit.edu	37	12	131161168	131161168	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131161168delA	uc001uim.2	-											RecName: Full=RIMS-binding protein 2;          Short=RIM-BP2;							cell junction|synapse				upper_aerodigestive_tract(3)|ovary(3)|large_intestine(2)|central_nervous_system(2)|pancreas(1)	11	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	12	131257447	131257447	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131257447delG								RIMBP2 (56621 upstream) : STX2 (16702 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	131390001	131390001	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131390001delT								RAN (29177 upstream) : GPR133 (48451 downstream)																																			---	---	---	---
GPR133	283383	broad.mit.edu	37	12	131473455	131473455	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131473455delC	uc001uit.3	+						GPR133_uc010tbm.1_Intron	NM_198827	NP_942122			G protein-coupled receptor 133 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(5)|ovary(3)|skin(2)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)														---	---	---	---
GPR133	283383	broad.mit.edu	37	12	131596160	131596160	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131596160delT	uc001uit.3	+						GPR133_uc010tbm.1_Intron|GPR133_uc009zyo.2_Intron|GPR133_uc001uiv.1_Intron|GPR133_uc009zyp.2_Intron	NM_198827	NP_942122			G protein-coupled receptor 133 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(5)|ovary(3)|skin(2)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)														---	---	---	---
LOC116437	116437	broad.mit.edu	37	12	131677394	131677394	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131677394delC	uc001uiw.2	+							NR_026670				Homo sapiens mRNA; cDNA DKFZp434L2430 (from clone DKFZp434L2430).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	12	131774158	131774158	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131774158delG								LOC116437 (76683 upstream) : SFRS8 (421477 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	131799767	131799767	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131799767delG								LOC116437 (102292 upstream) : SFRS8 (395868 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	131929361	131929361	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131929361delC								LOC116437 (231886 upstream) : SFRS8 (266274 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	132000111	132000112	+	IGR	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132000111_132000112insG								LOC116437 (302636 upstream) : SFRS8 (195523 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	12	133041014	133041016	+	IGR	DEL	CAT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133041014_133041016delCAT								GALNT9 (135109 upstream) : FBRSL1 (26141 downstream)																																			---	---	---	---
POLE	5426	broad.mit.edu	37	12	133236259	133236260	+	Intron	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133236259_133236260delAC	uc001uks.1	-						POLE_uc001ukr.1_5'Flank|POLE_uc010tbq.1_Intron|POLE_uc009zyu.1_Intron	NM_006231	NP_006222			DNA-directed DNA polymerase epsilon						base-excision repair, gap-filling|DNA synthesis involved in DNA repair|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	chromatin binding|DNA binding|DNA-directed DNA polymerase activity|nucleotide binding|protein binding|zinc ion binding			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)									DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
POLE	5426	broad.mit.edu	37	12	133241450	133241450	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133241450delC	uc001uks.1	-						POLE_uc010tbq.1_Intron|POLE_uc009zyu.1_Intron	NM_006231	NP_006222			DNA-directed DNA polymerase epsilon						base-excision repair, gap-filling|DNA synthesis involved in DNA repair|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	chromatin binding|DNA binding|DNA-directed DNA polymerase activity|nucleotide binding|protein binding|zinc ion binding			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)									DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
ANKLE2	23141	broad.mit.edu	37	12	133303359	133303359	+	3'UTR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133303359delC	uc001ukx.2	-	13					ANKLE2_uc009zyw.1_3'UTR	NM_015114	NP_055929			ankyrin repeat and LEM domain containing 2							cytoplasm|integral to membrane|nuclear envelope					0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.3e-08)|Epithelial(86;1.56e-07)|all cancers(50;4.94e-06)														---	---	---	---
GOLGA3	2802	broad.mit.edu	37	12	133363543	133363544	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133363543_133363544delTT	uc001ukz.1	-						GOLGA3_uc001ula.1_Intron|GOLGA3_uc001ulb.2_Intron	NM_005895	NP_005886			Golgi autoantigen, golgin subfamily a, 3						intra-Golgi vesicle-mediated transport	Golgi cisterna membrane|Golgi transport complex	protein binding|transporter activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)														---	---	---	---
GOLGA3	2802	broad.mit.edu	37	12	133374688	133374688	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133374688delG	uc001ukz.1	-						GOLGA3_uc001ula.1_Intron|GOLGA3_uc001ulb.2_Intron	NM_005895	NP_005886			Golgi autoantigen, golgin subfamily a, 3						intra-Golgi vesicle-mediated transport	Golgi cisterna membrane|Golgi transport complex	protein binding|transporter activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)														---	---	---	---
GOLGA3	2802	broad.mit.edu	37	12	133378165	133378165	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133378165delG	uc001ukz.1	-						GOLGA3_uc001ula.1_Intron|GOLGA3_uc001ulb.2_Intron	NM_005895	NP_005886			Golgi autoantigen, golgin subfamily a, 3						intra-Golgi vesicle-mediated transport	Golgi cisterna membrane|Golgi transport complex	protein binding|transporter activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)														---	---	---	---
CHFR	55743	broad.mit.edu	37	12	133455142	133455142	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133455142delG	uc001ulf.2	-						CHFR_uc001ulc.1_5'Flank|CHFR_uc001ule.2_Intron|CHFR_uc010tbs.1_Intron|CHFR_uc001uld.2_Intron|CHFR_uc010tbt.1_Intron	NM_001161344	NP_001154816			checkpoint with forkhead and ring finger domains						cell division|mitosis|mitotic cell cycle checkpoint|modification-dependent protein catabolic process|protein polyubiquitination	PML body	nucleotide binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			skin(1)	1	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.00552)|all_epithelial(31;0.226)		OV - Ovarian serous cystadenocarcinoma(86;2.59e-08)|Epithelial(86;6.38e-07)|all cancers(50;1.56e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	19542436	19542436	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19542436delT								LOC284232 (96327 upstream) : LOC348021 (39963 downstream)																																			---	---	---	---
TPTE2	93492	broad.mit.edu	37	13	20032483	20032483	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20032483delA	uc001umd.2	-						TPTE2_uc009zzk.2_Intron|TPTE2_uc009zzl.2_Intron|TPTE2_uc001ume.2_Intron|TPTE2_uc009zzm.2_Intron|TPTE2_uc010tcm.1_Intron	NM_199254	NP_954863			TPTE and PTEN homologous inositol lipid							endoplasmic reticulum membrane|integral to membrane	ion channel activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	20176939	20176939	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20176939delA								TPTE2 (41225 upstream) : MPHOSPH8 (30941 downstream)																																			---	---	---	---
PSPC1	55269	broad.mit.edu	37	13	20325236	20325238	+	Intron	DEL	TTC	-	-	rs76697490	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20325236_20325238delTTC	uc001uml.2	-						PSPC1_uc001umj.1_Intron|PSPC1_uc001umk.1_Intron	NM_001042414	NP_001035879			paraspeckle protein 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nuclear matrix|nucleolus	nucleotide binding|protein binding|RNA binding			breast(1)	1		all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483)														---	---	---	---
ZMYM2	7750	broad.mit.edu	37	13	20658328	20658328	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20658328delT	uc001umr.2	+						ZMYM2_uc001ums.2_Intron|ZMYM2_uc001umt.2_Intron|ZMYM2_uc001umv.2_Intron|ZMYM2_uc001umw.2_Intron	NM_003453	NP_003444			zinc finger protein 198						regulation of transcription, DNA-dependent|transcription, DNA-dependent	PML body	ubiquitin conjugating enzyme binding|zinc ion binding			lung(3)|ovary(2)|prostate(1)	6		all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856)														---	---	---	---
ZMYM2	7750	broad.mit.edu	37	13	20658799	20658799	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20658799delT	uc001umr.2	+						ZMYM2_uc001ums.2_Intron|ZMYM2_uc001umt.2_Intron|ZMYM2_uc001umv.2_Intron|ZMYM2_uc001umw.2_Intron	NM_003453	NP_003444			zinc finger protein 198						regulation of transcription, DNA-dependent|transcription, DNA-dependent	PML body	ubiquitin conjugating enzyme binding|zinc ion binding			lung(3)|ovary(2)|prostate(1)	6		all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	20745154	20745154	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20745154delT								GJA3 (9971 upstream) : GJB2 (16452 downstream)																																			---	---	---	---
CRYL1	51084	broad.mit.edu	37	13	21100427	21100428	+	5'Flank	INS	-	TCT	TCT	rs148134522	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21100427_21100428insTCT	uc001une.2	-						CRYL1_uc001unf.2_5'Flank|CRYL1_uc001ung.2_5'Flank	NM_015974	NP_057058			lambda-crystallin						fatty acid metabolic process	cytosol	3-hydroxyacyl-CoA dehydrogenase activity|L-gulonate 3-dehydrogenase activity|NAD+ binding|protein homodimerization activity				0		all_cancers(29;2.27e-23)|all_epithelial(30;1.69e-19)|all_lung(29;8.29e-18)|Lung SC(185;0.0262)|Ovarian(182;0.0827)|Hepatocellular(188;0.244)		all cancers(112;6.6e-05)|Epithelial(112;0.00178)|OV - Ovarian serous cystadenocarcinoma(117;0.0169)|Lung(94;0.0215)|GBM - Glioblastoma multiforme(144;0.0402)|LUSC - Lung squamous cell carcinoma(192;0.061)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	21484219	21484220	+	IGR	INS	-	TT	TT			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21484219_21484220insTT								XPO4 (7306 upstream) : LATS2 (62958 downstream)																																			---	---	---	---
EFHA1	221154	broad.mit.edu	37	13	22107048	22107048	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22107048delA	uc001uof.2	-							NM_152726	NP_689939			EF-hand domain family, member A1								calcium ion binding				0		all_cancers(29;1.24e-15)|all_epithelial(30;5.4e-14)|all_lung(29;2.04e-13)|Lung SC(185;0.0367)		all cancers(112;0.000171)|Epithelial(112;0.000398)|OV - Ovarian serous cystadenocarcinoma(117;0.00641)|Lung(94;0.189)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	22773900	22773900	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22773900delA	uc001uoi.2	+											Homo sapiens cDNA FLJ30283 fis, clone BRACE2002807.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	22885231	22885232	+	IGR	DEL	AA	-	-	rs67996361		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:22885231_22885232delAA								FGF9 (606591 upstream) : SGCG (869828 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	23338691	23338691	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23338691delA								None (None upstream) : SGCG (416369 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	23470231	23470232	+	IGR	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23470231_23470232delTC								None (None upstream) : SGCG (284828 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	23508297	23508300	+	IGR	DEL	CACT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23508297_23508300delCACT								None (None upstream) : SGCG (246760 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	24051338	24051338	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24051338delT	uc001uos.2	+											Homo sapiens mRNA; cDNA DKFZp313E1940 (from clone DKFZp313E1940).																														---	---	---	---
TNFRSF19	55504	broad.mit.edu	37	13	24156540	24156540	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24156540delA	uc001uov.1	+						TNFRSF19_uc001uot.2_Intron|TNFRSF19_uc010tcu.1_Intron|TNFRSF19_uc001uow.2_Intron|TNFRSF19_uc001uou.2_Intron	NM_018647	NP_061117			tumor necrosis factor receptor superfamily,						apoptosis|induction of apoptosis|JNK cascade	integral to membrane|mitochondrion	tumor necrosis factor receptor activity			kidney(1)|skin(1)	2		all_cancers(29;3.4e-22)|all_epithelial(30;8.75e-19)|all_lung(29;5.09e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00193)|Epithelial(112;0.0137)|OV - Ovarian serous cystadenocarcinoma(117;0.0465)|GBM - Glioblastoma multiforme(144;0.184)|Lung(94;0.19)														---	---	---	---
MIPEP	4285	broad.mit.edu	37	13	24366222	24366222	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24366222delT	uc001uox.3	-							NM_005932	NP_005923			mitochondrial intermediate peptidase precursor						protein processing involved in protein targeting to mitochondrion|proteolysis	mitochondrial matrix	metal ion binding|metalloendopeptidase activity			central_nervous_system(1)	1		all_cancers(29;1.83e-22)|all_epithelial(30;8.75e-19)|all_lung(29;9.17e-18)|Lung SC(185;0.0225)|Breast(139;0.14)		all cancers(112;0.00389)|Epithelial(112;0.0266)|OV - Ovarian serous cystadenocarcinoma(117;0.0717)|Lung(94;0.207)|GBM - Glioblastoma multiforme(144;0.232)														---	---	---	---
MIPEP	4285	broad.mit.edu	37	13	24409495	24409495	+	Intron	DEL	A	-	-	rs75925593		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24409495delA	uc001uox.3	-							NM_005932	NP_005923			mitochondrial intermediate peptidase precursor						protein processing involved in protein targeting to mitochondrion|proteolysis	mitochondrial matrix	metal ion binding|metalloendopeptidase activity			central_nervous_system(1)	1		all_cancers(29;1.83e-22)|all_epithelial(30;8.75e-19)|all_lung(29;9.17e-18)|Lung SC(185;0.0225)|Breast(139;0.14)		all cancers(112;0.00389)|Epithelial(112;0.0266)|OV - Ovarian serous cystadenocarcinoma(117;0.0717)|Lung(94;0.207)|GBM - Glioblastoma multiforme(144;0.232)														---	---	---	---
SPATA13	221178	broad.mit.edu	37	13	24707106	24707107	+	Intron	DEL	CT	-	-	rs144600368		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24707106_24707107delCT	uc001upd.1	+						C1QTNF9_uc001upe.2_Intron	NM_153023	NP_694568			spermatogenesis associated 13						cell migration|filopodium assembly|lamellipodium assembly|regulation of cell migration|regulation of Rho protein signal transduction	cytoplasm|filopodium|lamellipodium|ruffle membrane	protein binding|Rac guanyl-nucleotide exchange factor activity			skin(2)|ovary(1)	3		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)														---	---	---	---
C1QTNF9	338872	broad.mit.edu	37	13	24887106	24887108	+	Intron	DEL	AAG	-	-	rs56158660		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24887106_24887108delAAG	uc001upj.2	+						C1QTNF9_uc001upe.2_Intron	NM_178540	NP_848635			C1q and tumor necrosis factor related protein 9							collagen	hormone activity				0		all_cancers(29;3.55e-20)|all_epithelial(30;4.25e-17)|all_lung(29;1.04e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.00565)|Epithelial(112;0.027)|OV - Ovarian serous cystadenocarcinoma(117;0.115)|Lung(94;0.159)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	24930023	24930024	+	IGR	DEL	CA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24930023_24930024delCA								C1QTNF9 (33358 upstream) : PARP4 (65051 downstream)																																			---	---	---	---
PARP4	143	broad.mit.edu	37	13	25079277	25079278	+	Intron	INS	-	ACAC	ACAC	rs141835469	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25079277_25079278insACAC	uc001upl.2	-						PARP4_uc010tdc.1_Intron	NM_006437	NP_006428			poly (ADP-ribose) polymerase family, member 4						cell death|DNA repair|inflammatory response|protein ADP-ribosylation|response to drug|transport	cytoplasm|nucleus|ribonucleoprotein complex|spindle microtubule	DNA binding|enzyme binding|NAD+ ADP-ribosyltransferase activity			ovary(3)|skin(1)	4		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	25137146	25137147	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25137146_25137147insA								PARP4 (50198 upstream) : LOC374491 (3864 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	25600460	25600460	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25600460delA								TPTE2P1 (57853 upstream) : PABPC3 (69816 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	25613925	25613925	+	IGR	DEL	T	-	-	rs75270197		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25613925delT								TPTE2P1 (71318 upstream) : PABPC3 (56351 downstream)																																			---	---	---	---
ATP8A2	51761	broad.mit.edu	37	13	25969992	25969993	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25969992_25969993delTT	uc001uqk.2	+							NM_016529	NP_057613			ATPase, aminophospholipid transporter-like,						ATP biosynthetic process|negative regulation of cell proliferation	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|large_intestine(1)|skin(1)	4		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)														---	---	---	---
ATP8A2	51761	broad.mit.edu	37	13	25984355	25984356	+	Intron	DEL	TC	-	-	rs11617728	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25984355_25984356delTC	uc001uqk.2	+							NM_016529	NP_057613			ATPase, aminophospholipid transporter-like,						ATP biosynthetic process|negative regulation of cell proliferation	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|large_intestine(1)|skin(1)	4		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)														---	---	---	---
ATP8A2	51761	broad.mit.edu	37	13	25984356	25984356	+	Intron	DEL	C	-	-	rs11617728	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25984356delC	uc001uqk.2	+							NM_016529	NP_057613			ATPase, aminophospholipid transporter-like,						ATP biosynthetic process|negative regulation of cell proliferation	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|large_intestine(1)|skin(1)	4		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)														---	---	---	---
ATP8A2	51761	broad.mit.edu	37	13	26445248	26445249	+	Intron	DEL	GT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26445248_26445249delGT	uc001uqk.2	+						ATP8A2_uc010tdi.1_Intron|ATP8A2_uc010tdj.1_Intron|ATP8A2_uc010aaj.1_Intron	NM_016529	NP_057613			ATPase, aminophospholipid transporter-like,						ATP biosynthetic process|negative regulation of cell proliferation	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|large_intestine(1)|skin(1)	4		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)														---	---	---	---
ATP8A2	51761	broad.mit.edu	37	13	26521966	26521967	+	Intron	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26521966_26521967insG	uc001uqk.2	+						ATP8A2_uc010tdi.1_Intron|ATP8A2_uc010tdj.1_Intron	NM_016529	NP_057613			ATPase, aminophospholipid transporter-like,						ATP biosynthetic process|negative regulation of cell proliferation	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|large_intestine(1)|skin(1)	4		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)														---	---	---	---
ATP8A2	51761	broad.mit.edu	37	13	26523946	26523946	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26523946delT	uc001uqk.2	+						ATP8A2_uc010tdi.1_Intron|ATP8A2_uc010tdj.1_Intron	NM_016529	NP_057613			ATPase, aminophospholipid transporter-like,						ATP biosynthetic process|negative regulation of cell proliferation	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|large_intestine(1)|skin(1)	4		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	27100855	27100855	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27100855delA								CDK8 (122286 upstream) : WASF3 (30985 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	27495405	27495405	+	IGR	DEL	T	-	-	rs76427157		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27495405delT								GPR12 (160483 upstream) : USP12 (147033 downstream)																																			---	---	---	---
POLR1D	51082	broad.mit.edu	37	13	28230017	28230017	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28230017delA	uc001urp.2	+						POLR1D_uc010aam.2_Intron|POLR1D_uc001urq.2_Intron	NM_152705	NP_689918			polymerase (RNA) I polypeptide D isoform 2						termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|protein dimerization activity				0		Lung SC(185;0.0161)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	all cancers(112;0.0758)|OV - Ovarian serous cystadenocarcinoma(117;0.1)|Epithelial(112;0.213)														---	---	---	---
POLR1D	51082	broad.mit.edu	37	13	28239644	28239644	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28239644delT	uc001urp.2	+						POLR1D_uc010aam.2_Intron|POLR1D_uc001urq.2_Intron	NM_152705	NP_689918			polymerase (RNA) I polypeptide D isoform 2						termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|protein dimerization activity				0		Lung SC(185;0.0161)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	all cancers(112;0.0758)|OV - Ovarian serous cystadenocarcinoma(117;0.1)|Epithelial(112;0.213)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	28368608	28368608	+	IGR	DEL	T	-	-	rs74040898		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28368608delT								GSX1 (519 upstream) : PDX1 (125560 downstream)																																			---	---	---	---
FLT1	2321	broad.mit.edu	37	13	28905993	28905993	+	Intron	DEL	A	-	-	rs35686096		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28905993delA	uc001usb.3	-						FLT1_uc010aaq.2_5'Flank|FLT1_uc001usa.3_Intron	NM_002019	NP_002010			fms-related tyrosine kinase 1 isoform 1						cell differentiation|female pregnancy|positive regulation of vascular endothelial growth factor receptor signaling pathway	extracellular space|Golgi apparatus|integral to plasma membrane|nucleus	ATP binding|growth factor binding|vascular endothelial growth factor receptor activity			lung(10)|central_nervous_system(5)|ovary(3)|stomach(2)|skin(2)|urinary_tract(1)|breast(1)	24	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Sunitinib(DB01268)													---	---	---	---
FLT1	2321	broad.mit.edu	37	13	28959448	28959448	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28959448delT	uc001usb.3	-						FLT1_uc010aar.1_Intron	NM_002019	NP_002010			fms-related tyrosine kinase 1 isoform 1						cell differentiation|female pregnancy|positive regulation of vascular endothelial growth factor receptor signaling pathway	extracellular space|Golgi apparatus|integral to plasma membrane|nucleus	ATP binding|growth factor binding|vascular endothelial growth factor receptor activity			lung(10)|central_nervous_system(5)|ovary(3)|stomach(2)|skin(2)|urinary_tract(1)|breast(1)	24	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Sunitinib(DB01268)													---	---	---	---
FLT1	2321	broad.mit.edu	37	13	28961841	28961841	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28961841delT	uc001usb.3	-						FLT1_uc010aar.1_Intron|FLT1_uc001usc.3_3'UTR	NM_002019	NP_002010			fms-related tyrosine kinase 1 isoform 1						cell differentiation|female pregnancy|positive regulation of vascular endothelial growth factor receptor signaling pathway	extracellular space|Golgi apparatus|integral to plasma membrane|nucleus	ATP binding|growth factor binding|vascular endothelial growth factor receptor activity			lung(10)|central_nervous_system(5)|ovary(3)|stomach(2)|skin(2)|urinary_tract(1)|breast(1)	24	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Sunitinib(DB01268)													---	---	---	---
FLT1	2321	broad.mit.edu	37	13	29001275	29001275	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29001275delA	uc001usb.3	-						FLT1_uc010aar.1_Intron|FLT1_uc001usc.3_Intron|FLT1_uc010tdp.1_Intron	NM_002019	NP_002010			fms-related tyrosine kinase 1 isoform 1						cell differentiation|female pregnancy|positive regulation of vascular endothelial growth factor receptor signaling pathway	extracellular space|Golgi apparatus|integral to plasma membrane|nucleus	ATP binding|growth factor binding|vascular endothelial growth factor receptor activity			lung(10)|central_nervous_system(5)|ovary(3)|stomach(2)|skin(2)|urinary_tract(1)|breast(1)	24	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Sunitinib(DB01268)													---	---	---	---
Unknown	0	broad.mit.edu	37	13	29108269	29108269	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29108269delC								FLT1 (39004 upstream) : POMP (124972 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	29313915	29313916	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29313915_29313916delAA								SLC46A3 (20765 upstream) : MTUS2 (284832 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	29361136	29361136	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29361136delT								SLC46A3 (67986 upstream) : MTUS2 (237612 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	29361158	29361158	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29361158delT								SLC46A3 (68008 upstream) : MTUS2 (237590 downstream)																																			---	---	---	---
MTUS2	23281	broad.mit.edu	37	13	29616475	29616476	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29616475_29616476insT	uc001usl.3	+							NM_001033602	NP_001028774			hypothetical protein LOC23281 isoform a							cytoplasm|microtubule	microtubule binding|protein homodimerization activity				0																		---	---	---	---
MTUS2	23281	broad.mit.edu	37	13	29658501	29658502	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29658501_29658502delAA	uc001usl.3	+							NM_001033602	NP_001028774			hypothetical protein LOC23281 isoform a							cytoplasm|microtubule	microtubule binding|protein homodimerization activity				0																		---	---	---	---
MTUS2	23281	broad.mit.edu	37	13	29887389	29887389	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:29887389delA	uc001usl.3	+							NM_001033602	NP_001028774			hypothetical protein LOC23281 isoform a							cytoplasm|microtubule	microtubule binding|protein homodimerization activity				0																		---	---	---	---
MTUS2	23281	broad.mit.edu	37	13	30032049	30032049	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30032049delT	uc001usl.3	+						MTUS2_uc001usm.3_Intron|MTUS2_uc010aau.2_Intron	NM_001033602	NP_001028774			hypothetical protein LOC23281 isoform a							cytoplasm|microtubule	microtubule binding|protein homodimerization activity				0																		---	---	---	---
MTUS2	23281	broad.mit.edu	37	13	30066072	30066073	+	Intron	DEL	GT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30066072_30066073delGT	uc001usl.3	+						MTUS2_uc001usm.3_Intron|MTUS2_uc010aau.2_Intron	NM_001033602	NP_001028774			hypothetical protein LOC23281 isoform a							cytoplasm|microtubule	microtubule binding|protein homodimerization activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	30729253	30729253	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30729253delC								UBL3 (304433 upstream) : KATNAL1 (47515 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	30980716	30980718	+	IGR	DEL	AAA	-	-	rs72051461		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30980716_30980718delAAA								LOC100188949 (32680 upstream) : HMGB1 (52163 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	31005584	31005584	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31005584delG								LOC100188949 (57548 upstream) : HMGB1 (27297 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	31396852	31396854	+	IGR	DEL	AAA	-	-	rs75804177		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31396852_31396854delAAA								ALOX5AP (58296 upstream) : C13orf33 (83458 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	31635980	31635980	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31635980delA								C13orf26 (86829 upstream) : HSPH1 (74785 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	31664556	31664556	+	IGR	DEL	A	-	-	rs4941745	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31664556delA								C13orf26 (115405 upstream) : HSPH1 (46209 downstream)																																			---	---	---	---
HSPH1	10808	broad.mit.edu	37	13	31736846	31736847	+	5'Flank	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31736846_31736847delTT	uc001utj.2	-						HSPH1_uc001utk.2_5'Flank|HSPH1_uc010aaw.2_5'Flank|HSPH1_uc001utl.2_5'Flank|HSPH1_uc010tds.1_5'Flank|HSPH1_uc010tdt.1_5'Flank|HSPH1_uc010aax.1_5'Flank|HSPH1_uc010aay.1_5'Flank	NM_006644	NP_006635			heat shock 105kD						positive regulation of MHC class I biosynthetic process|positive regulation of NK T cell activation|response to unfolded protein	cytoplasm|extracellular region	ATP binding				0		Lung SC(185;0.0257)		all cancers(112;0.00385)|Epithelial(112;0.0328)|OV - Ovarian serous cystadenocarcinoma(117;0.0375)|GBM - Glioblastoma multiforme(144;0.125)														---	---	---	---
B3GALTL	145173	broad.mit.edu	37	13	31807569	31807569	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31807569delA	uc010aaz.2	+							NM_194318	NP_919299			beta 1,3-galactosyltransferase-like						fucose metabolic process	endoplasmic reticulum membrane|integral to membrane	transferase activity, transferring glycosyl groups			ovary(2)	2		Lung SC(185;0.0257)		all cancers(112;0.00436)|Epithelial(112;0.0285)|OV - Ovarian serous cystadenocarcinoma(117;0.0512)|GBM - Glioblastoma multiforme(144;0.184)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	32167057	32167057	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32167057delT								B3GALTL (260648 upstream) : RXFP2 (146622 downstream)																																			---	---	---	---
RXFP2	122042	broad.mit.edu	37	13	32316678	32316678	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32316678delA	uc001utt.2	+						RXFP2_uc010aba.2_Intron	NM_130806	NP_570718			relaxin/insulin-like family peptide receptor 2							integral to membrane|plasma membrane					0		Lung SC(185;0.0262)		all cancers(112;0.000559)|Epithelial(112;0.0017)|OV - Ovarian serous cystadenocarcinoma(117;0.0145)|BRCA - Breast invasive adenocarcinoma(63;0.0535)												OREG0022353	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	13	32600553	32600553	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32600553delT	uc001utw.2	-											Homo sapiens full length insert cDNA clone ZD78D03.																														---	---	---	---
FRY	10129	broad.mit.edu	37	13	32673954	32673954	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32673954delA	uc001utx.2	+						FRY_uc010tdw.1_Intron	NM_023037	NP_075463			furry homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)														---	---	---	---
FRY	10129	broad.mit.edu	37	13	32732281	32732282	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32732281_32732282insT	uc001utx.2	+						FRY_uc010tdw.1_Intron	NM_023037	NP_075463			furry homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)														---	---	---	---
FRY	10129	broad.mit.edu	37	13	32753208	32753208	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32753208delT	uc001utx.2	+						FRY_uc010tdw.1_Intron	NM_023037	NP_075463			furry homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)														---	---	---	---
FRY	10129	broad.mit.edu	37	13	32760689	32760689	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32760689delA	uc001utx.2	+						FRY_uc010tdw.1_Intron	NM_023037	NP_075463			furry homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)														---	---	---	---
FRY	10129	broad.mit.edu	37	13	32819585	32819585	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32819585delA	uc001utx.2	+						FRY_uc010tdw.1_Intron	NM_023037	NP_075463			furry homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)														---	---	---	---
N4BP2L2	10443	broad.mit.edu	37	13	33091402	33091402	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33091402delT	uc001uuk.3	-	6					N4BP2L2_uc001uuj.2_Intron|N4BP2L2_uc010abe.1_Intron|N4BP2L2_uc010tdz.1_Intron	NM_014887	NP_055702			phosphonoformate immuno-associated protein 5												0		Lung SC(185;0.0262)		all cancers(112;9.5e-07)|Epithelial(112;5.07e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00196)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.243)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	33129541	33129541	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33129541delA								N4BP2L2 (16605 upstream) : PDS5B (31051 downstream)																																			---	---	---	---
PDS5B	23047	broad.mit.edu	37	13	33186188	33186188	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33186188delT	uc010abf.2	+						PDS5B_uc001uun.2_Intron|PDS5B_uc001uuo.2_Intron|PDS5B_uc010abg.2_Intron	NM_015032	NP_055847			PDS5, regulator of cohesion maintenance, homolog						cell division|cell proliferation|mitotic sister chromatid cohesion|negative regulation of cell proliferation	chromatin|nucleus	ATP binding|DNA binding|identical protein binding			ovary(2)|lung(1)|pancreas(1)	4		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)														---	---	---	---
PDS5B	23047	broad.mit.edu	37	13	33283975	33283975	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33283975delT	uc010abf.2	+						PDS5B_uc010abg.2_Intron	NM_015032	NP_055847			PDS5, regulator of cohesion maintenance, homolog						cell division|cell proliferation|mitotic sister chromatid cohesion|negative regulation of cell proliferation	chromatin|nucleus	ATP binding|DNA binding|identical protein binding			ovary(2)|lung(1)|pancreas(1)	4		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	33523626	33523627	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33523626_33523627insT								PDS5B (171471 upstream) : KL (66574 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	34271507	34271507	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:34271507delT								STARD13 (20575 upstream) : RFC3 (120699 downstream)																																			---	---	---	---
RFC3	5983	broad.mit.edu	37	13	34398063	34398063	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:34398063delA	uc001uuz.2	+	3	345	c.235delA	c.(235-237)AAAfs	p.K79fs	RFC3_uc001uva.2_Frame_Shift_Del_p.K79fs|RFC3_uc010ted.1_Frame_Shift_Del_p.K79fs	NM_002915	NP_002906	P40938	RFC3_HUMAN	replication factor C 3 isoform 1	79					cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA synthesis involved in DNA repair|nucleotide-excision repair, DNA gap filling|response to organophosphorus|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|protein binding				0		Hepatocellular(188;0.0191)|Lung SC(185;0.0548)		all cancers(112;5.09e-06)|Epithelial(112;6.52e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00107)|OV - Ovarian serous cystadenocarcinoma(117;0.0285)|GBM - Glioblastoma multiforme(144;0.123)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	34646551	34646552	+	IGR	DEL	CA	-	-	rs66933289		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:34646551_34646552delCA								RFC3 (105857 upstream) : NBEA (869904 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	34775258	34775258	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:34775258delG								RFC3 (234564 upstream) : NBEA (741198 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	34820997	34820998	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:34820997_34820998delAA								RFC3 (280303 upstream) : NBEA (695458 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	35278671	35278671	+	IGR	DEL	A	-	-	rs35939253		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35278671delA								RFC3 (737977 upstream) : NBEA (237785 downstream)																																			---	---	---	---
NBEA	26960	broad.mit.edu	37	13	35771657	35771657	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:35771657delT	uc001uvb.2	+						NBEA_uc010abi.2_Intron	NM_015678	NP_056493			neurobeachin							cytosol|endomembrane system|plasma membrane|trans-Golgi network	protein binding			ovary(9)|large_intestine(2)	11		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)														---	---	---	---
NBEA	26960	broad.mit.edu	37	13	36182330	36182330	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36182330delT	uc001uvb.2	+						NBEA_uc010abi.2_Intron|NBEA_uc010tee.1_Intron|NBEA_uc010tef.1_Intron|NBEA_uc010teg.1_Intron|NBEA_uc001uvd.2_Intron	NM_015678	NP_056493			neurobeachin							cytosol|endomembrane system|plasma membrane|trans-Golgi network	protein binding			ovary(9)|large_intestine(2)	11		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	36982391	36982392	+	IGR	INS	-	GAG	GAG			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36982391_36982392insGAG								SPG20 (38074 upstream) : CCNA1 (23265 downstream)																																			---	---	---	---
CCNA1	8900	broad.mit.edu	37	13	37012576	37012576	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37012576delC	uc001uvr.3	+						CCNA1_uc010teo.1_Intron|CCNA1_uc010abq.2_Intron|CCNA1_uc010abp.2_Intron|CCNA1_uc001uvs.3_Intron|CCNA1_uc010abr.2_Intron	NM_003914	NP_003905			cyclin A1 isoform a						cell division|G2/M transition of mitotic cell cycle|male meiosis I|mitosis|regulation of cyclin-dependent protein kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|spermatogenesis	cytosol|microtubule cytoskeleton|nucleoplasm	protein kinase binding			lung(2)|skin(2)|ovary(1)	5		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.91e-07)|Epithelial(112;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0119)|GBM - Glioblastoma multiforme(144;0.0242)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	37067760	37067760	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37067760delT								CCNA1 (50742 upstream) : C13orf36 (180289 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	37075804	37075804	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37075804delT								CCNA1 (58786 upstream) : C13orf36 (172245 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	37160987	37160987	+	IGR	DEL	C	-	-	rs35113566		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37160987delC								CCNA1 (143969 upstream) : C13orf36 (87062 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	37170637	37170637	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37170637delT								CCNA1 (153619 upstream) : C13orf36 (77412 downstream)																																			---	---	---	---
SMAD9	4093	broad.mit.edu	37	13	37422329	37422329	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37422329delT	uc001uvw.2	-	7					SMAD9_uc001uvx.2_3'UTR|SMAD9_uc010tep.1_3'UTR	NM_001127217	NP_001120689			SMAD family member 9 isoform a						BMP signaling pathway|transforming growth factor beta receptor signaling pathway	cytosol|transcription factor complex	sequence-specific DNA binding transcription factor activity|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity				0		Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)		all cancers(112;3.38e-07)|Epithelial(112;1.93e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00804)|BRCA - Breast invasive adenocarcinoma(63;0.0129)|GBM - Glioblastoma multiforme(144;0.026)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	37730126	37730126	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37730126delT								CSNK1A1L (50325 upstream) : POSTN (406594 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	37981404	37981404	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37981404delC								CSNK1A1L (301603 upstream) : POSTN (155316 downstream)																																			---	---	---	---
POSTN	10631	broad.mit.edu	37	13	38171302	38171302	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38171302delA	uc001uwo.3	-						POSTN_uc001uwp.3_Intron|POSTN_uc001uwr.2_Intron|POSTN_uc001uwq.2_Intron|POSTN_uc010teu.1_Intron|POSTN_uc010tev.1_Intron|POSTN_uc010tew.1_Intron|POSTN_uc010tex.1_Intron	NM_006475	NP_006466			periostin, osteoblast specific factor isoform 1						cell adhesion|skeletal system development	proteinaceous extracellular matrix	heparin binding			ovary(2)	2		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)														---	---	---	---
POSTN	10631	broad.mit.edu	37	13	38172612	38172612	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38172612delT	uc001uwo.3	-						POSTN_uc001uwp.3_Intron|POSTN_uc001uwr.2_Intron|POSTN_uc001uwq.2_Intron|POSTN_uc010teu.1_Intron|POSTN_uc010tev.1_Intron|POSTN_uc010tew.1_Intron|POSTN_uc010tex.1_Intron	NM_006475	NP_006466			periostin, osteoblast specific factor isoform 1						cell adhesion|skeletal system development	proteinaceous extracellular matrix	heparin binding			ovary(2)	2		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	38197388	38197388	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38197388delA								POSTN (13825 upstream) : TRPC4 (13387 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	38633621	38633623	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38633621_38633623delTTT								TRPC4 (189682 upstream) : UFM1 (290319 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	38649778	38649784	+	IGR	DEL	TTTTTTT	-	-	rs112752318		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:38649778_38649784delTTTTTTT								TRPC4 (205839 upstream) : UFM1 (274158 downstream)																																			---	---	---	---
LHFP	10186	broad.mit.edu	37	13	39917882	39917882	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39917882delT	uc001uxf.2	-	4						NM_005780	NP_005771			lipoma HMGIC fusion partner precursor							integral to membrane	DNA binding		HMGA2/LHFP(2)	soft_tissue(2)|lung(1)|breast(1)	4		Lung NSC(96;3.55e-06)|Breast(139;0.00408)|Ovarian(182;0.0107)|Prostate(109;0.0118)|Lung SC(185;0.0719)|Hepatocellular(188;0.114)		OV - Ovarian serous cystadenocarcinoma(117;6.48e-46)|Epithelial(112;8.43e-42)|all cancers(112;1.42e-36)|GBM - Glioblastoma multiforme(144;0.00187)|BRCA - Breast invasive adenocarcinoma(63;0.00886)|KIRC - Kidney renal clear cell carcinoma(186;0.048)|Kidney(163;0.0601)|LUSC - Lung squamous cell carcinoma(192;0.105)				T	HMGA2	lipoma								---	---	---	---
LHFP	10186	broad.mit.edu	37	13	40173713	40173713	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40173713delA	uc001uxf.2	-							NM_005780	NP_005771			lipoma HMGIC fusion partner precursor							integral to membrane	DNA binding		HMGA2/LHFP(2)	soft_tissue(2)|lung(1)|breast(1)	4		Lung NSC(96;3.55e-06)|Breast(139;0.00408)|Ovarian(182;0.0107)|Prostate(109;0.0118)|Lung SC(185;0.0719)|Hepatocellular(188;0.114)		OV - Ovarian serous cystadenocarcinoma(117;6.48e-46)|Epithelial(112;8.43e-42)|all cancers(112;1.42e-36)|GBM - Glioblastoma multiforme(144;0.00187)|BRCA - Breast invasive adenocarcinoma(63;0.00886)|KIRC - Kidney renal clear cell carcinoma(186;0.048)|Kidney(163;0.0601)|LUSC - Lung squamous cell carcinoma(192;0.105)				T	HMGA2	lipoma								---	---	---	---
Unknown	0	broad.mit.edu	37	13	40211358	40211358	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40211358delT								LHFP (34002 upstream) : COG6 (18406 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	40428205	40428206	+	IGR	DEL	AT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:40428205_40428206delAT								COG6 (62403 upstream) : LOC646982 (493067 downstream)																																			---	---	---	---
FOXO1	2308	broad.mit.edu	37	13	41213001	41213001	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41213001delG	uc001uxl.3	-							NM_002015	NP_002006			forkhead box O1						anti-apoptosis|blood vessel development|embryo development|endocrine pancreas development|insulin receptor signaling pathway|negative regulation of stress-activated MAPK cascade|nerve growth factor receptor signaling pathway|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|response to DNA damage stimulus|tissue development	cytosol|transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding		PAX3/FOXO1(749)|PAX7/FOXO1(197)	soft_tissue(946)|lung(1)|central_nervous_system(1)	948		Lung NSC(96;1.18e-05)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;7.32e-09)|Epithelial(112;2.87e-06)|OV - Ovarian serous cystadenocarcinoma(117;6.98e-05)|GBM - Glioblastoma multiforme(144;0.00394)|BRCA - Breast invasive adenocarcinoma(63;0.0815)														---	---	---	---
MRPS31	10240	broad.mit.edu	37	13	41341226	41341226	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41341226delA	uc001uxm.3	-							NM_005830	NP_005821			mitochondrial ribosomal protein S31 precursor							mitochondrion|ribosome	protein domain specific binding				0		Lung NSC(96;3.55e-06)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;1.52e-08)|Epithelial(112;7.63e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000192)|GBM - Glioblastoma multiforme(144;0.00233)|BRCA - Breast invasive adenocarcinoma(63;0.0706)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	41728552	41728562	+	Intron	DEL	TTTTTTTTTTC	-	-	rs145185389		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41728552_41728562delTTTTTTTTTTC	uc001uxv.1	+											Homo sapiens cDNA FLJ31620 fis, clone NT2RI2003184.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	41729605	41729605	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41729605delA	uc001uxv.1	+											Homo sapiens cDNA FLJ31620 fis, clone NT2RI2003184.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	42116994	42116994	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42116994delC								C13orf15 (71981 upstream) : KIAA0564 (23968 downstream)																																			---	---	---	---
KIAA0564	23078	broad.mit.edu	37	13	42299335	42299335	+	Intron	DEL	A	-	-	rs67588391		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42299335delA	uc001uyj.2	-						KIAA0564_uc001uyk.2_Intron	NM_015058	NP_055873			hypothetical protein LOC23078 isoform a							extracellular region	ATP binding|ATPase activity			ovary(3)|upper_aerodigestive_tract(1)|kidney(1)|skin(1)	6		Lung NSC(96;4.61e-06)|Prostate(109;0.0167)|Lung SC(185;0.0262)|Breast(139;0.0854)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000368)|GBM - Glioblastoma multiforme(144;0.0033)|BRCA - Breast invasive adenocarcinoma(63;0.0969)														---	---	---	---
DGKH	160851	broad.mit.edu	37	13	42622287	42622287	+	5'Flank	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42622287delC	uc001uyl.1	+						DGKH_uc010tfh.1_Intron|DGKH_uc001uym.1_5'Flank	NM_178009	NP_821077			diacylglycerol kinase, eta isoform 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation|protein oligomerization	endosome|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(2)	2		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)														---	---	---	---
DGKH	160851	broad.mit.edu	37	13	42748332	42748332	+	Intron	DEL	A	-	-	rs77403765		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42748332delA	uc001uyl.1	+						DGKH_uc010tfh.1_Intron|DGKH_uc001uym.1_Intron|DGKH_uc010tfi.1_Intron|DGKH_uc010tfj.1_Intron|DGKH_uc001uyn.1_Intron|DGKH_uc001uyo.1_Intron|DGKH_uc001uyp.2_Intron	NM_178009	NP_821077			diacylglycerol kinase, eta isoform 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation|protein oligomerization	endosome|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(2)	2		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	43122850	43122850	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43122850delA								AKAP11 (225448 upstream) : TNFSF11 (14022 downstream)																																			---	---	---	---
TNFSF11	8600	broad.mit.edu	37	13	43136256	43136257	+	5'Flank	DEL	AA	-	-	rs10538049		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43136256_43136257delAA	uc001uyt.2	+							NM_033012	NP_143026			tumor necrosis factor ligand superfamily, member						immune response|monocyte chemotaxis|osteoclast differentiation|positive regulation of bone resorption|positive regulation of corticotropin-releasing hormone secretion|positive regulation of ERK1 and ERK2 cascade via TNFSF11-mediated signaling|positive regulation of fever generation by positive regulation of prostaglandin secretion|positive regulation of homotypic cell-cell adhesion|positive regulation of NF-kappaB transcription factor activity|positive regulation of osteoclast differentiation|positive regulation of T cell activation	cytoplasm|extracellular space|integral to plasma membrane	cytokine activity|receptor activity|tumor necrosis factor receptor binding				0		Lung NSC(96;1.11e-05)|Breast(139;0.00868)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000249)|GBM - Glioblastoma multiforme(144;0.00119)|BRCA - Breast invasive adenocarcinoma(63;0.073)														---	---	---	---
EPSTI1	94240	broad.mit.edu	37	13	43538282	43538282	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43538282delA	uc001uyw.1	-						EPSTI1_uc001uyx.1_Intron	NM_001002264	NP_001002264			epithelial stromal interaction 1 isoform 1											ovary(1)	1		Lung NSC(96;3.6e-06)|Breast(139;0.00869)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		GBM - Glioblastoma multiforme(144;0.000528)|BRCA - Breast invasive adenocarcinoma(63;0.0858)														---	---	---	---
ENOX1	55068	broad.mit.edu	37	13	43796517	43796518	+	Intron	DEL	AC	-	-	rs113908566		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43796517_43796518delAC	uc001uza.3	-						ENOX1_uc001uzb.3_Intron|ENOX1_uc001uzc.3_Intron|ENOX1_uc001uyz.3_Intron	NM_001127615	NP_001121087			ecto-NOX disulfide-thiol exchanger 1						electron transport chain|rhythmic process|transport	extracellular space|plasma membrane	nucleic acid binding|nucleotide binding|oxidoreductase activity			pancreas(1)|skin(1)	2		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)														---	---	---	---
ENOX1	55068	broad.mit.edu	37	13	43814705	43814705	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43814705delA	uc001uza.3	-						ENOX1_uc001uzb.3_Intron|ENOX1_uc001uzc.3_Intron|ENOX1_uc001uyz.3_Intron	NM_001127615	NP_001121087			ecto-NOX disulfide-thiol exchanger 1						electron transport chain|rhythmic process|transport	extracellular space|plasma membrane	nucleic acid binding|nucleotide binding|oxidoreductase activity			pancreas(1)|skin(1)	2		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)														---	---	---	---
ENOX1	55068	broad.mit.edu	37	13	43967723	43967726	+	Intron	DEL	TGGA	-	-	rs35153723		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:43967723_43967726delTGGA	uc001uza.3	-						ENOX1_uc001uzb.3_Intron|ENOX1_uc001uzc.3_Intron	NM_001127615	NP_001121087			ecto-NOX disulfide-thiol exchanger 1						electron transport chain|rhythmic process|transport	extracellular space|plasma membrane	nucleic acid binding|nucleotide binding|oxidoreductase activity			pancreas(1)|skin(1)	2		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)														---	---	---	---
ENOX1	55068	broad.mit.edu	37	13	44020305	44020306	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44020305_44020306delTT	uc001uza.3	-						ENOX1_uc001uzb.3_Intron|ENOX1_uc001uzc.3_Intron	NM_001127615	NP_001121087			ecto-NOX disulfide-thiol exchanger 1						electron transport chain|rhythmic process|transport	extracellular space|plasma membrane	nucleic acid binding|nucleotide binding|oxidoreductase activity			pancreas(1)|skin(1)	2		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)														---	---	---	---
ENOX1	55068	broad.mit.edu	37	13	44163308	44163308	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44163308delA	uc001uza.3	-						ENOX1_uc001uzb.3_Intron|ENOX1_uc001uzc.3_Intron	NM_001127615	NP_001121087			ecto-NOX disulfide-thiol exchanger 1						electron transport chain|rhythmic process|transport	extracellular space|plasma membrane	nucleic acid binding|nucleotide binding|oxidoreductase activity			pancreas(1)|skin(1)	2		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)														---	---	---	---
ENOX1	55068	broad.mit.edu	37	13	44280494	44280494	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44280494delA	uc001uzc.3	-							NM_017993	NP_060463			ecto-NOX disulfide-thiol exchanger 1						electron transport chain|rhythmic process|transport	extracellular space|plasma membrane	nucleic acid binding|nucleotide binding|oxidoreductase activity			pancreas(1)|skin(1)	2		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	44562753	44562753	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44562753delA								C13orf31 (94686 upstream) : LOC121838 (33718 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	44747154	44747155	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44747154_44747155delTT								LOC121838 (142556 upstream) : SERP2 (200823 downstream)																																			---	---	---	---
SERP2	387923	broad.mit.edu	37	13	44955678	44955678	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:44955678delA	uc001uzj.2	+						SERP2_uc001uzk.2_Intron	NM_001010897	NP_001010897			stress-associated endoplasmic reticulum protein						protein transport|transmembrane transport	endoplasmic reticulum membrane|integral to membrane					0		all_hematologic(4;1.49e-06)|Acute lymphoblastic leukemia(4;1.5e-06)|Lung NSC(96;0.00043)|Breast(139;0.0044)|Prostate(109;0.0137)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)		GBM - Glioblastoma multiforme(144;0.00026)|BRCA - Breast invasive adenocarcinoma(63;0.123)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	45170283	45170283	+	IGR	DEL	A	-	-	rs35230491		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45170283delA								TSC22D1 (19582 upstream) : NUFIP1 (343101 downstream)																																			---	---	---	---
NUFIP1	26747	broad.mit.edu	37	13	45562590	45562590	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45562590delA	uc001uzp.2	-						KIAA1704_uc010tfo.1_5'Flank|KIAA1704_uc001uzq.2_5'Flank|KIAA1704_uc001uzr.1_5'Flank|KIAA1704_uc001uzs.2_5'Flank	NM_012345	NP_036477			nuclear fragile X mental retardation protein						box C/D snoRNP assembly|positive regulation of transcription from RNA polymerase II promoter|RNA processing	actin cytoskeleton|cytosolic ribosome|nuclear matrix|nucleolus|perichromatin fibrils|pre-snoRNP complex|presynaptic active zone|transcription elongation factor complex	DNA binding|identical protein binding|protein binding, bridging|RNA binding|zinc ion binding				0		Lung NSC(96;8.23e-05)|Breast(139;0.00378)|Prostate(109;0.0107)|all_hematologic(4;0.014)|Lung SC(185;0.0262)|Hepatocellular(98;0.0524)|Acute lymphoblastic leukemia(4;0.143)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000306)|BRCA - Breast invasive adenocarcinoma(63;0.125)														---	---	---	---
KIAA1704	55425	broad.mit.edu	37	13	45601782	45601783	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45601782_45601783delAA	uc001uzq.2	+						KIAA1704_uc001uzr.1_Intron|KIAA1704_uc001uzs.2_Intron|KIAA1704_uc001uzt.2_Intron	NM_018559	NP_061029			hypothetical protein LOC55425											pancreas(1)|skin(1)	2		Lung NSC(96;0.00143)|Prostate(109;0.0137)|Breast(139;0.0192)|Lung SC(185;0.0367)|Hepatocellular(98;0.133)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000313)|BRCA - Breast invasive adenocarcinoma(63;0.126)														---	---	---	---
GTF2F2	2963	broad.mit.edu	37	13	45694215	45694215	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45694215delT	uc001uzw.2	+						GTF2F2_uc001uzv.2_5'Flank	NM_004128	NP_004119			general transcription factor IIF, polypeptide 2,						mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	microtubule cytoskeleton|transcription factor TFIIF complex	ATP binding|ATP-dependent helicase activity|DNA binding|protein binding				0		Lung NSC(96;0.00115)|Prostate(109;0.00578)|Breast(139;0.0192)|Lung SC(185;0.0367)|Hepatocellular(98;0.133)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000647)														---	---	---	---
LOC100190939	100190939	broad.mit.edu	37	13	45934841	45934841	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45934841delT	uc010tfr.1	+						LOC100190939_uc001vac.2_Intron	NR_024458				Homo sapiens pp13759 mRNA, complete cds.												0																		---	---	---	---
LCP1	3936	broad.mit.edu	37	13	46708464	46708464	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46708464delT	uc001vaz.3	-						LCP1_uc010ack.2_Intron|LCP1_uc001vay.3_Intron|LCP1_uc001vba.3_Intron	NM_002298	NP_002289			L-plastin						regulation of intracellular protein transport|T cell activation involved in immune response	cell junction|cytosol|ruffle membrane	calcium ion binding			lung(4)|ovary(3)	7		Lung NSC(96;1.27e-05)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.39e-05)				T	BCL6	NHL 								---	---	---	---
C13orf18	80183	broad.mit.edu	37	13	46962505	46962519	+	5'Flank	DEL	GAAGGAAGGAAGGGC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46962505_46962519delGAAGGAAGGAAGGGC	uc010acl.2	-						C13orf18_uc001vbf.3_5'Flank|C13orf18_uc001vbg.3_5'Flank|C13orf18_uc010tfz.1_5'Flank|C13orf18_uc010acm.2_5'Flank|C13orf18_uc010acn.2_5'Flank|C13orf18_uc001vbe.3_5'Flank|C13orf18_uc001vbh.3_Intron|C13orf18_uc001vbi.3_Intron	NM_025113	NP_079389			hypothetical protein LOC80183												0		Lung NSC(96;2.31e-05)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;2.19e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	47081842	47081842	+	IGR	DEL	G	-	-	rs34944979		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47081842delG								C13orf18 (69517 upstream) : LRCH1 (45454 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	47114786	47114788	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47114786_47114788delTTT								C13orf18 (102461 upstream) : LRCH1 (12508 downstream)																																			---	---	---	---
LRCH1	23143	broad.mit.edu	37	13	47224214	47224214	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47224214delA	uc001vbj.2	+						LRCH1_uc010acp.2_Intron|LRCH1_uc001vbk.2_Intron|LRCH1_uc001vbl.3_Intron	NM_015116	NP_055931			leucine-rich repeats and calponin homology (CH)											ovary(1)|central_nervous_system(1)	2		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)														---	---	---	---
LRCH1	23143	broad.mit.edu	37	13	47309115	47309115	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47309115delT	uc001vbj.2	+						LRCH1_uc001vbk.2_Intron|LRCH1_uc001vbl.3_Intron	NM_015116	NP_055931			leucine-rich repeats and calponin homology (CH)											ovary(1)|central_nervous_system(1)	2		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	47917367	47917367	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47917367delA								HTR2A (446317 upstream) : SUCLA2 (599425 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	48281651	48281651	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48281651delT								HTR2A (810601 upstream) : SUCLA2 (235141 downstream)																																			---	---	---	---
SUCLA2	8803	broad.mit.edu	37	13	48570880	48570881	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48570880_48570881insA	uc001vbs.2	-						SUCLA2_uc010tgb.1_Intron|SUCLA2_uc010tgc.1_Intron|SUCLA2_uc010tgd.1_Intron|SUCLA2_uc001vbt.1_Intron|SUCLA2_uc001vbu.1_Intron	NM_003850	NP_003841			succinate-CoA ligase, ADP-forming, beta subunit						succinyl-CoA pathway|tricarboxylic acid cycle	mitochondrial matrix	ATP binding|metal ion binding|protein binding|succinate-CoA ligase (ADP-forming) activity			central_nervous_system(1)	1		all_cancers(8;1.13e-24)|all_epithelial(8;1.78e-13)|all_lung(13;2.85e-06)|Breast(56;0.000141)|Lung NSC(96;0.000226)|all_hematologic(8;0.000885)|Prostate(109;0.00132)|Acute lymphoblastic leukemia(8;0.0167)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;2.1e-06)	Succinic acid(DB00139)													---	---	---	---
Unknown	0	broad.mit.edu	37	13	48726954	48726954	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48726954delA								MED4 (57703 upstream) : ITM2B (80320 downstream)																																			---	---	---	---
RB1	5925	broad.mit.edu	37	13	48955364	48955364	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48955364delT	uc001vcb.2	+							NM_000321	NP_000312			retinoblastoma 1						androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation	chromatin|PML body|Rb-E2F complex|SWI/SNF complex	androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding	p.?(7)		lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1)	358		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)		6	D|Mis|N|F|S		retinoblastoma|sarcoma|breast|small cell lung	retinoblastoma|sarcoma|breast|small cell lung			Hereditary_Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			---	---	---	---
Unknown	0	broad.mit.edu	37	13	49135267	49135267	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49135267delA								RCBTB2 (25149 upstream) : CYSLTR2 (92598 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	49415403	49415403	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49415403delA								CYSLTR2 (131905 upstream) : FNDC3A (134645 downstream)																																			---	---	---	---
FNDC3A	22862	broad.mit.edu	37	13	49559794	49559794	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49559794delA	uc001vcm.2	+						FNDC3A_uc001vcl.1_Intron|FNDC3A_uc001vcn.2_Intron|FNDC3A_uc001vco.2_Intron	NM_001079673	NP_001073141			fibronectin type III domain containing 3A							Golgi membrane|integral to membrane				lung(2)	2		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)														---	---	---	---
FNDC3A	22862	broad.mit.edu	37	13	49602351	49602351	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49602351delA	uc001vcm.2	+						FNDC3A_uc001vcl.1_Intron|FNDC3A_uc001vcn.2_Intron|FNDC3A_uc001vco.2_Intron	NM_001079673	NP_001073141			fibronectin type III domain containing 3A							Golgi membrane|integral to membrane				lung(2)	2		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)														---	---	---	---
CAB39L	81617	broad.mit.edu	37	13	49967302	49967302	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49967302delA	uc001vcw.2	-						CAB39L_uc001vcx.2_Intron|CAB39L_uc010adf.2_Intron	NM_030925	NP_112187			calcium binding protein 39-like						cell cycle arrest|insulin receptor signaling pathway|regulation of fatty acid oxidation	cytosol	protein binding				0		Lung NSC(96;2.11e-05)|Breast(56;0.00017)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;3.66e-09)|COAD - Colon adenocarcinoma(199;0.226)														---	---	---	---
SETDB2	83852	broad.mit.edu	37	13	50056660	50056660	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50056660delT	uc001vcz.2	+						SETDB2_uc001vcy.3_Intron|SETDB2_uc010adh.2_Intron|SETDB2_uc001vda.2_Intron	NM_031915	NP_114121			SET domain, bifurcated 2 isoform a						cell division|chromosome segregation|heart looping|left/right axis specification|mitosis|negative regulation of transcription, DNA-dependent	chromosome|nucleus	DNA binding|histone methyltransferase activity (H3-K9 specific)|zinc ion binding			ovary(1)|central_nervous_system(1)	2		Lung NSC(96;0.000408)|Breast(56;0.00131)|Prostate(109;0.00446)|Hepatocellular(98;0.0556)|Glioma(44;0.236)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;3.1e-09)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	50442051	50442052	+	IGR	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50442051_50442052delGA								KPNA3 (74994 upstream) : LOC220429 (22493 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	50446933	50446941	+	IGR	DEL	AAAAAAAAG	-	-	rs72288750		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50446933_50446941delAAAAAAAAG								KPNA3 (79876 upstream) : LOC220429 (17604 downstream)																																			---	---	---	---
DLEU1	10301	broad.mit.edu	37	13	50737310	50737310	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50737310delA	uc010adl.1	+						DLEU1_uc001vee.1_Intron|DLEU1_uc010adm.1_Intron|DLEU1_uc010adn.1_Intron|DLEU1_uc001vef.1_Intron|DLEU1_uc001veg.1_Intron|DLEU1_uc010tgn.1_Intron|DLEU1_uc001vei.1_Intron|DLEU1_uc010ado.1_Intron|DLEU1_uc010adp.1_Intron					Homo sapiens XTP6 (XTP6) mRNA, complete cds.												0																		---	---	---	---
DLEU1	10301	broad.mit.edu	37	13	50995715	50995715	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:50995715delT	uc001vee.1	+						DLEU1_uc010adm.1_Intron|DLEU1_uc010adn.1_Intron|DLEU1_uc001vef.1_Intron|DLEU1_uc001veg.1_Intron|DLEU1_uc010tgn.1_Intron|DLEU1_uc001vei.1_Intron|DLEU1_uc010ado.1_Intron|DLEU1_uc010adp.1_Intron|uc001vel.1_Intron|uc001vem.1_Intron|uc001veq.1_Intron|uc001ver.2_Intron|uc001ves.1_Intron|uc001vet.1_Intron|uc001veu.2_Intron|uc001vev.2_Intron					Homo sapiens XTP6 (XTP6) mRNA, complete cds.												0																		---	---	---	---
DLEU7	220107	broad.mit.edu	37	13	51364082	51364083	+	Intron	DEL	TT	-	-	rs59074825		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51364082_51364083delTT	uc001vex.2	-							NM_198989	NP_945340			deleted in lymphocytic leukemia, 7												0		Acute lymphoblastic leukemia(7;1.03e-07)|Lung NSC(96;0.000818)|Breast(56;0.00122)|Prostate(109;0.0047)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;3.25e-08)														---	---	---	---
GUCY1B2	2974	broad.mit.edu	37	13	51589121	51589122	+	Intron	DEL	CA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51589121_51589122delCA	uc001vfc.3	-							NR_003923				Homo sapiens soluble guanylyl cyclase subunit beta 2 (GUCY1B2) mRNA, complete cds.												0																		---	---	---	---
GUCY1B2	2974	broad.mit.edu	37	13	51600016	51600016	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51600016delG	uc001vfd.3	-						GUCY1B2_uc010tgo.1_Intron|GUCY1B2_uc001vfc.3_Intron					SubName: Full=Guanylate cyclase 1, soluble, beta 2;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	51903749	51903749	+	IGR	DEL	A	-	-	rs9634840	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:51903749delA								FAM124A (48133 upstream) : SERPINE3 (11419 downstream)																																			---	---	---	---
ATP7B	540	broad.mit.edu	37	13	52576533	52576533	+	Intron	DEL	A	-	-	rs111933118		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52576533delA	uc001vfw.2	-						ATP7B_uc010adv.2_Intron|ATP7B_uc001vfx.2_Intron|ATP7B_uc001vfy.2_Intron|ATP7B_uc010tgt.1_Intron|ATP7B_uc010tgu.1_Intron|ATP7B_uc010tgv.1_Intron	NM_000053	NP_000044			ATPase, Cu++ transporting, beta polypeptide						ATP biosynthetic process|cellular copper ion homeostasis|copper ion import|response to copper ion|sequestering of calcium ion	Golgi membrane|integral to plasma membrane|late endosome|mitochondrion	ATP binding|copper ion binding|copper-exporting ATPase activity|protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)										Wilson_disease				---	---	---	---
THSD1P1	374500	broad.mit.edu	37	13	52771584	52771584	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52771584delT	uc001vgm.1	-						THSD1P1_uc001vgl.1_5'Flank					Homo sapiens cDNA FLJ14630 fis, clone NT2RP2000459.												0																		---	---	---	---
TPTE2P3	220115	broad.mit.edu	37	13	53095129	53095129	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53095129delT	uc001vgw.2	+							NR_002793				Homo sapiens TPTE and PTEN homologous inositol lipid phosphatase pseudogene, mRNA (cDNA clone IMAGE:5298506), with apparent retained intron.												0																		---	---	---	---
LECT1	11061	broad.mit.edu	37	13	53299566	53299566	+	Intron	DEL	T	-	-	rs71739565		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53299566delT	uc001vhf.2	-						LECT1_uc001vhg.2_Intron|LECT1_uc001vhh.2_Intron	NM_007015	NP_008946			leukocyte cell derived chemotaxin 1 isoform 1						cartilage development|proteoglycan metabolic process	endomembrane system|extracellular region|integral to membrane				ovary(2)	2		Lung NSC(96;0.00212)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.38e-08)														---	---	---	---
PCDH8	5100	broad.mit.edu	37	13	53420216	53420216	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53420216delC	uc001vhi.2	-	1	2559	c.2356delG	c.(2356-2358)GCCfs	p.A786fs	PCDH8_uc001vhj.2_Intron	NM_002590	NP_002581	O95206	PCDH8_HUMAN	protocadherin 8 isoform 1 precursor	786	Cytoplasmic (Potential).				cell-cell signaling|homophilic cell adhesion	cell junction|dendrite|integral to plasma membrane|postsynaptic membrane|presynaptic membrane	calcium ion binding			breast(1)	1		Lung NSC(96;0.0019)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.19e-08)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	53548475	53548475	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53548475delC								PCDH8 (125701 upstream) : OLFM4 (54497 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	53650486	53650486	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53650486delA								OLFM4 (24300 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	54423368	54423368	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:54423368delC								OLFM4 (797182 upstream) : MIR1297 (462739 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	54475319	54475319	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:54475319delT								OLFM4 (849133 upstream) : MIR1297 (410788 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	55015539	55015539	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:55015539delT								MIR1297 (129356 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	55100882	55100882	+	IGR	DEL	A	-	-	rs67240658		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:55100882delA								MIR1297 (214699 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	55275474	55275474	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:55275474delA								MIR1297 (389291 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	55682045	55682045	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:55682045delT								MIR1297 (795862 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	56819186	56819186	+	IGR	DEL	T	-	-	rs77338174		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:56819186delT								None (None upstream) : PRR20C (895866 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	56995823	56995823	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:56995823delT								None (None upstream) : PRR20C (719229 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	57276624	57276624	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:57276624delT								None (None upstream) : PRR20C (438428 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	57348124	57348125	+	IGR	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:57348124_57348125delAC								None (None upstream) : PRR20C (366927 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	57545203	57545203	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:57545203delT								None (None upstream) : PRR20C (169849 downstream)																																			---	---	---	---
PCDH17	27253	broad.mit.edu	37	13	58209044	58209044	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:58209044delC	uc001vhq.1	+	1	3256	c.2364delC	c.(2362-2364)AGCfs	p.S788fs	PCDH17_uc010aec.1_Frame_Shift_Del_p.S788fs	NM_001040429	NP_001035519	O14917	PCD17_HUMAN	protocadherin 17 precursor	788	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding			ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	7		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)														---	---	---	---
PCDH17	27253	broad.mit.edu	37	13	58295718	58295718	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:58295718delA	uc001vhq.1	+						PCDH17_uc010aec.1_Intron|PCDH17_uc001vhr.1_Intron	NM_001040429	NP_001035519			protocadherin 17 precursor						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding			ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	7		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	58678051	58678051	+	IGR	DEL	T	-	-	rs7324018	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:58678051delT								PCDH17 (374986 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	58720268	58720268	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:58720268delC								PCDH17 (417203 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	59950394	59950394	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:59950394delT								None (None upstream) : DIAPH3 (289331 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	60192960	60192960	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60192960delA								None (None upstream) : DIAPH3 (46765 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	60769516	60769517	+	IGR	INS	-	AC	AC	rs36061441		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60769516_60769517insAC								DIAPH3 (31397 upstream) : TDRD3 (201074 downstream)																																			---	---	---	---
TDRD3	81550	broad.mit.edu	37	13	61141595	61141595	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61141595delT	uc001via.2	+						TDRD3_uc001vhz.3_Intron|TDRD3_uc010aeg.2_Intron|TDRD3_uc001vib.3_Intron	NM_030794	NP_110421			tudor domain containing 3 isoform 2						chromatin modification	cytoplasm|nucleus	chromatin binding|methylated histone residue binding|nucleic acid binding|transcription coactivator activity			upper_aerodigestive_tract(1)|skin(1)	2		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	61178311	61178312	+	IGR	INS	-	TG	TG	rs144928478	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61178311_61178312insTG								TDRD3 (30299 upstream) : PCDH20 (805509 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	61182759	61182759	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61182759delT								TDRD3 (34747 upstream) : PCDH20 (801062 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	61202364	61202365	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61202364_61202365insT								TDRD3 (54352 upstream) : PCDH20 (781456 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	62522858	62522858	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:62522858delA								PCDH20 (520779 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	63619537	63619537	+	IGR	DEL	T	-	-	rs148981749		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63619537delT								None (None upstream) : OR7E156P (692031 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	63629620	63629628	+	IGR	DEL	TAAGAAAAA	-	-	rs67126707		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63629620_63629628delTAAGAAAAA								None (None upstream) : OR7E156P (681940 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	63931284	63931285	+	IGR	INS	-	C	C	rs72521028		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:63931284_63931285insC								None (None upstream) : OR7E156P (380283 downstream)																																			---	---	---	---
OR7E156P	283491	broad.mit.edu	37	13	64316038	64316038	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:64316038delG	uc001vif.1	+						OR7E156P_uc001vig.1_Intron	NR_002171				Homo sapiens cDNA FLJ40150 fis, clone TESTI2013699.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	13	64441912	64441912	+	IGR	DEL	A	-	-	rs72560080		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:64441912delA								OR7E156P (125211 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	65179868	65179870	+	IGR	DEL	AAA	-	-	rs681730	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:65179868_65179870delAAA								OR7E156P (863167 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	65952751	65952751	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:65952751delT								None (None upstream) : PCDH9 (924216 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	66061840	66061840	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66061840delA								None (None upstream) : PCDH9 (815127 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	66695561	66695563	+	IGR	DEL	TTG	-	-	rs58541601		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:66695561_66695563delTTG								None (None upstream) : PCDH9 (181404 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	67894369	67894369	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67894369delT								PCDH9 (89901 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	67963380	67963380	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67963380delT								PCDH9 (158912 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	68507872	68507873	+	IGR	DEL	AC	-	-	rs72447195		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:68507872_68507873delAC								PCDH9 (703404 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	68543228	68543228	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:68543228delT								PCDH9 (738760 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	68570808	68570808	+	IGR	DEL	A	-	-	rs112890482		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:68570808delA								PCDH9 (766340 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	68967867	68967868	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:68967867_68967868delAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	69849551	69849551	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:69849551delT								None (None upstream) : KLHL1 (425175 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	71056628	71056628	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:71056628delA								ATXN8OS (342743 upstream) : DACH1 (955470 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	71569210	71569210	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:71569210delT								ATXN8OS (855325 upstream) : DACH1 (442888 downstream)																																			---	---	---	---
DACH1	1602	broad.mit.edu	37	13	72368199	72368199	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72368199delA	uc010thn.1	-						DACH1_uc010tho.1_Intron|DACH1_uc010thp.1_Intron	NM_080759	NP_542937			dachshund homolog 1 isoform a						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|nucleotide binding|protein binding			breast(1)	1		Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198)		GBM - Glioblastoma multiforme(99;0.00032)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	72919527	72919527	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:72919527delT								DACH1 (478197 upstream) : C13orf37 (362968 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	73010652	73010652	+	IGR	DEL	A	-	-	rs34945960		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73010652delA								DACH1 (569322 upstream) : C13orf37 (271843 downstream)																																			---	---	---	---
C13orf34	79866	broad.mit.edu	37	13	73302918	73302918	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73302918delT	uc001viv.1	+						C13orf37_uc001viu.2_5'Flank|C13orf34_uc010thq.1_Intron|C13orf34_uc010aen.1_Intron|C13orf34_uc010thr.1_Intron|C13orf34_uc001viw.1_Intron	NM_024808	NP_079084			aurora borealis						cell division|mitosis|regulation of mitosis|regulation of mitotic spindle organization|regulation of protein localization		protein kinase binding				0		Breast(118;0.0735)		GBM - Glioblastoma multiforme(99;0.000227)														---	---	---	---
DIS3	22894	broad.mit.edu	37	13	73349322	73349322	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73349322delA	uc001vix.3	-						DIS3_uc001viy.3_Intron|DIS3_uc001viz.2_Intron	NM_014953	NP_055768			DIS3 mitotic control isoform a						CUT catabolic process|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|rRNA catabolic process|rRNA processing	cytosol|exosome (RNase complex)|nucleolus|nucleoplasm	3'-5'-exoribonuclease activity|endonuclease activity|guanyl-nucleotide exchange factor activity|protein binding|RNA binding			central_nervous_system(1)	1		Breast(118;0.0074)|Acute lymphoblastic leukemia(28;0.0195)		GBM - Glioblastoma multiforme(99;0.000181)											Multiple Myeloma(4;0.011)			---	---	---	---
Unknown	0	broad.mit.edu	37	13	74722058	74722058	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:74722058delT								KLF12 (13664 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	75101999	75101999	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75101999delA								KLF12 (393605 upstream) : LOC647288 (709891 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	75523516	75523516	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75523516delA								KLF12 (815122 upstream) : LOC647288 (288374 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	75691131	75691131	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75691131delA								KLF12 (982737 upstream) : LOC647288 (120759 downstream)																																			---	---	---	---
TBC1D4	9882	broad.mit.edu	37	13	75894317	75894317	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75894317delT	uc001vjl.1	-						TBC1D4_uc010aer.2_Intron|TBC1D4_uc010aes.2_Intron	NM_014832	NP_055647			TBC1 domain family, member 4							cytoplasm	Rab GTPase activator activity			ovary(4)|central_nervous_system(1)|skin(1)	6		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)														---	---	---	---
TBC1D4	9882	broad.mit.edu	37	13	75911179	75911179	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:75911179delA	uc001vjl.1	-						TBC1D4_uc010aer.2_Intron|TBC1D4_uc010aes.2_Intron	NM_014832	NP_055647			TBC1 domain family, member 4							cytoplasm	Rab GTPase activator activity			ovary(4)|central_nervous_system(1)|skin(1)	6		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	76634871	76634871	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76634871delA								LMO7 (200867 upstream) : KCTD12 (819433 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	76642857	76642857	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76642857delT								LMO7 (208853 upstream) : KCTD12 (811447 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	76948305	76948305	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76948305delT								LMO7 (514301 upstream) : KCTD12 (505999 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	76960074	76960074	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76960074delT								LMO7 (526070 upstream) : KCTD12 (494230 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	77043903	77043903	+	IGR	DEL	T	-	-	rs34613221		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77043903delT								LMO7 (609899 upstream) : KCTD12 (410401 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	77124865	77124865	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77124865delA								LMO7 (690861 upstream) : KCTD12 (329439 downstream)																																			---	---	---	---
CLN5	1203	broad.mit.edu	37	13	77571278	77571278	+	Intron	DEL	G	-	-	rs851516	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77571278delG	uc001vkc.2	+							NM_006493	NP_006484			ceroid-lipofuscinosis, neuronal 5						brain development|cell death|lysosomal lumen acidification|neuron maturation|protein catabolic process	endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosomal membrane|perinuclear region of cytoplasm	protein binding			ovary(1)	1		Acute lymphoblastic leukemia(28;0.205)		GBM - Glioblastoma multiforme(99;0.0503)														---	---	---	---
MYCBP2	23077	broad.mit.edu	37	13	77834802	77834803	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77834802_77834803delAA	uc001vkf.2	-						MYCBP2_uc010aev.2_Intron	NM_015057	NP_055872			MYC binding protein 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ligase activity|protein binding|zinc ion binding			ovary(4)|breast(4)|skin(3)|lung(2)|pancreas(1)	14		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	77954535	77954535	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77954535delT								MYCBP2 (53358 upstream) : SCEL (155274 downstream)																																			---	---	---	---
SCEL	8796	broad.mit.edu	37	13	78137260	78137260	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78137260delC	uc001vki.2	+						SCEL_uc001vkj.2_Intron|SCEL_uc010thx.1_Intron	NM_144777	NP_659001			sciellin isoform 1						embryo development|keratinocyte differentiation	cornified envelope|cytoplasm|membrane	protein binding|zinc ion binding			ovary(4)|breast(1)	5		Acute lymphoblastic leukemia(28;0.0282)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0233)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	79166747	79166747	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79166747delT	uc001vku.1	+											Homo sapiens cDNA FLJ38460 fis, clone FEBRA2020801.																												OREG0004180	type=REGULATORY REGION|EvidenceSubtype=Dual luciferase reporter gene assay; In-vivo GFP Expression Assay	---	---	---	---
RNF219	79596	broad.mit.edu	37	13	79216517	79216517	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79216517delA	uc001vkw.1	-						RNF219_uc010afb.1_Intron|RNF219_uc010afc.2_Intron	NM_024546	NP_078822			ring finger protein 219								zinc ion binding			large_intestine(2)	2		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.0848)		GBM - Glioblastoma multiforme(99;0.0414)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	79295831	79295831	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79295831delT								RNF219 (61131 upstream) : RBM26 (598269 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	79822688	79822688	+	IGR	DEL	A	-	-	rs34442271		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:79822688delA								RNF219 (587988 upstream) : RBM26 (71412 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	80560117	80560117	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:80560117delT								NDFIP2 (429912 upstream) : SPRY2 (349997 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	80998466	80998466	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:80998466delT								SPRY2 (83380 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	81133800	81133800	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81133800delA								SPRY2 (218714 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	81327788	81327788	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81327788delC								SPRY2 (412702 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	81771980	81771980	+	IGR	DEL	A	-	-	rs5805114		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:81771980delA								SPRY2 (856894 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	82313452	82313452	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:82313452delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	83113378	83113378	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:83113378delT								None (None upstream) : None (None downstream)																																			---	---	---	---
SLITRK1	114798	broad.mit.edu	37	13	84458312	84458312	+	5'Flank	DEL	A	-	-	rs67444596		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:84458312delA	uc001vlk.2	-							NM_052910	NP_443142			slit and trk like 1 protein precursor							integral to membrane				ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5	Medulloblastoma(90;0.18)	Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.07)														---	---	---	---
Unknown	0	broad.mit.edu	37	13	85796175	85796175	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:85796175delA								None (None upstream) : SLITRK6 (570747 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	86204590	86204591	+	IGR	INS	-	T	T	rs149937095	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:86204590_86204591insT								None (None upstream) : SLITRK6 (162331 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	87569953	87569954	+	IGR	DEL	CA	-	-	rs112083893		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:87569953_87569954delCA								None (None upstream) : SLITRK5 (754916 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	87703898	87703900	+	IGR	DEL	AAA	-	-	rs71694077		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:87703898_87703900delAAA								None (None upstream) : SLITRK5 (620970 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	87882811	87882811	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:87882811delT								None (None upstream) : SLITRK5 (442059 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	88261673	88261674	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88261673_88261674insT	uc001vlm.1	-											Homo sapiens clone IMAGE:32106, mRNA sequence.																														---	---	---	---
Unknown	0	broad.mit.edu	37	13	88431947	88431950	+	IGR	DEL	GTGT	-	-	rs112998938		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88431947_88431950delGTGT								SLITRK5 (100079 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	88483362	88483363	+	IGR	DEL	TA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88483362_88483363delTA								SLITRK5 (151494 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	88675845	88675845	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88675845delG								SLITRK5 (343977 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	89561162	89561162	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:89561162delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	90732961	90732963	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:90732961_90732963delTTT								None (None upstream) : MIR622 (150473 downstream)																																			---	---	---	---
GPC5	2262	broad.mit.edu	37	13	92224303	92224304	+	Intron	DEL	AT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:92224303_92224304delAT	uc010tif.1	+							NM_004466	NP_004457			glypican 5 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding			ovary(2)|skin(2)|upper_aerodigestive_tract(1)	5	all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	Lung NSC(4;0.00454)																---	---	---	---
GPC5	2262	broad.mit.edu	37	13	92871815	92871815	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:92871815delT	uc010tif.1	+							NM_004466	NP_004457			glypican 5 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding			ovary(2)|skin(2)|upper_aerodigestive_tract(1)	5	all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	Lung NSC(4;0.00454)																---	---	---	---
GPC5	2262	broad.mit.edu	37	13	93404320	93404322	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:93404320_93404322delAAA	uc010tif.1	+							NM_004466	NP_004457			glypican 5 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding			ovary(2)|skin(2)|upper_aerodigestive_tract(1)	5	all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	Lung NSC(4;0.00454)																---	---	---	---
Unknown	0	broad.mit.edu	37	13	93746873	93746873	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:93746873delT								GPC5 (227388 upstream) : GPC6 (132205 downstream)																																			---	---	---	---
GPC6	10082	broad.mit.edu	37	13	94316868	94316869	+	Intron	INS	-	TTTG	TTTG	rs150836167	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94316868_94316869insTTTG	uc001vlt.2	+						GPC6_uc010tig.1_Intron|GPC6_uc001vlu.1_Intron	NM_005708	NP_005699			glypican 6 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)																---	---	---	---
GPC6	10082	broad.mit.edu	37	13	94363572	94363573	+	Intron	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94363572_94363573insG	uc001vlt.2	+						GPC6_uc010tig.1_Intron|GPC6_uc001vlu.1_Intron	NM_005708	NP_005699			glypican 6 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)																---	---	---	---
GPC6	10082	broad.mit.edu	37	13	94446936	94446936	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94446936delG	uc001vlt.2	+						GPC6_uc010tig.1_Intron|GPC6_uc001vlu.1_Intron	NM_005708	NP_005699			glypican 6 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)																---	---	---	---
Unknown	0	broad.mit.edu	37	13	95170489	95170489	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95170489delA								DCT (38553 upstream) : TGDS (55820 downstream)																																			---	---	---	---
GPR180	160897	broad.mit.edu	37	13	95260802	95260802	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95260802delT	uc001vly.2	+						GPR180_uc001vlz.2_Intron|GPR180_uc010afi.2_Intron	NM_180989	NP_851320			G protein-coupled receptor 180 precursor							integral to membrane				breast(1)	1	all_neural(89;0.0684)|Medulloblastoma(90;0.163)																	---	---	---	---
Unknown	0	broad.mit.edu	37	13	95354033	95354033	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95354033delC								GPR180 (72089 upstream) : SOX21 (7849 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	95357512	95357512	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95357512delA								GPR180 (75568 upstream) : SOX21 (4370 downstream)																																			---	---	---	---
ABCC4	10257	broad.mit.edu	37	13	95848885	95848886	+	Intron	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95848885_95848886insG	uc001vmd.3	-						ABCC4_uc010afk.2_Intron|ABCC4_uc001vme.2_Intron|ABCC4_uc010tih.1_Intron|ABCC4_uc001vmf.2_Intron|ABCC4_uc010afl.1_Intron|ABCC4_uc010afm.1_Intron	NM_005845	NP_005836			ATP-binding cassette, sub-family C, member 4						platelet activation|platelet degranulation	integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity			central_nervous_system(3)|skin(1)	4	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Cefazolin(DB01327)													---	---	---	---
ABCC4	10257	broad.mit.edu	37	13	95848985	95848991	+	Intron	DEL	AGAAGGG	-	-	rs113892410		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95848985_95848991delAGAAGGG	uc001vmd.3	-						ABCC4_uc010afk.2_Intron|ABCC4_uc001vme.2_Intron|ABCC4_uc010tih.1_Intron|ABCC4_uc001vmf.2_Intron|ABCC4_uc010afl.1_Intron|ABCC4_uc010afm.1_Intron	NM_005845	NP_005836			ATP-binding cassette, sub-family C, member 4						platelet activation|platelet degranulation	integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity			central_nervous_system(3)|skin(1)	4	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Cefazolin(DB01327)													---	---	---	---
CLDN10	9071	broad.mit.edu	37	13	96108853	96108854	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96108853_96108854delAA	uc001vmg.2	+						CLDN10_uc010tii.1_Intron	NM_182848	NP_878268			claudin 10 isoform a						calcium-independent cell-cell adhesion	integral to membrane|tight junction	identical protein binding|structural molecule activity			ovary(1)	1	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.18)															---	---	---	---
DNAJC3	5611	broad.mit.edu	37	13	96375824	96375824	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96375824delT	uc001vmq.2	+						DNAJC3_uc001vmp.2_Intron|DNAJC3_uc001vmr.2_Intron	NM_006260	NP_006251			DnaJ (Hsp40) homolog, subfamily C, member 3						protein folding|response to unfolded protein|response to virus		heat shock protein binding|protein kinase inhibitor activity|unfolded protein binding				0	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.126)															---	---	---	---
HS6ST3	266722	broad.mit.edu	37	13	96973656	96973656	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96973656delT	uc001vmw.2	+							NM_153456	NP_703157			heparan sulfate 6-O-sulfotransferase 3							integral to membrane	sulfotransferase activity			ovary(1)|skin(1)	2	all_neural(89;0.0878)|Medulloblastoma(90;0.163)																	---	---	---	---
HS6ST3	266722	broad.mit.edu	37	13	97141146	97141146	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97141146delT	uc001vmw.2	+							NM_153456	NP_703157			heparan sulfate 6-O-sulfotransferase 3							integral to membrane	sulfotransferase activity			ovary(1)|skin(1)	2	all_neural(89;0.0878)|Medulloblastoma(90;0.163)																	---	---	---	---
HS6ST3	266722	broad.mit.edu	37	13	97231817	97231818	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97231817_97231818delAA	uc001vmw.2	+							NM_153456	NP_703157			heparan sulfate 6-O-sulfotransferase 3							integral to membrane	sulfotransferase activity			ovary(1)|skin(1)	2	all_neural(89;0.0878)|Medulloblastoma(90;0.163)																	---	---	---	---
MBNL2	10150	broad.mit.edu	37	13	97913110	97913110	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:97913110delT	uc010aft.2	+						MBNL2_uc001vmz.2_Intron|MBNL2_uc001vna.2_Intron|MBNL2_uc001vnb.2_Intron	NM_144778	NP_659002			muscleblind-like 2 isoform 1						mRNA processing|regulation of RNA splicing|RNA splicing	cytoplasm|nucleus	RNA binding|zinc ion binding				0	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.218)															---	---	---	---
Unknown	0	broad.mit.edu	37	13	98315001	98315001	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98315001delA								RAP2A (194750 upstream) : IPO5 (290928 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	98517275	98517275	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98517275delT								RAP2A (397024 upstream) : IPO5 (88654 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	98710148	98710149	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98710148_98710149delAA								IPO5 (33599 upstream) : FARP1 (84667 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	98783722	98783722	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98783722delT								IPO5 (107173 upstream) : FARP1 (11094 downstream)																																			---	---	---	---
FARP1	10160	broad.mit.edu	37	13	98958116	98958116	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98958116delT	uc001vnj.2	+						FARP1_uc001vnh.2_Intron	NM_005766	NP_005757			FERM, RhoGEF, and pleckstrin domain protein 1						regulation of Rho protein signal transduction	cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|Rho guanyl-nucleotide exchange factor activity			breast(2)	2	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)															---	---	---	---
STK24	8428	broad.mit.edu	37	13	99105679	99105679	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99105679delA	uc001vnm.1	-						STK24_uc001vnn.1_Intron|STK24_uc010tim.1_Intron	NM_003576	NP_003567			serine/threonine kinase 24 isoform a						cellular component disassembly involved in apoptosis|signal transduction	cytosol|nucleoplasm	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(1)|lung(1)	2	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)															---	---	---	---
DOCK9	23348	broad.mit.edu	37	13	99450776	99450787	+	Intron	DEL	CCTGAAGACGAC	-	-	rs11275115		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99450776_99450787delCCTGAAGACGAC	uc001vnt.2	-						DOCK9_uc001vnw.2_Intron|DOCK9_uc001vnq.2_Intron|DOCK9_uc001vnr.2_Intron|DOCK9_uc010tin.1_Intron|DOCK9_uc001vns.2_Intron|DOCK9_uc010tio.1_Intron|DOCK9_uc010tip.1_Intron	NM_015296	NP_056111			dedicator of cytokinesis 9 isoform a						blood coagulation	cytosol|endomembrane system|membrane	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			central_nervous_system(1)	1	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)																	---	---	---	---
UBAC2	337867	broad.mit.edu	37	13	99885370	99885371	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99885370_99885371delTT	uc001voa.3	+						UBAC2_uc010tiu.1_Intron|UBAC2_uc001vob.3_Intron|UBAC2_uc010tiv.1_Intron|UBAC2_uc001vod.2_Intron|UBAC2_uc001voc.2_Intron|UBAC2_uc010tiw.1_Intron	NM_001144072	NP_001137544			UBA domain containing 2 isoform 1							integral to membrane				ovary(1)	1	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)																	---	---	---	---
UBAC2	337867	broad.mit.edu	37	13	99970257	99970257	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99970257delT	uc001voa.3	+						UBAC2_uc010tiu.1_Intron|UBAC2_uc001vob.3_Intron|UBAC2_uc010tiv.1_Intron|UBAC2_uc001vod.2_Intron|UBAC2_uc001voc.2_Intron|UBAC2_uc010tiw.1_Intron|UBAC2_uc001voh.2_Intron	NM_001144072	NP_001137544			UBA domain containing 2 isoform 1							integral to membrane				ovary(1)	1	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)																	---	---	---	---
Unknown	0	broad.mit.edu	37	13	100240683	100240698	+	IGR	DEL	TTCTTTCTTTCCTTCC	-	-	rs12560994	by1000genomes;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100240683_100240698delTTCTTTCTTTCCTTCC								TM9SF2 (25407 upstream) : CLYBL (18238 downstream)																																			---	---	---	---
CLYBL	171425	broad.mit.edu	37	13	100429134	100429134	+	Intron	DEL	T	-	-	rs114009483	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100429134delT	uc001vok.2	+						CLYBL_uc010tix.1_Intron|CLYBL_uc010tiy.1_Intron	NM_206808	NP_996531			citrate lyase beta like precursor						cellular aromatic compound metabolic process	citrate lyase complex|mitochondrion	citrate (pro-3S)-lyase activity|metal ion binding				0	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)																	---	---	---	---
CLYBL	171425	broad.mit.edu	37	13	100436132	100436133	+	Intron	DEL	AT	-	-	rs144542877		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100436132_100436133delAT	uc001vok.2	+						CLYBL_uc010tix.1_Intron|CLYBL_uc010tiy.1_Intron	NM_206808	NP_996531			citrate lyase beta like precursor						cellular aromatic compound metabolic process	citrate lyase complex|mitochondrion	citrate (pro-3S)-lyase activity|metal ion binding				0	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)																	---	---	---	---
PCCA	5095	broad.mit.edu	37	13	100803845	100803845	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100803845delA	uc001voo.2	+						PCCA_uc010aga.2_Intron|PCCA_uc010tiz.1_Intron	NM_000282	NP_000273			propionyl-Coenzyme A carboxylase, alpha						fatty acid beta-oxidation	mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|enzyme binding|metal ion binding|propionyl-CoA carboxylase activity			skin(2)	2	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Biotin(DB00121)													---	---	---	---
PCCA	5095	broad.mit.edu	37	13	101137297	101137298	+	Intron	DEL	CT	-	-	rs61970534		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101137297_101137298delCT	uc001voo.2	+						PCCA_uc010aga.2_Intron|PCCA_uc010tiz.1_Intron|PCCA_uc001vop.2_Intron	NM_000282	NP_000273			propionyl-Coenzyme A carboxylase, alpha						fatty acid beta-oxidation	mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|enzyme binding|metal ion binding|propionyl-CoA carboxylase activity			skin(2)	2	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Biotin(DB00121)													---	---	---	---
Unknown	0	broad.mit.edu	37	13	101651707	101651707	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101651707delA								TMTC4 (324604 upstream) : NALCN (54423 downstream)																																			---	---	---	---
NALCN	259232	broad.mit.edu	37	13	102042622	102042622	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102042622delT	uc001vox.1	-						NALCN_uc001voy.2_Intron|NALCN_uc001voz.2_Intron|NALCN_uc001vpa.2_Intron	NM_052867	NP_443099			voltage gated channel like 1							integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|skin(2)|pancreas(1)|central_nervous_system(1)	16	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)																	---	---	---	---
ITGBL1	9358	broad.mit.edu	37	13	102174189	102174189	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102174189delT	uc001vpb.2	+						ITGBL1_uc010agb.2_Intron|ITGBL1_uc001vpc.3_Intron	NM_004791	NP_004782			integrin, beta-like 1 (with EGF-like repeat						cell-matrix adhesion|integrin-mediated signaling pathway	extracellular region|integrin complex	binding|receptor activity			ovary(1)|skin(1)	2	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)																	---	---	---	---
ITGBL1	9358	broad.mit.edu	37	13	102263436	102263436	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102263436delG	uc001vpb.2	+						ITGBL1_uc010agb.2_Intron|ITGBL1_uc001vpc.3_Intron	NM_004791	NP_004782			integrin, beta-like 1 (with EGF-like repeat						cell-matrix adhesion|integrin-mediated signaling pathway	extracellular region|integrin complex	binding|receptor activity			ovary(1)|skin(1)	2	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)																	---	---	---	---
FGF14	2259	broad.mit.edu	37	13	102701823	102701823	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:102701823delA	uc001vpf.2	-							NM_175929	NP_787125			fibroblast growth factor 14 isoform 1B						cell death|cell-cell signaling|JNK cascade|nervous system development|signal transduction	nucleus	growth factor activity|heparin binding			ovary(2)|lung(1)|large_intestine(1)	4	all_neural(89;0.0239)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)																	---	---	---	---
FGF14	2259	broad.mit.edu	37	13	103022348	103022348	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103022348delT	uc001vpf.2	-						uc001vph.1_Intron|uc001vpg.1_5'Flank	NM_175929	NP_787125			fibroblast growth factor 14 isoform 1B						cell death|cell-cell signaling|JNK cascade|nervous system development|signal transduction	nucleus	growth factor activity|heparin binding			ovary(2)|lung(1)|large_intestine(1)	4	all_neural(89;0.0239)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)																	---	---	---	---
FGF14	2259	broad.mit.edu	37	13	103054180	103054180	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103054180delA	uc001vpf.2	-							NM_175929	NP_787125			fibroblast growth factor 14 isoform 1B						cell death|cell-cell signaling|JNK cascade|nervous system development|signal transduction	nucleus	growth factor activity|heparin binding			ovary(2)|lung(1)|large_intestine(1)	4	all_neural(89;0.0239)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)																	---	---	---	---
ERCC5	2073	broad.mit.edu	37	13	103507612	103507612	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103507612delT	uc001vpw.2	+						ERCC5_uc001vpu.1_Intron|ERCC5_uc010tjb.1_Intron|ERCC5_uc010tjc.1_Intron|ERCC5_uc010tjd.1_Intron	NM_000123	NP_000114			XPG-complementing protein						negative regulation of apoptosis|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|response to UV-C|transcription-coupled nucleotide-excision repair|UV protection	nucleoplasm	bubble DNA binding|double-stranded DNA binding|endodeoxyribonuclease activity|metal ion binding|protein homodimerization activity|protein N-terminus binding|single-stranded DNA binding			ovary(4)|lung(1)|central_nervous_system(1)|skin(1)	7	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)							Mis|N|F			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				---	---	---	---
Unknown	0	broad.mit.edu	37	13	104078562	104078562	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:104078562delA								SLC10A2 (359366 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	104339046	104339047	+	IGR	DEL	TA	-	-	rs1757384	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:104339046_104339047delTA								SLC10A2 (619850 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	104987647	104987648	+	IGR	INS	-	G	G	rs147579374	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:104987647_104987648insG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	105345902	105345902	+	IGR	DEL	T	-	-	rs71936974		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:105345902delT								None (None upstream) : DAOA (772314 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	106474042	106474042	+	IGR	DEL	T	-	-	rs11296552		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:106474042delT								DAOA (330660 upstream) : EFNB2 (668056 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	106905099	106905099	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:106905099delT								DAOA (761717 upstream) : EFNB2 (236999 downstream)																																			---	---	---	---
ARGLU1	55082	broad.mit.edu	37	13	107219284	107219285	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107219284_107219285insT	uc001vqk.3	-							NM_018011	NP_060481			arginine and glutamate rich 1												0	Lung NSC(43;0.015)|all_neural(89;0.0741)|Lung SC(71;0.14)|Medulloblastoma(90;0.169)																	---	---	---	---
Unknown	0	broad.mit.edu	37	13	107349078	107349078	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107349078delA								ARGLU1 (128564 upstream) : FAM155A (471802 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	107634221	107634221	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107634221delC								ARGLU1 (413707 upstream) : FAM155A (186659 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	107770556	107770557	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:107770556_107770557insT								ARGLU1 (550042 upstream) : FAM155A (50323 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	109034881	109034881	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109034881delT								TNFSF13B (75517 upstream) : MYO16 (213619 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	109175114	109175115	+	IGR	INS	-	TGTG	TGTG	rs138474693	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109175114_109175115insTGTG								TNFSF13B (215750 upstream) : MYO16 (73385 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	109220527	109220528	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109220527_109220528insT								TNFSF13B (261163 upstream) : MYO16 (27972 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	109234239	109234241	+	IGR	DEL	AAG	-	-	rs144492638		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109234239_109234241delAAG								TNFSF13B (274875 upstream) : MYO16 (14259 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	109903046	109903047	+	IGR	DEL	AA	-	-	rs34322724		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:109903046_109903047delAA								MYO16 (42691 upstream) : IRS2 (503139 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	110307104	110307105	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110307104_110307105delTG								MYO16 (446749 upstream) : IRS2 (99081 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	13	110327916	110327916	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110327916delG								MYO16 (467561 upstream) : IRS2 (78270 downstream)																																			---	---	---	---
COL4A1	1282	broad.mit.edu	37	13	110892935	110892935	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:110892935delC	uc001vqw.3	-						COL4A1_uc010agl.2_Intron	NM_001845	NP_001836			alpha 1 type IV collagen preproprotein						angiogenesis|axon guidance		extracellular matrix structural constituent|platelet-derived growth factor binding			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)															---	---	---	---
COL4A2	1284	broad.mit.edu	37	13	111105863	111105863	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111105863delA	uc001vqx.2	+							NM_001846	NP_001837			alpha 2 type IV collagen preproprotein						angiogenesis|axon guidance|extracellular matrix organization|negative regulation of angiogenesis	collagen type IV	extracellular matrix structural constituent|protein binding			skin(3)|central_nervous_system(2)|ovary(1)	6	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)															---	---	---	---
Unknown	0	broad.mit.edu	37	13	111237590	111237590	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111237590delT								RAB20 (23519 upstream) : CARKD (30291 downstream)																																			---	---	---	---
CARS2	79587	broad.mit.edu	37	13	111294555	111294555	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111294555delA	uc001vrd.2	-							NM_024537	NP_078813			cysteinyl-tRNA synthetase 2, mitochondrial						cysteinyl-tRNA aminoacylation	cytosol|mitochondrial matrix	ATP binding|cysteine-tRNA ligase activity|metal ion binding				0	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.163)		L-Cysteine(DB00151)													---	---	---	---
Unknown	0	broad.mit.edu	37	13	111433114	111433114	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111433114delA								ING1 (59694 upstream) : C13orf29 (83220 downstream)																																			---	---	---	---
C13orf29	283487	broad.mit.edu	37	13	111524168	111524168	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111524168delT	uc001vrk.2	-							NR_027701				Homo sapiens mRNA for hypothetical protein (ORF1), clone Telethon(Italy_B41)_Strait13785_FL302.												0																		---	---	---	---
ARHGEF7	8874	broad.mit.edu	37	13	111911437	111911437	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111911437delA	uc001vrs.2	+						ARHGEF7_uc001vrr.2_Intron|ARHGEF7_uc001vrt.2_Intron|ARHGEF7_uc010tjn.1_Intron|ARHGEF7_uc001vru.1_Intron|ARHGEF7_uc001vrv.3_Intron|ARHGEF7_uc001vrw.3_Intron|ARHGEF7_uc001vrx.3_Intron|ARHGEF7_uc010tjo.1_Intron|ARHGEF7_uc010tjp.1_Intron|ARHGEF7_uc010agn.1_Intron	NM_001113511	NP_001106983			PAK-interacting exchange factor beta isoform c						apoptosis|epidermal growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)															---	---	---	---
Unknown	0	broad.mit.edu	37	13	112328439	112328439	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:112328439delC								C13orf16 (331846 upstream) : SOX1 (393474 downstream)																																			---	---	---	---
ATP11A	23250	broad.mit.edu	37	13	113402151	113402152	+	Intron	INS	-	A	A	rs138507528	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113402151_113402152insA	uc001vsi.3	+						ATP11A_uc001vsj.3_Intron|uc001vsk.2_Intron	NM_015205	NP_056020			ATPase, class VI, type 11A isoform a						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			large_intestine(2)|ovary(2)	4	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)																---	---	---	---
ATP11A	23250	broad.mit.edu	37	13	113403385	113403385	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113403385delG	uc001vsi.3	+						ATP11A_uc001vsj.3_Intron|uc001vsk.2_Intron	NM_015205	NP_056020			ATPase, class VI, type 11A isoform a						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			large_intestine(2)|ovary(2)	4	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)																---	---	---	---
ATP11A	23250	broad.mit.edu	37	13	113425755	113425755	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113425755delC	uc001vsi.3	+						ATP11A_uc001vsj.3_Intron	NM_015205	NP_056020			ATPase, class VI, type 11A isoform a						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			large_intestine(2)|ovary(2)	4	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)																---	---	---	---
ATP11A	23250	broad.mit.edu	37	13	113447070	113447070	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113447070delC	uc001vsi.3	+						ATP11A_uc001vsj.3_Intron|ATP11A_uc001vsm.1_Intron	NM_015205	NP_056020			ATPase, class VI, type 11A isoform a						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			large_intestine(2)|ovary(2)	4	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)																---	---	---	---
ATP11A	23250	broad.mit.edu	37	13	113491010	113491011	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113491010_113491011delTT	uc001vsi.3	+						ATP11A_uc001vsj.3_Intron|ATP11A_uc001vsm.1_Intron	NM_015205	NP_056020			ATPase, class VI, type 11A isoform a						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			large_intestine(2)|ovary(2)	4	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)																---	---	---	---
MCF2L	23263	broad.mit.edu	37	13	113691013	113691014	+	Intron	INS	-	TTC	TTC	rs150383781	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113691013_113691014insTTC	uc001vsu.2	+						MCF2L_uc001vsq.2_Intron|MCF2L_uc010tjr.1_Intron|MCF2L_uc001vsr.2_Intron|MCF2L_uc001vss.3_Intron|MCF2L_uc010tjs.1_Intron	NM_001112732	NP_001106203			MCF.2 cell line derived transforming						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|plasma membrane	Rho guanyl-nucleotide exchange factor activity			ovary(1)|kidney(1)	2	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)																---	---	---	---
ADPRHL1	113622	broad.mit.edu	37	13	114094774	114094777	+	Intron	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114094774_114094777delTTTT	uc001vtq.1	-						ADPRHL1_uc001vtp.1_Intron	NM_138430	NP_612439			ADP-ribosylhydrolase like 1 isoform 1						protein de-ADP-ribosylation		ADP-ribosylarginine hydrolase activity|magnesium ion binding				0	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0395)|all_epithelial(44;0.011)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.0195)|GBM - Glioblastoma multiforme(44;0.116)															---	---	---	---
ATP4B	496	broad.mit.edu	37	13	114303832	114303832	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114303832delG	uc001vtz.2	-	7	775	c.733delC	c.(733-735)CTGfs	p.L245fs		NM_000705	NP_000696	P51164	ATP4B_HUMAN	hydrogen/potassium-exchanging ATPase 4B	245	Extracellular (Potential).				ATP biosynthetic process	integral to membrane|plasma membrane	hydrogen:potassium-exchanging ATPase activity|sodium:potassium-exchanging ATPase activity			ovary(1)	1	Lung NSC(43;0.0113)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.00696)|all_epithelial(44;0.00347)|all_lung(25;0.0221)|Breast(118;0.0411)|Lung NSC(25;0.0839)	all cancers(43;0.171)		Rabeprazole(DB01129)													---	---	---	---
RASA3	22821	broad.mit.edu	37	13	114877575	114877575	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114877575delC	uc001vui.2	-						RASA3_uc001vuj.2_Intron|RASA3_uc010tkl.1_Intron	NM_007368	NP_031394			RAS p21 protein activator 3						intracellular signal transduction|negative regulation of Ras protein signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	calcium-release channel activity|metal ion binding|Ras GTPase activator activity			lung(3)|skin(1)	4	Lung NSC(43;0.00814)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.016)|all_epithelial(44;0.00577)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.188)	BRCA - Breast invasive adenocarcinoma(86;0.128)															---	---	---	---
Unknown	0	broad.mit.edu	37	14	19034750	19034751	+	IGR	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19034750_19034751insC								None (None upstream) : OR11H12 (342843 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19090483	19090484	+	IGR	INS	-	T	T	rs71431940		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19090483_19090484insT								None (None upstream) : OR11H12 (287110 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19123817	19123818	+	IGR	DEL	AA	-	-	rs111719869		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19123817_19123818delAA								None (None upstream) : OR11H12 (253776 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19267332	19267332	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19267332delC								None (None upstream) : OR11H12 (110262 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19349895	19349895	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19349895delT								None (None upstream) : OR11H12 (27699 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	19432424	19432425	+	IGR	DEL	GT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19432424_19432425delGT								OR11H12 (53852 upstream) : POTEG (120940 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	20632792	20632792	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20632792delT								OR4N5 (19972 upstream) : OR11G2 (32703 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	20830429	20830439	+	IGR	DEL	AGGAAGAGAGA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20830429_20830439delAGGAAGAGAGA								PARP2 (4367 upstream) : TEP1 (3387 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	21114704	21114704	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21114704delT								OR6S1 (4854 upstream) : ANG (37632 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	21253823	21253823	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21253823delG								RNASE6 (3199 upstream) : RNASE1 (15693 downstream)																																			---	---	---	---
FLJ10357	55701	broad.mit.edu	37	14	21556192	21556192	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21556192delC	uc001vzp.2	+	22	4482	c.4453delC	c.(4453-4455)CCCfs	p.P1485fs	FLJ10357_uc010aij.2_RNA|FLJ10357_uc010tln.1_Frame_Shift_Del_p.P723fs	NM_018071	NP_060541	Q8TER5	ARH40_HUMAN	hypothetical protein LOC55701	1485					regulation of Rho protein signal transduction	cytoplasm	Rho guanyl-nucleotide exchange factor activity				0	all_cancers(95;0.00185)		OV - Ovarian serous cystadenocarcinoma(11;5.79e-11)|Epithelial(56;8.35e-09)|all cancers(55;4.23e-08)	GBM - Glioblastoma multiforme(265;0.0197)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	21592135	21592135	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21592135delG								ZNF219 (19272 upstream) : OR5AU1 (30962 downstream)																																			---	---	---	---
TOX4	9878	broad.mit.edu	37	14	21964624	21964625	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21964624_21964625delAA	uc001waz.2	+						TOX4_uc001wba.2_Intron|TOX4_uc010tlu.1_Intron|TOX4_uc010tlv.1_Intron	NM_014828	NP_055643			epidermal Langerhans cell protein LCP1							chromatin|nucleus|PTW/PP1 phosphatase complex	DNA binding|protein binding			ovary(1)	1	all_cancers(95;0.000465)		Epithelial(56;6.61e-06)|all cancers(55;5.15e-05)	GBM - Glioblastoma multiforme(265;0.0149)														---	---	---	---
SALL2	6297	broad.mit.edu	37	14	21994676	21994677	+	Intron	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21994676_21994677insC	uc001wbe.2	-						SALL2_uc010tly.1_5'Flank|SALL2_uc010tlz.1_5'Flank|SALL2_uc001wbf.3_5'Flank|SALL2_uc010tma.1_Intron|SALL2_uc001wbg.1_Intron	NM_005407	NP_005398			sal-like 2								DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|large_intestine(1)	3	all_cancers(95;0.000662)			GBM - Glioblastoma multiforme(265;0.0151)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	22164248	22164248	+	IGR	DEL	T	-	-	rs67526854		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22164248delT								OR4E2 (30012 upstream) : DAD1 (869559 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	22192926	22192927	+	IGR	INS	-	C	C	rs11453009		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22192926_22192927insC								OR4E2 (58690 upstream) : DAD1 (840880 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	22438736	22438736	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22438736delT	uc001wbw.2	+						uc010tmh.1_Intron|uc010aiv.1_Intron|uc010tmi.1_Intron|uc010tmj.1_Intron|uc010aja.1_Intron|uc010tmk.1_Intron					SubName: Full=Alpha-chain C region; Flags: Fragment;																														---	---	---	---
SLC7A7	9056	broad.mit.edu	37	14	23280190	23280190	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23280190delA	uc001wgr.3	-						SLC7A7_uc001wgs.3_Intron|SLC7A7_uc001wgt.3_Intron|SLC7A7_uc001wgu.3_Intron|SLC7A7_uc001wgv.3_Intron	NM_003982	NP_003973			solute carrier family 7 member 7						blood coagulation|cellular amino acid metabolic process|ion transport|leukocyte migration|protein complex assembly	basolateral plasma membrane|integral to plasma membrane	amino acid transmembrane transporter activity			ovary(1)|breast(1)	2	all_cancers(95;8.44e-05)			GBM - Glioblastoma multiforme(265;0.00741)														---	---	---	---
MRPL52	122704	broad.mit.edu	37	14	23296637	23296638	+	5'Flank	DEL	AA	-	-	rs113529547		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23296637_23296638delAA	uc001wgw.3	+						MRPL52_uc001wgx.3_5'Flank|MRPL52_uc001wgy.3_5'Flank|MRPL52_uc001wgz.3_5'Flank|MRPL52_uc001wha.3_5'Flank|MRPL52_uc001whb.3_5'Flank	NM_178336	NP_848026			mitochondrial ribosomal protein L52 isoform a						translation	mitochondrial large ribosomal subunit	structural constituent of ribosome				0	all_cancers(95;9.47e-05)			GBM - Glioblastoma multiforme(265;0.00551)														---	---	---	---
HAUS4	54930	broad.mit.edu	37	14	23422359	23422359	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23422359delT	uc001whp.2	-						HAUS4_uc001who.2_Intron|HAUS4_uc001whq.2_Intron|HAUS4_uc001whr.2_Intron|HAUS4_uc001whs.2_Intron|HAUS4_uc001wht.2_Intron|HAUS4_uc001whu.2_Intron|HAUS4_uc001whv.2_Intron|HAUS4_uc001whw.2_Intron|HAUS4_uc001whx.2_Intron	NM_017815	NP_060285			HAUS augmin-like complex, subunit 4						cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|spindle				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	23721023	23721024	+	IGR	INS	-	A	A	rs143097191		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23721023_23721024insA								SLC7A8 (68174 upstream) : HOMEZ (21820 downstream)																																			---	---	---	---
NGDN	25983	broad.mit.edu	37	14	23939095	23939095	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23939095delG	uc001wjy.2	+						NGDN_uc001wjz.2_Intron	NM_001042635	NP_001036100			neuroguidin isoform 1						regulation of translation	axon|cytoplasm|dendrite|filopodium|nucleus					0	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00654)												OREG0022601	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	14	24501823	24501823	+	IGR	DEL	A	-	-	rs79832782		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24501823delA								DHRS4 (26208 upstream) : DHRS4L1 (3887 downstream)																																			---	---	---	---
LRRC16B	90668	broad.mit.edu	37	14	24537638	24537638	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24537638delA	uc001wlj.2	+						LRRC16B_uc001wlk.2_Intron|CPNE6_uc010tnv.1_5'Flank|CPNE6_uc001wlm.2_5'Flank	NM_138360	NP_612369			leucine rich repeat containing 16B											ovary(2)|breast(2)|pancreas(1)	5				GBM - Glioblastoma multiforme(265;0.019)														---	---	---	---
TM9SF1	10548	broad.mit.edu	37	14	24673777	24673777	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24673777delG	uc010tob.1	-						TSSK4_uc001wne.2_5'Flank|TSSK4_uc001wnf.2_5'Flank|TSSK4_uc001wng.2_5'Flank|TSSK4_uc001wnh.2_5'Flank	NM_006405	NP_006396			transmembrane 9 superfamily member 1 isoform a						autophagy	autophagic vacuole membrane|cytoplasmic vesicle|integral to membrane|lysosomal membrane				ovary(1)	1				GBM - Glioblastoma multiforme(265;0.0183)														---	---	---	---
TGM1	7051	broad.mit.edu	37	14	24728736	24728736	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24728736delG	uc001wod.2	-						TGM1_uc010tog.1_Intron	NM_000359	NP_000350			transglutaminase 1						cell envelope organization|keratinization|peptide cross-linking	cornified envelope|intrinsic to membrane	acyltransferase activity|metal ion binding|protein binding|protein-glutamine gamma-glutamyltransferase activity			central_nervous_system(2)|ovary(1)	3				GBM - Glioblastoma multiforme(265;0.0186)	L-Glutamine(DB00130)													---	---	---	---
RABGGTA	5875	broad.mit.edu	37	14	24739364	24739364	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24739364delG	uc001wof.2	-						RABGGTA_uc001woe.2_5'Flank|RABGGTA_uc001wog.2_Intron|RABGGTA_uc001woh.2_Intron|RABGGTA_uc001woi.2_Intron	NM_004581	NP_004572			Rab geranylgeranyltransferase alpha						visual perception		Rab geranylgeranyltransferase activity|zinc ion binding				0				GBM - Glioblastoma multiforme(265;0.0184)														---	---	---	---
NFATC4	4776	broad.mit.edu	37	14	24841468	24841468	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24841468delT	uc001wpc.2	+						NFATC4_uc010tok.1_Intron|NFATC4_uc010tol.1_Intron|NFATC4_uc010alr.2_Intron|NFATC4_uc010als.2_Intron|NFATC4_uc010tom.1_Intron|NFATC4_uc010ton.1_Intron|NFATC4_uc010too.1_Intron|NFATC4_uc010alt.2_Intron|NFATC4_uc010top.1_Intron|NFATC4_uc010toq.1_Intron|NFATC4_uc010alu.2_Intron|NFATC4_uc010tor.1_Intron|NFATC4_uc010tos.1_Intron|NFATC4_uc010tot.1_Intron|NFATC4_uc010tou.1_Intron|NFATC4_uc010tov.1_Intron|NFATC4_uc010tow.1_Intron|NFATC4_uc010alv.2_Intron|NFATC4_uc010tox.1_Intron|NFATC4_uc001wpd.2_5'Flank|NFATC4_uc010toy.1_5'Flank|NFATC4_uc010toz.1_5'Flank|NFATC4_uc010tpa.1_5'Flank|NFATC4_uc010tpb.1_5'Flank	NM_004554	NP_004545			nuclear factor of activated T-cells,						cell differentiation|inflammatory response|transcription from RNA polymerase II promoter	cytoplasm|intermediate filament cytoskeleton|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(1)|central_nervous_system(1)|skin(1)	3				GBM - Glioblastoma multiforme(265;0.018)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	24969253	24969254	+	Intron	INS	-	A	A	rs142239985	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24969253_24969254insA	uc001wpo.1	+											Homo sapiens cDNA FLJ31806 fis, clone NT2RI2009151.																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	25042217	25042217	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25042217delT								CMA1 (64746 upstream) : CTSG (508 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	25545489	25545490	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25545489_25545490insT								STXBP6 (26318 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	25549699	25549700	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25549699_25549700delTT								STXBP6 (30528 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	25651182	25651183	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25651182_25651183delAA								STXBP6 (132011 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	25923639	25923639	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25923639delT								STXBP6 (404468 upstream) : NOVA1 (991451 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	26230426	26230426	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:26230426delT								STXBP6 (711255 upstream) : NOVA1 (684664 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	26270316	26270316	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:26270316delA								STXBP6 (751145 upstream) : NOVA1 (644774 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	26292900	26292901	+	IGR	INS	-	TG	TG	rs143200055	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:26292900_26292901insTG								STXBP6 (773729 upstream) : NOVA1 (622189 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	26701272	26701272	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:26701272delA								None (None upstream) : NOVA1 (213818 downstream)																																			---	---	---	---
NOVA1	4857	broad.mit.edu	37	14	26999147	26999147	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:26999147delT	uc001wpy.2	-						NOVA1_uc001wpz.2_Intron|NOVA1_uc001wqa.2_Intron|NOVA1_uc001wqb.2_Intron	NM_002515	NP_002506			neuro-oncological ventral antigen 1 isoform 1						locomotory behavior|RNA splicing|synaptic transmission	nucleus	RNA binding			skin(2)|upper_aerodigestive_tract(1)|breast(1)|liver(1)	5				GBM - Glioblastoma multiforme(265;0.0135)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	27546574	27546574	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:27546574delA								NOVA1 (479614 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	27776186	27776186	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:27776186delT								NOVA1 (709226 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	28762365	28762365	+	IGR	DEL	T	-	-	rs67757366		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:28762365delT								None (None upstream) : FOXG1 (473922 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	28973999	28973999	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:28973999delA								None (None upstream) : FOXG1 (262288 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	29198523	29198523	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:29198523delA								None (None upstream) : FOXG1 (37764 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	29409717	29409719	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:29409717_29409719delTTT								C14orf23 (145718 upstream) : PRKD1 (635970 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	29690399	29690399	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:29690399delA								C14orf23 (426400 upstream) : PRKD1 (355290 downstream)																																			---	---	---	---
PRKD1	5587	broad.mit.edu	37	14	30263712	30263712	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:30263712delA	uc001wqh.2	-							NM_002742	NP_002733			protein kinase D1						cell proliferation|intracellular signal transduction|sphingolipid metabolic process	cytosol|integral to plasma membrane	ATP binding|metal ion binding|protein binding|protein kinase C activity			lung(3)|large_intestine(2)|ovary(2)|skin(1)	8	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	30477123	30477124	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:30477123_30477124insA								PRKD1 (80224 upstream) : G2E3 (551205 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	30767973	30767973	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:30767973delT								PRKD1 (371074 upstream) : G2E3 (260356 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	30979887	30979887	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:30979887delA								PRKD1 (582988 upstream) : G2E3 (48442 downstream)																																			---	---	---	---
G2E3	55632	broad.mit.edu	37	14	31066757	31066757	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31066757delA	uc001wqk.2	+						G2E3_uc010tpe.1_Intron|G2E3_uc010tpf.1_Intron	NM_017769	NP_060239			G2/M-phase specific E3 ubiquitin ligase						apoptosis|multicellular organismal development|protein modification process	Golgi apparatus|nucleolus	acid-amino acid ligase activity|protein binding|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
SCFD1	23256	broad.mit.edu	37	14	31136131	31136131	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31136131delA	uc001wqm.1	+						SCFD1_uc001wqn.1_Intron|SCFD1_uc010tpg.1_Intron|SCFD1_uc010tph.1_Intron|SCFD1_uc010amf.1_Intron|SCFD1_uc010tpi.1_Intron|SCFD1_uc010amd.1_Intron|SCFD1_uc010ame.1_Intron	NM_016106	NP_057190			vesicle transport-related protein isoform a						post-Golgi vesicle-mediated transport|protein transport|regulation of ER to Golgi vesicle-mediated transport|response to toxin|retrograde vesicle-mediated transport, Golgi to ER|vesicle docking involved in exocytosis	cis-Golgi network|endoplasmic reticulum membrane|Golgi cisterna membrane|Golgi-associated vesicle|plasma membrane	syntaxin-5 binding				0	Hepatocellular(127;0.0877)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)	GBM - Glioblastoma multiforme(265;0.0181)														---	---	---	---
HECTD1	25831	broad.mit.edu	37	14	31647096	31647098	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31647096_31647098delTTT	uc001wrc.1	-							NM_015382	NP_056197			HECT domain containing 1						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	metal ion binding|protein binding|ubiquitin-protein ligase activity			ovary(3)|large_intestine(1)|lung(1)	5	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	31692794	31692794	+	IGR	DEL	A	-	-	rs77109546		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31692794delA								HECTD1 (15879 upstream) : HEATR5A (68201 downstream)																																			---	---	---	---
HEATR5A	25938	broad.mit.edu	37	14	31846166	31846166	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31846166delA	uc001wrf.3	-						HEATR5A_uc010ami.2_Intron|HEATR5A_uc001wrg.1_Intron|HEATR5A_uc010tpk.1_Intron	NM_015473	NP_056288			HEAT repeat containing 5A								binding			ovary(1)	1	Hepatocellular(127;0.0877)|Breast(36;0.137)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.0797)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0059)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	32019217	32019217	+	IGR	DEL	T	-	-	rs112510915		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32019217delT								HEATR5A (92537 upstream) : NUBPL (11374 downstream)																																			---	---	---	---
NUBPL	80224	broad.mit.edu	37	14	32142486	32142486	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32142486delA	uc001wrk.3	+						NUBPL_uc010amj.2_Intron|NUBPL_uc010tpl.1_Intron	NM_025152	NP_079428			nucleotide binding protein-like						mitochondrial respiratory chain complex I assembly|mitochondrion morphogenesis	mitochondrion	4 iron, 4 sulfur cluster binding|ATP binding|metal ion binding				0	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.214)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0677)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0102)														---	---	---	---
ARHGAP5	394	broad.mit.edu	37	14	32579416	32579417	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32579416_32579417delAA	uc001wrl.2	+						ARHGAP5_uc001wrm.2_Intron|ARHGAP5_uc001wrn.2_Intron|ARHGAP5_uc001wro.2_Intron|ARHGAP5_uc001wrp.2_Intron	NM_001173	NP_001025226			Rho GTPase activating protein 5 isoform b						cell adhesion|Rho protein signal transduction	cytosol|membrane	GTP binding|GTPase activity|Rho GTPase activator activity|SH2 domain binding			ovary(4)|central_nervous_system(1)	5	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	32754015	32754015	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:32754015delT								ARHGAP5 (125083 upstream) : AKAP6 (44464 downstream)																																			---	---	---	---
AKAP6	9472	broad.mit.edu	37	14	33294194	33294194	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33294194delA	uc001wrq.2	+							NM_004274	NP_004265			A-kinase anchor protein 6						protein targeting	calcium channel complex|nuclear membrane|sarcoplasmic reticulum	protein kinase A binding|receptor binding			breast(6)|ovary(5)|lung(4)|skin(3)|large_intestine(2)|pancreas(1)	21	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)														---	---	---	---
NPAS3	64067	broad.mit.edu	37	14	33518788	33518788	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33518788delC	uc001wru.2	+						NPAS3_uc001wrs.2_Intron|NPAS3_uc001wrt.2_Intron|NPAS3_uc001wrv.2_Intron	NM_173159	NP_071406			neuronal PAS domain protein 3 isoform 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			ovary(1)|skin(1)	2	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)														---	---	---	---
NPAS3	64067	broad.mit.edu	37	14	33766429	33766430	+	Intron	DEL	TT	-	-	rs71850110		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33766429_33766430delTT	uc001wru.2	+						NPAS3_uc001wrs.2_Intron|NPAS3_uc001wrt.2_Intron|NPAS3_uc001wrv.2_Intron|NPAS3_uc001wrw.2_Intron	NM_173159	NP_071406			neuronal PAS domain protein 3 isoform 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			ovary(1)|skin(1)	2	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)														---	---	---	---
NPAS3	64067	broad.mit.edu	37	14	33802794	33802794	+	Intron	DEL	T	-	-	rs5807716		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33802794delT	uc001wru.2	+						NPAS3_uc001wrs.2_Intron|NPAS3_uc001wrt.2_Intron|NPAS3_uc001wrv.2_Intron|NPAS3_uc001wrw.2_Intron	NM_173159	NP_071406			neuronal PAS domain protein 3 isoform 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			ovary(1)|skin(1)	2	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	35209488	35209488	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35209488delT								CFL2 (25459 upstream) : BAZ1A (12451 downstream)																																			---	---	---	---
FAM177A1	283635	broad.mit.edu	37	14	35550218	35550218	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35550218delT	uc001wsp.2	+						FAM177A1_uc001wsq.2_Intron	NM_001079519	NP_001072987			hypothetical protein LOC283635 isoform 2												0																		---	---	---	---
KIAA0391	9692	broad.mit.edu	37	14	35611090	35611090	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35611090delT	uc001wsy.1	+						KIAA0391_uc010tps.1_Intron|KIAA0391_uc001wsz.1_Intron|KIAA0391_uc001wta.2_Intron|KIAA0391_uc001wtb.1_Intron|KIAA0391_uc001wtc.1_Intron	NM_014672	NP_055487			mitochondrial RNase P protein 3 precursor						tRNA processing	mitochondrion					0	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;2.93e-05)|LUAD - Lung adenocarcinoma(48;3.86e-05)|Epithelial(34;0.0114)|all cancers(34;0.0277)	GBM - Glioblastoma multiforme(112;0.0593)														---	---	---	---
KIAA0391	9692	broad.mit.edu	37	14	35654492	35654492	+	Intron	DEL	T	-	-	rs11620951	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35654492delT	uc001wsy.1	+						KIAA0391_uc010tps.1_Intron|KIAA0391_uc001wsz.1_Intron|KIAA0391_uc001wta.2_Intron|KIAA0391_uc001wtb.1_Intron|KIAA0391_uc001wtc.1_Intron	NM_014672	NP_055487			mitochondrial RNase P protein 3 precursor						tRNA processing	mitochondrion					0	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;2.93e-05)|LUAD - Lung adenocarcinoma(48;3.86e-05)|Epithelial(34;0.0114)|all cancers(34;0.0277)	GBM - Glioblastoma multiforme(112;0.0593)														---	---	---	---
KIAA0391	9692	broad.mit.edu	37	14	35673462	35673462	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35673462delA	uc001wsy.1	+						KIAA0391_uc010tps.1_Intron|KIAA0391_uc001wsz.1_Intron|KIAA0391_uc001wta.2_Intron|KIAA0391_uc001wtb.1_Intron|KIAA0391_uc001wtc.1_Intron	NM_014672	NP_055487			mitochondrial RNase P protein 3 precursor						tRNA processing	mitochondrion					0	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;2.93e-05)|LUAD - Lung adenocarcinoma(48;3.86e-05)|Epithelial(34;0.0114)|all cancers(34;0.0277)	GBM - Glioblastoma multiforme(112;0.0593)														---	---	---	---
NFKBIA	4792	broad.mit.edu	37	14	35871169	35871169	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35871169delT	uc001wtf.3	-	6					NFKBIA_uc001wte.3_3'UTR|NFKBIA_uc001wtg.3_3'UTR|NFKBIA_uc010amo.2_RNA	NM_020529	NP_065390			nuclear factor of kappa light polypeptide gene						anti-apoptosis|apoptosis|cellular response to cold|cytoplasmic sequestering of NF-kappaB|innate immune response|interspecies interaction between organisms|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of DNA binding|negative regulation of lipid storage|negative regulation of macrophage derived foam cell differentiation|negative regulation of NF-kappaB transcription factor activity|nerve growth factor receptor signaling pathway|positive regulation of cellular protein metabolic process|positive regulation of cholesterol efflux|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|I-kappaB/NF-kappaB complex|nucleus|plasma membrane	identical protein binding|NF-kappaB binding|nuclear localization sequence binding|ubiquitin protein ligase binding			breast(2)	2	Breast(36;0.0484)|Hepatocellular(127;0.158)		Lung(238;9.25e-06)|LUAD - Lung adenocarcinoma(48;1.53e-05)|Epithelial(34;0.00314)|all cancers(34;0.00891)	GBM - Glioblastoma multiforme(112;0.0222)														---	---	---	---
RALGAPA1	253959	broad.mit.edu	37	14	36093802	36093802	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36093802delA	uc001wti.2	-						RALGAPA1_uc010amp.2_Intron|RALGAPA1_uc001wtj.2_Intron|RALGAPA1_uc010tpv.1_Intron|RALGAPA1_uc010tpw.1_Intron	NM_014990	NP_055805			Ral GTPase activating protein, alpha subunit 1						activation of Ral GTPase activity	cytosol|mitochondrion|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(3)|breast(1)	4																		---	---	---	---
RALGAPA1	253959	broad.mit.edu	37	14	36094781	36094781	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36094781delA	uc001wti.2	-						RALGAPA1_uc010amp.2_Intron|RALGAPA1_uc001wtj.2_Intron|RALGAPA1_uc010tpv.1_Intron|RALGAPA1_uc010tpw.1_Intron	NM_014990	NP_055805			Ral GTPase activating protein, alpha subunit 1						activation of Ral GTPase activity	cytosol|mitochondrion|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(3)|breast(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	36434784	36434784	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:36434784delA								BRMS1L (93616 upstream) : MBIP (332980 downstream)																																			---	---	---	---
PAX9	5083	broad.mit.edu	37	14	37143935	37143935	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:37143935delT	uc001wty.3	+						PAX9_uc010amq.2_Intron	NM_006194	NP_006185			paired box 9						multicellular organismal development|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	Hepatocellular(127;0.158)|Esophageal squamous(585;0.164)|Breast(36;0.218)		Lung(8;1.12e-09)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.00357)|all cancers(34;0.00998)|LUSC - Lung squamous cell carcinoma(13;0.0189)	GBM - Glioblastoma multiforme(112;0.0181)														---	---	---	---
MIPOL1	145282	broad.mit.edu	37	14	37865275	37865276	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:37865275_37865276insT	uc001wuc.2	+						MIPOL1_uc010amr.2_Intron|MIPOL1_uc001wub.3_Intron|MIPOL1_uc001wud.2_Intron|MIPOL1_uc010ams.2_Intron|MIPOL1_uc001wue.2_Intron|MIPOL1_uc010amt.2_Intron	NM_138731	NP_620059			mirror-image polydactyly 1											ovary(1)|central_nervous_system(1)	2	Breast(36;0.119)|Esophageal squamous(585;0.164)|Hepatocellular(127;0.213)		Lung(238;6.03e-07)|LUAD - Lung adenocarcinoma(48;2.48e-05)|Epithelial(34;0.047)|all cancers(34;0.0953)|LUSC - Lung squamous cell carcinoma(13;0.0975)|BRCA - Breast invasive adenocarcinoma(188;0.196)	GBM - Glioblastoma multiforme(112;0.0358)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	38144261	38144261	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38144261delT	uc001wug.2	+											Homo sapiens chromosome 14 open reading frame 25, mRNA (cDNA clone IMAGE:5268731), partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	38280521	38280521	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38280521delT	uc001wug.2	+						uc001wuh.2_Intron|uc001wui.2_Intron|uc001wuj.2_Intron					Homo sapiens chromosome 14 open reading frame 25, mRNA (cDNA clone IMAGE:5268731), partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	38655145	38655145	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38655145delC								FOXA1 (590656 upstream) : SSTR1 (22059 downstream)																																			---	---	---	---
TRAPPC6B	122553	broad.mit.edu	37	14	39635017	39635017	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:39635017delT	uc001wut.1	-						TRAPPC6B_uc001wuu.1_Intron|TRAPPC6B_uc001wuv.1_Intron|TRAPPC6B_uc010tqd.1_Intron	NM_001079537	NP_001073005			trafficking protein particle complex 6B isoform						vesicle-mediated transport	endoplasmic reticulum|Golgi apparatus	guanylate cyclase activity|heme binding				0	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0128)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	40370897	40370898	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:40370897_40370898delTT								FBXO33 (469193 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	41479847	41479847	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:41479847delA								None (None upstream) : LRFN5 (596917 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	41917734	41917737	+	IGR	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:41917734_41917737delTTTT								None (None upstream) : LRFN5 (159027 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	41966392	41966392	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:41966392delA								None (None upstream) : LRFN5 (110372 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	42666602	42666602	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:42666602delC								LRFN5 (292852 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	42924745	42924746	+	IGR	INS	-	A	A	rs147373174	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:42924745_42924746insA								LRFN5 (550995 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	43040581	43040583	+	IGR	DEL	TTC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:43040581_43040583delTTC								LRFN5 (666831 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	43298610	43298610	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:43298610delT								LRFN5 (924860 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	43459028	43459029	+	IGR	INS	-	A	A	rs150380153	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:43459028_43459029insA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	43664514	43664514	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:43664514delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	43821680	43821680	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:43821680delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	44102811	44102811	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44102811delA								None (None upstream) : FSCB (870544 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	44176473	44176473	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44176473delA								None (None upstream) : FSCB (796882 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	44190103	44190103	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44190103delT								None (None upstream) : FSCB (783252 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	44760816	44760817	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44760816_44760817delAA								None (None upstream) : FSCB (212538 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	44809159	44809160	+	IGR	DEL	AA	-	-	rs71446109		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44809159_44809160delAA								None (None upstream) : FSCB (164195 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	44867624	44867624	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:44867624delA								None (None upstream) : FSCB (105731 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	45182277	45182278	+	IGR	INS	-	CA	CA	rs141399288	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45182277_45182278insCA								FSCB (205778 upstream) : C14orf28 (184229 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	45317237	45317238	+	IGR	INS	-	AC	AC	rs140557876	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45317237_45317238insAC								FSCB (340738 upstream) : C14orf28 (49269 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	45328856	45328856	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45328856delT								FSCB (352357 upstream) : C14orf28 (37651 downstream)																																			---	---	---	---
FAM179B	23116	broad.mit.edu	37	14	45467013	45467018	+	Intron	DEL	AAAAAG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45467013_45467018delAAAAAG	uc001wvv.2	+						FAM179B_uc001wvw.2_Intron|FAM179B_uc010anc.2_Intron|FAM179B_uc001wvu.2_Intron	NM_015091	NP_055906			hypothetical protein LOC23116								binding			skin(2)|upper_aerodigestive_tract(1)	3																		---	---	---	---
C14orf106	55320	broad.mit.edu	37	14	45693014	45693014	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45693014delT	uc001wwf.2	-							NM_018353	NP_060823			chromosome 14 open reading frame 106						cell division|CenH3-containing nucleosome assembly at centromere|mitosis	chromosome, centromeric region|nucleoplasm	DNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	45769843	45769843	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45769843delT								C14orf106 (47238 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	45893922	45893922	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45893922delT								C14orf106 (171317 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	46303290	46303290	+	IGR	DEL	T	-	-	rs35677348		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:46303290delT								C14orf106 (580685 upstream) : RPL10L (816932 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	46699741	46699741	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:46699741delA								C14orf106 (977136 upstream) : RPL10L (420481 downstream)																																			---	---	---	---
MDGA2	161357	broad.mit.edu	37	14	47776895	47776896	+	Intron	DEL	AA	-	-	rs113956118		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:47776895_47776896delAA	uc001wwj.3	-						MDGA2_uc001wwi.3_Intron|MDGA2_uc010ani.2_Intron	NM_001113498	NP_001106970			MAM domain containing 1 isoform 1						spinal cord motor neuron differentiation	anchored to membrane|plasma membrane				ovary(4)|large_intestine(1)|pancreas(1)	6																		---	---	---	---
SDCCAG1	9147	broad.mit.edu	37	14	50096382	50096382	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50096382delA	uc010anj.1	-						C14orf104_uc001wws.3_Intron|C14orf104_uc001wwt.3_Intron	NM_004713	NP_004704			serologically defined colon cancer antigen 1							cytoplasm|nucleus					0	all_epithelial(31;0.000822)|Breast(41;0.0117)	all_lung(585;1.02e-05)		OV - Ovarian serous cystadenocarcinoma(311;5.99e-34)														---	---	---	---
SDCCAG1	9147	broad.mit.edu	37	14	50301039	50301039	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50301039delA	uc001wxc.2	-						SDCCAG1_uc010anj.1_Intron|SDCCAG1_uc010tqi.1_Intron|SDCCAG1_uc001wxe.2_Intron|SDCCAG1_uc001wxd.1_5'Flank|SDCCAG1_uc010anq.1_Intron	NM_004713	NP_004704			serologically defined colon cancer antigen 1							cytoplasm|nucleus					0	all_epithelial(31;0.000822)|Breast(41;0.0117)	all_lung(585;1.02e-05)		OV - Ovarian serous cystadenocarcinoma(311;5.99e-34)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	50398042	50398044	+	IGR	DEL	TTT	-	-	rs77737348		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50398042_50398044delTTT								ARF6 (34271 upstream) : C14orf182 (50386 downstream)																																			---	---	---	---
SOS2	6655	broad.mit.edu	37	14	50587455	50587460	+	Intron	DEL	TTTTTT	-	-	rs34012845		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50587455_50587460delTTTTTT	uc001wxs.3	-						SOS2_uc010ans.2_Intron|SOS2_uc010tql.1_Intron	NM_006939	NP_008870			son of sevenless homolog 2						apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	DNA binding|protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)	2	all_epithelial(31;0.000822)|Breast(41;0.0065)																	---	---	---	---
L2HGDH	79944	broad.mit.edu	37	14	50752627	50752627	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50752627delC	uc001wxu.2	-						L2HGDH_uc010tqn.1_Intron|L2HGDH_uc010tqo.1_Intron	NM_024884	NP_079160			L-2-hydroxyglutarate dehydrogenase precursor						2-oxoglutarate metabolic process|cellular protein metabolic process	integral to mitochondrial inner membrane	2-hydroxyglutarate dehydrogenase activity			ovary(2)	2	all_epithelial(31;0.000599)|Breast(41;0.0102)																	---	---	---	---
MAP4K5	11183	broad.mit.edu	37	14	50887605	50887605	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50887605delA	uc001wya.2	-						MAP4K5_uc001wyb.2_Intron	NM_006575	NP_006566			mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			large_intestine(1)	1	all_epithelial(31;0.000415)|Breast(41;0.0102)																	---	---	---	---
NIN	51199	broad.mit.edu	37	14	51273539	51273539	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51273539delA	uc001wym.2	-						NIN_uc001wyi.2_Intron|NIN_uc001wyj.2_Intron|NIN_uc001wyk.2_Intron|NIN_uc010tqp.1_Intron|NIN_uc001wyo.2_Intron|NIN_uc001wyp.1_Intron	NM_182946	NP_891991			ninein isoform 5						centrosome localization	centrosome|microtubule	calcium ion binding|GTP binding|protein binding			skin(3)|ovary(1)|kidney(1)|central_nervous_system(1)	6	all_epithelial(31;0.00244)|Breast(41;0.127)							T	PDGFRB	MPD								---	---	---	---
Unknown	0	broad.mit.edu	37	14	51316130	51316133	+	IGR	DEL	AAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51316130_51316133delAAAA								NIN (18291 upstream) : ABHD12B (22745 downstream)																																			---	---	---	---
ABHD12B	145447	broad.mit.edu	37	14	51370236	51370236	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51370236delT	uc001wys.2	+						ABHD12B_uc001wyq.2_Intron|ABHD12B_uc001wyr.2_Intron|ABHD12B_uc010any.2_Intron	NM_181533	NP_853511			abhydrolase domain containing 12B isoform b								hydrolase activity			breast(1)	1	all_epithelial(31;0.00481)|Breast(41;0.148)																	---	---	---	---
Unknown	0	broad.mit.edu	37	14	51603010	51603010	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51603010delA								TRIM9 (40588 upstream) : TMX1 (103876 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	51694489	51694489	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51694489delA								TRIM9 (132067 upstream) : TMX1 (12397 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	51788020	51788020	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51788020delT								TMX1 (63650 upstream) : FRMD6 (167835 downstream)																																			---	---	---	---
GNG2	54331	broad.mit.edu	37	14	52407094	52407094	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52407094delG	uc001wzi.2	+						GNG2_uc001wzh.2_Intron|GNG2_uc010aoc.1_Intron|GNG2_uc001wzj.2_Intron|GNG2_uc001wzk.2_Intron|GNG2_uc010aob.1_Intron	NM_053064	NP_444292			guanine nucleotide binding protein (G protein),						cellular response to glucagon stimulus|energy reserve metabolic process|platelet activation|synaptic transmission	heterotrimeric G-protein complex	protein binding|signal transducer activity				0	all_epithelial(31;0.0659)|Breast(41;0.0684)				Halothane(DB01159)													---	---	---	---
PTGDR	5729	broad.mit.edu	37	14	52734456	52734456	+	5'UTR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52734456delG	uc001wzq.2	+	1						NM_000953	NP_000944			prostaglandin D2 receptor							integral to membrane|plasma membrane	prostaglandin D receptor activity|protein binding			ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4	Breast(41;0.0639)|all_epithelial(31;0.0887)				Nedocromil(DB00716)													---	---	---	---
TXNDC16	57544	broad.mit.edu	37	14	52961258	52961258	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52961258delT	uc001wzs.2	-						TXNDC16_uc010tqu.1_Intron|TXNDC16_uc010aoe.2_Intron	NM_020784	NP_065835			thioredoxin domain containing 16 isoform 1						cell redox homeostasis	extracellular region					0	Breast(41;0.0716)																	---	---	---	---
TXNDC16	57544	broad.mit.edu	37	14	53012665	53012665	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53012665delT	uc001wzs.2	-						TXNDC16_uc010tqu.1_Intron|TXNDC16_uc010aoe.2_Intron	NM_020784	NP_065835			thioredoxin domain containing 16 isoform 1						cell redox homeostasis	extracellular region					0	Breast(41;0.0716)																	---	---	---	---
STYX	6815	broad.mit.edu	37	14	53213129	53213130	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53213129_53213130delTT	uc010tqy.1	+						STYX_uc001xaa.2_Intron	NM_001130701	NP_001124173			serine/threonine/tyrosine interacting protein						protein dephosphorylation|spermatogenesis	cytoplasm	protein tyrosine/serine/threonine phosphatase activity				0	Breast(41;0.176)																	---	---	---	---
Unknown	0	broad.mit.edu	37	14	53316063	53316064	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53316063_53316064insT								GNPNAT1 (57677 upstream) : FERMT2 (7926 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	53667001	53667001	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53667001delG								DDHD1 (46955 upstream) : BMP4 (749456 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	53746745	53746745	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53746745delA								DDHD1 (126699 upstream) : BMP4 (669712 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	53939511	53939511	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53939511delT								DDHD1 (319465 upstream) : BMP4 (476946 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	54176739	54176740	+	IGR	INS	-	AAC	AAC	rs138851738	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54176739_54176740insAAC								DDHD1 (556693 upstream) : BMP4 (239717 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	54723218	54723218	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54723218delT								BMP4 (299664 upstream) : CDKN3 (140455 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	54736888	54736888	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:54736888delT								BMP4 (313334 upstream) : CDKN3 (126785 downstream)																																			---	---	---	---
SAMD4A	23034	broad.mit.edu	37	14	55034317	55034317	+	5'Flank	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55034317delG	uc001xbb.2	+						SAMD4A_uc001xba.2_5'Flank|SAMD4A_uc001xbc.2_5'Flank	NM_015589	NP_056404			sterile alpha motif domain containing 4 isoform						positive regulation of translation	cell junction|cytoplasm|dendrite|synapse|synaptosome	translation repressor activity				0																		---	---	---	---
SAMD4A	23034	broad.mit.edu	37	14	55034376	55034377	+	5'Flank	DEL	TT	-	-	rs60147860		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55034376_55034377delTT	uc001xbb.2	+						SAMD4A_uc001xba.2_5'Flank|SAMD4A_uc001xbc.2_5'Flank	NM_015589	NP_056404			sterile alpha motif domain containing 4 isoform						positive regulation of translation	cell junction|cytoplasm|dendrite|synapse|synaptosome	translation repressor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	55681186	55681186	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55681186delA								DLGAP5 (22790 upstream) : FBXO34 (56835 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	56022631	56022631	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56022631delA								TBPL2 (115368 upstream) : C14orf33 (2059 downstream)																																			---	---	---	---
KTN1	3895	broad.mit.edu	37	14	56104387	56104387	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56104387delA	uc001xcb.2	+						KTN1_uc001xce.2_Intron|KTN1_uc001xcc.2_Intron|KTN1_uc001xcd.2_Intron|KTN1_uc010trb.1_Intron|KTN1_uc001xcf.1_Intron	NM_182926	NP_891556			kinectin 1 isoform a						microtubule-based movement	endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction				breast(3)|ovary(2)|lung(1)|central_nervous_system(1)	7								T	RET	papillary thryoid								---	---	---	---
C14orf34	645687	broad.mit.edu	37	14	56256797	56256798	+	Intron	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56256797_56256798delCT	uc010trd.1	-						C14orf34_uc010tre.1_Intron	NR_026796				Homo sapiens chromosome 14 open reading frame 34 (C14orf34), transcript variant 1, non-coding RNA.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	56537439	56537439	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56537439delC								C14orf34 (274047 upstream) : PELI2 (47654 downstream)																																			---	---	---	---
PELI2	57161	broad.mit.edu	37	14	56660141	56660141	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56660141delA	uc001xch.2	+							NM_021255	NP_067078			pellino 2						innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of MAPKKK cascade|positive regulation of protein phosphorylation|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	56818336	56818336	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56818336delG								PELI2 (50306 upstream) : C14orf101 (228002 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	56819829	56819830	+	IGR	INS	-	GAGA	GAGA	rs141936122	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56819829_56819830insGAGA								PELI2 (51799 upstream) : C14orf101 (226508 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	56847124	56847124	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:56847124delT								PELI2 (79094 upstream) : C14orf101 (199214 downstream)																																			---	---	---	---
C14orf101	54916	broad.mit.edu	37	14	57052707	57052707	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57052707delA	uc001xcm.2	+						C14orf101_uc001xcj.2_Intron|C14orf101_uc001xck.2_Intron|C14orf101_uc010aot.1_Intron|C14orf101_uc001xcl.1_Intron|C14orf101_uc001xcn.2_Intron|C14orf101_uc010trf.1_Intron	NM_017799	NP_060269			hypothetical protein LOC54916							integral to membrane				breast(1)|central_nervous_system(1)	2				OV - Ovarian serous cystadenocarcinoma(311;0.226)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	57183943	57183943	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57183943delT								C14orf101 (67713 upstream) : OTX2 (83484 downstream)																																			---	---	---	---
SLC35F4	341880	broad.mit.edu	37	14	58042222	58042222	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58042222delA	uc001xdb.1	-						SLC35F4_uc010aoz.1_Intron|SLC35F4_uc010apa.1_Intron	NM_001080455	NP_001073924			solute carrier family 35, member F4											ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	58424153	58424153	+	IGR	DEL	A	-	-	rs148498476		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58424153delA								SLC35F4 (360538 upstream) : C14orf37 (46656 downstream)																																			---	---	---	---
C14orf37	145407	broad.mit.edu	37	14	58528392	58528392	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58528392delT	uc001xdc.2	-						C14orf37_uc010tro.1_Intron|C14orf37_uc001xdd.2_Intron	NM_001001872	NP_001001872			hypothetical protein LOC145407 precursor							integral to membrane	binding				0																		---	---	---	---
C14orf37	145407	broad.mit.edu	37	14	58730645	58730645	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58730645delA	uc010tro.1	-						PSMA3_uc001xdj.1_Intron|PSMA3_uc001xdk.1_Intron	NM_001001872	NP_001001872			hypothetical protein LOC145407 precursor							integral to membrane	binding				0																		---	---	---	---
ARID4A	5926	broad.mit.edu	37	14	58795072	58795072	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58795072delA	uc001xdp.2	+						ARID4A_uc001xdo.2_Intron|ARID4A_uc001xdq.2_Intron	NM_002892	NP_002883			retinoblastoma-binding protein 1 isoform I						negative regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	transcriptional repressor complex	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|skin(2)|lung(1)	6																		---	---	---	---
KIAA0586	9786	broad.mit.edu	37	14	58956846	58956846	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58956846delT	uc001xdv.3	+						KIAA0586_uc010trr.1_Intron|KIAA0586_uc001xdt.3_Intron|KIAA0586_uc001xdu.3_Intron|KIAA0586_uc010trs.1_Intron|KIAA0586_uc010trt.1_Intron	NM_014749	NP_055564			talpid3 protein											ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	59846822	59846822	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59846822delT								DAAM1 (10351 upstream) : GPR135 (48918 downstream)																																			---	---	---	---
GPR135	64582	broad.mit.edu	37	14	59920130	59920130	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:59920130delA	uc001xed.2	-							NM_022571				G protein-coupled receptor 135							integral to membrane|plasma membrane	G-protein coupled receptor activity				0				OV - Ovarian serous cystadenocarcinoma(108;0.134)														---	---	---	---
SIX1	6495	broad.mit.edu	37	14	61113356	61113356	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61113356delA	uc001xfb.3	-							NM_005982	NP_005973			SIX homeobox 1						branching involved in ureteric bud morphogenesis|embryonic cranial skeleton morphogenesis|epithelial cell differentiation|inner ear morphogenesis|mesonephric tubule formation|metanephric mesenchyme development|myoblast migration|negative regulation of neuron apoptosis|organ induction|pattern specification process|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of ureteric bud formation|protein localization to nucleus|regulation of branch elongation involved in ureteric bud branching|regulation of neuron differentiation|skeletal muscle tissue development|thymus development|thyroid gland development	nucleolus|transcription factor complex	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding				0				OV - Ovarian serous cystadenocarcinoma(108;0.0201)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	61143807	61143809	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61143807_61143809delTTT								SIX1 (27652 upstream) : SIX4 (32447 downstream)																																			---	---	---	---
SIX4	51804	broad.mit.edu	37	14	61183965	61183966	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61183965_61183966insT	uc001xfc.2	-							NM_017420	NP_059116			sine oculis homeobox homolog 4							nucleus				breast(3)|ovary(1)	4				OV - Ovarian serous cystadenocarcinoma(108;0.0275)														---	---	---	---
MNAT1	4331	broad.mit.edu	37	14	61220127	61220127	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61220127delT	uc001xfd.2	+						MNAT1_uc010apq.1_Intron|MNAT1_uc001xfe.2_Intron	NM_002431	NP_002422			menage a trois 1 (CAK assembly factor)						cell proliferation|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mRNA capping|nucleotide-excision repair, DNA damage removal|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|protein complex assembly|protein phosphorylation|regulation of cyclin-dependent protein kinase activity|S phase of mitotic cell cycle|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	cytoplasm|holo TFIIH complex	protein N-terminus binding|zinc ion binding			ovary(1)|lung(1)	2				OV - Ovarian serous cystadenocarcinoma(108;0.0174)									Direct_reversal_of_damage|NER					---	---	---	---
MNAT1	4331	broad.mit.edu	37	14	61225325	61225325	+	Intron	DEL	C	-	-	rs1033738	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61225325delC	uc001xfd.2	+						MNAT1_uc010apq.1_Intron|MNAT1_uc001xfe.2_Intron	NM_002431	NP_002422			menage a trois 1 (CAK assembly factor)						cell proliferation|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mRNA capping|nucleotide-excision repair, DNA damage removal|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|protein complex assembly|protein phosphorylation|regulation of cyclin-dependent protein kinase activity|S phase of mitotic cell cycle|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	cytoplasm|holo TFIIH complex	protein N-terminus binding|zinc ion binding			ovary(1)|lung(1)	2				OV - Ovarian serous cystadenocarcinoma(108;0.0174)									Direct_reversal_of_damage|NER					---	---	---	---
MNAT1	4331	broad.mit.edu	37	14	61281941	61281942	+	Intron	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61281941_61281942delCT	uc001xfd.2	+						MNAT1_uc001xfe.2_Intron	NM_002431	NP_002422			menage a trois 1 (CAK assembly factor)						cell proliferation|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mRNA capping|nucleotide-excision repair, DNA damage removal|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|protein complex assembly|protein phosphorylation|regulation of cyclin-dependent protein kinase activity|S phase of mitotic cell cycle|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	cytoplasm|holo TFIIH complex	protein N-terminus binding|zinc ion binding			ovary(1)|lung(1)	2				OV - Ovarian serous cystadenocarcinoma(108;0.0174)									Direct_reversal_of_damage|NER					---	---	---	---
MNAT1	4331	broad.mit.edu	37	14	61299381	61299381	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61299381delT	uc001xfd.2	+						MNAT1_uc001xfe.2_Intron	NM_002431	NP_002422			menage a trois 1 (CAK assembly factor)						cell proliferation|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mRNA capping|nucleotide-excision repair, DNA damage removal|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|protein complex assembly|protein phosphorylation|regulation of cyclin-dependent protein kinase activity|S phase of mitotic cell cycle|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	cytoplasm|holo TFIIH complex	protein N-terminus binding|zinc ion binding			ovary(1)|lung(1)	2				OV - Ovarian serous cystadenocarcinoma(108;0.0174)									Direct_reversal_of_damage|NER					---	---	---	---
PRKCH	5583	broad.mit.edu	37	14	61656400	61656400	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61656400delT	uc010tsa.1	+							NM_006255	NP_006246			protein kinase C, eta						intracellular signal transduction|platelet activation	cytosol|plasma membrane	ATP binding|enzyme binding|metal ion binding|protein kinase C activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|large_intestine(1)|skin(1)	6				OV - Ovarian serous cystadenocarcinoma(108;0.045)|BRCA - Breast invasive adenocarcinoma(234;0.0906)|KIRC - Kidney renal clear cell carcinoma(182;0.182)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	62041069	62041070	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62041069_62041070insA	uc001xfp.2	+											Homo sapiens cDNA: FLJ22447 fis, clone HRC09479.																														---	---	---	---
SNAPC1	6617	broad.mit.edu	37	14	62259959	62259959	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62259959delT	uc001xft.2	+							NM_003082	NP_003073			small nuclear RNA activating complex,						regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding				0				OV - Ovarian serous cystadenocarcinoma(108;0.0639)|BRCA - Breast invasive adenocarcinoma(234;0.186)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	62439929	62439930	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62439929_62439930insT								SNAPC1 (176784 upstream) : SYT16 (13873 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	63134430	63134431	+	IGR	INS	-	CA	CA	rs149407658	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63134430_63134431insCA								FLJ43390 (537198 upstream) : KCNH5 (39516 downstream)																																			---	---	---	---
KCNH5	27133	broad.mit.edu	37	14	63529992	63529992	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63529992delA	uc001xfz.1	-						KCNH5_uc001xga.2_Intron	NM_172376	NP_758964			potassium voltage-gated channel, subfamily H,						regulation of transcription, DNA-dependent	integral to membrane	calmodulin binding|two-component sensor activity|voltage-gated potassium channel activity			ovary(4)|skin(4)|central_nervous_system(1)	9				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	63758672	63758672	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63758672delC								RHOJ (113 upstream) : GPHB5 (20971 downstream)																																			---	---	---	---
WDR89	112840	broad.mit.edu	37	14	64095657	64095657	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64095657delA	uc001xgh.2	-						WDR89_uc001xgi.2_Intron	NM_001008726	NP_001008726			WD repeat domain 89												0				OV - Ovarian serous cystadenocarcinoma(108;0.00543)|all cancers(60;0.0181)|BRCA - Breast invasive adenocarcinoma(234;0.101)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	65141011	65141011	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65141011delA								C14orf50 (84915 upstream) : PLEKHG3 (30182 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	65154122	65154122	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65154122delT								C14orf50 (98026 upstream) : PLEKHG3 (17071 downstream)																																			---	---	---	---
FNTB	2342	broad.mit.edu	37	14	65493580	65493580	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65493580delA	uc001xia.2	+						FNTB_uc010tsl.1_Intron|FNTB_uc010tsm.1_Intron|MAX_uc001xic.1_Intron|FNTB_uc001xid.2_Intron|FNTB_uc010tso.1_Intron	NM_002028	NP_002019			farnesyltransferase, CAAX box, beta						protein farnesylation	microtubule associated complex	protein binding|protein farnesyltransferase activity			ovary(1)	1				all cancers(60;0.00115)|OV - Ovarian serous cystadenocarcinoma(108;0.00412)|BRCA - Breast invasive adenocarcinoma(234;0.011)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	65618750	65618750	+	IGR	DEL	A	-	-	rs11368107		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65618750delA								MAX (49523 upstream) : LOC645431 (258563 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	66255837	66255838	+	IGR	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66255837_66255838delGA								FUT8 (45876 upstream) : C14orf53 (697271 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	66321518	66321519	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66321518_66321519insT								FUT8 (111557 upstream) : C14orf53 (631590 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	66561525	66561525	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66561525delT								FUT8 (351564 upstream) : C14orf53 (391584 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	66723833	66723833	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66723833delT								FUT8 (513872 upstream) : C14orf53 (229276 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	66772140	66772140	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66772140delT								FUT8 (562179 upstream) : C14orf53 (180969 downstream)																																			---	---	---	---
C14orf53	440184	broad.mit.edu	37	14	66953309	66953310	+	Intron	DEL	TC	-	-	rs10569333		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:66953309_66953310delTC	uc001xiu.3	+						C14orf53_uc010tsq.1_Intron|C14orf53_uc001xiv.3_Intron	NR_024338				Homo sapiens similar to CG32662-PA, mRNA (cDNA clone IMAGE:5163906).												0																		---	---	---	---
GPHN	10243	broad.mit.edu	37	14	67040484	67040484	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67040484delT	uc001xiy.2	+						GPHN_uc001xiw.2_Intron|GPHN_uc001xix.2_Intron|GPHN_uc010tss.1_Intron|GPHN_uc010tst.1_Intron	NM_001024218	NP_001019389			gephyrin isoform 2						Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cell junction|cytoplasm|cytoskeleton|postsynaptic membrane	ATP binding|metal ion binding|nucleotidyltransferase activity			ovary(2)	2		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)				T	MLL	AL								---	---	---	---
GPHN	10243	broad.mit.edu	37	14	67331491	67331491	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67331491delA	uc001xiy.2	+						GPHN_uc001xiw.2_Intron|GPHN_uc001xix.2_Intron|GPHN_uc010tss.1_Intron|GPHN_uc010tst.1_Intron|GPHN_uc010tsu.1_Intron	NM_001024218	NP_001019389			gephyrin isoform 2						Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cell junction|cytoplasm|cytoskeleton|postsynaptic membrane	ATP binding|metal ion binding|nucleotidyltransferase activity			ovary(2)	2		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)				T	MLL	AL								---	---	---	---
MPP5	64398	broad.mit.edu	37	14	67720562	67720564	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67720562_67720564delAAA	uc001xjc.2	+						MPP5_uc001xjd.2_Intron|MPP5_uc001xjb.1_Intron	NM_022474	NP_071919			membrane protein, palmitoylated 5						tight junction assembly	cytoplasm|endomembrane system|tight junction	protein domain specific binding			ovary(1)	1				all cancers(60;0.000388)|OV - Ovarian serous cystadenocarcinoma(108;0.00762)|BRCA - Breast invasive adenocarcinoma(234;0.0106)														---	---	---	---
MPP5	64398	broad.mit.edu	37	14	67786932	67786932	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67786932delT	uc001xjc.2	+						MPP5_uc001xjd.2_Intron|ATP6V1D_uc001xje.2_Intron	NM_022474	NP_071919			membrane protein, palmitoylated 5						tight junction assembly	cytoplasm|endomembrane system|tight junction	protein domain specific binding			ovary(1)	1				all cancers(60;0.000388)|OV - Ovarian serous cystadenocarcinoma(108;0.00762)|BRCA - Breast invasive adenocarcinoma(234;0.0106)														---	---	---	---
EIF2S1	1965	broad.mit.edu	37	14	67831425	67831425	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67831425delT	uc001xjg.2	+							NM_004094	NP_004085			eukaryotic translation initiation factor 2,							cytosol|eukaryotic translation initiation factor 2 complex|polysome|stress granule	protein binding|ribosome binding|translation initiation factor activity			ovary(1)	1				all cancers(60;0.000683)|OV - Ovarian serous cystadenocarcinoma(108;0.00579)|BRCA - Breast invasive adenocarcinoma(234;0.00937)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	68209454	68209454	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68209454delA								RDH12 (8287 upstream) : ZFYVE26 (3783 downstream)																																			---	---	---	---
ZFYVE26	23503	broad.mit.edu	37	14	68275906	68275907	+	Intron	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68275906_68275907delCT	uc001xka.2	-						ZFYVE26_uc010tsz.1_Intron|ZFYVE26_uc001xkc.3_Intron|ZFYVE26_uc010tta.1_Intron	NM_015346	NP_056161			zinc finger, FYVE domain containing 26						cell cycle|cell death|cytokinesis|double-strand break repair via homologous recombination	centrosome|midbody	metal ion binding|phosphatidylinositol-3-phosphate binding|protein binding			ovary(9)|breast(2)	11				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)														---	---	---	---
RAD51L1	5890	broad.mit.edu	37	14	68519346	68519347	+	Intron	DEL	TT	-	-	rs67773695		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68519346_68519347delTT	uc001xkf.1	+						RAD51L1_uc001xkd.2_Intron|RAD51L1_uc010aqr.2_Intron|RAD51L1_uc001xke.2_Intron|RAD51L1_uc010aqs.1_Intron|RAD51L1_uc001xkg.1_Intron	NM_133509	NP_598193			RAD51-like 1 isoform 3						blood coagulation|DNA repair|reciprocal meiotic recombination	nucleoplasm	ATP binding|DNA binding|DNA-dependent ATPase activity				0				UCEC - Uterine corpus endometrioid carcinoma (185;0.163)|all cancers(60;3.9e-06)|OV - Ovarian serous cystadenocarcinoma(108;0.000103)|BRCA - Breast invasive adenocarcinoma(234;0.000421)				T	HMGA2	lipoma|uterine leiomyoma			Direct_reversal_of_damage|Homologous_recombination					---	---	---	---
RAD51L1	5890	broad.mit.edu	37	14	68557158	68557158	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68557158delC	uc001xkf.1	+						RAD51L1_uc001xkd.2_Intron|RAD51L1_uc010aqr.2_Intron|RAD51L1_uc001xke.2_Intron|RAD51L1_uc010aqs.1_Intron|RAD51L1_uc001xkg.1_Intron	NM_133509	NP_598193			RAD51-like 1 isoform 3						blood coagulation|DNA repair|reciprocal meiotic recombination	nucleoplasm	ATP binding|DNA binding|DNA-dependent ATPase activity				0				UCEC - Uterine corpus endometrioid carcinoma (185;0.163)|all cancers(60;3.9e-06)|OV - Ovarian serous cystadenocarcinoma(108;0.000103)|BRCA - Breast invasive adenocarcinoma(234;0.000421)				T	HMGA2	lipoma|uterine leiomyoma			Direct_reversal_of_damage|Homologous_recombination					---	---	---	---
RAD51L1	5890	broad.mit.edu	37	14	68589749	68589749	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68589749delG	uc001xkf.1	+						RAD51L1_uc001xkd.2_Intron|RAD51L1_uc010aqr.2_Intron|RAD51L1_uc001xke.2_Intron|RAD51L1_uc010aqs.1_Intron|RAD51L1_uc001xkg.1_Intron	NM_133509	NP_598193			RAD51-like 1 isoform 3						blood coagulation|DNA repair|reciprocal meiotic recombination	nucleoplasm	ATP binding|DNA binding|DNA-dependent ATPase activity				0				UCEC - Uterine corpus endometrioid carcinoma (185;0.163)|all cancers(60;3.9e-06)|OV - Ovarian serous cystadenocarcinoma(108;0.000103)|BRCA - Breast invasive adenocarcinoma(234;0.000421)				T	HMGA2	lipoma|uterine leiomyoma			Direct_reversal_of_damage|Homologous_recombination					---	---	---	---
RAD51L1	5890	broad.mit.edu	37	14	68891092	68891092	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68891092delT	uc001xkf.1	+						RAD51L1_uc001xkd.2_Intron|RAD51L1_uc010aqr.2_Intron|RAD51L1_uc001xke.2_Intron|RAD51L1_uc010aqs.1_Intron|RAD51L1_uc001xkg.1_Intron	NM_133509	NP_598193			RAD51-like 1 isoform 3						blood coagulation|DNA repair|reciprocal meiotic recombination	nucleoplasm	ATP binding|DNA binding|DNA-dependent ATPase activity				0				UCEC - Uterine corpus endometrioid carcinoma (185;0.163)|all cancers(60;3.9e-06)|OV - Ovarian serous cystadenocarcinoma(108;0.000103)|BRCA - Breast invasive adenocarcinoma(234;0.000421)				T	HMGA2	lipoma|uterine leiomyoma			Direct_reversal_of_damage|Homologous_recombination					---	---	---	---
ACTN1	87	broad.mit.edu	37	14	69354296	69354296	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69354296delA	uc001xkl.2	-						ACTN1_uc001xkk.2_5'UTR|ACTN1_uc010ttb.1_Intron|ACTN1_uc001xkm.2_Intron|ACTN1_uc001xkn.2_Intron|ACTN1_uc010ttc.1_5'Flank|ACTN1_uc001xko.1_Intron|ACTN1_uc010ttd.1_Intron	NM_001102	NP_001093			actinin, alpha 1 isoform b						focal adhesion assembly|negative regulation of cellular component movement|platelet activation|platelet degranulation|regulation of apoptosis	actin cytoskeleton|cytosol|extracellular region|focal adhesion|nucleolus|platelet alpha granule lumen|pseudopodium|sarcomere	actin binding|calcium ion binding|integrin binding|vinculin binding			central_nervous_system(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00605)|all cancers(60;0.00846)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)														---	---	---	---
EXD2	55218	broad.mit.edu	37	14	69695979	69695979	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69695979delT	uc001xkt.2	+						EXD2_uc001xku.2_Intron|EXD2_uc001xkv.2_Intron|EXD2_uc001xkw.2_Intron|EXD2_uc001xkx.2_Intron|EXD2_uc010aqt.2_Intron|EXD2_uc010tte.1_Intron|EXD2_uc001xky.2_Intron	NM_018199	NP_060669			exonuclease 3'-5' domain containing 2						nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	intracellular	3'-5' exonuclease activity|nucleic acid binding				0																		---	---	---	---
ERH	2079	broad.mit.edu	37	14	69860742	69860744	+	Intron	DEL	AAA	-	-	rs76590310		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69860742_69860744delAAA	uc001xlc.2	-							NM_004450	NP_004441			enhancer of rudimentary homolog						cell cycle|pyrimidine nucleoside metabolic process	midbody	protein binding				0				all cancers(60;0.00365)|BRCA - Breast invasive adenocarcinoma(234;0.0137)|OV - Ovarian serous cystadenocarcinoma(108;0.0507)														---	---	---	---
SLC39A9	55334	broad.mit.edu	37	14	69868249	69868249	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69868249delA	uc001xle.2	+						SLC39A9_uc001xld.3_Intron|SLC39A9_uc010aqx.2_Intron|SLC39A9_uc001xlf.3_Intron|SLC39A9_uc001xlg.3_Intron	NM_018375	NP_060845			solute carrier family 39 (zinc transporter),						zinc ion transport	integral to membrane	metal ion transmembrane transporter activity				0				all cancers(60;0.00299)|BRCA - Breast invasive adenocarcinoma(234;0.0145)|OV - Ovarian serous cystadenocarcinoma(108;0.0373)														---	---	---	---
SLC39A9	55334	broad.mit.edu	37	14	69907832	69907832	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69907832delA	uc001xle.2	+						SLC39A9_uc010aqx.2_Intron|SLC39A9_uc001xlf.3_Intron|SLC39A9_uc001xlg.3_Intron	NM_018375	NP_060845			solute carrier family 39 (zinc transporter),						zinc ion transport	integral to membrane	metal ion transmembrane transporter activity				0				all cancers(60;0.00299)|BRCA - Breast invasive adenocarcinoma(234;0.0145)|OV - Ovarian serous cystadenocarcinoma(108;0.0373)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	70748946	70748947	+	IGR	DEL	TT	-	-	rs67914709		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70748946_70748947delTT								ADAM21P1 (34428 upstream) : COX16 (42852 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	71280447	71280448	+	IGR	DEL	AA	-	-	rs72231853		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71280447_71280448delAA								MAP3K9 (4559 upstream) : PCNX (93674 downstream)																																			---	---	---	---
PCNX	22990	broad.mit.edu	37	14	71502766	71502766	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71502766delT	uc001xmo.2	+						PCNX_uc010are.1_Intron|PCNX_uc010arf.1_Intron	NM_014982	NP_055797			pecanex-like 1							integral to membrane				ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	71715757	71715758	+	IGR	DEL	TG	-	-	rs112074337		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71715757_71715758delTG								PCNX (133658 upstream) : SNORD56B (149296 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	71752455	71752455	+	IGR	DEL	T	-	-	rs112680944		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71752455delT								PCNX (170356 upstream) : SNORD56B (112599 downstream)																																			---	---	---	---
SIPA1L1	26037	broad.mit.edu	37	14	71948236	71948236	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71948236delA	uc001xmr.1	+											Homo sapiens high-risk human papilloma viruses E6 oncoproteins targeted protein E6TP1 alpha mRNA, complete cds.						actin cytoskeleton reorganization|activation of Rap GTPase activity|regulation of dendritic spine morphogenesis	cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane|synaptosome	GTPase activator activity			ovary(3)|breast(1)	4				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)														---	---	---	---
SIPA1L1	26037	broad.mit.edu	37	14	72132259	72132259	+	Intron	DEL	A	-	-	rs79956828		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72132259delA	uc001xms.2	+						SIPA1L1_uc001xmt.2_Intron|SIPA1L1_uc001xmu.2_Intron|SIPA1L1_uc001xmv.2_Intron|SIPA1L1_uc010ttm.1_Intron	NM_015556	NP_056371			signal-induced proliferation-associated 1 like						actin cytoskeleton reorganization|activation of Rap GTPase activity|regulation of dendritic spine morphogenesis	cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane|synaptosome	GTPase activator activity			ovary(3)|breast(1)	4				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)														---	---	---	---
RGS6	9628	broad.mit.edu	37	14	72705746	72705746	+	Intron	DEL	T	-	-	rs11310093		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72705746delT	uc001xna.3	+						RGS6_uc010ttn.1_Intron|RGS6_uc001xmx.3_Intron|RGS6_uc010tto.1_Intron|RGS6_uc001xmy.3_Intron	NM_004296	NP_004287			regulator of G-protein signalling 6						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|signal transducer activity			upper_aerodigestive_tract(1)|lung(1)|skin(1)	3				all cancers(60;0.00309)|BRCA - Breast invasive adenocarcinoma(234;0.0281)|STAD - Stomach adenocarcinoma(64;0.0302)|OV - Ovarian serous cystadenocarcinoma(108;0.0476)														---	---	---	---
RGS6	9628	broad.mit.edu	37	14	72820691	72820693	+	Intron	DEL	CAG	-	-	rs66734260		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72820691_72820693delCAG	uc001xna.3	+						RGS6_uc010ttn.1_Intron|RGS6_uc001xmx.3_Intron|RGS6_uc010tto.1_Intron|RGS6_uc001xmy.3_Intron	NM_004296	NP_004287			regulator of G-protein signalling 6						G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|signal transducer activity			upper_aerodigestive_tract(1)|lung(1)|skin(1)	3				all cancers(60;0.00309)|BRCA - Breast invasive adenocarcinoma(234;0.0281)|STAD - Stomach adenocarcinoma(64;0.0302)|OV - Ovarian serous cystadenocarcinoma(108;0.0476)														---	---	---	---
DPF3	8110	broad.mit.edu	37	14	73249545	73249545	+	Intron	DEL	A	-	-	rs75960082		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73249545delA	uc001xnc.2	-						DPF3_uc001xnf.2_Intron|DPF3_uc010ari.1_Intron|DPF3_uc010ttq.1_Intron	NM_012074	NP_036206			D4, zinc and double PHD fingers, family 3						chromatin modification|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nBAF complex	nucleic acid binding|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00649)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)														---	---	---	---
RBM25	58517	broad.mit.edu	37	14	73586614	73586614	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73586614delT	uc001xno.2	+	19					RBM25_uc010ttu.1_3'UTR|RBM25_uc001xnp.2_3'UTR	NM_021239	NP_067062			RNA binding motif protein 25						apoptosis|mRNA processing|regulation of alternative nuclear mRNA splicing, via spliceosome|RNA splicing	cytoplasm|nuclear speck	mRNA binding|nucleotide binding|protein binding			central_nervous_system(2)|ovary(1)|breast(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)														---	---	---	---
NUMB	8650	broad.mit.edu	37	14	73798256	73798256	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73798256delA	uc001xny.1	-						NUMB_uc010aro.1_Intron|NUMB_uc010arp.1_Intron|NUMB_uc010arq.1_Intron|NUMB_uc010arr.1_Intron|NUMB_uc001xoa.1_Intron|NUMB_uc001xnz.1_Intron|NUMB_uc001xob.1_Intron|NUMB_uc001xod.1_Intron|NUMB_uc001xoc.1_Intron|NUMB_uc010ars.1_Intron|NUMB_uc001xof.1_Intron|NUMB_uc001xog.2_Intron|NUMB_uc001xoh.1_Intron	NM_001005743	NP_001005743			numb homolog isoform 1						axon guidance|lateral ventricle development|neuroblast division in subventricular zone|positive regulation of neurogenesis	integral to plasma membrane				ovary(2)|central_nervous_system(1)|skin(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.00471)|OV - Ovarian serous cystadenocarcinoma(108;0.161)														---	---	---	---
PTGR2	145482	broad.mit.edu	37	14	74327206	74327207	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74327206_74327207insT	uc001xow.2	+						PTGR2_uc010tue.1_Intron|PTGR2_uc001xox.2_Intron|ZNF410_uc001xoy.1_Intron	NM_001146154	NP_001139626			prostaglandin reductase 2						prostaglandin metabolic process		15-oxoprostaglandin 13-oxidase activity|zinc ion binding				0																		---	---	---	---
PTGR2	145482	broad.mit.edu	37	14	74342053	74342054	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74342053_74342054delTT	uc001xow.2	+						PTGR2_uc010tue.1_Intron|PTGR2_uc001xox.2_Intron|ZNF410_uc001xoy.1_Intron	NM_001146154	NP_001139626			prostaglandin reductase 2						prostaglandin metabolic process		15-oxoprostaglandin 13-oxidase activity|zinc ion binding				0																		---	---	---	---
COQ6	51004	broad.mit.edu	37	14	74420127	74420127	+	Intron	DEL	C	-	-	rs3213692	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74420127delC	uc001xph.2	+						COQ6_uc001xpe.2_Intron|COQ6_uc001xpf.2_Intron|COQ6_uc010tuk.1_Intron|COQ6_uc010tul.1_Intron|COQ6_uc010tum.1_Intron|COQ6_uc010tun.1_Intron|COQ6_uc001xpg.2_Intron	NM_182476	NP_872282			coenzyme Q6 homolog isoform a						ubiquinone biosynthetic process	mitochondrion	flavin adenine dinucleotide binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen				0				BRCA - Breast invasive adenocarcinoma(234;0.00337)														---	---	---	---
ENTPD5	957	broad.mit.edu	37	14	74437866	74437867	+	Intron	DEL	TT	-	-	rs113156308		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74437866_74437867delTT	uc010tuo.1	-						ENTPD5_uc001xpi.2_Intron	NM_001249	NP_001240			ectonucleoside triphosphate diphosphohydrolase 5						'de novo' posttranslational protein folding|ATP metabolic process|cell growth|cell proliferation|glycolysis|protein N-linked glycosylation|regulation of phosphatidylinositol 3-kinase cascade	endoplasmic reticulum lumen	guanosine-diphosphatase activity|uridine-diphosphatase activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00394)														---	---	---	---
LIN52	91750	broad.mit.edu	37	14	74659635	74659635	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74659635delG	uc001xpp.2	+						LIN52_uc010asb.2_Intron	NM_001024674	NP_001019845			lin-52 homolog											breast(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00471)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	74740891	74740891	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74740891delA								VSX2 (11457 upstream) : ABCD4 (11089 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	74785724	74785724	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74785724delT								ABCD4 (15957 upstream) : C14orf115 (29442 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	74907392	74907393	+	IGR	DEL	AA	-	-	rs79351727		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74907392_74907393delAA								TMEM90A (14587 upstream) : NPC2 (39251 downstream)																																			---	---	---	---
LTBP2	4053	broad.mit.edu	37	14	74965356	74965356	+	3'UTR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74965356delG	uc001xqa.2	-	36						NM_000428	NP_000419			latent transforming growth factor beta binding						protein secretion|protein targeting|transforming growth factor beta receptor signaling pathway	extracellular space|proteinaceous extracellular matrix	calcium ion binding|growth factor binding			liver(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)														---	---	---	---
KIAA0317	9870	broad.mit.edu	37	14	75131088	75131088	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75131088delT	uc001xqb.2	-						KIAA0317_uc010tut.1_Intron	NM_001039479	NP_001034568			hypothetical protein LOC9870						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	integral to membrane|intracellular	ubiquitin-protein ligase activity			ovary(2)|kidney(1)|central_nervous_system(1)|pancreas(1)	5				BRCA - Breast invasive adenocarcinoma(234;0.00404)														---	---	---	---
YLPM1	56252	broad.mit.edu	37	14	75260893	75260894	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75260893_75260894insT	uc001xqj.3	+						YLPM1_uc001xql.3_Intron	NM_019589	NP_062535			YLP motif containing 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck				ovary(2)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)														---	---	---	---
YLPM1	56252	broad.mit.edu	37	14	75269987	75269987	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75269987delT	uc001xqj.3	+						YLPM1_uc001xql.3_Intron	NM_019589	NP_062535			YLP motif containing 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck				ovary(2)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	75315101	75315101	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75315101delA								YLPM1 (11089 upstream) : PROX2 (6734 downstream)																																			---	---	---	---
RPS6KL1	83694	broad.mit.edu	37	14	75383387	75383388	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75383387_75383388delAA	uc010tux.1	-						RPS6KL1_uc001xqw.2_Intron|RPS6KL1_uc010asd.1_Intron|RPS6KL1_uc001xqy.1_Intron	NM_031464	NP_113652			ribosomal protein S6 kinase-like 1							ribosome	ATP binding|protein serine/threonine kinase activity			ovary(1)|stomach(1)|central_nervous_system(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.00658)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	75823387	75823387	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75823387delT								FOS (74452 upstream) : JDP2 (71122 downstream)																																			---	---	---	---
JDP2	122953	broad.mit.edu	37	14	75907822	75907823	+	Intron	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75907822_75907823delGA	uc010asj.2	+						JDP2_uc010tvb.1_Intron|JDP2_uc010tvc.1_Intron|JDP2_uc001xrq.2_Intron	NM_001135047	NP_001128519			Jun dimerization protein 2 isoform a							nucleus	sequence-specific DNA binding				0				BRCA - Breast invasive adenocarcinoma(234;0.0296)														---	---	---	---
FLVCR2	55640	broad.mit.edu	37	14	76073290	76073290	+	Intron	DEL	A	-	-	rs79782015		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76073290delA	uc001xrs.2	+						FLVCR2_uc010tvd.1_Intron	NM_017791	NP_060261			feline leukemia virus subgroup C cellular						transmembrane transport	integral to membrane|plasma membrane	heme binding|heme transporter activity				0				BRCA - Breast invasive adenocarcinoma(234;0.029)														---	---	---	---
FLVCR2	55640	broad.mit.edu	37	14	76090709	76090709	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76090709delA	uc001xrs.2	+						FLVCR2_uc010tvd.1_Intron	NM_017791	NP_060261			feline leukemia virus subgroup C cellular						transmembrane transport	integral to membrane|plasma membrane	heme binding|heme transporter activity				0				BRCA - Breast invasive adenocarcinoma(234;0.029)														---	---	---	---
TTLL5	23093	broad.mit.edu	37	14	76185973	76185973	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76185973delA	uc001xrx.2	+						TTLL5_uc010ask.1_Intron|TTLL5_uc001xry.1_Intron	NM_015072	NP_055887			tubulin tyrosine ligase-like family, member 5						protein modification process|transcription, DNA-dependent	centrosome|cilium|microtubule basal body|nucleus	tubulin-tyrosine ligase activity			ovary(2)|central_nervous_system(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.029)														---	---	---	---
TTLL5	23093	broad.mit.edu	37	14	76381441	76381441	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76381441delT	uc001xrx.2	+						TTLL5_uc001xsa.2_Intron	NM_015072	NP_055887			tubulin tyrosine ligase-like family, member 5						protein modification process|transcription, DNA-dependent	centrosome|cilium|microtubule basal body|nucleus	tubulin-tyrosine ligase activity			ovary(2)|central_nervous_system(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.029)														---	---	---	---
ESRRB	2103	broad.mit.edu	37	14	76965492	76965493	+	Intron	INS	-	C	C	rs150374889	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76965492_76965493insC	uc001xsr.2	+						ESRRB_uc001xso.2_Intron	NM_004452	NP_004443			estrogen-related receptor beta							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(234;0.0213)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	76980179	76980179	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76980179delT								ESRRB (12001 upstream) : VASH1 (248056 downstream)																																			---	---	---	---
TMEM63C	57156	broad.mit.edu	37	14	77652362	77652362	+	Intron	DEL	T	-	-	rs78577045		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77652362delT	uc001xtf.2	+						TMEM63C_uc010asq.1_Intron	NM_020431	NP_065164			transmembrane protein 63C							integral to membrane					0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0342)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	78557147	78557147	+	IGR	DEL	G	-	-	rs112512122		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78557147delG								ADCK1 (156851 upstream) : NRXN3 (79781 downstream)																																			---	---	---	---
NRXN3	9369	broad.mit.edu	37	14	78717617	78717617	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78717617delA	uc001xum.1	+											Homo sapiens mRNA for KIAA0743 protein, partial cds.						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)														---	---	---	---
NRXN3	9369	broad.mit.edu	37	14	78858342	78858342	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78858342delA	uc001xum.1	+											Homo sapiens mRNA for KIAA0743 protein, partial cds.						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)														---	---	---	---
NRXN3	9369	broad.mit.edu	37	14	78946320	78946320	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78946320delA	uc001xun.2	+						NRXN3_uc001xum.1_Intron	NM_004796	NP_004787			neurexin 3 isoform 1 precursor						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)														---	---	---	---
NRXN3	9369	broad.mit.edu	37	14	78990538	78990538	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78990538delT	uc001xun.2	+						NRXN3_uc001xum.1_Intron	NM_004796	NP_004787			neurexin 3 isoform 1 precursor						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)														---	---	---	---
NRXN3	9369	broad.mit.edu	37	14	78999084	78999084	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78999084delT	uc001xun.2	+						NRXN3_uc001xum.1_Intron	NM_004796	NP_004787			neurexin 3 isoform 1 precursor						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)														---	---	---	---
NRXN3	9369	broad.mit.edu	37	14	79460735	79460735	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79460735delA	uc001xun.2	+						NRXN3_uc001xum.1_Intron	NM_004796	NP_004787			neurexin 3 isoform 1 precursor						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)														---	---	---	---
NRXN3	9369	broad.mit.edu	37	14	79490463	79490463	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79490463delA	uc001xun.2	+						NRXN3_uc001xum.1_Intron	NM_004796	NP_004787			neurexin 3 isoform 1 precursor						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)														---	---	---	---
NRXN3	9369	broad.mit.edu	37	14	79857145	79857145	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:79857145delA	uc001xun.2	+						NRXN3_uc001xum.1_Intron|NRXN3_uc001xup.2_Intron|NRXN3_uc001xuq.2_Intron|NRXN3_uc010asw.2_Intron|NRXN3_uc001xur.3_Intron	NM_004796	NP_004787			neurexin 3 isoform 1 precursor						axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|upper_aerodigestive_tract(2)|pancreas(2)|central_nervous_system(1)|breast(1)|skin(1)	10		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	80342918	80342918	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80342918delT								NRXN3 (12160 upstream) : DIO2 (320952 downstream)																																			---	---	---	---
DIO2	1734	broad.mit.edu	37	14	80682474	80682474	+	5'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80682474delT	uc010asy.2	-	2					uc001xuw.1_Intron					RecName: Full=Iodothyronine deiodinase;						hormone biosynthetic process|selenocysteine incorporation|thyroid hormone generation	integral to membrane|plasma membrane	thyroxine 5'-deiodinase activity|ubiquitin protein ligase binding			central_nervous_system(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.0281)														---	---	---	---
C14orf145	145508	broad.mit.edu	37	14	80983473	80983473	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:80983473delT	uc001xux.2	-						C14orf145_uc010asz.1_Intron	NM_152446	NP_689659			hypothetical protein LOC145508							centriole|spindle pole					0				BRCA - Breast invasive adenocarcinoma(234;0.0586)														---	---	---	---
C14orf145	145508	broad.mit.edu	37	14	81143973	81143974	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81143973_81143974delAA	uc001xux.2	-						C14orf145_uc010asz.1_Intron	NM_152446	NP_689659			hypothetical protein LOC145508							centriole|spindle pole					0				BRCA - Breast invasive adenocarcinoma(234;0.0586)														---	---	---	---
SEL1L	6400	broad.mit.edu	37	14	81953653	81953653	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81953653delA	uc010tvv.1	-							NM_005065	NP_005056			sel-1 suppressor of lin-12-like precursor						Notch signaling pathway	endoplasmic reticulum membrane|integral to membrane	protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.0299)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	82079875	82079875	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:82079875delG	uc001xvp.3	-											Homo sapiens cDNA FLJ27344 fis, clone TST03461.																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	82122485	82122486	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:82122485_82122486delTG								SEL1L (122280 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	82226862	82226862	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:82226862delT								SEL1L (226657 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	82242795	82242795	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:82242795delG								SEL1L (242590 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	82290585	82290585	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:82290585delT								SEL1L (290380 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	82309552	82309554	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:82309552_82309554delTTT								SEL1L (309347 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	82796975	82796975	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:82796975delT								SEL1L (796770 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	83016034	83016034	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:83016034delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	83197046	83197046	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:83197046delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	83203621	83203621	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:83203621delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	83603826	83603827	+	IGR	INS	-	TG	TG	rs138920630	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:83603826_83603827insTG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	84616640	84616640	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:84616640delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	85689921	85689921	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:85689921delT								None (None upstream) : FLRT2 (306567 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	85865403	85865403	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:85865403delT								None (None upstream) : FLRT2 (131085 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	86320516	86320516	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:86320516delA								FLRT2 (226247 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	86471090	86471090	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:86471090delT								FLRT2 (376821 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	86693503	86693503	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:86693503delT								FLRT2 (599234 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	87159486	87159486	+	IGR	DEL	A	-	-	rs35371061		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:87159486delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	87476799	87476799	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:87476799delT								None (None upstream) : GALC (827365 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	87588523	87588523	+	IGR	DEL	T	-	-	rs111236890		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:87588523delT								None (None upstream) : GALC (715641 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	87758792	87758792	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:87758792delA								None (None upstream) : GALC (545372 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	88039963	88039963	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88039963delA								None (None upstream) : GALC (264201 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	88048513	88048513	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88048513delA								None (None upstream) : GALC (255651 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	88261316	88261316	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88261316delA								None (None upstream) : GALC (42848 downstream)																																			---	---	---	---
SPATA7	55812	broad.mit.edu	37	14	88868778	88868778	+	Intron	DEL	A	-	-	rs112520907		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88868778delA	uc001xwq.2	+						SPATA7_uc001xwr.2_Intron	NM_018418	NP_060888			spermatogenesis-associated protein 7 isoform a						response to stimulus|visual perception					ovary(1)	1																		---	---	---	---
PTPN21	11099	broad.mit.edu	37	14	88987753	88987753	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88987753delT	uc001xwv.3	-						PTPN21_uc010twc.1_Intron|PTPN21_uc010atf.1_Intron	NM_007039	NP_008970			protein tyrosine phosphatase, non-receptor type							cytoplasm|cytoskeleton	binding|protein tyrosine phosphatase activity			ovary(3)|skin(1)	4																		---	---	---	---
TTC8	123016	broad.mit.edu	37	14	89306606	89306606	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89306606delA	uc010ath.2	+						TTC8_uc010atg.1_Intron|TTC8_uc001xxl.2_Intron|TTC8_uc010ati.2_Intron|TTC8_uc001xxm.2_Intron|TTC8_uc010atj.2_Intron|TTC8_uc001xxi.2_Intron|TTC8_uc001xxj.2_Intron|TTC8_uc001xxk.2_Intron	NM_198309	NP_938051			tetratricopeptide repeat domain 8 isoform B						cilium assembly|establishment of anatomical structure orientation|sensory processing	BBSome|centrosome|cilium membrane|microtubule basal body	protein binding				0														Bardet-Biedl_syndrome				---	---	---	---
TTC8	123016	broad.mit.edu	37	14	89311056	89311056	+	Intron	DEL	T	-	-	rs35583525		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89311056delT	uc010ath.2	+						TTC8_uc010atg.1_Intron|TTC8_uc001xxl.2_Intron|TTC8_uc010ati.2_Intron|TTC8_uc001xxm.2_Intron|TTC8_uc010atj.2_Intron|TTC8_uc001xxi.2_Intron|TTC8_uc001xxj.2_Intron|TTC8_uc001xxk.2_Intron	NM_198309	NP_938051			tetratricopeptide repeat domain 8 isoform B						cilium assembly|establishment of anatomical structure orientation|sensory processing	BBSome|centrosome|cilium membrane|microtubule basal body	protein binding				0														Bardet-Biedl_syndrome				---	---	---	---
FOXN3	1112	broad.mit.edu	37	14	89714544	89714544	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89714544delA	uc001xxo.3	-						FOXN3_uc001xxn.3_Intron|FOXN3_uc010atk.2_Intron	NM_001085471	NP_001078940			checkpoint suppressor 1 isoform 1						DNA damage checkpoint|embryo development|G2 phase of mitotic cell cycle|negative regulation of transcription, DNA-dependent|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein C-terminus binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			skin(2)|ovary(1)	3																		---	---	---	---
FOXN3	1112	broad.mit.edu	37	14	90087719	90087724	+	5'Flank	DEL	AAAAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90087719_90087724delAAAAAA	uc001xxo.3	-						FOXN3_uc010atk.2_5'Flank|FOXN3_uc001xxp.2_5'Flank	NM_001085471	NP_001078940			checkpoint suppressor 1 isoform 1						DNA damage checkpoint|embryo development|G2 phase of mitotic cell cycle|negative regulation of transcription, DNA-dependent|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein C-terminus binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			skin(2)|ovary(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	90138562	90138565	+	IGR	DEL	TTTT	-	-	rs111986188		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90138562_90138565delTTTT								FOXN3 (53068 upstream) : C14orf143 (124906 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	90186501	90186501	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90186501delG								FOXN3 (101007 upstream) : C14orf143 (76970 downstream)																																			---	---	---	---
TDP1	55775	broad.mit.edu	37	14	90429218	90429218	+	Intron	DEL	A	-	-	rs113407792		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90429218delA	uc001xxy.2	+						TDP1_uc010atm.2_Intron|TDP1_uc001xxz.2_Intron|TDP1_uc010atn.2_Intron|TDP1_uc001xya.2_Intron|TDP1_uc001xyb.2_Intron|TDP1_uc010ato.2_5'Flank|TDP1_uc001xyc.1_5'Flank	NM_018319	NP_060789			tyrosyl-DNA phosphodiesterase 1						cell death|double-strand break repair|single strand break repair	cytoplasm|nucleus	3'-tyrosyl-DNA phosphodiesterase activity|double-stranded DNA binding|exonuclease activity|protein binding|single-stranded DNA binding			ovary(2)	2		all_cancers(154;0.185)		COAD - Colon adenocarcinoma(157;0.23)									Repair_of_DNA-protein_crosslinks					---	---	---	---
Unknown	0	broad.mit.edu	37	14	90512884	90512886	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90512884_90512886delTTT								TDP1 (1778 upstream) : KCNK13 (15222 downstream)																																			---	---	---	---
KCNK13	56659	broad.mit.edu	37	14	90544762	90544762	+	Intron	DEL	A	-	-	rs75988611		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90544762delA	uc001xye.1	+							NM_022054	NP_071337			potassium channel, subfamily K, member 13							integral to membrane	potassium channel activity|voltage-gated ion channel activity			skin(1)	1		all_cancers(154;0.186)																---	---	---	---
Unknown	0	broad.mit.edu	37	14	90803055	90803055	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90803055delA								C14orf102 (4776 upstream) : CALM1 (60318 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	90950748	90950748	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90950748delC								CALM1 (76138 upstream) : TTC7B (56185 downstream)																																			---	---	---	---
TTC7B	145567	broad.mit.edu	37	14	91021753	91021753	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91021753delG	uc001xyp.2	-						TTC7B_uc001xyo.2_Intron|TTC7B_uc010ats.2_Intron	NM_001010854	NP_001010854			tetratricopeptide repeat domain 7B								binding			ovary(2)	2		Melanoma(154;0.222)																---	---	---	---
TTC7B	145567	broad.mit.edu	37	14	91210127	91210127	+	Intron	DEL	A	-	-	rs34408594		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91210127delA	uc001xyp.2	-							NM_001010854	NP_001010854			tetratricopeptide repeat domain 7B								binding			ovary(2)	2		Melanoma(154;0.222)																---	---	---	---
TTC7B	145567	broad.mit.edu	37	14	91263201	91263201	+	Intron	DEL	T	-	-	rs35291655		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91263201delT	uc001xyp.2	-							NM_001010854	NP_001010854			tetratricopeptide repeat domain 7B								binding			ovary(2)	2		Melanoma(154;0.222)																---	---	---	---
RPS6KA5	9252	broad.mit.edu	37	14	91436205	91436206	+	Intron	DEL	TC	-	-	rs148958029	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91436205_91436206delTC	uc001xys.2	-						RPS6KA5_uc010twi.1_Intron|RPS6KA5_uc001xyt.2_Intron|RPS6KA5_uc010att.1_Intron	NM_004755	NP_004746			ribosomal protein S6 kinase, polypeptide 5						axon guidance|epidermal growth factor receptor signaling pathway|histone phosphorylation|innate immune response|interleukin-1-mediated signaling pathway|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of histone acetylation|positive regulation of histone phosphorylation|positive regulation of transcription from RNA polymerase II promoter|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytoplasm|nucleoplasm	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(1)	1		all_cancers(154;0.0148)|Melanoma(154;0.099)|all_epithelial(191;0.146)		Epithelial(152;0.182)|BRCA - Breast invasive adenocarcinoma(234;0.201)														---	---	---	---
C14orf159	80017	broad.mit.edu	37	14	91626762	91626770	+	Intron	DEL	AAAAAAAAA	-	-	rs34785372		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91626762_91626770delAAAAAAAAA	uc001xzb.2	+						C14orf159_uc010atu.1_Intron|C14orf159_uc010atv.1_Intron|C14orf159_uc001xyy.2_Intron|C14orf159_uc001xyx.2_Intron|C14orf159_uc001xyw.2_Intron|C14orf159_uc001xzc.2_Intron|C14orf159_uc001xza.2_Intron|C14orf159_uc001xyv.2_Intron|C14orf159_uc001xyz.2_Intron|C14orf159_uc010twj.1_Intron|C14orf159_uc001xze.2_Intron	NM_001102366	NP_001095836			hypothetical protein LOC80017 isoform a							mitochondrion				central_nervous_system(2)|ovary(1)	3		all_cancers(154;0.0191)|all_epithelial(191;0.241)		Epithelial(152;0.141)|OV - Ovarian serous cystadenocarcinoma(161;0.207)														---	---	---	---
CCDC88C	440193	broad.mit.edu	37	14	91775006	91775006	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91775006delG	uc010aty.2	-							NM_001080414	NP_001073883			DVL-binding protein DAPLE						microtubule cytoskeleton organization|protein destabilization|protein homooligomerization|regulation of protein phosphorylation|Wnt receptor signaling pathway	cytoplasm|insoluble fraction	microtubule binding|PDZ domain binding|protein self-association			ovary(3)	3		all_cancers(154;0.0468)																---	---	---	---
Unknown	0	broad.mit.edu	37	14	92036631	92036631	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92036631delG								SMEK1 (59818 upstream) : C14orf184 (2157 downstream)																																			---	---	---	---
TC2N	123036	broad.mit.edu	37	14	92287796	92287796	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92287796delA	uc001xzu.3	-						TC2N_uc001xzt.3_Intron|TC2N_uc010auc.2_Intron|TC2N_uc001xzv.3_Intron	NM_001128595	NP_001122067			tandem C2 domains, nuclear							nucleus				upper_aerodigestive_tract(1)	1				COAD - Colon adenocarcinoma(157;0.218)														---	---	---	---
FBLN5	10516	broad.mit.edu	37	14	92353000	92353001	+	Intron	INS	-	T	T	rs11458593		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92353000_92353001insT	uc001xzx.3	-						FBLN5_uc010aud.2_Intron|FBLN5_uc010aue.2_Intron	NM_006329	NP_006320			fibulin 5 precursor						cell-matrix adhesion|elastic fiber assembly|protein localization at cell surface|regulation of removal of superoxide radicals	extracellular space|proteinaceous extracellular matrix|soluble fraction	calcium ion binding|integrin binding|protein C-terminus binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	6		all_cancers(154;0.0722)																---	---	---	---
FBLN5	10516	broad.mit.edu	37	14	92414638	92414645	+	5'Flank	DEL	TGTTTGTT	-	-	rs71790778		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92414638_92414645delTGTTTGTT	uc001xzx.3	-						FBLN5_uc010aud.2_5'Flank|FBLN5_uc010aue.2_5'Flank	NM_006329	NP_006320			fibulin 5 precursor						cell-matrix adhesion|elastic fiber assembly|protein localization at cell surface|regulation of removal of superoxide radicals	extracellular space|proteinaceous extracellular matrix|soluble fraction	calcium ion binding|integrin binding|protein C-terminus binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	6		all_cancers(154;0.0722)																---	---	---	---
TRIP11	9321	broad.mit.edu	37	14	92454748	92454748	+	Intron	DEL	A	-	-	rs2273184	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92454748delA	uc001xzy.2	-						TRIP11_uc010auf.1_Intron	NM_004239	NP_004230			thyroid hormone receptor interactor 11						transcription from RNA polymerase II promoter	cytoskeleton|Golgi apparatus|membrane|nucleus	protein binding|transcription coactivator activity			ovary(6)|skin(2)|kidney(2)|central_nervous_system(1)|lung(1)|breast(1)	13				COAD - Colon adenocarcinoma(157;0.223)				T	PDGFRB	AML								---	---	---	---
CPSF2	53981	broad.mit.edu	37	14	92623949	92623949	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92623949delT	uc001yah.1	+							NM_017437	NP_059133			cleavage and polyadenylation specific factor 2						histone mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex	hydrolase activity|protein binding|RNA binding			ovary(2)	2		all_cancers(154;0.0766)		COAD - Colon adenocarcinoma(157;0.222)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	92714650	92714650	+	IGR	DEL	G	-	-	rs34739519		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92714650delG								CPSF2 (84107 upstream) : SLC24A4 (74275 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	92768093	92768093	+	IGR	DEL	A	-	-	rs139770063		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92768093delA								CPSF2 (137550 upstream) : SLC24A4 (20832 downstream)																																			---	---	---	---
SLC24A4	123041	broad.mit.edu	37	14	92818259	92818260	+	Intron	INS	-	AAGGA	AAGGA	rs57027749		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92818259_92818260insAAGGA	uc001yak.2	+						SLC24A4_uc001yai.2_Intron|SLC24A4_uc010twm.1_Intron|SLC24A4_uc001yaj.2_Intron	NM_153646	NP_705932			solute carrier family 24 member 4 isoform 1							integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			breast(2)|ovary(1)	3		all_cancers(154;0.0347)|all_epithelial(191;0.163)		Colorectal(1;0.00242)|COAD - Colon adenocarcinoma(157;0.047)|Epithelial(152;0.0781)|READ - Rectum adenocarcinoma(1;0.176)|all cancers(159;0.182)														---	---	---	---
RIN3	79890	broad.mit.edu	37	14	93017577	93017577	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93017577delC	uc001yap.2	+						RIN3_uc010auk.2_Intron	NM_024832	NP_079108			Ras and Rab interactor 3						endocytosis|signal transduction	cytoplasmic membrane-bounded vesicle|early endosome	GTPase activator activity|Ras GTPase binding			lung(2)|ovary(1)	3		all_cancers(154;0.0701)																---	---	---	---
C14orf142	84520	broad.mit.edu	37	14	93670800	93670800	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93670800delT	uc001ybl.1	-						UBR7_uc001ybm.3_5'Flank|UBR7_uc001ybn.3_5'Flank	NM_032490	NP_115879			hypothetical protein LOC84520												0		all_cancers(154;0.00528)|Acute lymphoblastic leukemia(33;0.0497)|all_epithelial(191;0.125)|all_neural(303;0.13)		Epithelial(152;0.177)|all cancers(159;0.198)|COAD - Colon adenocarcinoma(157;0.203)														---	---	---	---
BTBD7	55727	broad.mit.edu	37	14	93783250	93783250	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93783250delA	uc001ybo.2	-						BTBD7_uc001ybp.2_Intron|BTBD7_uc001ybr.2_Intron	NM_001002860	NP_001002860			BTB (POZ) domain containing 7 isoform 1											pancreas(1)	1		all_cancers(154;0.08)		Epithelial(152;0.196)|COAD - Colon adenocarcinoma(157;0.212)|all cancers(159;0.223)														---	---	---	---
KIAA1409	57578	broad.mit.edu	37	14	93991796	93991797	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93991796_93991797delAA	uc001ybv.1	+						KIAA1409_uc001ybs.1_Intron|KIAA1409_uc001ybu.1_Intron	NM_020818	NP_065869			hypothetical protein LOC57578							integral to membrane				ovary(10)|skin(4)|large_intestine(3)	17		all_cancers(154;0.0354)|all_epithelial(191;0.216)		Epithelial(152;0.188)														---	---	---	---
KIAA1409	57578	broad.mit.edu	37	14	94084806	94084806	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94084806delA	uc001ybv.1	+						KIAA1409_uc001ybs.1_Intron	NM_020818	NP_065869			hypothetical protein LOC57578							integral to membrane				ovary(10)|skin(4)|large_intestine(3)	17		all_cancers(154;0.0354)|all_epithelial(191;0.216)		Epithelial(152;0.188)														---	---	---	---
PRIMA1	145270	broad.mit.edu	37	14	94197999	94197999	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94197999delT	uc001ybw.1	-						PRIMA1_uc001ybx.1_Intron	NM_178013	NP_821092			proline rich membrane anchor 1 precursor						neurotransmitter catabolic process	cell junction|integral to membrane|synapse				large_intestine(1)|skin(1)	2		all_cancers(154;0.127)		Epithelial(152;0.138)|COAD - Colon adenocarcinoma(157;0.229)														---	---	---	---
PPP4R4	57718	broad.mit.edu	37	14	94686098	94686098	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94686098delT	uc001ycs.1	+						PPP4R4_uc001ycr.2_Intron	NM_058237	NP_478144			HEAT-like repeat-containing protein isoform 1							cytoplasm|protein serine/threonine phosphatase complex	protein binding			skin(3)|upper_aerodigestive_tract(1)	4																		---	---	---	---
PPP4R4	57718	broad.mit.edu	37	14	94702885	94702886	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94702885_94702886insT	uc001ycs.1	+							NM_058237	NP_478144			HEAT-like repeat-containing protein isoform 1							cytoplasm|protein serine/threonine phosphatase complex	protein binding			skin(3)|upper_aerodigestive_tract(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	94895117	94895118	+	IGR	DEL	TT	-	-	rs71937880		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94895117_94895118delTT								SERPINA1 (38088 upstream) : SERPINA11 (13683 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	95193580	95193582	+	IGR	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95193580_95193582delAAA								SERPINA13 (80250 upstream) : GSC (40979 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	95295034	95295034	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95295034delA								GSC (58535 upstream) : DICER1 (257531 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	95404696	95404697	+	IGR	DEL	GT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95404696_95404697delGT								GSC (168197 upstream) : DICER1 (147868 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	95466256	95466257	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95466256_95466257insA								GSC (229757 upstream) : DICER1 (86308 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	95485242	95485242	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95485242delA								GSC (248743 upstream) : DICER1 (67323 downstream)																																			---	---	---	---
DICER1	23405	broad.mit.edu	37	14	95581844	95581844	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95581844delA	uc001ydw.2	-						DICER1_uc001ydv.2_Intron|DICER1_uc001ydx.2_Intron	NM_030621	NP_085124			dicer1						negative regulation of Schwann cell proliferation|negative regulation of transcription from RNA polymerase II promoter|nerve development|neuron projection morphogenesis|peripheral nervous system myelin formation|positive regulation of myelination|positive regulation of Schwann cell differentiation|pre-miRNA processing|production of siRNA involved in RNA interference|targeting of mRNA for destruction involved in RNA interference	cytosol|RNA-induced silencing complex	ATP binding|ATP-dependent helicase activity|double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity			skin(2)|ovary(1)|pancreas(1)|lung(1)	5		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)				Mis F|N			pleuropulmonary blastoma			DICER_1_syndrome_|Familial_Multinodular_Goiter_				---	---	---	---
Unknown	0	broad.mit.edu	37	14	95951943	95951943	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95951943delT								C14orf49 (9770 upstream) : SNHG10 (47310 downstream)																																	OREG0031345	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	---	---	---	---
Unknown	0	broad.mit.edu	37	14	95994307	95994307	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95994307delA								C14orf49 (52134 upstream) : SNHG10 (4946 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	96366438	96366438	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96366438delT	uc001yfe.2	+											Homo sapiens cDNA FLJ12965 fis, clone NT2RP2005741.																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	96453787	96453788	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96453787_96453788delTT								TCL1A (273254 upstream) : C14orf132 (51874 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	96500970	96500970	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96500970delA								TCL1A (320437 upstream) : C14orf132 (4692 downstream)																																			---	---	---	---
PAPOLA	10914	broad.mit.edu	37	14	96999154	96999154	+	Intron	DEL	T	-	-	rs112354137		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96999154delT	uc001yfq.2	+						PAPOLA_uc001yfr.2_Intron|PAPOLA_uc010twv.1_Intron|PAPOLA_uc010avp.2_Intron	NM_032632	NP_116021			poly(A) polymerase alpha						mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	cytoplasm|nucleoplasm	ATP binding|magnesium ion binding|manganese ion binding|polynucleotide adenylyltransferase activity|RNA binding				0		all_cancers(154;0.0555)|all_epithelial(191;0.149)|Melanoma(154;0.155)		COAD - Colon adenocarcinoma(157;0.213)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	97593191	97593192	+	IGR	DEL	GT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97593191_97593192delGT								VRK1 (245241 upstream) : C14orf64 (798755 downstream)																																			---	---	---	---
C14orf64	388011	broad.mit.edu	37	14	98406115	98406116	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:98406115_98406116insA	uc001yfw.2	-						C14orf64_uc001yfx.2_Intron	NR_015430				Homo sapiens cDNA FLJ34349 fis, clone FEBRA2011063.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	99274415	99274415	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99274415delA								C14orf177 (90318 upstream) : BCL11B (361212 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	99497522	99497523	+	IGR	DEL	AC	-	-	rs35983861		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99497522_99497523delAC								C14orf177 (313425 upstream) : BCL11B (138104 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	99764447	99764447	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99764447delA								BCL11B (26625 upstream) : SETD3 (99637 downstream)																																			---	---	---	---
EML1	2009	broad.mit.edu	37	14	100217951	100217952	+	Intron	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100217951_100217952delGA	uc010avt.1	+							NM_004434	NP_004425			echinoderm microtubule associated protein like 1							cytoplasm|microtubule|microtubule associated complex	calcium ion binding|protein binding			large_intestine(2)|pancreas(1)|ovary(1)|skin(1)	5		Melanoma(154;0.0879)|all_epithelial(191;0.216)																---	---	---	---
YY1	7528	broad.mit.edu	37	14	100744638	100744638	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100744638delT	uc001ygy.1	+	5					uc001ygz.1_5'Flank	NM_003403	NP_003394			YY1 transcription factor						cell differentiation|cellular response to UV|double-strand break repair via homologous recombination|negative regulation of transcription from RNA polymerase II promoter|response to UV-C|spermatogenesis	Ino80 complex|nuclear matrix|plasma membrane	four-way junction DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|transcription regulatory region DNA binding|zinc ion binding				0		Melanoma(154;0.152)																---	---	---	---
Unknown	0	broad.mit.edu	37	14	101280148	101280149	+	IGR	INS	-	G	G	rs36015456		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101280148_101280149insG								DLK1 (78674 upstream) : MEG3 (12296 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	101380083	101380084	+	IGR	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101380083_101380084delAC								MIR370 (2533 upstream) : SNORD113-1 (11074 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	101500778	101500778	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101500778delT								MIR495 (605 upstream) : MIR376C (5249 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	101502830	101502830	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101502830delA								MIR495 (2657 upstream) : MIR376C (3197 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	101756627	101756628	+	IGR	DEL	AT	-	-	rs12879086		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101756627_101756628delAT								MIR656 (223489 upstream) : DIO3OS (261932 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	101829779	101829780	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101829779_101829780delTT								MIR656 (296641 upstream) : DIO3OS (188780 downstream)																																			---	---	---	---
PPP2R5C	5527	broad.mit.edu	37	14	102274428	102274430	+	5'Flank	DEL	GAG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102274428_102274430delGAG	uc001yko.2	+						PPP2R5C_uc001ykj.3_Intron|PPP2R5C_uc010txr.1_Intron|PPP2R5C_uc001ykk.2_Intron|PPP2R5C_uc010txt.1_5'Flank|PPP2R5C_uc001ykn.2_5'Flank|PPP2R5C_uc001ykp.2_5'Flank|PPP2R5C_uc010txs.1_5'Flank	NM_002719	NP_002710			gamma isoform of regulatory subunit B56, protein						DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|negative regulation of cell proliferation|proteasomal ubiquitin-dependent protein catabolic process|signal transduction	chromosome, centromeric region|nucleus|protein phosphatase type 2A complex	protein binding|protein binding|protein phosphatase type 2A regulator activity|protein phosphatase type 2A regulator activity			ovary(1)|breast(1)	2																		---	---	---	---
PPP2R5C	5527	broad.mit.edu	37	14	102276206	102276207	+	5'UTR	DEL	TT	-	-	rs78200543		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102276206_102276207delTT	uc001yko.2	+	1					PPP2R5C_uc001ykj.3_Intron|PPP2R5C_uc010txr.1_Intron|PPP2R5C_uc001ykk.2_Intron|PPP2R5C_uc010txt.1_5'UTR|PPP2R5C_uc001ykn.2_5'UTR|PPP2R5C_uc001ykp.2_5'UTR|PPP2R5C_uc010txs.1_5'UTR	NM_002719	NP_002710			gamma isoform of regulatory subunit B56, protein						DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|negative regulation of cell proliferation|proteasomal ubiquitin-dependent protein catabolic process|signal transduction	chromosome, centromeric region|nucleus|protein phosphatase type 2A complex	protein binding|protein binding|protein phosphatase type 2A regulator activity|protein phosphatase type 2A regulator activity			ovary(1)|breast(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	14	102418418	102418418	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102418418delT								PPP2R5C (24092 upstream) : DYNC1H1 (12447 downstream)																																			---	---	---	---
DYNC1H1	1778	broad.mit.edu	37	14	102450010	102450010	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102450010delT	uc001yks.2	+							NM_001376	NP_001367			cytoplasmic dynein 1 heavy chain 1						cytoplasmic mRNA processing body assembly|G2/M transition of mitotic cell cycle|microtubule-based movement|mitotic spindle organization|stress granule assembly|transport	centrosome|cytoplasmic dynein complex|cytosol|Golgi apparatus|microtubule	ATP binding|ATPase activity, coupled|microtubule motor activity|protein binding			ovary(7)|central_nervous_system(2)|pancreas(1)	10																		---	---	---	---
HSP90AA1	3320	broad.mit.edu	37	14	102548966	102548966	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102548966delT	uc001yku.3	-						HSP90AA1_uc001ykv.3_Intron	NM_005348	NP_005339			heat shock 90kDa protein 1, alpha isoform 2						axon guidance|cellular chaperone-mediated protein complex assembly|G2/M transition of mitotic cell cycle|nitric oxide metabolic process|positive regulation of nitric oxide biosynthetic process|protein import into mitochondrial outer membrane|protein refolding|regulation of nitric-oxide synthase activity|response to unfolded protein|signal transduction	cytosol|melanosome|plasma membrane	ATP binding|ATPase activity|nitric-oxide synthase regulator activity|protein homodimerization activity|TPR domain binding|unfolded protein binding			ovary(2)|central_nervous_system(2)|prostate(1)|lung(1)|breast(1)	7					Rifabutin(DB00615)													---	---	---	---
ANKRD9	122416	broad.mit.edu	37	14	102978188	102978189	+	5'Flank	DEL	TT	-	-	rs112127868		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102978188_102978189delTT	uc001yly.1	-						ANKRD9_uc001ylz.1_5'Flank|ANKRD9_uc001yma.1_5'Flank|ANKRD9_uc010awm.1_5'Flank	NM_152326	NP_689539			ankyrin repeat domain 9											pancreas(1)	1																		---	---	---	---
RCOR1	23186	broad.mit.edu	37	14	103084785	103084785	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103084785delG	uc001ymb.2	+							NM_015156	NP_055971			REST corepressor 1						blood coagulation|histone H4 deacetylation|interspecies interaction between organisms	transcriptional repressor complex	protein binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription|transcription regulatory region DNA binding			ovary(1)	1																		---	---	---	---
RCOR1	23186	broad.mit.edu	37	14	103119722	103119723	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103119722_103119723insT	uc001ymb.2	+							NM_015156	NP_055971			REST corepressor 1						blood coagulation|histone H4 deacetylation|interspecies interaction between organisms	transcriptional repressor complex	protein binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription|transcription regulatory region DNA binding			ovary(1)	1																		---	---	---	---
RCOR1	23186	broad.mit.edu	37	14	103124814	103124815	+	Intron	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103124814_103124815delCT	uc001ymb.2	+							NM_015156	NP_055971			REST corepressor 1						blood coagulation|histone H4 deacetylation|interspecies interaction between organisms	transcriptional repressor complex	protein binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription|transcription regulatory region DNA binding			ovary(1)	1																		---	---	---	---
PPP1R13B	23368	broad.mit.edu	37	14	104279570	104279572	+	Intron	DEL	AAA	-	-	rs11362801		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104279570_104279572delAAA	uc001yof.1	-						PPP1R13B_uc001yog.1_Intron	NM_015316	NP_056131			apoptosis-stimulating protein of p53, 1						apoptosis|induction of apoptosis|negative regulation of cell cycle	cytoplasm|nucleus|plasma membrane	protein binding			ovary(1)	1		all_cancers(154;0.173)|all_epithelial(191;0.131)|Melanoma(154;0.155)																---	---	---	---
C14orf2	9556	broad.mit.edu	37	14	104381692	104381692	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104381692delT	uc001yoi.3	-						C14orf2_uc001yoj.3_Intron|C14orf2_uc010aww.1_Intron|C14orf2_uc001yok.2_Intron	NM_004894	NP_004885			6.8 kDa mitochondrial proteolipid isoform 1							mitochondrion					0				Epithelial(152;0.223)														---	---	---	---
KIF26A	26153	broad.mit.edu	37	14	104639998	104639998	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104639998delG	uc001yos.3	+							NM_015656	NP_056471			kinesin family member 26A						blood coagulation|enteric nervous system development|microtubule-based movement|negative regulation of signal transduction|regulation of cell growth by extracellular stimulus	cytosol|microtubule	ATP binding|microtubule binding|microtubule motor activity			pancreas(1)	1		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767)	Epithelial(46;0.152)	Epithelial(152;0.161)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	104652635	104652635	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104652635delC								KIF26A (5401 upstream) : C14orf180 (393421 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	104659681	104659681	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104659681delC								KIF26A (12447 upstream) : C14orf180 (386375 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	104756339	104756339	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104756339delT								KIF26A (109105 upstream) : C14orf180 (289717 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	105131468	105131469	+	IGR	INS	-	ACAA	ACAA	rs113329447		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105131468_105131469insACAA								TMEM179 (60371 upstream) : INF2 (24474 downstream)																																			---	---	---	---
INF2	64423	broad.mit.edu	37	14	105324332	105324332	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105324332delT	uc010tyi.1	+							NM_022489	NP_071934			inverted formin 2 isoform 1						actin cytoskeleton organization	endoplasmic reticulum|nucleus|perinuclear region of cytoplasm	actin binding|Rho GTPase binding				0		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.176)														---	---	---	---
KIAA0284	283638	broad.mit.edu	37	14	105338624	105338625	+	Intron	INS	-	GCGTGTGTGT	GCGTGTGTGT	rs150438141	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105338624_105338625insGCGTGTGTGT	uc010axb.2	+						INF2_uc010tyi.1_Intron|KIAA0284_uc001ypr.2_Intron	NM_001112726	NP_001106197			hypothetical protein LOC283638 isoform 1							cytoplasm|microtubule				breast(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000472)|OV - Ovarian serous cystadenocarcinoma(23;0.00596)|Epithelial(46;0.0149)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.178)														---	---	---	---
C14orf79	122616	broad.mit.edu	37	14	105450584	105450584	+	5'Flank	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105450584delC	uc001ypy.1	+						C14orf79_uc001ypz.1_5'Flank|C14orf79_uc010tym.1_5'Flank	NM_174891	NP_777551			hypothetical protein LOC122616												0		all_cancers(154;0.0798)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.00326)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0181)															---	---	---	---
Unknown	0	broad.mit.edu	37	14	105547218	105547218	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105547218delT								GPR132 (15464 upstream) : JAG2 (60859 downstream)																																			---	---	---	---
NUDT14	256281	broad.mit.edu	37	14	105648174	105648174	+	5'Flank	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105648174delG	uc010tyn.1	-						NUDT14_uc001yqi.2_5'Flank	NM_177533	NP_803877			nudix-type motif 14							cytoplasm	metal ion binding|protein binding|UDP-sugar diphosphatase activity			skin(1)	1		all_cancers(154;0.0336)|all_epithelial(191;0.0729)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00989)|all cancers(16;0.0114)|Epithelial(46;0.0272)	Epithelial(152;0.047)|OV - Ovarian serous cystadenocarcinoma(161;0.148)|all cancers(159;0.208)											HNSCC(42;0.11)			---	---	---	---
BRF1	2972	broad.mit.edu	37	14	105736091	105736091	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105736091delC	uc001yqp.2	-						BRF1_uc010tyo.1_Intron|BRF1_uc010typ.1_Intron|BRF1_uc010axg.1_Intron|BRF1_uc001yqr.2_Intron	NM_001519	NP_001510			transcription initiation factor IIIB isoform 1						positive regulation of transcription, DNA-dependent|rRNA transcription|transcription initiation from RNA polymerase III promoter|tRNA transcription	transcription factor TFIIIB complex	translation initiation factor activity|zinc ion binding			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4		all_cancers(154;0.0231)|all_epithelial(191;0.0694)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00753)|all cancers(16;0.00925)|Epithelial(46;0.0221)	Epithelial(152;0.14)														---	---	---	---
PACS2	23241	broad.mit.edu	37	14	105787706	105787707	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105787706_105787707delTT	uc001yqt.2	+						PACS2_uc001yqs.2_Intron|PACS2_uc001yqv.2_Intron|PACS2_uc001yqu.2_Intron	NM_015197	NP_056012			phosphofurin acidic cluster sorting protein 2						apoptosis|interspecies interaction between organisms	endoplasmic reticulum lumen|mitochondrion				pancreas(1)	1		all_cancers(154;0.0351)|all_epithelial(191;0.153)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.0145)|Epithelial(46;0.036)	Epithelial(152;0.138)														---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106864554	106864555	+	Intron	INS	-	TC	TC			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106864554_106864555insTC	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	107093170	107093171	+	Intron	INS	-	G	G	rs149623573	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107093170_107093171insG	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	20144995	20144995	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20144995delG								None (None upstream) : GOLGA6L6 (592099 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20243064	20243064	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20243064delT								None (None upstream) : GOLGA6L6 (494030 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20438899	20438900	+	IGR	DEL	TT	-	-	rs113721779		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20438899_20438900delTT								None (None upstream) : GOLGA6L6 (298194 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20439843	20439843	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20439843delT								None (None upstream) : GOLGA6L6 (297251 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20463265	20463265	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20463265delT								None (None upstream) : GOLGA6L6 (273829 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20467496	20467498	+	IGR	DEL	TTG	-	-	rs7168907		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20467496_20467498delTTG								None (None upstream) : GOLGA6L6 (269596 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	20580172	20580173	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20580172_20580173insT								None (None upstream) : GOLGA6L6 (156921 downstream)																																			---	---	---	---
BCL8	606	broad.mit.edu	37	15	20884780	20884780	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:20884780delA	uc010tze.1	-							NR_027992				RecName: Full=Putative protein BCL8;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	21005621	21005621	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21005621delC								BCL8 (44141 upstream) : POTEB (35080 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	21960661	21960662	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21960661_21960662delTT								LOC646214 (19922 upstream) : CXADRP2 (53758 downstream)																																			---	---	---	---
GOLGA8DP	100132979	broad.mit.edu	37	15	22709287	22709288	+	Intron	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22709287_22709288delAG	uc010axw.2	-						GOLGA8DP_uc010axx.2_Intron|uc010tzw.1_5'Flank	NM_001012423	NP_001012423			golgi autoantigen, golgin subfamily a, 8E												0																		---	---	---	---
GOLGA8DP	100132979	broad.mit.edu	37	15	22709385	22709385	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22709385delG	uc010axw.2	-						GOLGA8DP_uc010axx.2_Intron|uc010tzw.1_5'Flank	NM_001012423	NP_001012423			golgi autoantigen, golgin subfamily a, 8E												0																		---	---	---	---
TUBGCP5	114791	broad.mit.edu	37	15	22838107	22838107	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22838107delT	uc001yur.3	+						TUBGCP5_uc001yuq.2_Intron	NM_052903	NP_443135			tubulin, gamma complex associated protein 5						G2/M transition of mitotic cell cycle|microtubule nucleation	centrosome|cytosol|gamma-tubulin ring complex|microtubule|spindle pole	microtubule binding			skin(1)	1		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.86e-06)|Epithelial(43;2.63e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000949)														---	---	---	---
TUBGCP5	114791	broad.mit.edu	37	15	22840983	22840983	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22840983delT	uc001yur.3	+						TUBGCP5_uc001yuq.2_Intron	NM_052903	NP_443135			tubulin, gamma complex associated protein 5						G2/M transition of mitotic cell cycle|microtubule nucleation	centrosome|cytosol|gamma-tubulin ring complex|microtubule|spindle pole	microtubule binding			skin(1)	1		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.86e-06)|Epithelial(43;2.63e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000949)														---	---	---	---
TUBGCP5	114791	broad.mit.edu	37	15	22848452	22848452	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22848452delA	uc001yur.3	+						TUBGCP5_uc001yuq.2_Intron|TUBGCP5_uc010axz.1_5'Flank	NM_052903	NP_443135			tubulin, gamma complex associated protein 5						G2/M transition of mitotic cell cycle|microtubule nucleation	centrosome|cytosol|gamma-tubulin ring complex|microtubule|spindle pole	microtubule binding			skin(1)	1		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.86e-06)|Epithelial(43;2.63e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000949)														---	---	---	---
TUBGCP5	114791	broad.mit.edu	37	15	22862068	22862069	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22862068_22862069delTT	uc001yur.3	+						TUBGCP5_uc001yuq.2_Intron|TUBGCP5_uc010axz.1_Intron	NM_052903	NP_443135			tubulin, gamma complex associated protein 5						G2/M transition of mitotic cell cycle|microtubule nucleation	centrosome|cytosol|gamma-tubulin ring complex|microtubule|spindle pole	microtubule binding			skin(1)	1		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.86e-06)|Epithelial(43;2.63e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000949)														---	---	---	---
TUBGCP5	114791	broad.mit.edu	37	15	22870060	22870060	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22870060delT	uc001yur.3	+						TUBGCP5_uc001yuq.2_Intron	NM_052903	NP_443135			tubulin, gamma complex associated protein 5						G2/M transition of mitotic cell cycle|microtubule nucleation	centrosome|cytosol|gamma-tubulin ring complex|microtubule|spindle pole	microtubule binding			skin(1)	1		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.86e-06)|Epithelial(43;2.63e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000949)														---	---	---	---
CYFIP1	23191	broad.mit.edu	37	15	22995453	22995454	+	Intron	INS	-	C	C	rs138313748	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22995453_22995454insC	uc001yus.2	+						CYFIP1_uc001yut.2_Intron|CYFIP1_uc001yuu.2_Intron|CYFIP1_uc001yuv.2_Intron	NM_014608	NP_055423			cytoplasmic FMR1 interacting protein 1 isoform						axon extension|lamellipodium assembly|regulation of cell shape|ruffle organization	cell junction|lamellipodium|mRNA cap binding complex|perinuclear region of cytoplasm|ruffle|synapse|synaptosome	actin filament binding|Rac GTPase binding			ovary(4)|pancreas(3)|liver(1)|skin(1)	9		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.22e-06)|Epithelial(43;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00101)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	23114116	23114116	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23114116delA	uc001yvf.2	-											Homo sapiens cDNA clone IMAGE:5275816.																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	23675490	23675490	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23675490delA								GOLGA8E (227067 upstream) : MKRN3 (134964 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	23776751	23776751	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23776751delT								GOLGA8E (328328 upstream) : MKRN3 (33703 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	24113602	24113602	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24113602delA								NDN (181152 upstream) : PWRN2 (296324 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	24305025	24305026	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24305025_24305026delTT								NDN (372575 upstream) : PWRN2 (104900 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	24317980	24317980	+	IGR	DEL	A	-	-	rs35704252		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24317980delA								NDN (385530 upstream) : PWRN2 (91946 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	24396084	24396084	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24396084delT								NDN (463634 upstream) : PWRN2 (13842 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	24446984	24446984	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24446984delT								PWRN2 (31889 upstream) : PWRN1 (331855 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	24734174	24734174	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24734174delA								PWRN2 (319079 upstream) : PWRN1 (44665 downstream)																																			---	---	---	---
SNRPN	6638	broad.mit.edu	37	15	25222784	25222784	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25222784delA	uc001ywp.1	+						SNRPN_uc001ywq.1_Intron|SNRPN_uc001ywr.1_Intron|SNRPN_uc001yws.1_Intron|SNRPN_uc001ywt.1_Intron|SNRPN_uc001ywv.1_Intron|SNRPN_uc001yww.1_Intron|SNRPN_uc001ywx.1_Intron|SNRPN_uc001ywz.1_Intron|PAR-SN_uc001yxa.1_Intron|SNRPN_uc001ywy.1_Intron	NM_022807	NP_073718			small nuclear ribonucleoprotein polypeptide N						RNA splicing	small nuclear ribonucleoprotein complex|spliceosomal complex	identical protein binding|RNA binding			ovary(1)	1		all_cancers(20;9.33e-22)|Breast(32;0.000625)		all cancers(64;3.38e-08)|Epithelial(43;3.45e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000207)|GBM - Glioblastoma multiforme(186;0.125)										Prader-Willi_syndrome				---	---	---	---
SNRPN	6638	broad.mit.edu	37	15	25227367	25227367	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25227367delT	uc001ywz.1	+						PAR-SN_uc001yxa.1_RNA|PAR-SN_uc001yxc.2_RNA|PAR-SN_uc001yxb.3_RNA|PAR5_uc001yxd.2_5'Flank					Homo sapiens SNRPN upstream reading frame protein (SNURF) mRNA, complete cds.						RNA splicing	small nuclear ribonucleoprotein complex|spliceosomal complex	identical protein binding|RNA binding			ovary(1)	1		all_cancers(20;9.33e-22)|Breast(32;0.000625)		all cancers(64;3.38e-08)|Epithelial(43;3.45e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000207)|GBM - Glioblastoma multiforme(186;0.125)										Prader-Willi_syndrome				---	---	---	---
IPW	3653	broad.mit.edu	37	15	25391837	25391838	+	Intron	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25391837_25391838delTC	uc001yyp.1	+						IPW_uc010aym.1_Intron					Homo sapiens clone kid12 SNURF-SNRPN mRNA, downstream untranslated exons, alternatively spliced.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	25581432	25581432	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25581432delA	uc001zae.2	+						uc001zan.1_Intron					Homo sapiens clone Rt-16 SNURF-SNRPN mRNA, downstream untranslated exons, alternatively spliced.																														---	---	---	---
UBE3A	7337	broad.mit.edu	37	15	25584423	25584423	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25584423delA	uc001zaq.2	-						uc001zae.2_Intron|UBE3A_uc001zar.2_Intron|UBE3A_uc001zas.2_Intron|UBE3A_uc001zat.2_Intron	NM_000462	NP_000453			ubiquitin protein ligase E3A isoform 2						brain development|interspecies interaction between organisms|protein K48-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus|proteasome complex	protein binding|ubiquitin-protein ligase activity			upper_aerodigestive_tract(1)|ovary(1)|breast(1)	3		all_cancers(20;3.47e-21)|Breast(32;0.00123)		all cancers(64;2.78e-08)|Epithelial(43;8.85e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0155)|Lung(196;0.0616)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	26244669	26244670	+	IGR	INS	-	TC	TC			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26244669_26244670insTC								ATP10A (134352 upstream) : GABRB3 (544025 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	26566414	26566414	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26566414delG								ATP10A (456097 upstream) : GABRB3 (222281 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	26743996	26743996	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26743996delT								ATP10A (633679 upstream) : GABRB3 (44699 downstream)																																			---	---	---	---
GABRG3	2567	broad.mit.edu	37	15	27387928	27387928	+	Intron	DEL	T	-	-	rs11366858		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27387928delT	uc001zbg.1	+						GABRG3_uc001zbf.2_Intron	NM_033223	NP_150092			gamma-aminobutyric acid (GABA) A receptor, gamma						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity				0		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)														---	---	---	---
GABRG3	2567	broad.mit.edu	37	15	27501588	27501590	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27501588_27501590delAAA	uc001zbg.1	+						GABRG3_uc001zbf.2_Intron	NM_033223	NP_150092			gamma-aminobutyric acid (GABA) A receptor, gamma						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity				0		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)														---	---	---	---
GABRG3	2567	broad.mit.edu	37	15	27715391	27715392	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27715391_27715392delTT	uc001zbg.1	+						GABRG3_uc001zbf.2_Intron	NM_033223	NP_150092			gamma-aminobutyric acid (GABA) A receptor, gamma						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity				0		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)														---	---	---	---
GABRG3	2567	broad.mit.edu	37	15	27748667	27748668	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27748667_27748668insT	uc001zbg.1	+							NM_033223	NP_150092			gamma-aminobutyric acid (GABA) A receptor, gamma						gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity				0		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	27954942	27954942	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:27954942delA								GABRG3 (176808 upstream) : OCA2 (45083 downstream)																																			---	---	---	---
OCA2	4948	broad.mit.edu	37	15	28071498	28071499	+	Intron	DEL	CA	-	-	rs10535869		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28071498_28071499delCA	uc001zbh.3	-						OCA2_uc010ayv.2_Intron	NM_000275	NP_000266			oculocutaneous albinism II						eye pigment biosynthetic process	endoplasmic reticulum membrane|endosome membrane|integral to membrane|lysosomal membrane|melanosome membrane	arsenite transmembrane transporter activity|citrate transmembrane transporter activity|L-tyrosine transmembrane transporter activity|protein binding			ovary(3)|breast(1)|pancreas(1)	5		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)										Oculocutaneous_Albinism				---	---	---	---
HERC2	8924	broad.mit.edu	37	15	28564441	28564441	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28564441delT	uc001zbj.2	-						HERC2_uc001zbl.1_Intron	NM_004667	NP_004658			hect domain and RLD 2						DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	29026725	29026726	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29026725_29026726insA								WHAMML2 (2440 upstream) : APBA2 (104442 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	29060451	29060451	+	5'Flank	DEL	T	-	-	rs77995187		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29060451delT	uc010uaq.1	+											DL491344																														---	---	---	---
APBA2	321	broad.mit.edu	37	15	29253481	29253481	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29253481delA	uc001zck.2	+						APBA2_uc010azj.2_Intron|APBA2_uc010uat.1_Intron|APBA2_uc001zcl.2_Intron|APBA2_uc010uas.1_Intron	NM_005503	NP_005494			amyloid beta A4 precursor protein-binding,						nervous system development|protein transport		protein binding				0		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)														---	---	---	---
FAM189A1	23359	broad.mit.edu	37	15	29795147	29795148	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29795147_29795148delAA	uc010azk.1	-							NM_015307	NP_056122			hypothetical protein LOC23359							integral to membrane					0																		---	---	---	---
FAM189A1	23359	broad.mit.edu	37	15	29846820	29846821	+	Intron	INS	-	AC	AC	rs150412748	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29846820_29846821insAC	uc010azk.1	-							NM_015307	NP_056122			hypothetical protein LOC23359							integral to membrane					0																		---	---	---	---
TJP1	7082	broad.mit.edu	37	15	30069231	30069231	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30069231delC	uc001zcr.2	-						TJP1_uc010azl.2_Intron|TJP1_uc001zcq.2_Intron|TJP1_uc001zcs.2_Intron	NM_003257	NP_003248			tight junction protein 1 isoform a						cell-cell junction assembly|cellular component disassembly involved in apoptosis	basolateral plasma membrane|cell-cell adherens junction|Golgi apparatus|tight junction				ovary(4)|central_nervous_system(1)|pancreas(1)	6		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	30282215	30282216	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30282215_30282216delTT								TJP1 (167509 upstream) : FAM7A3 (113719 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	31065489	31065490	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31065489_31065490delTT								ARHGAP11B (87680 upstream) : MTMR15 (130565 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	31138741	31138745	+	IGR	DEL	AAGAA	-	-	rs71473165		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31138741_31138745delAAGAA								ARHGAP11B (160932 upstream) : MTMR15 (57310 downstream)																																			---	---	---	---
TRPM1	4308	broad.mit.edu	37	15	31293996	31293996	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31293996delA	uc001zfm.2	-	27					TRPM1_uc010azy.2_3'UTR|TRPM1_uc001zfl.2_RNA	NM_002420	NP_002411			transient receptor potential cation channel,						cellular response to light stimulus|visual perception	integral to plasma membrane	calcium channel activity|receptor activity			ovary(2)|pancreas(1)|skin(1)	4		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)														---	---	---	---
TRPM1	4308	broad.mit.edu	37	15	31359898	31359899	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31359898_31359899delTT	uc001zfm.2	-						TRPM1_uc010azy.2_Intron|TRPM1_uc001zfl.2_Intron|uc010ubm.1_5'Flank|MIR211_hsa-mir-211|MI0000287_5'Flank|uc010ubn.1_5'Flank	NM_002420	NP_002411			transient receptor potential cation channel,						cellular response to light stimulus|visual perception	integral to plasma membrane	calcium channel activity|receptor activity			ovary(2)|pancreas(1)|skin(1)	4		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	31541751	31541751	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31541751delT								TRPM1 (147827 upstream) : KLF13 (77332 downstream)																																			---	---	---	---
OTUD7A	161725	broad.mit.edu	37	15	31928097	31928097	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31928097delC	uc001zfq.2	-						OTUD7A_uc001zfr.2_Intron|OTUD7A_uc001zfs.1_Intron|OTUD7A_uc010baa.1_Intron	NM_130901	NP_570971			OTU domain containing 7A							cytoplasm|nucleus	cysteine-type peptidase activity|DNA binding|zinc ion binding			pancreas(1)|skin(1)	2		all_lung(180;1.6e-09)		all cancers(64;2.44e-19)|Epithelial(43;6.82e-14)|GBM - Glioblastoma multiforme(186;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00189)|Lung(196;0.208)														---	---	---	---
OTUD7A	161725	broad.mit.edu	37	15	32109479	32109479	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:32109479delC	uc001zfr.2	-						OTUD7A_uc001zfs.1_Intron|OTUD7A_uc010baa.1_Intron	NM_130901	NP_570971			OTU domain containing 7A							cytoplasm|nucleus	cysteine-type peptidase activity|DNA binding|zinc ion binding			pancreas(1)|skin(1)	2		all_lung(180;1.6e-09)		all cancers(64;2.44e-19)|Epithelial(43;6.82e-14)|GBM - Glioblastoma multiforme(186;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00189)|Lung(196;0.208)														---	---	---	---
FMN1	342184	broad.mit.edu	37	15	33066565	33066565	+	Intron	DEL	A	-	-	rs76684755		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33066565delA	uc001zhf.3	-							NM_001103184	NP_001096654			formin 1						actin cytoskeleton organization	actin cytoskeleton|adherens junction|cytoplasm|nucleus	actin binding			ovary(1)	1		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	33456127	33456127	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33456127delT	uc001zhh.2	-											RecName: Full=Formin-1; AltName: Full=Limb deformity protein homolog;																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	33534938	33534939	+	IGR	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33534938_33534939delCT								FMN1 (174853 upstream) : RYR3 (68238 downstream)																																			---	---	---	---
RYR3	6263	broad.mit.edu	37	15	33975203	33975203	+	Intron	DEL	T	-	-	rs35327355		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33975203delT	uc001zhi.2	+						RYR3_uc010bar.2_Intron	NM_001036	NP_001027			ryanodine receptor 3						cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)														---	---	---	---
RYR3	6263	broad.mit.edu	37	15	34098049	34098050	+	Intron	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34098049_34098050delTC	uc001zhi.2	+						RYR3_uc010bar.2_Intron	NM_001036	NP_001027			ryanodine receptor 3						cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)														---	---	---	---
C15orf29	79768	broad.mit.edu	37	15	34492462	34492462	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34492462delT	uc001zhp.2	-						C15orf29_uc010ubz.1_Intron|C15orf29_uc010uca.1_Intron	NM_024713	NP_078989			hypothetical protein LOC79768							nucleolus				ovary(1)	1		all_lung(180;1.86e-06)		all cancers(64;5.49e-18)|GBM - Glioblastoma multiforme(113;8.91e-07)|BRCA - Breast invasive adenocarcinoma(123;0.026)|Lung(196;0.229)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	34508802	34508802	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34508802delA								C15orf29 (6505 upstream) : TMEM85 (8443 downstream)																																			---	---	---	---
SLC12A6	9990	broad.mit.edu	37	15	34543443	34543445	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34543443_34543445delTTT	uc001zhw.2	-						SLC12A6_uc001zhv.2_Intron|SLC12A6_uc001zhx.2_Intron|SLC12A6_uc001zhy.2_Intron|SLC12A6_uc001zhz.2_Intron|SLC12A6_uc001zia.2_Intron|SLC12A6_uc001zib.2_Intron|SLC12A6_uc001zic.2_Intron|SLC12A6_uc010bau.2_Intron|SLC12A6_uc001zid.2_Intron|SLC12A6_uc001zht.2_5'Flank|SLC12A6_uc001zhu.2_Intron	NM_133647	NP_598408			solute carrier family 12, member 6 isoform a						angiogenesis|cellular hypotonic salinity response|potassium ion transport|sodium ion transport	basolateral plasma membrane|integral to membrane	potassium:chloride symporter activity			central_nervous_system(5)|ovary(1)|skin(1)	7		all_lung(180;2.78e-08)		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	Potassium Chloride(DB00761)													---	---	---	---
SLC12A6	9990	broad.mit.edu	37	15	34578274	34578274	+	Intron	DEL	T	-	-	rs113383391		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34578274delT	uc001zhw.2	-						SLC12A6_uc001zhv.2_Intron|SLC12A6_uc001zhx.2_Intron|SLC12A6_uc001zhy.2_Intron|SLC12A6_uc001zhz.2_Intron|SLC12A6_uc001zia.2_Intron|SLC12A6_uc001zib.2_Intron|SLC12A6_uc001zic.2_Intron|SLC12A6_uc010bau.2_Intron|SLC12A6_uc001zid.2_Intron|SLC12A6_uc001zhu.2_Intron	NM_133647	NP_598408			solute carrier family 12, member 6 isoform a						angiogenesis|cellular hypotonic salinity response|potassium ion transport|sodium ion transport	basolateral plasma membrane|integral to membrane	potassium:chloride symporter activity			central_nervous_system(5)|ovary(1)|skin(1)	7		all_lung(180;2.78e-08)		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	Potassium Chloride(DB00761)													---	---	---	---
Unknown	0	broad.mit.edu	37	15	35305637	35305637	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35305637delT								ZNF770 (25183 upstream) : LOC723972 (223890 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	35975796	35975796	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35975796delA	uc001zjc.2	+											Homo sapiens, Similar to LOC161538, clone IMAGE:5199550, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	37541792	37541792	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37541792delT								MEIS2 (148292 upstream) : TMCO5A (685035 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	37802874	37802874	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37802874delT								MEIS2 (409374 upstream) : TMCO5A (423953 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	38339984	38339984	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38339984delT								TMCO5A (80059 upstream) : SPRED1 (205068 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	38402003	38402003	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38402003delT								TMCO5A (142078 upstream) : SPRED1 (143049 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	38507662	38507662	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38507662delA	uc001zjy.2	-											Homo sapiens, clone IMAGE:3923347, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	38865322	38865323	+	IGR	DEL	TG	-	-	rs35134214		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38865322_38865323delTG								RASGRP1 (8315 upstream) : C15orf53 (123476 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	38913887	38913887	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38913887delT								RASGRP1 (56880 upstream) : C15orf53 (74912 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	39143803	39143803	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39143803delT								C15orf53 (151564 upstream) : C15orf54 (399082 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	39621117	39621117	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39621117delA								C15orf54 (74069 upstream) : THBS1 (252163 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	39813045	39813045	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39813045delT								C15orf54 (265997 upstream) : THBS1 (60235 downstream)																																			---	---	---	---
GPR176	11245	broad.mit.edu	37	15	40207922	40207922	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40207922delA	uc001zkj.1	-						GPR176_uc001zkk.1_Intron	NM_007223	NP_009154			G protein-coupled receptor 176						synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity			ovary(2)|skin(2)|pancreas(1)|central_nervous_system(1)	6		all_cancers(109;4.05e-15)|all_epithelial(112;2.96e-13)|Lung NSC(122;8.53e-11)|all_lung(180;2.71e-09)|Melanoma(134;0.091)|Colorectal(260;0.198)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;4.4e-06)|BRCA - Breast invasive adenocarcinoma(123;0.123)														---	---	---	---
BMF	90427	broad.mit.edu	37	15	40380820	40380820	+	3'UTR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40380820delC	uc001zkv.2	-	4					BMF_uc001zkt.2_3'UTR|BMF_uc001zku.2_3'UTR|BMF_uc001zkw.2_3'UTR	NM_033503	NP_277038			Bcl2 modifying factor isoform bmf-1						activation of pro-apoptotic gene products|induction of apoptosis by intracellular signals|positive regulation of protein homooligomerization|positive regulation of release of cytochrome c from mitochondria	cytosol|mitochondrial outer membrane|myosin complex|plasma membrane	protein binding			ovary(1)	1		all_cancers(109;4.18e-18)|all_epithelial(112;6.15e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.29e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0516)														---	---	---	---
BUB1B	701	broad.mit.edu	37	15	40477243	40477243	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40477243delT	uc001zkx.3	+						BUB1B_uc010ucl.1_Intron	NM_001211	NP_001202			budding uninhibited by benzimidazoles 1 beta						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell division|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|phosphatidylinositol-mediated signaling|protein localization to kinetochore|spindle organization	anaphase-promoting complex|condensed chromosome outer kinetochore|cytosol|microtubule organizing center|perinuclear region of cytoplasm|spindle midzone	ATP binding|protein binding|protein serine/threonine kinase activity			stomach(2)|ovary(1)|kidney(1)	4		all_cancers(109;1.12e-18)|all_epithelial(112;1.61e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0556)				Mis|N|F|S			rhabdomyosarcoma			Mosaic_Variegated_Aneuploidy_Syndrome				---	---	---	---
BUB1B	701	broad.mit.edu	37	15	40501746	40501746	+	Intron	DEL	T	-	-	rs77735486		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40501746delT	uc001zkx.3	+							NM_001211	NP_001202			budding uninhibited by benzimidazoles 1 beta						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell division|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|phosphatidylinositol-mediated signaling|protein localization to kinetochore|spindle organization	anaphase-promoting complex|condensed chromosome outer kinetochore|cytosol|microtubule organizing center|perinuclear region of cytoplasm|spindle midzone	ATP binding|protein binding|protein serine/threonine kinase activity			stomach(2)|ovary(1)|kidney(1)	4		all_cancers(109;1.12e-18)|all_epithelial(112;1.61e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0556)				Mis|N|F|S			rhabdomyosarcoma			Mosaic_Variegated_Aneuploidy_Syndrome				---	---	---	---
Unknown	0	broad.mit.edu	37	15	40772837	40772838	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40772837_40772838delTT								CHST14 (7484 upstream) : MRPL42P5 (50702 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	40819377	40819377	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40819377delT	uc001zlx.1	+											full-length cDNA clone CS0DI072YL01 of Placenta Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
DNAJC17	55192	broad.mit.edu	37	15	41069919	41069920	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41069919_41069920delAA	uc001zms.1	-						DNAJC17_uc010bbz.1_Intron|DNAJC17_uc010bca.1_Intron|DNAJC17_uc010bcb.1_Intron	NM_018163	NP_060633			DnaJ (Hsp40) homolog, subfamily C, member 17						protein folding		heat shock protein binding|nucleotide binding|RNA binding|unfolded protein binding				0		all_cancers(109;4.16e-14)|all_epithelial(112;9.68e-12)|Lung NSC(122;3.19e-09)|all_lung(180;6.45e-08)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.91e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	41211098	41211098	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41211098delC								VPS18 (14926 upstream) : DLL4 (10449 downstream)																																			---	---	---	---
INO80	54617	broad.mit.edu	37	15	41278105	41278105	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41278105delA	uc001zni.2	-						INO80_uc010ucu.1_Intron	NM_017553	NP_060023			INO80 complex homolog 1						cell division|cellular response to ionizing radiation|cellular response to UV|chromatin remodeling|double-strand break repair via homologous recombination|mitotic sister chromatid segregation|positive regulation of cell growth|positive regulation of DNA replication involved in S phase|positive regulation of transcription from RNA polymerase II promoter|regulation of G1/S transition of mitotic cell cycle|spindle assembly|UV-damage excision repair	Ino80 complex|microtubule	actin binding|alpha-tubulin binding|ATP binding|ATPase activity|DNA binding|DNA helicase activity			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
INO80	54617	broad.mit.edu	37	15	41391521	41391522	+	Intron	DEL	AA	-	-	rs28837496		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41391521_41391522delAA	uc001zni.2	-						INO80_uc010ucu.1_Intron	NM_017553	NP_060023			INO80 complex homolog 1						cell division|cellular response to ionizing radiation|cellular response to UV|chromatin remodeling|double-strand break repair via homologous recombination|mitotic sister chromatid segregation|positive regulation of cell growth|positive regulation of DNA replication involved in S phase|positive regulation of transcription from RNA polymerase II promoter|regulation of G1/S transition of mitotic cell cycle|spindle assembly|UV-damage excision repair	Ino80 complex|microtubule	actin binding|alpha-tubulin binding|ATP binding|ATPase activity|DNA binding|DNA helicase activity			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
INO80	54617	broad.mit.edu	37	15	41403654	41403654	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41403654delT	uc001zni.2	-						INO80_uc010ucu.1_Intron	NM_017553	NP_060023			INO80 complex homolog 1						cell division|cellular response to ionizing radiation|cellular response to UV|chromatin remodeling|double-strand break repair via homologous recombination|mitotic sister chromatid segregation|positive regulation of cell growth|positive regulation of DNA replication involved in S phase|positive regulation of transcription from RNA polymerase II promoter|regulation of G1/S transition of mitotic cell cycle|spindle assembly|UV-damage excision repair	Ino80 complex|microtubule	actin binding|alpha-tubulin binding|ATP binding|ATPase activity|DNA binding|DNA helicase activity			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
NUSAP1	51203	broad.mit.edu	37	15	41647218	41647218	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41647218delA	uc001zns.3	+						NUSAP1_uc001znq.3_Intron|NUSAP1_uc001znr.3_Intron|NUSAP1_uc010bce.2_Intron|NUSAP1_uc001znt.3_Intron|NUSAP1_uc001znv.3_Intron|NUSAP1_uc001znu.3_Intron|NUSAP1_uc010ucw.1_Intron|NUSAP1_uc001znw.3_Intron	NM_016359	NP_057443			nucleolar and spindle associated protein 1						cytokinesis after mitosis|establishment of mitotic spindle localization|mitotic chromosome condensation|positive regulation of mitosis	chromosome|cytoplasm|nucleolus	DNA binding				0		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;9.63e-17)|GBM - Glioblastoma multiforme(113;1.59e-06)|BRCA - Breast invasive adenocarcinoma(123;0.168)														---	---	---	---
NUSAP1	51203	broad.mit.edu	37	15	41658490	41658492	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41658490_41658492delTTT	uc001zns.3	+						NUSAP1_uc001znq.3_Intron|NUSAP1_uc001znr.3_Intron|NUSAP1_uc010bce.2_Intron|NUSAP1_uc001znt.3_Intron|NUSAP1_uc001znv.3_Intron|NUSAP1_uc001znu.3_Intron|NUSAP1_uc010ucw.1_Intron|NUSAP1_uc001znw.3_Intron	NM_016359	NP_057443			nucleolar and spindle associated protein 1						cytokinesis after mitosis|establishment of mitotic spindle localization|mitotic chromosome condensation|positive regulation of mitosis	chromosome|cytoplasm|nucleolus	DNA binding				0		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;9.63e-17)|GBM - Glioblastoma multiforme(113;1.59e-06)|BRCA - Breast invasive adenocarcinoma(123;0.168)														---	---	---	---
NUSAP1	51203	broad.mit.edu	37	15	41672442	41672443	+	3'UTR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41672442_41672443delTT	uc001zns.3	+	11					NUSAP1_uc001znq.3_3'UTR|NUSAP1_uc001znr.3_3'UTR|NUSAP1_uc010bce.2_3'UTR|NUSAP1_uc001znt.3_3'UTR|NUSAP1_uc001znv.3_3'UTR|NUSAP1_uc001znu.3_3'UTR|NUSAP1_uc010ucw.1_3'UTR|NUSAP1_uc001znw.3_3'UTR	NM_016359	NP_057443			nucleolar and spindle associated protein 1						cytokinesis after mitosis|establishment of mitotic spindle localization|mitotic chromosome condensation|positive regulation of mitosis	chromosome|cytoplasm|nucleolus	DNA binding				0		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;9.63e-17)|GBM - Glioblastoma multiforme(113;1.59e-06)|BRCA - Breast invasive adenocarcinoma(123;0.168)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	41676967	41676968	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41676967_41676968insA								NUSAP1 (3720 upstream) : NDUFAF1 (2585 downstream)																																			---	---	---	---
MGA	23269	broad.mit.edu	37	15	41931340	41931340	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41931340delT	uc001zog.1	+							NM_001080541	NP_001074010			MAX-interacting protein isoform 2							MLL1 complex	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	12		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)														---	---	---	---
TMEM87A	25963	broad.mit.edu	37	15	42525641	42525641	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42525641delA	uc010udd.1	-						TMEM87A_uc001zpf.3_Intron|TMEM87A_uc010bcu.1_Intron	NM_015497	NP_056312			transmembrane protein 87A isoform 1							integral to membrane				ovary(1)	1		all_cancers(109;4.28e-16)|all_epithelial(112;1.04e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;1.03e-06)														---	---	---	---
GANC	2595	broad.mit.edu	37	15	42622913	42622913	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42622913delT	uc001zpi.2	+							NM_198141	NP_937784			glucosidase, alpha; neutral C						carbohydrate metabolic process		carbohydrate binding|maltose alpha-glucosidase activity			central_nervous_system(2)	2		all_cancers(109;3.08e-16)|all_epithelial(112;7.48e-15)|Lung NSC(122;3.08e-09)|all_lung(180;1.48e-08)|Melanoma(134;0.0574)|Colorectal(260;0.153)		GBM - Glioblastoma multiforme(94;1.06e-06)														---	---	---	---
ZFP106	64397	broad.mit.edu	37	15	42729133	42729133	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42729133delT	uc001zpw.2	-						ZFP106_uc001zpu.2_Intron|ZFP106_uc001zpv.2_Intron|ZFP106_uc001zpx.2_Intron	NM_022473	NP_071918			zinc finger protein 106 homolog							nucleolus	zinc ion binding			central_nervous_system(2)|ovary(1)	3		all_cancers(109;1.63e-12)|all_epithelial(112;3.97e-11)|Lung NSC(122;2.04e-07)|all_lung(180;8.31e-07)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(94;8.6e-07)														---	---	---	---
CDAN1	146059	broad.mit.edu	37	15	43025477	43025477	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43025477delT	uc001zql.2	-						CDAN1_uc001zqj.2_5'Flank|CDAN1_uc001zqk.2_Intron|CDAN1_uc010bcx.1_Intron	NM_138477	NP_612486			codanin 1							integral to membrane	protein binding			ovary(2)	2		all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;2.49e-07)														---	---	---	---
TTBK2	146057	broad.mit.edu	37	15	43183727	43183727	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43183727delA	uc001zqo.2	-						TTBK2_uc010bcy.2_Intron|TTBK2_uc001zqp.2_Intron|TTBK2_uc010bcz.1_Intron	NM_173500	NP_775771			tau tubulin kinase 2						cell death		ATP binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|stomach(1)|pancreas(1)|skin(1)	7		all_cancers(109;6.11e-16)|all_epithelial(112;5.5e-14)|Lung NSC(122;1.76e-08)|all_lung(180;6.04e-08)|Melanoma(134;0.0179)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;3.23e-07)														---	---	---	---
UBR1	197131	broad.mit.edu	37	15	43252975	43252975	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43252975delT	uc001zqq.2	-							NM_174916	NP_777576			ubiquitin protein ligase E3 component n-recognin						cellular response to leucine|negative regulation of TOR signaling cascade	cytosol	leucine binding|zinc ion binding			lung(1)	1		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)														---	---	---	---
UBR1	197131	broad.mit.edu	37	15	43321222	43321222	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43321222delG	uc001zqq.2	-						UBR1_uc010udk.1_Intron	NM_174916	NP_777576			ubiquitin protein ligase E3 component n-recognin						cellular response to leucine|negative regulation of TOR signaling cascade	cytosol	leucine binding|zinc ion binding			lung(1)	1		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)														---	---	---	---
UBR1	197131	broad.mit.edu	37	15	43336132	43336132	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43336132delA	uc001zqq.2	-						UBR1_uc010udk.1_Intron	NM_174916	NP_777576			ubiquitin protein ligase E3 component n-recognin						cellular response to leucine|negative regulation of TOR signaling cascade	cytosol	leucine binding|zinc ion binding			lung(1)	1		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)														---	---	---	---
UBR1	197131	broad.mit.edu	37	15	43340386	43340387	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43340386_43340387delAA	uc001zqq.2	-						UBR1_uc010udk.1_Intron	NM_174916	NP_777576			ubiquitin protein ligase E3 component n-recognin						cellular response to leucine|negative regulation of TOR signaling cascade	cytosol	leucine binding|zinc ion binding			lung(1)	1		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)														---	---	---	---
TGM5	9333	broad.mit.edu	37	15	43538098	43538098	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43538098delG	uc001zrd.1	-						TGM5_uc001zre.1_Intron	NM_201631	NP_963925			transglutaminase 5 isoform 1						epidermis development|peptide cross-linking	cytoplasm	acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			central_nervous_system(1)	1		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;4e-07)	L-Glutamine(DB00130)													---	---	---	---
CKMT1B	1159	broad.mit.edu	37	15	43888539	43888539	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43888539delT	uc001zsc.2	+						CKMT1B_uc010uds.1_Intron|CKMT1B_uc010udt.1_Intron|CKMT1B_uc010bdi.2_Intron|CKMT1B_uc010udu.1_Intron|CKMT1B_uc010udv.1_Intron|CKMT1B_uc001zsd.3_Intron|CKMT1B_uc010udw.1_Intron|CKMT1B_uc010udx.1_Intron|CKMT1B_uc010bdj.2_Intron|CKMT1B_uc010udy.1_Intron	NM_020990	NP_066270			creatine kinase, mitochondrial 1B precursor						creatine metabolic process	mitochondrial inner membrane	ATP binding|creatine kinase activity				0		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)	Creatine(DB00148)													---	---	---	---
MFAP1	4236	broad.mit.edu	37	15	44112537	44112537	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44112537delA	uc001zth.1	-							NM_005926	NP_005917			microfibrillar-associated protein 1							microfibril				skin(1)	1		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.33e-07)														---	---	---	---
MFAP1	4236	broad.mit.edu	37	15	44115580	44115582	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44115580_44115582delTTT	uc001zth.1	-							NM_005926	NP_005917			microfibrillar-associated protein 1							microfibril				skin(1)	1		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.33e-07)														---	---	---	---
FRMD5	84978	broad.mit.edu	37	15	44242095	44242095	+	Intron	DEL	A	-	-	rs112511482		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44242095delA	uc001ztl.2	-						FRMD5_uc001ztk.1_Intron|FRMD5_uc001ztm.2_Intron|FRMD5_uc001ztn.2_Intron	NM_032892	NP_116281			FERM domain containing 5 isoform 2							cytoplasm|cytoskeleton|extrinsic to membrane|integral to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(109;2.29e-15)|all_epithelial(112;9.98e-13)|Lung NSC(122;4.89e-08)|all_lung(180;5.08e-07)|Melanoma(134;0.0275)		all cancers(107;8.63e-20)|GBM - Glioblastoma multiforme(94;3.63e-06)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	44569208	44569208	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44569208delA								FRMD5 (81779 upstream) : CASC4 (11721 downstream)																																			---	---	---	---
CASC4	113201	broad.mit.edu	37	15	44705495	44705495	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44705495delA	uc001ztp.2	+						CASC4_uc001ztq.2_Intron	NM_138423	NP_612432			cancer susceptibility candidate 4 isoform a							integral to membrane				ovary(1)	1		all_cancers(109;1.69e-13)|all_epithelial(112;3.94e-11)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.027)		all cancers(107;2.91e-20)|GBM - Glioblastoma multiforme(94;1.57e-06)|COAD - Colon adenocarcinoma(120;0.217)|Colorectal(105;0.237)														---	---	---	---
CTDSPL2	51496	broad.mit.edu	37	15	44792078	44792078	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44792078delT	uc001ztr.2	+						CTDSPL2_uc001zts.2_Intron|CTDSPL2_uc001ztt.2_Intron|CTDSPL2_uc010bdv.2_Intron	NM_016396	NP_057480			CTD (carboxy-terminal domain, RNA polymerase II,								phosphoprotein phosphatase activity				0		all_cancers(109;4.36e-14)|all_epithelial(112;9.8e-12)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.0122)		all cancers(107;1.02e-20)|GBM - Glioblastoma multiforme(94;1.49e-06)|COAD - Colon adenocarcinoma(120;0.0857)|Colorectal(105;0.0905)														---	---	---	---
CTDSPL2	51496	broad.mit.edu	37	15	44811330	44811330	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44811330delT	uc001ztr.2	+						CTDSPL2_uc001zts.2_Intron|CTDSPL2_uc001ztt.2_Intron|CTDSPL2_uc010bdv.2_Intron	NM_016396	NP_057480			CTD (carboxy-terminal domain, RNA polymerase II,								phosphoprotein phosphatase activity				0		all_cancers(109;4.36e-14)|all_epithelial(112;9.8e-12)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.0122)		all cancers(107;1.02e-20)|GBM - Glioblastoma multiforme(94;1.49e-06)|COAD - Colon adenocarcinoma(120;0.0857)|Colorectal(105;0.0905)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	44826255	44826255	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44826255delT								CTDSPL2 (6828 upstream) : EIF3J (3011 downstream)																																			---	---	---	---
EIF3J	8669	broad.mit.edu	37	15	44852434	44852434	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44852434delT	uc001ztv.2	+						EIF3J_uc010ueg.1_Intron|EIF3J_uc001ztw.2_Intron	NM_003758	NP_003749			eukaryotic translation initiation factor 3,							cytosol|eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity				0		all_cancers(109;2.81e-14)|all_epithelial(112;2.8e-12)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.0122)		all cancers(107;3.13e-20)|GBM - Glioblastoma multiforme(94;9.81e-07)|COAD - Colon adenocarcinoma(120;0.0754)|Colorectal(105;0.0758)														---	---	---	---
SPG11	80208	broad.mit.edu	37	15	44931900	44931900	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44931900delA	uc001ztx.2	-						SPG11_uc010ueh.1_Intron|SPG11_uc010uei.1_Intron|SPG11_uc001zua.1_Intron	NM_025137	NP_079413			spatacsin isoform 1						cell death	cytosol|integral to membrane|nucleus	protein binding			ovary(4)|skin(1)	5		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	45128724	45128724	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45128724delT								TRIM69 (68699 upstream) : C15orf43 (120179 downstream)																																			---	---	---	---
SORD	6652	broad.mit.edu	37	15	45327312	45327312	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45327312delC	uc001zul.3	+						SORD_uc010uel.1_Intron|SORD_uc001zum.3_Intron|SORD_uc010bdz.2_Intron	NM_003104	NP_003095			sorbitol dehydrogenase						fructose biosynthetic process|glucose metabolic process|L-xylitol catabolic process|sorbitol catabolic process|sperm motility	cilium|extracellular space|flagellum|membrane fraction|mitochondrial membrane|soluble fraction	L-iditol 2-dehydrogenase activity|NAD binding|sugar binding|zinc ion binding				0		all_cancers(109;3.43e-12)|all_epithelial(112;2.33e-10)|Lung NSC(122;6.01e-07)|all_lung(180;4.38e-06)|Melanoma(134;0.0122)		all cancers(107;1.6e-18)|GBM - Glioblastoma multiforme(94;4.95e-07)|COAD - Colon adenocarcinoma(120;0.0704)|Colorectal(133;0.0706)	NADH(DB00157)													---	---	---	---
DUOXA1	90527	broad.mit.edu	37	15	45412115	45412115	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45412115delG	uc001zuq.1	-						DUOXA1_uc010uem.1_Intron|DUOXA1_uc001zup.2_Intron|DUOXA1_uc010bec.2_Intron|DUOXA1_uc001zur.1_Intron|DUOXA1_uc010bed.1_Intron	NM_144565	NP_653166			Numb-interacting protein						protein transport	endoplasmic reticulum membrane|integral to membrane				ovary(1)	1		all_cancers(109;6.02e-08)|all_epithelial(112;1.83e-06)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;3.82e-18)|GBM - Glioblastoma multiforme(94;4.39e-07)|COAD - Colon adenocarcinoma(120;0.0676)|Colorectal(133;0.0686)														---	---	---	---
DUOX1	53905	broad.mit.edu	37	15	45438309	45438309	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45438309delA	uc001zus.1	+						DUOX1_uc001zut.1_Intron|DUOX1_uc010bee.1_Intron|DUOX1_uc001zuu.2_5'Flank	NM_017434	NP_059130			dual oxidase 1 precursor						cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide biosynthetic process|hydrogen peroxide catabolic process|response to cAMP|superoxide anion generation	apical plasma membrane|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|NADP binding|peroxidase activity			ovary(5)|skin(2)|breast(1)	8		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	45848929	45848929	+	IGR	DEL	A	-	-	rs149072853		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45848929delA								C15orf21 (1 upstream) : PLDN (30488 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	45875254	45875254	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45875254delA								C15orf21 (26326 upstream) : PLDN (4163 downstream)																																			---	---	---	---
SQRDL	58472	broad.mit.edu	37	15	45930941	45930941	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45930941delA	uc001zvt.2	+						SQRDL_uc001zvu.2_Intron|SQRDL_uc001zvv.2_Intron	NM_021199	NP_067022			sulfide dehydrogenase like precursor								oxidoreductase activity			ovary(1)	1		Lung NSC(122;0.000117)|all_lung(180;0.000737)|Melanoma(134;0.0417)		all cancers(107;5.89e-18)|GBM - Glioblastoma multiforme(94;1.21e-06)|COAD - Colon adenocarcinoma(120;0.17)|Colorectal(133;0.188)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	46153190	46153190	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:46153190delT								SQRDL (169712 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	46807245	46807245	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:46807245delT								SQRDL (823767 upstream) : SEMA6D (669158 downstream)																																			---	---	---	---
SEMA6D	80031	broad.mit.edu	37	15	47754662	47754662	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:47754662delT	uc001zvw.2	+							NM_020858	NP_065909			semaphorin 6D isoform 1 precursor						axon guidance	cytoplasm|integral to membrane|plasma membrane	receptor activity			skin(3)|breast(1)	4		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)														---	---	---	---
SEMA6D	80031	broad.mit.edu	37	15	48054739	48054740	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:48054739_48054740delAA	uc010bek.2	+						SEMA6D_uc001zvw.2_Intron|SEMA6D_uc001zvx.1_Intron|SEMA6D_uc001zvy.2_Intron|SEMA6D_uc001zvz.2_Intron|SEMA6D_uc001zwa.2_Intron|SEMA6D_uc001zwb.2_Intron|SEMA6D_uc001zwc.2_Intron	NM_153618	NP_705871			semaphorin 6D isoform 4 precursor						axon guidance	cytoplasm|integral to membrane|plasma membrane	receptor activity			skin(3)|breast(1)	4		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)														---	---	---	---
CEP152	22995	broad.mit.edu	37	15	49076035	49076036	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49076035_49076036insT	uc001zwy.2	-						CEP152_uc001zwz.2_Intron|CEP152_uc001zxa.1_Intron	NM_014985	NP_055800			centrosomal protein 152kDa						centrosome duplication|G2/M transition of mitotic cell cycle	centrosome|cytosol	protein kinase binding			lung(2)	2		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)														---	---	---	---
SECISBP2L	9728	broad.mit.edu	37	15	49302416	49302416	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:49302416delT	uc001zxe.1	-						SECISBP2L_uc001zxd.1_Intron|SECISBP2L_uc010bep.1_Intron	NM_014701	NP_055516			SECIS binding protein 2-like											breast(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	50068919	50068919	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50068919delT								DTWD1 (131587 upstream) : ATP8B4 (81517 downstream)																																			---	---	---	---
ATP8B4	79895	broad.mit.edu	37	15	50405678	50405679	+	Intron	INS	-	A	A	rs113124308		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50405678_50405679insA	uc001zxu.2	-						ATP8B4_uc010ber.2_5'Flank|ATP8B4_uc010ufd.1_Intron|ATP8B4_uc010ufe.1_Intron	NM_024837	NP_079113			ATPase class I type 8B member 4						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			skin(3)|ovary(2)|breast(2)|large_intestine(1)	8		all_lung(180;0.00183)		all cancers(107;2.41e-07)|GBM - Glioblastoma multiforme(94;8.28e-05)														---	---	---	---
GABPB1	2553	broad.mit.edu	37	15	50617724	50617724	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50617724delT	uc001zyb.2	-						GABPB1_uc001zya.2_Intron|GABPB1_uc010ufg.1_Intron|GABPB1_uc001zyc.2_Intron|GABPB1_uc001zyd.2_Intron|GABPB1_uc001zye.2_Intron|GABPB1_uc001zyf.2_Intron	NM_005254	NP_005245			GA binding protein transcription factor, beta						positive regulation of transcription from RNA polymerase II promoter	nucleus	protein binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			large_intestine(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	50684432	50684432	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50684432delA								LOC100129387 (33931 upstream) : USP8 (32147 downstream)																																			---	---	---	---
USP8	9101	broad.mit.edu	37	15	50728391	50728391	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50728391delT	uc001zym.3	+						USP8_uc001zyk.1_Intron|USP8_uc001zyl.3_Intron|USP8_uc001zyn.3_Intron|USP8_uc010ufh.1_Intron|USP8_uc010bev.1_5'Flank	NM_001128611	NP_001122083			ubiquitin specific peptidase 8						cell cycle|cell proliferation|endosome organization|protein K48-linked deubiquitination|protein K63-linked deubiquitination|ubiquitin-dependent protein catabolic process	cytosol|early endosome|extrinsic to plasma membrane|nucleus	cysteine-type endopeptidase activity|SH3 domain binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			lung(1)|central_nervous_system(1)	2				all cancers(107;0.000225)|GBM - Glioblastoma multiforme(94;0.000771)														---	---	---	---
TRPM7	54822	broad.mit.edu	37	15	50861009	50861010	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50861009_50861010delAA	uc001zyt.3	-						TRPM7_uc001zyr.2_Intron	NM_017672	NP_060142			transient receptor potential cation channel,						cell death	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein serine/threonine kinase activity			ovary(4)|stomach(3)|breast(1)|central_nervous_system(1)|skin(1)	10				all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)														---	---	---	---
TRPM7	54822	broad.mit.edu	37	15	50862222	50862222	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:50862222delA	uc001zyt.3	-						TRPM7_uc001zyr.2_Intron	NM_017672	NP_060142			transient receptor potential cation channel,						cell death	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein serine/threonine kinase activity			ovary(4)|stomach(3)|breast(1)|central_nervous_system(1)|skin(1)	10				all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)														---	---	---	---
SPPL2A	84888	broad.mit.edu	37	15	51011275	51011275	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51011275delA	uc001zyv.2	-							NM_032802	NP_116191			signal peptide peptidase-like 2A							integral to membrane	aspartic-type endopeptidase activity				0				all cancers(107;0.000712)|GBM - Glioblastoma multiforme(94;0.00314)														---	---	---	---
SPPL2A	84888	broad.mit.edu	37	15	51024992	51024994	+	Intron	DEL	TTT	-	-	rs112777727		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51024992_51024994delTTT	uc001zyv.2	-							NM_032802	NP_116191			signal peptide peptidase-like 2A							integral to membrane	aspartic-type endopeptidase activity				0				all cancers(107;0.000712)|GBM - Glioblastoma multiforme(94;0.00314)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	51191129	51191130	+	IGR	DEL	TA	-	-	rs149764773		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51191129_51191130delTA								SPPL2A (133219 upstream) : AP4E1 (9816 downstream)																																			---	---	---	---
AP4E1	23431	broad.mit.edu	37	15	51276506	51276506	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51276506delT	uc001zyx.1	+							NM_007347	NP_031373			adaptor-related protein complex 4, epsilon 1						intracellular protein transport|vesicle-mediated transport	COPI vesicle coat	binding|structural molecule activity				0				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	51488112	51488113	+	IGR	DEL	TT	-	-	rs139322642		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51488112_51488113delTT								TNFAIP8L3 (90639 upstream) : CYP19A1 (12142 downstream)																																			---	---	---	---
CYP19A1	1588	broad.mit.edu	37	15	51587334	51587334	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51587334delT	uc001zyz.3	-						CYP19A1_uc001zza.3_Intron|CYP19A1_uc001zzb.2_Intron|CYP19A1_uc010bey.1_Intron|CYP19A1_uc001zze.1_Intron|uc002aaj.1_5'Flank|uc002aak.2_5'Flank|uc010ufr.1_5'Flank|uc010ufs.1_5'Flank	NM_031226	NP_112503			cytochrome P450, family 19						estrogen biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|membrane fraction	aromatase activity|electron carrier activity|heme binding|oxygen binding|steroid hydroxylase activity			skin(3)	3				all cancers(107;0.000372)|GBM - Glioblastoma multiforme(94;0.0128)	Aminoglutethimide(DB00357)|Anastrozole(DB01217)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Diethylstilbestrol(DB00255)|Exemestane(DB00990)|Letrozole(DB01006)|Testolactone(DB00894)|Testosterone(DB00624)													---	---	---	---
CYP19A1	1588	broad.mit.edu	37	15	51608522	51608523	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51608522_51608523insA	uc001zyz.3	-						CYP19A1_uc001zza.3_Intron|CYP19A1_uc001zzb.2_Intron|CYP19A1_uc010bey.1_Intron|CYP19A1_uc001zze.1_Intron|CYP19A1_uc002aaz.3_Intron	NM_031226	NP_112503			cytochrome P450, family 19						estrogen biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|membrane fraction	aromatase activity|electron carrier activity|heme binding|oxygen binding|steroid hydroxylase activity			skin(3)	3				all cancers(107;0.000372)|GBM - Glioblastoma multiforme(94;0.0128)	Aminoglutethimide(DB00357)|Anastrozole(DB01217)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Diethylstilbestrol(DB00255)|Exemestane(DB00990)|Letrozole(DB01006)|Testolactone(DB00894)|Testosterone(DB00624)													---	---	---	---
SCG3	29106	broad.mit.edu	37	15	52011041	52011042	+	Intron	DEL	AA	-	-	rs77984223		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52011041_52011042delAA	uc002abh.2	+						SCG3_uc010ufz.1_Intron	NM_013243	NP_037375			secretogranin III isoform 1 precursor						platelet activation|platelet degranulation	extracellular region|stored secretory granule				ovary(1)	1				all cancers(107;0.00488)														---	---	---	---
TMOD3	29766	broad.mit.edu	37	15	52194069	52194069	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52194069delT	uc002abm.2	+						TMOD3_uc010bfc.1_Intron	NM_014547	NP_055362			tropomodulin 3 (ubiquitous)							cytoplasm|cytoskeleton	actin binding|tropomyosin binding			ovary(1)	1				all cancers(107;0.00194)														---	---	---	---
TMOD3	29766	broad.mit.edu	37	15	52201131	52201131	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52201131delT	uc002abm.2	+	10					TMOD3_uc010bfc.1_Intron|TMOD3_uc002abn.2_5'Flank	NM_014547	NP_055362			tropomodulin 3 (ubiquitous)							cytoplasm|cytoskeleton	actin binding|tropomyosin binding			ovary(1)	1				all cancers(107;0.00194)														---	---	---	---
GNB5	10681	broad.mit.edu	37	15	52459395	52459395	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52459395delA	uc002abt.1	-						GNB5_uc002abr.1_Intron|GNB5_uc002abs.1_Intron|GNB5_uc002abu.3_Intron	NM_016194	NP_057278			guanine nucleotide-binding protein, beta-5							heterotrimeric G-protein complex	GTPase activity|signal transducer activity			lung(1)	1				all cancers(107;0.0163)														---	---	---	---
MYO5A	4644	broad.mit.edu	37	15	52794488	52794489	+	Intron	INS	-	ATAC	ATAC	rs150161899	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52794488_52794489insATAC	uc002aby.2	-						MYO5A_uc002abx.3_Intron|MYO5A_uc010uge.1_Intron	NM_000259	NP_000250			myosin VA isoform 1						actin filament-based movement|transport	cytoplasm|growth cone|myosin complex|ruffle	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|central_nervous_system(1)	4				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)														---	---	---	---
KIAA1370	56204	broad.mit.edu	37	15	52876875	52876875	+	Intron	DEL	A	-	-	rs12324699	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52876875delA	uc002acg.3	-						KIAA1370_uc002ach.3_Intron|KIAA1370_uc002acf.3_Intron|KIAA1370_uc010ugf.1_Intron	NM_019600	NP_062546			hypothetical protein LOC56204												0				all cancers(107;0.0803)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	54106447	54106448	+	IGR	DEL	AC	-	-	rs72732607	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54106447_54106448delAC								WDR72 (54588 upstream) : UNC13C (198653 downstream)																																			---	---	---	---
UNC13C	440279	broad.mit.edu	37	15	54492267	54492267	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54492267delG	uc002ack.2	+							NM_001080534	NP_001074003			unc-13 homolog C						exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(5)|pancreas(2)	7				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)														---	---	---	---
UNC13C	440279	broad.mit.edu	37	15	54560339	54560339	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54560339delT	uc002ack.2	+						UNC13C_uc002acl.2_Intron	NM_001080534	NP_001074003			unc-13 homolog C						exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(5)|pancreas(2)	7				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)														---	---	---	---
UNC13C	440279	broad.mit.edu	37	15	54587848	54587848	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54587848delA	uc002ack.2	+						UNC13C_uc002acl.2_Intron	NM_001080534	NP_001074003			unc-13 homolog C						exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(5)|pancreas(2)	7				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)														---	---	---	---
UNC13C	440279	broad.mit.edu	37	15	54915983	54915983	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:54915983delT	uc002ack.2	+						UNC13C_uc002acm.2_Intron	NM_001080534	NP_001074003			unc-13 homolog C						exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(5)|pancreas(2)	7				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	55155938	55155939	+	IGR	INS	-	T	T	rs146696057	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55155938_55155939insT								UNC13C (235133 upstream) : RSL24D1 (317582 downstream)																																			---	---	---	---
CCPG1	9236	broad.mit.edu	37	15	55783155	55783155	+	Intron	DEL	A	-	-	rs74830467		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55783155delA	uc002acy.2	-						DYX1C1_uc010ugh.1_Intron|DYX1C1_uc010ugi.1_Intron|DYX1C1_uc002adb.2_Intron|DYX1C1_uc002adc.2_Intron|DYX1C1_uc002add.2_Intron	NM_020739	NP_065790			cell cycle progression 1 isoform 2						cell cycle	integral to membrane				ovary(1)	1				all cancers(107;0.0354)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	55888356	55888356	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55888356delT								PYGO1 (7306 upstream) : PRTG (15392 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	56057322	56057323	+	IGR	DEL	AA	-	-	rs141660391		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56057322_56057323delAA								PRTG (22145 upstream) : NEDD4 (61808 downstream)																																			---	---	---	---
NEDD4	4734	broad.mit.edu	37	15	56166303	56166303	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56166303delT	uc002adj.2	-						NEDD4_uc002adl.2_Intron|NEDD4_uc002adi.2_Intron|NEDD4_uc010ugj.1_Intron|NEDD4_uc010bfm.2_Intron|NEDD4_uc002adk.2_Intron	NM_198400	NP_006145			neural precursor cell expressed, developmentally						development involved in symbiotic interaction|glucocorticoid receptor signaling pathway|negative regulation of sodium ion transport|negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage|negative regulation of vascular endothelial growth factor receptor signaling pathway|neuron projection development|positive regulation of nucleocytoplasmic transport|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein catabolic process|progesterone receptor signaling pathway|protein K63-linked ubiquitination|protein targeting to lysosome|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|receptor catabolic process|receptor internalization|regulation of dendrite morphogenesis|response to calcium ion|transmission of virus	apicolateral plasma membrane|cell cortex|chromatin|cytosol|perinuclear region of cytoplasm|ubiquitin ligase complex	beta-2 adrenergic receptor binding|phosphoserine binding|phosphothreonine binding|proline-rich region binding|protein domain specific binding|RNA polymerase binding|sodium channel inhibitor activity|ubiquitin binding|ubiquitin-protein ligase activity			skin(2)|ovary(1)|breast(1)	4				all cancers(107;0.0299)|GBM - Glioblastoma multiforme(80;0.113)														---	---	---	---
NEDD4	4734	broad.mit.edu	37	15	56179241	56179241	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56179241delA	uc002adj.2	-						NEDD4_uc002adl.2_Intron|NEDD4_uc002adi.2_Intron|NEDD4_uc010ugj.1_Intron|NEDD4_uc010bfm.2_Intron|NEDD4_uc002adk.2_Intron	NM_198400	NP_006145			neural precursor cell expressed, developmentally						development involved in symbiotic interaction|glucocorticoid receptor signaling pathway|negative regulation of sodium ion transport|negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage|negative regulation of vascular endothelial growth factor receptor signaling pathway|neuron projection development|positive regulation of nucleocytoplasmic transport|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein catabolic process|progesterone receptor signaling pathway|protein K63-linked ubiquitination|protein targeting to lysosome|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|receptor catabolic process|receptor internalization|regulation of dendrite morphogenesis|response to calcium ion|transmission of virus	apicolateral plasma membrane|cell cortex|chromatin|cytosol|perinuclear region of cytoplasm|ubiquitin ligase complex	beta-2 adrenergic receptor binding|phosphoserine binding|phosphothreonine binding|proline-rich region binding|protein domain specific binding|RNA polymerase binding|sodium channel inhibitor activity|ubiquitin binding|ubiquitin-protein ligase activity			skin(2)|ovary(1)|breast(1)	4				all cancers(107;0.0299)|GBM - Glioblastoma multiforme(80;0.113)														---	---	---	---
NEDD4	4734	broad.mit.edu	37	15	56183231	56183231	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56183231delA	uc002adj.2	-						NEDD4_uc002adl.2_Intron|NEDD4_uc002adi.2_Intron|NEDD4_uc010ugj.1_Intron|NEDD4_uc010bfm.2_Intron|NEDD4_uc002adk.2_Intron	NM_198400	NP_006145			neural precursor cell expressed, developmentally						development involved in symbiotic interaction|glucocorticoid receptor signaling pathway|negative regulation of sodium ion transport|negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage|negative regulation of vascular endothelial growth factor receptor signaling pathway|neuron projection development|positive regulation of nucleocytoplasmic transport|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein catabolic process|progesterone receptor signaling pathway|protein K63-linked ubiquitination|protein targeting to lysosome|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|receptor catabolic process|receptor internalization|regulation of dendrite morphogenesis|response to calcium ion|transmission of virus	apicolateral plasma membrane|cell cortex|chromatin|cytosol|perinuclear region of cytoplasm|ubiquitin ligase complex	beta-2 adrenergic receptor binding|phosphoserine binding|phosphothreonine binding|proline-rich region binding|protein domain specific binding|RNA polymerase binding|sodium channel inhibitor activity|ubiquitin binding|ubiquitin-protein ligase activity			skin(2)|ovary(1)|breast(1)	4				all cancers(107;0.0299)|GBM - Glioblastoma multiforme(80;0.113)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	56542006	56542006	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56542006delA								RFX7 (6523 upstream) : TEX9 (115638 downstream)																																			---	---	---	---
ZNF280D	54816	broad.mit.edu	37	15	56946272	56946272	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56946272delA	uc002adu.2	-						ZNF280D_uc002adv.2_Intron|ZNF280D_uc010bfq.2_Intron|ZNF280D_uc002adw.1_Intron|ZNF280D_uc010bfp.2_Intron	NM_017661	NP_060131			suppressor of hairy wing homolog 4 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)|skin(1)	3				all cancers(107;0.0399)|GBM - Glioblastoma multiforme(80;0.0787)														---	---	---	---
TCF12	6938	broad.mit.edu	37	15	57426955	57426955	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57426955delT	uc002aec.2	+						TCF12_uc010ugm.1_Intron|TCF12_uc010ugn.1_Intron|TCF12_uc002aea.2_Intron|TCF12_uc010bfs.2_Intron|TCF12_uc002aeb.2_Intron|TCF12_uc002aed.2_Intron	NM_207038	NP_996921			transcription factor 12 isoform b						immune response|muscle organ development|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(5)|ovary(2)|lung(1)	8		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)				T	TEC	extraskeletal myxoid chondrosarcoma								---	---	---	---
ALDH1A2	8854	broad.mit.edu	37	15	58464033	58464034	+	Intron	INS	-	ATC	ATC	rs146356656	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58464033_58464034insATC	uc010ugw.1	-						AQP9_uc010ugx.1_Intron|AQP9_uc002aez.2_Intron	NM_170697	NP_733798			aldehyde dehydrogenase 1A2 isoform 3						negative regulation of cell proliferation|neural tube development|response to cytokine stimulus	nucleus	3-chloroallyl aldehyde dehydrogenase activity|retinal binding|retinal dehydrogenase activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(80;0.152)|all cancers(107;0.18)	NADH(DB00157)|Tretinoin(DB00755)|Vitamin A(DB00162)													---	---	---	---
LIPC	3990	broad.mit.edu	37	15	58807916	58807916	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58807916delA	uc010bga.1	+						LIPC_uc010bfz.1_Intron|LIPC_uc002afa.1_Intron|LIPC_uc010bgb.1_Intron|LIPC_uc010ugy.1_Intron	NM_000236	NP_000227			lipase C precursor						cholesterol homeostasis|chylomicron remnant clearance|fatty acid biosynthetic process|high-density lipoprotein particle remodeling|intermediate-density lipoprotein particle remodeling|low-density lipoprotein particle remodeling|phosphatidylcholine catabolic process|triglyceride catabolic process|triglyceride homeostasis|very-low-density lipoprotein particle remodeling	high-density lipoprotein particle	apolipoprotein binding|heparin binding|low-density lipoprotein particle binding|phospholipase activity|triglyceride lipase activity			ovary(1)	1		Colorectal(260;0.215)		GBM - Glioblastoma multiforme(80;0.00213)|all cancers(107;0.00548)														---	---	---	---
ADAM10	102	broad.mit.edu	37	15	59009931	59009932	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59009931_59009932delAA	uc002afd.1	-						ADAM10_uc010bgc.1_Intron|ADAM10_uc010ugz.1_Intron|ADAM10_uc002afe.1_Intron|ADAM10_uc002afg.2_Intron	NM_001110	NP_001101			ADAM metallopeptidase domain 10 precursor						cell-cell signaling|constitutive protein ectodomain proteolysis|epidermal growth factor receptor signaling pathway|in utero embryonic development|integrin-mediated signaling pathway|monocyte activation|negative regulation of cell adhesion|Notch receptor processing|Notch signaling pathway|PMA-inducible membrane protein ectodomain proteolysis|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of T cell chemotaxis|protein phosphorylation|response to tumor necrosis factor	cell surface|endomembrane system|Golgi-associated vesicle|integral to membrane|nucleus|plasma membrane	integrin binding|metalloendopeptidase activity|protein homodimerization activity|protein kinase binding|SH3 domain binding|zinc ion binding			skin(2)	2				GBM - Glioblastoma multiforme(80;0.202)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	59052883	59052884	+	IGR	DEL	TT	-	-	rs75052780		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59052883_59052884delTT								ADAM10 (10706 upstream) : FAM63B (10509 downstream)																																			---	---	---	---
FAM63B	54629	broad.mit.edu	37	15	59086377	59086377	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59086377delC	uc002afj.2	+						FAM63B_uc002afi.2_Intron|FAM63B_uc002afk.2_Intron|FAM63B_uc002afl.2_Intron	NM_001040450	NP_001035540			hypothetical protein LOC54629 isoform a											central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	59268739	59268739	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59268739delA								SLTM (42887 upstream) : RNF111 (11126 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	59985851	59985851	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59985851delT								BNIP2 (4209 upstream) : FOXB1 (310570 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	60027036	60027036	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60027036delT								BNIP2 (45394 upstream) : FOXB1 (269385 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	60257613	60257613	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60257613delA								BNIP2 (275971 upstream) : FOXB1 (38808 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	60550315	60550315	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60550315delT								FOXB1 (221907 upstream) : ANXA2 (89036 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	61702750	61702750	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:61702750delA								RORA (181248 upstream) : VPS13C (441842 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	62386484	62386484	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62386484delG								C2CD4A (23375 upstream) : C2CD4B (69253 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	62433294	62433295	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62433294_62433295insT								C2CD4A (70185 upstream) : C2CD4B (22442 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	62563040	62563040	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62563040delA								C2CD4B (105558 upstream) : MGC15885 (366331 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	62575284	62575284	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62575284delT								C2CD4B (117802 upstream) : MGC15885 (354087 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	62895635	62895636	+	IGR	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62895635_62895636delAG								C2CD4B (438153 upstream) : MGC15885 (33735 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	62912068	62912068	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62912068delT								C2CD4B (454586 upstream) : MGC15885 (17303 downstream)																																			---	---	---	---
LACTB	114294	broad.mit.edu	37	15	63418062	63418063	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63418062_63418063delTT	uc002alw.2	+						LACTB_uc002alv.2_Intron	NM_032857	NP_116246			lactamase, beta isoform a							mitochondrion	hydrolase activity				0																		---	---	---	---
RPS27L	51065	broad.mit.edu	37	15	63446777	63446777	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63446777delA	uc002aly.2	-						RPS27L_uc002alx.2_Intron	NM_015920	NP_057004			ribosomal protein S27-like						DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA repair|mitotic cell cycle G1/S transition DNA damage checkpoint|positive regulation of anti-apoptosis|translation	nucleus|ribosome	caspase activator activity|metal ion binding|structural constituent of ribosome|translation activator activity				0																		---	---	---	---
APH1B	83464	broad.mit.edu	37	15	63571554	63571554	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63571554delT	uc002ama.2	+						APH1B_uc002amb.2_Intron|APH1B_uc010bgq.2_Intron|APH1B_uc010bgr.2_Intron	NM_031301	NP_112591			presenilin stabilization factor-like isoform 1						apoptosis|induction of apoptosis by extracellular signals|membrane protein intracellular domain proteolysis|nerve growth factor receptor signaling pathway|Notch receptor processing|Notch signaling pathway|positive regulation of catalytic activity|protein processing	integral to membrane|plasma membrane|transport vesicle	peptidase activity|protein binding				0																		---	---	---	---
HERC1	8925	broad.mit.edu	37	15	64055779	64055782	+	Intron	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64055779_64055782delTTTT	uc002amp.2	-						HERC1_uc010uil.1_Intron|HERC1_uc010bgt.1_Intron	NM_003922	NP_003913			hect domain and RCC1-like domain 1						protein modification process|transport	cytosol|Golgi apparatus|membrane	acid-amino acid ligase activity|ARF guanyl-nucleotide exchange factor activity			ovary(6)|breast(6)|lung(5)|central_nervous_system(2)	19																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	64142428	64142428	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64142428delA								HERC1 (16281 upstream) : MIR422A (20701 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	64161781	64161781	+	IGR	DEL	A	-	-	rs34722700		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64161781delA								HERC1 (35634 upstream) : MIR422A (1348 downstream)																																			---	---	---	---
SNX1	6642	broad.mit.edu	37	15	64419305	64419306	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64419305_64419306delAA	uc002amv.2	+						SNX1_uc010bgv.2_Intron|SNX1_uc010uio.1_Intron|SNX1_uc002amw.2_Intron|SNX1_uc002amx.2_Intron|SNX1_uc002amy.2_Intron|SNX1_uc010bgw.2_Intron	NM_003099	NP_003090			sorting nexin 1 isoform a						cell communication|early endosome to Golgi transport|endocytosis|intracellular protein transport	early endosome membrane|Golgi apparatus	phosphatidylinositol binding|protein binding|protein transporter activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	65015176	65015176	+	IGR	DEL	T	-	-	rs111590319		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65015176delT								OAZ2 (19714 upstream) : RBPMS2 (16922 downstream)																																			---	---	---	---
RBPMS2	348093	broad.mit.edu	37	15	65062387	65062388	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65062387_65062388delAA	uc002anq.2	-							NM_194272	NP_919248			RNA binding protein with multiple splicing 2								nucleic acid binding|nucleotide binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	65163283	65163283	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65163283delA								PLEKHO2 (3084 upstream) : ANKDD1A (40818 downstream)																																			---	---	---	---
ANKDD1A	348094	broad.mit.edu	37	15	65248896	65248897	+	Intron	INS	-	AAAC	AAAC	rs150588095	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65248896_65248897insAAAC	uc002aoa.2	+						ANKDD1A_uc002aoc.2_Intron|ANKDD1A_uc010bha.2_Intron	NM_182703	NP_874362			ankyrin repeat and death domain containing 1A						signal transduction					ovary(1)	1																		---	---	---	---
PARP16	54956	broad.mit.edu	37	15	65563924	65563924	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65563924delT	uc002aoo.2	-						PARP16_uc002aop.2_Intron|PARP16_uc002aoq.2_Intron	NM_017851	NP_060321			poly (ADP-ribose) polymerase family, member 16							integral to membrane	NAD+ ADP-ribosyltransferase activity			lung(2)	2																		---	---	---	---
IGDCC3	9543	broad.mit.edu	37	15	65626149	65626150	+	Intron	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65626149_65626150insG	uc002aos.2	-							NM_004884	NP_004875			putative neuronal cell adhesion molecule											ovary(3)	3																		---	---	---	---
DENND4A	10260	broad.mit.edu	37	15	66053228	66053228	+	Intron	DEL	A	-	-	rs77069014		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66053228delA	uc002aph.2	-						DENND4A_uc002api.2_Intron|DENND4A_uc002apj.3_Intron|DENND4A_uc010ujj.1_Intron	NM_005848	NP_005839			DENN/MADD domain containing 4A isoform 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4																		---	---	---	---
MEGF11	84465	broad.mit.edu	37	15	66241165	66241166	+	Intron	DEL	GT	-	-	rs72229548		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66241165_66241166delGT	uc002apm.2	-						MEGF11_uc002apl.2_Intron|MEGF11_uc002apn.1_Intron	NM_032445	NP_115821			multiple EGF-like-domains 11 precursor							basolateral plasma membrane|integral to membrane				pancreas(1)	1																		---	---	---	---
MEGF11	84465	broad.mit.edu	37	15	66321495	66321495	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66321495delT	uc002apm.2	-						MEGF11_uc002apl.2_Intron|MEGF11_uc002apn.1_Intron	NM_032445	NP_115821			multiple EGF-like-domains 11 precursor							basolateral plasma membrane|integral to membrane				pancreas(1)	1																		---	---	---	---
MEGF11	84465	broad.mit.edu	37	15	66462898	66462898	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66462898delA	uc002apm.2	-						MEGF11_uc002apl.2_Intron|MEGF11_uc002apn.1_Intron	NM_032445	NP_115821			multiple EGF-like-domains 11 precursor							basolateral plasma membrane|integral to membrane				pancreas(1)	1																		---	---	---	---
DIS3L	115752	broad.mit.edu	37	15	66609526	66609526	+	Intron	DEL	T	-	-	rs111454670		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66609526delT	uc010ujm.1	+						DIS3L_uc010ujl.1_Intron|DIS3L_uc002app.2_Intron|DIS3L_uc002apq.2_Intron|DIS3L_uc010bho.2_Intron	NM_001143688	NP_001137160			DIS3 mitotic control homolog (S.						rRNA catabolic process	cytoplasm|exosome (RNase complex)	exonuclease activity|protein binding|ribonuclease activity|RNA binding			ovary(2)	2																		---	---	---	---
MAP2K1	5604	broad.mit.edu	37	15	66686741	66686741	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66686741delT	uc010bhq.2	+							NM_002755	NP_002746			mitogen-activated protein kinase kinase 1						activation of MAPK activity|activation of MAPKK activity|axon guidance|cell cycle arrest|cellular senescence|epidermal growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of cell proliferation|nerve growth factor receptor signaling pathway|Ras protein signal transduction|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|plasma membrane	ATP binding|MAP kinase kinase activity|protein serine/threonine kinase activity|protein tyrosine kinase activity				0														Cardiofaciocutaneous_syndrome				---	---	---	---
ZWILCH	55055	broad.mit.edu	37	15	66832237	66832237	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66832237delT	uc002aqb.2	+						ZWILCH_uc010bhu.1_Intron|ZWILCH_uc002aqa.2_Intron|ZWILCH_uc010bhv.2_Intron	NM_017975	NP_060445			Zwilch						cell division|mitotic cell cycle checkpoint|mitotic prometaphase	condensed chromosome kinetochore|cytosol	protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	66951159	66951160	+	Intron	INS	-	TGTGTGAT	TGTGTGAT	rs140142949	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:66951159_66951160insTGTGTGAT	uc002aqe.2	+											Homo sapiens cDNA FLJ38816 fis, clone LIVER2007568.																														---	---	---	---
SMAD3	4088	broad.mit.edu	37	15	67381265	67381265	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67381265delA	uc002aqj.2	+							NM_005902	NP_005893			mothers against decapentaplegic homolog 3						activation of caspase activity|cell cycle arrest|cell-cell junction organization|evasion of host defenses by virus|immune response|induction of apoptosis|negative regulation of cell growth|negative regulation of mitotic cell cycle|negative regulation of protein catabolic process|negative regulation of protein phosphorylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription factor import into nucleus|positive regulation of transcription from RNA polymerase II promoter|primary miRNA processing|protein stabilization|regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|SMAD protein complex assembly|transforming growth factor beta receptor signaling pathway|transport|wound healing	cytosol|nuclear inner membrane|receptor complex	beta-catenin binding|co-SMAD binding|metal ion binding|protein homodimerization activity|protein kinase binding|R-SMAD binding|RNA polymerase II activating transcription factor binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transforming growth factor beta receptor binding|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity|ubiquitin protein ligase binding			large_intestine(2)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	5				Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(7;0.125)														---	---	---	---
IQCH	64799	broad.mit.edu	37	15	67709169	67709169	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67709169delT	uc002aqo.1	+						IQCH_uc002aqq.1_Intron|IQCH_uc002aqp.1_Intron|uc002aqr.1_Intron	NM_001031715	NP_001026885			IQ motif containing H isoform 1											skin(3)|ovary(1)	4				Colorectal(3;0.0856)														---	---	---	---
IQCH	64799	broad.mit.edu	37	15	67750832	67750832	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67750832delT	uc002aqo.1	+						IQCH_uc002aqq.1_Intron|IQCH_uc002aqp.1_Intron|uc002aqr.1_Intron	NM_001031715	NP_001026885			IQ motif containing H isoform 1											skin(3)|ovary(1)	4				Colorectal(3;0.0856)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	67800535	67800535	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67800535delA	uc002aqr.1	-											Homo sapiens cDNA FLJ42308 fis, clone TRACH2005796.																														---	---	---	---
MAP2K5	5607	broad.mit.edu	37	15	68000489	68000489	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68000489delA	uc002aqu.2	+						MAP2K5_uc002aqv.2_Intron|MAP2K5_uc002aqw.2_Intron|MAP2K5_uc002aqx.2_Intron	NM_145160	NP_660143			mitogen-activated protein kinase kinase 5						nerve growth factor receptor signaling pathway		ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(2)	2																		---	---	---	---
ITGA11	22801	broad.mit.edu	37	15	68617750	68617750	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68617750delG	uc002ari.2	-						ITGA11_uc010bib.2_Intron	NM_001004439	NP_001004439			integrin, alpha 11 precursor						cell-matrix adhesion|integrin-mediated signaling pathway|muscle organ development	integrin complex	collagen binding|receptor activity			kidney(2)|pancreas(1)	3					Tirofiban(DB00775)													---	---	---	---
ITGA11	22801	broad.mit.edu	37	15	68701460	68701461	+	Intron	INS	-	TGT	TGT	rs141029316	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68701460_68701461insTGT	uc002ari.2	-						ITGA11_uc010bib.2_Intron	NM_001004439	NP_001004439			integrin, alpha 11 precursor						cell-matrix adhesion|integrin-mediated signaling pathway|muscle organ development	integrin complex	collagen binding|receptor activity			kidney(2)|pancreas(1)	3					Tirofiban(DB00775)													---	---	---	---
CORO2B	10391	broad.mit.edu	37	15	69020047	69020047	+	3'UTR	DEL	T	-	-	rs71747415		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69020047delT	uc002arj.3	+	12					CORO2B_uc010bic.2_3'UTR|CORO2B_uc002ark.2_3'UTR	NM_006091	NP_006082			coronin, actin binding protein, 2B						actin cytoskeleton organization	actin cytoskeleton|cytoplasm|membrane	actin filament binding			ovary(3)|skin(2)|large_intestine(1)	6																		---	---	---	---
ANP32A	8125	broad.mit.edu	37	15	69072347	69072347	+	3'UTR	DEL	G	-	-	rs3214818		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69072347delG	uc002arl.2	-	7						NM_006305	NP_006296			acidic (leucine-rich) nuclear phosphoprotein 32						intracellular signal transduction|mRNA metabolic process|nucleocytoplasmic transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	endoplasmic reticulum|nucleoplasm|perinuclear region of cytoplasm	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	69126626	69126634	+	IGR	DEL	AAAAAAAAC	-	-	rs59781278		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69126626_69126634delAAAAAAAAC								ANP32A (13365 upstream) : NOX5 (96230 downstream)																																			---	---	---	---
PAQR5	54852	broad.mit.edu	37	15	69605048	69605049	+	Intron	DEL	AT	-	-	rs870336	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69605048_69605049delAT	uc002arz.2	+						PAQR5_uc002asa.2_5'Flank	NM_017705	NP_060175			progestin and adipoQ receptor family member V						cell differentiation|multicellular organismal development|oogenesis	integral to membrane	receptor activity|steroid binding			ovary(2)	2																		---	---	---	---
PAQR5	54852	broad.mit.edu	37	15	69619335	69619335	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69619335delT	uc002arz.2	+						PAQR5_uc002asa.2_Intron	NM_017705	NP_060175			progestin and adipoQ receptor family member V						cell differentiation|multicellular organismal development|oogenesis	integral to membrane	receptor activity|steroid binding			ovary(2)	2																		---	---	---	---
PAQR5	54852	broad.mit.edu	37	15	69685350	69685350	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69685350delA	uc002arz.2	+						PAQR5_uc002asa.2_Intron	NM_017705	NP_060175			progestin and adipoQ receptor family member V						cell differentiation|multicellular organismal development|oogenesis	integral to membrane	receptor activity|steroid binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	69701563	69701564	+	IGR	DEL	AC	-	-	rs62007330		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69701563_69701564delAC								PAQR5 (1587 upstream) : KIF23 (5124 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	70095397	70095397	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70095397delA								LOC145837 (231618 upstream) : C15orf50 (32176 downstream)																																			---	---	---	---
TLE3	7090	broad.mit.edu	37	15	70358681	70358681	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70358681delG	uc002asm.2	-						TLE3_uc002ask.2_Intron|TLE3_uc002asl.2_Intron|TLE3_uc010ukd.1_Intron|TLE3_uc010bik.1_Intron|TLE3_uc010bil.1_Intron|TLE3_uc002asn.2_Intron|TLE3_uc002asp.2_Intron|TLE3_uc002aso.2_Intron|TLE3_uc010bim.1_Intron	NM_005078	NP_005069			transducin-like enhancer protein 3 isoform a						organ morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	protein binding|protein binding			lung(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	70552390	70552390	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70552390delA								TLE3 (162134 upstream) : UACA (394505 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	70585777	70585777	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70585777delA								TLE3 (195521 upstream) : UACA (361118 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	70847537	70847537	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70847537delG								TLE3 (457281 upstream) : UACA (99358 downstream)																																			---	---	---	---
UACA	55075	broad.mit.edu	37	15	70987451	70987451	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:70987451delA	uc002asr.2	-						UACA_uc010uke.1_Intron|UACA_uc002asq.2_Intron|UACA_uc010bin.1_Intron	NM_018003	NP_060473			uveal autoantigen with coiled-coil domains and							cytoskeleton|extracellular region				ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	71384352	71384352	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71384352delT								LRRC49 (41918 upstream) : CT62 (18231 downstream)																																			---	---	---	---
THSD4	79875	broad.mit.edu	37	15	71633456	71633456	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71633456delT	uc002atb.1	+						THSD4_uc002atd.1_Intron	NM_024817	NP_079093			thrombospondin, type I, domain containing 4							proteinaceous extracellular matrix	metalloendopeptidase activity			ovary(2)	2																		---	---	---	---
THSD4	79875	broad.mit.edu	37	15	71886078	71886078	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71886078delA	uc002atb.1	+						THSD4_uc002atd.1_Intron|THSD4_uc010ukg.1_Intron|THSD4_uc002ate.2_Intron	NM_024817	NP_079093			thrombospondin, type I, domain containing 4							proteinaceous extracellular matrix	metalloendopeptidase activity			ovary(2)	2																		---	---	---	---
THSD4	79875	broad.mit.edu	37	15	71922481	71922481	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71922481delA	uc002atb.1	+						THSD4_uc002atd.1_Intron|THSD4_uc010ukg.1_Intron|THSD4_uc002ate.2_Intron	NM_024817	NP_079093			thrombospondin, type I, domain containing 4							proteinaceous extracellular matrix	metalloendopeptidase activity			ovary(2)	2																		---	---	---	---
HEXA	3073	broad.mit.edu	37	15	72659280	72659280	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72659280delT	uc002aun.3	-						CELF6_uc002auk.3_Intron|HEXA_uc010ukn.1_Intron|HEXA_uc002auo.3_Intron|HEXA_uc010bix.2_Intron|HEXA_uc010biy.2_Intron|HEXA_uc010uko.1_Intron|HEXA_uc010biz.1_Intron	NM_000520	NP_000511			hexosaminidase A preproprotein						cell death	lysosome	beta-N-acetylhexosaminidase activity|cation binding|protein heterodimerization activity			ovary(3)|upper_aerodigestive_tract(1)	4																		---	---	---	---
ARIH1	25820	broad.mit.edu	37	15	72795162	72795162	+	Intron	DEL	A	-	-	rs141264212	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72795162delA	uc002aut.3	+							NM_005744	NP_005735			ariadne ubiquitin-conjugating enzyme E2 binding						ubiquitin-dependent protein catabolic process	cytoplasm|ubiquitin ligase complex	ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding				0																		---	---	---	---
ARIH1	25820	broad.mit.edu	37	15	72833256	72833256	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72833256delC	uc002aut.3	+							NM_005744	NP_005735			ariadne ubiquitin-conjugating enzyme E2 binding						ubiquitin-dependent protein catabolic process	cytoplasm|ubiquitin ligase complex	ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding				0																		---	---	---	---
ADPGK	83440	broad.mit.edu	37	15	73053642	73053645	+	Intron	DEL	TGTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73053642_73053645delTGTT	uc002avg.3	-						ADPGK_uc010ukw.1_Intron|ADPGK_uc002avf.3_Intron|ADPGK_uc002avi.3_Intron|ADPGK_uc002avh.3_Intron	NM_031284	NP_112574			ADP-dependent glucokinase						glycolysis	extracellular region	ADP-specific glucokinase activity|metal ion binding				0																		---	---	---	---
NEO1	4756	broad.mit.edu	37	15	73349004	73349004	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73349004delC	uc002avm.3	+						NEO1_uc010ukx.1_Intron|NEO1_uc010uky.1_Intron|NEO1_uc010ukz.1_Intron	NM_002499	NP_002490			neogenin homolog 1 precursor						axon guidance|cell adhesion|positive regulation of muscle cell differentiation	Golgi apparatus|integral to plasma membrane|nucleus				pancreas(1)	1																		---	---	---	---
C15orf60	283677	broad.mit.edu	37	15	73797381	73797382	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73797381_73797382delTT	uc002avq.2	+						C15orf60_uc010bjb.2_Intron	NM_001042367	NP_001035826			hypothetical protein LOC283677											pancreas(1)	1																		---	---	---	---
C15orf60	283677	broad.mit.edu	37	15	73829828	73829829	+	Intron	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73829828_73829829insC	uc002avq.2	+						C15orf60_uc010bjb.2_Intron	NM_001042367	NP_001035826			hypothetical protein LOC283677											pancreas(1)	1																		---	---	---	---
C15orf60	283677	broad.mit.edu	37	15	73831240	73831240	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73831240delA	uc002avq.2	+						C15orf60_uc010bjb.2_Intron	NM_001042367	NP_001035826			hypothetical protein LOC283677											pancreas(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	74085928	74085929	+	IGR	DEL	TT	-	-	rs111893534		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74085928_74085929delTT								C15orf59 (42112 upstream) : TBC1D21 (80039 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	74107293	74107293	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74107293delG								C15orf59 (63477 upstream) : TBC1D21 (58675 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	74128390	74128391	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74128390_74128391delTT								C15orf59 (84574 upstream) : TBC1D21 (37577 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	74207028	74207029	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74207028_74207029insT								TBC1D21 (25475 upstream) : LOXL1 (11760 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	74247611	74247612	+	IGR	DEL	AA	-	-	rs72088517		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74247611_74247612delAA								LOXL1 (3133 upstream) : STOML1 (27949 downstream)																																			---	---	---	---
STOML1	9399	broad.mit.edu	37	15	74283490	74283490	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74283490delA	uc002awe.2	-						STOML1_uc002awf.2_Intron|STOML1_uc010bje.2_Intron|STOML1_uc010uld.1_Intron|STOML1_uc002awh.2_Intron|STOML1_uc002awg.2_Intron|STOML1_uc002awi.2_Intron	NM_004809	NP_004800			stomatin (EPB72)-like 1							integral to membrane	sterol binding			skin(1)	1																		---	---	---	---
PML	5371	broad.mit.edu	37	15	74295304	74295304	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74295304delA	uc002awv.2	+						PML_uc002awm.2_Intron|PML_uc002awl.2_Intron|PML_uc002awj.1_Intron|PML_uc002awk.2_Intron|PML_uc002awn.2_Intron|PML_uc002awo.2_Intron|PML_uc002awp.2_Intron|PML_uc002awq.2_Intron|PML_uc002awr.2_Intron|PML_uc002aws.2_Intron|PML_uc002awt.2_Intron|PML_uc002awu.2_Intron|PML_uc010ule.1_Intron|PML_uc002aww.1_Intron	NM_033238	NP_150241			promyelocytic leukemia protein isoform 1						cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction resulting in induction of apoptosis|endoplasmic reticulum calcium ion homeostasis|induction of apoptosis|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|maintenance of protein location in nucleus|negative regulation of angiogenesis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of mitotic cell cycle|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|negative regulation of telomerase activity|negative regulation of telomere maintenance via telomerase|negative regulation of transcription, DNA-dependent|negative regulation of translation in response to oxidative stress|PML body organization|PML body organization|positive regulation of defense response to virus by host|positive regulation of histone deacetylation|protein complex assembly|protein stabilization|protein targeting|regulation of calcium ion transport into cytosol|regulation of protein phosphorylation|response to hypoxia|response to virus|transcription, DNA-dependent	cytoplasm|cytosol|early endosome membrane|extrinsic to endoplasmic reticulum membrane|insoluble fraction|nuclear matrix|nuclear membrane|nucleolus|nucleus|PML body	cobalt ion binding|DNA binding|protein binding|protein binding|protein heterodimerization activity|protein homodimerization activity|SUMO binding|transcription coactivator activity|ubiquitin protein ligase binding|zinc ion binding|zinc ion binding			central_nervous_system(2)|kidney(2)|breast(1)	5								T	RARA|PAX5	APL|ALL								---	---	---	---
PML	5371	broad.mit.edu	37	15	74308032	74308032	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74308032delC	uc002awv.2	+						PML_uc002awm.2_Intron|PML_uc002awl.2_Intron|PML_uc002awj.1_Intron|PML_uc002awk.2_Intron|PML_uc002awn.2_Intron|PML_uc002awo.2_Intron|PML_uc002awp.2_Intron|PML_uc002awq.2_Intron|PML_uc002awr.2_Intron|PML_uc002aws.2_Intron|PML_uc002awt.2_Intron|PML_uc002awu.2_Intron|PML_uc010ule.1_Intron|PML_uc002aww.1_Intron	NM_033238	NP_150241			promyelocytic leukemia protein isoform 1						cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction resulting in induction of apoptosis|endoplasmic reticulum calcium ion homeostasis|induction of apoptosis|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|maintenance of protein location in nucleus|negative regulation of angiogenesis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of mitotic cell cycle|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|negative regulation of telomerase activity|negative regulation of telomere maintenance via telomerase|negative regulation of transcription, DNA-dependent|negative regulation of translation in response to oxidative stress|PML body organization|PML body organization|positive regulation of defense response to virus by host|positive regulation of histone deacetylation|protein complex assembly|protein stabilization|protein targeting|regulation of calcium ion transport into cytosol|regulation of protein phosphorylation|response to hypoxia|response to virus|transcription, DNA-dependent	cytoplasm|cytosol|early endosome membrane|extrinsic to endoplasmic reticulum membrane|insoluble fraction|nuclear matrix|nuclear membrane|nucleolus|nucleus|PML body	cobalt ion binding|DNA binding|protein binding|protein binding|protein heterodimerization activity|protein homodimerization activity|SUMO binding|transcription coactivator activity|ubiquitin protein ligase binding|zinc ion binding|zinc ion binding			central_nervous_system(2)|kidney(2)|breast(1)	5								T	RARA|PAX5	APL|ALL								---	---	---	---
ISLR	3671	broad.mit.edu	37	15	74463120	74463120	+	5'Flank	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74463120delG	uc002axg.1	+							NM_005545	NP_005536			immunoglobulin superfamily containing						cell adhesion	extracellular region				large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
CYP1A2	1544	broad.mit.edu	37	15	75039652	75039652	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75039652delA	uc002ayr.1	+							NM_000761	NP_000752			cytochrome P450, family 1, subfamily A,						alkaloid metabolic process|exogenous drug catabolic process|methylation|monocarboxylic acid metabolic process|monoterpenoid metabolic process|oxidative deethylation|oxidative demethylation|steroid catabolic process|toxin biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|caffeine oxidase activity|demethylase activity|electron carrier activity|enzyme binding|heme binding|oxygen binding			ovary(3)|breast(1)	4					Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Aciclovir(DB00787)|Alosetron(DB00969)|Aminophenazone(DB01424)|Amitriptyline(DB00321)|Anagrelide(DB00261)|Azelastine(DB00972)|Bortezomib(DB00188)|Caffeine(DB00201)|Carmustine(DB00262)|Chlordiazepoxide(DB00475)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Ciprofloxacin(DB00537)|Clomipramine(DB01242)|Clotrimazole(DB00257)|Clozapine(DB00363)|Conjugated Estrogens(DB00286)|Cyclobenzaprine(DB00924)|Dacarbazine(DB00851)|Desloratadine(DB00967)|Diazepam(DB00829)|Dibucaine(DB00527)|Diclofenac(DB00586)|Duloxetine(DB00476)|Enoxacin(DB00467)|Esomeprazole(DB00736)|Estradiol(DB00783)|Estrone(DB00655)|Fluorouracil(DB00544)|Flutamide(DB00499)|Fluvoxamine(DB00176)|Frovatriptan(DB00998)|Grepafloxacin(DB00365)|Haloperidol(DB00502)|Hesperetin(DB01094)|Imipramine(DB00458)|Ketoconazole(DB01026)|Leflunomide(DB01097)|Levobupivacaine(DB01002)|Levofloxacin(DB01137)|Lidocaine(DB00281)|Lomefloxacin(DB00978)|Melatonin(DB01065)|Mephenytoin(DB00532)|Mexiletine(DB00379)|Mirtazapine(DB00370)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ofloxacin(DB01165)|Olanzapine(DB00334)|Ondansetron(DB00904)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Pefloxacin(DB00487)|Pimozide(DB01100)|Propafenone(DB01182)|Propranolol(DB00571)|Quinidine(DB00908)|Ramelteon(DB00980)|Ranitidine(DB00863)|Rasagiline(DB01367)|Rifampin(DB01045)|Riluzole(DB00740)|Rofecoxib(DB00533)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Tacrine(DB00382)|Telithromycin(DB00976)|Terfenadine(DB00342)|Theophylline(DB00277)|Thiabendazole(DB00730)|Tizanidine(DB00697)|Tolbutamide(DB01124)|Verapamil(DB00661)|Warfarin(DB00682)|Zileuton(DB00744)|Zolmitriptan(DB00315)													---	---	---	---
Unknown	0	broad.mit.edu	37	15	75065431	75065431	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75065431delA								CYP1A2 (16490 upstream) : CSK (8994 downstream)																																			---	---	---	---
SCAMP2	10066	broad.mit.edu	37	15	75140576	75140576	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75140576delT	uc002azb.1	-						SCAMP2_uc002aza.1_Intron|SCAMP2_uc010bkg.1_Intron	NM_005697	NP_005688			secretory carrier membrane protein 2						post-Golgi vesicle-mediated transport|protein transport	integral to membrane|nucleus|recycling endosome membrane|trans-Golgi network membrane	protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	75533444	75533444	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75533444delA								C15orf39 (28936 upstream) : GOLGA6C (17455 downstream)																																			---	---	---	---
MAN2C1	4123	broad.mit.edu	37	15	75655170	75655170	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75655170delC	uc002baf.2	-						MAN2C1_uc002bag.2_Intron|MAN2C1_uc002bah.2_Intron|MAN2C1_uc010bkk.2_Intron|MAN2C1_uc010umi.1_Intron|MAN2C1_uc010umj.1_Intron	NM_006715	NP_006706			mannosidase, alpha, class 2C, member 1						mannose metabolic process		alpha-mannosidase activity|carbohydrate binding|protein binding|zinc ion binding				0																		---	---	---	---
SIN3A	25942	broad.mit.edu	37	15	75702784	75702784	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75702784delA	uc002bai.2	-						SIN3A_uc002baj.2_Intron|SIN3A_uc010uml.1_Intron	NM_015477	NP_056292			transcriptional co-repressor Sin3A						blood coagulation|cellular lipid metabolic process|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus|Sin3 complex	protein binding			skin(3)|ovary(1)|lung(1)	5																		---	---	---	---
SIN3A	25942	broad.mit.edu	37	15	75709485	75709485	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75709485delA	uc002bai.2	-						SIN3A_uc002baj.2_Intron|SIN3A_uc010uml.1_Intron	NM_015477	NP_056292			transcriptional co-repressor Sin3A						blood coagulation|cellular lipid metabolic process|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus|Sin3 complex	protein binding			skin(3)|ovary(1)|lung(1)	5																		---	---	---	---
SIN3A	25942	broad.mit.edu	37	15	75719271	75719272	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75719271_75719272delAA	uc002bai.2	-						SIN3A_uc002baj.2_Intron|SIN3A_uc010uml.1_Intron|SIN3A_uc002bak.3_Intron	NM_015477	NP_056292			transcriptional co-repressor Sin3A						blood coagulation|cellular lipid metabolic process|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus|Sin3 complex	protein binding			skin(3)|ovary(1)|lung(1)	5																		---	---	---	---
SNUPN	10073	broad.mit.edu	37	15	75904195	75904195	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75904195delA	uc002ban.2	-						SNUPN_uc002bao.2_Intron|SNUPN_uc002bap.2_Intron|SNUPN_uc002baq.2_Intron|SNUPN_uc002bar.2_Intron|SNUPN_uc002bas.2_Intron	NM_005701	NP_005692			snurportin 1						ncRNA metabolic process|protein import into nucleus|spliceosomal snRNP assembly	cytosol|nuclear pore	protein transporter activity|RNA cap binding			pancreas(1)	1																		---	---	---	---
SNUPN	10073	broad.mit.edu	37	15	75909934	75909935	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75909934_75909935delTT	uc002ban.2	-						SNUPN_uc002bao.2_Intron|SNUPN_uc002bap.2_Intron|SNUPN_uc002baq.2_Intron|SNUPN_uc002bar.2_Intron|SNUPN_uc002bas.2_Intron	NM_005701	NP_005692			snurportin 1						ncRNA metabolic process|protein import into nucleus|spliceosomal snRNP assembly	cytosol|nuclear pore	protein transporter activity|RNA cap binding			pancreas(1)	1																		---	---	---	---
C15orf27	123591	broad.mit.edu	37	15	76500333	76500333	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76500333delA	uc010bkp.2	+											RecName: Full=Transmembrane protein C15orf27;							integral to membrane					0																		---	---	---	---
ETFA	2108	broad.mit.edu	37	15	76576183	76576184	+	Intron	DEL	AA	-	-	rs144403864		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76576183_76576184delAA	uc002bbt.2	-						ETFA_uc010bkq.1_Intron|ETFA_uc002bbu.1_Intron	NM_000126	NP_000117			electron transfer flavoprotein, alpha						respiratory electron transport chain|transport	mitochondrial matrix	electron carrier activity|flavin adenine dinucleotide binding|oxidoreductase activity				0																		---	---	---	---
ETFA	2108	broad.mit.edu	37	15	76577920	76577920	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76577920delA	uc002bbt.2	-						ETFA_uc010bkq.1_Intron|ETFA_uc002bbu.1_Intron	NM_000126	NP_000117			electron transfer flavoprotein, alpha						respiratory electron transport chain|transport	mitochondrial matrix	electron carrier activity|flavin adenine dinucleotide binding|oxidoreductase activity				0																		---	---	---	---
ETFA	2108	broad.mit.edu	37	15	76588097	76588097	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76588097delA	uc002bbt.2	-						ETFA_uc010bkq.1_Intron|ETFA_uc002bbu.1_Intron	NM_000126	NP_000117			electron transfer flavoprotein, alpha						respiratory electron transport chain|transport	mitochondrial matrix	electron carrier activity|flavin adenine dinucleotide binding|oxidoreductase activity				0																		---	---	---	---
ISL2	64843	broad.mit.edu	37	15	76633897	76633897	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76633897delC	uc002bbw.1	+							NM_145805	NP_665804			ISL LIM homeobox 2							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0																		---	---	---	---
SCAPER	49855	broad.mit.edu	37	15	76879105	76879105	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76879105delT	uc002bby.2	-						SCAPER_uc010bkr.2_Intron|SCAPER_uc002bbx.2_Intron|SCAPER_uc002bbz.1_Intron	NM_020843	NP_065894			S-phase cyclin A-associated protein in the ER							endoplasmic reticulum|nucleus	zinc ion binding			large_intestine(1)|lung(1)|ovary(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	77202644	77202645	+	IGR	INS	-	AT	AT	rs58869888		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77202644_77202645insAT								SCAPER (4900 upstream) : RCN2 (21317 downstream)																																			---	---	---	---
TSPAN3	10099	broad.mit.edu	37	15	77348272	77348272	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77348272delA	uc002bcj.2	-						TSPAN3_uc002bck.2_Intron|TSPAN3_uc010ump.1_Intron|TSPAN3_uc010bkx.2_Intron	NM_005724	NP_005715			transmembrane 4 superfamily member 8 isoform 1							integral to membrane					0				all cancers(203;1.14e-19)														---	---	---	---
HMG20A	10363	broad.mit.edu	37	15	77753444	77753444	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77753444delA	uc002bcr.2	+						HMG20A_uc002bcq.1_Intron|HMG20A_uc002bcs.2_Intron	NM_018200	NP_060670			high-mobility group 20A						chromatin modification	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	77841222	77841222	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77841222delT								HMG20A (63279 upstream) : LINGO1 (64147 downstream)																																			---	---	---	---
TBC1D2B	23102	broad.mit.edu	37	15	78365388	78365388	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78365388delA	uc002bcy.3	-						TBC1D2B_uc010bla.2_Intron	NM_144572	NP_653173			TBC1 domain family, member 2B isoform a							intracellular	protein binding|Rab GTPase activator activity			ovary(1)|large_intestine(1)|breast(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	78534839	78534839	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78534839delT								ACSBG1 (7940 upstream) : DNAJA4 (21648 downstream)																																			---	---	---	---
DNAJA4	55466	broad.mit.edu	37	15	78563103	78563103	+	Intron	DEL	A	-	-	rs3169166	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78563103delA	uc002bdj.1	+						DNAJA4_uc002bdi.2_Intron|DNAJA4_uc002bdk.2_Intron|DNAJA4_uc002bdl.2_Intron	NM_001130182	NP_001123654			DnaJ (Hsp40) homolog, subfamily A, member 4						protein folding|response to heat	membrane	ATP binding|heat shock protein binding|metal ion binding|unfolded protein binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	78616409	78616409	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78616409delC								WDR61 (24469 upstream) : CRABP1 (16257 downstream)																																			---	---	---	---
CRABP1	1381	broad.mit.edu	37	15	78636799	78636800	+	Intron	DEL	AA	-	-	rs11364387		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78636799_78636800delAA	uc002bdp.2	+							NM_004378	NP_004369			cellular retinoic acid binding protein 1						multicellular organismal development|signal transduction	cytoplasm	retinal binding|retinol binding|transporter activity				0					Alitretinoin(DB00523)|Etretinate(DB00926)													---	---	---	---
Unknown	0	broad.mit.edu	37	15	78647693	78647693	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78647693delA								CRABP1 (7121 upstream) : IREB2 (82825 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	78726383	78726383	+	IGR	DEL	A	-	-	rs35031532		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78726383delA								CRABP1 (85811 upstream) : IREB2 (4135 downstream)																																			---	---	---	---
CHRNB4	1143	broad.mit.edu	37	15	78928264	78928264	+	Intron	DEL	G	-	-	rs12441088	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78928264delG	uc002bed.1	-						CHRNB4_uc002bee.1_Intron|CHRNB4_uc010blh.1_Intron	NM_000750	NP_000741			cholinergic receptor, nicotinic, beta 4						regulation of neurotransmitter secretion|synaptic transmission involved in micturition|synaptic transmission, cholinergic	cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity				0																		---	---	---	---
CHRNB4	1143	broad.mit.edu	37	15	78928955	78928957	+	Intron	DEL	TTT	-	-	rs77270762		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78928955_78928957delTTT	uc002bed.1	-						CHRNB4_uc002bee.1_Intron|CHRNB4_uc010blh.1_Intron	NM_000750	NP_000741			cholinergic receptor, nicotinic, beta 4						regulation of neurotransmitter secretion|synaptic transmission involved in micturition|synaptic transmission, cholinergic	cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity				0																		---	---	---	---
ADAMTS7	11173	broad.mit.edu	37	15	79058183	79058184	+	Frame_Shift_Ins	INS	-	TGGGTCC	TGGGTCC			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79058183_79058184insTGGGTCC	uc002bej.3	-	19	4280_4281	c.4069_4070insGGACCCA	c.(4069-4071)AAGfs	p.K1357fs	ADAMTS7_uc010und.1_3'UTR	NM_014272	NP_055087	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1357					proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0																		---	---	---	---
MTHFS	10588	broad.mit.edu	37	15	80165898	80165898	+	Intron	DEL	A	-	-	rs74972590		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80165898delA	uc002bex.3	-							NM_006441	NP_006432			5,10-methenyltetrahydrofolate synthetase						folic acid-containing compound biosynthetic process|formate metabolic process|tetrahydrofolate metabolic process	cytosol|Golgi apparatus|plasma membrane	5-formyltetrahydrofolate cyclo-ligase activity|ATP binding|folic acid binding				0				all cancers(203;0.00467)														---	---	---	---
MTHFS	10588	broad.mit.edu	37	15	80181808	80181808	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80181808delA	uc002bex.3	-							NM_006441	NP_006432			5,10-methenyltetrahydrofolate synthetase						folic acid-containing compound biosynthetic process|formate metabolic process|tetrahydrofolate metabolic process	cytosol|Golgi apparatus|plasma membrane	5-formyltetrahydrofolate cyclo-ligase activity|ATP binding|folic acid binding				0				all cancers(203;0.00467)														---	---	---	---
ST20	400410	broad.mit.edu	37	15	80205411	80205411	+	Intron	DEL	A	-	-	rs71453479		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80205411delA	uc002bez.3	-						ST20_uc002bfa.3_Intron	NM_001100879	NP_001094349			cervical cancer suppressor-1												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	80318308	80318308	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80318308delA								BCL2A1 (54665 upstream) : ZFAND6 (33713 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	80433285	80433285	+	IGR	DEL	A	-	-	rs77857889		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80433285delA								ZFAND6 (2575 upstream) : FAH (11846 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	80499645	80499645	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80499645delT								FAH (20963 upstream) : ARNT2 (197047 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	80549789	80549789	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80549789delA								FAH (71107 upstream) : ARNT2 (146903 downstream)																																			---	---	---	---
FAM108C1	58489	broad.mit.edu	37	15	81035932	81035933	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81035932_81035933insT	uc002bfu.2	+						FAM108C1_uc002bft.2_Intron	NM_021214	NP_067037			hypothetical protein LOC58489								hydrolase activity				0																		---	---	---	---
KIAA1199	57214	broad.mit.edu	37	15	81144738	81144738	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81144738delT	uc002bfw.1	+						KIAA1199_uc010unn.1_Intron	NM_018689	NP_061159			KIAA1199 precursor											upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3																		---	---	---	---
KIAA1199	57214	broad.mit.edu	37	15	81173728	81173728	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81173728delA	uc002bfw.1	+						KIAA1199_uc010unn.1_Intron	NM_018689	NP_061159			KIAA1199 precursor											upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	81359740	81359740	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81359740delT								MESDC1 (63396 upstream) : C15orf26 (32009 downstream)																																			---	---	---	---
C15orf26	161502	broad.mit.edu	37	15	81418688	81418688	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81418688delT	uc010blp.1	+							NM_173528	NP_775799			hypothetical protein LOC161502												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	81768189	81768191	+	IGR	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81768189_81768191delAAA								TMC3 (101771 upstream) : MEX3B (565937 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	82348260	82348260	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82348260delT								MEX3B (9899 upstream) : EFTUD1 (74301 downstream)																																			---	---	---	---
EFTUD1	79631	broad.mit.edu	37	15	82439824	82439824	+	Intron	DEL	A	-	-	rs76335360		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82439824delA	uc002bgt.1	-						EFTUD1_uc002bgs.1_Intron|EFTUD1_uc002bgu.1_Intron	NM_024580	NP_078856			elongation factor Tu GTP binding domain						mature ribosome assembly		GTP binding|GTPase activity|ribosome binding|translation elongation factor activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	83421332	83421332	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83421332delA								AP3B2 (42697 upstream) : SCARNA15 (3365 downstream)																																			---	---	---	---
HDGFRP3	50810	broad.mit.edu	37	15	83850237	83850237	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83850237delT	uc002bjs.1	-							NM_016073	NP_057157			hepatoma-derived growth factor, related protein						cell proliferation	nucleus	growth factor activity				0																		---	---	---	---
SH3GL3	6457	broad.mit.edu	37	15	84117177	84117177	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84117177delG	uc002bjw.2	+						SH3GL3_uc010bms.2_Intron|SH3GL3_uc010uot.1_Intron|SH3GL3_uc002bjx.2_Intron|SH3GL3_uc002bju.2_Intron|SH3GL3_uc002bjv.2_Intron	NM_003027	NP_003018			SH3-domain GRB2-like 3						central nervous system development|endocytosis|signal transduction	early endosome membrane	identical protein binding|lipid binding			pancreas(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
SH3GL3	6457	broad.mit.edu	37	15	84184873	84184873	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84184873delG	uc002bjw.2	+						SH3GL3_uc010bms.2_Intron|SH3GL3_uc010uot.1_Intron|SH3GL3_uc002bjx.2_Intron|SH3GL3_uc002bju.2_Intron|SH3GL3_uc002bjv.2_Intron	NM_003027	NP_003018			SH3-domain GRB2-like 3						central nervous system development|endocytosis|signal transduction	early endosome membrane	identical protein binding|lipid binding			pancreas(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
SH3GL3	6457	broad.mit.edu	37	15	84241967	84241967	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84241967delA	uc002bjw.2	+						SH3GL3_uc010uot.1_Intron|SH3GL3_uc002bjx.2_Intron|SH3GL3_uc002bju.2_Intron|SH3GL3_uc002bjv.2_Intron	NM_003027	NP_003018			SH3-domain GRB2-like 3						central nervous system development|endocytosis|signal transduction	early endosome membrane	identical protein binding|lipid binding			pancreas(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	84296351	84296351	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84296351delT								SH3GL3 (8860 upstream) : ADAMTSL3 (26487 downstream)																																			---	---	---	---
ADAMTSL3	57188	broad.mit.edu	37	15	84473326	84473330	+	Intron	DEL	TTTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84473326_84473330delTTTTT	uc002bjz.3	+						ADAMTSL3_uc002bjy.1_Intron|ADAMTSL3_uc010bmt.1_Intron|ADAMTSL3_uc010bmu.1_Intron	NM_207517	NP_997400			ADAMTS-like 3 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(6)|central_nervous_system(5)|lung(5)|large_intestine(4)|breast(3)|skin(2)|kidney(1)|pancreas(1)	27			BRCA - Breast invasive adenocarcinoma(143;0.211)															---	---	---	---
ADAMTSL3	57188	broad.mit.edu	37	15	84561733	84561733	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84561733delA	uc002bjz.3	+						ADAMTSL3_uc010bmt.1_Intron|ADAMTSL3_uc010bmu.1_Intron	NM_207517	NP_997400			ADAMTS-like 3 precursor							proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(6)|central_nervous_system(5)|lung(5)|large_intestine(4)|breast(3)|skin(2)|kidney(1)|pancreas(1)	27			BRCA - Breast invasive adenocarcinoma(143;0.211)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	84712190	84712190	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84712190delA								ADAMTSL3 (3599 upstream) : LOC388152 (155410 downstream)																																			---	---	---	---
ZSCAN2	54993	broad.mit.edu	37	15	85143052	85143052	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85143052delA	uc002bkr.2	+						ZSCAN2_uc002bkp.2_5'Flank|ZSCAN2_uc002bkq.2_5'Flank|ZSCAN2_uc010bmz.1_5'Flank|ZSCAN2_uc010bna.2_5'Flank	NM_181877	NP_870992			zinc finger protein 29 isoform 1						cell differentiation|multicellular organismal development|spermatogenesis|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2				UCEC - Uterine corpus endometrioid carcinoma (272;0.168)|all cancers(203;5.43e-22)														---	---	---	---
WDR73	84942	broad.mit.edu	37	15	85195108	85195108	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85195108delT	uc002bkw.2	-						WDR73_uc002bkv.2_Intron|WDR73_uc002bkx.2_Intron|WDR73_uc010upa.1_Intron	NM_032856	NP_116245			WD repeat domain 73												0																		---	---	---	---
SEC11A	23478	broad.mit.edu	37	15	85238695	85238695	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85238695delA	uc002blb.1	-						SEC11A_uc002blc.1_Intron	NM_014300	NP_055115			SEC11-like 1						energy reserve metabolic process|regulation of insulin secretion|signal peptide processing	endoplasmic reticulum membrane|integral to membrane|microsome	protein binding|serine-type peptidase activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(143;0.199)															---	---	---	---
ZNF592	9640	broad.mit.edu	37	15	85309834	85309834	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85309834delG	uc002bld.2	+							NM_014630	NP_055445			zinc finger protein 592						cell death|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(2)	6			BRCA - Breast invasive adenocarcinoma(143;0.0587)															---	---	---	---
SLC28A1	9154	broad.mit.edu	37	15	85440618	85440619	+	Intron	INS	-	A	A	rs79032718		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85440618_85440619insA	uc002blg.2	+						SLC28A1_uc010upd.1_Intron|SLC28A1_uc010bnb.2_Intron|SLC28A1_uc010upe.1_Intron|SLC28A1_uc010upf.1_Intron|SLC28A1_uc010upg.1_Intron	NM_004213	NP_004204			solute carrier family 28, member 1 isoform 1						nucleobase, nucleoside and nucleotide metabolic process	integral to plasma membrane|membrane fraction	nucleoside binding			skin(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(143;0.0587)															---	---	---	---
SLC28A1	9154	broad.mit.edu	37	15	85449163	85449164	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85449163_85449164delAA	uc002blg.2	+						SLC28A1_uc010upd.1_Intron|SLC28A1_uc010bnb.2_Intron|SLC28A1_uc010upe.1_Intron|SLC28A1_uc010upf.1_Intron|SLC28A1_uc010upg.1_Intron	NM_004213	NP_004204			solute carrier family 28, member 1 isoform 1						nucleobase, nucleoside and nucleotide metabolic process	integral to plasma membrane|membrane fraction	nucleoside binding			skin(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(143;0.0587)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	85901136	85901136	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85901136delT								PDE8A (218766 upstream) : AKAP13 (22735 downstream)																																			---	---	---	---
AKAP13	11214	broad.mit.edu	37	15	85958947	85958949	+	Intron	DEL	TTT	-	-	rs35819058		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85958947_85958949delTTT	uc002blv.1	+						AKAP13_uc002bls.2_Intron|AKAP13_uc002blt.1_Intron|AKAP13_uc002blu.1_Intron	NM_007200	NP_009131			A-kinase anchor protein 13 isoform 2						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane|membrane fraction|nucleus	cAMP-dependent protein kinase activity|metal ion binding|protein binding|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			central_nervous_system(3)|kidney(2)|urinary_tract(1)|liver(1)|skin(1)|ovary(1)	9																		---	---	---	---
AKAP13	11214	broad.mit.edu	37	15	86170030	86170030	+	Intron	DEL	T	-	-	rs80326405		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86170030delT	uc002blv.1	+						AKAP13_uc002blt.1_Intron|AKAP13_uc002blu.1_Intron|AKAP13_uc010bnf.1_Intron|AKAP13_uc010bne.1_Intron	NM_007200	NP_009131			A-kinase anchor protein 13 isoform 2						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane|membrane fraction|nucleus	cAMP-dependent protein kinase activity|metal ion binding|protein binding|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			central_nervous_system(3)|kidney(2)|urinary_tract(1)|liver(1)|skin(1)|ovary(1)	9																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	86400848	86400848	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86400848delA								KLHL25 (62659 upstream) : AGBL1 (284394 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	86519852	86519852	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86519852delT								KLHL25 (181663 upstream) : AGBL1 (165390 downstream)																																			---	---	---	---
AGBL1	123624	broad.mit.edu	37	15	87164042	87164042	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87164042delT	uc002blz.1	+							NM_152336	NP_689549			ATP/GTP binding protein-like 1						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding				0																		---	---	---	---
AGBL1	123624	broad.mit.edu	37	15	87533747	87533747	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:87533747delA	uc002blz.1	+							NM_152336	NP_689549			ATP/GTP binding protein-like 1						C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	88060607	88060607	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88060607delG								AGBL1 (488324 upstream) : NCRNA00052 (59553 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	88268639	88268639	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88268639delG								NCRNA00052 (145722 upstream) : NTRK3 (151349 downstream)																																			---	---	---	---
NTRK3	4916	broad.mit.edu	37	15	88607357	88607357	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88607357delG	uc002bme.1	-						NTRK3_uc002bmh.2_Intron|NTRK3_uc002bmf.1_Intron|NTRK3_uc010upl.1_Intron|NTRK3_uc010bnh.1_Intron|NTRK3_uc002bmg.2_Intron	NM_001012338	NP_001012338			neurotrophic tyrosine kinase, receptor, type 3						transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity		ETV6/NTRK3(234)	soft_tissue(85)|kidney(66)|breast(56)|salivary_gland(26)|lung(22)|large_intestine(6)|ovary(6)|stomach(5)|central_nervous_system(3)|pancreas(3)|haematopoietic_and_lymphoid_tissue(2)|skin(1)	281			BRCA - Breast invasive adenocarcinoma(143;0.211)					T	ETV6	congenital fibrosarcoma|Secretory breast 					TSP Lung(13;0.10)			---	---	---	---
NTRK3	4916	broad.mit.edu	37	15	88670279	88670279	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88670279delT	uc002bme.1	-						NTRK3_uc002bmh.2_Intron|NTRK3_uc002bmf.1_Intron|NTRK3_uc010upl.1_Intron|NTRK3_uc010bnh.1_Intron|NTRK3_uc002bmg.2_Intron	NM_001012338	NP_001012338			neurotrophic tyrosine kinase, receptor, type 3						transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity		ETV6/NTRK3(234)	soft_tissue(85)|kidney(66)|breast(56)|salivary_gland(26)|lung(22)|large_intestine(6)|ovary(6)|stomach(5)|central_nervous_system(3)|pancreas(3)|haematopoietic_and_lymphoid_tissue(2)|skin(1)	281			BRCA - Breast invasive adenocarcinoma(143;0.211)					T	ETV6	congenital fibrosarcoma|Secretory breast 					TSP Lung(13;0.10)			---	---	---	---
Unknown	0	broad.mit.edu	37	15	88907011	88907012	+	IGR	DEL	AG	-	-	rs2349982	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:88907011_88907012delAG								NTRK3 (107350 upstream) : MRPL46 (95696 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	89130409	89130409	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89130409delT	uc002bms.1	-											Homo sapiens cDNA FLJ30187 fis, clone BRACE2001239.																														---	---	---	---
ACAN	176	broad.mit.edu	37	15	89394009	89394009	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89394009delA	uc010upo.1	+						ACAN_uc002bmx.2_3'UTR|ACAN_uc010upp.1_Intron|ACAN_uc002bna.2_Intron	NM_013227	NP_037359			aggrecan isoform 2 precursor						cell adhesion		hyaluronic acid binding|sugar binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)															---	---	---	---
ABHD2	11057	broad.mit.edu	37	15	89744315	89744315	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89744315delA	uc002bnj.2	+	16					ABHD2_uc002bnk.2_3'UTR	NM_007011	NP_008942			alpha/beta hydrolase domain containing protein							integral to membrane	carboxylesterase activity			ovary(1)|lung(1)	2	Lung NSC(78;0.0472)|all_lung(78;0.089)																	---	---	---	---
FANCI	55215	broad.mit.edu	37	15	89811999	89811999	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89811999delA	uc010bnp.1	+						FANCI_uc002bnm.1_Intron|FANCI_uc002bnn.1_Intron|FANCI_uc002bnp.1_Intron	NM_001113378	NP_001106849			Fanconi anemia, complementation group I isoform						cell cycle|DNA repair	nucleoplasm	protein binding			ovary(2)	2	Lung NSC(78;0.0472)|all_lung(78;0.089)												Direct_reversal_of_damage|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
RHCG	51458	broad.mit.edu	37	15	90022354	90022354	+	Intron	DEL	A	-	-	rs66512382		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90022354delA	uc002bnz.2	-						RHCG_uc002bny.2_Intron|RHCG_uc002boa.2_Intron|RHCG_uc010bnq.1_Intron	NM_016321	NP_057405			Rh family, C glycoprotein						amine transport|cellular ion homeostasis|epithelial cell differentiation|transepithelial ammonium transport	apical plasma membrane|basolateral plasma membrane|cytoplasmic vesicle|integral to plasma membrane	ammonia transmembrane transporter activity|ammonium transmembrane transporter activity|ankyrin binding			kidney(1)	1	Lung NSC(78;0.0237)|all_lung(78;0.0478)																	---	---	---	---
LOC283761	283761	broad.mit.edu	37	15	90048926	90048927	+	RNA	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90048926_90048927delTT	uc002bob.2	-	4		c.704_705delAA			LOC283761_uc002bod.2_RNA|LOC283761_uc010upt.1_Intron|LOC283761_uc010upu.1_RNA|LOC283761_uc002boc.2_RNA	NR_027075				Homo sapiens cDNA FLJ25381 fis, clone TST02166.												0																		---	---	---	---
WDR93	56964	broad.mit.edu	37	15	90247559	90247559	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90247559delA	uc002boj.2	+						WDR93_uc002bok.3_3'UTR|WDR93_uc010bnr.2_Intron	NM_020212	NP_064597			WD repeat domain 93						electron transport chain	mitochondrial inner membrane	oxidoreductase activity, acting on NADH or NADPH			ovary(2)	2	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)															---	---	---	---
AP3S2	10239	broad.mit.edu	37	15	90414601	90414601	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90414601delA	uc002boq.3	-						AP3S2_uc002bos.3_Intron|AP3S2_uc010bns.2_Intron|AP3S2_uc002bor.3_Intron|AP3S2_uc010bnt.2_Intron	NM_005829	NP_005820			adaptor-related protein complex 3, sigma 2						intracellular protein transport|vesicle-mediated transport	cytoplasmic vesicle membrane|Golgi apparatus|membrane coat	protein transporter activity				0	Lung NSC(78;0.0181)|all_lung(78;0.0384)		BRCA - Breast invasive adenocarcinoma(143;0.0107)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.223)															---	---	---	---
C15orf38	348110	broad.mit.edu	37	15	90444749	90444749	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90444749delT	uc002bou.2	-	6					AP3S2_uc002bos.3_Intron|C15orf38_uc002bot.1_RNA	NM_182616	NP_872422			hypothetical protein LOC348110												0	Melanoma(11;0.0171)|Lung NSC(78;0.0181)|all_lung(78;0.0384)		BRCA - Breast invasive adenocarcinoma(143;0.0107)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.223)															---	---	---	---
ZNF710	374655	broad.mit.edu	37	15	90587139	90587139	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90587139delT	uc002bov.1	+							NM_198526	NP_940928			zinc finger protein 710						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.00769)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.129)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	90687059	90687059	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90687059delT								IDH2 (41351 upstream) : SEMA4B (41093 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	90701034	90701034	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90701034delA								IDH2 (55326 upstream) : SEMA4B (27118 downstream)																																			---	---	---	---
SEMA4B	10509	broad.mit.edu	37	15	90755359	90755377	+	Intron	DEL	CACTTCCTACTCAGAACCC	-	-	rs66854880		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90755359_90755377delCACTTCCTACTCAGAACCC	uc002boy.2	+						SEMA4B_uc002boz.2_Intron|SEMA4B_uc010uqd.1_Intron	NM_020210	NP_064595			semaphorin 4B precursor											ovary(1)|breast(1)|kidney(1)	3	Melanoma(11;0.00551)|Lung NSC(78;0.0125)|all_lung(78;0.0272)		BRCA - Breast invasive adenocarcinoma(143;0.0107)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.217)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	90829721	90829721	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90829721delA								TTLL13 (14278 upstream) : GABARAPL3 (60044 downstream)																																			---	---	---	---
IQGAP1	8826	broad.mit.edu	37	15	90944839	90944839	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90944839delA	uc002bpl.1	+							NM_003870	NP_003861			IQ motif containing GTPase activating protein 1						energy reserve metabolic process|regulation of insulin secretion|small GTPase mediated signal transduction	actin filament|cytoplasm|midbody|nucleus|plasma membrane	calmodulin binding|GTPase inhibitor activity|protein phosphatase binding|Ras GTPase activator activity			ovary(2)|lung(2)|central_nervous_system(2)|pancreas(1)|skin(1)	8	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	91251838	91251838	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91251838delA								CRTC3 (63262 upstream) : BLM (8741 downstream)																																			---	---	---	---
PRC1	9055	broad.mit.edu	37	15	91532907	91532907	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91532907delA	uc002bqm.2	-						PRC1_uc002bqn.2_Intron|PRC1_uc002bqo.2_Intron|PRC1_uc010uqs.1_Intron|PRC1_uc010uqt.1_Intron	NM_003981	NP_003972			protein regulator of cytokinesis 1 isoform 1						cytokinesis|mitotic spindle elongation	cytoplasm|nucleus|spindle microtubule|spindle pole	protein binding			ovary(1)|skin(1)	2	Lung NSC(78;0.0987)|all_lung(78;0.175)																	---	---	---	---
SV2B	9899	broad.mit.edu	37	15	91748340	91748340	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91748340delT	uc010uqv.1	+						SV2B_uc002bqt.2_Intron|SV2B_uc002bqu.3_Intron	NM_014848	NP_055663			synaptic vesicle protein 2B homolog						neurotransmitter transport	acrosomal vesicle|cell junction|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			ovary(3)|central_nervous_system(2)|skin(2)|upper_aerodigestive_tract(1)	8	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	91847614	91847615	+	IGR	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91847614_91847615delGA								SV2B (8966 upstream) : SLCO3A1 (549323 downstream)																																			---	---	---	---
SLCO3A1	28232	broad.mit.edu	37	15	92694020	92694021	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92694020_92694021delAA	uc002bqx.2	+						SLCO3A1_uc002bqy.2_Intron|SLCO3A1_uc010boc.1_Intron|SLCO3A1_uc002bqz.1_Intron	NM_013272	NP_037404			solute carrier organic anion transporter family,						sodium-independent organic anion transport	integral to membrane|plasma membrane	sodium-independent organic anion transmembrane transporter activity			skin(1)	1	Lung NSC(78;0.0158)|all_lung(78;0.0255)		BRCA - Breast invasive adenocarcinoma(143;0.0841)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	92743512	92743512	+	IGR	DEL	T	-	-	rs58365606	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92743512delT								SLCO3A1 (27847 upstream) : ST8SIA2 (193628 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	93080859	93080859	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93080859delC								C15orf32 (36512 upstream) : LOC100144604 (30189 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	93312778	93312779	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93312778_93312779delTT								FAM174B (35474 upstream) : CHD2 (116654 downstream)																																			---	---	---	---
CHD2	1106	broad.mit.edu	37	15	93510492	93510492	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93510492delT	uc002bsp.2	+						CHD2_uc002bso.1_Intron	NM_001271	NP_001262			chromodomain helicase DNA binding protein 2						regulation of transcription from RNA polymerase II promoter	nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding			ovary(1)|skin(1)	2	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	93725992	93725993	+	IGR	INS	-	T	T	rs145796429	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93725992_93725993insT								RGMA (93559 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	93963925	93963927	+	Intron	DEL	GGG	-	-	rs71758549		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:93963925_93963927delGGG	uc002bsu.1	+						uc002bta.1_Intron|uc010ure.1_5'Flank|uc010urf.1_5'Flank					Homo sapiens cDNA FLJ37033 fis, clone BRACE2011389.																														---	---	---	---
Unknown	0	broad.mit.edu	37	15	94202014	94202015	+	IGR	DEL	TT	-	-	rs80013660		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94202014_94202015delTT								RGMA (569581 upstream) : MCTP2 (572786 downstream)																																			---	---	---	---
MCTP2	55784	broad.mit.edu	37	15	94930203	94930203	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:94930203delA	uc002btj.2	+						MCTP2_uc010boj.2_Intron|MCTP2_uc010bok.2_Intron|MCTP2_uc002btk.3_Intron|MCTP2_uc002btl.2_Intron	NM_018349	NP_060819			multiple C2 domains, transmembrane 2 isoform 1						calcium-mediated signaling	integral to membrane|membrane fraction	calcium ion binding			ovary(1)|pancreas(1)|skin(1)	3	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	95099431	95099432	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:95099431_95099432insT								MCTP2 (72251 upstream) : LOC145820 (876890 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	95146195	95146195	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:95146195delT								MCTP2 (119015 upstream) : LOC145820 (830127 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	95400868	95400869	+	IGR	DEL	TG	-	-	rs113878476		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:95400868_95400869delTG								MCTP2 (373688 upstream) : LOC145820 (575453 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	95552960	95552960	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:95552960delA								MCTP2 (525780 upstream) : LOC145820 (423362 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	96067879	96067881	+	IGR	DEL	CTG	-	-	rs61257925	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:96067879_96067881delCTG								LOC145820 (16805 upstream) : NR2F2 (801276 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	96116089	96116089	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:96116089delA								LOC145820 (65015 upstream) : NR2F2 (753068 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	96501256	96501256	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:96501256delG								LOC145820 (450182 upstream) : NR2F2 (367901 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	96999426	96999426	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:96999426delC								NR2F2 (115936 upstream) : SPATA8 (327253 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	97266028	97266031	+	IGR	DEL	ACAG	-	-	rs71856857	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:97266028_97266031delACAG								NR2F2 (382538 upstream) : SPATA8 (60648 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	97389669	97389669	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:97389669delT								SPATA8 (60825 upstream) : LOC91948 (896177 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	97407640	97407640	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:97407640delT								SPATA8 (78796 upstream) : LOC91948 (878206 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	97817594	97817594	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:97817594delT								SPATA8 (488750 upstream) : LOC91948 (468252 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	97947396	97947396	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:97947396delT								SPATA8 (618552 upstream) : LOC91948 (338450 downstream)																																			---	---	---	---
LOC91948	91948	broad.mit.edu	37	15	98330327	98330327	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98330327delT	uc002buh.1	-						LOC91948_uc002bug.1_Intron	NR_024173				SubName: Full=Putative uncharacterized protein ENSP00000381347;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	15	98440769	98440769	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98440769delT								LOC91948 (23110 upstream) : ARRDC4 (22015 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	98556275	98556275	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98556275delA								ARRDC4 (39208 upstream) : FAM169B (424116 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	98710198	98710198	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98710198delA								ARRDC4 (193131 upstream) : FAM169B (270193 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	98873226	98873227	+	IGR	INS	-	TC	TC	rs145732236	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:98873226_98873227insTC								ARRDC4 (356159 upstream) : FAM169B (107164 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	99108118	99108118	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99108118delA								FAM169B (50507 upstream) : IGF1R (84643 downstream)																																			---	---	---	---
TTC23	64927	broad.mit.edu	37	15	99731161	99731162	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99731161_99731162insT	uc002bur.2	-						TTC23_uc002bus.2_Intron|TTC23_uc002but.2_Intron|TTC23_uc002buu.2_Intron|TTC23_uc002buv.2_Intron|TTC23_uc002bux.2_Intron|TTC23_uc002buw.2_Intron|TTC23_uc010boq.2_Intron|TTC23_uc002buy.2_Intron|TTC23_uc010bor.2_Intron|TTC23_uc002buz.2_Intron	NM_022905	NP_075056			tetratricopeptide repeat domain 23								binding				0	all_cancers(4;1.49e-13)|Lung NSC(78;0.000545)|all_lung(78;0.00121)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		all cancers(5;8.11e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00215)															---	---	---	---
TTC23	64927	broad.mit.edu	37	15	99740747	99740749	+	Intron	DEL	TAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99740747_99740749delTAA	uc002bur.2	-						TTC23_uc002bus.2_Intron|TTC23_uc002but.2_Intron|TTC23_uc002buu.2_Intron|TTC23_uc002buv.2_Intron|TTC23_uc002bux.2_Intron|TTC23_uc002buw.2_Intron|TTC23_uc010boq.2_Intron|TTC23_uc002buy.2_Intron|TTC23_uc010bor.2_Intron|TTC23_uc002buz.2_Intron	NM_022905	NP_075056			tetratricopeptide repeat domain 23								binding				0	all_cancers(4;1.49e-13)|Lung NSC(78;0.000545)|all_lung(78;0.00121)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		all cancers(5;8.11e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00215)															---	---	---	---
LRRC28	123355	broad.mit.edu	37	15	99842136	99842136	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99842136delT	uc002bva.1	+						LRRC28_uc010urs.1_Intron|LRRC28_uc002bvb.1_Intron|LRRC28_uc010urt.1_Intron|LRRC28_uc002bvc.1_Intron|LRRC28_uc010uru.1_Intron|LRRC28_uc002bvd.1_Intron	NM_144598	NP_653199			leucine rich repeat containing 28												0	Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00106)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	100014301	100014301	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100014301delT								LRRC28 (87021 upstream) : MEF2A (91832 downstream)																																			---	---	---	---
MEF2A	4205	broad.mit.edu	37	15	100153121	100153123	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100153121_100153123delAAA	uc002bve.2	+						MEF2A_uc010urv.1_Intron|MEF2A_uc010bos.2_Intron|MEF2A_uc002bvf.2_Intron|MEF2A_uc002bvg.2_Intron|MEF2A_uc002bvi.2_Intron	NM_001130926	NP_001124398			myocyte enhancer factor 2A isoform 2						apoptosis|BMK cascade|cardiac conduction|cellular response to calcium ion|dendrite morphogenesis|innate immune response|mitochondrial genome maintenance|mitochondrion distribution|muscle organ development|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of muscle cell differentiation|positive regulation of transcription from RNA polymerase II promoter|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|ventricular cardiac myofibril development	nuclear chromatin|nucleoplasm	activating transcription factor binding|histone acetyltransferase binding|histone deacetylase binding|protein heterodimerization activity|RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|SMAD binding			ovary(1)	1	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00085)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	100456098	100456099	+	IGR	DEL	AA	-	-	rs71993572		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100456098_100456099delAA								C15orf51 (108966 upstream) : ADAMTS17 (55544 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	100493197	100493197	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100493197delC								C15orf51 (146065 upstream) : ADAMTS17 (18446 downstream)																																			---	---	---	---
ADAMTS17	170691	broad.mit.edu	37	15	100598506	100598507	+	Intron	INS	-	T	T	rs150896439	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100598506_100598507insT	uc002bvv.1	-							NM_139057	NP_620688			ADAM metallopeptidase with thrombospondin type 1						proteolysis	intracellular|proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	101234275	101234275	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101234275delG								ASB7 (42373 upstream) : ALDH1A3 (185734 downstream)																																			---	---	---	---
ALDH1A3	220	broad.mit.edu	37	15	101435890	101435890	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101435890delC	uc002bwn.3	+						ALDH1A3_uc010bpb.2_Intron|uc002bwo.1_RNA	NM_000693	NP_000684			aldehyde dehydrogenase 1A3						retinal metabolic process	cytoplasm	aldehyde dehydrogenase|protein homodimerization activity			central_nervous_system(2)|lung(1)|pancreas(1)	4	Lung NSC(78;0.00144)|all_lung(78;0.0018)|Melanoma(26;0.00852)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.0766)|Lung(145;0.103)		NADH(DB00157)|Vitamin A(DB00162)													---	---	---	---
LRRK1	79705	broad.mit.edu	37	15	101589059	101589059	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101589059delC	uc002bwr.2	+						LRRK1_uc010usb.1_Intron|LRRK1_uc010usc.1_Intron	NM_024652	NP_078928			leucine-rich repeat kinase 1						small GTPase mediated signal transduction	mitochondrion	ATP binding|GTP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|lung(4)|central_nervous_system(3)|large_intestine(1)	12	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)															---	---	---	---
Unknown	0	broad.mit.edu	37	15	101798076	101798076	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101798076delT								CHSY1 (5950 upstream) : SELS (13138 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	15	102102382	102102382	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102102382delA								PCSK6 (72195 upstream) : TM2D3 (70798 downstream)																																			---	---	---	---
TM2D3	80213	broad.mit.edu	37	15	102185369	102185370	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102185369_102185370delAA	uc002bxi.2	-						TM2D3_uc010usg.1_Intron|TM2D3_uc002bxh.2_Intron|TM2D3_uc002bxj.2_Intron|TM2D3_uc002bxk.2_Intron	NM_078474	NP_510883			TM2 domain containing 3 isoform a							integral to membrane				ovary(1)	1	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000268)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)															---	---	---	---
TARSL2	123283	broad.mit.edu	37	15	102204200	102204201	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102204200_102204201insT	uc002bxm.2	-						TARSL2_uc002bxl.2_Intron|TARSL2_uc010usi.1_Intron	NM_152334	NP_689547			threonyl-tRNA synthetase-like 2						threonyl-tRNA aminoacylation	cytoplasm	ATP binding|threonine-tRNA ligase activity			ovary(2)	2	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000268)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)															---	---	---	---
MPG	4350	broad.mit.edu	37	16	133153	133153	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:133153delG	uc002cfn.2	+	4	736	c.418delG	c.(418-420)GGCfs	p.G140fs	MPG_uc002cfm.2_Frame_Shift_Del_p.G123fs|MPG_uc010bqp.2_Frame_Shift_Del_p.G123fs|MPG_uc002cfo.2_Frame_Shift_Del_p.G135fs	NM_002434	NP_002425	P29372	3MG_HUMAN	N-methylpurine-DNA glycosylase isoform a	140					depurination|DNA dealkylation involved in DNA repair	nucleoplasm	alkylbase DNA N-glycosylase activity|damaged DNA binding|identical protein binding			ovary(1)|skin(1)	2		all_cancers(16;9.01e-08)|all_epithelial(16;7.64e-07)|Hepatocellular(780;0.000325)|Lung NSC(18;0.0104)|all_lung(18;0.0239)											BER_DNA_glycosylases					---	---	---	---
NPRL3	8131	broad.mit.edu	37	16	136329	136329	+	3'UTR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:136329delG	uc002cfr.2	-	15					NPRL3_uc010uua.1_Intron|NPRL3_uc002cfp.1_RNA|NPRL3_uc002cfq.2_3'UTR|NPRL3_uc010uub.1_3'UTR	NM_001077350	NP_001070818			conserved gene telomeric to alpha globin cluster								protein binding			ovary(1)	1																		---	---	---	---
NPRL3	8131	broad.mit.edu	37	16	155508	155509	+	Intron	INS	-	CT	CT	rs146371565	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:155508_155509insCT	uc002cfr.2	-						NPRL3_uc010uua.1_Intron|NPRL3_uc002cfp.1_Intron|NPRL3_uc002cfq.2_Intron|NPRL3_uc010uub.1_Intron|NPRL3_uc010uuc.1_Intron|NPRL3_uc002cfs.1_Intron	NM_001077350	NP_001070818			conserved gene telomeric to alpha globin cluster								protein binding			ovary(1)	1																		---	---	---	---
RAB11FIP3	9727	broad.mit.edu	37	16	531512	531512	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:531512delA	uc002chf.2	+						RAB11FIP3_uc010uuf.1_Intron|RAB11FIP3_uc010uug.1_5'Flank	NM_014700	NP_055515			rab11-family interacting protein 3 isoform 1						cell cycle|cytokinesis|endocytic recycling|protein transport	centrosome|cleavage furrow|midbody|recycling endosome membrane	ADP-ribosylation factor binding|calcium ion binding|protein homodimerization activity|Rab GTPase binding				0		Hepatocellular(16;0.0218)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	1180596	1180597	+	IGR	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1180596_1180597insC								C1QTNF8 (34352 upstream) : CACNA1H (22644 downstream)																																			---	---	---	---
CACNA1H	8912	broad.mit.edu	37	16	1270496	1270496	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1270496delC	uc002cks.2	+	35	6812	c.6564delC	c.(6562-6564)AGCfs	p.S2188fs	CACNA1H_uc002ckt.2_Frame_Shift_Del_p.S2182fs|CACNA1H_uc002cku.2_Frame_Shift_Del_p.S883fs|CACNA1H_uc010brj.2_Frame_Shift_Del_p.S899fs|CACNA1H_uc002ckv.2_Frame_Shift_Del_p.S877fs	NM_021098	NP_066921	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type,	2188	Cytoplasmic (Potential).				aldosterone biosynthetic process|axon guidance|cellular response to hormone stimulus|cellular response to potassium ion|cortisol biosynthetic process|muscle contraction|myoblast fusion|positive regulation of acrosome reaction|regulation of heart contraction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(2)	2		Hepatocellular(780;0.00369)			Flunarizine(DB04841)|Mibefradil(DB01388)													---	---	---	---
UBE2I	7329	broad.mit.edu	37	16	1357172	1357173	+	5'Flank	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1357172_1357173delAA	uc002clc.1	+						uc010uuy.1_RNA|UBE2I_uc002cld.1_5'Flank|UBE2I_uc002cle.1_5'Flank|UBE2I_uc002clf.1_5'Flank|UBE2I_uc002clg.1_5'Flank	NM_194261	NP_919237			ubiquitin-conjugating enzyme E2I						cell division|chromosome segregation|interspecies interaction between organisms|mitosis|negative regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|protein sumoylation	cytoplasm|PML body|synaptonemal complex	ATP binding|enzyme binding|ubiquitin-protein ligase activity			breast(1)|skin(1)	2		Hepatocellular(780;0.00369)																---	---	---	---
UNKL	64718	broad.mit.edu	37	16	1434387	1434387	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1434387delC	uc010brn.1	-											SubName: Full=Putative ubiquitin-protein ligase;          EC=6.3.2.19; Flags: Fragment;							cytoplasm|nucleus	ligase activity|nucleic acid binding|zinc ion binding				0		Hepatocellular(780;0.0893)																---	---	---	---
CLCN7	1186	broad.mit.edu	37	16	1511034	1511034	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1511034delG	uc002clv.2	-						CLCN7_uc002clw.2_Intron	NM_001287	NP_001278			chloride channel 7 isoform a							integral to membrane|lysosomal membrane	antiporter activity|ATP binding|voltage-gated chloride channel activity			central_nervous_system(2)|ovary(1)|skin(1)	4		Hepatocellular(780;0.0893)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	1531481	1531481	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1531481delG								CLCN7 (6396 upstream) : PTX4 (4460 downstream)																																			---	---	---	---
RPL3L	6123	broad.mit.edu	37	16	2005269	2005269	+	5'Flank	DEL	A	-	-	rs116222346	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2005269delA	uc002cnh.2	-							NM_005061	NP_005052			ribosomal protein L3-like						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosol|ribosome	RNA binding|structural constituent of ribosome				0																		---	---	---	---
RNPS1	10921	broad.mit.edu	37	16	2306126	2306127	+	Intron	INS	-	A	A	rs75415289		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2306126_2306127insA	uc002cpt.2	-						RNPS1_uc002cpu.2_Intron|RNPS1_uc002cpv.2_Intron|RNPS1_uc002cpw.2_Intron|RNPS1_uc002cpx.2_Intron|RNPS1_uc010uwa.1_Intron	NM_080594	NP_542161			RNA-binding protein S1, serine-rich domain						mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|termination of RNA polymerase II transcription	cytosol|nuclear speck	mRNA 3'-UTR binding|nucleotide binding|protein binding			ovary(1)	1																		---	---	---	---
AMDHD2	51005	broad.mit.edu	37	16	2575307	2575307	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2575307delC	uc002cqq.2	+						AMDHD2_uc002cqp.2_Intron|AMDHD2_uc010uwc.1_Intron|AMDHD2_uc010uwd.1_Intron	NM_015944	NP_057028			amidohydrolase domain containing 2 isoform 1						N-acetylglucosamine metabolic process		N-acetylglucosamine-6-phosphate deacetylase activity			skin(2)|large_intestine(1)|breast(1)	4																		---	---	---	---
LOC652276	652276	broad.mit.edu	37	16	2657871	2657871	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2657871delT	uc002cqx.2	+						LOC652276_uc002cqy.3_Intron					Homo sapiens cDNA FLJ39075 fis, clone NT2RP7016911.												0																		---	---	---	---
PRSS27	83886	broad.mit.edu	37	16	2763103	2763104	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2763103_2763104delTT	uc002crf.2	-						PRSS27_uc002cre.2_Intron|PRSS27_uc002crg.2_Intron|PRSS27_uc010bst.1_3'UTR	NM_031948	NP_114154			marapsin precursor						proteolysis	extracellular region	serine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
SRRM2	23524	broad.mit.edu	37	16	2806346	2806346	+	5'UTR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2806346delC	uc002crk.2	+	2					SRRM2_uc002crj.1_Intron|SRRM2_uc002crl.1_5'UTR|SRRM2_uc010bsu.1_Intron	NM_016333	NP_057417			splicing coactivator subunit SRm300							Cajal body|catalytic step 2 spliceosome|nuclear speck	C2H2 zinc finger domain binding|protein N-terminus binding|RNA binding			ovary(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
PRSS22	64063	broad.mit.edu	37	16	2903146	2903146	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2903146delC	uc002cry.1	-	6	968	c.902delG	c.(901-903)GGTfs	p.G301fs	PRSS22_uc002crz.1_Frame_Shift_Del_p.G191fs	NM_022119	NP_071402	Q9GZN4	BSSP4_HUMAN	protease, serine, 22 precursor	301					proteolysis	extracellular region	serine-type endopeptidase activity			central_nervous_system(1)	1																		---	---	---	---
FLYWCH2	114984	broad.mit.edu	37	16	2947917	2947918	+	Intron	INS	-	AGA	AGA	rs151256526	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2947917_2947918insAGA	uc002csa.2	+						FLYWCH2_uc010uwj.1_Intron|FLYWCH2_uc010uwk.1_Intron	NM_138439	NP_612448			FLYWCH family member 2												0																		---	---	---	---
FLYWCH2	114984	broad.mit.edu	37	16	2949270	2949272	+	3'UTR	DEL	TTT	-	-	rs34090411		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2949270_2949272delTTT	uc002csa.2	+	4					FLYWCH2_uc010uwj.1_3'UTR|FLYWCH2_uc010uwk.1_3'UTR	NM_138439	NP_612448			FLYWCH family member 2												0																		---	---	---	---
HCFC1R1	54985	broad.mit.edu	37	16	3073252	3073252	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3073252delG	uc002csx.1	-	4	396	c.263delC	c.(262-264)CCAfs	p.P88fs	HCFC1R1_uc002csy.1_Frame_Shift_Del_p.P88fs|HCFC1R1_uc002csz.1_Frame_Shift_Del_p.P69fs|THOC6_uc002ctb.2_5'Flank|THOC6_uc002ctd.2_5'Flank|THOC6_uc002ctc.2_5'Flank|THOC6_uc002cta.2_5'Flank	NM_001002018	NP_001002018	Q9NWW0	HPIP_HUMAN	host cell factor C1 regulator 1 (XPO1 dependant)	88						cytoplasm|nucleus					0																		---	---	---	---
ZNF263	10127	broad.mit.edu	37	16	3325325	3325325	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3325325delA	uc010uww.1	+							NM_005741	NP_005732			zinc finger protein 263						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(3)|ovary(1)	4																		---	---	---	---
ZNF75A	7627	broad.mit.edu	37	16	3358947	3358948	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3358947_3358948delTT	uc002cut.3	+						ZNF75A_uc002cuv.3_Intron	NM_153028	NP_694573			zinc finger protein 75a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)	1																		---	---	---	---
DNASE1	1773	broad.mit.edu	37	16	3706902	3706902	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3706902delC	uc002cvr.2	+							NM_005223	NP_005214			deoxyribonuclease I precursor						apoptosis|DNA catabolic process	extracellular region|nuclear envelope	actin binding|deoxyribonuclease I activity				0		Ovarian(90;0.0261)		Kidney(780;0.0556)	Dornase Alfa(DB00003)								Direct_reversal_of_damage					---	---	---	---
TRAP1	10131	broad.mit.edu	37	16	3744352	3744352	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3744352delT	uc002cvt.3	-						TRAP1_uc010uxf.1_Intron	NM_016292	NP_057376			TNF receptor-associated protein 1 precursor						cellular response to oxidative stress|protein folding	mitochondrion	ATP binding|tumor necrosis factor receptor binding|unfolded protein binding			central_nervous_system(1)	1		Ovarian(90;0.0261)																---	---	---	---
CREBBP	1387	broad.mit.edu	37	16	3821078	3821078	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3821078delT	uc002cvv.2	-						CREBBP_uc002cvw.2_Intron	NM_004380	NP_004371			CREB binding protein isoform a						cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia	cytoplasm|nuclear body	histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1)	127		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)				T|N|F|Mis|O	MLL|MORF|RUNXBP2	ALL|AML|DLBCL|B-NHL 		Rubinstein-Taybi syndrome		Rubinstein-Taybi_syndrome				---	---	---	---
SRL	6345	broad.mit.edu	37	16	4255162	4255162	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4255162delA	uc002cvz.3	-						SRL_uc002cvy.3_Intron	NM_001098814	NP_001092284			sarcalumenin							sarcoplasmic reticulum lumen	GTP binding|GTPase activity			ovary(3)|skin(2)	5																		---	---	---	---
NMRAL1	57407	broad.mit.edu	37	16	4519045	4519045	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4519045delA	uc002cwm.2	-						NMRAL1_uc002cwn.2_Intron|NMRAL1_uc002cwo.2_Intron|NMRAL1_uc002cwp.2_Intron	NM_020677	NP_065728			NmrA-like family domain containing 1							nucleus|perinuclear region of cytoplasm	binding			kidney(1)	1																		---	---	---	---
ANKS3	124401	broad.mit.edu	37	16	4767804	4767804	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4767804delT	uc002cxj.1	-						ANKS3_uc002cxi.1_Intron|ANKS3_uc002cxk.2_Intron|ANKS3_uc002cxl.2_Intron|ANKS3_uc010uxs.1_Intron|ANKS3_uc002cxm.2_Intron	NM_133450	NP_597707			ankyrin repeat and sterile alpha motif domain												0																		---	---	---	---
UBN1	29855	broad.mit.edu	37	16	4907189	4907189	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4907189delA	uc002cyb.2	+						UBN1_uc010uxw.1_Intron|UBN1_uc002cyc.2_Intron	NM_001079514	NP_001072982			ubinuclein 1						chromatin modification|interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter	PML body|tight junction	DNA binding|sequence-specific DNA binding transcription factor activity			skin(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	5174693	5174693	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5174693delT								FAM86A (26904 upstream) : A2BP1 (894439 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	5223736	5223736	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5223736delT								FAM86A (75947 upstream) : A2BP1 (845396 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	5249753	5249753	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5249753delC								FAM86A (101964 upstream) : A2BP1 (819379 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	5508535	5508535	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:5508535delT	uc002cyq.1	+											Homo sapiens cDNA clone IMAGE:5244947, **** WARNING: chimeric clone ****.																														---	---	---	---
A2BP1	54715	broad.mit.edu	37	16	6150157	6150157	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6150157delT	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron	NM_018723	NP_061193			ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)														---	---	---	---
A2BP1	54715	broad.mit.edu	37	16	6258958	6258958	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6258958delT	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron	NM_018723	NP_061193			ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)														---	---	---	---
A2BP1	54715	broad.mit.edu	37	16	6766418	6766418	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:6766418delT	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Intron	NM_018723	NP_061193			ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)														---	---	---	---
A2BP1	54715	broad.mit.edu	37	16	7265727	7265730	+	Intron	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7265727_7265730delTTTT	uc002cys.2	+						A2BP1_uc010buf.1_Intron|A2BP1_uc002cyr.1_Intron|A2BP1_uc002cyt.2_Intron|A2BP1_uc010uxz.1_Intron|A2BP1_uc010uya.1_Intron|A2BP1_uc002cyv.1_Intron|A2BP1_uc010uyb.1_Intron	NM_018723	NP_061193			ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	8267610	8267610	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8267610delT								A2BP1 (504270 upstream) : TMEM114 (351893 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	8366722	8366722	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8366722delA								A2BP1 (603382 upstream) : TMEM114 (252781 downstream)																																			---	---	---	---
ABAT	18	broad.mit.edu	37	16	8777409	8777412	+	Intron	DEL	AAAA	-	-	rs145313959		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8777409_8777412delAAAA	uc002czc.3	+							NM_020686	NP_065737			4-aminobutyrate aminotransferase precursor						behavioral response to cocaine|gamma-aminobutyric acid catabolic process|neurotransmitter catabolic process|neurotransmitter secretion	4-aminobutyrate transaminase complex|mitochondrial matrix	(S)-3-amino-2-methylpropionate transaminase activity|4-aminobutyrate transaminase activity|protein homodimerization activity|pyridoxal phosphate binding|succinate-semialdehyde dehydrogenase binding			upper_aerodigestive_tract(1)	1					Divalproex sodium(DB00510)|Isoniazid(DB00951)|L-Alanine(DB00160)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)|Pyruvic acid(DB00119)|Tiagabine(DB00906)|Valproic Acid(DB00313)|Vigabatrin(DB01080)													---	---	---	---
Unknown	0	broad.mit.edu	37	16	9463125	9463126	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9463125_9463126insT								C16orf72 (249580 upstream) : GRIN2A (384141 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	9601206	9601206	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9601206delA								C16orf72 (387661 upstream) : GRIN2A (246061 downstream)																																			---	---	---	---
GRIN2A	2903	broad.mit.edu	37	16	10133857	10133858	+	Intron	DEL	AA	-	-	rs112753411		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10133857_10133858delAA	uc002czo.3	-						GRIN2A_uc010uym.1_Intron|GRIN2A_uc002czr.3_Intron	NM_001134407	NP_001127879			N-methyl-D-aspartate receptor subunit 2A isoform						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			skin(32)|NS(5)|ovary(4)|large_intestine(1)|lung(1)|breast(1)|kidney(1)	45					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)													---	---	---	---
Unknown	0	broad.mit.edu	37	16	10316095	10316095	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10316095delA								GRIN2A (39484 upstream) : ATF7IP2 (163817 downstream)																																			---	---	---	---
ATF7IP2	80063	broad.mit.edu	37	16	10546617	10546617	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10546617delT	uc002czu.2	+						ATF7IP2_uc002czv.2_Intron|ATF7IP2_uc010uyo.1_Intron|ATF7IP2_uc010uyp.1_Intron|ATF7IP2_uc002czw.2_Intron|ATF7IP2_uc010uyq.1_Intron	NM_024997	NP_079273			activating transcription factor 7 interacting						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0																		---	---	---	---
CLEC16A	23274	broad.mit.edu	37	16	11108387	11108387	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11108387delA	uc002dao.2	+						CLEC16A_uc002dan.3_Intron	NM_015226	NP_056041			C-type lectin domain family 16, member A									p.0?(1)		ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	11529465	11529465	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11529465delT								C16orf75 (83848 upstream) : LITAF (112117 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	11758793	11758793	+	IGR	DEL	G	-	-	rs67091316		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11758793delG								LITAF (77471 upstream) : SNN (3508 downstream)																																			---	---	---	---
TXNDC11	51061	broad.mit.edu	37	16	11812128	11812128	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11812128delA	uc010buu.1	-						TXNDC11_uc002dbg.1_Intron	NM_015914	NP_056998			thioredoxin domain containing 11						cell redox homeostasis	endoplasmic reticulum membrane|integral to membrane					0																		---	---	---	---
SNX29	92017	broad.mit.edu	37	16	12246078	12246079	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12246078_12246079delAA	uc002dby.3	+						SNX29_uc010uyx.1_Intron	NM_001080530	NP_001073999			sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1																		---	---	---	---
SNX29	92017	broad.mit.edu	37	16	12445068	12445069	+	Intron	DEL	GG	-	-	rs142994621		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12445068_12445069delGG	uc002dby.3	+							NM_001080530	NP_001073999			sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1																		---	---	---	---
SNX29	92017	broad.mit.edu	37	16	12475232	12475233	+	Intron	INS	-	CATC	CATC	rs147339601	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12475232_12475233insCATC	uc002dby.3	+							NM_001080530	NP_001073999			sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1																		---	---	---	---
SNX29	92017	broad.mit.edu	37	16	12503836	12503836	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12503836delT	uc002dby.3	+							NM_001080530	NP_001073999			sorting nexin 29						cell communication		phosphatidylinositol binding			ovary(1)	1																		---	---	---	---
CPPED1	55313	broad.mit.edu	37	16	12840928	12840930	+	Intron	DEL	TAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:12840928_12840930delTAA	uc002dca.3	-						CPPED1_uc002dcb.3_Intron	NM_018340	NP_060810			calcineurin-like phosphoesterase domain								hydrolase activity|metal ion binding				0																		---	---	---	---
SHISA9	729993	broad.mit.edu	37	16	13168526	13168526	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:13168526delT	uc010uyy.1	+							NM_001145204	NP_001138676			shisa homolog 9 isoform 1						regulation of short-term neuronal synaptic plasticity	cell junction|dendritic spine membrane|ionotropic glutamate receptor complex|synapse					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	14006629	14006629	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14006629delA								SHISA9 (672357 upstream) : ERCC4 (7385 downstream)																																			---	---	---	---
ERCC4	2072	broad.mit.edu	37	16	14016110	14016111	+	Intron	DEL	TT	-	-	rs113434368		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14016110_14016111delTT	uc002dce.2	+						ERCC4_uc010bva.2_Intron	NM_005236	NP_005227			excision repair cross-complementing rodent						double-strand break repair via homologous recombination|meiotic mismatch repair|negative regulation of telomere maintenance|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|nucleotide-excision repair, DNA incision, 5'-to lesion|resolution of meiotic recombination intermediates|telomere maintenance via telomere shortening|transcription-coupled nucleotide-excision repair	nuclear chromosome, telomeric region|nucleoplasm|nucleotide-excision repair factor 1 complex	damaged DNA binding|protein C-terminus binding|protein N-terminus binding|single-stranded DNA binding|single-stranded DNA specific endodeoxyribonuclease activity			lung(4)|ovary(3)|skin(2)|pancreas(1)	10								Mis|N|F			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				---	---	---	---
MKL2	57496	broad.mit.edu	37	16	14312561	14312561	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14312561delT	uc010uza.1	+						MKL2_uc002dcg.2_Intron|MKL2_uc002dch.2_Intron|MKL2_uc010uzb.1_Intron	NM_014048	NP_054767			megakaryoblastic leukemia 2 protein						cell differentiation|muscle organ development|positive regulation of striated muscle tissue development|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		identical protein binding|nucleic acid binding|transcription coactivator activity			ovary(3)|kidney(1)|pancreas(1)	5																		---	---	---	---
MKL2	57496	broad.mit.edu	37	16	14317169	14317169	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14317169delC	uc010uza.1	+						MKL2_uc002dcg.2_Intron|MKL2_uc002dch.2_Intron|MKL2_uc010uzb.1_Intron	NM_014048	NP_054767			megakaryoblastic leukemia 2 protein						cell differentiation|muscle organ development|positive regulation of striated muscle tissue development|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		identical protein binding|nucleic acid binding|transcription coactivator activity			ovary(3)|kidney(1)|pancreas(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	14405007	14405010	+	IGR	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14405007_14405010delTTTT								MIR365-1 (1779 upstream) : PARN (124549 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	14416445	14416445	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14416445delA								MIR365-1 (13217 upstream) : PARN (113114 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	15053924	15053924	+	IGR	DEL	T	-	-	rs78217806		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15053924delT								NPIP (7994 upstream) : PDXDC1 (14675 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	15058709	15058709	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15058709delT								NPIP (12779 upstream) : PDXDC1 (9890 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	15061934	15061934	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15061934delA								NPIP (16004 upstream) : PDXDC1 (6665 downstream)																																			---	---	---	---
PDXDC1	23042	broad.mit.edu	37	16	15073155	15073155	+	Intron	DEL	T	-	-	rs112064828		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15073155delT	uc002dda.3	+						PDXDC1_uc010uzl.1_Intron|PDXDC1_uc010uzm.1_Intron|PDXDC1_uc010bvc.1_Intron|PDXDC1_uc002dcz.2_Intron|PDXDC1_uc002ddb.3_Intron|PDXDC1_uc010uzn.1_Intron|PDXDC1_uc002ddc.2_Intron	NM_015027	NP_055842			pyridoxal-dependent decarboxylase domain						carboxylic acid metabolic process		carboxy-lyase activity|protein binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)													---	---	---	---
PDXDC1	23042	broad.mit.edu	37	16	15079956	15079957	+	Intron	DEL	AA	-	-	rs72009445		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15079956_15079957delAA	uc002dda.3	+						PDXDC1_uc010uzl.1_Intron|PDXDC1_uc010uzm.1_Intron|PDXDC1_uc010bvc.1_Intron|PDXDC1_uc002dcz.2_Intron|PDXDC1_uc002ddb.3_Intron|PDXDC1_uc010uzn.1_Intron|PDXDC1_uc002ddc.2_Intron	NM_015027	NP_055842			pyridoxal-dependent decarboxylase domain						carboxylic acid metabolic process		carboxy-lyase activity|protein binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)													---	---	---	---
Unknown	0	broad.mit.edu	37	16	15299832	15299832	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15299832delT								PDXDC1 (66637 upstream) : MPV17L (189779 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	15992055	15992055	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15992055delC								C16orf63 (9608 upstream) : ABCC1 (51379 downstream)																																			---	---	---	---
ABCC1	4363	broad.mit.edu	37	16	16170975	16170976	+	Intron	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16170975_16170976delCT	uc010bvi.2	+						ABCC1_uc010bvj.2_Intron|ABCC1_uc010bvk.2_Intron|ABCC1_uc010bvl.2_Intron|ABCC1_uc010bvm.2_Intron|ABCC1_uc002del.3_Intron	NM_004996	NP_004987			ATP-binding cassette, sub-family C, member 1						hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process|response to drug	Golgi apparatus|integral to plasma membrane|membrane fraction|nucleus	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)	4					Daunorubicin(DB00694)|Glibenclamide(DB01016)|Probenecid(DB01032)|Saquinavir(DB01232)|Sulfinpyrazone(DB01138)													---	---	---	---
ABCC1	4363	broad.mit.edu	37	16	16180249	16180249	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16180249delG	uc010bvi.2	+						ABCC1_uc010bvj.2_Intron|ABCC1_uc010bvk.2_Intron|ABCC1_uc010bvl.2_Intron|ABCC1_uc010bvm.2_Intron|ABCC1_uc002del.3_Intron	NM_004996	NP_004987			ATP-binding cassette, sub-family C, member 1						hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process|response to drug	Golgi apparatus|integral to plasma membrane|membrane fraction|nucleus	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)	4					Daunorubicin(DB00694)|Glibenclamide(DB01016)|Probenecid(DB01032)|Saquinavir(DB01232)|Sulfinpyrazone(DB01138)													---	---	---	---
ABCC6	368	broad.mit.edu	37	16	16271088	16271088	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16271088delT	uc002den.3	-						ABCC6_uc010bvo.2_Intron	NM_001171	NP_001162			ATP-binding cassette, sub-family C, member 6						response to drug|visual perception	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			skin(2)|ovary(1)	3				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	16690613	16690613	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16690613delA								LOC339047 (246176 upstream) : XYLT1 (505570 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	16725090	16725090	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16725090delC								LOC339047 (280653 upstream) : XYLT1 (471093 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	17142371	17142371	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17142371delT								LOC339047 (697934 upstream) : XYLT1 (53812 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	17185703	17185703	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17185703delG								LOC339047 (741266 upstream) : XYLT1 (10480 downstream)																																			---	---	---	---
XYLT1	64131	broad.mit.edu	37	16	17247947	17247948	+	Intron	INS	-	A	A	rs145212515	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17247947_17247948insA	uc002dfa.2	-							NM_022166	NP_071449			xylosyltransferase I						glycosaminoglycan biosynthetic process	endoplasmic reticulum membrane|extracellular region|Golgi membrane|integral to membrane	acetylglucosaminyltransferase activity|protein xylosyltransferase activity			ovary(4)	4																		---	---	---	---
XYLT1	64131	broad.mit.edu	37	16	17306157	17306158	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17306157_17306158insT	uc002dfa.2	-							NM_022166	NP_071449			xylosyltransferase I						glycosaminoglycan biosynthetic process	endoplasmic reticulum membrane|extracellular region|Golgi membrane|integral to membrane	acetylglucosaminyltransferase activity|protein xylosyltransferase activity			ovary(4)	4																		---	---	---	---
XYLT1	64131	broad.mit.edu	37	16	17425363	17425364	+	Intron	INS	-	AT	AT	rs72532618		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17425363_17425364insAT	uc002dfa.2	-							NM_022166	NP_071449			xylosyltransferase I						glycosaminoglycan biosynthetic process	endoplasmic reticulum membrane|extracellular region|Golgi membrane|integral to membrane	acetylglucosaminyltransferase activity|protein xylosyltransferase activity			ovary(4)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	17813446	17813446	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:17813446delA								XYLT1 (248708 upstream) : NOMO2 (697737 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	18045183	18045183	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18045183delA								XYLT1 (480445 upstream) : NOMO2 (466000 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	18941060	18941060	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18941060delA								SMG1 (3334 upstream) : TMC7 (54196 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	19156391	19156391	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19156391delG								ITPRIPL2 (23443 upstream) : SYT17 (23247 downstream)																																			---	---	---	---
TMC5	79838	broad.mit.edu	37	16	19446907	19446908	+	Intron	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19446907_19446908delAC	uc002dgc.3	+						TMC5_uc010vaq.1_Intron|TMC5_uc002dgb.3_Intron|TMC5_uc010var.1_Intron	NM_001105248	NP_001098718			transmembrane channel-like 5 isoform a							integral to membrane				skin(1)	1																		---	---	---	---
TMC5	79838	broad.mit.edu	37	16	19457337	19457337	+	Intron	DEL	A	-	-	rs113174029		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19457337delA	uc002dgc.3	+						TMC5_uc010vaq.1_Intron|TMC5_uc002dgb.3_Intron|TMC5_uc010var.1_Intron	NM_001105248	NP_001098718			transmembrane channel-like 5 isoform a							integral to membrane				skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	19715403	19715403	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19715403delT								C16orf62 (2959 upstream) : C16orf88 (2273 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	20255998	20255998	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20255998delT								GPR139 (170898 upstream) : GP2 (65814 downstream)																																			---	---	---	---
ACSM1	116285	broad.mit.edu	37	16	20648048	20648048	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20648048delG	uc002dhm.1	-						ACSM1_uc002dhn.1_Intron|ACSM1_uc010bwg.1_Intron	NM_052956	NP_443188			acyl-CoA synthetase medium-chain family member						benzoate metabolic process|butyrate metabolic process|energy derivation by oxidation of organic compounds|fatty acid oxidation|xenobiotic metabolic process	mitochondrial matrix	acyl-CoA ligase activity|ATP binding|butyrate-CoA ligase activity|GTP binding|metal ion binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
LOC81691	81691	broad.mit.edu	37	16	20825412	20825415	+	Intron	DEL	TTTT	-	-	rs78714567		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20825412_20825415delTTTT	uc002dhv.2	+						ERI2_uc002dht.3_Intron|LOC81691_uc002dhx.2_Intron|LOC81691_uc002dhw.2_Intron|LOC81691_uc002dhy.3_Intron	NM_030941	NP_112203			exonuclease NEF-sp isoform 1							nucleolus	exonuclease activity|nucleotide binding|RNA binding			ovary(1)|kidney(1)	2																		---	---	---	---
DNAH3	55567	broad.mit.edu	37	16	20954569	20954569	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20954569delT	uc010vbe.1	-						DNAH3_uc010vbd.1_Intron	NM_017539	NP_060009			dynein, axonemal, heavy chain 3						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)														---	---	---	---
DNAH3	55567	broad.mit.edu	37	16	20954720	20954720	+	Intron	DEL	T	-	-	rs78447992		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20954720delT	uc010vbe.1	-						DNAH3_uc010vbd.1_Intron	NM_017539	NP_060009			dynein, axonemal, heavy chain 3						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)														---	---	---	---
DNAH3	55567	broad.mit.edu	37	16	20980749	20980750	+	Intron	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20980749_20980750delTC	uc010vbe.1	-						DNAH3_uc010vbd.1_Intron	NM_017539	NP_060009			dynein, axonemal, heavy chain 3						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)														---	---	---	---
ANKS4B	257629	broad.mit.edu	37	16	21249490	21249491	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21249490_21249491insA	uc010bwp.1	+							NM_145865	NP_665872			harmonin-interacting ankyrin-repeat containing											ovary(2)	2				GBM - Glioblastoma multiforme(48;0.0565)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	21365649	21365649	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21365649delT								NCRNA00169 (35737 upstream) : NPIPL3 (47802 downstream)																																			---	---	---	---
LOC100271836	100271836	broad.mit.edu	37	16	21484708	21484708	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21484708delA	uc002djc.2	-						uc002diq.3_Intron|LOC100271836_uc002dja.2_Intron|LOC100271836_uc002djb.2_Intron					SubName: Full=Putative uncharacterized protein DKFZp547E087;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	21902237	21902240	+	Intron	DEL	AAAA	-	-	rs55836110		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21902237_21902240delAAAA	uc002djs.3	-						uc010vbo.1_Intron|uc002dju.1_5'Flank					Homo sapiens cDNA FLJ45371 fis, clone BRHIP3017855, highly  similar to Homo sapiens nuclear pore complex interacting protein (NPIP).																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	22099357	22099357	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22099357delT								C16orf52 (505 upstream) : VWA3A (4506 downstream)																																			---	---	---	---
VWA3A	146177	broad.mit.edu	37	16	22134675	22134676	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22134675_22134676delAA	uc010vbq.1	+						VWA3A_uc010bxd.2_Intron|VWA3A_uc010bxc.2_Intron	NM_173615	NP_775886			von Willebrand factor A domain containing 3A							extracellular region				skin(1)	1				GBM - Glioblastoma multiforme(48;0.0439)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	22400006	22400006	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22400006delA								CDR2 (14068 upstream) : RRN3P3 (30861 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	22662052	22662054	+	IGR	DEL	AAA	-	-	rs112918197		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22662052_22662054delAAA								LOC653786 (73866 upstream) : HS3ST2 (163806 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	22730475	22730475	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22730475delC								LOC653786 (142289 upstream) : HS3ST2 (95385 downstream)																																			---	---	---	---
HS3ST2	9956	broad.mit.edu	37	16	22862156	22862156	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22862156delA	uc002dli.2	+						HS3ST2_uc002dlj.2_Intron	NM_006043	NP_006034			heparan sulfate D-glucosaminyl							Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine 3-sulfotransferase 2 activity			ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(48;0.0299)														---	---	---	---
COG7	91949	broad.mit.edu	37	16	23404439	23404439	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23404439delA	uc002dlo.2	-							NM_153603	NP_705831			component of oligomeric golgi complex 7						intracellular protein transport|protein glycosylation|protein localization in Golgi apparatus|protein stabilization|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane|Golgi transport complex	protein binding				0				GBM - Glioblastoma multiforme(48;0.0401)														---	---	---	---
COG7	91949	broad.mit.edu	37	16	23417774	23417774	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23417774delA	uc002dlo.2	-							NM_153603	NP_705831			component of oligomeric golgi complex 7						intracellular protein transport|protein glycosylation|protein localization in Golgi apparatus|protein stabilization|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane|Golgi transport complex	protein binding				0				GBM - Glioblastoma multiforme(48;0.0401)														---	---	---	---
CHP2	63928	broad.mit.edu	37	16	23767633	23767633	+	Intron	DEL	G	-	-	rs77005706	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23767633delG	uc002dmb.1	+							NM_022097	NP_071380			hepatocellular carcinoma antigen gene 520								calcium ion binding			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(48;0.0144)														---	---	---	---
PRKCB	5579	broad.mit.edu	37	16	23888308	23888309	+	Intron	INS	-	G	G	rs140697938	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23888308_23888309insG	uc002dmd.2	+						PRKCB_uc002dme.2_Intron	NM_212535	NP_997700			protein kinase C, beta isoform 1						apoptosis|B cell activation|B cell receptor signaling pathway|intracellular signal transduction|lipoprotein transport|platelet activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|synaptic transmission|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|histone binding|histone kinase activity (H3-T6 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|zinc ion binding			ovary(3)|central_nervous_system(3)|lung(2)|large_intestine(1)	9					Vitamin E(DB00163)													---	---	---	---
PRKCB	5579	broad.mit.edu	37	16	23973021	23973022	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23973021_23973022insT	uc002dmd.2	+						PRKCB_uc002dme.2_Intron	NM_212535	NP_997700			protein kinase C, beta isoform 1						apoptosis|B cell activation|B cell receptor signaling pathway|intracellular signal transduction|lipoprotein transport|platelet activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|synaptic transmission|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|histone binding|histone kinase activity (H3-T6 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|zinc ion binding			ovary(3)|central_nervous_system(3)|lung(2)|large_intestine(1)	9					Vitamin E(DB00163)													---	---	---	---
PRKCB	5579	broad.mit.edu	37	16	24001489	24001489	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24001489delT	uc002dmd.2	+						PRKCB_uc002dme.2_Intron	NM_212535	NP_997700			protein kinase C, beta isoform 1						apoptosis|B cell activation|B cell receptor signaling pathway|intracellular signal transduction|lipoprotein transport|platelet activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|synaptic transmission|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|histone binding|histone kinase activity (H3-T6 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|zinc ion binding			ovary(3)|central_nervous_system(3)|lung(2)|large_intestine(1)	9					Vitamin E(DB00163)													---	---	---	---
PRKCB	5579	broad.mit.edu	37	16	24040914	24040923	+	Intron	DEL	CAGACTAATA	-	-	rs140560821		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24040914_24040923delCAGACTAATA	uc002dmd.2	+						PRKCB_uc002dme.2_Intron	NM_212535	NP_997700			protein kinase C, beta isoform 1						apoptosis|B cell activation|B cell receptor signaling pathway|intracellular signal transduction|lipoprotein transport|platelet activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|synaptic transmission|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|histone binding|histone kinase activity (H3-T6 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|zinc ion binding			ovary(3)|central_nervous_system(3)|lung(2)|large_intestine(1)	9					Vitamin E(DB00163)													---	---	---	---
PRKCB	5579	broad.mit.edu	37	16	24219934	24219934	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24219934delT	uc002dmd.2	+						PRKCB_uc002dme.2_Intron	NM_212535	NP_997700			protein kinase C, beta isoform 1						apoptosis|B cell activation|B cell receptor signaling pathway|intracellular signal transduction|lipoprotein transport|platelet activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|synaptic transmission|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|histone binding|histone kinase activity (H3-T6 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|zinc ion binding			ovary(3)|central_nervous_system(3)|lung(2)|large_intestine(1)	9					Vitamin E(DB00163)													---	---	---	---
Unknown	0	broad.mit.edu	37	16	24232607	24232607	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24232607delT								PRKCB (677 upstream) : CACNG3 (34269 downstream)																																			---	---	---	---
CACNG3	10368	broad.mit.edu	37	16	24350679	24350679	+	Intron	DEL	C	-	-	rs74421888		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24350679delC	uc002dmf.2	+							NM_006539	NP_006530			voltage-dependent calcium channel gamma-3						regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|endocytic vesicle membrane|voltage-gated calcium channel complex	voltage-gated calcium channel activity				0				GBM - Glioblastoma multiforme(48;0.0809)														---	---	---	---
SLC5A11	115584	broad.mit.edu	37	16	24874160	24874160	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24874160delA	uc002dmu.2	+						SLC5A11_uc002dms.2_Intron|SLC5A11_uc010vcd.1_Intron|SLC5A11_uc002dmt.2_Intron|SLC5A11_uc010vce.1_Intron|SLC5A11_uc010bxt.2_Intron	NM_052944	NP_443176			solute carrier family 5 (sodium/glucose						apoptosis|carbohydrate transport|sodium ion transport	integral to membrane|plasma membrane	polyol transmembrane transporter activity|symporter activity			ovary(2)	2				GBM - Glioblastoma multiforme(48;0.0365)														---	---	---	---
ARHGAP17	55114	broad.mit.edu	37	16	24985910	24985910	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24985910delT	uc002dnb.2	-						ARHGAP17_uc002dnc.2_Intron|ARHGAP17_uc010vcf.1_Intron|ARHGAP17_uc002dng.1_Intron	NM_001006634	NP_001006635			nadrin isoform 1						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|tight junction	GTPase activator activity|SH3 domain binding				0				GBM - Glioblastoma multiforme(48;0.0407)														---	---	---	---
LCMT1	51451	broad.mit.edu	37	16	25151697	25151697	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25151697delT	uc002dnx.1	+						LCMT1_uc002dny.1_Intron|LCMT1_uc002dnz.1_Intron|LCMT1_uc002doa.1_Intron	NM_016309	NP_057393			leucine carboxyl methyltransferase 1 isoform a								protein binding|protein C-terminal carboxyl O-methyltransferase activity|S-adenosylmethionine-dependent methyltransferase activity				0				GBM - Glioblastoma multiforme(48;0.0336)	L-Leucine(DB00149)													---	---	---	---
Unknown	0	broad.mit.edu	37	16	25418365	25418365	+	IGR	DEL	T	-	-	rs67584508		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25418365delT								ZKSCAN2 (149510 upstream) : HS3ST4 (284982 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	25535327	25535327	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25535327delT								ZKSCAN2 (266472 upstream) : HS3ST4 (168020 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	25639530	25639530	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25639530delT								ZKSCAN2 (370675 upstream) : HS3ST4 (63817 downstream)																																			---	---	---	---
HS3ST4	9951	broad.mit.edu	37	16	25799844	25799844	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25799844delT	uc002dof.2	+							NM_006040	NP_006031			heparan sulfate D-glucosaminyl						heparan sulfate proteoglycan metabolic process	extracellular region|Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity			large_intestine(1)|breast(1)	2				GBM - Glioblastoma multiforme(48;0.0988)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	26272081	26272081	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26272081delA								HS3ST4 (123073 upstream) : C16orf82 (806138 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	26537211	26537214	+	IGR	DEL	ACTC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26537211_26537214delACTC								HS3ST4 (388203 upstream) : C16orf82 (541005 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	26711423	26711424	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26711423_26711424insA								HS3ST4 (562415 upstream) : C16orf82 (366795 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	26735917	26735917	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26735917delT								HS3ST4 (586909 upstream) : C16orf82 (342302 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	26770435	26770435	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26770435delT								HS3ST4 (621427 upstream) : C16orf82 (307784 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	27204467	27204468	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27204467_27204468delAA								C16orf82 (123981 upstream) : JMJD5 (10339 downstream)																																			---	---	---	---
JMJD5	79831	broad.mit.edu	37	16	27230013	27230013	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27230013delA	uc002doh.2	+						JMJD5_uc010vcn.1_Intron|JMJD5_uc010bxw.2_Intron|JMJD5_uc010bxx.2_Intron	NM_024773	NP_079049			jumonji domain containing 5 isoform 2						G2/M transition of mitotic cell cycle|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	chromatin binding|histone demethylase activity (H3-K36 specific)|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			ovary(2)|upper_aerodigestive_tract(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	27315288	27315291	+	IGR	DEL	TCCA	-	-	rs139616028		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27315288_27315291delTCCA								NSMCE1 (35175 upstream) : IL4R (9960 downstream)																																			---	---	---	---
GTF3C1	2975	broad.mit.edu	37	16	27509762	27509762	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27509762delT	uc002dov.1	-						GTF3C1_uc002dou.2_Intron	NM_001520	NP_001511			general transcription factor IIIC, polypeptide							transcription factor TFIIIC complex	DNA binding|protein binding			ovary(2)|pancreas(1)|breast(1)|skin(1)	5																		---	---	---	---
KIAA0556	23247	broad.mit.edu	37	16	27627394	27627394	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27627394delA	uc002dow.2	+							NM_015202	NP_056017			hypothetical protein LOC23247											ovary(4)|large_intestine(2)|upper_aerodigestive_tract(1)|skin(1)	8																		---	---	---	---
KIAA0556	23247	broad.mit.edu	37	16	27688009	27688010	+	Intron	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27688009_27688010delTG	uc002dow.2	+						KIAA0556_uc002dox.1_Intron	NM_015202	NP_056017			hypothetical protein LOC23247											ovary(4)|large_intestine(2)|upper_aerodigestive_tract(1)|skin(1)	8																		---	---	---	---
GSG1L	146395	broad.mit.edu	37	16	27846906	27846906	+	Intron	DEL	C	-	-	rs772957	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27846906delC	uc002doz.2	-						GSG1L_uc010bya.1_Intron|GSG1L_uc010bxz.1_Intron|GSG1L_uc002doy.2_Intron	NM_001109763	NP_001103233			GSG1-like isoform 1							integral to membrane				ovary(1)	1																		---	---	---	---
GSG1L	146395	broad.mit.edu	37	16	27862131	27862132	+	Intron	DEL	TA	-	-	rs59567686	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27862131_27862132delTA	uc002doz.2	-						GSG1L_uc010bya.1_Intron|GSG1L_uc010bxz.1_Intron|GSG1L_uc002doy.2_Intron	NM_001109763	NP_001103233			GSG1-like isoform 1							integral to membrane				ovary(1)	1																		---	---	---	---
GSG1L	146395	broad.mit.edu	37	16	27865592	27865592	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27865592delG	uc002doz.2	-						GSG1L_uc010bya.1_Intron|GSG1L_uc010bxz.1_Intron|GSG1L_uc002doy.2_Intron	NM_001109763	NP_001103233			GSG1-like isoform 1							integral to membrane				ovary(1)	1																		---	---	---	---
GSG1L	146395	broad.mit.edu	37	16	27909996	27909999	+	Intron	DEL	TCTC	-	-	rs71389507		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27909996_27909999delTCTC	uc002doz.2	-						GSG1L_uc010bya.1_Intron	NM_001109763	NP_001103233			GSG1-like isoform 1							integral to membrane				ovary(1)	1																		---	---	---	---
XPO6	23214	broad.mit.edu	37	16	28124902	28124902	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28124902delA	uc002dpa.1	-						XPO6_uc002dpb.1_Intron|XPO6_uc010vcp.1_Intron	NM_015171	NP_055986			exportin 6						protein export from nucleus		protein binding|protein transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
XPO6	23214	broad.mit.edu	37	16	28192840	28192843	+	Intron	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28192840_28192843delTTTT	uc002dpa.1	-						XPO6_uc002dpb.1_Intron|XPO6_uc010vcp.1_Intron	NM_015171	NP_055986			exportin 6						protein export from nucleus		protein binding|protein transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
RABEP2	79874	broad.mit.edu	37	16	28933886	28933886	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28933886delA	uc002drq.2	-						uc010vct.1_Intron|RABEP2_uc010vdf.1_Intron|RABEP2_uc010byn.2_Intron|RABEP2_uc002drr.2_Intron	NM_024816	NP_079092			rabaptin, RAB GTPase binding effector protein 2						endocytosis|protein transport	early endosome	growth factor activity|GTPase activator activity			ovary(1)|breast(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	29359269	29359269	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29359269delA	uc010vct.1	-						RUNDC2C_uc010bys.1_Intron					RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor;																														---	---	---	---
BOLA2	552900	broad.mit.edu	37	16	29636194	29636194	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29636194delA	uc010bzb.1	-						uc002dtf.2_Intron					SubName: Full=Putative uncharacterized protein ENSP00000369970; Flags: Fragment;												0																		---	---	---	---
TMEM219	124446	broad.mit.edu	37	16	29981007	29981007	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29981007delA	uc002duw.2	+						uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|TMEM219_uc002duy.2_Intron|TMEM219_uc010bzk.1_Intron|TMEM219_uc002duz.2_Intron|TMEM219_uc010bzl.1_Intron	NM_194280	NP_919256			transmembrane protein 219							integral to membrane					0																		---	---	---	---
INO80E	283899	broad.mit.edu	37	16	30012043	30012043	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30012043delC	uc002dvg.1	+						uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|INO80E_uc002dvh.1_Intron|INO80E_uc002dvi.1_Intron|INO80E_uc002dvj.1_Intron|INO80E_uc002dvk.1_Intron	NM_173618	NP_775889			INO80 complex subunit E						DNA recombination|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	Ino80 complex				skin(1)	1																		---	---	---	---
LOC595101	595101	broad.mit.edu	37	16	30291742	30291742	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30291742delA	uc002dxp.1	-							NR_002453				Homo sapiens cDNA FLJ39663 fis, clone SMINT2007187.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	30559135	30559137	+	IGR	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30559135_30559137delAAA								ZNF768 (12916 upstream) : ZNF764 (5949 downstream)																																			---	---	---	---
ZNF764	92595	broad.mit.edu	37	16	30568626	30568626	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30568626delA	uc002dyq.2	-						ZNF764_uc002dyr.1_Intron	NM_033410	NP_219363			zinc finger protein 764						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
ZNF689	115509	broad.mit.edu	37	16	30617821	30617821	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30617821delT	uc002dyx.2	-						ZNF689_uc010bzy.2_Intron	NM_138447	NP_612456			zinc finger protein HIT-39						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0			Colorectal(24;0.198)															---	---	---	---
RNF40	9810	broad.mit.edu	37	16	30775886	30775886	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30775886delG	uc002dzq.2	+						C16orf93_uc002dzm.2_5'Flank|C16orf93_uc002dzn.2_5'Flank|C16orf93_uc002dzo.2_5'Flank|C16orf93_uc002dzp.2_5'Flank|RNF40_uc010caa.2_Intron|RNF40_uc010cab.2_Intron|RNF40_uc010vfa.1_Intron|RNF40_uc002dzr.2_Intron|RNF40_uc010vfb.1_Intron	NM_014771	NP_055586			ring finger protein 40						histone H2B ubiquitination|histone monoubiquitination|ubiquitin-dependent protein catabolic process	nucleus|synaptosome|ubiquitin ligase complex	protein homodimerization activity|ubiquitin protein ligase binding|zinc ion binding			central_nervous_system(1)	1			Colorectal(24;0.198)															---	---	---	---
BCL7C	9274	broad.mit.edu	37	16	30894680	30894680	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30894680delT	uc002dzt.1	-						uc002dzu.2_Intron	NM_004765	NP_004756			B-cell CLL/lymphoma 7C						apoptosis						0			Colorectal(24;0.198)															---	---	---	---
ORAI3	93129	broad.mit.edu	37	16	30960896	30960896	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30960896delG	uc002eac.2	+							NM_152288	NP_689501			ORAI calcium release-activated calcium modulator							integral to membrane	protein binding				0																		---	---	---	---
PRSS53	339105	broad.mit.edu	37	16	31106666	31106666	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31106666delA	uc002ear.2	-						VKORC1_uc002eas.2_5'Flank|VKORC1_uc002eat.2_5'Flank|VKORC1_uc002eau.2_5'Flank	NM_001039503	NP_001034592			polyserase 3 precursor						proteolysis	extracellular region	serine-type endopeptidase activity				0																		---	---	---	---
PRSS36	146547	broad.mit.edu	37	16	31151942	31151942	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31151942delG	uc002ebd.2	-	13	2097	c.2038delC	c.(2038-2040)CTGfs	p.L680fs	PRSS36_uc010vff.1_Frame_Shift_Del_p.L455fs|PRSS36_uc010vfg.1_Frame_Shift_Del_p.L675fs|PRSS36_uc010vfh.1_Intron	NM_173502	NP_775773	Q5K4E3	POLS2_HUMAN	protease, serine, 36 precursor	680	Peptidase S1 3.				proteolysis	cytoplasm|proteinaceous extracellular matrix	serine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
FUS	2521	broad.mit.edu	37	16	31188818	31188818	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31188818delT	uc002ebf.2	+						FUS_uc002ebe.1_5'Flank|FUS_uc002ebh.2_5'Flank|FUS_uc002ebg.2_5'Flank|FUS_uc002ebi.2_5'Flank|FUS_uc002ebj.2_5'Flank|FUS_uc010vfi.1_5'Flank	NM_004960	NP_004951			fusion (involved in t(12;16) in malignant						cell death|nuclear mRNA splicing, via spliceosome	nucleoplasm	DNA binding|nucleotide binding|protein binding|RNA binding|zinc ion binding		FUS/DDIT3(623)|FUS/ERG(163)|FUS/CREB3L2(158)|FUS/CREB3L1(6)|FUS/ATF1(4)|FUS/FEV(2)	soft_tissue(791)|haematopoietic_and_lymphoid_tissue(153)|bone(12)|breast(2)	958		Renal(780;0.000219)|Breast(268;0.00957)|Hepatocellular(780;0.121)		GBM - Glioblastoma multiforme(240;2.31e-05)|Kidney(780;0.000209)				T	DDIT3|ERG|FEV|ATF1|CREB3L2|CREB3L1	liposarcoma|AML|Ewing sarcoma|angiomatoid fibrous histiocytoma|fibromyxoid sarcoma								---	---	---	---
Unknown	0	broad.mit.edu	37	16	31261613	31261613	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31261613delT								TRIM72 (25103 upstream) : ITGAM (9675 downstream)																																			---	---	---	---
ITGAX	3687	broad.mit.edu	37	16	31373986	31373986	+	Frame_Shift_Del	DEL	C	-	-	rs150562711		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31373986delC	uc002ebu.1	+	12	1338	c.1271delC	c.(1270-1272)GCCfs	p.A424fs	ITGAX_uc002ebt.2_Frame_Shift_Del_p.A424fs|ITGAX_uc010vfk.1_Frame_Shift_Del_p.A74fs	NM_000887	NP_000878	P20702	ITAX_HUMAN	integrin alpha X precursor	424	FG-GAP 4.|Extracellular (Potential).				blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration|organ morphogenesis	integrin complex	protein binding|receptor activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	31588752	31588752	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31588752delA								CSDAP1 (7907 upstream) : KIAA0664P3 (123182 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	31598776	31598776	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31598776delT								CSDAP1 (17931 upstream) : KIAA0664P3 (113158 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	31698052	31698052	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31698052delT								CSDAP1 (117207 upstream) : KIAA0664P3 (13882 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32279740	32279740	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32279740delT								HERC2P4 (115866 upstream) : TP53TG3B (405101 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32283768	32283768	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32283768delA								HERC2P4 (119894 upstream) : TP53TG3B (401073 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32327287	32327288	+	IGR	INS	-	A	A	rs144798927		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32327287_32327288insA								HERC2P4 (163413 upstream) : TP53TG3B (357553 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32522596	32522596	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32522596delA								HERC2P4 (358722 upstream) : TP53TG3B (162245 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32526249	32526250	+	IGR	INS	-	A	A	rs148676631		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32526249_32526250insA								HERC2P4 (362375 upstream) : TP53TG3B (158591 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32546636	32546637	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32546636_32546637insA								HERC2P4 (382762 upstream) : TP53TG3B (138204 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32548384	32548384	+	IGR	DEL	G	-	-	rs112617757		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32548384delG								HERC2P4 (384510 upstream) : TP53TG3B (136457 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32831165	32831165	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32831165delA								TP53TG3B (142287 upstream) : SLC6A10P (57632 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	32841066	32841066	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:32841066delC								TP53TG3B (152188 upstream) : SLC6A10P (47731 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33056628	33056629	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33056628_33056629insA								SLC6A10P (160165 upstream) : MIR1826 (908879 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33420314	33420314	+	IGR	DEL	G	-	-	rs3933842	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33420314delG								SLC6A10P (523851 upstream) : MIR1826 (545194 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33441507	33441507	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33441507delA								SLC6A10P (545044 upstream) : MIR1826 (524001 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33599448	33599448	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33599448delA								SLC6A10P (702985 upstream) : MIR1826 (366060 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33866816	33866817	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33866816_33866817insT								SLC6A10P (970353 upstream) : MIR1826 (98691 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	33993687	33993687	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:33993687delG								MIR1826 (28095 upstream) : UBE2MP1 (410115 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	34468013	34468013	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34468013delT								UBE2MP1 (63251 upstream) : LOC283914 (129774 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	34686678	34686678	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34686678delT								LOC283914 (60594 upstream) : LOC146481 (25107 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	34868297	34868298	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:34868297_34868298insT								LOC146481 (153330 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	35151053	35151053	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:35151053delT								LOC146481 (436086 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	35184833	35184834	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:35184833_35184834delTG								LOC146481 (469866 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	46441770	46441771	+	IGR	INS	-	TGGAATCAAG	TGGAATCAAG			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46441770_46441771insTGGAATCAAG								None (None upstream) : ANKRD26P1 (61478 downstream)																																			---	---	---	---
SHCBP1	79801	broad.mit.edu	37	16	46644385	46644385	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46644385delT	uc002eec.3	-							NM_024745	NP_079021			SHC SH2-domain binding protein 1											ovary(1)|breast(1)	2		all_cancers(37;0.00404)|all_epithelial(9;0.00527)|all_lung(18;0.0413)|Lung NSC(13;0.213)																---	---	---	---
SHCBP1	79801	broad.mit.edu	37	16	46652089	46652090	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46652089_46652090delAA	uc002eec.3	-							NM_024745	NP_079021			SHC SH2-domain binding protein 1											ovary(1)|breast(1)	2		all_cancers(37;0.00404)|all_epithelial(9;0.00527)|all_lung(18;0.0413)|Lung NSC(13;0.213)																---	---	---	---
SHCBP1	79801	broad.mit.edu	37	16	46652287	46652289	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46652287_46652289delAAA	uc002eec.3	-							NM_024745	NP_079021			SHC SH2-domain binding protein 1											ovary(1)|breast(1)	2		all_cancers(37;0.00404)|all_epithelial(9;0.00527)|all_lung(18;0.0413)|Lung NSC(13;0.213)																---	---	---	---
VPS35	55737	broad.mit.edu	37	16	46717645	46717645	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46717645delT	uc002eef.3	-						VPS35_uc002eee.2_Intron	NM_018206	NP_060676			vacuolar protein sorting 35						protein transport|retrograde transport, endosome to Golgi	cytosol|endosome|membrane	protein binding				0		all_cancers(37;7.65e-05)|all_epithelial(9;0.000154)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)																---	---	---	---
MYLK3	91807	broad.mit.edu	37	16	46787660	46787660	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46787660delA	uc010vge.1	-											SubName: Full=cDNA FLJ50066, highly similar to Homo sapiens cardiac-MyBP-C associated Ca/CaM kinase (MLCK), mRNA;						cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis	cytosol	ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity			stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1)	7		all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	46826009	46826009	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46826009delA								MYLK3 (28851 upstream) : C16orf87 (9950 downstream)																																			---	---	---	---
GPT2	84706	broad.mit.edu	37	16	46915793	46915793	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46915793delA	uc002eel.2	+							NM_133443	NP_597700			glutamic pyruvate transaminase 2 isoform 1						2-oxoglutarate metabolic process|cellular amino acid biosynthetic process|L-alanine metabolic process	mitochondrial matrix	L-alanine:2-oxoglutarate aminotransferase activity|pyridoxal phosphate binding			ovary(1)|skin(1)	2		all_cancers(37;0.0276)|all_epithelial(9;0.0498)|all_lung(18;0.0522)			L-Alanine(DB00160)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)													---	---	---	---
Unknown	0	broad.mit.edu	37	16	46974659	46974661	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:46974659_46974661delTTT								GPT2 (9459 upstream) : DNAJA2 (14613 downstream)																																			---	---	---	---
NETO2	81831	broad.mit.edu	37	16	47122024	47122025	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47122024_47122025delTT	uc002eer.1	-						NETO2_uc002eeq.1_Intron|NETO2_uc010vgf.1_Intron|NETO2_uc002ees.1_Intron	NM_018092	NP_060562			neuropilin- and tolloid-like protein 2							integral to membrane	receptor activity				0		all_cancers(37;0.00114)|all_lung(18;0.00432)|Lung NSC(13;0.0384)|Breast(268;0.174)													HNSCC(25;0.065)			---	---	---	---
ITFG1	81533	broad.mit.edu	37	16	47485385	47485385	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47485385delA	uc002eet.2	-						ITFG1_uc010vgh.1_Intron|ITFG1_uc010cbf.1_Intron	NM_030790	NP_110417			integrin alpha FG-GAP repeat containing 1							extracellular region|integral to membrane				ovary(1)|central_nervous_system(1)	2		all_cancers(37;0.0613)|all_lung(18;0.0543)|Lung NSC(13;0.227)																---	---	---	---
PHKB	5257	broad.mit.edu	37	16	47672757	47672758	+	Intron	INS	-	GT	GT	rs142809009	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47672757_47672758insGT	uc002eev.3	+						PHKB_uc002eeu.3_Intron	NM_000293	NP_000284			phosphorylase kinase, beta isoform a						glucose metabolic process|glycogen catabolic process	cytosol|plasma membrane	calmodulin binding|glucan 1,4-alpha-glucosidase activity			ovary(1)|large_intestine(1)|breast(1)	3		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	47989871	47989871	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47989871delT								PHKB (254438 upstream) : ABCC12 (127013 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	47992802	47992803	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:47992802_47992803delTT								PHKB (257369 upstream) : ABCC12 (124081 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	48009325	48009331	+	IGR	DEL	AAAAAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48009325_48009331delAAAAAAA								PHKB (273892 upstream) : ABCC12 (107553 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	48072341	48072341	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48072341delA								PHKB (336908 upstream) : ABCC12 (44543 downstream)																																			---	---	---	---
SIAH1	6477	broad.mit.edu	37	16	48442400	48442400	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48442400delC	uc002efl.2	-											Homo sapiens SIAH1 mRNA for seven in absentia homolog 1 isoform a, complete cds, clone: FLJ08065AAAN.						axon guidance|cell cycle|neuron apoptosis|proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|spermatogenesis	beta-catenin destruction complex|cytosol|nucleus	protein C-terminus binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1		all_cancers(37;0.157)|all_lung(18;0.11)|Breast(268;0.238)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	48677191	48677191	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48677191delT								N4BP1 (33071 upstream) : CBLN1 (635020 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	48765887	48765887	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48765887delA								N4BP1 (121767 upstream) : CBLN1 (546324 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	49497331	49497331	+	IGR	DEL	A	-	-	rs147042866		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49497331delA								C16orf78 (64014 upstream) : ZNF423 (27191 downstream)																																			---	---	---	---
ZNF423	23090	broad.mit.edu	37	16	49765035	49765035	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49765035delT	uc002efs.2	-							NM_015069	NP_055884			zinc finger protein 423						cell differentiation|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(1)|lung(1)|kidney(1)|pancreas(1)	4		all_cancers(37;0.0155)																---	---	---	---
ZNF423	23090	broad.mit.edu	37	16	49801493	49801493	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49801493delA	uc002efs.2	-							NM_015069	NP_055884			zinc finger protein 423						cell differentiation|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(1)|lung(1)|kidney(1)|pancreas(1)	4		all_cancers(37;0.0155)																---	---	---	---
ZNF423	23090	broad.mit.edu	37	16	49804485	49804485	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49804485delC	uc002efs.2	-							NM_015069	NP_055884			zinc finger protein 423						cell differentiation|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(1)|lung(1)|kidney(1)|pancreas(1)	4		all_cancers(37;0.0155)																---	---	---	---
PAPD5	64282	broad.mit.edu	37	16	50249543	50249543	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50249543delA	uc010vgo.1	+						PAPD5_uc010cbi.2_Intron|PAPD5_uc002efz.2_Intron|PAPD5_uc002ega.2_Intron	NM_001040284	NP_001035374			PAP associated domain containing 5 isoform a						cell division|DNA replication|histone mRNA catabolic process|mitosis	cytoplasm|nucleus	DNA binding|DNA-directed DNA polymerase activity|metal ion binding				0		all_cancers(37;0.0452)		BRCA - Breast invasive adenocarcinoma(181;0.0843)|GBM - Glioblastoma multiforme(240;0.231)														---	---	---	---
PAPD5	64282	broad.mit.edu	37	16	50263428	50263428	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50263428delA	uc010vgo.1	+	13					PAPD5_uc010cbi.2_Intron|PAPD5_uc002efz.2_3'UTR|PAPD5_uc002ega.2_3'UTR	NM_001040284	NP_001035374			PAP associated domain containing 5 isoform a						cell division|DNA replication|histone mRNA catabolic process|mitosis	cytoplasm|nucleus	DNA binding|DNA-directed DNA polymerase activity|metal ion binding				0		all_cancers(37;0.0452)		BRCA - Breast invasive adenocarcinoma(181;0.0843)|GBM - Glioblastoma multiforme(240;0.231)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	50466577	50466578	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50466577_50466578insT								BRD7 (63748 upstream) : NKD1 (115663 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	50692826	50692826	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50692826delA								NKD1 (24185 upstream) : SNX20 (7385 downstream)																																			---	---	---	---
SNX20	124460	broad.mit.edu	37	16	50707236	50707236	+	3'UTR	DEL	A	-	-	rs75121949	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50707236delA	uc002egk.2	-	4					SNX20_uc010vgp.1_Intron|SNX20_uc002egi.3_Intron	NM_182854	NP_878274			sorting nexin 20 isoform 1						cell communication|protein transport	endosome membrane|nucleus|plasma membrane	phosphatidylinositol binding|protein binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	50862395	50862396	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50862395_50862396insT								CYLD (26549 upstream) : SALL1 (307490 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	51036851	51036857	+	IGR	DEL	AAAAAAA	-	-	rs35821164		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51036851_51036857delAAAAAAA								CYLD (201005 upstream) : SALL1 (133029 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	51534873	51534874	+	IGR	DEL	AT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:51534873_51534874delAT								SALL1 (349690 upstream) : TOX3 (937044 downstream)																																			---	---	---	---
TOX3	27324	broad.mit.edu	37	16	52478412	52478415	+	Intron	DEL	CACA	-	-	rs66485654		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:52478412_52478415delCACA	uc002egw.2	-						TOX3_uc010vgt.1_Intron|TOX3_uc010vgu.1_Intron	NM_001080430	NP_001073899			TOX high mobility group box family member 3						apoptosis|negative regulation of neuron apoptosis|positive regulation of anti-apoptosis|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	chromatin binding|estrogen response element binding|phosphoprotein binding|protein homodimerization activity				0																		---	---	---	---
CHD9	80205	broad.mit.edu	37	16	53342553	53342553	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53342553delT	uc002ehb.2	+						CHD9_uc002egy.2_Intron|CHD9_uc002ehc.2_Intron|CHD9_uc002ehf.2_Intron|CHD9_uc010cbw.2_Intron|CHD9_uc002ehg.1_Intron	NM_025134	NP_079410			chromodomain helicase DNA binding protein 9						cellular lipid metabolic process|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleoplasm	ATP binding|DNA binding|helicase activity|protein binding			lung(2)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|kidney(1)	7		all_cancers(37;0.0212)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	53368579	53368579	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53368579delA								CHD9 (7166 upstream) : RBL2 (99772 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	53411374	53411375	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53411374_53411375insT								CHD9 (49961 upstream) : RBL2 (56976 downstream)																																			---	---	---	---
RBL2	5934	broad.mit.edu	37	16	53487750	53487750	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53487750delT	uc002ehi.3	+						RBL2_uc010vgv.1_Intron|RBL2_uc002ehj.2_Intron|RBL2_uc010vgw.1_Intron	NM_005611	NP_005602			retinoblastoma-like 2 (p130)						cell cycle|chromatin modification|regulation of cell cycle|regulation of lipid kinase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding			ovary(2)|lung(2)|upper_aerodigestive_tract(1)	5																		---	---	---	---
RBL2	5934	broad.mit.edu	37	16	53515565	53515566	+	Intron	DEL	TT	-	-	rs72027669		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53515565_53515566delTT	uc002ehi.3	+						RBL2_uc002ehj.2_Intron|RBL2_uc010vgw.1_Intron	NM_005611	NP_005602			retinoblastoma-like 2 (p130)						cell cycle|chromatin modification|regulation of cell cycle|regulation of lipid kinase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding			ovary(2)|lung(2)|upper_aerodigestive_tract(1)	5																		---	---	---	---
FTO	79068	broad.mit.edu	37	16	53876405	53876406	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53876405_53876406insT	uc002ehr.2	+						FTO_uc010vha.1_Intron	NM_001080432	NP_001073901			fat mass and obesity associated						DNA dealkylation involved in DNA repair|oxidative single-stranded DNA demethylation|oxidative single-stranded RNA demethylation|RNA repair	nucleus	DNA-N1-methyladenine dioxygenase activity|ferrous iron binding|oxidative DNA demethylase activity|oxidative RNA demethylase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0																		---	---	---	---
FTO	79068	broad.mit.edu	37	16	53887220	53887220	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53887220delA	uc002ehr.2	+						FTO_uc010vha.1_Intron	NM_001080432	NP_001073901			fat mass and obesity associated						DNA dealkylation involved in DNA repair|oxidative single-stranded DNA demethylation|oxidative single-stranded RNA demethylation|RNA repair	nucleus	DNA-N1-methyladenine dioxygenase activity|ferrous iron binding|oxidative DNA demethylase activity|oxidative RNA demethylase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0																		---	---	---	---
FTO	79068	broad.mit.edu	37	16	53896976	53896976	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:53896976delA	uc002ehr.2	+						FTO_uc010vha.1_Intron	NM_001080432	NP_001073901			fat mass and obesity associated						DNA dealkylation involved in DNA repair|oxidative single-stranded DNA demethylation|oxidative single-stranded RNA demethylation|RNA repair	nucleus	DNA-N1-methyladenine dioxygenase activity|ferrous iron binding|oxidative DNA demethylase activity|oxidative RNA demethylase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	54157216	54157217	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54157216_54157217delTT								FTO (8838 upstream) : IRX3 (159995 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	54719620	54719622	+	IGR	DEL	CTC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54719620_54719622delCTC								IRX3 (399242 upstream) : IRX5 (245489 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	54913260	54913261	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54913260_54913261delAA								IRX3 (592882 upstream) : IRX5 (51850 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	55123107	55123107	+	IGR	DEL	C	-	-	rs57373911		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55123107delC								IRX5 (154714 upstream) : IRX6 (235364 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	55455663	55455663	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55455663delC								IRX6 (90992 upstream) : MMP2 (57418 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	55681358	55681359	+	IGR	DEL	GA	-	-	rs118144951	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55681358_55681359delGA								LPCAT2 (60777 upstream) : SLC6A2 (8663 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	55832336	55832336	+	IGR	DEL	G	-	-	rs71149632		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55832336delG								CES4 (23512 upstream) : CES1 (4430 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	56036394	56036394	+	IGR	DEL	A	-	-	rs137929028		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56036394delA								CES7 (77022 upstream) : LOC283856 (90505 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	56082046	56082047	+	IGR	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56082046_56082047delCT								CES7 (122674 upstream) : LOC283856 (44852 downstream)																																			---	---	---	---
GNAO1	2775	broad.mit.edu	37	16	56322940	56322940	+	Intron	DEL	A	-	-	rs111415218		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56322940delA	uc002eit.3	+						GNAO1_uc002eiu.3_Intron	NM_138736	NP_620073			guanine nucleotide binding protein, alpha						dopamine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|muscle contraction	heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|GTP binding|GTPase activity|metabotropic serotonin receptor binding|signal transducer activity			lung(1)|breast(1)	2		all_neural(199;0.159)																---	---	---	---
OGFOD1	55239	broad.mit.edu	37	16	56492433	56492433	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56492433delT	uc002ejb.2	+						OGFOD1_uc002ejc.2_Intron	NM_018233	NP_060703			2-oxoglutarate and iron-dependent oxygenase								iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			skin(1)	1					Vitamin C(DB00126)													---	---	---	---
Unknown	0	broad.mit.edu	37	16	56743379	56743381	+	IGR	DEL	AGG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56743379_56743381delAGG								MT1X (25272 upstream) : NUP93 (20636 downstream)																																			---	---	---	---
SLC12A3	6559	broad.mit.edu	37	16	56904753	56904753	+	Intron	DEL	T	-	-	rs71882529		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56904753delT	uc010ccm.2	+						SLC12A3_uc002ekd.3_Intron|SLC12A3_uc010ccn.2_Intron	NM_001126108	NP_001119580			solute carrier family 12, member 3 isoform 3						sodium ion transmembrane transport	apical plasma membrane|integral to plasma membrane|membrane fraction	sodium:chloride symporter activity			ovary(2)|breast(1)	3					Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Metolazone(DB00524)|Polythiazide(DB01324)|Quinethazone(DB01325)													---	---	---	---
NLRC5	84166	broad.mit.edu	37	16	57038083	57038083	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57038083delG	uc002ekk.1	+							NM_032206	NP_115582			nucleotide-binding oligomerization domains 27						defense response to virus|innate immune response|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|negative regulation of type I interferon-mediated signaling pathway|positive regulation of interferon-gamma-mediated signaling pathway|positive regulation of MHC class I biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of type I interferon-mediated signaling pathway|regulation of kinase activity	cytosol|nucleus	ATP binding|protein binding|RNA polymerase II core promoter sequence-specific DNA binding			ovary(4)|skin(2)|breast(1)	7		all_neural(199;0.225)																---	---	---	---
NLRC5	84166	broad.mit.edu	37	16	57091977	57091978	+	Frame_Shift_Del	DEL	TC	-	-	rs7206703	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57091977_57091978delTC	uc002ekk.1	+	28	3972_3973	c.3747_3748delTC	c.(3745-3750)GATCTCfs	p.D1249fs	NLRC5_uc002ekn.2_Intron|NLRC5_uc002ekl.2_Frame_Shift_Del_p.D1053fs|NLRC5_uc002ekm.2_Frame_Shift_Del_p.D1023fs|NLRC5_uc010ccr.1_RNA|NLRC5_uc010ccs.1_RNA|NLRC5_uc002eko.1_RNA|NLRC5_uc002ekp.1_Frame_Shift_Del_p.D164fs|NLRC5_uc002ekq.1_5'UTR|NLRC5_uc002ekr.1_Frame_Shift_Del_p.G136fs	NM_032206	NP_115582	Q86WI3	NLRC5_HUMAN	nucleotide-binding oligomerization domains 27	1249_1250	LRR 13.				defense response to virus|innate immune response|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|negative regulation of type I interferon-mediated signaling pathway|positive regulation of interferon-gamma-mediated signaling pathway|positive regulation of MHC class I biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of type I interferon-mediated signaling pathway|regulation of kinase activity	cytosol|nucleus	ATP binding|protein binding|RNA polymerase II core promoter sequence-specific DNA binding			ovary(4)|skin(2)|breast(1)	7		all_neural(199;0.225)																---	---	---	---
RSPRY1	89970	broad.mit.edu	37	16	57242151	57242152	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57242151_57242152insA	uc002elb.2	+						RSPRY1_uc002elc.2_Intron|RSPRY1_uc002eld.2_Intron	NM_133368	NP_588609			ring finger and SPRY domain containing 1							extracellular region	zinc ion binding			ovary(1)	1																		---	---	---	---
RSPRY1	89970	broad.mit.edu	37	16	57248940	57248942	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57248940_57248942delAAA	uc002elb.2	+						RSPRY1_uc002elc.2_Intron|RSPRY1_uc002eld.2_Intron	NM_133368	NP_588609			ring finger and SPRY domain containing 1							extracellular region	zinc ion binding			ovary(1)	1																		---	---	---	---
CIAPIN1	57019	broad.mit.edu	37	16	57477840	57477840	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57477840delA	uc002ell.1	-						CIAPIN1_uc002elk.1_5'Flank|CIAPIN1_uc002elm.1_Intron|CIAPIN1_uc002eln.1_Intron|CIAPIN1_uc010cda.1_Intron|CIAPIN1_uc002elo.1_Intron|CIAPIN1_uc010vhm.1_5'Flank	NM_020313	NP_064709			cytokine induced apoptosis inhibitor 1						anti-apoptosis|apoptosis	cytoplasm|nucleolus					0																		---	---	---	---
COQ9	57017	broad.mit.edu	37	16	57494403	57494403	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57494403delA	uc002elq.2	+						COQ9_uc002elr.2_Intron|COQ9_uc002els.2_Intron|POLR2C_uc010vhq.1_5'Flank|POLR2C_uc002elt.1_5'Flank	NM_020312	NP_064708			coenzyme Q9 homolog precursor						ubiquinone biosynthetic process	mitochondrion				breast(1)	1																		---	---	---	---
KIFC3	3801	broad.mit.edu	37	16	57805033	57805033	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57805033delC	uc002emp.2	-						KIFC3_uc010vhw.1_Intron|KIFC3_uc002emn.2_Intron|KIFC3_uc002emm.2_Intron|KIFC3_uc010vhx.1_Intron|KIFC3_uc010cdf.2_Intron|KIFC3_uc002emo.3_Intron|KIFC3_uc010vhy.1_Intron|KIFC3_uc002emq.2_Intron|KIFC3_uc010vhz.1_Intron|KIFC3_uc002emr.1_Intron	NM_005550	NP_005541			kinesin family member C3 isoform 1						epithelial cell-cell adhesion|microtubule-based movement|visual perception|zonula adherens maintenance	centrosome|cytoplasmic vesicle membrane|kinesin complex|microtubule|zonula adherens	ATP binding|microtubule motor activity			central_nervous_system(2)|ovary(1)	3		all_neural(199;0.224)																---	---	---	---
C16orf57	79650	broad.mit.edu	37	16	58036140	58036140	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58036140delC	uc002emz.2	+						ZNF319_uc002emx.1_5'Flank|C16orf57_uc010via.1_Intron|C16orf57_uc002emy.2_Intron|C16orf57_uc010vib.1_Intron|C16orf57_uc010vic.1_Intron	NM_024598	NP_078874			hypothetical protein LOC79650												0																		---	---	---	---
C16orf57	79650	broad.mit.edu	37	16	58040567	58040567	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58040567delA	uc002emz.2	+						C16orf57_uc010via.1_Intron|C16orf57_uc002emy.2_Intron|C16orf57_uc010vib.1_Intron|C16orf57_uc010vic.1_Intron	NM_024598	NP_078874			hypothetical protein LOC79650												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	58097052	58097053	+	IGR	DEL	GG	-	-	rs66695416		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58097052_58097053delGG								MMP15 (16250 upstream) : C16orf80 (50444 downstream)																																			---	---	---	---
CSNK2A2	1459	broad.mit.edu	37	16	58195986	58195986	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58195986delA	uc002enc.2	-							NM_001896	NP_001887			casein kinase 2, alpha prime polypeptide						axon guidance|Wnt receptor signaling pathway	cytosol|nucleus	ATP binding|protein N-terminus binding|protein serine/threonine kinase activity			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	58494484	58494487	+	IGR	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58494484_58494487delTTTT								GINS3 (54437 upstream) : NDRG4 (3062 downstream)																																			---	---	---	---
NDRG4	65009	broad.mit.edu	37	16	58528233	58528233	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58528233delC	uc002enm.2	+						NDRG4_uc002enk.2_Intron|NDRG4_uc010vif.1_Intron	NM_001130487	NP_001123959			NDRG family member 4 isoform 2						cell differentiation|cell growth|multicellular organismal development|response to stress	cytoplasm				skin(1)	1																		---	---	---	---
NDRG4	65009	broad.mit.edu	37	16	58531863	58531864	+	5'Flank	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58531863_58531864delAA	uc002eno.2	+						NDRG4_uc002enk.2_Intron|NDRG4_uc002enm.2_Intron|NDRG4_uc010vif.1_Intron|NDRG4_uc010cdk.2_5'Flank|NDRG4_uc010vig.1_5'Flank|NDRG4_uc010vih.1_5'Flank|NDRG4_uc010vii.1_5'Flank|NDRG4_uc002enp.2_5'Flank	NM_022910	NP_075061			NDRG family member 4 isoform 1						cell differentiation|cell growth|multicellular organismal development|response to stress	cytoplasm				skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	58670626	58670626	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58670626delT								CNOT1 (6876 upstream) : SLC38A7 (29672 downstream)																																			---	---	---	---
GOT2	2806	broad.mit.edu	37	16	58743249	58743249	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58743249delA	uc002eof.1	-						GOT2_uc010vim.1_Intron	NM_002080	NP_002071			aspartate aminotransferase 2 precursor						aspartate catabolic process|fatty acid transport|gluconeogenesis|response to ethanol	mitochondrial matrix|plasma membrane	L-aspartate:2-oxoglutarate aminotransferase activity|protein binding|pyridoxal phosphate binding			central_nervous_system(1)|skin(1)	2					L-Aspartic Acid(DB00128)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)													---	---	---	---
Unknown	0	broad.mit.edu	37	16	58929932	58929932	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58929932delT								GOT2 (161686 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	58983955	58983955	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58983955delT								GOT2 (215709 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	59121953	59121954	+	IGR	DEL	TT	-	-	rs148998026	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59121953_59121954delTT								GOT2 (353707 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	59864610	59864610	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:59864610delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	60319439	60319442	+	IGR	DEL	AAAA	-	-	rs34664782		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:60319439_60319442delAAAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	60481268	60481268	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:60481268delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	60538937	60538937	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:60538937delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	60794929	60794930	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:60794929_60794930delAA								None (None upstream) : CDH8 (892305 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	61008325	61008325	+	IGR	DEL	A	-	-	rs11301780		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61008325delA								None (None upstream) : CDH8 (678910 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	61312830	61312830	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61312830delC								None (None upstream) : CDH8 (374405 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	61348294	61348295	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61348294_61348295delAA								None (None upstream) : CDH8 (338940 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	61561887	61561888	+	IGR	DEL	TG	-	-	rs112566879		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61561887_61561888delTG								None (None upstream) : CDH8 (125347 downstream)																																			---	---	---	---
CDH8	1006	broad.mit.edu	37	16	61728994	61728994	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61728994delC	uc002eog.1	-							NM_001796	NP_001787			cadherin 8, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|skin(2)|breast(1)	9		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)														---	---	---	---
CDH8	1006	broad.mit.edu	37	16	61883226	61883227	+	Intron	DEL	AA	-	-	rs66664910		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61883226_61883227delAA	uc002eog.1	-						CDH8_uc002eoh.2_Intron	NM_001796	NP_001787			cadherin 8, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|skin(2)|breast(1)	9		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)														---	---	---	---
CDH8	1006	broad.mit.edu	37	16	61904736	61904736	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61904736delT	uc002eog.1	-							NM_001796	NP_001787			cadherin 8, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|skin(2)|breast(1)	9		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	62563600	62563607	+	IGR	DEL	CACACACA	-	-	rs67536942		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:62563600_62563607delCACACACA								CDH8 (493564 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	63024388	63024388	+	IGR	DEL	T	-	-	rs72014706		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:63024388delT								CDH8 (954352 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	63801764	63801765	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:63801764_63801765delAA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	64705719	64705720	+	IGR	DEL	AC	-	-	rs13335704		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:64705719_64705720delAC								None (None upstream) : CDH11 (274965 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	65616772	65616773	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65616772_65616773delAA								LOC283867 (6569 upstream) : CDH5 (783752 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	65719651	65719651	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65719651delA								LOC283867 (109448 upstream) : CDH5 (680874 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	65769963	65769963	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65769963delG								LOC283867 (159760 upstream) : CDH5 (630562 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	65979880	65979881	+	IGR	INS	-	CACA	CACA	rs148592826	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:65979880_65979881insCACA								LOC283867 (369677 upstream) : CDH5 (420644 downstream)																																			---	---	---	---
BEAN	146227	broad.mit.edu	37	16	66482132	66482133	+	Intron	INS	-	TTG	TTG	rs142279114	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66482132_66482133insTTG	uc002eoq.2	+						BEAN_uc002eop.1_Intron	NM_001136106	NP_001129578			brain expressed, associated with Nedd4						cell death	integral to membrane					0																		---	---	---	---
CMTM2	146225	broad.mit.edu	37	16	66618247	66618248	+	Intron	INS	-	AAG	AAG	rs148905784	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66618247_66618248insAAG	uc002ept.2	+						CMTM2_uc010cdu.2_Intron	NM_144673	NP_653274			chemokine-like factor superfamily 2						chemotaxis	extracellular space|integral to membrane	cytokine activity			ovary(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.068)|Epithelial(162;0.212)														---	---	---	---
CMTM4	146223	broad.mit.edu	37	16	66683184	66683184	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66683184delT	uc002epz.2	-						CMTM4_uc002eqa.2_Intron	NM_178818	NP_848933			chemokine-like factor superfamily 4 isoform 1						chemotaxis	extracellular space|integral to membrane	cytokine activity			pancreas(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0811)|Epithelial(162;0.214)														---	---	---	---
CCDC79	283847	broad.mit.edu	37	16	66811036	66811036	+	Intron	DEL	A	-	-	rs71671589		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66811036delA	uc010viv.1	-						CCDC79_uc002eqc.1_Intron|CCDC79_uc002eqd.1_Intron	NM_001136505	NP_001129977			coiled-coil domain containing 79						regulation of transcription, DNA-dependent		DNA binding				0																		---	---	---	---
NAE1	8883	broad.mit.edu	37	16	66844128	66844128	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66844128delA	uc002eqf.2	-						NAE1_uc002eqe.2_Intron|NAE1_uc002eqg.2_Intron|NAE1_uc010cdv.2_Intron	NM_003905	NP_003896			NEDD8 activating enzyme E1 subunit 1 isoform a						apoptosis|cell cycle|DNA replication|mitotic cell cycle DNA replication checkpoint|protein neddylation|signal transduction	cytoplasm|insoluble fraction|plasma membrane	catalytic activity|protein heterodimerization activity			ovary(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0914)|Epithelial(162;0.214)	Adenosine triphosphate(DB00171)													---	---	---	---
CES3	23491	broad.mit.edu	37	16	67003309	67003309	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67003309delA	uc002eqt.2	+						CES3_uc010cdz.2_Intron|CES3_uc010cea.2_Intron|CES3_uc010viw.1_Intron	NM_024922	NP_079198			carboxylesterase 3 precursor							endoplasmic reticulum lumen	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity			ovary(3)|central_nervous_system(2)	5		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0488)|Epithelial(162;0.127)														---	---	---	---
CBFB	865	broad.mit.edu	37	16	67132464	67132464	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67132464delT	uc002era.2	+						CBFB_uc002erb.2_Intron|CBFB_uc010vja.1_Intron	NM_001755	NP_001746			core-binding factor, beta subunit isoform 2						transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			breast(2)	2		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00189)|Epithelial(162;0.00755)|all cancers(182;0.066)				T	MYH11	AML								---	---	---	---
LRRC29	26231	broad.mit.edu	37	16	67242832	67242835	+	Intron	DEL	AAGG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67242832_67242835delAAGG	uc002esd.2	-						LRRC29_uc002ese.2_Intron|LRRC29_uc002esf.2_Intron|LRRC29_uc002esg.2_Intron	NM_012163	NP_036295			F-box and leucine-rich repeat protein 9												0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000691)|Epithelial(162;0.00462)|all cancers(182;0.0434)														---	---	---	---
LRRC29	26231	broad.mit.edu	37	16	67248625	67248625	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67248625delA	uc002ese.2	-						LRRC29_uc002esf.2_Intron|LRRC29_uc002esg.2_Intron|LRRC29_uc010vjg.1_Intron	NM_012163	NP_036295			F-box and leucine-rich repeat protein 9												0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000691)|Epithelial(162;0.00462)|all cancers(182;0.0434)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	67524403	67524403	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67524403delT								AGRP (6687 upstream) : FAM65A (38351 downstream)																																			---	---	---	---
CTCF	10664	broad.mit.edu	37	16	67602282	67602283	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67602282_67602283insT	uc002etl.2	+						CTCF_uc010cek.2_Intron	NM_006565	NP_006556			CCCTC-binding factor						chromatin modification|chromosome segregation|negative regulation of transcription, DNA-dependent|nucleosome positioning|positive regulation of transcription, DNA-dependent|regulation of centromeric sister chromatid cohesion|regulation of molecular function, epigenetic	chromosome, centromeric region|condensed chromosome|nucleolus|nucleoplasm	chromatin insulator sequence binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0166)|Epithelial(162;0.0577)														---	---	---	---
CTCF	10664	broad.mit.edu	37	16	67639285	67639285	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67639285delT	uc002etl.2	+						CTCF_uc010cek.2_Intron	NM_006565	NP_006556			CCCTC-binding factor						chromatin modification|chromosome segregation|negative regulation of transcription, DNA-dependent|nucleosome positioning|positive regulation of transcription, DNA-dependent|regulation of centromeric sister chromatid cohesion|regulation of molecular function, epigenetic	chromosome, centromeric region|condensed chromosome|nucleolus|nucleoplasm	chromatin insulator sequence binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0166)|Epithelial(162;0.0577)														---	---	---	---
CENPT	80152	broad.mit.edu	37	16	67863425	67863427	+	Intron	DEL	AAG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67863425_67863427delAAG	uc002eun.3	-						CENPT_uc002eum.3_Intron|CENPT_uc010vkc.1_Intron|CENPT_uc010vkd.1_Intron	NM_025082	NP_079358			centromere protein T						mitotic prometaphase	condensed chromosome kinetochore|cytosol|nucleus	DNA binding				0		Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00429)|Epithelial(162;0.019)|all cancers(182;0.124)														---	---	---	---
CENPT	80152	broad.mit.edu	37	16	67872525	67872527	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67872525_67872527delAAA	uc002eun.3	-							NM_025082	NP_079358			centromere protein T						mitotic prometaphase	condensed chromosome kinetochore|cytosol|nucleus	DNA binding				0		Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00429)|Epithelial(162;0.019)|all cancers(182;0.124)														---	---	---	---
NUTF2	10204	broad.mit.edu	37	16	67884112	67884113	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67884112_67884113delTT	uc002eup.2	+						NUTF2_uc010vkf.1_Intron|CENPT_uc002eun.3_5'Flank	NM_005796	NP_005787			nuclear transport factor 2						protein transport	cytosol|nuclear pore	protein binding|transporter activity				0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00443)|Epithelial(162;0.0199)|all cancers(182;0.129)														---	---	---	---
DPEP2	64174	broad.mit.edu	37	16	68026099	68026099	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68026099delG	uc010cey.2	-						DPEP2_uc002evd.3_Intron|DPEP2_uc002eve.2_Intron|DPEP2_uc002evf.2_Intron|DPEP2_uc002evg.2_Intron	NM_022355	NP_071750			dipeptidase 2 precursor						hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process|proteolysis	anchored to membrane|plasma membrane	dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metalloexopeptidase activity			skin(1)	1		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0489)|all cancers(182;0.239)														---	---	---	---
DUS2L	54920	broad.mit.edu	37	16	68063109	68063109	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68063109delA	uc002evi.2	+						DUS2L_uc002evj.2_Intron|DUS2L_uc010vkk.1_Intron	NM_017803	NP_060273			dihydrouridine synthase 2-like, SMM1 homolog						tRNA processing	endoplasmic reticulum	double-stranded RNA binding|flavin adenine dinucleotide binding|tRNA dihydrouridine synthase activity				0		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0131)|Epithelial(162;0.0564)														---	---	---	---
PRMT7	54496	broad.mit.edu	37	16	68381784	68381784	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68381784delT	uc002evy.1	+						PRMT7_uc002evx.1_Intron|PRMT7_uc010vlg.1_Intron|PRMT7_uc002evz.1_Intron	NM_019023	NP_061896			protein arginine methyltransferase 7						cell differentiation|DNA methylation involved in gamete generation|regulation of gene expression by genetic imprinting|regulation of transcription, DNA-dependent|spliceosomal snRNP assembly|transcription, DNA-dependent	cytosol|nucleus	[myelin basic protein]-arginine N-methyltransferase activity|histone methyltransferase activity (H4-R3 specific)|protein-arginine omega-N monomethyltransferase activity|protein-arginine omega-N symmetric methyltransferase activity|ribonucleoprotein binding				0		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0155)|Epithelial(162;0.0629)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	68627911	68627911	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68627911delT								ZFP90 (26873 upstream) : CDH3 (50240 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	68640760	68640760	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68640760delT								ZFP90 (39722 upstream) : CDH3 (37391 downstream)														p.?(1)																					---	---	---	---
CDH3	1001	broad.mit.edu	37	16	68732680	68732680	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68732680delT	uc002ewf.2	+	16					CDH3_uc010vli.1_3'UTR	NM_001793	NP_001784			cadherin 3, type 1 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion|response to stimulus|visual perception	integral to membrane	calcium ion binding	p.?(1)		ovary(3)|breast(1)|skin(1)	5		Ovarian(137;0.0564)		OV - Ovarian serous cystadenocarcinoma(108;0.000782)|Epithelial(162;0.0054)|all cancers(182;0.0384)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	68739330	68739330	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68739330delG								CDH3 (6373 upstream) : CDH1 (31865 downstream)														p.?(1)																					---	---	---	---
Unknown	0	broad.mit.edu	37	16	68746592	68746592	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68746592delT								CDH3 (13635 upstream) : CDH1 (24603 downstream)														p.?(1)																					---	---	---	---
Unknown	0	broad.mit.edu	37	16	68754522	68754522	+	IGR	DEL	T	-	-	rs5817649		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68754522delT								CDH3 (21565 upstream) : CDH1 (16673 downstream)														p.?(1)																					---	---	---	---
CIRH1A	84916	broad.mit.edu	37	16	69178104	69178104	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69178104delT	uc002ews.3	+						CIRH1A_uc002ewr.2_Intron|CIRH1A_uc002ewt.3_Intron|CIRH1A_uc010cfi.2_Intron|CIRH1A_uc010cfj.1_Intron	NM_032830	NP_116219			cirhin							nucleolus	protein binding				0				OV - Ovarian serous cystadenocarcinoma(108;0.125)														---	---	---	---
NFAT5	10725	broad.mit.edu	37	16	69600928	69600928	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69600928delT	uc002exm.1	+						NFAT5_uc002exh.1_Intron|NFAT5_uc002exi.2_Intron|NFAT5_uc002exj.1_Intron|NFAT5_uc002exk.1_Intron|NFAT5_uc002exl.1_Intron|NFAT5_uc002exn.1_Intron|MIR1538_hsa-mir-1538|MI0007259_5'Flank	NM_006599	NP_006590			nuclear factor of activated T-cells 5 isoform c						excretion|signal transduction|transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
NOB1	28987	broad.mit.edu	37	16	69785968	69785969	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69785968_69785969delAA	uc002exs.2	-							NM_014062	NP_054781			nin one binding protein							nucleus	metal ion binding|protein binding				0																		---	---	---	---
WWP2	11060	broad.mit.edu	37	16	69815425	69815425	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69815425delT	uc002exu.1	+						WWP2_uc002ext.2_Intron|WWP2_uc002exv.1_Intron	NM_007014	NP_008945			WW domain containing E3 ubiquitin protein ligase						entry of virus into host cell|negative regulation of protein transport|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transporter activity|proteasomal ubiquitin-dependent protein catabolic process|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus|ubiquitin ligase complex	RNA polymerase II transcription factor binding|ubiquitin-protein ligase activity			lung(3)|ovary(1)|breast(1)|skin(1)	6																		---	---	---	---
CLEC18C	283971	broad.mit.edu	37	16	70030143	70030143	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70030143delA	uc002exy.2	+						PDXDC2_uc002eyb.2_Intron|PDXDC2_uc002eyc.2_Intron	NM_182619	NP_872425			secretory protein LOC348174 precursor							extracellular region	sugar binding				0																		---	---	---	---
CLEC18C	283971	broad.mit.edu	37	16	70057194	70057194	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70057194delT	uc002exy.2	+						PDXDC2_uc002eyb.2_Intron|PDXDC2_uc002eyc.2_Intron	NM_182619	NP_872425			secretory protein LOC348174 precursor							extracellular region	sugar binding				0																		---	---	---	---
CLEC18C	283971	broad.mit.edu	37	16	70072984	70072984	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70072984delT	uc002exy.2	+						PDXDC2_uc002eyb.2_RNA|PDXDC2_uc002eyc.2_Intron	NM_182619	NP_872425			secretory protein LOC348174 precursor							extracellular region	sugar binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	70250376	70250376	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70250376delA								CLEC18C (29580 upstream) : EXOSC6 (33758 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	70280996	70280996	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70280996delA								CLEC18C (60200 upstream) : EXOSC6 (3138 downstream)																																			---	---	---	---
DDX19A	55308	broad.mit.edu	37	16	70349528	70349528	+	Intron	DEL	T	-	-	rs72351659		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70349528delT	uc002eys.2	+						DDX19B_uc010vly.1_Intron|DDX19B_uc010vlv.1_Intron|DDX19B_uc010vlw.1_Intron|DDX19B_uc002eyo.2_Intron|DDX19B_uc002eyp.2_Intron|DDX19B_uc002eyq.2_Intron|DDX19B_uc002eyr.2_Intron|DDX19B_uc010vlx.1_Intron	NM_007242	NP_009173			DEAD (Asp-Glu-Ala-As) box polypeptide 19 isoform						mRNA transport|protein transport|transmembrane transport	cytoplasm|nuclear membrane|nuclear pore	ATP binding|ATP-dependent helicase activity|RNA binding				0		Ovarian(137;0.221)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	70479749	70479751	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70479749_70479751delTTT								ST3GAL2 (6758 upstream) : FUK (8747 downstream)																																			---	---	---	---
SF3B3	23450	broad.mit.edu	37	16	70566194	70566194	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70566194delA	uc002ezf.2	+							NM_012426	NP_036558			splicing factor 3b, subunit 3						protein complex assembly	catalytic step 2 spliceosome|nucleoplasm|small nuclear ribonucleoprotein complex|U12-type spliceosomal complex	nucleic acid binding|protein binding			ovary(1)	1		Ovarian(137;0.0694)																---	---	---	---
Unknown	0	broad.mit.edu	37	16	70621181	70621181	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70621181delT								SF3B3 (9611 upstream) : IL34 (59287 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	71289225	71289225	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71289225delA								HYDIN (24600 upstream) : FTSJD1 (26979 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	71371224	71371228	+	IGR	DEL	AAAAG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71371224_71371228delAAAAG								FTSJD1 (47711 upstream) : CALB2 (21398 downstream)																																			---	---	---	---
CALB2	794	broad.mit.edu	37	16	71391231	71391232	+	5'Flank	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71391231_71391232insC	uc002faa.3	+						CALB2_uc010vme.1_5'Flank|CALB2_uc002fac.3_5'Flank	NM_001740	NP_001731			calbindin 2 isoform 1								calcium ion binding				0		Ovarian(137;0.125)																---	---	---	---
ZNF23	7571	broad.mit.edu	37	16	71520262	71520262	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71520262delA	uc002fai.2	-						ZNF19_uc002fak.1_5'Flank|ZNF19_uc010cgc.1_Intron|ZNF19_uc002fal.1_Intron|ZNF19_uc002fam.1_Intron	NM_145911	NP_666016			zinc finger protein 23						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Ovarian(137;0.00768)		BRCA - Breast invasive adenocarcinoma(221;0.0686)														---	---	---	---
PHLPP2	23035	broad.mit.edu	37	16	71720675	71720676	+	Intron	DEL	TT	-	-	rs10685121		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71720675_71720676delTT	uc002fax.2	-						PHLPP2_uc010cgf.2_Intron|PHLPP2_uc002fay.1_Intron	NM_015020	NP_055835			PH domain and leucine rich repeat protein							cytoplasm|membrane|nucleus	metal ion binding|phosphoprotein phosphatase activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
AP1G1	164	broad.mit.edu	37	16	71784038	71784038	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71784038delA	uc010cgg.2	-						AP1G1_uc002fba.2_Intron|AP1G1_uc002fbb.2_Intron|AP1G1_uc002faz.2_5'Flank	NM_001128	NP_001119			adaptor-related protein complex 1, gamma 1						endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport|regulation of defense response to virus by virus|viral reproduction	clathrin adaptor complex|clathrin coated vesicle membrane|cytosol|Golgi membrane|lysosomal membrane|recycling endosome	kinesin binding|protein transporter activity			ovary(2)	2		Ovarian(137;0.125)																---	---	---	---
AP1G1	164	broad.mit.edu	37	16	71789340	71789340	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71789340delA	uc010cgg.2	-						AP1G1_uc002fba.2_Intron|AP1G1_uc002fbb.2_Intron	NM_001128	NP_001119			adaptor-related protein complex 1, gamma 1						endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport|regulation of defense response to virus by virus|viral reproduction	clathrin adaptor complex|clathrin coated vesicle membrane|cytosol|Golgi membrane|lysosomal membrane|recycling endosome	kinesin binding|protein transporter activity			ovary(2)	2		Ovarian(137;0.125)																---	---	---	---
AP1G1	164	broad.mit.edu	37	16	71795578	71795579	+	Intron	DEL	AA	-	-	rs142639197	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71795578_71795579delAA	uc010cgg.2	-						AP1G1_uc002fba.2_Intron|AP1G1_uc002fbb.2_Intron|AP1G1_uc010vmg.1_Intron	NM_001128	NP_001119			adaptor-related protein complex 1, gamma 1						endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport|regulation of defense response to virus by virus|viral reproduction	clathrin adaptor complex|clathrin coated vesicle membrane|cytosol|Golgi membrane|lysosomal membrane|recycling endosome	kinesin binding|protein transporter activity			ovary(2)	2		Ovarian(137;0.125)																---	---	---	---
ZNF821	55565	broad.mit.edu	37	16	71907225	71907226	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71907225_71907226delAA	uc010vmj.1	-						ATXN1L_uc010vmi.1_Intron|ZNF821_uc002fbe.2_Intron|ZNF821_uc002fbf.2_Intron|ZNF821_uc002fbg.3_Intron|ZNF821_uc002fbh.3_Intron|ZNF821_uc002fbi.3_Intron	NM_017530	NP_060000			zinc finger protein 821						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
KIAA0174	9798	broad.mit.edu	37	16	71949731	71949731	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71949731delT	uc002fbj.1	+						KIAA0174_uc010cgh.1_Intron|KIAA0174_uc002fbk.1_Intron|KIAA0174_uc002fbm.1_Intron|KIAA0174_uc002fbl.1_Intron|KIAA0174_uc002fbn.1_Intron|KIAA0174_uc010cgi.1_Intron|KIAA0174_uc010cgj.1_5'Flank|KIAA0174_uc010vmk.1_Intron					SubName: Full=cDNA FLJ32696 fis, clone TESTI2000358; SubName: Full=cDNA FLJ77725;						cell cycle|cell division	cytoplasmic membrane-bounded vesicle|ER-Golgi intermediate compartment	protein binding			ovary(1)	1																		---	---	---	---
PKD1L3	342372	broad.mit.edu	37	16	71973137	71973137	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71973137delT	uc010vmm.1	-							NM_181536	NP_853514			polycystin 1-like 3 precursor												0																		---	---	---	---
PKD1L3	342372	broad.mit.edu	37	16	72003267	72003268	+	Intron	INS	-	ACA	ACA	rs144427410	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72003267_72003268insACA	uc010vmm.1	-							NM_181536	NP_853514			polycystin 1-like 3 precursor												0																		---	---	---	---
TXNL4B	54957	broad.mit.edu	37	16	72120088	72120091	+	3'UTR	DEL	GTGT	-	-	rs113545197		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72120088_72120091delGTGT	uc002fca.2	-	4					TXNL4B_uc010cgl.2_Intron|TXNL4B_uc010vmn.1_3'UTR|TXNL4B_uc010vmo.1_3'UTR	NM_017853	NP_060323			thioredoxin-like 4B						mitosis|mRNA processing|RNA splicing	spliceosomal complex				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	72322380	72322380	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72322380delA	uc002fcg.1	-											full-length cDNA clone CS0DC011YD03 of Neuroblastoma Cot 25-normalized of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	73442009	73442010	+	Intron	DEL	TT	-	-	rs66906978		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73442009_73442010delTT	uc002fco.1	+											Homo sapiens cDNA clone IMAGE:5272469.																														---	---	---	---
Unknown	0	broad.mit.edu	37	16	73578094	73578094	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:73578094delA								HTA (450424 upstream) : PSMD7 (752587 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	74082002	74082002	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74082002delA								HTA (954332 upstream) : PSMD7 (248679 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	74116775	74116775	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74116775delT								HTA (989105 upstream) : PSMD7 (213906 downstream)																																			---	---	---	---
PSMD7	5713	broad.mit.edu	37	16	74334932	74334932	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74334932delT	uc002fcq.2	+						PSMD7_uc010vmr.1_Intron	NM_002811	NP_002802			proteasome 26S non-ATPase subunit 7						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome regulatory particle	protein binding				0																		---	---	---	---
GLG1	2734	broad.mit.edu	37	16	74505408	74505408	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74505408delT	uc002fcy.3	-						GLG1_uc002fcx.2_Intron|GLG1_uc002fcw.3_Intron|GLG1_uc002fcz.3_Intron	NM_001145667	NP_001139139			golgi apparatus protein 1 isoform 3							Golgi membrane|integral to membrane	receptor binding			ovary(1)|breast(1)	2																		---	---	---	---
GLG1	2734	broad.mit.edu	37	16	74636683	74636683	+	Intron	DEL	A	-	-	rs72349063		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74636683delA	uc002fcy.3	-						GLG1_uc002fcx.2_Intron|GLG1_uc002fcw.3_Intron|GLG1_uc002fcz.3_Intron	NM_001145667	NP_001139139			golgi apparatus protein 1 isoform 3							Golgi membrane|integral to membrane	receptor binding			ovary(1)|breast(1)	2																		---	---	---	---
RFWD3	55159	broad.mit.edu	37	16	74681194	74681194	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74681194delT	uc002fda.2	-						RFWD3_uc010cgq.2_Intron	NM_018124	NP_060594			ring finger and WD repeat domain 3						DNA repair|mitotic cell cycle G1/S transition DNA damage checkpoint|response to ionizing radiation	nucleus	MDM2 binding|p53 binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)|breast(1)	3																		---	---	---	---
WDR59	79726	broad.mit.edu	37	16	75004946	75004946	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75004946delA	uc002fdh.1	-						WDR59_uc002fdi.2_Intron|WDR59_uc002fdj.2_Intron	NM_030581	NP_085058			WD repeat domain 59											ovary(1)|breast(1)	2																		---	---	---	---
CFDP1	10428	broad.mit.edu	37	16	75453296	75453296	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75453296delA	uc002fdy.2	-						CFDP1_uc002fdz.2_Intron|CFDP1_uc002fea.1_Intron	NM_006324	NP_006315			craniofacial development protein 1						multicellular organismal development					upper_aerodigestive_tract(1)	1																		---	---	---	---
CFDP1	10428	broad.mit.edu	37	16	75460585	75460585	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75460585delA	uc002fdy.2	-						CFDP1_uc002fdz.2_Intron|CFDP1_uc002fea.1_Intron	NM_006324	NP_006315			craniofacial development protein 1						multicellular organismal development					upper_aerodigestive_tract(1)	1																		---	---	---	---
TMEM170A	124491	broad.mit.edu	37	16	75479598	75479600	+	3'UTR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75479598_75479600delTTT	uc002fec.2	-	3					TMEM170A_uc002feb.2_3'UTR|TMEM170A_uc002fed.1_Intron					RecName: Full=Transmembrane protein 170A;							integral to membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	75545702	75545703	+	IGR	INS	-	T	T	rs141190453	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75545702_75545703insT								CHST6 (16776 upstream) : CHST5 (16727 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	75554509	75554509	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75554509delA								CHST6 (25583 upstream) : CHST5 (7921 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	75557022	75557022	+	IGR	DEL	T	-	-	rs145144464		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75557022delT								CHST6 (28096 upstream) : CHST5 (5408 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	75626098	75626100	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75626098_75626100delTTT								GABARAPL2 (14320 upstream) : ADAT1 (6898 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	76081469	76081469	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76081469delT								TERF2IP (390141 upstream) : CNTNAP4 (229707 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	77128129	77128129	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77128129delT								CNTNAP4 (534994 upstream) : MON1B (96707 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	77193828	77193828	+	IGR	DEL	T	-	-	rs68066912		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77193828delT								CNTNAP4 (600693 upstream) : MON1B (31008 downstream)																																			---	---	---	---
NUDT7	283927	broad.mit.edu	37	16	77764208	77764208	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77764208delC	uc010chd.2	+						NUDT7_uc010vnj.1_Intron	NM_001105663	NP_001099133			nudix motif 7						nucleoside diphosphate metabolic process	peroxisome	hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides|magnesium ion binding|manganese ion binding			ovary(1)|kidney(1)	2																		---	---	---	---
VAT1L	57687	broad.mit.edu	37	16	77912301	77912301	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77912301delA	uc002ffg.1	+							NM_020927	NP_065978			vesicle amine transport protein 1 homolog (T.								oxidoreductase activity|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	78109167	78109167	+	IGR	DEL	A	-	-	rs2344925		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78109167delA								CLEC3A (43170 upstream) : WWOX (24384 downstream)																																			---	---	---	---
WWOX	51741	broad.mit.edu	37	16	78153194	78153194	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78153194delT	uc002ffk.2	+						WWOX_uc010vnk.1_Intron|WWOX_uc002ffl.2_Intron|WWOX_uc010che.2_Intron|WWOX_uc002ffj.1_Intron	NM_016373	NP_057457			WW domain-containing oxidoreductase isoform 1						apoptosis|negative regulation of Wnt receptor signaling pathway|steroid metabolic process|Wnt receptor signaling pathway	Golgi apparatus|mitochondrion|nucleus	coenzyme binding|oxidoreductase activity|protein dimerization activity				0		all_cancers(2;1.97e-181)|all_epithelial(2;3.85e-160)|all_lung(2;2.03e-39)|Lung NSC(2;7.16e-35)|Colorectal(2;6.96e-21)|all_hematologic(2;1.13e-16)|Melanoma(2;5.16e-06)|all_neural(2;8.84e-06)|Renal(2;5.26e-05)|Medulloblastoma(2;0.00498)|Breast(2;0.00631)|Lung SC(2;0.0261)|Prostate(104;0.167)		UCEC - Uterine corpus endometrioid carcinoma (2;0.012)|Epithelial(1;2.65e-39)|all cancers(1;3.26e-34)|STAD - Stomach adenocarcinoma(1;5.1e-20)|COAD - Colon adenocarcinoma(1;1.04e-11)|Colorectal(1;3.4e-11)|OV - Ovarian serous cystadenocarcinoma(1;1.01e-10)|BRCA - Breast invasive adenocarcinoma(1;0.00196)|Kidney(780;0.232)														---	---	---	---
WWOX	51741	broad.mit.edu	37	16	78433014	78433014	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78433014delA	uc002ffk.2	+						WWOX_uc010vnk.1_Intron|WWOX_uc002ffl.2_Intron|WWOX_uc010che.2_Intron	NM_016373	NP_057457			WW domain-containing oxidoreductase isoform 1						apoptosis|negative regulation of Wnt receptor signaling pathway|steroid metabolic process|Wnt receptor signaling pathway	Golgi apparatus|mitochondrion|nucleus	coenzyme binding|oxidoreductase activity|protein dimerization activity				0		all_cancers(2;1.97e-181)|all_epithelial(2;3.85e-160)|all_lung(2;2.03e-39)|Lung NSC(2;7.16e-35)|Colorectal(2;6.96e-21)|all_hematologic(2;1.13e-16)|Melanoma(2;5.16e-06)|all_neural(2;8.84e-06)|Renal(2;5.26e-05)|Medulloblastoma(2;0.00498)|Breast(2;0.00631)|Lung SC(2;0.0261)|Prostate(104;0.167)		UCEC - Uterine corpus endometrioid carcinoma (2;0.012)|Epithelial(1;2.65e-39)|all cancers(1;3.26e-34)|STAD - Stomach adenocarcinoma(1;5.1e-20)|COAD - Colon adenocarcinoma(1;1.04e-11)|Colorectal(1;3.4e-11)|OV - Ovarian serous cystadenocarcinoma(1;1.01e-10)|BRCA - Breast invasive adenocarcinoma(1;0.00196)|Kidney(780;0.232)														---	---	---	---
WWOX	51741	broad.mit.edu	37	16	78641542	78641544	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78641542_78641544delTTT	uc002ffk.2	+						WWOX_uc010vnk.1_Intron|WWOX_uc002ffl.2_Intron|WWOX_uc010che.2_Intron	NM_016373	NP_057457			WW domain-containing oxidoreductase isoform 1						apoptosis|negative regulation of Wnt receptor signaling pathway|steroid metabolic process|Wnt receptor signaling pathway	Golgi apparatus|mitochondrion|nucleus	coenzyme binding|oxidoreductase activity|protein dimerization activity				0		all_cancers(2;1.97e-181)|all_epithelial(2;3.85e-160)|all_lung(2;2.03e-39)|Lung NSC(2;7.16e-35)|Colorectal(2;6.96e-21)|all_hematologic(2;1.13e-16)|Melanoma(2;5.16e-06)|all_neural(2;8.84e-06)|Renal(2;5.26e-05)|Medulloblastoma(2;0.00498)|Breast(2;0.00631)|Lung SC(2;0.0261)|Prostate(104;0.167)		UCEC - Uterine corpus endometrioid carcinoma (2;0.012)|Epithelial(1;2.65e-39)|all cancers(1;3.26e-34)|STAD - Stomach adenocarcinoma(1;5.1e-20)|COAD - Colon adenocarcinoma(1;1.04e-11)|Colorectal(1;3.4e-11)|OV - Ovarian serous cystadenocarcinoma(1;1.01e-10)|BRCA - Breast invasive adenocarcinoma(1;0.00196)|Kidney(780;0.232)														---	---	---	---
WWOX	51741	broad.mit.edu	37	16	78720408	78720408	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:78720408delA	uc002ffk.2	+						WWOX_uc010vnk.1_Intron|WWOX_uc002ffl.2_Intron|WWOX_uc010che.2_Intron	NM_016373	NP_057457			WW domain-containing oxidoreductase isoform 1						apoptosis|negative regulation of Wnt receptor signaling pathway|steroid metabolic process|Wnt receptor signaling pathway	Golgi apparatus|mitochondrion|nucleus	coenzyme binding|oxidoreductase activity|protein dimerization activity				0		all_cancers(2;1.97e-181)|all_epithelial(2;3.85e-160)|all_lung(2;2.03e-39)|Lung NSC(2;7.16e-35)|Colorectal(2;6.96e-21)|all_hematologic(2;1.13e-16)|Melanoma(2;5.16e-06)|all_neural(2;8.84e-06)|Renal(2;5.26e-05)|Medulloblastoma(2;0.00498)|Breast(2;0.00631)|Lung SC(2;0.0261)|Prostate(104;0.167)		UCEC - Uterine corpus endometrioid carcinoma (2;0.012)|Epithelial(1;2.65e-39)|all cancers(1;3.26e-34)|STAD - Stomach adenocarcinoma(1;5.1e-20)|COAD - Colon adenocarcinoma(1;1.04e-11)|Colorectal(1;3.4e-11)|OV - Ovarian serous cystadenocarcinoma(1;1.01e-10)|BRCA - Breast invasive adenocarcinoma(1;0.00196)|Kidney(780;0.232)														---	---	---	---
WWOX	51741	broad.mit.edu	37	16	79192746	79192746	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79192746delT	uc002ffk.2	+						WWOX_uc010vnk.1_Intron|WWOX_uc002ffl.2_Intron|WWOX_uc010che.2_Intron	NM_016373	NP_057457			WW domain-containing oxidoreductase isoform 1						apoptosis|negative regulation of Wnt receptor signaling pathway|steroid metabolic process|Wnt receptor signaling pathway	Golgi apparatus|mitochondrion|nucleus	coenzyme binding|oxidoreductase activity|protein dimerization activity				0		all_cancers(2;1.97e-181)|all_epithelial(2;3.85e-160)|all_lung(2;2.03e-39)|Lung NSC(2;7.16e-35)|Colorectal(2;6.96e-21)|all_hematologic(2;1.13e-16)|Melanoma(2;5.16e-06)|all_neural(2;8.84e-06)|Renal(2;5.26e-05)|Medulloblastoma(2;0.00498)|Breast(2;0.00631)|Lung SC(2;0.0261)|Prostate(104;0.167)		UCEC - Uterine corpus endometrioid carcinoma (2;0.012)|Epithelial(1;2.65e-39)|all cancers(1;3.26e-34)|STAD - Stomach adenocarcinoma(1;5.1e-20)|COAD - Colon adenocarcinoma(1;1.04e-11)|Colorectal(1;3.4e-11)|OV - Ovarian serous cystadenocarcinoma(1;1.01e-10)|BRCA - Breast invasive adenocarcinoma(1;0.00196)|Kidney(780;0.232)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	79414647	79414648	+	IGR	DEL	TA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79414647_79414648delTA								WWOX (168084 upstream) : MAF (213098 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	79452543	79452543	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79452543delA								WWOX (205980 upstream) : MAF (175203 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	79781782	79781782	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79781782delA								MAF (147160 upstream) : DYNLRB2 (793072 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	79912466	79912466	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:79912466delT								MAF (277844 upstream) : DYNLRB2 (662388 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	80189938	80189938	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80189938delA								MAF (555316 upstream) : DYNLRB2 (384916 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	80384283	80384284	+	IGR	DEL	TT	-	-	rs72062671		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80384283_80384284delTT								MAF (749661 upstream) : DYNLRB2 (190570 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	80386054	80386055	+	IGR	DEL	AA	-	-	rs2019809	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80386054_80386055delAA								MAF (751432 upstream) : DYNLRB2 (188799 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	80462357	80462357	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:80462357delT								MAF (827735 upstream) : DYNLRB2 (112497 downstream)																																			---	---	---	---
CENPN	55839	broad.mit.edu	37	16	81051343	81051343	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81051343delT	uc002ffx.2	+						CENPN_uc002ffw.3_Intron|CENPN_uc010vnl.1_Intron|CENPN_uc010vnm.1_Intron|CENPN_uc002ffy.3_Intron	NM_001100624	NP_001094094			centromere protein N isoform 2						CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	condensed chromosome kinetochore|cytosol|nucleoplasm					0																		---	---	---	---
C16orf46	123775	broad.mit.edu	37	16	81097648	81097648	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81097648delA	uc002fgc.3	-						C16orf46_uc010chf.2_Intron|C16orf46_uc010vno.1_Intron	NM_152337	NP_689550			chromosome 16 open reading frame 46 isoform 2												0																		---	---	---	---
CMIP	80790	broad.mit.edu	37	16	81518559	81518559	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81518559delT	uc002fgp.2	+							NM_198390	NP_938204			c-Maf-inducing protein isoform C-mip							cytoplasm|nucleus					0																		---	---	---	---
CMIP	80790	broad.mit.edu	37	16	81534101	81534101	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81534101delT	uc002fgp.2	+						CMIP_uc002fgq.1_Intron	NM_198390	NP_938204			c-Maf-inducing protein isoform C-mip							cytoplasm|nucleus					0																		---	---	---	---
CMIP	80790	broad.mit.edu	37	16	81570358	81570359	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81570358_81570359insT	uc002fgp.2	+						CMIP_uc002fgq.1_Intron	NM_198390	NP_938204			c-Maf-inducing protein isoform C-mip							cytoplasm|nucleus					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	82303971	82303971	+	IGR	DEL	C	-	-	rs11337036		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82303971delC								MPHOSPH6 (100142 upstream) : CDH13 (356607 downstream)																																			---	---	---	---
CDH13	1012	broad.mit.edu	37	16	82750254	82750254	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82750254delT	uc002fgx.2	+						CDH13_uc010chh.2_Intron|CDH13_uc010vns.1_Intron|CDH13_uc010vnt.1_Intron|CDH13_uc010vnu.1_Intron	NM_001257	NP_001248			cadherin 13 preproprotein						adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)														---	---	---	---
CDH13	1012	broad.mit.edu	37	16	82794623	82794632	+	Intron	DEL	TTTTTTTTTT	-	-	rs4783267		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82794623_82794632delTTTTTTTTTT	uc002fgx.2	+						CDH13_uc010chh.2_Intron|CDH13_uc010vns.1_Intron|CDH13_uc010vnt.1_Intron|CDH13_uc010vnu.1_Intron	NM_001257	NP_001248			cadherin 13 preproprotein						adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)														---	---	---	---
CDH13	1012	broad.mit.edu	37	16	82852298	82852298	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82852298delA	uc002fgx.2	+						CDH13_uc010chh.2_Intron|CDH13_uc010vns.1_Intron|CDH13_uc010vnt.1_Intron|CDH13_uc010vnu.1_Intron	NM_001257	NP_001248			cadherin 13 preproprotein						adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)														---	---	---	---
CDH13	1012	broad.mit.edu	37	16	82893341	82893343	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:82893341_82893343delAAA	uc002fgx.2	+						CDH13_uc010chh.2_Intron|CDH13_uc010vns.1_Intron|CDH13_uc010vnt.1_Intron|CDH13_uc010vnu.1_Intron	NM_001257	NP_001248			cadherin 13 preproprotein						adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)														---	---	---	---
CDH13	1012	broad.mit.edu	37	16	83409163	83409164	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83409163_83409164insA	uc002fgx.2	+						CDH13_uc010vns.1_Intron|CDH13_uc010vnt.1_Intron|CDH13_uc010vnu.1_Intron	NM_001257	NP_001248			cadherin 13 preproprotein						adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)														---	---	---	---
CDH13	1012	broad.mit.edu	37	16	83561054	83561054	+	Intron	DEL	A	-	-	rs113406128		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83561054delA	uc002fgx.2	+						CDH13_uc010vns.1_Intron|CDH13_uc010vnt.1_Intron|CDH13_uc010vnu.1_Intron	NM_001257	NP_001248			cadherin 13 preproprotein						adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)														---	---	---	---
CDH13	1012	broad.mit.edu	37	16	83807981	83807981	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83807981delT	uc002fgx.2	+						CDH13_uc010vns.1_Intron|CDH13_uc010vnt.1_Intron|CDH13_uc010vnu.1_Intron	NM_001257	NP_001248			cadherin 13 preproprotein						adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)														---	---	---	---
MBTPS1	8720	broad.mit.edu	37	16	84137923	84137923	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84137923delA	uc002fhi.2	-							NM_003791	NP_003782			membrane-bound transcription factor site-1						cholesterol metabolic process|proteolysis	endoplasmic reticulum lumen|endoplasmic reticulum membrane|Golgi membrane|integral to membrane	serine-type endopeptidase activity			ovary(2)	2																		---	---	---	---
TAF1C	9013	broad.mit.edu	37	16	84219510	84219510	+	Intron	DEL	A	-	-	rs112040715		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84219510delA	uc002fhn.2	-						TAF1C_uc002fhm.2_Intron|TAF1C_uc010vnx.1_Intron|TAF1C_uc010vny.1_Intron|TAF1C_uc010vnz.1_Intron|TAF1C_uc002fho.2_Intron|TAF1C_uc010voa.1_Intron|TAF1C_uc002fhp.1_Intron|TAF1C_uc010vob.1_Intron	NM_005679	NP_005670			TBP-associated factor 1C isoform 1						regulation of transcription, DNA-dependent|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	84390679	84390679	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84390679delG								WFDC1 (27233 upstream) : ATP2C2 (11454 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	84596674	84596677	+	IGR	DEL	AAAA	-	-	rs5818494		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84596674_84596677delAAAA								KIAA1609 (58386 upstream) : COTL1 (2529 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	84722126	84722126	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84722126delT								KLHL36 (26211 upstream) : USP10 (11429 downstream)																																			---	---	---	---
CRISPLD2	83716	broad.mit.edu	37	16	84895819	84895819	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84895819delT	uc010voh.1	+						CRISPLD2_uc010vog.1_Intron|CRISPLD2_uc002fio.2_Intron|CRISPLD2_uc002fim.2_Intron|CRISPLD2_uc002fin.3_Intron	NM_031476	NP_113664			cysteine-rich secretory protein LCCL domain							extracellular region|transport vesicle					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	85254386	85254386	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85254386delT								FAM92B (108272 upstream) : KIAA0182 (390643 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	85589281	85589282	+	IGR	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85589281_85589282insC								FAM92B (443167 upstream) : KIAA0182 (55747 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	85599001	85599001	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85599001delA								FAM92B (452887 upstream) : KIAA0182 (46028 downstream)																																			---	---	---	---
KIAA0182	23199	broad.mit.edu	37	16	85686968	85686968	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85686968delT	uc002fix.2	+						KIAA0182_uc002fiw.2_Intron|KIAA0182_uc002fiy.2_Intron	NM_014615	NP_055430			genetic suppressor element 1 isoform 1								protein binding			large_intestine(3)|ovary(1)|skin(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	16	85958989	85958989	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85958989delT								IRF8 (2780 upstream) : LOC732275 (406467 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	86321237	86321242	+	IGR	DEL	GCGTGC	-	-	rs55750318		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86321237_86321242delGCGTGC								IRF8 (365028 upstream) : LOC732275 (44214 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	86437584	86437584	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86437584delA								LOC732275 (58299 upstream) : FOXF1 (106549 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	86640755	86640755	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86640755delT								FOXL1 (25452 upstream) : FBXO31 (722189 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	86671298	86671299	+	IGR	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86671298_86671299delGA								FOXL1 (55995 upstream) : FBXO31 (691645 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	16	87353276	87353279	+	5'Flank	DEL	AAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87353276_87353279delAAAA	uc002fju.2	-											SubName: Full=cDNA: FLJ22477 fis, clone HRC10815;																														---	---	---	---
JPH3	57338	broad.mit.edu	37	16	87721531	87721531	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87721531delC	uc002fkd.2	+						JPH3_uc010vou.1_Intron	NM_020655	NP_065706			junctophilin 3						calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional sarcoplasmic reticulum membrane|plasma membrane	protein binding			ovary(1)|pancreas(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0287)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	88366325	88366325	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88366325delG								BANP (255402 upstream) : ZNF469 (127554 downstream)																																			---	---	---	---
MVD	4597	broad.mit.edu	37	16	88720515	88720515	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88720515delG	uc002flg.1	-						MVD_uc002flf.1_Intron	NM_002461	NP_002452			diphosphomevalonate decarboxylase						cholesterol biosynthetic process|positive regulation of cell proliferation	cytosol	ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity				0				BRCA - Breast invasive adenocarcinoma(80;0.0478)														---	---	---	---
MVD	4597	broad.mit.edu	37	16	88724562	88724562	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88724562delG	uc002flg.1	-						MVD_uc002flf.1_5'Flank	NM_002461	NP_002452			diphosphomevalonate decarboxylase						cholesterol biosynthetic process|positive regulation of cell proliferation	cytosol	ATP binding|diphosphomevalonate decarboxylase activity|Hsp70 protein binding|kinase activity|protein homodimerization activity				0				BRCA - Breast invasive adenocarcinoma(80;0.0478)														---	---	---	---
FAM38A	9780	broad.mit.edu	37	16	88826780	88826781	+	Intron	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88826780_88826781delCT	uc010vpb.1	-							NM_001142864	NP_001136336			family with sequence similarity 38, member A							endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|integral to membrane|plasma membrane	ion channel activity				0																		---	---	---	---
GALNS	2588	broad.mit.edu	37	16	88913543	88913543	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:88913543delT	uc002fly.3	-						GALNS_uc010cid.2_Intron|GALNS_uc002flz.3_Intron	NM_000512	NP_000503			galactosamine (N-acetyl)-6-sulfate sulfatase							lysosome	metal ion binding|N-acetylgalactosamine-4-sulfatase activity|N-acetylgalactosamine-6-sulfatase activity			large_intestine(2)	2				BRCA - Breast invasive adenocarcinoma(80;0.0496)	Hyaluronidase(DB00070)													---	---	---	---
Unknown	0	broad.mit.edu	37	16	89156409	89156409	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89156409delG								CBFA2T3 (113008 upstream) : ACSF3 (3845 downstream)																																			---	---	---	---
CDH15	1013	broad.mit.edu	37	16	89255736	89255737	+	Intron	DEL	GG	-	-	rs66969920		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89255736_89255737delGG	uc002fmt.2	+							NM_004933	NP_004924			cadherin 15 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion|muscle cell differentiation|positive regulation of muscle cell differentiation	integral to membrane|plasma membrane	calcium ion binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0261)														---	---	---	---
ZNF778	197320	broad.mit.edu	37	16	89291883	89291883	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89291883delT	uc002fmv.2	+						ZNF778_uc010vpf.1_Intron|ZNF778_uc002fmw.1_Intron|ZNF778_uc010vpg.1_Intron	NM_182531	NP_872337			zinc finger protein 778						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				BRCA - Breast invasive adenocarcinoma(80;0.0269)														---	---	---	---
ANKRD11	29123	broad.mit.edu	37	16	89545684	89545684	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89545684delA	uc002fmx.1	-						ANKRD11_uc002fmy.1_Intron|ANKRD11_uc002fnc.1_Intron|ANKRD11_uc002fne.2_Intron|ANKRD11_uc002fng.1_Intron	NM_013275	NP_037407			ankyrin repeat domain 11							nucleus				ovary(4)|large_intestine(1)|central_nervous_system(1)	6		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)														---	---	---	---
DPEP1	1800	broad.mit.edu	37	16	89701416	89701417	+	Intron	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89701416_89701417insC	uc010cin.2	+						DPEP1_uc002fnr.3_Intron|DPEP1_uc002fns.3_Intron	NM_001128141	NP_001121613			dipeptidase 1 precursor						proteolysis	anchored to membrane|apical plasma membrane|microvillus membrane	dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metalloexopeptidase activity|protein binding			large_intestine(1)	1		all_lung(18;0.0054)|all_hematologic(23;0.094)		BRCA - Breast invasive adenocarcinoma(80;0.0258)	Cilastatin(DB01597)													---	---	---	---
CDK10	8558	broad.mit.edu	37	16	89759056	89759056	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89759056delT	uc010cio.2	+						CDK10_uc010cip.2_Intron|CDK10_uc010vpl.1_Intron|CDK10_uc002fob.2_Intron|CDK10_uc002fod.2_Intron|CDK10_uc002foe.2_Intron|CDK10_uc002fof.2_Intron|CDK10_uc002fog.3_Intron|CDK10_uc002foh.3_Intron|CDK10_uc002foi.2_5'Flank	NM_052988	NP_443714			cyclin-dependent kinase 10 isoform a						negative regulation of cell proliferation|traversing start control point of mitotic cell cycle		ATP binding|cyclin-dependent protein kinase activity|protein binding			ovary(1)	1		Lung NSC(15;2.19e-05)|all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.0276)														---	---	---	---
FANCA	2175	broad.mit.edu	37	16	89823551	89823551	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89823551delT	uc002fou.1	-						FANCA_uc010vpn.1_Intron|FANCA_uc010vpo.1_Intron	NM_000135	NP_000126			Fanconi anemia, complementation group A isoform						DNA repair|protein complex assembly	cytoplasm|nucleoplasm	protein binding			ovary(2)|breast(2)|central_nervous_system(1)|skin(1)	6		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)				D|Mis|N|F|S			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
FANCA	2175	broad.mit.edu	37	16	89843254	89843255	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89843254_89843255insA	uc002fou.1	-						FANCA_uc010vpn.1_Intron	NM_000135	NP_000126			Fanconi anemia, complementation group A isoform						DNA repair|protein complex assembly	cytoplasm|nucleoplasm	protein binding			ovary(2)|breast(2)|central_nervous_system(1)|skin(1)	6		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)				D|Mis|N|F|S			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
TCF25	22980	broad.mit.edu	37	16	89954031	89954031	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89954031delT	uc002fpb.2	+						TCF25_uc002fpc.2_Intron	NM_014972	NP_055787			NULP1						heart development|negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0		all_cancers(9;4.71e-08)|Lung NSC(15;0.000192)|all_lung(18;0.000319)|all_neural(9;0.0122)|all_hematologic(23;0.027)		BRCA - Breast invasive adenocarcinoma(80;0.0288)														---	---	---	---
Unknown	0	broad.mit.edu	37	16	89980552	89980553	+	RNA	DEL	TG	-	-	rs72318787		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89980552_89980553delTG	uc010ciy.1	+	2		c.1055_1056delTG								Homo sapiens cDNA clone IMAGE:40002380.																														---	---	---	---
MC1R	4157	broad.mit.edu	37	16	89981381	89981382	+	5'Flank	INS	-	TG	TG	rs144448880	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89981381_89981382insTG	uc002fpe.3	+						uc010ciy.1_RNA	NM_002386	NP_002377			melanocortin 1 receptor						G-protein signaling, coupled to cyclic nucleotide second messenger|intracellular protein kinase cascade|multicellular organismal development|negative regulation of tumor necrosis factor production|pigmentation|positive regulation of cAMP biosynthetic process|positive regulation of protein kinase A signaling cascade|positive regulation of protein kinase B signaling cascade|positive regulation of protein kinase C signaling cascade|positive regulation of transcription from RNA polymerase II promoter|UV protection|UV-damage excision repair	integral to plasma membrane	melanocyte-stimulating hormone receptor activity|ubiquitin protein ligase binding				0		all_cancers(9;1.69e-11)|Lung NSC(15;8.94e-06)|all_lung(18;1.39e-05)|all_neural(9;0.00581)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0273)										Melanoma_Familial_Clustering_of				---	---	---	---
DEF8	54849	broad.mit.edu	37	16	90028045	90028045	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:90028045delC	uc002fpn.1	+						DEF8_uc002fpo.1_Intron|DEF8_uc002fpp.1_Intron|DEF8_uc010vpq.1_Intron|DEF8_uc010vpr.1_Intron|DEF8_uc002fpq.1_5'Flank	NM_207514	NP_997397			differentially expressed in FDCP 8 isoform 1						intracellular signal transduction		zinc ion binding			central_nervous_system(1)	1		all_cancers(9;7.59e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.0019)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0274)														---	---	---	---
PRDM7	11105	broad.mit.edu	37	16	90138639	90138639	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:90138639delA	uc010cje.2	-						PRDM7_uc010cjf.2_Intron|PRDM7_uc010cjh.1_Intron	NM_001098173	NP_001091643			PR domain containing 7 isoform 1							chromosome|nucleus	nucleic acid binding			ovary(1)	1		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0278)														---	---	---	---
RPH3AL	9501	broad.mit.edu	37	17	64561	64561	+	Intron	DEL	A	-	-	rs112783318		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64561delA	uc002frd.1	-						RPH3AL_uc010vpy.1_Intron|RPH3AL_uc002fre.1_Intron|RPH3AL_uc002frf.1_Intron|RPH3AL_uc010cjl.1_Intron	NM_006987	NP_008918			rabphilin 3A-like (without C2 domains)						exocytosis|intracellular protein transport	transport vesicle membrane	cytoskeletal protein binding|Rab GTPase binding|zinc ion binding			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.023)|all cancers(1;4.96e-06)|Epithelial(1;2.86e-05)|BRCA - Breast invasive adenocarcinoma(1;0.00453)|OV - Ovarian serous cystadenocarcinoma(1;0.0716)|LUAD - Lung adenocarcinoma(1115;0.102)|COAD - Colon adenocarcinoma(4;0.107)														---	---	---	---
RPH3AL	9501	broad.mit.edu	37	17	111141	111142	+	Intron	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:111141_111142delCT	uc002frd.1	-						RPH3AL_uc010vpy.1_Intron|RPH3AL_uc002fre.1_Intron|RPH3AL_uc002frf.1_Intron|RPH3AL_uc010cjl.1_Intron	NM_006987	NP_008918			rabphilin 3A-like (without C2 domains)						exocytosis|intracellular protein transport	transport vesicle membrane	cytoskeletal protein binding|Rab GTPase binding|zinc ion binding			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.023)|all cancers(1;4.96e-06)|Epithelial(1;2.86e-05)|BRCA - Breast invasive adenocarcinoma(1;0.00453)|OV - Ovarian serous cystadenocarcinoma(1;0.0716)|LUAD - Lung adenocarcinoma(1115;0.102)|COAD - Colon adenocarcinoma(4;0.107)														---	---	---	---
ABR	29	broad.mit.edu	37	17	969772	969772	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:969772delT	uc002fsd.2	-						ABR_uc002fse.2_Intron|ABR_uc010vqg.1_Intron|ABR_uc002fsg.2_Intron|ABR_uc002fsh.1_Intron	NM_021962	NP_068781			active breakpoint cluster region-related						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding|Rho guanyl-nucleotide exchange factor activity			upper_aerodigestive_tract(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)														---	---	---	---
ABR	29	broad.mit.edu	37	17	986962	986963	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:986962_986963insA	uc002fsd.2	-						ABR_uc002fse.2_Intron|ABR_uc002fsg.2_Intron|ABR_uc002fsh.1_Intron	NM_021962	NP_068781			active breakpoint cluster region-related						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding|Rho guanyl-nucleotide exchange factor activity			upper_aerodigestive_tract(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)														---	---	---	---
ABR	29	broad.mit.edu	37	17	1002327	1002327	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1002327delT	uc002fsd.2	-						ABR_uc002fse.2_Intron|ABR_uc002fsg.2_Intron|ABR_uc010cjq.1_Intron	NM_021962	NP_068781			active breakpoint cluster region-related						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding|Rho guanyl-nucleotide exchange factor activity			upper_aerodigestive_tract(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	1107754	1107754	+	IGR	DEL	A	-	-	rs77929899		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1107754delA								ABR (17138 upstream) : TUSC5 (75203 downstream)																																			---	---	---	---
SLC43A2	124935	broad.mit.edu	37	17	1513210	1513210	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1513210delT	uc002fsv.2	-						SLC43A2_uc002fsu.2_Intron|SLC43A2_uc002fsw.2_Intron|SLC43A2_uc002fsx.2_Intron	NM_152346	NP_689559			solute carrier family 43, member 2						cellular nitrogen compound metabolic process|ion transport	integral to membrane|plasma membrane					0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0883)														---	---	---	---
PRPF8	10594	broad.mit.edu	37	17	1566597	1566597	+	Intron	DEL	A	-	-	rs116168685	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1566597delA	uc002fte.2	-							NM_006445	NP_006436			U5 snRNP-specific protein							catalytic step 2 spliceosome|nuclear speck|U5 snRNP	protein binding|RNA binding			lung(4)|ovary(2)	6				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)														---	---	---	---
PRPF8	10594	broad.mit.edu	37	17	1581619	1581619	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1581619delA	uc002fte.2	-							NM_006445	NP_006436			U5 snRNP-specific protein							catalytic step 2 spliceosome|nuclear speck|U5 snRNP	protein binding|RNA binding			lung(4)|ovary(2)	6				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	1607926	1607926	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1607926delT								PRPF8 (19750 upstream) : C17orf91 (6878 downstream)																																			---	---	---	---
RPA1	6117	broad.mit.edu	37	17	1758626	1758627	+	Intron	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1758626_1758627delTG	uc002fto.2	+							NM_002945	NP_002936			replication protein A1						cell cycle checkpoint|DNA recombinase assembly|DNA strand elongation involved in DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	actin cytoskeleton|cytoplasm|DNA replication factor A complex|PML body	metal ion binding|protein binding|single-stranded DNA binding				0													NER					---	---	---	---
RPA1	6117	broad.mit.edu	37	17	1797163	1797163	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1797163delT	uc002fto.2	+							NM_002945	NP_002936			replication protein A1						cell cycle checkpoint|DNA recombinase assembly|DNA strand elongation involved in DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	actin cytoskeleton|cytoplasm|DNA replication factor A complex|PML body	metal ion binding|protein binding|single-stranded DNA binding				0													NER					---	---	---	---
Unknown	0	broad.mit.edu	37	17	1821654	1821654	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1821654delT								RPA1 (18806 upstream) : RTN4RL1 (16319 downstream)																																			---	---	---	---
RTN4RL1	146760	broad.mit.edu	37	17	1915891	1915891	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1915891delT	uc002ftp.2	-							NM_178568	NP_848663			reticulon 4 receptor-like 1 precursor						axon regeneration	anchored to plasma membrane	receptor activity				0																		---	---	---	---
SMG6	23293	broad.mit.edu	37	17	1964768	1964770	+	3'UTR	DEL	GGC	-	-	rs36097261		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1964768_1964770delGGC	uc002fub.1	-	19					SMG6_uc010vqv.1_3'UTR	NM_017575	NP_060045			Smg-6 homolog, nonsense mediated mRNA decay						mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation|telomere maintenance	chromosome, telomeric region|cytosol|nucleolus|telomerase holoenzyme complex	endoribonuclease activity|metal ion binding|protein binding|telomeric DNA binding			central_nervous_system(2)|lung(1)|kidney(1)	4																		---	---	---	---
SMG6	23293	broad.mit.edu	37	17	1982773	1982773	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1982773delA	uc002fub.1	-						SMG6_uc010vqv.1_Intron	NM_017575	NP_060045			Smg-6 homolog, nonsense mediated mRNA decay						mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation|telomere maintenance	chromosome, telomeric region|cytosol|nucleolus|telomerase holoenzyme complex	endoribonuclease activity|metal ion binding|protein binding|telomeric DNA binding			central_nervous_system(2)|lung(1)|kidney(1)	4																		---	---	---	---
SMG6	23293	broad.mit.edu	37	17	2075774	2075774	+	Intron	DEL	T	-	-	rs75172492		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2075774delT	uc002fub.1	-						SMG6_uc010vqv.1_Intron	NM_017575	NP_060045			Smg-6 homolog, nonsense mediated mRNA decay						mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation|telomere maintenance	chromosome, telomeric region|cytosol|nucleolus|telomerase holoenzyme complex	endoribonuclease activity|metal ion binding|protein binding|telomeric DNA binding			central_nervous_system(2)|lung(1)|kidney(1)	4																		---	---	---	---
PAFAH1B1	5048	broad.mit.edu	37	17	2516550	2516550	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2516550delC	uc002fuw.3	+						PAFAH1B1_uc010ckb.1_Intron	NM_000430	NP_000421			platelet-activating factor acetylhydrolase,						acrosome assembly|actin cytoskeleton organization|adult locomotory behavior|brain morphogenesis|corpus callosum morphogenesis|establishment of mitotic spindle orientation|G2/M transition of mitotic cell cycle|hippocampus development|layer formation in cerebral cortex|learning or memory|lipid catabolic process|microtubule organizing center organization|mitotic prometaphase|neuroblast proliferation|neuromuscular process controlling balance|neuron migration|platelet activating factor metabolic process|regulation of Rho GTPase activity|retrograde axon cargo transport|synaptic transmission|vesicle transport along microtubule	astral microtubule|cell cortex|centrosome|cytosol|kinetochore|motile primary cilium|nuclear membrane|perinuclear region of cytoplasm	dynactin binding|heparin binding|microtubule binding|phospholipase binding|phosphoprotein binding|protein homodimerization activity			skin(1)	1																		---	---	---	---
KIAA0664	23277	broad.mit.edu	37	17	2596961	2596962	+	Intron	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2596961_2596962insG	uc002fuy.1	-						KIAA0664_uc002fux.1_Intron|KIAA0664_uc010ckc.1_Intron	NM_015229	NP_056044			hypothetical protein LOC23277								binding			breast(2)	2																		---	---	---	---
RAP1GAP2	23108	broad.mit.edu	37	17	2805515	2805516	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2805515_2805516delTT	uc010ckd.2	+						RAP1GAP2_uc010cke.2_Intron	NM_015085	NP_055900			RAP1 GTPase activating protein 2 isoform 1						regulation of small GTPase mediated signal transduction	centrosome|cytosol|perinuclear region of cytoplasm	GTPase activator activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	2942592	2942592	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2942592delT								RAP1GAP2 (1558 upstream) : OR1D4 (23372 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	3190096	3190096	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3190096delG								OR3A2 (7828 upstream) : OR3A1 (4833 downstream)																																			---	---	---	---
TRPV3	162514	broad.mit.edu	37	17	3429777	3429777	+	Intron	DEL	A	-	-	rs112541565		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3429777delA	uc002fvt.1	-						TRPV3_uc002fvs.1_Intron|TRPV3_uc010vrh.1_Intron|TRPV3_uc010vri.1_Intron|TRPV3_uc010vrj.1_Intron|TRPV3_uc010vrk.1_Intron|TRPV3_uc010vrl.1_Intron|TRPV3_uc010vrm.1_Intron|TRPV3_uc002fvr.2_Intron|TRPV3_uc002fvu.2_Intron|TRPV3_uc010vrn.1_Intron	NM_145068	NP_659505			transient receptor potential cation channel,							integral to membrane	calcium channel activity			ovary(4)	4					Menthol(DB00825)													---	---	---	---
TRPV3	162514	broad.mit.edu	37	17	3430380	3430380	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3430380delG	uc002fvt.1	-						TRPV3_uc002fvs.1_Intron|TRPV3_uc010vrh.1_Intron|TRPV3_uc010vri.1_Intron|TRPV3_uc010vrj.1_Intron|TRPV3_uc010vrk.1_Intron|TRPV3_uc010vrl.1_Intron|TRPV3_uc010vrm.1_Intron|TRPV3_uc002fvr.2_Intron|TRPV3_uc002fvu.2_Intron|TRPV3_uc010vrn.1_Intron	NM_145068	NP_659505			transient receptor potential cation channel,							integral to membrane	calcium channel activity			ovary(4)	4					Menthol(DB00825)													---	---	---	---
TRPV1	7442	broad.mit.edu	37	17	3469471	3469471	+	3'UTR	DEL	A	-	-	rs77350414		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3469471delA	uc010vrr.1	-	15					TRPV1_uc010vro.1_3'UTR|TRPV1_uc010vrp.1_3'UTR|TRPV1_uc010vrq.1_3'UTR|TRPV1_uc010vrs.1_3'UTR|TRPV1_uc010vrt.1_3'UTR|TRPV1_uc010vru.1_3'UTR	NM_080706	NP_542437			transient receptor potential cation channel,						cell surface receptor linked signaling pathway|chemosensory behavior|thermoception	cell junction|dendritic spine membrane|integral to plasma membrane|postsynaptic membrane	ATP binding|calcium channel activity|calmodulin binding			ovary(1)	1				Lung(1;0.055)|COAD - Colon adenocarcinoma(5;0.0896)|LUAD - Lung adenocarcinoma(1115;0.131)	Alpha-Linolenic Acid(DB00132)|Aspartame(DB00168)|Icosapent(DB00159)													---	---	---	---
C17orf85	55421	broad.mit.edu	37	17	3725406	3725406	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3725406delT	uc010ckl.1	-						C17orf85_uc002fwr.2_Intron|C17orf85_uc002fwq.2_Intron	NM_001114118	NP_001107590			ELG protein isoform a								nucleotide binding			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (3;0.0725)														---	---	---	---
ZZEF1	23140	broad.mit.edu	37	17	3999601	3999601	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3999601delA	uc002fxe.2	-						ZZEF1_uc002fxk.1_Intron	NM_015113	NP_055928			zinc finger, ZZ type with EF hand domain 1								calcium ion binding|zinc ion binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
UBE2G1	7326	broad.mit.edu	37	17	4207466	4207466	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4207466delT	uc002fxs.2	-							NM_003342	NP_003333			ubiquitin-conjugating enzyme E2G 1						protein K48-linked ubiquitination|protein K63-linked ubiquitination|ubiquitin-dependent protein catabolic process		ATP binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity				0																		---	---	---	---
SMTNL2	342527	broad.mit.edu	37	17	4509421	4509421	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4509421delT	uc002fyf.1	+						SMTNL2_uc002fye.2_Intron	NM_001114974	NP_001108446			smoothelin-like 2 isoform 1												0				READ - Rectum adenocarcinoma(115;0.0325)														---	---	---	---
SMTNL2	342527	broad.mit.edu	37	17	4511254	4511255	+	3'UTR	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4511254_4511255delAG	uc002fyf.1	+	8					SMTNL2_uc002fye.2_3'UTR|uc002fyg.1_5'Flank	NM_001114974	NP_001108446			smoothelin-like 2 isoform 1												0				READ - Rectum adenocarcinoma(115;0.0325)														---	---	---	---
MINK1	50488	broad.mit.edu	37	17	4743682	4743682	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4743682delA	uc010vsl.1	+						MINK1_uc010vsk.1_Intron|MINK1_uc010vsm.1_Intron|MINK1_uc010vsn.1_Intron|MINK1_uc010vso.1_Intron	NM_153827	NP_722549			misshapen-like kinase 1 isoform 3						JNK cascade	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			central_nervous_system(2)|stomach(1)|large_intestine(1)|lung(1)|skin(1)	6																		---	---	---	---
PFN1	5216	broad.mit.edu	37	17	4848973	4848973	+	3'UTR	DEL	A	-	-	rs77350166		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4848973delA	uc002gaa.2	-	3					PFN1_uc002fzz.2_3'UTR	NM_005022	NP_005013			profilin 1						actin cytoskeleton organization|platelet activation|platelet degranulation	actin cytoskeleton|cytoplasm	actin binding|proline-rich region binding				0																		---	---	---	---
ZFP3	124961	broad.mit.edu	37	17	4990738	4990738	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4990738delT	uc002gaq.2	+							NM_153018	NP_694563			zinc finger protein-3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
USP6	9098	broad.mit.edu	37	17	5044641	5044642	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5044641_5044642delAA	uc002gau.1	+						USP6_uc002gav.1_Intron|USP6_uc010ckz.1_Intron	NM_004505	NP_004496			ubiquitin specific protease 6						protein deubiquitination|regulation of vesicle-mediated transport|ubiquitin-dependent protein catabolic process	lysosome|plasma membrane|recycling endosome	calmodulin binding|cysteine-type endopeptidase activity|nucleic acid binding|protein binding|Rab GTPase activator activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			skin(2)|upper_aerodigestive_tract(1)|lung(1)|breast(1)	5								T	COL1A1|CDH11|ZNF9|OMD	aneurysmal bone cysts								---	---	---	---
RABEP1	9135	broad.mit.edu	37	17	5271654	5271654	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5271654delT	uc002gbm.3	+						RABEP1_uc010clc.1_Intron|RABEP1_uc010cld.1_Intron|RABEP1_uc010vsw.1_Intron|RABEP1_uc002gbl.3_Intron|NUP88_uc002gbn.2_Intron	NM_004703	NP_004694			rabaptin, RAB GTPase binding effector protein 1						apoptosis|cellular membrane fusion|endocytosis|protein transport	centrosome|early endosome|endocytic vesicle|recycling endosome	growth factor activity|GTPase activator activity|protein homodimerization activity			large_intestine(1)|ovary(1)	2																		---	---	---	---
NUP88	4927	broad.mit.edu	37	17	5317524	5317524	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5317524delT	uc002gbo.1	-						NUP88_uc010vsx.1_Intron|NUP88_uc010cle.1_Intron|NUP88_uc010vsy.1_Intron	NM_002532	NP_002523			nucleoporin 88kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	transporter activity			kidney(1)	1																		---	---	---	---
C1QBP	708	broad.mit.edu	37	17	5344447	5344448	+	5'Flank	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5344447_5344448delAA	uc002gby.1	-							NM_001212	NP_001203			complement component 1, q subcomponent binding						blood coagulation, intrinsic pathway|immune response|interspecies interaction between organisms	mitochondrial matrix|nucleus|plasma membrane				ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	5623109	5623110	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5623109_5623110delAA								NLRP1 (135277 upstream) : WSCD1 (349327 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	5834917	5834917	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5834917delT								NLRP1 (347085 upstream) : WSCD1 (137520 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	5921031	5921031	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5921031delA								NLRP1 (433199 upstream) : WSCD1 (51406 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	5968000	5968000	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5968000delT								NLRP1 (480168 upstream) : WSCD1 (4437 downstream)																																			---	---	---	---
AIPL1	23746	broad.mit.edu	37	17	6338530	6338530	+	5'Flank	DEL	G	-	-	rs7211442	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6338530delG	uc002gcp.2	-						AIPL1_uc002gcq.2_5'Flank|AIPL1_uc002gcr.2_5'Flank|AIPL1_uc010clk.2_5'Flank|AIPL1_uc010cll.2_5'Flank|AIPL1_uc002gcs.2_5'Flank	NM_014336	NP_055151			aryl hydrocarbon receptor interacting						protein farnesylation|protein folding|visual perception	cytoplasm|nucleus	farnesylated protein binding|unfolded protein binding				0				COAD - Colon adenocarcinoma(228;0.141)														---	---	---	---
KIAA0753	9851	broad.mit.edu	37	17	6498378	6498378	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6498378delA	uc002gde.3	-						KIAA0753_uc010vtd.1_Intron|KIAA0753_uc010clo.2_Intron|KIAA0753_uc010vte.1_Intron	NM_014804	NP_055619			hypothetical protein LOC9851							centrosome					0				COAD - Colon adenocarcinoma(228;0.157)														---	---	---	---
MED31	51003	broad.mit.edu	37	17	6547714	6547714	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6547714delT	uc002gdg.3	-	4					MED31_uc002gdh.3_RNA|TXNDC17_uc002gdf.3_3'UTR	NM_016060	NP_057144			mediator of RNA polymerase II transcription,						regulation of transcription, DNA-dependent|transcription, DNA-dependent	mediator complex	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	6653556	6653556	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6653556delA								SLC13A5 (36816 upstream) : XAF1 (5238 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	6825876	6825876	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6825876delA								ALOX12P2 (22209 upstream) : ALOX12 (73508 downstream)																																			---	---	---	---
ALOX12	239	broad.mit.edu	37	17	6909554	6909554	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6909554delG	uc002gdx.3	+						uc002gdy.1_Intron	NM_000697	NP_000688			arachidonate 12-lipoxygenase						anti-apoptosis|cellular component movement|fatty acid oxidation|leukotriene biosynthetic process|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of cell proliferation|superoxide anion generation	cytosol|sarcolemma	arachidonate 12-lipoxygenase activity|hepoxilin-epoxide hydrolase activity|iron ion binding|lipoxygenase activity|protein binding			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	6957757	6957757	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6957757delT								SLC16A11 (10515 upstream) : CLEC10A (20100 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	7042385	7042385	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7042385delA								ASGR2 (24093 upstream) : ASGR1 (34367 downstream)																																			---	---	---	---
DLG4	1742	broad.mit.edu	37	17	7100722	7100722	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7100722delT	uc002get.3	-						DLG4_uc010vtm.1_Intron|DLG4_uc010vtn.1_Intron|DLG4_uc010cly.2_Intron|DLG4_uc010vto.1_Intron	NM_001365	NP_001356			post-synaptic density protein 95 isoform 1						axon guidance|learning|protein complex assembly|protein localization to synapse|signal transduction|synaptic transmission	cell junction|cortical cytoskeleton|endocytic vesicle membrane|neuron spine|postsynaptic density|postsynaptic membrane|synaptosome	protein binding|protein C-terminus binding			ovary(1)|breast(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	7260827	7260827	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7260827delA								TMEM95 (289 upstream) : TNK1 (23538 downstream)																																			---	---	---	---
NLGN2	57555	broad.mit.edu	37	17	7315332	7315332	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7315332delT	uc002ggt.1	+							NM_020795	NP_065846			neuroligin 2 precursor						cell-cell junction maintenance|neuron cell-cell adhesion|positive regulation of synaptogenesis|regulation of inhibitory postsynaptic membrane potential|synapse assembly	cell surface|integral to plasma membrane|postsynaptic membrane	neurexin binding|receptor activity			central_nervous_system(1)	1		Prostate(122;0.157)																---	---	---	---
NLGN2	57555	broad.mit.edu	37	17	7321449	7321449	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7321449delT	uc002ggt.1	+	7					FGF11_uc010vtw.1_5'Flank|SPEM1_uc002ggv.2_5'Flank	NM_020795	NP_065846			neuroligin 2 precursor						cell-cell junction maintenance|neuron cell-cell adhesion|positive regulation of synaptogenesis|regulation of inhibitory postsynaptic membrane potential|synapse assembly	cell surface|integral to plasma membrane|postsynaptic membrane	neurexin binding|receptor activity			central_nervous_system(1)	1		Prostate(122;0.157)																---	---	---	---
ATP1B2	482	broad.mit.edu	37	17	7557763	7557763	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7557763delT	uc002gif.1	+							NM_001678	NP_001669			Na+/K+ -ATPase beta 2 subunit						ATP biosynthetic process|blood coagulation|leukocyte migration	integral to membrane|plasma membrane	protein binding|sodium:potassium-exchanging ATPase activity	p.0?(2)|p.?(1)		central_nervous_system(1)|pancreas(1)	2		all_cancers(10;0.000178)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;2.55e-06)|READ - Rectum adenocarcinoma(115;0.168)														---	---	---	---
TP53	7157	broad.mit.edu	37	17	7581269	7581271	+	Intron	DEL	TTC	-	-	rs1794284	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7581269_7581271delTTC	uc002gim.2	-						TP53_uc002gig.1_5'Flank|TP53_uc002gih.2_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Intron|TP53_uc010cni.1_Intron|TP53_uc002gij.2_Intron|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Intron|TP53_uc002gio.2_Intron|TP53_uc010vug.1_Intron|TP53_uc010cnk.1_Intron	NM_001126112	NP_001119584			tumor protein p53 isoform a						activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.0?(2)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)			111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			---	---	---	---
WRAP53	55135	broad.mit.edu	37	17	7603375	7603375	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7603375delT	uc010vuh.1	+						WRAP53_uc010vui.1_Intron|WRAP53_uc002gip.2_Intron|WRAP53_uc002gir.2_Intron|WRAP53_uc002giq.2_Intron|WRAP53_uc010cnl.2_Intron|WRAP53_uc010vuj.1_5'Flank	NM_001143990	NP_001137462			WD repeat domain 79 isoform 2						positive regulation of telomerase activity|telomere formation via telomerase	Cajal body|cytoplasm|telomerase holoenzyme complex	protein binding|RNA binding				0																		---	---	---	---
WRAP53	55135	broad.mit.edu	37	17	7603866	7603866	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7603866delA	uc010vuh.1	+						WRAP53_uc010vui.1_Intron|WRAP53_uc002gip.2_Intron|WRAP53_uc002gir.2_Intron|WRAP53_uc002giq.2_Intron|WRAP53_uc010cnl.2_Intron|WRAP53_uc010vuj.1_5'Flank	NM_001143990	NP_001137462			WD repeat domain 79 isoform 2						positive regulation of telomerase activity|telomere formation via telomerase	Cajal body|cytoplasm|telomerase holoenzyme complex	protein binding|RNA binding				0																		---	---	---	---
DNAH2	146754	broad.mit.edu	37	17	7716573	7716573	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7716573delT	uc002giu.1	+						DNAH2_uc010cnm.1_Intron	NM_020877	NP_065928			dynein heavy chain domain 3						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|skin(6)|central_nervous_system(1)	13		all_cancers(10;4.66e-07)|Prostate(122;0.081)																---	---	---	---
Unknown	0	broad.mit.edu	37	17	7858584	7858584	+	IGR	DEL	A	-	-	rs78611358		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7858584delA								CNTROB (5689 upstream) : GUCY2D (47404 downstream)																																			---	---	---	---
ALOX15B	247	broad.mit.edu	37	17	7947411	7947412	+	Intron	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7947411_7947412delGA	uc002gju.2	+						ALOX15B_uc002gjv.2_Intron|ALOX15B_uc002gjw.2_Intron|ALOX15B_uc010vun.1_Intron|ALOX15B_uc010cnp.2_Intron	NM_001141	NP_001132			arachidonate 15-lipoxygenase, second type						induction of apoptosis|leukotriene biosynthetic process|negative regulation of cell cycle|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of growth|prostate gland development|regulation of epithelial cell differentiation	cytoplasm	arachidonate 15-lipoxygenase activity|iron ion binding|lipoxygenase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	7958215	7958216	+	5'Flank	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7958215_7958216delTT	uc002gjx.1	+											Homo sapiens cDNA FLJ35294 fis, clone PROST2008724.																														---	---	---	---
ALOX12B	242	broad.mit.edu	37	17	7984601	7984601	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7984601delG	uc002gjy.1	-						uc010cnq.1_RNA	NM_001139	NP_001130			arachidonate 12-lipoxygenase, 12R type						epidermis development|leukotriene biosynthetic process		arachidonate 12-lipoxygenase activity|iron ion binding|lipoxygenase activity				0															Multiple Myeloma(8;0.094)			---	---	---	---
PER1	5187	broad.mit.edu	37	17	8055075	8055075	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8055075delC	uc002gkd.2	-						PER1_uc010vuq.1_5'Flank|PER1_uc010vur.1_Intron|PER1_uc010vus.1_5'Flank	NM_002616	NP_002607			period 1						circadian rhythm|entrainment of circadian clock|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	signal transducer activity			lung(2)|breast(2)|skin(2)|large_intestine(1)|ovary(1)|kidney(1)	9								T	ETV6	AML|CMML			Other_conserved_DNA_damage_response_genes					---	---	---	---
Unknown	0	broad.mit.edu	37	17	8187100	8187100	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8187100delT								PFAS (13292 upstream) : SLC25A35 (3982 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	8258578	8258578	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8258578delA								ODF4 (9215 upstream) : LOC100128288 (3153 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	8259333	8259334	+	IGR	INS	-	T	T	rs76058201		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8259333_8259334insT								ODF4 (9970 upstream) : LOC100128288 (2397 downstream)																																			---	---	---	---
RPL26	6154	broad.mit.edu	37	17	8285832	8285832	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8285832delT	uc002glh.1	-							NM_000987	NP_000978			ribosomal protein L26						endocrine pancreas development|ribosomal large subunit biogenesis|rRNA processing|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	protein binding|RNA binding|structural constituent of ribosome				0																		---	---	---	---
MYH10	4628	broad.mit.edu	37	17	8508327	8508328	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8508327_8508328delAA	uc002gll.2	-						MYH10_uc002glm.2_Intron|MYH10_uc010cnx.2_Intron	NM_005964	NP_005955			myosin, heavy polypeptide 10, non-muscle						actin filament-based movement|axon guidance|cytokinesis after mitosis|regulation of cell shape	cell cortex|cleavage furrow|midbody|myosin complex|stress fiber	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	8579617	8579617	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8579617delT								MYH10 (45581 upstream) : CCDC42 (53630 downstream)																																			---	---	---	---
NTN1	9423	broad.mit.edu	37	17	8966871	8966871	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8966871delT	uc002glw.3	+							NM_004822	NP_004813			netrin 1 precursor						apoptosis|axon guidance		protein binding				0																		---	---	---	---
STX8	9482	broad.mit.edu	37	17	9434334	9434334	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9434334delT	uc002glx.2	-							NM_004853	NP_004844			syntaxin 8						transport	endoplasmic reticulum|integral to plasma membrane				central_nervous_system(1)	1																		---	---	---	---
DHRS7C	201140	broad.mit.edu	37	17	9675931	9675931	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9675931delC	uc010vvb.1	-						DHRS7C_uc010cof.2_Intron	NM_001105571	NP_001099041			dehydrogenase/reductase (SDR family) member 7C							extracellular region	binding|oxidoreductase activity				0																		---	---	---	---
GAS7	8522	broad.mit.edu	37	17	9975450	9975450	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9975450delC	uc002gmg.1	-						GAS7_uc010coh.1_Intron	NM_201433	NP_958839			growth arrest-specific 7 isoform c						cell cycle arrest	cytoplasm	sequence-specific DNA binding transcription factor activity			lung(1)|pancreas(1)	2								T	MLL	AML*								---	---	---	---
GAS7	8522	broad.mit.edu	37	17	9979525	9979530	+	Intron	DEL	GGGAGG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9979525_9979530delGGGAGG	uc002gmg.1	-						GAS7_uc010coh.1_Intron	NM_201433	NP_958839			growth arrest-specific 7 isoform c						cell cycle arrest	cytoplasm	sequence-specific DNA binding transcription factor activity			lung(1)|pancreas(1)	2								T	MLL	AML*								---	---	---	---
MYH8	4626	broad.mit.edu	37	17	10318982	10318982	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10318982delA	uc002gmm.2	-						uc002gml.1_Intron	NM_002472	NP_002463			myosin, heavy chain 8, skeletal muscle,						muscle filament sliding	cytosol|muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			skin(6)|ovary(3)|breast(2)	11														Trismus-Pseudocamptodactyly_Syndrome_with_Cardiac_Myxoma_and_Freckling				---	---	---	---
MYH2	4620	broad.mit.edu	37	17	10428511	10428511	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10428511delT	uc010coi.2	-						uc002gml.1_Intron|MYH2_uc002gmp.3_Intron|MYH2_uc010coj.2_Intron	NM_001100112	NP_001093582			myosin heavy chain IIa						muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(5)|pancreas(4)|skin(3)|lung(1)|kidney(1)	14																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	11038615	11038615	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11038615delT								PIRT (297197 upstream) : SHISA6 (106125 downstream)																																			---	---	---	---
DNAH9	1770	broad.mit.edu	37	17	11708371	11708371	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11708371delA	uc002gne.2	+						DNAH9_uc010coo.2_Intron	NM_001372	NP_001363			dynein, axonemal, heavy chain 9 isoform 2						cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	12459384	12459384	+	Intron	DEL	T	-	-	rs67951351		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12459384delT	uc002gnl.1	+						uc002gnm.1_Intron					Homo sapiens cDNA FLJ34690 fis, clone MESAN2000894.																														---	---	---	---
Unknown	0	broad.mit.edu	37	17	12535172	12535173	+	Intron	INS	-	A	A	rs71369332		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12535172_12535173insA	uc002gnl.1	+						uc002gnm.1_Intron					Homo sapiens cDNA FLJ34690 fis, clone MESAN2000894.																														---	---	---	---
Unknown	0	broad.mit.edu	37	17	14285343	14285344	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14285343_14285344insA								HS3ST3B1 (35851 upstream) : PMP22 (847753 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	14724361	14724361	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14724361delT								HS3ST3B1 (474869 upstream) : PMP22 (408736 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	14904838	14904838	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:14904838delG								HS3ST3B1 (655346 upstream) : PMP22 (228259 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	15281346	15281346	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15281346delA								TEKT3 (36388 upstream) : CDRT4 (57992 downstream)																																			---	---	---	---
FAM18B2	201158	broad.mit.edu	37	17	15433126	15433126	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15433126delT	uc002goq.2	-						CDRT4_uc010vvw.1_Intron|FAM18B2_uc010vvx.1_Intron	NM_145301	NP_660344			hypothetical protein LOC201158 isoform 1							integral to membrane					0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0872)|BRCA - Breast invasive adenocarcinoma(8;0.0581)|READ - Rectum adenocarcinoma(1115;0.0967)														---	---	---	---
NCOR1	9611	broad.mit.edu	37	17	15961099	15961099	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15961099delA	uc002gpo.2	-						NCOR1_uc002gpn.2_Intron|NCOR1_uc002gpl.2_Intron|NCOR1_uc002gpm.2_Intron|NCOR1_uc010vwb.1_Intron|NCOR1_uc010coy.2_Intron|NCOR1_uc010vwc.1_Intron	NM_006311	NP_006302			nuclear receptor co-repressor 1						cellular lipid metabolic process|chromatin modification|negative regulation of JNK cascade|regulation of glycolysis by negative regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by negative regulation of transcription from an RNA polymerase II promoter|spindle assembly|transcription from RNA polymerase II promoter	nuclear chromatin|spindle microtubule|transcriptional repressor complex	histone deacetylase binding|transcription corepressor activity|transcription regulatory region DNA binding			upper_aerodigestive_tract(2)|ovary(1)|central_nervous_system(1)|kidney(1)	5				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)														---	---	---	---
NCOR1	9611	broad.mit.edu	37	17	15961519	15961519	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15961519delA	uc002gpo.2	-						NCOR1_uc002gpn.2_Intron|NCOR1_uc002gpl.2_5'UTR|NCOR1_uc002gpm.2_Intron|NCOR1_uc010vwb.1_Intron|NCOR1_uc010coy.2_Intron|NCOR1_uc010vwc.1_Intron	NM_006311	NP_006302			nuclear receptor co-repressor 1						cellular lipid metabolic process|chromatin modification|negative regulation of JNK cascade|regulation of glycolysis by negative regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by negative regulation of transcription from an RNA polymerase II promoter|spindle assembly|transcription from RNA polymerase II promoter	nuclear chromatin|spindle microtubule|transcriptional repressor complex	histone deacetylase binding|transcription corepressor activity|transcription regulatory region DNA binding			upper_aerodigestive_tract(2)|ovary(1)|central_nervous_system(1)|kidney(1)	5				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)														---	---	---	---
NCOR1	9611	broad.mit.edu	37	17	16062401	16062401	+	Intron	DEL	A	-	-	rs35251798		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16062401delA	uc002gpo.2	-						NCOR1_uc002gpn.2_Intron|NCOR1_uc002gpp.1_Intron|NCOR1_uc002gpr.2_Intron|NCOR1_uc002gps.1_Intron|NCOR1_uc010coz.1_Intron|NCOR1_uc010cpb.1_Intron|NCOR1_uc010cpa.1_Intron	NM_006311	NP_006302			nuclear receptor co-repressor 1						cellular lipid metabolic process|chromatin modification|negative regulation of JNK cascade|regulation of glycolysis by negative regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by negative regulation of transcription from an RNA polymerase II promoter|spindle assembly|transcription from RNA polymerase II promoter	nuclear chromatin|spindle microtubule|transcriptional repressor complex	histone deacetylase binding|transcription corepressor activity|transcription regulatory region DNA binding			upper_aerodigestive_tract(2)|ovary(1)|central_nervous_system(1)|kidney(1)	5				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)														---	---	---	---
PIGL	9487	broad.mit.edu	37	17	16148156	16148156	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16148156delT	uc002gpv.2	+						PIGL_uc010vwd.1_Intron	NM_004278	NP_004269			phosphatidylinositol glycan anchor biosynthesis,						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	N-acetylglucosaminylphosphatidylinositol deacetylase activity				0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0934)														---	---	---	---
PIGL	9487	broad.mit.edu	37	17	16159343	16159343	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16159343delA	uc002gpv.2	+						PIGL_uc010vwd.1_Intron	NM_004278	NP_004269			phosphatidylinositol glycan anchor biosynthesis,						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	N-acetylglucosaminylphosphatidylinositol deacetylase activity				0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0934)														---	---	---	---
C17orf76	388341	broad.mit.edu	37	17	16356663	16356670	+	Intron	DEL	CACACACA	-	-	rs72023119		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16356663_16356670delCACACACA	uc010cph.1	-						C17orf76_uc002gqh.2_Intron|NCRNA00188_uc010vwl.1_Intron|NCRNA00188_uc010vwm.1_Intron|NCRNA00188_uc010vwn.1_Intron|NCRNA00188_uc010cpe.2_Intron|NCRNA00188_uc010vwo.1_Intron|NCRNA00188_uc010vwp.1_Intron	NM_001113567	NP_001107039			hypothetical protein LOC388341 isoform 1												0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0887)														---	---	---	---
COPS3	8533	broad.mit.edu	37	17	17168716	17168716	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17168716delT	uc002grd.2	-						COPS3_uc010vwv.1_Intron|COPS3_uc010vww.1_Intron	NM_003653	NP_003644			COP9 constitutive photomorphogenic homolog						cullin deneddylation|response to light stimulus|signal transduction	cytoplasm|signalosome	protein binding			skin(1)	1																		---	---	---	---
COPS3	8533	broad.mit.edu	37	17	17173472	17173473	+	Intron	DEL	AA	-	-	rs112388445		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17173472_17173473delAA	uc002grd.2	-						COPS3_uc010vwv.1_Intron|COPS3_uc010vww.1_Intron	NM_003653	NP_003644			COP9 constitutive photomorphogenic homolog						cullin deneddylation|response to light stimulus|signal transduction	cytoplasm|signalosome	protein binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	17265861	17265861	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17265861delT								NT5M (14886 upstream) : MED9 (114439 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	17311086	17311086	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17311086delT								NT5M (60111 upstream) : MED9 (69214 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	17315498	17315498	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17315498delT								NT5M (64523 upstream) : MED9 (64802 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	17315673	17315673	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17315673delT								NT5M (64698 upstream) : MED9 (64627 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	17332986	17332986	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17332986delT								NT5M (82011 upstream) : MED9 (47314 downstream)																																			---	---	---	---
TOM1L2	146691	broad.mit.edu	37	17	17795944	17795944	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17795944delC	uc002grz.3	-						TOM1L2_uc002gry.3_Intron|TOM1L2_uc010vwy.1_Intron|TOM1L2_uc010cpr.2_Intron|TOM1L2_uc010vwz.1_Intron|TOM1L2_uc010vxa.1_Intron|TOM1L2_uc010vxb.1_Intron	NM_001082968	NP_001076437			target of myb1-like 2 isoform 3						intracellular protein transport	intracellular					0	all_neural(463;0.228)																	---	---	---	---
TOP3A	7156	broad.mit.edu	37	17	18203388	18203389	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18203388_18203389delAA	uc002gsx.1	-						TOP3A_uc010vxr.1_5'Flank|TOP3A_uc002gsw.1_Intron|TOP3A_uc010vxs.1_Intron|TOP3A_uc010cqa.1_Intron	NM_004618	NP_004609			topoisomerase (DNA) III alpha						DNA topological change|meiosis	chromosome|PML body	ATP binding|DNA topoisomerase type I activity|protein binding|zinc ion binding			skin(3)	3																		---	---	---	---
TBC1D28	254272	broad.mit.edu	37	17	18542715	18542717	+	Intron	DEL	GAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18542715_18542717delGAA	uc002gud.2	-							NM_001039397	NP_001034486			TBC1 domain family, member 28							intracellular	Rab GTPase activator activity			ovary(1)	1																		---	---	---	---
PRPSAP2	5636	broad.mit.edu	37	17	18768167	18768167	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18768167delT	uc002gup.1	+						PRPSAP2_uc002guo.1_Intron|PRPSAP2_uc010vyi.1_Intron|PRPSAP2_uc010vyj.1_Intron|PRPSAP2_uc010vyk.1_5'Flank	NM_002767	NP_002758			phosphoribosyl pyrophosphate						nucleotide biosynthetic process		enzyme inhibitor activity|magnesium ion binding|ribose phosphate diphosphokinase activity			skin(1)	1																		---	---	---	---
EPN2	22905	broad.mit.edu	37	17	19165498	19165499	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19165498_19165499insA	uc002gvd.3	+						EPN2_uc002gvc.2_Intron|EPN2_uc010vyn.1_Intron|EPN2_uc010cql.1_Intron|EPN2_uc002gve.3_Intron|EPN2_uc002gvf.3_Intron|EPN2_uc010vyo.1_Intron	NM_014964	NP_055779			epsin 2 isoform b						endocytosis		lipid binding			skin(1)	1	all_cancers(12;3.11e-05)|all_epithelial(12;0.00121)|Hepatocellular(7;0.00345)|Breast(13;0.143)																	---	---	---	---
AKAP10	11216	broad.mit.edu	37	17	19861222	19861222	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19861222delA	uc002gwo.2	-						AKAP10_uc002gwp.1_Intron|AKAP10_uc010cqw.1_Intron|AKAP10_uc010vze.1_Intron	NM_007202	NP_009133			A-kinase anchor protein 10 precursor						blood coagulation|protein localization	cytosol|mitochondrion|plasma membrane	signal transducer activity			skin(1)	1	all_cancers(12;2.08e-05)|all_epithelial(12;0.00158)|Breast(13;0.165)																	---	---	---	---
CYTSB	92521	broad.mit.edu	37	17	20194866	20194867	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20194866_20194867delTT	uc002gwq.2	+						CYTSB_uc002gws.2_Intron|CYTSB_uc002gwv.2_Intron|CYTSB_uc010vzf.1_Intron|CYTSB_uc002gww.2_Intron	NM_001033553	NP_001028725			spectrin domain with coiled-coils 1 NSP5b3b							nucleus					0																		---	---	---	---
CYTSB	92521	broad.mit.edu	37	17	20209172	20209173	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20209172_20209173delTT	uc002gwq.2	+						CYTSB_uc002gws.2_Intron|CYTSB_uc002gwv.2_Intron|CYTSB_uc010vzf.1_Intron|CYTSB_uc002gww.2_Intron	NM_001033553	NP_001028725			spectrin domain with coiled-coils 1 NSP5b3b							nucleus					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	20321840	20321840	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20321840delA								CCDC144C (16336 upstream) : LGALS9B (31336 downstream)																																			---	---	---	---
LGALS9B	284194	broad.mit.edu	37	17	20358814	20358814	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20358814delG	uc002gxa.1	-						LGALS9B_uc002gwz.1_Intron|LGALS9B_uc010vzh.1_Intron	NM_001042685	NP_001036150			galectin-9 like								sugar binding			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	20492076	20492077	+	IGR	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20492076_20492077delAC								LGALS9B (121228 upstream) : CCDC144NL (274633 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	20675883	20675883	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20675883delT								LGALS9B (305035 upstream) : CCDC144NL (90827 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	20683349	20683350	+	IGR	INS	-	C	C	rs141043289	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20683349_20683350insC								LGALS9B (312501 upstream) : CCDC144NL (83360 downstream)																																			---	---	---	---
DHRS7B	25979	broad.mit.edu	37	17	21052466	21052466	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21052466delA	uc002gyo.2	+							NM_015510	NP_056325			dehydrogenase/reductase (SDR family) member 7B							integral to membrane|peroxisomal membrane	binding|oxidoreductase activity			pancreas(1)	1																		---	---	---	---
DHRS7B	25979	broad.mit.edu	37	17	21057049	21057049	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21057049delA	uc002gyo.2	+							NM_015510	NP_056325			dehydrogenase/reductase (SDR family) member 7B							integral to membrane|peroxisomal membrane	binding|oxidoreductase activity			pancreas(1)	1																		---	---	---	---
TMEM11	8834	broad.mit.edu	37	17	21106814	21106814	+	Intron	DEL	G	-	-	rs11357405		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21106814delG	uc002gyp.2	-						TMEM11_uc002gyq.2_Intron	NM_003876	NP_003867			transmembrane protein 11						mitochondrion organization	integral to mitochondrial inner membrane|integral to plasma membrane	protein binding				0																		---	---	---	---
TMEM11	8834	broad.mit.edu	37	17	21119986	21119986	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21119986delT	uc002gyp.2	-						TMEM11_uc002gyq.2_5'Flank	NM_003876	NP_003867			transmembrane protein 11						mitochondrion organization	integral to mitochondrial inner membrane|integral to plasma membrane	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	21161866	21161867	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21161866_21161867delAA								C17orf103 (5288 upstream) : MAP2K3 (26101 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21324811	21324815	+	IGR	DEL	AGGGT	-	-	rs141749648		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21324811_21324815delAGGGT								KCNJ12 (1632 upstream) : C17orf51 (106757 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21516327	21516328	+	IGR	INS	-	CAG	CAG	rs138704073	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21516327_21516328insCAG								C17orf51 (38596 upstream) : FAM27L (309042 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21518737	21518737	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21518737delA								C17orf51 (41006 upstream) : FAM27L (306633 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21541903	21541904	+	IGR	INS	-	G	G	rs146783355		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21541903_21541904insG								C17orf51 (64172 upstream) : FAM27L (283466 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21545305	21545305	+	IGR	DEL	T	-	-	rs71303754		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21545305delT								C17orf51 (67574 upstream) : FAM27L (280065 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21545864	21545865	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21545864_21545865insT								C17orf51 (68133 upstream) : FAM27L (279505 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21564474	21564475	+	IGR	INS	-	G	G	rs148417302		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21564474_21564475insG								C17orf51 (86743 upstream) : FAM27L (260895 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	21729415	21729415	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21729415delA	uc002gyy.3	+											SubName: Full=cDNA FLJ51326, highly similar to Homo sapiens ubiquitin B (UBB), mRNA;																														---	---	---	---
Unknown	0	broad.mit.edu	37	17	25278530	25278531	+	IGR	DEL	TT	-	-	rs141329779		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25278530_25278531delTT								None (None upstream) : WSB1 (342575 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	25279403	25279403	+	IGR	DEL	G	-	-	rs148242435	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25279403delG								None (None upstream) : WSB1 (341703 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	25291546	25291548	+	IGR	DEL	TAG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25291546_25291548delTAG								None (None upstream) : WSB1 (329558 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	25314079	25314079	+	IGR	DEL	A	-	-	rs113118575		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25314079delA								None (None upstream) : WSB1 (307027 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	25380546	25380546	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25380546delA								None (None upstream) : WSB1 (240560 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	25549656	25549656	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25549656delA								None (None upstream) : WSB1 (71450 downstream)																																			---	---	---	---
WSB1	26118	broad.mit.edu	37	17	25621293	25621293	+	5'UTR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25621293delC	uc002gzd.1	+	1					WSB1_uc010vzy.1_5'UTR|WSB1_uc010vzz.1_5'UTR|WSB1_uc010crf.1_5'UTR|WSB1_uc002gze.1_5'UTR|WSB1_uc002gzf.1_RNA	NM_015626	NP_056441			WD repeat and SOCS box-containing 1 isoform 1						intracellular signal transduction	intracellular	protein binding				0	all_cancers(1;2e-13)|all_epithelial(1;4.8e-15)|Lung NSC(42;0.00152)		BRCA - Breast invasive adenocarcinoma(3;0.0152)	UCEC - Uterine corpus endometrioid carcinoma (53;0.154)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	25753329	25753329	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25753329delC	uc002gzg.2	+						uc002gzi.1_5'Flank					Homo sapiens similar to ubiquitin specific protease 6, mRNA (cDNA clone IMAGE:5168266), with apparent retained intron.																														---	---	---	---
KSR1	8844	broad.mit.edu	37	17	25848361	25848361	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25848361delT	uc010crg.2	+						KSR1_uc002gzj.1_Intron	NM_014238	NP_055053			kinase suppressor of ras						Ras protein signal transduction	cytoplasm|membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|central_nervous_system(1)	4	Lung NSC(42;0.00836)		BRCA - Breast invasive adenocarcinoma(3;0.00122)	UCEC - Uterine corpus endometrioid carcinoma (53;0.168)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	25988693	25988702	+	IGR	DEL	CACAGGTGGC	-	-	rs3217511		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:25988693_25988702delCACAGGTGGC								LGALS9 (12108 upstream) : NOS2 (95091 downstream)																																			---	---	---	---
NOS2	4843	broad.mit.edu	37	17	26145563	26145563	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26145563delA	uc010crh.1	-							NM_000625	NP_000616			nitric oxide synthase 2A						arginine catabolic process|defense response to Gram-negative bacterium|innate immune response in mucosa|nitric oxide biosynthetic process|peptidyl-cysteine S-nitrosylation|platelet activation|positive regulation of killing of cells of other organism|positive regulation of leukocyte mediated cytotoxicity|regulation of cellular respiration|regulation of insulin secretion|superoxide metabolic process	cytosol|nucleus	arginine binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|protein homodimerization activity|tetrahydrobiopterin binding			skin(2)|ovary(1)|breast(1)	4					Dexamethasone(DB01234)|Hydrocortisone(DB00741)|L-Arginine(DB00125)|L-Citrulline(DB00155)													---	---	---	---
NOS2	4843	broad.mit.edu	37	17	26201836	26201836	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26201836delT	uc010crh.1	-							NM_000625	NP_000616			nitric oxide synthase 2A						arginine catabolic process|defense response to Gram-negative bacterium|innate immune response in mucosa|nitric oxide biosynthetic process|peptidyl-cysteine S-nitrosylation|platelet activation|positive regulation of killing of cells of other organism|positive regulation of leukocyte mediated cytotoxicity|regulation of cellular respiration|regulation of insulin secretion|superoxide metabolic process	cytosol|nucleus	arginine binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|protein homodimerization activity|tetrahydrobiopterin binding			skin(2)|ovary(1)|breast(1)	4					Dexamethasone(DB01234)|Hydrocortisone(DB00741)|L-Arginine(DB00125)|L-Citrulline(DB00155)													---	---	---	---
Unknown	0	broad.mit.edu	37	17	26235904	26235904	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26235904delT								NOS2 (15495 upstream) : NLK (133784 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	26284561	26284561	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26284561delT								NOS2 (64152 upstream) : NLK (85127 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	26568936	26568936	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26568936delA								PYY2 (13853 upstream) : PPY2 (5534 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	26585291	26585291	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26585291delA								PPY2 (9977 upstream) : FLJ40504 (18317 downstream)																																			---	---	---	---
TNFAIP1	7126	broad.mit.edu	37	17	26660285	26660285	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26660285delC	uc002hax.1	+						IFT20_uc002hau.1_Intron|IFT20_uc002hav.1_Intron|IFT20_uc002haw.1_Intron|IFT20_uc010wae.1_Intron|TNFAIP1_uc002hay.2_5'Flank|TNFAIP1_uc010waf.1_5'Flank	NM_021137	NP_066960			tumor necrosis factor, alpha-induced protein 1						apoptosis|cell migration|DNA replication|embryo development|immune response|negative regulation of Rho protein signal transduction|proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination|stress fiber assembly	Cul3-RING ubiquitin ligase complex|endosome|nucleus|voltage-gated potassium channel complex	GTP-Rho binding|voltage-gated potassium channel activity				0	all_lung(13;0.000294)|Lung NSC(42;0.000964)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)														---	---	---	---
POLDIP2	26073	broad.mit.edu	37	17	26677324	26677324	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26677324delT	uc002haz.2	-						POLDIP2_uc010wag.1_Intron	NM_015584	NP_056399			DNA polymerase delta interacting protein 2							mitochondrial nucleoid|nucleus					0	all_lung(13;0.000354)|Lung NSC(42;0.00115)			UCEC - Uterine corpus endometrioid carcinoma (53;0.154)														---	---	---	---
DHRS13	147015	broad.mit.edu	37	17	27226057	27226057	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27226057delA	uc002hde.3	-						FLOT2_uc002hdc.2_5'Flank|DHRS13_uc002hdd.3_Intron|DHRS13_uc010wba.1_Intron	NM_144683	NP_653284			dehydrogenase/reductase (SDR family) member 13							extracellular region	binding|oxidoreductase activity				0	all_cancers(5;2.12e-15)|all_epithelial(6;3.44e-19)|Lung NSC(42;0.01)		Epithelial(11;1.59e-06)|all cancers(11;9.27e-06)|BRCA - Breast invasive adenocarcinoma(11;5.78e-05)|OV - Ovarian serous cystadenocarcinoma(11;0.0602)															---	---	---	---
PHF12	57649	broad.mit.edu	37	17	27242444	27242446	+	Intron	DEL	GGA	-	-	rs10529696		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27242444_27242446delGGA	uc002hdg.1	-						PHF12_uc010wbb.1_Intron|PHF12_uc002hdi.1_Intron|PHF12_uc002hdj.1_Intron|PHF12_uc010crw.1_Intron|PHF12_uc002hdh.1_Intron	NM_001033561	NP_001028733			PHD finger protein 12 isoform 1						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	transcriptional repressor complex	protein binding|zinc ion binding			ovary(1)	1	all_cancers(5;1.95e-14)|all_epithelial(6;5e-18)|Lung NSC(42;0.01)		Epithelial(11;1.64e-05)|all cancers(11;7.47e-05)|BRCA - Breast invasive adenocarcinoma(11;9.79e-05)															---	---	---	---
PHF12	57649	broad.mit.edu	37	17	27261065	27261065	+	Intron	DEL	A	-	-	rs35582292		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27261065delA	uc002hdg.1	-						PHF12_uc010wbb.1_Intron|PHF12_uc002hdi.1_Intron|PHF12_uc002hdj.1_Intron|PHF12_uc010crw.1_Intron|PHF12_uc002hdk.1_Intron|uc002hdl.2_Intron	NM_001033561	NP_001028733			PHD finger protein 12 isoform 1						negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	transcriptional repressor complex	protein binding|zinc ion binding			ovary(1)	1	all_cancers(5;1.95e-14)|all_epithelial(6;5e-18)|Lung NSC(42;0.01)		Epithelial(11;1.64e-05)|all cancers(11;7.47e-05)|BRCA - Breast invasive adenocarcinoma(11;9.79e-05)															---	---	---	---
MYO18A	399687	broad.mit.edu	37	17	27503406	27503406	+	Intron	DEL	A	-	-	rs71359276		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27503406delA	uc002hdt.1	-						MYO18A_uc010csa.1_Intron|MYO18A_uc002hdu.1_Intron	NM_078471	NP_510880			myosin 18A isoform a						anti-apoptosis|DNA metabolic process	ER-Golgi intermediate compartment|myosin complex	ATP binding|DNA binding|DNA-dependent ATPase activity|identical protein binding|motor activity				0			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)															---	---	---	---
SSH2	85464	broad.mit.edu	37	17	28041552	28041552	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28041552delT	uc002heo.1	-						SSH2_uc010wbh.1_Intron|SSH2_uc002hep.1_Intron|SSH2_uc002heq.2_Intron|SSH2_uc002her.2_Intron|SSH2_uc010csc.1_Intron	NM_033389	NP_203747			slingshot 2						actin cytoskeleton organization|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of lamellipodium assembly	cytoplasm|cytoskeleton	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			skin(2)	2																		---	---	---	---
SSH2	85464	broad.mit.edu	37	17	28047745	28047745	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28047745delA	uc002heo.1	-						SSH2_uc010wbh.1_Intron|SSH2_uc002hep.1_Intron|SSH2_uc002heq.2_Intron|SSH2_uc002her.2_Intron|SSH2_uc010csc.1_Intron	NM_033389	NP_203747			slingshot 2						actin cytoskeleton organization|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of lamellipodium assembly	cytoplasm|cytoskeleton	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			skin(2)	2																		---	---	---	---
EFCAB5	374786	broad.mit.edu	37	17	28292087	28292088	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28292087_28292088delTT	uc002het.2	+						EFCAB5_uc010wbi.1_Intron|EFCAB5_uc010wbj.1_Intron|EFCAB5_uc010wbk.1_Intron|EFCAB5_uc010csd.2_Intron	NM_198529	NP_940931			EF-hand calcium binding domain 5 isoform a								calcium ion binding			ovary(1)|skin(1)	2																		---	---	---	---
EFCAB5	374786	broad.mit.edu	37	17	28360101	28360102	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28360101_28360102delTT	uc002het.2	+						EFCAB5_uc010wbi.1_Intron|EFCAB5_uc010wbj.1_Intron|EFCAB5_uc010wbk.1_Intron|EFCAB5_uc010csd.2_Intron|EFCAB5_uc010cse.2_Intron|EFCAB5_uc010csf.2_Intron	NM_198529	NP_940931			EF-hand calcium binding domain 5 isoform a								calcium ion binding			ovary(1)|skin(1)	2																		---	---	---	---
CPD	1362	broad.mit.edu	37	17	28773196	28773197	+	Intron	DEL	TT	-	-	rs141561458		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28773196_28773197delTT	uc002hfb.1	+						CPD_uc010wbo.1_Intron|CPD_uc010wbp.1_Intron	NM_001304	NP_001295			carboxypeptidase D precursor						proteolysis	integral to membrane	metallocarboxypeptidase activity|serine-type carboxypeptidase activity|zinc ion binding			liver(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	28857770	28857770	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:28857770delT								GOSR1 (3939 upstream) : TBC1D29 (28272 downstream)																																			---	---	---	---
ATAD5	79915	broad.mit.edu	37	17	29206584	29206584	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29206584delT	uc002hfs.1	+							NM_024857	NP_079133			ATPase family, AAA domain containing 5						response to DNA damage stimulus	nucleus	ATP binding|nucleoside-triphosphatase activity			ovary(3)	3		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)																---	---	---	---
NF1	4763	broad.mit.edu	37	17	29528326	29528326	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29528326delT	uc002hgg.2	+						NF1_uc002hge.1_Intron|NF1_uc002hgf.1_Intron|NF1_uc002hgh.2_Intron|NF1_uc010csn.1_Intron	NM_001042492	NP_001035957			neurofibromin isoform 1						actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.?(2)		soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)				D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			---	---	---	---
RAB11FIP4	84440	broad.mit.edu	37	17	29809609	29809609	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29809609delA	uc002hgn.1	+							NM_032932	NP_116321			RAB11 family interacting protein 4 (class II)						cytokinesis|interspecies interaction between organisms|protein transport	cleavage furrow|endocytic vesicle|midbody|recycling endosome membrane	ADP-ribosylation factor binding|calcium ion binding|protein homodimerization activity|Rab GTPase binding			skin(1)	1		all_cancers(10;3.62e-13)|all_epithelial(10;0.000387)|all_lung(9;0.0132)|Breast(31;0.014)|all_hematologic(16;0.015)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0259)|Ovarian(249;0.0423)|Lung NSC(157;0.066)																---	---	---	---
Unknown	0	broad.mit.edu	37	17	29871395	29871396	+	IGR	INS	-	A	A	rs141600569	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29871395_29871396insA								RAB11FIP4 (6163 upstream) : MIR193A (15619 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	29991528	29991528	+	IGR	DEL	A	-	-	rs111697401		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29991528delA								MIR365-2 (88988 upstream) : C17orf79 (187357 downstream)																																			---	---	---	---
UTP6	55813	broad.mit.edu	37	17	30207445	30207446	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30207445_30207446delAA	uc002hgr.2	-						UTP6_uc002hgq.2_Intron|UTP6_uc010cst.2_Intron|UTP6_uc010wbw.1_3'UTR	NM_018428	NP_060898			hepatocellular carcinoma-associated antigen 66						rRNA processing	nucleolus	binding			ovary(1)	1		all_hematologic(16;0.0149)|Ovarian(249;0.021)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|Breast(31;0.231)																---	---	---	---
SUZ12	23512	broad.mit.edu	37	17	30293274	30293274	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30293274delA	uc002hgs.2	+						SUZ12_uc002hgt.2_Intron	NM_015355	NP_056170			joined to JAZF1						negative regulation of cell differentiation|transcription, DNA-dependent	ESC/E(Z) complex	histone methyltransferase activity|methylated histone residue binding|zinc ion binding		JAZF1/SUZ12(131)	soft_tissue(98)|endometrium(33)	131		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.041)|Ovarian(249;0.182)|Breast(31;0.231)						T	JAZF1	endometrial stromal tumours								---	---	---	---
Unknown	0	broad.mit.edu	37	17	30330030	30330033	+	IGR	DEL	AAAT	-	-	rs71142100		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30330030_30330033delAAAT								SUZ12 (1973 upstream) : LRRC37B (5004 downstream)																																			---	---	---	---
LRRC37B	114659	broad.mit.edu	37	17	30365150	30365150	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30365150delA	uc002hgu.2	+						LRRC37B_uc010wbx.1_Intron|LRRC37B_uc010csu.2_Intron	NM_052888	NP_443120			leucine rich repeat containing 37B precursor							integral to membrane				upper_aerodigestive_tract(1)|ovary(1)	2		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.111)|Ovarian(249;0.182)|Breast(31;0.244)																---	---	---	---
Unknown	0	broad.mit.edu	37	17	30449638	30449638	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30449638delT								LRRC37B (69121 upstream) : RHOT1 (19835 downstream)																																			---	---	---	---
RHOT1	55288	broad.mit.edu	37	17	30477376	30477377	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30477376_30477377delTT	uc002hgz.2	+						RHOT1_uc002hgw.2_Intron|RHOT1_uc002hgy.2_Intron|RHOT1_uc002hha.2_Intron|RHOT1_uc010csv.2_Intron|RHOT1_uc002hgx.2_Intron|RHOT1_uc010wby.1_Intron|RHOT1_uc002hhb.2_Intron|RHOT1_uc002hgv.2_Intron	NM_018307	NP_060777			ras homolog gene family, member T1 isoform 3						apoptosis|cellular homeostasis|mitochondrion transport along microtubule|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|integral to mitochondrial outer membrane|plasma membrane	calcium ion binding|GTP binding|GTPase activity|protein binding			ovary(3)|central_nervous_system(1)	4		Myeloproliferative disorder(56;0.0255)|Breast(31;0.116)|Ovarian(249;0.182)																---	---	---	---
MYO1D	4642	broad.mit.edu	37	17	31103177	31103177	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31103177delA	uc002hho.1	-						MYO1D_uc002hhp.1_Intron|MYO1D_uc010wcb.1_Intron	NM_015194	NP_056009			myosin ID							myosin complex	actin binding|ATP binding|calmodulin binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3			BRCA - Breast invasive adenocarcinoma(9;0.0362)															---	---	---	---
ACCN1	40	broad.mit.edu	37	17	31745386	31745386	+	Intron	DEL	A	-	-	rs113180295		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31745386delA	uc002hhu.2	-							NM_001094	NP_001085			amiloride-sensitive cation channel 1, neuronal						central nervous system development|peripheral nervous system development|synaptic transmission	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Breast(31;0.042)|Ovarian(249;0.202)		UCEC - Uterine corpus endometrioid carcinoma (308;0.13)|BRCA - Breast invasive adenocarcinoma(366;0.215)	Amiloride(DB00594)													---	---	---	---
ACCN1	40	broad.mit.edu	37	17	31946861	31946861	+	Intron	DEL	A	-	-	rs111653636		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:31946861delA	uc002hhu.2	-							NM_001094	NP_001085			amiloride-sensitive cation channel 1, neuronal						central nervous system development|peripheral nervous system development|synaptic transmission	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Breast(31;0.042)|Ovarian(249;0.202)		UCEC - Uterine corpus endometrioid carcinoma (308;0.13)|BRCA - Breast invasive adenocarcinoma(366;0.215)	Amiloride(DB00594)													---	---	---	---
ACCN1	40	broad.mit.edu	37	17	32024616	32024617	+	Intron	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32024616_32024617insC	uc002hhu.2	-							NM_001094	NP_001085			amiloride-sensitive cation channel 1, neuronal						central nervous system development|peripheral nervous system development|synaptic transmission	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Breast(31;0.042)|Ovarian(249;0.202)		UCEC - Uterine corpus endometrioid carcinoma (308;0.13)|BRCA - Breast invasive adenocarcinoma(366;0.215)	Amiloride(DB00594)													---	---	---	---
ACCN1	40	broad.mit.edu	37	17	32264445	32264447	+	Intron	DEL	TTT	-	-	rs111454004		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:32264445_32264447delTTT	uc002hhu.2	-							NM_001094	NP_001085			amiloride-sensitive cation channel 1, neuronal						central nervous system development|peripheral nervous system development|synaptic transmission	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Breast(31;0.042)|Ovarian(249;0.202)		UCEC - Uterine corpus endometrioid carcinoma (308;0.13)|BRCA - Breast invasive adenocarcinoma(366;0.215)	Amiloride(DB00594)													---	---	---	---
RAD51L3	5892	broad.mit.edu	37	17	33438585	33438586	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33438585_33438586delAA	uc002hir.2	-						RFFL_uc002hiq.2_Intron|RAD51L3_uc010wcd.1_Intron|RAD51L3_uc002his.2_Intron|RAD51L3_uc010ctk.2_Intron|RAD51L3_uc010wce.1_Intron|RAD51L3_uc002hit.2_Intron|RAD51L3_uc002hiu.2_Intron|RAD51L3_uc010wcf.1_Intron|RAD51L3_uc002hiw.1_Intron|RAD51L3_uc002hiv.1_Intron|RAD51L3_uc010ctl.1_Intron|RAD51L3_uc010ctm.1_Intron	NM_002878	NP_002869			RAD51-like 3 isoform 1						DNA repair|reciprocal meiotic recombination	nucleus	ATP binding|DNA binding|DNA-dependent ATPase activity|protein binding				0		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)									Direct_reversal_of_damage|Homologous_recombination					---	---	---	---
NLE1	54475	broad.mit.edu	37	17	33466212	33466212	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33466212delA	uc002hiy.1	-						NLE1_uc010ctn.1_Intron|NLE1_uc002hiz.1_Intron	NM_018096	NP_060566			Notchless gene homolog isoform a							nucleolus				breast(3)|ovary(1)	4		Ovarian(249;0.17)																---	---	---	---
Unknown	0	broad.mit.edu	37	17	33893887	33893888	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33893887_33893888delAA								SLFN14 (8777 upstream) : SNORD7 (6788 downstream)																																			---	---	---	---
AP2B1	163	broad.mit.edu	37	17	34046379	34046379	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34046379delA	uc002hjr.2	+						AP2B1_uc002hjq.2_Intron|AP2B1_uc010wci.1_Intron|AP2B1_uc002hjs.2_Intron|AP2B1_uc002hjt.2_Intron|AP2B1_uc010ctv.2_Intron|AP2B1_uc010wcj.1_Intron	NM_001282	NP_001273			adaptor-related protein complex 2, beta 1						axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of defense response to virus by virus|synaptic transmission|vesicle-mediated transport|viral reproduction	clathrin adaptor complex|coated pit|cytosol|endocytic vesicle membrane|plasma membrane	clathrin binding|protein transporter activity			ovary(1)	1		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)														---	---	---	---
C17orf66	256957	broad.mit.edu	37	17	34188868	34188869	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34188868_34188869delTT	uc002hke.1	-						C17orf66_uc010wck.1_Intron|C17orf66_uc010wcl.1_Intron|C17orf66_uc010wcm.1_Intron	NM_152781	NP_689994			hypothetical protein LOC256957								binding			breast(2)|skin(1)	3		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0184)														---	---	---	---
C17orf66	256957	broad.mit.edu	37	17	34193242	34193242	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34193242delA	uc002hke.1	-						C17orf66_uc010wck.1_Intron|C17orf66_uc010wcl.1_Intron|C17orf66_uc010wcm.1_Intron	NM_152781	NP_689994			hypothetical protein LOC256957								binding			breast(2)|skin(1)	3		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0184)														---	---	---	---
GGNBP2	79893	broad.mit.edu	37	17	34937715	34937715	+	Intron	DEL	A	-	-	rs76574496		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34937715delA	uc002hnb.2	+						GGNBP2_uc002hna.2_Intron|GGNBP2_uc002hnc.1_Intron	NM_024835	NP_079111			zinc finger protein 403						cell differentiation|multicellular organismal development|spermatogenesis	cytoplasmic membrane-bounded vesicle				ovary(2)	2		Breast(25;0.00957)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)														---	---	---	---
MRM1	79922	broad.mit.edu	37	17	34964976	34964977	+	3'UTR	DEL	GA	-	-	rs4796229	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34964976_34964977delGA	uc002hne.2	+	5					MRM1_uc002hnf.2_3'UTR	NM_024864	NP_079140			mitochondrial rRNA methyltransferase 1 homolog						RNA processing	mitochondrion	RNA binding|RNA methyltransferase activity				0		Breast(25;0.00957)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0184)												OREG0024339	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	17	35123467	35123468	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35123467_35123468insA								MRM1 (158061 upstream) : LHX1 (171031 downstream)																																			---	---	---	---
AATF	26574	broad.mit.edu	37	17	35346372	35346372	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35346372delT	uc002hni.2	+						AATF_uc002hnj.2_Intron	NM_012138	NP_036270			apoptosis antagonizing transcription factor						anti-apoptosis|apoptosis|induction of apoptosis by extracellular signals|negative regulation of superoxide anion generation|nerve growth factor receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to DNA damage stimulus	centrosome|focal adhesion|nucleolus	leucine zipper domain binding|sequence-specific DNA binding transcription factor activity				0		Breast(25;0.00607)																---	---	---	---
ACACA	31	broad.mit.edu	37	17	35548923	35548923	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35548923delT	uc002hnm.2	-						ACACA_uc002hnk.2_Intron|ACACA_uc002hnl.2_Intron|ACACA_uc002hnn.2_Intron|ACACA_uc002hno.2_Intron|ACACA_uc010cuy.2_Intron	NM_198836	NP_942133			acetyl-Coenzyme A carboxylase alpha isoform 2						acetyl-CoA metabolic process|energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|triglyceride biosynthetic process	cytosol	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			large_intestine(1)|ovary(1)	2		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)													---	---	---	---
ACACA	31	broad.mit.edu	37	17	35612023	35612024	+	Intron	DEL	AA	-	-	rs76757920		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35612023_35612024delAA	uc002hnm.2	-						ACACA_uc002hnk.2_Intron|ACACA_uc002hnl.2_Intron|ACACA_uc002hnn.2_Intron|ACACA_uc002hno.2_Intron|ACACA_uc010cuz.2_Intron	NM_198836	NP_942133			acetyl-Coenzyme A carboxylase alpha isoform 2						acetyl-CoA metabolic process|energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|triglyceride biosynthetic process	cytosol	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			large_intestine(1)|ovary(1)	2		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)													---	---	---	---
ACACA	31	broad.mit.edu	37	17	35627767	35627767	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35627767delA	uc002hnm.2	-						ACACA_uc002hnk.2_Intron|ACACA_uc002hnl.2_Intron|ACACA_uc002hnn.2_Intron|ACACA_uc002hno.2_Intron|ACACA_uc010cuz.2_Intron	NM_198836	NP_942133			acetyl-Coenzyme A carboxylase alpha isoform 2						acetyl-CoA metabolic process|energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|triglyceride biosynthetic process	cytosol	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			large_intestine(1)|ovary(1)	2		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)													---	---	---	---
SYNRG	11276	broad.mit.edu	37	17	35881137	35881142	+	Intron	DEL	TTTTTT	-	-	rs66478744		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35881137_35881142delTTTTTT	uc002hoa.2	-						SYNRG_uc010wde.1_Intron|SYNRG_uc010wdf.1_Intron|SYNRG_uc002hoc.2_Intron|SYNRG_uc002hoe.2_Intron|SYNRG_uc002hod.2_Intron|SYNRG_uc010wdg.1_Intron|SYNRG_uc002hob.2_Intron	NM_007247	NP_009178			synergin, gamma isoform 1						endocytosis|intracellular protein transport	AP-1 adaptor complex	calcium ion binding			ovary(2)	2																		---	---	---	---
DDX52	11056	broad.mit.edu	37	17	35988719	35988719	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35988719delA	uc002hoi.1	-						DDX52_uc002hoh.1_Intron	NM_007010	NP_008941			ATP-dependent RNA helicase ROK1 isoform a							nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)|skin(1)	2		Breast(25;0.00637)|Ovarian(249;0.15)																---	---	---	---
Unknown	0	broad.mit.edu	37	17	36013972	36013973	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36013972_36013973delTT								DDX52 (10485 upstream) : HNF1B (32462 downstream)																																			---	---	---	---
HNF1B	6928	broad.mit.edu	37	17	36072236	36072236	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36072236delG	uc002hok.3	-						HNF1B_uc010wdi.1_Intron	NM_000458	NP_000449			hepatocyte nuclear factor 1-beta isoform 1						endocrine pancreas development|genitalia development|kidney development|positive regulation of transcription initiation from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|pronephric nephron tubule development|regulation of pronephros size	nucleus	DNA binding|protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)	3		Breast(25;0.00765)|Ovarian(249;0.15)	STAD - Stomach adenocarcinoma(1;0.0142)											Hereditary_Prostate_Cancer				---	---	---	---
Unknown	0	broad.mit.edu	37	17	36109087	36109088	+	IGR	INS	-	T	T	rs149308286	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36109087_36109088insT								HNF1B (3991 upstream) : LOC284100 (93485 downstream)																																			---	---	---	---
LOC284100	284100	broad.mit.edu	37	17	36239622	36239624	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36239622_36239624delAAA	uc002hon.1	-							NR_024178				Homo sapiens cDNA FLJ37577 fis, clone BRCOC2003513, moderately similar to 14-3-3 protein epsilon (14-3-3E).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	36386143	36386143	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36386143delA	uc002hpx.2	-											Homo sapiens cDNA FLJ43844 fis, clone TESTI4006308, highly  similar to Puromycin-sensitive aminopeptidase (EC 3.4.11.-).																														---	---	---	---
GPR179	440435	broad.mit.edu	37	17	36498001	36498001	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36498001delA	uc002hpz.2	-							NM_001004334	NP_001004334			GPR158-like 1 precursor							integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(3)	3	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)																---	---	---	---
MLLT6	4302	broad.mit.edu	37	17	36883484	36883484	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36883484delT	uc002hqi.3	+	20					MLLT6_uc002hqk.3_3'UTR|MLLT6_uc010cvn.1_5'Flank	NM_005937	NP_005928			myeloid/lymphoid or mixed-lineage leukemia						regulation of transcription, DNA-dependent	nucleus	protein binding|zinc ion binding			breast(3)|prostate(1)|lung(1)|skin(1)	6	Breast(7;4.43e-21)							T	MLL	AL								---	---	---	---
Unknown	0	broad.mit.edu	37	17	37017655	37017655	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37017655delA								RPL23 (7602 upstream) : LASP1 (8457 downstream)																																			---	---	---	---
LASP1	3927	broad.mit.edu	37	17	37041896	37041897	+	Intron	INS	-	C	C	rs139928162	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37041896_37041897insC	uc002hra.2	+						LASP1_uc010wdy.1_Intron|LASP1_uc010cvq.2_Intron|LASP1_uc010wdz.1_Intron	NM_006148	NP_006139			LIM and SH3 protein 1							cortical actin cytoskeleton	ion transmembrane transporter activity|SH3/SH2 adaptor activity|zinc ion binding			lung(1)	1								T	MLL	AML								---	---	---	---
Unknown	0	broad.mit.edu	37	17	37162039	37162040	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37162039_37162040delTT								FBXO47 (38384 upstream) : PLXDC1 (57516 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	37209433	37209433	+	RNA	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37209433delT	uc002hrd.1	+	5		c.3555delT								Homo sapiens cDNA FLJ43826 fis, clone TESTI4002703.																														---	---	---	---
PLXDC1	57125	broad.mit.edu	37	17	37289082	37289082	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37289082delA	uc002hrg.2	-						PLXDC1_uc002hrh.2_Intron|PLXDC1_uc002hri.2_Intron|PLXDC1_uc002hrj.1_Intron|PLXDC1_uc002hrk.1_Intron	NM_020405	NP_065138			plexin domain containing 1 precursor						angiogenesis	cytoplasm|extracellular region|integral to membrane|tight junction				ovary(1)|kidney(1)|skin(1)	3																		---	---	---	---
FBXL20	84961	broad.mit.edu	37	17	37505343	37505343	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37505343delA	uc010wed.1	-						FBXL20_uc002hrt.2_Intron|FBXL20_uc010cvu.2_Intron	NM_032875	NP_116264			F-box and leucine-rich repeat protein 20							cytoplasm				ovary(1)	1			LUAD - Lung adenocarcinoma(14;0.146)															---	---	---	---
MED1	5469	broad.mit.edu	37	17	37597110	37597110	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37597110delA	uc002hrv.3	-						MED1_uc010wee.1_Intron|MED1_uc002hru.2_Intron	NM_004774	NP_004765			mediator complex subunit 1						androgen biosynthetic process|androgen receptor signaling pathway|cellular lipid metabolic process|fat cell differentiation|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription initiation from RNA polymerase II promoter	mediator complex	DNA binding|estrogen receptor binding|ligand-dependent nuclear receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|peroxisome proliferator activated receptor binding|receptor activity|retinoic acid receptor binding|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			lung(2)|ovary(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	8		Ovarian(249;1.78e-06)|Lung SC(565;0.0262)	Lung(15;0.0178)|LUAD - Lung adenocarcinoma(14;0.146)	UCEC - Uterine corpus endometrioid carcinoma (308;6.64e-05)|BRCA - Breast invasive adenocarcinoma(366;0.00136)|READ - Rectum adenocarcinoma(1115;0.0649)											HNSCC(31;0.082)			---	---	---	---
CDK12	51755	broad.mit.edu	37	17	37668056	37668056	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37668056delT	uc010cvv.2	+						CDK12_uc010wef.1_Intron|CDK12_uc002hrw.3_Intron	NM_016507	NP_057591			Cdc2-related kinase, arginine/serine-rich						mRNA processing|phosphorylation of RNA polymerase II C-terminal domain|protein autophosphorylation|regulation of MAP kinase activity|RNA splicing	nuclear cyclin-dependent protein kinase holoenzyme complex|nuclear speck|nucleolus	ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity			ovary(10)|lung(4)|breast(2)|skin(2)|large_intestine(1)	19															TCGA Ovarian(9;0.13)			---	---	---	---
STARD3	10948	broad.mit.edu	37	17	37793780	37793780	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37793780delG	uc002hsd.2	+						STARD3_uc010weg.1_Intron|STARD3_uc010weh.1_Intron|STARD3_uc002hse.2_Intron|STARD3_uc010wei.1_Intron	NM_006804	NP_006795			StAR-related lipid transfer (START) domain						cholesterol metabolic process|mitochondrial transport|steroid biosynthetic process	integral to membrane|late endosome membrane	cholesterol binding|cholesterol transporter activity				0	Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;1.04e-44)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)															---	---	---	---
IKZF3	22806	broad.mit.edu	37	17	37967509	37967510	+	Intron	DEL	GG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37967509_37967510delGG	uc002hsu.2	-						IKZF3_uc002htd.2_Intron|IKZF3_uc010cwd.2_Intron|IKZF3_uc002hsv.2_Intron|IKZF3_uc010cwe.2_Intron|IKZF3_uc010cwf.2_Intron|IKZF3_uc010cwg.2_Intron|IKZF3_uc002hsw.2_Intron|IKZF3_uc002hsx.2_Intron|IKZF3_uc002hsy.2_Intron|IKZF3_uc002hsz.2_Intron|IKZF3_uc002hta.2_Intron|IKZF3_uc002htb.2_Intron|IKZF3_uc010cwh.2_Intron|IKZF3_uc002htc.2_Intron	NM_012481	NP_036613			aiolos isoform 1						B cell activation|mesoderm development|regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(2)|kidney(2)|skin(2)	6	Breast(7;4.5e-103)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)															---	---	---	---
IKZF3	22806	broad.mit.edu	37	17	37995848	37995848	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37995848delT	uc002hsu.2	-						IKZF3_uc002htd.2_Intron|IKZF3_uc010cwd.2_Intron|IKZF3_uc002hsv.2_Intron|IKZF3_uc010cwe.2_Intron|IKZF3_uc010cwf.2_Intron|IKZF3_uc010cwg.2_Intron|IKZF3_uc002hsw.2_Intron|IKZF3_uc002hsx.2_Intron|IKZF3_uc002hsy.2_Intron|IKZF3_uc002hsz.2_Intron|IKZF3_uc002hta.2_Intron|IKZF3_uc002htb.2_Intron|IKZF3_uc010cwh.2_Intron|IKZF3_uc002htc.2_Intron	NM_012481	NP_036613			aiolos isoform 1						B cell activation|mesoderm development|regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			lung(2)|kidney(2)|skin(2)	6	Breast(7;4.5e-103)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)															---	---	---	---
GSDMA	284110	broad.mit.edu	37	17	38130039	38130039	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38130039delT	uc002htl.1	+						GSDMA_uc002htm.1_Intron	NM_178171	NP_835465			gasdermin 1						apoptosis|induction of apoptosis	perinuclear region of cytoplasm					0																		---	---	---	---
GSDMA	284110	broad.mit.edu	37	17	38130567	38130568	+	Frame_Shift_Ins	INS	-	AG	AG			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38130567_38130568insAG	uc002htl.1	+	9	911_912	c.793_794insAG	c.(793-795)CAGfs	p.Q265fs	GSDMA_uc002htm.1_Frame_Shift_Ins_p.Q265fs	NM_178171	NP_835465	Q96QA5	GSDMA_HUMAN	gasdermin 1	265					apoptosis|induction of apoptosis	perinuclear region of cytoplasm					0																		---	---	---	---
WIPF2	147179	broad.mit.edu	37	17	38394149	38394149	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38394149delA	uc002hug.1	+						WIPF2_uc010cwv.1_Intron|WIPF2_uc002huh.1_Intron|WIPF2_uc010cww.1_Intron|WIPF2_uc002hui.1_Intron|WIPF2_uc010cwx.1_Intron|WIPF2_uc010cwy.1_Intron	NM_133264	NP_573571			WIRE protein							cytoplasm|cytoskeleton	actin binding			upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	3															HNSCC(43;0.11)			---	---	---	---
WIPF2	147179	broad.mit.edu	37	17	38420599	38420606	+	Intron	DEL	AAAAAAAG	-	-	rs113326809		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38420599_38420606delAAAAAAAG	uc002hug.1	+						WIPF2_uc002huh.1_Intron|WIPF2_uc010cww.1_Intron|WIPF2_uc002hui.1_Intron|WIPF2_uc010cwx.1_Intron|WIPF2_uc010cwy.1_Intron	NM_133264	NP_573571			WIRE protein							cytoplasm|cytoskeleton	actin binding			upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	3															HNSCC(43;0.11)			---	---	---	---
CDC6	990	broad.mit.edu	37	17	38453261	38453261	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38453261delT	uc002huj.1	+							NM_001254	NP_001245			cell division cycle 6 protein						cell division|DNA replication|DNA replication checkpoint|M/G1 transition of mitotic cell cycle|mitosis|negative regulation of cell proliferation|negative regulation of DNA replication|positive regulation of cell cycle cytokinesis|positive regulation of chromosome segregation|regulation of cyclin-dependent protein kinase activity|regulation of mitotic anaphase|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|traversing start control point of mitotic cell cycle	cytosol|nucleoplasm|spindle midzone|spindle pole	ATP binding|kinase binding|nucleoside-triphosphatase activity			ovary(2)|breast(1)	3																		---	---	---	---
RARA	5914	broad.mit.edu	37	17	38465901	38465902	+	Intron	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38465901_38465902delAG	uc002huk.1	+							NM_000964	NP_000955			retinoic acid receptor, alpha isoform 1						apoptotic cell clearance|cellular response to estrogen stimulus|cellular response to retinoic acid|estrogen receptor signaling pathway|negative regulation of granulocyte differentiation|negative regulation of interferon-gamma production|negative regulation of tumor necrosis factor production|positive regulation of binding|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of interleukin-13 production|positive regulation of interleukin-4 production|positive regulation of interleukin-5 production|positive regulation of T-helper 2 cell differentiation|positive regulation of transcription from RNA polymerase II promoter|protein phosphorylation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to estradiol stimulus	cytoplasm|nucleoplasm	chromatin DNA binding|enzyme binding|protein domain specific binding|protein heterodimerization activity|receptor binding|retinoic acid binding|retinoic acid receptor activity|retinoic acid-responsive element binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(1)|lung(1)|breast(1)	3		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00143)		Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Isotretinoin(DB00982)|Tamibarotene(DB04942)|Tazarotene(DB00799)			T	PML|ZNF145|TIF1|NUMA1|NPM1	APL								---	---	---	---
TOP2A	7153	broad.mit.edu	37	17	38556930	38556930	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38556930delA	uc002huq.2	-							NM_001067	NP_001058			DNA topoisomerase II, alpha isozyme						apoptotic chromosome condensation|DNA ligation|DNA repair|DNA topological change|DNA-dependent DNA replication|mitotic cell cycle G2/M transition decatenation checkpoint|mitotic recombination|phosphatidylinositol-mediated signaling|positive regulation of apoptosis|positive regulation of retroviral genome replication|resolution of meiotic recombination intermediates|sister chromatid segregation	cytoplasm|DNA topoisomerase complex (ATP-hydrolyzing)|nucleolus|nucleoplasm|synaptonemal complex	ATP binding|chromatin binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA-dependent ATPase activity|drug binding|histone deacetylase binding|protein C-terminus binding|protein heterodimerization activity|protein homodimerization activity|protein kinase C binding|sequence-specific DNA binding transcription factor activity|ubiquitin binding			ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Gatifloxacin(DB01044)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)													---	---	---	---
TNS4	84951	broad.mit.edu	37	17	38660112	38660112	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38660112delA	uc010cxb.2	-							NM_032865	NP_116254			tensin 4 precursor						apoptosis|protein localization	cytoplasm|cytoskeleton|focal adhesion	actin binding			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(5;5.91e-05)															---	---	---	---
SMARCE1	6605	broad.mit.edu	37	17	38802116	38802117	+	Intron	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38802116_38802117delAG	uc002hux.2	-						SMARCE1_uc010wff.1_Intron|SMARCE1_uc010wfg.1_Intron|SMARCE1_uc002huy.2_Intron|SMARCE1_uc010wfh.1_Intron|SMARCE1_uc010wfi.1_Intron|SMARCE1_uc002huz.1_Intron|SMARCE1_uc010wfj.1_5'Flank|SMARCE1_uc002hva.2_Intron	NM_003079	NP_003070			SWI/SNF-related matrix-associated						chromatin modification|negative regulation of transcription, DNA-dependent|nervous system development|nucleosome disassembly|regulation of transcription from RNA polymerase II promoter	nBAF complex|npBAF complex|nuclear chromosome|SWI/SNF complex|transcriptional repressor complex	chromatin binding|DNA binding|N-acetyltransferase activity|protein binding|protein N-terminus binding|transcription coactivator activity				0		Breast(137;0.000812)																---	---	---	---
Unknown	0	broad.mit.edu	37	17	38943214	38943216	+	IGR	DEL	AAA	-	-	rs35249446		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38943214_38943216delAAA								KRT27 (4428 upstream) : KRT28 (5232 downstream)																																			---	---	---	---
KRT40	125115	broad.mit.edu	37	17	39139511	39139511	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39139511delT	uc010cxh.1	-						KRT40_uc002hvq.1_Intron	NM_182497	NP_872303			type I hair keratin KA36							intermediate filament	structural molecule activity				0		Breast(137;0.00043)																---	---	---	---
Unknown	0	broad.mit.edu	37	17	39244574	39244575	+	IGR	INS	-	T	T	rs140740206		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39244574_39244575insT								KRTAP4-7 (3180 upstream) : KRTAP4-8 (8661 downstream)																																			---	---	---	---
JUP	3728	broad.mit.edu	37	17	39739452	39739452	+	Intron	DEL	G	-	-	rs67735391		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39739452delG	uc010wfs.1	-						KRT14_uc002hxf.1_Intron|KRT14_uc010cxp.1_Intron	NM_021991	NP_068831			junction plakoglobin						adherens junction organization|atrioventricular valve morphogenesis|cell migration|cell morphogenesis|cellular response to indole-3-methanol|cytoskeletal anchoring at plasma membrane|detection of mechanical stimulus|ectoderm development|endothelial cell-cell adhesion|gastrulation|morphogenesis of embryonic epithelium|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of Wnt receptor signaling pathway involved in heart development|nervous system development|oocyte development|positive regulation of protein import into nucleus|positive regulation of sequence-specific DNA binding transcription factor activity|skin development	actin cytoskeleton|Axin-APC-beta-catenin-GSK3B complex|basolateral plasma membrane|catenin complex|desmosome|fascia adherens|gamma-catenin-TCF7L2 complex|internal side of plasma membrane|nucleus|protein-DNA complex|Z disc|zonula adherens	alpha-catenin binding|cadherin binding|protein homodimerization activity|protein kinase binding|protein phosphatase binding|RPTP-like protein binding|specific RNA polymerase II transcription factor activity|transcription coactivator activity			ovary(2)|lung(2)|breast(1)	5		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)														---	---	---	---
JUP	3728	broad.mit.edu	37	17	39804445	39804445	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39804445delC	uc010wfs.1	-							NM_021991	NP_068831			junction plakoglobin						adherens junction organization|atrioventricular valve morphogenesis|cell migration|cell morphogenesis|cellular response to indole-3-methanol|cytoskeletal anchoring at plasma membrane|detection of mechanical stimulus|ectoderm development|endothelial cell-cell adhesion|gastrulation|morphogenesis of embryonic epithelium|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of Wnt receptor signaling pathway involved in heart development|nervous system development|oocyte development|positive regulation of protein import into nucleus|positive regulation of sequence-specific DNA binding transcription factor activity|skin development	actin cytoskeleton|Axin-APC-beta-catenin-GSK3B complex|basolateral plasma membrane|catenin complex|desmosome|fascia adherens|gamma-catenin-TCF7L2 complex|internal side of plasma membrane|nucleus|protein-DNA complex|Z disc|zonula adherens	alpha-catenin binding|cadherin binding|protein homodimerization activity|protein kinase binding|protein phosphatase binding|RPTP-like protein binding|specific RNA polymerase II transcription factor activity|transcription coactivator activity			ovary(2)|lung(2)|breast(1)	5		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)												OREG0024406	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
JUP	3728	broad.mit.edu	37	17	39902403	39902403	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39902403delT	uc010wfs.1	-							NM_021991	NP_068831			junction plakoglobin						adherens junction organization|atrioventricular valve morphogenesis|cell migration|cell morphogenesis|cellular response to indole-3-methanol|cytoskeletal anchoring at plasma membrane|detection of mechanical stimulus|ectoderm development|endothelial cell-cell adhesion|gastrulation|morphogenesis of embryonic epithelium|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of Wnt receptor signaling pathway involved in heart development|nervous system development|oocyte development|positive regulation of protein import into nucleus|positive regulation of sequence-specific DNA binding transcription factor activity|skin development	actin cytoskeleton|Axin-APC-beta-catenin-GSK3B complex|basolateral plasma membrane|catenin complex|desmosome|fascia adherens|gamma-catenin-TCF7L2 complex|internal side of plasma membrane|nucleus|protein-DNA complex|Z disc|zonula adherens	alpha-catenin binding|cadherin binding|protein homodimerization activity|protein kinase binding|protein phosphatase binding|RPTP-like protein binding|specific RNA polymerase II transcription factor activity|transcription coactivator activity			ovary(2)|lung(2)|breast(1)	5		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	39954462	39954463	+	IGR	INS	-	CC	CC	rs143349904	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39954462_39954463insCC								JUP (11498 upstream) : SC65 (3743 downstream)																																			---	---	---	---
NT5C3L	115024	broad.mit.edu	37	17	39990634	39990634	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39990634delA	uc002hyc.3	-						NT5C3L_uc002hxx.3_5'Flank|NT5C3L_uc010wfu.1_Intron|NT5C3L_uc002hyb.3_Intron|NT5C3L_uc002hyd.3_Intron|NT5C3L_uc002hxy.3_Intron|NT5C3L_uc002hxz.3_Intron|NT5C3L_uc002hya.3_Intron	NM_052935	NP_443167			5'-nucleotidase, cytosolic III-like							cytoplasm	5'-nucleotidase activity|magnesium ion binding				0		Breast(137;0.000162)		BRCA - Breast invasive adenocarcinoma(366;0.15)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	40200395	40200395	+	IGR	DEL	A	-	-	rs138023948		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40200395delA								NKIRAS2 (22741 upstream) : DHX58 (53027 downstream)																																			---	---	---	---
GHDC	84514	broad.mit.edu	37	17	40347086	40347086	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40347086delA	uc002hzd.2	-						GHDC_uc002hzg.1_5'Flank|GHDC_uc010wgg.1_5'Flank|GHDC_uc002hze.3_5'Flank|GHDC_uc002hzf.3_5'Flank|GHDC_uc010cxz.2_5'Flank	NM_032484	NP_115873			LGP1 homolog isoform 1							endoplasmic reticulum|nuclear envelope					0		all_cancers(22;0.000229)|Breast(137;0.00104)|all_epithelial(22;0.00304)		BRCA - Breast invasive adenocarcinoma(366;0.124)														---	---	---	---
STAT5B	6777	broad.mit.edu	37	17	40375459	40375459	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40375459delT	uc002hzh.2	-	5	660	c.491delA	c.(490-492)AAGfs	p.K164fs	STAT5B_uc002hzi.3_Frame_Shift_Del_p.K164fs	NM_012448	NP_036580	P51692	STA5B_HUMAN	signal transducer and activator of transcription	164					2-oxoglutarate metabolic process|allantoin metabolic process|citrate metabolic process|creatine metabolic process|creatinine metabolic process|fatty acid metabolic process|isoleucine metabolic process|JAK-STAT cascade involved in growth hormone signaling pathway|oxaloacetate metabolic process|response to estradiol stimulus|succinate metabolic process|taurine metabolic process|valine metabolic process	cytosol|nucleoplasm	calcium ion binding|glucocorticoid receptor binding|sequence-specific DNA binding transcription factor activity			ovary(3)|lung(2)|skin(1)	6		all_cancers(22;4.15e-07)|all_epithelial(22;2.83e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.135)	Dasatinib(DB01254)													---	---	---	---
STAT3	6774	broad.mit.edu	37	17	40468976	40468977	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40468976_40468977delAA	uc002hzl.1	-						STAT3_uc002hzk.1_Intron|STAT3_uc002hzm.1_Intron|STAT3_uc010wgh.1_Intron|STAT3_uc002hzn.1_Intron|STAT3_uc010cyf.1_5'Flank	NM_139276	NP_644805			signal transducer and activator of transcription						cellular component movement|eating behavior|eye photoreceptor cell differentiation|glucose homeostasis|interleukin-6-mediated signaling pathway|interspecies interaction between organisms|JAK-STAT cascade involved in growth hormone signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|protein import into nucleus|response to estradiol stimulus|sexual reproduction|temperature homeostasis	cytosol|nucleus|plasma membrane	calcium ion binding|ligand-regulated transcription factor activity|protein dimerization activity|protein kinase binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription factor binding|transcription regulatory region DNA binding			ovary(1)|lung(1)|breast(1)|central_nervous_system(1)	4		all_cancers(22;1.39e-06)|all_epithelial(22;2.95e-05)|Breast(137;0.000135)		BRCA - Breast invasive adenocarcinoma(366;0.139)										Hyperimmunoglobulin_E_Recurrent_Infection_Syndrome				---	---	---	---
VPS25	84313	broad.mit.edu	37	17	40927065	40927065	+	Intron	DEL	T	-	-	rs151270458	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40927065delT	uc002ibi.2	+							NM_032353	NP_115729			vacuolar protein sorting 25						cellular membrane organization|endosome transport|protein transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|endosome membrane|nucleoplasm					0		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0745)														---	---	---	---
G6PC	2538	broad.mit.edu	37	17	41055723	41055724	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41055723_41055724delAA	uc002icb.1	+						G6PC_uc010whf.1_Intron	NM_000151	NP_000142			glucose-6-phosphatase, catalytic subunit						gluconeogenesis|glucose homeostasis|transmembrane transport	integral to endoplasmic reticulum membrane	glucose-6-phosphatase activity|phosphate binding			ovary(1)|breast(1)|kidney(1)|skin(1)	4		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.113)										Glycogen_Storage_Disease_type_Ia				---	---	---	---
Unknown	0	broad.mit.edu	37	17	41086668	41086669	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41086668_41086669delAA								G6PC (21282 upstream) : AARSD1 (15876 downstream)																																			---	---	---	---
VAT1	10493	broad.mit.edu	37	17	41171639	41171639	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41171639delC	uc002icm.1	-						VAT1_uc010cyw.1_Intron|VAT1_uc010whk.1_Intron	NM_006373	NP_006364			vesicle amine transport protein 1							cytoplasm|integral to membrane	oxidoreductase activity|zinc ion binding				0		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.156)														---	---	---	---
BRCA1	672	broad.mit.edu	37	17	41243954	41243955	+	Frame_Shift_Ins	INS	-	A	A	rs80357562		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41243954_41243955insA	uc002icq.2	-	10	3825_3826	c.3593_3594insT	c.(3592-3594)TTGfs	p.L1198fs	BRCA1_uc010whp.1_Intron|BRCA1_uc010whl.1_Intron|BRCA1_uc010whm.1_Intron|BRCA1_uc002icp.3_Frame_Shift_Ins_p.L1127fs|BRCA1_uc002icu.2_Intron|BRCA1_uc010cyx.2_Frame_Shift_Ins_p.L1151fs|BRCA1_uc002ict.2_Frame_Shift_Ins_p.L1198fs|BRCA1_uc010whn.1_Intron|BRCA1_uc010who.1_Intron|BRCA1_uc010whq.1_Intron|BRCA1_uc002idc.1_Intron|BRCA1_uc010whr.1_Intron|BRCA1_uc002idd.2_Frame_Shift_Ins_p.L1198fs|BRCA1_uc002ide.1_Frame_Shift_Ins_p.L1029fs|BRCA1_uc010cyy.1_Frame_Shift_Ins_p.L1198fs|BRCA1_uc010whs.1_Frame_Shift_Ins_p.L1198fs|BRCA1_uc010cyz.2_Frame_Shift_Ins_p.L1151fs|BRCA1_uc010cza.2_Frame_Shift_Ins_p.L1172fs|BRCA1_uc010wht.1_Frame_Shift_Ins_p.L902fs	NM_007294	NP_009225	P38398	BRCA1_HUMAN	breast cancer 1, early onset isoform 1	1198					androgen receptor signaling pathway|apoptosis|cellular response to indole-3-methanol|chromosome segregation|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|DNA damage response, signal transduction resulting in induction of apoptosis|double-strand break repair via homologous recombination|fatty acid biosynthetic process|G2/M transition DNA damage checkpoint|negative regulation of centriole replication|negative regulation of fatty acid biosynthetic process|negative regulation of histone H3-K9 methylation|negative regulation of transcription, DNA-dependent|positive regulation of cell cycle arrest|positive regulation of DNA repair|positive regulation of histone acetylation|positive regulation of histone H3-K4 methylation|positive regulation of histone H4-K20 methylation|positive regulation of protein ubiquitination|positive regulation of transcription from RNA polymerase II promoter|postreplication repair|protein autoubiquitination|protein K6-linked ubiquitination|regulation of cell motility|regulation of cell proliferation|regulation of transcription from RNA polymerase III promoter|response to estrogen stimulus|response to ionizing radiation|substrate adhesion-dependent cell spreading	BRCA1-A complex|BRCA1-BARD1 complex|gamma-tubulin ring complex|nucleoplasm|plasma membrane|ribonucleoprotein complex|ruffle	androgen receptor binding|identical protein binding|protein binding|RNA binding|transcription coactivator activity|transcription regulatory region DNA binding|tubulin binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(24)|breast(21)|lung(4)|central_nervous_system(1)|endometrium(1)|urinary_tract(1)	52		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)				D|Mis|N|F|S		ovarian	breast|ovarian		Homologous_recombination	Hereditary_Breast-Ovarian_Cancer_BRCA1_type	TCGA Ovarian(2;0.000030)			---	---	---	---
Unknown	0	broad.mit.edu	37	17	41500982	41500982	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41500982delT								ARL4D (22479 upstream) : MIR2117 (21192 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	41713037	41713037	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41713037delT								ETV4 (89275 upstream) : MEOX1 (4730 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	41839658	41839658	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41839658delT								SOST (3502 upstream) : DUSP3 (3832 downstream)																																			---	---	---	---
PYY	5697	broad.mit.edu	37	17	42077137	42077137	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42077137delA	uc002ieq.2	-							NM_004160	NP_004151			peptide YY precursor						cell proliferation|cell-cell signaling|cellular component movement|cytoskeleton organization|digestion|G-protein coupled receptor protein signaling pathway	soluble fraction					0		Breast(137;0.00314)|Prostate(33;0.0724)		BRCA - Breast invasive adenocarcinoma(366;0.12)														---	---	---	---
HDAC5	10014	broad.mit.edu	37	17	42165217	42165218	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42165217_42165218delTT	uc002ifd.1	-						HDAC5_uc002ife.1_Intron|HDAC5_uc002iff.1_Intron|HDAC5_uc010czp.1_Intron|HDAC5_uc002ifg.1_5'Flank|HDAC5_uc002ifh.2_Intron	NM_005474	NP_005465			histone deacetylase 5 isoform 1						B cell differentiation|cellular response to insulin stimulus|chromatin remodeling|chromatin silencing|inflammatory response|negative regulation of cell migration involved in sprouting angiogenesis|negative regulation of myotube differentiation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|transcription, DNA-dependent	cytoplasm|histone deacetylase complex	histone deacetylase activity (H3-K16 specific)|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein kinase C binding|repressing transcription factor binding			ovary(1)	1		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.118)														---	---	---	---
ITGA2B	3674	broad.mit.edu	37	17	42453970	42453971	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42453970_42453971delTT	uc002igt.1	-						ITGA2B_uc002igu.1_Intron	NM_000419	NP_000410			integrin alpha 2b preproprotein						axon guidance|integrin-mediated signaling pathway|platelet activation|platelet degranulation	integrin complex|platelet alpha granule membrane	identical protein binding|receptor activity			ovary(2)|lung(1)	3		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.191)	Tirofiban(DB00775)													---	---	---	---
CCDC43	124808	broad.mit.edu	37	17	42756253	42756253	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42756253delT	uc002ihc.2	-	5	690	c.646delA	c.(646-648)AGGfs	p.R216fs	CCDC43_uc010czw.1_3'UTR	NM_144609	NP_653210	Q96MW1	CCD43_HUMAN	coiled-coil domain containing 43 isoform 1	216	Potential.										0		Prostate(33;0.0322)																---	---	---	---
GFAP	2670	broad.mit.edu	37	17	42990963	42990963	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42990963delG	uc002ihq.2	-						GFAP_uc002ihr.2_Intron|GFAP_uc010wjg.1_Intron	NM_002055	NP_002046			glial fibrillary acidic protein isoform 1							cytoplasm|intermediate filament	structural constituent of cytoskeleton			ovary(1)|pancreas(1)	2		Prostate(33;0.0959)																---	---	---	---
DCAKD	79877	broad.mit.edu	37	17	43110841	43110841	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43110841delT	uc002ihx.2	-						DCAKD_uc010daa.1_Intron|DCAKD_uc010dab.1_Intron	NM_024819	NP_079095			dephospho-CoA kinase domain containing						coenzyme A biosynthetic process		ATP binding|dephospho-CoA kinase activity				0		Prostate(33;0.155)																---	---	---	---
NMT1	4836	broad.mit.edu	37	17	43149935	43149936	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43149935_43149936delTT	uc002ihz.2	+						NMT1_uc010dac.1_Intron|NMT1_uc002iia.2_Intron	NM_021079	NP_066565			N-myristoyltransferase 1						activation of pro-apoptotic gene products|induction of apoptosis by intracellular signals|N-terminal protein myristoylation|protein lipoylation	actin cytoskeleton|cell junction|cytosol	glycylpeptide N-tetradecanoyltransferase activity				0		Prostate(33;0.155)																---	---	---	---
HEXIM2	124790	broad.mit.edu	37	17	43246192	43246193	+	Intron	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43246192_43246193insG	uc002iih.1	+						HEXIM2_uc010daf.1_Intron|HEXIM2_uc002iii.1_Intron|HEXIM2_uc002iij.1_Intron|uc002iik.1_RNA	NM_144608	NP_653209			hexamthylene bis-acetamide inducible 2						negative regulation of cyclin-dependent protein kinase activity|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	cyclin-dependent protein kinase inhibitor activity|protein binding|snRNA binding				0																		---	---	---	---
LOC100133991	100133991	broad.mit.edu	37	17	43330777	43330777	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43330777delT	uc010dah.2	+							NR_024434				Homo sapiens cDNA FLJ39900 fis, clone SPLEN2017121.												0																		---	---	---	---
ARHGAP27	201176	broad.mit.edu	37	17	43480446	43480446	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43480446delC	uc002iix.2	-						ARHGAP27_uc010dak.2_Intron|ARHGAP27_uc010wjl.1_Intron	NM_199282	NP_954976			Rho GTPase activating protein 27 isoform a						positive regulation of Cdc42 GTPase activity|receptor-mediated endocytosis|signal transduction	cytoplasm|membrane	Rac GTPase activator activity|SH3 domain binding				0	Renal(3;0.0405)																	---	---	---	---
Unknown	0	broad.mit.edu	37	17	43663214	43663214	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43663214delA								LRRC37A4 (67698 upstream) : LOC644172 (14277 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	43675963	43675963	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43675963delA								LRRC37A4 (80447 upstream) : LOC644172 (1528 downstream)																																			---	---	---	---
CRHR1	1394	broad.mit.edu	37	17	43702020	43702020	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43702020delA	uc002ijp.2	+						CRHR1_uc010wjx.1_Intron|MGC57346_uc010dan.2_Intron|MGC57346_uc002ijj.3_Intron					SubName: Full=cDNA FLJ60308, highly similar to Corticotropin-releasing factor receptor 1;						female pregnancy|immune response|parturition	integral to plasma membrane	corticotrophin-releasing factor receptor activity|protein binding			lung(3)	3	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.161)														---	---	---	---
MAPT	4137	broad.mit.edu	37	17	44066409	44066409	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44066409delG	uc002ijr.3	+						MAPT_uc010dau.2_Intron|MAPT_uc002ijs.3_Intron|MAPT_uc002ijx.3_Intron|MAPT_uc002ijt.3_Intron|MAPT_uc002iju.3_Intron|MAPT_uc002ijv.3_Intron	NM_016835	NP_058519			microtubule-associated protein tau isoform 1						cellular component disassembly involved in apoptosis|microtubule cytoskeleton organization|negative regulation of microtubule depolymerization|positive regulation of axon extension|positive regulation of microtubule polymerization|regulation of autophagy	axon|cytosol|growth cone|microtubule|microtubule associated complex|nuclear periphery|plasma membrane|tubulin complex	apolipoprotein E binding|enzyme binding|identical protein binding|lipoprotein particle binding|microtubule binding|protein binding|SH3 domain binding|structural constituent of cytoskeleton			pancreas(1)	1		Melanoma(429;0.216)																---	---	---	---
LRRC37A	9884	broad.mit.edu	37	17	44400765	44400765	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44400765delT	uc002ikg.2	+						ARL17A_uc002iki.3_Intron|ARL17A_uc002ikh.3_Intron|ARL17B_uc002ikf.2_Intron	NM_014834	NP_055649			leucine rich repeat containing 37A precursor							integral to membrane					0		Melanoma(429;0.211)		BRCA - Breast invasive adenocarcinoma(366;0.232)														---	---	---	---
Unknown	0	broad.mit.edu	37	17	44568242	44568243	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44568242_44568243delTT								ARL17A (129079 upstream) : LRRC37A2 (21833 downstream)																																			---	---	---	---
NPEPPS	9520	broad.mit.edu	37	17	45679340	45679340	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45679340delA	uc002ilr.3	+						NPEPPS_uc010wkt.1_Intron|NPEPPS_uc010wku.1_Intron|NPEPPS_uc010wkv.1_Intron|NPEPPS_uc002ils.1_5'Flank	NM_006310	NP_006301			aminopeptidase puromycin sensitive						proteolysis	cytosol|nucleus	aminopeptidase activity|metallopeptidase activity|protein binding|zinc ion binding				0																		---	---	---	---
KPNB1	3837	broad.mit.edu	37	17	45753217	45753217	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45753217delT	uc002ilt.1	+						KPNB1_uc010wkw.1_Intron|KPNB1_uc010wkx.1_Intron	NM_002265	NP_002256			karyopherin beta 1						DNA fragmentation involved in apoptotic nuclear change|NLS-bearing substrate import into nucleus|protein import into nucleus, translocation|ribosomal protein import into nucleus|viral genome transport in host cell|viral infectious cycle	cytosol|nuclear pore|nucleoplasm	nuclear localization sequence binding|protein domain specific binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
TBX21	30009	broad.mit.edu	37	17	45817128	45817130	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45817128_45817130delAAA	uc002ilv.1	+							NM_013351	NP_037483			T-box 21						lymphocyte migration|multicellular organismal development|positive regulation of transcription, DNA-dependent|response to virus	nucleus	sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding				0																		---	---	---	---
OSBPL7	114881	broad.mit.edu	37	17	45894763	45894763	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45894763delT	uc002ilx.1	-						OSBPL7_uc002ilw.1_5'Flank	NM_145798	NP_665741			oxysterol-binding protein-like protein 7						lipid transport		lipid binding				0																		---	---	---	---
SKAP1	8631	broad.mit.edu	37	17	46423471	46423471	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46423471delA	uc002ini.1	-						SKAP1_uc002inj.1_Intron|SKAP1_uc010dbd.1_Intron|SKAP1_uc010dbe.1_Intron	NM_003726	NP_003717			src kinase associated phosphoprotein 1 isoform						positive regulation of transcription from RNA polymerase II promoter|T cell receptor signaling pathway	cytoplasm|nucleus|plasma membrane	antigen binding|protein kinase binding|SH2 domain binding				0																		---	---	---	---
SKAP1	8631	broad.mit.edu	37	17	46454551	46454551	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46454551delA	uc002ini.1	-						SKAP1_uc002inj.1_Intron|SKAP1_uc010dbd.1_Intron|SKAP1_uc010dbe.1_Intron	NM_003726	NP_003717			src kinase associated phosphoprotein 1 isoform						positive regulation of transcription from RNA polymerase II promoter|T cell receptor signaling pathway	cytoplasm|nucleus|plasma membrane	antigen binding|protein kinase binding|SH2 domain binding				0																		---	---	---	---
HOXB3	3213	broad.mit.edu	37	17	46655143	46655143	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46655143delC	uc010dbf.2	-						HOXB3_uc010wlm.1_Intron|HOXB3_uc010dbg.2_Intron|HOXB3_uc010wlk.1_5'Flank|HOXB3_uc010wll.1_Intron|HOXB4_uc002inp.2_Intron	NM_002146	NP_002137			homeobox B3						angiogenesis	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
PRAC	84366	broad.mit.edu	37	17	46801722	46801723	+	5'Flank	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46801722_46801723insG	uc002iny.2	-						C17orf93_uc002inz.1_RNA	NM_032391	NP_115767			prostate cancer susceptibility candidate							nucleus					0																OREG0024525	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CALCOCO2	10241	broad.mit.edu	37	17	46929187	46929190	+	Intron	DEL	TAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46929187_46929190delTAAA	uc002iof.2	+						CALCOCO2_uc010wlp.1_Intron|CALCOCO2_uc010wlq.1_Intron|CALCOCO2_uc010wlr.1_Intron|CALCOCO2_uc010wls.1_Intron	NM_005831	NP_005822			calcium binding and coiled-coil domain 2						response to interferon-gamma|viral reproduction	cytoskeleton|Golgi apparatus|nucleus|perinuclear region of cytoplasm|soluble fraction	protein homodimerization activity			ovary(1)	1																		---	---	---	---
B4GALNT2	124872	broad.mit.edu	37	17	47218386	47218386	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47218386delT	uc002ion.2	+						B4GALNT2_uc010wlt.1_Intron|B4GALNT2_uc010wlu.1_Intron	NM_153446	NP_703147			beta-1,4-N-acetyl-galactosaminyl transferase 2						lipid glycosylation|negative regulation of cell-cell adhesion|UDP-N-acetylgalactosamine metabolic process	integral to Golgi membrane	acetylgalactosaminyltransferase activity			large_intestine(1)|ovary(1)	2			all cancers(6;0.000316)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	47331141	47331142	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47331141_47331142insA	uc002iot.1	+											Homo sapiens cDNA FLJ40194 fis, clone TESTI2019481.																														---	---	---	---
ZNF652	22834	broad.mit.edu	37	17	47378324	47378325	+	Intron	DEL	TA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47378324_47378325delTA	uc002iov.3	-						ZNF652_uc002iow.2_Intron|ZNF652_uc002iou.3_Intron	NM_001145365	NP_001138837			zinc finger protein 652						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(1)	1	all_cancers(4;6.81e-14)|Breast(4;4.97e-29)|all_epithelial(4;1.53e-17)		BRCA - Breast invasive adenocarcinoma(1;3.1e-14)|Epithelial(5;2.92e-06)|all cancers(6;3.15e-05)															---	---	---	---
PHB	5245	broad.mit.edu	37	17	47494094	47494096	+	5'Flank	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47494094_47494096delTTT	uc002iox.1	-							NM_002634	NP_002625			prohibitin						cellular response to interleukin-6|DNA replication|glucocorticoid receptor signaling pathway|histone deacetylation|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of transcription by competitive promoter binding|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|progesterone receptor signaling pathway|regulation of apoptosis	integral to plasma membrane|mitochondrial inner membrane|nucleoplasm	histone deacetylase binding|transcription regulatory region DNA binding				0	all_cancers(4;2.62e-14)|Breast(4;4.21e-29)|all_epithelial(4;6.9e-18)		Epithelial(5;8.1e-06)|all cancers(6;7.71e-05)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	47505240	47505241	+	IGR	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47505240_47505241delAC								PHB (12998 upstream) : NGFR (67414 downstream)																																			---	---	---	---
NGFR	4804	broad.mit.edu	37	17	47571322	47571322	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47571322delT	uc002ioz.3	+							NM_002507	NP_002498			nerve growth factor receptor precursor						anti-apoptosis|apoptosis|induction of apoptosis by extracellular signals|membrane protein intracellular domain proteolysis|negative regulation of axonogenesis|negative regulation of cell cycle|nerve growth factor receptor signaling pathway|positive regulation of axonogenesis	cell surface|cytosol|endosome|extracellular region|integral to plasma membrane|nucleoplasm				ovary(1)|lung(1)	2	all_cancers(4;1.45e-13)|Breast(4;6.34e-28)|all_epithelial(4;4.95e-17)																	---	---	---	---
Unknown	0	broad.mit.edu	37	17	47663448	47663448	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47663448delT								NXPH3 (2279 upstream) : SPOP (12800 downstream)																																			---	---	---	---
SPOP	8405	broad.mit.edu	37	17	47740049	47740051	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47740049_47740051delAAA	uc002ipb.2	-						SPOP_uc002ipc.2_Intron|SPOP_uc002ipd.2_Intron|SPOP_uc002ipe.2_Intron|SPOP_uc002ipf.2_Intron|SPOP_uc002ipg.2_Intron|SPOP_uc010wlx.1_Intron	NM_001007226	NP_001007227			speckle-type POZ protein						mRNA processing	nucleus	protein binding			prostate(2)|ovary(2)|lung(2)	6															Prostate(2;0.17)			---	---	---	---
EME1	146956	broad.mit.edu	37	17	48455122	48455123	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48455122_48455123delTT	uc002iqs.1	+						EME1_uc010dbp.1_Intron|EME1_uc010dbq.1_5'Flank	NM_152463	NP_689676			essential meiotic endonuclease 1 homolog 1						DNA recombination|DNA repair	nucleolus	DNA binding|endonuclease activity|metal ion binding|protein binding				0	Breast(11;5.62e-19)		BRCA - Breast invasive adenocarcinoma(22;2.43e-08)										Direct_reversal_of_damage|Homologous_recombination					---	---	---	---
Unknown	0	broad.mit.edu	37	17	48871670	48871670	+	IGR	DEL	A	-	-	rs71353674		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48871670delA								C17orf73 (26752 upstream) : WFIKKN2 (40341 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	48956112	48956112	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48956112delT								TOB1 (10773 upstream) : SPAG9 (83424 downstream)																																			---	---	---	---
SPAG9	9043	broad.mit.edu	37	17	49048275	49048275	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49048275delT	uc002itc.2	-						SPAG9_uc002itb.2_Intron|SPAG9_uc002itd.2_Intron|SPAG9_uc002ita.2_Intron	NM_001130528	NP_001124000			sperm associated antigen 9 isoform 1						positive regulation of cell migration|positive regulation of muscle cell differentiation|retrograde transport, endosome to Golgi|spermatogenesis	acrosomal vesicle|integral to membrane|perinuclear region of cytoplasm				lung(4)|breast(1)	5			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)															---	---	---	---
SPAG9	9043	broad.mit.edu	37	17	49081519	49081519	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49081519delT	uc002itc.2	-						SPAG9_uc002itb.2_Intron|SPAG9_uc002itd.2_Intron|SPAG9_uc002itf.2_Intron|SPAG9_uc002ita.2_Intron|SPAG9_uc002ite.2_Intron	NM_001130528	NP_001124000			sperm associated antigen 9 isoform 1						positive regulation of cell migration|positive regulation of muscle cell differentiation|retrograde transport, endosome to Golgi|spermatogenesis	acrosomal vesicle|integral to membrane|perinuclear region of cytoplasm				lung(4)|breast(1)	5			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	49208029	49208030	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49208029_49208030delTT								SPAG9 (9803 upstream) : NME1 (22890 downstream)																																			---	---	---	---
NME1-NME2	654364	broad.mit.edu	37	17	49231519	49231521	+	Intron	DEL	TCT	-	-	rs60023424	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49231519_49231521delTCT	uc002itk.2	+						NME1_uc010dbx.1_Intron|NME1_uc002ith.1_Intron|NME1_uc002iti.1_Intron|NME1-NME2_uc002itj.2_Intron	NM_002512	NP_002503			nucleoside diphosphate kinase B						cell adhesion|CTP biosynthetic process|GTP biosynthetic process|negative regulation of apoptosis|nucleobase, nucleoside and nucleotide interconversion|positive regulation of epithelial cell proliferation|positive regulation of keratinocyte differentiation|UTP biosynthetic process	cytosol|lamellipodium|nucleus|ruffle	ATP binding|DNA binding|metal ion binding|nucleoside diphosphate kinase activity|protein binding|protein histidine kinase activity|sequence-specific DNA binding transcription factor activity				0			BRCA - Breast invasive adenocarcinoma(22;1.54e-08)															---	---	---	---
UTP18	51096	broad.mit.edu	37	17	49351985	49351986	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49351985_49351986insT	uc002its.2	+							NM_016001	NP_057085			UTP18, small subunit processome component						rRNA processing	nucleolus					0			BRCA - Breast invasive adenocarcinoma(22;2.09e-07)															---	---	---	---
UTP18	51096	broad.mit.edu	37	17	49353083	49353084	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49353083_49353084delTT	uc002its.2	+							NM_016001	NP_057085			UTP18, small subunit processome component						rRNA processing	nucleolus					0			BRCA - Breast invasive adenocarcinoma(22;2.09e-07)															---	---	---	---
CA10	56934	broad.mit.edu	37	17	49799745	49799746	+	Intron	INS	-	GT	GT			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49799745_49799746insGT	uc002itw.3	-						CA10_uc002itu.3_Intron|CA10_uc002itv.3_Intron|CA10_uc002itx.3_Intron|CA10_uc002ity.3_Intron|CA10_uc002itz.2_Intron	NM_020178	NP_064563			carbonic anhydrase X						brain development					ovary(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(22;4.74e-06)															---	---	---	---
CA10	56934	broad.mit.edu	37	17	49914086	49914086	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49914086delA	uc002itw.3	-						CA10_uc002itv.3_Intron|CA10_uc002itx.3_Intron|CA10_uc002ity.3_Intron|CA10_uc002itz.2_Intron	NM_020178	NP_064563			carbonic anhydrase X						brain development					ovary(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(22;4.74e-06)															---	---	---	---
CA10	56934	broad.mit.edu	37	17	50176519	50176519	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:50176519delA	uc002itw.3	-						CA10_uc002itv.3_Intron|CA10_uc002itx.3_Intron|CA10_uc002ity.3_Intron|CA10_uc002itz.2_Intron	NM_020178	NP_064563			carbonic anhydrase X						brain development					ovary(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(22;4.74e-06)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	50304105	50304106	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:50304105_50304106delTT								CA10 (66728 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	50955632	50955633	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:50955632_50955633delAA								CA10 (718255 upstream) : KIF2B (944606 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	51065183	51065183	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51065183delA								CA10 (827806 upstream) : KIF2B (835056 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	51536885	51536887	+	IGR	DEL	TTG	-	-	rs112539811	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51536885_51536887delTTG								None (None upstream) : KIF2B (363352 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	51682743	51682744	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:51682743_51682744insA								None (None upstream) : KIF2B (217495 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	52764641	52764642	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:52764641_52764642delTG								KIF2B (862068 upstream) : TOM1L1 (213410 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	52782183	52782183	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:52782183delA								KIF2B (879610 upstream) : TOM1L1 (195869 downstream)																																			---	---	---	---
TOM1L1	10040	broad.mit.edu	37	17	53006174	53006174	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53006174delT	uc002iud.2	+						TOM1L1_uc002iuc.2_Intron|TOM1L1_uc010dca.1_Intron|TOM1L1_uc010wnb.1_Intron|TOM1L1_uc010wnc.1_Intron|TOM1L1_uc010dbz.2_Intron|TOM1L1_uc010wnd.1_Intron|TOM1L1_uc010dcb.1_Intron	NM_005486	NP_005477			target of myb1-like 1						intracellular protein transport|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	cytosol|endosome membrane|Golgi stack|lysosome	SH3 domain binding|ubiquitin binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	53312861	53312861	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53312861delC								STXBP4 (71412 upstream) : HLF (29460 downstream)																																			---	---	---	---
MMD	23531	broad.mit.edu	37	17	53476911	53476911	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:53476911delC	uc002iui.2	-							NM_012329	NP_036461			monocyte to macrophage						cytolysis	integral to plasma membrane|late endosome membrane|lysosomal membrane|membrane fraction	receptor activity				0																		---	---	---	---
ANKFN1	162282	broad.mit.edu	37	17	54555176	54555176	+	Intron	DEL	T	-	-	rs113151852		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54555176delT	uc002iun.1	+							NM_153228	NP_694960			ankyrin-repeat and fibronectin type III domain											large_intestine(1)|ovary(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	54619401	54619401	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54619401delA								ANKFN1 (59394 upstream) : NOG (51659 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	55101348	55101348	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55101348delA								SCPEP1 (17221 upstream) : RNF126P1 (21491 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	55155897	55155900	+	IGR	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55155897_55155900delTTTT								RNF126P1 (31742 upstream) : AKAP1 (6653 downstream)																																			---	---	---	---
MSI2	124540	broad.mit.edu	37	17	55334529	55334529	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55334529delC	uc002iuz.1	+						MSI2_uc010wnm.1_Intron|MSI2_uc002iva.2_Intron	NM_138962	NP_620412			musashi 2 isoform a							cytoplasm	nucleotide binding|RNA binding			central_nervous_system(1)|pancreas(1)	2	Breast(9;1.78e-08)			GBM - Glioblastoma multiforme(1;0.0025)				T	HOXA9	CML								---	---	---	---
MSI2	124540	broad.mit.edu	37	17	55377566	55377566	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55377566delT	uc002iuz.1	+						MSI2_uc010wnm.1_Intron|MSI2_uc002iva.2_Intron	NM_138962	NP_620412			musashi 2 isoform a							cytoplasm	nucleotide binding|RNA binding			central_nervous_system(1)|pancreas(1)	2	Breast(9;1.78e-08)			GBM - Glioblastoma multiforme(1;0.0025)				T	HOXA9	CML								---	---	---	---
CUEDC1	404093	broad.mit.edu	37	17	56021161	56021161	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56021161delA	uc002ive.1	-							NM_017949	NP_060419			CUE domain-containing 1											skin(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	56252779	56252779	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56252779delT								OR4D2 (4840 upstream) : EPX (17343 downstream)																																			---	---	---	---
MKS1	54903	broad.mit.edu	37	17	56291371	56291371	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56291371delA	uc002ivr.1	-						MKS1_uc010wnq.1_Intron|MKS1_uc002ivs.1_Intron	NM_017777	NP_060247			Meckel syndrome type 1 protein isoform 1						cilium assembly	centrosome|cilium|microtubule basal body	protein binding			ovary(1)	1																		---	---	---	---
BZRAP1	9256	broad.mit.edu	37	17	56391568	56391568	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56391568delA	uc002ivx.3	-						BZRAP1_uc010dcs.2_Intron|BZRAP1_uc010wnt.1_Intron	NM_004758	NP_004749			peripheral benzodiazepine receptor-associated							mitochondrion	benzodiazepine receptor binding			upper_aerodigestive_tract(2)|skin(1)	3	Medulloblastoma(34;0.127)|all_neural(34;0.237)																	---	---	---	---
RNF43	54894	broad.mit.edu	37	17	56435161	56435161	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56435161delC	uc002iwf.2	-	8	3932	c.1976delG	c.(1975-1977)GGTfs	p.G659fs	RNF43_uc010wnv.1_Frame_Shift_Del_p.G618fs|RNF43_uc002iwh.3_Frame_Shift_Del_p.G659fs|RNF43_uc002iwg.3_Frame_Shift_Del_p.G659fs|RNF43_uc010dcw.2_Frame_Shift_Del_p.G532fs	NM_017763	NP_060233	Q68DV7	RNF43_HUMAN	ring finger protein 43 precursor	659	Pro-rich.|Cytoplasmic (Potential).					endoplasmic reticulum membrane|integral to membrane|nuclear envelope	ligase activity|protein binding|zinc ion binding			ovary(1)	1	Medulloblastoma(34;0.127)|all_neural(34;0.237)																	---	---	---	---
TEX14	56155	broad.mit.edu	37	17	56671192	56671192	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56671192delT	uc010dcz.1	-						TEX14_uc002iwr.1_Intron|TEX14_uc002iws.1_Intron|TEX14_uc010dda.1_Intron	NM_198393	NP_938207			testis expressed sequence 14 isoform a							cytoplasm	ATP binding|protein kinase activity			stomach(4)|lung(3)|breast(3)|ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)|pancreas(1)	17	Medulloblastoma(34;0.127)|all_neural(34;0.237)																	---	---	---	---
TEX14	56155	broad.mit.edu	37	17	56678882	56678883	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56678882_56678883insA	uc010dcz.1	-						TEX14_uc002iwr.1_Intron|TEX14_uc002iws.1_Intron|TEX14_uc010dda.1_Intron	NM_198393	NP_938207			testis expressed sequence 14 isoform a							cytoplasm	ATP binding|protein kinase activity			stomach(4)|lung(3)|breast(3)|ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)|pancreas(1)	17	Medulloblastoma(34;0.127)|all_neural(34;0.237)																	---	---	---	---
RAD51C	5889	broad.mit.edu	37	17	56785577	56785577	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56785577delT	uc002iwu.2	+						RAD51C_uc010woa.1_Intron|RAD51C_uc010ddc.2_Intron|RAD51C_uc002iwv.2_Intron|RAD51C_uc002iww.2_Intron	NM_058216	NP_478123			RAD51 homolog C isoform 1						blood coagulation|DNA repair	mitochondrion|nucleoplasm|perinuclear region of cytoplasm	ATP binding|DNA binding|DNA-dependent ATPase activity				0	Medulloblastoma(34;0.127)|all_neural(34;0.237)												Homologous_recombination	Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2				---	---	---	---
TRIM37	4591	broad.mit.edu	37	17	57119311	57119311	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57119311delT	uc002iwy.3	-						TRIM37_uc002iwz.3_Intron|TRIM37_uc002ixa.3_Intron|TRIM37_uc010woc.1_Intron	NM_001005207	NP_001005207			tripartite motif-containing 37 protein							perinuclear region of cytoplasm|peroxisome	ligase activity|protein binding|zinc ion binding			lung(2)|pancreas(2)|ovary(1)|skin(1)|breast(1)	7	Medulloblastoma(34;0.0922)|all_neural(34;0.101)													Mulibrey_Nanism				---	---	---	---
Unknown	0	broad.mit.edu	37	17	57283412	57283412	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57283412delA								PRR11 (2527 upstream) : C17orf71 (3959 downstream)																																			---	---	---	---
YPEL2	388403	broad.mit.edu	37	17	57427450	57427450	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57427450delT	uc002ixm.1	+						YPEL2_uc002ixl.1_Intron	NM_001005404	NP_001005404			yippee-like 2							nucleolus					0	all_neural(34;0.0837)|Medulloblastoma(34;0.0922)																	---	---	---	---
Unknown	0	broad.mit.edu	37	17	57488063	57488063	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57488063delT								YPEL2 (8968 upstream) : DHX40 (154823 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	57575292	57575292	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57575292delT								YPEL2 (96197 upstream) : DHX40 (67594 downstream)																																			---	---	---	---
CLTC	1213	broad.mit.edu	37	17	57706486	57706486	+	Intron	DEL	A	-	-	rs34915361		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57706486delA	uc002ixq.1	+						CLTC_uc002ixp.2_Intron|CLTC_uc002ixr.1_Intron	NM_004859	NP_004850			clathrin heavy chain 1						axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|mitosis|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport|receptor internalization|transferrin transport	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|cytosol|melanosome|spindle	protein binding|structural molecule activity		CLTC/ALK(44)|CLTC/TFE3(2)	haematopoietic_and_lymphoid_tissue(33)|soft_tissue(11)|kidney(2)|ovary(1)|breast(1)	48	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)							T	ALK|TFE3	ALCL|renal 								---	---	---	---
CLTC	1213	broad.mit.edu	37	17	57728361	57728361	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57728361delT	uc002ixq.1	+						CLTC_uc002ixp.2_Intron|CLTC_uc002ixr.1_Intron	NM_004859	NP_004850			clathrin heavy chain 1						axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|mitosis|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport|receptor internalization|transferrin transport	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|cytosol|melanosome|spindle	protein binding|structural molecule activity		CLTC/ALK(44)|CLTC/TFE3(2)	haematopoietic_and_lymphoid_tissue(33)|soft_tissue(11)|kidney(2)|ovary(1)|breast(1)	48	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)							T	ALK|TFE3	ALCL|renal 								---	---	---	---
CLTC	1213	broad.mit.edu	37	17	57764446	57764446	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57764446delT	uc002ixq.1	+						CLTC_uc002ixp.2_Intron|CLTC_uc002ixr.1_Intron	NM_004859	NP_004850			clathrin heavy chain 1						axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|mitosis|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport|receptor internalization|transferrin transport	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|cytosol|melanosome|spindle	protein binding|structural molecule activity		CLTC/ALK(44)|CLTC/TFE3(2)	haematopoietic_and_lymphoid_tissue(33)|soft_tissue(11)|kidney(2)|ovary(1)|breast(1)	48	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)							T	ALK|TFE3	ALCL|renal 								---	---	---	---
HEATR6	63897	broad.mit.edu	37	17	58153604	58153604	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58153604delA	uc002iyk.1	-						HEATR6_uc010wos.1_5'Flank	NM_022070	NP_071353			HEAT repeat containing 6								binding			ovary(1)|skin(1)	2	all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10)															---	---	---	---
USP32	84669	broad.mit.edu	37	17	58332410	58332411	+	Intron	DEL	TT	-	-	rs35284371		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58332410_58332411delTT	uc002iyo.1	-						USP32_uc002iyn.1_Intron|USP32_uc010wov.1_Intron	NM_032582	NP_115971			ubiquitin specific protease 32						protein deubiquitination|ubiquitin-dependent protein catabolic process	Golgi apparatus|membrane	calcium ion binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|breast(2)|large_intestine(1)	5	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)															---	---	---	---
APPBP2	10513	broad.mit.edu	37	17	58576694	58576696	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58576694_58576696delAAA	uc002iys.1	-						APPBP2_uc010ddl.1_Intron	NM_006380	NP_006371			amyloid beta precursor protein-binding protein						intracellular protein transport	cytoplasmic vesicle membrane|microtubule|microtubule associated complex|nucleus	microtubule motor activity|protein binding				0	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;3.67e-13)|all cancers(12;1.44e-11)|Colorectal(3;0.01)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	58654417	58654418	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58654417_58654418delAA								APPBP2 (50837 upstream) : PPM1D (23136 downstream)																																			---	---	---	---
PPM1D	8493	broad.mit.edu	37	17	58708967	58708967	+	Intron	DEL	A	-	-	rs34657053		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58708967delA	uc002iyt.1	+						PPM1D_uc010ddm.1_Intron	NM_003620	NP_003611			protein phosphatase 1D						negative regulation of cell proliferation|protein dephosphorylation|response to radiation	nucleus|protein serine/threonine phosphatase complex	metal ion binding|protein binding|protein serine/threonine phosphatase activity			upper_aerodigestive_tract(1)	1	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;6.75e-12)|all cancers(12;1.96e-10)															---	---	---	---
BCAS3	54828	broad.mit.edu	37	17	58771861	58771862	+	Intron	DEL	AA	-	-	rs77243661		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:58771861_58771862delAA	uc002iyv.3	+						BCAS3_uc010wow.1_Intron|BCAS3_uc002iyu.3_Intron|BCAS3_uc002iyw.3_Intron	NM_001099432	NP_001092902			breast carcinoma amplified sequence 3 isoform 1							nucleus				ovary(2)|central_nervous_system(2)|skin(1)	5			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	59735109	59735109	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59735109delT								NACA2 (66546 upstream) : BRIP1 (24876 downstream)																																			---	---	---	---
BRIP1	83990	broad.mit.edu	37	17	59824782	59824782	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:59824782delA	uc002izk.1	-						BRIP1_uc002izl.1_Intron	NM_032043	NP_114432			BRCA1 interacting protein C-terminal helicase 1						DNA damage checkpoint|double-strand break repair|regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding			ovary(1)	1								F|N|Mis			AML|leukemia|breast		Direct_reversal_of_damage|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
Unknown	0	broad.mit.edu	37	17	60365931	60365932	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60365931_60365932insA								TBC1D3P2 (12915 upstream) : EFCAB3 (81647 downstream)																																			---	---	---	---
MARCH10	162333	broad.mit.edu	37	17	60848936	60848940	+	Intron	DEL	TTTTT	-	-	rs71990711		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60848936_60848940delTTTTT	uc010ddr.2	-						MARCH10_uc002jag.3_Intron|MARCH10_uc010dds.2_Intron|MARCH10_uc002jah.2_Intron	NM_001100875	NP_001094345			ring finger protein 190								ligase activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	60904063	60904063	+	IGR	DEL	T	-	-	rs66832023		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60904063delT								MARCH10 (18358 upstream) : MIR633 (117513 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	60950101	60950101	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60950101delT								MARCH10 (64396 upstream) : MIR633 (71475 downstream)																																			---	---	---	---
TANC2	26115	broad.mit.edu	37	17	61278353	61278353	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61278353delT	uc002jal.3	+						TANC2_uc010wpe.1_Intron	NM_025185	NP_079461			tetratricopeptide repeat, ankyrin repeat and								binding			ovary(2)	2																		---	---	---	---
TANC2	26115	broad.mit.edu	37	17	61489994	61489994	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61489994delT	uc002jal.3	+						TANC2_uc010wpe.1_Intron|TANC2_uc002jao.3_Intron	NM_025185	NP_079461			tetratricopeptide repeat, ankyrin repeat and								binding			ovary(2)	2																		---	---	---	---
CYB561	1534	broad.mit.edu	37	17	61522538	61522538	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61522538delA	uc002jas.2	-						CYB561_uc010ddt.2_Intron|CYB561_uc002jat.2_Intron|CYB561_uc010wpf.1_Intron|CYB561_uc010wpg.1_Intron	NM_001017916	NP_001017916			cytochrome b-561						electron transport chain|transport	integral to plasma membrane	cytochrome-b5 reductase activity|ferric-chelate reductase activity|metal ion binding			ovary(1)	1				READ - Rectum adenocarcinoma(1115;0.0689)														---	---	---	---
KCNH6	81033	broad.mit.edu	37	17	61625627	61625627	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61625627delA	uc002jaz.1	+						DCAF7_uc002jbb.2_5'Flank|DCAF7_uc002jbc.2_5'Flank|DCAF7_uc010wpn.1_5'Flank	NM_173092	NP_775115			potassium voltage-gated channel, subfamily H,						regulation of transcription, DNA-dependent|signal transduction					skin(1)	1					Ibutilide(DB00308)													---	---	---	---
MAP3K3	4215	broad.mit.edu	37	17	61737570	61737571	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61737570_61737571delTT	uc002jbg.2	+						MAP3K3_uc002jbe.2_Intron|MAP3K3_uc002jbf.2_Intron|MAP3K3_uc002jbh.2_Intron|MAP3K3_uc010wpo.1_Intron|MAP3K3_uc010wpp.1_Intron	NM_002401	NP_002392			mitogen-activated protein kinase kinase kinase 3						MAPKKK cascade|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autophosphorylation	cytosol	ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein binding			lung(3)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)	6																		---	---	---	---
STRADA	92335	broad.mit.edu	37	17	61819681	61819681	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61819681delT	uc002jbm.2	-						STRADA_uc002jbn.2_5'Flank|STRADA_uc002jbo.2_5'Flank|STRADA_uc002jbp.2_5'Flank|STRADA_uc002jbq.2_5'Flank|STRADA_uc010wpq.1_5'Flank|STRADA_uc010wpr.1_5'Flank|STRADA_uc010ddw.2_5'Flank|STRADA_uc002jbr.2_5'Flank	NM_001003787	NP_001003787			STE20-related kinase adaptor alpha isoform 1						activation of protein kinase activity|cell cycle arrest|insulin receptor signaling pathway|protein export from nucleus|regulation of fatty acid oxidation	cytosol|nucleus	ATP binding|kinase binding|protein kinase activity			ovary(1)	1																		---	---	---	---
SCN4A	6329	broad.mit.edu	37	17	62021503	62021504	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62021503_62021504insT	uc002jds.1	-							NM_000334	NP_000325			voltage-gated sodium channel type 4 alpha						muscle contraction	voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(1)|pancreas(1)|skin(1)	3					Lamotrigine(DB00555)													---	---	---	---
Unknown	0	broad.mit.edu	37	17	62058997	62058997	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62058997delT								SCN4A (8719 upstream) : C17orf72 (16714 downstream)																																			---	---	---	---
ERN1	2081	broad.mit.edu	37	17	62144967	62144969	+	Intron	DEL	AAA	-	-	rs35232508		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62144967_62144969delAAA	uc002jdz.2	-							NM_001433	NP_001424			endoplasmic reticulum to nucleus signalling 1						activation of signaling protein activity involved in unfolded protein response|apoptosis|cell cycle arrest|induction of apoptosis|mRNA processing|regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to endoplasmic reticulum membrane	ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|magnesium ion binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(4)|lung(2)|stomach(1)|ovary(1)|kidney(1)	9																		---	---	---	---
SMURF2	64750	broad.mit.edu	37	17	62541845	62541855	+	3'UTR	DEL	AAAAAAAGGGG	-	-	rs59188589		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62541845_62541855delAAAAAAAGGGG	uc002jep.1	-	19					SMURF2_uc002jeq.1_3'UTR|SMURF2_uc002jer.1_3'UTR	NM_022739	NP_073576			SMAD specific E3 ubiquitin protein ligase 2						BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent SMAD protein catabolic process	cytosol|membrane raft|nucleus|plasma membrane|ubiquitin ligase complex	identical protein binding|SMAD binding|ubiquitin-protein ligase activity			skin(3)|lung(1)	4	Breast(5;1.32e-14)		BRCA - Breast invasive adenocarcinoma(8;9.88e-12)															---	---	---	---
SMURF2	64750	broad.mit.edu	37	17	62634042	62634042	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62634042delA	uc002jep.1	-						SMURF2_uc002jeq.1_Intron|SMURF2_uc002jer.1_Intron	NM_022739	NP_073576			SMAD specific E3 ubiquitin protein ligase 2						BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent SMAD protein catabolic process	cytosol|membrane raft|nucleus|plasma membrane|ubiquitin ligase complex	identical protein binding|SMAD binding|ubiquitin-protein ligase activity			skin(3)|lung(1)	4	Breast(5;1.32e-14)		BRCA - Breast invasive adenocarcinoma(8;9.88e-12)															---	---	---	---
SMURF2	64750	broad.mit.edu	37	17	62656308	62656308	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62656308delT	uc002jep.1	-						SMURF2_uc002jeq.1_Intron|SMURF2_uc002jer.1_Intron	NM_022739	NP_073576			SMAD specific E3 ubiquitin protein ligase 2						BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent SMAD protein catabolic process	cytosol|membrane raft|nucleus|plasma membrane|ubiquitin ligase complex	identical protein binding|SMAD binding|ubiquitin-protein ligase activity			skin(3)|lung(1)	4	Breast(5;1.32e-14)		BRCA - Breast invasive adenocarcinoma(8;9.88e-12)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	62932555	62932556	+	IGR	DEL	GT	-	-	rs35142297		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62932555_62932556delGT								LRRC37A3 (16969 upstream) : AMZ2P1 (30112 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	63457339	63457339	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63457339delT								RGS9 (233520 upstream) : AXIN2 (67346 downstream)																																			---	---	---	---
AXIN2	8313	broad.mit.edu	37	17	63535294	63535294	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63535294delC	uc002jfi.2	-						AXIN2_uc010den.1_Intron|AXIN2_uc002jfh.2_Intron	NM_004655	NP_004646			axin 2						cellular protein localization|cellular response to organic cyclic compound|dorsal/ventral axis specification|intramembranous ossification|maintenance of DNA repeat elements|mRNA stabilization|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of cell proliferation|negative regulation of osteoblast differentiation|odontogenesis|positive regulation of cell death|positive regulation of epithelial to mesenchymal transition|positive regulation of protein phosphorylation|regulation of centromeric sister chromatid cohesion|regulation of mismatch repair|Wnt receptor signaling pathway involved in somitogenesis	Axin-APC-beta-catenin-GSK3B complex|cell cortex|centrosome|cytoplasmic membrane-bounded vesicle|cytoplasmic microtubule|nucleus|plasma membrane|postsynaptic density	armadillo repeat domain binding|beta-catenin binding|GTPase activator activity|protein kinase binding|signal transducer activity|ubiquitin protein ligase binding			central_nervous_system(1)|skin(1)	2														Oligodontia_Ectodermal_Dysplasia_and_Colorectal_Polyp_syndrome				---	---	---	---
AXIN2	8313	broad.mit.edu	37	17	63553624	63553625	+	Intron	INS	-	CT	CT	rs150521485	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63553624_63553625insCT	uc002jfi.2	-						AXIN2_uc010den.1_Intron|AXIN2_uc002jfh.2_Intron	NM_004655	NP_004646			axin 2						cellular protein localization|cellular response to organic cyclic compound|dorsal/ventral axis specification|intramembranous ossification|maintenance of DNA repeat elements|mRNA stabilization|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of cell proliferation|negative regulation of osteoblast differentiation|odontogenesis|positive regulation of cell death|positive regulation of epithelial to mesenchymal transition|positive regulation of protein phosphorylation|regulation of centromeric sister chromatid cohesion|regulation of mismatch repair|Wnt receptor signaling pathway involved in somitogenesis	Axin-APC-beta-catenin-GSK3B complex|cell cortex|centrosome|cytoplasmic membrane-bounded vesicle|cytoplasmic microtubule|nucleus|plasma membrane|postsynaptic density	armadillo repeat domain binding|beta-catenin binding|GTPase activator activity|protein kinase binding|signal transducer activity|ubiquitin protein ligase binding			central_nervous_system(1)|skin(1)	2														Oligodontia_Ectodermal_Dysplasia_and_Colorectal_Polyp_syndrome				---	---	---	---
CCDC46	201134	broad.mit.edu	37	17	63888640	63888641	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63888640_63888641delTT	uc002jfl.2	-						CCDC46_uc010deo.2_Intron|CCDC46_uc002jfm.2_Intron|CCDC46_uc010dep.2_Intron	NM_145036	NP_659473			coiled-coil domain containing 46 isoform a							centrosome					0			BRCA - Breast invasive adenocarcinoma(6;1.53e-06)															---	---	---	---
CCDC46	201134	broad.mit.edu	37	17	63962155	63962155	+	Intron	DEL	T	-	-	rs147502023		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63962155delT	uc002jfl.2	-						CCDC46_uc010deo.2_Intron|CCDC46_uc002jfm.2_Intron|CCDC46_uc010dep.2_Intron	NM_145036	NP_659473			coiled-coil domain containing 46 isoform a							centrosome					0			BRCA - Breast invasive adenocarcinoma(6;1.53e-06)															---	---	---	---
CCDC46	201134	broad.mit.edu	37	17	64106456	64106456	+	Intron	DEL	A	-	-	rs12942145		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64106456delA	uc002jfl.2	-						CCDC46_uc002jfm.2_Intron|CCDC46_uc010dep.2_Intron	NM_145036	NP_659473			coiled-coil domain containing 46 isoform a							centrosome					0			BRCA - Breast invasive adenocarcinoma(6;1.53e-06)															---	---	---	---
PRKCA	5578	broad.mit.edu	37	17	64390191	64390191	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64390191delA	uc002jfp.1	+						PRKCA_uc002jfo.1_Intron	NM_002737	NP_002728			protein kinase C, alpha						activation of phospholipase C activity|energy reserve metabolic process|induction of apoptosis by extracellular signals|intracellular signal transduction|mRNA metabolic process|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of blood vessel endothelial cell migration|regulation of insulin secretion|response to interleukin-1|synaptic transmission	cytosol|endoplasmic reticulum|membrane fraction|nucleoplasm|plasma membrane	ATP binding|enzyme binding|histone kinase activity (H3-T6 specific)|protein kinase C activity|zinc ion binding			central_nervous_system(4)|large_intestine(1)|stomach(1)|lung(1)|breast(1)|ovary(1)	9			BRCA - Breast invasive adenocarcinoma(6;4.68e-09)		Phosphatidylserine(DB00144)|Vitamin E(DB00163)													---	---	---	---
Unknown	0	broad.mit.edu	37	17	64896725	64896725	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64896725delT								CACNG5 (15369 upstream) : CACNG4 (64288 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	64939709	64939710	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64939709_64939710insA								CACNG5 (58353 upstream) : CACNG4 (21303 downstream)																																			---	---	---	---
PSMD12	5718	broad.mit.edu	37	17	65336874	65336874	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65336874delA	uc002jfy.2	-	11					PSMD12_uc002jga.2_3'UTR|PSMD12_uc002jfz.2_3'UTR	NM_002816	NP_002807			proteasome 26S non-ATPase subunit 12 isoform 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome regulatory particle	protein binding				0	all_cancers(12;2.38e-11)|all_epithelial(3;8.27e-13)																	---	---	---	---
PITPNC1	26207	broad.mit.edu	37	17	65439750	65439752	+	Intron	DEL	TTT	-	-	rs147888519		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65439750_65439752delTTT	uc002jgc.2	+						PITPNC1_uc002jgb.2_Intron	NM_012417	NP_036549			phosphatidylinositol transfer protein,						signal transduction	cytoplasm	lipid binding|phosphatidylinositol transporter activity|protein binding			skin(1)	1	all_cancers(12;3.03e-10)		BRCA - Breast invasive adenocarcinoma(8;2.08e-08)|Colorectal(3;0.198)															---	---	---	---
PITPNC1	26207	broad.mit.edu	37	17	65469456	65469456	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65469456delT	uc002jgc.2	+						PITPNC1_uc002jgb.2_Intron|MIR548D2_hsa-mir-548d-2|MI0003671_5'Flank	NM_012417	NP_036549			phosphatidylinositol transfer protein,						signal transduction	cytoplasm	lipid binding|phosphatidylinositol transporter activity|protein binding			skin(1)	1	all_cancers(12;3.03e-10)		BRCA - Breast invasive adenocarcinoma(8;2.08e-08)|Colorectal(3;0.198)															---	---	---	---
PITPNC1	26207	broad.mit.edu	37	17	65523823	65523823	+	Intron	DEL	A	-	-	rs74712107		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65523823delA	uc002jgc.2	+						PITPNC1_uc002jgb.2_Intron	NM_012417	NP_036549			phosphatidylinositol transfer protein,						signal transduction	cytoplasm	lipid binding|phosphatidylinositol transporter activity|protein binding			skin(1)	1	all_cancers(12;3.03e-10)		BRCA - Breast invasive adenocarcinoma(8;2.08e-08)|Colorectal(3;0.198)															---	---	---	---
PITPNC1	26207	broad.mit.edu	37	17	65558656	65558656	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65558656delT	uc002jgc.2	+						PITPNC1_uc002jgb.2_Intron	NM_012417	NP_036549			phosphatidylinositol transfer protein,						signal transduction	cytoplasm	lipid binding|phosphatidylinositol transporter activity|protein binding			skin(1)	1	all_cancers(12;3.03e-10)		BRCA - Breast invasive adenocarcinoma(8;2.08e-08)|Colorectal(3;0.198)															---	---	---	---
PITPNC1	26207	broad.mit.edu	37	17	65582715	65582715	+	Intron	DEL	A	-	-	rs111765556		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65582715delA	uc002jgc.2	+						PITPNC1_uc002jgb.2_Intron	NM_012417	NP_036549			phosphatidylinositol transfer protein,						signal transduction	cytoplasm	lipid binding|phosphatidylinositol transporter activity|protein binding			skin(1)	1	all_cancers(12;3.03e-10)		BRCA - Breast invasive adenocarcinoma(8;2.08e-08)|Colorectal(3;0.198)															---	---	---	---
PITPNC1	26207	broad.mit.edu	37	17	65592511	65592511	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65592511delA	uc002jgc.2	+						PITPNC1_uc002jgb.2_Intron	NM_012417	NP_036549			phosphatidylinositol transfer protein,						signal transduction	cytoplasm	lipid binding|phosphatidylinositol transporter activity|protein binding			skin(1)	1	all_cancers(12;3.03e-10)		BRCA - Breast invasive adenocarcinoma(8;2.08e-08)|Colorectal(3;0.198)															---	---	---	---
BPTF	2186	broad.mit.edu	37	17	65955102	65955102	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65955102delA	uc002jgf.2	+						BPTF_uc002jge.2_Intron|BPTF_uc002jgg.2_Intron|BPTF_uc002jgh.2_Intron	NM_182641	NP_872579			bromodomain PHD finger transcription factor						brain development|chromatin remodeling|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|NURF complex	sequence-specific DNA binding|transcription factor binding|zinc ion binding			ovary(2)|skin(2)	4	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)															---	---	---	---
ARSG	22901	broad.mit.edu	37	17	66332361	66332361	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66332361delT	uc002jhc.2	+						ARSG_uc002jhb.1_Intron	NM_014960	NP_055775			Arylsulfatase G precursor						sulfur compound metabolic process	endoplasmic reticulum|extracellular space|lysosome	arylsulfatase activity|metal ion binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(8;5.34e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)															---	---	---	---
WIPI1	55062	broad.mit.edu	37	17	66449342	66449342	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66449342delA	uc010dey.2	-						WIPI1_uc002jhd.3_Intron|WIPI1_uc010wqo.1_Intron|WIPI1_uc002jhe.3_Intron	NM_017983	NP_060453			WD repeat domain, phosphoinositide interacting						macroautophagy|vesicle targeting, trans-Golgi to endosome	autophagic vacuole membrane|clathrin-coated vesicle|cytosol|endosome membrane|PAS complex|pre-autophagosomal structure membrane|trans-Golgi network	androgen receptor binding|estrogen receptor binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding				0																		---	---	---	---
PRKAR1A	5573	broad.mit.edu	37	17	66518742	66518742	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66518742delT	uc002jhg.2	+						PRKAR1A_uc002jhh.2_Intron|PRKAR1A_uc002jhi.2_Intron|PRKAR1A_uc002jhj.2_Intron|PRKAR1A_uc002jhk.2_Intron|PRKAR1A_uc002jhl.2_Intron|PRKAR1A_uc002jhm.2_Intron	NM_212471	NP_997636			cAMP-dependent protein kinase, regulatory						activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|intracellular signal transduction|nerve growth factor receptor signaling pathway|regulation of insulin secretion|regulation of transcription from RNA polymerase II promoter|transmembrane transport|water transport	cAMP-dependent protein kinase complex|cytosol	cAMP binding|cAMP-dependent protein kinase regulator activity|protein binding			adrenal_gland(4)|lung(3)|thyroid(2)|soft_tissue(2)|breast(1)	12	Breast(10;1.64e-13)							T|Mis|N|F|S	RET	papillary thyroid	myxoma|endocrine|papillary thyroid			Carney_Complex|Primary_Pigmented_Nodular_Adrenocortical_Disease_Familial|Cardiac_Myxomas_Familial_Clustering_of				---	---	---	---
Unknown	0	broad.mit.edu	37	17	66712982	66712982	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66712982delA								FAM20A (115887 upstream) : ABCA8 (150451 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	66774948	66774948	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66774948delT								FAM20A (177853 upstream) : ABCA8 (88485 downstream)																																			---	---	---	---
ABCA8	10351	broad.mit.edu	37	17	66872446	66872446	+	Intron	DEL	T	-	-	rs4148026		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66872446delT	uc002jhp.2	-						ABCA8_uc002jhq.2_Intron|ABCA8_uc010wqq.1_Intron	NM_007168	NP_009099			ATP-binding cassette, sub-family A member 8							integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)|skin(1)	3	Breast(10;4.56e-13)																	---	---	---	---
ABCA10	10349	broad.mit.edu	37	17	67218640	67218640	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67218640delA	uc010dfa.1	-						ABCA10_uc010wqt.1_Intron|ABCA10_uc010dfc.1_Intron	NM_080282	NP_525021			ATP-binding cassette, sub-family A, member 10						transport	integral to membrane	ATP binding|ATPase activity			ovary(2)|central_nervous_system(1)|skin(1)	4	Breast(10;6.95e-12)																	---	---	---	---
ABCA5	23461	broad.mit.edu	37	17	67248055	67248055	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67248055delA	uc002jif.2	-						ABCA5_uc002jib.2_Intron|ABCA5_uc002jic.2_Intron|ABCA5_uc002jid.2_Intron|ABCA5_uc002jie.2_Intron|ABCA5_uc002jig.2_Intron	NM_018672	NP_061142			ATP-binding cassette, sub-family A , member 5						cholesterol efflux|high-density lipoprotein particle remodeling|negative regulation of macrophage derived foam cell differentiation	Golgi membrane|integral to membrane|late endosome membrane|lysosomal membrane	ATP binding|ATPase activity			ovary(2)|central_nervous_system(1)|skin(1)	4	Breast(10;3.72e-11)																	---	---	---	---
ABCA5	23461	broad.mit.edu	37	17	67281850	67281850	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67281850delA	uc002jif.2	-						ABCA5_uc002jic.2_Intron|ABCA5_uc002jid.2_Intron|ABCA5_uc002jie.2_Intron|ABCA5_uc002jig.2_Intron|ABCA5_uc002jih.2_Intron|ABCA5_uc010dfe.2_Intron	NM_018672	NP_061142			ATP-binding cassette, sub-family A , member 5						cholesterol efflux|high-density lipoprotein particle remodeling|negative regulation of macrophage derived foam cell differentiation	Golgi membrane|integral to membrane|late endosome membrane|lysosomal membrane	ATP binding|ATPase activity			ovary(2)|central_nervous_system(1)|skin(1)	4	Breast(10;3.72e-11)																	---	---	---	---
MAP2K6	5608	broad.mit.edu	37	17	67522543	67522543	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67522543delA	uc002jij.2	+							NM_002758	NP_002749			mitogen-activated protein kinase kinase 6						activation of MAPK activity|cell cycle arrest|DNA damage induced protein phosphorylation|innate immune response|muscle cell differentiation|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of muscle cell differentiation|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|pancreas(1)	5	Breast(10;6.05e-10)																	---	---	---	---
Unknown	0	broad.mit.edu	37	17	67683962	67683963	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67683962_67683963delTT								MAP2K6 (145500 upstream) : KCNJ16 (387463 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	67703228	67703228	+	IGR	DEL	T	-	-	rs79991562		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67703228delT								MAP2K6 (164766 upstream) : KCNJ16 (368198 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	68535292	68535293	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68535292_68535293delAA								KCNJ2 (359111 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	68920322	68920325	+	IGR	DEL	TTTC	-	-	rs145545590		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68920322_68920325delTTTC								KCNJ2 (744141 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	69235096	69235096	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:69235096delT								None (None upstream) : SOX9 (882065 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	69415003	69415003	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:69415003delT								None (None upstream) : SOX9 (702158 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	69495821	69495821	+	IGR	DEL	A	-	-	rs35858146		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:69495821delA								None (None upstream) : SOX9 (621340 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	69588833	69588833	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:69588833delA								None (None upstream) : SOX9 (528328 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	70144126	70144126	+	IGR	DEL	A	-	-	rs36119433		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70144126delA								SOX9 (21574 upstream) : SLC39A11 (497960 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	70188455	70188455	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70188455delT								SOX9 (65903 upstream) : SLC39A11 (453631 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	70251887	70251887	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70251887delA								SOX9 (129335 upstream) : SLC39A11 (390199 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	70254324	70254325	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70254324_70254325insT								SOX9 (131772 upstream) : SLC39A11 (387761 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	70270801	70270802	+	IGR	INS	-	CA	CA	rs143583122	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70270801_70270802insCA								SOX9 (148249 upstream) : SLC39A11 (371284 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	70435095	70435095	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70435095delA	uc002jix.2	-						uc002jiz.1_Intron					Homo sapiens cDNA FLJ20470 fis, clone KAT06815.																														---	---	---	---
SLC39A11	201266	broad.mit.edu	37	17	70780464	70780465	+	Intron	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70780464_70780465delAG	uc002jjb.2	-						SLC39A11_uc002jja.2_Intron	NM_001159770	NP_001153242			solute carrier family 39, member 11 isoform 1						zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			ovary(1)	1																		---	---	---	---
SLC39A11	201266	broad.mit.edu	37	17	70806831	70806831	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70806831delT	uc002jjb.2	-						SLC39A11_uc002jja.2_Intron	NM_001159770	NP_001153242			solute carrier family 39, member 11 isoform 1						zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			ovary(1)	1																		---	---	---	---
SLC39A11	201266	broad.mit.edu	37	17	71035052	71035052	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71035052delA	uc002jjb.2	-						SLC39A11_uc002jja.2_Intron|SLC39A11_uc002jjc.1_Intron	NM_001159770	NP_001153242			solute carrier family 39, member 11 isoform 1						zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	71170700	71170701	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71170700_71170701delAA								SSTR2 (2640 upstream) : COG1 (18472 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	71323244	71323244	+	IGR	DEL	C	-	-	rs11651652	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71323244delC								CDC42EP4 (15101 upstream) : SDK2 (7280 downstream)																																			---	---	---	---
SDK2	54549	broad.mit.edu	37	17	71606536	71606536	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71606536delA	uc010dfm.2	-							NM_001144952	NP_001138424			sidekick 2						cell adhesion	integral to membrane				ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	71879059	71879059	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71879059delT								C17orf54 (54383 upstream) : RPL38 (320736 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	71896624	71896624	+	IGR	DEL	T	-	-	rs140468570		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71896624delT								C17orf54 (71948 upstream) : RPL38 (303171 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	71909537	71909537	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71909537delA								C17orf54 (84861 upstream) : RPL38 (290258 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	71927556	71927556	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71927556delT								C17orf54 (102880 upstream) : RPL38 (272239 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	71935447	71935448	+	IGR	INS	-	ACAC	ACAC	rs113615491		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71935447_71935448insACAC								C17orf54 (110771 upstream) : RPL38 (264347 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	72103130	72103130	+	IGR	DEL	A	-	-	rs113811112		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72103130delA								C17orf54 (278454 upstream) : RPL38 (96665 downstream)																																			---	---	---	---
CD300LF	146722	broad.mit.edu	37	17	72705707	72705707	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72705707delT	uc002jlg.2	-						RAB37_uc002jlc.2_Intron|RAB37_uc010dfu.2_Intron|RAB37_uc002jld.2_Intron|CD300LF_uc002jlh.2_Intron|CD300LF_uc002jli.2_Intron|CD300LF_uc010wra.1_Intron	NM_139018	NP_620587			NK inhibitory receptor precursor							integral to membrane|plasma membrane	receptor activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
SLC16A5	9121	broad.mit.edu	37	17	73098833	73098833	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73098833delT	uc002jmr.2	+						SLC16A5_uc002jms.1_Intron|SLC16A5_uc002jmt.2_Intron|SLC16A5_uc002jmu.2_Intron|SLC16A5_uc010wrt.1_Intron	NM_004695	NP_004686			solute carrier family 16, member 5						organic anion transport	integral to plasma membrane|membrane fraction	secondary active monocarboxylate transmembrane transporter activity|symporter activity			central_nervous_system(1)	1	all_lung(278;0.226)		LUSC - Lung squamous cell carcinoma(166;0.162)|Lung(188;0.235)		Pyruvic acid(DB00119)													---	---	---	---
HN1	51155	broad.mit.edu	37	17	73144523	73144524	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73144523_73144524insT	uc002jna.1	-						HN1_uc002jmz.1_Intron|HN1_uc002jnb.1_Intron|HN1_uc010dgc.1_Intron|HN1_uc002jnc.2_Intron|HN1_uc002jnd.2_Intron	NM_016185	NP_057269			hematological and neurological expressed 1							nucleus					0	all_lung(278;0.14)|Lung NSC(278;0.168)																	---	---	---	---
NUP85	79902	broad.mit.edu	37	17	73205894	73205894	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73205894delT	uc002jng.1	+						NUP85_uc010dgd.1_Intron|NUP85_uc010wrv.1_Intron	NM_024844	NP_079120			nucleoporin 85						carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|nuclear membrane|Nup107-160 complex|spindle	protein binding			ovary(1)	1	all_lung(278;0.14)|Lung NSC(278;0.168)		all cancers(21;3.45e-06)															---	---	---	---
GRB2	2885	broad.mit.edu	37	17	73380459	73380459	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73380459delA	uc002jnx.3	-						GRB2_uc002jny.3_Intron	NM_002086	NP_002077			growth factor receptor-bound protein 2 isoform						axon guidance|blood coagulation|cell junction assembly|cell-cell signaling|cellular response to ionizing radiation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of reactive oxygen species metabolic process|Ras protein signal transduction|receptor internalization|signal transduction in response to DNA damage|T cell costimulation	cytosol|Golgi apparatus	epidermal growth factor receptor binding|insulin receptor substrate binding|SH3/SH2 adaptor activity			ovary(3)	3	all_cancers(13;5.44e-09)|all_epithelial(9;1.1e-09)|Breast(9;1.85e-09)|all_lung(278;0.222)		all cancers(21;1.09e-07)|Epithelial(20;1.23e-06)|Lung(188;0.185)		Pegademase bovine(DB00061)													---	---	---	---
LLGL2	3993	broad.mit.edu	37	17	73536131	73536132	+	Intron	INS	-	C	C	rs147170564	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73536131_73536132insC	uc002joh.2	+						LLGL2_uc002jog.1_Intron|LLGL2_uc010dgf.1_Intron|LLGL2_uc002joi.2_Intron|LLGL2_uc010dgg.1_Intron	NM_001031803	NP_001026973			lethal giant larvae homolog 2 isoform c						cell cycle|cell division|exocytosis|regulation of establishment or maintenance of cell polarity	cytoplasm|intracellular membrane-bounded organelle	PDZ domain binding			ovary(2)	2	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)															---	---	---	---
MRPL38	64978	broad.mit.edu	37	17	73898037	73898037	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73898037delG	uc010wso.1	-						FBF1_uc002jqa.1_Intron|MRPL38_uc002jpz.1_Intron	NM_032478	NP_115867			mitochondrial ribosomal protein L38 precursor							actin cytoskeleton|mitochondrion|ribosome				pancreas(1)	1			all cancers(21;0.000154)|Epithelial(20;0.000156)|BRCA - Breast invasive adenocarcinoma(9;0.00936)|LUSC - Lung squamous cell carcinoma(166;0.154)															---	---	---	---
ACOX1	51	broad.mit.edu	37	17	73939622	73939622	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73939622delA	uc002jqf.2	-	14					FBF1_uc002jqc.2_5'Flank|FBF1_uc002jqd.1_5'Flank|ACOX1_uc010wsq.1_3'UTR|ACOX1_uc002jqe.2_3'UTR|ACOX1_uc010wsr.1_3'UTR	NM_007292	NP_009223			acyl-Coenzyme A oxidase 1 isoform b						fatty acid beta-oxidation using acyl-CoA oxidase|generation of precursor metabolites and energy|prostaglandin metabolic process|very long-chain fatty acid metabolic process	peroxisomal matrix	acyl-CoA dehydrogenase activity|acyl-CoA oxidase activity|flavin adenine dinucleotide binding|protein N-terminus binding			ovary(1)	1																		---	---	---	---
ACOX1	51	broad.mit.edu	37	17	73944640	73944640	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73944640delT	uc002jqf.2	-						ACOX1_uc010wsq.1_Intron|ACOX1_uc002jqe.2_Intron|ACOX1_uc010wsr.1_Intron	NM_007292	NP_009223			acyl-Coenzyme A oxidase 1 isoform b						fatty acid beta-oxidation using acyl-CoA oxidase|generation of precursor metabolites and energy|prostaglandin metabolic process|very long-chain fatty acid metabolic process	peroxisomal matrix	acyl-CoA dehydrogenase activity|acyl-CoA oxidase activity|flavin adenine dinucleotide binding|protein N-terminus binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	74115923	74115924	+	IGR	DEL	TT	-	-	rs35859558		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74115923_74115924delTT								EXOC7 (16055 upstream) : FOXJ1 (16493 downstream)																																			---	---	---	---
RNF157	114804	broad.mit.edu	37	17	74153037	74153037	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74153037delT	uc002jqz.2	-						RNF157_uc002jra.2_Intron	NM_052916	NP_443148			ring finger protein 157								zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(166;0.187)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	74362628	74362630	+	IGR	DEL	TTT	-	-	rs11350131		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74362628_74362630delTTT								PRPSAP1 (12349 upstream) : SPHK1 (10112 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	74500717	74500717	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74500717delT								RHBDF2 (3209 upstream) : CYGB (22723 downstream)																																			---	---	---	---
MGAT5B	146664	broad.mit.edu	37	17	74866830	74866830	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74866830delG	uc002jtg.3	+						MGAT5B_uc002jth.2_Intron|MGAT5B_uc002jti.2_5'Flank					Homo sapiens GnT-IX mRNA for N-Acetylglucosaminyltransferase IX, complete cds.							Golgi membrane|integral to membrane	alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(2)|skin(1)	3																		---	---	---	---
MGAT5B	146664	broad.mit.edu	37	17	74910181	74910181	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74910181delA	uc002jti.2	+						MGAT5B_uc002jth.2_Intron	NM_198955	NP_945193			N-acetylglucosaminyltranferase VB isoform 2							Golgi membrane|integral to membrane	alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(2)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	17	75096476	75096476	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75096476delT								C17orf86 (5409 upstream) : SEC14L1 (40529 downstream)																																			---	---	---	---
SEC14L1	6397	broad.mit.edu	37	17	75182484	75182485	+	Intron	INS	-	CT	CT			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75182484_75182485insCT	uc002jto.2	+						SEC14L1_uc010dhc.2_Intron|SEC14L1_uc010wth.1_Intron|SEC14L1_uc002jtm.2_Intron|SEC14L1_uc010wti.1_Intron	NM_003003	NP_002994			SEC14 (S. cerevisiae)-like 1 isoform a						transport	Golgi apparatus|integral to membrane	binding			ovary(2)	2																		---	---	---	---
SEC14L1	6397	broad.mit.edu	37	17	75203535	75203535	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75203535delT	uc002jto.2	+						SEC14L1_uc010dhc.2_Intron|SEC14L1_uc010wth.1_Intron|SEC14L1_uc002jtm.2_Intron|SEC14L1_uc010wti.1_Intron|SEC14L1_uc010wtj.1_Intron|SEC14L1_uc002jtr.2_5'Flank	NM_003003	NP_002994			SEC14 (S. cerevisiae)-like 1 isoform a						transport	Golgi apparatus|integral to membrane	binding			ovary(2)	2																		---	---	---	---
SEPT9	10801	broad.mit.edu	37	17	75422379	75422379	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75422379delC	uc002jts.3	+						SEPT9_uc010wtk.1_Intron|SEPT9_uc002jtt.3_Intron|SEPT9_uc002jtu.3_Intron|SEPT9_uc002jtv.2_Intron|SEPT9_uc002jtw.2_Intron|SEPT9_uc002jtx.1_Intron|SEPT9_uc010wtl.1_Intron	NM_001113491	NP_001106963			septin 9 isoform a						cell cycle|cell division|protein heterooligomerization	microtubule|perinuclear region of cytoplasm|stress fiber	GTP binding|GTPase activity|protein binding|protein binding			breast(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(99;0.153)															---	---	---	---
SEPT9	10801	broad.mit.edu	37	17	75482602	75482613	+	Intron	DEL	GTGCGCGCACGC	-	-	rs139526675	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75482602_75482613delGTGCGCGCACGC	uc002jts.3	+						SEPT9_uc010wtk.1_Intron|SEPT9_uc002jtt.3_Intron|SEPT9_uc002jtu.3_Intron|SEPT9_uc002jtv.2_Intron|SEPT9_uc002jtw.2_Intron|SEPT9_uc010wtl.1_Intron|SEPT9_uc002jty.3_Intron|SEPT9_uc010wtm.1_Intron|SEPT9_uc010wtn.1_Intron|SEPT9_uc010dhd.2_Intron	NM_001113491	NP_001106963			septin 9 isoform a						cell cycle|cell division|protein heterooligomerization	microtubule|perinuclear region of cytoplasm|stress fiber	GTP binding|GTPase activity|protein binding|protein binding			breast(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(99;0.153)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	75736108	75736108	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75736108delT								SEPT9 (239432 upstream) : FLJ45079 (139001 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	75849166	75849166	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75849166delG								SEPT9 (352490 upstream) : FLJ45079 (25943 downstream)																																			---	---	---	---
TNRC6C	57690	broad.mit.edu	37	17	76064881	76064881	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76064881delA	uc002jud.2	+						TNRC6C_uc002juf.2_Intron|TNRC6C_uc002jue.2_Intron	NM_018996	NP_061869			trinucleotide repeat containing 6C isoform 2						gene silencing by RNA|regulation of translation		nucleotide binding|RNA binding			ovary(1)|central_nervous_system(1)	2			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)															---	---	---	---
TMC8	147138	broad.mit.edu	37	17	76132551	76132551	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76132551delA	uc002jup.2	+						TMC8_uc002juq.2_Intron|TMC8_uc010wtr.1_Intron|TMC8_uc002jur.1_5'Flank	NM_152468	NP_689681			transmembrane channel-like 8							endoplasmic reticulum membrane|integral to membrane					0			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)|OV - Ovarian serous cystadenocarcinoma(97;0.192)											Epidermodysplasia_Verruciformis_Familial_Clustering_of				---	---	---	---
AFMID	125061	broad.mit.edu	37	17	76192762	76192762	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76192762delA	uc002jva.3	+						AFMID_uc002juy.3_Intron|AFMID_uc010dhj.2_Intron|AFMID_uc002jvb.3_Intron|AFMID_uc002juz.3_Intron	NM_001010982	NP_001010982			arylformamidase isoform 1							cytosol|nucleus	arylformamidase activity			large_intestine(1)|pancreas(1)	2			BRCA - Breast invasive adenocarcinoma(99;0.00269)|OV - Ovarian serous cystadenocarcinoma(97;0.134)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	76255992	76255993	+	IGR	DEL	AT	-	-	rs71363702		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76255992_76255993delAT								LOC283999 (18925 upstream) : SOCS3 (96866 downstream)																																			---	---	---	---
SOCS3	9021	broad.mit.edu	37	17	76354878	76354878	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76354878delC	uc002jvl.2	-	2	715	c.299delG	c.(298-300)GGCfs	p.G100fs		NM_003955	NP_003946	O14543	SOCS3_HUMAN	suppressor of cytokine signaling 3	100	SH2.				anti-apoptosis|interferon-gamma-mediated signaling pathway|JAK-STAT cascade|regulation of growth|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway	cytosol	protein kinase inhibitor activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(99;0.000688)|OV - Ovarian serous cystadenocarcinoma(97;0.0554)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	76488937	76488938	+	IGR	INS	-	TTT	TTT	rs35406046		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76488937_76488938insTTT								DNAH17 (20081 upstream) : CYTH1 (181193 downstream)																																			---	---	---	---
CYTH1	9267	broad.mit.edu	37	17	76704466	76704467	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76704466_76704467insA	uc002jvw.2	-						CYTH1_uc010wtw.1_Intron|CYTH1_uc010wtx.1_Intron	NM_017456	NP_059430			cytohesin 1 isoform 2						regulation of ARF protein signal transduction|regulation of cell adhesion|vesicle-mediated transport	cytoplasm|plasma membrane	ARF guanyl-nucleotide exchange factor activity|protein binding			ovary(1)	1																		---	---	---	---
ENGASE	64772	broad.mit.edu	37	17	77083687	77083687	+	3'UTR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77083687delG	uc002jwv.2	+	14					ENGASE_uc002jww.2_3'UTR	NM_001042573	NP_001036038			endo-beta-N-acetylglucosaminidase							cytosol	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity			skin(1)	1																OREG0024793	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
HRNBP3	146713	broad.mit.edu	37	17	77260177	77260178	+	Intron	DEL	TT	-	-	rs79664648		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77260177_77260178delTT	uc010dhs.2	-						HRNBP3_uc010wua.1_Intron	NM_001082575	NP_001076044			hexaribonucleotide binding protein 3						mRNA processing|RNA splicing	cytoplasm|nucleus	nucleotide binding|RNA binding				0			BRCA - Breast invasive adenocarcinoma(99;0.0577)|OV - Ovarian serous cystadenocarcinoma(97;0.112)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	77638042	77638042	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77638042delT								HRNBP3 (159362 upstream) : ENPP7 (66840 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	77660186	77660186	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77660186delG								HRNBP3 (181506 upstream) : ENPP7 (44696 downstream)																																			---	---	---	---
CBX4	8535	broad.mit.edu	37	17	77809592	77809593	+	Intron	DEL	CC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77809592_77809593delCC	uc002jxe.2	-							NM_003655	NP_003646			chromobox homolog 4						anti-apoptosis|chromatin modification|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|PcG protein complex	enzyme binding|transcription corepressor activity			skin(2)	2			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)													OREG0024799	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CBX4	8535	broad.mit.edu	37	17	77812414	77812414	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77812414delT	uc002jxe.2	-							NM_003655	NP_003646			chromobox homolog 4						anti-apoptosis|chromatin modification|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|PcG protein complex	enzyme binding|transcription corepressor activity			skin(2)	2			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)															---	---	---	---
CCDC40	55036	broad.mit.edu	37	17	78030018	78030019	+	Intron	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78030018_78030019delTC	uc010dht.2	+						CCDC40_uc010wub.1_Intron|CCDC40_uc002jxm.3_Intron	NM_017950	NP_060420			coiled-coil domain containing 40						axonemal dynein complex assembly|ciliary cell motility|cilium movement involved in determination of left/right asymmetry|flagellar cell motility	cilium|cytoplasm				ovary(3)	3	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.149)															---	---	---	---
GAA	2548	broad.mit.edu	37	17	78084940	78084941	+	Intron	DEL	GC	-	-	rs12945868	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78084940_78084941delGC	uc002jxo.2	+						GAA_uc002jxp.2_Intron|GAA_uc002jxq.2_Intron	NM_001079803	NP_001073271			acid alpha-glucosidase preproprotein						cardiac muscle contraction|diaphragm contraction|glycogen catabolic process|lysosome organization|tongue morphogenesis|vacuolar sequestering|ventricular cardiac muscle tissue morphogenesis	lysosomal membrane	carbohydrate binding|maltose alpha-glucosidase activity			ovary(1)	1	all_neural(118;0.117)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.139)		Acarbose(DB00284)													---	---	---	---
EIF4A3	9775	broad.mit.edu	37	17	78109705	78109705	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78109705delA	uc010wuc.1	-						EIF4A3_uc002jxs.2_Intron	NM_014740	NP_055555			eukaryotic translation initiation factor 4A,						mRNA transport|negative regulation of translation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of translation|rRNA processing	catalytic step 2 spliceosome|cytoplasm|exon-exon junction complex|nuclear speck	ATP binding|ATP-dependent RNA helicase activity|poly(A) RNA binding|protein binding			ovary(1)	1	all_neural(118;0.117)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.139)															---	---	---	---
CARD14	79092	broad.mit.edu	37	17	78169065	78169065	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78169065delC	uc002jxw.1	+	10	1627	c.1432delC	c.(1432-1434)CCCfs	p.P478fs	CARD14_uc002jxt.1_RNA|CARD14_uc002jxv.2_Frame_Shift_Del_p.P478fs|CARD14_uc010wud.1_RNA|CARD14_uc002jxx.2_Frame_Shift_Del_p.P241fs|CARD14_uc010dhu.1_Frame_Shift_Del_p.P276fs	NM_024110	NP_077015	Q9BXL6	CAR14_HUMAN	caspase recruitment domain protein 14 isoform 1	478					activation of NF-kappaB-inducing kinase activity|positive regulation of protein phosphorylation|regulation of apoptosis	aggresome|cytoplasm|plasma membrane	CARD domain binding			ovary(4)|skin(1)	5	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.017)|BRCA - Breast invasive adenocarcinoma(99;0.0908)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	78230774	78230775	+	IGR	INS	-	T	T	rs150246623	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78230774_78230775insT								SLC26A11 (3477 upstream) : RNF213 (82951 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	78240078	78240078	+	Intron	DEL	A	-	-	rs76011856		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78240078delA	uc002jye.1	+						uc002jyf.2_Intron					Homo sapiens mRNA for KIAA1618 protein, partial cds.																														---	---	---	---
RNF213	57674	broad.mit.edu	37	17	78335325	78335325	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78335325delA	uc002jyh.1	+						uc002jyi.1_Intron|RNF213_uc010dhw.1_Intron	NM_020914	NP_065965			ring finger protein 213											ovary(8)|lung(6)|breast(3)|large_intestine(2)|central_nervous_system(1)|pancreas(1)	21	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	78471639	78471639	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78471639delA								NPTX1 (21235 upstream) : RPTOR (46986 downstream)																																			---	---	---	---
RPTOR	57521	broad.mit.edu	37	17	78867196	78867197	+	Intron	DEL	GT	-	-	rs35931098		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78867196_78867197delGT	uc002jyt.1	+						RPTOR_uc010wug.1_Intron	NM_020761	NP_065812			raptor isoform 1						cell cycle arrest|cell growth|cellular response to amino acid stimulus|cellular response to nutrient levels|insulin receptor signaling pathway|positive regulation of protein serine/threonine kinase activity|positive regulation of TOR signaling cascade|TOR signaling cascade	cytosol|lysosome|TORC1 complex	protein complex binding			lung(4)|urinary_tract(1)|ovary(1)	6																		---	---	---	---
FLJ90757	440465	broad.mit.edu	37	17	79005508	79005508	+	3'UTR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79005508delC	uc002jyy.2	-	2						NR_026857				Homo sapiens cDNA FLJ14444 fis, clone HEMBB1001153.												0																		---	---	---	---
BAHCC1	57597	broad.mit.edu	37	17	79429724	79429724	+	Intron	DEL	C	-	-	rs1471442		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79429724delC	uc002kaf.2	+							NM_001080519	NP_001073988			BAH domain and coiled-coil containing 1								DNA binding			ovary(1)	1	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0224)|OV - Ovarian serous cystadenocarcinoma(97;0.116)															---	---	---	---
FSCN2	25794	broad.mit.edu	37	17	79498531	79498536	+	Intron	DEL	TGGTGA	-	-	rs138521587	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79498531_79498536delTGGTGA	uc010wup.1	+						FSCN2_uc010wuo.1_Intron	NM_012418	NP_036550			fascin 2 isoform 1						actin filament bundle assembly|anatomical structure morphogenesis|visual perception	actin cytoskeleton|cytoplasm|stereocilium	actin filament binding|protein binding, bridging				0	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0371)															---	---	---	---
STRA13	201254	broad.mit.edu	37	17	79977796	79977796	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79977796delG	uc002kdc.2	-						STRA13_uc002kdd.2_Intron	NM_144998	NP_659435			stimulated by retinoic acid 13						DNA repair	chromosome, centromeric region|Fanconi anaemia nuclear complex	DNA binding|protein binding				0	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)															---	---	---	---
FASN	2194	broad.mit.edu	37	17	80047566	80047566	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80047566delG	uc002kdu.2	-	12	2024	c.1907delC	c.(1906-1908)CCGfs	p.P636fs	FASN_uc002kdw.1_5'Flank	NM_004104	NP_004095	P49327	FAS_HUMAN	fatty acid synthase	636	Acyl and malonyl transferases (By similarity).				energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|pantothenate metabolic process|positive regulation of cellular metabolic process|triglyceride biosynthetic process	cytosol|Golgi apparatus|melanosome|plasma membrane	3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity|3-oxoacyl-[acyl-carrier-protein] synthase activity|[acyl-carrier-protein] S-acetyltransferase activity|[acyl-carrier-protein] S-malonyltransferase activity|acyl carrier activity|cofactor binding|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity|myristoyl-[acyl-carrier-protein] hydrolase activity|oleoyl-[acyl-carrier-protein] hydrolase activity|palmitoyl-[acyl-carrier-protein] hydrolase activity|phosphopantetheine binding|protein binding|zinc ion binding			central_nervous_system(1)	1	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)|Pyrazinamide(DB00339)													---	---	---	---
CCDC57	284001	broad.mit.edu	37	17	80143495	80143495	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80143495delA	uc002kdz.1	-						CCDC57_uc002kdx.1_Intron|CCDC57_uc010dik.1_5'Flank	NM_198082	NP_932348			coiled-coil domain containing 57											ovary(2)	2	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)															---	---	---	---
HEXDC	284004	broad.mit.edu	37	17	80377960	80377961	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80377960_80377961delAA	uc002kew.2	+						C17orf101_uc002ket.1_5'Flank|C17orf101_uc002keu.1_5'Flank|C17orf101_uc010dip.1_5'Flank|HEXDC_uc002kev.3_Intron|HEXDC_uc010diq.2_Intron					SubName: Full=Hexosaminidase (Glycosyl hydrolase family 20, catalytic domain) containing, isoform CRA_c; SubName: Full=Hexosaminidase D;						carbohydrate metabolic process	cytoplasm|nucleus	beta-N-acetylhexosaminidase activity|cation binding			ovary(1)|skin(1)	2	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)															---	---	---	---
RAB40B	10966	broad.mit.edu	37	17	80615786	80615786	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80615786delG	uc002kft.2	-	6	916	c.790delC	c.(790-792)CAGfs	p.Q264fs	RAB40B_uc002kfs.2_RNA	NM_006822	NP_006813	Q12829	RB40B_HUMAN	RAB40B, member RAS oncogene family	264					protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding	p.Q264P(1)		central_nervous_system(1)	1	Breast(20;0.00132)|all_neural(118;0.0952)	all_cancers(8;0.072)|all_epithelial(8;0.139)	BRCA - Breast invasive adenocarcinoma(99;0.0262)|OV - Ovarian serous cystadenocarcinoma(97;0.061)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	80663290	80663290	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80663290delG								RAB40B (6692 upstream) : FN3KRP (11292 downstream)																																			---	---	---	---
TBCD	6904	broad.mit.edu	37	17	80719598	80719599	+	Intron	INS	-	TC	TC	rs71168147		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80719598_80719599insTC	uc002kfz.2	+						TBCD_uc002kfx.1_Intron|TBCD_uc002kfy.1_Intron	NM_005993	NP_005984			beta-tubulin cofactor D						'de novo' posttranslational protein folding|adherens junction assembly|negative regulation of cell-substrate adhesion|negative regulation of microtubule polymerization|post-chaperonin tubulin folding pathway|tight junction assembly	adherens junction|cytoplasm|lateral plasma membrane|microtubule|tight junction	beta-tubulin binding|chaperone binding|GTPase activator activity				0	Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)															---	---	---	---
TBCD	6904	broad.mit.edu	37	17	80731605	80731605	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80731605delT	uc002kfz.2	+						TBCD_uc002kfx.1_Intron|TBCD_uc002kfy.1_Intron	NM_005993	NP_005984			beta-tubulin cofactor D						'de novo' posttranslational protein folding|adherens junction assembly|negative regulation of cell-substrate adhesion|negative regulation of microtubule polymerization|post-chaperonin tubulin folding pathway|tight junction assembly	adherens junction|cytoplasm|lateral plasma membrane|microtubule|tight junction	beta-tubulin binding|chaperone binding|GTPase activator activity				0	Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)															---	---	---	---
TBCD	6904	broad.mit.edu	37	17	80799197	80799198	+	Intron	DEL	TT	-	-	rs112302012		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80799197_80799198delTT	uc002kfz.2	+						TBCD_uc002kfx.1_Intron|TBCD_uc002kfy.1_Intron|ZNF750_uc002kga.2_5'Flank	NM_005993	NP_005984			beta-tubulin cofactor D						'de novo' posttranslational protein folding|adherens junction assembly|negative regulation of cell-substrate adhesion|negative regulation of microtubule polymerization|post-chaperonin tubulin folding pathway|tight junction assembly	adherens junction|cytoplasm|lateral plasma membrane|microtubule|tight junction	beta-tubulin binding|chaperone binding|GTPase activator activity				0	Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)															---	---	---	---
TBCD	6904	broad.mit.edu	37	17	80878978	80878978	+	Intron	DEL	T	-	-	rs3214867		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80878978delT	uc002kfz.2	+						TBCD_uc002kfx.1_Intron|TBCD_uc002kfy.1_Intron|TBCD_uc002kgb.1_Intron	NM_005993	NP_005984			beta-tubulin cofactor D						'de novo' posttranslational protein folding|adherens junction assembly|negative regulation of cell-substrate adhesion|negative regulation of microtubule polymerization|post-chaperonin tubulin folding pathway|tight junction assembly	adherens junction|cytoplasm|lateral plasma membrane|microtubule|tight junction	beta-tubulin binding|chaperone binding|GTPase activator activity				0	Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)															---	---	---	---
B3GNTL1	146712	broad.mit.edu	37	17	80926329	80926329	+	Intron	DEL	C	-	-	rs66784069		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80926329delC	uc002kgg.1	-						B3GNTL1_uc002kgf.1_Intron|B3GNTL1_uc002kge.1_Intron	NM_001009905	NP_001009905			UDP-GlcNAc:betaGal								transferase activity, transferring glycosyl groups			ovary(1)|pancreas(1)	2	Breast(20;0.000443)|all_neural(118;0.0779)	all_cancers(8;0.0396)|all_epithelial(8;0.0556)	BRCA - Breast invasive adenocarcinoma(99;0.0517)|OV - Ovarian serous cystadenocarcinoma(97;0.0868)															---	---	---	---
B3GNTL1	146712	broad.mit.edu	37	17	80967300	80967300	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80967300delA	uc002kgg.1	-						B3GNTL1_uc002kgf.1_Intron|B3GNTL1_uc002kge.1_5'Flank	NM_001009905	NP_001009905			UDP-GlcNAc:betaGal								transferase activity, transferring glycosyl groups			ovary(1)|pancreas(1)	2	Breast(20;0.000443)|all_neural(118;0.0779)	all_cancers(8;0.0396)|all_epithelial(8;0.0556)	BRCA - Breast invasive adenocarcinoma(99;0.0517)|OV - Ovarian serous cystadenocarcinoma(97;0.0868)															---	---	---	---
Unknown	0	broad.mit.edu	37	18	86862	86862	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:86862delA								None (None upstream) : USP14 (71621 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	139806	139806	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:139806delT								None (None upstream) : USP14 (18677 downstream)																																			---	---	---	---
USP14	9097	broad.mit.edu	37	18	164404	164405	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:164404_164405delTT	uc002kkf.1	+						USP14_uc002kkg.1_Intron|USP14_uc010wyr.1_Intron	NM_005151	NP_005142			ubiquitin specific protease 14 isoform a						regulation of chemotaxis|regulation of proteasomal protein catabolic process|ubiquitin-dependent protein catabolic process	cell surface|cytoplasmic membrane-bounded vesicle|plasma membrane|proteasome complex	cysteine-type endopeptidase activity|endopeptidase inhibitor activity|proteasome binding|tRNA guanylyltransferase activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(2)	2		all_cancers(4;0.0896)|Myeloproliferative disorder(11;0.0412)																---	---	---	---
USP14	9097	broad.mit.edu	37	18	180062	180062	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:180062delT	uc002kkf.1	+						USP14_uc002kkg.1_Intron|USP14_uc010wyr.1_Intron	NM_005151	NP_005142			ubiquitin specific protease 14 isoform a						regulation of chemotaxis|regulation of proteasomal protein catabolic process|ubiquitin-dependent protein catabolic process	cell surface|cytoplasmic membrane-bounded vesicle|plasma membrane|proteasome complex	cysteine-type endopeptidase activity|endopeptidase inhibitor activity|proteasome binding|tRNA guanylyltransferase activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(2)	2		all_cancers(4;0.0896)|Myeloproliferative disorder(11;0.0412)																---	---	---	---
THOC1	9984	broad.mit.edu	37	18	265533	265533	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:265533delA	uc002kkj.3	-						THOC1_uc002kkk.3_Intron|THOC1_uc002kkl.2_Intron	NM_005131	NP_005122			THO complex 1						apoptosis|intronless viral mRNA export from host nucleus|mRNA processing|regulation of transcription elongation, DNA-dependent|RNA splicing|signal transduction|transcription, DNA-dependent	cytoplasm|nuclear matrix|nuclear speck|THO complex part of transcription export complex	DNA binding|protein binding|RNA binding			ovary(1)	1		all_cancers(4;0.0896)|Myeloproliferative disorder(11;0.0412)																---	---	---	---
COLEC12	81035	broad.mit.edu	37	18	389209	389214	+	Intron	DEL	ACACAC	-	-	rs112963606		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:389209_389214delACACAC	uc002kkm.2	-							NM_130386	NP_569057			collectin sub-family member 12						carbohydrate mediated signaling|innate immune response|phagocytosis, recognition|protein homooligomerization	collagen|integral to membrane	galactose binding|low-density lipoprotein particle binding|metal ion binding|pattern recognition receptor activity|scavenger receptor activity			ovary(1)|pancreas(1)	2		all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426)																---	---	---	---
COLEC12	81035	broad.mit.edu	37	18	399163	399163	+	Intron	DEL	C	-	-	rs4798133	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:399163delC	uc002kkm.2	-							NM_130386	NP_569057			collectin sub-family member 12						carbohydrate mediated signaling|innate immune response|phagocytosis, recognition|protein homooligomerization	collagen|integral to membrane	galactose binding|low-density lipoprotein particle binding|metal ion binding|pattern recognition receptor activity|scavenger receptor activity			ovary(1)|pancreas(1)	2		all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426)																---	---	---	---
COLEC12	81035	broad.mit.edu	37	18	449288	449288	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:449288delA	uc002kkm.2	-							NM_130386	NP_569057			collectin sub-family member 12						carbohydrate mediated signaling|innate immune response|phagocytosis, recognition|protein homooligomerization	collagen|integral to membrane	galactose binding|low-density lipoprotein particle binding|metal ion binding|pattern recognition receptor activity|scavenger receptor activity			ovary(1)|pancreas(1)	2		all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426)																---	---	---	---
COLEC12	81035	broad.mit.edu	37	18	471948	471948	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:471948delA	uc002kkm.2	-							NM_130386	NP_569057			collectin sub-family member 12						carbohydrate mediated signaling|innate immune response|phagocytosis, recognition|protein homooligomerization	collagen|integral to membrane	galactose binding|low-density lipoprotein particle binding|metal ion binding|pattern recognition receptor activity|scavenger receptor activity			ovary(1)|pancreas(1)	2		all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426)																---	---	---	---
COLEC12	81035	broad.mit.edu	37	18	481706	481706	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:481706delA	uc002kkm.2	-							NM_130386	NP_569057			collectin sub-family member 12						carbohydrate mediated signaling|innate immune response|phagocytosis, recognition|protein homooligomerization	collagen|integral to membrane	galactose binding|low-density lipoprotein particle binding|metal ion binding|pattern recognition receptor activity|scavenger receptor activity			ovary(1)|pancreas(1)	2		all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426)																---	---	---	---
CLUL1	27098	broad.mit.edu	37	18	623035	623037	+	Intron	DEL	TTT	-	-	rs72439563		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:623035_623037delTTT	uc002kkp.2	+						CLUL1_uc010wys.1_Intron|CLUL1_uc002kkq.2_Intron	NM_014410	NP_055225			clusterin-like 1 (retinal) precursor						cell death	extracellular region				ovary(2)	2																		---	---	---	---
CLUL1	27098	broad.mit.edu	37	18	645263	645263	+	Intron	DEL	A	-	-	rs112345887		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:645263delA	uc002kkp.2	+						CLUL1_uc010wys.1_Intron|CLUL1_uc002kkq.2_Intron	NM_014410	NP_055225			clusterin-like 1 (retinal) precursor						cell death	extracellular region				ovary(2)	2																		---	---	---	---
ENOSF1	55556	broad.mit.edu	37	18	680848	680848	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:680848delT	uc002kku.3	-						ENOSF1_uc002kkt.3_Intron|ENOSF1_uc010dke.2_Intron|ENOSF1_uc010dkf.2_Intron|ENOSF1_uc002kkv.3_Intron|ENOSF1_uc002kkw.3_Intron|ENOSF1_uc002kkx.3_Intron	NM_017512	NP_059982			enolase superfamily 1 isoform rTS beta						cellular amino acid catabolic process	mitochondrion	isomerase activity|metal ion binding			ovary(1)	1																		---	---	---	---
YES1	7525	broad.mit.edu	37	18	728323	728324	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:728323_728324delAA	uc002kky.2	-						YES1_uc002kkz.2_Intron	NM_005433	NP_005424			viral oncogene yes-1 homolog 1						blood coagulation|leukocyte migration|regulation of vascular permeability|T cell costimulation	cytosol|plasma membrane	ATP binding|ion channel binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|ovary(1)	3					Dasatinib(DB01254)													---	---	---	---
YES1	7525	broad.mit.edu	37	18	791264	791265	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:791264_791265delAA	uc002kky.2	-						YES1_uc002kkz.2_Intron	NM_005433	NP_005424			viral oncogene yes-1 homolog 1						blood coagulation|leukocyte migration|regulation of vascular permeability|T cell costimulation	cytosol|plasma membrane	ATP binding|ion channel binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|ovary(1)	3					Dasatinib(DB01254)													---	---	---	---
Unknown	0	broad.mit.edu	37	18	1250079	1250080	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:1250079_1250080delTT								ADCYAP1 (337908 upstream) : C18orf2 (4310 downstream)																																			---	---	---	---
C18orf2	56651	broad.mit.edu	37	18	1261404	1261404	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:1261404delA	uc002klb.1	-											Homo sapiens C18orf2 isoform 1 mRNA, complete sequence, alternatively spliced.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	1450680	1450681	+	IGR	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:1450680_1450681insG								C18orf2 (43499 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	1473258	1473259	+	IGR	DEL	GA	-	-	rs218517	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:1473258_1473259delGA								C18orf2 (66077 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	1541288	1541288	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:1541288delA								C18orf2 (134107 upstream) : METTL4 (996237 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	1652443	1652443	+	IGR	DEL	A	-	-	rs78994591		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:1652443delA								C18orf2 (245262 upstream) : METTL4 (885082 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	1654490	1654492	+	IGR	DEL	AAA	-	-	rs35540645		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:1654490_1654492delAAA								C18orf2 (247309 upstream) : METTL4 (883033 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	1775474	1775474	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:1775474delT								C18orf2 (368293 upstream) : METTL4 (762051 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	1832192	1832192	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:1832192delT								C18orf2 (425011 upstream) : METTL4 (705333 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	2276194	2276194	+	IGR	DEL	A	-	-	rs71742907		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2276194delA								C18orf2 (869013 upstream) : METTL4 (261331 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	2280155	2280156	+	IGR	INS	-	CA	CA			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2280155_2280156insCA								C18orf2 (872974 upstream) : METTL4 (257369 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	2283096	2283097	+	IGR	INS	-	G	G	rs146536581	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2283096_2283097insG								C18orf2 (875915 upstream) : METTL4 (254428 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	2289680	2289680	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2289680delT								C18orf2 (882499 upstream) : METTL4 (247845 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	2503126	2503126	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2503126delA								None (None upstream) : METTL4 (34399 downstream)																																			---	---	---	---
SMCHD1	23347	broad.mit.edu	37	18	2672860	2672860	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2672860delA	uc002klm.3	+							NM_015295	NP_056110			structural maintenance of chromosomes flexible						chromosome organization		ATP binding				0																		---	---	---	---
SMCHD1	23347	broad.mit.edu	37	18	2711263	2711265	+	Intron	DEL	TTT	-	-	rs78107873		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2711263_2711265delTTT	uc002klm.3	+						SMCHD1_uc002klk.3_Intron|SMCHD1_uc002kll.3_Intron	NM_015295	NP_056110			structural maintenance of chromosomes flexible						chromosome organization		ATP binding				0																		---	---	---	---
SMCHD1	23347	broad.mit.edu	37	18	2732489	2732492	+	Splice_Site	DEL	AAGT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2732489_2732492delAAGT	uc002klm.3	+	25	3465	c.3276_splice	c.e25+1	p.K1092_splice	SMCHD1_uc002klk.3_Splice_Site|SMCHD1_uc002kll.3_Splice_Site	NM_015295	NP_056110			structural maintenance of chromosomes flexible						chromosome organization		ATP binding				0																		---	---	---	---
SMCHD1	23347	broad.mit.edu	37	18	2772110	2772110	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2772110delT	uc002klm.3	+						SMCHD1_uc002klk.3_Intron|SMCHD1_uc002kll.3_Intron	NM_015295	NP_056110			structural maintenance of chromosomes flexible						chromosome organization		ATP binding				0																		---	---	---	---
SMCHD1	23347	broad.mit.edu	37	18	2774576	2774576	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2774576delT	uc002klm.3	+						SMCHD1_uc002klk.3_Intron|SMCHD1_uc002kll.3_Intron	NM_015295	NP_056110			structural maintenance of chromosomes flexible						chromosome organization		ATP binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	2840131	2840132	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2840131_2840132delTG								SMCHD1 (35117 upstream) : EMILIN2 (6896 downstream)																																			---	---	---	---
LPIN2	9663	broad.mit.edu	37	18	2920647	2920649	+	Intron	DEL	GAG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2920647_2920649delGAG	uc002klo.2	-							NM_014646	NP_055461			lipin 2						fatty acid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent|triglyceride biosynthetic process	cytosol|endoplasmic reticulum membrane|nucleus	phosphatidate phosphatase activity|transcription coactivator activity			ovary(1)|skin(1)	2				READ - Rectum adenocarcinoma(2;0.0419)|Colorectal(6;0.156)														---	---	---	---
LPIN2	9663	broad.mit.edu	37	18	2934455	2934455	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2934455delA	uc002klo.2	-							NM_014646	NP_055461			lipin 2						fatty acid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent|triglyceride biosynthetic process	cytosol|endoplasmic reticulum membrane|nucleus	phosphatidate phosphatase activity|transcription coactivator activity			ovary(1)|skin(1)	2				READ - Rectum adenocarcinoma(2;0.0419)|Colorectal(6;0.156)														---	---	---	---
LOC727896	727896	broad.mit.edu	37	18	2946534	2946534	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2946534delT	uc010wyu.1	-	1	88	c.1delA	c.(1-3)ATGfs	p.M1fs	LPIN2_uc002klo.2_Intron	NR_026659				Homo sapiens cDNA clone IMAGE:4614712, containing frame-shift errors.												0																		---	---	---	---
MYOM1	8736	broad.mit.edu	37	18	3076075	3076075	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3076075delT	uc002klp.2	-						MYOM1_uc002klq.2_Intron	NM_003803	NP_003794			myomesin 1 isoform a							striated muscle myosin thick filament	structural constituent of muscle			ovary(3)|central_nervous_system(1)|pancreas(1)	5																		---	---	---	---
MYOM1	8736	broad.mit.edu	37	18	3094667	3094667	+	Intron	DEL	T	-	-	rs111967746		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3094667delT	uc002klp.2	-						MYOM1_uc002klq.2_Intron	NM_003803	NP_003794			myomesin 1 isoform a							striated muscle myosin thick filament	structural constituent of muscle			ovary(3)|central_nervous_system(1)|pancreas(1)	5																		---	---	---	---
MYOM1	8736	broad.mit.edu	37	18	3118350	3118351	+	Intron	INS	-	T	T	rs141436615	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3118350_3118351insT	uc002klp.2	-						MYOM1_uc002klq.2_Intron	NM_003803	NP_003794			myomesin 1 isoform a							striated muscle myosin thick filament	structural constituent of muscle			ovary(3)|central_nervous_system(1)|pancreas(1)	5																		---	---	---	---
MYOM1	8736	broad.mit.edu	37	18	3142264	3142264	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3142264delT	uc002klp.2	-						MYOM1_uc002klq.2_Intron	NM_003803	NP_003794			myomesin 1 isoform a							striated muscle myosin thick filament	structural constituent of muscle			ovary(3)|central_nervous_system(1)|pancreas(1)	5																		---	---	---	---
MYOM1	8736	broad.mit.edu	37	18	3155228	3155228	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3155228delT	uc002klp.2	-						MYOM1_uc002klq.2_Intron	NM_003803	NP_003794			myomesin 1 isoform a							striated muscle myosin thick filament	structural constituent of muscle			ovary(3)|central_nervous_system(1)|pancreas(1)	5																		---	---	---	---
MYOM1	8736	broad.mit.edu	37	18	3221180	3221180	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3221180delT	uc002klp.2	-						MYOM1_uc002klq.2_5'Flank	NM_003803	NP_003794			myomesin 1 isoform a							striated muscle myosin thick filament	structural constituent of muscle			ovary(3)|central_nervous_system(1)|pancreas(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	3258373	3258373	+	IGR	DEL	C	-	-	rs4798076	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3258373delC								MYL12A (2145 upstream) : MYL12B (3738 downstream)																																			---	---	---	---
MYL12B	103910	broad.mit.edu	37	18	3272865	3272865	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3272865delT	uc010dkl.2	+						MYL12B_uc002klt.3_Intron|MYL12B_uc010wyv.1_Intron	NM_001144944	NP_001138416			myosin regulatory light chain MRCL2 isoform A						axon guidance|muscle contraction	cytosol|myosin complex	calcium ion binding				0																		---	---	---	---
TGIF1	7050	broad.mit.edu	37	18	3457982	3457982	+	3'UTR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3457982delG	uc002klz.2	+	3					TGIF1_uc002klu.2_3'UTR|TGIF1_uc002klv.2_3'UTR|TGIF1_uc002klx.2_3'UTR|TGIF1_uc002klw.2_3'UTR|TGIF1_uc002kly.2_3'UTR|TGIF1_uc002kma.2_3'UTR|TGIF1_uc002kmb.2_3'UTR|TGIF1_uc002kmc.2_3'UTR	NM_170695	NP_733796			TG-interacting factor isoform a						negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(1)	1	Esophageal squamous(4;0.0859)	Colorectal(8;0.0104)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	3488686	3488686	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3488686delT								TGIF1 (30282 upstream) : DLGAP1 (10151 downstream)																																			---	---	---	---
DLGAP1	9229	broad.mit.edu	37	18	3663264	3663265	+	Intron	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3663264_3663265insC	uc002kmf.2	-						DLGAP1_uc010wyz.1_Intron|DLGAP1_uc002kme.1_Intron|DLGAP1_uc010dkn.2_Intron|DLGAP1_uc010wyw.1_Intron|DLGAP1_uc010wyx.1_Intron|DLGAP1_uc010wyy.1_Intron|DLGAP1_uc002kmg.2_Intron	NM_004746	NP_004737			discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)																---	---	---	---
DLGAP1	9229	broad.mit.edu	37	18	3734461	3734461	+	Intron	DEL	T	-	-	rs111917190		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3734461delT	uc002kmf.2	-						DLGAP1_uc010wyz.1_Intron|DLGAP1_uc002kme.1_Intron|DLGAP1_uc010dkn.2_Intron|DLGAP1_uc010wyw.1_Intron|DLGAP1_uc010wyx.1_Intron|DLGAP1_uc010wyy.1_Intron|DLGAP1_uc002kmg.2_Intron|DLGAP1_uc002kmk.2_Intron	NM_004746	NP_004737			discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)																---	---	---	---
DLGAP1	9229	broad.mit.edu	37	18	3761579	3761581	+	Intron	DEL	TTT	-	-	rs57318116		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3761579_3761581delTTT	uc002kmf.2	-						DLGAP1_uc010wyz.1_Intron|DLGAP1_uc002kme.1_Intron|DLGAP1_uc010dkn.2_Intron|DLGAP1_uc010wyw.1_Intron|DLGAP1_uc010wyx.1_Intron|DLGAP1_uc010wyy.1_Intron|DLGAP1_uc002kmg.2_Intron|DLGAP1_uc002kmk.2_Intron	NM_004746	NP_004737			discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)																---	---	---	---
DLGAP1	9229	broad.mit.edu	37	18	3780524	3780525	+	Intron	INS	-	T	T	rs146949665	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3780524_3780525insT	uc002kmf.2	-						DLGAP1_uc010wyz.1_Intron|DLGAP1_uc002kme.1_Intron|DLGAP1_uc010dkn.2_Intron|DLGAP1_uc010wyw.1_Intron|DLGAP1_uc010wyx.1_Intron|DLGAP1_uc010wyy.1_Intron|DLGAP1_uc002kmg.2_Intron|DLGAP1_uc002kmk.2_Intron	NM_004746	NP_004737			discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)																---	---	---	---
DLGAP1	9229	broad.mit.edu	37	18	3784301	3784301	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3784301delC	uc002kmf.2	-						DLGAP1_uc010wyz.1_Intron|DLGAP1_uc002kme.1_Intron|DLGAP1_uc010dkn.2_Intron|DLGAP1_uc010wyw.1_Intron|DLGAP1_uc010wyx.1_Intron|DLGAP1_uc010wyy.1_Intron|DLGAP1_uc002kmg.2_Intron|DLGAP1_uc002kmk.2_Intron	NM_004746	NP_004737			discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)																---	---	---	---
DLGAP1	9229	broad.mit.edu	37	18	3791515	3791516	+	Intron	INS	-	GT	GT	rs145967187	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3791515_3791516insGT	uc002kmf.2	-						DLGAP1_uc010wyz.1_Intron|DLGAP1_uc002kme.1_Intron|DLGAP1_uc010dkn.2_Intron|DLGAP1_uc010wyw.1_Intron|DLGAP1_uc010wyx.1_Intron|DLGAP1_uc010wyy.1_Intron|DLGAP1_uc002kmg.2_Intron|DLGAP1_uc002kmk.2_Intron	NM_004746	NP_004737			discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)																---	---	---	---
DLGAP1	9229	broad.mit.edu	37	18	3810539	3810539	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3810539delA	uc002kmf.2	-						DLGAP1_uc010wyz.1_Intron|DLGAP1_uc002kme.1_Intron|DLGAP1_uc010dkn.2_Intron|DLGAP1_uc010wyw.1_Intron|DLGAP1_uc010wyx.1_Intron|DLGAP1_uc010wyy.1_Intron|DLGAP1_uc002kmg.2_Intron|DLGAP1_uc002kmk.2_Intron	NM_004746	NP_004737			discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)																---	---	---	---
DLGAP1	9229	broad.mit.edu	37	18	3974080	3974081	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3974080_3974081delTT	uc010wyz.1	-							NM_004746	NP_004737			discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)																---	---	---	---
DLGAP1	9229	broad.mit.edu	37	18	4185263	4185264	+	Intron	DEL	TT	-	-	rs11336512		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4185263_4185264delTT	uc010wyz.1	-						uc002kmm.2_Intron	NM_004746	NP_004737			discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)																---	---	---	---
DLGAP1	9229	broad.mit.edu	37	18	4261398	4261398	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4261398delC	uc010wyz.1	-							NM_004746	NP_004737			discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)																---	---	---	---
DLGAP1	9229	broad.mit.edu	37	18	4335825	4335825	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4335825delA	uc010wyz.1	-							NM_004746	NP_004737			discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)																---	---	---	---
DLGAP1	9229	broad.mit.edu	37	18	4366707	4366707	+	Intron	DEL	A	-	-	rs56398398	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4366707delA	uc010wyz.1	-							NM_004746	NP_004737			discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)																---	---	---	---
DLGAP1	9229	broad.mit.edu	37	18	4392726	4392729	+	Intron	DEL	CTTA	-	-	rs72425749		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4392726_4392729delCTTA	uc010wyz.1	-							NM_004746	NP_004737			discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	4505563	4505563	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4505563delA								DLGAP1 (50297 upstream) : LOC642597 (638109 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	4789513	4789514	+	IGR	DEL	CC	-	-	rs71368759		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:4789513_4789514delCC								DLGAP1 (334247 upstream) : LOC642597 (354158 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	5096584	5096587	+	IGR	DEL	AAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5096584_5096587delAAAA								DLGAP1 (641318 upstream) : LOC642597 (47085 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	5136489	5136489	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5136489delA								DLGAP1 (681223 upstream) : LOC642597 (7183 downstream)																																			---	---	---	---
LOC339290	339290	broad.mit.edu	37	18	5245396	5245397	+	RNA	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5245396_5245397delAG	uc002kmo.2	+	3		c.2868_2869delAG			LOC339290_uc010dko.2_RNA|LOC339290_uc002kmp.2_RNA	NR_015389				Homo sapiens cDNA FLJ32367 fis, clone PUAEN1000239.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	5265410	5265410	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5265410delA								LOC339290 (18907 upstream) : ZFP161 (23609 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	5300013	5300013	+	IGR	DEL	T	-	-	rs71368783		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5300013delT								ZFP161 (3974 upstream) : EPB41L3 (92375 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	5385391	5385392	+	IGR	INS	-	TG	TG	rs144880628	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5385391_5385392insTG								ZFP161 (89352 upstream) : EPB41L3 (6996 downstream)																																			---	---	---	---
EPB41L3	23136	broad.mit.edu	37	18	5450173	5450174	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5450173_5450174insT	uc002kmt.1	-						EPB41L3_uc010wzh.1_Intron|EPB41L3_uc002kmu.1_Intron|EPB41L3_uc010dkq.1_Intron|EPB41L3_uc010dks.1_Intron|EPB41L3_uc002kmv.1_Intron	NM_012307	NP_036439			erythrocyte membrane protein band 4.1-like 3						cortical actin cytoskeleton organization	cell-cell junction|cytoplasm|cytoskeleton|extrinsic to membrane	actin binding|structural molecule activity			ovary(5)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	5782778	5782779	+	Intron	INS	-	G	G	rs145585600	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5782778_5782779insG	uc002kmw.2	+											Homo sapiens chromosome 18 unknown mRNA sequence.																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	5791825	5791826	+	Intron	DEL	CA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5791825_5791826delCA	uc002kmw.2	+											Homo sapiens chromosome 18 unknown mRNA sequence.																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	5952719	5952719	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5952719delT								TMEM200C (60616 upstream) : L3MBTL4 (1987 downstream)																																			---	---	---	---
L3MBTL4	91133	broad.mit.edu	37	18	6085264	6085265	+	Intron	INS	-	A	A	rs139081498	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6085264_6085265insA	uc002kmz.3	-						L3MBTL4_uc010dkt.2_Intron|L3MBTL4_uc002kmy.3_Intron	NM_173464	NP_775735			l(3)mbt-like 4						chromatin modification	nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|pancreas(1)	3		Colorectal(10;0.0249)																---	---	---	---
L3MBTL4	91133	broad.mit.edu	37	18	6090632	6090633	+	Intron	DEL	TT	-	-	rs10556087		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6090632_6090633delTT	uc002kmz.3	-						L3MBTL4_uc010dkt.2_Intron|L3MBTL4_uc002kmy.3_Intron	NM_173464	NP_775735			l(3)mbt-like 4						chromatin modification	nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|pancreas(1)	3		Colorectal(10;0.0249)																---	---	---	---
L3MBTL4	91133	broad.mit.edu	37	18	6241559	6241559	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6241559delA	uc002kmz.3	-						L3MBTL4_uc010dkt.2_Intron|L3MBTL4_uc002kmy.3_5'Flank	NM_173464	NP_775735			l(3)mbt-like 4						chromatin modification	nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|pancreas(1)	3		Colorectal(10;0.0249)																---	---	---	---
L3MBTL4	91133	broad.mit.edu	37	18	6322510	6322510	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6322510delA	uc002kmz.3	-						L3MBTL4_uc010dkt.2_Intron	NM_173464	NP_775735			l(3)mbt-like 4						chromatin modification	nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|pancreas(1)	3		Colorectal(10;0.0249)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	6587439	6587439	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6587439delA								L3MBTL4 (172529 upstream) : ARHGAP28 (201054 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	6677086	6677086	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6677086delT								L3MBTL4 (262176 upstream) : ARHGAP28 (111407 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	6729191	6729191	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6729191delA								L3MBTL4 (314281 upstream) : ARHGAP28 (59302 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	6783242	6783242	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6783242delT								L3MBTL4 (368332 upstream) : ARHGAP28 (5251 downstream)																																			---	---	---	---
ARHGAP28	79822	broad.mit.edu	37	18	6809422	6809422	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6809422delA	uc002knc.2	+							NM_030672	NP_109597			Rho GTPase activating protein 28 isoform b						signal transduction	intracellular				pancreas(1)	1		Colorectal(10;0.168)																---	---	---	---
ARHGAP28	79822	broad.mit.edu	37	18	6910852	6910852	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6910852delT	uc010wzi.1	+						ARHGAP28_uc002kne.2_Intron					SubName: Full=Putative uncharacterized protein ARHGAP28;						signal transduction	intracellular				pancreas(1)	1		Colorectal(10;0.168)																---	---	---	---
LAMA1	284217	broad.mit.edu	37	18	7015437	7015437	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7015437delT	uc002knm.2	-						LAMA1_uc010wzj.1_Intron	NM_005559	NP_005550			laminin, alpha 1 precursor						axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|upper_aerodigestive_tract(2)|breast(2)|skin(2)|pancreas(2)|central_nervous_system(1)	21		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
LAMA1	284217	broad.mit.edu	37	18	7026190	7026191	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7026190_7026191delAA	uc002knm.2	-						LAMA1_uc010wzj.1_Intron	NM_005559	NP_005550			laminin, alpha 1 precursor						axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|upper_aerodigestive_tract(2)|breast(2)|skin(2)|pancreas(2)|central_nervous_system(1)	21		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
LAMA1	284217	broad.mit.edu	37	18	7118786	7118786	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7118786delA	uc002knm.2	-						LAMA1_uc010wzj.1_5'Flank	NM_005559	NP_005550			laminin, alpha 1 precursor						axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|upper_aerodigestive_tract(2)|breast(2)|skin(2)|pancreas(2)|central_nervous_system(1)	21		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
Unknown	0	broad.mit.edu	37	18	7167788	7167788	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7167788delC								LAMA1 (49975 upstream) : LRRC30 (63349 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	7358310	7358310	+	IGR	DEL	A	-	-	rs113855928		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7358310delA								LRRC30 (126269 upstream) : PTPRM (209004 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	7367673	7367673	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7367673delG								LRRC30 (135632 upstream) : PTPRM (199641 downstream)																																			---	---	---	---
PTPRM	5797	broad.mit.edu	37	18	7565300	7565300	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7565300delT	uc002knn.3	+						PTPRM_uc010dkv.2_5'Flank	NM_002845	NP_002836			protein tyrosine phosphatase, receptor type, M						homophilic cell adhesion|negative regulation of angiogenesis|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|response to drug|retina layer formation|retinal ganglion cell axon guidance	cell-cell adherens junction|integral to plasma membrane|lamellipodium|perinuclear region of cytoplasm	cadherin binding|transmembrane receptor protein tyrosine phosphatase activity			lung(3)|ovary(2)|central_nervous_system(1)	6		Colorectal(10;0.234)																---	---	---	---
PTPRM	5797	broad.mit.edu	37	18	7602649	7602649	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7602649delT	uc002knn.3	+						PTPRM_uc010dkv.2_Intron	NM_002845	NP_002836			protein tyrosine phosphatase, receptor type, M						homophilic cell adhesion|negative regulation of angiogenesis|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|response to drug|retina layer formation|retinal ganglion cell axon guidance	cell-cell adherens junction|integral to plasma membrane|lamellipodium|perinuclear region of cytoplasm	cadherin binding|transmembrane receptor protein tyrosine phosphatase activity			lung(3)|ovary(2)|central_nervous_system(1)	6		Colorectal(10;0.234)																---	---	---	---
PTPRM	5797	broad.mit.edu	37	18	7669730	7669730	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7669730delT	uc002knn.3	+						PTPRM_uc010dkv.2_Intron	NM_002845	NP_002836			protein tyrosine phosphatase, receptor type, M						homophilic cell adhesion|negative regulation of angiogenesis|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|response to drug|retina layer formation|retinal ganglion cell axon guidance	cell-cell adherens junction|integral to plasma membrane|lamellipodium|perinuclear region of cytoplasm	cadherin binding|transmembrane receptor protein tyrosine phosphatase activity			lung(3)|ovary(2)|central_nervous_system(1)	6		Colorectal(10;0.234)																---	---	---	---
PTPRM	5797	broad.mit.edu	37	18	8001532	8001532	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8001532delT	uc002knn.3	+						PTPRM_uc010dkv.2_Intron|PTPRM_uc010wzl.1_Intron	NM_002845	NP_002836			protein tyrosine phosphatase, receptor type, M						homophilic cell adhesion|negative regulation of angiogenesis|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|response to drug|retina layer formation|retinal ganglion cell axon guidance	cell-cell adherens junction|integral to plasma membrane|lamellipodium|perinuclear region of cytoplasm	cadherin binding|transmembrane receptor protein tyrosine phosphatase activity			lung(3)|ovary(2)|central_nervous_system(1)	6		Colorectal(10;0.234)																---	---	---	---
PTPRM	5797	broad.mit.edu	37	18	8004861	8004862	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8004861_8004862insT	uc002knn.3	+						PTPRM_uc010dkv.2_Intron|PTPRM_uc010wzl.1_Intron	NM_002845	NP_002836			protein tyrosine phosphatase, receptor type, M						homophilic cell adhesion|negative regulation of angiogenesis|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|response to drug|retina layer formation|retinal ganglion cell axon guidance	cell-cell adherens junction|integral to plasma membrane|lamellipodium|perinuclear region of cytoplasm	cadherin binding|transmembrane receptor protein tyrosine phosphatase activity			lung(3)|ovary(2)|central_nervous_system(1)	6		Colorectal(10;0.234)																---	---	---	---
PTPRM	5797	broad.mit.edu	37	18	8073014	8073019	+	Intron	DEL	ACCAGT	-	-	rs139547527		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8073014_8073019delACCAGT	uc002knn.3	+						PTPRM_uc010dkv.2_Intron|PTPRM_uc010wzl.1_Intron	NM_002845	NP_002836			protein tyrosine phosphatase, receptor type, M						homophilic cell adhesion|negative regulation of angiogenesis|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|response to drug|retina layer formation|retinal ganglion cell axon guidance	cell-cell adherens junction|integral to plasma membrane|lamellipodium|perinuclear region of cytoplasm	cadherin binding|transmembrane receptor protein tyrosine phosphatase activity			lung(3)|ovary(2)|central_nervous_system(1)	6		Colorectal(10;0.234)																---	---	---	---
PTPRM	5797	broad.mit.edu	37	18	8180135	8180135	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8180135delA	uc002knn.3	+						PTPRM_uc010dkv.2_Intron|PTPRM_uc010wzl.1_Intron	NM_002845	NP_002836			protein tyrosine phosphatase, receptor type, M						homophilic cell adhesion|negative regulation of angiogenesis|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|response to drug|retina layer formation|retinal ganglion cell axon guidance	cell-cell adherens junction|integral to plasma membrane|lamellipodium|perinuclear region of cytoplasm	cadherin binding|transmembrane receptor protein tyrosine phosphatase activity			lung(3)|ovary(2)|central_nervous_system(1)	6		Colorectal(10;0.234)																---	---	---	---
PTPRM	5797	broad.mit.edu	37	18	8299754	8299754	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8299754delT	uc002knn.3	+						PTPRM_uc010dkv.2_Intron|PTPRM_uc010wzl.1_Intron	NM_002845	NP_002836			protein tyrosine phosphatase, receptor type, M						homophilic cell adhesion|negative regulation of angiogenesis|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|response to drug|retina layer formation|retinal ganglion cell axon guidance	cell-cell adherens junction|integral to plasma membrane|lamellipodium|perinuclear region of cytoplasm	cadherin binding|transmembrane receptor protein tyrosine phosphatase activity			lung(3)|ovary(2)|central_nervous_system(1)	6		Colorectal(10;0.234)																---	---	---	---
PTPRM	5797	broad.mit.edu	37	18	8384458	8384458	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8384458delA	uc002knn.3	+						PTPRM_uc010dkv.2_Intron|PTPRM_uc010wzl.1_Intron	NM_002845	NP_002836			protein tyrosine phosphatase, receptor type, M						homophilic cell adhesion|negative regulation of angiogenesis|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|response to drug|retina layer formation|retinal ganglion cell axon guidance	cell-cell adherens junction|integral to plasma membrane|lamellipodium|perinuclear region of cytoplasm	cadherin binding|transmembrane receptor protein tyrosine phosphatase activity			lung(3)|ovary(2)|central_nervous_system(1)	6		Colorectal(10;0.234)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	8561431	8561432	+	IGR	INS	-	GG	GG	rs148203207	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8561431_8561432insGG								PTPRM (154573 upstream) : RAB12 (48003 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	8565892	8565892	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8565892delA								PTPRM (159034 upstream) : RAB12 (43543 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	8665093	8665093	+	IGR	DEL	A	-	-	rs144630128		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8665093delA								RAB12 (25714 upstream) : KIAA0802 (42316 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	8839261	8839261	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8839261delG								KIAA0802 (6486 upstream) : NDUFV2 (263414 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	8883962	8883962	+	IGR	DEL	T	-	-	rs8087347	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8883962delT								KIAA0802 (51187 upstream) : NDUFV2 (218713 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	8989893	8989893	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8989893delT								KIAA0802 (157118 upstream) : NDUFV2 (112782 downstream)																																			---	---	---	---
ANKRD12	23253	broad.mit.edu	37	18	9176275	9176275	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9176275delT	uc002knv.2	+						ANKRD12_uc010wzn.1_Intron|ANKRD12_uc002knw.2_Intron|ANKRD12_uc002knx.2_Intron	NM_015208	NP_056023			ankyrin repeat domain 12 isoform 1							nucleus				ovary(2)|central_nervous_system(1)	3																		---	---	---	---
ANKRD12	23253	broad.mit.edu	37	18	9216637	9216637	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9216637delT	uc002knv.2	+						ANKRD12_uc010wzn.1_Intron|ANKRD12_uc002knw.2_Intron|ANKRD12_uc002knx.2_Intron|ANKRD12_uc010dkx.1_5'Flank	NM_015208	NP_056023			ankyrin repeat domain 12 isoform 1							nucleus				ovary(2)|central_nervous_system(1)	3																		---	---	---	---
ANKRD12	23253	broad.mit.edu	37	18	9230654	9230655	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9230654_9230655delTT	uc002knv.2	+						ANKRD12_uc010wzn.1_Intron|ANKRD12_uc002knw.2_Intron|ANKRD12_uc002knx.2_Intron|ANKRD12_uc010dkx.1_Intron	NM_015208	NP_056023			ankyrin repeat domain 12 isoform 1							nucleus				ovary(2)|central_nervous_system(1)	3																		---	---	---	---
ANKRD12	23253	broad.mit.edu	37	18	9273305	9273305	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9273305delA	uc002knv.2	+						ANKRD12_uc002knw.2_Intron|ANKRD12_uc002knx.2_Intron	NM_015208	NP_056023			ankyrin repeat domain 12 isoform 1							nucleus				ovary(2)|central_nervous_system(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	9408595	9408596	+	IGR	INS	-	T	T	rs138332977	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9408595_9408596insT								TWSG1 (6178 upstream) : RALBP1 (66411 downstream)																																			---	---	---	---
RALBP1	10928	broad.mit.edu	37	18	9478243	9478244	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9478243_9478244delTT	uc002kob.2	+						RALBP1_uc002koc.2_Intron	NM_006788	NP_006779			ralA binding protein 1						chemotaxis|positive regulation of Cdc42 GTPase activity|small GTPase mediated signal transduction|transport	cytosol|membrane	ATPase activity, coupled to movement of substances|Rac GTPase activator activity|Rac GTPase binding|Ral GTPase binding			central_nervous_system(1)	1																		---	---	---	---
RALBP1	10928	broad.mit.edu	37	18	9513298	9513298	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9513298delT	uc002kob.2	+						RALBP1_uc002koc.2_Intron	NM_006788	NP_006779			ralA binding protein 1						chemotaxis|positive regulation of Cdc42 GTPase activity|small GTPase mediated signal transduction|transport	cytosol|membrane	ATPase activity, coupled to movement of substances|Rac GTPase activator activity|Rac GTPase binding|Ral GTPase binding			central_nervous_system(1)	1																		---	---	---	---
RALBP1	10928	broad.mit.edu	37	18	9525921	9525921	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9525921delT	uc002kob.2	+						RALBP1_uc002koc.2_Intron	NM_006788	NP_006779			ralA binding protein 1						chemotaxis|positive regulation of Cdc42 GTPase activity|small GTPase mediated signal transduction|transport	cytosol|membrane	ATPase activity, coupled to movement of substances|Rac GTPase activator activity|Rac GTPase binding|Ral GTPase binding			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	9625641	9625641	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:9625641delT								PPP4R1 (11041 upstream) : RAB31 (82587 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	10015912	10015912	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10015912delT								VAPA (55895 upstream) : APCDD1 (438713 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	10025643	10025644	+	IGR	INS	-	T	T	rs35969329		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10025643_10025644insT								VAPA (65626 upstream) : APCDD1 (428981 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	10042452	10042452	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10042452delT								VAPA (82435 upstream) : APCDD1 (412173 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	10110661	10110662	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10110661_10110662delTT								VAPA (150644 upstream) : APCDD1 (343963 downstream)																																			---	---	---	---
APCDD1	147495	broad.mit.edu	37	18	10451721	10451721	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10451721delA	uc002kom.3	+							NM_153000	NP_694545			adenomatosis polyposis coli down-regulated 1						hair follicle development|negative regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to plasma membrane	Wnt-protein binding				0				READ - Rectum adenocarcinoma(15;0.08)														---	---	---	---
NAPG	8774	broad.mit.edu	37	18	10542225	10542227	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10542225_10542227delTTT	uc002kon.2	+						NAPG_uc010wzr.1_Intron|NAPG_uc002koo.2_Intron|NAPG_uc002kop.2_Intron	NM_003826	NP_003817			N-ethylmaleimide-sensitive factor attachment						cellular membrane fusion|intra-Golgi vesicle-mediated transport|intracellular protein transport|protein complex assembly|protein stabilization	membrane|membrane fraction|mitochondrion	protein binding				0																		---	---	---	---
NAPG	8774	broad.mit.edu	37	18	10544973	10544974	+	Intron	DEL	GT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10544973_10544974delGT	uc002kon.2	+						NAPG_uc010wzr.1_Intron|NAPG_uc002koo.2_Intron|NAPG_uc002kop.2_Intron	NM_003826	NP_003817			N-ethylmaleimide-sensitive factor attachment						cellular membrane fusion|intra-Golgi vesicle-mediated transport|intracellular protein transport|protein complex assembly|protein stabilization	membrane|membrane fraction|mitochondrion	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	10586098	10586099	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10586098_10586099insT								NAPG (33336 upstream) : FAM38B (84761 downstream)																																			---	---	---	---
FAM38B	63895	broad.mit.edu	37	18	10829267	10829267	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10829267delA	uc002kow.1	-											RecName: Full=Uncharacterized protein C18orf58;							integral to membrane	ion channel activity			ovary(1)	1																		---	---	---	---
FAM38B	63895	broad.mit.edu	37	18	10884693	10884693	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10884693delC	uc002kow.1	-											RecName: Full=Uncharacterized protein C18orf58;							integral to membrane	ion channel activity			ovary(1)	1																		---	---	---	---
FAM38B	63895	broad.mit.edu	37	18	10892652	10892653	+	5'Flank	DEL	GG	-	-	rs196956	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10892652_10892653delGG	uc002kow.1	-											RecName: Full=Uncharacterized protein C18orf58;							integral to membrane	ion channel activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	10932932	10932933	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10932932_10932933delAA								FAM38B (230953 upstream) : GNAL (756203 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	10940859	10940859	+	IGR	DEL	A	-	-	rs77372334		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:10940859delA								FAM38B (238880 upstream) : GNAL (748277 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	11170451	11170451	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11170451delA								FAM38B (468472 upstream) : GNAL (518685 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	11232078	11232078	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11232078delA								FAM38B (530099 upstream) : GNAL (457058 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	11316225	11316225	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11316225delT								FAM38B (614246 upstream) : GNAL (372911 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	11354860	11354861	+	IGR	INS	-	TG	TG	rs143655375	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11354860_11354861insTG								FAM38B (652881 upstream) : GNAL (334275 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	11376956	11376956	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11376956delT								FAM38B (674977 upstream) : GNAL (312180 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	11480372	11480372	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11480372delA								FAM38B (778393 upstream) : GNAL (208764 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	11622352	11622355	+	IGR	DEL	CTCT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11622352_11622355delCTCT								FAM38B (920373 upstream) : GNAL (66781 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	11644934	11644934	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11644934delA								FAM38B (942955 upstream) : GNAL (44202 downstream)																																			---	---	---	---
GNAL	2774	broad.mit.edu	37	18	11775185	11775185	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11775185delG	uc010dkz.2	+						GNAL_uc002kqc.2_Intron|GNAL_uc002kqd.2_Intron	NM_001142339	NP_001135811			guanine nucleotide binding protein (G protein),						activation of adenylate cyclase activity by dopamine receptor signaling pathway|inhibition of adenylate cyclase activity by G-protein signaling pathway|sensory perception of smell|synaptic transmission	heterotrimeric G-protein complex	adenylate cyclase activity|G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			ovary(1)	1																		---	---	---	---
CHMP1B	57132	broad.mit.edu	37	18	11853467	11853467	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11853467delT	uc002kqe.2	+	1					GNAL_uc002kqc.2_Intron|GNAL_uc010dkz.2_Intron|GNAL_uc002kqd.2_Intron	NM_020412	NP_065145			chromatin modifying protein 1B						cell cycle|cell division|protein transport	cytosol|late endosome membrane	protein domain specific binding				0																		---	---	---	---
GNAL	2774	broad.mit.edu	37	18	11876464	11876464	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11876464delA	uc010dkz.2	+						GNAL_uc002kqc.2_Intron|GNAL_uc002kqd.2_Intron|GNAL_uc010wzt.1_Intron	NM_001142339	NP_001135811			guanine nucleotide binding protein (G protein),						activation of adenylate cyclase activity by dopamine receptor signaling pathway|inhibition of adenylate cyclase activity by G-protein signaling pathway|sensory perception of smell|synaptic transmission	heterotrimeric G-protein complex	adenylate cyclase activity|G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	11937253	11937253	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11937253delA								MPPE1 (28612 upstream) : IMPA2 (43804 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	11975911	11975911	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11975911delA								MPPE1 (67270 upstream) : IMPA2 (5146 downstream)																																			---	---	---	---
IMPA2	3613	broad.mit.edu	37	18	11996999	11997000	+	Intron	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11996999_11997000delAC	uc002kqp.1	+						IMPA2_uc002kqo.1_Intron|IMPA2_uc010dlb.1_Intron|IMPA2_uc002kqq.1_Intron	NM_014214	NP_055029			inositol(myo)-1(or 4)-monophosphatase 2						inositol phosphate dephosphorylation|signal transduction	cytoplasm	inositol-1(or 4)-monophosphatase activity|metal ion binding|protein homodimerization activity			skin(2)	2					Lithium(DB01356)													---	---	---	---
IMPA2	3613	broad.mit.edu	37	18	12007130	12007130	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12007130delA	uc002kqp.1	+						IMPA2_uc002kqo.1_Intron|IMPA2_uc010dlb.1_Intron|IMPA2_uc002kqq.1_Intron	NM_014214	NP_055029			inositol(myo)-1(or 4)-monophosphatase 2						inositol phosphate dephosphorylation|signal transduction	cytoplasm	inositol-1(or 4)-monophosphatase activity|metal ion binding|protein homodimerization activity			skin(2)	2					Lithium(DB01356)													---	---	---	---
Unknown	0	broad.mit.edu	37	18	12241053	12241053	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12241053delT								IMPA2 (210177 upstream) : CIDEA (13265 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	12242879	12242879	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12242879delT								IMPA2 (212003 upstream) : CIDEA (11439 downstream)																																			---	---	---	---
AFG3L2	10939	broad.mit.edu	37	18	12355580	12355580	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12355580delA	uc002kqz.1	-							NM_006796	NP_006787			AFG3 ATPase family gene 3-like 2						cell death|protein catabolic process|proteolysis	integral to membrane	ATP binding|metalloendopeptidase activity|nucleoside-triphosphatase activity|unfolded protein binding|zinc ion binding				0					Adenosine triphosphate(DB00171)													---	---	---	---
SPIRE1	56907	broad.mit.edu	37	18	12593953	12593953	+	Intron	DEL	A	-	-	rs71371279		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12593953delA	uc002kre.2	-						SPIRE1_uc002krc.2_Intron|SPIRE1_uc010wzw.1_Intron|SPIRE1_uc010wzx.1_Intron|SPIRE1_uc010wzy.1_Intron	NM_001128626	NP_001122098			spire homolog 1 isoform a							cytoskeleton|perinuclear region of cytoplasm	actin binding				0																		---	---	---	---
PSMG2	56984	broad.mit.edu	37	18	12705066	12705066	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12705066delT	uc002krk.2	+						PSMG2_uc002krg.2_Intron|PSMG2_uc002krj.1_Intron|CEP76_uc002krh.3_5'Flank|CEP76_uc002kri.2_5'Flank|CEP76_uc010wzz.1_5'Flank|CEP76_uc010xab.1_5'Flank	NM_020232	NP_064617			proteasome (prosome, macropain) assembly						proteasome assembly	nucleus	protein binding				0																		---	---	---	---
PTPN2	5771	broad.mit.edu	37	18	12809714	12809714	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12809714delT	uc002krp.2	-						PTPN2_uc002krl.2_Intron|PTPN2_uc002krn.2_Intron|PTPN2_uc002kro.2_Intron|PTPN2_uc002krm.2_Intron	NM_002828	NP_002819			protein tyrosine phosphatase, non-receptor type						interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway	endoplasmic reticulum|nucleoplasm	protein binding			skin(2)	2		Lung NSC(161;8.94e-06)																---	---	---	---
SEH1L	81929	broad.mit.edu	37	18	12954079	12954079	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12954079delA	uc002krr.2	+						SEH1L_uc002krq.2_Intron	NM_031216	NP_112493			sec13-like protein isoform 2						attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation|carbohydrate metabolic process|cell division|glucose transport|mitotic metaphase plate congression|mitotic prometaphase|mRNA transport|nuclear pore organization|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex					0																		---	---	---	---
CEP192	55125	broad.mit.edu	37	18	13010851	13010852	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13010851_13010852insA	uc010xac.1	+						CEP192_uc002krs.1_Intron	NM_032142	NP_115518			centrosomal protein 192kDa											ovary(4)|pancreas(1)	5																		---	---	---	---
CEP192	55125	broad.mit.edu	37	18	13026917	13026917	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13026917delT	uc010xac.1	+						CEP192_uc010dlf.1_5'Flank|CEP192_uc010xad.1_5'Flank|CEP192_uc002kru.2_5'Flank|CEP192_uc002krs.1_Intron	NM_032142	NP_115518			centrosomal protein 192kDa											ovary(4)|pancreas(1)	5																		---	---	---	---
C18orf1	753	broad.mit.edu	37	18	13221336	13221336	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13221336delT	uc002ksa.2	+						C18orf1_uc002ksb.2_Intron	NM_181481	NP_852146			hypothetical protein LOC753 isoform alpha 1							integral to membrane|plasma membrane				ovary(2)|skin(1)	3				READ - Rectum adenocarcinoma(73;0.0642)														---	---	---	---
C18orf1	753	broad.mit.edu	37	18	13381089	13381092	+	Intron	DEL	TTTG	-	-	rs74856912		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13381089_13381092delTTTG	uc002ksa.2	+						C18orf1_uc002ksb.2_Intron	NM_181481	NP_852146			hypothetical protein LOC753 isoform alpha 1							integral to membrane|plasma membrane				ovary(2)|skin(1)	3				READ - Rectum adenocarcinoma(73;0.0642)														---	---	---	---
C18orf1	753	broad.mit.edu	37	18	13493325	13493325	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13493325delT	uc002ksa.2	+						C18orf1_uc002ksb.2_Intron	NM_181481	NP_852146			hypothetical protein LOC753 isoform alpha 1							integral to membrane|plasma membrane				ovary(2)|skin(1)	3				READ - Rectum adenocarcinoma(73;0.0642)														---	---	---	---
C18orf1	753	broad.mit.edu	37	18	13557408	13557408	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13557408delT	uc002ksa.2	+						C18orf1_uc002ksb.2_Intron	NM_181481	NP_852146			hypothetical protein LOC753 isoform alpha 1							integral to membrane|plasma membrane				ovary(2)|skin(1)	3				READ - Rectum adenocarcinoma(73;0.0642)														---	---	---	---
C18orf1	753	broad.mit.edu	37	18	13588571	13588573	+	Intron	DEL	TTA	-	-	rs1785201	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13588571_13588573delTTA	uc002ksa.2	+						C18orf1_uc002ksb.2_Intron	NM_181481	NP_852146			hypothetical protein LOC753 isoform alpha 1							integral to membrane|plasma membrane				ovary(2)|skin(1)	3				READ - Rectum adenocarcinoma(73;0.0642)														---	---	---	---
C18orf19	125228	broad.mit.edu	37	18	13673425	13673425	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13673425delC	uc010dlh.2	-						C18orf19_uc010dlg.2_Intron|C18orf19_uc010dli.2_Intron|C18orf19_uc002ksj.3_Intron|C18orf19_uc010dlj.2_Intron	NM_001098801	NP_001092271			hypothetical protein LOC125228							integral to membrane				breast(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	13954613	13954613	+	IGR	DEL	T	-	-	rs66745674		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13954613delT								MC2R (39078 upstream) : ZNF519 (121376 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	14023986	14023987	+	IGR	INS	-	T	T	rs8091227		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14023986_14023987insT								MC2R (108451 upstream) : ZNF519 (52002 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	14061626	14061626	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14061626delT								MC2R (146091 upstream) : ZNF519 (14363 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	14074901	14074901	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14074901delT								MC2R (159366 upstream) : ZNF519 (1088 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	14301902	14301902	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14301902delA								ZNF519 (169473 upstream) : LOC284233 (35520 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	14410521	14410521	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14410521delT								LOC284233 (67999 upstream) : CXADRP3 (67435 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	14433026	14433027	+	IGR	INS	-	A	A	rs142174423		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14433026_14433027insA								LOC284233 (90504 upstream) : CXADRP3 (44929 downstream)																																			---	---	---	---
POTEC	388468	broad.mit.edu	37	18	14542585	14542585	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14542585delC	uc010dln.2	-						POTEC_uc010xaj.1_Intron	NM_001137671	NP_001131143			ANKRD26-like family B, member 2											skin(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	14936310	14936310	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14936310delT								ANKRD30B (83573 upstream) : LOC644669 (377245 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	15152420	15152421	+	IGR	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15152420_15152421insC								ANKRD30B (299683 upstream) : LOC644669 (161134 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	15279149	15279149	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15279149delA								ANKRD30B (426412 upstream) : LOC644669 (34406 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	15397846	15397846	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15397846delG								LOC644669 (71928 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	15402425	15402425	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:15402425delT								LOC644669 (76507 upstream) : None (None downstream)																																			---	---	---	---
ROCK1	6093	broad.mit.edu	37	18	18619417	18619417	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:18619417delA	uc002kte.2	-							NM_005406	NP_005397			Rho-associated, coiled-coil containing protein						actin cytoskeleton organization|axon guidance|cellular component disassembly involved in apoptosis|cytokinesis|leukocyte tethering or rolling|membrane to membrane docking|Rho protein signal transduction	centriole|cytosol|Golgi membrane	ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity			lung(2)|breast(2)|central_nervous_system(1)	5	Melanoma(1;0.165)																	---	---	---	---
SNRPD1	6632	broad.mit.edu	37	18	19201129	19201129	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19201129delA	uc002ktj.1	+							NM_006938	NP_008869			small nuclear ribonucleoprotein D1 polypeptide						ncRNA metabolic process|spliceosomal snRNP assembly|spliceosome assembly	catalytic step 2 spliceosome|cytosol|nucleoplasm|small nuclear ribonucleoprotein complex|U12-type spliceosomal complex	protein binding|RNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	19478109	19478109	+	IGR	DEL	T	-	-	rs112096983		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19478109delT								MIB1 (27199 upstream) : GATA6 (271307 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	20481015	20481015	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20481015delT								CTAGE1 (483137 upstream) : RBBP8 (32280 downstream)																																			---	---	---	---
RBBP8	5932	broad.mit.edu	37	18	20526569	20526569	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20526569delA	uc002ktw.2	+						RBBP8_uc002kty.2_Intron|RBBP8_uc002ktz.2_Intron|RBBP8_uc002kua.2_Intron|RBBP8_uc002ktx.1_Intron	NM_002894	NP_002885			retinoblastoma binding protein 8 isoform a						cell cycle checkpoint|DNA double-strand break processing involved in repair via single-strand annealing|meiosis|regulation of transcription from RNA polymerase II promoter	nucleus	damaged DNA binding|protein binding|single-stranded DNA specific endodeoxyribonuclease activity			ovary(1)|lung(1)|skin(1)	3	all_cancers(21;4.34e-05)|all_epithelial(16;8.3e-07)|Lung NSC(20;0.0107)|Colorectal(14;0.0202)|all_lung(20;0.0291)|Ovarian(20;0.19)		OV - Ovarian serous cystadenocarcinoma(1;0.00196)										Direct_reversal_of_damage|Homologous_recombination					---	---	---	---
CABLES1	91768	broad.mit.edu	37	18	20776161	20776161	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20776161delT	uc002kuc.2	+						CABLES1_uc002kub.2_Intron|CABLES1_uc002kud.2_Intron	NM_001100619	NP_001094089			Cdk5 and Abl enzyme substrate 1 isoform 2						blood coagulation|cell cycle|cell division|regulation of cell cycle|regulation of cell division	cytosol|nucleus	cyclin-dependent protein kinase regulator activity|protein binding			breast(1)	1	all_cancers(21;0.000102)|all_epithelial(16;2.48e-06)|Lung NSC(20;0.00696)|all_lung(20;0.0197)|Colorectal(14;0.0202)|Ovarian(20;0.127)																	---	---	---	---
C18orf45	85019	broad.mit.edu	37	18	21010721	21010721	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21010721delA	uc002kuf.2	-						C18orf45_uc010xaq.1_Intron|C18orf45_uc010xar.1_Intron|C18orf45_uc002kug.2_Intron|C18orf45_uc002kuh.2_Intron	NM_032933	NP_116322			hypothetical protein LOC85019							integral to membrane					0	all_cancers(21;0.000238)|all_epithelial(16;5.29e-06)|Lung NSC(20;0.00925)|Colorectal(14;0.0202)|all_lung(20;0.0255)|Ovarian(20;0.127)																	---	---	---	---
NPC1	4864	broad.mit.edu	37	18	21156386	21156386	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21156386delA	uc002kum.3	-						NPC1_uc010xba.1_Intron	NM_000271	NP_000262			Niemann-Pick disease, type C1 precursor						autophagy|bile acid metabolic process|cholesterol efflux|cholesterol homeostasis|lysosomal transport	endoplasmic reticulum|integral to plasma membrane|late endosome membrane|lysosomal membrane|nuclear envelope|perinuclear region of cytoplasm	hedgehog receptor activity|protein binding|sterol transporter activity			ovary(2)	2	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)																	---	---	---	---
ANKRD29	147463	broad.mit.edu	37	18	21189059	21189061	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21189059_21189061delAAA	uc002kun.2	-						ANKRD29_uc002kuo.2_Intron	NM_173505	NP_775776			ankyrin repeat domain 29											ovary(3)|breast(1)	4	all_cancers(21;5.07e-05)|all_epithelial(16;2.49e-07)|Lung NSC(20;0.00211)|all_lung(20;0.00676)|Colorectal(14;0.0202)|Ovarian(20;0.127)																	---	---	---	---
ANKRD29	147463	broad.mit.edu	37	18	21197464	21197464	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21197464delT	uc002kun.2	-						ANKRD29_uc002kuo.2_Intron	NM_173505	NP_775776			ankyrin repeat domain 29											ovary(3)|breast(1)	4	all_cancers(21;5.07e-05)|all_epithelial(16;2.49e-07)|Lung NSC(20;0.00211)|all_lung(20;0.00676)|Colorectal(14;0.0202)|Ovarian(20;0.127)																	---	---	---	---
Unknown	0	broad.mit.edu	37	18	21568165	21568166	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21568165_21568166delAA								LAMA3 (33138 upstream) : TTC39C (4571 downstream)																																			---	---	---	---
TTC39C	125488	broad.mit.edu	37	18	21644471	21644471	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21644471delG	uc002kuw.2	+						TTC39C_uc002kuu.2_Intron	NM_001135993	NP_001129465			tetratricopeptide repeat domain 39C isoform 1								binding			ovary(1)	1																		---	---	---	---
TTC39C	125488	broad.mit.edu	37	18	21653497	21653498	+	Intron	DEL	TT	-	-	rs10711494		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21653497_21653498delTT	uc002kuw.2	+						TTC39C_uc002kuu.2_Intron	NM_001135993	NP_001129465			tetratricopeptide repeat domain 39C isoform 1								binding			ovary(1)	1																		---	---	---	---
TTC39C	125488	broad.mit.edu	37	18	21675678	21675679	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21675678_21675679insA	uc002kuw.2	+						TTC39C_uc002kuu.2_Intron	NM_001135993	NP_001129465			tetratricopeptide repeat domain 39C isoform 1								binding			ovary(1)	1																		---	---	---	---
TTC39C	125488	broad.mit.edu	37	18	21698619	21698621	+	Intron	DEL	TTT	-	-	rs67869116		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21698619_21698621delTTT	uc002kuw.2	+						TTC39C_uc002kuu.2_Intron	NM_001135993	NP_001129465			tetratricopeptide repeat domain 39C isoform 1								binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	22062255	22062255	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22062255delT								HRH4 (2335 upstream) : ZNF521 (579633 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	22165991	22165991	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22165991delA								HRH4 (106071 upstream) : ZNF521 (475897 downstream)																																			---	---	---	---
ZNF521	25925	broad.mit.edu	37	18	22871899	22871899	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22871899delA	uc002kvk.2	-						ZNF521_uc010xbe.1_Intron|ZNF521_uc010dly.2_Intron|ZNF521_uc002kvl.2_Intron	NM_015461	NP_056276			zinc finger protein 521						cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein domain specific binding|zinc ion binding			ovary(4)|large_intestine(2)|lung(1)	7	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)							T	PAX5	ALL								---	---	---	---
Unknown	0	broad.mit.edu	37	18	23181308	23181308	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:23181308delT								ZNF521 (249094 upstream) : SS18 (414911 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	23379445	23379445	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:23379445delT								ZNF521 (447231 upstream) : SS18 (216774 downstream)																																			---	---	---	---
PSMA8	143471	broad.mit.edu	37	18	23769498	23769498	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:23769498delA	uc002kvq.2	+						PSMA8_uc002kvo.2_Intron|PSMA8_uc002kvp.2_Intron|PSMA8_uc002kvr.2_Intron	NM_144662	NP_653263			proteasome alpha 8 subunit isoform 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|M/G1 transition of mitotic cell cycle|mRNA metabolic process|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome core complex, alpha-subunit complex	threonine-type endopeptidase activity			skin(1)	1	all_cancers(21;0.000585)|Lung NSC(5;0.00148)|all_lung(6;0.0038)|Ovarian(20;0.124)		OV - Ovarian serous cystadenocarcinoma(3;0.000324)|all cancers(3;0.000954)|LUSC - Lung squamous cell carcinoma(2;0.181)															---	---	---	---
TAF4B	6875	broad.mit.edu	37	18	23845111	23845111	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:23845111delT	uc002kvu.3	+						TAF4B_uc002kvs.3_Intron|TAF4B_uc002kvt.3_Intron	NM_005640	NP_005631			TAF4b RNA polymerase II, TATA box binding						transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|nucleolus|transcription factor TFIID complex	DNA binding|NF-kappaB binding|sequence-specific DNA binding transcription factor activity			lung(1)|central_nervous_system(1)|skin(1)	3	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)															---	---	---	---
Unknown	0	broad.mit.edu	37	18	25497972	25497973	+	IGR	DEL	TG	-	-	rs112861067		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25497972_25497973delTG								C18orf16 (727322 upstream) : CDH2 (32957 downstream)																																			---	---	---	---
CDH2	1000	broad.mit.edu	37	18	25729520	25729520	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25729520delA	uc002kwg.2	-							NM_001792	NP_001783			cadherin 2, type 1 preproprotein						adherens junction organization|cell junction assembly|positive regulation of muscle cell differentiation	catenin complex|integral to membrane	alpha-catenin binding|beta-catenin binding|calcium ion binding|gamma-catenin binding			ovary(3)|lung(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	25968358	25968358	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:25968358delC								CDH2 (210913 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	26030161	26030162	+	IGR	DEL	AA	-	-	rs113687176		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:26030161_26030162delAA								CDH2 (272716 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	26121303	26121303	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:26121303delA								CDH2 (363858 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	26219359	26219362	+	IGR	DEL	CAGT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:26219359_26219362delCAGT								CDH2 (461914 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	26348483	26348487	+	IGR	DEL	TCCTA	-	-	rs141153145		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:26348483_26348487delTCCTA								CDH2 (591038 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	26585983	26585984	+	IGR	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:26585983_26585984delAC								CDH2 (828538 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	26657993	26657993	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:26657993delT								CDH2 (900548 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	27451238	27451238	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:27451238delA								None (None upstream) : MIR302F (427638 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	27473485	27473485	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:27473485delT								None (None upstream) : MIR302F (405391 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	27653526	27653526	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:27653526delA								None (None upstream) : MIR302F (225350 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	27660542	27660542	+	IGR	DEL	T	-	-	rs113236419		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:27660542delT								None (None upstream) : MIR302F (218334 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	28364625	28364625	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28364625delG								MIR302F (485699 upstream) : DSC3 (205428 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	28526984	28526985	+	IGR	INS	-	TC	TC			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28526984_28526985insTC								MIR302F (648058 upstream) : DSC3 (43068 downstream)																																			---	---	---	---
DSC3	1825	broad.mit.edu	37	18	28616212	28616212	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28616212delT	uc002kwj.3	-						DSC3_uc002kwi.3_Intron	NM_001941	NP_001932			desmocollin 3 isoform Dsc3a preproprotein						homophilic cell adhesion|protein stabilization	desmosome|integral to membrane|membrane fraction	calcium ion binding|gamma-catenin binding			ovary(2)|skin(2)	4			OV - Ovarian serous cystadenocarcinoma(10;0.125)															---	---	---	---
DSG1	1828	broad.mit.edu	37	18	28923779	28923779	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28923779delT	uc002kwp.2	+						DSG1_uc010xbp.1_5'UTR	NM_001942	NP_001933			desmoglein 1 preproprotein						calcium-dependent cell-cell adhesion|cell-cell junction assembly|cellular component disassembly involved in apoptosis|homophilic cell adhesion|protein stabilization	cytosol|desmosome|integral to membrane|internal side of plasma membrane	calcium ion binding|gamma-catenin binding|toxin binding			skin(3)|ovary(2)|central_nervous_system(2)	7			OV - Ovarian serous cystadenocarcinoma(10;0.00559)															---	---	---	---
Unknown	0	broad.mit.edu	37	18	29199286	29199286	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29199286delG								TTR (20302 upstream) : B4GALT6 (2924 downstream)																																			---	---	---	---
B4GALT6	9331	broad.mit.edu	37	18	29210381	29210384	+	Intron	DEL	TTTT	-	-	rs71842456		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29210381_29210384delTTTT	uc002kwz.3	-						B4GALT6_uc010dma.2_Intron|B4GALT6_uc010dmb.2_Intron	NM_004775	NP_004766			beta-1,4-galactosyltransferase 6						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	metal ion binding				0			OV - Ovarian serous cystadenocarcinoma(10;0.00791)															---	---	---	---
B4GALT6	9331	broad.mit.edu	37	18	29246379	29246379	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29246379delT	uc002kwz.3	-						B4GALT6_uc010dma.2_Intron|B4GALT6_uc010dmb.2_Intron	NM_004775	NP_004766			beta-1,4-galactosyltransferase 6						post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	metal ion binding				0			OV - Ovarian serous cystadenocarcinoma(10;0.00791)															---	---	---	---
KIAA1012	22878	broad.mit.edu	37	18	29450857	29450857	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29450857delA	uc002kxc.3	-						KIAA1012_uc002kxb.3_Intron|KIAA1012_uc002kxd.3_Intron	NM_014939	NP_055754			hypothetical protein LOC22878						ER to Golgi vesicle-mediated transport	cis-Golgi network					0																		---	---	---	---
KIAA1012	22878	broad.mit.edu	37	18	29489050	29489050	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29489050delA	uc002kxc.3	-						KIAA1012_uc002kxb.3_Intron|KIAA1012_uc002kxd.3_Intron|KIAA1012_uc002kxe.2_Intron	NM_014939	NP_055754			hypothetical protein LOC22878						ER to Golgi vesicle-mediated transport	cis-Golgi network					0																		---	---	---	---
RNF125	54941	broad.mit.edu	37	18	29607894	29607895	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29607894_29607895delAA	uc002kxf.1	+							NM_017831	NP_060301			ring finger protein 125						negative regulation of type I interferon production	intracellular	ligase activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	29745285	29745288	+	IGR	DEL	TTTT	-	-	rs113048652		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29745285_29745288delTTTT								RNF138 (33762 upstream) : MEP1B (24699 downstream)																																			---	---	---	---
MEP1B	4225	broad.mit.edu	37	18	29795258	29795258	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29795258delT	uc002kxj.3	+							NM_005925	NP_005916			meprin A beta precursor						digestion|proteolysis	extracellular space|integral to plasma membrane	metalloendopeptidase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
FAM59A	64762	broad.mit.edu	37	18	29883880	29883880	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29883880delA	uc002kxl.2	-						FAM59A_uc002kxk.1_Intron	NM_022751	NP_073588			family with sequence similarity 59, member A											ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	30068884	30068885	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30068884_30068885insA								FAM59A (18437 upstream) : WBP11P1 (22741 downstream)																																			---	---	---	---
C18orf34	374864	broad.mit.edu	37	18	30827526	30827526	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30827526delA	uc002kxn.2	-						C18orf34_uc010dme.1_Intron|C18orf34_uc010xbr.1_Intron|C18orf34_uc010dmf.1_Intron|C18orf34_uc002kxo.2_Intron|C18orf34_uc002kxp.2_Intron	NM_001105528	NP_001098998			hypothetical protein LOC374864 isoform 1											ovary(1)	1																		---	---	---	---
DTNA	1837	broad.mit.edu	37	18	32446137	32446137	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32446137delG	uc010dmn.1	+						DTNA_uc010xbx.1_3'UTR|DTNA_uc002kxv.3_3'UTR|DTNA_uc002kxw.2_Intron|DTNA_uc010dmj.2_Intron|DTNA_uc002kxz.2_Intron|DTNA_uc002kxy.2_Intron|DTNA_uc010dml.2_3'UTR|DTNA_uc002kyb.3_3'UTR|DTNA_uc010dmm.2_3'UTR|DTNA_uc010xby.1_Intron|DTNA_uc010dmo.2_3'UTR|DTNA_uc002kyd.3_3'UTR|DTNA_uc010xbz.1_Intron|DTNA_uc010xca.1_Intron|DTNA_uc002kye.2_Intron	NM_001390	NP_001381			dystrobrevin alpha isoform 1						neuromuscular synaptic transmission|signal transduction|striated muscle contraction	cell junction|cytoplasm|synapse	calcium ion binding|protein binding|zinc ion binding				0																		---	---	---	---
DTNA	1837	broad.mit.edu	37	18	32449990	32449990	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32449990delA	uc010dmn.1	+						DTNA_uc002kxw.2_Intron|DTNA_uc010dmj.2_Intron|DTNA_uc002kxz.2_Intron|DTNA_uc002kxy.2_Intron|DTNA_uc010xby.1_Intron|DTNA_uc010xbz.1_Intron|DTNA_uc010xca.1_Intron|DTNA_uc002kye.2_Intron	NM_001390	NP_001381			dystrobrevin alpha isoform 1						neuromuscular synaptic transmission|signal transduction|striated muscle contraction	cell junction|cytoplasm|synapse	calcium ion binding|protein binding|zinc ion binding				0																		---	---	---	---
DTNA	1837	broad.mit.edu	37	18	32459771	32459771	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32459771delT	uc010dmn.1	+						DTNA_uc002kxw.2_Intron|DTNA_uc010dmj.2_Intron|DTNA_uc002kxz.2_Intron|DTNA_uc002kxy.2_Intron|DTNA_uc010xby.1_Intron|DTNA_uc010xbz.1_Intron|DTNA_uc010xca.1_Intron|DTNA_uc002kye.2_Intron	NM_001390	NP_001381			dystrobrevin alpha isoform 1						neuromuscular synaptic transmission|signal transduction|striated muscle contraction	cell junction|cytoplasm|synapse	calcium ion binding|protein binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	32484897	32484897	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32484897delT								DTNA (13089 upstream) : MAPRE2 (71995 downstream)																																			---	---	---	---
MAPRE2	10982	broad.mit.edu	37	18	32710115	32710115	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32710115delG	uc002kyg.2	+						MAPRE2_uc010xcb.1_Intron|MAPRE2_uc010xcc.1_Intron|MAPRE2_uc002kyh.2_Intron|MAPRE2_uc010xcd.1_Intron	NM_014268	NP_055083			microtubule-associated protein, RP/EB family,						cell division|cell proliferation|mitosis|signal transduction	cytoplasm|microtubule	microtubule binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	32729172	32729174	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:32729172_32729174delTTT								MAPRE2 (6795 upstream) : ZNF397 (91824 downstream)																																			---	---	---	---
INO80C	125476	broad.mit.edu	37	18	33058374	33058374	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33058374delT	uc002kyy.3	-						INO80C_uc002kyw.1_Intron|INO80C_uc002kyx.3_Intron|INO80C_uc010dmt.2_Intron	NM_194281	NP_919257			Ies6-similar protein isoform 2						DNA recombination|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	Ino80 complex|MLL1 complex					0																		---	---	---	---
GALNT1	2589	broad.mit.edu	37	18	33234733	33234733	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33234733delA	uc010dmu.2	+	2	160	c.107delA	c.(106-108)GAAfs	p.E36fs	GALNT1_uc002kyz.3_5'UTR|GALNT1_uc002kza.2_Frame_Shift_Del_p.E36fs|GALNT1_uc002kzb.2_Frame_Shift_Del_p.E36fs	NM_020474	NP_065207	Q10472	GALT1_HUMAN	polypeptide N-acetylgalactosaminyltransferase 1	36	Lumenal (Potential).				protein O-linked glycosylation via serine|protein O-linked glycosylation via threonine	extracellular region|Golgi cisterna membrane|integral to membrane|perinuclear region of cytoplasm	manganese ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	33488232	33488232	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33488232delT								MIR187 (3343 upstream) : C18orf21 (64356 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	33659744	33659744	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33659744delC								RPRD1A (12371 upstream) : SLC39A6 (28751 downstream)																																			---	---	---	---
ELP2	55250	broad.mit.edu	37	18	33723066	33723066	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33723066delT	uc002kzk.1	+						ELP2_uc010xcg.1_Intron|ELP2_uc002kzl.1_Intron|ELP2_uc002kzm.1_Intron|ELP2_uc010xch.1_Intron|ELP2_uc002kzn.1_Intron|ELP2_uc002kzo.1_Intron	NM_018255	NP_060725			elongator protein 2						regulation of transcription from RNA polymerase II promoter	Golgi apparatus|transcription elongation factor complex				breast(2)|ovary(1)|skin(1)	4																		---	---	---	---
MOCOS	55034	broad.mit.edu	37	18	33789140	33789140	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33789140delT	uc002kzq.3	+							NM_017947	NP_060417			molybdenum cofactor sulfurase						Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cytosol	lyase activity|Mo-molybdopterin cofactor sulfurase activity|molybdenum ion binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)													---	---	---	---
FHOD3	80206	broad.mit.edu	37	18	34205516	34205516	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34205516delC	uc002kzt.1	+	10	1097	c.1000delC	c.(1000-1002)CCCfs	p.P334fs	FHOD3_uc002kzr.1_Frame_Shift_Del_p.P334fs|FHOD3_uc002kzs.1_Frame_Shift_Del_p.P334fs|FHOD3_uc002kzu.1_Frame_Shift_Del_p.P159fs|FHOD3_uc010dmz.1_Frame_Shift_Del_p.P87fs	NM_025135	NP_079411	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	334	GBD/FH3.				actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding			skin(3)|large_intestine(2)|breast(2)|ovary(1)	8		all_epithelial(2;0.0181)|Colorectal(2;0.0195)																---	---	---	---
FHOD3	80206	broad.mit.edu	37	18	34329909	34329910	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34329909_34329910delTT	uc002kzt.1	+						FHOD3_uc002kzs.1_Intron|FHOD3_uc010dmz.1_Intron|FHOD3_uc010dnb.1_Intron	NM_025135	NP_079411			formin homology 2 domain containing 3						actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding			skin(3)|large_intestine(2)|breast(2)|ovary(1)	8		all_epithelial(2;0.0181)|Colorectal(2;0.0195)																---	---	---	---
C18orf10	25941	broad.mit.edu	37	18	34385648	34385648	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34385648delA	uc002kzw.1	-						C18orf10_uc002kzv.1_Intron|C18orf10_uc010xci.1_Intron|C18orf10_uc002kzx.1_Intron|C18orf10_uc002kzy.3_Intron	NM_015476	NP_056291			tubulin polyglutamylase complex subunit 2							cytoplasm|microtubule				skin(1)	1																		---	---	---	---
C18orf10	25941	broad.mit.edu	37	18	34390315	34390315	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34390315delT	uc002kzw.1	-						C18orf10_uc002kzv.1_Intron|C18orf10_uc010xci.1_Intron|C18orf10_uc002kzx.1_Intron|C18orf10_uc002kzy.3_Intron	NM_015476	NP_056291			tubulin polyglutamylase complex subunit 2							cytoplasm|microtubule				skin(1)	1																		---	---	---	---
CELF4	56853	broad.mit.edu	37	18	34837049	34837049	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34837049delA	uc002lae.2	-						CELF4_uc010dnd.1_Intron|CELF4_uc002lag.2_Intron|CELF4_uc002laf.2_Intron	NM_020180	NP_064565			bruno-like 4, RNA binding protein isoform 1						embryo development|germ cell development|regulation of alternative nuclear mRNA splicing, via spliceosome	cytoplasm|nucleus	BRE binding|nucleotide binding|translation repressor activity, nucleic acid binding			ovary(2)	2																		---	---	---	---
CELF4	56853	broad.mit.edu	37	18	34915446	34915447	+	Intron	DEL	GT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34915446_34915447delGT	uc002lae.2	-						CELF4_uc010dnd.1_Intron|CELF4_uc002lag.2_Intron|CELF4_uc002laf.2_Intron|CELF4_uc002lai.2_Intron	NM_020180	NP_064565			bruno-like 4, RNA binding protein isoform 1						embryo development|germ cell development|regulation of alternative nuclear mRNA splicing, via spliceosome	cytoplasm|nucleus	BRE binding|nucleotide binding|translation repressor activity, nucleic acid binding			ovary(2)	2																OREG0024928	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	18	35637922	35637922	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35637922delG								CELF4 (491922 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	35669392	35669392	+	IGR	DEL	A	-	-	rs35678779		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:35669392delA								CELF4 (523392 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	36112789	36112790	+	IGR	INS	-	A	A	rs144888933	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:36112789_36112790insA								CELF4 (966789 upstream) : LOC647946 (674098 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	36417139	36417140	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:36417139_36417140insA								None (None upstream) : LOC647946 (369748 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	36460620	36460620	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:36460620delA								None (None upstream) : LOC647946 (326268 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	36624444	36624444	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:36624444delT								None (None upstream) : LOC647946 (162444 downstream)																																			---	---	---	---
LOC647946	647946	broad.mit.edu	37	18	37271249	37271249	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37271249delT	uc010xcj.1	-						LOC647946_uc002lal.1_Intron	NR_024391				Homo sapiens cDNA FLJ33284 fis, clone ASTRO2009458.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	37476943	37476943	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37476943delA								LOC647946 (96661 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	37603089	37603089	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37603089delT								LOC647946 (222807 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	38450981	38450982	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:38450981_38450982delTT								None (None upstream) : KC6 (609256 downstream)																																			---	---	---	---
KC6	641516	broad.mit.edu	37	18	39085444	39085444	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39085444delT	uc002lan.2	-							NR_002838				Homo sapiens KC6 mRNA, complete sequence.												0																		---	---	---	---
PIK3C3	5289	broad.mit.edu	37	18	39629473	39629473	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39629473delT	uc002lap.2	+						PIK3C3_uc010xcl.1_Intron|PIK3C3_uc002laq.2_Intron|PIK3C3_uc002lar.1_Intron	NM_002647	NP_002638			catalytic phosphatidylinositol 3-kinase 3						cell cycle|cytokinesis|fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway	midbody|phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|protein binding			lung(8)|ovary(1)|breast(1)	10															TSP Lung(28;0.18)			---	---	---	---
Unknown	0	broad.mit.edu	37	18	40001158	40001158	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:40001158delT	uc002las.1	+						uc002lat.2_Intron|uc002lau.2_Intron					Homo sapiens hypothetical gene supported by BC011527; BC021928; BC011527; BC021928, mRNA (cDNA clone IMAGE:3872963), with apparent retained intron.																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	40005325	40005326	+	Intron	DEL	CT	-	-	rs112513135		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:40005325_40005326delCT	uc002las.1	+						uc002lat.2_Intron|uc002lau.2_Intron					Homo sapiens hypothetical gene supported by BC011527; BC021928; BC011527; BC021928, mRNA (cDNA clone IMAGE:3872963), with apparent retained intron.																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	40053932	40053932	+	Intron	DEL	A	-	-	rs59413587	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:40053932delA	uc002las.1	+						uc002lat.2_Intron|uc002lau.2_Intron					Homo sapiens hypothetical gene supported by BC011527; BC021928; BC011527; BC021928, mRNA (cDNA clone IMAGE:3872963), with apparent retained intron.																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	40223907	40223907	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:40223907delA	uc002lau.2	+											Homo sapiens hypothetical gene supported by BC011527; BC021928; BC011527; BC021928, mRNA (cDNA clone IMAGE:3872963), with apparent retained intron.																														---	---	---	---
RIT2	6014	broad.mit.edu	37	18	40488102	40488102	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:40488102delA	uc002lav.2	-						RIT2_uc010dnf.2_Intron	NM_002930	NP_002921			Ras-like without CAAX 2						nerve growth factor receptor signaling pathway|small GTPase mediated signal transduction|synaptic transmission	intracellular|plasma membrane	calmodulin binding|GTP binding|GTPase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	41443416	41443416	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:41443416delT								SYT4 (585801 upstream) : SETBP1 (816722 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	41503906	41503906	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:41503906delT								SYT4 (646291 upstream) : SETBP1 (756232 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	41677228	41677228	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:41677228delT								SYT4 (819613 upstream) : SETBP1 (582910 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	41795587	41795588	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:41795587_41795588delTG								SYT4 (937972 upstream) : SETBP1 (464550 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	42062363	42062363	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42062363delA	uc002lax.3	-											Homo sapiens cDNA clone IMAGE:5265929.																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	42200790	42200790	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42200790delA								None (None upstream) : SETBP1 (59348 downstream)																																			---	---	---	---
SLC14A2	8170	broad.mit.edu	37	18	43187044	43187044	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43187044delT	uc010dnj.2	+						SLC14A2_uc002lbb.2_Intron	NM_007163	NP_009094			solute carrier family 14 (urea transporter),							apical plasma membrane|integral to membrane|membrane fraction	protein binding|urea transmembrane transporter activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
SLC14A2	8170	broad.mit.edu	37	18	43238546	43238547	+	Intron	DEL	AA	-	-	rs36007266		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43238546_43238547delAA	uc010dnj.2	+						SLC14A2_uc002lbe.2_Intron	NM_007163	NP_009094			solute carrier family 14 (urea transporter),							apical plasma membrane|integral to membrane|membrane fraction	protein binding|urea transmembrane transporter activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
SLC14A1	6563	broad.mit.edu	37	18	43310598	43310598	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43310598delT	uc010xcn.1	+						SLC14A1_uc010dnk.2_Intron|SLC14A1_uc002lbf.3_Intron|SLC14A1_uc002lbg.3_Intron|SLC14A1_uc010xco.1_Intron|SLC14A1_uc002lbh.3_Intron|SLC14A1_uc002lbi.3_Intron|SLC14A1_uc002lbj.3_Intron|SLC14A1_uc002lbk.3_Intron	NM_001146036	NP_001139508			solute carrier family 14 (urea transporter),							integral to plasma membrane	urea transmembrane transporter activity			central_nervous_system(1)|pancreas(1)	2																		---	---	---	---
SIGLEC15	284266	broad.mit.edu	37	18	43422408	43422409	+	3'UTR	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43422408_43422409delGA	uc002lbl.1	+	6					SIGLEC15_uc010xcp.1_RNA	NM_213602	NP_998767			sialic acid binding Ig-like lectin 15 precursor							integral to membrane					0																		---	---	---	---
KIAA1632	57724	broad.mit.edu	37	18	43456752	43456753	+	Intron	DEL	TT	-	-	rs72383953		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43456752_43456753delTT	uc002lbm.2	-						KIAA1632_uc010xcq.1_Intron|KIAA1632_uc010xcr.1_Intron|KIAA1632_uc010xcs.1_Intron|KIAA1632_uc002lbn.2_Intron	NM_020964	NP_066015			hypothetical protein LOC57724						autophagy						0																		---	---	---	---
KIAA1632	57724	broad.mit.edu	37	18	43476410	43476410	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43476410delT	uc002lbm.2	-						KIAA1632_uc010xcq.1_Intron|KIAA1632_uc010xcr.1_Intron|KIAA1632_uc010xcs.1_Intron|KIAA1632_uc002lbn.2_Intron	NM_020964	NP_066015			hypothetical protein LOC57724						autophagy						0																		---	---	---	---
KIAA1632	57724	broad.mit.edu	37	18	43529365	43529365	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43529365delT	uc002lbm.2	-						KIAA1632_uc002lbo.1_Intron	NM_020964	NP_066015			hypothetical protein LOC57724						autophagy						0																		---	---	---	---
PSTPIP2	9050	broad.mit.edu	37	18	43568402	43568402	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43568402delA	uc002lbp.3	-						PSTPIP2_uc002lbq.3_Intron	NM_024430	NP_077748			proline-serine-threonine phosphatase interacting							membrane				ovary(1)	1																		---	---	---	---
HAUS1	115106	broad.mit.edu	37	18	43705697	43705697	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43705697delT	uc002lbu.2	+						HAUS1_uc002lbv.2_Intron	NM_138443	NP_612452			coiled-coil domain containing 5						cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|spindle pole				ovary(1)	1																		---	---	---	---
C18orf25	147339	broad.mit.edu	37	18	43760670	43760670	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43760670delA	uc002lbw.2	+						C18orf25_uc002lbx.2_Intron	NM_145055	NP_659492			ARKadia-like 1 isoform a											central_nervous_system(2)	2																		---	---	---	---
C18orf25	147339	broad.mit.edu	37	18	43780750	43780750	+	Intron	DEL	T	-	-	rs72249968		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43780750delT	uc002lbw.2	+						C18orf25_uc002lbx.2_Intron	NM_145055	NP_659492			ARKadia-like 1 isoform a											central_nervous_system(2)	2																		---	---	---	---
PIAS2	9063	broad.mit.edu	37	18	44498165	44498165	+	5'Flank	DEL	C	-	-	rs79609991	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44498165delC	uc002lck.2	-						PIAS2_uc010dnp.2_5'Flank|PIAS2_uc002lcl.2_5'Flank|PIAS2_uc010xda.1_5'Flank|PIAS2_uc002lcm.2_5'Flank|PIAS2_uc002lcn.1_Intron|KATNAL2_uc010dnq.1_Intron	NM_004671	NP_004662			protein inhibitor of activated STAT X isoform						androgen receptor signaling pathway|negative regulation of androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck|PML body	androgen receptor binding|DNA binding|protein binding|SUMO ligase activity|transcription coactivator activity|zinc ion binding			ovary(2)|breast(1)|skin(1)	4																		---	---	---	---
KATNAL2	83473	broad.mit.edu	37	18	44531468	44531468	+	Intron	DEL	T	-	-	rs75960197		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44531468delT	uc002lco.2	+						KATNAL2_uc010dnq.1_Intron|KATNAL2_uc002lcp.3_Intron	NM_031303	NP_112593			katanin p60 subunit A-like 2							cytoplasm|microtubule	ATP binding|microtubule-severing ATPase activity			ovary(1)|skin(1)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	44733055	44733055	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44733055delC								IER3IP1 (30310 upstream) : SMAD2 (626412 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	45087950	45087950	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45087950delC	uc002lcx.2	+											Homo sapiens, clone IMAGE:5538207, mRNA.																														---	---	---	---
SMAD2	4087	broad.mit.edu	37	18	45389925	45389925	+	Intron	DEL	T	-	-	rs146121005		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45389925delT	uc002lcy.2	-						SMAD2_uc002lcz.2_Intron|SMAD2_uc010xdc.1_Intron|SMAD2_uc010xdd.1_Intron	NM_005901	NP_005892			Sma- and Mad-related protein 2 isoform 1						anterior/posterior pattern formation|cell fate commitment|common-partner SMAD protein phosphorylation|intracellular signal transduction|mesoderm formation|negative regulation of transcription, DNA-dependent|palate development|paraxial mesoderm morphogenesis|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription from RNA polymerase II promoter|primary miRNA processing|regulation of binding|regulation of transforming growth factor beta receptor signaling pathway|response to cholesterol|SMAD protein complex assembly|transforming growth factor beta receptor signaling pathway|zygotic specification of dorsal/ventral axis	activin responsive factor complex|cytosol	activating transcription factor binding|co-SMAD binding|double-stranded DNA binding|I-SMAD binding|R-SMAD binding|sequence-specific DNA binding transcription factor activity|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity|type I transforming growth factor beta receptor binding|ubiquitin protein ligase binding			large_intestine(3)|lung(1)|central_nervous_system(1)	5																		---	---	---	---
SMAD2	4087	broad.mit.edu	37	18	45443440	45443440	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45443440delG	uc002lcy.2	-						SMAD2_uc002lcz.2_Intron|SMAD2_uc010xdc.1_Intron|SMAD2_uc010xdd.1_Intron	NM_005901	NP_005892			Sma- and Mad-related protein 2 isoform 1						anterior/posterior pattern formation|cell fate commitment|common-partner SMAD protein phosphorylation|intracellular signal transduction|mesoderm formation|negative regulation of transcription, DNA-dependent|palate development|paraxial mesoderm morphogenesis|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription from RNA polymerase II promoter|primary miRNA processing|regulation of binding|regulation of transforming growth factor beta receptor signaling pathway|response to cholesterol|SMAD protein complex assembly|transforming growth factor beta receptor signaling pathway|zygotic specification of dorsal/ventral axis	activin responsive factor complex|cytosol	activating transcription factor binding|co-SMAD binding|double-stranded DNA binding|I-SMAD binding|R-SMAD binding|sequence-specific DNA binding transcription factor activity|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity|type I transforming growth factor beta receptor binding|ubiquitin protein ligase binding			large_intestine(3)|lung(1)|central_nervous_system(1)	5																		---	---	---	---
ZBTB7C	201501	broad.mit.edu	37	18	45650241	45650241	+	Intron	DEL	T	-	-	rs74421474		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45650241delT	uc010dnv.2	-						ZBTB7C_uc002ldb.2_Intron|ZBTB7C_uc010dnu.2_Intron|ZBTB7C_uc010dnw.2_Intron|ZBTB7C_uc010dnx.1_Intron|ZBTB7C_uc010dny.1_Intron|ZBTB7C_uc010dnz.1_Intron|ZBTB7C_uc010dob.1_Intron|ZBTB7C_uc010doc.1_Intron|ZBTB7C_uc010dod.1_Intron|ZBTB7C_uc010doe.1_Intron|ZBTB7C_uc010dof.1_Intron|ZBTB7C_uc010dog.1_Intron|ZBTB7C_uc010doh.1_Intron|ZBTB7C_uc010doi.1_Intron|ZBTB7C_uc010doj.1_Intron|ZBTB7C_uc010dok.1_Intron|ZBTB7C_uc010dol.1_Intron|ZBTB7C_uc010doa.1_Intron|ZBTB7C_uc010don.1_Intron|ZBTB7C_uc010doo.1_Intron|ZBTB7C_uc010dop.1_Intron|ZBTB7C_uc010doq.1_Intron|ZBTB7C_uc010dor.1_Intron|ZBTB7C_uc010dos.1_Intron|ZBTB7C_uc010dot.1_Intron|ZBTB7C_uc010dou.1_Intron|ZBTB7C_uc010dom.1_Intron	NM_001039360	NP_001034449			zinc finger and BTB domain containing 7C							intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1																		---	---	---	---
KIAA0427	9811	broad.mit.edu	37	18	46105874	46105874	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46105874delT	uc002ldc.2	+						KIAA0427_uc002ldd.2_Intron	NM_014772	NP_055587			hypothetical protein LOC9811 isoform 1						nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translational initiation	perinuclear region of cytoplasm	protein binding				0																		---	---	---	---
KIAA0427	9811	broad.mit.edu	37	18	46261918	46261920	+	Intron	DEL	AGA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46261918_46261920delAGA	uc002ldc.2	+						KIAA0427_uc002ldd.2_Intron	NM_014772	NP_055587			hypothetical protein LOC9811 isoform 1						nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translational initiation	perinuclear region of cytoplasm	protein binding				0																		---	---	---	---
KIAA0427	9811	broad.mit.edu	37	18	46384841	46384842	+	Intron	INS	-	CACA	CACA	rs141502397	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46384841_46384842insCACA	uc002ldc.2	+						KIAA0427_uc002ldd.2_Intron|KIAA0427_uc002lde.3_Intron	NM_014772	NP_055587			hypothetical protein LOC9811 isoform 1						nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translational initiation	perinuclear region of cytoplasm	protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	46422122	46422122	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46422122delT								KIAA0427 (32544 upstream) : SMAD7 (24102 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	46544029	46544029	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46544029delT								SMAD7 (66948 upstream) : DYM (26143 downstream)																																			---	---	---	---
DYM	54808	broad.mit.edu	37	18	46808324	46808324	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46808324delA	uc002ldi.1	-						DYM_uc010xdf.1_Intron|DYM_uc002ldj.3_Intron	NM_017653	NP_060123			dymeclin							Golgi apparatus					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	47147669	47147669	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47147669delA								LIPG (28393 upstream) : ACAA2 (162206 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	47202345	47202345	+	IGR	DEL	A	-	-	rs35295951		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47202345delA								LIPG (83069 upstream) : ACAA2 (107530 downstream)																																			---	---	---	---
MYO5B	4645	broad.mit.edu	37	18	47643215	47643216	+	Intron	DEL	AA	-	-	rs35037356		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47643215_47643216delAA	uc002leb.2	-							NM_001080467	NP_001073936			myosin VB						protein transport	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|skin(2)|central_nervous_system(1)	5				READ - Rectum adenocarcinoma(32;0.103)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	47834403	47834403	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47834403delA								CXXC1 (19711 upstream) : SKA1 (66989 downstream)																																			---	---	---	---
MAPK4	5596	broad.mit.edu	37	18	48207445	48207445	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48207445delT	uc002lev.2	+						MAPK4_uc010xdm.1_Intron|MAPK4_uc010doz.2_Intron	NM_002747	NP_002738			mitogen-activated protein kinase 4						cell cycle		ATP binding|MAP kinase activity			lung(4)|skin(2)	6		Colorectal(6;0.0297)		Colorectal(21;0.156)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	48365292	48365292	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48365292delA								MRO (13538 upstream) : ME2 (40143 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	48383722	48383722	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48383722delC								MRO (31968 upstream) : ME2 (21713 downstream)																																			---	---	---	---
ME2	4200	broad.mit.edu	37	18	48439041	48439041	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48439041delT	uc002ley.2	+						ME2_uc010dpd.2_Intron	NM_002396	NP_002387			malic enzyme 2, NAD(+)-dependent, mitochondrial						malate metabolic process	mitochondrial matrix	electron carrier activity|malate dehydrogenase (decarboxylating) activity|malate dehydrogenase (oxaloacetate-decarboxylating) activity|metal ion binding|NAD binding				0		Colorectal(6;0.0273)|all_epithelial(6;0.118)		Colorectal(21;0.0313)|READ - Rectum adenocarcinoma(32;0.105)|STAD - Stomach adenocarcinoma(97;0.184)	NADH(DB00157)													---	---	---	---
ME2	4200	broad.mit.edu	37	18	48458053	48458054	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48458053_48458054delTT	uc002ley.2	+						ME2_uc010dpd.2_Intron	NM_002396	NP_002387			malic enzyme 2, NAD(+)-dependent, mitochondrial						malate metabolic process	mitochondrial matrix	electron carrier activity|malate dehydrogenase (decarboxylating) activity|malate dehydrogenase (oxaloacetate-decarboxylating) activity|metal ion binding|NAD binding				0		Colorectal(6;0.0273)|all_epithelial(6;0.118)		Colorectal(21;0.0313)|READ - Rectum adenocarcinoma(32;0.105)|STAD - Stomach adenocarcinoma(97;0.184)	NADH(DB00157)													---	---	---	---
Unknown	0	broad.mit.edu	37	18	48742427	48742427	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48742427delT								MEX3C (18737 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	49373784	49373785	+	IGR	DEL	TG	-	-	rs35041360		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:49373784_49373785delTG								MEX3C (650094 upstream) : DCC (492786 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	49677234	49677234	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:49677234delT								MEX3C (953544 upstream) : DCC (189337 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	49769501	49769501	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:49769501delT								None (None upstream) : DCC (97070 downstream)																																			---	---	---	---
DCC	1630	broad.mit.edu	37	18	50628198	50628203	+	Intron	DEL	TTTGTG	-	-	rs66953859	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50628198_50628203delTTTGTG	uc002lfe.1	+						DCC_uc010xdr.1_Intron|DCC_uc010dpf.1_Intron	NM_005215	NP_005206			netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)														---	---	---	---
DCC	1630	broad.mit.edu	37	18	50707700	50707700	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50707700delT	uc002lfe.1	+						DCC_uc010xdr.1_Intron|DCC_uc010dpf.1_Intron	NM_005215	NP_005206			netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)														---	---	---	---
DCC	1630	broad.mit.edu	37	18	50820417	50820417	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50820417delT	uc002lfe.1	+						DCC_uc010xdr.1_Intron|DCC_uc010dpf.1_Intron	NM_005215	NP_005206			netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)														---	---	---	---
DCC	1630	broad.mit.edu	37	18	50854868	50854870	+	Intron	DEL	AAG	-	-	rs35156113		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50854868_50854870delAAG	uc002lfe.1	+						DCC_uc010xdr.1_Intron|DCC_uc010dpf.1_Intron	NM_005215	NP_005206			netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	51387848	51387849	+	IGR	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51387848_51387849insG								DCC (330066 upstream) : MBD2 (292726 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	51447358	51447359	+	IGR	DEL	GT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51447358_51447359delGT								DCC (389576 upstream) : MBD2 (233216 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	51827710	51827710	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:51827710delA								POLI (3108 upstream) : STARD6 (23353 downstream)																																			---	---	---	---
RAB27B	5874	broad.mit.edu	37	18	52551371	52551371	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:52551371delA	uc002lfr.2	+							NM_004163	NP_004154			RAB27B, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	Golgi apparatus|plasma membrane	GTP binding|GTPase activity				0				Colorectal(16;0.0273)|READ - Rectum adenocarcinoma(59;0.219)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	52785080	52785081	+	Intron	DEL	TT	-	-	rs4363927	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:52785080_52785081delTT	uc002lfu.1	-											Homo sapiens cDNA FLJ36621 fis, clone TRACH2016651.																														---	---	---	---
TCF4	6925	broad.mit.edu	37	18	53131956	53131956	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53131956delT	uc002lfz.2	-						TCF4_uc002lfy.2_Intron|TCF4_uc010xdx.1_Intron|TCF4_uc010dph.1_Intron|TCF4_uc010xdy.1_Intron|TCF4_uc002lga.2_Intron|TCF4_uc010dpi.2_Intron|TCF4_uc002lgc.3_5'Flank	NM_003199	NP_003190			transcription factor 4 isoform b						positive regulation of neuron differentiation|protein-DNA complex assembly|transcription initiation from RNA polymerase II promoter	transcription factor complex	E-box binding|protein C-terminus binding|protein heterodimerization activity|RNA polymerase II core promoter proximal region sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|sequence-specific DNA binding RNA polymerase recruiting transcription factor activity|TFIIB-class binding transcription factor activity|TFIIB-class transcription factor binding			ovary(1)|lung(1)	2				Colorectal(16;0.00108)|READ - Rectum adenocarcinoma(59;0.0649)|COAD - Colon adenocarcinoma(17;0.0718)														---	---	---	---
TCF4	6925	broad.mit.edu	37	18	53252311	53252311	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53252311delA	uc002lfz.2	-						TCF4_uc010xdx.1_Intron|TCF4_uc010dph.1_Intron|TCF4_uc010xdy.1_Intron|TCF4_uc002lga.2_Intron|TCF4_uc010dpi.2_Intron	NM_003199	NP_003190			transcription factor 4 isoform b						positive regulation of neuron differentiation|protein-DNA complex assembly|transcription initiation from RNA polymerase II promoter	transcription factor complex	E-box binding|protein C-terminus binding|protein heterodimerization activity|RNA polymerase II core promoter proximal region sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|sequence-specific DNA binding RNA polymerase recruiting transcription factor activity|TFIIB-class binding transcription factor activity|TFIIB-class transcription factor binding			ovary(1)|lung(1)	2				Colorectal(16;0.00108)|READ - Rectum adenocarcinoma(59;0.0649)|COAD - Colon adenocarcinoma(17;0.0718)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	54088400	54088401	+	IGR	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54088400_54088401insC								TCF4 (785215 upstream) : TXNL1 (181654 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	54150405	54150405	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54150405delA								TCF4 (847220 upstream) : TXNL1 (119650 downstream)																																			---	---	---	---
WDR7	23335	broad.mit.edu	37	18	54374658	54374659	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:54374658_54374659delTT	uc002lgk.1	+						WDR7_uc010dpk.1_Intron|WDR7_uc002lgl.1_Intron	NM_015285	NP_056100			rabconnectin-3 beta isoform 1											ovary(2)|skin(1)	3				Lung(128;0.0238)|Colorectal(16;0.0296)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	55686289	55686289	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55686289delC								ATP8B1 (287250 upstream) : NEDD4L (25330 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	56086847	56086848	+	IGR	INS	-	ATGG	ATGG	rs113192967		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56086847_56086848insATGG								NEDD4L (18075 upstream) : MIR122 (31458 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	56508725	56508726	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56508725_56508726delTT								MALT1 (91355 upstream) : ZNF532 (21335 downstream)																																			---	---	---	---
ZNF532	55205	broad.mit.edu	37	18	56650832	56650832	+	Intron	DEL	C	-	-	rs112612807		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56650832delC	uc002lho.2	+						ZNF532_uc002lhp.2_Intron|ZNF532_uc010xeg.1_Intron|ZNF532_uc002lhr.2_Intron|ZNF532_uc002lhs.2_Intron|ZNF532_uc010xeh.1_Intron	NM_018181	NP_060651			zinc finger protein 532						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	57094104	57094104	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57094104delA								LMAN1 (67596 upstream) : CCBE1 (7045 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	57526799	57526800	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:57526799_57526800delAA								CCBE1 (162155 upstream) : PMAIP1 (40392 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	58703787	58703787	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58703787delA								MC4R (663786 upstream) : CDH20 (297201 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	58859352	58859353	+	IGR	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:58859352_58859353insC								MC4R (819351 upstream) : CDH20 (141635 downstream)																																			---	---	---	---
CDH20	28316	broad.mit.edu	37	18	59158388	59158388	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59158388delT	uc010dps.1	+						CDH20_uc002lif.2_Intron	NM_031891	NP_114097			cadherin 20, type 2 preproprotein						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(3)|ovary(1)|pancreas(1)	5		Colorectal(73;0.186)																---	---	---	---
KIAA1468	57614	broad.mit.edu	37	18	59950871	59950871	+	Intron	DEL	A	-	-	rs9320007	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59950871delA	uc002lil.2	+						KIAA1468_uc010xel.1_Intron|KIAA1468_uc002lim.2_Intron	NM_020854	NP_065905			hypothetical protein LOC57614								binding			ovary(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)	6		Colorectal(73;0.186)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	59983691	59983691	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59983691delA								KIAA1468 (9337 upstream) : TNFRSF11A (8857 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	60362542	60362542	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60362542delC								ZCCHC2 (108580 upstream) : PHLPP1 (20192 downstream)																																			---	---	---	---
PHLPP1	23239	broad.mit.edu	37	18	60476934	60476935	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60476934_60476935delAA	uc002lis.2	+							NM_194449	NP_919431			PH domain and leucine rich repeat protein						apoptosis|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling	cytosol|membrane|nucleus	metal ion binding|protein serine/threonine phosphatase activity				0																		---	---	---	---
PHLPP1	23239	broad.mit.edu	37	18	60569902	60569902	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60569902delT	uc002lis.2	+							NM_194449	NP_919431			PH domain and leucine rich repeat protein						apoptosis|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling	cytosol|membrane|nucleus	metal ion binding|protein serine/threonine phosphatase activity				0																		---	---	---	---
BCL2	596	broad.mit.edu	37	18	60868385	60868386	+	Intron	DEL	AT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60868385_60868386delAT	uc002lit.1	-						BCL2_uc002liu.1_Intron	NM_000633	NP_000624			B-cell lymphoma protein 2 alpha isoform						activation of pro-apoptotic gene products|anti-apoptosis|apoptosis in response to endoplasmic reticulum stress|B cell proliferation|B cell receptor signaling pathway|defense response to virus|female pregnancy|humoral immune response|induction of apoptosis by intracellular signals|negative regulation of cellular pH reduction|negative regulation of mitochondrial depolarization|negative regulation of neuron apoptosis|neuron apoptosis|positive regulation of B cell proliferation|positive regulation of cell growth|protein polyubiquitination|regulation of mitochondrial membrane permeability|regulation of mitochondrial membrane potential|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|regulation of transmembrane transporter activity|release of cytochrome c from mitochondria|response to cytokine stimulus|response to DNA damage stimulus|response to drug|response to iron ion|response to nicotine|response to toxin	endoplasmic reticulum membrane|mitochondrial outer membrane|nuclear membrane|pore complex	BH3 domain binding|channel activity|protease binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|ubiquitin protein ligase binding			central_nervous_system(1)	1		all_hematologic(56;1.18e-20)|Prostate(75;0.0872)		Lung(128;0.0234)|READ - Rectum adenocarcinoma(59;0.0935)	Docetaxel(DB01248)|Fludarabine(DB01073)|Melatonin(DB01065)|Paclitaxel(DB01229)|Rasagiline(DB01367)			T	IGH@	NHL|CLL								---	---	---	---
BCL2	596	broad.mit.edu	37	18	60885975	60885975	+	Intron	DEL	T	-	-	rs113355863	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60885975delT	uc002lit.1	-						BCL2_uc002liu.1_Intron	NM_000633	NP_000624			B-cell lymphoma protein 2 alpha isoform						activation of pro-apoptotic gene products|anti-apoptosis|apoptosis in response to endoplasmic reticulum stress|B cell proliferation|B cell receptor signaling pathway|defense response to virus|female pregnancy|humoral immune response|induction of apoptosis by intracellular signals|negative regulation of cellular pH reduction|negative regulation of mitochondrial depolarization|negative regulation of neuron apoptosis|neuron apoptosis|positive regulation of B cell proliferation|positive regulation of cell growth|protein polyubiquitination|regulation of mitochondrial membrane permeability|regulation of mitochondrial membrane potential|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|regulation of transmembrane transporter activity|release of cytochrome c from mitochondria|response to cytokine stimulus|response to DNA damage stimulus|response to drug|response to iron ion|response to nicotine|response to toxin	endoplasmic reticulum membrane|mitochondrial outer membrane|nuclear membrane|pore complex	BH3 domain binding|channel activity|protease binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|ubiquitin protein ligase binding			central_nervous_system(1)	1		all_hematologic(56;1.18e-20)|Prostate(75;0.0872)		Lung(128;0.0234)|READ - Rectum adenocarcinoma(59;0.0935)	Docetaxel(DB01248)|Fludarabine(DB01073)|Melatonin(DB01065)|Paclitaxel(DB01229)|Rasagiline(DB01367)			T	IGH@	NHL|CLL								---	---	---	---
SERPINB8	5271	broad.mit.edu	37	18	61642346	61642347	+	Intron	INS	-	AC	AC	rs142389462	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61642346_61642347insAC	uc002ljv.2	+						SERPINB8_uc002ljs.1_Intron|SERPINB8_uc002ljt.2_Intron|SERPINB8_uc002lju.2_Intron|SERPINB8_uc010xex.1_Intron	NM_198833	NP_942130			serine (or cysteine) proteinase inhibitor, clade						regulation of proteolysis	cytosol	protein binding|serine-type endopeptidase inhibitor activity			skin(1)	1		Esophageal squamous(42;0.129)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	61783811	61783811	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61783811delT	uc002ljx.2	+						C18orf20_uc002ljw.3_Intron					Homo sapiens hypothetical protein LOC284294, mRNA (cDNA clone IMAGE:4823205).																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	61855334	61855335	+	Intron	DEL	GT	-	-	rs35788959		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61855334_61855335delGT	uc002ljx.2	+											Homo sapiens hypothetical protein LOC284294, mRNA (cDNA clone IMAGE:4823205).																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	62130101	62130101	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62130101delA								C18orf20 (313841 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	62595467	62595467	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62595467delA								C18orf20 (779207 upstream) : CDH7 (822021 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	62831304	62831304	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62831304delA								None (None upstream) : CDH7 (586184 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	62933737	62933737	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62933737delA								None (None upstream) : CDH7 (483751 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	62994789	62994792	+	IGR	DEL	TATG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:62994789_62994792delTATG								None (None upstream) : CDH7 (422696 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	63248354	63248354	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63248354delA								None (None upstream) : CDH7 (169134 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	63327270	63327270	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63327270delT								None (None upstream) : CDH7 (90218 downstream)																																			---	---	---	---
CDH7	1005	broad.mit.edu	37	18	63483429	63483429	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:63483429delT	uc002ljz.2	+						CDH7_uc002lka.2_Intron|CDH7_uc002lkb.2_Intron	NM_033646	NP_387450			cadherin 7, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|pancreas(1)|skin(1)	4		Esophageal squamous(42;0.129)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	64170618	64170619	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:64170618_64170619insA								CDH7 (622444 upstream) : CDH19 (702 downstream)																																			---	---	---	---
CDH19	28513	broad.mit.edu	37	18	64190855	64190855	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:64190855delG	uc002lkc.1	-						CDH19_uc010dql.1_Intron|CDH19_uc010xey.1_Intron	NM_021153	NP_066976			cadherin 19, type 2 preproprotein						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|skin(1)	2		Esophageal squamous(42;0.0132)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	65770759	65770759	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:65770759delA								DSEL (586792 upstream) : TMX3 (570168 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	66147007	66147010	+	IGR	DEL	TTTT	-	-	rs148284600		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66147007_66147010delTTTT								DSEL (963040 upstream) : TMX3 (193917 downstream)																																			---	---	---	---
CCDC102B	79839	broad.mit.edu	37	18	66503864	66503867	+	Intron	DEL	AAAT	-	-	rs71369199	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:66503864_66503867delAAAT	uc002lkk.2	+						CCDC102B_uc002lki.2_Intron|CCDC102B_uc002lkj.1_Intron	NM_001093729	NP_001087198			coiled-coil domain containing 102B											ovary(1)|lung(1)|skin(1)	3		Esophageal squamous(42;0.0559)|Colorectal(73;0.0604)																---	---	---	---
DOK6	220164	broad.mit.edu	37	18	67264768	67264769	+	Intron	INS	-	C	C	rs146975687	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67264768_67264769insC	uc002lkl.2	+							NM_152721	NP_689934			docking protein 6								insulin receptor binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3		Colorectal(73;0.083)|Esophageal squamous(42;0.131)																---	---	---	---
Unknown	0	broad.mit.edu	37	18	68098399	68098399	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:68098399delG								SOCS6 (100965 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	68164753	68164754	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:68164753_68164754insA								SOCS6 (167319 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	69174241	69174241	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:69174241delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	69332613	69332613	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:69332613delT								None (None upstream) : CBLN2 (871302 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	70287488	70287488	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:70287488delT								CBLN2 (75765 upstream) : NETO1 (122063 downstream)																																			---	---	---	---
NETO1	81832	broad.mit.edu	37	18	70526037	70526037	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:70526037delT	uc002lkw.2	-						NETO1_uc002lkx.1_Intron|NETO1_uc002lky.1_Intron|NETO1_uc002lkz.2_Intron	NM_138966	NP_620416			neuropilin- and tolloid-like protein 1 isoform 3						memory|regulation of long-term neuronal synaptic plasticity|visual learning	cell junction|excitatory synapse|extracellular region|integral to membrane|postsynaptic density|postsynaptic membrane	receptor activity			ovary(2)|skin(2)	4		Esophageal squamous(42;0.129)		READ - Rectum adenocarcinoma(1;0.0487)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	70569094	70569094	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:70569094delA								NETO1 (34284 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	71011068	71011068	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71011068delT	uc002llc.1	+											Homo sapiens cDNA clone IMAGE:4667929, partial cds.																														---	---	---	---
Unknown	0	broad.mit.edu	37	18	72027376	72027376	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72027376delA								CYB5A (68155 upstream) : FAM69C (75588 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	73060109	73060109	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73060109delT								TSHZ1 (58209 upstream) : C18orf62 (61718 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	73087135	73087136	+	IGR	INS	-	CT	CT			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73087135_73087136insCT								TSHZ1 (85235 upstream) : C18orf62 (34691 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	73574340	73574341	+	IGR	DEL	AA	-	-	rs138984721	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73574340_73574341delAA								C18orf62 (434751 upstream) : ZNF516 (497278 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	73701104	73701105	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73701104_73701105delAA								C18orf62 (561515 upstream) : ZNF516 (370514 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	73767896	73767896	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73767896delA								C18orf62 (628307 upstream) : ZNF516 (303723 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	73900766	73900766	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:73900766delA								C18orf62 (761177 upstream) : ZNF516 (170853 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	74282220	74282221	+	IGR	INS	-	G	G	rs4609939		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74282220_74282221insG								LOC284276 (10437 upstream) : ZNF236 (253895 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	74324365	74324366	+	IGR	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74324365_74324366insG								LOC284276 (52582 upstream) : ZNF236 (211750 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	75490586	75490586	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75490586delG								GALR1 (508492 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	75600772	75600772	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:75600772delT								GALR1 (618678 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	76199234	76199235	+	IGR	INS	-	G	G	rs144984091	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76199234_76199235insG								None (None upstream) : SALL3 (541040 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	76377454	76377455	+	IGR	DEL	CA	-	-	rs62098734		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76377454_76377455delCA								None (None upstream) : SALL3 (362820 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	76386792	76386792	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76386792delA								None (None upstream) : SALL3 (353483 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	76659006	76659006	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76659006delG								None (None upstream) : SALL3 (81269 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	76710346	76710347	+	IGR	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76710346_76710347insG								None (None upstream) : SALL3 (29928 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	18	76785814	76785814	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76785814delA								SALL3 (27623 upstream) : ATP9B (43583 downstream)																																			---	---	---	---
ATP9B	374868	broad.mit.edu	37	18	76960564	76960564	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:76960564delA	uc002lmx.2	+						ATP9B_uc002lmv.1_Intron|ATP9B_uc002lmw.1_Intron|ATP9B_uc002lmy.1_Intron|ATP9B_uc002lmz.1_Intron	NM_198531	NP_940933			ATPase, class II, type 9B						ATP biosynthetic process	integral to membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)	3		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)														---	---	---	---
NFATC1	4772	broad.mit.edu	37	18	77169333	77169336	+	Intron	DEL	CATC	-	-	rs114755141		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77169333_77169336delCATC	uc010xfg.1	+						NFATC1_uc002lnc.1_Intron|NFATC1_uc010xff.1_Intron|NFATC1_uc002lnd.2_Intron|NFATC1_uc002lne.2_Intron|NFATC1_uc010xfh.1_Intron|NFATC1_uc010xfi.1_Intron|NFATC1_uc010xfj.1_Intron|NFATC1_uc002lnf.2_Intron|NFATC1_uc002lng.2_Intron|NFATC1_uc010xfk.1_Intron	NM_006162	NP_006153			nuclear factor of activated T-cells, cytosolic						intracellular signal transduction|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleus	FK506 binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			large_intestine(1)|ovary(1)	2		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;3.73e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0257)														---	---	---	---
NFATC1	4772	broad.mit.edu	37	18	77246179	77246180	+	Intron	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77246179_77246180insC	uc010xfg.1	+						NFATC1_uc002lnd.2_Intron|NFATC1_uc002lne.2_Intron|NFATC1_uc010xfh.1_Intron|NFATC1_uc010xfj.1_Intron|NFATC1_uc002lnf.2_Intron|NFATC1_uc002lng.2_Intron|NFATC1_uc010xfk.1_Intron	NM_006162	NP_006153			nuclear factor of activated T-cells, cytosolic						intracellular signal transduction|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleus	FK506 binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			large_intestine(1)|ovary(1)	2		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;3.73e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0257)														---	---	---	---
Unknown	0	broad.mit.edu	37	18	77426319	77426319	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77426319delA								NFATC1 (136997 upstream) : CTDP1 (13482 downstream)																																			---	---	---	---
C18orf22	79863	broad.mit.edu	37	18	77796872	77796872	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77796872delA	uc002lns.2	+						TXNL4A_uc010drg.2_5'Flank|C18orf22_uc010drh.2_Intron|C18orf22_uc010dri.1_Intron	NM_024805	NP_079081			hypothetical protein LOC79863 precursor						rRNA processing	mitochondrion					0		all_cancers(4;3.21e-14)|all_epithelial(4;7.11e-09)|all_lung(4;0.00366)|Lung NSC(4;0.00683)|Esophageal squamous(42;0.0212)|Ovarian(4;0.0545)|all_hematologic(56;0.15)|Melanoma(33;0.2)		OV - Ovarian serous cystadenocarcinoma(15;6.46e-08)|BRCA - Breast invasive adenocarcinoma(31;0.00376)														---	---	---	---
C18orf22	79863	broad.mit.edu	37	18	77839178	77839178	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77839178delT	uc010dri.1	+						uc002lnu.2_RNA					Homo sapiens hypothetical p38 protein mRNA, complete cds.						rRNA processing	mitochondrion					0		all_cancers(4;3.21e-14)|all_epithelial(4;7.11e-09)|all_lung(4;0.00366)|Lung NSC(4;0.00683)|Esophageal squamous(42;0.0212)|Ovarian(4;0.0545)|all_hematologic(56;0.15)|Melanoma(33;0.2)		OV - Ovarian serous cystadenocarcinoma(15;6.46e-08)|BRCA - Breast invasive adenocarcinoma(31;0.00376)														---	---	---	---
ADNP2	22850	broad.mit.edu	37	18	77867942	77867942	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77867942delT	uc002lnw.2	+							NM_014913	NP_055728			ADNP homeobox 2						cellular response to oxidative stress|cellular response to retinoic acid|negative regulation of cell death|neuron differentiation|positive regulation of cell growth	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|breast(3)|central_nervous_system(1)	8		all_cancers(4;1.06e-15)|all_epithelial(4;2.36e-10)|all_lung(4;0.000302)|Lung NSC(4;0.000518)|Esophageal squamous(42;0.0212)|Ovarian(4;0.0256)|all_hematologic(56;0.15)|Melanoma(33;0.2)		Epithelial(2;1.1e-11)|OV - Ovarian serous cystadenocarcinoma(15;7.54e-09)|BRCA - Breast invasive adenocarcinoma(31;0.00247)|STAD - Stomach adenocarcinoma(84;0.164)														---	---	---	---
PARD6G	84552	broad.mit.edu	37	18	77922426	77922426	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77922426delG	uc002lny.2	-						LOC100130522_uc002lnx.2_Intron|LOC100130522_uc010xfn.1_Intron|LOC100130522_uc010xfo.1_Intron	NM_032510	NP_115899			PAR-6 gamma protein						cell cycle|cell division|tight junction assembly	cytosol|tight junction	protein binding				0		all_cancers(4;5.63e-22)|all_epithelial(4;5.86e-15)|all_lung(4;1.32e-05)|Ovarian(4;1.33e-05)|Lung NSC(4;2.77e-05)|Esophageal squamous(42;0.0157)|all_hematologic(56;0.13)|Melanoma(33;0.144)		Epithelial(2;1.48e-13)|all cancers(1;5.77e-13)|OV - Ovarian serous cystadenocarcinoma(15;2.74e-10)|BRCA - Breast invasive adenocarcinoma(31;0.00166)|STAD - Stomach adenocarcinoma(84;0.18)|Lung(128;0.23)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	93471	93473	+	IGR	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:93471_93473delAAA								FAM138F (15781 upstream) : OR4F17 (13673 downstream)																																			---	---	---	---
PPAP2C	8612	broad.mit.edu	37	19	292653	292653	+	5'Flank	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:292653delG	uc002loi.2	-						PPAP2C_uc002loh.2_5'Flank|PPAP2C_uc002loj.2_5'Flank	NM_003712	NP_003703			phosphatidic acid phosphatase type 2C isoform 1						sphingolipid metabolic process	integral to membrane|plasma membrane	phosphatidate phosphatase activity|phosphoprotein phosphatase activity|sphingosine-1-phosphate phosphatase activity			central_nervous_system(1)	1		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
MADCAM1	8174	broad.mit.edu	37	19	496564	496564	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:496564delG	uc002los.2	+						MADCAM1_uc002lot.2_Intron|MADCAM1_uc010drq.2_Intron	NM_130760	NP_570116			mucosal vascular addressin cell adhesion						cell adhesion|immune response|regulation of immune response|signal transduction	integral to membrane|membrane fraction|plasma membrane					0		all_cancers(10;4.25e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	526595	526596	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:526595_526596delTT								C19orf20 (6942 upstream) : CDC34 (5137 downstream)																																			---	---	---	---
FGF22	27006	broad.mit.edu	37	19	643528	643528	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:643528delG	uc010xfq.1	+	3	437	c.437delG	c.(436-438)AGGfs	p.R146fs	FGF22_uc010xfr.1_Frame_Shift_Del_p.E138fs	NM_020637	NP_065688	Q9HCT0	FGF22_HUMAN	fibroblast growth factor 22 precursor	146					cell differentiation|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway	extracellular space	growth factor activity				0		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
RNF126	55658	broad.mit.edu	37	19	656343	656343	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:656343delA	uc010drs.2	-							NM_194460	NP_919442			ring finger protein 126								protein binding|zinc ion binding				0		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
PRSSL1	400668	broad.mit.edu	37	19	691213	691213	+	Intron	DEL	A	-	-	rs147436553		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:691213delA	uc002lpl.1	-						PRSSL1_uc010xfs.1_Intron	NM_214710	NP_999875			protease, serine-like 1 precursor						proteolysis	extracellular region	serine-type endopeptidase activity				0		all_epithelial(18;2.19e-21)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
PALM	5064	broad.mit.edu	37	19	708192	708192	+	5'Flank	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:708192delC	uc002lpm.1	+						PALM_uc010xft.1_5'Flank|PALM_uc002lpn.1_5'Flank	NM_002579	NP_002570			paralemmin isoform 1						cellular component movement|negative regulation of adenylate cyclase activity|negative regulation of dopamine receptor signaling pathway|positive regulation of filopodium assembly|regulation of cell shape	cytoplasmic membrane-bounded vesicle|filopodium membrane|integral to plasma membrane					0		all_epithelial(18;2.19e-21)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)|Lung(535;0.201)														---	---	---	---
PALM	5064	broad.mit.edu	37	19	738527	738527	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:738527delA	uc002lpm.1	+						PALM_uc002lpn.1_Intron|PALM_uc010xfu.1_Intron	NM_002579	NP_002570			paralemmin isoform 1						cellular component movement|negative regulation of adenylate cyclase activity|negative regulation of dopamine receptor signaling pathway|positive regulation of filopodium assembly|regulation of cell shape	cytoplasmic membrane-bounded vesicle|filopodium membrane|integral to plasma membrane					0		all_epithelial(18;2.19e-21)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)|Lung(535;0.201)														---	---	---	---
MED16	10025	broad.mit.edu	37	19	873770	873771	+	Intron	DEL	CC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:873770_873771delCC	uc002lqd.1	-						MED16_uc010drw.1_Intron|MED16_uc002lqe.2_Intron|MED16_uc002lqf.2_Intron|MED16_uc010xfv.1_Intron|MED16_uc010xfw.1_Intron|MED16_uc010xfx.1_Intron|MED16_uc010xfy.1_Intron|MED16_uc010xfz.1_RNA	NM_005481	NP_005472			mediator complex subunit 16						androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	receptor activity|thyroid hormone receptor binding|thyroid hormone receptor coactivator activity|vitamin D receptor binding				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
MED16	10025	broad.mit.edu	37	19	877295	877296	+	Intron	INS	-	CT	CT	rs140629440	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:877295_877296insCT	uc002lqd.1	-						MED16_uc010drw.1_Intron|MED16_uc002lqe.2_Intron|MED16_uc002lqf.2_Intron|MED16_uc010xfv.1_Intron|MED16_uc010xfw.1_Intron|MED16_uc010xfx.1_Intron|MED16_uc010xfy.1_Intron	NM_005481	NP_005472			mediator complex subunit 16						androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	receptor activity|thyroid hormone receptor binding|thyroid hormone receptor coactivator activity|vitamin D receptor binding				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
ARID3A	1820	broad.mit.edu	37	19	962233	962233	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:962233delT	uc002lql.2	+							NM_005224	NP_005215			AT rich interactive domain 3A (BRIGHT- like)							cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	1282480	1282480	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1282480delG								C19orf24 (3238 upstream) : EFNA2 (3688 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	1318482	1318482	+	IGR	DEL	A	-	-	rs78582206		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1318482delA								EFNA2 (18538 upstream) : MUM1 (36494 downstream)																																			---	---	---	---
MUM1	84939	broad.mit.edu	37	19	1358189	1358192	+	Intron	DEL	AAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1358189_1358192delAAAA	uc010xgm.1	+						MUM1_uc010dsi.2_Intron|MUM1_uc002lrz.2_Intron|MUM1_uc002lsb.2_Intron|MUM1_uc002lsc.1_5'UTR					SubName: Full=MUM1 protein;						chromatin organization|DNA repair	nucleus	nucleosome binding|protein binding				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
DAZAP1	26528	broad.mit.edu	37	19	1418939	1418939	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1418939delA	uc002lsn.2	+						DAZAP1_uc002lsm.2_Intron|DAZAP1_uc002lso.2_Intron|DAZAP1_uc002lsl.1_Intron	NM_018959	NP_061832			DAZ associated protein 1 isoform b						cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm|nucleus	nucleotide binding|RNA binding			breast(1)	1		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
UQCR11	10975	broad.mit.edu	37	19	1602164	1602165	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1602164_1602165delAA	uc002ltm.2	-							NM_006830	NP_006821			ubiquinol-cytochrome c reductase, 6.4kDa						respiratory electron transport chain	integral to membrane|mitochondrial inner membrane|respiratory chain	electron carrier activity			ovary(1)|breast(1)	2																		---	---	---	---
UQCR11	10975	broad.mit.edu	37	19	1607562	1607562	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1607562delT	uc002ltm.2	-							NM_006830	NP_006821			ubiquinol-cytochrome c reductase, 6.4kDa						respiratory electron transport chain	integral to membrane|mitochondrial inner membrane|respiratory chain	electron carrier activity			ovary(1)|breast(1)	2																		---	---	---	---
BTBD2	55643	broad.mit.edu	37	19	1992580	1992580	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1992580delT	uc002lup.1	-						BTBD2_uc002luo.1_5'Flank	NM_017797	NP_060267			BTB (POZ) domain containing 2							cytoplasmic mRNA processing body	protein binding			ovary(1)|skin(1)	2		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
BTBD2	55643	broad.mit.edu	37	19	1997185	1997185	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1997185delA	uc002lup.1	-							NM_017797	NP_060267			BTB (POZ) domain containing 2							cytoplasmic mRNA processing body	protein binding			ovary(1)|skin(1)	2		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
MKNK2	2872	broad.mit.edu	37	19	2037835	2037836	+	3'UTR	DEL	AA	-	-	rs80059214		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2037835_2037836delAA	uc002lus.2	-	14					MKNK2_uc002luq.1_Intron|MKNK2_uc010xgu.1_3'UTR|MKNK2_uc010xgv.1_3'UTR|MKNK2_uc002lur.2_Intron|MKNK2_uc002lut.1_3'UTR	NM_199054	NP_951009			MAP kinase-interacting serine/threonine kinase 2						cell surface receptor linked signaling pathway|intracellular protein kinase cascade|regulation of translation		ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(1)|breast(1)	2		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
MOBKL2A	126308	broad.mit.edu	37	19	2080384	2080384	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2080384delT	uc002luu.2	-						MOBKL2A_uc002luv.2_Intron	NM_130807	NP_570719			MOB-LAK							intracellular	metal ion binding			lung(1)	1		Ovarian(11;1.78e-06)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
MOBKL2A	126308	broad.mit.edu	37	19	2093161	2093161	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2093161delT	uc002luv.2	-							NM_130807	NP_570719			MOB-LAK							intracellular	metal ion binding			lung(1)	1		Ovarian(11;1.78e-06)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
AP3D1	8943	broad.mit.edu	37	19	2108687	2108687	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2108687delT	uc002luz.2	-	29	3588	c.3365delA	c.(3364-3366)AAGfs	p.K1122fs	AP3D1_uc010dsv.2_Frame_Shift_Del_p.K212fs|AP3D1_uc002luy.2_Frame_Shift_Del_p.K1081fs|AP3D1_uc002lva.2_Frame_Shift_Del_p.K1184fs	NM_003938	NP_003929	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1	1122					eye pigment biosynthetic process|intracellular protein transport|regulation of sequestering of zinc ion|vesicle-mediated transport	endosome membrane|Golgi membrane|membrane coat	binding|protein transporter activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
DOT1L	84444	broad.mit.edu	37	19	2177768	2177768	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2177768delT	uc002lvb.3	+							NM_032482	NP_115871			DOT1-like, histone H3 methyltransferase							nucleus	DNA binding|histone-lysine N-methyltransferase activity|protein binding			pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
SF3A2	8175	broad.mit.edu	37	19	2245187	2245189	+	Intron	DEL	AAA	-	-	rs113747822		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2245187_2245189delAAA	uc002lvg.2	+							NM_007165	NP_009096			splicing factor 3a, subunit 2						nuclear mRNA 3'-splice site recognition	catalytic step 2 spliceosome|nucleoplasm|small nuclear ribonucleoprotein complex	nucleic acid binding|zinc ion binding				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	2263641	2263641	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2263641delA								JSRP1 (7225 upstream) : OAZ1 (5879 downstream)																																			---	---	---	---
GNG7	2788	broad.mit.edu	37	19	2593070	2593070	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2593070delA	uc002lwd.2	-							NM_052847	NP_443079			guanine nucleotide binding protein (G protein),						cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	heterotrimeric G-protein complex	signal transducer activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
GNG7	2788	broad.mit.edu	37	19	2635362	2635362	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2635362delA	uc002lwd.2	-							NM_052847	NP_443079			guanine nucleotide binding protein (G protein),						cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	heterotrimeric G-protein complex	signal transducer activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	2863474	2863474	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2863474delT								ZNF555 (9268 upstream) : ZNF556 (3859 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	2930621	2930622	+	IGR	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2930621_2930622delAG								ZNF57 (12154 upstream) : ZNF77 (2595 downstream)																																			---	---	---	---
CELF5	60680	broad.mit.edu	37	19	3239267	3239268	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3239267_3239268insT	uc002lxm.2	+						CELF5_uc002lxl.1_Intron|CELF5_uc010dtj.1_Intron|CELF5_uc010xhg.1_Intron	NM_021938	NP_068757			bruno-like 5, RNA binding protein						mRNA processing	cytoplasm|nucleus	nucleotide binding|RNA binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	3485476	3485476	+	IGR	DEL	T	-	-	rs78966300		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3485476delT								C19orf77 (4936 upstream) : DOHH (5344 downstream)																																			---	---	---	---
ITGB1BP3	27231	broad.mit.edu	37	19	3941216	3941216	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3941216delG	uc002lyz.3	+						ITGB1BP3_uc010xia.1_Intron	NM_170678	NP_733778			integrin beta 1 binding protein 3						pyridine nucleotide biosynthetic process		ATP binding|metal ion binding|protein binding|ribosylnicotinamide kinase activity			skin(2)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00463)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	4088647	4088647	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4088647delT								ZBTB7A (21831 upstream) : MAP2K2 (1682 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	4133783	4133783	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4133783delA								MAP2K2 (9657 upstream) : CREB3L3 (19846 downstream)																																			---	---	---	---
PLIN4	729359	broad.mit.edu	37	19	4515193	4515193	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4515193delA	uc002mar.1	-							NM_001080400	NP_001073869			plasma membrane associated protein, S3-12							lipid particle|plasma membrane					0																		---	---	---	---
PTPRS	5802	broad.mit.edu	37	19	5168816	5168817	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5168816_5168817insT	uc002mbu.1	-							NM_130853	NP_570923			protein tyrosine phosphatase, receptor type,						cell adhesion	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			large_intestine(2)|ovary(1)|central_nervous_system(1)	4				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	5451345	5451345	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5451345delG								PTPRS (110531 upstream) : ZNRF4 (4081 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	5471325	5471325	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5471325delA								ZNRF4 (14459 upstream) : PLAC2 (86855 downstream)																																			---	---	---	---
TMEM146	257062	broad.mit.edu	37	19	5742351	5742352	+	Intron	DEL	AT	-	-	rs10561033		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5742351_5742352delAT	uc002mda.2	+						TMEM146_uc010duj.1_Intron	NM_152784	NP_689997			transmembrane protein 146 precursor							integral to membrane				ovary(1)|central_nervous_system(1)|pancreas(1)	3																		---	---	---	---
ACSBG2	81616	broad.mit.edu	37	19	6147130	6147130	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6147130delA	uc002mef.1	+						ACSBG2_uc002mee.1_Intron|ACSBG2_uc002meg.1_Intron|ACSBG2_uc002meh.1_Intron|ACSBG2_uc002mei.1_Intron|ACSBG2_uc010xiz.1_Intron	NM_030924	NP_112186			bubblegum-related acyl-CoA synthetase 2						cell differentiation|fatty acid metabolic process|multicellular organismal development|spermatogenesis	membrane|microsome|mitochondrion	acyl-CoA thioesterase activity|ATP binding|long-chain fatty acid-CoA ligase activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	6288375	6288376	+	IGR	INS	-	GT	GT			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6288375_6288376insGT								MLLT1 (8416 upstream) : ACER1 (18134 downstream)																																			---	---	---	---
ACER1	125981	broad.mit.edu	37	19	6311676	6311678	+	Intron	DEL	AGG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6311676_6311678delAGG	uc002mel.2	-							NM_133492	NP_597999			alkaline ceramidase 1							endoplasmic reticulum membrane|integral to membrane	ceramidase activity				0																		---	---	---	---
SLC25A41	284427	broad.mit.edu	37	19	6432330	6432330	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6432330delT	uc010dus.2	-						SLC25A41_uc010dut.2_Intron	NM_173637	NP_775908			solute carrier family 25, member 41						transmembrane transport	integral to membrane|mitochondrial inner membrane	binding				0																		---	---	---	---
DENND1C	79958	broad.mit.edu	37	19	6469736	6469737	+	Intron	DEL	TT	-	-	rs74772168		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6469736_6469737delTT	uc002mfe.2	-						DENND1C_uc002mfb.2_Intron|DENND1C_uc002mfc.2_Intron|DENND1C_uc002mfd.2_Intron|DENND1C_uc010xje.1_Intron	NM_024898	NP_079174			DENN/MADD domain containing 1C							clathrin-coated vesicle|cytosol	guanyl-nucleotide exchange factor activity			large_intestine(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	6547121	6547122	+	IGR	INS	-	TG	TG	rs149663040	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6547121_6547122insTG								TNFSF9 (11182 upstream) : CD70 (36013 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	6608067	6608067	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6608067delA								CD70 (16904 upstream) : TNFSF14 (56499 downstream)																																			---	---	---	---
GPR108	56927	broad.mit.edu	37	19	6731752	6731752	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6731752delG	uc002mfp.2	-						GPR108_uc010duv.2_Intron|GPR108_uc002mfn.2_Intron|GPR108_uc002mfo.3_Intron|GPR108_uc010duw.2_Intron	NM_001080452	NP_001073921			G protein-coupled receptor 108 isoform 1							integral to membrane					0																		---	---	---	---
VAV1	7409	broad.mit.edu	37	19	6800803	6800804	+	Intron	INS	-	TG	TG	rs143603038	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6800803_6800804insTG	uc002mfu.1	+						VAV1_uc010xjh.1_Intron|VAV1_uc010dva.1_Intron|VAV1_uc002mfv.1_Intron	NM_005428	NP_005419			vav 1 guanine nucleotide exchange factor						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|T cell costimulation	cytosol|plasma membrane	metal ion binding|protein binding|sequence-specific DNA binding transcription factor activity			lung(4)|ovary(4)|breast(3)|central_nervous_system(2)|kidney(2)|skin(1)	16																		---	---	---	---
EMR4P	326342	broad.mit.edu	37	19	6974645	6974645	+	5'UTR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6974645delC	uc010xjk.1	-	8					EMR4P_uc010dve.1_Intron	NR_024075				RecName: Full=Putative EGF-like module-containing mucin-like hormone receptor-like 4; AltName: Full=G-protein coupled receptor 127; AltName: Full=G-protein coupled receptor PGR16; Flags: Precursor;												0																		---	---	---	---
INSR	3643	broad.mit.edu	37	19	7151161	7151190	+	Intron	DEL	CTTTCTTTCTTTCTCTTTCTTTCTTTCTTT	-	-	rs10422180		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7151161_7151190delCTTTCTTTCTTTCTCTTTCTTTCTTTCTTT	uc002mgd.1	-						INSR_uc002mge.1_Intron	NM_000208	NP_000199			insulin receptor isoform Long precursor						activation of MAPK activity|activation of protein kinase B activity|carbohydrate metabolic process|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|glucose homeostasis|heart morphogenesis|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of developmental growth|positive regulation of DNA replication|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of MAPKKK cascade|positive regulation of mitosis|positive regulation of nitric oxide biosynthetic process|positive regulation of protein kinase B signaling cascade|positive regulation of protein phosphorylation|positive regulation of respiratory burst|protein autophosphorylation|protein heterotetramerization|regulation of embryonic development|regulation of transcription, DNA-dependent|transformation of host cell by virus	caveola|endosome membrane|insulin receptor complex|microsome	ATP binding|GTP binding|insulin binding|insulin receptor activity|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor II binding|insulin-like growth factor receptor binding|metal ion binding|phosphatidylinositol 3-kinase binding|PTB domain binding|receptor signaling protein tyrosine kinase activity|SH2 domain binding			ovary(4)|lung(3)|central_nervous_system(2)|large_intestine(1)|stomach(1)|skin(1)	12					Insulin Glargine recombinant(DB00047)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
INSR	3643	broad.mit.edu	37	19	7279824	7279825	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7279824_7279825delAA	uc002mgd.1	-						INSR_uc002mge.1_Intron|INSR_uc002mgf.2_Intron	NM_000208	NP_000199			insulin receptor isoform Long precursor						activation of MAPK activity|activation of protein kinase B activity|carbohydrate metabolic process|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|glucose homeostasis|heart morphogenesis|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of developmental growth|positive regulation of DNA replication|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of MAPKKK cascade|positive regulation of mitosis|positive regulation of nitric oxide biosynthetic process|positive regulation of protein kinase B signaling cascade|positive regulation of protein phosphorylation|positive regulation of respiratory burst|protein autophosphorylation|protein heterotetramerization|regulation of embryonic development|regulation of transcription, DNA-dependent|transformation of host cell by virus	caveola|endosome membrane|insulin receptor complex|microsome	ATP binding|GTP binding|insulin binding|insulin receptor activity|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor II binding|insulin-like growth factor receptor binding|metal ion binding|phosphatidylinositol 3-kinase binding|PTB domain binding|receptor signaling protein tyrosine kinase activity|SH2 domain binding			ovary(4)|lung(3)|central_nervous_system(2)|large_intestine(1)|stomach(1)|skin(1)	12					Insulin Glargine recombinant(DB00047)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
XAB2	56949	broad.mit.edu	37	19	7685993	7685993	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7685993delC	uc002mgx.2	-							NM_020196	NP_064581			XPA binding protein 2						transcription, DNA-dependent|transcription-coupled nucleotide-excision repair	catalytic step 2 spliceosome|nucleoplasm	protein binding			central_nervous_system(2)|breast(1)|skin(1)	4													Direct_reversal_of_damage|NER					---	---	---	---
Unknown	0	broad.mit.edu	37	19	7770197	7770197	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7770197delT								FCER2 (3165 upstream) : CLEC4G (23647 downstream)																																			---	---	---	---
FBN3	84467	broad.mit.edu	37	19	8151014	8151014	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8151014delG	uc002mjf.2	-						FBN3_uc002mje.2_Intron	NM_032447	NP_115823			fibrillin 3 precursor							proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(6)|skin(3)|pancreas(1)|central_nervous_system(1)	11																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	8217724	8217726	+	IGR	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8217724_8217726delAAA								FBN3 (5343 upstream) : LASS4 (56491 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	8227353	8227353	+	IGR	DEL	A	-	-	rs78855495		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8227353delA								FBN3 (14972 upstream) : LASS4 (46864 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	8267153	8267153	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8267153delA								FBN3 (54772 upstream) : LASS4 (7064 downstream)																																			---	---	---	---
MARCH2	51257	broad.mit.edu	37	19	8481945	8481946	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8481945_8481946delTT	uc002mjv.2	+						MARCH2_uc002mjw.2_Intron|MARCH2_uc002mjx.2_Intron	NM_016496	NP_057580			membrane-associated ring finger (C3HC4) 2						endocytosis	cytoplasmic vesicle|endoplasmic reticulum membrane|endosome membrane|integral to membrane|lysosomal membrane	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
HNRNPM	4670	broad.mit.edu	37	19	8549919	8549919	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8549919delT	uc010dwe.2	+						HNRNPM_uc010xke.1_Intron|HNRNPM_uc010dwd.2_Intron|HNRNPM_uc002mka.2_Intron|HNRNPM_uc002mkb.1_5'Flank	NM_005968	NP_005959			heterogeneous nuclear ribonucleoprotein M						alternative nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|integral to plasma membrane|nuclear matrix|nucleolus|paraspeckles	nucleotide binding|protein domain specific binding|RNA binding				0																		---	---	---	---
HNRNPM	4670	broad.mit.edu	37	19	8553928	8553929	+	3'UTR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8553928_8553929insT	uc010dwe.2	+	16					HNRNPM_uc010dwd.2_3'UTR|HNRNPM_uc002mka.2_3'UTR|HNRNPM_uc002mkb.1_RNA	NM_005968	NP_005959			heterogeneous nuclear ribonucleoprotein M						alternative nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|integral to plasma membrane|nuclear matrix|nucleolus|paraspeckles	nucleotide binding|protein domain specific binding|RNA binding				0																		---	---	---	---
PRAM1	84106	broad.mit.edu	37	19	8567648	8567648	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8567648delT	uc002mkd.2	-						PRAM1_uc002mkc.2_5'Flank	NM_032152	NP_115528			PML-RARA regulated adaptor molecule 1								lipid binding|protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	8900338	8900339	+	IGR	DEL	GT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8900338_8900339delGT								OR2Z1 (58004 upstream) : ZNF558 (20043 downstream)																																			---	---	---	---
MUC16	94025	broad.mit.edu	37	19	9079451	9079451	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9079451delA	uc002mkp.2	-							NM_024690	NP_078966			mucin 16						cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	9184450	9184450	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9184450delA								MUC16 (92432 upstream) : OR1M1 (19471 downstream)																																			---	---	---	---
ZNF562	54811	broad.mit.edu	37	19	9778430	9778431	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9778430_9778431delTT	uc010xks.1	-						ZNF562_uc002mly.2_Intron|ZNF562_uc002mlx.2_Intron|ZNF562_uc010xkt.1_Intron|ZNF562_uc010xku.1_Intron|ZNF562_uc010xkv.1_Intron|ZNF562_uc010xkw.1_Intron	NM_001130032	NP_001123504			zinc finger protein 562 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	9851519	9851519	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9851519delA								ZNF562 (65743 upstream) : ZNF846 (11297 downstream)																																			---	---	---	---
OLFM2	93145	broad.mit.edu	37	19	10028428	10028429	+	Intron	INS	-	GTAGA	GTAGA	rs112357016		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10028428_10028429insGTAGA	uc002mmp.2	-							NM_058164	NP_477512			olfactomedin 2 precursor							extracellular region				large_intestine(1)|skin(1)	2																		---	---	---	---
COL5A3	50509	broad.mit.edu	37	19	10109877	10109877	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10109877delT	uc002mmq.1	-							NM_015719	NP_056534			collagen, type V, alpha 3 preproprotein						collagen fibril organization|skin development	collagen type V	collagen binding|extracellular matrix structural constituent			ovary(7)|lung(1)|central_nervous_system(1)|skin(1)	10			Epithelial(33;7.11e-05)															---	---	---	---
C3P1	388503	broad.mit.edu	37	19	10176515	10176515	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10176515delA	uc010dwx.1	+							NR_027300				Synthetic construct DNA, clone: pF1KB7402, Homo sapiens LOC388503 gene, without stop codon, in Flexi system.												0																		---	---	---	---
DNMT1	1786	broad.mit.edu	37	19	10288073	10288073	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10288073delA	uc002mng.2	-						DNMT1_uc010xlc.1_Intron|DNMT1_uc002mnh.2_Intron|DNMT1_uc010xld.1_Intron|DNMT1_uc010dxb.1_Intron	NM_001379	NP_001370			DNA (cytosine-5-)-methyltransferase 1 isoform b						chromatin modification|maintenance of DNA methylation|negative regulation of histone H3-K9 methylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of gene expression|positive regulation of histone H3-K4 methylation|transcription, DNA-dependent	nucleus	DNA (cytosine-5-)-methyltransferase activity|DNA binding|transcription factor binding			ovary(2)|prostate(1)|lung(1)|breast(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Ifosfamide(DB01181)|Procainamide(DB01035)													---	---	---	---
S1PR2	9294	broad.mit.edu	37	19	10342677	10342678	+	5'Flank	INS	-	G	G	rs148394477	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10342677_10342678insG	uc002mnl.2	-							NM_004230	NP_004221			endothelial differentiation, sphingolipid						activation of MAPK activity|positive regulation of cell proliferation	integral to membrane|plasma membrane	lipid binding|lysosphingolipid and lysophosphatidic acid receptor activity			lung(1)|central_nervous_system(1)	2																		---	---	---	---
MRPL4	51073	broad.mit.edu	37	19	10364701	10364701	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10364701delT	uc002mnm.2	+						MRPL4_uc002mnn.2_Intron|MRPL4_uc002mno.2_Intron	NM_146387	NP_666499			mitochondrial ribosomal protein L4 isoform a						translation	mitochondrion|ribosome	structural constituent of ribosome			ovary(1)	1		Renal(1328;0.0112)	OV - Ovarian serous cystadenocarcinoma(20;1.39e-09)|Epithelial(33;1.99e-06)|all cancers(31;4.81e-06)	Lung(535;0.00705)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	10377498	10377498	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10377498delT								MRPL4 (6764 upstream) : ICAM1 (4019 downstream)																																			---	---	---	---
RAVER1	125950	broad.mit.edu	37	19	10439226	10439227	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10439226_10439227delAA	uc002moa.2	-							NM_133452	NP_597709			RAVER1							cytoplasm|nucleus	nucleotide binding|protein binding|RNA binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(20;1.81e-09)|Epithelial(33;3.65e-06)|all cancers(31;8.35e-06)															---	---	---	---
RAVER1	125950	broad.mit.edu	37	19	10443951	10443952	+	Intron	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10443951_10443952insC	uc002moa.2	-							NM_133452	NP_597709			RAVER1							cytoplasm|nucleus	nucleotide binding|protein binding|RNA binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(20;1.81e-09)|Epithelial(33;3.65e-06)|all cancers(31;8.35e-06)															---	---	---	---
TYK2	7297	broad.mit.edu	37	19	10475179	10475179	+	Intron	DEL	A	-	-	rs80231890		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10475179delA	uc002moc.3	-						TYK2_uc010dxe.2_Intron|TYK2_uc002mod.2_Intron	NM_003331	NP_003322			tyrosine kinase 2						intracellular protein kinase cascade|regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway	cytoskeleton|cytosol|membrane|nucleus	ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity			lung(5)|large_intestine(2)|ovary(1)|breast(1)	9			OV - Ovarian serous cystadenocarcinoma(20;1.77e-09)|Epithelial(33;3.92e-06)|all cancers(31;8.95e-06)															---	---	---	---
PDE4A	5141	broad.mit.edu	37	19	10576680	10576681	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10576680_10576681delTT	uc002moj.2	+						PDE4A_uc002mok.2_Intron|PDE4A_uc002mol.2_Intron|PDE4A_uc002mom.2_Intron|PDE4A_uc002mon.2_Intron|PDE4A_uc002moo.2_Intron	NM_001111307	NP_001104777			phosphodiesterase 4A isoform 1						signal transduction	cytosol|membrane fraction|perinuclear region of cytoplasm|ruffle membrane|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|protein binding			ovary(1)|breast(1)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(20;5.8e-10)|Epithelial(33;7.58e-07)|all cancers(31;3.91e-06)		Cilostazol(DB01166)|Dipyridamole(DB00975)|Dyphylline(DB00651)|Enprofylline(DB00824)|Iloprost(DB01088)|Milrinone(DB00235)|Pentoxifylline(DB00806)|Phentolamine(DB00692)|Tadalafil(DB00820)|Theophylline(DB00277)													---	---	---	---
SLC44A2	57153	broad.mit.edu	37	19	10735810	10735810	+	5'Flank	DEL	A	-	-	rs78297952		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10735810delA	uc002mpf.2	+						SLC44A2_uc002mpe.3_Intron	NM_020428	NP_065161			solute carrier family 44, member 2 isoform 1						positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to membrane|plasma membrane	choline transmembrane transporter activity|signal transducer activity			ovary(1)	1			Epithelial(33;8.7e-06)|all cancers(31;2.77e-05)		Choline(DB00122)													---	---	---	---
DNM2	1785	broad.mit.edu	37	19	10928493	10928494	+	Intron	DEL	GC	-	-	rs76440766		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10928493_10928494delGC	uc002mps.1	+						DNM2_uc010dxk.2_Intron|DNM2_uc002mpt.1_Intron|DNM2_uc002mpv.1_Intron|DNM2_uc002mpu.1_Intron|DNM2_uc010dxl.1_Intron|DNM2_uc002mpw.2_Intron|uc010xlj.1_5'Flank|MIR199A1_hsa-mir-199a-1|MI0000242_5'Flank	NM_001005361	NP_001005361			dynamin 2 isoform 2						G2/M transition of mitotic cell cycle|positive regulation of apoptosis|positive regulation of transcription, DNA-dependent|post-Golgi vesicle-mediated transport|receptor internalization|signal transduction|synaptic vesicle transport|transferrin transport	cell junction|cytosol|Golgi membrane|microtubule|postsynaptic density|postsynaptic membrane	GTP binding|GTPase activity|microtubule binding			central_nervous_system(2)|skin(2)|ovary(1)|breast(1)	6			Epithelial(33;4.17e-05)|all cancers(31;8.48e-05)															---	---	---	---
YIPF2	78992	broad.mit.edu	37	19	11035133	11035134	+	Intron	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11035133_11035134delCT	uc002mqb.2	-						YIPF2_uc002mqc.2_Intron	NM_024029	NP_076934			Yip1 domain family, member 2							integral to membrane|transport vesicle					0																		---	---	---	---
SMARCA4	6597	broad.mit.edu	37	19	11121909	11121910	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11121909_11121910delTT	uc002mqf.3	+						SMARCA4_uc010dxp.2_Intron|SMARCA4_uc010dxo.2_Intron|SMARCA4_uc002mqg.1_Intron|SMARCA4_uc010dxq.2_Intron|SMARCA4_uc010dxr.2_Intron|SMARCA4_uc002mqj.3_Intron|SMARCA4_uc010dxs.2_Intron|SMARCA4_uc010dxt.1_5'Flank	NM_003072	NP_003063			SWI/SNF-related matrix-associated						chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex	androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity	p.?(1)		lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1)	67		all_lung(6;0.0512)|Lung NSC(9;0.0568)						F|N|Mis		NSCLC				Rhabdoid_Predisposition_syndrome				---	---	---	---
DOCK6	57572	broad.mit.edu	37	19	11326767	11326767	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11326767delT	uc002mqs.3	-						DOCK6_uc010xlq.1_Intron	NM_020812	NP_065863			dedicator of cytokinesis 6						blood coagulation	cytosol	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(2)|skin(1)	3																		---	---	---	---
RGL3	57139	broad.mit.edu	37	19	11521522	11521522	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11521522delT	uc002mrp.2	-						RGL3_uc002mrn.2_Intron|RGL3_uc002mrm.2_Intron|RGL3_uc002mro.2_Intron	NM_001035223	NP_001030300			ral guanine nucleotide dissociation						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular				ovary(1)	1																		---	---	---	---
ELAVL3	1995	broad.mit.edu	37	19	11564773	11564773	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11564773delT	uc002mry.1	-	7					ELAVL3_uc002mrx.1_3'UTR	NM_001420	NP_001411			ELAV-like protein 3 isoform 1						cell differentiation|nervous system development		AU-rich element binding|nucleotide binding			ovary(1)|breast(1)|skin(1)	3																		---	---	---	---
ELAVL3	1995	broad.mit.edu	37	19	11577605	11577605	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11577605delC	uc002mry.1	-	2	427	c.47delG	c.(46-48)GGCfs	p.G16fs	ELAVL3_uc002mrx.1_Frame_Shift_Del_p.G16fs	NM_001420	NP_001411	Q14576	ELAV3_HUMAN	ELAV-like protein 3 isoform 1	16					cell differentiation|nervous system development		AU-rich element binding|nucleotide binding			ovary(1)|breast(1)|skin(1)	3																		---	---	---	---
ELAVL3	1995	broad.mit.edu	37	19	11591325	11591326	+	Intron	DEL	CC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11591325_11591326delCC	uc002mry.1	-						ELAVL3_uc002mrx.1_Intron	NM_001420	NP_001411			ELAV-like protein 3 isoform 1						cell differentiation|nervous system development		AU-rich element binding|nucleotide binding			ovary(1)|breast(1)|skin(1)	3																		---	---	---	---
CNN1	1264	broad.mit.edu	37	19	11656018	11656018	+	Intron	DEL	A	-	-	rs34908887		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11656018delA	uc002msc.1	+						CNN1_uc010xmb.1_Intron|CNN1_uc010xmc.1_Intron	NM_001299	NP_001290			calponin 1, basic, smooth muscle						actomyosin structure organization|regulation of smooth muscle contraction	cytoskeleton	actin binding|calmodulin binding				0																		---	---	---	---
CNN1	1264	broad.mit.edu	37	19	11660769	11660769	+	3'UTR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11660769delG	uc002msc.1	+	7					CNN1_uc010xmb.1_3'UTR|CNN1_uc010xmc.1_3'UTR	NM_001299	NP_001290			calponin 1, basic, smooth muscle						actomyosin structure organization|regulation of smooth muscle contraction	cytoskeleton	actin binding|calmodulin binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	11730587	11730587	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11730587delT								ZNF627 (613 upstream) : ZNF833 (20004 downstream)																																			---	---	---	---
ZNF441	126068	broad.mit.edu	37	19	11890728	11890728	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11890728delA	uc010dyj.2	+						ZNF441_uc002msn.3_Intron	NM_152355	NP_689568			zinc finger protein 441						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	11896114	11896114	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11896114delA								ZNF441 (1228 upstream) : ZNF491 (13277 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	12094338	12094338	+	IGR	DEL	A	-	-	rs80321679		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12094338delA								ZNF763 (3142 upstream) : ZNF433 (31194 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	12413706	12413707	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12413706_12413707insA								ZNF44 (7992 upstream) : ZNF563 (14599 downstream)																																			---	---	---	---
ZNF442	79973	broad.mit.edu	37	19	12467442	12467443	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12467442_12467443delAA	uc002mtr.1	-						ZNF442_uc010xmk.1_Intron	NM_030824	NP_110451			zinc finger protein 442						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(2)|breast(1)|kidney(1)	4																		---	---	---	---
CALR	811	broad.mit.edu	37	19	13052108	13052108	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13052108delA	uc002mvu.2	+						CALR_uc002mvv.2_5'Flank	NM_004343	NP_004334			calreticulin precursor						cell cycle arrest|cellular senescence|glucocorticoid receptor signaling pathway|negative regulation of neuron differentiation|negative regulation of retinoic acid receptor signaling pathway|negative regulation of steroid hormone receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative regulation of translation|peptide antigen assembly with MHC class I protein complex|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of DNA replication|positive regulation of phagocytosis|post-translational protein modification|protein export from nucleus|protein maturation by protein folding|protein N-linked glycosylation via asparagine|protein stabilization|regulation of apoptosis|sequestering of calcium ion	cytosol|endoplasmic reticulum lumen|extracellular space|MHC class I peptide loading complex|nucleus|perinuclear region of cytoplasm|polysome|proteinaceous extracellular matrix	androgen receptor binding|calcium ion binding|chaperone binding|complement component C1q binding|DNA binding|integrin binding|mRNA binding|protein binding involved in protein folding|sugar binding|ubiquitin protein ligase binding|unfolded protein binding|zinc ion binding			ovary(1)	1					Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
NFIX	4784	broad.mit.edu	37	19	13199534	13199534	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13199534delC	uc010xmx.1	+						NFIX_uc002mwd.2_Intron|NFIX_uc002mwe.2_Intron|NFIX_uc002mwf.2_Intron|NFIX_uc002mwg.1_Intron					RecName: Full=Nuclear factor 1;						DNA replication|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			breast(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(19;8.2e-22)															---	---	---	---
LYL1	4066	broad.mit.edu	37	19	13209934	13209934	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13209934delT	uc002mwi.2	-	4						NM_005583	NP_005574			lymphoblastic leukemia derived sequence 1						B cell differentiation|blood vessel maturation|definitive hemopoiesis|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding				0			OV - Ovarian serous cystadenocarcinoma(19;6.08e-22)					T	TRB@	T-ALL								---	---	---	---
CACNA1A	773	broad.mit.edu	37	19	13365183	13365183	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13365183delT	uc010dze.2	-						CACNA1A_uc010xnd.1_Intron|CACNA1A_uc002mwx.3_Intron|CACNA1A_uc010dzc.2_Intron|CACNA1A_uc002mwy.3_Intron|CACNA1A_uc010xne.1_Intron|CACNA1A_uc002mwv.3_Intron	NM_001127221	NP_001120693			calcium channel, alpha 1A subunit isoform 3						cell death|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|membrane depolarization|regulation of insulin secretion	cytoplasm|nucleus	syntaxin binding			large_intestine(2)	2			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Cinnarizine(DB00568)|Loperamide(DB00836)|Nisoldipine(DB00401)|Pregabalin(DB00230)													---	---	---	---
CACNA1A	773	broad.mit.edu	37	19	13443865	13443865	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13443865delA	uc010dze.2	-						CACNA1A_uc010dzc.2_5'Flank|CACNA1A_uc002mwy.3_Intron|CACNA1A_uc010xne.1_5'Flank	NM_001127221	NP_001120693			calcium channel, alpha 1A subunit isoform 3						cell death|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|membrane depolarization|regulation of insulin secretion	cytoplasm|nucleus	syntaxin binding			large_intestine(2)	2			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Cinnarizine(DB00568)|Loperamide(DB00836)|Nisoldipine(DB00401)|Pregabalin(DB00230)													---	---	---	---
CACNA1A	773	broad.mit.edu	37	19	13597672	13597673	+	Intron	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13597672_13597673delTC	uc010dze.2	-						CACNA1A_uc002mwy.3_Intron	NM_001127221	NP_001120693			calcium channel, alpha 1A subunit isoform 3						cell death|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|membrane depolarization|regulation of insulin secretion	cytoplasm|nucleus	syntaxin binding			large_intestine(2)	2			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Cinnarizine(DB00568)|Loperamide(DB00836)|Nisoldipine(DB00401)|Pregabalin(DB00230)													---	---	---	---
CACNA1A	773	broad.mit.edu	37	19	13601680	13601695	+	Intron	DEL	AAGGAAGGAAAGGAGG	-	-	rs28407756		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13601680_13601695delAAGGAAGGAAAGGAGG	uc010dze.2	-						CACNA1A_uc002mwy.3_Intron	NM_001127221	NP_001120693			calcium channel, alpha 1A subunit isoform 3						cell death|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|membrane depolarization|regulation of insulin secretion	cytoplasm|nucleus	syntaxin binding			large_intestine(2)	2			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Cinnarizine(DB00568)|Loperamide(DB00836)|Nisoldipine(DB00401)|Pregabalin(DB00230)													---	---	---	---
CACNA1A	773	broad.mit.edu	37	19	13606475	13606475	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13606475delC	uc010dze.2	-						CACNA1A_uc002mwy.3_Intron	NM_001127221	NP_001120693			calcium channel, alpha 1A subunit isoform 3						cell death|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|membrane depolarization|regulation of insulin secretion	cytoplasm|nucleus	syntaxin binding			large_intestine(2)	2			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Cinnarizine(DB00568)|Loperamide(DB00836)|Nisoldipine(DB00401)|Pregabalin(DB00230)													---	---	---	---
CCDC130	81576	broad.mit.edu	37	19	13846344	13846347	+	Intron	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13846344_13846347delTTTT	uc002mxb.1	+						CCDC130_uc010xnf.1_Intron	NM_030818	NP_110445			coiled-coil domain containing 130						response to virus		protein binding				0			OV - Ovarian serous cystadenocarcinoma(19;6.02e-23)|Epithelial(5;2.58e-18)															---	---	---	---
CCDC130	81576	broad.mit.edu	37	19	13850557	13850557	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13850557delT	uc002mxb.1	+						CCDC130_uc010xnf.1_Intron	NM_030818	NP_110445			coiled-coil domain containing 130						response to virus		protein binding				0			OV - Ovarian serous cystadenocarcinoma(19;6.02e-23)|Epithelial(5;2.58e-18)															---	---	---	---
ZSWIM4	65249	broad.mit.edu	37	19	13924429	13924429	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13924429delA	uc002mxh.1	+						ZSWIM4_uc010xng.1_Intron	NM_023072	NP_075560			zinc finger, SWIM-type containing 4								zinc ion binding			central_nervous_system(2)	2			OV - Ovarian serous cystadenocarcinoma(19;2.94e-23)|Epithelial(5;4.58e-19)															---	---	---	---
ZSWIM4	65249	broad.mit.edu	37	19	13941995	13941995	+	3'UTR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13941995delG	uc002mxh.1	+	13					ZSWIM4_uc010xng.1_3'UTR	NM_023072	NP_075560			zinc finger, SWIM-type containing 4								zinc ion binding			central_nervous_system(2)	2			OV - Ovarian serous cystadenocarcinoma(19;2.94e-23)|Epithelial(5;4.58e-19)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	13972746	13972746	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13972746delG								MIR23A (25273 upstream) : MIR181C (12767 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	14440883	14440884	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14440883_14440884delTT								LPHN1 (123886 upstream) : CD97 (51329 downstream)																																			---	---	---	---
PKN1	5585	broad.mit.edu	37	19	14554904	14554904	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14554904delC	uc002myp.2	+						PKN1_uc002myq.2_Intron	NM_002741	NP_002732			protein kinase N1 isoform 2						activation of JUN kinase activity|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	endosome|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|GTP-Rho binding|histone binding|histone deacetylase binding|histone kinase activity (H3-T11 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|Rac GTPase binding			ovary(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)	8																		---	---	---	---
PKN1	5585	broad.mit.edu	37	19	14558367	14558367	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14558367delT	uc002myp.2	+						PKN1_uc002myq.2_Intron	NM_002741	NP_002732			protein kinase N1 isoform 2						activation of JUN kinase activity|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	endosome|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|GTP-Rho binding|histone binding|histone deacetylase binding|histone kinase activity (H3-T11 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|Rac GTPase binding			ovary(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)	8																		---	---	---	---
TECR	9524	broad.mit.edu	37	19	14642244	14642245	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14642244_14642245insT	uc002mza.2	+						DNAJB1_uc010xnr.1_5'Flank|TECR_uc002mzb.2_Intron|TECR_uc010xns.1_Intron|TECR_uc002mzc.2_Intron|TECR_uc002mzd.2_Intron	NM_138501	NP_612510			glycoprotein, synaptic 2						fatty acid elongation|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process|very long-chain fatty acid biosynthetic process	integral to endoplasmic reticulum membrane	trans-2-enoyl-CoA reductase (NADPH) activity|very long-chain-acyl-CoA dehydrogenase activity				0																		---	---	---	---
TECR	9524	broad.mit.edu	37	19	14668577	14668577	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14668577delT	uc002mza.2	+						TECR_uc002mzb.2_Intron|TECR_uc010xns.1_Intron|TECR_uc002mzc.2_Intron|TECR_uc002mzd.2_Intron	NM_138501	NP_612510			glycoprotein, synaptic 2						fatty acid elongation|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process|very long-chain fatty acid biosynthetic process	integral to endoplasmic reticulum membrane	trans-2-enoyl-CoA reductase (NADPH) activity|very long-chain-acyl-CoA dehydrogenase activity				0																		---	---	---	---
EMR3	84658	broad.mit.edu	37	19	14765714	14765714	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14765714delT	uc002mzi.3	-						EMR3_uc010dzp.2_Intron|EMR3_uc010xnv.1_Intron	NM_032571	NP_115960			egf-like module-containing mucin-like receptor						neuropeptide signaling pathway	extracellular space|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(5)|skin(1)	6																		---	---	---	---
AKAP8L	26993	broad.mit.edu	37	19	15505847	15505847	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15505847delT	uc002naw.1	-						AKAP8L_uc002nax.1_Intron|AKAP8L_uc010xoh.1_Intron	NM_014371	NP_055186			A kinase (PRKA) anchor protein 8-like							cytoplasm|nuclear matrix	DEAD/H-box RNA helicase binding|DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
CIB3	117286	broad.mit.edu	37	19	16278297	16278297	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16278297delG	uc002nds.2	-						CIB3_uc010eae.2_Intron|CIB3_uc010eaf.2_Intron|CIB3_uc010eag.2_Intron	NM_054113	NP_473454			DNA-dependent protein kinase catalytic								calcium ion binding			ovary(1)	1																		---	---	---	---
AP1M1	8907	broad.mit.edu	37	19	16320149	16320150	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16320149_16320150insT	uc002ndu.2	+						AP1M1_uc002ndv.2_Intron|AP1M1_uc010xpd.1_Intron	NM_032493	NP_115882			adaptor-related protein complex 1, mu 1 subunit						cellular membrane organization|endosome to melanosome transport|interspecies interaction between organisms|intracellular protein transport|melanosome organization|post-Golgi vesicle-mediated transport|regulation of defense response to virus by virus|viral reproduction	clathrin adaptor complex|clathrin coated vesicle membrane|cytosol|Golgi membrane|lysosomal membrane	protein binding			ovary(3)|breast(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	16442141	16442141	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16442141delA								KLF2 (3804 upstream) : EPS15L1 (23920 downstream)																																			---	---	---	---
C19orf44	84167	broad.mit.edu	37	19	16628185	16628186	+	Intron	DEL	CG	-	-	rs114467203	by1000genomes;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16628185_16628186delCG	uc002neh.1	+						MED26_uc002nee.2_Intron|C19orf44_uc002neg.2_Intron|C19orf44_uc010eai.1_Intron	NM_032207	NP_115583			hypothetical protein LOC84167												0																		---	---	---	---
C19orf42	79086	broad.mit.edu	37	19	16755248	16755249	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16755248_16755249delTT	uc002neo.1	-						C19orf42_uc002nep.1_Intron					Homo sapiens cDNA: FLJ21949 fis, clone HEP04922.							integral to membrane					0																		---	---	---	---
NWD1	284434	broad.mit.edu	37	19	16872616	16872616	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16872616delA	uc002neu.3	+						NWD1_uc002net.3_Intron|NWD1_uc002nev.3_Intron					RecName: Full=NACHT and WD repeat domain-containing protein 1;								ATP binding			skin(3)|ovary(2)|pancreas(2)	7																		---	---	---	---
NWD1	284434	broad.mit.edu	37	19	16893673	16893676	+	Intron	DEL	TTCT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16893673_16893676delTTCT	uc002neu.3	+						NWD1_uc002net.3_Intron|NWD1_uc002nev.3_Intron					RecName: Full=NACHT and WD repeat domain-containing protein 1;								ATP binding			skin(3)|ovary(2)|pancreas(2)	7																		---	---	---	---
SIN3B	23309	broad.mit.edu	37	19	16941876	16941878	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16941876_16941878delTTT	uc002ney.1	+						SIN3B_uc002new.2_Intron|SIN3B_uc002nex.2_Intron|SIN3B_uc002nez.1_Intron	NM_015260	NP_056075			SIN3 homolog B, transcription regulator						cellular lipid metabolic process|transcription, DNA-dependent	nucleoplasm	protein binding			ovary(2)	2																		---	---	---	---
HAUS8	93323	broad.mit.edu	37	19	17170524	17170524	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17170524delT	uc002nfe.2	-						HAUS8_uc002nff.2_Intron|HAUS8_uc002nfg.1_Intron|HAUS8_uc002nfh.1_Intron	NM_033417	NP_219485			sarcoma antigen NY-SAR-48 isoform a						cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|spindle pole					0																		---	---	---	---
USHBP1	83878	broad.mit.edu	37	19	17369974	17369974	+	Intron	DEL	A	-	-	rs80351288		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17369974delA	uc002nfs.1	-						USHBP1_uc002nfr.1_5'Flank|USHBP1_uc002nft.1_Intron|USHBP1_uc010xpk.1_Intron|USHBP1_uc010eam.1_Intron	NM_031941	NP_114147			Usher syndrome 1C binding protein 1								PDZ domain binding			ovary(1)	1																		---	---	---	---
USHBP1	83878	broad.mit.edu	37	19	17374674	17374674	+	Intron	DEL	A	-	-	rs77430153		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17374674delA	uc002nfs.1	-						USHBP1_uc002nft.1_Intron|USHBP1_uc010xpk.1_Intron|USHBP1_uc010eam.1_5'UTR	NM_031941	NP_114147			Usher syndrome 1C binding protein 1								PDZ domain binding			ovary(1)	1																		---	---	---	---
ANKLE1	126549	broad.mit.edu	37	19	17395193	17395193	+	Intron	DEL	T	-	-	rs68029926		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17395193delT	uc002nga.2	+						ANKLE1_uc010xpm.1_Intron|ANKLE1_uc010eao.1_Intron|ANKLE1_uc010xpn.1_Intron|ANKLE1_uc002nfy.2_Intron|ANKLE1_uc002nfz.2_Intron	NM_152363	NP_689576			ankyrin repeat domain 41							nuclear envelope					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	17494010	17494010	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17494010delT								PLVAP (5873 upstream) : BST2 (19746 downstream)																																			---	---	---	---
FAM129C	199786	broad.mit.edu	37	19	17638883	17638883	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17638883delT	uc010xpr.1	+						FAM129C_uc010xpq.1_Intron|FAM129C_uc010xps.1_Intron|FAM129C_uc010xpt.1_Intron	NM_173544	NP_775815			B-cell novel protein 1 isoform a												0																		---	---	---	---
UNC13A	23025	broad.mit.edu	37	19	17789381	17789382	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17789381_17789382insT	uc002nhd.2	-							NM_001080421	NP_001073890			unc-13 homolog A						exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	17824162	17824163	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17824162_17824163delTT								UNC13A (24761 upstream) : MAP1S (6140 downstream)																																			---	---	---	---
MAP1S	55201	broad.mit.edu	37	19	17840322	17840323	+	Intron	INS	-	T	T	rs75073135		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17840322_17840323insT	uc002nhe.1	+						MAP1S_uc010eba.1_Intron|MAP1S_uc002nhf.1_Intron|MAP1S_uc010xpv.1_Intron	NM_018174	NP_060644			BPY2 interacting protein 1						apoptosis|brain development|microtubule bundle formation|mitochondrion transport along microtubule|neuron projection morphogenesis	cytosol|dendrite|microtubule|neuronal cell body|nucleus|perinuclear region of cytoplasm|spindle|synapse	actin filament binding|beta-tubulin binding|DNA binding|microtubule binding			central_nervous_system(1)	1																		---	---	---	---
ARRDC2	27106	broad.mit.edu	37	19	18111475	18111476	+	5'Flank	INS	-	GGAA	GGAA	rs141584055	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18111475_18111476insGGAA	uc002nhu.2	+							NM_001025604	NP_001020775			arrestin domain containing 2 isoform 2											pancreas(1)	1																		---	---	---	---
PGPEP1	54858	broad.mit.edu	37	19	18475058	18475058	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18475058delT	uc002nis.1	+	5					PGPEP1_uc002nit.1_3'UTR|PGPEP1_uc010xqg.1_3'UTR	NM_017712	NP_060182			pyroglutamyl-peptidase I								cysteine-type peptidase activity				0																		---	---	---	---
ELL	8178	broad.mit.edu	37	19	18555752	18555752	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18555752delC	uc002njh.2	-						ELL_uc010ebq.2_Intron|ELL_uc002njg.2_Intron	NM_006532	NP_006523			elongation factor RNA polymerase II						positive regulation of transcription elongation, DNA-dependent|positive regulation of viral transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	Cajal body|nuclear speck|transcription elongation factor complex	protein binding			lung(1)	1				GBM - Glioblastoma multiforme(1328;7.81e-07)				T	MLL	AL								---	---	---	---
C19orf50	79036	broad.mit.edu	37	19	18676041	18676044	+	Intron	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18676041_18676044delTTTT	uc002njo.2	+						C19orf50_uc002njp.2_Intron|C19orf50_uc002njq.2_Intron	NM_024069	NP_076974			hypothetical protein LOC79036								protein binding				0																		---	---	---	---
TMEM59L	25789	broad.mit.edu	37	19	18727191	18727191	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18727191delT	uc002njy.3	+						TMEM59L_uc010ebu.1_Intron	NM_012109	NP_036241			brain-specific membrane-anchored protein							Golgi membrane|integral to membrane|membrane fraction				ovary(2)|skin(2)	4																		---	---	---	---
CRTC1	23373	broad.mit.edu	37	19	18863456	18863457	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18863456_18863457delTT	uc002nkb.3	+						CRTC1_uc010ebv.2_Intron|CRTC1_uc010ebw.2_Intron|CRTC1_uc002nkc.3_Intron	NM_015321	NP_056136			mucoepidermoid carcinoma translocated 1 isoform						interspecies interaction between organisms|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	cAMP response element binding protein binding|protein binding		CRTC1/MAML2(516)	salivary_gland(474)|lung(35)|thyroid(4)|breast(3)|skin(2)|ovary(1)	519																		---	---	---	---
COPE	11316	broad.mit.edu	37	19	19023131	19023131	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19023131delT	uc002nkk.2	-						COPE_uc002nkl.2_Intron|COPE_uc002nkm.2_Intron|COPE_uc002nkn.2_Intron|HOMER3_uc002nko.1_Intron|HOMER3_uc002nkp.1_Intron	NM_007263	NP_009194			epsilon subunit of coatomer protein complex						COPI coating of Golgi vesicle|intra-Golgi vesicle-mediated transport|protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol	binding|structural molecule activity				0																		---	---	---	---
SLC25A42	284439	broad.mit.edu	37	19	19218457	19218457	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19218457delA	uc002nlf.1	+							NM_178526	NP_848621			solute carrier family 25, member 42						transmembrane transport	integral to membrane|mitochondrial inner membrane	binding				0			OV - Ovarian serous cystadenocarcinoma(5;5.4e-06)|Epithelial(12;0.000497)															---	---	---	---
MEF2B	100271849	broad.mit.edu	37	19	19279582	19279582	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19279582delT	uc002nlm.2	-						MEF2B_uc002nln.2_Intron|MEF2B_uc002nll.2_Intron|LOC729991-MEF2B_uc010xqo.1_Intron|LOC729991-MEF2B_uc010xqp.1_Intron|LOC729991-MEF2B_uc002nlo.2_Intron|LOC729991-MEF2B_uc002nlp.2_Intron|MEF2B_uc002nlk.2_Intron	NM_001145785	NP_001139257			myocyte enhancer factor 2B isoform a											skin(1)	1			OV - Ovarian serous cystadenocarcinoma(5;0.00011)|Epithelial(12;0.00412)															---	---	---	---
ZNF93	81931	broad.mit.edu	37	19	20025912	20025912	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20025912delT	uc002non.2	+						ZNF93_uc002nom.2_Intron	NM_031218	NP_112495			zinc finger protein 93							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			pancreas(1)	1																		---	---	---	---
ZNF826	664701	broad.mit.edu	37	19	20471388	20471388	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20471388delA	uc002now.1	-						ZNF826_uc010ecl.1_Intron					Homo sapiens cDNA FLJ44894 fis, clone BRAMY3000692, moderately similar to Zinc finger protein 91.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	20905475	20905475	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20905475delT								ZNF626 (61073 upstream) : ZNF85 (200605 downstream)																																			---	---	---	---
ZNF430	80264	broad.mit.edu	37	19	21238433	21238433	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21238433delT	uc002npj.2	+						ZNF430_uc002npk.2_Intron	NM_025189	NP_079465			zinc finger protein 430						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)	2																		---	---	---	---
ZNF493	284443	broad.mit.edu	37	19	21586460	21586460	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21586460delT	uc002npx.2	+						ZNF493_uc002npu.2_Intron|ZNF493_uc002npw.2_Intron|ZNF493_uc002npy.2_Intron	NM_175910	NP_787106			zinc finger protein 493 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
ZNF429	353088	broad.mit.edu	37	19	21728866	21728866	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21728866delT	uc010ecu.1	+											Homo sapiens KRAB zinc finger protein HZF26 (HZF26) mRNA, partial cds.						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2																		---	---	---	---
ZNF43	7594	broad.mit.edu	37	19	22002026	22002026	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22002026delA	uc002nqj.2	-						ZNF43_uc010ecv.2_Intron|ZNF43_uc002nql.2_Intron|ZNF43_uc002nqm.2_Intron|ZNF43_uc002nqk.2_Intron	NM_003423	NP_003414			zinc finger protein 43						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2		Renal(1328;0.000219)|Hepatocellular(1079;0.121)		GBM - Glioblastoma multiforme(1328;5.97e-05)|STAD - Stomach adenocarcinoma(1328;0.0127)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	22074949	22074949	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22074949delT								ZNF43 (40119 upstream) : ZNF208 (40811 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	22293004	22293005	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22293004_22293005delTT								ZNF257 (19103 upstream) : ZNF676 (68898 downstream)																																			---	---	---	---
ZNF98	148198	broad.mit.edu	37	19	22583777	22583777	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22583777delA	uc002nqt.2	-							NM_001098626	NP_001092096			zinc finger protein 98						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)																---	---	---	---
Unknown	0	broad.mit.edu	37	19	22678835	22678835	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22678835delT								ZNF98 (73687 upstream) : ZNF492 (138291 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	22936591	22936591	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22936591delT								ZNF492 (86119 upstream) : ZNF99 (2418 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	23277010	23277010	+	IGR	DEL	T	-	-	rs113278715		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23277010delT								ZNF99 (324226 upstream) : ZNF91 (244409 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	23309536	23309536	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23309536delT	uc002nrb.1	+											Homo sapiens cDNA FLJ16640 fis, clone TESTI4028938, moderately similar to Zinc finger protein 85.																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	23404386	23404387	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23404386_23404387delTT								ZNF99 (451602 upstream) : ZNF91 (117032 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	23652669	23652669	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23652669delT								ZNF91 (74400 upstream) : ZNF675 (183040 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	23676196	23676196	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:23676196delT								ZNF91 (97927 upstream) : ZNF675 (159513 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	24117301	24117301	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24117301delT	uc002nrp.1	-											Homo sapiens cDNA FLJ43698 fis, clone TCERX2000998.																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	24434342	24434343	+	IGR	INS	-	T	T	rs141420540	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24434342_24434343insT								LOC100101266 (88093 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	24497483	24497483	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24497483delT								LOC100101266 (151234 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	24557741	24557742	+	IGR	INS	-	AT	AT	rs142570266	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24557741_24557742insAT								LOC100101266 (211492 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	24562814	24562825	+	IGR	DEL	TCTTTTGATTGA	-	-	rs113432942		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24562814_24562825delTCTTTTGATTGA								LOC100101266 (216565 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	24572153	24572154	+	IGR	INS	-	T	T	rs112196152		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:24572153_24572154insT								LOC100101266 (225904 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	27775532	27775532	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27775532delT								None (None upstream) : LOC148189 (505870 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	27858710	27858710	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:27858710delA								None (None upstream) : LOC148189 (422692 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	28214331	28214332	+	IGR	INS	-	T	T	rs117603506	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28214331_28214332insT								None (None upstream) : LOC148189 (67070 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	28650412	28650413	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28650412_28650413delTG								LOC148189 (365564 upstream) : LOC148145 (805627 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	28723197	28723197	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28723197delA								LOC148189 (438349 upstream) : LOC148145 (732843 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	28747184	28747184	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:28747184delA								LOC148189 (462336 upstream) : LOC148145 (708856 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	29327007	29327008	+	IGR	INS	-	G	G	rs149030613	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29327007_29327008insG								None (None upstream) : LOC148145 (129032 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	29348795	29348796	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29348795_29348796delTT								None (None upstream) : LOC148145 (107244 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	29487688	29487689	+	IGR	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:29487688_29487689delCT								LOC148145 (27633 upstream) : UQCRFS1 (210478 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	30149535	30149535	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30149535delT								POP4 (41373 upstream) : PLEKHF1 (6792 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	30379711	30379711	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30379711delA								CCNE1 (64493 upstream) : C19orf2 (34840 downstream)																																			---	---	---	---
C19orf2	8725	broad.mit.edu	37	19	30477171	30477171	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30477171delT	uc002nsr.2	+						C19orf2_uc002nsq.2_Intron|C19orf2_uc002nss.2_Intron|C19orf2_uc002nst.2_Intron	NM_003796	NP_003787			RPB5-mediating protein isoform a						protein folding|regulation of transcription from RNA polymerase II promoter|response to virus	DNA-directed RNA polymerase II, core complex|prefoldin complex	transcription corepressor activity|unfolded protein binding			ovary(1)|kidney(1)	2	Ovarian(5;0.000902)|Breast(6;0.0203)|Esophageal squamous(110;0.195)	Hepatocellular(1079;0.137)|Renal(1328;0.228)	STAD - Stomach adenocarcinoma(5;5.36e-06)|Lung(7;0.0144)|LUAD - Lung adenocarcinoma(5;0.115)	STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	30565350	30565350	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30565350delC								C19orf2 (58739 upstream) : ZNF536 (297978 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	30696789	30696789	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30696789delA								C19orf2 (190178 upstream) : ZNF536 (166539 downstream)																																			---	---	---	---
ZNF536	9745	broad.mit.edu	37	19	30960319	30960319	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30960319delA	uc002nsu.1	+						ZNF536_uc010edd.1_Intron	NM_014717	NP_055532			zinc finger protein 536						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(7)|large_intestine(2)|skin(2)	11	Esophageal squamous(110;0.0834)																	---	---	---	---
Unknown	0	broad.mit.edu	37	19	31185583	31185583	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31185583delT								ZNF536 (136618 upstream) : DKFZp566F0947 (455200 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	31461400	31461400	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31461400delT								ZNF536 (412435 upstream) : DKFZp566F0947 (179383 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	31603838	31603839	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31603838_31603839insT								ZNF536 (554873 upstream) : DKFZp566F0947 (36944 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	31873812	31873813	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31873812_31873813delTG								TSHZ3 (33622 upstream) : ZNF507 (962701 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	31942304	31942305	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31942304_31942305insA								TSHZ3 (102114 upstream) : ZNF507 (894209 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	32526652	32526652	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32526652delA	uc002ntb.1	+											Homo sapiens cDNA FLJ40174 fis, clone TESTI2016996.																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	32699105	32699105	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32699105delC								TSHZ3 (858915 upstream) : ZNF507 (137409 downstream)																																			---	---	---	---
DPY19L3	147991	broad.mit.edu	37	19	32952165	32952165	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32952165delG	uc002ntg.2	+						DPY19L3_uc002nth.1_Intron|DPY19L3_uc002nti.1_Intron	NM_207325	NP_997208			dpy-19-like 3							integral to membrane				ovary(4)	4	Esophageal squamous(110;0.162)																	---	---	---	---
Unknown	0	broad.mit.edu	37	19	33087386	33087390	+	IGR	DEL	AAAAC	-	-	rs4805775		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33087386_33087390delAAAAC								PDCD5 (9064 upstream) : ANKRD27 (517 downstream)																																			---	---	---	---
TDRD12	91646	broad.mit.edu	37	19	33228446	33228447	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33228446_33228447insT	uc002ntq.2	+						TDRD12_uc002ntr.3_Intron					RecName: Full=Tudor domain-containing protein 12; AltName: Full=ES cell-associated transcript 8 protein;								ATP binding|ATP-dependent helicase activity|nucleic acid binding				0	Esophageal squamous(110;0.137)																	---	---	---	---
Unknown	0	broad.mit.edu	37	19	33317585	33317586	+	Intron	DEL	AC	-	-	rs67597657		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33317585_33317586delAC	uc002nts.1	+											Homo sapiens cDNA FLJ13072 fis, clone NT2RP3001844.																														---	---	---	---
CCDC123	84902	broad.mit.edu	37	19	33440291	33440291	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33440291delT	uc002nty.2	-						CCDC123_uc002ntx.2_Intron|CCDC123_uc010edg.2_Intron|CCDC123_uc002ntz.1_Intron|CCDC123_uc002nua.2_Intron|CCDC123_uc002nub.1_Intron	NM_032816	NP_116205			coiled-coil domain containing 123							centrosome|spindle pole					0	Esophageal squamous(110;0.137)																	---	---	---	---
RHPN2	85415	broad.mit.edu	37	19	33499157	33499161	+	Intron	DEL	TTTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33499157_33499161delTTTTT	uc002nuf.2	-						RHPN2_uc010xro.1_Intron|RHPN2_uc002nue.2_Intron	NM_033103	NP_149094			rhophilin, Rho GTPase binding protein 2						signal transduction	perinuclear region of cytoplasm	protein binding			central_nervous_system(5)|ovary(1)	6	Esophageal squamous(110;0.137)																	---	---	---	---
GPATCH1	55094	broad.mit.edu	37	19	33582956	33582957	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33582956_33582957delTT	uc002nug.1	+							NM_018025	NP_060495			G patch domain containing 1							catalytic step 2 spliceosome	nucleic acid binding			skin(1)	1	Esophageal squamous(110;0.137)																	---	---	---	---
GPATCH1	55094	broad.mit.edu	37	19	33587442	33587442	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33587442delT	uc002nug.1	+							NM_018025	NP_060495			G patch domain containing 1							catalytic step 2 spliceosome	nucleic acid binding			skin(1)	1	Esophageal squamous(110;0.137)																	---	---	---	---
GPATCH1	55094	broad.mit.edu	37	19	33617450	33617450	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33617450delA	uc002nug.1	+						GPATCH1_uc002nuh.1_Intron	NM_018025	NP_060495			G patch domain containing 1							catalytic step 2 spliceosome	nucleic acid binding			skin(1)	1	Esophageal squamous(110;0.137)															OREG0025410	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SLC7A10	56301	broad.mit.edu	37	19	33708250	33708250	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33708250delG	uc002num.2	-						SLC7A10_uc010xrq.1_Intron	NM_019849	NP_062823			solute carrier family 7, member 10						blood coagulation|cellular nitrogen compound metabolic process|ion transport|leukocyte migration	integral to plasma membrane	L-serine transmembrane transporter activity			ovary(1)|central_nervous_system(1)	2	Esophageal squamous(110;0.137)																	---	---	---	---
Unknown	0	broad.mit.edu	37	19	33827824	33827825	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33827824_33827825delAA								LOC80054 (31862 upstream) : CEBPG (36784 downstream)																																			---	---	---	---
PEPD	5184	broad.mit.edu	37	19	33887538	33887538	+	Intron	DEL	C	-	-	rs74713374		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33887538delC	uc002nur.3	-						PEPD_uc010xrr.1_Intron|PEPD_uc010xrs.1_Intron	NM_000285	NP_000276			prolidase isoform 1						cellular amino acid metabolic process|collagen catabolic process|proteolysis		aminopeptidase activity|dipeptidase activity|manganese ion binding|metallocarboxypeptidase activity			ovary(2)	2	Esophageal squamous(110;0.137)																	---	---	---	---
PEPD	5184	broad.mit.edu	37	19	33888617	33888617	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33888617delG	uc002nur.3	-						PEPD_uc010xrr.1_Intron|PEPD_uc010xrs.1_Intron	NM_000285	NP_000276			prolidase isoform 1						cellular amino acid metabolic process|collagen catabolic process|proteolysis		aminopeptidase activity|dipeptidase activity|manganese ion binding|metallocarboxypeptidase activity			ovary(2)	2	Esophageal squamous(110;0.137)																	---	---	---	---
PEPD	5184	broad.mit.edu	37	19	33984135	33984135	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33984135delC	uc002nur.3	-						PEPD_uc010xrr.1_Intron|PEPD_uc010xrs.1_Intron	NM_000285	NP_000276			prolidase isoform 1						cellular amino acid metabolic process|collagen catabolic process|proteolysis		aminopeptidase activity|dipeptidase activity|manganese ion binding|metallocarboxypeptidase activity			ovary(2)	2	Esophageal squamous(110;0.137)																	---	---	---	---
CHST8	64377	broad.mit.edu	37	19	34156544	34156545	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34156544_34156545delAA	uc002nus.3	+						CHST8_uc002nut.3_Intron	NM_001127895	NP_001121367			carbohydrate (N-acetylgalactosamine 4-0)						carbohydrate biosynthetic process|central nervous system development|hormone biosynthetic process|proteoglycan biosynthetic process|sulfur compound metabolic process	Golgi membrane|integral to membrane	N-acetylgalactosamine 4-O-sulfotransferase activity			skin(2)|large_intestine(1)|ovary(1)	4	Esophageal squamous(110;0.162)																	---	---	---	---
Unknown	0	broad.mit.edu	37	19	34425424	34425424	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34425424delA								KCTD15 (118759 upstream) : LSM14A (237928 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	34432331	34432331	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34432331delT								KCTD15 (125666 upstream) : LSM14A (231021 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	34443675	34443675	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34443675delT								KCTD15 (137010 upstream) : LSM14A (219677 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	34450442	34450444	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34450442_34450444delTTT								KCTD15 (143777 upstream) : LSM14A (212908 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	34609020	34609020	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34609020delA								KCTD15 (302355 upstream) : LSM14A (54332 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	35021191	35021192	+	IGR	INS	-	T	T	rs57251432	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35021191_35021192insT								WTIP (29107 upstream) : LOC643719 (46447 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	35390729	35390730	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35390729_35390730insT								ZNF599 (126595 upstream) : ZNF30 (27077 downstream)																																			---	---	---	---
HPN	3249	broad.mit.edu	37	19	35532835	35532835	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35532835delC	uc002nxq.1	+						HPN_uc002nxr.1_5'UTR|HPN_uc002nxs.1_Intron	NM_002151	NP_002142			hepsin						cell growth|proteolysis	cytoplasm|integral to plasma membrane	scavenger receptor activity|serine-type endopeptidase activity			ovary(1)|central_nervous_system(1)	2	all_lung(56;5.38e-08)|Lung NSC(56;8.61e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)		Coagulation factor VIIa(DB00036)													---	---	---	---
LOC100128675	100128675	broad.mit.edu	37	19	35550387	35550388	+	3'UTR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35550387_35550388delAA	uc010xsi.1	-	4					HPN_uc002nxq.1_Intron|HPN_uc002nxr.1_Intron|HPN_uc002nxs.1_Intron|HPN_uc010xsh.1_Intron|HPN_uc002nxt.1_Intron	NR_024562				SubName: Full=cDNA FLJ57934;												0																		---	---	---	---
HPN	3249	broad.mit.edu	37	19	35556034	35556034	+	Intron	DEL	T	-	-	rs113406953		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35556034delT	uc002nxq.1	+						HPN_uc002nxr.1_Intron|HPN_uc002nxs.1_Intron|HPN_uc010xsh.1_Intron|HPN_uc002nxt.1_Intron|LOC100128675_uc010xsi.1_Intron	NM_002151	NP_002142			hepsin						cell growth|proteolysis	cytoplasm|integral to plasma membrane	scavenger receptor activity|serine-type endopeptidase activity			ovary(1)|central_nervous_system(1)	2	all_lung(56;5.38e-08)|Lung NSC(56;8.61e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)		Coagulation factor VIIa(DB00036)													---	---	---	---
LOC100128675	100128675	broad.mit.edu	37	19	35567519	35567519	+	Intron	DEL	A	-	-	rs111841547		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35567519delA	uc010xsi.1	-						LOC100128675_uc002nxu.2_Intron	NR_024562				SubName: Full=cDNA FLJ57934;												0																		---	---	---	---
LOC100128675	100128675	broad.mit.edu	37	19	35588534	35588534	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35588534delC	uc010xsi.1	-						LOC100128675_uc002nxu.2_Intron	NR_024562				SubName: Full=cDNA FLJ57934;												0																		---	---	---	---
TMEM147	10430	broad.mit.edu	37	19	36037111	36037111	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36037111delT	uc002oaj.1	+						uc010eec.1_5'Flank|uc002oag.2_5'Flank|TMEM147_uc002oai.1_Intron|TMEM147_uc002oak.1_Intron	NM_032635	NP_116024			transmembrane protein 147							endoplasmic reticulum membrane|integral to membrane	protein binding				0	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	36074583	36074583	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36074583delT								ATP4A (20023 upstream) : HAUS5 (29063 downstream)																																			---	---	---	---
MLL4	9757	broad.mit.edu	37	19	36224445	36224445	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36224445delG	uc010eei.2	+							NM_014727	NP_055542			myeloid/lymphoid or mixed-lineage leukemia 4						chromatin-mediated maintenance of transcription		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(6)|breast(2)|ovary(1)|kidney(1)|skin(1)	11	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	36375308	36375310	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36375308_36375310delTTT								APLP1 (4610 upstream) : NFKBID (3833 downstream)																																			---	---	---	---
CLIP3	25999	broad.mit.edu	37	19	36520925	36520925	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36520925delC	uc010eeq.1	-						uc002ocy.2_Intron|CLIP3_uc002ocz.1_Intron	NM_015526	NP_056341			CAP-GLY domain containing linker protein 3						chaperone-mediated protein transport|fat cell differentiation|membrane biogenesis|negative regulation of microtubule polymerization|peptidyl-L-cysteine S-palmitoylation|positive regulation of apoptosis|positive regulation of endocytosis|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose transport|positive regulation of protein phosphorylation	early endosome membrane|Golgi stack|membrane raft|microsome|plasma membrane|recycling endosome membrane|trans-Golgi network membrane	ganglioside binding|microtubule binding			ovary(2)|pancreas(1)|skin(1)	4	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)															---	---	---	---
COX7A1	1346	broad.mit.edu	37	19	36642553	36642553	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36642553delC	uc002odm.1	-							NM_001864	NP_001855			cytochrome c oxidase subunit VIIa polypeptide 1						generation of precursor metabolites and energy	integral to membrane|mitochondrial respiratory chain	cytochrome-c oxidase activity|electron carrier activity				0	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)															---	---	---	---
ZNF565	147929	broad.mit.edu	37	19	36679283	36679283	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36679283delA	uc002odn.2	-						ZNF565_uc010ees.2_Intron|ZNF565_uc002odo.2_Intron	NM_152477	NP_689690			zinc finger protein 565						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.206)															---	---	---	---
ZNF146	7705	broad.mit.edu	37	19	36728810	36728810	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36728810delA	uc002odq.3	+	4					ZNF146_uc010eet.2_3'UTR|ZNF146_uc010eeu.2_3'UTR	NM_007145	NP_009076			zinc finger protein 146						regulation of transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|heparin binding|zinc ion binding				0	Esophageal squamous(110;0.162)																	---	---	---	---
ZFP14	57677	broad.mit.edu	37	19	36836248	36836248	+	Intron	DEL	T	-	-	rs111615942		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36836248delT	uc002odx.1	-						ZFP14_uc010xtd.1_Intron|ZFP14_uc010eex.1_Intron	NM_020917	NP_065968			zinc finger protein 14-like						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Esophageal squamous(110;0.162)																	---	---	---	---
ZFP14	57677	broad.mit.edu	37	19	36866898	36866898	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36866898delT	uc010eex.1	-							NM_020917	NP_065968			zinc finger protein 14-like						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Esophageal squamous(110;0.162)																	---	---	---	---
Unknown	0	broad.mit.edu	37	19	37548509	37548509	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37548509delT								ZNF568 (59675 upstream) : ZNF420 (20873 downstream)																																			---	---	---	---
HKR1	284459	broad.mit.edu	37	19	37828133	37828133	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37828133delC	uc002ogb.2	+						HKR1_uc002ofx.2_Intron|HKR1_uc002ofy.2_Intron|HKR1_uc002ofz.2_Intron|HKR1_uc002oga.2_Intron|HKR1_uc010xto.1_Intron|HKR1_uc002ogc.2_Intron|HKR1_uc010xtp.1_Intron	NM_181786	NP_861451			GLI-Kruppel family member HKR1						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)															---	---	---	---
HKR1	284459	broad.mit.edu	37	19	37831546	37831547	+	Intron	INS	-	TT	TT			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37831546_37831547insTT	uc002ogb.2	+						HKR1_uc002ofx.2_Intron|HKR1_uc002ofy.2_Intron|HKR1_uc002ofz.2_Intron|HKR1_uc002oga.2_Intron|HKR1_uc010xto.1_Intron|HKR1_uc002ogc.2_Intron|HKR1_uc010xtp.1_Intron	NM_181786	NP_861451			GLI-Kruppel family member HKR1						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)															---	---	---	---
SIPA1L3	23094	broad.mit.edu	37	19	38504046	38504046	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38504046delA	uc002ohk.2	+							NM_015073	NP_055888			signal-induced proliferation-associated 1 like						regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(1)|central_nervous_system(1)	2			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	38733427	38733428	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38733427_38733428insA								DPF1 (13110 upstream) : PPP1R14A (8451 downstream)																																			---	---	---	---
RYR1	6261	broad.mit.edu	37	19	39021450	39021450	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39021450delT	uc002oit.2	+						RYR1_uc002oiu.2_Intron|RYR1_uc002oiv.1_Intron|RYR1_uc010xuf.1_Intron	NM_000540	NP_000531			skeletal muscle ryanodine receptor isoform 1						muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)													---	---	---	---
MAP4K1	11184	broad.mit.edu	37	19	39096484	39096485	+	Intron	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39096484_39096485insC	uc002oix.1	-						MAP4K1_uc002oiw.1_Intron|MAP4K1_uc002oiy.1_Intron|MAP4K1_uc010xug.1_Intron	NM_007181	NP_009112			mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity|peptidyl-serine phosphorylation		ATP binding|MAP kinase kinase kinase kinase activity|protein binding|small GTPase regulator activity			skin(4)|lung(3)|ovary(1)	8	all_cancers(60;6.42e-06)|Ovarian(47;0.103)		Lung(45;0.000751)|LUSC - Lung squamous cell carcinoma(53;0.00272)															---	---	---	---
EIF3K	27335	broad.mit.edu	37	19	39125240	39125241	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39125240_39125241delAA	uc002oiz.1	+						EIF3K_uc010xuh.1_Intron|EIF3K_uc010xui.1_Intron	NM_013234	NP_037366			eukaryotic translation initiation factor 3,						regulation of translational initiation	cytosol|eukaryotic translation initiation factor 3 complex|nucleus	protein binding|ribosome binding|translation initiation factor activity			ovary(1)|central_nervous_system(1)	2	all_cancers(60;6.42e-06)|Ovarian(47;0.103)		Lung(45;0.000751)|LUSC - Lung squamous cell carcinoma(53;0.00272)															---	---	---	---
LGALS4	3960	broad.mit.edu	37	19	39293326	39293327	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39293326_39293327delTT	uc002ojg.2	-							NM_006149	NP_006140			galectin-4						cell adhesion	cytosol|plasma membrane	sugar binding			ovary(1)|skin(1)	2	all_cancers(60;1.02e-05)|Ovarian(47;0.0454)		Lung(45;0.00416)|LUSC - Lung squamous cell carcinoma(53;0.00741)															---	---	---	---
LGALS4	3960	broad.mit.edu	37	19	39294122	39294122	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39294122delC	uc002ojg.2	-						LGALS4_uc010xuj.1_3'UTR	NM_006149	NP_006140			galectin-4						cell adhesion	cytosol|plasma membrane	sugar binding			ovary(1)|skin(1)	2	all_cancers(60;1.02e-05)|Ovarian(47;0.0454)		Lung(45;0.00416)|LUSC - Lung squamous cell carcinoma(53;0.00741)															---	---	---	---
SARS2	54938	broad.mit.edu	37	19	39407123	39407123	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39407123delA	uc002oka.2	-						SARS2_uc002ojz.2_Intron|SARS2_uc010xup.1_Intron|SARS2_uc002okb.2_Intron|SARS2_uc010xuq.1_Intron	NM_017827	NP_060297			seryl-tRNA synthetase 2 isoform b precursor						seryl-tRNA aminoacylation	mitochondrial matrix	ATP binding|protein binding|serine-tRNA ligase activity			ovary(1)|pancreas(1)|skin(1)	3	all_cancers(60;2.74e-06)|all_epithelial(25;4.36e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)															---	---	---	---
SARS2	54938	broad.mit.edu	37	19	39408522	39408522	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39408522delC	uc002oka.2	-						SARS2_uc002ojz.2_Intron|SARS2_uc010xup.1_Intron|SARS2_uc002okb.2_Intron|SARS2_uc010xuq.1_Intron|SARS2_uc010xur.1_Intron	NM_017827	NP_060297			seryl-tRNA synthetase 2 isoform b precursor						seryl-tRNA aminoacylation	mitochondrial matrix	ATP binding|protein binding|serine-tRNA ligase activity			ovary(1)|pancreas(1)|skin(1)	3	all_cancers(60;2.74e-06)|all_epithelial(25;4.36e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)															---	---	---	---
NCCRP1	342897	broad.mit.edu	37	19	39686777	39686778	+	5'Flank	INS	-	A	A	rs147413791	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39686777_39686778insA	uc002okq.1	+							NM_001001414	NP_001001414			non-specific cytotoxic cell receptor protein 1						protein catabolic process					ovary(1)	1																		---	---	---	---
SAMD4B	55095	broad.mit.edu	37	19	39864427	39864427	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39864427delC	uc002olb.2	+						SAMD4B_uc002ola.2_Intron	NM_018028	NP_060498			sterile alpha motif domain containing 4B								protein binding				0	all_cancers(60;2.5e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;9.6e-28)|all cancers(26;9.14e-25)|Lung(45;0.000168)|LUSC - Lung squamous cell carcinoma(53;0.000199)															---	---	---	---
ZFP36	7538	broad.mit.edu	37	19	39899575	39899575	+	3'UTR	DEL	A	-	-	rs75936692		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39899575delA	uc002olh.1	+	2					ZFP36_uc010egn.1_3'UTR	NM_003407	NP_003398			zinc finger protein 36, C3H type, homolog						positive regulation of nuclear-transcribed mRNA poly(A) tail shortening	cytosol|nucleus	AU-rich element binding|DNA binding|mRNA binding|protein binding|single-stranded RNA binding|zinc ion binding			pancreas(1)	1	all_cancers(60;6.54e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;1.53e-06)|Ovarian(47;0.0512)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)															---	---	---	---
TIMM50	92609	broad.mit.edu	37	19	39981205	39981206	+	3'UTR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39981205_39981206insT	uc002olu.1	+	11					TIMM50_uc002olv.1_3'UTR	NM_001001563	NP_001001563			translocase of inner mitochondrial membrane 50						mitochondrial membrane organization|protein transport|release of cytochrome c from mitochondria|transmembrane transport	integral to membrane|mitochondrial inner membrane presequence translocase complex|nuclear speck	interleukin-2 receptor binding|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|ribonucleoprotein binding|RNA binding			ovary(1)	1	all_cancers(60;4.04e-06)|all_lung(34;1.77e-07)|Lung NSC(34;2.09e-07)|all_epithelial(25;1.13e-05)|Ovarian(47;0.159)		Epithelial(26;5.89e-26)|all cancers(26;1.96e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)															---	---	---	---
Unknown	0	broad.mit.edu	37	19	40058635	40058635	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40058635delT								EID2 (27797 upstream) : LGALS13 (34534 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	40101393	40101393	+	IGR	DEL	C	-	-	rs67358923		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40101393delC								LGALS13 (3280 upstream) : LOC100129935 (27932 downstream)																																			---	---	---	---
LOC400696	400696	broad.mit.edu	37	19	40175482	40175482	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40175482delT	uc010xve.1	+	4					LOC400696_uc010xvf.1_Intron	NM_207646	NP_997529			hypothetical protein LOC400696												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	40247370	40247370	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40247370delT								CLC (18702 upstream) : LEUTX (19864 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	40469949	40469949	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40469949delA								FCGBP (29416 upstream) : PSMC4 (7124 downstream)																																			---	---	---	---
LTBP4	8425	broad.mit.edu	37	19	41134754	41134754	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41134754delT	uc002ooh.1	+						LTBP4_uc002oog.1_Intron|LTBP4_uc002ooi.1_Intron|LTBP4_uc002ooj.1_Intron|LTBP4_uc002ool.1_Intron|LTBP4_uc010xvp.1_Intron	NM_001042544	NP_001036009			latent transforming growth factor beta binding						growth hormone secretion|multicellular organismal development|protein folding|regulation of cell differentiation|regulation of cell growth|regulation of proteolysis|regulation of transforming growth factor beta receptor signaling pathway	extracellular space|proteinaceous extracellular matrix	calcium ion binding|glycosaminoglycan binding|integrin binding|transforming growth factor beta binding|transforming growth factor beta receptor activity			central_nervous_system(1)	1			Lung(22;0.000158)|LUSC - Lung squamous cell carcinoma(20;0.000384)															---	---	---	---
EGLN2	112398	broad.mit.edu	37	19	41293441	41293441	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41293441delA	uc010ehd.2	+						RAB4B_uc002opc.1_Intron|RAB4B_uc002opd.1_Intron|RAB4B_uc002ope.1_Intron|RAB4B_uc002opf.1_Intron	NM_080732	NP_542770			EGL nine (C.elegans) homolog 2						cell redox homeostasis|estrogen receptor signaling pathway|positive regulation of protein catabolic process|regulation of cell growth|response to hypoxia	cytoplasm|nucleus	ferrous iron binding|L-ascorbic acid binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|oxygen sensor activity			ovary(2)	2			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Vitamin C(DB00126)													---	---	---	---
AXL	558	broad.mit.edu	37	19	41761985	41761986	+	Intron	INS	-	GT	GT	rs146112923	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41761985_41761986insGT	uc010ehj.2	+						CYP2F1_uc010xvw.1_Intron|AXL_uc010ehk.2_Intron	NM_021913	NP_068713			AXL receptor tyrosine kinase isoform 1							integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(4)|stomach(3)|ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)	13																		---	---	---	---
CEACAM3	1084	broad.mit.edu	37	19	42308324	42308325	+	Intron	DEL	CC	-	-	rs147364650		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42308324_42308325delCC	uc002orn.1	+						CEACAM3_uc010eia.1_Intron|CEACAM3_uc002oro.1_Intron	NM_001815	NP_001806			carcinoembryonic antigen-related cell adhesion							integral to membrane				skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	42318470	42318470	+	IGR	DEL	C	-	-	rs35918720		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42318470delC								CEACAM3 (2879 upstream) : LYPD4 (22680 downstream)																																			---	---	---	---
CD79A	973	broad.mit.edu	37	19	42384462	42384463	+	Intron	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42384462_42384463delAG	uc002orv.2	+						CD79A_uc002oru.2_Intron|ARHGEF1_uc002orw.1_5'Flank|ARHGEF1_uc002orx.2_5'Flank|ARHGEF1_uc002ory.2_5'Flank|ARHGEF1_uc002orz.2_5'Flank	NM_001783	NP_001774			CD79A antigen isoform 1 precursor						B cell differentiation|B cell proliferation|B cell receptor signaling pathway	B cell receptor complex|external side of plasma membrane|integral to membrane|membrane raft|multivesicular body	transmembrane receptor activity			ovary(2)|pancreas(1)	3								O|S		DLBCL								---	---	---	---
ARHGEF1	9138	broad.mit.edu	37	19	42416126	42416126	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42416126delC	uc002osc.2	+											SubName: Full=ARHGEF1 protein; SubName: Full=Rho guanine nucleotide exchange factor (GEF) 1, isoform CRA_g;						cell proliferation|negative regulation of axonogenesis|nerve growth factor receptor signaling pathway|positive regulation of axonogenesis|regulation of Rho protein signal transduction|Rho protein signal transduction	cytosol|plasma membrane	GTPase activator activity|protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(3)|large_intestine(1)	4		Renal(1328;0.000518)|Hepatocellular(1079;0.0046)|Medulloblastoma(540;0.0425)		Epithelial(262;5.89e-46)|GBM - Glioblastoma multiforme(1328;2.49e-12)|STAD - Stomach adenocarcinoma(1328;0.00644)														---	---	---	---
RABAC1	10567	broad.mit.edu	37	19	42466457	42466457	+	5'Flank	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42466457delG	uc002osf.2	-							NM_006423	NP_006414			Rab acceptor 1							cell junction|Golgi apparatus|integral to membrane|synaptic vesicle	identical protein binding				0																		---	---	---	---
GRIK5	2901	broad.mit.edu	37	19	42564732	42564735	+	Intron	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42564732_42564735delTTTT	uc002osj.1	-						GRIK5_uc010eib.1_Intron	NM_002088	NP_002079			glutamate receptor KA2 precursor							cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity				0		Prostate(69;0.059)			L-Glutamic Acid(DB00142)													---	---	---	---
Unknown	0	broad.mit.edu	37	19	42773911	42773911	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42773911delG								ERF (14602 upstream) : CIC (14906 downstream)																																			---	---	---	---
CIC	23152	broad.mit.edu	37	19	42792902	42792902	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42792902delT	uc002otf.1	+							NM_015125	NP_055940			capicua homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			ovary(4)|breast(4)|lung(1)|central_nervous_system(1)|skin(1)	11		Prostate(69;0.00682)						T	DUX4	soft tissue sarcoma								---	---	---	---
CIC	23152	broad.mit.edu	37	19	42797376	42797376	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42797376delC	uc002otf.1	+	15	3778	c.3738delC	c.(3736-3738)AGCfs	p.S1246fs		NM_015125	NP_055940	Q96RK0	CIC_HUMAN	capicua homolog	1246	Pro-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			ovary(4)|breast(4)|lung(1)|central_nervous_system(1)|skin(1)	11		Prostate(69;0.00682)						T	DUX4	soft tissue sarcoma								---	---	---	---
CNFN	84518	broad.mit.edu	37	19	42895172	42895172	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42895172delA	uc002otp.3	-						CNFN_uc002otq.3_5'Flank	NM_032488	NP_115877			cornifelin						keratinization	cornified envelope|cytoplasm					0		Prostate(69;0.00899)																---	---	---	---
CEACAM8	1088	broad.mit.edu	37	19	43086348	43086348	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43086348delG	uc002oud.2	-						uc010eif.1_Intron|uc010eig.1_Intron|uc010eih.1_Intron	NM_001816	NP_001807			carcinoembryonic antigen-related cell adhesion						immune response	anchored to membrane|extracellular space|integral to plasma membrane				ovary(1)	1		Prostate(69;0.00899)																---	---	---	---
Unknown	0	broad.mit.edu	37	19	43155321	43155321	+	RNA	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43155321delC	uc010eif.1	+	3		c.262delC			uc010eig.1_RNA|uc010eih.1_RNA					Homo sapiens cDNA FLJ39530 fis, clone PUAEN2004400.																														---	---	---	---
PSG8	440533	broad.mit.edu	37	19	43269031	43269031	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43269031delT	uc002ouo.2	-						PSG3_uc002ouf.2_Intron|PSG1_uc002oug.1_Intron|PSG8_uc002oui.2_Intron|PSG8_uc002ouh.2_Intron|PSG8_uc010ein.2_Intron|PSG8_uc002ouj.3_Intron|PSG8_uc002ouk.3_Intron|PSG8_uc002oul.3_Intron|PSG8_uc002oum.3_Intron|PSG1_uc002oun.2_Intron|PSG8_uc002oup.3_Intron	NM_182707	NP_874366			pregnancy specific beta-1-glycoprotein 8 isoform							extracellular region					0		Prostate(69;0.00899)																---	---	---	---
PSG8	440533	broad.mit.edu	37	19	43339875	43339875	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43339875delA	uc002oul.3	-						PSG3_uc002ouf.2_Intron|PSG1_uc002oug.1_Intron|PSG8_uc002ouj.3_Intron|PSG8_uc002ouk.3_Intron|PSG8_uc002oum.3_Intron|PSG1_uc002oun.2_Intron|PSG8_uc002oup.3_Intron	NM_001130168	NP_001123640			pregnancy specific beta-1-glycoprotein 8 isoform							extracellular region					0		Prostate(69;0.00899)																---	---	---	---
PSG1	5669	broad.mit.edu	37	19	43343691	43343691	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43343691delT	uc010eio.1	-						PSG3_uc002ouf.2_Intron|PSG1_uc002oug.1_Intron|PSG11_uc002ouw.2_Intron|PSG7_uc002ous.1_Intron|PSG7_uc002out.1_Intron|PSG10_uc002ouv.1_Intron|PSG8_uc002ouj.3_Intron|PSG8_uc002ouk.3_Intron|PSG8_uc002oul.3_Intron|PSG8_uc002oum.3_Intron|PSG1_uc002oun.2_Intron|PSG8_uc002oup.3_Intron|PSG10_uc010eip.2_Intron|PSG1_uc002our.1_Intron	NM_006905	NP_008836			pregnancy specific beta-1-glycoprotein 1						female pregnancy	extracellular region				ovary(2)	2		Prostate(69;0.00682)																---	---	---	---
PSG6	5675	broad.mit.edu	37	19	43423536	43423536	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43423536delT	uc002ovj.1	-						PSG3_uc002ouf.2_Intron|PSG11_uc002ouw.2_Intron|PSG7_uc002ous.1_Intron|PSG7_uc002out.1_Intron|PSG10_uc002ouv.1_Intron|PSG6_uc002ovh.1_Intron|PSG6_uc002ovi.2_Intron|PSG6_uc010xwk.1_Intron|PSG11_uc002ovk.1_Intron|PSG6_uc002ovf.1_5'Flank|PSG6_uc002ovg.1_5'Flank	NM_002782	NP_002773			pregnancy specific beta-1-glycoprotein 6 isoform						female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00899)																---	---	---	---
PSG6	5675	broad.mit.edu	37	19	43460948	43460948	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43460948delA	uc002ovh.1	-						PSG11_uc002ouw.2_Intron|PSG10_uc002ouv.1_Intron|PSG6_uc002ovi.2_Intron|PSG6_uc010xwk.1_Intron|PSG11_uc002ovk.1_Intron					SubName: Full=Putative uncharacterized protein PSG6;						female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00899)																---	---	---	---
PSG6	5675	broad.mit.edu	37	19	43570913	43570913	+	Intron	DEL	T	-	-	rs139918672	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43570913delT	uc002ovi.2	-						PSG10_uc002ouv.1_5'Flank|PSG6_uc010xwk.1_Intron|PSG2_uc002ovr.2_Intron|PSG2_uc002ovq.3_Intron|PSG2_uc010eiq.1_Intron|PSG2_uc002ovs.3_Intron|PSG2_uc002ovt.3_Intron					SubName: Full=Putative uncharacterized protein PSG6;						female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00899)																---	---	---	---
PSG5	5673	broad.mit.edu	37	19	43674451	43674452	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43674451_43674452delTT	uc002ovu.2	-						PSG6_uc010xwk.1_Intron|PSG5_uc010eir.2_Intron|PSG5_uc002ovx.2_Intron|PSG5_uc002ovv.2_Intron|PSG5_uc002ovw.2_Intron	NM_002781	NP_002772			pregnancy specific beta-1-glycoprotein 5						female pregnancy	extracellular region				skin(3)	3		Prostate(69;0.00899)																---	---	---	---
Unknown	0	broad.mit.edu	37	19	43756544	43756545	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43756544_43756545delAA								PSG4 (46754 upstream) : PSG9 (891 downstream)																																			---	---	---	---
PHLDB3	653583	broad.mit.edu	37	19	43994164	43994165	+	Intron	DEL	AA	-	-	rs77696385		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43994164_43994165delAA	uc002own.3	-						PHLDB3_uc010eit.2_Intron	NM_198850	NP_942147			pleckstrin homology-like domain, family B,												0		Prostate(69;0.0153)																---	---	---	---
KCNN4	3783	broad.mit.edu	37	19	44272893	44272894	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44272893_44272894delTT	uc002oxl.2	-						KCNN4_uc010eiz.2_Intron	NM_002250	NP_002241			intermediate conductance calcium-activated						defense response	voltage-gated potassium channel complex	calcium-activated potassium channel activity|calmodulin binding			ovary(2)	2		Prostate(69;0.0352)			Clotrimazole(DB00257)|Halothane(DB01159)|Quinine(DB00468)													---	---	---	---
KCNN4	3783	broad.mit.edu	37	19	44278256	44278256	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44278256delG	uc002oxl.2	-						KCNN4_uc010eiz.2_Intron	NM_002250	NP_002241			intermediate conductance calcium-activated						defense response	voltage-gated potassium channel complex	calcium-activated potassium channel activity|calmodulin binding			ovary(2)	2		Prostate(69;0.0352)			Clotrimazole(DB00257)|Halothane(DB01159)|Quinine(DB00468)													---	---	---	---
ZFP112	7771	broad.mit.edu	37	19	44853520	44853520	+	Intron	DEL	A	-	-	rs66786961		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44853520delA	uc010ejj.2	-						ZFP112_uc002ozc.3_Intron|ZFP112_uc010xwy.1_Intron|ZFP112_uc010xwz.1_Intron	NM_001083335	NP_001076804			zinc finger protein 228 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|skin(2)	5																		---	---	---	---
ZNF180	7733	broad.mit.edu	37	19	45005834	45005836	+	5'Flank	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45005834_45005836delAAA	uc002ozf.3	-						ZNF180_uc002ozh.3_5'Flank|ZNF180_uc002ozi.3_5'Flank|ZNF180_uc002ozg.3_5'Flank|ZNF180_uc010ejm.2_5'Flank	NM_013256	NP_037388			zinc finger protein 180						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Prostate(69;0.0435)																---	---	---	---
PVR	5817	broad.mit.edu	37	19	45159345	45159345	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45159345delA	uc002ozm.2	+						PVR_uc010ejs.2_Intron|PVR_uc010xxb.1_Intron|PVR_uc010xxc.1_Intron|PVR_uc002ozn.2_Intron	NM_006505	NP_006496			poliovirus receptor isoform alpha						adherens junction organization|cell adhesion|cell junction assembly|interspecies interaction between organisms|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target|susceptibility to natural killer cell mediated cytotoxicity|susceptibility to T cell mediated cytotoxicity	cell junction|cell surface|cytoplasm|extracellular space|integral to membrane|nucleus	cell adhesion molecule binding|receptor activity				0	Lung NSC(12;0.00608)|all_lung(12;0.0148)	Medulloblastoma(540;0.0425)|Ovarian(192;0.0728)|Prostate(69;0.081)|all_neural(266;0.112)		Epithelial(262;0.000601)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	45268891	45268892	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45268891_45268892insA								BCL3 (5591 upstream) : CBLC (12234 downstream)																																			---	---	---	---
CBLC	23624	broad.mit.edu	37	19	45280550	45280552	+	5'Flank	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45280550_45280552delAAA	uc002ozs.2	+						CBLC_uc010ejt.2_5'Flank	NM_012116	NP_036248			Cas-Br-M (murine) ecotropic retroviral						cell surface receptor linked signaling pathway|negative regulation of epidermal growth factor receptor activity|negative regulation of MAP kinase activity|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	calcium ion binding|epidermal growth factor receptor binding|phosphotyrosine binding|SH3 domain binding|signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(1)|skin(1)	6	Lung NSC(12;0.00136)|all_lung(12;0.00371)	Ovarian(192;0.231)						M		AML								---	---	---	---
BCAM	4059	broad.mit.edu	37	19	45316993	45316993	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45316993delA	uc002ozu.2	+						BCAM_uc002ozt.1_Intron	NM_005581	NP_005572			basal cell adhesion molecule isoform 1						cell-matrix adhesion	integral to plasma membrane	laminin binding|laminin receptor activity			skin(1)	1	Lung NSC(12;0.000789)|all_lung(12;0.00218)	Ovarian(192;0.0728)|all_neural(266;0.112)																---	---	---	---
MARK4	57787	broad.mit.edu	37	19	45781627	45781628	+	Intron	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45781627_45781628delGA	uc002pbb.1	+						MARK4_uc002paz.1_Intron|MARK4_uc002pba.1_Intron|MARK4_uc002pbc.1_Intron					RecName: Full=MAP/microtubule affinity-regulating kinase 4;          EC=2.7.11.1; AltName: Full=MAP/microtubule affinity-regulating kinase-like 1;						microtubule bundle formation|nervous system development|positive regulation of programmed cell death	centrosome|neuron projection	ATP binding|gamma-tubulin binding|microtubule binding|protein serine/threonine kinase activity|tau-protein kinase activity|ubiquitin binding			central_nervous_system(2)|large_intestine(1)	3		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0102)														---	---	---	---
MARK4	57787	broad.mit.edu	37	19	45783055	45783055	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45783055delT	uc002pbb.1	+						MARK4_uc002paz.1_Intron|MARK4_uc002pba.1_Intron|MARK4_uc002pbc.1_Intron					RecName: Full=MAP/microtubule affinity-regulating kinase 4;          EC=2.7.11.1; AltName: Full=MAP/microtubule affinity-regulating kinase-like 1;						microtubule bundle formation|nervous system development|positive regulation of programmed cell death	centrosome|neuron projection	ATP binding|gamma-tubulin binding|microtubule binding|protein serine/threonine kinase activity|tau-protein kinase activity|ubiquitin binding			central_nervous_system(2)|large_intestine(1)	3		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0102)														---	---	---	---
EML2	24139	broad.mit.edu	37	19	46116146	46116147	+	Intron	INS	-	T	T	rs144273191	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46116146_46116147insT	uc002pcn.2	-						EML2_uc002pco.2_Intron|EML2_uc002pcp.2_Intron|EML2_uc010xxl.1_Intron|EML2_uc010xxm.1_Intron	NM_012155	NP_036287			echinoderm microtubule associated protein like						sensory perception of sound|visual perception	cytoplasm|intracellular membrane-bounded organelle|microtubule|microtubule associated complex	catalytic activity|protein binding			large_intestine(1)|ovary(1)	2		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)														---	---	---	---
EML2	24139	broad.mit.edu	37	19	46150063	46150064	+	5'Flank	INS	-	TTGT	TTGT	rs148730309	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46150063_46150064insTTGT	uc010xxm.1	-						EML2_uc010xxn.1_5'Flank|uc010ekl.2_5'Flank	NM_012155	NP_036287			echinoderm microtubule associated protein like						sensory perception of sound|visual perception	cytoplasm|intracellular membrane-bounded organelle|microtubule|microtubule associated complex	catalytic activity|protein binding			large_intestine(1)|ovary(1)	2		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)														---	---	---	---
GIPR	2696	broad.mit.edu	37	19	46175977	46175979	+	Intron	DEL	ATC	-	-	rs13306396		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46175977_46175979delATC	uc002pcu.1	+						GIPR_uc002pct.1_Intron|GIPR_uc010xxp.1_Intron|GIPR_uc010xxq.1_Intron|MIR642_hsa-mir-642|MI0003657_5'Flank	NM_000164	NP_000155			gastric inhibitory polypeptide receptor						generation of precursor metabolites and energy|response to nutrient	integral to membrane|plasma membrane				skin(1)	1		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0056)|GBM - Glioblastoma multiforme(486;0.0832)|Epithelial(262;0.199)														---	---	---	---
NOVA2	4858	broad.mit.edu	37	19	46461612	46461613	+	Intron	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46461612_46461613delTG	uc002pdv.2	-							NM_002516	NP_002507			neuro-oncological ventral antigen 2							nucleus	RNA binding				0		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00245)|GBM - Glioblastoma multiforme(486;0.0782)|Epithelial(262;0.179)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	46683188	46683188	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46683188delA								IGFL2 (18629 upstream) : DKFZp434J0226 (23495 downstream)																																			---	---	---	---
HIF3A	64344	broad.mit.edu	37	19	46843766	46843766	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46843766delT	uc002peh.2	+	15					HIF3A_uc002pek.2_3'UTR|HIF3A_uc010xxy.1_3'UTR|HIF3A_uc002pel.2_3'UTR	NM_152795	NP_690008			hypoxia inducible factor 3, alpha subunit						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3		Ovarian(192;0.00965)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00204)|all cancers(93;0.0107)|GBM - Glioblastoma multiforme(486;0.0489)|Epithelial(262;0.136)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	47019966	47019966	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47019966delG								PNMAL2 (20797 upstream) : CALM3 (84546 downstream)																																			---	---	---	---
GRLF1	2909	broad.mit.edu	37	19	47444309	47444309	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47444309delT	uc010ekv.2	+							NM_004491	NP_004482			glucocorticoid receptor DNA binding factor 1						axon guidance|negative regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|transcription, DNA-dependent	cytosol	DNA binding|Rho GTPase activator activity|transcription corepressor activity			central_nervous_system(1)	1		all_cancers(25;1.51e-09)|all_epithelial(76;1.87e-07)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|Ovarian(192;0.0129)|all_neural(266;0.026)|Breast(70;0.077)		all cancers(93;2.03e-05)|OV - Ovarian serous cystadenocarcinoma(262;2.57e-05)|Epithelial(262;0.00135)|GBM - Glioblastoma multiforme(486;0.0289)														---	---	---	---
GRLF1	2909	broad.mit.edu	37	19	47503884	47503884	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47503884delC	uc010ekv.2	+	6	4439	c.4439delC	c.(4438-4440)ACCfs	p.T1480fs		NM_004491	NP_004482	Q9NRY4	RHG35_HUMAN	glucocorticoid receptor DNA binding factor 1	1480	Pro-rich.				axon guidance|negative regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|transcription, DNA-dependent	cytosol	DNA binding|Rho GTPase activator activity|transcription corepressor activity			central_nervous_system(1)	1		all_cancers(25;1.51e-09)|all_epithelial(76;1.87e-07)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|Ovarian(192;0.0129)|all_neural(266;0.026)|Breast(70;0.077)		all cancers(93;2.03e-05)|OV - Ovarian serous cystadenocarcinoma(262;2.57e-05)|Epithelial(262;0.00135)|GBM - Glioblastoma multiforme(486;0.0289)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	47514063	47514063	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47514063delA								GRLF1 (5740 upstream) : NPAS1 (9038 downstream)																																			---	---	---	---
CCDC9	26093	broad.mit.edu	37	19	47772367	47772367	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47772367delA	uc010xym.1	+							NM_015603	NP_056418			coiled-coil domain containing 9												0		all_cancers(25;0.0432)|all_epithelial(76;0.00812)|Medulloblastoma(540;0.0208)|all_neural(266;0.0416)|Hepatocellular(1079;0.114)		OV - Ovarian serous cystadenocarcinoma(262;8.51e-95)|Epithelial(262;1.15e-92)|all cancers(93;7.67e-84)|GBM - Glioblastoma multiforme(486;0.024)|STAD - Stomach adenocarcinoma(1328;0.183)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	47890417	47890418	+	IGR	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47890417_47890418delAG								DHX34 (4456 upstream) : MEIS3 (15964 downstream)																																			---	---	---	---
MEIS3	56917	broad.mit.edu	37	19	47918145	47918145	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47918145delG	uc002pgu.2	-						MEIS3_uc002pgo.2_5'Flank|MEIS3_uc002pgp.2_5'UTR|MEIS3_uc002pgq.2_Intron|MEIS3_uc002pgr.2_Intron|MEIS3_uc002pgt.2_Intron|MEIS3_uc002pgv.2_Intron|MEIS3_uc002pgs.2_Intron|MEIS3_uc010eld.2_Intron	NM_001009813	NP_001009813			Meis1, myeloid ecotropic viral integration site							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;0.000198)|OV - Ovarian serous cystadenocarcinoma(262;0.000439)|Epithelial(262;0.0113)|GBM - Glioblastoma multiforme(486;0.0223)														---	---	---	---
MEIS3	56917	broad.mit.edu	37	19	47923844	47923845	+	5'Flank	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47923844_47923845delGA	uc002pgu.2	-						MEIS3_uc002pgq.2_5'Flank|MEIS3_uc002pgr.2_5'Flank|MEIS3_uc002pgt.2_5'Flank|MEIS3_uc002pgv.2_5'Flank|MEIS3_uc002pgs.2_5'Flank|MEIS3_uc010eld.2_5'Flank|MEIS3_uc002pgw.2_5'Flank	NM_001009813	NP_001009813			Meis1, myeloid ecotropic viral integration site							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;0.000198)|OV - Ovarian serous cystadenocarcinoma(262;0.000439)|Epithelial(262;0.0113)|GBM - Glioblastoma multiforme(486;0.0223)														---	---	---	---
ELSPBP1	64100	broad.mit.edu	37	19	48497639	48497640	+	5'Flank	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48497639_48497640delAA	uc002pht.2	+							NM_022142	NP_071425			epididymal sperm binding protein 1 precursor						single fertilization	extracellular region					0		all_cancers(25;8.7e-09)|all_lung(116;1.15e-06)|all_epithelial(76;1.17e-06)|Lung NSC(112;2.56e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000253)|all cancers(93;0.00129)|Epithelial(262;0.0314)|GBM - Glioblastoma multiforme(486;0.0606)														---	---	---	---
CARD8	22900	broad.mit.edu	37	19	48724211	48724211	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48724211delA	uc002pie.3	-						CARD8_uc002pii.3_Intron|CARD8_uc002pid.1_5'Flank|CARD8_uc010xzi.1_Intron|CARD8_uc010els.2_Intron|CARD8_uc010xzj.1_Intron|CARD8_uc010xzk.1_Intron|CARD8_uc002pif.3_Intron|CARD8_uc002pig.3_Intron|CARD8_uc002pih.3_Intron|CARD8_uc010xzl.1_Intron|CARD8_uc010xzm.1_Intron	NM_014959	NP_055774			caspase recruitment domain family, member 8						negative regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-1 beta secretion	cytoplasm|nucleus	caspase activator activity|NACHT domain binding|protein homodimerization activity				0		all_lung(116;0.000112)|Lung NSC(112;0.000192)|all_epithelial(76;0.000349)|all_neural(266;0.0228)|Ovarian(192;0.113)|Prostate(7;0.184)		OV - Ovarian serous cystadenocarcinoma(262;0.000112)|all cancers(93;0.000293)|Epithelial(262;0.0129)|GBM - Glioblastoma multiforme(486;0.0336)														---	---	---	---
CARD8	22900	broad.mit.edu	37	19	48727228	48727228	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48727228delT	uc002pie.3	-						CARD8_uc002pii.3_Intron|CARD8_uc010xzi.1_Intron|CARD8_uc010els.2_Intron|CARD8_uc010xzj.1_Intron|CARD8_uc010xzk.1_Intron|CARD8_uc002pif.3_Intron|CARD8_uc002pig.3_Intron|CARD8_uc002pih.3_Intron|CARD8_uc010xzl.1_Intron|CARD8_uc010xzm.1_Intron	NM_014959	NP_055774			caspase recruitment domain family, member 8						negative regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-1 beta secretion	cytoplasm|nucleus	caspase activator activity|NACHT domain binding|protein homodimerization activity				0		all_lung(116;0.000112)|Lung NSC(112;0.000192)|all_epithelial(76;0.000349)|all_neural(266;0.0228)|Ovarian(192;0.113)|Prostate(7;0.184)		OV - Ovarian serous cystadenocarcinoma(262;0.000112)|all cancers(93;0.000293)|Epithelial(262;0.0129)|GBM - Glioblastoma multiforme(486;0.0336)														---	---	---	---
ZNF114	163071	broad.mit.edu	37	19	48779785	48779785	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48779785delT	uc002pil.1	+						ZNF114_uc010elv.1_Intron|ZNF114_uc002pim.1_Intron	NM_153608	NP_705836			zinc finger protein 114						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_epithelial(76;8.01e-05)|all_lung(116;0.000112)|Lung NSC(112;0.000192)|Prostate(7;0.0187)|all_neural(266;0.0228)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;7.56e-05)|all cancers(93;0.000113)|Epithelial(262;0.00962)|GBM - Glioblastoma multiforme(486;0.0153)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	48791158	48791158	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48791158delA								ZNF114 (295 upstream) : CCDC114 (8551 downstream)																																			---	---	---	---
EMP3	2014	broad.mit.edu	37	19	48829365	48829366	+	Intron	DEL	GG	-	-	rs113422662		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48829365_48829366delGG	uc002piv.2	+							NM_001425	NP_001416			epithelial membrane protein 3						cell growth|negative regulation of cell proliferation	integral to membrane					0		all_epithelial(76;6.08e-07)|all_lung(116;5.76e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.00989)|Prostate(7;0.0143)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000138)|all cancers(93;0.00017)|Epithelial(262;0.0138)|GBM - Glioblastoma multiforme(486;0.0146)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	48883723	48883725	+	IGR	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48883723_48883725delAAA								SYNGR4 (4096 upstream) : KDELR1 (2102 downstream)																																			---	---	---	---
KCNJ14	3770	broad.mit.edu	37	19	48958346	48958347	+	5'Flank	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48958346_48958347delCT	uc002pje.1	+							NM_013348	NP_037480			potassium inwardly-rectifying channel J14							voltage-gated potassium channel complex	inward rectifier potassium channel activity			skin(1)	1		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000109)|all cancers(93;0.000129)|Epithelial(262;0.0081)|GBM - Glioblastoma multiforme(486;0.0222)														---	---	---	---
HSD17B14	51171	broad.mit.edu	37	19	49336585	49336585	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49336585delG	uc002pkv.1	-						HSD17B14_uc010emk.1_Intron	NM_016246	NP_057330			dehydrogenase/reductase (SDR family) member 10						steroid catabolic process	centrosome|cytosol	estradiol 17-beta-dehydrogenase activity|protein binding|testosterone 17-beta-dehydrogenase (NADP+) activity				0		all_epithelial(76;7e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000341)|all cancers(93;0.000764)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.0346)														---	---	---	---
PLEKHA4	57664	broad.mit.edu	37	19	49365224	49365224	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49365224delA	uc002pkx.2	-						PLEKHA4_uc002pkw.1_5'Flank|PLEKHA4_uc010eml.2_Intron	NM_020904	NP_065955			pleckstrin homology domain containing family A							cytoplasm|membrane	1-phosphatidylinositol binding			ovary(1)|central_nervous_system(1)|skin(1)	3		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;0.000108)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.00027)|all cancers(93;0.00084)|GBM - Glioblastoma multiforme(486;0.0244)|Epithelial(262;0.0364)														---	---	---	---
TULP2	7288	broad.mit.edu	37	19	49392589	49392590	+	Intron	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49392589_49392590delAC	uc002pkz.2	-							NM_003323	NP_003314			tubby like protein 2						visual perception	cytoplasm|extracellular region				ovary(1)|kidney(1)|skin(1)	3		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000259)|all cancers(93;0.000435)|Epithelial(262;0.0221)|GBM - Glioblastoma multiforme(486;0.0234)														---	---	---	---
SNRNP70	6625	broad.mit.edu	37	19	49598420	49598421	+	Intron	INS	-	C	C	rs112804267		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49598420_49598421insC	uc002pmk.2	+						SNRNP70_uc002pmh.1_Intron|SNRNP70_uc002pmi.1_Intron|SNRNP70_uc002pml.2_Intron|SNRNP70_uc002pmm.2_Intron	NM_003089	NP_003080			U1 small nuclear ribonucleoprotein 70 kDa						nuclear mRNA splicing, via spliceosome|regulation of RNA splicing	nucleoplasm|spliceosomal complex	nucleotide binding|protein binding|RNA binding				0																		---	---	---	---
SLC17A7	57030	broad.mit.edu	37	19	49937768	49937768	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49937768delC	uc002pnp.2	-						SLC17A7_uc002pnq.1_Intron|SLC17A7_uc002pno.2_Intron	NM_020309	NP_064705			solute carrier family 17, member 7						glutamate secretion|neurotransmitter secretion	cell junction|clathrin sculpted glutamate transport vesicle membrane|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|sodium-dependent phosphate transmembrane transporter activity|sodium:inorganic phosphate symporter activity			ovary(1)|pancreas(1)|skin(1)	3		all_lung(116;1.62e-07)|Lung NSC(112;8.47e-07)|all_neural(266;0.0381)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(486;0.0245)														---	---	---	---
FLT3LG	2323	broad.mit.edu	37	19	49975255	49975255	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49975255delT	uc010yau.1	+						FLT3LG_uc002pnv.2_5'Flank|FLT3LG_uc002pnw.2_5'Flank|FLT3LG_uc002pnu.2_5'Flank|FLT3LG_uc002pnx.2_5'Flank|FLT3LG_uc010yav.1_5'Flank	NM_001459	NP_001450			fms-related tyrosine kinase 3 ligand precursor						positive regulation of cell proliferation|signal transduction	extracellular space|integral to membrane|plasma membrane|soluble fraction	cytokine activity				0		all_lung(116;1.62e-07)|Lung NSC(112;8.47e-07)|all_neural(266;0.0381)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00154)|GBM - Glioblastoma multiforme(486;0.0246)														---	---	---	---
PRR12	57479	broad.mit.edu	37	19	50099026	50099026	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50099026delC	uc002poo.3	+	4	1434	c.1434delC	c.(1432-1434)GGCfs	p.G478fs		NM_020719	NP_065770	Q9ULL5	PRR12_HUMAN	proline rich 12	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment							DNA binding			central_nervous_system(1)|pancreas(1)	2		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)														---	---	---	---
RRAS	6237	broad.mit.edu	37	19	50143144	50143144	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50143144delC	uc002pop.1	-						SCAF1_uc002poq.2_5'Flank	NM_006270	NP_006261			related RAS viral (r-ras) oncogene homolog						axon guidance|Ras protein signal transduction|synaptic transmission	intracellular|plasma membrane	GDP binding|GTP binding|GTPase activity|protein binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(262;0.00114)|GBM - Glioblastoma multiforme(134;0.0206)														---	---	---	---
IRF3	3661	broad.mit.edu	37	19	50165584	50165585	+	Frame_Shift_Del	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50165584_50165585delCT	uc010end.1	-	6	984_985	c.602_603delAG	c.(601-603)GAGfs	p.E201fs	IRF3_uc002pos.1_5'Flank|IRF3_uc002pot.1_Intron|IRF3_uc002pox.1_Frame_Shift_Del_p.E201fs|IRF3_uc002poy.1_Frame_Shift_Del_p.E201fs|IRF3_uc002pou.2_Frame_Shift_Del_p.E201fs|IRF3_uc002pov.2_Frame_Shift_Del_p.E55fs|IRF3_uc002pow.2_Frame_Shift_Del_p.E201fs|IRF3_uc002poz.1_Frame_Shift_Del_p.E201fs|BCL2L12_uc002ppa.2_5'Flank|BCL2L12_uc002ppb.2_5'Flank	NM_001571	NP_001562	Q14653	IRF3_HUMAN	interferon regulatory factor 3	201	Involved in HERC5 binding.				interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|MyD88-independent toll-like receptor signaling pathway|negative regulation of type I interferon production|response to virus|Toll signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	cytosol|endosome membrane|nucleoplasm|plasma membrane	DNA binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription cofactor activity			ovary(2)	2		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.0011)|GBM - Glioblastoma multiforme(134;0.02)														---	---	---	---
CPT1C	126129	broad.mit.edu	37	19	50215601	50215603	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50215601_50215603delAAA	uc002ppj.2	+						CPT1C_uc002ppi.2_Intron|CPT1C_uc002ppk.2_Intron|CPT1C_uc010eng.2_Intron|CPT1C_uc010enh.2_Intron|CPT1C_uc010eni.1_Intron	NM_152359	NP_689572			carnitine palmitoyltransferase 1C isoform 2						fatty acid metabolic process	integral to membrane|mitochondrial outer membrane	carnitine O-palmitoyltransferase activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0011)|GBM - Glioblastoma multiforme(134;0.00786)														---	---	---	---
MED25	81857	broad.mit.edu	37	19	50331486	50331490	+	Intron	DEL	AAAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50331486_50331490delAAAAA	uc002ppw.1	+						MED25_uc010ybe.1_Intron	NM_030973	NP_112235			mediator complex subunit 25						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm				ovary(1)	1		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00822)|GBM - Glioblastoma multiforme(134;0.0122)														---	---	---	---
MYH14	79784	broad.mit.edu	37	19	50805542	50805544	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50805542_50805544delAAA	uc002prr.1	+						MYH14_uc010enu.1_Intron|MYH14_uc002prq.1_Intron|MYH14_uc010ycb.1_Intron|MYH14_uc002prs.1_Intron	NM_024729	NP_079005			myosin, heavy chain 14 isoform 2						axon guidance|regulation of cell shape	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			central_nervous_system(1)	1		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)														---	---	---	---
FAM71E1	112703	broad.mit.edu	37	19	50973232	50973232	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50973232delT	uc002psh.2	-						FAM71E1_uc002psg.2_Intron|FAM71E1_uc002psi.2_Intron	NM_138411	NP_612420			hypothetical protein LOC112703											breast(1)	1		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.0077)|GBM - Glioblastoma multiforme(134;0.026)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	50989430	50989431	+	RNA	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50989430_50989431insT	uc002psm.1	+	1		c.1267_1268insT								Homo sapiens cDNA FLJ33174 fis, clone ADRGL2002260, weakly similar to DIAPHANOUS PROTEIN HOMOLOG 1 (P140MDIA).																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	51160207	51160207	+	IGR	DEL	A	-	-	rs67847799		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51160207delA								SYT3 (17115 upstream) : SHANK1 (4877 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	51235017	51235017	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51235017delA								CLEC11A (6038 upstream) : GPR32 (38841 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	51288852	51288852	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51288852delG								GPR32 (13925 upstream) : ACPT (4820 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	51289260	51289261	+	IGR	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51289260_51289261insG								GPR32 (14333 upstream) : ACPT (4411 downstream)																																			---	---	---	---
KLK6	5653	broad.mit.edu	37	19	51475458	51475459	+	5'Flank	DEL	AA	-	-	rs112633459		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51475458_51475459delAA	uc002pul.2	-						KLK6_uc002pum.2_5'Flank	NM_002774	NP_002765			kallikrein-related peptidase 6 isoform A						amyloid precursor protein metabolic process|central nervous system development|collagen catabolic process|hormone metabolic process|myelination|positive regulation of G-protein coupled receptor protein signaling pathway|protein autoprocessing|proteolysis|regulation of cell differentiation|tissue regeneration	endoplasmic reticulum|extracellular region|microsome|mitochondrion|nucleolus	protein binding|serine-type endopeptidase activity				0		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00372)|GBM - Glioblastoma multiforme(134;0.00871)														---	---	---	---
KLK12	43849	broad.mit.edu	37	19	51536291	51536291	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51536291delA	uc002pvg.1	-						KLK12_uc010ycp.1_Intron|KLK12_uc010ycq.1_Intron|KLK12_uc010ycr.1_Intron|KLK12_uc010ycs.1_Intron|KLK12_uc002pvh.1_Intron|KLK12_uc002pvi.1_Intron|KLK12_uc002pvj.1_Intron	NM_145894	NP_665901			kallikrein 12 isoform 2						proteolysis	extracellular region|soluble fraction	serine-type endopeptidase activity			ovary(1)	1		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00399)														---	---	---	---
KLK14	43847	broad.mit.edu	37	19	51586228	51586229	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51586228_51586229delTT	uc002pvs.1	-							NM_022046	NP_071329			kallikrein 14 preproprotein						epidermis morphogenesis|fertilization|negative regulation of G-protein coupled receptor protein signaling pathway|positive regulation of G-protein coupled receptor protein signaling pathway|proteolysis|seminal clot liquefaction	extracellular space	serine-type endopeptidase activity			skin(1)	1		all_neural(266;0.0199)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00422)														---	---	---	---
KLK14	43847	broad.mit.edu	37	19	51586545	51586546	+	Intron	INS	-	GAGAGG	GAGAGG			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51586545_51586546insGAGAGG	uc002pvs.1	-							NM_022046	NP_071329			kallikrein 14 preproprotein						epidermis morphogenesis|fertilization|negative regulation of G-protein coupled receptor protein signaling pathway|positive regulation of G-protein coupled receptor protein signaling pathway|proteolysis|seminal clot liquefaction	extracellular space	serine-type endopeptidase activity			skin(1)	1		all_neural(266;0.0199)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00422)														---	---	---	---
SIGLEC8	27181	broad.mit.edu	37	19	51956351	51956351	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51956351delT	uc002pwt.2	-						SIGLEC8_uc010yda.1_Intron|SIGLEC8_uc002pwu.2_Intron|SIGLEC8_uc010eox.2_Intron	NM_014442	NP_055257			sialic acid binding Ig-like lectin 8 precursor						cell adhesion	integral to membrane	sugar binding|transmembrane receptor activity			ovary(2)|kidney(1)|central_nervous_system(1)|skin(1)	5		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000627)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	52097561	52097561	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52097561delA	uc002pxd.1	-	1	70	c.14delT	c.(13-15)TTCfs	p.F5fs						SubName: Full=cDNA FLJ30403 fis, clone BRACE2008480; SubName: Full=HCG2008157;																														---	---	---	---
Unknown	0	broad.mit.edu	37	19	52210229	52210229	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52210229delA								NCRNA00085 (1787 upstream) : HAS1 (6136 downstream)																																			---	---	---	---
ZNF577	84765	broad.mit.edu	37	19	52391029	52391029	+	Intron	DEL	A	-	-	rs73065045	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52391029delA	uc010yde.1	-						ZNF577_uc010ydd.1_Intron|ZNF577_uc002pxx.3_Intron|ZNF577_uc002pxv.2_5'UTR|ZNF577_uc002pxw.2_5'UTR|ZNF577_uc010ydf.1_Intron	NM_032679	NP_116068			zinc finger protein 577 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.019)														---	---	---	---
ZNF841	284371	broad.mit.edu	37	19	52597277	52597278	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52597277_52597278insA	uc002pyl.1	-						ZNF841_uc010ydh.1_Intron	NM_001136499	NP_001129971			zinc finger protein 841						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
PPP2R1A	5518	broad.mit.edu	37	19	52724056	52724056	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52724056delA	uc002pyp.2	+						PPP2R1A_uc010ydk.1_Intron|PPP2R1A_uc002pyq.2_Intron	NM_014225	NP_055040			alpha isoform of regulatory subunit A, protein						ceramide metabolic process|chromosome segregation|G2/M transition of mitotic cell cycle|inactivation of MAPK activity|induction of apoptosis|negative regulation of cell growth|negative regulation of tyrosine phosphorylation of Stat3 protein|protein complex assembly|protein dephosphorylation|regulation of cell adhesion|regulation of cell differentiation|regulation of DNA replication|regulation of transcription, DNA-dependent|regulation of Wnt receptor signaling pathway|response to organic substance|RNA splicing|second-messenger-mediated signaling	chromosome, centromeric region|cytosol|membrane|microtubule cytoskeleton|mitochondrion|nucleus|protein phosphatase type 2A complex|soluble fraction	antigen binding|protein heterodimerization activity|protein phosphatase type 2A regulator activity			endometrium(31)|ovary(28)|lung(2)|breast(2)|skin(1)|kidney(1)|pancreas(1)	66				GBM - Glioblastoma multiforme(134;0.00456)|OV - Ovarian serous cystadenocarcinoma(262;0.015)				Mis		clear cell ovarian carcinoma								---	---	---	---
ZNF880	400713	broad.mit.edu	37	19	52880498	52880498	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52880498delT	uc002pzc.2	+							NM_001145434	NP_001138906			zinc finger protein LOC400713						regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	52926250	52926250	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52926250delT								ZNF528 (4594 upstream) : ZNF534 (6190 downstream)																																			---	---	---	---
ZNF83	55769	broad.mit.edu	37	19	53174700	53174701	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53174700_53174701delTT	uc010epz.2	-						ZNF83_uc010eqb.1_Intron	NM_001105554	NP_001099024			zinc finger protein 83 isoform b							nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(262;0.00841)|GBM - Glioblastoma multiforme(134;0.0244)														---	---	---	---
ZNF611	81856	broad.mit.edu	37	19	53214845	53214845	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53214845delG	uc002pzz.2	-						ZNF611_uc010eqc.2_Intron|ZNF611_uc010ydo.1_Intron|ZNF611_uc010ydr.1_Intron|ZNF611_uc010ydp.1_Intron|ZNF611_uc010ydq.1_Intron|ZNF611_uc002qaa.3_Intron	NM_030972	NP_112234			zinc finger protein 611 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(262;0.0233)|GBM - Glioblastoma multiforme(134;0.04)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	53775884	53775884	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53775884delA								VN1R4 (4966 upstream) : BIRC8 (16972 downstream)																																			---	---	---	---
ZNF813	126017	broad.mit.edu	37	19	53982356	53982356	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53982356delT	uc002qbu.2	+							NM_001004301	NP_001004301			zinc finger protein 813						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	54528922	54528923	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54528922_54528923insT								CACNG6 (13004 upstream) : VSTM1 (15162 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	54591362	54591362	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54591362delT								TARM1 (6728 upstream) : OSCAR (6573 downstream)																																			---	---	---	---
PRPF31	26121	broad.mit.edu	37	19	54621362	54621363	+	Intron	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54621362_54621363insC	uc002qdh.2	+						TFPT_uc010yej.1_5'Flank|TFPT_uc010erd.2_5'Flank|PRPF31_uc010yek.1_Intron	NM_015629	NP_056444			pre-mRNA processing factor 31 homolog						assembly of spliceosomal tri-snRNP	Cajal body|MLL1 complex|nuclear speck|U4 snRNP|U4/U6 x U5 tri-snRNP complex|U4atac snRNP	RNA binding|snRNP binding			ovary(1)	1	all_cancers(19;0.00681)|all_epithelial(19;0.00362)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)																	---	---	---	---
LAIR2	3904	broad.mit.edu	37	19	55008669	55008669	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55008669delT	uc002qga.1	+						LAIR2_uc002qgb.1_5'Flank					Homo sapiens leukocyte-associated Ig-like receptor-2 (LAIR-2) mRNA, complete cds.							extracellular region	receptor activity			ovary(1)	1	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0967)														---	---	---	---
LILRB1	10859	broad.mit.edu	37	19	55148385	55148385	+	3'UTR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55148385delC	uc002qgj.2	+	16					LILRB1_uc002qgl.2_3'UTR|LILRB1_uc002qgk.2_3'UTR|LILRB1_uc002qgm.2_3'UTR|LILRB1_uc010erq.2_3'UTR|LILRB1_uc010err.2_RNA	NM_006669	NP_006660			leukocyte immunoglobulin-like receptor,						regulation of immune response|response to virus	integral to membrane|plasma membrane	protein phosphatase 1 binding|receptor activity			large_intestine(1)|ovary(1)|skin(1)	3				GBM - Glioblastoma multiforme(193;0.0188)											HNSCC(37;0.09)			---	---	---	---
KIR2DL3	3804	broad.mit.edu	37	19	55271765	55271766	+	Intron	DEL	GA	-	-	rs112795662		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55271765_55271766delGA	uc010erw.1	+						KIR2DS4_uc010yfj.1_Intron|KIR2DL1_uc002qgz.1_Intron|KIR2DL3_uc002qha.1_Intron|KIR3DP1_uc010yfi.1_Intron	NM_015868	NP_056952			killer cell immunoglobulin-like receptor, two						immune response|regulation of immune response	integral to plasma membrane	antigen binding|protein binding|receptor activity			ovary(2)	2				GBM - Glioblastoma multiforme(193;0.0192)														---	---	---	---
RDH13	112724	broad.mit.edu	37	19	55578086	55578087	+	Intron	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55578086_55578087delTG	uc002qip.2	-						RDH13_uc002qiq.1_5'Flank	NM_138412	NP_612421			retinol dehydrogenase 13 isoform 2								binding|oxidoreductase activity			large_intestine(1)|ovary(1)|skin(1)	3			BRCA - Breast invasive adenocarcinoma(297;0.199)	GBM - Glioblastoma multiforme(193;0.0504)	Vitamin A(DB00162)													---	---	---	---
TNNT1	7138	broad.mit.edu	37	19	55645049	55645051	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55645049_55645051delAAA	uc002qjb.3	-						TNNT1_uc002qiz.3_Intron|TNNT1_uc002qja.3_Intron|TNNT1_uc002qjc.3_Intron|TNNT1_uc002qje.3_Intron|TNNT1_uc002qjd.3_Intron	NM_003283	NP_003274			troponin T1, skeletal, slow isoform a						muscle filament sliding|negative regulation of muscle contraction	cytosol|troponin complex	tropomyosin binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.047)														---	---	---	---
TNNT1	7138	broad.mit.edu	37	19	55648876	55648877	+	Intron	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55648876_55648877insC	uc002qjb.3	-						TNNT1_uc002qiz.3_Intron|TNNT1_uc002qja.3_Intron|TNNT1_uc002qjc.3_Intron|TNNT1_uc002qje.3_Intron|TNNT1_uc002qjd.3_Intron	NM_003283	NP_003274			troponin T1, skeletal, slow isoform a						muscle filament sliding|negative regulation of muscle contraction	cytosol|troponin complex	tropomyosin binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.047)														---	---	---	---
TMEM150B	284417	broad.mit.edu	37	19	55834810	55834810	+	Intron	DEL	A	-	-	rs151204950		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55834810delA	uc010esw.1	-						TMEM150B_uc010yfu.1_Intron|TMEM150B_uc010yfv.1_Intron|TMEM150B_uc010yfw.1_Intron|TMEM150B_uc002qki.2_Intron	NM_001085488	NP_001078957			transmembrane protein 150B precursor							integral to membrane					0																		---	---	---	---
EPN1	29924	broad.mit.edu	37	19	56206220	56206220	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56206220delC	uc002qlw.2	+	10	1735	c.1393delC	c.(1393-1395)CCCfs	p.P465fs	EPN1_uc002qlv.2_Frame_Shift_Del_p.P439fs|EPN1_uc010etd.2_Frame_Shift_Del_p.P464fs|EPN1_uc002qlx.2_Frame_Shift_Del_p.P551fs	NM_001130072	NP_001123544	Q9Y6I3	EPN1_HUMAN	epsin 1 isoform b	465	Ala/Gly/Pro-rich.				endocytosis|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway	coated pit|cytoplasm|nucleus|plasma membrane	lipid binding				0		Colorectal(82;0.00244)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.112)														---	---	---	---
NLRP5	126206	broad.mit.edu	37	19	56511728	56511728	+	Intron	DEL	T	-	-	rs35449342		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56511728delT	uc002qmj.2	+						NLRP5_uc002qmi.2_Intron	NM_153447	NP_703148			NACHT, LRR and PYD containing protein 5							mitochondrion|nucleolus	ATP binding			ovary(3)|skin(2)|kidney(1)|central_nervous_system(1)	7		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)														---	---	---	---
ZSCAN5A	79149	broad.mit.edu	37	19	56745028	56745028	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56745028delA	uc002qmr.2	-						ZSCAN5A_uc010ygi.1_Intron	NM_024303	NP_077279			zinc finger and SCAN domain containing 5A						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			large_intestine(1)|ovary(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	56948985	56948985	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56948985delT								ZNF583 (12585 upstream) : ZNF667 (2219 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	19	57270078	57270079	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57270078_57270079insA	uc010ygp.1	+											Homo sapiens cDNA clone IMAGE:4793694.																														---	---	---	---
DUXA	503835	broad.mit.edu	37	19	57670785	57670785	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57670785delT	uc002qoa.1	-							NM_001012729	NP_001012747			double homeobox A							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0123)														---	---	---	---
AURKC	6795	broad.mit.edu	37	19	57745123	57745124	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57745123_57745124delTT	uc002qoe.2	+						AURKC_uc002qoc.2_Intron|AURKC_uc002qod.2_Intron|AURKC_uc010etv.2_Intron	NM_001015878	NP_001015878			aurora kinase C isoform 1						cell cycle|cytokinesis	condensed chromosome|cytoplasm|midbody|spindle midzone	ATP binding|protein serine/threonine kinase activity			lung(4)|ovary(2)	6		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0122)														---	---	---	---
ZNF805	390980	broad.mit.edu	37	19	57765542	57765542	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57765542delA	uc010ygt.1	+	4	1562	c.1355delA	c.(1354-1356)GAAfs	p.E452fs	ZNF805_uc010ygu.1_Frame_Shift_Del_p.E319fs	NM_001023563	NP_001018857	Q5CZA5	ZN805_HUMAN	zinc finger protein 805 isoform 1	452					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	19	57848992	57848992	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57848992delT								ZNF543 (6848 upstream) : ZNF304 (13653 downstream)																																			---	---	---	---
ZNF749	388567	broad.mit.edu	37	19	57948629	57948629	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57948629delT	uc002qoq.2	+						ZNF547_uc002qpm.3_Intron	NM_001023561	NP_001018855			zinc finger protein 749						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0264)|Lung(386;0.177)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	58163788	58163789	+	IGR	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58163788_58163789delCT								ZNF211 (9641 upstream) : ZSCAN4 (16514 downstream)																																			---	---	---	---
ZNF776	284309	broad.mit.edu	37	19	58215377	58215377	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58215377delA	uc002qpx.2	+						ZNF154_uc002qpy.2_Intron|ZNF154_uc010euf.2_Intron	NM_173632	NP_775903			zinc finger protein 776						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0256)														---	---	---	---
ZNF329	79673	broad.mit.edu	37	19	58657842	58657842	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58657842delA	uc002qrn.2	-						ZNF329_uc010euk.1_Intron|ZNF329_uc002qro.1_Intron|ZNF329_uc002qrp.1_Intron	NM_024620	NP_078896			zinc finger protein 329						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.029)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.017)|Lung(386;0.216)														---	---	---	---
ZNF544	27300	broad.mit.edu	37	19	58748995	58748995	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58748995delT	uc010euo.2	+						ZNF544_uc010eun.1_Intron|ZNF544_uc010yhw.1_Intron|ZNF544_uc010yhx.1_Intron|ZNF544_uc010yhy.1_Intron|ZNF544_uc002qrt.3_Intron|ZNF544_uc002qru.3_Intron|ZNF544_uc002qrv.2_Intron	NM_014480	NP_055295			zinc finger protein 544						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1		all_cancers(17;4.17e-12)|all_epithelial(17;1.25e-08)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.17)|GBM - Glioblastoma multiforme(193;0.018)														---	---	---	---
ZNF837	116412	broad.mit.edu	37	19	58885421	58885421	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58885421delA	uc002qsm.2	-						ZNF837_uc002qsl.3_Intron	NM_001129730	NP_001123202			zinc finger protein 837 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	104949	104949	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:104949delA								DEFB125 (27654 upstream) : DEFB126 (18303 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	282109	282109	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:282109delT								ZCCHC3 (1148 upstream) : SOX12 (24130 downstream)																																			---	---	---	---
NRSN2	80023	broad.mit.edu	37	20	335199	335200	+	3'UTR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:335199_335200insT	uc002wdi.3	+	4					NRSN2_uc002wdj.2_RNA|NRSN2_uc002wdl.2_Intron	NM_024958	NP_079234			neurensin 2							integral to membrane|plasma membrane|transport vesicle					0		all_cancers(10;0.0834)														OREG0025706	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	20	346118	346118	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:346118delG								NRSN2 (5774 upstream) : TRIB3 (15190 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	569924	569924	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:569924delC								CSNK2A1 (45442 upstream) : TCF15 (14715 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	581647	581647	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:581647delA								CSNK2A1 (57165 upstream) : TCF15 (2992 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	681624	681624	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:681624delT								SRXN1 (24801 upstream) : C20orf54 (59101 downstream)																																			---	---	---	---
ANGPT4	51378	broad.mit.edu	37	20	894906	894906	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:894906delA	uc002wei.2	-						ANGPT4_uc010zpn.1_Intron	NM_015985	NP_057069			angiopoietin 4 precursor						anti-apoptosis|blood coagulation|cellular response to hypoxia|leukocyte migration|negative regulation of angiogenesis|negative regulation of blood vessel endothelial cell migration|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of peptidyl-tyrosine phosphorylation|signal transduction	extracellular space	receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity			ovary(2)	2																		---	---	---	---
PSMF1	9491	broad.mit.edu	37	20	1132715	1132715	+	Intron	DEL	T	-	-	rs77960434		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1132715delT	uc002wel.3	+						PSMF1_uc010zpo.1_Intron|PSMF1_uc002wem.3_Intron|PSMF1_uc010zpp.1_Intron|PSMF1_uc002wen.3_Intron|PSMF1_uc002wep.3_Intron	NM_178578	NP_848693			proteasome inhibitor subunit 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome core complex	endopeptidase inhibitor activity|protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	1237348	1237350	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1237348_1237350delTTT								RAD21L1 (2203 upstream) : SNPH (9610 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	1747985	1747986	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1747985_1747986insA								SIRPG (109560 upstream) : SIRPA (126827 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	1947664	1947665	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1947664_1947665delAA	uc002wfu.1	+											Homo sapiens cDNA FLJ33362 fis, clone BRACE2005337.																														---	---	---	---
STK35	140901	broad.mit.edu	37	20	2119148	2119148	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2119148delA	uc002wfw.3	+						STK35_uc010zpu.1_Intron	NM_080836	NP_543026			serine/threonine kinase 35							cytoplasm|nucleolus	ATP binding|protein serine/threonine kinase activity			ovary(1)	1																		---	---	---	---
TGM6	343641	broad.mit.edu	37	20	2405999	2406001	+	Intron	DEL	AAA	-	-	rs71329364		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2405999_2406001delAAA	uc002wfy.1	+						TGM6_uc010gal.1_Intron	NM_198994	NP_945345			transglutaminase 6						cell death|peptide cross-linking		acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(3)|skin(1)	4					L-Glutamine(DB00130)													---	---	---	---
NOP56	10528	broad.mit.edu	37	20	2638355	2638355	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2638355delT	uc002wgh.2	+						NOP56_uc010zpy.1_Intron|NOP56_uc002wgi.2_Intron|NOP56_uc002wgm.1_3'UTR	NM_006392	NP_006383			nucleolar protein 5A						rRNA processing	box C/D snoRNP complex|pre-snoRNP complex	protein binding|snoRNA binding			ovary(1)|pancreas(1)	2																		---	---	---	---
EBF4	57593	broad.mit.edu	37	20	2671971	2671971	+	5'Flank	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2671971delG	uc002wgt.3	+						EBF4_uc002wgs.3_5'Flank	NM_001110514	NP_001103984			early B-cell factor 4						multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|metal ion binding				0																		---	---	---	---
PTPRA	5786	broad.mit.edu	37	20	2955700	2955700	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2955700delA	uc010zqb.1	+						PTPRA_uc002whj.2_Intron|PTPRA_uc010zqc.1_Intron|PTPRA_uc002whk.2_Intron|PTPRA_uc010zqd.1_Intron|PTPRA_uc002whl.2_Intron|PTPRA_uc002whm.2_Intron|PTPRA_uc002whn.2_Intron					SubName: Full=cDNA FLJ60525, highly similar to Receptor-type tyrosine-protein phosphatase alpha (EC 3.1.3.48);						axon guidance|protein phosphorylation	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	3029673	3029673	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3029673delT								MRPS26 (778 upstream) : OXT (22593 downstream)																																			---	---	---	---
ATRN	8455	broad.mit.edu	37	20	3601166	3601167	+	Intron	INS	-	AC	AC	rs11471428		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3601166_3601167insAC	uc002wim.2	+							NM_139321	NP_647537			attractin isoform 1						inflammatory response	extracellular space|integral to plasma membrane	receptor activity|sugar binding			ovary(1)|breast(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	4117880	4117880	+	IGR	DEL	A	-	-	rs11482353		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4117880delA								RNF24 (121664 upstream) : SMOX (11570 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	4338555	4338555	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4338555delA								ADRA1D (108896 upstream) : PRNP (328242 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	4342932	4342932	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4342932delC								ADRA1D (113273 upstream) : PRNP (323865 downstream)																																			---	---	---	---
SLC23A2	9962	broad.mit.edu	37	20	4945546	4945547	+	Intron	DEL	AA	-	-	rs11087663		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4945546_4945547delAA	uc002wlg.1	-						SLC23A2_uc010zqr.1_Intron|SLC23A2_uc002wlh.1_Intron|SLC23A2_uc002wli.2_Intron|SLC23A2_uc002wlj.1_Intron	NM_005116	NP_005107			solute carrier family 23 (nucleobase						L-ascorbic acid metabolic process|molecular hydrogen transport|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|transepithelial L-ascorbic acid transport	apical plasma membrane|integral to plasma membrane|membrane fraction	nucleobase transmembrane transporter activity|sodium-dependent L-ascorbate transmembrane transporter activity|sodium-dependent multivitamin transmembrane transporter activity			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	5026647	5026647	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5026647delA								SLC23A2 (35708 upstream) : C20orf30 (22483 downstream)																																			---	---	---	---
C20orf30	29058	broad.mit.edu	37	20	5071383	5071383	+	Intron	DEL	A	-	-	rs5840069		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5071383delA	uc010gbi.2	-							NM_014145	NP_054864			hypothetical protein LOC29058 isoform 2							integral to membrane					0																		---	---	---	---
GPCPD1	56261	broad.mit.edu	37	20	5554390	5554390	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5554390delA	uc002wme.3	-						GPCPD1_uc002wmd.3_Intron	NM_019593	NP_062539			hypothetical protein LOC56261						glycerol metabolic process|lipid metabolic process		carbohydrate binding|glycerophosphodiester phosphodiesterase activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	5596971	5596974	+	IGR	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5596971_5596974delTTTT								GPCPD1 (5299 upstream) : C20orf196 (134069 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	5626382	5626382	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5626382delA								GPCPD1 (34710 upstream) : C20orf196 (104661 downstream)																																			---	---	---	---
TRMT6	51605	broad.mit.edu	37	20	5924808	5924808	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:5924808delT	uc002wmh.1	-	4	580	c.458delA	c.(457-459)AAAfs	p.K153fs	TRMT6_uc010zra.1_5'UTR|TRMT6_uc010gbn.1_5'UTR|TRMT6_uc010gbo.1_RNA	NM_015939	NP_057023	Q9UJA5	TRM6_HUMAN	tRNA methyltransferase 6	153					regulation of translational initiation|tRNA processing	nucleus	protein binding|translation initiation factor activity			pancreas(1)	1																		---	---	---	---
FERMT1	55612	broad.mit.edu	37	20	6087512	6087512	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:6087512delC	uc002wmr.2	-						FERMT1_uc010gbt.2_Intron|FERMT1_uc002wms.2_Intron|FERMT1_uc002wmt.2_Intron	NM_017671	NP_060141			kindlin-1						cell adhesion|establishment of epithelial cell polarity|keratinocyte migration|keratinocyte proliferation	cytosol|focal adhesion|ruffle membrane	binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	6531644	6531644	+	IGR	DEL	T	-	-	rs10712166		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:6531644delT								FERMT1 (427453 upstream) : BMP2 (217101 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	7048830	7048830	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7048830delT								BMP2 (287920 upstream) : HAO1 (814801 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	7116161	7116161	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:7116161delT								BMP2 (355251 upstream) : HAO1 (747470 downstream)																																			---	---	---	---
PLCB1	23236	broad.mit.edu	37	20	8114865	8114865	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8114865delA	uc002wnb.2	+						PLCB1_uc010zrb.1_Intron|PLCB1_uc010gbv.1_Intron|PLCB1_uc002wmz.1_Intron|PLCB1_uc002wna.2_Intron	NM_015192	NP_056007			phosphoinositide-specific phospholipase C beta 1						activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of monocyte extravasation|negative regulation of transcription, DNA-dependent|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|positive regulation of transcription, DNA-dependent|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	cytosol|nuclear chromatin|nuclear speck	calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity			ovary(4)|breast(3)|upper_aerodigestive_tract(2)|skin(2)|lung(1)	12																		---	---	---	---
PLCB1	23236	broad.mit.edu	37	20	8175414	8175415	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8175414_8175415insA	uc002wnb.2	+						PLCB1_uc010zrb.1_Intron|PLCB1_uc010gbv.1_Intron|PLCB1_uc002wmz.1_Intron|PLCB1_uc002wna.2_Intron	NM_015192	NP_056007			phosphoinositide-specific phospholipase C beta 1						activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of monocyte extravasation|negative regulation of transcription, DNA-dependent|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|positive regulation of transcription, DNA-dependent|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	cytosol|nuclear chromatin|nuclear speck	calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity			ovary(4)|breast(3)|upper_aerodigestive_tract(2)|skin(2)|lung(1)	12																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	8920281	8920282	+	IGR	INS	-	AGA	AGA	rs145520579	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8920281_8920282insAGA								PLCB1 (54736 upstream) : PLCB4 (129419 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	8966949	8966951	+	IGR	DEL	ATG	-	-	rs11481585		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8966949_8966951delATG								PLCB1 (101404 upstream) : PLCB4 (82750 downstream)																																			---	---	---	---
PLCB4	5332	broad.mit.edu	37	20	9387309	9387309	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9387309delT	uc002wnf.2	+						PLCB4_uc010gbw.1_Intron|PLCB4_uc010gbx.2_Intron|PLCB4_uc002wne.2_Intron|PLCB4_uc002wnh.2_Intron	NM_182797	NP_877949			phospholipase C beta 4 isoform b						intracellular signal transduction|lipid catabolic process	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			skin(11)|ovary(3)|pancreas(1)	15																		---	---	---	---
PLCB4	5332	broad.mit.edu	37	20	9388020	9388021	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9388020_9388021delTT	uc002wnf.2	+						PLCB4_uc010gbw.1_Intron|PLCB4_uc010gbx.2_Intron|PLCB4_uc002wne.2_Intron|PLCB4_uc002wnh.2_Intron	NM_182797	NP_877949			phospholipase C beta 4 isoform b						intracellular signal transduction|lipid catabolic process	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			skin(11)|ovary(3)|pancreas(1)	15																		---	---	---	---
PAK7	57144	broad.mit.edu	37	20	9645734	9645737	+	Intron	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9645734_9645737delTTTT	uc002wnl.2	-						PAK7_uc002wnk.2_Intron|PAK7_uc002wnj.2_Intron|PAK7_uc010gby.1_Intron	NM_020341	NP_065074			p21-activated kinase 7								ATP binding|protein binding|protein serine/threonine kinase activity			lung(11)|skin(5)|central_nervous_system(3)|ovary(2)|large_intestine(1)|stomach(1)	23			COAD - Colon adenocarcinoma(9;0.194)															---	---	---	---
SNAP25	6616	broad.mit.edu	37	20	10227262	10227262	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10227262delA	uc002wnq.1	+						SNAP25_uc002wnr.1_Intron|SNAP25_uc002wns.1_Intron|SNAP25_uc010gca.1_Intron|SNAP25_uc010gcb.1_Intron|SNAP25_uc010gcc.1_Intron	NM_130811	NP_570824			synaptosomal-associated protein 25 isoform						energy reserve metabolic process|glutamate secretion|neurotransmitter uptake|synaptic vesicle docking involved in exocytosis	cell junction|growth cone|perinuclear region of cytoplasm|synapse|synaptosome				skin(2)	2					Botulinum Toxin Type A(DB00083)													---	---	---	---
SNAP25	6616	broad.mit.edu	37	20	10278757	10278757	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10278757delT	uc002wnq.1	+						SNAP25_uc002wnr.1_Intron|SNAP25_uc002wns.1_Intron|SNAP25_uc010gca.1_Intron|SNAP25_uc010gcb.1_Intron|SNAP25_uc010gcc.1_Intron	NM_130811	NP_570824			synaptosomal-associated protein 25 isoform						energy reserve metabolic process|glutamate secretion|neurotransmitter uptake|synaptic vesicle docking involved in exocytosis	cell junction|growth cone|perinuclear region of cytoplasm|synapse|synaptosome				skin(2)	2					Botulinum Toxin Type A(DB00083)													---	---	---	---
Unknown	0	broad.mit.edu	37	20	10288808	10288808	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10288808delT								SNAP25 (743 upstream) : MKKS (97025 downstream)																																			---	---	---	---
C20orf94	128710	broad.mit.edu	37	20	10485606	10485607	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10485606_10485607delAA	uc010zre.1	+							NM_001009608	NP_001009608			hypothetical protein LOC128710								protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	10773038	10773038	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10773038delT								JAG1 (118344 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	10870575	10870575	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10870575delA								JAG1 (215881 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	11454632	11454632	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11454632delA								JAG1 (799938 upstream) : BTBD3 (416845 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	11569687	11569687	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11569687delT								JAG1 (914993 upstream) : BTBD3 (301790 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	12259611	12259611	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:12259611delA								BTBD3 (352369 upstream) : SPTLC3 (730016 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	12766053	12766053	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:12766053delT								BTBD3 (858811 upstream) : SPTLC3 (223574 downstream)																																			---	---	---	---
ISM1	140862	broad.mit.edu	37	20	13241691	13241691	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13241691delA	uc010gce.1	+							NM_080826	NP_543016			isthmin 1 homolog precursor							extracellular region					0																		---	---	---	---
TASP1	55617	broad.mit.edu	37	20	13295662	13295662	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13295662delA	uc010zri.1	-											Homo sapiens cDNA FLJ20212 fis, clone COLF1860.						asparagine catabolic process via L-aspartate|positive regulation of transcription, DNA-dependent|protein maturation		threonine-type endopeptidase activity				0																		---	---	---	---
TASP1	55617	broad.mit.edu	37	20	13415647	13415647	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13415647delA	uc002woi.2	-						TASP1_uc010zri.1_Intron|TASP1_uc002woh.2_Intron	NM_017714	NP_060184			taspase 1 precursor						asparagine catabolic process via L-aspartate|positive regulation of transcription, DNA-dependent|protein maturation		threonine-type endopeptidase activity				0																		---	---	---	---
C20orf7	79133	broad.mit.edu	37	20	13782444	13782444	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13782444delT	uc002wom.2	+						C20orf7_uc002won.2_Intron|C20orf7_uc002woo.2_Intron	NM_024120	NP_077025			hypothetical protein LOC79133 isoform 1						mitochondrial respiratory chain complex I assembly	extrinsic to mitochondrial inner membrane	methyltransferase activity				0		Myeloproliferative disorder(85;0.00878)																---	---	---	---
SEL1L2	80343	broad.mit.edu	37	20	13832191	13832191	+	Intron	DEL	T	-	-	rs74736880		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13832191delT	uc010gcf.2	-						SEL1L2_uc002woq.3_Intron|SEL1L2_uc010zrl.1_Intron|SEL1L2_uc002wor.2_Intron	NM_025229	NP_079505			sel-1 suppressor of lin-12-like 2 precursor							integral to membrane	binding			ovary(2)	2																		---	---	---	---
MACROD2	140733	broad.mit.edu	37	20	14010865	14010865	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14010865delG	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002wos.2_Intron	NM_080676	NP_542407			MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)																---	---	---	---
MACROD2	140733	broad.mit.edu	37	20	14713347	14713347	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14713347delT	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002wox.2_Intron	NM_080676	NP_542407			MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)																---	---	---	---
MACROD2	140733	broad.mit.edu	37	20	15255123	15255123	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15255123delC	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002woz.2_Intron	NM_080676	NP_542407			MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)																---	---	---	---
MACROD2	140733	broad.mit.edu	37	20	15284466	15284466	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15284466delT	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002woz.2_Intron	NM_080676	NP_542407			MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)																---	---	---	---
MACROD2	140733	broad.mit.edu	37	20	15680208	15680208	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:15680208delG	uc002wou.2	+						MACROD2_uc002wot.2_Intron|MACROD2_uc002woz.2_Intron|MACROD2_uc002wpb.2_5'Flank	NM_080676	NP_542407			MACRO domain containing 2 isoform 1												0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	16119067	16119067	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16119067delA								MACROD2 (85228 upstream) : KIF16B (133682 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	16199501	16199501	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16199501delA								MACROD2 (165662 upstream) : KIF16B (53248 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	16227249	16227249	+	IGR	DEL	A	-	-	rs77632141		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16227249delA								MACROD2 (193410 upstream) : KIF16B (25500 downstream)																																			---	---	---	---
KIF16B	55614	broad.mit.edu	37	20	16415377	16415377	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16415377delT	uc002wpg.1	-						KIF16B_uc010gch.1_Intron|KIF16B_uc010gci.1_Intron|KIF16B_uc010gcj.1_Intron	NM_024704	NP_078980			kinesin-like motor protein C20orf23						cell communication|early endosome to late endosome transport|endoderm development|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|formation of primary germ layer|Golgi to endosome transport|microtubule-based movement|receptor catabolic process|regulation of receptor recycling	early endosome membrane|microtubule	ATP binding|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|plus-end-directed microtubule motor activity			skin(2)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|ovary(1)|kidney(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	16885504	16885504	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16885504delA								OTOR (152696 upstream) : PCSK2 (321248 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	16894384	16894384	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:16894384delA								OTOR (161576 upstream) : PCSK2 (312368 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	17172744	17172744	+	IGR	DEL	A	-	-	rs80084657		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17172744delA								OTOR (439936 upstream) : PCSK2 (34008 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	17804031	17804031	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17804031delT								BANF2 (87514 upstream) : SNX5 (118215 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	17904712	17904712	+	IGR	DEL	T	-	-	rs117981024	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17904712delT								BANF2 (188195 upstream) : SNX5 (17534 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	17993443	17993444	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:17993443_17993444insA								C20orf72 (21684 upstream) : OVOL2 (11352 downstream)																																			---	---	---	---
DTD1	92675	broad.mit.edu	37	20	18690520	18690520	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18690520delT	uc002wrf.3	+							NM_080820	NP_543010			D-tyrosyl-tRNA deacylase 1						D-amino acid catabolic process	cytoplasm	hydrolase activity, acting on ester bonds			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	18895467	18895467	+	IGR	DEL	G	-	-	rs35640774		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:18895467delG								C20orf79 (100434 upstream) : SLC24A3 (297823 downstream)																																			---	---	---	---
SLC24A3	57419	broad.mit.edu	37	20	19312157	19312157	+	Intron	DEL	A	-	-	rs74173320		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19312157delA	uc002wrl.2	+							NM_020689	NP_065740			solute carrier family 24							integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			ovary(1)	1																		---	---	---	---
SLC24A3	57419	broad.mit.edu	37	20	19468812	19468812	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19468812delC	uc002wrl.2	+							NM_020689	NP_065740			solute carrier family 24							integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			ovary(1)	1																		---	---	---	---
SLC24A3	57419	broad.mit.edu	37	20	19629097	19629098	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19629097_19629098delTT	uc002wrl.2	+							NM_020689	NP_065740			solute carrier family 24							integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	19804029	19804031	+	IGR	DEL	CTG	-	-	rs78184693	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19804029_19804031delCTG								SLC24A3 (100489 upstream) : RIN2 (66179 downstream)																																			---	---	---	---
C20orf26	26074	broad.mit.edu	37	20	20171229	20171230	+	Intron	DEL	CA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20171229_20171230delCA	uc002wru.2	+						C20orf26_uc010zse.1_Intron	NM_015585	NP_056400			hypothetical protein LOC26074											ovary(3)|pancreas(1)	4				READ - Rectum adenocarcinoma(2;0.171)														---	---	---	---
Unknown	0	broad.mit.edu	37	20	20752650	20752650	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20752650delC								RALGAPA2 (59384 upstream) : PLK1S1 (353974 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	20888751	20888751	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20888751delT								RALGAPA2 (195485 upstream) : PLK1S1 (217873 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	21446624	21446624	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21446624delT								NKX2-4 (68577 upstream) : NKX2-2 (45040 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	22846653	22846654	+	IGR	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:22846653_22846654delGA								FOXA2 (280552 upstream) : SSTR4 (169403 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	23493480	23493480	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23493480delG								CST8 (16825 upstream) : CSTT (6303 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	24228014	24228014	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24228014delA								GGTLC1 (258598 upstream) : TMEM90B (221821 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	24286437	24286438	+	IGR	INS	-	CTTT	CTTT	rs11473434		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24286437_24286438insCTTT								GGTLC1 (317021 upstream) : TMEM90B (163397 downstream)																																			---	---	---	---
TMEM90B	79953	broad.mit.edu	37	20	24642150	24642153	+	Intron	DEL	GGAG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24642150_24642153delGGAG	uc002wtw.1	+							NM_024893	NP_079169			transmembrane protein 90B						response to biotic stimulus	early endosome membrane|integral to membrane|plasma membrane					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	24762759	24762759	+	IGR	DEL	A	-	-	rs72280446		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24762759delA								TMEM90B (115592 upstream) : CST7 (167107 downstream)																																			---	---	---	---
PYGB	5834	broad.mit.edu	37	20	25262537	25262539	+	Intron	DEL	CTC	-	-	rs146665561		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25262537_25262539delCTC	uc002wup.2	+							NM_002862	NP_002853			brain glycogen phosphorylase						glucose metabolic process|glycogen catabolic process	cytoplasm	glycogen phosphorylase activity|pyridoxal phosphate binding			central_nervous_system(1)|skin(1)	2					Pyridoxal Phosphate(DB00114)													---	---	---	---
GINS1	9837	broad.mit.edu	37	20	25407160	25407160	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25407160delT	uc002wuv.1	+						GINS1_uc010zte.1_Intron	NM_021067	NP_066545			GINS complex subunit 1						DNA strand elongation involved in DNA replication|S phase of mitotic cell cycle	cytoplasm|nucleoplasm				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	25649846	25649846	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25649846delA	uc002wuz.2	+											Homo sapiens zinc finger protein 337, mRNA (cDNA clone IMAGE:4826085).																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	25858966	25858967	+	IGR	INS	-	A	A	rs57493078		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25858966_25858967insA								FAM182B (10180 upstream) : LOC100134868 (131468 downstream)																																			---	---	---	---
C20orf191	149934	broad.mit.edu	37	20	26088971	26088971	+	Intron	DEL	A	-	-	rs76867961	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26088971delA	uc002wvj.3	-							NR_003678				SubName: Full=Putative uncharacterized protein ENSP00000323172;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	26132119	26132119	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26132119delT								C20orf191 (37442 upstream) : MIR663 (56703 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	26133151	26133152	+	IGR	DEL	GC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26133151_26133152delGC								C20orf191 (38474 upstream) : MIR663 (55670 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	26148286	26148289	+	IGR	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:26148286_26148289delTTTT								C20orf191 (53609 upstream) : MIR663 (40533 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29427513	29427514	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29427513_29427514insA								None (None upstream) : FRG1B (184365 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29470213	29470213	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29470213delA								None (None upstream) : FRG1B (141666 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29507910	29507911	+	IGR	DEL	GT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29507910_29507911delGT								None (None upstream) : FRG1B (103968 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	29849021	29849022	+	IGR	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:29849021_29849022insC								DEFB115 (1586 upstream) : DEFB116 (41994 downstream)																																			---	---	---	---
HM13	81502	broad.mit.edu	37	20	30155848	30155848	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30155848delT	uc002wwe.2	+						HM13_uc002wwc.2_Intron|HM13_uc002wwd.2_Intron|HM13_uc002wwf.2_Intron|HM13_uc010gdu.2_Intron	NM_030789	NP_110416			minor histocompatibility antigen 13 isoform 1						membrane protein proteolysis	cell surface|endoplasmic reticulum membrane|integral to membrane|plasma membrane	aspartic-type endopeptidase activity|protein binding			breast(1)	1	all_cancers(5;3.44e-05)|Lung NSC(7;4.38e-06)|all_lung(7;7.65e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		all cancers(5;0.000479)|Colorectal(19;0.00202)|COAD - Colon adenocarcinoma(19;0.0264)															---	---	---	---
TTLL9	164395	broad.mit.edu	37	20	30477770	30477773	+	Intron	DEL	TCTC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30477770_30477773delTCTC	uc010gdx.1	+						TTLL9_uc002wwy.1_Intron|TTLL9_uc002wwz.1_Intron|TTLL9_uc002wxa.1_Intron|TTLL9_uc002wxb.1_Intron|TTLL9_uc010zto.1_Intron|TTLL9_uc002wxc.2_Intron|TTLL9_uc010ztp.1_Intron	NM_001008409	NP_001008409			tubulin tyrosine ligase-like family, member 9						protein modification process	cilium|microtubule|microtubule basal body	ATP binding|tubulin-tyrosine ligase activity			ovary(2)	2			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)															---	---	---	---
PDRG1	81572	broad.mit.edu	37	20	30536717	30536717	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30536717delT	uc002wxd.2	-							NM_030815	NP_110442			p53 and DNA damage-regulated protein						protein folding	prefoldin complex	unfolded protein binding				0			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)															---	---	---	---
PLAGL2	5326	broad.mit.edu	37	20	30789952	30789952	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30789952delG	uc002wxn.2	-	2	247	c.30delC	c.(28-30)CCCfs	p.P10fs		NM_002657	NP_002648	Q9UPG8	PLAL2_HUMAN	pleiomorphic adenoma gene-like 2	10						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)															---	---	---	---
POFUT1	23509	broad.mit.edu	37	20	30812195	30812195	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30812195delA	uc002wxp.2	+						POFUT1_uc010ztt.1_Intron|POFUT1_uc010ztu.1_Intron	NM_015352	NP_056167			protein O-fucosyltransferase 1 isoform 1						fucose metabolic process|Notch signaling pathway|O-glycan processing|regulation of transcription, DNA-dependent	endoplasmic reticulum|membrane	peptide-O-fucosyltransferase activity			breast(1)	1			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)															---	---	---	---
KIF3B	9371	broad.mit.edu	37	20	30911917	30911918	+	Intron	DEL	AA	-	-	rs72063467		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30911917_30911918delAA	uc002wxq.2	+						KIF3B_uc010ztw.1_Intron	NM_004798	NP_004789			kinesin family member 3B						anterograde axon cargo transport|blood coagulation|determination of left/right symmetry|mitotic centrosome separation|plus-end-directed vesicle transport along microtubule|spindle assembly involved in mitosis	centrosome|cytosol|kinesin II complex|plus-end kinesin complex|spindle microtubule	ATP binding|plus-end-directed microtubule motor activity|Rho GTPase binding			central_nervous_system(3)|ovary(2)	5			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)															---	---	---	---
ASXL1	171023	broad.mit.edu	37	20	30972775	30972775	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30972775delA	uc002wxs.2	+						ASXL1_uc002wxr.1_Intron|ASXL1_uc010geb.2_Intron	NM_015338	NP_056153			additional sex combs like 1 isoform 1						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	PR-DUB complex	metal ion binding|protein binding			haematopoietic_and_lymphoid_tissue(239)|large_intestine(6)|central_nervous_system(2)|ovary(1)	248								F|N|Mis		MDS|CMML								---	---	---	---
DNMT3B	1789	broad.mit.edu	37	20	31358095	31358095	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31358095delT	uc002wyc.2	+						DNMT3B_uc010ztx.1_Intron|DNMT3B_uc010zty.1_Intron|DNMT3B_uc002wyd.2_Intron|DNMT3B_uc002wye.2_Intron|DNMT3B_uc010gee.2_Intron|DNMT3B_uc010gef.2_Intron|DNMT3B_uc010ztz.1_Intron|DNMT3B_uc010zua.1_Intron	NM_006892	NP_008823			DNA cytosine-5 methyltransferase 3 beta isoform						negative regulation of histone H3-K9 methylation|positive regulation of gene expression|positive regulation of histone H3-K4 methylation		metal ion binding|protein binding|transcription corepressor activity			lung(3)|ovary(2)	5																		---	---	---	---
DNMT3B	1789	broad.mit.edu	37	20	31390643	31390643	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31390643delA	uc002wyc.2	+						DNMT3B_uc002wyd.2_Intron|DNMT3B_uc002wye.2_Intron|DNMT3B_uc010gee.2_Intron|DNMT3B_uc010gef.2_Intron|DNMT3B_uc010ztz.1_Intron|DNMT3B_uc010zua.1_Intron|DNMT3B_uc002wyf.2_Intron|DNMT3B_uc002wyg.2_Intron|DNMT3B_uc010geg.2_Intron|DNMT3B_uc010geh.2_Intron	NM_006892	NP_008823			DNA cytosine-5 methyltransferase 3 beta isoform						negative regulation of histone H3-K9 methylation|positive regulation of gene expression|positive regulation of histone H3-K4 methylation		metal ion binding|protein binding|transcription corepressor activity			lung(3)|ovary(2)	5																		---	---	---	---
C20orf70	140683	broad.mit.edu	37	20	31768033	31768033	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31768033delA	uc002wyo.1	+							NM_080574	NP_542141			chromosome 20 open reading frame 70 precursor							extracellular region	lipid binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
CBFA2T2	9139	broad.mit.edu	37	20	32217923	32217923	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32217923delT	uc002wzg.1	+						CBFA2T2_uc010zug.1_Intron|CBFA2T2_uc002wze.1_Intron|CBFA2T2_uc002wzf.1_Intron|CBFA2T2_uc002wzh.1_Intron|CBFA2T2_uc002wzi.1_Intron|CBFA2T2_uc002wzj.1_Intron	NM_005093	NP_005084			core-binding factor, runt domain, alpha subunit							nucleus	protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			pancreas(1)|skin(1)	2																		---	---	---	---
E2F1	1869	broad.mit.edu	37	20	32266465	32266466	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32266465_32266466delAA	uc002wzu.3	-							NM_005225	NP_005216			E2F transcription factor 1						apoptosis|cell proliferation|G1 phase of mitotic cell cycle|G2 phase of mitotic cell cycle|mRNA stabilization|negative regulation of transcription involved in G1/S phase of mitotic cell cycle|positive regulation of fibroblast proliferation|positive regulation of transcription from RNA polymerase II promoter|regulation of G1/S transition of mitotic cell cycle	mitochondrion|Rb-E2F complex	sequence-specific DNA binding transcription factor activity|transcription corepressor activity|transcription factor binding				0																		---	---	---	---
ZNF341	84905	broad.mit.edu	37	20	32341970	32341970	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32341970delA	uc002wzy.2	+						ZNF341_uc002wzx.2_Intron|ZNF341_uc010geq.2_Intron|ZNF341_uc010ger.2_Intron	NM_032819	NP_116208			zinc finger protein 341						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2																		---	---	---	---
ZNF341	84905	broad.mit.edu	37	20	32364199	32364200	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32364199_32364200delTT	uc002wzy.2	+						ZNF341_uc002wzx.2_Intron|ZNF341_uc010geq.2_Intron|ZNF341_uc010ger.2_Intron	NM_032819	NP_116208			zinc finger protein 341						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	32461579	32461579	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32461579delC								CHMP4B (19410 upstream) : RALY (120153 downstream)																																			---	---	---	---
RALY	22913	broad.mit.edu	37	20	32652434	32652435	+	Intron	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32652434_32652435insC	uc002xab.2	+						RALY_uc010zui.1_Intron|RALY_uc002xac.2_Intron|RALY_uc002xad.2_Intron|RALY_uc002xae.1_Intron	NM_016732	NP_057951			RNA binding protein (autoantigenic,							catalytic step 2 spliceosome|heterogeneous nuclear ribonucleoprotein complex	nucleotide binding|RNA binding			ovary(1)	1																		---	---	---	---
MIR644	693229	broad.mit.edu	37	20	33054130	33054130	+	RNA	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33054130delT	hsa-mir-644|MI0003659	+			c.1delT			ITCH_uc002xak.2_Intron|ITCH_uc010geu.1_Intron|ITCH_uc010zuj.1_Intron																	0																		---	---	---	---
PIGU	128869	broad.mit.edu	37	20	33197170	33197171	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33197170_33197171insT	uc002xas.2	-						PIGU_uc010zul.1_Intron|PIGU_uc002xat.2_Intron|PIGU_uc010gev.1_Intron	NM_080476	NP_536724			phosphatidylinositol glycan anchor biosynthesis,						attachment of GPI anchor to protein|C-terminal protein lipidation|regulation of JAK-STAT cascade	GPI-anchor transamidase complex|plasma membrane					0																		---	---	---	---
PIGU	128869	broad.mit.edu	37	20	33260364	33260364	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33260364delA	uc002xas.2	-						PIGU_uc010zul.1_Intron|PIGU_uc002xat.2_Intron|PIGU_uc010gev.1_Intron	NM_080476	NP_536724			phosphatidylinositol glycan anchor biosynthesis,						attachment of GPI anchor to protein|C-terminal protein lipidation|regulation of JAK-STAT cascade	GPI-anchor transamidase complex|plasma membrane					0																		---	---	---	---
NCOA6	23054	broad.mit.edu	37	20	33342832	33342832	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33342832delA	uc002xav.2	-						NCOA6_uc002xaw.2_Intron	NM_014071	NP_054790			nuclear receptor coactivator 6						brain development|cellular lipid metabolic process|DNA recombination|DNA repair|DNA replication|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|heart development|myeloid cell differentiation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus|transcription initiation from RNA polymerase II promoter	transcription factor complex	chromatin binding|enzyme binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|retinoid X receptor binding|thyroid hormone receptor binding			ovary(3)|breast(3)|central_nervous_system(1)	7																		---	---	---	---
EDEM2	55741	broad.mit.edu	37	20	33726560	33726560	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33726560delT	uc002xbo.2	-						EDEM2_uc010zuv.1_Intron|EDEM2_uc010zus.1_Intron|EDEM2_uc002xbq.2_Intron|EDEM2_uc010zut.1_Intron|EDEM2_uc002xbp.2_Intron|EDEM2_uc002xbn.2_Intron|EDEM2_uc002xbr.2_Intron|EDEM2_uc010zuu.1_Intron	NM_018217	NP_060687			ER degradation enhancer, mannosidase alpha-like						post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|response to unfolded protein	endoplasmic reticulum lumen|endoplasmic reticulum membrane|extracellular region	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity|misfolded protein binding				0			BRCA - Breast invasive adenocarcinoma(18;0.00936)															---	---	---	---
MMP24	10893	broad.mit.edu	37	20	33819259	33819259	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33819259delA	uc002xbu.2	+						EDEM2_uc010zuv.1_Intron	NM_006690	NP_006681			matrix metalloproteinase 24 preproprotein						proteolysis	integral to plasma membrane|proteinaceous extracellular matrix	calcium ion binding|enzyme activator activity|metalloendopeptidase activity|zinc ion binding				0			BRCA - Breast invasive adenocarcinoma(18;0.00252)															---	---	---	---
MMP24	10893	broad.mit.edu	37	20	33863920	33863920	+	3'UTR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33863920delC	uc002xbu.2	+	9					EDEM2_uc010zuv.1_Intron	NM_006690	NP_006681			matrix metalloproteinase 24 preproprotein						proteolysis	integral to plasma membrane|proteinaceous extracellular matrix	calcium ion binding|enzyme activator activity|metalloendopeptidase activity|zinc ion binding				0			BRCA - Breast invasive adenocarcinoma(18;0.00252)															---	---	---	---
GDF5	8200	broad.mit.edu	37	20	33935201	33935201	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33935201delT	uc010gfc.1	-						UQCC_uc010zuy.1_Intron|UQCC_uc002xcd.2_Intron|UQCC_uc010zuz.1_Intron|UQCC_uc010zva.1_Intron|UQCC_uc002xce.2_Intron|UQCC_uc002xcg.2_Intron|UQCC_uc010gfb.2_Intron|UQCC_uc010zvb.1_Intron|UQCC_uc002xcf.2_Intron|UQCC_uc002xci.1_Intron|UQCC_uc010gfd.1_Intron	NM_000557	NP_000548			growth differentiation factor 5 preproprotein						cartilage development|cell-cell signaling|growth|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity				0	Lung NSC(9;0.00642)|all_lung(11;0.0094)		BRCA - Breast invasive adenocarcinoma(18;0.00663)															---	---	---	---
GDF5	8200	broad.mit.edu	37	20	33969913	33969913	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33969913delT	uc010gfc.1	-						UQCC_uc010zuy.1_Intron|UQCC_uc002xcd.2_Intron|UQCC_uc010zuz.1_Intron|UQCC_uc010zva.1_Intron|UQCC_uc002xce.2_Intron|UQCC_uc002xcg.2_Intron|UQCC_uc010gfb.2_Intron|UQCC_uc010zvb.1_Intron|UQCC_uc002xcf.2_Intron|UQCC_uc002xci.1_Intron|UQCC_uc010gfd.1_Intron	NM_000557	NP_000548			growth differentiation factor 5 preproprotein						cartilage development|cell-cell signaling|growth|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity				0	Lung NSC(9;0.00642)|all_lung(11;0.0094)		BRCA - Breast invasive adenocarcinoma(18;0.00663)															---	---	---	---
CEP250	11190	broad.mit.edu	37	20	34063758	34063758	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34063758delC	uc002xcm.2	+						CEP250_uc010zve.1_Intron|CEP250_uc010zvd.1_Intron	NM_007186	NP_009117			centrosomal protein 2						centriole-centriole cohesion|G2/M transition of mitotic cell cycle|protein localization|regulation of centriole-centriole cohesion	centriole|cilium|cytosol|microtubule basal body|perinuclear region of cytoplasm|protein complex	protein C-terminus binding|protein kinase binding			ovary(4)|central_nervous_system(1)	5	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)															---	---	---	---
FER1L4	80307	broad.mit.edu	37	20	34185345	34185345	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34185345delC	uc002xcy.3	-							NR_024377				Homo sapiens clone PP3795 unknown mRNA.												0																		---	---	---	---
NFS1	9054	broad.mit.edu	37	20	34284587	34284587	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34284587delT	uc002xdw.1	-						NFS1_uc002xdt.1_Intron|NFS1_uc002xdu.1_Intron|NFS1_uc002xdv.1_Intron|NFS1_uc010zvk.1_Intron|NFS1_uc010zvl.1_Intron|NFS1_uc002xdx.2_Intron|ROMO1_uc002xdy.2_5'Flank|ROMO1_uc010gfm.2_5'Flank	NM_021100	NP_066923			NFS1 nitrogen fixation 1 precursor						cysteine metabolic process|iron incorporation into metallo-sulfur cluster|Mo-molybdopterin cofactor biosynthetic process|protein complex assembly|water-soluble vitamin metabolic process	cytosol|mitochondrial matrix|nucleus	cysteine desulfurase activity|protein homodimerization activity|pyridoxal phosphate binding			ovary(1)|skin(1)	2	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.0886)		L-Alanine(DB00160)|L-Cysteine(DB00151)|Pyridoxal Phosphate(DB00114)													---	---	---	---
Unknown	0	broad.mit.edu	37	20	34337434	34337434	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34337434delT								RBM39 (7241 upstream) : PHF20 (22489 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	34341658	34341659	+	IGR	DEL	AA	-	-	rs79208525		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34341658_34341659delAA								RBM39 (11465 upstream) : PHF20 (18264 downstream)																																			---	---	---	---
PHF20	51230	broad.mit.edu	37	20	34396798	34396798	+	Intron	DEL	T	-	-	rs79627785		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34396798delT	uc002xek.1	+						PHF20_uc002xei.1_Intron|PHF20_uc010gfo.1_Intron|PHF20_uc002xej.1_Intron|PHF20_uc002xeh.2_Intron	NM_016436	NP_057520			PHD finger protein 20						regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex	DNA binding|zinc ion binding			ovary(1)	1	Breast(12;0.00631)|all_lung(11;0.0145)																	---	---	---	---
PHF20	51230	broad.mit.edu	37	20	34407571	34407572	+	Intron	DEL	TG	-	-	rs72112610		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34407571_34407572delTG	uc002xek.1	+						PHF20_uc002xei.1_Intron|PHF20_uc010gfo.1_Intron|PHF20_uc002xej.1_Intron|PHF20_uc002xeh.2_Intron	NM_016436	NP_057520			PHD finger protein 20						regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex	DNA binding|zinc ion binding			ovary(1)	1	Breast(12;0.00631)|all_lung(11;0.0145)																	---	---	---	---
Unknown	0	broad.mit.edu	37	20	34887954	34887955	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34887954_34887955delAA								C20orf4 (29114 upstream) : DLGAP4 (6348 downstream)																																			---	---	---	---
TGIF2	60436	broad.mit.edu	37	20	35207584	35207584	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35207584delT	uc002xfn.2	+						C20orf24_uc002xfo.2_Intron	NM_021809	NP_068581			TGFB-induced factor homeobox 2							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			pancreas(1)|skin(1)	2	Breast(12;0.114)	Myeloproliferative disorder(115;0.00878)																---	---	---	---
TGIF2	60436	broad.mit.edu	37	20	35212312	35212312	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35212312delA	uc002xfn.2	+						C20orf24_uc002xfo.2_Intron	NM_021809	NP_068581			TGFB-induced factor homeobox 2							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			pancreas(1)|skin(1)	2	Breast(12;0.114)	Myeloproliferative disorder(115;0.00878)																---	---	---	---
TGIF2	60436	broad.mit.edu	37	20	35216315	35216315	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35216315delA	uc002xfn.2	+						C20orf24_uc002xfo.2_Intron	NM_021809	NP_068581			TGFB-induced factor homeobox 2							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			pancreas(1)|skin(1)	2	Breast(12;0.114)	Myeloproliferative disorder(115;0.00878)																---	---	---	---
NDRG3	57446	broad.mit.edu	37	20	35343913	35343914	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35343913_35343914delTT	uc002xfw.2	-						NDRG3_uc002xfx.2_Intron|NDRG3_uc010zvq.1_Intron|NDRG3_uc010zvr.1_Intron	NM_032013	NP_114402			N-myc downstream regulated gene 3 isoform a						cell differentiation|negative regulation of cell growth|spermatogenesis	cytoplasm				ovary(1)	1		Myeloproliferative disorder(115;0.00878)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	35592915	35592916	+	IGR	DEL	AG	-	-	rs9636529		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35592915_35592916delAG								SAMHD1 (12739 upstream) : RBL1 (32156 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	35601111	35601111	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35601111delA								SAMHD1 (20935 upstream) : RBL1 (23961 downstream)																																			---	---	---	---
RBL1	5933	broad.mit.edu	37	20	35633449	35633449	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35633449delA	uc002xgi.2	-						RBL1_uc010zvt.1_Intron|RBL1_uc002xgj.1_Intron	NM_002895	NP_002886			retinoblastoma-like protein 1 isoform a						cell cycle|chromatin modification|interspecies interaction between organisms|regulation of cell cycle|regulation of lipid kinase activity|transcription, DNA-dependent		transcription factor binding			lung(5)|skin(3)|ovary(2)	10		Myeloproliferative disorder(115;0.00878)																---	---	---	---
RBL1	5933	broad.mit.edu	37	20	35663914	35663914	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35663914delA	uc002xgi.2	-						RBL1_uc010zvt.1_Intron|RBL1_uc002xgj.1_Intron	NM_002895	NP_002886			retinoblastoma-like protein 1 isoform a						cell cycle|chromatin modification|interspecies interaction between organisms|regulation of cell cycle|regulation of lipid kinase activity|transcription, DNA-dependent		transcription factor binding			lung(5)|skin(3)|ovary(2)	10		Myeloproliferative disorder(115;0.00878)																---	---	---	---
RBL1	5933	broad.mit.edu	37	20	35708866	35708869	+	Intron	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35708866_35708869delTTTT	uc002xgi.2	-						RBL1_uc010zvt.1_Intron|RBL1_uc002xgj.1_Intron|RBL1_uc010gfv.1_Intron	NM_002895	NP_002886			retinoblastoma-like protein 1 isoform a						cell cycle|chromatin modification|interspecies interaction between organisms|regulation of cell cycle|regulation of lipid kinase activity|transcription, DNA-dependent		transcription factor binding			lung(5)|skin(3)|ovary(2)	10		Myeloproliferative disorder(115;0.00878)																---	---	---	---
C20orf132	140699	broad.mit.edu	37	20	35729832	35729832	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35729832delA	uc010zvu.1	-						C20orf132_uc002xgk.2_Intron	NM_152503	NP_689716			hypothetical protein LOC140699 isoform 1												0		Myeloproliferative disorder(115;0.00878)																---	---	---	---
C20orf132	140699	broad.mit.edu	37	20	35761047	35761047	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35761047delT	uc010zvu.1	-						C20orf132_uc002xgk.2_Intron|C20orf132_uc002xgm.2_Intron|C20orf132_uc002xgn.2_Intron	NM_152503	NP_689716			hypothetical protein LOC140699 isoform 1												0		Myeloproliferative disorder(115;0.00878)																---	---	---	---
RPN2	6185	broad.mit.edu	37	20	35835477	35835477	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35835477delA	uc002xgp.2	+						RPN2_uc002xgo.3_Intron|RPN2_uc010gfw.2_Intron|RPN2_uc002xgq.2_Intron	NM_002951	NP_002942			ribophorin II isoform 1 precursor						post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|nucleus|oligosaccharyltransferase complex	dolichyl-diphosphooligosaccharide-protein glycotransferase activity|protein binding			ovary(2)|skin(1)	3		Myeloproliferative disorder(115;0.00878)																---	---	---	---
RPN2	6185	broad.mit.edu	37	20	35840889	35840889	+	Intron	DEL	T	-	-	rs148357955		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35840889delT	uc002xgp.2	+						RPN2_uc002xgo.3_Intron|RPN2_uc010gfw.2_Intron|RPN2_uc002xgq.2_Intron	NM_002951	NP_002942			ribophorin II isoform 1 precursor						post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|nucleus|oligosaccharyltransferase complex	dolichyl-diphosphooligosaccharide-protein glycotransferase activity|protein binding			ovary(2)|skin(1)	3		Myeloproliferative disorder(115;0.00878)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	36065582	36065582	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36065582delA								SRC (31763 upstream) : BLCAP (80238 downstream)																																			---	---	---	---
CTNNBL1	56259	broad.mit.edu	37	20	36407392	36407392	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36407392delT	uc010zvw.1	+						CTNNBL1_uc002xhh.2_Intron|CTNNBL1_uc002xhi.2_Intron|CTNNBL1_uc002xhj.2_Intron	NM_030877	NP_110517			beta catenin-like 1						apoptosis|positive regulation of apoptosis|somatic diversification of immunoglobulins	nucleus	enzyme binding			ovary(2)	2		Myeloproliferative disorder(115;0.00878)																---	---	---	---
CTNNBL1	56259	broad.mit.edu	37	20	36417509	36417509	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36417509delA	uc010zvw.1	+						CTNNBL1_uc002xhh.2_Intron|CTNNBL1_uc002xhi.2_Intron|CTNNBL1_uc002xhj.2_Intron	NM_030877	NP_110517			beta catenin-like 1						apoptosis|positive regulation of apoptosis|somatic diversification of immunoglobulins	nucleus	enzyme binding			ovary(2)	2		Myeloproliferative disorder(115;0.00878)																---	---	---	---
RPRD1B	58490	broad.mit.edu	37	20	36676670	36676670	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36676670delT	uc002xho.3	+							NM_021215	NP_067038			Regulation of nuclear pre-mRNA domain containing											pancreas(1)	1																		---	---	---	---
LOC388796	388796	broad.mit.edu	37	20	37051739	37051740	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37051739_37051740delAA	uc002xie.3	-						LOC388796_uc002xii.3_Intron|LOC388796_uc002xig.3_Intron|LOC388796_uc002xih.3_Intron|LOC388796_uc002xij.3_Intron|LOC388796_uc002xif.3_Intron					Homo sapiens cDNA FLJ12683 fis, clone NT2RM4002457.												0																		---	---	---	---
RALGAPB	57148	broad.mit.edu	37	20	37123942	37123942	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37123942delT	uc002xiw.2	+						RALGAPB_uc010zvz.1_Intron|RALGAPB_uc002xix.2_Intron|RALGAPB_uc002xiy.1_Intron|RALGAPB_uc002xiz.2_Intron	NM_020336	NP_065069			Ral GTPase activating protein, beta subunit						activation of Ral GTPase activity	intracellular	protein heterodimerization activity|Ral GTPase activator activity			pancreas(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	37277257	37277257	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37277257delT								ADIG (60153 upstream) : SLC32A1 (75848 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	38095377	38095377	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:38095377delT								LOC339568 (241986 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	38808859	38808859	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:38808859delA								LOC339568 (955468 upstream) : MAFB (505660 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	38858534	38858535	+	IGR	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:38858534_38858535delAC								None (None upstream) : MAFB (455984 downstream)																																			---	---	---	---
PLCG1	5335	broad.mit.edu	37	20	39794631	39794631	+	Intron	DEL	C	-	-	rs74464491		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39794631delC	uc002xjp.1	+						PLCG1_uc002xjo.1_Intron|PLCG1_uc010zwe.1_Intron|PLCG1_uc010ggf.2_5'Flank	NM_182811	NP_877963			phospholipase C, gamma 1 isoform b						activation of phospholipase C activity|axon guidance|blood coagulation|cellular response to epidermal growth factor stimulus|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|interspecies interaction between organisms|intracellular signal transduction|leukocyte migration|nerve growth factor receptor signaling pathway|phospholipid catabolic process|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of epithelial cell migration|T cell receptor signaling pathway	cytosol|lamellipodium|plasma membrane|ruffle	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|receptor signaling protein activity			lung(3)|breast(3)|skin(2)	8		Myeloproliferative disorder(115;0.00878)																---	---	---	---
PLCG1	5335	broad.mit.edu	37	20	39801752	39801752	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39801752delT	uc002xjp.1	+						PLCG1_uc002xjo.1_Intron|PLCG1_uc010zwe.1_Intron	NM_182811	NP_877963			phospholipase C, gamma 1 isoform b						activation of phospholipase C activity|axon guidance|blood coagulation|cellular response to epidermal growth factor stimulus|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|interspecies interaction between organisms|intracellular signal transduction|leukocyte migration|nerve growth factor receptor signaling pathway|phospholipid catabolic process|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of epithelial cell migration|T cell receptor signaling pathway	cytosol|lamellipodium|plasma membrane|ruffle	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|receptor signaling protein activity			lung(3)|breast(3)|skin(2)	8		Myeloproliferative disorder(115;0.00878)														OREG0025953	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CHD6	84181	broad.mit.edu	37	20	40226364	40226365	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40226364_40226365delTT	uc002xka.1	-						CHD6_uc002xkd.2_Intron|CHD6_uc002xkc.2_Intron	NM_032221	NP_115597			chromodomain helicase DNA binding protein 6						chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding			ovary(6)|skin(5)|lung(2)|central_nervous_system(1)	14		Myeloproliferative disorder(115;0.00425)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	40318828	40318829	+	IGR	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40318828_40318829delAC								CHD6 (71695 upstream) : PTPRT (382564 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	40393018	40393018	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40393018delA								CHD6 (145885 upstream) : PTPRT (308375 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	40522785	40522786	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40522785_40522786delTG								CHD6 (275652 upstream) : PTPRT (178607 downstream)																																			---	---	---	---
PTPRT	11122	broad.mit.edu	37	20	40875242	40875242	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40875242delC	uc002xkg.2	-						PTPRT_uc010ggj.2_Intron	NM_007050	NP_008981			protein tyrosine phosphatase, receptor type, T						homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			skin(8)|ovary(7)|lung(5)	20		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)																---	---	---	---
PTPRT	11122	broad.mit.edu	37	20	41175651	41175652	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41175651_41175652insA	uc002xkg.2	-						PTPRT_uc010ggj.2_Intron	NM_007050	NP_008981			protein tyrosine phosphatase, receptor type, T						homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			skin(8)|ovary(7)|lung(5)	20		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)																---	---	---	---
PTPRT	11122	broad.mit.edu	37	20	41305179	41305182	+	Intron	DEL	CTCT	-	-	rs67125859		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41305179_41305182delCTCT	uc002xkg.2	-						PTPRT_uc010ggj.2_Intron	NM_007050	NP_008981			protein tyrosine phosphatase, receptor type, T						homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			skin(8)|ovary(7)|lung(5)	20		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)																---	---	---	---
PTPRT	11122	broad.mit.edu	37	20	41737717	41737717	+	Intron	DEL	T	-	-	rs74366329		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41737717delT	uc002xkg.2	-						PTPRT_uc010ggj.2_Intron	NM_007050	NP_008981			protein tyrosine phosphatase, receptor type, T						homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			skin(8)|ovary(7)|lung(5)	20		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	41903347	41903348	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:41903347_41903348insT								PTPRT (84790 upstream) : SFRS6 (183156 downstream)																																			---	---	---	---
IFT52	51098	broad.mit.edu	37	20	42262646	42262646	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42262646delT	uc002xkw.2	+						IFT52_uc002xky.2_Intron|IFT52_uc002xkx.2_Intron|IFT52_uc010ggn.2_Intron|IFT52_uc002xkz.2_Intron	NM_016004	NP_057088			intraflagellar transport 52 homolog							intraflagellar transport particle B|microtubule-based flagellum	protein C-terminus binding			ovary(2)	2		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	42456035	42456035	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42456035delT								GTSF1L (100393 upstream) : TOX2 (87457 downstream)																																			---	---	---	---
TOX2	84969	broad.mit.edu	37	20	42634582	42634582	+	Intron	DEL	A	-	-	rs142869884		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42634582delA	uc002xlf.3	+						TOX2_uc010ggo.2_Intron|TOX2_uc002xle.3_Intron|TOX2_uc010ggp.2_Intron|TOX2_uc002xlg.2_Intron	NM_001098798	NP_001092268			TOX high mobility group box family member 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.00189)															---	---	---	---
STK4	6789	broad.mit.edu	37	20	43621775	43621775	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43621775delT	uc002xnb.2	+						STK4_uc010ggx.2_Intron|STK4_uc010ggy.2_Intron|STK4_uc010ggw.1_Intron	NM_006282	NP_006273			serine/threonine kinase 4						apoptosis|cell morphogenesis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|peptidyl-serine phosphorylation|positive regulation of apoptosis|protein autophosphorylation	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein homodimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity|transcription factor binding			ovary(1)|skin(1)	2		Myeloproliferative disorder(115;0.0122)																---	---	---	---
SYS1-DBNDD2	767557	broad.mit.edu	37	20	44019203	44019203	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44019203delA	uc002xnx.2	+							NM_001048225	NP_001041690			SCF apoptosis response protein 1 isoform a												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	44119407	44119407	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44119407delA								WFDC2 (9236 upstream) : SPINT3 (21694 downstream)																																			---	---	---	---
SPINLW1	57119	broad.mit.edu	37	20	44174618	44174618	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44174618delC	uc002xou.2	-						SPINLW1_uc010zxc.1_Intron|SPINLW1_uc002xot.2_5'UTR|SPINLW1_uc002xov.1_Intron	NM_020398	NP_065131			serine peptidase inhibitor-like, with Kunitz and							extracellular region	serine-type endopeptidase inhibitor activity			pancreas(1)	1		Myeloproliferative disorder(115;0.0122)																---	---	---	---
DNTTIP1	116092	broad.mit.edu	37	20	44430268	44430268	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44430268delA	uc002xpk.2	+							NM_052951	NP_443183			terminal deoxynucleotidyltransferase interacting							nucleus				ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(115;0.0122)																---	---	---	---
ZNF335	63925	broad.mit.edu	37	20	44600345	44600345	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44600345delC	uc002xqw.2	-						ZNF335_uc010zxk.1_Intron|ZNF335_uc002xqx.1_5'Flank|ZNF335_uc002xqy.2_5'Flank	NM_022095	NP_071378			zinc finger protein 335						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(3)|ovary(1)	4		Myeloproliferative disorder(115;0.0122)																---	---	---	---
NCOA5	57727	broad.mit.edu	37	20	44692139	44692139	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44692139delC	uc002xrd.2	-	6	1538	c.1010delG	c.(1009-1011)GGCfs	p.G337fs	NCOA5_uc002xrc.2_Frame_Shift_Del_p.G225fs|NCOA5_uc002xre.2_Frame_Shift_Del_p.G337fs	NM_020967	NP_066018	Q9HCD5	NCOA5_HUMAN	nuclear receptor coactivator 5	337					regulation of transcription, DNA-dependent|transcription, DNA-dependent|translation	nucleus	aminoacyl-tRNA ligase activity|ATP binding			central_nervous_system(1)|skin(1)	2		Myeloproliferative disorder(115;0.0122)																---	---	---	---
Unknown	0	broad.mit.edu	37	20	45103444	45103444	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45103444delG								LOC100240726 (9513 upstream) : ZNF334 (26265 downstream)																																			---	---	---	---
SLC13A3	64849	broad.mit.edu	37	20	45273077	45273077	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45273077delT	uc002xsf.1	-						SLC13A3_uc010zxw.1_Intron|SLC13A3_uc002xsg.1_Intron|SLC13A3_uc010gho.1_Intron|SLC13A3_uc010zxx.1_Intron|SLC13A3_uc002xsi.3_Intron	NM_022829	NP_073740			solute carrier family 13 member 3 isoform a							integral to membrane|plasma membrane	high affinity sodium:dicarboxylate symporter activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)													---	---	---	---
EYA2	2139	broad.mit.edu	37	20	45781024	45781026	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45781024_45781026delTTT	uc002xsm.2	+						EYA2_uc010ghp.2_Intron|EYA2_uc002xsn.2_Intron|EYA2_uc002xso.2_Intron|EYA2_uc002xsp.2_Intron|EYA2_uc002xsq.2_Intron	NM_005244	NP_005235			eyes absent 2 isoform a						DNA repair|histone dephosphorylation|mesodermal cell fate specification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	magnesium ion binding|protein binding|protein tyrosine phosphatase activity			ovary(1)	1		Myeloproliferative disorder(115;0.0241)																---	---	---	---
ZMYND8	23613	broad.mit.edu	37	20	45848175	45848178	+	Intron	DEL	AAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45848175_45848178delAAAA	uc002xta.1	-						ZMYND8_uc010ghq.1_Intron|ZMYND8_uc010ghr.1_Intron|ZMYND8_uc002xst.1_Intron|ZMYND8_uc002xsu.1_Intron|ZMYND8_uc002xsv.1_Intron|ZMYND8_uc002xsw.1_Intron|ZMYND8_uc002xsx.1_Intron|ZMYND8_uc002xsy.1_Intron|ZMYND8_uc002xsz.1_Intron|ZMYND8_uc010zxy.1_Intron|ZMYND8_uc002xtb.1_Intron|ZMYND8_uc002xss.2_Intron|ZMYND8_uc010zxz.1_Intron|ZMYND8_uc002xtc.1_Intron|ZMYND8_uc002xtd.1_Intron|ZMYND8_uc002xte.1_Intron|ZMYND8_uc010zya.1_Intron|ZMYND8_uc002xtf.1_Intron|ZMYND8_uc002xsr.1_Intron	NM_012408	NP_036540			zinc finger, MYND-type containing 8 isoform b								protein binding|zinc ion binding			central_nervous_system(2)|urinary_tract(1)|ovary(1)|skin(1)	5			Epithelial(1;0.0289)|all cancers(1;0.0962)|OV - Ovarian serous cystadenocarcinoma(1;0.154)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	46072239	46072239	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46072239delA								ZMYND8 (86765 upstream) : NCOA3 (58418 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	46082448	46082449	+	IGR	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46082448_46082449delGA								ZMYND8 (96974 upstream) : NCOA3 (48208 downstream)																																			---	---	---	---
NCOA3	8202	broad.mit.edu	37	20	46190722	46190722	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46190722delT	uc002xtk.2	+						NCOA3_uc010ght.1_Intron|NCOA3_uc002xtl.2_Intron|NCOA3_uc002xtm.2_Intron|NCOA3_uc002xtn.2_Intron	NM_181659	NP_858045			nuclear receptor coactivator 3 isoform a						androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleoplasm	androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding			ovary(3)|lung(1)|skin(1)	5																		---	---	---	---
NCOA3	8202	broad.mit.edu	37	20	46240081	46240081	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46240081delT	uc002xtk.2	+						NCOA3_uc010ght.1_Intron|NCOA3_uc002xtl.2_Intron|NCOA3_uc002xtm.2_Intron|NCOA3_uc002xtn.2_Intron	NM_181659	NP_858045			nuclear receptor coactivator 3 isoform a						androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleoplasm	androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding			ovary(3)|lung(1)|skin(1)	5																		---	---	---	---
SULF2	55959	broad.mit.edu	37	20	46300886	46300886	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46300886delC	uc002xto.2	-						SULF2_uc002xtr.2_Intron|SULF2_uc002xtq.2_Intron	NM_018837	NP_061325			sulfatase 2 isoform a precursor						bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding			ovary(2)|breast(2)|pancreas(1)|skin(1)	6																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	46588141	46588141	+	RNA	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46588141delC	uc002xts.1	+	4		c.2549delC								Homo sapiens mRNA; cDNA DKFZp686I1537 (from clone DKFZp686I1537).																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	46736889	46736890	+	IGR	DEL	AA	-	-	rs72121166		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46736889_46736890delAA								SULF2 (321529 upstream) : LOC284749 (251764 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	46856857	46856857	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46856857delA								SULF2 (441497 upstream) : LOC284749 (131797 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	46980056	46980057	+	IGR	DEL	CA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46980056_46980057delCA								SULF2 (564696 upstream) : LOC284749 (8597 downstream)																																			---	---	---	---
PREX1	57580	broad.mit.edu	37	20	47365015	47365016	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47365015_47365016delTT	uc002xtw.1	-							NM_020820	NP_065871			phosphatidylinositol-3,4,						actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)															---	---	---	---
PREX1	57580	broad.mit.edu	37	20	47387246	47387247	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47387246_47387247insA	uc002xtw.1	-							NM_020820	NP_065871			phosphatidylinositol-3,4,						actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	47815508	47815509	+	IGR	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47815508_47815509insC								STAU1 (10220 upstream) : DDX27 (20323 downstream)																																			---	---	---	---
DDX27	55661	broad.mit.edu	37	20	47853289	47853291	+	Intron	DEL	AGA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47853289_47853291delAGA	uc002xuh.2	+							NM_017895	NP_060365			DEAD (Asp-Glu-Ala-Asp) box polypeptide 27							nucleus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			kidney(2)	2			BRCA - Breast invasive adenocarcinoma(12;0.000899)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)															---	---	---	---
ZNFX1	57169	broad.mit.edu	37	20	47877326	47877326	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47877326delA	uc002xui.2	-							NM_021035	NP_066363			zinc finger, NFX1-type containing 1								metal ion binding			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)															---	---	---	---
ZNFX1	57169	broad.mit.edu	37	20	47893558	47893558	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47893558delA	uc002xui.2	-						C20orf199_uc002xuj.2_5'Flank|C20orf199_uc002xul.3_5'Flank|C20orf199_uc002xun.3_5'Flank|C20orf199_uc002xum.3_5'Flank|C20orf199_uc002xuo.2_5'Flank|SNORD12C_uc010ghz.2_5'Flank	NM_021035	NP_066363			zinc finger, NFX1-type containing 1								metal ion binding			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	47957296	47957297	+	IGR	INS	-	CT	CT	rs151036392	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47957296_47957297insCT								C20orf199 (51503 upstream) : KCNB1 (31208 downstream)																																			---	---	---	---
PTGIS	5740	broad.mit.edu	37	20	48156558	48156558	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48156558delG	uc002xut.2	-						PTGIS_uc010zyi.1_Intron	NM_000961	NP_000952			prostaglandin I2 synthase						hormone biosynthetic process|prostaglandin biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|prostaglandin-I synthase activity			skin(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(12;2.37e-05)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		Phenylbutazone(DB00812)													---	---	---	---
Unknown	0	broad.mit.edu	37	20	48218201	48218201	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48218201delT								PTGIS (33494 upstream) : B4GALT5 (31284 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	48240396	48240396	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48240396delA								PTGIS (55689 upstream) : B4GALT5 (9089 downstream)																																			---	---	---	---
SLC9A8	23315	broad.mit.edu	37	20	48432281	48432282	+	Intron	DEL	AA	-	-	rs77498910		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48432281_48432282delAA	uc002xuv.1	+						SLC9A8_uc010zym.1_Intron|SLC9A8_uc010zyj.1_Intron|SLC9A8_uc010zyk.1_Intron|SLC9A8_uc010zyl.1_Intron|SLC9A8_uc010gib.1_Intron	NM_015266	NP_056081			sodium/hydrogen exchanger 8							Golgi membrane|integral to membrane	sodium:hydrogen antiporter activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(9;3.91e-07)															---	---	---	---
SLC9A8	23315	broad.mit.edu	37	20	48447098	48447098	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48447098delG	uc002xuv.1	+						SLC9A8_uc010zym.1_Intron|SLC9A8_uc010zyj.1_Intron|SLC9A8_uc010zyk.1_Intron|SLC9A8_uc010zyl.1_Intron|SLC9A8_uc010gib.1_Intron	NM_015266	NP_056081			sodium/hydrogen exchanger 8							Golgi membrane|integral to membrane	sodium:hydrogen antiporter activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(9;3.91e-07)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	48591444	48591445	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48591444_48591445insT								RNF114 (21024 upstream) : SNAI1 (8082 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	48694317	48694317	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48694317delA								SNAI1 (88899 upstream) : TMEM189-UBE2V1 (3346 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	48830682	48830682	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48830682delT								CEBPB (21470 upstream) : PTPN1 (296209 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	48844964	48844964	+	IGR	DEL	T	-	-	rs72326949		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48844964delT								CEBPB (35752 upstream) : PTPN1 (281927 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	49117163	49117163	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49117163delT								CEBPB (307951 upstream) : PTPN1 (9728 downstream)																																			---	---	---	---
FAM65C	140876	broad.mit.edu	37	20	49244218	49244218	+	Intron	DEL	A	-	-	rs77257844		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49244218delA	uc002xvm.2	-						FAM65C_uc010zyt.1_Intron|FAM65C_uc010zyu.1_Intron|FAM65C_uc002xvn.1_Intron	NM_080829	NP_543019			hypothetical protein LOC140876											ovary(2)	2																		---	---	---	---
FAM65C	140876	broad.mit.edu	37	20	49286399	49286401	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49286399_49286401delAAA	uc010zyt.1	-						FAM65C_uc010zyu.1_Intron	NM_080829	NP_543019			hypothetical protein LOC140876											ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	49396898	49396898	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49396898delG								PARD6B (26621 upstream) : BCAS4 (14569 downstream)																																			---	---	---	---
BCAS4	55653	broad.mit.edu	37	20	49410197	49410197	+	5'Flank	DEL	T	-	-	rs76931943		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49410197delT	uc002xvq.2	+						BCAS4_uc002xvp.1_5'Flank|BCAS4_uc002xvr.2_5'Flank|BCAS4_uc002xvs.2_5'Flank	NM_017843	NP_060313			breast carcinoma amplified sequence 4 isoform a							cytoplasm					0																		---	---	---	---
BCAS4	55653	broad.mit.edu	37	20	49430375	49430377	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49430375_49430377delAAA	uc002xvq.2	+						BCAS4_uc002xvp.1_Intron|BCAS4_uc002xvr.2_Intron|BCAS4_uc002xvs.2_Intron	NM_017843	NP_060313			breast carcinoma amplified sequence 4 isoform a							cytoplasm					0																		---	---	---	---
ADNP	23394	broad.mit.edu	37	20	49548722	49548722	+	5'Flank	DEL	A	-	-	rs79919566		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49548722delA	uc002xvt.1	-						ADNP_uc002xvu.1_5'Flank	NM_015339	NP_056154			activity-dependent neuroprotector							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2																		---	---	---	---
DPM1	8813	broad.mit.edu	37	20	49565355	49565355	+	Intron	DEL	A	-	-	rs76899294		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49565355delA	uc002xvw.1	-						DPM1_uc002xvv.1_5'Flank|DPM1_uc002xvx.1_Intron	NM_003859	NP_003850			dolichyl-phosphate mannosyltransferase 1						C-terminal protein lipidation|dolichol metabolic process|dolichol-linked oligosaccharide biosynthetic process|GPI anchor biosynthetic process|protein N-linked glycosylation via asparagine|protein O-linked mannosylation	dolichol-phosphate-mannose synthase complex|endoplasmic reticulum membrane|membrane fraction	dolichyl-phosphate beta-D-mannosyltransferase activity|dolichyl-phosphate-mannose-protein mannosyltransferase activity|protein binding			ovary(1)	1																		---	---	---	---
KCNG1	3755	broad.mit.edu	37	20	49623091	49623091	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49623091delT	uc002xwa.3	-							NM_002237	NP_002228			potassium voltage-gated channel, subfamily G,							voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	50519024	50519024	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50519024delT								SALL4 (99976 upstream) : ZFP64 (181527 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	50690038	50690039	+	IGR	DEL	AA	-	-	rs112663481		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50690038_50690039delAA								SALL4 (270990 upstream) : ZFP64 (10512 downstream)																																			---	---	---	---
TSHZ2	128553	broad.mit.edu	37	20	51642064	51642064	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51642064delG	uc002xwo.2	+							NM_173485	NP_775756			teashirt zinc finger homeobox 2						multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|haematopoietic_and_lymphoid_tissue(1)	6			STAD - Stomach adenocarcinoma(23;0.1)															---	---	---	---
TSHZ2	128553	broad.mit.edu	37	20	51718182	51718182	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51718182delT	uc002xwo.2	+							NM_173485	NP_775756			teashirt zinc finger homeobox 2						multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|haematopoietic_and_lymphoid_tissue(1)	6			STAD - Stomach adenocarcinoma(23;0.1)															---	---	---	---
TSHZ2	128553	broad.mit.edu	37	20	51765863	51765863	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51765863delT	uc002xwo.2	+							NM_173485	NP_775756			teashirt zinc finger homeobox 2						multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|haematopoietic_and_lymphoid_tissue(1)	6			STAD - Stomach adenocarcinoma(23;0.1)															---	---	---	---
TSHZ2	128553	broad.mit.edu	37	20	52057730	52057730	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52057730delT	uc002xwo.2	+						uc002xwp.1_Intron	NM_173485	NP_775756			teashirt zinc finger homeobox 2						multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|haematopoietic_and_lymphoid_tissue(1)	6			STAD - Stomach adenocarcinoma(23;0.1)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	52306050	52306051	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52306050_52306051delTT								ZNF217 (95249 upstream) : SUMO1P1 (184991 downstream)																																			---	---	---	---
SUMO1P1	391257	broad.mit.edu	37	20	52492322	52492322	+	5'Flank	DEL	T	-	-	rs6068700	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52492322delT	uc010gik.2	-							NR_002189				Homo sapiens SUMO1 pseudogene 1, mRNA (cDNA clone IMAGE:6619211).												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	52930590	52930590	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:52930590delA								PFDN4 (94099 upstream) : DOK5 (161667 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	53489178	53489179	+	IGR	INS	-	T	T	rs142243629	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53489178_53489179insT								DOK5 (221469 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	53721226	53721226	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:53721226delA								DOK5 (453517 upstream) : CBLN4 (851271 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	54123936	54123937	+	IGR	INS	-	TG	TG	rs144292581	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54123936_54123937insTG								DOK5 (856227 upstream) : CBLN4 (448560 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	54538603	54538605	+	IGR	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54538603_54538605delTTT								None (None upstream) : CBLN4 (33892 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	54591966	54591966	+	IGR	DEL	T	-	-	rs11477059		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54591966delT								CBLN4 (11954 upstream) : MC3R (231822 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	54645518	54645518	+	IGR	DEL	T	-	-	rs7509319		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54645518delT								CBLN4 (65506 upstream) : MC3R (178270 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	54722027	54722030	+	IGR	DEL	AAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54722027_54722030delAAAA								CBLN4 (142015 upstream) : MC3R (101758 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	54735373	54735374	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54735373_54735374delAA								CBLN4 (155361 upstream) : MC3R (88414 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	54764376	54764379	+	IGR	DEL	AAAA	-	-	rs146477534		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54764376_54764379delAAAA								CBLN4 (184364 upstream) : MC3R (59409 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	54836991	54836991	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54836991delA								MC3R (12120 upstream) : C20orf108 (96992 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	54870245	54870245	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54870245delG								MC3R (45374 upstream) : C20orf108 (63738 downstream)																																			---	---	---	---
AURKA	6790	broad.mit.edu	37	20	54959235	54959235	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:54959235delT	uc002xxd.1	-						AURKA_uc002xxe.1_Intron|AURKA_uc002xxf.1_Intron|AURKA_uc002xxg.1_Intron|AURKA_uc002xxh.1_Intron|AURKA_uc002xxi.1_Intron|AURKA_uc002xxj.1_Intron|AURKA_uc002xxk.1_Intron|AURKA_uc010zzd.1_Intron	NM_198433	NP_940835			serine/threonine protein kinase 6						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitosis|phosphatidylinositol-mediated signaling|regulation of protein stability|spindle organization	cytosol|nucleus|perinuclear region of cytoplasm|spindle microtubule|spindle pole centrosome	ATP binding|protein kinase binding|protein serine/threonine kinase activity			lung(3)|ovary(2)|breast(1)|large_intestine(1)|skin(1)	8			Colorectal(105;0.202)															---	---	---	---
CASS4	57091	broad.mit.edu	37	20	55018124	55018124	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55018124delG	uc002xxp.2	+						CASS4_uc002xxq.3_Intron|CASS4_uc002xxr.2_Intron|CASS4_uc010zze.1_Intron|CASS4_uc010gio.2_Intron	NM_001164116	NP_001157588			HEF-like protein isoform a						cell adhesion	cytoplasm|cytoskeleton|focal adhesion	two-component sensor activity			ovary(2)|skin(1)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	55147896	55147896	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55147896delA								C20orf107 (36322 upstream) : TFAP2C (56462 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	55149400	55149400	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55149400delC								C20orf107 (37826 upstream) : TFAP2C (54958 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	55256428	55256428	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55256428delT								TFAP2C (42092 upstream) : BMP7 (487381 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	55283396	55283396	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55283396delG								TFAP2C (69060 upstream) : BMP7 (460413 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	55717425	55717425	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55717425delG								TFAP2C (503089 upstream) : BMP7 (26384 downstream)																																			---	---	---	---
BMP7	655	broad.mit.edu	37	20	55745772	55745772	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:55745772delT	uc010gip.1	-	7					BMP7_uc010giq.1_3'UTR	NM_001719	NP_001710			bone morphogenetic protein 7 precursor						BMP signaling pathway|cartilage development|cellular response to hypoxia|epithelial to mesenchymal transition|growth|mesonephros development|negative regulation of glomerular mesangial cell proliferation|negative regulation of MAP kinase activity|negative regulation of mitosis|negative regulation of neuron differentiation|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|negative regulation of phosphorylation|negative regulation of striated muscle cell apoptosis|negative regulation of transcription, DNA-dependent|ossification|pathway-restricted SMAD protein phosphorylation|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|protein localization to nucleus|regulation of removal of superoxide radicals|SMAD protein signal transduction|steroid hormone mediated signaling pathway|ureteric bud development	extracellular space	cytokine activity|growth factor activity			skin(1)	1	all_lung(29;0.0133)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;2.49e-13)|Epithelial(14;1.74e-08)|all cancers(14;2.05e-07)															---	---	---	---
CTCFL	140690	broad.mit.edu	37	20	56077408	56077409	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56077408_56077409insT	uc010gix.1	-						CTCFL_uc010giw.1_Intron|CTCFL_uc002xym.2_Intron|CTCFL_uc010giz.1_Intron|CTCFL_uc010giy.1_Intron|CTCFL_uc010gja.1_Intron|CTCFL_uc010gjb.1_Intron|CTCFL_uc010gjc.1_Intron|CTCFL_uc010gjd.1_Intron|CTCFL_uc010gje.2_Intron|CTCFL_uc010gjf.2_Intron|CTCFL_uc010gjg.2_Intron|CTCFL_uc010giu.2_Intron|CTCFL_uc010giv.2_Intron	NM_080618	NP_542185			CCCTC-binding factor-like protein						cell cycle|DNA methylation involved in gamete generation|histone methylation|positive regulation of transcription, DNA-dependent|regulation of gene expression by genetic imprinting|regulation of histone H3-K4 methylation|transcription, DNA-dependent	cytoplasm|nucleus	histone binding|sequence-specific DNA binding|transcription regulatory region DNA binding|zinc ion binding			ovary(2)|large_intestine(1)|skin(1)	4	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)															---	---	---	---
PCK1	5105	broad.mit.edu	37	20	56137683	56137683	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56137683delA	uc002xyn.3	+						PCK1_uc010zzm.1_Intron	NM_002591	NP_002582			cytosolic phosphoenolpyruvate carboxykinase 1						gluconeogenesis|glucose homeostasis|glycerol biosynthetic process from pyruvate|response to insulin stimulus	cytosol|nucleus	carboxylic acid binding|GTP binding|magnesium ion binding|manganese ion binding|phosphoenolpyruvate carboxykinase (GTP) activity			skin(1)	1	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)															---	---	---	---
ZBP1	81030	broad.mit.edu	37	20	56183183	56183184	+	Intron	INS	-	T	T	rs143371271		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56183183_56183184insT	uc002xyo.2	-						ZBP1_uc010gjm.2_Intron|ZBP1_uc002xyp.2_Intron	NM_030776	NP_110403			Z-DNA binding protein 1 isoform a							cytoplasm|nucleus	double-stranded RNA adenosine deaminase activity|left-handed Z-DNA binding|RNA binding			ovary(2)	2	Lung NSC(12;0.000545)|all_lung(29;0.00195)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;7.87e-13)|Epithelial(14;3.26e-09)|all cancers(14;3.62e-08)															---	---	---	---
PMEPA1	56937	broad.mit.edu	37	20	56288102	56288103	+	5'Flank	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56288102_56288103delAA	uc002xys.2	-						PMEPA1_uc002xyr.2_5'Flank|PMEPA1_uc002xyt.2_5'Flank	NM_199169	NP_954638			transmembrane prostate androgen-induced protein						androgen receptor signaling pathway	integral to membrane|plasma membrane	WW domain binding			pancreas(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	20	56329969	56329969	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56329969delT								PMEPA1 (43428 upstream) : C20orf85 (396014 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	56418926	56418926	+	IGR	DEL	G	-	-	rs67890274		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56418926delG								PMEPA1 (132385 upstream) : C20orf85 (307057 downstream)																																			---	---	---	---
PPP4R1L	55370	broad.mit.edu	37	20	56833771	56833771	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56833771delA	uc002xyy.1	-						PPP4R1L_uc010gjn.1_Intron					SubName: Full=cDNA FLJ50842, moderately similar to Serine/threonine-protein phosphatase 4regulatory subunit 1;												0																		---	---	---	---
PPP4R1L	55370	broad.mit.edu	37	20	56869410	56869410	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56869410delT	uc002xyy.1	-						PPP4R1L_uc010gjn.1_Intron					SubName: Full=cDNA FLJ50842, moderately similar to Serine/threonine-protein phosphatase 4regulatory subunit 1;												0																		---	---	---	---
VAPB	9217	broad.mit.edu	37	20	57014202	57014202	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57014202delA	uc002xza.2	+						VAPB_uc002xzb.2_Intron|VAPB_uc010zzo.1_Intron|VAPB_uc002xzc.2_Intron	NM_004738	NP_004729			VAMP-associated protein B/C						cell death|endoplasmic reticulum unfolded protein response|positive regulation of viral genome replication|sphingolipid metabolic process|virus-host interaction	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane	beta-tubulin binding|enzyme binding|protein heterodimerization activity|protein homodimerization activity|structural molecule activity			kidney(1)	1	Lung NSC(12;0.000615)|all_lung(29;0.00186)		BRCA - Breast invasive adenocarcinoma(13;6.2e-12)|Epithelial(14;3.7e-08)|all cancers(14;3.88e-07)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	57117043	57117043	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57117043delA	uc002xzg.1	+											Homo sapiens cDNA FLJ30075 fis, clone BGGI11000285.																														---	---	---	---
GNAS	2778	broad.mit.edu	37	20	57446669	57446669	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57446669delA	uc002xzw.2	+						GNAS_uc002xzt.2_Intron|GNAS_uc002xzu.3_Intron|GNAS_uc010gjq.2_Intron|GNAS_uc002xzv.2_Intron	NM_080425	NP_536350			GNAS complex locus XLas						activation of adenylate cyclase activity|cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|intracellular transport|platelet activation|regulation of insulin secretion|sensory perception of smell|transmembrane transport|water transport	heterotrimeric G-protein complex|intrinsic to membrane|trans-Golgi network membrane	adenylate cyclase activity|GTP binding|GTPase activity|guanyl-nucleotide exchange factor activity|identical protein binding|signal transducer activity			pituitary(201)|thyroid(35)|ovary(15)|adrenal_gland(9)|liver(7)|large_intestine(5)|parathyroid(5)|kidney(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|testis(1)|stomach(1)|small_intestine(1)|autonomic_ganglia(1)|pancreas(1)	292	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)					Mis		pituitary adenoma		McCune-Albright syndrome; pseudohypoparathyroidism|type IA		3-Methylglutaconic_Aciduria_and_Myelodysplasia|McCune-Albright_syndrome|Mazabraud_syndrome	TSP Lung(22;0.16)			---	---	---	---
GNAS	2778	broad.mit.edu	37	20	57473310	57473310	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57473310delT	uc002xzw.2	+						GNAS_uc002xzt.2_Intron|GNAS_uc002xzu.3_Intron|GNAS_uc010gjq.2_Intron|GNAS_uc002xzv.2_Intron|GNAS_uc002xzx.2_Intron|GNAS_uc010gjr.2_Intron|GNAS_uc002xzy.2_Intron|GNAS_uc002yaa.2_Intron|GNAS_uc010zzt.1_Intron|GNAS_uc002yab.2_Intron|GNAS_uc002yad.2_5'UTR	NM_080425	NP_536350			GNAS complex locus XLas						activation of adenylate cyclase activity|cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|intracellular transport|platelet activation|regulation of insulin secretion|sensory perception of smell|transmembrane transport|water transport	heterotrimeric G-protein complex|intrinsic to membrane|trans-Golgi network membrane	adenylate cyclase activity|GTP binding|GTPase activity|guanyl-nucleotide exchange factor activity|identical protein binding|signal transducer activity			pituitary(201)|thyroid(35)|ovary(15)|adrenal_gland(9)|liver(7)|large_intestine(5)|parathyroid(5)|kidney(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|testis(1)|stomach(1)|small_intestine(1)|autonomic_ganglia(1)|pancreas(1)	292	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)					Mis		pituitary adenoma		McCune-Albright syndrome; pseudohypoparathyroidism|type IA		3-Methylglutaconic_Aciduria_and_Myelodysplasia|McCune-Albright_syndrome|Mazabraud_syndrome	TSP Lung(22;0.16)			---	---	---	---
CDH26	60437	broad.mit.edu	37	20	58578026	58578026	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58578026delA	uc002ybe.2	+						CDH26_uc002ybf.1_Intron|CDH26_uc010zzy.1_Intron|CDH26_uc002ybg.2_Intron|CDH26_uc002ybh.2_Intron|CDH26_uc002ybi.2_Intron	NM_177980	NP_817089			cadherin-like 26 isoform a						homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|central_nervous_system(1)	4	all_lung(29;0.00963)		BRCA - Breast invasive adenocarcinoma(7;5.58e-09)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	58661144	58661145	+	5'Flank	INS	-	A	A	rs140706847	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58661144_58661145insA	uc002ybk.1	+											full-length cDNA clone CS0DJ007YF24 of T cells (Jurkat cell line) Cot 10-normalized of Homo sapiens (human).																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	58744888	58744888	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58744888delG	uc002ybl.2	+						uc010gjw.1_Intron					Homo sapiens cDNA FLJ35486 fis, clone SMINT2008491.																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	59131696	59131696	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59131696delA	uc010gjw.1	+											Homo sapiens cDNA FLJ35486 fis, clone SMINT2008491.																														---	---	---	---
Unknown	0	broad.mit.edu	37	20	59232560	59232560	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59232560delA								MIR646 (348935 upstream) : CDH4 (594999 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	59268077	59268077	+	IGR	DEL	A	-	-	rs111244940		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59268077delA								MIR646 (384452 upstream) : CDH4 (559482 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	59339199	59339200	+	IGR	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59339199_59339200delAC								MIR646 (455574 upstream) : CDH4 (488359 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	59360836	59360836	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59360836delA								MIR646 (477211 upstream) : CDH4 (466723 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	59389913	59389913	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59389913delT								MIR646 (506288 upstream) : CDH4 (437646 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	59529289	59529291	+	IGR	DEL	CTC	-	-	rs73628173		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59529289_59529291delCTC								MIR646 (645664 upstream) : CDH4 (298268 downstream)																																			---	---	---	---
CDH4	1002	broad.mit.edu	37	20	59858001	59858001	+	Intron	DEL	G	-	-	rs67326049		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59858001delG	uc002ybn.1	+							NM_001794	NP_001785			cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)															---	---	---	---
CDH4	1002	broad.mit.edu	37	20	60315653	60315653	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60315653delC	uc002ybn.1	+						CDH4_uc002ybo.1_Intron|CDH4_uc002ybp.1_Intron	NM_001794	NP_001785			cadherin 4, type 1 preproprotein						adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)															---	---	---	---
Unknown	0	broad.mit.edu	37	20	60534080	60534080	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60534080delG								MIR1257 (5362 upstream) : TAF4 (15775 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	60536883	60536883	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60536883delT								MIR1257 (8165 upstream) : TAF4 (12972 downstream)																																			---	---	---	---
LSM14B	149986	broad.mit.edu	37	20	60695151	60695151	+	5'Flank	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60695151delG	uc010gjy.1	+						LSM14B_uc002ybt.2_5'Flank|LSM14B_uc010gjx.1_5'Flank|LSM14B_uc002ybv.2_5'Flank	NM_144703	NP_653304			LSM14 homolog B						multicellular organismal development|regulation of translation	ribonucleoprotein complex					0	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.28e-07)															---	---	---	---
SS18L1	26039	broad.mit.edu	37	20	60740566	60740566	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60740566delG	uc002ycb.2	+	8	967	c.912delG	c.(910-912)GAGfs	p.E304fs	SS18L1_uc011aaa.1_Frame_Shift_Del_p.E304fs|SS18L1_uc002ybz.1_RNA|SS18L1_uc002yca.1_RNA|SS18L1_uc002ycc.1_RNA	NM_198935	NP_945173	O75177	CREST_HUMAN	SS18-like protein 1	304	Gln-rich.|MFD domain (By similarity).				chromatin modification|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	condensed chromosome kinetochore				ovary(2)	2	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.92e-08)					T	SSX1	synovial sarcoma								---	---	---	---
SS18L1	26039	broad.mit.edu	37	20	60749514	60749514	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60749514delA	uc002ycb.2	+						SS18L1_uc011aaa.1_Intron|SS18L1_uc002ybz.1_Intron|SS18L1_uc002yca.1_Intron|SS18L1_uc002ycc.1_Intron	NM_198935	NP_945173			SS18-like protein 1						chromatin modification|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	condensed chromosome kinetochore				ovary(2)	2	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.92e-08)					T	SSX1	synovial sarcoma								---	---	---	---
GATA5	140628	broad.mit.edu	37	20	61041057	61041057	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61041057delC	uc002ycx.1	-							NM_080473	NP_536721			GATA binding protein 5						blood coagulation|intestinal epithelial cell differentiation|positive regulation of transcription from RNA polymerase II promoter	nucleoplasm	sequence-specific DNA binding|transcription regulatory region DNA binding|zinc ion binding				0	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;3.08e-06)															---	---	---	---
CHRNA4	1137	broad.mit.edu	37	20	61987950	61987951	+	Intron	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61987950_61987951insG	uc002yes.2	-						CHRNA4_uc002yet.1_Intron|CHRNA4_uc011aaw.1_Intron|CHRNA4_uc010gke.1_Intron|CHRNA4_uc002yev.1_Intron|CHRNA4_uc010gkf.1_Intron	NM_000744	NP_000735			cholinergic receptor, nicotinic, alpha 4 subunit						B cell activation|behavioral response to nicotine|calcium ion transport|cognition|DNA repair|membrane depolarization|regulation of action potential|regulation of dopamine secretion|regulation of inhibitory postsynaptic membrane potential|response to hypoxia|response to oxidative stress|sensory perception of pain|synaptic transmission, cholinergic	cell junction|dendrite|external side of plasma membrane|membrane fraction|neuronal cell body|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity			central_nervous_system(1)|skin(1)	2	all_cancers(38;1.71e-10)				Nicotine(DB00184)|Varenicline(DB01273)													---	---	---	---
PRIC285	85441	broad.mit.edu	37	20	62193251	62193251	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62193251delG	uc002yfm.2	-	12	7508	c.6616delC	c.(6616-6618)CGTfs	p.R2206fs	PRIC285_uc002yfl.1_Frame_Shift_Del_p.R1637fs	NM_001037335	NP_001032412	Q9BYK8	PR285_HUMAN	PPAR-alpha interacting complex protein 285	2206					cellular lipid metabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	ATP binding|DNA binding|helicase activity|ribonuclease activity|RNA binding|transcription coactivator activity|zinc ion binding			central_nervous_system(2)	2	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;1.27e-08)|all cancers(9;7.32e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)															---	---	---	---
ZBTB46	140685	broad.mit.edu	37	20	62420481	62420481	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62420481delA	uc002ygv.1	-						ZBTB46_uc002ygu.2_Intron	NM_025224	NP_079500			zinc finger and BTB domain containing 46						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			large_intestine(1)|ovary(1)	2	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)																	---	---	---	---
Unknown	0	broad.mit.edu	37	20	62752952	62752952	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62752952delT								NPBWR2 (14768 upstream) : MYT1 (30192 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	20	62959951	62959951	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62959951delG								PCMTD2 (52373 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	9418367	9418367	+	IGR	DEL	A	-	-	rs80128862		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9418367delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	9659217	9659217	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9659217delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	9668163	9668163	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9668163delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	9730386	9730386	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9730386delT	uc011abu.1	+											Homo sapiens, clone IMAGE:4720764, mRNA.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	10408482	10408482	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10408482delG								None (None upstream) : TPTE (498261 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10498470	10498470	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10498470delA	uc011abv.1	-											Homo sapiens cDNA, FLJ18615.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	10530817	10530817	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10530817delA	uc011abv.1	-											Homo sapiens cDNA, FLJ18615.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	10589178	10589179	+	Intron	DEL	AA	-	-	rs78105979		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10589178_10589179delAA	uc011abv.1	-											Homo sapiens cDNA, FLJ18615.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	10599058	10599058	+	5'Flank	DEL	A	-	-	rs71270017		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10599058delA	uc011abv.1	-											Homo sapiens cDNA, FLJ18615.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	10610945	10610946	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10610945_10610946insA								None (None upstream) : TPTE (295797 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10727383	10727384	+	IGR	INS	-	T	T	rs149998033		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10727383_10727384insT								None (None upstream) : TPTE (179359 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10795987	10795991	+	IGR	DEL	GTGAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10795987_10795991delGTGAA								None (None upstream) : TPTE (110752 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	10857683	10857687	+	IGR	DEL	GAATA	-	-	rs113195832		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:10857683_10857687delGAATA								None (None upstream) : TPTE (49056 downstream)																																			---	---	---	---
BAGE2	85319	broad.mit.edu	37	21	11100729	11100729	+	5'Flank	DEL	T	-	-	rs150061043		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11100729delT	uc002yit.1	-						BAGE_uc002yix.2_5'Flank	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	11134502	11134502	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11134502delA								BAGE (35565 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	14360492	14360493	+	IGR	INS	-	AT	AT			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14360492_14360493insAT								None (None upstream) : C21orf99 (49994 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	14392473	14392473	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14392473delA								None (None upstream) : C21orf99 (18014 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	14627286	14627286	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:14627286delT								C21orf99 (136717 upstream) : POTED (355212 downstream)																																			---	---	---	---
RBM11	54033	broad.mit.edu	37	21	15591835	15591836	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15591835_15591836delAA	uc002yjo.3	+						RBM11_uc002yjn.3_Intron|RBM11_uc002yjp.3_Intron	NM_144770	NP_658983			RNA binding motif protein 11								nucleotide binding|RNA binding				0				Epithelial(23;0.000314)|COAD - Colon adenocarcinoma(22;0.00242)|Colorectal(24;0.0129)|Lung(58;0.141)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	15642030	15642031	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15642030_15642031insT								RBM11 (41339 upstream) : ABCC13 (4089 downstream)																																			---	---	---	---
SAMSN1	64092	broad.mit.edu	37	21	15914309	15914311	+	Intron	DEL	AAA	-	-	rs67987845		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15914309_15914311delAAA	uc002yju.1	-						SAMSN1_uc010gky.1_Intron|SAMSN1_uc002yjv.1_Intron	NM_022136	NP_071419			SAM domain, SH3 domain and nuclear localization						negative regulation of adaptive immune response|negative regulation of B cell activation|negative regulation of peptidyl-tyrosine phosphorylation	cytoplasm|nucleus|ruffle	phosphotyrosine binding			ovary(3)|pancreas(1)	4				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.00118)|Colorectal(24;0.00961)|Lung(58;0.164)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	16192972	16192972	+	IGR	DEL	C	-	-	rs71916718		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16192972delC								SAMSN1 (237249 upstream) : NRIP1 (140584 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	16241835	16241835	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16241835delA								SAMSN1 (286112 upstream) : NRIP1 (91721 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	16672170	16672171	+	IGR	DEL	GC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16672170_16672171delGC								NRIP1 (235044 upstream) : USP25 (430325 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	16853596	16853596	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:16853596delA								NRIP1 (416470 upstream) : USP25 (248900 downstream)																																			---	---	---	---
USP25	29761	broad.mit.edu	37	21	17181079	17181079	+	Intron	DEL	T	-	-	rs141423317	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:17181079delT	uc002yjy.1	+						USP25_uc011aby.1_Intron|USP25_uc002yjz.1_Intron|USP25_uc010gla.1_Intron	NM_013396	NP_037528			ubiquitin specific peptidase 25						protein modification process|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)|liver(2)	5				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)														---	---	---	---
USP25	29761	broad.mit.edu	37	21	17203605	17203605	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:17203605delA	uc002yjy.1	+						USP25_uc011aby.1_Intron|USP25_uc002yjz.1_Intron|USP25_uc010gla.1_Intron	NM_013396	NP_037528			ubiquitin specific peptidase 25						protein modification process|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)|liver(2)	5				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)														---	---	---	---
USP25	29761	broad.mit.edu	37	21	17203704	17203704	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:17203704delT	uc002yjy.1	+						USP25_uc011aby.1_Intron|USP25_uc002yjz.1_Intron|USP25_uc010gla.1_Intron	NM_013396	NP_037528			ubiquitin specific peptidase 25						protein modification process|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)|liver(2)	5				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)														---	---	---	---
C21orf34	388815	broad.mit.edu	37	21	17480883	17480883	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:17480883delA	uc002ykb.2	+						C21orf34_uc010glc.2_Intron	NR_027790				Homo sapiens C21ORF34 (C21orf34) mRNA, partial cds, alternatively spliced.												0		Breast(209;0.152)		Epithelial(23;8.3e-05)|all cancers(11;0.000383)|Colorectal(24;0.00387)|COAD - Colon adenocarcinoma(22;0.0113)|OV - Ovarian serous cystadenocarcinoma(11;0.0127)|LUSC - Lung squamous cell carcinoma(23;0.153)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	18688317	18688317	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:18688317delC								C21orf34 (706223 upstream) : CXADR (197013 downstream)																																			---	---	---	---
CXADR	1525	broad.mit.edu	37	21	18924014	18924014	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:18924014delT	uc002yki.2	+						CXADR_uc002ykh.1_Intron|CXADR_uc010gld.1_Intron|CXADR_uc010gle.1_Intron|CXADR_uc002ykj.1_Intron	NM_001338	NP_001329			coxsackie virus and adenovirus receptor						blood coagulation|cell adhesion|interspecies interaction between organisms|leukocyte migration|regulation of immune response	adherens junction|basolateral plasma membrane|extracellular region|integral to plasma membrane|nucleus|tight junction	receptor activity			ovary(1)	1				Epithelial(23;0.000206)|all cancers(11;0.000302)|OV - Ovarian serous cystadenocarcinoma(11;0.0194)|Lung(58;0.0233)|COAD - Colon adenocarcinoma(22;0.0389)|Colorectal(24;0.0483)|LUSC - Lung squamous cell carcinoma(23;0.0782)														---	---	---	---
C21orf91	54149	broad.mit.edu	37	21	19152086	19152086	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19152086delC	uc002ykm.2	-						C21orf91_uc002ykn.2_Intron					Homo sapiens partial mRNA; ID YG81-6.											ovary(1)	1				Epithelial(23;8.76e-05)|all cancers(11;0.000422)|OV - Ovarian serous cystadenocarcinoma(11;0.0107)|Lung(58;0.0129)|COAD - Colon adenocarcinoma(22;0.0303)|LUSC - Lung squamous cell carcinoma(23;0.0381)|Colorectal(24;0.0929)														---	---	---	---
CHODL	140578	broad.mit.edu	37	21	19628340	19628340	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19628340delA	uc002ykv.2	+						CHODL_uc002ykr.2_Intron|CHODL_uc002yks.2_Intron|CHODL_uc002ykt.2_Intron|CHODL_uc002yku.2_Intron	NM_024944	NP_079220			chondrolectin precursor						muscle organ development	integral to membrane|perinuclear region of cytoplasm	sugar binding			upper_aerodigestive_tract(1)	1		all_epithelial(11;0.21)		Epithelial(23;0.000191)|all cancers(11;0.000827)|LUSC - Lung squamous cell carcinoma(23;0.00646)|Lung(58;0.0129)|OV - Ovarian serous cystadenocarcinoma(11;0.017)|COAD - Colon adenocarcinoma(22;0.03)|Colorectal(24;0.0917)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	20230803	20230803	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:20230803delA								TMPRSS15 (454833 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	20708303	20708303	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:20708303delA								TMPRSS15 (932333 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	21885524	21885524	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:21885524delT								None (None upstream) : C21orf131 (229390 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	21967630	21967630	+	IGR	DEL	T	-	-	rs112642004		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:21967630delT								None (None upstream) : C21orf131 (147284 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	21991980	21991980	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:21991980delA								None (None upstream) : C21orf131 (122934 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	23092562	23092563	+	IGR	INS	-	TTCC	TTCC	rs62214663		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:23092562_23092563insTTCC								NCAM2 (181348 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	24147448	24147448	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:24147448delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	24384294	24384295	+	IGR	INS	-	GAGA	GAGA	rs139889205	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:24384294_24384295insGAGA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	24463466	24463466	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:24463466delT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	25369890	25369892	+	IGR	DEL	TTG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:25369890_25369892delTTG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	25560932	25560932	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:25560932delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	26593785	26593785	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26593785delT								None (None upstream) : NCRNA00158 (164349 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	26705324	26705324	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26705324delA								None (None upstream) : NCRNA00158 (52810 downstream)																																			---	---	---	---
MRPL39	54148	broad.mit.edu	37	21	26976400	26976400	+	Intron	DEL	A	-	-	rs11303574		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:26976400delA	uc002ylo.2	-						MRPL39_uc002yln.2_Intron	NM_017446	NP_059142			mitochondrial ribosomal protein L39 isoform a							mitochondrial ribosome	nucleotide binding				0																		---	---	---	---
GABPA	2551	broad.mit.edu	37	21	27114009	27114009	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27114009delT	uc002ylx.3	+						GABPA_uc002yly.3_Intron	NM_002040	NP_002031			GA binding protein transcription factor, alpha						positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	protein heterodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription regulatory region DNA binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
GABPA	2551	broad.mit.edu	37	21	27124278	27124278	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27124278delT	uc002ylx.3	+						GABPA_uc002yly.3_Intron	NM_002040	NP_002031			GA binding protein transcription factor, alpha						positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	protein heterodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription regulatory region DNA binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
APP	351	broad.mit.edu	37	21	27487012	27487012	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27487012delT	uc002ylz.2	-						APP_uc010glk.2_Intron|APP_uc002yma.2_Intron|APP_uc011ach.1_Intron|APP_uc002ymb.2_Intron|APP_uc010glj.2_Intron|APP_uc011aci.1_Intron|APP_uc011acj.1_Intron	NM_000484	NP_000475			amyloid beta A4 protein isoform a precursor						adult locomotory behavior|axon cargo transport|axon midline choice point recognition|cell adhesion|cellular copper ion homeostasis|collateral sprouting in absence of injury|dendrite development|endocytosis|extracellular matrix organization|G2 phase of mitotic cell cycle|innate immune response|ionotropic glutamate receptor signaling pathway|mating behavior|mRNA polyadenylation|neuron apoptosis|neuron remodeling|Notch signaling pathway|platelet activation|platelet degranulation|positive regulation of mitotic cell cycle|protein phosphorylation|regulation of epidermal growth factor receptor activity|regulation of multicellular organism growth|regulation of synapse structure and activity|regulation of translation|visual learning	axon|cell surface|coated pit|dendritic shaft|dendritic spine|extracellular region|Golgi apparatus|integral to plasma membrane|platelet alpha granule lumen	acetylcholine receptor binding|DNA binding|heparin binding|identical protein binding|metal ion binding|protein binding|protein binding|PTB domain binding|serine-type endopeptidase inhibitor activity			ovary(1)	1		Breast(209;0.00295)																---	---	---	---
Unknown	0	broad.mit.edu	37	21	27748628	27748628	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27748628delT								APP (205182 upstream) : CYYR1 (89901 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	27752650	27752651	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27752650_27752651insT								APP (209204 upstream) : CYYR1 (85878 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	28056321	28056321	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28056321delT								CYYR1 (110740 upstream) : ADAMTS1 (152287 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	28531560	28531561	+	IGR	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28531560_28531561insG								ADAMTS5 (192121 upstream) : NCRNA00113 (563137 downstream)																																			---	---	---	---
C21orf94	246705	broad.mit.edu	37	21	29392969	29392970	+	Intron	DEL	CA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:29392969_29392970delCA	uc002ymj.3	+							NR_027246				Homo sapiens C21orf94 protein (C21orf94) mRNA, complete cds.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	29504318	29504319	+	Intron	INS	-	AA	AA	rs144567549	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:29504318_29504319insAA	uc002ymk.1	+						uc002yml.2_Intron					Homo sapiens cDNA FLJ35800 fis, clone TESTI2005933.																														---	---	---	---
Unknown	0	broad.mit.edu	37	21	29914830	29914830	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:29914830delT								NCRNA00161 (2154 upstream) : N6AMT1 (329683 downstream)																																			---	---	---	---
RNF160	26046	broad.mit.edu	37	21	30343173	30343173	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30343173delA	uc002ymr.2	-						RNF160_uc010gll.1_Intron	NM_015565	NP_056380			zinc finger protein 294								ligase activity|zinc ion binding				0																		---	---	---	---
RNF160	26046	broad.mit.edu	37	21	30354539	30354539	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30354539delA	uc002ymr.2	-						RNF160_uc010gll.1_Intron	NM_015565	NP_056380			zinc finger protein 294								ligase activity|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	30369867	30369867	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30369867delG								RNF160 (4590 upstream) : RWDD2B (8215 downstream)																																			---	---	---	---
USP16	10600	broad.mit.edu	37	21	30416255	30416255	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30416255delT	uc002ymy.2	+						USP16_uc002ymx.2_Intron|USP16_uc002ymw.2_Intron|USP16_uc011acm.1_Intron|USP16_uc011acn.1_Intron|USP16_uc011aco.1_Intron	NM_006447	NP_006438			ubiquitin specific protease 16 isoform a						cell division|histone deubiquitination|mitosis|positive regulation of transcription, DNA-dependent|protein homotetramerization|transcription, DNA-dependent|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	cysteine-type endopeptidase activity|histone binding|transcription coactivator activity|ubiquitin binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			ovary(2)|breast(1)|pancreas(1)	4																		---	---	---	---
GRIK1	2897	broad.mit.edu	37	21	31169452	31169452	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31169452delA	uc002yno.1	-						GRIK1_uc002ynn.2_Intron|GRIK1_uc011acs.1_Intron|GRIK1_uc011act.1_Intron|GRIK1_uc010glq.1_Intron|GRIK1_uc002ynr.2_Intron	NM_000830	NP_000821			glutamate receptor, ionotropic, kainate 1						central nervous system development|synaptic transmission	cell junction|postsynaptic membrane	kainate selective glutamate receptor activity			large_intestine(1)|ovary(1)|skin(1)	3					L-Glutamic Acid(DB00142)|Topiramate(DB00273)													---	---	---	---
GRIK1	2897	broad.mit.edu	37	21	31287138	31287138	+	Intron	DEL	A	-	-	rs72334363		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31287138delA	uc002yno.1	-						GRIK1_uc002ynn.2_Intron|GRIK1_uc011acs.1_Intron|GRIK1_uc011act.1_Intron|GRIK1_uc010glq.1_Intron|GRIK1_uc002ynr.2_Intron	NM_000830	NP_000821			glutamate receptor, ionotropic, kainate 1						central nervous system development|synaptic transmission	cell junction|postsynaptic membrane	kainate selective glutamate receptor activity			large_intestine(1)|ovary(1)|skin(1)	3					L-Glutamic Acid(DB00142)|Topiramate(DB00273)													---	---	---	---
Unknown	0	broad.mit.edu	37	21	31407667	31407667	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31407667delA								GRIK1 (95385 upstream) : CLDN17 (130596 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	31411874	31411874	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31411874delT								GRIK1 (99592 upstream) : CLDN17 (126389 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	31815295	31815295	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31815295delT								KRTAP15-1 (2198 upstream) : KRTAP19-1 (37071 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	32052643	32052643	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32052643delA								KRTAP20-3 (37188 upstream) : KRTAP21-2 (66628 downstream)																																			---	---	---	---
TIAM1	7074	broad.mit.edu	37	21	32845409	32845409	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32845409delT	uc002yow.1	-						TIAM1_uc002yox.1_Intron	NM_003253	NP_003244			T-cell lymphoma invasion and metastasis 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cell-cell junction|cytosol	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|breast(3)|ovary(2)|large_intestine(2)	10																		---	---	---	---
TIAM1	7074	broad.mit.edu	37	21	32928733	32928734	+	Intron	INS	-	TGTT	TGTT	rs141560656	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32928733_32928734insTGTT	uc002yow.1	-						TIAM1_uc002yox.1_Intron|uc002yoy.2_5'Flank	NM_003253	NP_003244			T-cell lymphoma invasion and metastasis 1						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cell-cell junction|cytosol	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|breast(3)|ovary(2)|large_intestine(2)	10																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	33017919	33017919	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33017919delT								TIAM1 (85629 upstream) : SOD1 (14016 downstream)																																			---	---	---	---
SFRS15	57466	broad.mit.edu	37	21	33068866	33068867	+	Intron	DEL	AA	-	-	rs33982658		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33068866_33068867delAA	uc002ypd.2	-						SFRS15_uc002ype.2_Intron|SFRS15_uc010glu.2_Intron|SFRS15_uc002ypf.1_Intron	NM_020706	NP_065757			splicing factor, arginine/serine-rich 15 isoform							nucleus	nucleotide binding|RNA binding				0																		---	---	---	---
SFRS15	57466	broad.mit.edu	37	21	33074822	33074823	+	Intron	DEL	AA	-	-	rs72441176		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33074822_33074823delAA	uc002ypd.2	-						SFRS15_uc002ype.2_Intron|SFRS15_uc010glu.2_Intron|SFRS15_uc002ypf.1_5'Flank|SFRS15_uc002ypg.2_Intron	NM_020706	NP_065757			splicing factor, arginine/serine-rich 15 isoform							nucleus	nucleotide binding|RNA binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	33568332	33568333	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33568332_33568333delAA								NCRNA00159 (39516 upstream) : C21orf45 (72199 downstream)																																			---	---	---	---
URB1	9875	broad.mit.edu	37	21	33735979	33735979	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33735979delT	uc002ypn.2	-							NM_014825	NP_055640			URB1 ribosome biogenesis 1 homolog							nucleolus	protein binding				0																		---	---	---	---
URB1	9875	broad.mit.edu	37	21	33749473	33749473	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:33749473delT	uc002ypn.2	-							NM_014825	NP_055640			URB1 ribosome biogenesis 1 homolog							nucleolus	protein binding				0																		---	---	---	---
SYNJ1	8867	broad.mit.edu	37	21	34082839	34082840	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34082839_34082840delTT	uc002yqh.2	-						SYNJ1_uc011ads.1_Intron|SYNJ1_uc002yqf.2_Intron|SYNJ1_uc002yqg.2_Intron|SYNJ1_uc002yqi.2_Intron	NM_003895	NP_003886			synaptojanin 1 isoform a								inositol-polyphosphate 5-phosphatase activity|nucleotide binding|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|RNA binding			ovary(4)|skin(1)	5																		---	---	---	---
C21orf62	56245	broad.mit.edu	37	21	34187574	34187574	+	5'Flank	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34187574delT	uc010glz.2	-						C21orf62_uc011adt.1_5'Flank|C21orf62_uc011adu.1_5'Flank	NM_001162495	NP_001155967			hypothetical protein LOC56245											ovary(1)	1		Myeloproliferative disorder(46;0.0255)																---	---	---	---
C21orf54	728409	broad.mit.edu	37	21	34541429	34541430	+	Intron	INS	-	TTG	TTG	rs146898284	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34541429_34541430insTTG	uc002yra.2	-							NR_024102				Homo sapiens cDNA clone IMAGE:8144118.												0																		---	---	---	---
ITSN1	6453	broad.mit.edu	37	21	35048343	35048343	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35048343delT	uc002yta.1	+						DONSON_uc002ysn.1_Intron|ITSN1_uc002yth.3_Intron|ITSN1_uc002ysz.2_Intron|ITSN1_uc010gmg.2_Intron|ITSN1_uc010gmh.2_Intron|ITSN1_uc002ysw.2_Intron|ITSN1_uc010gmi.2_Intron|ITSN1_uc010gmj.2_Intron|ITSN1_uc002ysy.2_Intron|ITSN1_uc002ysx.2_Intron|ITSN1_uc002ytb.1_Intron	NM_003024	NP_003015			intersectin 1 isoform ITSN-l						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic vesicle endocytosis	cell junction|coated pit|cytosol|lamellipodium|synapse|synaptosome	calcium ion binding|proline-rich region binding|protein complex scaffold|Rho guanyl-nucleotide exchange factor activity			ovary(3)|skin(1)	4																		---	---	---	---
ITSN1	6453	broad.mit.edu	37	21	35183100	35183101	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35183100_35183101delTT	uc002yta.1	+						DONSON_uc002ysn.1_Intron|ITSN1_uc002yth.3_Intron|ITSN1_uc002ysz.2_Intron|ITSN1_uc010gmg.2_Intron|ITSN1_uc010gmh.2_Intron|ITSN1_uc002ysw.2_Intron|ITSN1_uc010gmi.2_Intron|ITSN1_uc010gmj.2_Intron|ITSN1_uc002ysy.2_Intron|ITSN1_uc002ysx.2_Intron|ITSN1_uc002ytb.1_Intron|ITSN1_uc002ytc.1_Intron|ITSN1_uc002ytd.2_Intron|ITSN1_uc010gmk.2_Intron|ITSN1_uc010gml.2_Intron|ITSN1_uc002ytj.2_Intron|ITSN1_uc010gmm.1_Intron|ITSN1_uc002yte.2_Intron|ITSN1_uc002ytf.1_Intron	NM_003024	NP_003015			intersectin 1 isoform ITSN-l						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic vesicle endocytosis	cell junction|coated pit|cytosol|lamellipodium|synapse|synaptosome	calcium ion binding|proline-rich region binding|protein complex scaffold|Rho guanyl-nucleotide exchange factor activity			ovary(3)|skin(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	35352235	35352235	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35352235delT								ATP5O (64077 upstream) : MRPS6 (93588 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	35383554	35383555	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35383554_35383555delTT								ATP5O (95396 upstream) : MRPS6 (62268 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	35710594	35710594	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35710594delA								C21orf82 (148374 upstream) : KCNE2 (25729 downstream)																																			---	---	---	---
RUNX1	861	broad.mit.edu	37	21	36248865	36248865	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:36248865delT	uc002yuh.2	-						RUNX1_uc002yui.2_Intron|RUNX1_uc010gmu.2_Intron|RUNX1_uc010gmv.2_Intron|RUNX1_uc002yuj.3_Intron|RUNX1_uc002yuk.3_Intron|RUNX1_uc002yum.1_Intron|RUNX1_uc010gmw.1_Intron|RUNX1_uc002yuo.1_Intron|RUNX1_uc002yur.1_Intron	NM_001001890	NP_001001890			runt-related transcription factor 1 isoform						myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387								T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				---	---	---	---
RUNX1	861	broad.mit.edu	37	21	36264005	36264005	+	Intron	DEL	A	-	-	rs2298322	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:36264005delA	uc010gmu.2	-						RUNX1_uc002yut.1_Intron|RUNX1_uc010gmv.2_Intron|RUNX1_uc002yuj.3_Intron|RUNX1_uc002yuk.3_Intron|RUNX1_uc002yum.1_Intron|RUNX1_uc010gmw.1_Intron	NM_001754	NP_001745			runt-related transcription factor 1 isoform						myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387								T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				---	---	---	---
RUNX1	861	broad.mit.edu	37	21	36341697	36341697	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:36341697delA	uc010gmu.2	-						RUNX1_uc002yut.1_Intron|RUNX1_uc010gmv.2_Intron|RUNX1_uc002yuj.3_Intron|RUNX1_uc002yuk.3_Intron|RUNX1_uc002yum.1_Intron|RUNX1_uc010gmw.1_Intron	NM_001754	NP_001745			runt-related transcription factor 1 isoform						myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387								T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				---	---	---	---
RUNX1	861	broad.mit.edu	37	21	36351628	36351628	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:36351628delT	uc010gmu.2	-						RUNX1_uc002yut.1_Intron|RUNX1_uc010gmv.2_Intron|RUNX1_uc002yuj.3_Intron|RUNX1_uc002yuk.3_Intron|RUNX1_uc002yum.1_Intron|RUNX1_uc010gmw.1_Intron	NM_001754	NP_001745			runt-related transcription factor 1 isoform						myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387								T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				---	---	---	---
RUNX1	861	broad.mit.edu	37	21	36575656	36575656	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:36575656delT	uc002yut.1	-											Synthetic construct DNA, clone: pF1KB4846, Homo sapiens RUNX1 gene for runt-related transcription factor 1, complete cds, without stop codon, in Flexi system.						myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387								T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				---	---	---	---
RUNX1	861	broad.mit.edu	37	21	36617577	36617577	+	Intron	DEL	C	-	-	rs68064991		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:36617577delC	uc002yut.1	-											Synthetic construct DNA, clone: pF1KB4846, Homo sapiens RUNX1 gene for runt-related transcription factor 1, complete cds, without stop codon, in Flexi system.						myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387								T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				---	---	---	---
Unknown	0	broad.mit.edu	37	21	37400984	37400985	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37400984_37400985insA								RUNX1 (43937 upstream) : SETD4 (5855 downstream)																																	OREG0026191	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	21	37451907	37451907	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37451907delT	uc011aea.1	-						SETD4_uc002yva.2_5'Flank					Homo sapiens cDNA FLJ59082 complete cds.																														---	---	---	---
DOPEY2	9980	broad.mit.edu	37	21	37595487	37595487	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37595487delT	uc002yvg.2	+						DOPEY2_uc011aeb.1_Intron	NM_005128	NP_005119			pad-1-like						endoplasmic reticulum organization|Golgi to endosome transport|multicellular organismal development|protein transport	Golgi membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
DOPEY2	9980	broad.mit.edu	37	21	37649590	37649590	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37649590delT	uc002yvg.2	+						DOPEY2_uc011aeb.1_Intron	NM_005128	NP_005119			pad-1-like						endoplasmic reticulum organization|Golgi to endosome transport|multicellular organismal development|protein transport	Golgi membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
DOPEY2	9980	broad.mit.edu	37	21	37663564	37663564	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37663564delA	uc002yvg.2	+						DOPEY2_uc011aeb.1_Intron	NM_005128	NP_005119			pad-1-like						endoplasmic reticulum organization|Golgi to endosome transport|multicellular organismal development|protein transport	Golgi membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
MORC3	23515	broad.mit.edu	37	21	37701599	37701599	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37701599delA	uc002yvi.2	+							NM_015358	NP_056173			MORC family CW-type zinc finger 3						cell aging|maintenance of protein location in nucleus|negative regulation of fibroblast proliferation|peptidyl-serine phosphorylation|protein stabilization	aggresome|intermediate filament cytoskeleton|PML body	ATP binding|zinc ion binding			ovary(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	37966689	37966690	+	IGR	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37966689_37966690delTC								CLDN14 (17822 upstream) : SIM2 (105301 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	38001910	38001910	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38001910delA								CLDN14 (53043 upstream) : SIM2 (70081 downstream)																																			---	---	---	---
HLCS	3141	broad.mit.edu	37	21	38278663	38278663	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38278663delA	uc010gnb.2	-						HLCS_uc002yvs.2_Intron	NM_000411	NP_000402			holocarboxylase synthetase						cell proliferation|histone biotinylation|response to biotin	chromatin|cytosol|mitochondrion|nuclear lamina|nuclear matrix	ATP binding|biotin binding|biotin-[acetyl-CoA-carboxylase] ligase activity|biotin-[methylcrotonoyl-CoA-carboxylase] ligase activity|biotin-[methylmalonyl-CoA-carboxytransferase] ligase activity|biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase activity|enzyme binding			ovary(2)|breast(1)|kidney(1)|liver(1)	5		Myeloproliferative disorder(46;0.0422)			Biotin(DB00121)													---	---	---	---
TTC3	7267	broad.mit.edu	37	21	38512779	38512779	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38512779delA	uc002yvz.2	+						TTC3_uc011aee.1_Intron|TTC3_uc002ywa.2_Intron|TTC3_uc002ywb.2_Intron|TTC3_uc010gnf.2_Intron|TTC3_uc002ywc.2_Intron|TTC3_uc011aed.1_Intron|TTC3_uc010gne.1_Intron	NM_001001894	NP_001001894			tetratricopeptide repeat domain 3						protein K48-linked ubiquitination|ubiquitin-dependent protein catabolic process	nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			skin(3)|ovary(2)|lung(2)|breast(2)	9		Myeloproliferative disorder(46;0.0412)																---	---	---	---
DYRK1A	1859	broad.mit.edu	37	21	38748799	38748800	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38748799_38748800delTT	uc002ywi.2	+						DYRK1A_uc002ywg.1_Intron|DYRK1A_uc010gno.1_Intron|DYRK1A_uc002ywh.1_Intron	NM_101395	NP_567824			dual-specificity tyrosine-(Y)-phosphorylation						nervous system development|peptidyl-tyrosine phosphorylation|protein autophosphorylation	nuclear speck	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding|protein self-association|protein serine/threonine kinase activity			ovary(2)|lung(1)|breast(1)	4																		---	---	---	---
DYRK1A	1859	broad.mit.edu	37	21	38830138	38830138	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38830138delT	uc002ywk.2	+						DYRK1A_uc002ywg.1_Intron|DYRK1A_uc010gno.1_Intron|DYRK1A_uc002ywh.1_Intron|DYRK1A_uc002ywi.2_Intron|DYRK1A_uc002ywj.2_Intron|DYRK1A_uc002ywl.2_Intron|DYRK1A_uc002ywm.2_Intron	NM_001396	NP_001387			dual-specificity tyrosine-(Y)-phosphorylation						nervous system development|peptidyl-tyrosine phosphorylation|protein autophosphorylation	nuclear speck	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding|protein self-association|protein serine/threonine kinase activity			ovary(2)|lung(1)|breast(1)	4																		---	---	---	---
ERG	2078	broad.mit.edu	37	21	39926928	39926928	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39926928delA	uc010gnw.2	-						ERG_uc010gnv.2_Intron|ERG_uc010gnx.2_Intron|ERG_uc011ael.1_Intron|ERG_uc002yxb.2_Intron|ERG_uc002yxc.3_Intron|ERG_uc010gnz.2_Intron	NM_001136155	NP_001129627			ets-related isoform 4						cell proliferation|multicellular organismal development|protein phosphorylation	cytoplasm|nucleus|ribonucleoprotein complex	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity		TMPRSS2/ERG(2499)|FUS/ERG(163)|EWSR1/ERG(162)	prostate(2499)|bone(167)|haematopoietic_and_lymphoid_tissue(153)|soft_tissue(5)|lung(2)|skin(1)|ovary(1)	2828		Prostate(19;3.6e-06)																---	---	---	---
NCRNA00114	400866	broad.mit.edu	37	21	40125377	40125378	+	5'Flank	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40125377_40125378delTC	uc010goa.2	-						NCRNA00114_uc011aen.1_Intron|NCRNA00114_uc002yxd.3_Intron	NR_027067				Homo sapiens chromosome 21 open reading frame 24 isoform 1 (C21orf24) mRNA, complete sequence.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	40332485	40332485	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40332485delT								ETS2 (135609 upstream) : PSMG1 (214905 downstream)																																			---	---	---	---
BRWD1	54014	broad.mit.edu	37	21	40584804	40584804	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40584804delA	uc002yxk.1	-						BRWD1_uc010goc.1_Intron|BRWD1_uc002yxl.2_Intron|BRWD1_uc010god.1_Intron	NM_018963	NP_061836			bromodomain and WD repeat domain containing 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				skin(3)|ovary(1)	4		Prostate(19;8.44e-08)|all_epithelial(19;0.223)																---	---	---	---
BRWD1	54014	broad.mit.edu	37	21	40604601	40604601	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40604601delA	uc002yxk.1	-						BRWD1_uc010goc.1_Intron|BRWD1_uc002yxl.2_Intron	NM_018963	NP_061836			bromodomain and WD repeat domain containing 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				skin(3)|ovary(1)	4		Prostate(19;8.44e-08)|all_epithelial(19;0.223)																---	---	---	---
BRWD1	54014	broad.mit.edu	37	21	40633672	40633672	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40633672delA	uc002yxk.1	-						BRWD1_uc010goc.1_Intron|BRWD1_uc002yxl.2_Intron|BRWD1_uc010goe.1_Intron|BRWD1_uc010gof.1_Intron|BRWD1_uc010gog.1_Intron|BRWD1_uc010goh.1_Intron|BRWD1_uc010goi.1_Intron	NM_018963	NP_061836			bromodomain and WD repeat domain containing 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				skin(3)|ovary(1)	4		Prostate(19;8.44e-08)|all_epithelial(19;0.223)																---	---	---	---
BRWD1	54014	broad.mit.edu	37	21	40651964	40651964	+	Intron	DEL	A	-	-	rs71846273		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40651964delA	uc002yxk.1	-						BRWD1_uc002yxl.2_Intron|BRWD1_uc010goe.1_Intron|BRWD1_uc010gof.1_Intron|BRWD1_uc010gog.1_Intron|BRWD1_uc010goh.1_Intron|BRWD1_uc010goi.1_Intron	NM_018963	NP_061836			bromodomain and WD repeat domain containing 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				skin(3)|ovary(1)	4		Prostate(19;8.44e-08)|all_epithelial(19;0.223)																---	---	---	---
SH3BGR	6450	broad.mit.edu	37	21	40822904	40822905	+	5'Flank	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40822904_40822905insT	uc002yya.2	+						SH3BGR_uc002yxz.2_Intron	NM_007341	NP_031367			SH3-binding domain and glutamic acid-rich						protein complex assembly	cytosol	SH3 domain binding|SH3/SH2 adaptor activity				0		all_cancers(19;1.16e-23)|all_epithelial(19;1.22e-20)|Prostate(19;2.55e-06)|Breast(209;0.0133)		STAD - Stomach adenocarcinoma(101;0.00151)														---	---	---	---
SH3BGR	6450	broad.mit.edu	37	21	40871691	40871691	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40871691delT	uc002yya.2	+						SH3BGR_uc002yxz.2_Intron	NM_007341	NP_031367			SH3-binding domain and glutamic acid-rich						protein complex assembly	cytosol	SH3 domain binding|SH3/SH2 adaptor activity				0		all_cancers(19;1.16e-23)|all_epithelial(19;1.22e-20)|Prostate(19;2.55e-06)|Breast(209;0.0133)		STAD - Stomach adenocarcinoma(101;0.00151)														---	---	---	---
B3GALT5	10317	broad.mit.edu	37	21	40926684	40926684	+	5'Flank	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40926684delG	uc002yyb.1	+							NM_033173	NP_149363			UDP-Gal:betaGlcNAc beta						protein glycosylation	endoplasmic reticulum|Golgi membrane|integral to membrane	UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity			skin(1)	1		Prostate(19;2.55e-06)																---	---	---	---
DSCAM	1826	broad.mit.edu	37	21	41392456	41392459	+	Intron	DEL	GTGA	-	-	rs140985038	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41392456_41392459delGTGA	uc002yyq.1	-						DSCAM_uc002yyr.1_Intron	NM_001389	NP_001380			Down syndrome cell adhesion molecule isoform						cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)|skin(4)|upper_aerodigestive_tract(1)	11		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)																---	---	---	---
DSCAM	1826	broad.mit.edu	37	21	41735180	41735182	+	Intron	DEL	TTT	-	-	rs146361159		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41735180_41735182delTTT	uc002yyq.1	-						DSCAM_uc002yyr.1_Intron	NM_001389	NP_001380			Down syndrome cell adhesion molecule isoform						cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)|skin(4)|upper_aerodigestive_tract(1)	11		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)																---	---	---	---
DSCAM	1826	broad.mit.edu	37	21	41741250	41741251	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41741250_41741251delTT	uc002yyq.1	-						DSCAM_uc002yyr.1_Intron	NM_001389	NP_001380			Down syndrome cell adhesion molecule isoform						cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)|skin(4)|upper_aerodigestive_tract(1)	11		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)																---	---	---	---
DSCAM	1826	broad.mit.edu	37	21	41848783	41848783	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41848783delA	uc002yyq.1	-						DSCAM_uc002yyr.1_Intron	NM_001389	NP_001380			Down syndrome cell adhesion molecule isoform						cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)|skin(4)|upper_aerodigestive_tract(1)	11		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)																---	---	---	---
Unknown	0	broad.mit.edu	37	21	42341991	42341991	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42341991delA								DSCAM (122952 upstream) : C21orf130 (171436 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	42507065	42507066	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42507065_42507066delTT								DSCAM (288026 upstream) : C21orf130 (6361 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	42908380	42908380	+	IGR	DEL	T	-	-	rs55931937		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42908380delT								TMPRSS2 (5337 upstream) : NCRNA00111 (191082 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	43022314	43022314	+	IGR	DEL	T	-	-	rs11336725		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43022314delT								TMPRSS2 (119271 upstream) : NCRNA00111 (77148 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	43065928	43065929	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43065928_43065929insT								TMPRSS2 (162885 upstream) : NCRNA00111 (33533 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	43080786	43080787	+	IGR	DEL	TT	-	-	rs75629022		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43080786_43080787delTT								TMPRSS2 (177743 upstream) : NCRNA00111 (18675 downstream)																																			---	---	---	---
RIPK4	54101	broad.mit.edu	37	21	43176484	43176485	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43176484_43176485insT	uc002yzn.1	-							NM_020639	NP_065690			ankyrin repeat domain 3							cytoplasm|nucleus	ATP binding|protein serine/threonine kinase activity			ovary(2)|central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)	7																		---	---	---	---
PRDM15	63977	broad.mit.edu	37	21	43255983	43255984	+	Intron	DEL	CC	-	-	rs71999286		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43255983_43255984delCC	uc002yzq.1	-						PRDM15_uc002yzo.2_Intron|PRDM15_uc002yzp.2_Intron|PRDM15_uc002yzr.1_Intron	NM_022115	NP_071398			PR domain containing 15 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
UMODL1	89766	broad.mit.edu	37	21	43517623	43517623	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43517623delT	uc002zaf.1	+						UMODL1_uc002zad.1_Intron|UMODL1_uc002zae.1_Intron|UMODL1_uc002zag.1_Intron|UMODL1_uc010gow.1_Intron|UMODL1_uc002zai.1_Intron|UMODL1_uc010gox.1_Intron|UMODL1_uc010goy.1_Intron|UMODL1_uc002zaj.1_Intron|UMODL1_uc010goz.1_Intron	NM_001004416	NP_001004416			uromodulin-like 1 isoform 1 precursor							cytoplasm|extracellular region|integral to membrane|plasma membrane	calcium ion binding|peptidase inhibitor activity			ovary(2)|skin(1)	3																		---	---	---	---
ABCG1	9619	broad.mit.edu	37	21	43664672	43664672	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43664672delT	uc002zaq.2	+						ABCG1_uc002zan.2_Intron|ABCG1_uc002zam.2_Intron|ABCG1_uc002zao.2_Intron|ABCG1_uc002zap.2_Intron|ABCG1_uc002zar.2_Intron|ABCG1_uc011aev.1_Intron	NM_004915	NP_004906			ATP-binding cassette sub-family G member 1						amyloid precursor protein catabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|detection of hormone stimulus|high-density lipoprotein particle remodeling|intracellular cholesterol transport|lipoprotein metabolic process|low-density lipoprotein particle remodeling|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|positive regulation of cholesterol biosynthetic process|regulation of cholesterol esterification|regulation of transcription, DNA-dependent|response to lipid|reverse cholesterol transport	endoplasmic reticulum membrane|external side of plasma membrane|Golgi membrane|recycling endosome	ADP binding|ATP binding|cholesterol transporter activity|glycoprotein transporter activity|phospholipid transporter activity|protein heterodimerization activity|protein homodimerization activity|sterol-transporting ATPase activity|toxin transporter activity			ovary(2)|central_nervous_system(1)	3					Adenosine triphosphate(DB00171)													---	---	---	---
SLC37A1	54020	broad.mit.edu	37	21	43956585	43956585	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43956585delT	uc002zbi.2	+						SLC37A1_uc002zbj.2_Intron	NM_018964	NP_061837			solute carrier family 37 member 1						carbohydrate transport|transmembrane transport	integral to membrane					0																		---	---	---	---
SLC37A1	54020	broad.mit.edu	37	21	43994125	43994126	+	Intron	INS	-	CCT	CCT	rs151204684	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43994125_43994126insCCT	uc002zbi.2	+						SLC37A1_uc002zbj.2_Intron	NM_018964	NP_061837			solute carrier family 37 member 1						carbohydrate transport|transmembrane transport	integral to membrane					0																		---	---	---	---
PDE9A	5152	broad.mit.edu	37	21	44090377	44090378	+	Intron	DEL	AT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44090377_44090378delAT	uc002zbm.2	+						PDE9A_uc002zbn.2_Intron|PDE9A_uc002zbo.2_Intron|PDE9A_uc002zbp.2_Intron|PDE9A_uc002zbq.2_Intron|PDE9A_uc002zbs.2_Intron|PDE9A_uc002zbr.2_Intron|PDE9A_uc002zbt.2_Intron|PDE9A_uc002zbu.2_Intron|PDE9A_uc002zbv.2_Intron|PDE9A_uc002zbw.2_Intron|PDE9A_uc002zbx.2_Intron|PDE9A_uc002zby.2_Intron|PDE9A_uc002zbz.2_Intron|PDE9A_uc002zca.2_Intron|PDE9A_uc002zcb.2_Intron|PDE9A_uc002zcc.2_Intron|PDE9A_uc002zcd.2_Intron|PDE9A_uc002zce.2_Intron|PDE9A_uc002zcf.2_Intron|PDE9A_uc002zcg.2_Intron	NM_002606	NP_002597			phosphodiesterase 9A isoform a						platelet activation|signal transduction	cytosol|endoplasmic reticulum|Golgi apparatus|perinuclear region of cytoplasm|ruffle membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding|protein binding			ovary(1)|skin(1)	2																		---	---	---	---
PDE9A	5152	broad.mit.edu	37	21	44114072	44114073	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44114072_44114073delTT	uc002zbm.2	+						PDE9A_uc002zbn.2_Intron|PDE9A_uc002zbo.2_Intron|PDE9A_uc002zbp.2_Intron|PDE9A_uc002zbq.2_Intron|PDE9A_uc002zbs.2_Intron|PDE9A_uc002zbr.2_Intron|PDE9A_uc002zbt.2_Intron|PDE9A_uc002zbu.2_Intron|PDE9A_uc002zbv.2_Intron|PDE9A_uc002zbw.2_Intron|PDE9A_uc002zbx.2_Intron|PDE9A_uc002zby.2_Intron|PDE9A_uc002zbz.2_Intron|PDE9A_uc002zca.2_Intron|PDE9A_uc002zcb.2_Intron|PDE9A_uc002zcc.2_Intron|PDE9A_uc002zcd.2_Intron|PDE9A_uc002zce.2_Intron|PDE9A_uc002zcf.2_Intron|PDE9A_uc002zcg.2_Intron	NM_002606	NP_002597			phosphodiesterase 9A isoform a						platelet activation|signal transduction	cytosol|endoplasmic reticulum|Golgi apparatus|perinuclear region of cytoplasm|ruffle membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding|protein binding			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	44223842	44223844	+	IGR	DEL	TAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44223842_44223844delTAA								PDE9A (28226 upstream) : WDR4 (39362 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	44252281	44252287	+	IGR	DEL	TTTTTTT	-	-	rs67029934		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44252281_44252287delTTTTTTT								PDE9A (56665 upstream) : WDR4 (10919 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	44363267	44363267	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44363267delT								NDUFV3 (33495 upstream) : PKNOX1 (31376 downstream)																																			---	---	---	---
U2AF1	7307	broad.mit.edu	37	21	44514137	44514137	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44514137delA	uc002zda.1	-						U2AF1_uc002zcy.1_Intron|U2AF1_uc002zcz.1_Intron|U2AF1_uc002zdb.1_Intron|U2AF1_uc010gpi.1_3'UTR	NM_001025203	NP_001020374			U2 small nuclear RNA auxillary factor 1 isoform						mRNA 3'-end processing|mRNA export from nucleus|termination of RNA polymerase II transcription	Cajal body|catalytic step 2 spliceosome|nuclear speck	nucleotide binding|RNA binding|zinc ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	44805444	44805445	+	IGR	DEL	GT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44805444_44805445delGT								CRYAA (212531 upstream) : SIK1 (28953 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	21	44906012	44906012	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44906012delC								C21orf84 (7909 upstream) : HSF2BP (43061 downstream)																																			---	---	---	---
AGPAT3	56894	broad.mit.edu	37	21	45353308	45353308	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45353308delT	uc002zdv.2	+						AGPAT3_uc002zdw.2_Intron	NM_020132	NP_064517			1-acylglycerol-3-phosphate O-acyltransferase 3						phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|plasma membrane	1-acylglycerol-3-phosphate O-acyltransferase activity				0				STAD - Stomach adenocarcinoma(101;0.18)|Colorectal(79;0.24)														---	---	---	---
AGPAT3	56894	broad.mit.edu	37	21	45389547	45389548	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45389547_45389548insT	uc002zdv.2	+						AGPAT3_uc002zdw.2_Intron|AGPAT3_uc002zdx.2_Intron|AGPAT3_uc002zdy.2_Intron	NM_020132	NP_064517			1-acylglycerol-3-phosphate O-acyltransferase 3						phospholipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|plasma membrane	1-acylglycerol-3-phosphate O-acyltransferase activity				0				STAD - Stomach adenocarcinoma(101;0.18)|Colorectal(79;0.24)														---	---	---	---
TRAPPC10	7109	broad.mit.edu	37	21	45434274	45434277	+	Intron	DEL	TTCC	-	-	rs11413186		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45434274_45434277delTTCC	uc002zea.2	+						TRAPPC10_uc010gpo.2_Intron|TRAPPC10_uc002zdz.2_Intron	NM_003274	NP_003265			trafficking protein particle complex 10						vesicle-mediated transport	Golgi apparatus|integral to membrane	binding|sodium ion transmembrane transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
TRAPPC10	7109	broad.mit.edu	37	21	45453852	45453852	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45453852delA	uc002zea.2	+						TRAPPC10_uc010gpo.2_Intron|TRAPPC10_uc002zdz.2_Intron	NM_003274	NP_003265			trafficking protein particle complex 10						vesicle-mediated transport	Golgi apparatus|integral to membrane	binding|sodium ion transmembrane transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	21	46180600	46180600	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46180600delG								C21orf29 (49105 upstream) : UBE2G2 (8356 downstream)																																			---	---	---	---
ITGB2	3689	broad.mit.edu	37	21	46323507	46323507	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46323507delG	uc002zgd.2	-						ITGB2_uc002zge.2_Intron|ITGB2_uc002zgf.3_Intron|ITGB2_uc011afl.1_Intron|ITGB2_uc010gpw.2_Intron|ITGB2_uc002zgg.2_Intron	NM_001127491	NP_001120963			integrin, beta 2 precursor						apoptosis|blood coagulation|cell-cell signaling|cell-matrix adhesion|inflammatory response|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|multicellular organismal development|neutrophil chemotaxis|regulation of cell shape|regulation of immune response|regulation of peptidyl-tyrosine phosphorylation	integrin complex	glycoprotein binding|protein kinase binding|receptor activity			ovary(4)|central_nervous_system(3)|breast(2)	9				Colorectal(79;0.0669)	Simvastatin(DB00641)													---	---	---	---
Unknown	0	broad.mit.edu	37	21	46490462	46490462	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46490462delG								NCRNA00162 (65820 upstream) : C21orf122 (411 downstream)																																			---	---	---	---
ADARB1	104	broad.mit.edu	37	21	46615523	46615526	+	Intron	DEL	TTTT	-	-	rs139330122	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46615523_46615526delTTTT	uc002zgy.2	+						ADARB1_uc002zgr.2_Intron|ADARB1_uc002zgs.2_Intron|ADARB1_uc002zgw.2_Intron|ADARB1_uc002zgv.2_Intron|ADARB1_uc002zgt.2_Intron|ADARB1_uc010gpx.2_Intron|ADARB1_uc002zgq.2_Intron|ADARB1_uc002zgu.2_Intron	NM_015833	NP_056648			RNA-specific adenosine deaminase B1 isoform 2						adenosine to inosine editing|mRNA modification|mRNA processing|RNA processing	nucleoplasm|nucleus	double-stranded RNA adenosine deaminase activity|double-stranded RNA adenosine deaminase activity|double-stranded RNA binding|double-stranded RNA binding|metal ion binding|mRNA binding|RNA binding			skin(1)	1				Colorectal(79;0.115)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	46667414	46667414	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46667414delA	uc002zgz.1	+											Homo sapiens C21orf89 protein (C21orf89) mRNA, complete cds.																														---	---	---	---
COL18A1	80781	broad.mit.edu	37	21	46835453	46835453	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46835453delC	uc002zhg.2	+							NM_130445	NP_569712			alpha 1 type XVIII collagen isoform 2 precursor						cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception	collagen|extracellular space	extracellular matrix structural constituent|metal ion binding|protein binding			central_nervous_system(1)	1				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)														---	---	---	---
COL18A1	80781	broad.mit.edu	37	21	46858120	46858121	+	Intron	INS	-	CA	CA			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46858120_46858121insCA	uc002zhg.2	+							NM_130445	NP_569712			alpha 1 type XVIII collagen isoform 2 precursor						cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception	collagen|extracellular space	extracellular matrix structural constituent|metal ion binding|protein binding			central_nervous_system(1)	1				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)														---	---	---	---
SLC19A1	6573	broad.mit.edu	37	21	46950276	46950277	+	Intron	DEL	GT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46950276_46950277delGT	uc002zhl.1	-						SLC19A1_uc010gpy.1_Intron|SLC19A1_uc011aft.1_Intron|SLC19A1_uc002zhm.1_Intron|SLC19A1_uc010gpz.1_Intron	NM_194255	NP_919231			solute carrier family 19 member 1						folic acid metabolic process	integral to plasma membrane|membrane fraction	folic acid binding|folic acid transporter activity|methotrexate transporter activity|reduced folate carrier activity				0				Colorectal(79;0.0569)|READ - Rectum adenocarcinoma(84;0.172)														---	---	---	---
PCBP3	54039	broad.mit.edu	37	21	47061266	47061267	+	5'Flank	DEL	AA	-	-	rs4819138	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47061266_47061267delAA	uc010gqb.2	+							NM_020528	NP_065389			poly(rC) binding protein 3 isoform 1						mRNA metabolic process	cytosol|mitochondrion|nucleus|ribonucleoprotein complex	DNA binding|RNA binding			skin(1)	1	all_hematologic(128;0.24)			Colorectal(79;0.0411)|READ - Rectum adenocarcinoma(84;0.0649)														---	---	---	---
PCBP3	54039	broad.mit.edu	37	21	47319496	47319496	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47319496delT	uc002zhq.1	+						PCBP3_uc010gqb.2_Intron|PCBP3_uc002zhp.1_Intron|PCBP3_uc010gqc.1_Intron|PCBP3_uc002zhs.1_Intron|PCBP3_uc002zhr.1_Intron|PCBP3_uc002zht.1_Intron	NM_020528	NP_065389			poly(rC) binding protein 3 isoform 1						mRNA metabolic process	cytosol|mitochondrion|nucleus|ribonucleoprotein complex	DNA binding|RNA binding			skin(1)	1	all_hematologic(128;0.24)			Colorectal(79;0.0411)|READ - Rectum adenocarcinoma(84;0.0649)														---	---	---	---
PCBP3	54039	broad.mit.edu	37	21	47341732	47341734	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47341732_47341734delAAA	uc002zhq.1	+						PCBP3_uc010gqb.2_Intron|PCBP3_uc002zhp.1_Intron|PCBP3_uc002zhs.1_Intron|PCBP3_uc002zhr.1_Intron|PCBP3_uc002zht.1_Intron	NM_020528	NP_065389			poly(rC) binding protein 3 isoform 1						mRNA metabolic process	cytosol|mitochondrion|nucleus|ribonucleoprotein complex	DNA binding|RNA binding			skin(1)	1	all_hematologic(128;0.24)			Colorectal(79;0.0411)|READ - Rectum adenocarcinoma(84;0.0649)														---	---	---	---
Unknown	0	broad.mit.edu	37	21	47498885	47498886	+	IGR	INS	-	CCCGCAT	CCCGCAT	rs146689281	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47498885_47498886insCCCGCAT								COL6A1 (73922 upstream) : COL6A2 (19147 downstream)																																			---	---	---	---
DIP2A	23181	broad.mit.edu	37	21	47928949	47928949	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47928949delA	uc002zjo.2	+						DIP2A_uc011afy.1_Intron|DIP2A_uc011afz.1_Intron|DIP2A_uc002zjl.2_Intron|DIP2A_uc002zjm.2_Intron|DIP2A_uc010gql.2_Intron|DIP2A_uc002zjn.2_Intron|DIP2A_uc002zjp.1_Intron	NM_015151	NP_055966			disco-interacting protein 2A isoform a						multicellular organismal development	nucleus	catalytic activity|transcription factor binding			ovary(2)	2	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)														---	---	---	---
PRMT2	3275	broad.mit.edu	37	21	48063246	48063246	+	Intron	DEL	T	-	-	rs78162248		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:48063246delT	uc002zjx.2	+						PRMT2_uc002zjw.2_Intron|PRMT2_uc002zjy.2_Intron|PRMT2_uc010gqm.2_Intron|PRMT2_uc011aga.1_Intron|PRMT2_uc011agb.1_Intron|PRMT2_uc011agc.1_Intron|PRMT2_uc002zjz.1_5'UTR	NM_206962	NP_996845			HMT1 hnRNP methyltransferase-like 1						developmental cell growth|induction of apoptosis|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of NF-kappaB transcription factor activity|negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of androgen receptor signaling pathway	cytosol|nucleus	androgen receptor binding|estrogen receptor binding|histone-arginine N-methyltransferase activity|peroxisome proliferator activated receptor binding|progesterone receptor binding|protein homodimerization activity|retinoic acid receptor binding|signal transducer activity|thyroid hormone receptor binding|transcription coactivator activity			ovary(1)	1	Breast(49;0.247)	Lung NSC(3;0.245)		Epithelial(3;1.03e-07)|OV - Ovarian serous cystadenocarcinoma(3;4.68e-07)|all cancers(3;7.48e-07)|Colorectal(79;0.167)|Lung(125;0.203)|LUSC - Lung squamous cell carcinoma(216;0.23)|READ - Rectum adenocarcinoma(84;0.248)														---	---	---	---
Unknown	0	broad.mit.edu	37	22	16311421	16311422	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16311421_16311422delAA								POTEH (23484 upstream) : OR11H1 (137404 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	16360805	16360806	+	IGR	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16360805_16360806delCT								POTEH (72868 upstream) : OR11H1 (88020 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	17034027	17034027	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17034027delT								OR11H1 (584223 upstream) : CCT8L2 (37621 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	17353883	17353884	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17353883_17353884insA								HSFYL1 (43658 upstream) : GAB4 (88945 downstream)																																			---	---	---	---
GAB4	128954	broad.mit.edu	37	22	17451924	17451924	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17451924delA	uc002zlw.2	-						GAB4_uc010gqs.1_Intron	NM_001037814	NP_001032903			GRB2-associated binding protein family, member											large_intestine(1)|ovary(1)	2		all_epithelial(15;0.112)|Lung NSC(13;0.248)																---	---	---	---
IL17RA	23765	broad.mit.edu	37	22	17576486	17576486	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17576486delT	uc002zly.2	+						IL17RA_uc010gqt.2_Intron	NM_014339	NP_055154			interleukin 17A receptor precursor						fibroblast activation|positive regulation of interleukin-23 production	integral to plasma membrane	interleukin-17 receptor activity			skin(2)	2		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)		Colorectal(9;0.241)												OREG0026280	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	22	17658599	17658599	+	IGR	DEL	A	-	-	rs139307973	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17658599delA								CECR4 (12265 upstream) : CECR1 (1593 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	17738784	17738785	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17738784_17738785delTT								CECR1 (36046 upstream) : CECR2 (102054 downstream)																																			---	---	---	---
TUBA8	51807	broad.mit.edu	37	22	18562906	18562906	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18562906delT	uc002znr.2	+						PEX26_uc002znp.3_Intron|PEX26_uc002znq.3_Intron|uc002zns.2_5'Flank|PEX26_uc002znt.2_Intron	NM_018943	NP_061816			tubulin, alpha 8						microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|structural molecule activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	19311553	19311553	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19311553delA								CLTCL1 (32314 upstream) : HIRA (6671 downstream)																																			---	---	---	---
HIRA	7290	broad.mit.edu	37	22	19413119	19413120	+	Intron	INS	-	C	C	rs142071393	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19413119_19413120insC	uc002zpf.1	-						HIRA_uc011agx.1_Intron|HIRA_uc010grn.1_Intron|HIRA_uc010gro.1_Intron|HIRA_uc010grp.2_Intron	NM_003325	NP_003316			HIR histone cell cycle regulation defective						chromatin modification|regulation of transcription from RNA polymerase II promoter	PML body	chromatin binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(1)	1	Colorectal(54;0.0993)																	---	---	---	---
HIRA	7290	broad.mit.edu	37	22	19432107	19432107	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19432107delT	uc010gro.1	-						HIRA_uc010grp.2_Intron|C22orf39_uc002zpi.2_Intron|C22orf39_uc002zpj.2_5'Flank|C22orf39_uc002zpk.1_Intron	NM_003325	NP_003316			HIR histone cell cycle regulation defective						chromatin modification|regulation of transcription from RNA polymerase II promoter	PML body	chromatin binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(1)	1	Colorectal(54;0.0993)																	---	---	---	---
CDC45	8318	broad.mit.edu	37	22	19492873	19492873	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19492873delT	uc002zpr.2	+						CDC45_uc011agz.1_Intron|CDC45_uc011aha.1_Intron|CDC45_uc002zps.2_Intron|CDC45_uc002zpt.2_Intron	NM_003504	NP_003495			CDC45-like						DNA replication checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle	centrosome|nucleoplasm	protein binding			lung(1)	1																		---	---	---	---
CDC45	8318	broad.mit.edu	37	22	19495509	19495509	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19495509delA	uc002zpr.2	+						CDC45_uc011agz.1_Intron|CDC45_uc011aha.1_Intron|CDC45_uc002zps.2_Intron|CDC45_uc002zpt.2_Intron	NM_003504	NP_003495			CDC45-like						DNA replication checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle	centrosome|nucleoplasm	protein binding			lung(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	19597951	19597951	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19597951delG								LOC150185 (43589 upstream) : SEPT5 (104036 downstream)																																			---	---	---	---
GNB1L	54584	broad.mit.edu	37	22	19782867	19782867	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19782867delA	uc002zqe.1	-						GNB1L_uc002zqd.1_Intron|GNB1L_uc002zqf.1_Intron	NM_053004	NP_443730			guanine nucleotide binding protein						G-protein coupled receptor protein signaling pathway|intracellular signal transduction	internal side of plasma membrane|intracellular				breast(1)	1	Colorectal(54;0.0993)																	---	---	---	---
TXNRD2	10587	broad.mit.edu	37	22	19868926	19868926	+	Intron	DEL	G	-	-	rs34318203		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19868926delG	uc011ahc.1	-						TXNRD2_uc002zql.1_Intron|TXNRD2_uc002zqm.1_Intron|TXNRD2_uc002zqn.1_Intron|TXNRD2_uc002zqo.1_Intron|TXNRD2_uc002zqp.1_Intron|TXNRD2_uc002zqr.1_Intron|TXNRD2_uc002zqj.1_Intron|TXNRD2_uc002zqq.1_5'Flank	NM_006440	NP_006431			thioredoxin reductase 2 precursor						cell redox homeostasis|response to oxygen radical	mitochondrion	flavin adenine dinucleotide binding|NADP binding|thioredoxin-disulfide reductase activity			ovary(2)	2	Colorectal(54;0.0993)																	---	---	---	---
C22orf25	128989	broad.mit.edu	37	22	20011062	20011063	+	Intron	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20011062_20011063delGA	uc010grw.1	+						C22orf25_uc002zrb.1_Intron|C22orf25_uc002zrc.1_Intron|C22orf25_uc002zrd.1_Intron|C22orf25_uc002zre.2_Intron|C22orf25_uc010grx.2_Intron|C22orf25_uc011ahe.1_Intron|C22orf25_uc011ahf.1_Intron|C22orf25_uc011ahg.1_Intron|C22orf25_uc002zrg.2_Intron|C22orf25_uc011ahh.1_Intron|C22orf25_uc002zrf.2_Intron|C22orf25_uc011ahi.1_Intron	NM_152906	NP_690870			hypothetical protein LOC128989												0	Colorectal(54;0.0533)																	---	---	---	---
Unknown	0	broad.mit.edu	37	22	20281317	20281317	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20281317delC								RTN4R (25501 upstream) : DGCR6L (20485 downstream)																																			---	---	---	---
PI4KA	5297	broad.mit.edu	37	22	21170228	21170229	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21170228_21170229delTT	uc002zsz.3	-						PI4KA_uc010gsq.1_Intron	NM_058004	NP_477352			phosphatidylinositol 4-kinase type 3 alpha						phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling|synaptic transmission	Golgi-associated vesicle	1-phosphatidylinositol 4-kinase activity|ATP binding|protein binding			lung(2)|upper_aerodigestive_tract(1)|salivary_gland(1)	4	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)															---	---	---	---
SNAP29	9342	broad.mit.edu	37	22	21213874	21213874	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21213874delT	uc011ahw.1	+						PI4KA_uc002zsz.3_5'Flank|PI4KA_uc010gsq.1_5'Flank	NM_004782	NP_004773			synaptosomal-associated protein 29						cellular membrane fusion|exocytosis|protein transport|vesicle targeting	cell junction|cytoplasm|nucleus|synapse|synaptosome	SNAP receptor activity				0	all_cancers(11;2.77e-25)|all_epithelial(7;8.92e-24)|Lung NSC(8;1.49e-15)|all_lung(8;2.54e-14)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000592)|Lung(15;0.0117)															---	---	---	---
UBE2L3	7332	broad.mit.edu	37	22	21934066	21934066	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21934066delA	uc002zva.1	+						UBE2L3_uc011aig.1_Intron|UBE2L3_uc002zuz.1_Intron	NM_003347	NP_003338			ubiquitin-conjugating enzyme E2L 3						cell proliferation|cellular response to glucocorticoid stimulus|protein K11-linked ubiquitination|regulation of S phase of mitotic cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus|ubiquitin ligase complex	ATP binding|transcription coactivator activity|ubiquitin protein ligase binding|ubiquitin-protein ligase activity				0	Colorectal(54;0.105)																	---	---	---	---
Unknown	0	broad.mit.edu	37	22	22240532	22240532	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22240532delA								MAPK1 (18562 upstream) : PPM1F (33261 downstream)																																			---	---	---	---
TOP3B	8940	broad.mit.edu	37	22	22330660	22330660	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22330660delC	uc002zvs.2	-						TOP3B_uc010gtl.2_Intron|TOP3B_uc002zvt.3_Intron	NM_003935	NP_003926			topoisomerase (DNA) III beta						DNA topological change	nucleus	ATP binding|DNA topoisomerase type I activity|protein binding			kidney(1)	1	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.145)														---	---	---	---
LOC96610	96610	broad.mit.edu	37	22	22486531	22486531	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22486531delT	uc011aim.1	+											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
LOC96610	96610	broad.mit.edu	37	22	22654928	22654929	+	Intron	DEL	TT	-	-	rs111234971		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22654928_22654929delTT	uc011aim.1	+						LOC96610_uc011aiq.1_Intron|LOC96610_uc011aip.1_Intron|LOC96610_uc010gto.2_Intron					Parts of antibodies, mostly variable regions.												0																		---	---	---	---
RAB36	9609	broad.mit.edu	37	22	23506388	23506388	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23506388delT	uc002zwv.1	+	11					RAB36_uc010gtw.1_3'UTR	NM_004914	NP_004905			RAB36, member RAS oncogene family						protein transport|small GTPase mediated signal transduction	Golgi membrane	GTP binding			ovary(1)|central_nervous_system(1)	2	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.155)														---	---	---	---
BCR	613	broad.mit.edu	37	22	23550604	23550604	+	Intron	DEL	T	-	-	rs66521339		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23550604delT	uc002zww.2	+						BCR_uc002zwx.2_Intron	NM_004327	NP_004318			breakpoint cluster region isoform 1						regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	ATP binding|GTPase activator activity|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity		BCR/JAK2(6)	haematopoietic_and_lymphoid_tissue(6)|central_nervous_system(3)|urinary_tract(1)|lung(1)|skin(1)	12								T	ABL1| FGFR1|JAK2 	CML|ALL|AML								---	---	---	---
Unknown	0	broad.mit.edu	37	22	23691466	23691466	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23691466delT								BCR (31243 upstream) : ZDHHC8P1 (41327 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	23712779	23712780	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23712779_23712780delAA								BCR (52556 upstream) : ZDHHC8P1 (20013 downstream)																																			---	---	---	---
LOC91316	91316	broad.mit.edu	37	22	24000115	24000115	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24000115delT	uc002zxh.3	-						LOC91316_uc002zxi.3_Intron|LOC91316_uc002zxk.3_Intron|LOC91316_uc010gua.2_Intron|LOC91316_uc002zxl.3_Intron|LOC91316_uc011aiz.1_Intron|LOC91316_uc002zxm.3_Intron					Homo sapiens cDNA FLJ32313 fis, clone PROST2003232, weakly similar to BETA-GLUCURONIDASE PRECURSOR (EC 3.2.1.31).												0																		---	---	---	---
DDT	1652	broad.mit.edu	37	22	24271364	24271364	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24271364delC	uc011ajf.1	-							NM_001355	NP_001346			D-dopachrome tautomerase						melanin biosynthetic process	cytoplasm	D-dopachrome decarboxylase activity|dopachrome isomerase activity|protein binding				0																		---	---	---	---
CABIN1	23523	broad.mit.edu	37	22	24495100	24495100	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24495100delG	uc002zzi.1	+						CABIN1_uc002zzj.1_Intron|CABIN1_uc002zzl.1_Intron	NM_012295	NP_036427			calcineurin binding protein 1						cell surface receptor linked signaling pathway|chromatin modification	nucleus	protein phosphatase inhibitor activity			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	24614413	24614414	+	IGR	INS	-	A	A	rs150183646	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24614413_24614414insA								SUSD2 (29339 upstream) : GGT5 (1209 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	25101709	25101710	+	IGR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25101709_25101710delAA								POM121L10P (46595 upstream) : PIWIL3 (13291 downstream)																																			---	---	---	---
PIWIL3	440822	broad.mit.edu	37	22	25145193	25145193	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25145193delC	uc003abd.1	-						PIWIL3_uc011ajx.1_Intron|PIWIL3_uc011ajy.1_Intron|PIWIL3_uc010gut.1_Intron	NM_001008496	NP_001008496			piwi-like 3						cell differentiation|gene silencing by RNA|meiosis|multicellular organismal development|regulation of translation|spermatogenesis	cytoplasm	RNA binding			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	25196501	25196502	+	IGR	INS	-	TG	TG			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25196501_25196502insTG								PIWIL3 (25818 upstream) : SGSM1 (5634 downstream)																																			---	---	---	---
SGSM1	129049	broad.mit.edu	37	22	25240493	25240493	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25240493delA	uc003abg.2	+						SGSM1_uc003abh.2_Intron|SGSM1_uc010guu.1_Intron|SGSM1_uc003abj.2_Intron|SGSM1_uc003abi.1_5'UTR|SGSM1_uc003abf.2_Intron	NM_001039948	NP_001035037			RUN and TBC1 domain containing 2 isoform 1							Golgi apparatus	Rab GTPase activator activity			ovary(2)|central_nervous_system(2)|pancreas(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	25329496	25329496	+	IGR	DEL	A	-	-	rs59254088		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25329496delA								SGSM1 (6683 upstream) : TMEM211 (1712 downstream)																																			---	---	---	---
KIAA1671	85379	broad.mit.edu	37	22	25471470	25471470	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25471470delT	uc003abn.2	+						KIAA1671_uc003abl.2_Intron	NM_001145206	NP_001138678			hypothetical protein LOC85379											lung(1)	1																		---	---	---	---
CRYBB3	1417	broad.mit.edu	37	22	25598254	25598254	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25598254delT	uc003abo.1	+							NM_004076	NP_004067			crystallin, beta B3						visual perception		protein binding|structural constituent of eye lens				0																OREG0026423	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	22	25648076	25648076	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25648076delT								CRYBB2 (20240 upstream) : IGLL3 (65812 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	25862007	25862007	+	Intron	DEL	T	-	-	rs76502343		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25862007delT	uc003abv.2	+											Homo sapiens cDNA clone IMAGE:3542716, partial cds.																														---	---	---	---
ADRBK2	157	broad.mit.edu	37	22	26104196	26104196	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26104196delA	uc003abx.3	+						ADRBK2_uc010gux.2_Intron|ADRBK2_uc003abw.2_Intron|ADRBK2_uc003aby.3_Intron	NM_005160	NP_005151			beta-adrenergic receptor kinase 2								ATP binding|beta-adrenergic receptor kinase activity|signal transducer activity			lung(3)|ovary(2)|stomach(1)|central_nervous_system(1)	7					Adenosine triphosphate(DB00171)													---	---	---	---
MYO18B	84700	broad.mit.edu	37	22	26183238	26183255	+	Intron	DEL	CGCACACACACACACACA	-	-	rs144822452	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26183238_26183255delCGCACACACACACACACA	uc003abz.1	+						MYO18B_uc003aca.1_Intron|MYO18B_uc010guy.1_Intron|MYO18B_uc010guz.1_Intron|MYO18B_uc011aka.1_Intron|MYO18B_uc011akb.1_Intron	NM_032608	NP_115997			myosin XVIIIB							nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12																		---	---	---	---
MYO18B	84700	broad.mit.edu	37	22	26204921	26204921	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26204921delT	uc003abz.1	+						MYO18B_uc003aca.1_Intron|MYO18B_uc010guy.1_Intron|MYO18B_uc010guz.1_Intron|MYO18B_uc011aka.1_Intron|MYO18B_uc011akb.1_Intron	NM_032608	NP_115997			myosin XVIIIB							nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12																		---	---	---	---
MYO18B	84700	broad.mit.edu	37	22	26243046	26243048	+	Intron	DEL	AAA	-	-	rs71901912		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26243046_26243048delAAA	uc003abz.1	+						MYO18B_uc003aca.1_Intron|MYO18B_uc010guy.1_Intron|MYO18B_uc010guz.1_Intron|MYO18B_uc011aka.1_Intron|MYO18B_uc011akb.1_Intron	NM_032608	NP_115997			myosin XVIIIB							nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12																		---	---	---	---
MYO18B	84700	broad.mit.edu	37	22	26326762	26326762	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26326762delC	uc003abz.1	+						MYO18B_uc003aca.1_Intron|MYO18B_uc010guy.1_Intron|MYO18B_uc010guz.1_Intron|MYO18B_uc011aka.1_Intron|MYO18B_uc011akb.1_Intron	NM_032608	NP_115997			myosin XVIIIB							nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12																		---	---	---	---
MYO18B	84700	broad.mit.edu	37	22	26344285	26344285	+	Intron	DEL	A	-	-	rs150160143		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26344285delA	uc003abz.1	+						MYO18B_uc003aca.1_Intron|MYO18B_uc010guy.1_Intron|MYO18B_uc010guz.1_Intron|MYO18B_uc011aka.1_Intron|MYO18B_uc011akb.1_Intron	NM_032608	NP_115997			myosin XVIIIB							nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12																		---	---	---	---
MYO18B	84700	broad.mit.edu	37	22	26367913	26367913	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26367913delA	uc003abz.1	+						MYO18B_uc003aca.1_Intron|MYO18B_uc010guy.1_Intron|MYO18B_uc010guz.1_Intron|MYO18B_uc011aka.1_Intron|MYO18B_uc011akb.1_Intron|MYO18B_uc010gva.1_Intron	NM_032608	NP_115997			myosin XVIIIB							nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	26509818	26509821	+	IGR	DEL	TGTG	-	-	rs66959333		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26509818_26509821delTGTG								MYO18B (82811 upstream) : SEZ6L (55659 downstream)																																			---	---	---	---
SEZ6L	23544	broad.mit.edu	37	22	26672020	26672021	+	Intron	INS	-	CT	CT			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26672020_26672021insCT	uc003acb.2	+						SEZ6L_uc003acc.2_Intron|SEZ6L_uc011akc.1_Intron|SEZ6L_uc003acd.2_Intron|SEZ6L_uc011akd.1_Intron|SEZ6L_uc003ace.2_Intron	NM_021115	NP_066938			seizure related 6 homolog (mouse)-like							endoplasmic reticulum membrane|integral to membrane				ovary(4)|central_nervous_system(1)|pancreas(1)	6																		---	---	---	---
TFIP11	24144	broad.mit.edu	37	22	26894669	26894670	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26894669_26894670delAA	uc003acr.2	-						TFIP11_uc003acs.2_Intron|TFIP11_uc003act.2_Intron	NM_012143	NP_036275			tuftelin interacting protein 11						biomineral tissue development	catalytic step 2 spliceosome|cytoplasm|nuclear speck	DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
TPST2	8459	broad.mit.edu	37	22	26947528	26947528	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26947528delT	uc003acw.2	-						TPST2_uc003acx.2_Intron|TPST2_uc011akf.1_Intron	NM_001008566	NP_001008566			tyrosylprotein sulfotransferase 2						peptidyl-tyrosine sulfation	endoplasmic reticulum|Golgi membrane|integral to membrane|membrane fraction	protein-tyrosine sulfotransferase activity			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	27303405	27303405	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27303405delT								MIAT (188456 upstream) : MN1 (840861 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	27330690	27330691	+	IGR	INS	-	T	T	rs151254739	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27330690_27330691insT								MIAT (215741 upstream) : MN1 (813575 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	27365154	27365154	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27365154delA								MIAT (250205 upstream) : MN1 (779112 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	27683034	27683034	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:27683034delA								MIAT (568085 upstream) : MN1 (461232 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	28002656	28002656	+	IGR	DEL	A	-	-	rs67865435		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28002656delA								MIAT (887707 upstream) : MN1 (141610 downstream)																																			---	---	---	---
MN1	4330	broad.mit.edu	37	22	28180871	28180871	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28180871delG	uc003adj.2	-						MN1_uc010gvg.2_Intron	NM_002430	NP_002421			meningioma  1								binding			central_nervous_system(3)|lung(3)|large_intestine(1)|breast(1)|skin(1)|ovary(1)	10								T	ETV6	AML|meningioma								---	---	---	---
LOC284900	284900	broad.mit.edu	37	22	28373784	28373785	+	Intron	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28373784_28373785insC	uc003ado.2	+							NR_026963				Homo sapiens mRNA for KIAA1648 protein, partial cds.												0																		---	---	---	---
TTC28	23331	broad.mit.edu	37	22	28395900	28395900	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28395900delT	uc003adp.3	-						LOC284900_uc003ado.2_RNA|LOC284900_uc003adq.1_RNA	NM_001145418	NP_001138890			tetratricopeptide repeat domain 28								binding				0																		---	---	---	---
TTC28	23331	broad.mit.edu	37	22	28769244	28769246	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28769244_28769246delAAA	uc003adp.3	-							NM_001145418	NP_001138890			tetratricopeptide repeat domain 28								binding				0																		---	---	---	---
TTC28	23331	broad.mit.edu	37	22	28795475	28795476	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:28795475_28795476insT	uc003adp.3	-							NM_001145418	NP_001138890			tetratricopeptide repeat domain 28								binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	29234824	29234824	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29234824delT								XBP1 (38264 upstream) : ZNRF3 (45066 downstream)																																			---	---	---	---
KREMEN1	83999	broad.mit.edu	37	22	29477190	29477191	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29477190_29477191insT	uc011akm.1	+						KREMEN1_uc003ael.2_Intron	NM_032045	NP_114434			kringle-containing transmembrane protein 1						cell communication|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to membrane|membrane fraction	protein binding			ovary(3)|lung(2)	5																		---	---	---	---
KREMEN1	83999	broad.mit.edu	37	22	29491863	29491863	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29491863delA	uc011akm.1	+						KREMEN1_uc003ael.2_Intron|KREMEN1_uc011akn.1_Intron	NM_032045	NP_114434			kringle-containing transmembrane protein 1						cell communication|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to membrane|membrane fraction	protein binding			ovary(3)|lung(2)	5																		---	---	---	---
KREMEN1	83999	broad.mit.edu	37	22	29559918	29559919	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29559918_29559919delAA	uc011akm.1	+							NM_032045	NP_114434			kringle-containing transmembrane protein 1						cell communication|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to membrane|membrane fraction	protein binding			ovary(3)|lung(2)	5																		---	---	---	---
THOC5	8563	broad.mit.edu	37	22	29942833	29942836	+	Intron	DEL	TTTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29942833_29942836delTTTT	uc003afr.2	-						THOC5_uc003afs.2_Intron|THOC5_uc003aft.2_Intron|THOC5_uc003afu.2_Intron|THOC5_uc010gvo.2_Intron|THOC5_uc003afv.1_Intron	NM_001002878	NP_001002878			THO complex 5						intronless viral mRNA export from host nucleus|monocyte differentiation|mRNA processing|primitive hemopoiesis|RNA splicing	cytoplasm|intermediate filament cytoskeleton|THO complex part of transcription export complex	protein binding|RNA binding			breast(3)	3																		---	---	---	---
MTMR3	8897	broad.mit.edu	37	22	30422038	30422038	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30422038delT	uc003agv.3	+	20					MTMR3_uc003agu.3_3'UTR|MTMR3_uc003agw.3_3'UTR	NM_021090	NP_066576			myotubularin-related protein 3 isoform c						phosphatidylinositol dephosphorylation	cytoplasm|membrane|membrane fraction|nucleus	metal ion binding|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity			breast(3)|ovary(1)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(5;0.00204)|Epithelial(10;0.06)|all cancers(5;0.107)															---	---	---	---
Unknown	0	broad.mit.edu	37	22	30427106	30427107	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30427106_30427107insA								MTMR3 (251 upstream) : HORMAD2 (49346 downstream)																																			---	---	---	---
SF3A1	10291	broad.mit.edu	37	22	30747291	30747291	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30747291delA	uc003ahl.2	-							NM_005877	NP_005868			splicing factor 3a, subunit 1, 120kDa isoform 1						nuclear mRNA 3'-splice site recognition	catalytic step 2 spliceosome|nucleoplasm|U2-type spliceosomal complex	protein binding|RNA binding			ovary(3)|large_intestine(1)|pancreas(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	30827721	30827721	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30827721delT								MTP18 (2680 upstream) : SEC14L3 (27496 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	30829057	30829057	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30829057delT								MTP18 (4016 upstream) : SEC14L3 (26160 downstream)																																			---	---	---	---
TCN2	6948	broad.mit.edu	37	22	31022191	31022191	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31022191delC	uc003aip.1	+						TCN2_uc003aiq.1_Intron|TCN2_uc003air.1_Intron	NM_000355	NP_000346			transcobalamin II precursor						cobalamin metabolic process|cobalamin transport|cobalt ion transport	extracellular space	cobalamin binding			central_nervous_system(1)	1					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)													---	---	---	---
Unknown	0	broad.mit.edu	37	22	31067329	31067329	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31067329delC								SLC35E4 (2327 upstream) : OSBP2 (22440 downstream)																																			---	---	---	---
OSBP2	23762	broad.mit.edu	37	22	31302452	31302452	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31302452delT	uc003aiy.1	+	14					OSBP2_uc011ala.1_3'UTR|OSBP2_uc010gwc.1_3'UTR|OSBP2_uc011alb.1_3'UTR|OSBP2_uc003aiz.1_3'UTR|OSBP2_uc003aja.1_3'UTR|OSBP2_uc011alc.1_3'UTR|OSBP2_uc003ajb.2_3'UTR|OSBP2_uc011ald.1_3'UTR|OSBP2_uc010gwd.1_3'UTR	NM_030758	NP_110385			oxysterol binding protein 2 isoform a						lipid transport	membrane	lipid binding			breast(1)|skin(1)	2																		---	---	---	---
MORC2	22880	broad.mit.edu	37	22	31329912	31329912	+	Intron	DEL	G	-	-	rs71740454		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31329912delG	uc003aje.1	-							NM_014941	NP_055756			MORC family CW-type zinc finger 2								ATP binding|zinc ion binding			ovary(1)|pancreas(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	32325458	32325458	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32325458delG								DEPDC5 (22458 upstream) : C22orf24 (4050 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	32780017	32780018	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32780017_32780018insT								RFPL3S (12954 upstream) : C22orf28 (3544 downstream)																																			---	---	---	---
SYN3	8224	broad.mit.edu	37	22	32921002	32921002	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32921002delA	uc003amx.2	-						SYN3_uc003amy.2_Intron|SYN3_uc003amz.2_Intron|SYN3_uc011amc.1_Intron	NM_003490	NP_003481			synapsin III isoform IIIa						neurotransmitter secretion	cell junction|synaptic vesicle membrane	ATP binding|ligase activity			skin(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	33577521	33577521	+	IGR	DEL	T	-	-	rs71686584		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33577521delT								SYN3 (123144 upstream) : LARGE (91542 downstream)																																			---	---	---	---
LARGE	9215	broad.mit.edu	37	22	34043747	34043747	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34043747delT	uc003and.3	-						LARGE_uc003ane.3_Intron|LARGE_uc010gwp.2_Intron|LARGE_uc011ame.1_Intron|LARGE_uc011amf.1_Intron	NM_004737	NP_004728			like-glycosyltransferase						glycosphingolipid biosynthetic process|muscle cell homeostasis|N-acetylglucosamine metabolic process|protein glycosylation	integral to Golgi membrane	acetylglucosaminyltransferase activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(1;0.219)																---	---	---	---
LARGE	9215	broad.mit.edu	37	22	34052045	34052046	+	Intron	DEL	GT	-	-	rs36081368		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34052045_34052046delGT	uc003and.3	-						LARGE_uc003ane.3_Intron|LARGE_uc010gwp.2_Intron|LARGE_uc011ame.1_Intron|LARGE_uc011amf.1_Intron	NM_004737	NP_004728			like-glycosyltransferase						glycosphingolipid biosynthetic process|muscle cell homeostasis|N-acetylglucosamine metabolic process|protein glycosylation	integral to Golgi membrane	acetylglucosaminyltransferase activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(1;0.219)																---	---	---	---
Unknown	0	broad.mit.edu	37	22	34530058	34530058	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34530058delG								LARGE (211474 upstream) : ISX (932071 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	35762124	35762124	+	IGR	DEL	A	-	-	rs35195870		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35762124delA								TOM1 (18139 upstream) : HMOX1 (14963 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	35886572	35886572	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35886572delG								MCM5 (66078 upstream) : RASD2 (50780 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	35969441	35969441	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35969441delT								RASD2 (19398 upstream) : MB (33371 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	36037102	36037102	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36037102delT								MB (17701 upstream) : APOL6 (7322 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	36101022	36101022	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36101022delA								APOL6 (36567 upstream) : APOL5 (12897 downstream)																																			---	---	---	---
RBM9	23543	broad.mit.edu	37	22	36290684	36290684	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36290684delA	uc003aon.3	-						RBM9_uc010gwu.2_Intron|RBM9_uc003aoo.3_Intron	NM_001082578	NP_001076047			RNA binding motif protein 9 isoform 5						estrogen receptor signaling pathway|mRNA processing|negative regulation of transcription, DNA-dependent|regulation of cell proliferation|RNA splicing	cytoplasm|nucleus	nucleotide binding|RNA binding|transcription corepressor activity|transcription factor binding				0																		---	---	---	---
MYH9	4627	broad.mit.edu	37	22	36714813	36714813	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36714813delT	uc003apg.2	-						MYH9_uc003aph.1_Intron	NM_002473	NP_002464			myosin, heavy polypeptide 9, non-muscle						actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape	actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity			breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1)	11								T	ALK	ALCL		Deafness|autosomal dominant 17|Epstein syndrome|Fechtner syndrome|May-Hegglin anomaly|Sebastian syndrome		Hereditary_Macrothrombocytopenia_MYH9-associated				---	---	---	---
MYH9	4627	broad.mit.edu	37	22	36742654	36742654	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36742654delT	uc003apg.2	-						MYH9_uc003api.1_Intron	NM_002473	NP_002464			myosin, heavy polypeptide 9, non-muscle						actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape	actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity			breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1)	11								T	ALK	ALCL		Deafness|autosomal dominant 17|Epstein syndrome|Fechtner syndrome|May-Hegglin anomaly|Sebastian syndrome		Hereditary_Macrothrombocytopenia_MYH9-associated				---	---	---	---
MYH9	4627	broad.mit.edu	37	22	36746959	36746959	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36746959delT	uc003apg.2	-						MYH9_uc003api.1_Intron	NM_002473	NP_002464			myosin, heavy polypeptide 9, non-muscle						actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape	actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity			breast(3)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|lung(1)|skin(1)|kidney(1)|pancreas(1)	11								T	ALK	ALCL		Deafness|autosomal dominant 17|Epstein syndrome|Fechtner syndrome|May-Hegglin anomaly|Sebastian syndrome		Hereditary_Macrothrombocytopenia_MYH9-associated				---	---	---	---
CACNG2	10369	broad.mit.edu	37	22	36963769	36963769	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36963769delT	uc003aps.1	-							NM_006078	NP_006069			voltage-dependent calcium channel gamma-2						membrane depolarization|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|endocytic vesicle membrane|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity				0																		---	---	---	---
CACNG2	10369	broad.mit.edu	37	22	37021969	37021969	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37021969delT	uc003aps.1	-							NM_006078	NP_006069			voltage-dependent calcium channel gamma-2						membrane depolarization|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|endocytic vesicle membrane|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	37236630	37236630	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37236630delA								PVALB (21113 upstream) : NCF4 (20400 downstream)																																			---	---	---	---
NCF4	4689	broad.mit.edu	37	22	37263152	37263153	+	Intron	INS	-	GT	GT	rs146306103	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37263152_37263153insGT	uc003apy.3	+						NCF4_uc003apz.3_Intron	NM_000631	NP_000622			neutrophil cytosolic factor 4 isoform 1						cell communication|immune response|oxidation-reduction process	cytosol|NADPH oxidase complex	phosphatidylinositol binding|protein dimerization activity			ovary(1)	1																		---	---	---	---
TMPRSS6	164656	broad.mit.edu	37	22	37468255	37468258	+	Intron	DEL	GATG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37468255_37468258delGATG	uc003aqs.1	-						TMPRSS6_uc003aqt.1_Intron	NM_153609	NP_705837			transmembrane protease, serine 6						angiogenesis|extracellular matrix organization|fibrinolysis|intracellular signal transduction|proteolysis	integral to membrane|intracellular|plasma membrane	serine-type endopeptidase activity			breast(4)|ovary(1)|skin(1)	6																		---	---	---	---
TMPRSS6	164656	broad.mit.edu	37	22	37470921	37470922	+	Intron	INS	-	AC	AC			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37470921_37470922insAC	uc003aqs.1	-						TMPRSS6_uc003aqt.1_Intron	NM_153609	NP_705837			transmembrane protease, serine 6						angiogenesis|extracellular matrix organization|fibrinolysis|intracellular signal transduction|proteolysis	integral to membrane|intracellular|plasma membrane	serine-type endopeptidase activity			breast(4)|ovary(1)|skin(1)	6																		---	---	---	---
TMPRSS6	164656	broad.mit.edu	37	22	37471557	37471558	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37471557_37471558delAA	uc003aqs.1	-						TMPRSS6_uc003aqt.1_Intron	NM_153609	NP_705837			transmembrane protease, serine 6						angiogenesis|extracellular matrix organization|fibrinolysis|intracellular signal transduction|proteolysis	integral to membrane|intracellular|plasma membrane	serine-type endopeptidase activity			breast(4)|ovary(1)|skin(1)	6																		---	---	---	---
TMPRSS6	164656	broad.mit.edu	37	22	37496454	37496455	+	Intron	INS	-	G	G	rs149146010	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37496454_37496455insG	uc003aqs.1	-						TMPRSS6_uc003aqt.1_Intron|TMPRSS6_uc003aqu.2_Intron	NM_153609	NP_705837			transmembrane protease, serine 6						angiogenesis|extracellular matrix organization|fibrinolysis|intracellular signal transduction|proteolysis	integral to membrane|intracellular|plasma membrane	serine-type endopeptidase activity			breast(4)|ovary(1)|skin(1)	6																		---	---	---	---
CYTH4	27128	broad.mit.edu	37	22	37682149	37682151	+	Intron	DEL	GGT	-	-	rs146828966	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37682149_37682151delGGT	uc003arf.2	+						CYTH4_uc003ard.3_Intron|CYTH4_uc003are.2_Intron|CYTH4_uc011amw.1_Intron|CYTH4_uc010gxe.2_Intron	NM_013385	NP_037517			cytohesin 4						regulation of ARF protein signal transduction|regulation of cell adhesion	cytoplasm|plasma membrane	ARF guanyl-nucleotide exchange factor activity			ovary(2)	2																		---	---	---	---
CARD10	29775	broad.mit.edu	37	22	37897444	37897445	+	Intron	INS	-	A	A	rs140768331	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37897444_37897445insA	uc003asx.1	-						CARD10_uc003ast.1_Intron|CARD10_uc003asw.1_Intron|CARD10_uc003asy.1_Intron	NM_014550	NP_055365			caspase recruitment domain protein 10						activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis	CBM complex	receptor signaling complex scaffold activity			upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1)	6	Melanoma(58;0.0574)																	---	---	---	---
Unknown	0	broad.mit.edu	37	22	37984040	37984040	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37984040delC								LGALS2 (8016 upstream) : GGA1 (20463 downstream)																																			---	---	---	---
TRIOBP	11078	broad.mit.edu	37	22	38103429	38103429	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38103429delT	uc003atr.2	+						TRIOBP_uc003atu.2_Intron|TRIOBP_uc003atq.1_Intron|TRIOBP_uc003ats.1_Intron	NM_001039141	NP_001034230			TRIO and F-actin binding protein isoform 6						actin modification|barbed-end actin filament capping	actin cytoskeleton|cytoplasm|nucleus	actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding			central_nervous_system(1)	1	Melanoma(58;0.0574)																	---	---	---	---
TRIOBP	11078	broad.mit.edu	37	22	38132293	38132294	+	Intron	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38132293_38132294delCT	uc003atr.2	+						TRIOBP_uc003atu.2_Intron	NM_001039141	NP_001034230			TRIO and F-actin binding protein isoform 6						actin modification|barbed-end actin filament capping	actin cytoskeleton|cytoplasm|nucleus	actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding			central_nervous_system(1)	1	Melanoma(58;0.0574)																	---	---	---	---
Unknown	0	broad.mit.edu	37	22	38473599	38473599	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38473599delG								PICK1 (1892 upstream) : SLC16A8 (546 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	38581068	38581068	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38581068delT								PLA2G6 (3232 upstream) : MAFF (16871 downstream)																																			---	---	---	---
CSNK1E	1454	broad.mit.edu	37	22	38742235	38742235	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38742235delA	uc003avm.1	-						LOC400927_uc010gxm.2_Intron|LOC400927_uc011ans.1_Intron	NM_152221	NP_689407			casein kinase 1 epsilon						DNA repair|G2/M transition of mitotic cell cycle|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|signal transduction	cytosol|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(1)|lung(1)|central_nervous_system(1)	3	Melanoma(58;0.045)																	---	---	---	---
CBY1	25776	broad.mit.edu	37	22	39064376	39064376	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39064376delT	uc003awb.2	+						CBY1_uc011any.1_Intron|CBY1_uc003awc.2_Intron	NM_001002880	NP_001002880			PKD2 interactor, golgi and endoplasmic reticulum						cardiac muscle cell differentiation|fat cell differentiation|negative regulation of transcription, DNA-dependent|protein localization	nuclear speck|trans-Golgi network	beta-catenin binding|identical protein binding			ovary(1)	1	Melanoma(58;0.04)																	---	---	---	---
GTPBP1	9567	broad.mit.edu	37	22	39103781	39103782	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39103781_39103782insA	uc003awg.2	+							NM_004286	NP_004277			GTP binding protein 1						immune response|positive regulation of mRNA catabolic process|signal transduction	cytoplasmic exosome (RNase complex)|cytosol	GTP binding|GTPase activity			ovary(1)	1	Melanoma(58;0.04)																	---	---	---	---
DNAL4	10126	broad.mit.edu	37	22	39174876	39174876	+	3'UTR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39174876delG	uc003awj.2	-	4					SUN2_uc010gxr.1_Intron	NM_005740	NP_005731			dynein light chain 4, axonemal						microtubule-based movement|nerve growth factor receptor signaling pathway	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule|plasma membrane	ATPase activity, coupled|microtubule motor activity				0	Melanoma(58;0.04)																	---	---	---	---
Unknown	0	broad.mit.edu	37	22	39210299	39210299	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39210299delT								SUN2 (20138 upstream) : NPTXR (4159 downstream)																																			---	---	---	---
APOBEC3A	200315	broad.mit.edu	37	22	39354337	39354339	+	Intron	DEL	TTC	-	-	rs139583460	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39354337_39354339delTTC	uc003awn.2	+						APOBEC3A_uc011aob.1_Intron|APOBEC3A_uc011aoc.1_Intron	NM_145699	NP_663745			phorbolin 1						cellular response to xenobiotic stimulus|defense response to virus|DNA cytosine deamination|DNA demethylation|innate immune response|negative regulation of transposition|negative regulation of viral genome replication	cytoplasm|nucleus	cytidine deaminase activity|zinc ion binding			ovary(1)	1	Melanoma(58;0.04)																	---	---	---	---
PDGFB	5155	broad.mit.edu	37	22	39622076	39622076	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39622076delG	uc003axf.2	-						PDGFB_uc003axe.2_Intron	NM_002608	NP_002599			platelet-derived growth factor beta isoform 1						activation of protein kinase B activity|cellular response to mycophenolic acid|embryonic placenta development|heart development|hemopoiesis|metanephric glomerular mesangial cell development|monocyte chemotaxis|negative regulation of phosphatidylinositol biosynthetic process|negative regulation of platelet activation|negative regulation of transcription, DNA-dependent|paracrine signaling|peptidyl-serine phosphorylation|peptidyl-tyrosine phosphorylation|platelet activation|platelet degranulation|positive regulation of blood vessel endothelial cell migration|positive regulation of calcium ion import|positive regulation of cell division|positive regulation of chemotaxis|positive regulation of cyclin-dependent protein kinase activity|positive regulation of DNA biosynthetic process|positive regulation of DNA replication|positive regulation of endothelial cell proliferation|positive regulation of ERK1 and ERK2 cascade|positive regulation of fibroblast proliferation|positive regulation of glomerular filtration|positive regulation of glomerular mesangial cell proliferation|positive regulation of MAP kinase activity|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway|positive regulation of mitosis|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein autophosphorylation|positive regulation of protein tyrosine kinase activity|positive regulation of reactive oxygen species metabolic process|positive regulation of smooth muscle cell migration|positive regulation of smooth muscle cell proliferation|positive regulation of transcription, DNA-dependent|reactive oxygen species metabolic process|transforming growth factor beta receptor signaling pathway	basolateral plasma membrane|cell surface|endoplasmic reticulum lumen|extracellular region|Golgi membrane|platelet alpha granule lumen	collagen binding|eukaryotic cell surface binding|growth factor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein heterodimerization activity|protein homodimerization activity|superoxide-generating NADPH oxidase activator activity		COL1A1/PDGFB(372)	soft_tissue(372)|central_nervous_system(1)	373	Melanoma(58;0.04)				Becaplermin(DB00102)			T	COL1A1	DFSP								---	---	---	---
Unknown	0	broad.mit.edu	37	22	39672573	39672573	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39672573delC								PDGFB (31616 upstream) : RPL3 (36315 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	39696410	39696411	+	IGR	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39696410_39696411insC								PDGFB (55453 upstream) : RPL3 (12477 downstream)																																			---	---	---	---
SMCR7L	54471	broad.mit.edu	37	22	39908658	39908658	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39908658delT	uc003axx.2	+						SMCR7L_uc003axw.2_Intron|SMCR7L_uc010gxz.1_Intron|SMCR7L_uc003axy.2_Intron	NM_019008	NP_061881			hypothetical protein LOC54471							integral to membrane|mitochondrion				central_nervous_system(1)	1	Melanoma(58;0.04)																	---	---	---	---
TNRC6B	23112	broad.mit.edu	37	22	40574037	40574037	+	5'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40574037delA	uc011aor.1	+	1					TNRC6B_uc003aym.2_Intron|TNRC6B_uc003ayn.3_5'UTR	NM_001162501	NP_001155973			trinucleotide repeat containing 6B isoform 1						gene silencing by RNA|regulation of translation	cytoplasmic mRNA processing body	nucleotide binding|RNA binding				0																		---	---	---	---
TNRC6B	23112	broad.mit.edu	37	22	40593293	40593293	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40593293delT	uc011aor.1	+						TNRC6B_uc003aym.2_Intron|TNRC6B_uc003ayn.3_Intron	NM_001162501	NP_001155973			trinucleotide repeat containing 6B isoform 1						gene silencing by RNA|regulation of translation	cytoplasmic mRNA processing body	nucleotide binding|RNA binding				0																		---	---	---	---
TNRC6B	23112	broad.mit.edu	37	22	40684549	40684551	+	Intron	DEL	TTT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40684549_40684551delTTT	uc011aor.1	+						TNRC6B_uc003aym.2_Intron|TNRC6B_uc003ayn.3_Intron|TNRC6B_uc003ayo.2_Intron	NM_001162501	NP_001155973			trinucleotide repeat containing 6B isoform 1						gene silencing by RNA|regulation of translation	cytoplasmic mRNA processing body	nucleotide binding|RNA binding				0																		---	---	---	---
TNRC6B	23112	broad.mit.edu	37	22	40708460	40708460	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40708460delT	uc011aor.1	+						TNRC6B_uc003aym.2_Intron|TNRC6B_uc003ayn.3_Intron|TNRC6B_uc003ayo.2_Intron	NM_001162501	NP_001155973			trinucleotide repeat containing 6B isoform 1						gene silencing by RNA|regulation of translation	cytoplasmic mRNA processing body	nucleotide binding|RNA binding				0																		---	---	---	---
MKL1	57591	broad.mit.edu	37	22	40806782	40806782	+	3'UTR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40806782delC	uc003ayv.1	-	12					MKL1_uc003ayw.1_3'UTR|MKL1_uc010gye.1_3'UTR|MKL1_uc010gyf.1_3'UTR	NM_020831	NP_065882			megakaryoblastic leukemia 1 protein						positive regulation of transcription from RNA polymerase II promoter|smooth muscle cell differentiation|transcription, DNA-dependent	cytoplasm|nucleus	actin monomer binding|leucine zipper domain binding|nucleic acid binding|transcription coactivator activity			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5								T	RBM15	acute megakaryocytic leukemia								---	---	---	---
MKL1	57591	broad.mit.edu	37	22	40961557	40961557	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40961557delA	uc003ayw.1	-						MKL1_uc010gye.1_Intron|MKL1_uc010gyf.1_Intron|MKL1_uc003ayy.1_Intron	NM_020831	NP_065882			megakaryoblastic leukemia 1 protein						positive regulation of transcription from RNA polymerase II promoter|smooth muscle cell differentiation|transcription, DNA-dependent	cytoplasm|nucleus	actin monomer binding|leucine zipper domain binding|nucleic acid binding|transcription coactivator activity			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5								T	RBM15	acute megakaryocytic leukemia								---	---	---	---
Unknown	0	broad.mit.edu	37	22	41150543	41150543	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41150543delA								MCHR1 (71726 upstream) : SLC25A17 (15098 downstream)																																			---	---	---	---
SLC25A17	10478	broad.mit.edu	37	22	41190622	41190622	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41190622delA	uc003azc.2	-						SLC25A17_uc010gyg.2_Intron|SLC25A17_uc011aou.1_Intron|SLC25A17_uc003azd.2_Intron|SLC25A17_uc011aov.1_Intron	NM_006358	NP_006349			solute carrier family 25 (mitochondrial carrier;						fatty acid alpha-oxidation	integral to plasma membrane|mitochondrial inner membrane|peroxisomal membrane	adenine nucleotide transmembrane transporter activity|protein binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	41381588	41381588	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41381588delA								RBX1 (12922 upstream) : MIR1281 (106929 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	41431905	41431906	+	IGR	INS	-	A	A	rs145611631	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41431905_41431906insA								RBX1 (63239 upstream) : MIR1281 (56611 downstream)																																			---	---	---	---
RANGAP1	5905	broad.mit.edu	37	22	41672684	41672684	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41672684delA	uc003azs.2	-						RANGAP1_uc003azt.2_Intron|RANGAP1_uc003azu.2_Intron|RANGAP1_uc011aoz.1_Intron	NM_002883	NP_002874			Ran GTPase activating protein 1						mitotic prometaphase|signal transduction	condensed chromosome kinetochore|cytosol|nuclear membrane|nuclear pore|soluble fraction|spindle pole	protein binding|Ran GTPase activator activity				0																		---	---	---	---
ZC3H7B	23264	broad.mit.edu	37	22	41720075	41720076	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41720075_41720076delAA	uc003azw.2	+						ZC3H7B_uc003azv.1_Intron|ZC3H7B_uc010gyl.1_Intron	NM_017590	NP_060060			zinc finger CCCH-type containing 7B						interspecies interaction between organisms	nucleus	nucleic acid binding|protein binding|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	41800526	41800527	+	IGR	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41800526_41800527insA								TEF (5198 upstream) : TOB2 (28965 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	41851716	41851716	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41851716delA								TOB2 (8689 upstream) : PHF5A (4006 downstream)																																			---	---	---	---
CSDC2	27254	broad.mit.edu	37	22	41961164	41961164	+	Intron	DEL	A	-	-	rs34446853		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41961164delA	uc003bak.1	+							NM_014460	NP_055275			RNA-binding protein pippin						histone mRNA 3'-end processing|regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding|RNA binding				0																		---	---	---	---
MEI1	150365	broad.mit.edu	37	22	42105620	42105620	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42105620delT	uc003baz.1	+						MEI1_uc003bay.3_Intron|MEI1_uc011apd.1_Intron	NM_152513	NP_689726			meiosis defective 1								binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	42626649	42626650	+	IGR	DEL	AA	-	-	rs67137457		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42626649_42626650delAA								TCF20 (15204 upstream) : NFAM1 (149765 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	42892830	42892830	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42892830delA								NFAM1 (64429 upstream) : SERHL (3755 downstream)																																			---	---	---	---
SERHL	94009	broad.mit.edu	37	22	42905257	42905257	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42905257delC	uc011apm.1	+						SERHL_uc011apl.1_Intron					RecName: Full=Serine hydrolase-like protein;          EC=3.1.-.-;												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	43014731	43014731	+	IGR	DEL	A	-	-	rs28602842		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43014731delA								POLDIP3 (3769 upstream) : CYB5R3 (83 downstream)																																			---	---	---	---
ARFGAP3	26286	broad.mit.edu	37	22	43216681	43216681	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43216681delA	uc003bdd.2	-						ARFGAP3_uc010gzf.2_Intron|ARFGAP3_uc011apu.1_Intron	NM_014570	NP_055385			ADP-ribosylation factor GTPase activating						intracellular protein transport|protein secretion|regulation of ARF GTPase activity|vesicle-mediated transport	cytosol|Golgi membrane	ARF GTPase activator activity|protein transporter activity|zinc ion binding			breast(1)	1																OREG0026610	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
BIK	638	broad.mit.edu	37	22	43509624	43509624	+	Intron	DEL	T	-	-	rs71670982		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43509624delT	uc003bdk.2	+							NM_001197	NP_001188			BCL2-interacting killer						apoptosis|induction of apoptosis|positive regulation of protein homooligomerization|positive regulation of release of cytochrome c from mitochondria	endomembrane system|integral to membrane					0		Ovarian(80;0.0694)																---	---	---	---
SCUBE1	80274	broad.mit.edu	37	22	43641384	43641384	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43641384delG	uc003bdt.1	-						SCUBE1_uc003bdu.1_Intron	NM_173050	NP_766638			signal peptide, CUB domain, EGF-like 1						adult heart development|blood coagulation|endothelial cell differentiation|inflammatory response|post-embryonic development|protein homooligomerization	external side of plasma membrane|extracellular space|extrinsic to plasma membrane	calcium ion binding|identical protein binding|protein heterodimerization activity			central_nervous_system(2)|ovary(1)|lung(1)|skin(1)	5		all_neural(38;0.0414)|Ovarian(80;0.07)																---	---	---	---
MPPED1	758	broad.mit.edu	37	22	43834583	43834584	+	Intron	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43834583_43834584delTC	uc011apv.1	+						MPPED1_uc011apw.1_Intron|MPPED1_uc011apx.1_Intron|MPPED1_uc011apy.1_Intron|MPPED1_uc011apz.1_Intron	NM_001044370	NP_001037835			metallophosphoesterase domain containing 1								hydrolase activity				0		all_neural(38;0.0244)|Ovarian(80;0.0694)																---	---	---	---
Unknown	0	broad.mit.edu	37	22	44213730	44213730	+	IGR	DEL	A	-	-	rs142988801		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44213730delA								EFCAB6 (5612 upstream) : SULT4A1 (6657 downstream)																																			---	---	---	---
PNPLA3	80339	broad.mit.edu	37	22	44317000	44317001	+	5'Flank	DEL	GA	-	-	rs36045052		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44317000_44317001delGA	uc003bei.1	+						PNPLA3_uc010gzm.1_5'Flank	NM_025225	NP_079501			patatin-like phospholipase domain containing 3						triglyceride biosynthetic process|triglyceride catabolic process	integral to membrane	diolein transacylation activity|mono-olein transacylation activity|phospholipase A2 activity|triglyceride lipase activity				0		Ovarian(80;0.024)|all_neural(38;0.0416)																---	---	---	---
PARVB	29780	broad.mit.edu	37	22	44395568	44395568	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44395568delA	uc003bem.2	+							NM_001003828	NP_001003828			parvin, beta isoform a						cell adhesion|cell junction assembly	cytoskeleton|cytosol|focal adhesion	actin binding				0		Ovarian(80;0.0246)|all_neural(38;0.0423)																---	---	---	---
PARVB	29780	broad.mit.edu	37	22	44432929	44432929	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44432929delA	uc003ben.2	+						PARVB_uc003bem.2_Intron|PARVB_uc010gzn.2_Intron	NM_013327	NP_037459			parvin, beta isoform b						cell adhesion|cell junction assembly	cytoskeleton|cytosol|focal adhesion	actin binding				0		Ovarian(80;0.0246)|all_neural(38;0.0423)																---	---	---	---
PARVB	29780	broad.mit.edu	37	22	44542173	44542174	+	Intron	INS	-	CA	CA	rs148878216	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44542173_44542174insCA	uc003ben.2	+						PARVB_uc003bem.2_Intron|PARVB_uc010gzn.2_Intron|PARVB_uc003beo.2_Intron	NM_013327	NP_037459			parvin, beta isoform b						cell adhesion|cell junction assembly	cytoskeleton|cytosol|focal adhesion	actin binding				0		Ovarian(80;0.0246)|all_neural(38;0.0423)																---	---	---	---
Unknown	0	broad.mit.edu	37	22	44604074	44604074	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44604074delA								PARVG (1040 upstream) : KIAA1644 (35483 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	44976431	44976431	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44976431delG								NCRNA00207 (8102 upstream) : PRR5 (88162 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	45027274	45027274	+	IGR	DEL	A	-	-	rs113216958		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45027274delA								NCRNA00207 (58945 upstream) : PRR5 (37319 downstream)																																			---	---	---	---
PRR5-ARHGAP8	553158	broad.mit.edu	37	22	45157846	45157846	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45157846delC	uc003bfd.2	+						PRR5-ARHGAP8_uc003bfc.2_Intron|PRR5-ARHGAP8_uc011aqi.1_Intron|PRR5-ARHGAP8_uc011aqj.1_Intron|ARHGAP8_uc003bfi.2_Intron|ARHGAP8_uc010gzv.2_Intron|ARHGAP8_uc003bfj.2_Intron|ARHGAP8_uc003bfk.2_Intron|PRR5-ARHGAP8_uc003bfg.1_Intron	NM_181335	NP_851852			Rho GTPase activating protein 8 isoform 2											skin(2)	2																		---	---	---	---
PHF21B	112885	broad.mit.edu	37	22	45373445	45373447	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45373445_45373447delAAA	uc003bfn.2	-						PHF21B_uc003bfm.2_Intron|PHF21B_uc011aqk.1_Intron|PHF21B_uc011aql.1_Intron|PHF21B_uc011aqm.1_Intron	NM_138415	NP_612424			PHD finger protein 21B isoform 1								zinc ion binding			ovary(2)|skin(1)	3		all_neural(38;0.00802)|Glioma(61;0.0353)|Ovarian(80;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0203)														---	---	---	---
Unknown	0	broad.mit.edu	37	22	45538412	45538421	+	Intron	DEL	CACACACGCG	-	-	rs517149	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45538412_45538421delCACACACGCG	uc003bfp.1	-						uc003bfq.2_Intron					Homo sapiens, clone IMAGE:5228959, mRNA.																														---	---	---	---
UPK3A	7380	broad.mit.edu	37	22	45682631	45682633	+	Intron	DEL	AGA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45682631_45682633delAGA	uc003bfy.2	+						UPK3A_uc010gzy.2_Intron	NM_006953	NP_008884			uroplakin 3A precursor						epithelial cell differentiation	endoplasmic reticulum membrane|integral to membrane					0		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)														---	---	---	---
Unknown	0	broad.mit.edu	37	22	45867281	45867282	+	IGR	DEL	CT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45867281_45867282delCT								RIBC2 (38988 upstream) : FBLN1 (31437 downstream)																																			---	---	---	---
FBLN1	2192	broad.mit.edu	37	22	45939157	45939157	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45939157delA	uc003bgj.1	+						FBLN1_uc003bgg.1_Intron|FBLN1_uc003bgh.2_Intron|FBLN1_uc010gzz.2_Intron|FBLN1_uc003bgi.1_Intron	NM_006486	NP_006477			fibulin 1 isoform D						interspecies interaction between organisms	extracellular space|soluble fraction	calcium ion binding|extracellular matrix structural constituent|protein binding			ovary(1)|central_nervous_system(1)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)														---	---	---	---
FBLN1	2192	broad.mit.edu	37	22	45952328	45952329	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45952328_45952329delTT	uc003bgj.1	+						FBLN1_uc003bgg.1_Intron|FBLN1_uc003bgh.2_Intron|FBLN1_uc010gzz.2_Intron|FBLN1_uc003bgi.1_Intron	NM_006486	NP_006477			fibulin 1 isoform D						interspecies interaction between organisms	extracellular space|soluble fraction	calcium ion binding|extracellular matrix structural constituent|protein binding			ovary(1)|central_nervous_system(1)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)														---	---	---	---
ATXN10	25814	broad.mit.edu	37	22	46090664	46090664	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46090664delA	uc003bgm.1	+						ATXN10_uc011aqt.1_Intron|ATXN10_uc003bgn.1_Intron	NM_013236	NP_037368			ataxin 10						cell death|neuron projection development	dendrite|neuronal cell body|perinuclear region of cytoplasm				ovary(1)|kidney(1)	2		Ovarian(80;0.00973)|all_neural(38;0.0417)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0223)														---	---	---	---
ATXN10	25814	broad.mit.edu	37	22	46159642	46159642	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46159642delA	uc003bgm.1	+						ATXN10_uc011aqt.1_Intron|ATXN10_uc003bgn.1_Intron	NM_013236	NP_037368			ataxin 10						cell death|neuron projection development	dendrite|neuronal cell body|perinuclear region of cytoplasm				ovary(1)|kidney(1)	2		Ovarian(80;0.00973)|all_neural(38;0.0417)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0223)														---	---	---	---
Unknown	0	broad.mit.edu	37	22	46256786	46256786	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46256786delG								ATXN10 (15957 upstream) : WNT7B (59462 downstream)																																			---	---	---	---
LOC400931	400931	broad.mit.edu	37	22	46484518	46484518	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46484518delT	uc003bgr.3	+						LOC400931_uc003bgu.2_Intron|LOC400931_uc003bgt.3_Intron					SubName: Full=FLJ27365 protein, isoform CRA_a; SubName: Full=Novel transcript;												0																		---	---	---	---
CELSR1	9620	broad.mit.edu	37	22	46796229	46796229	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46796229delA	uc003bhw.1	-						CELSR1_uc011arc.1_Intron	NM_014246	NP_055061			cadherin EGF LAG seven-pass G-type receptor 1						central nervous system development|homophilic cell adhesion|neural tube closure|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein dimerization activity			lung(4)|breast(4)|pancreas(2)|skin(1)	11		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)														---	---	---	---
CELSR1	9620	broad.mit.edu	37	22	46809948	46809948	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46809948delA	uc003bhw.1	-							NM_014246	NP_055061			cadherin EGF LAG seven-pass G-type receptor 1						central nervous system development|homophilic cell adhesion|neural tube closure|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein dimerization activity			lung(4)|breast(4)|pancreas(2)|skin(1)	11		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)														---	---	---	---
CELSR1	9620	broad.mit.edu	37	22	46882936	46882941	+	Intron	DEL	CACTCC	-	-	rs66729539		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46882936_46882941delCACTCC	uc003bhw.1	-							NM_014246	NP_055061			cadherin EGF LAG seven-pass G-type receptor 1						central nervous system development|homophilic cell adhesion|neural tube closure|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein dimerization activity			lung(4)|breast(4)|pancreas(2)|skin(1)	11		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)														---	---	---	---
GRAMD4	23151	broad.mit.edu	37	22	47068576	47068576	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47068576delG	uc003bhx.2	+						GRAMD4_uc010had.2_Intron|GRAMD4_uc003bhy.2_5'Flank	NM_015124	NP_055939			death-inducing-protein						apoptosis	integral to membrane|mitochondrial membrane				ovary(1)	1		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|BRCA - Breast invasive adenocarcinoma(115;0.166)														---	---	---	---
CERK	64781	broad.mit.edu	37	22	47085434	47085435	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47085434_47085435insT	uc003bia.2	-						CERK_uc010hae.2_Intron	NM_022766	NP_073603			ceramide kinase						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|ceramide metabolic process	integral to membrane of membrane fraction|membrane|nucleus	ATP binding|ceramide kinase activity|diacylglycerol kinase activity|magnesium ion binding			skin(1)	1		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)|BRCA - Breast invasive adenocarcinoma(115;0.171)														---	---	---	---
Unknown	0	broad.mit.edu	37	22	47154314	47154315	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47154314_47154315insT								CERK (20162 upstream) : TBC1D22A (4234 downstream)																																			---	---	---	---
TBC1D22A	25771	broad.mit.edu	37	22	47348235	47348237	+	Intron	DEL	TTC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47348235_47348237delTTC	uc003bib.2	+						TBC1D22A_uc010haf.2_Intron|TBC1D22A_uc003bic.2_Intron|TBC1D22A_uc003bie.2_Intron|TBC1D22A_uc003bid.2_Intron|TBC1D22A_uc010hag.2_Intron|TBC1D22A_uc003bif.2_Intron	NM_014346	NP_055161			TBC1 domain family, member 22A							intracellular	protein homodimerization activity|Rab GTPase activator activity			ovary(1)	1		all_cancers(38;4.44e-05)|all_epithelial(38;0.000507)|Breast(42;0.0488)|all_lung(38;0.0682)|Ovarian(80;0.0731)|all_neural(38;0.0966)|Glioma(61;0.222)|Lung SC(80;0.236)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0347)|BRCA - Breast invasive adenocarcinoma(115;0.231)														---	---	---	---
Unknown	0	broad.mit.edu	37	22	48013463	48013463	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48013463delA								TBC1D22A (443741 upstream) : FAM19A5 (871825 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	48390049	48390050	+	IGR	INS	-	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48390049_48390050insG								TBC1D22A (820327 upstream) : FAM19A5 (495238 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	48492313	48492314	+	IGR	INS	-	G	G	rs145694638	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48492313_48492314insG								TBC1D22A (922591 upstream) : FAM19A5 (392974 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	48761059	48761059	+	IGR	DEL	A	-	-	rs67488850		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:48761059delA								None (None upstream) : FAM19A5 (124229 downstream)																																			---	---	---	---
FAM19A5	25817	broad.mit.edu	37	22	49142415	49142415	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49142415delG	uc003bim.3	+						FAM19A5_uc003bio.3_Intron	NM_001082967	NP_001076436			family with sequence similarity 19 (chemokine							extracellular region|integral to membrane				large_intestine(1)	1		all_cancers(38;2.95e-11)|all_epithelial(38;3.07e-10)|all_lung(38;2.89e-05)|Breast(42;0.000396)|Lung NSC(38;0.000471)|Ovarian(80;0.00934)|Lung SC(80;0.195)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0227)|BRCA - Breast invasive adenocarcinoma(115;0.119)														---	---	---	---
Unknown	0	broad.mit.edu	37	22	49446283	49446284	+	IGR	DEL	AT	-	-	rs34164031		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49446283_49446284delAT								FAM19A5 (298541 upstream) : C22orf34 (361892 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	49473542	49473542	+	IGR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49473542delG								FAM19A5 (325800 upstream) : C22orf34 (334634 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	49613447	49613447	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49613447delA								FAM19A5 (465705 upstream) : C22orf34 (194729 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	22	49700848	49700848	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49700848delA								FAM19A5 (553106 upstream) : C22orf34 (107328 downstream)																																			---	---	---	---
C22orf34	348645	broad.mit.edu	37	22	49869542	49869542	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49869542delT	uc003biq.2	-											Homo sapiens cDNA FLJ42972 fis, clone BRSTN2019129.												0																		---	---	---	---
C22orf34	348645	broad.mit.edu	37	22	49894333	49894335	+	Intron	DEL	CAT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49894333_49894335delCAT	uc003biq.2	-											Homo sapiens cDNA FLJ42972 fis, clone BRSTN2019129.												0																		---	---	---	---
C22orf34	348645	broad.mit.edu	37	22	49902218	49902218	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49902218delA	uc003biq.2	-											Homo sapiens cDNA FLJ42972 fis, clone BRSTN2019129.												0																		---	---	---	---
C22orf34	348645	broad.mit.edu	37	22	49973122	49973123	+	Intron	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:49973122_49973123delAC	uc003biq.2	-											Homo sapiens cDNA FLJ42972 fis, clone BRSTN2019129.												0																		---	---	---	---
TTLL8	164714	broad.mit.edu	37	22	50467576	50467577	+	Intron	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50467576_50467577insC	uc011ark.1	-							NM_001080447	NP_001073916			tubulin tyrosine ligase-like family, member 8											ovary(2)	2		all_cancers(38;3.44e-07)|all_epithelial(38;2.44e-06)|all_lung(38;0.00141)|Breast(42;0.00519)|Lung NSC(38;0.0199)|Ovarian(80;0.142)|Lung SC(80;0.162)		READ - Rectum adenocarcinoma(2;0.000882)|Colorectal(2;0.00311)|BRCA - Breast invasive adenocarcinoma(115;0.226)														---	---	---	---
TTLL8	164714	broad.mit.edu	37	22	50495750	50495767	+	5'Flank	DEL	GTCAGGTCTGGGTTGTGA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50495750_50495767delGTCAGGTCTGGGTTGTGA	uc011ark.1	-							NM_001080447	NP_001073916			tubulin tyrosine ligase-like family, member 8											ovary(2)	2		all_cancers(38;3.44e-07)|all_epithelial(38;2.44e-06)|all_lung(38;0.00141)|Breast(42;0.00519)|Lung NSC(38;0.0199)|Ovarian(80;0.142)|Lung SC(80;0.162)		READ - Rectum adenocarcinoma(2;0.000882)|Colorectal(2;0.00311)|BRCA - Breast invasive adenocarcinoma(115;0.226)														---	---	---	---
TRABD	80305	broad.mit.edu	37	22	50626111	50626111	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50626111delA	uc003bjq.1	+						TRABD_uc003bjr.1_Intron|TRABD_uc003bjs.1_Intron|TRABD_uc003bjt.1_Intron|TRABD_uc003bju.1_5'Flank	NM_025204	NP_079480			TraB domain containing												0		all_cancers(38;1.07e-07)|all_epithelial(38;9.6e-07)|all_lung(38;0.00141)|Breast(42;0.00387)|Lung NSC(38;0.0199)|Ovarian(80;0.142)|Lung SC(80;0.162)		LUAD - Lung adenocarcinoma(64;0.105)														---	---	---	---
TUBGCP6	85378	broad.mit.edu	37	22	50656444	50656444	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50656444delC	uc003bkb.1	-	24	5783	c.5271delG	c.(5269-5271)GGGfs	p.G1757fs	TUBGCP6_uc003bka.1_Frame_Shift_Del_p.G827fs|TUBGCP6_uc010har.1_Frame_Shift_Del_p.G1749fs|TUBGCP6_uc010has.1_RNA	NM_020461	NP_065194	Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	1757					G2/M transition of mitotic cell cycle|microtubule nucleation	centrosome|cytosol|gamma-tubulin ring complex|microtubule|spindle pole	microtubule binding			ovary(2)|central_nervous_system(2)	4		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)														---	---	---	---
MAPK12	6300	broad.mit.edu	37	22	50689168	50689168	+	3'UTR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50689168delC	uc003bkl.1	-	11					HDAC10_uc003bke.2_Intron|HDAC10_uc003bkf.2_Intron|HDAC10_uc003bkg.2_Intron|HDAC10_uc010hav.2_Intron|HDAC10_uc003bkh.2_Intron|HDAC10_uc003bki.2_Intron|HDAC10_uc003bkj.2_Intron|HDAC10_uc003bkk.1_5'Flank|MAPK12_uc003bkn.2_3'UTR|MAPK12_uc003bko.2_3'UTR	NM_002969	NP_002960			mitogen-activated protein kinase 12						cell cycle arrest|DNA damage induced protein phosphorylation|muscle organ development|myoblast differentiation|nerve growth factor receptor signaling pathway|positive regulation of muscle cell differentiation|Ras protein signal transduction	mitochondrion|nucleoplasm	ATP binding|magnesium ion binding|MAP kinase activity|protein binding				0		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)														---	---	---	---
CPT1B	1375	broad.mit.edu	37	22	51010856	51010856	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:51010856delT	uc003bmk.3	-						CPT1B_uc003bml.2_Intron|CPT1B_uc003bmm.2_Intron|CPT1B_uc003bmo.2_Intron|CPT1B_uc011asa.1_Intron|CPT1B_uc003bmn.2_Intron|CPT1B_uc011asb.1_Intron|CHKB-CPT1B_uc003bmp.2_Intron|uc003bmr.1_RNA	NM_001145137	NP_001138609			carnitine palmitoyltransferase 1B isoform a						carnitine shuttle|fatty acid beta-oxidation|regulation of fatty acid oxidation	integral to membrane|mitochondrial outer membrane	carnitine O-palmitoyltransferase activity			ovary(1)|central_nervous_system(1)	2		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		all cancers(3;3.56e-77)|OV - Ovarian serous cystadenocarcinoma(4;5.39e-74)|Epithelial(4;5.58e-70)|GBM - Glioblastoma multiforme(4;5.59e-08)|LUAD - Lung adenocarcinoma(64;0.0016)|Lung(4;0.00942)|BRCA - Breast invasive adenocarcinoma(115;0.207)														---	---	---	---
SHANK3	85358	broad.mit.edu	37	22	51147577	51147578	+	Intron	DEL	GA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:51147577_51147578delGA	uc003bne.1	+						SHANK3_uc003bnf.1_Intron	NM_001080420	NP_001073889			SH3 and multiple ankyrin repeat domains 3											central_nervous_system(1)	1		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)														---	---	---	---
Unknown	0	broad.mit.edu	37	X	287049	287049	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:287049delT								NCRNA00107 (4997 upstream) : PPP2R3B (7923 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	485038	485039	+	IGR	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:485038_485039delTC								PPP2R3B (137411 upstream) : SHOX (100040 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	495401	495401	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:495401delT								PPP2R3B (147774 upstream) : SHOX (89678 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	521619	521620	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:521619_521620delTT								PPP2R3B (173992 upstream) : SHOX (63459 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	728944	728945	+	IGR	DEL	AC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:728944_728945delAC								SHOX (108799 upstream) : CRLF2 (585942 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	872648	872648	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:872648delT								SHOX (252503 upstream) : CRLF2 (442239 downstream)																																			---	---	---	---
IL3RA	3563	broad.mit.edu	37	X	1479071	1479072	+	Intron	DEL	TC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1479071_1479072delTC	uc004cps.2	+						IL3RA_uc011mhd.1_Intron	NM_002183	NP_002174			interleukin 3 receptor, alpha precursor							integral to membrane|plasma membrane	interleukin-3 receptor activity			skin(2)|lung(1)	3		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Sargramostim(DB00020)													---	---	---	---
P2RY8	286530	broad.mit.edu	37	X	1592419	1592422	+	Intron	DEL	TGGA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1592419_1592422delTGGA	uc004cpz.2	-							NM_178129	NP_835230			G-protein coupled purinergic receptor P2Y8							integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			lung(5)	5		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)						T	CRLF2	B-ALL|Downs associated ALL								---	---	---	---
Unknown	0	broad.mit.edu	37	X	1696526	1696529	+	IGR	DEL	ATGG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1696526_1696529delATGG								P2RY8 (40489 upstream) : SFRS17A (13957 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	1701911	1701911	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1701911delA								P2RY8 (45874 upstream) : SFRS17A (8575 downstream)																																			---	---	---	---
ASMT	438	broad.mit.edu	37	X	1744516	1744517	+	Intron	DEL	AG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1744516_1744517delAG	uc004cqd.2	+						ASMT_uc010ncy.2_Intron|ASMT_uc004cqe.2_Intron	NM_004043	NP_004034			acetylserotonin O-methyltransferase						melatonin biosynthetic process|translation	cytosol	acetylserotonin O-methyltransferase activity|S-methyltransferase activity			skin(1)	1		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)																---	---	---	---
Unknown	0	broad.mit.edu	37	X	2053055	2053056	+	IGR	DEL	TG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2053055_2053056delTG								ASMT (291082 upstream) : DHRSX (84501 downstream)																																			---	---	---	---
DHRSX	207063	broad.mit.edu	37	X	2145720	2145720	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2145720delA	uc004cqf.3	-							NM_145177	NP_660160			dehydrogenase/reductase (SDR family) X-linked								binding|oxidoreductase activity				0		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)																---	---	---	---
DHRSX	207063	broad.mit.edu	37	X	2354701	2354701	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2354701delT	uc004cqf.3	-							NM_145177	NP_660160			dehydrogenase/reductase (SDR family) X-linked								binding|oxidoreductase activity				0		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)																---	---	---	---
PRKX	5613	broad.mit.edu	37	X	3573501	3573501	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:3573501delG	uc010nde.2	-							NM_005044	NP_005035			protein kinase, X-linked								ATP binding|cAMP-dependent protein kinase activity			skin(2)|lung(1)	3		all_lung(23;0.000396)|Lung NSC(23;0.00123)																---	---	---	---
Unknown	0	broad.mit.edu	37	X	5586515	5586516	+	IGR	DEL	TG	-	-	rs878251	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:5586515_5586516delTG								None (None upstream) : NLGN4X (221568 downstream)																																			---	---	---	---
HDHD1A	8226	broad.mit.edu	37	X	7023727	7023728	+	Frame_Shift_Ins	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:7023727_7023728insT	uc004crv.2	-	2	290_291	c.213_214insA	c.(211-216)AAAGAGfs	p.K71fs	HDHD1A_uc011mhm.1_Frame_Shift_Ins_p.K94fs|HDHD1A_uc011mhn.1_Intron|HDHD1A_uc010ndl.2_Frame_Shift_Ins_p.K71fs|HDHD1A_uc011mho.1_Frame_Shift_Ins_p.K71fs	NM_012080	NP_036212	Q08623	HDHD1_HUMAN	haloacid dehalogenase-like hydrolase domain	71_72					nucleotide metabolic process		metal ion binding|phosphatase activity				0		Colorectal(8;0.0114)|Medulloblastoma(8;0.184)																---	---	---	---
FAM9B	171483	broad.mit.edu	37	X	9000595	9000597	+	Intron	DEL	GGG	-	-	rs111614282		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9000595_9000597delGGG	uc011mhu.1	-						FAM9B_uc011mhv.1_Intron|FAM9B_uc004csh.2_Intron	NM_205849	NP_995321			family with sequence similarity 9, member B							nucleus					0		Hepatocellular(5;0.219)																---	---	---	---
TBL1X	6907	broad.mit.edu	37	X	9660309	9660309	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9660309delC	uc010ndq.2	+						TBL1X_uc004csq.3_Intron|TBL1X_uc010ndr.2_Intron|TBL1X_uc004csr.2_Intron|TBL1X_uc004css.2_Intron	NM_001139466	NP_001132938			transducin beta-like 1X isoform a						canonical Wnt receptor signaling pathway|cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|proteasomal ubiquitin-dependent protein catabolic process|sensory perception of sound|transcription, DNA-dependent	spindle microtubule|transcriptional repressor complex	beta-catenin binding|histone binding|protein C-terminus binding|protein domain specific binding|transcription corepressor activity|transcription factor binding|transcription regulatory region DNA binding			ovary(1)	1		Hepatocellular(5;0.000888)																---	---	---	---
OFD1	8481	broad.mit.edu	37	X	13787350	13787350	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13787350delT	uc004cvp.3	+	23					OFD1_uc004cvr.3_3'UTR|OFD1_uc011mil.1_3'UTR|OFD1_uc004cvq.3_3'UTR|OFD1_uc010nen.2_3'UTR|OFD1_uc004cvs.3_RNA|OFD1_uc004cvu.3_3'UTR|OFD1_uc004cvv.3_3'UTR	NM_003611	NP_003602			oral-facial-digital syndrome 1						cilium movement involved in determination of left/right asymmetry|G2/M transition of mitotic cell cycle	centriole|cilium|cytosol|microtubule basal body|nuclear membrane	alpha-tubulin binding|gamma-tubulin binding				0																		---	---	---	---
MOSPD2	158747	broad.mit.edu	37	X	14913296	14913296	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:14913296delT	uc004cwi.2	+						MOSPD2_uc004cwj.2_Intron	NM_152581	NP_689794			motile sperm domain containing 2							integral to membrane	structural molecule activity			lung(1)	1	Hepatocellular(33;0.183)																	---	---	---	---
TMEM27	57393	broad.mit.edu	37	X	15682932	15682933	+	5'UTR	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15682932_15682933delAA	uc004cxc.1	-	1						NM_020665	NP_065716			transmembrane protein 27 precursor						proteolysis	integral to membrane	metallopeptidase activity|peptidyl-dipeptidase activity			ovary(1)	1	Hepatocellular(33;0.183)																	---	---	---	---
RBBP7	5931	broad.mit.edu	37	X	16871713	16871713	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:16871713delA	uc004cxt.2	-						RBBP7_uc004cxs.1_Intron|RBBP7_uc004cxu.2_Intron|RBBP7_uc010nez.2_3'UTR	NM_002893	NP_002884			retinoblastoma binding protein 7						cell proliferation|cellular heat acclimation|CenH3-containing nucleosome assembly at centromere|DNA replication|multicellular organismal development|negative regulation of cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex|NuRD complex	protein binding			upper_aerodigestive_tract(1)|ovary(1)	2	Hepatocellular(33;0.0997)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	17999166	17999166	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:17999166delT								RAI2 (119709 upstream) : BEND2 (181887 downstream)																																			---	---	---	---
SCML2	10389	broad.mit.edu	37	X	18275161	18275161	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18275161delA	uc004cyl.2	-						SCML2_uc004cyk.3_Intron|SCML2_uc010nfd.1_Intron|SCML2_uc011miz.1_Intron|SCML2_uc010nfc.2_Intron	NM_006089	NP_006080			sex comb on midleg-like 2						anatomical structure morphogenesis	PcG protein complex	DNA binding|sequence-specific DNA binding transcription factor activity				0	Hepatocellular(33;0.183)																	---	---	---	---
CDKL5	6792	broad.mit.edu	37	X	18597856	18597856	+	Intron	DEL	A	-	-	rs12013924		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18597856delA	uc004cym.2	+						CDKL5_uc004cyn.2_Intron	NM_003159	NP_003150			cyclin-dependent kinase-like 5						neuron migration|positive regulation of axon extension|positive regulation of dendrite morphogenesis|positive regulation of Rac GTPase activity|protein autophosphorylation	dendrite cytoplasm|dendritic growth cone|nucleus	ATP binding|cyclin-dependent protein kinase activity|Rac GTPase binding			ovary(2)|large_intestine(1)|stomach(1)|central_nervous_system(1)|skin(1)	6	Hepatocellular(33;0.183)																	---	---	---	---
CDKL5	6792	broad.mit.edu	37	X	18665265	18665265	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18665265delT	uc004cym.2	+						CDKL5_uc004cyn.2_Intron|RS1_uc004cyo.2_Intron	NM_003159	NP_003150			cyclin-dependent kinase-like 5						neuron migration|positive regulation of axon extension|positive regulation of dendrite morphogenesis|positive regulation of Rac GTPase activity|protein autophosphorylation	dendrite cytoplasm|dendritic growth cone|nucleus	ATP binding|cyclin-dependent protein kinase activity|Rac GTPase binding			ovary(2)|large_intestine(1)|stomach(1)|central_nervous_system(1)|skin(1)	6	Hepatocellular(33;0.183)																	---	---	---	---
PPEF1	5475	broad.mit.edu	37	X	18748213	18748213	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18748213delT	uc004cyq.2	+						PPEF1_uc004cyp.2_Intron|PPEF1_uc004cyr.2_Intron|PPEF1_uc004cys.2_Intron|PPEF1_uc011mja.1_Intron|PPEF1_uc011mjb.1_5'Flank	NM_006240	NP_006231			protein phosphatase with EF hand calcium-binding						detection of stimulus involved in sensory perception|protein dephosphorylation		calcium ion binding|iron ion binding|manganese ion binding|protein binding|protein serine/threonine phosphatase activity				0	Hepatocellular(33;0.183)																	---	---	---	---
PPEF1	5475	broad.mit.edu	37	X	18800472	18800473	+	Intron	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18800472_18800473insT	uc004cyq.2	+						PPEF1_uc004cyp.2_Intron|PPEF1_uc004cyr.2_Intron|PPEF1_uc004cys.2_Intron|PPEF1_uc011mja.1_Intron|PPEF1_uc011mjb.1_Intron	NM_006240	NP_006231			protein phosphatase with EF hand calcium-binding						detection of stimulus involved in sensory perception|protein dephosphorylation		calcium ion binding|iron ion binding|manganese ion binding|protein binding|protein serine/threonine phosphatase activity				0	Hepatocellular(33;0.183)																	---	---	---	---
GPR64	10149	broad.mit.edu	37	X	19014281	19014281	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19014281delA	uc004cyx.2	-						GPR64_uc004cyy.2_Intron|GPR64_uc004cyz.2_Intron|GPR64_uc004czb.2_Intron|GPR64_uc004czc.2_Intron|GPR64_uc004czd.2_Intron|GPR64_uc004cze.2_Intron|GPR64_uc004czf.2_Intron|GPR64_uc004cza.2_Intron|GPR64_uc004cyw.2_Intron|GPR64_uc010nfj.2_Intron	NM_001079858	NP_001073327			G protein-coupled receptor 64 isoform 1						neuropeptide signaling pathway|spermatogenesis	cytoplasm|integral to plasma membrane	G-protein coupled receptor activity				0	Hepatocellular(33;0.183)																	---	---	---	---
GPR64	10149	broad.mit.edu	37	X	19058292	19058292	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19058292delA	uc004cyx.2	-						GPR64_uc004cyy.2_Intron|GPR64_uc004cyz.2_Intron|GPR64_uc004czb.2_Intron|GPR64_uc004czc.2_Intron|GPR64_uc004czd.2_Intron|GPR64_uc004cze.2_Intron|GPR64_uc004czf.2_Intron|GPR64_uc004cza.2_Intron|GPR64_uc004cyw.2_Intron|GPR64_uc010nfj.2_Intron	NM_001079858	NP_001073327			G protein-coupled receptor 64 isoform 1						neuropeptide signaling pathway|spermatogenesis	cytoplasm|integral to plasma membrane	G-protein coupled receptor activity				0	Hepatocellular(33;0.183)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	19258041	19258041	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19258041delC								GPR64 (117364 upstream) : PDHA1 (103970 downstream)																																			---	---	---	---
CXorf23	256643	broad.mit.edu	37	X	19935293	19935293	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19935293delA	uc004czp.2	-	11					CXorf23_uc004czn.3_5'Flank|CXorf23_uc010nfn.2_RNA|CXorf23_uc011mjg.1_3'UTR|CXorf23_uc004czo.2_3'UTR	NM_198279	NP_938020			hypothetical protein LOC256643							mitochondrion				lung(1)|skin(1)	2																		---	---	---	---
CXorf23	256643	broad.mit.edu	37	X	19948068	19948068	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:19948068delA	uc004czp.2	-						CXorf23_uc010nfn.2_Intron|CXorf23_uc011mjg.1_Intron|CXorf23_uc004czo.2_Intron	NM_198279	NP_938020			hypothetical protein LOC256643							mitochondrion				lung(1)|skin(1)	2																		---	---	---	---
EIF1AX	1964	broad.mit.edu	37	X	20156751	20156751	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:20156751delA	uc004czt.2	-						SCARNA9L_uc010nfp.2_5'Flank	NM_001412	NP_001403			X-linked eukaryotic translation initiation							cytosol	translation initiation factor activity			ovary(1)	1																		---	---	---	---
CNKSR2	22866	broad.mit.edu	37	X	21488873	21488873	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21488873delT	uc004czx.1	+						CNKSR2_uc004czw.2_Intron|CNKSR2_uc011mjn.1_Intron|CNKSR2_uc011mjo.1_Intron	NM_014927	NP_055742			connector enhancer of kinase suppressor of Ras						regulation of signal transduction	cytoplasm|membrane	protein binding			large_intestine(1)|lung(1)	2																		---	---	---	---
SMS	6611	broad.mit.edu	37	X	21989957	21989957	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21989957delT	uc004dag.2	+						SMS_uc011mjq.1_Intron|SMS_uc004daf.1_Intron	NM_004595	NP_004586			spermine synthase						methionine metabolic process|spermine biosynthetic process	cytosol	spermidine synthase activity|spermine synthase activity			ovary(1)	1					Spermine(DB00127)													---	---	---	---
KLHL15	80311	broad.mit.edu	37	X	24006015	24006015	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24006015delT	uc004dba.3	-	4						NM_030624	NP_085127			kelch-like 15											ovary(1)|breast(1)	2																		---	---	---	---
POLA1	5422	broad.mit.edu	37	X	24733418	24733418	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:24733418delT	uc004dbl.2	+						POLA1_uc004dbm.2_Intron|POLA1_uc004dbn.2_Intron	NM_016937	NP_058633			DNA-directed DNA polymerase alpha 1						cell proliferation|DNA replication checkpoint|DNA replication, synthesis of RNA primer|DNA-dependent DNA replication initiation|double-strand break repair via nonhomologous end joining|interspecies interaction between organisms|lagging strand elongation|leading strand elongation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|cytoplasm|nuclear envelope|nuclear matrix|nucleolus|nucleoplasm	chromatin binding|DNA-directed DNA polymerase activity|metal ion binding|nucleoside binding			ovary(2)|skin(1)	3					Clofarabine(DB00631)|Fludarabine(DB01073)													---	---	---	---
DMD	1756	broad.mit.edu	37	X	31195898	31195898	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:31195898delA	uc004dda.1	-						DMD_uc004dcq.1_Intron|DMD_uc004dcr.1_Intron|DMD_uc004dcs.1_Intron|DMD_uc004dct.1_Intron|DMD_uc004dcu.1_Intron|DMD_uc004dcv.1_Intron|DMD_uc004dcw.2_Intron|DMD_uc004dcx.2_Intron|DMD_uc004dcz.2_Intron|DMD_uc004dcy.1_Intron|DMD_uc004ddb.1_Intron|DMD_uc004dcm.1_Intron|DMD_uc004dcn.1_Intron|DMD_uc004dco.1_Intron|DMD_uc004dcp.1_Intron|DMD_uc011mkb.1_Intron	NM_004006	NP_003997			dystrophin Dp427m isoform						muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)																---	---	---	---
CXorf22	170063	broad.mit.edu	37	X	35984670	35984670	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:35984670delT	uc004ddj.2	+						CXorf22_uc010ngv.2_Intron	NM_152632	NP_689845			hypothetical protein LOC170063											large_intestine(1)|lung(1)|ovary(1)	3																		---	---	---	---
CXorf59	286464	broad.mit.edu	37	X	36117799	36117799	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:36117799delA	uc004ddk.1	+							NM_173695	NP_775966			hypothetical protein LOC286464							integral to membrane				central_nervous_system(1)	1																		---	---	---	---
FAM47C	442444	broad.mit.edu	37	X	37028265	37028265	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:37028265delC	uc004ddl.1	+	1	1796	c.1782delC	c.(1780-1782)CTCfs	p.L594fs		NM_001013736	NP_001013758	Q5HY64	FA47C_HUMAN	hypothetical protein LOC442444	594										ovary(3)	3																		---	---	---	---
ATP6AP2	10159	broad.mit.edu	37	X	40457911	40457912	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40457911_40457912delTT	uc004det.2	+						ATP6AP2_uc010nhc.2_Intron|ATP6AP2_uc011mkl.1_Intron|ATP6AP2_uc011mkm.1_Intron|ATP6AP2_uc011mkn.1_Intron|ATP6AP2_uc004deu.1_Intron	NM_005765	NP_005756			ATPase, H+ transporting, lysosomal accessory						angiotensin maturation|positive regulation of transforming growth factor-beta1 production|regulation of MAPKKK cascade	external side of plasma membrane|integral to membrane	protein binding|receptor activity				0																		---	---	---	---
MED14	9282	broad.mit.edu	37	X	40511007	40511007	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:40511007delT	uc004dex.3	-	31						NM_004229	NP_004220			mediator complex subunit 14						androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			breast(2)|kidney(1)|skin(1)	4																		---	---	---	---
DDX3X	1654	broad.mit.edu	37	X	41207100	41207100	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41207100delT	uc004dfe.2	+	17					DDX3X_uc004dff.2_3'UTR|DDX3X_uc011mkq.1_3'UTR|DDX3X_uc011mkr.1_3'UTR|DDX3X_uc011mks.1_3'UTR|DDX3X_uc004dfg.2_RNA	NM_001356	NP_001347			DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3						interspecies interaction between organisms	cytoplasm|nuclear speck	ATP binding|ATP-dependent RNA helicase activity|DNA binding|protein binding|RNA binding			ovary(2)|breast(2)|central_nervous_system(1)|skin(1)	6															HNSCC(61;0.18)			---	---	---	---
Unknown	0	broad.mit.edu	37	X	42718731	42718732	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:42718731_42718732delTT								PPP1R2P9 (81245 upstream) : MAOA (796677 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	44505033	44505033	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44505033delA								FUNDC1 (102812 upstream) : DUSP21 (198216 downstream)																																			---	---	---	---
KDM6A	7403	broad.mit.edu	37	X	44938317	44938317	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44938317delA	uc004dge.3	+						KDM6A_uc010nhk.2_Intron|KDM6A_uc011mkz.1_Intron|KDM6A_uc011mla.1_Intron|KDM6A_uc011mlb.1_Intron|KDM6A_uc011mlc.1_Intron|KDM6A_uc011mld.1_Intron	NM_021140	NP_066963			ubiquitously transcribed tetratricopeptide						histone H3-K4 methylation		metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			kidney(24)|haematopoietic_and_lymphoid_tissue(23)|oesophagus(11)|large_intestine(7)|lung(5)|breast(4)|central_nervous_system(3)|urinary_tract(3)|endometrium(2)|pancreas(2)	84								D|N|F|S		renal|oesophageal SCC|MM								---	---	---	---
KDM6A	7403	broad.mit.edu	37	X	44941830	44941831	+	Frame_Shift_Ins	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:44941830_44941831insA	uc004dge.3	+	21	3529_3530	c.3154_3155insA	c.(3154-3156)GAAfs	p.E1052fs	KDM6A_uc011mkz.1_Frame_Shift_Ins_p.E1104fs|KDM6A_uc011mla.1_Frame_Shift_Ins_p.E1007fs|KDM6A_uc011mlb.1_Frame_Shift_Ins_p.E1059fs|KDM6A_uc011mlc.1_Frame_Shift_Ins_p.E756fs|KDM6A_uc011mld.1_Frame_Shift_Ins_p.E691fs	NM_021140	NP_066963	O15550	KDM6A_HUMAN	ubiquitously transcribed tetratricopeptide	1052					histone H3-K4 methylation		metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			kidney(24)|haematopoietic_and_lymphoid_tissue(23)|oesophagus(11)|large_intestine(7)|lung(5)|breast(4)|central_nervous_system(3)|urinary_tract(3)|endometrium(2)|pancreas(2)	84								D|N|F|S		renal|oesophageal SCC|MM								---	---	---	---
SLC9A7	84679	broad.mit.edu	37	X	46539207	46539207	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46539207delA	uc004dgu.1	-						SLC9A7_uc004dgv.1_Intron	NM_032591	NP_115980			solute carrier family 9, member 7						regulation of pH	Golgi membrane|integral to membrane|recycling endosome membrane|trans-Golgi network	potassium:hydrogen antiporter activity|protein homodimerization activity|sodium:hydrogen antiporter activity			ovary(2)	2																		---	---	---	---
RP2	6102	broad.mit.edu	37	X	46719653	46719653	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46719653delT	uc004dgw.3	+							NM_006915	NP_008846			XRP2 protein						cell morphogenesis|CTP biosynthetic process|GTP biosynthetic process|protein folding|UTP biosynthetic process|visual perception	cytoplasm|plasma membrane	ATP binding|GTP binding|GTPase activator activity|nucleoside diphosphate kinase activity|unfolded protein binding				0																		---	---	---	---
ARAF	369	broad.mit.edu	37	X	47426415	47426415	+	Frame_Shift_Del	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47426415delC	uc011mlq.1	+	9	891	c.758delC	c.(757-759)ACCfs	p.T253fs	ARAF_uc011mln.1_RNA|ARAF_uc011mlo.1_Frame_Shift_Del_p.T119fs|ARAF_uc011mlp.1_Frame_Shift_Del_p.T253fs|ARAF_uc004dic.1_Frame_Shift_Del_p.T34fs	NM_001654	NP_001645	P10398	ARAF_HUMAN	v-raf murine sarcoma 3611 viral oncogene	253					intracellular signal transduction|negative regulation of apoptosis|positive regulation of peptidyl-serine phosphorylation		ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|receptor signaling protein activity			large_intestine(3)|lung(2)|ovary(1)|skin(1)	7					Adenosine triphosphate(DB00171)													---	---	---	---
ELK1	2002	broad.mit.edu	37	X	47500596	47500596	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47500596delG	uc004dik.3	-						ELK1_uc010nhv.2_Intron|ELK1_uc010nhw.2_5'UTR|ELK1_uc004dil.3_Intron	NM_001114123	NP_001107595			ELK1 protein						innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway		protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2																		---	---	---	---
SSX5	6758	broad.mit.edu	37	X	48054295	48054295	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48054295delA	uc004dja.1	-						SSX5_uc004diz.1_Intron	NM_175723	NP_783729			synovial sarcoma, X breakpoint 5 isoform b						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	48158876	48158876	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48158876delT	uc010nib.1	-							NM_174962	NP_777622			synovial sarcoma, X breakpoint 9																														---	---	---	---
SSX3	10214	broad.mit.edu	37	X	48209231	48209231	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48209231delT	uc004djd.1	-						SSX3_uc004dje.2_Intron	NM_021014	NP_066294			synovial sarcoma, X breakpoint 3 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding				0																		---	---	---	---
SSX3	10214	broad.mit.edu	37	X	48218345	48218345	+	5'Flank	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48218345delA	uc004djd.1	-						SSX3_uc004dje.2_5'Flank|SSX3_uc010nic.2_5'Flank	NM_021014	NP_066294			synovial sarcoma, X breakpoint 3 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	48635378	48635378	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48635378delA								GLOD5 (3316 upstream) : GATA1 (9604 downstream)																																			---	---	---	---
HDAC6	10013	broad.mit.edu	37	X	48681900	48681901	+	Frame_Shift_Ins	INS	-	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48681900_48681901insC	uc011mmi.1	+	25	3186_3187	c.3091_3092insC	c.(3091-3093)ACCfs	p.T1031fs	HDAC6_uc004dks.1_Frame_Shift_Ins_p.T1031fs|HDAC6_uc010nig.1_Frame_Shift_Ins_p.T879fs|HDAC6_uc004dkt.1_Frame_Shift_Ins_p.T1031fs|HDAC6_uc011mmk.1_Frame_Shift_Ins_p.T1012fs|HDAC6_uc004dkv.1_Frame_Shift_Ins_p.T679fs|HDAC6_uc004dkw.1_Frame_Shift_Ins_p.T679fs|HDAC6_uc004dkx.1_Frame_Shift_Ins_p.T394fs	NM_006044	NP_006035	Q9UBN7	HDAC6_HUMAN	histone deacetylase 6	1031					aggresome assembly|cellular response to hydrogen peroxide|Hsp90 deacetylation|lysosome localization|macroautophagy|misfolded or incompletely synthesized protein catabolic process|negative regulation of proteolysis|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|polyubiquitinated misfolded protein transport|positive regulation of apoptosis|positive regulation of cellular chaperone-mediated protein complex assembly|positive regulation of epithelial cell migration|positive regulation of receptor biosynthetic process|positive regulation of signal transduction|regulation of androgen receptor signaling pathway|regulation of receptor activity|response to growth factor stimulus|response to toxin|transcription, DNA-dependent|tubulin deacetylation	aggresome|caveola|cell leading edge|cytosol|histone deacetylase complex|microtubule associated complex|perinuclear region of cytoplasm	actin binding|alpha-tubulin binding|beta-catenin binding|dynein complex binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|Hsp90 protein binding|microtubule binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|polyubiquitin binding|tau protein binding|tubulin deacetylase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)	4					Vorinostat(DB02546)													---	---	---	---
CACNA1F	778	broad.mit.edu	37	X	49072018	49072018	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49072018delG	uc004dnb.2	-						CACNA1F_uc010nip.2_Intron	NM_005183	NP_005174			calcium channel, voltage-dependent, L type,						axon guidance|detection of light stimulus involved in visual perception	voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			breast(3)|ovary(1)|kidney(1)|skin(1)	6					Verapamil(DB00661)													---	---	---	---
GAGE10	643832	broad.mit.edu	37	X	49158062	49158063	+	5'Flank	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49158062_49158063delTT	uc010nir.1	+							NM_001098413	NP_001091883			G antigen 10												0	Ovarian(276;0.236)																	---	---	---	---
GAGE12J	729396	broad.mit.edu	37	X	49199452	49199453	+	Intron	INS	-	TG	TG			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49199452_49199453insTG	uc004dnl.3	+						GAGE13_uc004dnn.3_Intron|GAGE8_uc011mne.1_Intron|GAGE8_uc011mnf.1_Intron|GAGE8_uc011mng.1_Intron|GAGE2A_uc004dnr.3_Intron|GAGE8_uc004dnq.3_Intron|GAGE10_uc010nis.2_Intron|GAGE12J_uc004dnk.3_Intron|GAGE2D_uc004dnp.3_Intron|GAGE2C_uc004dno.3_Intron|GAGE2E_uc010njb.2_Intron|GAGE8_uc011mnh.1_Intron	NM_001098406	NP_001465			G antigen 12J												0	Ovarian(276;0.236)																	---	---	---	---
IQSEC2	23096	broad.mit.edu	37	X	53296225	53296227	+	Intron	DEL	CTC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53296225_53296227delCTC	uc004dsd.2	-						IQSEC2_uc004dsc.2_Intron|IQSEC2_uc004dse.2_RNA|IQSEC2_uc004dsf.2_RNA	NM_001111125	NP_001104595			IQ motif and Sec7 domain 2 isoform1						regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	53390519	53390519	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53390519delA								IQSEC2 (39997 upstream) : SMC1A (10553 downstream)																																			---	---	---	---
HUWE1	10075	broad.mit.edu	37	X	53658442	53658442	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53658442delA	uc004dsp.2	-							NM_031407	NP_113584			HECT, UBA and WWE domain containing 1						base-excision repair|cell differentiation|histone ubiquitination|protein monoubiquitination|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	DNA binding|protein binding|ubiquitin-protein ligase activity			ovary(8)|large_intestine(4)|breast(4)|kidney(1)	17																		---	---	---	---
WNK3	65267	broad.mit.edu	37	X	54228636	54228636	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54228636delA	uc004dtd.1	-						WNK3_uc004dtc.1_Intron	NM_001002838	NP_001002838			WNK lysine deficient protein kinase 3 isoform 2						intracellular protein kinase cascade|positive regulation of establishment of protein localization in plasma membrane|positive regulation of peptidyl-threonine phosphorylation|positive regulation of rubidium ion transmembrane transporter activity|positive regulation of rubidium ion transport|positive regulation of sodium ion transmembrane transporter activity|positive regulation of sodium ion transport|protein autophosphorylation	adherens junction|tight junction	ATP binding|protein binding|protein serine/threonine kinase activity|rubidium ion transmembrane transporter activity|sodium ion transmembrane transporter activity			lung(4)|ovary(3)|kidney(2)|central_nervous_system(2)	11																		---	---	---	---
GNL3L	54552	broad.mit.edu	37	X	54585147	54585147	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54585147delT	uc004dth.1	+						GNL3L_uc004dti.2_Intron	NM_019067	NP_061940			guanine nucleotide binding protein-like 3						ribosome biogenesis	nucleolus	GTP binding			ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	54868437	54868437	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54868437delT								MAGED2 (25992 upstream) : TRO (78812 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	55230847	55230847	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:55230847delT								FAM104B (43238 upstream) : PAGE5 (15944 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	61700353	61700353	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:61700353delA								None (None upstream) : SPIN4 (866755 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	62519009	62519009	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:62519009delT								None (None upstream) : SPIN4 (48099 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	62825422	62825422	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:62825422delA								LOC92249 (44549 upstream) : ARHGEF9 (29426 downstream)																																			---	---	---	---
YIPF6	286451	broad.mit.edu	37	X	67742761	67742761	+	Splice_Site	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:67742761delT	uc004dwy.2	+	6	615	c.592_splice	c.e6+2	p.A198_splice	YIPF6_uc011mph.1_Splice_Site_p.A155_splice	NM_173834	NP_776195			Yip1 domain family, member 6							endoplasmic reticulum|integral to membrane					0																		---	---	---	---
AWAT2	158835	broad.mit.edu	37	X	69262972	69262974	+	In_Frame_Del	DEL	AGA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69262972_69262974delAGA	uc004dxt.1	-	5	598_600	c.592_594delTCT	c.(592-594)TCTdel	p.S198del		NM_001002254	NP_001002254	Q6E213	AWAT2_HUMAN	wax synthase 2	198						endoplasmic reticulum membrane|integral to membrane	long-chain-alcohol O-fatty-acyltransferase activity				0																		---	---	---	---
KIF4A	24137	broad.mit.edu	37	X	69640183	69640183	+	3'UTR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69640183delT	uc004dyg.2	+	31					KIF4A_uc010nkw.2_3'UTR|GDPD2_uc010nkx.1_5'Flank|GDPD2_uc010nky.1_5'Flank|GDPD2_uc004dyh.2_5'Flank|GDPD2_uc011mpk.1_5'Flank|GDPD2_uc011mpl.1_5'Flank|GDPD2_uc011mpm.1_5'Flank	NM_012310	NP_036442			kinesin family member 4						anterograde axon cargo transport|axon guidance|blood coagulation|organelle organization	chromosome|cytosol|midbody|nuclear matrix|spindle microtubule	ATP binding|DNA binding|microtubule motor activity|protein binding			ovary(4)	4																		---	---	---	---
TEX11	56159	broad.mit.edu	37	X	69811475	69811475	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69811475delA	uc004dyl.2	-						TEX11_uc004dyk.2_Intron|TEX11_uc004dym.2_Intron	NM_001003811	NP_001003811			testis expressed sequence 11 isoform 1								protein binding			ovary(3)|breast(1)|skin(1)	5	Renal(35;0.156)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	70144112	70144112	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70144112delT								TEX11 (15545 upstream) : SLC7A3 (1323 downstream)																																			---	---	---	---
TAF1	6872	broad.mit.edu	37	X	70612706	70612706	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70612706delT	uc004dzu.3	+						BCYRN1_uc011mpt.1_Intron|TAF1_uc004dzt.3_Intron|TAF1_uc004dzv.3_Intron	NM_138923	NP_620278			TBP-associated factor 1 isoform 2						G1 phase of mitotic cell cycle|interspecies interaction between organisms|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription initiation from RNA polymerase II promoter|protein autophosphorylation|regulation of transcription involved in G2/M-phase of mitotic cell cycle|RNA polymerase II transcriptional preinitiation complex assembly|transcription elongation from RNA polymerase II promoter|viral reproduction	MLL1 complex|transcription factor TFIID complex	ATP binding|histone acetyl-lysine binding|histone acetyltransferase activity|p53 binding|protein binding|protein serine/threonine kinase activity|sequence-specific DNA binding|TBP-class protein binding|transcription coactivator activity			ovary(7)|breast(4)|large_intestine(2)|central_nervous_system(2)|lung(1)|skin(1)	17	Renal(35;0.156)	all_lung(315;0.000321)																---	---	---	---
NHSL2	340527	broad.mit.edu	37	X	71264810	71264812	+	Intron	DEL	AAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71264810_71264812delAAA	uc011mqa.1	+							NM_001013627	NP_001013649			NHS-like 2												0	Renal(35;0.156)																	---	---	---	---
PIN4	5303	broad.mit.edu	37	X	71416535	71416535	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71416535delT	uc004eam.2	+						PIN4_uc004eao.1_Intron	NM_006223	NP_006214			protein (peptidyl-prolyl cis/trans isomerase)						protein folding|rRNA processing	cytoplasm|mitochondrial matrix|mitochondrial matrix|nucleolus|nucleolus|preribosome|spindle|spindle	bent DNA binding|DNA binding|double-stranded DNA binding|peptidyl-prolyl cis-trans isomerase activity				0	Renal(35;0.156)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	71492424	71492424	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71492424delA								PIN4 (7612 upstream) : RPS4X (30 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	72026439	72026440	+	IGR	DEL	TC	-	-	rs114320514	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:72026439_72026440delTC								PHKA1 (92410 upstream) : DMRTC1B (36360 downstream)																																			---	---	---	---
TSIX	9383	broad.mit.edu	37	X	73046080	73046080	+	RNA	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73046080delT	uc004ebn.2	+	1		c.34041delT			XIST_uc004ebm.1_RNA	NR_003255				Homo sapiens XIST antisense RNA (non-protein coding) (TSIX), non-coding RNA.												0																		---	---	---	---
XIST	7503	broad.mit.edu	37	X	73072587	73072587	+	RNA	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73072587delG	uc004ebm.1	-	1		c.2delC				NR_001564				Homo sapiens cDNA: FLJ21545 fis, clone COL06195.												0																		---	---	---	---
ZDHHC15	158866	broad.mit.edu	37	X	74649036	74649036	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:74649036delA	uc004ecg.2	-						ZDHHC15_uc004ech.2_Intron|ZDHHC15_uc011mqo.1_Intron	NM_144969	NP_659406			zinc finger, DHHC-type containing 15 isoform 1							integral to membrane	zinc ion binding			ovary(2)	2																		---	---	---	---
ZDHHC15	158866	broad.mit.edu	37	X	74651360	74651361	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:74651360_74651361delAA	uc004ecg.2	-						ZDHHC15_uc004ech.2_Intron|ZDHHC15_uc011mqo.1_Intron	NM_144969	NP_659406			zinc finger, DHHC-type containing 15 isoform 1							integral to membrane	zinc ion binding			ovary(2)	2																		---	---	---	---
ATRX	546	broad.mit.edu	37	X	76777075	76777076	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:76777075_76777076insA	uc004ecp.3	-						ATRX_uc004ecq.3_Intron|ATRX_uc004eco.3_Intron	NM_000489	NP_000480			transcriptional regulator ATRX isoform 1						DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30					Phosphatidylserine(DB00144)			Mis|F|N		Pancreatic neuroendocrine tumors		ATR-X (alpha thalassemia/mental retardation) syndrome						---	---	---	---
ATP7A	538	broad.mit.edu	37	X	77264922	77264922	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77264922delT	uc004ecx.3	+						ATP7A_uc004ecw.2_3'UTR	NM_000052	NP_000043			ATPase, Cu++ transporting, alpha polypeptide						ATP biosynthetic process|blood vessel development|blood vessel remodeling|cartilage development|cellular copper ion homeostasis|cerebellar Purkinje cell differentiation|collagen fibril organization|copper ion import|detoxification of copper ion|dopamine metabolic process|elastic fiber assembly|elastin biosynthetic process|epinephrine metabolic process|hair follicle morphogenesis|locomotory behavior|lung alveolus development|negative regulation of metalloenzyme activity|neuroprotection|peptidyl-lysine modification|pigmentation|positive regulation of metalloenzyme activity|positive regulation of oxidoreductase activity|pyramidal neuron development|regulation of oxidative phosphorylation|removal of superoxide radicals|serotonin metabolic process|skin development|T-helper cell differentiation|tryptophan metabolic process	basolateral plasma membrane|cytosol|endoplasmic reticulum|endoplasmic reticulum|integral to membrane|late endosome|neuron projection|neuronal cell body|perinuclear region of cytoplasm|trans-Golgi network|trans-Golgi network transport vesicle	ATP binding|copper-dependent protein binding|copper-exporting ATPase activity|superoxide dismutase copper chaperone activity				0																		---	---	---	---
BRWD3	254065	broad.mit.edu	37	X	79946538	79946538	+	Intron	DEL	A	-	-	rs73502699	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:79946538delA	uc004edt.2	-						BRWD3_uc010nmi.1_Intron|BRWD3_uc004edo.2_Intron|BRWD3_uc004edp.2_Intron|BRWD3_uc004edq.2_Intron|BRWD3_uc010nmj.1_Intron|BRWD3_uc004edr.2_Intron|BRWD3_uc004eds.2_Intron|BRWD3_uc004edu.2_Intron|BRWD3_uc004edv.2_Intron|BRWD3_uc004edw.2_Intron|BRWD3_uc004edx.2_Intron|BRWD3_uc004edy.2_Intron|BRWD3_uc004edz.2_Intron|BRWD3_uc004eea.2_Intron|BRWD3_uc004eeb.2_Intron	NM_153252	NP_694984			bromodomain and WD repeat domain containing 3											ovary(4)	4																		---	---	---	---
HMGN5	79366	broad.mit.edu	37	X	80373885	80373886	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:80373885_80373886insA	uc004eee.1	-							NM_030763	NP_110390			high-mobility group nucleosome binding domain 5						chromatin modification|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin|nucleolus	chromatin binding|DNA binding			lung(1)	1																		---	---	---	---
HMGN5	79366	broad.mit.edu	37	X	80376944	80376944	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:80376944delA	uc004eee.1	-							NM_030763	NP_110390			high-mobility group nucleosome binding domain 5						chromatin modification|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin|nucleolus	chromatin binding|DNA binding			lung(1)	1																OREG0019884	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
Unknown	0	broad.mit.edu	37	X	83305886	83305886	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:83305886delT								CYLC1 (164260 upstream) : RPS6KA6 (13098 downstream)																																			---	---	---	---
HDX	139324	broad.mit.edu	37	X	83577029	83577029	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:83577029delA	uc004eek.1	-						HDX_uc011mqv.1_Intron|HDX_uc004eel.1_Intron	NM_144657	NP_653258			highly divergent homeobox							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
POF1B	79983	broad.mit.edu	37	X	84563107	84563108	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:84563107_84563108insA	uc004eer.2	-						POF1B_uc004ees.2_Intron	NM_024921	NP_079197			premature ovarian failure, 1B								actin binding				0																		---	---	---	---
CHM	1121	broad.mit.edu	37	X	85119900	85119900	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:85119900delA	uc004eet.2	-						CHM_uc011mqz.1_Intron	NM_000390	NP_000381			choroideremia isoform a						intracellular protein transport|protein geranylgeranylation|response to stimulus|visual perception	Rab-protein geranylgeranyltransferase complex	GTPase activator activity|Rab geranylgeranyltransferase activity			ovary(1)	1		all_lung(315;5.41e-06)																---	---	---	---
DACH2	117154	broad.mit.edu	37	X	86087097	86087097	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:86087097delT	uc004eew.2	+						DACH2_uc004eex.2_Intron|DACH2_uc010nmq.2_Intron|DACH2_uc011mra.1_Intron|DACH2_uc010nmr.2_Intron	NM_053281	NP_444511			dachshund 2 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|nucleotide binding			ovary(4)|pancreas(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	86619918	86619918	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:86619918delT								DACH2 (532313 upstream) : KLHL4 (152797 downstream)																																			---	---	---	---
KLHL4	56062	broad.mit.edu	37	X	86888740	86888740	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:86888740delT	uc004efb.2	+						KLHL4_uc004efa.2_Intron	NM_019117	NP_061990			kelch-like 4 isoform 1							cytoplasm|microtubule cytoskeleton|nucleolus	actin binding			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	93283076	93283077	+	IGR	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:93283076_93283077delTT								FAM133A (315815 upstream) : None (None downstream)																																			---	---	---	---
RPA4	29935	broad.mit.edu	37	X	96140150	96140151	+	3'UTR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:96140150_96140151insT	uc004efv.3	+	1					DIAPH2_uc004eft.3_Intron|DIAPH2_uc004efu.3_Intron|DIAPH2_uc004efs.2_Intron	NM_013347	NP_037479			replication protein A4, 34kDa						DNA damage checkpoint|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair	DNA replication factor A complex|nucleoplasm	single-stranded DNA binding				0													Other_identified_genes_with_known_or_suspected_DNA_repair_function					---	---	---	---
RPA4	29935	broad.mit.edu	37	X	96140184	96140184	+	3'UTR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:96140184delA	uc004efv.3	+	1					DIAPH2_uc004eft.3_Intron|DIAPH2_uc004efu.3_Intron|DIAPH2_uc004efs.2_Intron	NM_013347	NP_037479			replication protein A4, 34kDa						DNA damage checkpoint|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair	DNA replication factor A complex|nucleoplasm	single-stranded DNA binding				0													Other_identified_genes_with_known_or_suspected_DNA_repair_function					---	---	---	---
Unknown	0	broad.mit.edu	37	X	97346456	97346456	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:97346456delT								DIAPH2 (490860 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	97677254	97677254	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:97677254delT								DIAPH2 (821658 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	X	100057018	100057028	+	IGR	DEL	AGCCAACTATG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100057018_100057028delAGCCAACTATG								SYTL4 (69887 upstream) : CSTF2 (18320 downstream)																																			---	---	---	---
XKRX	402415	broad.mit.edu	37	X	100178116	100178116	+	Intron	DEL	A	-	-	rs35360189		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100178116delA	uc004egn.2	-						XKRX_uc011mre.1_Intron	NM_212559	NP_997724			XK, Kell blood group complex subunit-related,							integral to membrane|plasma membrane				breast(1)	1																		---	---	---	---
HNRNPH2	3188	broad.mit.edu	37	X	100667857	100667857	+	Frame_Shift_Del	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100667857delG	uc004ehm.2	+	2	1051	c.881delG	c.(880-882)AGGfs	p.R294fs	HNRNPH2_uc004ehn.2_Frame_Shift_Del_p.R294fs	NM_019597	NP_062543	P55795	HNRH2_HUMAN	heterogeneous nuclear ribonucleoprotein H2	294	RRM 3.|2 X 16 AA Gly-rich approximate repeats.				nuclear mRNA splicing, via spliceosome	actin cytoskeleton|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|RNA binding				0																		---	---	---	---
NXF2B	728343	broad.mit.edu	37	X	101677220	101677221	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101677220_101677221delTT	uc004ejb.3	-						NXF2B_uc004eiz.3_Intron|NXF2B_uc004eja.3_Intron|NXF2B_uc004ejc.1_Intron|NXF2_uc004eiy.3_Intron	NM_001099686	NP_001093156			nuclear RNA export factor 2B						mRNA export from nucleus|multicellular organismal development	actin cytoskeleton|cytoplasm|nuclear RNA export factor complex	nucleocytoplasmic transporter activity|nucleotide binding|RNA binding			ovary(1)	1																		---	---	---	---
PLP1	5354	broad.mit.edu	37	X	103040729	103040729	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:103040729delT	uc010nov.2	+						RAB9B_uc004eli.1_Intron|PLP1_uc004elk.2_Intron|PLP1_uc004elj.2_Intron|PLP1_uc011msf.1_Intron|PLP1_uc010now.1_Intron|PLP1_uc010nox.2_5'Flank	NM_001128834	NP_001122306			proteolipid protein 1 isoform 1						cell death|synaptic transmission	integral to membrane				ovary(1)	1																		---	---	---	---
NRK	203447	broad.mit.edu	37	X	105139188	105139188	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105139188delT	uc004emd.2	+						NRK_uc010npc.1_Intron	NM_198465	NP_940867			Nik related kinase								ATP binding|protein serine/threonine kinase activity|small GTPase regulator activity			breast(7)|ovary(3)|lung(2)|large_intestine(1)|central_nervous_system(1)	14															HNSCC(51;0.14)			---	---	---	---
NRK	203447	broad.mit.edu	37	X	105156736	105156736	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105156736delA	uc004emd.2	+	14	2641	c.2338delA	c.(2338-2340)AAAfs	p.K780fs	NRK_uc010npc.1_Frame_Shift_Del_p.K448fs	NM_198465	NP_940867	Q7Z2Y5	NRK_HUMAN	Nik related kinase	780							ATP binding|protein serine/threonine kinase activity|small GTPase regulator activity			breast(7)|ovary(3)|lung(2)|large_intestine(1)|central_nervous_system(1)	14															HNSCC(51;0.14)			---	---	---	---
CXorf57	55086	broad.mit.edu	37	X	105905170	105905170	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105905170delT	uc004emi.3	+						CXorf57_uc004emj.3_Intron	NM_018015	NP_060485			hypothetical protein LOC55086											ovary(1)|lung(1)|breast(1)	3																		---	---	---	---
RNF128	79589	broad.mit.edu	37	X	105937256	105937256	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:105937256delT	uc004emk.2	+	1	189	c.24delT	c.(22-24)AGTfs	p.S8fs		NM_024539	NP_078815	Q8TEB7	RN128_HUMAN	ring finger protein 128 isoform 2	Error:Variant_position_missing_in_Q8TEB7_after_alignment						endomembrane system|integral to membrane|perinuclear region of cytoplasm	zinc ion binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
COL4A6	1288	broad.mit.edu	37	X	107431944	107431944	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107431944delT	uc004enw.3	-						COL4A6_uc004env.3_Intron|COL4A6_uc011msn.1_Intron|COL4A6_uc010npk.2_Intron	NM_001847	NP_001838			type IV alpha 6 collagen isoform A precursor						cell adhesion|extracellular matrix organization	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(6)|urinary_tract(1)|large_intestine(1)	8														Alport_syndrome_with_Diffuse_Leiomyomatosis				---	---	---	---
COL4A6	1288	broad.mit.edu	37	X	107438185	107438186	+	Intron	INS	-	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107438185_107438186insA	uc004enw.3	-						COL4A6_uc004env.3_Intron|COL4A6_uc011msn.1_Intron|COL4A6_uc010npk.2_Intron	NM_001847	NP_001838			type IV alpha 6 collagen isoform A precursor						cell adhesion|extracellular matrix organization	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(6)|urinary_tract(1)|large_intestine(1)	8														Alport_syndrome_with_Diffuse_Leiomyomatosis				---	---	---	---
ACSL4	2182	broad.mit.edu	37	X	108902743	108902743	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:108902743delA	uc004eoi.2	-						ACSL4_uc004eoj.2_Intron|ACSL4_uc004eok.2_Intron	NM_022977	NP_075266			acyl-CoA synthetase long-chain family member 4						fatty acid metabolic process|learning or memory|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane|peroxisomal membrane	ATP binding|long-chain fatty acid-CoA ligase activity			large_intestine(1)|lung(1)|ovary(1)	3					Icosapent(DB00159)|Troglitazone(DB00197)													---	---	---	---
AMMECR1	9949	broad.mit.edu	37	X	109468163	109468163	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:109468163delT	uc004eoo.2	-						AMMECR1_uc004eop.2_Intron|AMMECR1_uc004eoq.2_Intron	NM_015365	NP_056180			AMMECR1 protein isoform 1												0																		---	---	---	---
LRCH2	57631	broad.mit.edu	37	X	114347905	114347905	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114347905delA	uc010nqe.2	-						LRCH2_uc004epz.2_Intron	NM_020871	NP_065922			leucine-rich repeats and calponin homology (CH)											ovary(1)	1																		---	---	---	---
LUZP4	51213	broad.mit.edu	37	X	114537781	114537781	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:114537781delA	uc004eqa.2	+						LUZP4_uc004eqb.2_Intron	NM_016383	NP_057467			leucine zipper protein 4							nucleus				ovary(2)	2																		---	---	---	---
DOCK11	139818	broad.mit.edu	37	X	117743229	117743229	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117743229delT	uc004eqp.2	+						DOCK11_uc004eqq.2_Intron	NM_144658	NP_653259			dedicator of cytokinesis 11						blood coagulation	cytosol	GTP binding			ovary(3)	3																		---	---	---	---
IL13RA1	3597	broad.mit.edu	37	X	117880827	117880827	+	Intron	DEL	A	-	-	rs144642926	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117880827delA	uc004eqs.2	+						IL13RA1_uc004eqr.1_Intron|IL13RA1_uc004eqt.1_Intron	NM_001560	NP_001551			interleukin 13 receptor, alpha 1 precursor							interleukin-13 receptor complex	cytokine receptor activity				0																		---	---	---	---
LONRF3	79836	broad.mit.edu	37	X	118151699	118151699	+	3'UTR	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118151699delG	uc004eqw.2	+	11					LONRF3_uc004eqx.2_3'UTR|LONRF3_uc004eqy.2_RNA|LONRF3_uc004eqz.2_3'UTR	NM_001031855	NP_001027026			LON peptidase N-terminal domain and ring finger						proteolysis		ATP-dependent peptidase activity|protein binding|zinc ion binding			breast(1)|central_nervous_system(1)	2																		---	---	---	---
CXorf56	63932	broad.mit.edu	37	X	118694020	118694020	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118694020delA	uc004erk.1	-						CXorf56_uc004erj.1_Intron|CXorf56_uc011mtu.1_Intron	NM_022101	NP_071384			hypothetical protein LOC63932								protein binding				0																		---	---	---	---
NKAP	79576	broad.mit.edu	37	X	119071662	119071662	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119071662delT	uc004esh.2	-						NKAP_uc004esg.2_5'UTR	NM_024528	NP_078804			NFKB activating protein						negative regulation of transcription, DNA-dependent|Notch signaling pathway|positive regulation of alpha-beta T cell differentiation|transcription, DNA-dependent	cytoplasm|nucleus	chromatin binding|protein binding			ovary(2)	2																		---	---	---	---
LAMP2	3920	broad.mit.edu	37	X	119580473	119580473	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119580473delA	uc004est.3	-						LAMP2_uc004ess.3_Intron|LAMP2_uc011mtz.1_Intron|LAMP2_uc011mua.1_Intron|LAMP2_uc010nqp.1_Intron	NM_002294	NP_002285			lysosomal-associated membrane protein 2 isoform						platelet activation|platelet degranulation	endosome membrane|integral to membrane|late endosome|lysosomal membrane|membrane fraction|plasma membrane|platelet dense granule membrane				ovary(1)	1																		---	---	---	---
THOC2	57187	broad.mit.edu	37	X	122753440	122753440	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:122753440delA	uc004etu.2	-						THOC2_uc010nqt.1_Intron|THOC2_uc004etw.1_Intron	NM_001081550	NP_001075019			THO complex 2						intronless viral mRNA export from host nucleus|mRNA processing|RNA splicing	THO complex part of transcription export complex	protein binding|RNA binding			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	129072491	129072491	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129072491delT								UTP14A (8764 upstream) : BCORL1 (44178 downstream)																																			---	---	---	---
ZNF280C	55609	broad.mit.edu	37	X	129349321	129349321	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129349321delA	uc004evm.2	-						ZNF280C_uc010nrf.1_Intron	NM_017666	NP_060136			zinc finger protein 280C						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)|ovary(1)	3																		---	---	---	---
RBMX2	51634	broad.mit.edu	37	X	129546352	129546352	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129546352delA	uc004evt.2	+	6	563	c.499delA	c.(499-501)AAAfs	p.K167fs		NM_016024	NP_057108	Q9Y388	RBMX2_HUMAN	RNA binding motif protein, X-linked 2	167	Lys-rich.						nucleotide binding|RNA binding			breast(3)|ovary(1)	4																		---	---	---	---
PHF6	84295	broad.mit.edu	37	X	133511863	133511863	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133511863delA	uc004exj.2	+						PHF6_uc004exk.2_Intron|PHF6_uc011mvk.1_Intron|PHF6_uc004exh.2_Intron|PHF6_uc010nrr.2_Intron|PHF6_uc004exi.2_Intron	NM_001015877	NP_001015877			PHD finger protein 6 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	zinc ion binding			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
PHF6	84295	broad.mit.edu	37	X	133527689	133527689	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133527689delT	uc004exj.2	+						PHF6_uc004exk.2_Intron|PHF6_uc011mvk.1_Intron|PHF6_uc004exh.2_Intron|PHF6_uc010nrr.2_Intron|PHF6_uc004exi.2_Intron	NM_001015877	NP_001015877			PHD finger protein 6 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	zinc ion binding			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
PHF6	84295	broad.mit.edu	37	X	133548080	133548080	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133548080delT	uc004exj.2	+						PHF6_uc004exk.2_Intron|PHF6_uc011mvk.1_Intron|PHF6_uc004exh.2_Intron|PHF6_uc010nrr.2_Intron|PHF6_uc004exi.2_Intron	NM_001015877	NP_001015877			PHD finger protein 6 isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	zinc ion binding			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
PLAC1	10761	broad.mit.edu	37	X	133728165	133728165	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:133728165delT	uc004exo.1	-						PLAC1_uc004exp.1_Intron	NM_021796	NP_068568			placenta-specific 1 precursor						placenta development	extracellular region				pancreas(1)	1	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
MOSPD1	56180	broad.mit.edu	37	X	134033048	134033048	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134033048delT	uc004eyb.2	-						MOSPD1_uc004eya.2_Intron|MOSPD1_uc010nrv.2_Intron|MOSPD1_uc011mvr.1_Intron	NM_019556	NP_062456			motile sperm domain containing 1						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter	integral to membrane|nucleus|perinuclear region of cytoplasm	structural molecule activity			ovary(1)|breast(1)	2	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
ZNF449	203523	broad.mit.edu	37	X	134493962	134493962	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134493962delA	uc004eys.2	+						ZNF449_uc004eyt.2_Intron|ZNF449_uc004eyu.2_Intron	NM_152695	NP_689908			zinc finger protein 449						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	134807304	134807305	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:134807304_134807305insT								DDX26B (90845 upstream) : CT45A1 (39880 downstream)																																			---	---	---	---
VGLL1	51442	broad.mit.edu	37	X	135630679	135630679	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135630679delA	uc004ezy.2	+						MIR934_hsa-mir-934|MI0005756_5'Flank	NM_016267	NP_057351			vestigial like 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	transcription coactivator activity				0	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
RBMX	27316	broad.mit.edu	37	X	135960247	135960248	+	Splice_Site	INS	-	A	A	rs35488933		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135960247_135960248insA	uc004fae.1	-	4	427	c.217_splice	c.e4-1	p.S73_splice	RBMX_uc011mwf.1_Intron|RBMX_uc004fad.1_Splice_Site_p.S73_splice|RBMX_uc011mwg.1_Splice_Site_p.S34_splice|RBMX_uc004faf.1_Intron|RBMX_uc010nsf.1_Splice_Site_p.S34_splice|RBMX_uc004fag.1_Splice_Site	NM_002139	NP_002130			RNA binding motif protein, X-linked isoform 1							catalytic step 2 spliceosome|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|RNA binding			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
MCF2	4168	broad.mit.edu	37	X	138700010	138700011	+	Intron	DEL	AA	-	-	rs72084181		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138700010_138700011delAA	uc004fau.2	-						MCF2_uc004fav.2_Intron|MCF2_uc011mwl.1_Intron|MCF2_uc010nsh.1_Intron|MCF2_uc011mwm.1_Intron|MCF2_uc011mwn.1_Intron|MCF2_uc004faw.2_Intron|MCF2_uc011mwo.1_Intron	NM_005369	NP_005360			MCF.2 cell line derived transforming sequence						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytoskeleton|cytosol|membrane|membrane fraction	protein binding|Rho guanyl-nucleotide exchange factor activity			lung(1)|pleura(1)	2	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
ATP11C	286410	broad.mit.edu	37	X	138865164	138865164	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:138865164delA	uc004faz.2	-						ATP11C_uc004fay.2_Intron|ATP11C_uc004fba.2_Intron	NM_173694	NP_775965			ATPase, class VI, type 11C isoform a						ATP biosynthetic process	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(5)|large_intestine(3)	8	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
MAGEC1	9947	broad.mit.edu	37	X	140994072	140994072	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:140994072delT	uc004fbt.2	+	4	1168	c.882delT	c.(880-882)ACTfs	p.T294fs	MAGEC1_uc010nsl.1_Intron	NM_005462	NP_005453	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	294							protein binding			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4	Acute lymphoblastic leukemia(192;6.56e-05)														HNSCC(15;0.026)			---	---	---	---
Unknown	0	broad.mit.edu	37	X	143923051	143923052	+	IGR	INS	-	GAT	GAT			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:143923051_143923052insGAT								UBE2NL (954696 upstream) : SPANXN1 (406055 downstream)																																			---	---	---	---
HSFX2	100130086	broad.mit.edu	37	X	148731302	148731303	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:148731302_148731303delAA	uc004fdl.2	-						HSFX1_uc004fdm.2_Intron	NM_016153	NP_057237			heat shock transcription factor family, X linked							cytoplasm|nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
MTM1	4534	broad.mit.edu	37	X	149783252	149783253	+	Intron	DEL	AA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149783252_149783253delAA	uc004fef.3	+						MTM1_uc011mxx.1_Intron|MTM1_uc011mxy.1_Intron|MTM1_uc011mxz.1_Intron|MTM1_uc010nte.2_Intron	NM_000252	NP_000243			myotubularin						endosome to lysosome transport|intermediate filament organization|mitochondrion distribution|mitochondrion morphogenesis|phosphatidylinositol dephosphorylation|protein transport|regulation of vacuole organization	filopodium|late endosome|plasma membrane|ruffle	intermediate filament binding|phosphatidylinositol binding|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein tyrosine phosphatase activity			upper_aerodigestive_tract(1)|ovary(1)|kidney(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
MTM1	4534	broad.mit.edu	37	X	149828974	149828974	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149828974delT	uc004fef.3	+						MTM1_uc011mxx.1_Intron|MTM1_uc011mxy.1_Intron|MTM1_uc011mxz.1_Intron|MTM1_uc010nte.2_Intron	NM_000252	NP_000243			myotubularin						endosome to lysosome transport|intermediate filament organization|mitochondrion distribution|mitochondrion morphogenesis|phosphatidylinositol dephosphorylation|protein transport|regulation of vacuole organization	filopodium|late endosome|plasma membrane|ruffle	intermediate filament binding|phosphatidylinositol binding|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein tyrosine phosphatase activity			upper_aerodigestive_tract(1)|ovary(1)|kidney(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
PASD1	139135	broad.mit.edu	37	X	150816900	150816900	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150816900delT	uc004fev.3	+							NM_173493	NP_775764			PAS domain containing 1							nucleus	signal transducer activity			ovary(3)	3	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	152879758	152879758	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152879758delT								FAM58A (15126 upstream) : DUSP9 (28139 downstream)																																			---	---	---	---
IDH3G	3421	broad.mit.edu	37	X	153053246	153053246	+	Intron	DEL	G	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153053246delG	uc004fip.2	-						IDH3G_uc004fio.2_Intron|IDH3G_uc004fiq.2_Intron|IDH3G_uc010num.2_Intron|IDH3G_uc004fir.2_Intron|IDH3G_uc004fit.1_Intron|IDH3G_uc004fis.2_Intron|IDH3G_uc004fiu.2_5'Flank	NM_004135	NP_004126			isocitrate dehydrogenase 3 (NAD+) gamma isoform						carbohydrate metabolic process|isocitrate metabolic process|tricarboxylic acid cycle	mitochondrial matrix|nucleolus	ATP binding|isocitrate dehydrogenase (NAD+) activity|magnesium ion binding|NAD binding				0	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)				NADH(DB00157)													---	---	---	---
MECP2	4204	broad.mit.edu	37	X	153297558	153297558	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153297558delC	uc004fjv.2	-						MECP2_uc004fjw.2_Intron	NM_004992	NP_004983			methyl CpG binding protein 2 isoform 1						negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	heterochromatin|nucleus	double-stranded methylated DNA binding|protein domain specific binding|protein N-terminus binding|transcription corepressor activity				0	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
MECP2	4204	broad.mit.edu	37	X	153357615	153357617	+	Intron	DEL	AAA	-	-	rs79072307		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153357615_153357617delAAA	uc004fjv.2	-						MECP2_uc004fjw.2_Intron	NM_004992	NP_004983			methyl CpG binding protein 2 isoform 1						negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	heterochromatin|nucleus	double-stranded methylated DNA binding|protein domain specific binding|protein N-terminus binding|transcription corepressor activity				0	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
CLIC2	1193	broad.mit.edu	37	X	154520373	154520373	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154520373delT	uc004fnf.2	-						CLIC2_uc010nvj.1_Intron	NM_001289	NP_001280			chloride intracellular channel 2						signal transduction	chloride channel complex|cytoplasm|nucleus	voltage-gated chloride channel activity			large_intestine(1)|ovary(1)|skin(1)	3	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)																	---	---	---	---
CLIC2	1193	broad.mit.edu	37	X	154522807	154522807	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154522807delA	uc004fnf.2	-						CLIC2_uc010nvj.1_Intron	NM_001289	NP_001280			chloride intracellular channel 2						signal transduction	chloride channel complex|cytoplasm|nucleus	voltage-gated chloride channel activity			large_intestine(1)|ovary(1)|skin(1)	3	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	155035037	155035039	+	IGR	DEL	AAC	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:155035037_155035039delAAC								SPRY3 (22920 upstream) : VAMP7 (75908 downstream)																																			---	---	---	---
VAMP7	6845	broad.mit.edu	37	X	155128055	155128055	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:155128055delA	uc004fnr.2	+						VAMP7_uc004fnt.2_Intron|VAMP7_uc011naa.1_Intron|VAMP7_uc011nab.1_Intron|VAMP7_uc004fns.2_Intron|VAMP7_uc011nac.1_Intron	NM_005638	NP_005629			vesicle-associated membrane protein 7 isoform 1						calcium ion-dependent exocytosis|endosome to lysosome transport|eosinophil degranulation|ER to Golgi vesicle-mediated transport|neutrophil degranulation|phagocytosis, engulfment|post-Golgi vesicle-mediated transport|protein transport|vesicle fusion	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|phagocytic vesicle membrane|plasma membrane|SNARE complex|transport vesicle membrane	protein binding				0	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)																	---	---	---	---
Unknown	0	broad.mit.edu	37	X	155202294	155202294	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:155202294delT								VAMP7 (28862 upstream) : IL9R (24952 downstream)																																			---	---	---	---
RPS4Y1	6192	broad.mit.edu	37	Y	2710309	2710310	+	Intron	DEL	TT	-	-	rs34402762		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:2710309_2710310delTT	uc004fqi.2	+							NM_001008	NP_000999			ribosomal protein S4, Y-linked 1 Y isoform						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit|polysome	rRNA binding|structural constituent of ribosome				0																		---	---	---	---
ZFY	7544	broad.mit.edu	37	Y	2843719	2843719	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:2843719delT	uc004fqj.2	+						ZFY_uc010nwd.1_Intron|ZFY_uc011nan.1_Intron|ZFY_uc010nwe.2_Intron	NM_003411	NP_003402			zinc finger protein, Y-linked isoform 1						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ZFY	7544	broad.mit.edu	37	Y	2847675	2847675	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:2847675delA	uc004fqj.2	+	8	2368	c.2047delA	c.(2047-2049)AAAfs	p.K683fs	ZFY_uc011nan.1_Frame_Shift_Del_p.K492fs|ZFY_uc010nwe.2_Frame_Shift_Del_p.K606fs	NM_003411	NP_003402	P08048	ZFY_HUMAN	zinc finger protein, Y-linked isoform 1	683					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
PCDH11Y	83259	broad.mit.edu	37	Y	4966326	4966326	+	Frame_Shift_Del	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:4966326delA	uc004fqo.2	+	2	1441	c.707delA	c.(706-708)CAAfs	p.Q236fs	PCDH11Y_uc010nwg.1_Frame_Shift_Del_p.Q225fs|PCDH11Y_uc004fql.1_Frame_Shift_Del_p.Q225fs|PCDH11Y_uc004fqm.1_Frame_Shift_Del_p.Q225fs|PCDH11Y_uc004fqn.1_Frame_Shift_Del_p.Q236fs|PCDH11Y_uc004fqp.1_Frame_Shift_Del_p.Q7fs	NM_032973	NP_116755	Q9BZA8	PC11Y_HUMAN	protocadherin 11 Y-linked isoform c	236	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	Y	7644475	7644475	+	Intron	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:7644475delC	uc004frg.2	-											Homo sapiens raftlin, lipid raft linker 1, mRNA (cDNA clone IMAGE:5298352).																														---	---	---	---
Unknown	0	broad.mit.edu	37	Y	9951328	9951329	+	IGR	DEL	AA	-	-	rs148567096		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:9951328_9951329delAA								TTTY22 (300474 upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	13392769	13392769	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13392769delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	13400003	13400004	+	IGR	INS	-	C	C	rs113389937		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13400003_13400004insC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	13448783	13448787	+	IGR	DEL	CCACA	-	-	rs113649973		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13448783_13448787delCCACA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	13456418	13456422	+	IGR	DEL	CACTG	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13456418_13456422delCACTG								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	13464699	13464699	+	IGR	DEL	C	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13464699delC								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	13867011	13867011	+	IGR	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13867011delT								None (None upstream) : TTTY15 (907287 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	14548627	14548627	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:14548627delA								None (None upstream) : TTTY15 (225671 downstream)																																			---	---	---	---
USP9Y	8287	broad.mit.edu	37	Y	14923725	14923725	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:14923725delT	uc004fst.1	+						USP9Y_uc010nwu.1_Intron	NM_004654	NP_004645			ubiquitin specific protease 9, Y-linked						BMP signaling pathway|protein deubiquitination|spermatogenesis|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity				0																		---	---	---	---
USP9Y	8287	broad.mit.edu	37	Y	14945827	14945828	+	Intron	DEL	TT	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:14945827_14945828delTT	uc004fst.1	+						USP9Y_uc010nwu.1_Intron	NM_004654	NP_004645			ubiquitin specific protease 9, Y-linked						BMP signaling pathway|protein deubiquitination|spermatogenesis|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity				0																		---	---	---	---
DDX3Y	8653	broad.mit.edu	37	Y	15025445	15025445	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:15025445delA	uc004fsu.1	+						DDX3Y_uc010nwv.1_Intron|DDX3Y_uc011naq.1_Intron|DDX3Y_uc004fsv.2_Intron|DDX3Y_uc010nww.1_Intron|DDX3Y_uc011nar.1_Intron	NM_001122665	NP_001116137			DEAD (Asp-Glu-Ala-Asp) box polypeptide 3,							cytoplasm|nucleus	ATP binding|ATP-dependent helicase activity|DNA binding|RNA binding				0																		---	---	---	---
UTY	7404	broad.mit.edu	37	Y	15522997	15522997	+	Intron	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:15522997delA	uc004fsx.1	-						UTY_uc004fsy.2_Intron|UTY_uc004fsz.2_Intron	NM_007125	NP_009056			tetratricopeptide repeat protein isoform 3						chromatin modification	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	Y	21065875	21065875	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:21065875delA								NCRNA00185 (25761 upstream) : TTTY14 (28712 downstream)																																			---	---	---	---
CYorf15B	84663	broad.mit.edu	37	Y	21758039	21758042	+	5'Flank	DEL	AAAA	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:21758039_21758042delAAAA	uc011nay.1	+							NM_032576	NP_115965			lipopolysaccaride-specific response 5-like												0																		---	---	---	---
RBMY2EP	159125	broad.mit.edu	37	Y	23557693	23557693	+	Intron	DEL	T	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:23557693delT	uc004fun.1	-							NR_001574				Homo sapiens RNA binding motif protein, Y-linked, family 2, member E pseudogene (RBMY2EP), non-coding RNA.												0																		---	---	---	---
Unknown	0	broad.mit.edu	37	Y	28774180	28774180	+	IGR	DEL	A	-	-			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:28774180delA								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	Y	28813935	28813936	+	IGR	INS	-	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:28813935_28813936insT								None (None upstream) : None (None downstream)																																			---	---	---	---
PLEKHN1	84069	broad.mit.edu	37	1	909406	909406	+	Missense_Mutation	SNP	C	T	T	rs149299504	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:909406C>T	uc001ace.2	+	13	1819	c.1784C>T	c.(1783-1785)CCG>CTG	p.P595L	PLEKHN1_uc001acd.2_Missense_Mutation_p.P543L|PLEKHN1_uc001acf.2_Missense_Mutation_p.P508L	NM_032129	NP_115505	Q494U1	PKHN1_HUMAN	pleckstrin homology domain containing, family N	595											0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.93e-23)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.00095)|Kidney(185;0.0023)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.199)														---	---	---	---
DVL1	1855	broad.mit.edu	37	1	1273708	1273708	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1273708G>A	uc001aer.3	-	13	1420	c.1373C>T	c.(1372-1374)ACG>ATG	p.T458M	DVL1_uc002quu.2_Missense_Mutation_p.T200M|DVL1_uc009vka.2_Missense_Mutation_p.T141M|DVL1_uc001aeu.1_Missense_Mutation_p.T217M	NM_004421	NP_004412	O14640	DVL1_HUMAN	dishevelled 1	483	DEP.				canonical Wnt receptor signaling pathway|dendrite morphogenesis|intracellular signal transduction|negative regulation of protein binding|negative regulation of protein kinase activity|neural tube development|neuromuscular junction development|neurotransmitter secretion|positive regulation of transcription, DNA-dependent|positive regulation of Wnt receptor signaling pathway|protein localization to nucleus|receptor clustering|transcription from RNA polymerase II promoter|Wnt receptor signaling pathway, planar cell polarity pathway	cytoplasmic membrane-bounded vesicle|cytosol|plasma membrane|synapse|synaptosome	frizzled binding|identical protein binding|protein kinase binding|signal transducer activity				0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)														---	---	---	---
DVL1	1855	broad.mit.edu	37	1	1273764	1273764	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1273764C>T	uc001aer.3	-	13	1364	c.1317G>A	c.(1315-1317)CGG>CGA	p.R439R	DVL1_uc002quu.2_Silent_p.R181R|DVL1_uc009vka.2_Silent_p.R122R|DVL1_uc001aeu.1_Silent_p.R198R	NM_004421	NP_004412	O14640	DVL1_HUMAN	dishevelled 1	464	DEP.				canonical Wnt receptor signaling pathway|dendrite morphogenesis|intracellular signal transduction|negative regulation of protein binding|negative regulation of protein kinase activity|neural tube development|neuromuscular junction development|neurotransmitter secretion|positive regulation of transcription, DNA-dependent|positive regulation of Wnt receptor signaling pathway|protein localization to nucleus|receptor clustering|transcription from RNA polymerase II promoter|Wnt receptor signaling pathway, planar cell polarity pathway	cytoplasmic membrane-bounded vesicle|cytosol|plasma membrane|synapse|synaptosome	frizzled binding|identical protein binding|protein kinase binding|signal transducer activity				0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)														---	---	---	---
CDK11A	728642	broad.mit.edu	37	1	1635056	1635056	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1635056C>A	uc009vks.2	-	18	2027	c.1919G>T	c.(1918-1920)GGG>GTG	p.G640V	CDK11B_uc001ags.1_Intron|CDK11B_uc001agt.1_Intron|CDK11B_uc001aha.1_Intron|CDK11B_uc001agw.1_Intron|CDK11B_uc001agv.1_Intron|CDK11B_uc001agy.1_Intron|CDK11B_uc001agx.1_Intron|CDK11B_uc001agz.1_Intron|SLC35E2B_uc001ahh.3_Intron|SLC35E2_uc009vkm.1_Intron|CDK11A_uc001ahj.3_Missense_Mutation_p.G147V|CDK11A_uc009vkp.2_Missense_Mutation_p.G257V|CDK11A_uc009vkq.2_RNA|CDK11A_uc009vkr.2_Missense_Mutation_p.G630V	NM_024011	NP_076916	Q9UQ88	CD11A_HUMAN	cell division cycle 2-like 2 isoform 1	643	Protein kinase.				apoptosis|mitosis|regulation of cell growth|regulation of mRNA processing|regulation of transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|cyclin-dependent protein kinase activity|protein binding			stomach(1)	1																		---	---	---	---
NADK	65220	broad.mit.edu	37	1	1685986	1685986	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1685986G>A	uc009vkw.2	-	8	961	c.840C>T	c.(838-840)TAC>TAT	p.Y280Y	NADK_uc001aic.2_Silent_p.Y280Y|NADK_uc001aid.3_Silent_p.Y280Y|NADK_uc001aie.2_Silent_p.Y425Y|NADK_uc010nyv.1_Silent_p.Y248Y|NADK_uc009vkx.1_Silent_p.Y158Y	NM_023018	NP_075394	O95544	NADK_HUMAN	NAD kinase	280					ATP metabolic process|NAD metabolic process|water-soluble vitamin metabolic process	cytosol	ATP binding|metal ion binding|NAD+ kinase activity|protein binding				0	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.61e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;8.75e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.33e-23)|GBM - Glioblastoma multiforme(42;1.35e-07)|Colorectal(212;0.000203)|COAD - Colon adenocarcinoma(227;0.000225)|Kidney(185;0.00265)|STAD - Stomach adenocarcinoma(132;0.00655)|BRCA - Breast invasive adenocarcinoma(365;0.00855)|KIRC - Kidney renal clear cell carcinoma(229;0.0382)|Lung(427;0.207)														---	---	---	---
MORN1	79906	broad.mit.edu	37	1	2303987	2303987	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2303987T>G	uc001ajb.1	-	8	699	c.678A>C	c.(676-678)GAA>GAC	p.E226D	MORN1_uc009vld.2_Missense_Mutation_p.E202D|MORN1_uc001ajd.1_Missense_Mutation_p.E226D	NM_024848	NP_079124	Q5T089	MORN1_HUMAN	MORN repeat containing 1	226										ovary(2)|central_nervous_system(1)	3	all_cancers(77;0.000194)|all_epithelial(69;9.96e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;3.3e-15)|all_lung(118;1.15e-06)|Lung NSC(185;6.26e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;2.21e-37)|OV - Ovarian serous cystadenocarcinoma(86;5.01e-23)|GBM - Glioblastoma multiforme(42;2.8e-08)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00137)|BRCA - Breast invasive adenocarcinoma(365;0.00488)|STAD - Stomach adenocarcinoma(132;0.00665)|KIRC - Kidney renal clear cell carcinoma(229;0.0203)|Lung(427;0.212)														---	---	---	---
MORN1	79906	broad.mit.edu	37	1	2318901	2318901	+	Silent	SNP	G	A	A	rs142498651	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:2318901G>A	uc001ajb.1	-	4	336	c.315C>T	c.(313-315)GCC>GCT	p.A105A	MORN1_uc009vld.2_Silent_p.A81A|MORN1_uc001ajd.1_Silent_p.A105A|MORN1_uc010nyy.1_Missense_Mutation_p.P48L	NM_024848	NP_079124	Q5T089	MORN1_HUMAN	MORN repeat containing 1	105	MORN 3.									ovary(2)|central_nervous_system(1)	3	all_cancers(77;0.000194)|all_epithelial(69;9.96e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;3.3e-15)|all_lung(118;1.15e-06)|Lung NSC(185;6.26e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;2.21e-37)|OV - Ovarian serous cystadenocarcinoma(86;5.01e-23)|GBM - Glioblastoma multiforme(42;2.8e-08)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00137)|BRCA - Breast invasive adenocarcinoma(365;0.00488)|STAD - Stomach adenocarcinoma(132;0.00665)|KIRC - Kidney renal clear cell carcinoma(229;0.0203)|Lung(427;0.212)														---	---	---	---
PRDM16	63976	broad.mit.edu	37	1	3301858	3301858	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3301858C>T	uc001akf.2	+						PRDM16_uc001akc.2_Intron|PRDM16_uc001akd.2_Intron|PRDM16_uc001ake.2_Intron|PRDM16_uc009vlh.2_Intron	NM_022114	NP_071397			PR domain containing 16 isoform 1						brown fat cell differentiation|negative regulation of granulocyte differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of cellular respiration|transcription, DNA-dependent	transcriptional repressor complex	protein binding|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding			lung(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)				T	EVI1	MDS|AML								---	---	---	---
TP73	7161	broad.mit.edu	37	1	3644714	3644714	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3644714C>T	uc001akp.2	+	9	1117	c.1007C>T	c.(1006-1008)GCC>GTC	p.A336V	TP73_uc001akq.2_Missense_Mutation_p.A336V|TP73_uc010nzj.1_Missense_Mutation_p.A287V|TP73_uc001akr.2_Missense_Mutation_p.A287V|TP73_uc009vlk.1_Missense_Mutation_p.A287V|TP73_uc001aks.2_Missense_Mutation_p.A287V|TP73_uc010nzk.1_Missense_Mutation_p.A265V|TP73_uc010nzl.1_5'UTR	NM_005427	NP_005418	O15350	P73_HUMAN	tumor protein p73 isoform a	336					cellular response to UV|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|mismatch repair|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of JUN kinase activity|negative regulation of neuron apoptosis|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|protein tetramerization|response to gamma radiation|response to X-ray	chromatin|cytosol|transcription factor complex	chromatin binding|damaged DNA binding|double-stranded DNA binding|metal ion binding|p53 binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding|transcription repressor activity			ovary(1)|lung(1)	2	all_cancers(77;0.0395)|Ovarian(185;0.0634)|Lung NSC(156;0.188)|all_lung(157;0.198)	all_epithelial(116;7.42e-17)|all_lung(118;1.86e-06)|Lung NSC(185;0.000163)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.109)|Ovarian(437;0.127)		Epithelial(90;5.57e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.87e-22)|GBM - Glioblastoma multiforme(42;5.72e-16)|Colorectal(212;2.22e-05)|COAD - Colon adenocarcinoma(227;8.48e-05)|Kidney(185;0.000539)|BRCA - Breast invasive adenocarcinoma(365;0.000868)|STAD - Stomach adenocarcinoma(132;0.0072)|KIRC - Kidney renal clear cell carcinoma(229;0.00751)|Lung(427;0.226)														---	---	---	---
TP73	7161	broad.mit.edu	37	1	3644746	3644746	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3644746C>T	uc001akp.2	+	9	1149	c.1039C>T	c.(1039-1041)CGG>TGG	p.R347W	TP73_uc001akq.2_Missense_Mutation_p.R347W|TP73_uc010nzj.1_Missense_Mutation_p.R298W|TP73_uc001akr.2_Missense_Mutation_p.R298W|TP73_uc009vlk.1_Missense_Mutation_p.R298W|TP73_uc001aks.2_Missense_Mutation_p.R298W|TP73_uc010nzk.1_Missense_Mutation_p.R276W|TP73_uc010nzl.1_5'UTR	NM_005427	NP_005418	O15350	P73_HUMAN	tumor protein p73 isoform a	347	Oligomerization (Potential).|Interaction with HIPK2.				cellular response to UV|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|mismatch repair|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of JUN kinase activity|negative regulation of neuron apoptosis|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|protein tetramerization|response to gamma radiation|response to X-ray	chromatin|cytosol|transcription factor complex	chromatin binding|damaged DNA binding|double-stranded DNA binding|metal ion binding|p53 binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding|transcription repressor activity			ovary(1)|lung(1)	2	all_cancers(77;0.0395)|Ovarian(185;0.0634)|Lung NSC(156;0.188)|all_lung(157;0.198)	all_epithelial(116;7.42e-17)|all_lung(118;1.86e-06)|Lung NSC(185;0.000163)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.109)|Ovarian(437;0.127)		Epithelial(90;5.57e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.87e-22)|GBM - Glioblastoma multiforme(42;5.72e-16)|Colorectal(212;2.22e-05)|COAD - Colon adenocarcinoma(227;8.48e-05)|Kidney(185;0.000539)|BRCA - Breast invasive adenocarcinoma(365;0.000868)|STAD - Stomach adenocarcinoma(132;0.0072)|KIRC - Kidney renal clear cell carcinoma(229;0.00751)|Lung(427;0.226)														---	---	---	---
KIAA0562	9731	broad.mit.edu	37	1	3764134	3764134	+	Missense_Mutation	SNP	G	A	A	rs144370302	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3764134G>A	uc001aky.2	-	4	690	c.331C>T	c.(331-333)CGG>TGG	p.R111W	KIAA0562_uc010nzm.1_RNA|KIAA0562_uc001akz.2_Missense_Mutation_p.R111W	NM_014704	NP_055519	O60308	CE104_HUMAN	glycine-, glutamate-,	111						centriole	binding				0	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_epithelial(116;3.96e-21)|all_lung(118;2.74e-08)|Lung NSC(185;6.4e-06)|Breast(487;0.00066)|Renal(390;0.00121)|Hepatocellular(190;0.00335)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.031)|Lung SC(97;0.0548)|Medulloblastoma(700;0.212)		Epithelial(90;6.85e-39)|OV - Ovarian serous cystadenocarcinoma(86;1.59e-22)|GBM - Glioblastoma multiforme(42;3.16e-16)|Colorectal(212;2.01e-05)|COAD - Colon adenocarcinoma(227;7.99e-05)|BRCA - Breast invasive adenocarcinoma(365;0.000389)|Kidney(185;0.000513)|STAD - Stomach adenocarcinoma(132;0.00709)|KIRC - Kidney renal clear cell carcinoma(229;0.00714)|Lung(427;0.137)														---	---	---	---
C1orf174	339448	broad.mit.edu	37	1	3807160	3807160	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:3807160C>T	uc001alf.2	-	3	698	c.591G>A	c.(589-591)CGG>CGA	p.R197R	C1orf174_uc009vls.2_RNA	NM_207356	NP_997239	Q8IYL3	CA174_HUMAN	hypothetical protein LOC339448	197											0	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_cancers(23;5.09e-25)|all_epithelial(116;9.35e-17)|all_lung(118;1.09e-06)|Lung NSC(185;0.000139)|all_neural(13;0.00287)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0219)|all_hematologic(16;0.027)|Colorectal(325;0.0276)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.0743)|Ovarian(437;0.127)		Epithelial(90;1.55e-39)|OV - Ovarian serous cystadenocarcinoma(86;5.99e-23)|GBM - Glioblastoma multiforme(42;2.22e-17)|Colorectal(212;1.08e-05)|COAD - Colon adenocarcinoma(227;5.49e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.000365)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.19)														---	---	---	---
AJAP1	55966	broad.mit.edu	37	1	4772065	4772065	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:4772065C>A	uc001alm.1	+	2	516	c.135C>A	c.(133-135)GGC>GGA	p.G45G	AJAP1_uc001aln.2_Silent_p.G45G	NM_001042478	NP_001035943	Q9UKB5	AJAP1_HUMAN	adherens junction associated protein 1	45	Extracellular (Potential).				cell adhesion	adherens junction|apical plasma membrane|basolateral plasma membrane|integral to membrane				lung(1)	1	all_cancers(77;0.071)|Ovarian(185;0.0721)	all_cancers(23;1.77e-36)|all_epithelial(116;1.26e-21)|all_lung(118;3.51e-08)|Lung NSC(185;3.47e-06)|all_neural(13;8.84e-06)|all_hematologic(16;7.61e-05)|Breast(487;0.000507)|Renal(390;0.0007)|Colorectal(325;0.00117)|Hepatocellular(190;0.0071)|Glioma(11;0.0155)|Myeloproliferative disorder(586;0.0258)|Ovarian(437;0.0409)|Lung SC(97;0.133)|Medulloblastoma(700;0.215)		Epithelial(90;3.89e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.97e-19)|GBM - Glioblastoma multiforme(42;3.71e-19)|Colorectal(212;4.57e-06)|COAD - Colon adenocarcinoma(227;0.00019)|Kidney(185;0.000969)|BRCA - Breast invasive adenocarcinoma(365;0.00122)|STAD - Stomach adenocarcinoma(132;0.00578)|KIRC - Kidney renal clear cell carcinoma(229;0.0126)|READ - Rectum adenocarcinoma(331;0.0689)														---	---	---	---
ICMT	23463	broad.mit.edu	37	1	6285180	6285180	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6285180G>A	uc001amk.2	-	5	888	c.815C>T	c.(814-816)ACG>ATG	p.T272M	ICMT_uc001aml.2_Missense_Mutation_p.T176M	NM_012405	NP_036537	O60725	ICMT_HUMAN	isoprenylcysteine carboxyl methyltransferase	272					protein targeting to membrane	endoplasmic reticulum membrane|integral to membrane|membrane fraction	protein C-terminal S-isoprenylcysteine carboxyl O-methyltransferase activity				0	Ovarian(185;0.0634)	all_cancers(23;5.85e-39)|all_epithelial(116;2.4e-22)|all_lung(118;2.65e-08)|Lung NSC(185;6.45e-07)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000688)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211)		Epithelial(90;5.52e-38)|GBM - Glioblastoma multiforme(13;6.51e-32)|OV - Ovarian serous cystadenocarcinoma(86;3.03e-19)|Colorectal(212;7.08e-08)|COAD - Colon adenocarcinoma(227;8.35e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(365;0.00109)|STAD - Stomach adenocarcinoma(132;0.00313)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)														---	---	---	---
TAS1R1	80835	broad.mit.edu	37	1	6637065	6637065	+	Missense_Mutation	SNP	C	T	T	rs145341910		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6637065C>T	uc001ant.2	+	5	1529	c.1529C>T	c.(1528-1530)ACG>ATG	p.T510M	TAS1R1_uc001anu.2_Missense_Mutation_p.T256M|TAS1R1_uc001anv.2_Missense_Mutation_p.T256M|TAS1R1_uc001anw.2_Intron|ZBTB48_uc009vmc.1_5'Flank|ZBTB48_uc001anx.2_5'Flank	NM_138697	NP_619642	Q7RTX1	TS1R1_HUMAN	sweet taste receptor T1r isoform b	510	Extracellular (Potential).				sensory perception of umami taste	plasma membrane	protein heterodimerization activity|taste receptor activity			ovary(1)|central_nervous_system(1)|skin(1)	3	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;8.73e-34)|all_epithelial(116;9.26e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Breast(487;0.000353)|Renal(390;0.0007)|Colorectal(325;0.00104)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443)		Colorectal(212;1.29e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00108)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0642)														---	---	---	---
ZBTB48	3104	broad.mit.edu	37	1	6640751	6640751	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:6640751G>A	uc009vmc.1	+	2	205	c.82G>A	c.(82-84)GCC>ACC	p.A28T	ZBTB48_uc001anx.2_Missense_Mutation_p.A28T|ZBTB48_uc009vmd.1_Missense_Mutation_p.A28T	NM_005341	NP_005332	P10074	ZBT48_HUMAN	zinc finger and BTB domain containing 48	28	BTB.					cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;7.39e-28)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;1.35e-07)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(304;0.00109)|STAD - Stomach adenocarcinoma(132;0.017)|READ - Rectum adenocarcinoma(331;0.0642)														---	---	---	---
CAMTA1	23261	broad.mit.edu	37	1	7723742	7723742	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7723742A>C	uc001aoi.2	+	9	1342	c.1135A>C	c.(1135-1137)ACA>CCA	p.T379P		NM_015215	NP_056030	Q9Y6Y1	CMTA1_HUMAN	calmodulin-binding transcription activator 1	379					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)														---	---	---	---
CAMTA1	23261	broad.mit.edu	37	1	7811283	7811283	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7811283C>T	uc001aoi.2	+	20	4921	c.4714C>T	c.(4714-4716)CAG>TAG	p.Q1572*	CAMTA1_uc001aok.3_Nonsense_Mutation_p.Q615*|CAMTA1_uc001aoj.2_Nonsense_Mutation_p.Q535*|CAMTA1_uc009vmf.2_Nonsense_Mutation_p.Q162*	NM_015215	NP_056030	Q9Y6Y1	CMTA1_HUMAN	calmodulin-binding transcription activator 1	1572	IQ 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	calmodulin binding			ovary(5)|central_nervous_system(2)|breast(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)														---	---	---	---
PER3	8863	broad.mit.edu	37	1	7845496	7845496	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7845496T>C	uc001aoo.2	+						PER3_uc009vmg.1_Intron|PER3_uc009vmh.1_Intron|PER3_uc001aop.2_Intron|PER3_uc010nzw.1_Intron|PER3_uc001aon.2_Intron	NM_016831	NP_058515			period 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	signal transducer activity			ovary(1)|pancreas(1)|skin(1)	3	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
PER3	8863	broad.mit.edu	37	1	7886681	7886681	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:7886681A>G	uc001aoo.2	+	16	2250	c.2075A>G	c.(2074-2076)GAT>GGT	p.D692G	PER3_uc009vmg.1_Missense_Mutation_p.D700G|PER3_uc009vmh.1_Missense_Mutation_p.D693G|PER3_uc001aop.2_Missense_Mutation_p.D700G|PER3_uc010nzw.1_Missense_Mutation_p.D381G	NM_016831	NP_058515	P56645	PER3_HUMAN	period 3	692	CSNK1E binding domain (By similarity).				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	signal transducer activity			ovary(1)|pancreas(1)|skin(1)	3	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
RERE	473	broad.mit.edu	37	1	8421529	8421529	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8421529G>A	uc001ape.2	-	19	2848	c.2038C>T	c.(2038-2040)CCA>TCA	p.P680S	RERE_uc001apf.2_Missense_Mutation_p.P680S|RERE_uc010nzx.1_Missense_Mutation_p.P412S|RERE_uc001apd.2_Missense_Mutation_p.P126S	NM_012102	NP_036234	Q9P2R6	RERE_HUMAN	atrophin-1 like protein isoform a	680					multicellular organismal development|NLS-bearing substrate import into nucleus	mitochondrion	poly-glutamine tract binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)														---	---	---	---
ENO1	2023	broad.mit.edu	37	1	8924086	8924086	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8924086C>T	uc001apj.1	-	9	1082	c.931G>A	c.(931-933)GCA>ACA	p.A311T	ENO1_uc001api.1_Missense_Mutation_p.A215T|ENO1_uc001apk.1_Missense_Mutation_p.A256T|ENO1_uc001apl.1_Missense_Mutation_p.A311T|ENO1_uc009vmi.1_Missense_Mutation_p.A268T|ENO1_uc009vmj.1_Missense_Mutation_p.A311T|ENO1_uc009vmk.1_Missense_Mutation_p.A185T|ENO1_uc009vml.1_Missense_Mutation_p.A311T	NM_001428	NP_001419	P06733	ENOA_HUMAN	enolase 1	311					gluconeogenesis|glycolysis|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|response to virus	phosphopyruvate hydratase complex|plasma membrane|sarcomere	DNA binding|magnesium ion binding|phosphopyruvate hydratase activity|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(2)|kidney(1)|central_nervous_system(1)	4	Ovarian(185;0.0661)|all_lung(157;0.127)	all_epithelial(116;2.54e-20)|all_lung(118;2.99e-06)|Lung NSC(185;6.25e-06)|Renal(390;0.000147)|Breast(348;0.00086)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;2.42e-07)|COAD - Colon adenocarcinoma(227;2.78e-05)|Kidney(185;0.000249)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.00177)|BRCA - Breast invasive adenocarcinoma(304;0.00185)|READ - Rectum adenocarcinoma(331;0.0642)														---	---	---	---
SLC2A5	6518	broad.mit.edu	37	1	9097834	9097834	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9097834C>T	uc001apo.2	-	12	1609	c.1317G>A	c.(1315-1317)CCG>CCA	p.P439P	SLC2A5_uc010nzy.1_Silent_p.P380P|SLC2A5_uc010nzz.1_Silent_p.P324P|SLC2A5_uc010oaa.1_Silent_p.P395P|SLC2A5_uc010oab.1_Silent_p.P439P	NM_003039	NP_003030	P22732	GTR5_HUMAN	solute carrier family 2 (facilitated	439	Extracellular (Potential).				carbohydrate metabolic process	integral to membrane|plasma membrane	fructose transmembrane transporter activity|glucose transmembrane transporter activity			pancreas(2)|ovary(1)	3	Ovarian(185;0.112)|all_lung(157;0.185)	all_epithelial(116;1.34e-15)|all_lung(118;9.46e-05)|Lung NSC(185;0.000172)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.00715)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;7.78e-07)|COAD - Colon adenocarcinoma(227;8.83e-05)|Kidney(185;0.000286)|KIRC - Kidney renal clear cell carcinoma(229;0.00103)|STAD - Stomach adenocarcinoma(132;0.0019)|BRCA - Breast invasive adenocarcinoma(304;0.00199)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
SPSB1	80176	broad.mit.edu	37	1	9427540	9427540	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9427540G>A	uc010oae.1	+	3	1067	c.728G>A	c.(727-729)CGC>CAC	p.R243H	SPSB1_uc001apv.2_Missense_Mutation_p.R243H	NM_025106	NP_079382	Q96BD6	SPSB1_HUMAN	splA/ryanodine receptor domain and SOCS box	243	SOCS box.				intracellular signal transduction	cytoplasm					0	all_lung(157;0.194)	all_epithelial(116;4.38e-15)|all_lung(118;0.000156)|Lung NSC(185;0.000446)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;2.72e-07)|COAD - Colon adenocarcinoma(227;9.12e-05)|Kidney(185;0.000296)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00193)|BRCA - Breast invasive adenocarcinoma(304;0.00202)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
CLSTN1	22883	broad.mit.edu	37	1	9795139	9795139	+	Silent	SNP	G	A	A	rs35981252	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:9795139G>A	uc001aqh.2	-	14	2736	c.1977C>T	c.(1975-1977)GGC>GGT	p.G659G	CLSTN1_uc001aqi.2_Silent_p.G649G|CLSTN1_uc010oag.1_Silent_p.G640G|CLSTN1_uc001aqf.2_5'Flank	NM_001009566	NP_001009566	O94985	CSTN1_HUMAN	calsyntenin 1 isoform 1	659	Extracellular (Potential).				homophilic cell adhesion	cell junction|cell projection|endoplasmic reticulum membrane|Golgi membrane|integral to membrane|nucleus|postsynaptic membrane	calcium ion binding			skin(1)	1	all_lung(157;0.222)	all_lung(284;4.03e-05)|Lung NSC(185;6.93e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;8.36e-08)|COAD - Colon adenocarcinoma(227;1.93e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|STAD - Stomach adenocarcinoma(132;0.00644)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
UBE4B	10277	broad.mit.edu	37	1	10166605	10166605	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10166605C>T	uc001aqs.3	+	7	1873	c.1160C>T	c.(1159-1161)ACG>ATG	p.T387M	UBE4B_uc001aqr.3_Intron|UBE4B_uc010oai.1_Intron|UBE4B_uc010oaj.1_Intron	NM_001105562	NP_001099032	O95155	UBE4B_HUMAN	ubiquitination factor E4B isoform 1	387					apoptosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to UV	cytoplasm|ubiquitin ligase complex	enzyme binding			ovary(2)|skin(2)	4		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)														---	---	---	---
UBE4B	10277	broad.mit.edu	37	1	10211445	10211445	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10211445A>G	uc001aqs.3	+	21	3465	c.2752A>G	c.(2752-2754)ATG>GTG	p.M918V	UBE4B_uc001aqr.3_Missense_Mutation_p.M789V|UBE4B_uc010oai.1_RNA|UBE4B_uc010oaj.1_Missense_Mutation_p.M373V|UBE4B_uc001aqt.1_Missense_Mutation_p.M258V	NM_001105562	NP_001099032	O95155	UBE4B_HUMAN	ubiquitination factor E4B isoform 1	918					apoptosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to UV	cytoplasm|ubiquitin ligase complex	enzyme binding			ovary(2)|skin(2)	4		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)														---	---	---	---
KIF1B	23095	broad.mit.edu	37	1	10318559	10318559	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10318559T>A	uc001aqx.3	+	4	394	c.192T>A	c.(190-192)GAT>GAA	p.D64E	KIF1B_uc001aqv.3_Missense_Mutation_p.D64E|KIF1B_uc001aqw.3_Missense_Mutation_p.D64E|KIF1B_uc001aqy.2_Missense_Mutation_p.D64E|KIF1B_uc001aqz.2_Missense_Mutation_p.D64E|KIF1B_uc001ara.2_Missense_Mutation_p.D64E|KIF1B_uc001arb.2_Missense_Mutation_p.D64E|KIF1B_uc009vmt.2_RNA	NM_015074	NP_055889	O60333	KIF1B_HUMAN	kinesin family member 1B isoform b	64	Kinesin-motor.				anterograde axon cargo transport|apoptosis|neuromuscular synaptic transmission|neuron-neuron synaptic transmission	cytoplasmic vesicle membrane|microtubule|microtubule associated complex|mitochondrion	ATP binding|ATPase activity|kinesin binding|microtubule motor activity|protein binding			ovary(2)|upper_aerodigestive_tract(1)	3	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)														---	---	---	---
KIF1B	23095	broad.mit.edu	37	1	10327512	10327512	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10327512G>A	uc001aqx.3	+	6	706	c.504G>A	c.(502-504)GTG>GTA	p.V168V	KIF1B_uc001aqv.3_Silent_p.V168V|KIF1B_uc001aqw.3_Silent_p.V168V|KIF1B_uc001aqy.2_Silent_p.V168V|KIF1B_uc001aqz.2_Silent_p.V168V|KIF1B_uc001ara.2_Silent_p.V168V|KIF1B_uc001arb.2_Silent_p.V168V|KIF1B_uc009vmt.2_RNA	NM_015074	NP_055889	O60333	KIF1B_HUMAN	kinesin family member 1B isoform b	168	Kinesin-motor.				anterograde axon cargo transport|apoptosis|neuromuscular synaptic transmission|neuron-neuron synaptic transmission	cytoplasmic vesicle membrane|microtubule|microtubule associated complex|mitochondrion	ATP binding|ATPase activity|kinesin binding|microtubule motor activity|protein binding			ovary(2)|upper_aerodigestive_tract(1)	3	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)														---	---	---	---
KIF1B	23095	broad.mit.edu	37	1	10364001	10364001	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10364001C>T	uc001aqx.3	+						KIF1B_uc001aqv.3_Missense_Mutation_p.R920C|KIF1B_uc001aqw.3_Intron|KIF1B_uc001aqy.2_Intron|KIF1B_uc001aqz.2_Intron|KIF1B_uc001ara.2_Intron|KIF1B_uc001arb.2_Intron	NM_015074	NP_055889			kinesin family member 1B isoform b						anterograde axon cargo transport|apoptosis|neuromuscular synaptic transmission|neuron-neuron synaptic transmission	cytoplasmic vesicle membrane|microtubule|microtubule associated complex|mitochondrion	ATP binding|ATPase activity|kinesin binding|microtubule motor activity|protein binding			ovary(2)|upper_aerodigestive_tract(1)	3	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)														---	---	---	---
KIF1B	23095	broad.mit.edu	37	1	10364477	10364477	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10364477T>C	uc001aqx.3	+						KIF1B_uc001aqv.3_Silent_p.G1078G|KIF1B_uc001aqw.3_Intron|KIF1B_uc001aqy.2_Intron|KIF1B_uc001aqz.2_Intron|KIF1B_uc001ara.2_Intron|KIF1B_uc001arb.2_Intron	NM_015074	NP_055889			kinesin family member 1B isoform b						anterograde axon cargo transport|apoptosis|neuromuscular synaptic transmission|neuron-neuron synaptic transmission	cytoplasmic vesicle membrane|microtubule|microtubule associated complex|mitochondrion	ATP binding|ATPase activity|kinesin binding|microtubule motor activity|protein binding			ovary(2)|upper_aerodigestive_tract(1)	3	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)														---	---	---	---
KIF1B	23095	broad.mit.edu	37	1	10423344	10423344	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:10423344T>C	uc001aqx.3	+	41	4510	c.4308T>C	c.(4306-4308)AAT>AAC	p.N1436N	KIF1B_uc001aqw.3_Silent_p.N1390N|KIF1B_uc001aqy.2_Silent_p.N1410N|KIF1B_uc001aqz.2_Silent_p.N1436N|KIF1B_uc001ara.2_Silent_p.N1396N|KIF1B_uc001arb.2_Silent_p.N1422N	NM_015074	NP_055889	O60333	KIF1B_HUMAN	kinesin family member 1B isoform b	1436					anterograde axon cargo transport|apoptosis|neuromuscular synaptic transmission|neuron-neuron synaptic transmission	cytoplasmic vesicle membrane|microtubule|microtubule associated complex|mitochondrion	ATP binding|ATPase activity|kinesin binding|microtubule motor activity|protein binding			ovary(2)|upper_aerodigestive_tract(1)	3	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)														---	---	---	---
C1orf127	148345	broad.mit.edu	37	1	11018761	11018761	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11018761G>A	uc010oao.1	-						C1orf127_uc001arr.1_Intron|C1orf127_uc001ars.1_Intron	NM_173507	NP_775778			hypothetical protein LOC148345											ovary(1)	1	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)														---	---	---	---
UBIAD1	29914	broad.mit.edu	37	1	11345835	11345835	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11345835G>A	uc001asg.2	+	2	998	c.664G>A	c.(664-666)GCC>ACC	p.A222T		NM_013319	NP_037451	Q9Y5Z9	UBIA1_HUMAN	UbiA prenyltransferase domain containing 1	222	Helical; (Potential).				menaquinone biosynthetic process	endoplasmic reticulum membrane|integral to membrane|mitochondrion|nucleus	prenyltransferase activity				0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.000818)|all_lung(284;0.00105)|Colorectal(325;0.0062)|Breast(348;0.012)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.52e-06)|COAD - Colon adenocarcinoma(227;0.000254)|BRCA - Breast invasive adenocarcinoma(304;0.000299)|Kidney(185;0.000754)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0487)														---	---	---	---
PTCHD2	57540	broad.mit.edu	37	1	11561608	11561608	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:11561608C>T	uc001ash.3	+	2	697	c.559C>T	c.(559-561)CGG>TGG	p.R187W	PTCHD2_uc001asi.1_Missense_Mutation_p.R187W	NM_020780	NP_065831	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	187	Extracellular (Potential).				cholesterol homeostasis|regulation of lipid transport|smoothened signaling pathway	endoplasmic reticulum|integral to membrane|nuclear membrane	hedgehog receptor activity			skin(3)|ovary(2)|pancreas(1)|breast(1)	7	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)														---	---	---	---
PLOD1	5351	broad.mit.edu	37	1	12030838	12030838	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12030838A>G	uc001atm.2	+	17	1958	c.1867A>G	c.(1867-1869)ATG>GTG	p.M623V	PLOD1_uc010obb.1_Missense_Mutation_p.M670V	NM_000302	NP_000293	Q02809	PLOD1_HUMAN	lysyl hydroxylase 1 precursor	623					epidermis development|hydroxylysine biosynthetic process|protein modification process|response to hypoxia	rough endoplasmic reticulum membrane	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-lysine 5-dioxygenase activity|protein homodimerization activity			ovary(2)|breast(1)	3	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.06e-06)|COAD - Colon adenocarcinoma(227;0.000273)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000809)|KIRC - Kidney renal clear cell carcinoma(229;0.00267)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)	Minoxidil(DB00350)|Succinic acid(DB00139)|Vitamin C(DB00126)													---	---	---	---
VPS13D	55187	broad.mit.edu	37	1	12317132	12317132	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12317132C>T	uc001atv.2	+	9	1070	c.929C>T	c.(928-930)GCG>GTG	p.A310V	VPS13D_uc001atw.2_Missense_Mutation_p.A310V	NM_015378	NP_056193	Q5THJ4	VP13D_HUMAN	vacuolar protein sorting 13D isoform 1	310					protein localization					ovary(4)|pancreas(1)	5	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)														---	---	---	---
VPS13D	55187	broad.mit.edu	37	1	12335999	12335999	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12335999G>A	uc001atv.2	+	19	2495	c.2354G>A	c.(2353-2355)AGC>AAC	p.S785N	VPS13D_uc001atw.2_Missense_Mutation_p.S785N|VPS13D_uc001atx.2_5'UTR	NM_015378	NP_056193	Q5THJ4	VP13D_HUMAN	vacuolar protein sorting 13D isoform 1	785					protein localization					ovary(4)|pancreas(1)	5	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)												OREG0013110	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
VPS13D	55187	broad.mit.edu	37	1	12416051	12416051	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12416051C>A	uc001atv.2	+	48	9916	c.9775C>A	c.(9775-9777)CGT>AGT	p.R3259S	VPS13D_uc001atw.2_Missense_Mutation_p.R3234S|VPS13D_uc001atx.2_Missense_Mutation_p.R2446S	NM_015378	NP_056193	Q5THJ4	VP13D_HUMAN	vacuolar protein sorting 13D isoform 1	3258					protein localization					ovary(4)|pancreas(1)	5	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)														---	---	---	---
VPS13D	55187	broad.mit.edu	37	1	12463978	12463978	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12463978G>T	uc001atv.2	+	63	12123	c.11982G>T	c.(11980-11982)CAG>CAT	p.Q3994H	VPS13D_uc001atw.2_Missense_Mutation_p.Q3969H|VPS13D_uc001atx.2_Missense_Mutation_p.Q3181H|VPS13D_uc009vnl.2_RNA	NM_015378	NP_056193	Q5THJ4	VP13D_HUMAN	vacuolar protein sorting 13D isoform 1	3993				Q -> R (in Ref. 6; CAE46021).	protein localization					ovary(4)|pancreas(1)	5	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)														---	---	---	---
AADACL3	126767	broad.mit.edu	37	1	12779610	12779610	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12779610T>G	uc009vnn.1	+	2	364	c.131T>G	c.(130-132)CTG>CGG	p.L44R	AADACL3_uc001aug.1_Intron	NM_001103170	NP_001096640	Q5VUY0	ADCL3_HUMAN	arylacetamide deacetylase-like 3 isoform 1	44							hydrolase activity				0	Ovarian(185;0.249)	Lung NSC(185;8.27e-05)|all_lung(284;9.47e-05)|Renal(390;0.000147)|Colorectal(325;0.000583)|Breast(348;0.000596)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00217)|KIRC - Kidney renal clear cell carcinoma(229;0.00579)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
LOC649330	649330	broad.mit.edu	37	1	12907990	12907990	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12907990G>T	uc009vno.2	-	1	248	c.153C>A	c.(151-153)GGC>GGA	p.G51G	HNRNPCL1_uc010obf.1_Silent_p.G51G	NM_001146181	NP_001139653	B7ZW38	B7ZW38_HUMAN	heterogeneous nuclear ribonucleoprotein C-like	51							nucleic acid binding|nucleotide binding				0																		---	---	---	---
PRAMEF17	391004	broad.mit.edu	37	1	13716820	13716820	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:13716820C>A	uc009vnz.1	+	2	337	c.307C>A	c.(307-309)CTG>ATG	p.L103M		NM_001099851	NP_001093321	Q5VTA0	PRA17_HUMAN	PRAME family member 17	103											0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;9.86e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|COAD - Colon adenocarcinoma(227;0.000502)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
PRDM2	7799	broad.mit.edu	37	1	14109219	14109219	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:14109219G>A	uc001avi.2	+	8	5785	c.4929G>A	c.(4927-4929)GAG>GAA	p.E1643E	PRDM2_uc001avg.2_Intron|PRDM2_uc001avh.2_Silent_p.E1643E|PRDM2_uc001avj.2_Intron|PRDM2_uc001avk.2_Silent_p.E1442E|PRDM2_uc009voe.2_Intron|PRDM2_uc009vof.2_Intron	NM_012231	NP_036363	Q13029	PRDM2_HUMAN	retinoblastoma protein-binding zinc finger	1643						Golgi apparatus|nucleus	DNA binding|histone-lysine N-methyltransferase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)														---	---	---	---
CELA2A	63036	broad.mit.edu	37	1	15789298	15789298	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15789298G>A	uc001awk.2	+	4	324	c.298G>A	c.(298-300)GTC>ATC	p.V100I		NM_033440	NP_254275	P08217	CEL2A_HUMAN	elastase 2A preproprotein	100	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			ovary(2)	2																		---	---	---	---
CASP9	842	broad.mit.edu	37	1	15834411	15834411	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15834411G>A	uc001awn.2	-						CASP9_uc001awm.1_Intron|CASP9_uc001awo.2_Intron|CASP9_uc001awp.2_Intron|CASP9_uc009voi.2_Intron|CASP9_uc010obm.1_Intron|CASP9_uc001awq.2_Intron	NM_001229	NP_001220			caspase 9 isoform alpha preproprotein						activation of caspase activity by cytochrome c|induction of apoptosis by intracellular signals|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling	cytosol	cysteine-type endopeptidase activity|enzyme activator activity|protein binding			central_nervous_system(1)|kidney(1)	2		Breast(348;0.000207)|all_lung(284;0.000211)|Colorectal(325;0.000259)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;8.49e-07)|COAD - Colon adenocarcinoma(227;4.36e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00013)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00763)|READ - Rectum adenocarcinoma(331;0.0655)														---	---	---	---
AGMAT	79814	broad.mit.edu	37	1	15904339	15904339	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15904339A>G	uc001awv.1	-	5	884	c.741T>C	c.(739-741)GCT>GCC	p.A247A	DNAJC16_uc001awu.2_Intron	NM_024758	NP_079034	Q9BSE5	SPEB_HUMAN	agmatine ureohydrolase (agmatinase) precursor	247					putrescine biosynthetic process|spermidine biosynthetic process	mitochondrion	agmatinase activity|metal ion binding			skin(1)	1		Breast(348;0.000207)|Colorectal(325;0.000258)|Lung NSC(340;0.000359)|all_lung(284;0.000486)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.93e-07)|COAD - Colon adenocarcinoma(227;3.91e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000121)|KIRC - Kidney renal clear cell carcinoma(229;0.00257)|STAD - Stomach adenocarcinoma(313;0.00734)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
AGMAT	79814	broad.mit.edu	37	1	15905387	15905387	+	Silent	SNP	C	T	T	rs138589883		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15905387C>T	uc001awv.1	-	4	830	c.687G>A	c.(685-687)ACG>ACA	p.T229T	DNAJC16_uc001awu.2_Intron	NM_024758	NP_079034	Q9BSE5	SPEB_HUMAN	agmatine ureohydrolase (agmatinase) precursor	229					putrescine biosynthetic process|spermidine biosynthetic process	mitochondrion	agmatinase activity|metal ion binding			skin(1)	1		Breast(348;0.000207)|Colorectal(325;0.000258)|Lung NSC(340;0.000359)|all_lung(284;0.000486)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.93e-07)|COAD - Colon adenocarcinoma(227;3.91e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000121)|KIRC - Kidney renal clear cell carcinoma(229;0.00257)|STAD - Stomach adenocarcinoma(313;0.00734)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
RSC1A1	6248	broad.mit.edu	37	1	15987634	15987634	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:15987634T>C	uc010obn.1	+	1	1271	c.1271T>C	c.(1270-1272)GTG>GCG	p.V424A		NM_006511	NP_006502	Q92681	RSCA1_HUMAN	regulatory solute carrier protein, family 1,	424					negative regulation of transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent|transport	cell junction|Golgi apparatus|nucleus	ion channel inhibitor activity			ovary(1)	1		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00276)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.73e-07)|COAD - Colon adenocarcinoma(227;3.49e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000114)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
SPEN	23013	broad.mit.edu	37	1	16261933	16261933	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16261933G>T	uc001axk.1	+	11	9402	c.9198G>T	c.(9196-9198)CAG>CAT	p.Q3066H	SPEN_uc010obp.1_Missense_Mutation_p.Q3025H	NM_015001	NP_055816	Q96T58	MINT_HUMAN	spen homolog, transcriptional regulator	3066					interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway	nucleus	nucleotide binding|protein binding|RNA binding			ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	15		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)														---	---	---	---
ZBTB17	7709	broad.mit.edu	37	1	16269994	16269994	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16269994C>A	uc001axl.3	-	12	1836	c.1597G>T	c.(1597-1599)GTG>TTG	p.V533L	ZBTB17_uc010obq.1_Missense_Mutation_p.V450L|ZBTB17_uc010obr.1_Missense_Mutation_p.V533L|ZBTB17_uc010obs.1_Missense_Mutation_p.V457L	NM_003443	NP_003434	Q13105	ZBT17_HUMAN	zinc finger and BTB domain containing 17	533	C2H2-type 9.				negative regulation of cell cycle	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Colorectal(325;0.000257)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|Colorectal(212;4.12e-07)|COAD - Colon adenocarcinoma(227;2.43e-05)|BRCA - Breast invasive adenocarcinoma(304;9.97e-05)|Kidney(64;0.000182)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
CLCNKA	1187	broad.mit.edu	37	1	16351323	16351323	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16351323T>C	uc001axu.2	+	4	375	c.295T>C	c.(295-297)TAC>CAC	p.Y99H	CLCNKA_uc001axt.2_Intron|CLCNKA_uc001axv.2_Missense_Mutation_p.Y99H|CLCNKA_uc010obw.1_Intron|CLCNKB_uc001axw.3_Intron	NM_004070	NP_004061	P51800	CLCKA_HUMAN	chloride channel Ka isoform 1	99					excretion	chloride channel complex|integral to plasma membrane	voltage-gated chloride channel activity			ovary(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	Niflumic Acid(DB04552)													---	---	---	---
FAM131C	348487	broad.mit.edu	37	1	16388625	16388625	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16388625G>A	uc001axz.3	-	4	427	c.237C>T	c.(235-237)AAC>AAT	p.N79N	FAM131C_uc010obz.1_Silent_p.N79N	NM_182623	NP_872429	Q96AQ9	F131C_HUMAN	hypothetical protein LOC348487	79											0		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.32e-08)|COAD - Colon adenocarcinoma(227;5.56e-06)|BRCA - Breast invasive adenocarcinoma(304;9.12e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
CROCC	9696	broad.mit.edu	37	1	17249201	17249201	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17249201C>T	uc001azt.2	+	2	173	c.104C>T	c.(103-105)GCG>GTG	p.A35V	CROCC_uc009voy.1_Intron|CROCC_uc009voz.1_5'UTR	NM_014675	NP_055490	Q5TZA2	CROCC_HUMAN	ciliary rootlet coiled-coil	35					cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)|central_nervous_system(1)	5		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)														---	---	---	---
ATP13A2	23400	broad.mit.edu	37	1	17314722	17314722	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17314722G>A	uc001baa.2	-	25	2960	c.2770C>T	c.(2770-2772)CGC>TGC	p.R924C	ATP13A2_uc001azz.1_Missense_Mutation_p.R71C|ATP13A2_uc001bab.2_Missense_Mutation_p.R919C|ATP13A2_uc001bac.2_Missense_Mutation_p.R880C	NM_022089	NP_071372	Q9NQ11	AT132_HUMAN	ATPase type 13A2 isoform 1	924	Cytoplasmic (Potential).				ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			skin(2)|ovary(1)|central_nervous_system(1)	4		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)														---	---	---	---
ATP13A2	23400	broad.mit.edu	37	1	17326947	17326947	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17326947A>G	uc001baa.2	-	9	978	c.788T>C	c.(787-789)ATC>ACC	p.I263T	ATP13A2_uc001bab.2_Missense_Mutation_p.I258T|ATP13A2_uc001bac.2_Missense_Mutation_p.I258T|ATP13A2_uc009vpa.1_5'Flank|ATP13A2_uc001bad.1_5'UTR	NM_022089	NP_071372	Q9NQ11	AT132_HUMAN	ATPase type 13A2 isoform 1	263	Helical; (Potential).				ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			skin(2)|ovary(1)|central_nervous_system(1)	4		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)														---	---	---	---
PADI2	11240	broad.mit.edu	37	1	17413088	17413088	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17413088G>A	uc001baf.2	-	7	844	c.762C>T	c.(760-762)GGC>GGT	p.G254G	PADI2_uc010ocm.1_Missense_Mutation_p.A173V|PADI2_uc001bag.1_Silent_p.G254G	NM_007365	NP_031391	Q9Y2J8	PADI2_HUMAN	peptidyl arginine deiminase, type II	254					peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm	calcium ion binding|protein-arginine deiminase activity			ovary(3)|pancreas(1)|central_nervous_system(1)|skin(1)	6		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)	L-Citrulline(DB00155)													---	---	---	---
PADI1	29943	broad.mit.edu	37	1	17548925	17548925	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17548925T>C	uc001bah.1	+	2	325	c.233T>C	c.(232-234)GTA>GCA	p.V78A		NM_013358	NP_037490	Q9ULC6	PADI1_HUMAN	peptidylarginine deiminase type I	78					peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm	calcium ion binding|protein-arginine deiminase activity				0		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00054)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00522)|BRCA - Breast invasive adenocarcinoma(304;1.3e-05)|COAD - Colon adenocarcinoma(227;1.31e-05)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(196;0.0069)|READ - Rectum adenocarcinoma(331;0.0681)|Lung(427;0.197)	L-Citrulline(DB00155)													---	---	---	---
PADI6	353238	broad.mit.edu	37	1	17715368	17715368	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17715368C>A	uc001bak.1	+	8	955	c.955C>A	c.(955-957)CTG>ATG	p.L319M		NM_207421	NP_997304	Q6TGC4	PADI6_HUMAN	peptidylarginine deiminase type 6	311					peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm|nucleus	calcium ion binding|protein-arginine deiminase activity			breast(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;7.59e-06)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.0134)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)													---	---	---	---
IGSF21	84966	broad.mit.edu	37	1	18703458	18703458	+	Silent	SNP	C	T	T	rs151094752		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:18703458C>T	uc001bau.1	+	8	1649	c.1266C>T	c.(1264-1266)ACC>ACT	p.T422T	IGSF21_uc001bav.1_Silent_p.T243T	NM_032880	NP_116269	Q96ID5	IGS21_HUMAN	immunoglobin superfamily, member 21 precursor	422	Ig-like 2.					extracellular region				ovary(2)|large_intestine(1)|skin(1)	4		Colorectal(325;0.000147)|Renal(390;0.00145)|all_lung(284;0.00366)|Lung NSC(340;0.00376)|Breast(348;0.00387)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0121)|BRCA - Breast invasive adenocarcinoma(304;5.52e-05)|Kidney(64;0.00103)|KIRC - Kidney renal clear cell carcinoma(64;0.0102)|STAD - Stomach adenocarcinoma(196;0.0118)|READ - Rectum adenocarcinoma(331;0.157)														---	---	---	---
UBR4	23352	broad.mit.edu	37	1	19511581	19511581	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19511581A>G	uc001bbi.2	-							NM_020765	NP_065816			retinoblastoma-associated factor 600						interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(10)|ovary(7)|breast(4)|pancreas(2)|skin(2)	25		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)														---	---	---	---
UBR4	23352	broad.mit.edu	37	1	19525293	19525293	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19525293C>T	uc001bbi.2	-	4	512	c.508G>A	c.(508-510)GTG>ATG	p.V170M		NM_020765	NP_065816	Q5T4S7	UBR4_HUMAN	retinoblastoma-associated factor 600	170					interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(10)|ovary(7)|breast(4)|pancreas(2)|skin(2)	25		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)														---	---	---	---
KIAA0090	23065	broad.mit.edu	37	1	19566343	19566343	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:19566343C>T	uc001bbo.2	-	8	966	c.923G>A	c.(922-924)GGA>GAA	p.G308E	KIAA0090_uc001bbp.2_Missense_Mutation_p.G308E|KIAA0090_uc001bbq.2_Missense_Mutation_p.G308E|KIAA0090_uc001bbr.2_Missense_Mutation_p.G286E	NM_015047	NP_055862	Q8N766	K0090_HUMAN	hypothetical protein LOC23065 precursor	308	Extracellular (Potential).					integral to membrane	protein binding			ovary(1)	1		Colorectal(325;0.000147)|Renal(390;0.000469)|Breast(348;0.00366)|all_lung(284;0.00519)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00492)|BRCA - Breast invasive adenocarcinoma(304;3.84e-05)|Kidney(64;0.000191)|KIRC - Kidney renal clear cell carcinoma(64;0.00274)|GBM - Glioblastoma multiforme(114;0.005)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0656)														---	---	---	---
OTUD3	23252	broad.mit.edu	37	1	20216881	20216881	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20216881T>C	uc001bcs.3	+	2	344	c.225T>C	c.(223-225)AAT>AAC	p.N75N		NM_015207	NP_056022	Q5T2D3	OTUD3_HUMAN	OTU domain containing 3	75	OTU.										0		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000276)|Lung NSC(340;0.000338)|Breast(348;0.000812)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.12e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000142)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.000408)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
UBXN10	127733	broad.mit.edu	37	1	20517866	20517866	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20517866T>C	uc001bdb.2	+	2	896	c.812T>C	c.(811-813)ATC>ACC	p.I271T		NM_152376	NP_689589	Q96LJ8	UBX10_HUMAN	UBX domain protein 10	271	UBX.									ovary(1)	1																		---	---	---	---
MUL1	79594	broad.mit.edu	37	1	20827289	20827289	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20827289C>A	uc001bdi.3	-	4	1110	c.953G>T	c.(952-954)GGG>GTG	p.G318V		NM_024544	NP_078820	Q969V5	MUL1_HUMAN	mitochondrial ubiquitin ligase activator of NFKB	318	Cytoplasmic (Potential).|RING-type.				activation of caspase activity|activation of JUN kinase activity|induction of apoptosis|mitochondrial fission|mitochondrion localization|negative regulation of cell growth|positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to mitochondrial outer membrane|nucleus|peroxisome	identical protein binding|signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding				0		Colorectal(325;0.000147)|Renal(390;0.000469)|Lung NSC(340;0.00412)|all_lung(284;0.00419)|Breast(348;0.00748)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000137)|Kidney(64;0.00017)|GBM - Glioblastoma multiforme(114;0.00124)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.198)														---	---	---	---
CDA	978	broad.mit.edu	37	1	20931448	20931448	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20931448C>T	uc001bdk.2	+	2	361	c.182C>T	c.(181-183)CCG>CTG	p.P61L	CDA_uc001bdl.2_RNA|CDA_uc009vpv.2_Intron	NM_001785	NP_001776	P32320	CDD_HUMAN	cytidine deaminase	61					cell surface receptor linked signaling pathway|cytosine metabolic process|negative regulation of cell growth|negative regulation of nucleotide metabolic process|protein homotetramerization|pyrimidine nucleoside salvage	cytosol|extracellular region	cytidine deaminase activity|nucleoside binding|protein homodimerization activity|zinc ion binding			ovary(1)	1		Lung NSC(340;1.75e-08)|all_lung(284;5.99e-08)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|GBM - Glioblastoma multiforme(114;1.06e-08)|COAD - Colon adenocarcinoma(152;1.22e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000148)|Kidney(64;0.000184)|KIRC - Kidney renal clear cell carcinoma(64;0.0027)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0652)|Lung(427;0.199)	Azacitidine(DB00928)|Capecitabine(DB01101)|Cytarabine(DB00987)|Gemcitabine(DB00441)													---	---	---	---
CDA	978	broad.mit.edu	37	1	20944987	20944987	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20944987A>G	uc001bdk.2	+	4	546	c.367A>G	c.(367-369)ACG>GCG	p.T123A	CDA_uc001bdl.2_RNA|CDA_uc009vpv.2_RNA	NM_001785	NP_001776	P32320	CDD_HUMAN	cytidine deaminase	123					cell surface receptor linked signaling pathway|cytosine metabolic process|negative regulation of cell growth|negative regulation of nucleotide metabolic process|protein homotetramerization|pyrimidine nucleoside salvage	cytosol|extracellular region	cytidine deaminase activity|nucleoside binding|protein homodimerization activity|zinc ion binding			ovary(1)	1		Lung NSC(340;1.75e-08)|all_lung(284;5.99e-08)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|GBM - Glioblastoma multiforme(114;1.06e-08)|COAD - Colon adenocarcinoma(152;1.22e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000148)|Kidney(64;0.000184)|KIRC - Kidney renal clear cell carcinoma(64;0.0027)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0652)|Lung(427;0.199)	Azacitidine(DB00928)|Capecitabine(DB01101)|Cytarabine(DB00987)|Gemcitabine(DB00441)													---	---	---	---
DDOST	1650	broad.mit.edu	37	1	20987798	20987798	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20987798G>A	uc001bdo.1	-	1	240	c.97C>T	c.(97-99)CTG>TTG	p.L33L	DDOST_uc009vpw.1_Silent_p.L33L|DDOST_uc010odd.1_5'UTR|DDOST_uc010ode.1_Silent_p.L33L	NM_005216	NP_005207	P39656	OST48_HUMAN	dolichyl-diphosphooligosaccharide-protein	33					innate immune response|post-translational protein modification|response to cytokine stimulus|T cell activation	integral to membrane|microsome|oligosaccharyltransferase complex	dolichyl-diphosphooligosaccharide-protein glycotransferase activity|protein binding				0		all_lung(284;2.98e-05)|Lung NSC(340;3.25e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.17e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000141)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.00046)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)												OREG0013196	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
KIF17	57576	broad.mit.edu	37	1	21031106	21031106	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21031106G>A	uc001bdr.3	-	5	1075	c.957C>T	c.(955-957)TAC>TAT	p.Y319Y	KIF17_uc001bds.3_Silent_p.Y319Y	NM_020816	NP_065867	Q9P2E2	KIF17_HUMAN	kinesin family member 17 isoform a	319					microtubule-based movement|protein transport	cytoplasm|microtubule	ATP binding			ovary(3)|skin(1)	4		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)														---	---	---	---
EIF4G3	8672	broad.mit.edu	37	1	21268465	21268465	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21268465T>G	uc001bec.2	-	9	1270	c.1014A>C	c.(1012-1014)AAA>AAC	p.K338N	EIF4G3_uc010odi.1_5'UTR|EIF4G3_uc010odj.1_Missense_Mutation_p.K337N|EIF4G3_uc009vpz.2_Intron|EIF4G3_uc001bed.2_Missense_Mutation_p.K338N|EIF4G3_uc001bef.2_Missense_Mutation_p.K337N|EIF4G3_uc001bee.2_Missense_Mutation_p.K344N|EIF4G3_uc001beg.2_Missense_Mutation_p.K337N|EIF4G3_uc010odk.1_Missense_Mutation_p.K338N|EIF4G3_uc001beh.2_Missense_Mutation_p.K349N	NM_003760	NP_003751	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4	338					interspecies interaction between organisms|regulation of translational initiation|RNA metabolic process	eukaryotic translation initiation factor 4F complex	protein binding|RNA cap binding|translation initiation factor activity			skin(1)	1		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)														---	---	---	---
ECE1	1889	broad.mit.edu	37	1	21573803	21573803	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21573803G>A	uc001bek.2	-	9	1149	c.1074C>T	c.(1072-1074)CCC>CCT	p.P358P	ECE1_uc001bem.2_Silent_p.P342P|ECE1_uc001bej.2_Silent_p.P346P|ECE1_uc001bei.2_Silent_p.P355P|ECE1_uc010odl.1_Silent_p.P358P|ECE1_uc009vqa.1_Silent_p.P358P	NM_001397	NP_001388	P42892	ECE1_HUMAN	endothelin converting enzyme 1 isoform 1	358	Extracellular (Potential).				bradykinin catabolic process|calcitonin catabolic process|ear development|embryonic digit morphogenesis|endothelin maturation|heart development|positive regulation of receptor recycling|substance P catabolic process	early endosome|external side of plasma membrane|integral to membrane|intrinsic to endosome membrane|membrane fraction|perinuclear region of cytoplasm|plasma membrane|Weibel-Palade body	metal ion binding|metalloendopeptidase activity|protein homodimerization activity			ovary(2)|skin(1)	3		Lung NSC(340;1.14e-05)|all_lung(284;1.23e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00147)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0183)|OV - Ovarian serous cystadenocarcinoma(117;4.83e-27)|COAD - Colon adenocarcinoma(152;1.36e-06)|GBM - Glioblastoma multiforme(114;1.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000162)|STAD - Stomach adenocarcinoma(196;0.00326)|KIRC - Kidney renal clear cell carcinoma(1967;0.00755)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.206)														---	---	---	---
ECE1	1889	broad.mit.edu	37	1	21582577	21582577	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21582577C>T	uc001bek.2	-	8	958	c.883G>A	c.(883-885)GGG>AGG	p.G295R	ECE1_uc001bem.2_Missense_Mutation_p.G279R|ECE1_uc001bej.2_Missense_Mutation_p.G283R|ECE1_uc001bei.2_Missense_Mutation_p.G292R|ECE1_uc010odl.1_Missense_Mutation_p.G295R|ECE1_uc009vqa.1_Missense_Mutation_p.G295R	NM_001397	NP_001388	P42892	ECE1_HUMAN	endothelin converting enzyme 1 isoform 1	295	Extracellular (Potential).				bradykinin catabolic process|calcitonin catabolic process|ear development|embryonic digit morphogenesis|endothelin maturation|heart development|positive regulation of receptor recycling|substance P catabolic process	early endosome|external side of plasma membrane|integral to membrane|intrinsic to endosome membrane|membrane fraction|perinuclear region of cytoplasm|plasma membrane|Weibel-Palade body	metal ion binding|metalloendopeptidase activity|protein homodimerization activity			ovary(2)|skin(1)	3		Lung NSC(340;1.14e-05)|all_lung(284;1.23e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00147)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0183)|OV - Ovarian serous cystadenocarcinoma(117;4.83e-27)|COAD - Colon adenocarcinoma(152;1.36e-06)|GBM - Glioblastoma multiforme(114;1.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000162)|STAD - Stomach adenocarcinoma(196;0.00326)|KIRC - Kidney renal clear cell carcinoma(1967;0.00755)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.206)														---	---	---	---
RAP1GAP	5909	broad.mit.edu	37	1	21926081	21926081	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21926081G>A	uc001bex.2	-	21	1940	c.1682C>T	c.(1681-1683)GCG>GTG	p.A561V	RAP1GAP_uc001bev.2_Missense_Mutation_p.A646V|RAP1GAP_uc001bew.2_Missense_Mutation_p.A625V|RAP1GAP_uc001bey.2_Missense_Mutation_p.A587V	NM_002885	NP_002876	P47736	RPGP1_HUMAN	RAP1 GTPase activating protein isoform c	561					regulation of Ras GTPase activity|signal transduction	cytosol|Golgi membrane|membrane fraction	GTPase activator activity|GTPase activity|protein homodimerization activity|Ras GTPase binding			breast(2)|ovary(1)	3		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000861)|all_lung(284;0.000901)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;2.3e-26)|COAD - Colon adenocarcinoma(152;1.59e-05)|GBM - Glioblastoma multiforme(114;2.7e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000354)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00862)|READ - Rectum adenocarcinoma(331;0.0625)|Lung(427;0.146)														---	---	---	---
RAP1GAP	5909	broad.mit.edu	37	1	21934828	21934828	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21934828C>T	uc001bex.2	-	17	1432	c.1174G>A	c.(1174-1176)GCC>ACC	p.A392T	RAP1GAP_uc001bev.2_Missense_Mutation_p.A392T|RAP1GAP_uc001bew.2_Missense_Mutation_p.A456T|RAP1GAP_uc001bey.2_Missense_Mutation_p.A392T	NM_002885	NP_002876	P47736	RPGP1_HUMAN	RAP1 GTPase activating protein isoform c	392	Rap-GAP.				regulation of Ras GTPase activity|signal transduction	cytosol|Golgi membrane|membrane fraction	GTPase activator activity|GTPase activity|protein homodimerization activity|Ras GTPase binding			breast(2)|ovary(1)	3		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000861)|all_lung(284;0.000901)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;2.3e-26)|COAD - Colon adenocarcinoma(152;1.59e-05)|GBM - Glioblastoma multiforme(114;2.7e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000354)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00862)|READ - Rectum adenocarcinoma(331;0.0625)|Lung(427;0.146)														---	---	---	---
HSPG2	3339	broad.mit.edu	37	1	22159765	22159765	+	Silent	SNP	G	A	A	rs141904589		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22159765G>A	uc001bfj.2	-	80	11131	c.11091C>T	c.(11089-11091)GCC>GCT	p.A3697A	HSPG2_uc001bfi.2_5'Flank|HSPG2_uc009vqd.2_Silent_p.A3698A	NM_005529	NP_005520	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2 precursor	3697	Laminin G-like 1.				angiogenesis|cell adhesion|lipid metabolic process|lipoprotein metabolic process	basement membrane|extracellular space|plasma membrane	protein C-terminus binding			ovary(5)|large_intestine(2)|central_nervous_system(1)|skin(1)	9		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Becaplermin(DB00102)|Palifermin(DB00039)													---	---	---	---
HSPG2	3339	broad.mit.edu	37	1	22170701	22170701	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22170701C>T	uc001bfj.2	-	65	8596	c.8556G>A	c.(8554-8556)GGG>GGA	p.G2852G	HSPG2_uc009vqd.2_Silent_p.G2853G	NM_005529	NP_005520	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2 precursor	2852	Ig-like C2-type 14.				angiogenesis|cell adhesion|lipid metabolic process|lipoprotein metabolic process	basement membrane|extracellular space|plasma membrane	protein C-terminus binding			ovary(5)|large_intestine(2)|central_nervous_system(1)|skin(1)	9		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Becaplermin(DB00102)|Palifermin(DB00039)													---	---	---	---
HSPG2	3339	broad.mit.edu	37	1	22182007	22182007	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22182007G>A	uc001bfj.2	-						HSPG2_uc009vqd.2_Intron	NM_005529	NP_005520			heparan sulfate proteoglycan 2 precursor						angiogenesis|cell adhesion|lipid metabolic process|lipoprotein metabolic process	basement membrane|extracellular space|plasma membrane	protein C-terminus binding			ovary(5)|large_intestine(2)|central_nervous_system(1)|skin(1)	9		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Becaplermin(DB00102)|Palifermin(DB00039)													---	---	---	---
ZBTB40	9923	broad.mit.edu	37	1	22838295	22838295	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22838295A>G	uc001bft.2	+	12	2640	c.2129A>G	c.(2128-2130)GAT>GGT	p.D710G	ZBTB40_uc001bfu.2_Missense_Mutation_p.D710G|ZBTB40_uc009vqi.1_Missense_Mutation_p.D598G|ZBTB40_uc001bfv.1_Missense_Mutation_p.D339G	NM_001083621	NP_001077090	Q9NUA8	ZBT40_HUMAN	zinc finger and BTB domain containing 40	710					bone mineralization|regulation of transcription, DNA-dependent|response to DNA damage stimulus|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.86e-26)|Colorectal(126;8.55e-08)|COAD - Colon adenocarcinoma(152;4.1e-06)|GBM - Glioblastoma multiforme(114;1.39e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000712)|KIRC - Kidney renal clear cell carcinoma(1967;0.00374)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0693)|Lung(427;0.216)														---	---	---	---
EPHA8	2046	broad.mit.edu	37	1	22915822	22915822	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22915822C>T	uc001bfx.1	+						EPHA8_uc001bfw.2_Missense_Mutation_p.P480S	NM_020526	NP_065387			ephrin receptor EphA8 isoform 1 precursor							integral to plasma membrane	ATP binding|ephrin receptor activity			central_nervous_system(5)|breast(3)|lung(2)|large_intestine(1)|stomach(1)|skin(1)	13		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)														---	---	---	---
EPHA8	2046	broad.mit.edu	37	1	22927873	22927873	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22927873A>G	uc001bfx.1	+	16	2935	c.2810A>G	c.(2809-2811)GAC>GGC	p.D937G		NM_020526	NP_065387	P29322	EPHA8_HUMAN	ephrin receptor EphA8 isoform 1 precursor	937	Cytoplasmic (Potential).|SAM.					integral to plasma membrane	ATP binding|ephrin receptor activity			central_nervous_system(5)|breast(3)|lung(2)|large_intestine(1)|stomach(1)|skin(1)	13		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)														---	---	---	---
KDM1A	23028	broad.mit.edu	37	1	23408739	23408739	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:23408739G>C	uc001bgi.2	+	18	2402	c.2253G>C	c.(2251-2253)TGG>TGC	p.W751C	KDM1A_uc001bgj.2_Missense_Mutation_p.W775C	NM_015013	NP_055828	O60341	KDM1A_HUMAN	lysine-specific histone demethylase 1 isoform b	751	Demethylase activity.				blood coagulation|muscle cell development|negative regulation of apoptosis|negative regulation of DNA damage response, signal transduction by p53 class mediator|negative regulation of protein binding|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nuclear chromatin	androgen receptor binding|chromatin binding|enzyme binding|flavin adenine dinucleotide binding|histone demethylase activity (H3-dimethyl-K4 specific)|histone demethylase activity (H3-K9 specific)|ligand-dependent nuclear receptor transcription coactivator activity|MyoD binding|oxidoreductase activity|p53 binding|transcription regulatory region DNA binding			ovary(1)|lung(1)	2																		---	---	---	---
TCEB3	6924	broad.mit.edu	37	1	24077971	24077971	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24077971A>C	uc001bho.2	+	4	1014	c.954A>C	c.(952-954)AAA>AAC	p.K318N		NM_003198	NP_003189	Q14241	ELOA1_HUMAN	elongin A	318					positive regulation of viral transcription|regulation of transcription from RNA polymerase II promoter|transcription elongation from RNA polymerase II promoter|viral reproduction	integral to membrane	DNA binding			ovary(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.42e-24)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;4.74e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000973)|KIRC - Kidney renal clear cell carcinoma(1967;0.00334)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)												OREG0013232	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
HMGCL	3155	broad.mit.edu	37	1	24140723	24140723	+	Missense_Mutation	SNP	C	T	T	rs146306707		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24140723C>T	uc001bib.2	-	5	498	c.454G>A	c.(454-456)GCA>ACA	p.A152T	HMGCL_uc010oec.1_Intron|HMGCL_uc009vqr.2_Intron|HMGCL_uc001bic.2_Missense_Mutation_p.A127T|HMGCL_uc009vqs.1_Intron|HMGCL_uc001bid.1_Missense_Mutation_p.A152T	NM_000191	NP_000182	P35914	HMGCL_HUMAN	3-hydroxy-3-methylglutaryl CoA lyase isoform 1	152					acetoacetic acid biosynthetic process|ketone body biosynthetic process	mitochondrial matrix	hydroxymethylglutaryl-CoA lyase activity|metal ion binding			central_nervous_system(1)	1		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.0044)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.38e-24)|Colorectal(126;5.58e-08)|COAD - Colon adenocarcinoma(152;3.12e-06)|GBM - Glioblastoma multiforme(114;4.9e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000982)|KIRC - Kidney renal clear cell carcinoma(1967;0.0034)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0856)|LUSC - Lung squamous cell carcinoma(448;0.188)														---	---	---	---
NIPAL3	57185	broad.mit.edu	37	1	24775978	24775978	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24775978C>T	uc001bjh.2	+	6	809	c.402C>T	c.(400-402)TAC>TAT	p.Y134Y	NIPAL3_uc010oek.1_Silent_p.Y134Y|NIPAL3_uc001bjg.2_Silent_p.Y134Y|NIPAL3_uc009vrc.2_Silent_p.Y52Y	NM_020448	NP_065181	Q6P499	NPAL3_HUMAN	NIPA-like domain containing 3	134						integral to membrane					0																		---	---	---	---
CLIC4	25932	broad.mit.edu	37	1	25166518	25166518	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25166518C>T	uc001bjo.2	+	5	868	c.583C>T	c.(583-585)CTG>TTG	p.L195L	CLIC4_uc001bjn.2_RNA|CLIC4_uc001bjp.1_Silent_p.L175L	NM_013943	NP_039234	Q9Y696	CLIC4_HUMAN	chloride intracellular channel 4	195	GST C-terminal.				cellular response to calcium ion|establishment or maintenance of apical/basal cell polarity|keratinocyte differentiation|negative regulation of cell migration|regulation of cytoskeleton organization	actin cytoskeleton|apical part of cell|cell surface|cell-cell junction|centrosome|chloride channel complex|cytoplasmic vesicle membrane|cytosol|microvillus|midbody|mitochondrion|nuclear matrix|perinuclear region of cytoplasm|soluble fraction	voltage-gated chloride channel activity				0		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000778)|all_lung(284;0.00106)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0479)|OV - Ovarian serous cystadenocarcinoma(117;1.06e-24)|Colorectal(126;1.03e-07)|COAD - Colon adenocarcinoma(152;4.93e-06)|STAD - Stomach adenocarcinoma(196;0.000418)|GBM - Glioblastoma multiforme(114;0.000451)|BRCA - Breast invasive adenocarcinoma(304;0.00215)|KIRC - Kidney renal clear cell carcinoma(1967;0.00216)|READ - Rectum adenocarcinoma(331;0.0693)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.18)														---	---	---	---
RHD	6007	broad.mit.edu	37	1	25611169	25611169	+	Missense_Mutation	SNP	C	T	T	rs139501061	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25611169C>T	uc001bjz.2	+	2	312	c.254C>T	c.(253-255)GCG>GTG	p.A85V	RHD_uc010oep.1_Missense_Mutation_p.A85V|RHD_uc001bkc.2_Missense_Mutation_p.A85V|RHD_uc009vrm.2_5'UTR|RHD_uc001bka.2_Missense_Mutation_p.A85V|RHD_uc001bkb.2_Missense_Mutation_p.A85V|RHD_uc009vrn.2_Missense_Mutation_p.A85V|RHD_uc009vro.2_Missense_Mutation_p.A85V|RHD_uc009vrp.2_Missense_Mutation_p.A85V	NM_016124	NP_057208	Q02161	RHD_HUMAN	Rh blood group D antigen isoform 1	85	Helical; (Potential).					integral to plasma membrane				breast(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;7.39e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;6.43e-07)|STAD - Stomach adenocarcinoma(196;0.000332)|BRCA - Breast invasive adenocarcinoma(304;0.000438)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.000908)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)														---	---	---	---
RHD	6007	broad.mit.edu	37	1	25611201	25611201	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25611201G>A	uc001bjz.2	+	2	344	c.286G>A	c.(286-288)GGC>AGC	p.G96S	RHD_uc010oep.1_Missense_Mutation_p.G96S|RHD_uc001bkc.2_Missense_Mutation_p.G96S|RHD_uc009vrm.2_5'UTR|RHD_uc001bka.2_Missense_Mutation_p.G96S|RHD_uc001bkb.2_Missense_Mutation_p.G96S|RHD_uc009vrn.2_Missense_Mutation_p.G96S|RHD_uc009vro.2_Missense_Mutation_p.G96S|RHD_uc009vrp.2_Missense_Mutation_p.G96S	NM_016124	NP_057208	Q02161	RHD_HUMAN	Rh blood group D antigen isoform 1	96	Helical; (Potential).					integral to plasma membrane				breast(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;7.39e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;6.43e-07)|STAD - Stomach adenocarcinoma(196;0.000332)|BRCA - Breast invasive adenocarcinoma(304;0.000438)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.000908)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)														---	---	---	---
RHCE	6006	broad.mit.edu	37	1	25717229	25717229	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:25717229G>A	uc001bkf.2	-						RHCE_uc001bkg.2_Intron|RHCE_uc001bkh.2_Intron|RHCE_uc001bki.2_Intron|RHCE_uc001bkj.2_Intron	NM_020485	NP_065231			Rhesus blood group, CcEe antigens isoform 1							integral to plasma membrane					0		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0426)|OV - Ovarian serous cystadenocarcinoma(117;2.12e-27)|Colorectal(126;3.16e-08)|COAD - Colon adenocarcinoma(152;1.72e-06)|STAD - Stomach adenocarcinoma(196;0.00035)|KIRC - Kidney renal clear cell carcinoma(1967;0.000769)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|GBM - Glioblastoma multiforme(114;0.00458)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
CNKSR1	10256	broad.mit.edu	37	1	26514963	26514963	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26514963C>T	uc001bln.3	+	18	1638	c.1580C>T	c.(1579-1581)CCG>CTG	p.P527L	CNKSR1_uc001blm.3_Missense_Mutation_p.P520L|CNKSR1_uc009vsd.2_Missense_Mutation_p.P262L|CNKSR1_uc009vse.2_Missense_Mutation_p.P262L|CNKSR1_uc001blo.2_Missense_Mutation_p.P262L|CATSPER4_uc010oey.1_5'Flank|CATSPER4_uc010oez.1_5'Flank|CATSPER4_uc009vsf.2_5'Flank	NM_006314	NP_006305	Q969H4	CNKR1_HUMAN	connector enhancer of kinase suppressor of Ras	527					Rho protein signal transduction|transmembrane receptor protein tyrosine kinase signaling pathway	cell cortex|cell-cell junction	protein binding, bridging			lung(1)|kidney(1)	2		Colorectal(325;3.46e-05)|all_lung(284;0.000116)|Lung NSC(340;0.000154)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0133)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;2.72e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00072)|BRCA - Breast invasive adenocarcinoma(304;0.000959)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00823)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
AIM1L	55057	broad.mit.edu	37	1	26672659	26672659	+	5'Flank	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26672659C>A	uc001bmd.3	-						uc009vsi.1_Missense_Mutation_p.G164C	NM_001039775	NP_001034864			absent in melanoma 1-like								sugar binding			pancreas(1)	1		all_cancers(24;4.67e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.51e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000792)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.00858)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.165)|LUSC - Lung squamous cell carcinoma(448;0.239)														---	---	---	---
ARID1A	8289	broad.mit.edu	37	1	27089711	27089711	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27089711C>T	uc001bmv.1	+	8	3040	c.2667C>T	c.(2665-2667)GGC>GGT	p.G889G	ARID1A_uc001bmt.1_Silent_p.G889G|ARID1A_uc001bmu.1_Silent_p.G889G|ARID1A_uc001bmw.1_Silent_p.G506G	NM_006015	NP_006006	O14497	ARI1A_HUMAN	AT rich interactive domain 1A isoform a	889					androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent	nBAF complex|npBAF complex|SWI/SNF complex	DNA binding|protein binding			ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	142		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)				Mis|N|F|S|D		clear cell ovarian carcinoma|RCC								---	---	---	---
ARID1A	8289	broad.mit.edu	37	1	27100887	27100887	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27100887G>T	uc001bmv.1	+	18	4542	c.4169G>T	c.(4168-4170)AGC>ATC	p.S1390I	ARID1A_uc001bmt.1_Missense_Mutation_p.S1389I|ARID1A_uc001bmu.1_Intron|ARID1A_uc001bmw.1_Missense_Mutation_p.S1007I|ARID1A_uc001bmx.1_Missense_Mutation_p.S236I|ARID1A_uc009vsm.1_Intron|ARID1A_uc009vsn.1_5'UTR	NM_006015	NP_006006	O14497	ARI1A_HUMAN	AT rich interactive domain 1A isoform a	1390	Gln-rich.				androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent	nBAF complex|npBAF complex|SWI/SNF complex	DNA binding|protein binding			ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	142		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)				Mis|N|F|S|D		clear cell ovarian carcinoma|RCC								---	---	---	---
NR0B2	8431	broad.mit.edu	37	1	27240257	27240257	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27240257C>G	uc001bnf.2	-	1	311	c.175G>C	c.(175-177)GCC>CCC	p.A59P		NM_021969	NP_068804	Q15466	NR0B2_HUMAN	short heterodimer partner	59	Ligand-binding (By similarity).				cholesterol metabolic process|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	DNA binding|protein domain specific binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription corepressor activity				0		all_cancers(24;1.23e-26)|all_epithelial(13;1.19e-23)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Breast(348;0.00017)|Renal(390;0.0007)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;1.01e-51)|OV - Ovarian serous cystadenocarcinoma(117;8.22e-30)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
MAP3K6	9064	broad.mit.edu	37	1	27687644	27687644	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27687644G>A	uc001bny.1	-						MAP3K6_uc009vsw.1_Intron|MAP3K6_uc001bnz.1_Intron	NM_004672	NP_004663			mitogen-activated protein kinase kinase kinase						activation of JUN kinase activity		ATP binding|magnesium ion binding|MAP kinase kinase kinase activity			breast(4)|lung(3)|ovary(1)|central_nervous_system(1)	9		all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.69e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00132)|KIRC - Kidney renal clear cell carcinoma(1967;0.00163)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
FCN3	8547	broad.mit.edu	37	1	27700836	27700836	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27700836G>A	uc001boa.2	-						FCN3_uc001bob.2_Intron	NM_003665	NP_003656			ficolin 3 isoform 1 precursor						complement activation, lectin pathway|signal transduction	collagen|extracellular space	receptor binding|sugar binding				0		all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;1.42e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00128)|KIRC - Kidney renal clear cell carcinoma(1967;0.00155)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
AHDC1	27245	broad.mit.edu	37	1	27875225	27875225	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27875225G>A	uc009vsy.2	-	6	4371	c.3402C>T	c.(3400-3402)TGC>TGT	p.C1134C	AHDC1_uc009vsz.1_Silent_p.C1134C	NM_001029882	NP_001025053	Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	1134							DNA binding			central_nervous_system(1)	1		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)														---	---	---	---
SMPDL3B	27293	broad.mit.edu	37	1	28271748	28271748	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28271748T>C	uc001bpg.2	+	2	258	c.67T>C	c.(67-69)TTC>CTC	p.F23L	SMPDL3B_uc001bpf.2_Missense_Mutation_p.F23L|SMPDL3B_uc010ofq.1_5'UTR|SMPDL3B_uc010ofr.1_Missense_Mutation_p.F23L	NM_014474	NP_055289	Q92485	ASM3B_HUMAN	acid sphingomyelinase-like phosphodiesterase 3B	23					sphingomyelin catabolic process	extracellular space	hydrolase activity, acting on glycosyl bonds|sphingomyelin phosphodiesterase activity			ovary(3)	3		Colorectal(325;3.46e-05)|all_lung(284;0.000414)|Lung NSC(340;0.000431)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0419)|OV - Ovarian serous cystadenocarcinoma(117;5.68e-24)|Colorectal(126;1.65e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00303)|BRCA - Breast invasive adenocarcinoma(304;0.00587)|READ - Rectum adenocarcinoma(331;0.055)														---	---	---	---
PHACTR4	65979	broad.mit.edu	37	1	28785684	28785684	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28785684C>T	uc001bpw.2	+	3	387	c.105C>T	c.(103-105)AGC>AGT	p.S35S	PHACTR4_uc001bpu.2_Silent_p.S35S|PHACTR4_uc001bpv.1_RNA|PHACTR4_uc001bpx.2_Silent_p.S19S|PHACTR4_uc001bpy.2_Silent_p.S45S	NM_001048183	NP_001041648	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4 isoform 1	35							actin binding|protein phosphatase inhibitor activity				0		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
RCC1	1104	broad.mit.edu	37	1	28861871	28861871	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28861871C>T	uc001bqg.1	+	6	725	c.640C>T	c.(640-642)CGT>TGT	p.R214C	SNHG3-RCC1_uc001bqa.1_Missense_Mutation_p.R214C|SNHG3-RCC1_uc001bqb.1_Missense_Mutation_p.R214C|SNHG3-RCC1_uc001bqc.1_Missense_Mutation_p.R214C|RCC1_uc001bqe.1_Missense_Mutation_p.R231C|RCC1_uc001bqf.1_Missense_Mutation_p.R245C	NM_001269	NP_001260	P18754	RCC1_HUMAN	regulator of chromosome condensation 1 isoform	214	RCC1 4.				cell division|chromosome segregation|G1/S transition of mitotic cell cycle|mitosis|mitotic spindle organization|regulation of mitosis|regulation of S phase of mitotic cell cycle|spindle assembly|viral reproduction	condensed nuclear chromosome|cytoplasm|nuclear chromatin|nuclear membrane|nucleoplasm	histone binding|nucleosomal DNA binding|Ran guanyl-nucleotide exchange factor activity			ovary(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;0.000318)|all_lung(284;0.000434)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.00989)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)|Medulloblastoma(700;0.123)		Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|KIRC - Kidney renal clear cell carcinoma(1967;0.0101)|BRCA - Breast invasive adenocarcinoma(304;0.022)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
RCC1	1104	broad.mit.edu	37	1	28864405	28864405	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:28864405C>T	uc001bqg.1	+	10	1237	c.1152C>T	c.(1150-1152)GAC>GAT	p.D384D	SNHG3-RCC1_uc001bqa.1_Silent_p.D384D|SNHG3-RCC1_uc001bqb.1_Silent_p.D384D|SNHG3-RCC1_uc001bqc.1_Silent_p.D384D|RCC1_uc001bqe.1_Silent_p.D401D|RCC1_uc001bqf.1_Silent_p.D415D	NM_001269	NP_001260	P18754	RCC1_HUMAN	regulator of chromosome condensation 1 isoform	384	RCC1 7.				cell division|chromosome segregation|G1/S transition of mitotic cell cycle|mitosis|mitotic spindle organization|regulation of mitosis|regulation of S phase of mitotic cell cycle|spindle assembly|viral reproduction	condensed nuclear chromosome|cytoplasm|nuclear chromatin|nuclear membrane|nucleoplasm	histone binding|nucleosomal DNA binding|Ran guanyl-nucleotide exchange factor activity			ovary(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;0.000318)|all_lung(284;0.000434)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.00989)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)|Medulloblastoma(700;0.123)		Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|KIRC - Kidney renal clear cell carcinoma(1967;0.0101)|BRCA - Breast invasive adenocarcinoma(304;0.022)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
EPB41	2035	broad.mit.edu	37	1	29323758	29323758	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29323758G>A	uc001brm.1	+	3	720	c.713G>A	c.(712-714)CGA>CAA	p.R238Q	EPB41_uc001brg.1_Missense_Mutation_p.R29Q|EPB41_uc001brh.1_Missense_Mutation_p.R29Q|EPB41_uc001bri.1_Intron|EPB41_uc001brj.1_Missense_Mutation_p.R29Q|EPB41_uc009vtk.1_Intron|EPB41_uc001brk.2_Missense_Mutation_p.R238Q|EPB41_uc001brl.1_Missense_Mutation_p.R238Q|EPB41_uc009vtl.1_Missense_Mutation_p.R29Q|EPB41_uc009vtm.1_Intron	NM_203342	NP_976217	P11171	41_HUMAN	erythrocyte membrane protein band 4.1	238	FERM.				blood circulation|cortical actin cytoskeleton organization|positive regulation of protein binding	extrinsic to membrane|Golgi apparatus|nucleus|plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	1-phosphatidylinositol binding|actin binding|spectrin binding|structural constituent of cytoskeleton			ovary(1)	1		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)														---	---	---	---
PTPRU	10076	broad.mit.edu	37	1	29585787	29585787	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29585787C>T	uc001bru.2	+	4	602	c.492C>T	c.(490-492)GCC>GCT	p.A164A	PTPRU_uc001brv.2_Silent_p.A164A|PTPRU_uc001brw.2_Silent_p.A164A|PTPRU_uc009vtq.2_Silent_p.A164A|PTPRU_uc009vtr.2_Silent_p.A164A	NM_005704	NP_005695	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U	164	Extracellular (Potential).|MAM.				canonical Wnt receptor signaling pathway|cell differentiation|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|protein localization at cell surface|transmembrane receptor protein tyrosine phosphatase signaling pathway	cell-cell junction|integral to plasma membrane	beta-catenin binding|transmembrane receptor protein tyrosine phosphatase activity			large_intestine(3)|ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	7		Colorectal(325;0.000399)|Lung NSC(340;0.00953)|all_lung(284;0.0112)|Breast(348;0.0126)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;6.99e-07)|COAD - Colon adenocarcinoma(152;3.18e-05)|STAD - Stomach adenocarcinoma(196;0.0234)|READ - Rectum adenocarcinoma(331;0.0686)|BRCA - Breast invasive adenocarcinoma(304;0.0871)														---	---	---	---
SDC3	9672	broad.mit.edu	37	1	31351588	31351588	+	Splice_Site	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31351588C>A	uc001bse.2	-	2	186	c.139_splice	c.e2-1	p.A47_splice	SDC3_uc001bsd.2_Splice_Site	NM_014654	NP_055469			syndecan 3							integral to membrane	cytoskeletal protein binding			ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(586;0.0393)|Colorectal(325;0.0466)|all_neural(195;0.0966)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)		STAD - Stomach adenocarcinoma(196;0.0197)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
PUM1	9698	broad.mit.edu	37	1	31414911	31414911	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:31414911G>A	uc001bsi.1	-	19	3161	c.3048C>T	c.(3046-3048)CAC>CAT	p.H1016H	PUM1_uc001bsf.1_Silent_p.H684H|PUM1_uc001bsg.1_Silent_p.H750H|PUM1_uc001bsh.1_Silent_p.H1018H|PUM1_uc001bsj.1_Silent_p.H992H|PUM1_uc010oga.1_Silent_p.H874H|PUM1_uc001bsk.1_Silent_p.H1054H|PUM1_uc010ogb.1_Silent_p.H957H|SNORD103A_uc009vts.1_Intron	NM_014676	NP_055491	Q14671	PUM1_HUMAN	pumilio 1 isoform 2	1016	PUM-HD.|Pumilio 5.				cellular membrane organization|post-Golgi vesicle-mediated transport|regulation of translation	cytosol	RNA binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)														---	---	---	---
COL16A1	1307	broad.mit.edu	37	1	32133817	32133817	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32133817A>G	uc001btk.1	-	51	3617	c.3252T>C	c.(3250-3252)GGT>GGC	p.G1084G	COL16A1_uc001bti.1_5'UTR|COL16A1_uc001btj.1_Silent_p.G882G	NM_001856	NP_001847	Q07092	COGA1_HUMAN	alpha 1 type XVI collagen precursor	1084	Triple-helical region 2 (COL2) with 2 imperfections.				cell adhesion|female pregnancy|integrin-mediated signaling pathway	collagen type XVI	integrin binding|structural molecule activity			ovary(8)	8		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)														---	---	---	---
COL16A1	1307	broad.mit.edu	37	1	32155378	32155378	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32155378C>T	uc001btk.1	-	23	1949	c.1584G>A	c.(1582-1584)GGG>GGA	p.G528G	COL16A1_uc001btj.1_Silent_p.G357G|COL16A1_uc001btl.3_Silent_p.G528G	NM_001856	NP_001847	Q07092	COGA1_HUMAN	alpha 1 type XVI collagen precursor	528	Triple-helical region 8 (COL8) with 1 imperfection.				cell adhesion|female pregnancy|integrin-mediated signaling pathway	collagen type XVI	integrin binding|structural molecule activity			ovary(8)	8		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)														---	---	---	---
COL16A1	1307	broad.mit.edu	37	1	32157648	32157648	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32157648G>A	uc001btk.1	-	17	1580	c.1215C>T	c.(1213-1215)GGC>GGT	p.G405G	COL16A1_uc001btj.1_Silent_p.G234G|COL16A1_uc001btl.3_Silent_p.G405G	NM_001856	NP_001847	Q07092	COGA1_HUMAN	alpha 1 type XVI collagen precursor	405	Triple-helical region 9 (COL9) with 3 imperfections.				cell adhesion|female pregnancy|integrin-mediated signaling pathway	collagen type XVI	integrin binding|structural molecule activity			ovary(8)	8		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)														---	---	---	---
BAI2	576	broad.mit.edu	37	1	32201444	32201444	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32201444G>A	uc001btn.2	-	23	3605	c.3251C>T	c.(3250-3252)GCA>GTA	p.A1084V	BAI2_uc001btm.2_5'Flank|BAI2_uc001btp.1_5'UTR|BAI2_uc010ogn.1_Missense_Mutation_p.A87V|BAI2_uc010ogo.1_Missense_Mutation_p.A726V|BAI2_uc010ogp.1_Missense_Mutation_p.A1017V|BAI2_uc010ogq.1_Missense_Mutation_p.A1084V|BAI2_uc001bto.2_Missense_Mutation_p.A1084V	NM_001703	NP_001694	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	1084	Helical; Name=5; (Potential).				negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(5)|breast(4)|ovary(2)|central_nervous_system(1)|skin(1)	13		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)		STAD - Stomach adenocarcinoma(196;0.0557)														---	---	---	---
EIF3I	8668	broad.mit.edu	37	1	32694368	32694368	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32694368G>A	uc001bur.3	+	9	1213	c.680G>A	c.(679-681)CGG>CAG	p.R227Q	EIF3I_uc009vuc.2_Missense_Mutation_p.R227Q|EIF3I_uc001bus.2_Missense_Mutation_p.R179Q	NM_003757	NP_003748	Q13347	EIF3I_HUMAN	eukaryotic translation initiation factor 3,	227						cytosol|eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			ovary(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.212)																---	---	---	---
LCK	3932	broad.mit.edu	37	1	32745597	32745597	+	Splice_Site	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32745597T>C	uc001bux.2	+	11	1333	c.1195_splice	c.e11+2	p.G399_splice	LCK_uc001buy.2_Splice_Site_p.G399_splice|LCK_uc001buz.2_Splice_Site_p.G429_splice|LCK_uc010ohc.1_Splice_Site_p.G443_splice|LCK_uc001bva.2_Splice_Site_p.G406_splice	NM_005356	NP_005347			lymphocyte-specific protein tyrosine kinase						activation of caspase activity|cellular zinc ion homeostasis|induction of apoptosis|interspecies interaction between organisms|leukocyte migration|platelet activation|positive regulation of T cell receptor signaling pathway|regulation of defense response to virus by virus|release of sequestered calcium ion into cytosol|response to drug|T cell costimulation|T cell differentiation|T cell receptor signaling pathway|viral reproduction	cytosol|Golgi apparatus|membrane raft|pericentriolar material|plasma membrane	ATP binding|ATPase binding|CD4 receptor binding|CD8 receptor binding|glycoprotein binding|non-membrane spanning protein tyrosine kinase activity|phosphatidylinositol 3-kinase binding|protein C-terminus binding|protein kinase binding|protein serine/threonine phosphatase activity|SH2 domain binding			lung(3)|central_nervous_system(2)|ovary(1)	6		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.212)			Dasatinib(DB01254)			T	TRB@	T-ALL								---	---	---	---
BSDC1	55108	broad.mit.edu	37	1	32842014	32842014	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32842014C>T	uc001bvh.3	-	9	1052	c.1005G>A	c.(1003-1005)AAG>AAA	p.K335K	BSDC1_uc010ohg.1_Silent_p.K352K|BSDC1_uc010ohh.1_Silent_p.K279K|BSDC1_uc010ohi.1_Silent_p.K240K|BSDC1_uc001bvg.3_RNA|BSDC1_uc001bvj.2_Silent_p.K231K|BSDC1_uc001bvi.2_Silent_p.K352K	NM_018045	NP_060515	Q9NW68	BSDC1_HUMAN	BSD domain containing 1 isoform b	335							protein binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)																---	---	---	---
ZNF362	149076	broad.mit.edu	37	1	33745780	33745780	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33745780C>T	uc001bxc.1	+	5	575	c.405C>T	c.(403-405)GGC>GGT	p.G135G		NM_152493	NP_689706	Q5T0B9	ZN362_HUMAN	zinc finger protein 362	135					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)																---	---	---	---
ZSCAN20	7579	broad.mit.edu	37	1	33960132	33960132	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:33960132C>T	uc001bxj.3	+	8	2355	c.2188C>T	c.(2188-2190)CGA>TGA	p.R730*	ZSCAN20_uc009vui.2_Nonsense_Mutation_p.R729*	NM_145238	NP_660281	P17040	ZSC20_HUMAN	zinc finger protein 31	730	C2H2-type 1.				viral reproduction	mitochondrion|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)																---	---	---	---
CSMD2	114784	broad.mit.edu	37	1	34035024	34035024	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34035024C>T	uc001bxn.1	-	53	8116	c.8087G>A	c.(8086-8088)CGT>CAT	p.R2696H	CSMD2_uc001bxm.1_Missense_Mutation_p.R2694H	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	2696	Sushi 17.|Extracellular (Potential).					integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)																---	---	---	---
CSMD2	114784	broad.mit.edu	37	1	34209061	34209061	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34209061C>T	uc001bxn.1	-	14	1902	c.1873G>A	c.(1873-1875)GTG>ATG	p.V625M	CSMD2_uc001bxm.1_Missense_Mutation_p.V665M	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	625	Extracellular (Potential).|CUB 4.					integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)																---	---	---	---
CSMD2	114784	broad.mit.edu	37	1	34254228	34254228	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:34254228A>G	uc001bxn.1	-	12	1545	c.1516T>C	c.(1516-1518)TCC>CCC	p.S506P	CSMD2_uc001bxm.1_Missense_Mutation_p.S546P	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	506	CUB 3.|Extracellular (Potential).					integral to membrane|plasma membrane	protein binding			ovary(6)|skin(5)|pancreas(1)	12		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)																---	---	---	---
ZMYM4	9202	broad.mit.edu	37	1	35847315	35847315	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35847315T>G	uc001byt.2	+	9	1605	c.1525T>G	c.(1525-1527)TCT>GCT	p.S509A	ZMYM4_uc009vuu.2_Missense_Mutation_p.S477A|ZMYM4_uc001byu.2_Missense_Mutation_p.S185A|ZMYM4_uc009vuv.2_Missense_Mutation_p.S248A	NM_005095	NP_005086	Q5VZL5	ZMYM4_HUMAN	zinc finger protein 262	509					multicellular organismal development		DNA binding|zinc ion binding			large_intestine(2)|ovary(1)|kidney(1)|skin(1)	5		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
ZMYM4	9202	broad.mit.edu	37	1	35865080	35865080	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35865080T>C	uc001byt.2	+						ZMYM4_uc009vuu.2_Intron|ZMYM4_uc001byu.2_Intron|ZMYM4_uc009vuv.2_Intron	NM_005095	NP_005086			zinc finger protein 262						multicellular organismal development		DNA binding|zinc ion binding			large_intestine(2)|ovary(1)|kidney(1)|skin(1)	5		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
ZMYM4	9202	broad.mit.edu	37	1	35881325	35881325	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35881325A>G	uc001byt.2	+						ZMYM4_uc009vuu.2_Intron|ZMYM4_uc001byu.2_Intron|ZMYM4_uc009vuv.2_Intron	NM_005095	NP_005086			zinc finger protein 262						multicellular organismal development		DNA binding|zinc ion binding			large_intestine(2)|ovary(1)|kidney(1)|skin(1)	5		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
EIF2C1	26523	broad.mit.edu	37	1	36359747	36359747	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36359747C>T	uc001bzl.2	+	6	972	c.759C>T	c.(757-759)CGC>CGT	p.R253R	EIF2C1_uc001bzk.2_Silent_p.R178R|EIF2C1_uc009vuy.2_5'Flank	NM_012199	NP_036331	Q9UL18	AGO1_HUMAN	eukaryotic translation initiation factor 2C, 1	253	PAZ.				negative regulation of translation involved in gene silencing by miRNA|nuclear-transcribed mRNA catabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|micro-ribonucleoprotein complex|polysome	protein binding|RNA binding			ovary(2)|skin(1)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
EIF2C3	192669	broad.mit.edu	37	1	36411297	36411297	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36411297C>T	uc001bzp.2	+	2	280	c.24C>T	c.(22-24)CCC>CCT	p.P8P	EIF2C3_uc001bzn.1_Silent_p.P8P|EIF2C3_uc001bzo.2_RNA|EIF2C3_uc001bzq.2_5'UTR	NM_024852	NP_079128	Q9H9G7	AGO3_HUMAN	eukaryotic translation initiation factor 2C, 3	8					mRNA catabolic process|negative regulation of translation involved in gene silencing by miRNA	cytoplasmic mRNA processing body|cytosol	protein binding|RNA binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)																---	---	---	---
THRAP3	9967	broad.mit.edu	37	1	36762280	36762280	+	Nonsense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:36762280A>T	uc001cae.3	+	9	2436	c.2212A>T	c.(2212-2214)AGA>TGA	p.R738*	THRAP3_uc001caf.3_Nonsense_Mutation_p.R738*	NM_005119	NP_005110	Q9Y2W1	TR150_HUMAN	thyroid hormone receptor associated protein 3	738					androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ATP binding|ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(5)|lung(3)|breast(1)	9		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)						T	USP6	aneurysmal bone cysts								---	---	---	---
GRIK3	2899	broad.mit.edu	37	1	37325543	37325543	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:37325543C>T	uc001caz.2	-	6	997	c.862G>A	c.(862-864)GAC>AAC	p.D288N	GRIK3_uc001cba.1_Missense_Mutation_p.D288N	NM_000831	NP_000822	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3	288	Extracellular (Potential).				negative regulation of synaptic transmission, glutamatergic|regulation of membrane potential|synaptic transmission	cell junction|dendrite cytoplasm|integral to plasma membrane|perikaryon|postsynaptic membrane|terminal button	adenylate cyclase inhibiting metabotropic glutamate receptor activity|extracellular-glutamate-gated ion channel activity|G-protein-coupled receptor binding|kainate selective glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)|breast(1)	7		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)			L-Glutamic Acid(DB00142)													---	---	---	---
SNIP1	79753	broad.mit.edu	37	1	38003596	38003596	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38003596C>T	uc001cbi.2	-	4	1017	c.944G>A	c.(943-945)CGT>CAT	p.R315H	SNIP1_uc010oid.1_RNA	NM_024700	NP_078976	Q8TAD8	SNIP1_HUMAN	Smad nuclear interacting protein	315	FHA.				production of miRNAs involved in gene silencing by miRNA	nucleus	protein binding			upper_aerodigestive_tract(1)|lung(1)	2		Myeloproliferative disorder(586;0.0393)																---	---	---	---
SNIP1	79753	broad.mit.edu	37	1	38005841	38005841	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38005841G>A	uc001cbi.2	-	3	916	c.843C>T	c.(841-843)TAC>TAT	p.Y281Y	SNIP1_uc010oid.1_RNA	NM_024700	NP_078976	Q8TAD8	SNIP1_HUMAN	Smad nuclear interacting protein	281	FHA.				production of miRNAs involved in gene silencing by miRNA	nucleus	protein binding			upper_aerodigestive_tract(1)|lung(1)	2		Myeloproliferative disorder(586;0.0393)																---	---	---	---
GNL2	29889	broad.mit.edu	37	1	38052955	38052955	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38052955G>A	uc001cbk.2	-	5	689	c.526C>T	c.(526-528)CAG>TAG	p.Q176*	GNL2_uc010oif.1_Nonsense_Mutation_p.Q17*|GNL2_uc009vve.2_Intron	NM_013285	NP_037417	Q13823	NOG2_HUMAN	guanine nucleotide binding protein-like 2	176					ribosome biogenesis	nucleolus	GTP binding|GTPase activity|protein binding			ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(586;0.0393)																---	---	---	---
GNL2	29889	broad.mit.edu	37	1	38059363	38059363	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38059363C>A	uc001cbk.2	-	2	312	c.149G>T	c.(148-150)AGG>ATG	p.R50M	GNL2_uc010oif.1_Translation_Start_Site|GNL2_uc009vve.2_Missense_Mutation_p.R50M	NM_013285	NP_037417	Q13823	NOG2_HUMAN	guanine nucleotide binding protein-like 2	50					ribosome biogenesis	nucleolus	GTP binding|GTPase activity|protein binding			ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(586;0.0393)																---	---	---	---
RRAGC	64121	broad.mit.edu	37	1	39305271	39305271	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39305271C>T	uc001ccq.2	-	7	1176	c.1154G>A	c.(1153-1155)AGT>AAT	p.S385N	RRAGC_uc010oim.1_Missense_Mutation_p.S351N|RRAGC_uc001ccr.2_Missense_Mutation_p.S307N	NM_022157	NP_071440	Q9HB90	RRAGC_HUMAN	Ras-related GTP binding C	385					apoptosis|cell growth|cellular protein localization|cellular response to amino acid stimulus|positive regulation of TOR signaling cascade|RNA splicing|small GTPase mediated signal transduction|transcription, DNA-dependent	lysosome|nucleus	GDP binding|GTP binding|GTPase activity|magnesium ion binding|protein heterodimerization activity			ovary(1)	1	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)																---	---	---	---
MACF1	23499	broad.mit.edu	37	1	39788347	39788347	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39788347G>A	uc010ois.1	+	33	4317	c.4112G>A	c.(4111-4113)CGC>CAC	p.R1371H	MACF1_uc001cda.1_Missense_Mutation_p.R1279H|MACF1_uc001cdc.1_Missense_Mutation_p.R458H|MACF1_uc009vvq.1_Missense_Mutation_p.R428H|MACF1_uc001cdb.1_Missense_Mutation_p.R458H	NM_012090	NP_036222	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker	1371					cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)|skin(2)	16	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)															---	---	---	---
MACF1	23499	broad.mit.edu	37	1	39797537	39797537	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39797537G>A	uc010oiu.1	+	1	728	c.597G>A	c.(595-597)AGG>AGA	p.R199R	MACF1_uc010ois.1_Intron|MACF1_uc001cda.1_Intron|MACF1_uc001cdc.1_Intron|MACF1_uc001cdb.1_Intron	NM_033044	NP_149033	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker	1764					cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)|skin(2)	16	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)															---	---	---	---
MACF1	23499	broad.mit.edu	37	1	39838264	39838264	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39838264G>A	uc010oiu.1	+	16	8660	c.8529G>A	c.(8527-8529)AAG>AAA	p.K2843K	MACF1_uc010ois.1_Silent_p.K2341K|MACF1_uc001cda.1_Silent_p.K2249K|MACF1_uc001cdc.1_Silent_p.K1428K|MACF1_uc001cdb.1_Silent_p.K1428K	NM_033044	NP_149033	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker	4408					cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)|skin(2)	16	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)															---	---	---	---
MACF1	23499	broad.mit.edu	37	1	39893940	39893940	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39893940G>T	uc010oiu.1	+	27	12235	c.12104G>T	c.(12103-12105)AGG>ATG	p.R4035M	MACF1_uc010ois.1_Missense_Mutation_p.R3533M|MACF1_uc001cda.1_Missense_Mutation_p.R3420M|MACF1_uc001cdc.1_Intron	NM_033044	NP_149033	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)|skin(2)	16	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)															---	---	---	---
HEYL	26508	broad.mit.edu	37	1	40095922	40095922	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40095922A>G	uc001cdp.2	-	4	341	c.290T>C	c.(289-291)ATG>ACG	p.M97T	HEYL_uc010oiw.1_Missense_Mutation_p.M69T	NM_014571	NP_055386	Q9NQ87	HEYL_HUMAN	hairy/enhancer-of-split related with YRPW	97	Transcriptional repression and interaction with NCOR1 and SIN3A (By similarity).|Helix-loop-helix motif.				multicellular organismal development|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1	Lung NSC(20;3.81e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.1e-18)|Epithelial(16;2.77e-17)|all cancers(16;5.64e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)															---	---	---	---
MFSD2A	84879	broad.mit.edu	37	1	40424485	40424485	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40424485G>A	uc001cev.2	+	3	561	c.380G>A	c.(379-381)CGC>CAC	p.R127H	MFSD2A_uc010ojb.1_Missense_Mutation_p.R77H|MFSD2A_uc001ceu.2_Missense_Mutation_p.R114H|MFSD2A_uc010ojc.1_Intron|MFSD2A_uc009vvy.2_RNA	NM_001136493	NP_001129965	Q8NA29	MFS2A_HUMAN	major facilitator superfamily domain containing	127					transmembrane transport	endoplasmic reticulum membrane|integral to membrane				ovary(1)|pancreas(1)	2																		---	---	---	---
COL9A2	1298	broad.mit.edu	37	1	40779928	40779928	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40779928G>A	uc001cfh.1	-	4	268	c.198C>T	c.(196-198)GGC>GGT	p.G66G	COL9A2_uc001cfi.1_5'UTR	NM_001852	NP_001843	Q14055	CO9A2_HUMAN	alpha 2 type IX collagen precursor	66	Triple-helical region 4 (COL4).				axon guidance|skeletal system development	collagen type IX				ovary(2)	2	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;2.08e-17)															---	---	---	---
ZNF642	339559	broad.mit.edu	37	1	40961657	40961657	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40961657G>A	uc001cfo.2	+	6	1801	c.1507G>A	c.(1507-1509)GCC>ACC	p.A503T	ZNF642_uc009vwb.2_Missense_Mutation_p.A503T|ZNF642_uc010ojk.1_Missense_Mutation_p.A504T	NM_198494	NP_940896	Q49AA0	ZN642_HUMAN	zinc finger protein 642	503	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;8.81e-19)															---	---	---	---
DEM1	64789	broad.mit.edu	37	1	40981297	40981297	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40981297C>T	uc001cfp.2	+	3	1286	c.1081C>T	c.(1081-1083)CTC>TTC	p.L361F	DEM1_uc001cfq.2_Missense_Mutation_p.L361F|DEM1_uc001cfr.2_Missense_Mutation_p.L361F|DEM1_uc001cfs.2_Missense_Mutation_p.L361F	NM_022774	NP_073611	Q9H790	EXO5_HUMAN	defects in morphology 1 homolog	361							DNA binding|exonuclease activity				0																		---	---	---	---
NFYC	4802	broad.mit.edu	37	1	41236467	41236467	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41236467C>T	uc001cge.2	+	10	1352	c.1344C>T	c.(1342-1344)TCC>TCT	p.S448S	NFYC_uc001cfx.3_Silent_p.S344S|NFYC_uc009vwd.2_Silent_p.S325S|NFYC_uc001cfz.2_Silent_p.S324S|NFYC_uc010ojn.1_Silent_p.S287S|NFYC_uc001cfy.3_Silent_p.S325S|NFYC_uc001cgc.2_Silent_p.S291S|NFYC_uc001cgb.2_Silent_p.S429S|NFYC_uc001cgd.3_Silent_p.S325S	NM_001142588	NP_001136060	Q13952	NFYC_HUMAN	nuclear transcription factor Y, gamma isoform 1	448					protein folding|regulation of transcription from RNA polymerase II promoter	CCAAT-binding factor complex	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			breast(2)|kidney(1)	3	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.72e-17)															---	---	---	---
HIVEP3	59269	broad.mit.edu	37	1	42047611	42047611	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42047611T>G	uc001cgz.3	-	4	4071	c.2858A>C	c.(2857-2859)GAC>GCC	p.D953A	HIVEP3_uc001cha.3_Missense_Mutation_p.D953A|HIVEP3_uc001cgy.2_RNA	NM_024503	NP_078779	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer	953	No DNA binding activity or transactivation activity, but complete prevention of TRAF-dependent NF-Kappa-B activation; associates with TRAF2 and JUN (By similarity).				positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)																---	---	---	---
FOXJ3	22887	broad.mit.edu	37	1	42654551	42654551	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42654551T>C	uc001che.2	-	13	1814	c.1502A>G	c.(1501-1503)GAC>GGC	p.D501G	FOXJ3_uc001chf.2_Missense_Mutation_p.D501G|FOXJ3_uc001chg.2_Missense_Mutation_p.D501G	NM_014947	NP_055762	Q9UPW0	FOXJ3_HUMAN	forkhead box J3	501					embryo development|organ development|pattern specification process|positive regulation of transcription, DNA-dependent|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein domain specific binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			ovary(2)	2	Ovarian(52;0.01)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)																---	---	---	---
MED8	112950	broad.mit.edu	37	1	43851674	43851674	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43851674T>C	uc001cjg.3	-	6	765	c.717A>G	c.(715-717)GTA>GTG	p.V239V	MED8_uc001cje.1_Silent_p.V239V|MED8_uc001cjf.3_Silent_p.V150V	NM_201542	NP_963836	Q96G25	MED8_HUMAN	mediator complex subunit 8 isoform 1	239					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex					0	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)																---	---	---	---
KIAA0467	23334	broad.mit.edu	37	1	43908573	43908573	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43908573C>A	uc001cjk.1	+	44	6000	c.5538C>A	c.(5536-5538)GGC>GGA	p.G1846G		NM_015284	NP_056099	Q5T011	SZT2_HUMAN	hypothetical protein LOC23334	2745						peroxisome					0	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)																---	---	---	---
IPO13	9670	broad.mit.edu	37	1	44423781	44423781	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44423781G>A	uc001ckx.2	+	8	2468	c.1673G>A	c.(1672-1674)TGC>TAC	p.C558Y		NM_014652	NP_055467	O94829	IPO13_HUMAN	importin 13	558	HEAT 9.				protein import into nucleus	cytoplasm|nucleus	protein binding|protein transporter activity			central_nervous_system(1)	1	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0821)																---	---	---	---
IPO13	9670	broad.mit.edu	37	1	44425992	44425992	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44425992G>T	uc001ckx.2	+	12	2895	c.2100G>T	c.(2098-2100)CAG>CAT	p.Q700H		NM_014652	NP_055467	O94829	IPO13_HUMAN	importin 13	700	HEAT 12.				protein import into nucleus	cytoplasm|nucleus	protein binding|protein transporter activity			central_nervous_system(1)	1	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0821)																---	---	---	---
IPO13	9670	broad.mit.edu	37	1	44432666	44432666	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44432666G>A	uc001ckx.2	+	18	3383	c.2588G>A	c.(2587-2589)CGT>CAT	p.R863H	IPO13_uc001cky.2_Missense_Mutation_p.R81H	NM_014652	NP_055467	O94829	IPO13_HUMAN	importin 13	863					protein import into nucleus	cytoplasm|nucleus	protein binding|protein transporter activity			central_nervous_system(1)	1	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0821)																---	---	---	---
RNF220	55182	broad.mit.edu	37	1	45088448	45088448	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45088448G>T	uc001clv.1	+	4	1153	c.793G>T	c.(793-795)GGC>TGC	p.G265C	RNF220_uc001clw.1_Missense_Mutation_p.G265C|RNF220_uc010okx.1_Missense_Mutation_p.G26C|RNF220_uc010oky.1_Missense_Mutation_p.G26C	NM_018150	NP_060620	Q5VTB9	RN220_HUMAN	ring finger protein 220	265					protein autoubiquitination	cytoplasm	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
MUTYH	4595	broad.mit.edu	37	1	45798130	45798130	+	Missense_Mutation	SNP	G	A	A	rs34126013		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45798130G>A	uc001cnm.2	-	9	928	c.712C>T	c.(712-714)CGG>TGG	p.R238W	MUTYH_uc009vxn.2_Missense_Mutation_p.R63W|MUTYH_uc001cnf.2_Missense_Mutation_p.R213W|MUTYH_uc009vxo.2_Missense_Mutation_p.R213W|MUTYH_uc001cng.2_Missense_Mutation_p.R224W|MUTYH_uc001cnj.2_Missense_Mutation_p.R121W|MUTYH_uc001cni.2_Missense_Mutation_p.R213W|MUTYH_uc001cnh.2_Missense_Mutation_p.R214W|MUTYH_uc001cno.2_Missense_Mutation_p.R121W|MUTYH_uc001cnk.2_Missense_Mutation_p.R98W|MUTYH_uc010oll.1_Intron|MUTYH_uc001cnl.2_Missense_Mutation_p.R227W|MUTYH_uc009vxp.2_Missense_Mutation_p.R241W|MUTYH_uc001cnn.2_Missense_Mutation_p.R228W	NM_012222	NP_036354	Q9UIF7	MUTYH_HUMAN	mutY homolog isoform 1	238					depurination|mismatch repair	nucleoplasm	4 iron, 4 sulfur cluster binding|DNA N-glycosylase activity|endonuclease activity|metal ion binding|MutSalpha complex binding				0	Acute lymphoblastic leukemia(166;0.155)							Mis			colorectal		BER_DNA_glycosylases	MUTYH-associated_polyposis				---	---	---	---
MUTYH	4595	broad.mit.edu	37	1	45798144	45798144	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45798144T>G	uc001cnm.2	-	9	914	c.698A>C	c.(697-699)GAT>GCT	p.D233A	MUTYH_uc009vxn.2_Missense_Mutation_p.D58A|MUTYH_uc001cnf.2_Missense_Mutation_p.D208A|MUTYH_uc009vxo.2_Missense_Mutation_p.D208A|MUTYH_uc001cng.2_Missense_Mutation_p.D219A|MUTYH_uc001cnj.2_Missense_Mutation_p.D116A|MUTYH_uc001cni.2_Missense_Mutation_p.D208A|MUTYH_uc001cnh.2_Missense_Mutation_p.D209A|MUTYH_uc001cno.2_Missense_Mutation_p.D116A|MUTYH_uc001cnk.2_Missense_Mutation_p.D93A|MUTYH_uc010oll.1_Intron|MUTYH_uc001cnl.2_Missense_Mutation_p.D222A|MUTYH_uc009vxp.2_Missense_Mutation_p.D236A|MUTYH_uc001cnn.2_Missense_Mutation_p.D223A	NM_012222	NP_036354	Q9UIF7	MUTYH_HUMAN	mutY homolog isoform 1	233					depurination|mismatch repair	nucleoplasm	4 iron, 4 sulfur cluster binding|DNA N-glycosylase activity|endonuclease activity|metal ion binding|MutSalpha complex binding				0	Acute lymphoblastic leukemia(166;0.155)							Mis			colorectal		BER_DNA_glycosylases	MUTYH-associated_polyposis				---	---	---	---
PRDX1	5052	broad.mit.edu	37	1	45981487	45981487	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45981487G>A	uc001cnz.2	-						PRDX1_uc001coa.2_Intron|PRDX1_uc001cob.2_Intron|PRDX1_uc001coc.2_Intron	NM_181697	NP_859048			peroxiredoxin 1						cell proliferation|cell redox homeostasis|hydrogen peroxide catabolic process|skeletal system development	melanosome|mitochondrion|nucleus	protein binding|thioredoxin peroxidase activity				0	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
AKR1A1	10327	broad.mit.edu	37	1	46027556	46027556	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46027556G>A	uc001cod.2	+						AKR1A1_uc009vxw.2_Intron|AKR1A1_uc001coe.2_Intron	NM_006066	NP_006057			aldo-keto reductase family 1, member A1						glucose metabolic process		alditol:NADP+ 1-oxidoreductase activity|electron carrier activity|protein binding				0	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
AKR1A1	10327	broad.mit.edu	37	1	46033771	46033771	+	Silent	SNP	G	A	A	rs147059021	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46033771G>A	uc001cod.2	+	6	938	c.474G>A	c.(472-474)GCG>GCA	p.A158A	AKR1A1_uc001coe.2_Silent_p.A158A|AKR1A1_uc001cof.2_Missense_Mutation_p.R31H|AKR1A1_uc001cog.2_RNA	NM_006066	NP_006057	P14550	AK1A1_HUMAN	aldo-keto reductase family 1, member A1	158					glucose metabolic process		alditol:NADP+ 1-oxidoreductase activity|electron carrier activity|protein binding				0	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
MAST2	23139	broad.mit.edu	37	1	46495235	46495235	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46495235C>T	uc001cov.2	+	19	2599	c.2316C>T	c.(2314-2316)GGC>GGT	p.G772G	MAST2_uc001cow.2_Silent_p.G772G|MAST2_uc001coy.1_Silent_p.G446G|MAST2_uc001coz.1_Silent_p.G657G|MAST2_uc001cpa.2_RNA	NM_015112	NP_055927	Q6P0Q8	MAST2_HUMAN	microtubule associated serine/threonine kinase	772	Protein kinase.				regulation of interleukin-12 biosynthetic process|spermatid differentiation	cytoplasm|cytoskeleton|plasma membrane	ATP binding|magnesium ion binding|phosphatase binding|protein serine/threonine kinase activity			ovary(5)|lung(3)|stomach(2)|breast(1)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)																	---	---	---	---
PIK3R3	8503	broad.mit.edu	37	1	46511720	46511720	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46511720A>G	uc001cpb.3	-	9	1813	c.1057T>C	c.(1057-1059)TAT>CAT	p.Y353H	PIK3R3_uc009vyb.2_Missense_Mutation_p.Y294H|PIK3R3_uc009vyc.2_Missense_Mutation_p.Y370H|PIK3R3_uc001cpc.3_Missense_Mutation_p.Y353H|PIK3R3_uc010olw.1_Missense_Mutation_p.Y399H|PIK3R3_uc010olv.1_Missense_Mutation_p.Y143H	NM_003629	NP_003620	Q92569	P55G_HUMAN	phosphoinositide-3-kinase, regulatory subunit 3	353					insulin receptor signaling pathway|platelet activation|T cell costimulation		1-phosphatidylinositol-3-kinase activity|protein binding				0	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
POMGNT1	55624	broad.mit.edu	37	1	46661505	46661505	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46661505C>T	uc001cpe.2	-	6	676	c.512G>A	c.(511-513)CGA>CAA	p.R171Q	POMGNT1_uc010olx.1_Missense_Mutation_p.R149Q|POMGNT1_uc010oly.1_RNA|POMGNT1_uc010olz.1_Missense_Mutation_p.R28Q|POMGNT1_uc001cpg.2_Missense_Mutation_p.R171Q|POMGNT1_uc001cpf.2_5'UTR|POMGNT1_uc001cpj.2_Missense_Mutation_p.R155Q|POMGNT1_uc001cpi.1_5'Flank	NM_017739	NP_060209	Q8WZA1	PMGT1_HUMAN	O-linked mannose	171	Lumenal (Potential).				protein N-linked glycosylation|protein O-linked glycosylation	Golgi membrane|integral to membrane|microsome	alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity|beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
RAD54L	8438	broad.mit.edu	37	1	46743574	46743574	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46743574T>C	uc009vye.2	+	18	2069	c.1955T>C	c.(1954-1956)GTA>GCA	p.V652A	RAD54L_uc001cpl.2_Missense_Mutation_p.V652A|RAD54L_uc001cpm.1_Missense_Mutation_p.V435A	NM_001142548	NP_001136020	Q92698	RAD54_HUMAN	RAD54-like protein	652	Helicase C-terminal.				meiosis	nucleus	ATP binding|DNA binding|helicase activity			ovary(2)|skin(1)	3	Acute lymphoblastic leukemia(166;0.155)	Breast(1374;0.0634)		KIRC - Kidney renal clear cell carcinoma(1967;0.000896)									Direct_reversal_of_damage|Homologous_recombination					---	---	---	---
LRRC41	10489	broad.mit.edu	37	1	46745938	46745938	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46745938A>G	uc001cpn.2	-	7	1990	c.1946T>C	c.(1945-1947)CTG>CCG	p.L649P	LRRC41_uc010omb.1_Missense_Mutation_p.L649P	NM_006369	NP_006360	Q15345	LRC41_HUMAN	MUF1 protein	649	LRR 5.									ovary(2)|breast(1)|pancreas(1)	4	Acute lymphoblastic leukemia(166;0.155)																	---	---	---	---
FAAH	2166	broad.mit.edu	37	1	46878752	46878752	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46878752G>A	uc001cpu.2	+	14	1553	c.1471G>A	c.(1471-1473)GTC>ATC	p.V491I	FAAH_uc001cpv.2_Intron	NM_001441	NP_001432	O00519	FAAH1_HUMAN	fatty acid amide hydrolase	491	Cytoplasmic (By similarity).				fatty acid catabolic process	cytoplasm|cytoskeleton|endomembrane system|integral to membrane|organelle membrane	carbon-nitrogen ligase activity, with glutamine as amido-N-donor|fatty acid amide hydrolase activity			ovary(1)|breast(1)	2	Acute lymphoblastic leukemia(166;0.155)				Propofol(DB00818)|Thiopental(DB00599)													---	---	---	---
CYP4X1	260293	broad.mit.edu	37	1	47514266	47514266	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47514266C>T	uc001cqt.2	+	10	1487	c.1237C>T	c.(1237-1239)CTT>TTT	p.L413F	CYP4X1_uc001cqr.2_Missense_Mutation_p.L412F|CYP4X1_uc001cqs.2_Missense_Mutation_p.L348F	NM_178033	NP_828847	Q8N118	CP4X1_HUMAN	cytochrome P450, family 4, subfamily X,	413						endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding			ovary(1)|skin(1)	2																		---	---	---	---
STIL	6491	broad.mit.edu	37	1	47726077	47726077	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47726077T>C	uc001crc.1	-	16	3116	c.2961A>G	c.(2959-2961)AGA>AGG	p.R987R	TAL1_uc001crb.1_Intron|STIL_uc010omn.1_Silent_p.R941R|STIL_uc010omo.1_Silent_p.R970R|STIL_uc001crd.1_Silent_p.R988R|STIL_uc001cre.1_Silent_p.R987R|STIL_uc001crf.1_Silent_p.R600R|STIL_uc001crg.1_Silent_p.R923R	NM_003035	NP_003026	Q15468	STIL_HUMAN	SCL/TAL1 interrupting locus isoform 2	987					cell proliferation|multicellular organismal development	centrosome|cytosol				lung(2)|skin(1)	3		Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444)																---	---	---	---
ELAVL4	1996	broad.mit.edu	37	1	50661359	50661359	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50661359A>G	uc001csb.2	+	5	903	c.635A>G	c.(634-636)AAC>AGC	p.N212S	ELAVL4_uc001cry.3_Missense_Mutation_p.N215S|ELAVL4_uc001crz.3_Missense_Mutation_p.N212S|ELAVL4_uc001csa.3_Missense_Mutation_p.N229S|ELAVL4_uc001csc.3_Missense_Mutation_p.N212S|ELAVL4_uc009vyu.2_Missense_Mutation_p.N217S|ELAVL4_uc010omz.1_Missense_Mutation_p.N217S	NM_021952	NP_068771	P26378	ELAV4_HUMAN	ELAV-like 4 isoform 1	212	RRM 2.				mRNA processing		AU-rich element binding|mRNA 3'-UTR binding|nucleotide binding			ovary(1)|pancreas(1)	2																		---	---	---	---
EPS15	2060	broad.mit.edu	37	1	51873795	51873795	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:51873795A>G	uc001csq.1	-						EPS15_uc009vyz.1_Intron|EPS15_uc001csp.3_Intron	NM_001981	NP_001972			epidermal growth factor receptor pathway						cell proliferation|clathrin coat assembly|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|protein transport	cytosol|early endosome membrane	calcium ion binding|SH3 domain binding			lung(1)|kidney(1)	2								T	MLL	ALL								---	---	---	---
NRD1	4898	broad.mit.edu	37	1	52289381	52289381	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52289381G>A	uc001ctc.3	-	9	1640	c.1318C>T	c.(1318-1320)CGT>TGT	p.R440C	NRD1_uc009vzb.2_Missense_Mutation_p.R135C|NRD1_uc001ctd.3_Missense_Mutation_p.R372C|NRD1_uc001cte.2_Missense_Mutation_p.R308C|NRD1_uc001ctf.2_Missense_Mutation_p.R372C|NRD1_uc010ong.1_RNA|NRD1_uc009vzc.1_Missense_Mutation_p.R240C	NM_002525	NP_002516	O43847	NRDC_HUMAN	nardilysin isoform a	371					cell migration|cell proliferation|neuromuscular junction development|positive regulation of membrane protein ectodomain proteolysis|proteolysis|regulation of endopeptidase activity	cell surface|cytosol	epidermal growth factor binding|metalloendopeptidase activity|zinc ion binding				0																		---	---	---	---
CC2D1B	200014	broad.mit.edu	37	1	52825821	52825821	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52825821G>A	uc001ctq.1	-	7	826	c.688C>T	c.(688-690)CGG>TGG	p.R230W	CC2D1B_uc001ctr.2_5'Flank|CC2D1B_uc001cts.2_5'UTR	NM_032449	NP_115825	Q5T0F9	C2D1B_HUMAN	coiled-coil and C2 domain containing 1B	230	Pro-rich.									ovary(2)	2																		---	---	---	---
ZCCHC11	23318	broad.mit.edu	37	1	52896886	52896886	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:52896886G>T	uc001ctx.2	-	28	4741	c.4507C>A	c.(4507-4509)CCG>ACG	p.P1503T	ZCCHC11_uc001cty.2_Missense_Mutation_p.P1504T|ZCCHC11_uc001ctz.2_Missense_Mutation_p.P1499T|ZCCHC11_uc001cua.1_Missense_Mutation_p.P421T	NM_015269	NP_056084	Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11 isoform	1503	Pro-rich.				miRNA catabolic process|pre-miRNA processing|RNA 3'-end processing|stem cell maintenance	cytoplasm|nucleolus	nucleic acid binding|protein binding|protein binding|RNA uridylyltransferase activity|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
DMRTB1	63948	broad.mit.edu	37	1	53930432	53930432	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53930432G>A	uc001cvq.1	+	3	928	c.873G>A	c.(871-873)GCG>GCA	p.A291A		NM_033067	NP_149056	Q96MA1	DMRTB_HUMAN	DMRT-like family B with proline-rich C-terminal,	291	Pro-rich.				sex differentiation	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity			ovary(1)|skin(1)	2																		---	---	---	---
CDCP2	200008	broad.mit.edu	37	1	54605750	54605750	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54605750G>A	uc001cwv.1	-	4	1641	c.793C>T	c.(793-795)CGG>TGG	p.R265W		NM_201546	NP_963840	Q5VXM1	CDCP2_HUMAN	CUB domain containing protein 2 precursor	265	CUB 3.					extracellular region				ovary(1)	1																		---	---	---	---
CYB5RL	606495	broad.mit.edu	37	1	54644993	54644993	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54644993C>T	uc009vzo.2	-	7	893	c.573G>A	c.(571-573)ACG>ACA	p.T191T	CYB5RL_uc001cww.2_Silent_p.T81T|CYB5RL_uc001cwx.3_RNA|CYB5RL_uc001cwy.3_Silent_p.T43T	NM_001031672	NP_001026842	Q6IPT4	NB5R5_HUMAN	cytochrome b5 reductase-like	191	FAD (By similarity).						cytochrome-b5 reductase activity				0																		---	---	---	---
BSND	7809	broad.mit.edu	37	1	55464947	55464947	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55464947C>A	uc001cye.2	+	1	331	c.88C>A	c.(88-90)CGG>AGG	p.R30R		NM_057176	NP_476517	Q8WZ55	BSND_HUMAN	barttin	30	Extracellular (Potential).					basolateral plasma membrane|cytoplasm|integral to plasma membrane|protein complex				ovary(1)|skin(1)	2																		---	---	---	---
PCSK9	255738	broad.mit.edu	37	1	55521680	55521680	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55521680C>T	uc001cyf.1	+	6	1105	c.814C>T	c.(814-816)CGG>TGG	p.R272W	PCSK9_uc010oom.1_RNA	NM_174936	NP_777596	Q8NBP7	PCSK9_HUMAN	proprotein convertase subtilisin/kexin type 9	272	Peptidase S8.				cellular response to insulin stimulus|cellular response to starvation|cholesterol homeostasis|cholesterol metabolic process|kidney development|liver development|low-density lipoprotein particle receptor catabolic process|lysosomal transport|negative regulation of catalytic activity|negative regulation of low-density lipoprotein particle clearance|negative regulation of receptor recycling|neuron differentiation|positive regulation of neuron apoptosis|positive regulation of receptor internalization|protein autoprocessing|regulation of receptor activity	extracellular space|late endosome|lysosome|perinuclear region of cytoplasm	apolipoprotein receptor binding|identical protein binding|low-density lipoprotein particle receptor binding|serine-type endopeptidase activity|very-low-density lipoprotein particle receptor binding			ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
USP24	23358	broad.mit.edu	37	1	55559690	55559690	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55559690G>A	uc001cyg.3	-	49	5794	c.5794C>T	c.(5794-5796)CTG>TTG	p.L1932L		NM_015306	NP_056121	Q9UPU5	UBP24_HUMAN	ubiquitin specific protease 24	2092					ubiquitin-dependent protein catabolic process		binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(6)|kidney(6)|breast(1)	13																		---	---	---	---
C8B	732	broad.mit.edu	37	1	57411609	57411609	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57411609G>A	uc001cyp.2	-	7	1057	c.990C>T	c.(988-990)TAC>TAT	p.Y330Y	C8B_uc010oon.1_Silent_p.Y268Y|C8B_uc010ooo.1_Silent_p.Y278Y	NM_000066	NP_000057	P07358	CO8B_HUMAN	complement component 8, beta polypeptide	330	MACPF.				complement activation, alternative pathway|complement activation, classical pathway|cytolysis	membrane attack complex				central_nervous_system(2)|large_intestine(1)|ovary(1)	4																		---	---	---	---
DAB1	1600	broad.mit.edu	37	1	57537190	57537190	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57537190T>C	uc001cys.1	-						DAB1_uc001cyt.1_Intron|DAB1_uc001cyq.1_Intron|DAB1_uc001cyr.1_Intron|DAB1_uc009vzw.1_Intron|DAB1_uc009vzx.1_Intron	NM_021080	NP_066566			disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3																		---	---	---	---
ROR1	4919	broad.mit.edu	37	1	64515548	64515548	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64515548C>T	uc001dbj.2	+	3	748	c.349C>T	c.(349-351)CGG>TGG	p.R117W	ROR1_uc001dbi.3_Missense_Mutation_p.R117W	NM_005012	NP_005003	Q01973	ROR1_HUMAN	receptor tyrosine kinase-like orphan receptor 1	117	Ig-like C2-type.|Extracellular (Potential).				transmembrane receptor protein tyrosine kinase signaling pathway	cytoplasm|integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			ovary(6)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|central_nervous_system(1)|skin(1)|kidney(1)	19																		---	---	---	---
ROR1	4919	broad.mit.edu	37	1	64644490	64644490	+	Silent	SNP	C	T	T	rs75566046	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:64644490C>T	uc001dbj.2	+	9	3165	c.2766C>T	c.(2764-2766)GAC>GAT	p.D922D	uc001dbm.2_5'Flank	NM_005012	NP_005003	Q01973	ROR1_HUMAN	receptor tyrosine kinase-like orphan receptor 1	922	Cytoplasmic (Potential).				transmembrane receptor protein tyrosine kinase signaling pathway	cytoplasm|integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			ovary(6)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|central_nervous_system(1)|skin(1)|kidney(1)	19																		---	---	---	---
JAK1	3716	broad.mit.edu	37	1	65325840	65325840	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:65325840C>G	uc001dbu.1	-	9	1531	c.1282G>C	c.(1282-1284)GCC>CCC	p.A428P	JAK1_uc009wam.1_Missense_Mutation_p.A416P	NM_002227	NP_002218	P23458	JAK1_HUMAN	janus kinase 1	428					interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to antibiotic|type I interferon-mediated signaling pathway	cytoskeleton|cytosol|endomembrane system|membrane|nucleus	ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity	p.A428fs*25(1)		haematopoietic_and_lymphoid_tissue(34)|prostate(7)|soft_tissue(6)|lung(4)|breast(3)|central_nervous_system(2)|liver(2)|large_intestine(1)|stomach(1)|ovary(1)	61				BRCA - Breast invasive adenocarcinoma(111;0.0485)				Mis		ALL								---	---	---	---
LEPR	3953	broad.mit.edu	37	1	66083695	66083695	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66083695T>C	uc001dci.2	+	16	2463	c.2261T>C	c.(2260-2262)GTG>GCG	p.V754A	LEPR_uc001dcg.2_Missense_Mutation_p.V754A|LEPR_uc001dch.2_Missense_Mutation_p.V754A|LEPR_uc009waq.2_Intron|LEPR_uc001dcj.2_Missense_Mutation_p.V754A|LEPR_uc001dck.2_Missense_Mutation_p.V754A	NM_002303	NP_002294	P48357	LEPR_HUMAN	leptin receptor isoform 1	754	Extracellular (Potential).|Fibronectin type-III 4.				energy reserve metabolic process|multicellular organismal development	extracellular region|integral to membrane|plasma membrane	cytokine receptor activity			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)														---	---	---	---
PDE4B	5142	broad.mit.edu	37	1	66829193	66829193	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:66829193G>A	uc001dcn.2	+	12	1414	c.1223G>A	c.(1222-1224)AGC>AAC	p.S408N	PDE4B_uc009war.2_Missense_Mutation_p.S316N|PDE4B_uc001dco.2_Missense_Mutation_p.S408N|PDE4B_uc001dcp.2_Missense_Mutation_p.S393N|PDE4B_uc001dcq.2_Missense_Mutation_p.S236N|PDE4B_uc009was.2_Missense_Mutation_p.S175N	NM_001037341	NP_001032418	Q07343	PDE4B_HUMAN	phosphodiesterase 4B isoform 1	408	cAMP.				signal transduction	cytosol|insoluble fraction|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			ovary(2)|central_nervous_system(1)	3					Adenosine monophosphate(DB00131)|Amrinone(DB01427)|Caffeine(DB00201)|Cilostazol(DB01166)|Dyphylline(DB00651)|Enprofylline(DB00824)|Papaverine(DB01113)|Pentoxifylline(DB00806)|Theophylline(DB00277)													---	---	---	---
WDR78	79819	broad.mit.edu	37	1	67288091	67288091	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67288091A>G	uc001dcx.2	-	16	2505	c.2449T>C	c.(2449-2451)TCT>CCT	p.S817P	WDR78_uc009waw.2_Missense_Mutation_p.S530P|WDR78_uc009wax.2_RNA	NM_024763	NP_079039	Q5VTH9	WDR78_HUMAN	WD repeat domain 78 isoform 1	817	WD 6.									ovary(2)	2																		---	---	---	---
WDR78	79819	broad.mit.edu	37	1	67288098	67288098	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67288098T>C	uc001dcx.2	-	16	2498	c.2442A>G	c.(2440-2442)GGA>GGG	p.G814G	WDR78_uc009waw.2_Silent_p.G527G|WDR78_uc009wax.2_RNA	NM_024763	NP_079039	Q5VTH9	WDR78_HUMAN	WD repeat domain 78 isoform 1	814	WD 6.									ovary(2)	2																		---	---	---	---
IL12RB2	3595	broad.mit.edu	37	1	67816695	67816695	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67816695C>T	uc001ddu.2	+	9	1821	c.1181C>T	c.(1180-1182)GCT>GTT	p.A394V	IL12RB2_uc010oqi.1_Missense_Mutation_p.A394V|IL12RB2_uc010oqj.1_Missense_Mutation_p.A394V|IL12RB2_uc010oqk.1_RNA|IL12RB2_uc010oql.1_Missense_Mutation_p.A394V|IL12RB2_uc010oqm.1_Missense_Mutation_p.A394V|IL12RB2_uc010oqn.1_RNA	NM_001559	NP_001550	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2 precursor	394	Fibronectin type-III 3.|Extracellular (Potential).				positive regulation of cell proliferation|positive regulation of interferon-gamma production	integral to plasma membrane	cytokine receptor activity			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
LRRC7	57554	broad.mit.edu	37	1	70504559	70504559	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70504559C>T	uc001dep.2	+	19	2968	c.2938C>T	c.(2938-2940)CGA>TGA	p.R980*	LRRC7_uc009wbg.2_Nonsense_Mutation_p.R264*|LRRC7_uc001deq.2_Nonsense_Mutation_p.R221*	NM_020794	NP_065845	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	980						centrosome|focal adhesion|nucleolus	protein binding			ovary(9)|breast(2)|central_nervous_system(2)|liver(1)	14																		---	---	---	---
TNNI3K	51086	broad.mit.edu	37	1	74663953	74663953	+	5'UTR	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74663953A>G	uc001dge.1	+	1					LRRIQ3_uc001dfy.3_5'Flank|LRRIQ3_uc001dfz.3_5'Flank|TNNI3K_uc001dgc.1_5'UTR|TNNI3K_uc001dgd.2_5'UTR|FPGT_uc010oqt.1_5'UTR|FPGT_uc010oqu.1_5'UTR|FPGT_uc001dgb.1_5'UTR|FPGT_uc010oqv.1_5'UTR	NM_001112808	NP_001106279			TNNI3 interacting kinase isoform a							cytoplasm|nucleus	ATP binding|metal ion binding|protein C-terminus binding|protein serine/threonine kinase activity|troponin I binding			large_intestine(4)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	10																		---	---	---	---
TNNI3K	51086	broad.mit.edu	37	1	74665366	74665366	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74665366G>T	uc001dge.1	+	2	117	c.101G>T	c.(100-102)GGA>GTA	p.G34V	LRRIQ3_uc001dfy.3_5'Flank|LRRIQ3_uc001dfz.3_5'Flank|TNNI3K_uc001dgc.1_Missense_Mutation_p.G34V|TNNI3K_uc001dgd.2_Missense_Mutation_p.G34V|FPGT_uc010oqt.1_5'UTR|FPGT_uc010oqu.1_Missense_Mutation_p.G34V|FPGT_uc001dgb.1_Missense_Mutation_p.G34V|FPGT_uc010oqv.1_Missense_Mutation_p.G34V	NM_001112808	NP_001106279	Q59H18	TNI3K_HUMAN	TNNI3 interacting kinase isoform a	Error:Variant_position_missing_in_Q59H18_after_alignment						cytoplasm|nucleus	ATP binding|metal ion binding|protein C-terminus binding|protein serine/threonine kinase activity|troponin I binding			large_intestine(4)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	10																		---	---	---	---
SLC44A5	204962	broad.mit.edu	37	1	75672365	75672365	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75672365G>T	uc001dgu.2	-	24	2231	c.2087C>A	c.(2086-2088)CCC>CAC	p.P696H	SLC44A5_uc001dgt.2_Intron|SLC44A5_uc001dgs.2_Intron|SLC44A5_uc001dgr.2_Intron|SLC44A5_uc010oqz.1_Intron|SLC44A5_uc010ora.1_Missense_Mutation_p.P690H|SLC44A5_uc010orb.1_Missense_Mutation_p.P566H	NM_152697	NP_689910	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5 isoform A	696	Cytoplasmic (Potential).					integral to membrane|plasma membrane	choline transmembrane transporter activity			ovary(2)|skin(2)	4																		---	---	---	---
SLC44A5	204962	broad.mit.edu	37	1	75805265	75805265	+	Splice_Site	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:75805265A>G	uc001dgu.2	-	4	245	c.101_splice	c.e4+1	p.R34_splice	SLC44A5_uc001dgt.2_Splice_Site_p.R34_splice|SLC44A5_uc001dgs.2_Splice_Site|SLC44A5_uc001dgr.2_Splice_Site|SLC44A5_uc010oqz.1_Splice_Site_p.R73_splice|SLC44A5_uc010ora.1_Splice_Site_p.R28_splice|SLC44A5_uc010orb.1_Splice_Site	NM_152697	NP_689910			solute carrier family 44, member 5 isoform A							integral to membrane|plasma membrane	choline transmembrane transporter activity			ovary(2)|skin(2)	4																		---	---	---	---
AK5	26289	broad.mit.edu	37	1	77984325	77984325	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:77984325C>T	uc001dhn.2	+	11	1481	c.1224C>T	c.(1222-1224)GGC>GGT	p.G408G	AK5_uc001dho.2_Silent_p.G382G	NM_174858	NP_777283	Q9Y6K8	KAD5_HUMAN	adenylate kinase 5 isoform 1	408					ADP biosynthetic process|ATP metabolic process|dADP biosynthetic process|nucleobase, nucleoside and nucleotide interconversion|pyrimidine ribonucleotide biosynthetic process|signal transduction	centrosome|cytosol	adenylate kinase activity|ATP binding|cAMP-dependent protein kinase regulator activity|nucleoside kinase activity			skin(1)	1																		---	---	---	---
ZZZ3	26009	broad.mit.edu	37	1	78050307	78050307	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78050307G>A	uc001dhq.2	-	6	2015	c.1539C>T	c.(1537-1539)CTC>CTT	p.L513L	ZZZ3_uc001dhr.2_Silent_p.L19L|ZZZ3_uc009wbz.1_3'UTR|ZZZ3_uc001dhp.2_Silent_p.L513L	NM_015534	NP_056349	Q8IYH5	ZZZ3_HUMAN	zinc finger, ZZ-type containing 3	513					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|large_intestine(1)	5																		---	---	---	---
DNAJB4	11080	broad.mit.edu	37	1	78479298	78479298	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78479298C>T	uc001dij.2	+	2	934	c.775C>T	c.(775-777)CGA>TGA	p.R259*	DNAJB4_uc010orn.1_Nonsense_Mutation_p.R144*	NM_007034	NP_008965	Q9UDY4	DNJB4_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 4	259					protein folding|response to heat|response to unfolded protein	cytoplasm|plasma membrane	heat shock protein binding|unfolded protein binding				0																		---	---	---	---
ELTD1	64123	broad.mit.edu	37	1	79383580	79383580	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:79383580T>C	uc001diq.3	-	11	1773	c.1617A>G	c.(1615-1617)CTA>CTG	p.L539L		NM_022159	NP_071442	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain	539	Helical; Name=4; (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(1)|skin(1)	2				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)														---	---	---	---
DNASE2B	58511	broad.mit.edu	37	1	84880274	84880274	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:84880274G>A	uc001djt.1	+	6	842	c.809G>A	c.(808-810)CGA>CAA	p.R270Q	DNASE2B_uc001dju.1_Missense_Mutation_p.R62Q|DNASE2B_uc009wch.1_Missense_Mutation_p.R62Q	NM_021233	NP_067056	Q8WZ79	DNS2B_HUMAN	deoxyribonuclease II beta isoform 1 precursor	270					DNA metabolic process	lysosome	deoxyribonuclease II activity				0				all cancers(265;0.00303)|Epithelial(280;0.0112)|OV - Ovarian serous cystadenocarcinoma(397;0.0808)									Direct_reversal_of_damage					---	---	---	---
ZNHIT6	54680	broad.mit.edu	37	1	86167894	86167894	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:86167894A>C	uc001dlh.2	-	5	1099	c.965T>G	c.(964-966)CTT>CGT	p.L322R	ZNHIT6_uc010osc.1_Missense_Mutation_p.L283R	NM_017953	NP_060423	Q9NWK9	BCD1_HUMAN	zinc finger, HIT type 6	322					box C/D snoRNP assembly|ribosome biogenesis	pre-snoRNP complex	identical protein binding|metal ion binding			large_intestine(1)	1																		---	---	---	---
CLCA4	22802	broad.mit.edu	37	1	87031123	87031123	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87031123A>C	uc009wcs.2	+	5	768	c.724A>C	c.(724-726)AGT>CGT	p.S242R	CLCA4_uc009wct.2_Missense_Mutation_p.S5R|CLCA4_uc009wcu.2_Missense_Mutation_p.S62R	NM_012128	NP_036260	Q14CN2	CLCA4_HUMAN	chloride channel accessory 4	242						apical plasma membrane|extracellular region|integral to plasma membrane	chloride channel activity			ovary(2)	2		Lung NSC(277;0.238)		all cancers(265;0.0202)|Epithelial(280;0.0404)														---	---	---	---
HS2ST1	9653	broad.mit.edu	37	1	87538659	87538659	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87538659G>A	uc010osk.1	+	2	552	c.167G>A	c.(166-168)CGA>CAA	p.R56Q	HS2ST1_uc001dmc.3_Missense_Mutation_p.R56Q|LOC339524_uc001dme.1_Missense_Mutation_p.R17Q	NM_012262	NP_036394	Q7LGA3	HS2ST_HUMAN	heparan sulfate 2-O-sulfotransferase 1 isoform	56	Lumenal (Potential).					Golgi membrane|integral to membrane				central_nervous_system(1)	1		Lung NSC(277;0.153)		all cancers(265;0.00699)|Epithelial(280;0.0261)														---	---	---	---
GBP1	2633	broad.mit.edu	37	1	89528881	89528881	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89528881G>T	uc001dmx.2	-	2	257	c.37C>A	c.(37-39)CTC>ATC	p.L13I		NM_002053	NP_002044	P32455	GBP1_HUMAN	guanylate binding protein 1,	13					interferon-gamma-mediated signaling pathway	plasma membrane	GTP binding|GTPase activity			ovary(1)|skin(1)	2		Lung NSC(277;0.123)		all cancers(265;0.0156)|Epithelial(280;0.0291)														---	---	---	---
GBP4	115361	broad.mit.edu	37	1	89659076	89659076	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89659076G>A	uc001dnb.2	-	4	499	c.383C>T	c.(382-384)TCG>TTG	p.S128L		NM_052941	NP_443173	Q96PP9	GBP4_HUMAN	guanylate binding protein 4	128						cytoplasm	GTP binding|GTPase activity				0				all cancers(265;0.00723)|Epithelial(280;0.0291)														---	---	---	---
GBP5	115362	broad.mit.edu	37	1	89735132	89735132	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:89735132T>C	uc001dnc.2	-	3	644	c.107A>G	c.(106-108)CAA>CGA	p.Q36R	GBP5_uc001dnd.2_Missense_Mutation_p.Q36R|GBP5_uc001dne.1_Missense_Mutation_p.Q36R	NM_052942	NP_443174	Q96PP8	GBP5_HUMAN	guanylate-binding protein 5	36						plasma membrane	GTP binding|GTPase activity			ovary(1)	1				all cancers(265;0.00784)|Epithelial(280;0.0286)														---	---	---	---
LRRC8D	55144	broad.mit.edu	37	1	90398977	90398977	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:90398977G>A	uc001dnm.2	+	3	775	c.350G>A	c.(349-351)CGC>CAC	p.R117H	LRRC8D_uc001dnn.2_Missense_Mutation_p.R117H	NM_001134479	NP_001127951	Q7L1W4	LRC8D_HUMAN	leucine rich repeat containing 8 family, member	117						integral to membrane	protein binding			ovary(2)	2		all_lung(203;0.0894)|Lung NSC(277;0.227)		all cancers(265;0.0109)|Epithelial(280;0.0427)														---	---	---	---
LRRC8D	55144	broad.mit.edu	37	1	90399768	90399768	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:90399768C>A	uc001dnm.2	+	3	1566	c.1141C>A	c.(1141-1143)CTC>ATC	p.L381I	LRRC8D_uc001dnn.2_Missense_Mutation_p.L381I	NM_001134479	NP_001127951	Q7L1W4	LRC8D_HUMAN	leucine rich repeat containing 8 family, member	381	Helical; (Potential).					integral to membrane	protein binding			ovary(2)	2		all_lung(203;0.0894)|Lung NSC(277;0.227)		all cancers(265;0.0109)|Epithelial(280;0.0427)														---	---	---	---
ZNF644	84146	broad.mit.edu	37	1	91382427	91382427	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91382427C>T	uc001dnw.2	-	6	4054	c.3912G>A	c.(3910-3912)ACG>ACA	p.T1304T	ZNF644_uc001dnv.2_Silent_p.T82T|ZNF644_uc001dnx.2_Silent_p.T82T	NM_201269	NP_958357	Q9H582	ZN644_HUMAN	zinc finger protein 644 isoform 1	1304					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|breast(1)|skin(1)	3		all_lung(203;0.00206)|Lung NSC(277;0.0519)|Lung SC(238;0.101)		all cancers(265;0.00102)|Epithelial(280;0.00766)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)|OV - Ovarian serous cystadenocarcinoma(397;0.173)														---	---	---	---
ZNF644	84146	broad.mit.edu	37	1	91405592	91405592	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91405592C>T	uc001dnw.2	-	3	1461	c.1319G>A	c.(1318-1320)CGC>CAC	p.R440H	ZNF644_uc001dnv.2_Intron|ZNF644_uc001dnx.2_Intron|ZNF644_uc001dny.1_Missense_Mutation_p.R440H	NM_201269	NP_958357	Q9H582	ZN644_HUMAN	zinc finger protein 644 isoform 1	440					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|breast(1)|skin(1)	3		all_lung(203;0.00206)|Lung NSC(277;0.0519)|Lung SC(238;0.101)		all cancers(265;0.00102)|Epithelial(280;0.00766)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)|OV - Ovarian serous cystadenocarcinoma(397;0.173)														---	---	---	---
HFM1	164045	broad.mit.edu	37	1	91859791	91859791	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91859791G>A	uc001doa.3	-	4	453	c.353C>T	c.(352-354)GCT>GTT	p.A118V	HFM1_uc010osu.1_Intron|HFM1_uc010osv.1_Intron|HFM1_uc001doc.1_Missense_Mutation_p.A118V	NM_001017975	NP_001017975	A2PYH4	HFM1_HUMAN	HFM1 protein	118							ATP binding|ATP-dependent helicase activity|nucleic acid binding				0		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)														---	---	---	---
BRDT	676	broad.mit.edu	37	1	92430235	92430235	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92430235C>T	uc001dok.3	+	3	593	c.244C>T	c.(244-246)CGC>TGC	p.R82C	BRDT_uc001dol.3_Missense_Mutation_p.R82C|BRDT_uc010osz.1_Missense_Mutation_p.R82C|BRDT_uc009wdf.2_Missense_Mutation_p.R9C|BRDT_uc010ota.1_Intron|BRDT_uc010otb.1_Intron|BRDT_uc001dom.3_Missense_Mutation_p.R82C	NM_207189	NP_997072	Q58F21	BRDT_HUMAN	testis-specific bromodomain protein	82	Bromo 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein serine/threonine kinase activity|transcription coactivator activity			stomach(2)|ovary(1)|lung(1)	4		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)														---	---	---	---
EPHX4	253152	broad.mit.edu	37	1	92511085	92511085	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92511085A>G	uc001don.2	+							NM_173567	NP_775838			abhydrolase domain containing 7							integral to membrane	hydrolase activity			central_nervous_system(1)	1																		---	---	---	---
BTBD8	284697	broad.mit.edu	37	1	92595245	92595245	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92595245G>A	uc001doo.2	+	5	931	c.664G>A	c.(664-666)GCC>ACC	p.A222T	BTBD8_uc010otc.1_RNA	NM_183242	NP_899065	Q5XKL5	BTBD8_HUMAN	BTB (POZ) domain containing 8	222	BTB 2.					nucleus				ovary(1)	1		all_lung(203;0.0484)|Lung NSC(277;0.126)|Glioma(108;0.222)		all cancers(265;0.0153)|Epithelial(280;0.0982)														---	---	---	---
RPAP2	79871	broad.mit.edu	37	1	92798988	92798988	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:92798988A>C	uc001dot.2	+	9	1605	c.1496A>C	c.(1495-1497)AAC>ACC	p.N499T	RPAP2_uc009wdh.2_RNA	NM_024813	NP_079089	Q8IXW5	RPAP2_HUMAN	RNA polymerase II associated protein 2	499						integral to membrane|nucleus	metal ion binding|phosphoprotein phosphatase activity			ovary(1)	1		all_lung(203;0.0565)|Lung NSC(277;0.152)|Glioma(108;0.222)		all cancers(265;0.00647)|GBM - Glioblastoma multiforme(16;0.0234)|Epithelial(280;0.115)														---	---	---	---
TMED5	50999	broad.mit.edu	37	1	93645672	93645672	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93645672C>T	uc001dpn.2	-	1	575	c.128G>A	c.(127-129)GGC>GAC	p.G43D	CCDC18_uc001dpq.2_5'Flank|TMED5_uc001dpo.2_Missense_Mutation_p.G43D|TMED5_uc001dpp.2_RNA	NM_016040	NP_057124	Q9Y3A6	TMED5_HUMAN	transmembrane emp24 protein transport domain	43	Lumenal (Potential).				transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment|integral to membrane				ovary(1)	1		all_lung(203;0.0223)|Lung NSC(277;0.071)|Melanoma(281;0.147)|Glioma(108;0.188)		all cancers(265;0.00108)|GBM - Glioblastoma multiforme(16;0.00407)|Epithelial(280;0.0797)														---	---	---	---
CCDC18	343099	broad.mit.edu	37	1	93721964	93721964	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:93721964C>T	uc001dpq.2	+	25	3937	c.3769C>T	c.(3769-3771)CTG>TTG	p.L1257L	CCDC18_uc001dpr.1_Silent_p.L52L	NM_206886	NP_996769	Q5T9S5	CCD18_HUMAN	sarcoma antigen NY-SAR-41	1138	Potential.									ovary(2)|breast(2)|pancreas(1)	5		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)														---	---	---	---
BCAR3	8412	broad.mit.edu	37	1	94037354	94037354	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94037354C>T	uc001dpz.2	-	9	2122	c.1847G>A	c.(1846-1848)TGC>TAC	p.C616Y	BCAR3_uc001dqa.2_Missense_Mutation_p.C616Y|BCAR3_uc001dqb.2_Missense_Mutation_p.C616Y|BCAR3_uc001dpx.3_Missense_Mutation_p.C292Y|BCAR3_uc001dpy.2_Missense_Mutation_p.C525Y|BCAR3_uc009wdm.1_Missense_Mutation_p.C292Y	NM_003567	NP_003558	O75815	BCAR3_HUMAN	breast cancer antiestrogen resistance 3	616	Ras-GEF.				response to drug|small GTPase mediated signal transduction	intracellular	guanyl-nucleotide exchange factor activity|protein binding			ovary(1)|lung(1)|central_nervous_system(1)	3		all_lung(203;0.00145)|Lung NSC(277;0.00662)		all cancers(265;0.0126)|GBM - Glioblastoma multiforme(16;0.0467)|Epithelial(280;0.166)														---	---	---	---
ARHGAP29	9411	broad.mit.edu	37	1	94643642	94643642	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94643642C>T	uc001dqj.3	-	21	2931	c.2562G>A	c.(2560-2562)AGG>AGA	p.R854R	ARHGAP29_uc009wdq.1_RNA|ARHGAP29_uc001dqk.2_Silent_p.R420R	NM_004815	NP_004806	Q52LW3	RHG29_HUMAN	PTPL1-associated RhoGAP 1	854	Rho-GAP.				Rho protein signal transduction	cytosol	metal ion binding|Rho GTPase activator activity			breast(4)|skin(3)|lung(2)|upper_aerodigestive_tract(1)|ovary(1)	11		all_lung(203;0.000732)|Lung NSC(277;0.00328)		all cancers(265;0.0187)|Epithelial(280;0.159)														---	---	---	---
ARHGAP29	9411	broad.mit.edu	37	1	94649849	94649849	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:94649849A>G	uc001dqj.3	-						ARHGAP29_uc009wdq.1_Intron|ARHGAP29_uc001dqk.2_Intron	NM_004815	NP_004806			PTPL1-associated RhoGAP 1						Rho protein signal transduction	cytosol	metal ion binding|Rho GTPase activator activity			breast(4)|skin(3)|lung(2)|upper_aerodigestive_tract(1)|ovary(1)	11		all_lung(203;0.000732)|Lung NSC(277;0.00328)		all cancers(265;0.0187)|Epithelial(280;0.159)														---	---	---	---
CNN3	1266	broad.mit.edu	37	1	95363384	95363384	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:95363384C>T	uc010otw.1	-	8	986	c.904G>A	c.(904-906)GCA>ACA	p.A302T	CNN3_uc010otv.1_Missense_Mutation_p.A261T|CNN3_uc001dqz.3_Missense_Mutation_p.A302T|CNN3_uc010otx.1_Missense_Mutation_p.A256T	NM_001839	NP_001830	Q15417	CNN3_HUMAN	calponin 3	302	Asp/Glu-rich (acidic).				actomyosin structure organization|smooth muscle contraction		actin binding|calmodulin binding|tropomyosin binding|troponin C binding				0		all_lung(203;0.00206)|Lung NSC(277;0.00948)		all cancers(265;0.0325)|Epithelial(280;0.0861)														---	---	---	---
DPYD	1806	broad.mit.edu	37	1	97700416	97700416	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:97700416C>T	uc001drv.2	-	19	2571	c.2434G>A	c.(2434-2436)GTC>ATC	p.V812I		NM_000110	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase isoform 1	812					'de novo' pyrimidine base biosynthetic process|purine base catabolic process|thymidine catabolic process|thymine catabolic process|UMP biosynthetic process|uracil catabolic process	cytosol	4 iron, 4 sulfur cluster binding|dihydroorotate oxidase activity|dihydropyrimidine dehydrogenase (NADP+) activity|electron carrier activity|flavin adenine dinucleotide binding|metal ion binding|NADP binding|protein homodimerization activity			ovary(3)|skin(3)|breast(2)	8		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Enfuvirtide(DB00109)													---	---	---	---
DPYD	1806	broad.mit.edu	37	1	98060666	98060666	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:98060666A>C	uc001drv.2	-	9	1044	c.907T>G	c.(907-909)TTT>GTT	p.F303V		NM_000110	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase isoform 1	303					'de novo' pyrimidine base biosynthetic process|purine base catabolic process|thymidine catabolic process|thymine catabolic process|UMP biosynthetic process|uracil catabolic process	cytosol	4 iron, 4 sulfur cluster binding|dihydroorotate oxidase activity|dihydropyrimidine dehydrogenase (NADP+) activity|electron carrier activity|flavin adenine dinucleotide binding|metal ion binding|NADP binding|protein homodimerization activity			ovary(3)|skin(3)|breast(2)	8		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Enfuvirtide(DB00109)													---	---	---	---
SNX7	51375	broad.mit.edu	37	1	99150493	99150493	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:99150493C>G	uc010ouc.1	+	2	285	c.233C>G	c.(232-234)CCT>CGT	p.P78R	SNX7_uc001dsa.2_Missense_Mutation_p.P14R|SNX7_uc010oud.1_Missense_Mutation_p.P78R	NM_015976	NP_057060	Q9UNH6	SNX7_HUMAN	sorting nexin 7 isoform a	14					cell communication|protein transport	cytoplasmic vesicle membrane	phosphatidylinositol binding|protein binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3		all_epithelial(167;7.64e-07)|all_lung(203;0.0006)|Lung NSC(277;0.00137)		Epithelial(280;0.0521)|all cancers(265;0.0687)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.207)|Colorectal(170;0.234)														---	---	---	---
LPPR4	9890	broad.mit.edu	37	1	99772130	99772130	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:99772130G>T	uc001dse.2	+	7	1962	c.1856G>T	c.(1855-1857)GGG>GTG	p.G619V	LPPR4_uc010oue.1_Missense_Mutation_p.G561V	NM_014839	NP_055654	Q7Z2D5	LPPR4_HUMAN	plasticity related gene 1	619							phosphatidate phosphatase activity			ovary(3)	3		all_epithelial(167;3.54e-06)|all_lung(203;0.00139)|Lung NSC(277;0.00202)		Epithelial(280;0.0736)|all cancers(265;0.0975)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)|Colorectal(170;0.22)														---	---	---	---
HIAT1	64645	broad.mit.edu	37	1	100544110	100544110	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100544110T>C	uc001dst.2	+							NM_033055	NP_149044			hippocampus abundant transcript 1						transmembrane transport	integral to membrane|plasma membrane	transporter activity				0		all_epithelial(167;2.96e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.0832)|all cancers(265;0.136)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.195)														---	---	---	---
DBT	1629	broad.mit.edu	37	1	100676244	100676244	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100676244G>A	uc001dta.2	-						DBT_uc010oug.1_Intron	NM_001918	NP_001909			dihydrolipoamide branched chain transacylase						branched chain family amino acid catabolic process|fatty-acyl-CoA biosynthetic process	microtubule cytoskeleton|mitochondrial alpha-ketoglutarate dehydrogenase complex|mitochondrial nucleoid	acyltransferase activity|cofactor binding|dihydrolipoyllysine-residue (2-methylpropanoyl)transferase activity|protein binding			pancreas(1)	1		all_epithelial(167;5.4e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.0739)|all cancers(265;0.123)|COAD - Colon adenocarcinoma(174;0.154)|Lung(183;0.199)														---	---	---	---
OLFM3	118427	broad.mit.edu	37	1	102270097	102270097	+	Silent	SNP	G	T	T	rs139403729		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:102270097G>T	uc001duf.2	-	6	1205	c.1134C>A	c.(1132-1134)ACC>ACA	p.T378T	OLFM3_uc001dug.2_Silent_p.T358T|OLFM3_uc001duh.2_RNA|OLFM3_uc001dui.2_RNA|OLFM3_uc001duj.2_Silent_p.T283T|OLFM3_uc001due.2_RNA	NM_058170	NP_477518	Q96PB7	NOE3_HUMAN	olfactomedin 3	378	Olfactomedin-like.					extracellular region				ovary(2)|skin(1)	3		all_epithelial(167;1.87e-06)|all_lung(203;8.12e-05)|Lung NSC(277;0.000189)		all cancers(265;0.0843)|Epithelial(280;0.0921)|COAD - Colon adenocarcinoma(174;0.145)														---	---	---	---
COL11A1	1301	broad.mit.edu	37	1	103444294	103444294	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:103444294G>A	uc001dul.2	-	35	3042	c.2724C>T	c.(2722-2724)GGC>GGT	p.G908G	COL11A1_uc001duk.2_Silent_p.G104G|COL11A1_uc001dum.2_Silent_p.G920G|COL11A1_uc001dun.2_Silent_p.G869G|COL11A1_uc009weh.2_Silent_p.G792G	NM_001854	NP_001845	P12107	COBA1_HUMAN	alpha 1 type XI collagen isoform A	908	Triple-helical region.				collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	12		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)														---	---	---	---
VAV3	10451	broad.mit.edu	37	1	108116660	108116660	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108116660C>T	uc001dvk.1	-						VAV3_uc010ouu.1_Intron|VAV3_uc001dvj.1_Intron|VAV3_uc010ouv.1_Intron|VAV3_uc010ouw.1_Intron	NM_006113	NP_006104			vav 3 guanine nucleotide exchange factor isoform						angiogenesis|apoptosis|B cell receptor signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of B cell proliferation|regulation of Rho protein signal transduction|response to DNA damage stimulus|response to drug|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(5)|lung(2)|breast(2)	9		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)														---	---	---	---
SLC25A24	29957	broad.mit.edu	37	1	108690925	108690925	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:108690925T>C	uc001dvn.3	-	7	1120	c.906A>G	c.(904-906)GCA>GCG	p.A302A	SLC25A24_uc001dvm.2_Silent_p.A283A	NM_013386	NP_037518	Q6NUK1	SCMC1_HUMAN	solute carrier family 25 member 24 isoform 1	302	Solcar 2.|Helical; Name=3; (Potential).				transmembrane transport	integral to membrane|mitochondrial inner membrane	calcium ion binding			ovary(1)	1		all_epithelial(167;3.72e-05)|all_lung(203;0.000567)|Lung NSC(277;0.0011)|Melanoma(281;0.211)		Colorectal(144;0.0345)|Lung(183;0.0971)|COAD - Colon adenocarcinoma(174;0.127)|Epithelial(280;0.134)														---	---	---	---
SARS	6301	broad.mit.edu	37	1	109774299	109774299	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109774299G>A	uc001dwu.1	+	6	713	c.638G>A	c.(637-639)CGC>CAC	p.R213H	SARS_uc001dwt.1_Missense_Mutation_p.R213H|SARS_uc001dwv.1_Missense_Mutation_p.R213H|SARS_uc001dww.1_Missense_Mutation_p.R146H|SARS_uc001dwx.1_Missense_Mutation_p.R165H|SARS_uc009wfa.1_Missense_Mutation_p.R213H|SARS_uc001dwy.1_Missense_Mutation_p.R38H|SARS_uc001dwz.1_Missense_Mutation_p.R38H	NM_006513	NP_006504	P49591	SYSC_HUMAN	seryl-tRNA synthetase	213					seryl-tRNA aminoacylation|tRNA processing	cytosol	ATP binding|protein binding|RNA binding|serine-tRNA ligase activity			central_nervous_system(1)	1		all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0301)|Lung(183;0.0677)|COAD - Colon adenocarcinoma(174;0.116)|Epithelial(280;0.233)	L-Serine(DB00133)													---	---	---	---
CELSR2	1952	broad.mit.edu	37	1	109803813	109803813	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109803813C>T	uc001dxa.3	+	3	4169	c.4108C>T	c.(4108-4110)CGC>TGC	p.R1370C		NM_001408	NP_001399	Q9HCU4	CELR2_HUMAN	cadherin EGF LAG seven-pass G-type receptor 2	1370	Extracellular (Potential).|Laminin G-like 1.				dendrite morphogenesis|homophilic cell adhesion|neural plate anterior/posterior regionalization|neuropeptide signaling pathway|regulation of cell-cell adhesion|regulation of transcription, DNA-dependent|Wnt receptor signaling pathway	cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(4)|lung(3)|skin(1)	8		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)														---	---	---	---
CELSR2	1952	broad.mit.edu	37	1	109804971	109804971	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109804971C>T	uc001dxa.3	+	6	4510	c.4449C>T	c.(4447-4449)ACC>ACT	p.T1483T		NM_001408	NP_001399	Q9HCU4	CELR2_HUMAN	cadherin EGF LAG seven-pass G-type receptor 2	1483	Extracellular (Potential).|Laminin G-like 1.				dendrite morphogenesis|homophilic cell adhesion|neural plate anterior/posterior regionalization|neuropeptide signaling pathway|regulation of cell-cell adhesion|regulation of transcription, DNA-dependent|Wnt receptor signaling pathway	cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(4)|lung(3)|skin(1)	8		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)														---	---	---	---
SORT1	6272	broad.mit.edu	37	1	109859576	109859576	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109859576G>A	uc001dxm.1	-	17	2195	c.2146C>T	c.(2146-2148)CGG>TGG	p.R716W	SORT1_uc010ovi.1_Missense_Mutation_p.R579W	NM_002959	NP_002950	Q99523	SORT_HUMAN	sortilin 1 preproprotein	716	Interactions with LRPAP1 and NGFB.|Extracellular (Potential).				endocytosis|endosome to lysosome transport|endosome transport via multivesicular body sorting pathway|glucose import|Golgi to endosome transport|induction of apoptosis by extracellular signals|myotube differentiation|negative regulation of apoptosis|negative regulation of lipoprotein lipase activity|neuropeptide signaling pathway|ossification|plasma membrane to endosome transport|regulation of gene expression|response to insulin stimulus|vesicle organization	cell surface|coated pit|early endosome|endoplasmic reticulum membrane|endosome membrane|Golgi cisterna membrane|integral to membrane|lysosomal membrane|microsome|nuclear membrane|perinuclear region of cytoplasm|plasma membrane	enzyme binding|nerve growth factor binding|nerve growth factor receptor activity|neurotensin receptor activity, non-G-protein coupled			ovary(1)	1		all_epithelial(167;4.69e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.0529)|Colorectal(144;0.142)|Epithelial(280;0.145)|Kidney(133;0.169)|all cancers(265;0.184)														---	---	---	---
ATXN7L2	127002	broad.mit.edu	37	1	110031505	110031505	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110031505C>T	uc001dxr.2	+	7	835	c.820C>T	c.(820-822)CGG>TGG	p.R274W	ATXN7L2_uc001dxs.2_5'UTR|ATXN7L2_uc001dxt.2_5'Flank	NM_153340	NP_699171	Q5T6C5	AT7L2_HUMAN	ataxin 7-like 2	274	SCA7.									ovary(2)	2		all_epithelial(167;0.00197)|all_lung(203;0.00291)|Lung NSC(277;0.00453)		Colorectal(144;0.0129)|Lung(183;0.0426)|Epithelial(280;0.0675)|READ - Rectum adenocarcinoma(129;0.0693)|all cancers(265;0.071)|LUSC - Lung squamous cell carcinoma(189;0.228)														---	---	---	---
GNAI3	2773	broad.mit.edu	37	1	110128869	110128869	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110128869C>T	uc001dxz.2	+	6	779	c.622C>T	c.(622-624)CGA>TGA	p.R208*		NM_006496	NP_006487	P08754	GNAI3_HUMAN	guanine nucleotide binding protein (G protein),	208					cell cycle|cell division|inhibition of adenylate cyclase activity by G-protein signaling pathway|platelet activation|synaptic transmission	centrosome|heterotrimeric G-protein complex|midbody	G-protein beta/gamma-subunit complex binding|GTP binding|GTPase activity|metabotropic serotonin receptor binding|signal transducer activity			ovary(1)	1		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Lung(183;0.046)|Colorectal(144;0.119)|Epithelial(280;0.139)|all cancers(265;0.147)|LUSC - Lung squamous cell carcinoma(189;0.237)														---	---	---	---
GSTM1	2944	broad.mit.edu	37	1	110231736	110231736	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110231736C>T	uc001dyk.2	+	4	322	c.244C>T	c.(244-246)CGC>TGC	p.R82C	GSTM1_uc001dyl.2_Missense_Mutation_p.R82C	NM_000561	NP_000552	P09488	GSTM1_HUMAN	glutathione S-transferase mu 1 isoform 1	82	GST N-terminal.				xenobiotic metabolic process	cytosol	glutathione transferase activity				0		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		all cancers(265;0.0122)|Colorectal(144;0.0129)|Epithelial(280;0.0146)|Lung(183;0.0422)|COAD - Colon adenocarcinoma(174;0.047)|LUSC - Lung squamous cell carcinoma(189;0.227)	Glutathione(DB00143)									Melanoma_Familial_Clustering_of|ACTH-independent_macronodular_adrenal_hyperplasia|Naso-/Oropharyngeal/Laryngeal_Cancer_Familial_Clustering_of				---	---	---	---
EPS8L3	79574	broad.mit.edu	37	1	110302449	110302449	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110302449T>C	uc001dyr.1	-	4	251	c.106A>G	c.(106-108)ACA>GCA	p.T36A	EPS8L3_uc001dys.1_Missense_Mutation_p.T36A|EPS8L3_uc001dyq.1_Missense_Mutation_p.T36A|EPS8L3_uc009wfm.1_Missense_Mutation_p.T2A|EPS8L3_uc009wfn.1_Missense_Mutation_p.T2A|EPS8L3_uc009wfo.1_Intron	NM_133181	NP_573444	Q8TE67	ES8L3_HUMAN	epidermal growth factor receptor pathway	36						cytoplasm	protein binding			ovary(2)|skin(1)	3		all_epithelial(167;1.95e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)		Lung(183;0.0245)|Colorectal(144;0.0365)|all cancers(265;0.103)|Epithelial(280;0.109)|LUSC - Lung squamous cell carcinoma(189;0.137)|COAD - Colon adenocarcinoma(174;0.141)														---	---	---	---
FAM40A	85369	broad.mit.edu	37	1	110582142	110582142	+	Intron	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110582142G>T	uc001dza.1	+						FAM40A_uc001dyz.1_Intron|FAM40A_uc009wfp.1_Intron	NM_033088	NP_149079			hypothetical protein LOC85369							nucleus	protein binding			ovary(3)|large_intestine(1)	4		all_cancers(81;8.51e-05)|all_epithelial(167;3.58e-05)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0154)|all cancers(265;0.0732)|Epithelial(280;0.0781)|Colorectal(144;0.115)|LUSC - Lung squamous cell carcinoma(189;0.137)														---	---	---	---
SLC6A17	388662	broad.mit.edu	37	1	110716714	110716714	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110716714C>T	uc009wfq.2	+	4	1025	c.564C>T	c.(562-564)AGC>AGT	p.S188S		NM_001010898	NP_001010898	Q9H1V8	S6A17_HUMAN	solute carrier family 6, member 17	188	Extracellular (Potential).				alanine transport|glycine transport|leucine transport|proline transport	cell junction|integral to plasma membrane|synaptic vesicle membrane	neurotransmitter:sodium symporter activity			ovary(1)|pancreas(1)	2		all_cancers(81;9.9e-06)|all_epithelial(167;3.24e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0282)|Epithelial(280;0.0372)|all cancers(265;0.0378)|Colorectal(144;0.0438)|LUSC - Lung squamous cell carcinoma(189;0.151)|COAD - Colon adenocarcinoma(174;0.151)														---	---	---	---
SLC6A17	388662	broad.mit.edu	37	1	110734843	110734843	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110734843G>A	uc009wfq.2	+						SLC6A17_uc001dze.1_5'Flank	NM_001010898	NP_001010898			solute carrier family 6, member 17						alanine transport|glycine transport|leucine transport|proline transport	cell junction|integral to plasma membrane|synaptic vesicle membrane	neurotransmitter:sodium symporter activity			ovary(1)|pancreas(1)	2		all_cancers(81;9.9e-06)|all_epithelial(167;3.24e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0282)|Epithelial(280;0.0372)|all cancers(265;0.0378)|Colorectal(144;0.0438)|LUSC - Lung squamous cell carcinoma(189;0.151)|COAD - Colon adenocarcinoma(174;0.151)														---	---	---	---
RBM15	64783	broad.mit.edu	37	1	110888215	110888215	+	Missense_Mutation	SNP	C	T	T	rs138022193		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110888215C>T	uc001dzl.1	+	2	3001	c.2918C>T	c.(2917-2919)GCG>GTG	p.A973V	RBM15_uc001dzm.1_Intron|uc001dzn.1_RNA	NM_022768	NP_073605	Q96T37	RBM15_HUMAN	RNA binding motif protein 15	973					interspecies interaction between organisms	nucleus	nucleotide binding|protein binding|RNA binding			ovary(3)	3		all_cancers(81;2.89e-06)|all_epithelial(167;2.96e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Breast(1374;0.0634)		BRCA - Breast invasive adenocarcinoma(282;0.000224)|Epithelial(280;0.000476)|Kidney(133;0.000539)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|all cancers(265;0.00144)|Lung(183;0.0238)|Colorectal(144;0.103)|LUSC - Lung squamous cell carcinoma(189;0.135)				T	MKL1	acute megakaryocytic leukemia								---	---	---	---
KCNA3	3738	broad.mit.edu	37	1	111216996	111216996	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111216996C>T	uc001dzv.1	-	1	660	c.436G>A	c.(436-438)GAG>AAG	p.E146K		NM_002232	NP_002223	P22001	KCNA3_HUMAN	potassium voltage-gated channel, shaker-related	146						voltage-gated potassium channel complex	delayed rectifier potassium channel activity			ovary(4)|pancreas(1)	5		all_cancers(81;3.92e-06)|all_epithelial(167;1.28e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Lung(183;0.0235)|Colorectal(144;0.0306)|all cancers(265;0.0752)|Epithelial(280;0.0821)|COAD - Colon adenocarcinoma(174;0.132)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
C1orf103	55791	broad.mit.edu	37	1	111494613	111494613	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111494613T>C	uc001eaa.2	-	2	1149	c.893A>G	c.(892-894)CAG>CGG	p.Q298R	C1orf103_uc001dzz.2_Intron|C1orf103_uc001eab.2_Intron|C1orf103_uc001eac.1_Intron	NM_018372	NP_060842	Q5T3J3	LRIF1_HUMAN	receptor-interacting factor 1 isoform 1	298					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear matrix	protein binding				0		all_cancers(81;1.02e-05)|all_epithelial(167;1.87e-05)|all_lung(203;0.000234)|Lung NSC(277;0.000451)		Lung(183;0.0155)|Colorectal(144;0.0314)|all cancers(265;0.082)|LUSC - Lung squamous cell carcinoma(189;0.0826)|Epithelial(280;0.0891)|COAD - Colon adenocarcinoma(174;0.134)														---	---	---	---
CEPT1	10390	broad.mit.edu	37	1	111702135	111702135	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111702135A>T	uc001eah.1	+	3	681	c.473A>T	c.(472-474)GAT>GTT	p.D158V	CEPT1_uc001eag.2_Missense_Mutation_p.D158V|CEPT1_uc001eai.1_Missense_Mutation_p.D158V|CEPT1_uc001eaj.1_Missense_Mutation_p.D158V	NM_001007794	NP_001007795	Q9Y6K0	CEPT1_HUMAN	choline/ethanolaminephosphotransferase	158						endoplasmic reticulum membrane|integral to membrane|nuclear membrane	diacylglycerol cholinephosphotransferase activity|ethanolaminephosphotransferase activity|metal ion binding				0		all_cancers(81;2.27e-05)|all_epithelial(167;7.36e-06)|all_lung(203;0.00018)|Lung NSC(277;0.000359)		Lung(183;0.0173)|Colorectal(144;0.0375)|all cancers(265;0.0701)|LUSC - Lung squamous cell carcinoma(189;0.0888)|Epithelial(280;0.103)|COAD - Colon adenocarcinoma(174;0.141)	Choline(DB00122)													---	---	---	---
DENND2D	79961	broad.mit.edu	37	1	111731322	111731322	+	Splice_Site	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111731322A>G	uc001eak.1	-	10	1299	c.1099_splice	c.e10+1	p.T367_splice	DENND2D_uc001eal.1_Splice_Site_p.T364_splice	NM_024901	NP_079177			DENN/MADD domain containing 2D											ovary(1)	1		all_cancers(81;0.00198)|all_epithelial(167;0.000686)|all_lung(203;0.00318)|Lung NSC(277;0.00499)		Lung(183;0.0162)|Colorectal(144;0.069)|all cancers(265;0.0757)|LUSC - Lung squamous cell carcinoma(189;0.0845)|Epithelial(280;0.114)|COAD - Colon adenocarcinoma(174;0.14)														---	---	---	---
DENND2D	79961	broad.mit.edu	37	1	111737212	111737212	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111737212G>A	uc001eak.1	-	7	982	c.782C>T	c.(781-783)GCG>GTG	p.A261V	DENND2D_uc001eal.1_Missense_Mutation_p.A258V	NM_024901	NP_079177	Q9H6A0	DEN2D_HUMAN	DENN/MADD domain containing 2D	261	DENN.									ovary(1)	1		all_cancers(81;0.00198)|all_epithelial(167;0.000686)|all_lung(203;0.00318)|Lung NSC(277;0.00499)		Lung(183;0.0162)|Colorectal(144;0.069)|all cancers(265;0.0757)|LUSC - Lung squamous cell carcinoma(189;0.0845)|Epithelial(280;0.114)|COAD - Colon adenocarcinoma(174;0.14)														---	---	---	---
OVGP1	5016	broad.mit.edu	37	1	111958951	111958951	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:111958951G>A	uc001eba.2	-	10	1206	c.1150C>T	c.(1150-1152)CGG>TGG	p.R384W	OVGP1_uc001eaz.2_Missense_Mutation_p.R346W|OVGP1_uc010owb.1_Missense_Mutation_p.R32W	NM_002557	NP_002548	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1 precursor	384					chitin catabolic process|female pregnancy|single fertilization	transport vesicle	cation binding|chitinase activity			ovary(4)|large_intestine(1)	5		all_cancers(81;8.18e-06)|all_epithelial(167;5.64e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000302)		Lung(183;0.0253)|Colorectal(144;0.033)|all cancers(265;0.0552)|Epithelial(280;0.0802)|COAD - Colon adenocarcinoma(174;0.123)|LUSC - Lung squamous cell carcinoma(189;0.14)														---	---	---	---
CAPZA1	829	broad.mit.edu	37	1	113212692	113212692	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113212692A>G	uc001ecj.1	+	10	1191	c.799A>G	c.(799-801)ACC>GCC	p.T267A		NM_006135	NP_006126	P52907	CAZA1_HUMAN	F-actin capping protein alpha-1 subunit	267					actin cytoskeleton organization|actin filament capping|blood coagulation|cellular component movement|innate immune response|protein complex assembly	cytosol|extracellular region|F-actin capping protein complex|WASH complex	actin binding				0	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
LRIG2	9860	broad.mit.edu	37	1	113655152	113655152	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113655152C>T	uc001edf.1	+	14	2048	c.1850C>T	c.(1849-1851)GCC>GTC	p.A617V	LRIG2_uc009wgn.1_Missense_Mutation_p.A514V	NM_014813	NP_055628	O94898	LRIG2_HUMAN	leucine-rich repeats and immunoglobulin-like	617	Ig-like C2-type 2.|Extracellular (Potential).					cytoplasm|integral to membrane|plasma membrane				ovary(3)	3	Lung SC(450;0.246)	all_cancers(81;1.56e-05)|all_epithelial(167;2.62e-05)|all_lung(203;0.000665)|Lung NSC(69;0.000986)		Lung(183;0.0279)|Colorectal(144;0.0885)|COAD - Colon adenocarcinoma(174;0.134)|all cancers(265;0.139)|Epithelial(280;0.143)|LUSC - Lung squamous cell carcinoma(189;0.15)														---	---	---	---
LRIG2	9860	broad.mit.edu	37	1	113666541	113666541	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:113666541C>A	uc001edf.1	+	18	3214	c.3016C>A	c.(3016-3018)CTG>ATG	p.L1006M	LRIG2_uc009wgn.1_Missense_Mutation_p.L903M	NM_014813	NP_055628	O94898	LRIG2_HUMAN	leucine-rich repeats and immunoglobulin-like	1006	Cytoplasmic (Potential).					cytoplasm|integral to membrane|plasma membrane				ovary(3)	3	Lung SC(450;0.246)	all_cancers(81;1.56e-05)|all_epithelial(167;2.62e-05)|all_lung(203;0.000665)|Lung NSC(69;0.000986)		Lung(183;0.0279)|Colorectal(144;0.0885)|COAD - Colon adenocarcinoma(174;0.134)|all cancers(265;0.139)|Epithelial(280;0.143)|LUSC - Lung squamous cell carcinoma(189;0.15)														---	---	---	---
AP4B1	10717	broad.mit.edu	37	1	114442577	114442577	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114442577A>C	uc001eeb.2	-	5	1206	c.1063T>G	c.(1063-1065)TAC>GAC	p.Y355D	uc001edv.1_RNA|AP4B1_uc001eec.2_Missense_Mutation_p.Y187D|AP4B1_uc001eed.2_Missense_Mutation_p.Y355D|AP4B1_uc010owp.1_Missense_Mutation_p.Y256D|AP4B1_uc001eea.1_Missense_Mutation_p.Y149D|AP4B1_uc001eee.1_5'Flank|AP4B1_uc010owq.1_Missense_Mutation_p.Y262D	NM_006594	NP_006585	Q9Y6B7	AP4B1_HUMAN	adaptor-related protein complex 4, beta 1	355					intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|soluble fraction|trans-Golgi network	protein binding|protein transporter activity			ovary(3)|central_nervous_system(1)	4	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.1e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
HIPK1	204851	broad.mit.edu	37	1	114483192	114483192	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:114483192G>A	uc001eem.2	+	2	348	c.187G>A	c.(187-189)GCA>ACA	p.A63T	HIPK1_uc001eel.2_Missense_Mutation_p.A63T|HIPK1_uc001een.2_Missense_Mutation_p.A63T	NM_198268	NP_938009	Q86Z02	HIPK1_HUMAN	homeodomain-interacting protein kinase 1 isoform	63					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(4)	4	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
CSDE1	7812	broad.mit.edu	37	1	115263212	115263212	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:115263212G>A	uc001efk.2	-	17	2466	c.2000C>T	c.(1999-2001)GCT>GTT	p.A667V	CSDE1_uc001efi.2_Missense_Mutation_p.A713V|CSDE1_uc001efj.2_RNA|CSDE1_uc001efl.2_Missense_Mutation_p.A636V|CSDE1_uc001efm.2_Missense_Mutation_p.A682V|CSDE1_uc009wgv.2_Missense_Mutation_p.A667V|CSDE1_uc001efn.2_Missense_Mutation_p.A636V	NM_001007553	NP_001007554	O75534	CSDE1_HUMAN	upstream of NRAS isoform 1	667	CSD 8.				male gonad development|regulation of transcription, DNA-dependent	cytoplasm	DNA binding|protein binding|RNA binding			ovary(1)	1	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)														---	---	---	---
CASQ2	845	broad.mit.edu	37	1	116275531	116275531	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:116275531A>G	uc001efx.3	-	5	861	c.597T>C	c.(595-597)TTT>TTC	p.F199F	CASQ2_uc010owu.1_Silent_p.F128F	NM_001232	NP_001223	O14958	CASQ2_HUMAN	cardiac calsequestrin 2 precursor	199					heart development|striated muscle contraction	sarcoplasmic reticulum lumen	calcium ion binding			skin(1)	1	Lung SC(450;0.211)	all_cancers(81;1.25e-06)|all_epithelial(167;1.02e-06)|all_lung(203;8.03e-06)|Lung NSC(69;5.01e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)														---	---	---	---
IGSF3	3321	broad.mit.edu	37	1	117146595	117146595	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117146595G>A	uc001egr.1	-	6	1980	c.1275C>T	c.(1273-1275)GGC>GGT	p.G425G	IGSF3_uc001egq.1_Silent_p.G445G|IGSF3_uc001egs.1_Silent_p.G98G	NM_001007237	NP_001007238	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3 isoform 2	425	Ig-like C2-type 4.|Extracellular (Potential).					integral to membrane				ovary(2)	2	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)														---	---	---	---
CD101	9398	broad.mit.edu	37	1	117552700	117552700	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117552700G>A	uc010oxb.1	+	2	330	c.272G>A	c.(271-273)AGC>AAC	p.S91N	CD101_uc009whd.2_Missense_Mutation_p.S91N|CD101_uc010oxc.1_Missense_Mutation_p.S91N|CD101_uc010oxd.1_Missense_Mutation_p.S91N	NM_004258	NP_004249	Q93033	IGSF2_HUMAN	immunoglobulin superfamily, member 2 precursor	91	Extracellular (Potential).|Ig-like C2-type 1.			S -> G (in Ref. 1; CAA83923).	cell surface receptor linked signaling pathway	integral to membrane|plasma membrane	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides			skin(2)|upper_aerodigestive_tract(1)|ovary(1)	4																		---	---	---	---
TRIM45	80263	broad.mit.edu	37	1	117656070	117656070	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:117656070C>T	uc001egz.2	-	5	2093	c.1505G>A	c.(1504-1506)CGC>CAC	p.R502H	TRIM45_uc009whe.2_Missense_Mutation_p.R484H|TRIM45_uc001eha.2_Missense_Mutation_p.R398H	NM_025188	NP_079464	Q9H8W5	TRI45_HUMAN	tripartite motif-containing 45 isoform 1	502						cytoplasm|nucleus	zinc ion binding			central_nervous_system(1)	1	Lung SC(450;0.225)	all_cancers(81;0.000979)|all_lung(203;7.65e-05)|all_epithelial(167;0.000134)|Lung NSC(69;0.000389)		Lung(183;0.0537)|Colorectal(144;0.172)|LUSC - Lung squamous cell carcinoma(189;0.187)														---	---	---	---
ZNF697	90874	broad.mit.edu	37	1	120166716	120166716	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120166716C>A	uc001ehy.1	-	3	364	c.250G>T	c.(250-252)GGC>TGC	p.G84C		NM_001080470	NP_001073939	Q5TEC3	ZN697_HUMAN	zinc finger protein 697	84					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_neural(166;0.219)	all_lung(203;3.66e-05)|Lung NSC(69;0.000202)|all_epithelial(167;0.0266)		Lung(183;0.011)|LUSC - Lung squamous cell carcinoma(189;0.0577)														---	---	---	---
PHGDH	26227	broad.mit.edu	37	1	120269488	120269488	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120269488C>T	uc001ehz.2	+	4	598	c.371C>T	c.(370-372)GCG>GTG	p.A124V	PHGDH_uc009whl.2_Missense_Mutation_p.A26V|PHGDH_uc009whm.2_Missense_Mutation_p.A22V|PHGDH_uc001eia.2_Missense_Mutation_p.A124V|PHGDH_uc009whn.2_Missense_Mutation_p.A124V|PHGDH_uc001eib.2_Missense_Mutation_p.A90V	NM_006623	NP_006614	O43175	SERA_HUMAN	phosphoglycerate dehydrogenase	124					brain development|L-serine biosynthetic process		electron carrier activity|NAD binding|phosphoglycerate dehydrogenase activity			ovary(1)	1	all_cancers(5;1.18e-09)|all_epithelial(5;2.16e-10)|Melanoma(3;1.93e-05)|all_neural(166;0.219)	all_lung(203;3.66e-05)|Lung NSC(69;0.000202)|all_epithelial(167;0.0347)		Lung(183;0.0111)|LUSC - Lung squamous cell carcinoma(189;0.0593)	NADH(DB00157)													---	---	---	---
NOTCH2	4853	broad.mit.edu	37	1	120459067	120459067	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120459067C>T	uc001eik.2	-	34	6534	c.6278G>A	c.(6277-6279)AGC>AAC	p.S2093N		NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein	2093	Cytoplasmic (Potential).				anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1)	27	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)				N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				---	---	---	---
NOTCH2	4853	broad.mit.edu	37	1	120462034	120462034	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120462034C>A	uc001eik.2	-	31	5938	c.5682G>T	c.(5680-5682)AAG>AAT	p.K1894N		NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein	1894	Cytoplasmic (Potential).|ANK 2.				anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1)	27	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)				N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				---	---	---	---
NOTCH2	4853	broad.mit.edu	37	1	120484288	120484288	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120484288T>G	uc001eik.2	-	18	3098	c.2842A>C	c.(2842-2844)ACA>CCA	p.T948P	NOTCH2_uc001eil.2_Missense_Mutation_p.T948P	NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein	948	Extracellular (Potential).				anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			lung(8)|haematopoietic_and_lymphoid_tissue(7)|ovary(4)|central_nervous_system(2)|skin(2)|kidney(2)|breast(1)|prostate(1)	27	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)				N|F|Mis		marginal zone lymphoma|DLBCL				Alagille_Syndrome				---	---	---	---
PDE4DIP	9659	broad.mit.edu	37	1	144881594	144881594	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144881594G>T	uc001elw.3	-	25	3893	c.3602C>A	c.(3601-3603)CCT>CAT	p.P1201H	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Missense_Mutation_p.P1157H|PDE4DIP_uc001elv.3_Missense_Mutation_p.P208H	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform	1201					cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)				T	PDGFRB	MPD								---	---	---	---
PDE4DIP	9659	broad.mit.edu	37	1	145015938	145015938	+	Silent	SNP	C	T	T	rs144857876	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145015938C>T	uc001elx.3	-	3	485	c.150G>A	c.(148-150)CCG>CCA	p.P50P	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elm.3_5'UTR|PDE4DIP_uc001eln.3_Silent_p.P50P|PDE4DIP_uc001elo.2_Silent_p.P121P|PDE4DIP_uc001emh.2_Silent_p.P121P|uc001emj.2_Intron	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform	Error:Variant_position_missing_in_Q5VU43_after_alignment					cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)				T	PDGFRB	MPD								---	---	---	---
ITGA10	8515	broad.mit.edu	37	1	145531027	145531027	+	Splice_Site	SNP	G	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145531027G>C	uc001eoa.2	+	7	834	c.758_splice	c.e7+1	p.C253_splice	NBPF10_uc001emp.3_Intron|ITGA10_uc010oyv.1_Splice_Site_p.C122_splice|ITGA10_uc009wiw.2_Splice_Site_p.C110_splice|ITGA10_uc010oyw.1_Splice_Site_p.C198_splice	NM_003637	NP_003628			integrin, alpha 10 precursor						cell-matrix adhesion|integrin-mediated signaling pathway	integrin complex	collagen binding|receptor activity			lung(2)|ovary(2)|kidney(2)|large_intestine(1)|skin(1)	8	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)																	---	---	---	---
RNF115	27246	broad.mit.edu	37	1	145650495	145650495	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145650495T>C	uc001eoj.2	+	3	378	c.174T>C	c.(172-174)GGT>GGC	p.G58G	NBPF10_uc001emp.3_Intron|RNF115_uc001eok.2_Silent_p.G25G|RNF115_uc009wiy.2_5'UTR	NM_014455	NP_055270	Q9Y4L5	RN115_HUMAN	Rabring 7	58					protein autoubiquitination	cytosol	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1																		---	---	---	---
BCL9	607	broad.mit.edu	37	1	147095924	147095924	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147095924C>T	uc001epq.2	+	10	4185	c.3445C>T	c.(3445-3447)CAG>TAG	p.Q1149*	BCL9_uc010ozr.1_Nonsense_Mutation_p.Q1063*	NM_004326	NP_004317	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	1149	Pro-rich.				Wnt receptor signaling pathway	nucleus	protein binding			ovary(2)|large_intestine(2)|breast(1)|skin(1)	6	all_hematologic(923;0.115)							T	IGH@|IGL@	B-ALL								---	---	---	---
SV2A	9900	broad.mit.edu	37	1	149882490	149882490	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149882490G>A	uc001etg.2	-	4	1334	c.843C>T	c.(841-843)TCC>TCT	p.S281S	SV2A_uc001eth.2_Silent_p.S281S	NM_014849	NP_055664	Q7L0J3	SV2A_HUMAN	synaptic vesicle glycoprotein 2	281	Helical; (Potential).				neurotransmitter transport	cell junction|endoplasmic reticulum|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			ovary(6)|pancreas(1)	7	Breast(34;0.00769)|all_hematologic(923;0.127)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)		Levetiracetam(DB01202)													---	---	---	---
OTUD7B	56957	broad.mit.edu	37	1	149939438	149939438	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149939438G>A	uc001etn.2	-	4	639	c.283C>T	c.(283-285)CTG>TTG	p.L95L	OTUD7B_uc001eto.2_Intron	NM_020205	NP_064590	Q6GQQ9	OTU7B_HUMAN	zinc finger protein Cezanne	95					negative regulation of I-kappaB kinase/NF-kappaB cascade	cytoplasm|microtubule cytoskeleton|nucleus	cysteine-type peptidase activity|DNA binding|protein binding|zinc ion binding			ovary(1)|breast(1)|skin(1)	3	Breast(34;0.0009)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.247)															---	---	---	---
PLEKHO1	51177	broad.mit.edu	37	1	150131040	150131040	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150131040G>T	uc001ett.2	+	6	830	c.552G>T	c.(550-552)ATG>ATT	p.M184I	PLEKHO1_uc001etr.2_Missense_Mutation_p.M12I|PLEKHO1_uc001ets.2_Missense_Mutation_p.M1I|PLEKHO1_uc001etu.2_Missense_Mutation_p.M12I	NM_016274	NP_057358	Q53GL0	PKHO1_HUMAN	pleckstrin homology domain containing, family O	184	Interaction with ATM, CKIP, IFP35 and NMI.|Interaction with capping proteins (CPs).					cytoplasm|nucleus|plasma membrane				lung(1)	1	Lung NSC(24;7.78e-28)|Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
PLEKHO1	51177	broad.mit.edu	37	1	150131110	150131110	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150131110C>T	uc001ett.2	+	6	900	c.622C>T	c.(622-624)CGG>TGG	p.R208W	PLEKHO1_uc001etr.2_Missense_Mutation_p.R36W|PLEKHO1_uc001ets.2_Missense_Mutation_p.R25W|PLEKHO1_uc001etu.2_Missense_Mutation_p.R36W	NM_016274	NP_057358	Q53GL0	PKHO1_HUMAN	pleckstrin homology domain containing, family O	208	Interaction with ATM, CKIP, IFP35 and NMI.					cytoplasm|nucleus|plasma membrane				lung(1)	1	Lung NSC(24;7.78e-28)|Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
TARS2	80222	broad.mit.edu	37	1	150459931	150459931	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150459931C>T	uc001euq.2	+	1	12	c.5C>T	c.(4-6)GCC>GTC	p.A2V	TARS2_uc010pcd.1_RNA|TARS2_uc001eur.2_Missense_Mutation_p.A2V|TARS2_uc009wlt.2_5'UTR|TARS2_uc009wls.2_Missense_Mutation_p.A2V	NM_025150	NP_079426	Q9BW92	SYTM_HUMAN	threonyl-tRNA synthetase 2, mitochondrial	2					threonyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|threonine-tRNA ligase activity			ovary(1)	1	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.51e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)		L-Threonine(DB00156)													---	---	---	---
TARS2	80222	broad.mit.edu	37	1	150469090	150469090	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150469090C>T	uc001euq.2	+	8	914	c.907C>T	c.(907-909)CGG>TGG	p.R303W	TARS2_uc010pcd.1_RNA|TARS2_uc001eur.2_Intron|TARS2_uc009wlt.2_Intron|TARS2_uc009wls.2_Intron	NM_025150	NP_079426	Q9BW92	SYTM_HUMAN	threonyl-tRNA synthetase 2, mitochondrial	303					threonyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|threonine-tRNA ligase activity			ovary(1)	1	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.51e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)		L-Threonine(DB00156)													---	---	---	---
ADAMTSL4	54507	broad.mit.edu	37	1	150526055	150526055	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150526055C>T	uc001eux.2	+	6	824	c.588C>T	c.(586-588)TCC>TCT	p.S196S	ADAMTSL4_uc001euw.2_Silent_p.S196S|ADAMTSL4_uc009wlw.2_Silent_p.S196S|ADAMTSL4_uc010pcg.1_Silent_p.S196S	NM_019032	NP_061905	Q6UY14	ATL4_HUMAN	thrombospondin repeat containing 1 isoform 1	196					apoptosis|positive regulation of apoptosis		metalloendopeptidase activity|protease binding			ovary(1)|skin(1)	2	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)															---	---	---	---
CTSS	1520	broad.mit.edu	37	1	150720339	150720339	+	Silent	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150720339T>G	uc001evn.2	-	7	943	c.810A>C	c.(808-810)CCA>CCC	p.P270P	CTSS_uc010pcj.1_Silent_p.P220P	NM_004079	NP_004070	P25774	CATS_HUMAN	cathepsin S preproprotein	270					immune response|proteolysis	extracellular region|lysosome	cysteine-type endopeptidase activity				0	all_cancers(9;6.17e-52)|all_epithelial(9;9.7e-43)|all_lung(15;5.74e-35)|Lung NSC(24;2.09e-31)|Breast(34;0.00146)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0485)|Epithelial(6;5.02e-21)|all cancers(9;1.28e-20)|OV - Ovarian serous cystadenocarcinoma(6;1.09e-14)|BRCA - Breast invasive adenocarcinoma(12;0.00501)|LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
CTSK	1513	broad.mit.edu	37	1	150772083	150772083	+	Nonsense_Mutation	SNP	G	A	A	rs74315303		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:150772083G>A	uc001evp.1	-	6	845	c.721C>T	c.(721-723)CGA>TGA	p.R241*	CTSK_uc001evq.1_Nonsense_Mutation_p.R152*	NM_000396	NP_000387	P43235	CATK_HUMAN	cathepsin K preproprotein	241					proteolysis	lysosome	cysteine-type endopeptidase activity|protein binding			skin(1)	1	all_cancers(9;2.32e-51)|all_epithelial(9;3.89e-42)|all_lung(15;4.59e-35)|Lung NSC(24;1.7e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Colorectal(459;0.171)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0485)|BRCA - Breast invasive adenocarcinoma(12;0.00606)|LUSC - Lung squamous cell carcinoma(543;0.211)															---	---	---	---
BNIPL	149428	broad.mit.edu	37	1	151015609	151015609	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151015609A>G	uc001ewl.2	+	5	784	c.611A>G	c.(610-612)CAT>CGT	p.H204R	BNIPL_uc009wmi.2_Missense_Mutation_p.H122R|BNIPL_uc009wmj.2_RNA	NM_138278	NP_612122	Q7Z465	BNIPL_HUMAN	BCL2/adenovirus E1B 19kD interacting protein	204	CRAL-TRIO.				apoptosis|induction of apoptosis|negative regulation of cell proliferation|regulation of growth rate	cytosol|nucleus	identical protein binding				0	Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)															---	---	---	---
CDC42SE1	56882	broad.mit.edu	37	1	151028192	151028192	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151028192C>T	uc001ewo.2	-	3	585	c.15G>A	c.(13-15)TGG>TGA	p.W5*	CDC42SE1_uc001ewp.2_Nonsense_Mutation_p.W5*	NM_001038707	NP_001033796	Q9NRR8	C42S1_HUMAN	CDC42 small effector 1	5					phagocytosis|regulation of cell shape|signal transduction	cytoplasm|cytoskeleton|plasma membrane	GTPase inhibitor activity				0	Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)															---	---	---	---
SNX27	81609	broad.mit.edu	37	1	151665453	151665453	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151665453T>G	uc001eyn.1	+	10	1472	c.1456T>G	c.(1456-1458)TTC>GTC	p.F486V	SNX27_uc001eyo.2_Missense_Mutation_p.F393V|SNX27_uc001eyp.2_Missense_Mutation_p.F300V	NM_030918	NP_112180	Q96L92	SNX27_HUMAN	sorting nexin family member 27	486					cell communication|protein transport|signal transduction	cytosol|early endosome	phosphatidylinositol binding|protein binding			ovary(2)|central_nervous_system(1)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
TDRKH	11022	broad.mit.edu	37	1	151751710	151751710	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151751710C>A	uc009wnb.1	-	5	612	c.430G>T	c.(430-432)GGC>TGC	p.G144C	TDRKH_uc001eyy.2_5'UTR|TDRKH_uc001ezb.3_Missense_Mutation_p.G140C|TDRKH_uc001ezc.3_Intron|TDRKH_uc001eza.3_Missense_Mutation_p.G144C|TDRKH_uc001ezd.3_Missense_Mutation_p.G144C|TDRKH_uc010pdn.1_5'UTR	NM_006862	NP_006853	Q9Y2W6	TDRKH_HUMAN	tudor and KH domain containing isoform a	144	KH 2.						RNA binding			ovary(1)|pancreas(1)	2	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
THEM5	284486	broad.mit.edu	37	1	151820732	151820732	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151820732G>A	uc009wnd.2	-	4	633	c.501C>T	c.(499-501)GAC>GAT	p.D167D		NM_182578	NP_872384	Q8N1Q8	THEM5_HUMAN	thioesterase superfamily member 5	167							hydrolase activity			ovary(1)|skin(1)	2	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
TCHH	7062	broad.mit.edu	37	1	152084354	152084354	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152084354G>A	uc001ezp.2	-	2	1339	c.1339C>T	c.(1339-1341)CTG>TTG	p.L447L	TCHH_uc009wne.1_Silent_p.L447L	NM_007113	NP_009044	Q07283	TRHY_HUMAN	trichohyalin	447	9 X 28 AA approximate tandem repeats.				keratinization	cytoskeleton	calcium ion binding			ovary(3)|kidney(1)|central_nervous_system(1)	5	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)															---	---	---	---
HRNR	388697	broad.mit.edu	37	1	152192843	152192843	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152192843C>A	uc001ezt.1	-	3	1338	c.1262G>T	c.(1261-1263)GGC>GTC	p.G421V		NM_001009931	NP_001009931	Q86YZ3	HORN_HUMAN	hornerin	421	4.				keratinization		calcium ion binding|protein binding			skin(2)|ovary(1)	3	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)															---	---	---	---
HRNR	388697	broad.mit.edu	37	1	152193233	152193233	+	Missense_Mutation	SNP	C	T	T	rs143206493		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152193233C>T	uc001ezt.1	-	3	948	c.872G>A	c.(871-873)CGT>CAT	p.R291H		NM_001009931	NP_001009931	Q86YZ3	HORN_HUMAN	hornerin	291	3.				keratinization		calcium ion binding|protein binding			skin(2)|ovary(1)	3	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)															---	---	---	---
FLG	2312	broad.mit.edu	37	1	152276822	152276822	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152276822C>T	uc001ezu.1	-	3	10576	c.10540G>A	c.(10540-10542)GAC>AAC	p.D3514N		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	3514	Ser-rich.|Filaggrin 21.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)|skin(4)|upper_aerodigestive_tract(3)	16	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											Ichthyosis				---	---	---	---
FLG	2312	broad.mit.edu	37	1	152285981	152285981	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152285981G>T	uc001ezu.1	-	3	1417	c.1381C>A	c.(1381-1383)CGG>AGG	p.R461R	uc001ezv.2_RNA	NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	461	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)|skin(4)|upper_aerodigestive_tract(3)	16	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											Ichthyosis				---	---	---	---
FLG	2312	broad.mit.edu	37	1	152285992	152285992	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152285992C>T	uc001ezu.1	-	3	1406	c.1370G>A	c.(1369-1371)CGG>CAG	p.R457Q	uc001ezv.2_RNA	NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	457	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)|skin(4)|upper_aerodigestive_tract(3)	16	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											Ichthyosis				---	---	---	---
FLG2	388698	broad.mit.edu	37	1	152326287	152326287	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152326287G>A	uc001ezw.3	-	3	4048	c.3975C>T	c.(3973-3975)GGC>GGT	p.G1325G	uc001ezv.2_Intron	NM_001014342	NP_001014364	Q5D862	FILA2_HUMAN	filaggrin family member 2	1325							calcium ion binding|structural molecule activity			ovary(10)|skin(5)|upper_aerodigestive_tract(1)|breast(1)	17	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)															---	---	---	---
CRCT1	54544	broad.mit.edu	37	1	152488020	152488020	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152488020G>A	uc001ezz.2	+	2	234	c.161G>A	c.(160-162)GGC>GAC	p.G54D		NM_019060	NP_061933	Q9UGL9	CRCT1_HUMAN	cysteine-rich C-terminal 1	54	Cys-rich.										0	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)															---	---	---	---
PGLYRP3	114771	broad.mit.edu	37	1	153275003	153275003	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153275003C>A	uc001fbn.1	-	5	663	c.610G>T	c.(610-612)GTC>TTC	p.V204F		NM_052891	NP_443123	Q96LB9	PGRP3_HUMAN	peptidoglycan recognition protein 3 precursor	204					defense response to Gram-positive bacterium|detection of bacterium|innate immune response|peptidoglycan catabolic process	extracellular region|intracellular|membrane	N-acetylmuramoyl-L-alanine amidase activity|peptidoglycan receptor activity|zinc ion binding			ovary(2)|pancreas(1)|skin(1)	4	all_lung(78;3.35e-32)|Lung NSC(65;1.22e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
ILF2	3608	broad.mit.edu	37	1	153635714	153635714	+	Silent	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153635714A>C	uc001fcr.2	-	11	864	c.783T>G	c.(781-783)CCT>CCG	p.P261P	ILF2_uc010pdy.1_Silent_p.P223P|ILF2_uc009wok.2_Silent_p.P239P	NM_004515	NP_004506	Q12905	ILF2_HUMAN	interleukin enhancer binding factor 2	261	DZF.				immune response|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus|ribonucleoprotein complex	ATP binding|DNA binding|double-stranded RNA binding|protein binding|transferase activity				0	all_lung(78;1.84e-32)|Lung NSC(65;6.67e-31)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)															---	---	---	---
INTS3	65123	broad.mit.edu	37	1	153713803	153713803	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153713803C>A	uc009wom.2	+	4	498	c.277C>A	c.(277-279)CTG>ATG	p.L93M	INTS3_uc001fct.2_Missense_Mutation_p.L93M|INTS3_uc001fcu.2_Translation_Start_Site|INTS3_uc001fcv.2_Translation_Start_Site	NM_023015	NP_075391	Q68E01	INT3_HUMAN	integrator complex subunit 3	93					DNA repair|G2/M transition checkpoint|response to ionizing radiation|snRNA processing	integrator complex|SOSS complex	protein binding			ovary(2)|upper_aerodigestive_tract(1)	3	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)															---	---	---	---
SLC27A3	11000	broad.mit.edu	37	1	153749212	153749212	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153749212C>T	uc001fcz.2	+						SLC27A3_uc009won.2_Intron	NM_024330	NP_077306			solute carrier family 27 member 3						fatty acid metabolic process	integral to membrane|mitochondrial membrane	ligase activity|nucleotide binding			ovary(1)	1	all_lung(78;6.47e-32)|Lung NSC(65;2.52e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)															---	---	---	---
DENND4B	9909	broad.mit.edu	37	1	153907312	153907312	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153907312C>T	uc001fdd.1	-	18	3098	c.2697G>A	c.(2695-2697)CAG>CAA	p.Q899Q	uc001fdc.1_RNA	NM_014856	NP_055671	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	899	Gln-rich.									ovary(1)	1	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)															---	---	---	---
CREB3L4	148327	broad.mit.edu	37	1	153946380	153946380	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153946380G>A	uc001fdn.3	+	10	1293	c.1027G>A	c.(1027-1029)GTA>ATA	p.V343I	CREB3L4_uc010pef.1_Missense_Mutation_p.V196I|CREB3L4_uc001fdo.3_Missense_Mutation_p.V323I|CREB3L4_uc001fdm.1_Missense_Mutation_p.V343I|CREB3L4_uc001fdp.1_Missense_Mutation_p.V323I|CREB3L4_uc001fdr.2_Missense_Mutation_p.V343I|CREB3L4_uc001fdq.2_Missense_Mutation_p.V323I	NM_130898	NP_570968	Q8TEY5	CR3L4_HUMAN	cAMP responsive element binding protein 3-like	343	Lumenal (Potential).				response to unfolded protein	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)															---	---	---	---
TPM3	7170	broad.mit.edu	37	1	154141803	154141803	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154141803C>T	uc001fec.1	-	9	947	c.832G>A	c.(832-834)GCC>ACC	p.A278T	TPM3_uc001fdx.1_Intron|TPM3_uc010pei.1_Intron|TPM3_uc001fdy.1_Intron|TPM3_uc001fdz.1_Intron|TPM3_uc001fea.1_Intron|TPM3_uc001feb.1_Intron|TPM3_uc010pej.1_Intron|TPM3_uc009wor.2_Intron|TPM3_uc001fed.1_Missense_Mutation_p.A241T	NM_152263	NP_689476	P06753	TPM3_HUMAN	tropomyosin 3 isoform 1	277	By similarity.				cellular component movement|muscle filament sliding|regulation of muscle contraction	cytosol|muscle thin filament tropomyosin|stress fiber	actin binding		TPM3/ALK(33)	haematopoietic_and_lymphoid_tissue(22)|soft_tissue(11)|skin(1)	34	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)							T	NTRK1|ALK	papillary thyroid|ALCL								---	---	---	---
AQP10	89872	broad.mit.edu	37	1	154296060	154296060	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154296060C>T	uc001feu.2	+						AQP10_uc001fev.2_Intron|ATP8B2_uc001few.2_5'Flank	NM_080429	NP_536354			aquaporin 10						response to toxin|transmembrane transport|water transport	integral to membrane|plasma membrane	transporter activity			central_nervous_system(1)	1	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)															---	---	---	---
ATP8B2	57198	broad.mit.edu	37	1	154303924	154303924	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154303924G>A	uc001fey.1	+	5	554	c.365G>A	c.(364-366)CGC>CAC	p.R122H	ATP8B2_uc001few.2_Missense_Mutation_p.R103H|ATP8B2_uc001fex.2_Missense_Mutation_p.R136H	NM_001005855	NP_001005855	P98198	AT8B2_HUMAN	ATPase, class I, type 8B, member 2 isoform b	122	Cytoplasmic (Potential).				ATP biosynthetic process	plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(1)|skin(1)	2	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)															---	---	---	---
KCNN3	3782	broad.mit.edu	37	1	154687391	154687391	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154687391A>G	uc001ffp.2	-	6	2104	c.1790T>C	c.(1789-1791)GTG>GCG	p.V597A	KCNN3_uc001ffo.2_Missense_Mutation_p.V292A	NM_002249	NP_002240	Q9UGI6	KCNN3_HUMAN	small conductance calcium-activated potassium	602	Calmodulin-binding (By similarity).					integral to membrane	calmodulin binding			lung(1)	1	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)															---	---	---	---
KCNN3	3782	broad.mit.edu	37	1	154698393	154698393	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154698393C>T	uc001ffp.2	-	5	2014	c.1700G>A	c.(1699-1701)CGG>CAG	p.R567Q	KCNN3_uc001ffo.2_Missense_Mutation_p.R262Q	NM_002249	NP_002240	Q9UGI6	KCNN3_HUMAN	small conductance calcium-activated potassium	572	Calmodulin-binding (By similarity).					integral to membrane	calmodulin binding			lung(1)	1	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)															---	---	---	---
PBXIP1	57326	broad.mit.edu	37	1	154923805	154923805	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154923805G>A	uc001ffr.2	-	5	371	c.312C>T	c.(310-312)GAC>GAT	p.D104D	PBXIP1_uc001ffs.2_Silent_p.D75D|PBXIP1_uc010pep.1_Intron|PBXIP1_uc009woy.1_RNA	NM_020524	NP_065385	Q96AQ6	PBIP1_HUMAN	pre-B-cell leukemia homeobox interacting protein	104					cell differentiation|multicellular organismal development|negative regulation of transcription, DNA-dependent	cytosol|microtubule|nucleus	protein binding|transcription corepressor activity			large_intestine(1)	1	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)															---	---	---	---
THBS3	7059	broad.mit.edu	37	1	155172603	155172603	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155172603C>T	uc001fix.2	-	8	980	c.957G>A	c.(955-957)GAG>GAA	p.E319E	RAG1AP1_uc010pey.1_Intron|THBS3_uc009wqi.2_Silent_p.E310E|THBS3_uc001fiz.2_Silent_p.E319E|THBS3_uc001fiy.2_Translation_Start_Site|THBS3_uc010pfu.1_Silent_p.E199E|THBS3_uc010pfv.1_RNA|THBS3_uc001fja.2_RNA	NM_007112	NP_009043	P49746	TSP3_HUMAN	thrombospondin 3 precursor	319	EGF-like 2; calcium-binding (Potential).				cell-matrix adhesion	extracellular region|perinuclear region of cytoplasm	calcium ion binding|heparin binding|structural molecule activity			breast(3)|ovary(2)	5	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)															---	---	---	---
FAM189B	10712	broad.mit.edu	37	1	155221574	155221574	+	Silent	SNP	C	T	T	rs149524897		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155221574C>T	uc001fjm.2	-	6	1350	c.744G>A	c.(742-744)CCG>CCA	p.P248P	RAG1AP1_uc010pey.1_Intron|FAM189B_uc009wql.2_Silent_p.P14P|FAM189B_uc001fjn.2_Silent_p.P152P|FAM189B_uc001fjo.2_Silent_p.P230P|FAM189B_uc001fjp.2_Intron	NM_006589	NP_006580	P81408	F189B_HUMAN	hypothetical protein LOC10712 isoform a	248	Poly-Pro.					integral to membrane	WW domain binding			ovary(1)|breast(1)	2																		---	---	---	---
CLK2	1196	broad.mit.edu	37	1	155234552	155234552	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155234552C>T	uc001fjy.2	-	9	1237	c.947G>A	c.(946-948)CGC>CAC	p.R316H	RAG1AP1_uc010pey.1_Intron|SCAMP3_uc001fjs.2_5'Flank|SCAMP3_uc001fju.2_5'Flank|SCAMP3_uc001fjv.2_5'Flank|SCAMP3_uc001fjt.2_5'Flank|CLK2_uc001fjw.2_Missense_Mutation_p.R315H|CLK2_uc001fjx.2_Missense_Mutation_p.R88H|CLK2_uc009wqm.2_Missense_Mutation_p.R316H	NM_003993	NP_003984	P49760	CLK2_HUMAN	CDC-like kinase 2	316	Protein kinase.					nucleus	ATP binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)										Other_conserved_DNA_damage_response_genes					---	---	---	---
HCN3	57657	broad.mit.edu	37	1	155257627	155257627	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155257627T>C	uc001fjz.1	+	8	1706	c.1698T>C	c.(1696-1698)AGT>AGC	p.S566S	RAG1AP1_uc010pey.1_Intron|HCN3_uc010pfz.1_Silent_p.S261S	NM_020897	NP_065948	Q9P1Z3	HCN3_HUMAN	hyperpolarization activated cyclic	566	Cytoplasmic (Potential).					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)|breast(1)	2	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)															---	---	---	---
ASH1L	55870	broad.mit.edu	37	1	155313102	155313102	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155313102T>C	uc009wqq.2	-						RAG1AP1_uc010pey.1_Intron|ASH1L_uc001fkt.2_Intron	NM_018489	NP_060959			absent, small, or homeotic 1-like						cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)															---	---	---	---
ASH1L	55870	broad.mit.edu	37	1	155348076	155348076	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155348076T>C	uc009wqq.2	-	10	6823	c.6343A>G	c.(6343-6345)AAT>GAT	p.N2115D	RAG1AP1_uc010pey.1_Intron|ASH1L_uc001fkt.2_Missense_Mutation_p.N2110D	NM_018489	NP_060959	Q9NR48	ASH1L_HUMAN	absent, small, or homeotic 1-like	2115	AWS.				cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)															---	---	---	---
ASH1L	55870	broad.mit.edu	37	1	155448114	155448114	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155448114C>T	uc009wqq.2	-	3	5027	c.4547G>A	c.(4546-4548)CGC>CAC	p.R1516H	ASH1L_uc001fkt.2_Missense_Mutation_p.R1516H|ASH1L_uc009wqr.1_Missense_Mutation_p.R1516H	NM_018489	NP_060959	Q9NR48	ASH1L_HUMAN	absent, small, or homeotic 1-like	1516					cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)															---	---	---	---
YY1AP1	55249	broad.mit.edu	37	1	155629956	155629956	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155629956G>A	uc001fln.2	-	11	1907	c.1883C>T	c.(1882-1884)GCC>GTC	p.A628V	YY1AP1_uc001flg.2_Missense_Mutation_p.A367V|YY1AP1_uc010pgg.1_Missense_Mutation_p.A467V|YY1AP1_uc010pgh.1_Missense_Mutation_p.A571V|YY1AP1_uc010pgi.1_Missense_Mutation_p.A720V|YY1AP1_uc001flh.2_Missense_Mutation_p.A700V|YY1AP1_uc009wqt.2_Missense_Mutation_p.A551V|YY1AP1_uc001flk.2_Missense_Mutation_p.A571V|YY1AP1_uc001fll.2_Missense_Mutation_p.A582V|YY1AP1_uc009wqv.2_Missense_Mutation_p.A299V|YY1AP1_uc001flm.2_Missense_Mutation_p.A571V|YY1AP1_uc001fli.2_Missense_Mutation_p.A582V|YY1AP1_uc009wqu.2_Missense_Mutation_p.A415V|YY1AP1_uc001flj.2_Missense_Mutation_p.A562V|YY1AP1_uc009wqw.2_Missense_Mutation_p.A551V|YY1AP1_uc001flo.2_Missense_Mutation_p.A516V|YY1AP1_uc001flp.2_Missense_Mutation_p.A582V	NM_139118	NP_620829	Q9H869	YYAP1_HUMAN	YY1-associated protein isoform 2	628					regulation of cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	protein binding			ovary(2)|skin(1)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)																	---	---	---	---
YY1AP1	55249	broad.mit.edu	37	1	155646524	155646524	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155646524G>A	uc001fln.2	-	5	361	c.337C>T	c.(337-339)CTG>TTG	p.L113L	YY1AP1_uc010pgg.1_5'UTR|YY1AP1_uc010pgh.1_Silent_p.L36L|YY1AP1_uc010pgi.1_Silent_p.L185L|YY1AP1_uc001flh.2_Silent_p.L185L|YY1AP1_uc009wqt.2_Silent_p.L36L|YY1AP1_uc001flk.2_Silent_p.L36L|YY1AP1_uc001fll.2_Silent_p.L47L|YY1AP1_uc009wqv.2_5'UTR|YY1AP1_uc001flm.2_Silent_p.L36L|YY1AP1_uc001fli.2_Silent_p.L47L|YY1AP1_uc009wqu.2_5'UTR|YY1AP1_uc001flj.2_Silent_p.L47L|YY1AP1_uc009wqw.2_Silent_p.L36L|YY1AP1_uc001flo.2_5'UTR|YY1AP1_uc001flp.2_Silent_p.L47L|YY1AP1_uc010pgj.1_Silent_p.L113L|YY1AP1_uc009wqx.2_Silent_p.L185L|YY1AP1_uc010pgk.1_Silent_p.L185L	NM_139118	NP_620829	Q9H869	YYAP1_HUMAN	YY1-associated protein isoform 2	113					regulation of cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	protein binding			ovary(2)|skin(1)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)																	---	---	---	---
RXFP4	339403	broad.mit.edu	37	1	155912230	155912230	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155912230G>A	uc010pgs.1	+	1	751	c.730G>A	c.(730-732)GTG>ATG	p.V244M		NM_181885	NP_871001	Q8TDU9	RL3R2_HUMAN	relaxin 3 receptor 2	244	Cytoplasmic (Potential).					integral to membrane|plasma membrane	angiotensin type II receptor activity				0	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)																	---	---	---	---
UBQLN4	56893	broad.mit.edu	37	1	156013836	156013836	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156013836G>A	uc001fna.2	-	6	1103	c.1079C>T	c.(1078-1080)CCG>CTG	p.P360L	UBQLN4_uc010pgx.1_Missense_Mutation_p.P340L	NM_020131	NP_064516	Q9NRR5	UBQL4_HUMAN	ataxin-1 ubiquitin-like interacting protein	360						cytosol|endoplasmic reticulum membrane|nucleus	identical protein binding			pancreas(1)|skin(1)	2	Hepatocellular(266;0.133)|all_neural(408;0.195)																	---	---	---	---
SEMA4A	64218	broad.mit.edu	37	1	156130789	156130789	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156130789T>C	uc001fnl.2	+	8	883	c.779T>C	c.(778-780)CTC>CCC	p.L260P	SEMA4A_uc009wrq.2_Missense_Mutation_p.L260P|SEMA4A_uc001fnm.2_Missense_Mutation_p.L260P|SEMA4A_uc001fnn.2_Missense_Mutation_p.L128P|SEMA4A_uc001fno.2_Missense_Mutation_p.L260P	NM_022367	NP_071762	Q9H3S1	SEM4A_HUMAN	semaphorin B precursor	260	Sema.|Extracellular (Potential).				axon guidance	integral to membrane|plasma membrane	receptor activity			ovary(1)|skin(1)	2	Hepatocellular(266;0.158)																	---	---	---	---
PMF1	11243	broad.mit.edu	37	1	156182866	156182866	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156182866G>A	uc001fnq.2	+	1	83	c.60G>A	c.(58-60)GGG>GGA	p.G20G	PMF1_uc009wru.1_RNA|PMF1_uc001fnr.2_Silent_p.G20G|BGLAP_uc001fns.1_Silent_p.G20G	NM_007221	NP_009152	Q6P1K2	PMF1_HUMAN	polyamine-modulated factor 1	20					cell division|chromosome segregation|mitotic prometaphase|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytosol|MIS12/MIND type complex|transcription factor complex	leucine zipper domain binding|transcription coactivator activity				0	Hepatocellular(266;0.158)																	---	---	---	---
C1orf85	112770	broad.mit.edu	37	1	156264003	156264003	+	Nonsense_Mutation	SNP	G	A	A	rs140283956		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156264003G>A	uc001foh.2	-	4	617	c.604C>T	c.(604-606)CGA>TGA	p.R202*	C1orf85_uc001fof.3_5'Flank|C1orf85_uc001fog.1_Intron|C1orf85_uc001foi.2_Nonsense_Mutation_p.R202*|C1orf85_uc009wrx.2_Nonsense_Mutation_p.R135*|C1orf85_uc001foj.2_Nonsense_Mutation_p.R116*	NM_144580	NP_653181	Q8WWB7	NCUG1_HUMAN	kidney predominant protein NCU-G1 precursor	202	Lumenal (Potential).				positive regulation of transcription from RNA polymerase II promoter	cytosol|integral to membrane|lysosomal membrane|nucleus	ligand-dependent nuclear receptor activity|protein binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			ovary(2)	2	Hepatocellular(266;0.158)																	---	---	---	---
C1orf182	128229	broad.mit.edu	37	1	156316633	156316633	+	Missense_Mutation	SNP	G	A	A	rs117266642	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156316633G>A	uc001foo.2	+	4	600	c.238G>A	c.(238-240)GCC>ACC	p.A80T	C1orf182_uc009wry.2_Missense_Mutation_p.A80T|C1orf182_uc001fop.3_Missense_Mutation_p.A80T	NM_144627	NP_653228	Q96A04	CA182_HUMAN	SSTK-interacting protein	80											0	Hepatocellular(266;0.158)																	---	---	---	---
C1orf61	10485	broad.mit.edu	37	1	156377716	156377716	+	Silent	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156377716T>G	uc001fou.1	-	5	340	c.223A>C	c.(223-225)AGG>CGG	p.R75R	C1orf61_uc001fot.1_5'Flank|C1orf61_uc001fov.1_RNA|C1orf61_uc001fow.1_Intron|C1orf61_uc001fox.1_Intron	NM_006365	NP_006356	Q13536	CROC4_HUMAN	transcriptional activator of the c-fos promoter	75						nucleus				skin(1)	1	Hepatocellular(266;0.158)																	---	---	---	---
IQGAP3	128239	broad.mit.edu	37	1	156498841	156498841	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156498841G>A	uc001fpf.2	-	35	4513	c.4438C>T	c.(4438-4440)CGG>TGG	p.R1480W		NM_178229	NP_839943	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	1480					small GTPase mediated signal transduction	intracellular	calmodulin binding|Ras GTPase activator activity			ovary(5)|skin(1)	6	all_hematologic(923;0.088)|Hepatocellular(266;0.158)																	---	---	---	---
IQGAP3	128239	broad.mit.edu	37	1	156524098	156524098	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156524098G>T	uc001fpf.2	-	13	1452	c.1377C>A	c.(1375-1377)GCC>GCA	p.A459A	IQGAP3_uc009wsb.1_Silent_p.A416A	NM_178229	NP_839943	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	459					small GTPase mediated signal transduction	intracellular	calmodulin binding|Ras GTPase activator activity			ovary(5)|skin(1)	6	all_hematologic(923;0.088)|Hepatocellular(266;0.158)																	---	---	---	---
PEAR1	375033	broad.mit.edu	37	1	156876512	156876512	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156876512G>A	uc001fqj.1	+	6	600	c.484G>A	c.(484-486)GTA>ATA	p.V162I	PEAR1_uc009wsl.1_Splice_Site_p.G23_splice|PEAR1_uc001fqk.1_5'UTR	NM_001080471	NP_001073940	Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	162						integral to membrane				ovary(2)|central_nervous_system(1)	3	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)																	---	---	---	---
ARHGEF11	9826	broad.mit.edu	37	1	156910082	156910082	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156910082C>T	uc001fqo.2	-	35	4570	c.3530G>A	c.(3529-3531)GGC>GAC	p.G1177D	ARHGEF11_uc010phu.1_Missense_Mutation_p.G593D|ARHGEF11_uc001fqn.2_Missense_Mutation_p.G1217D	NM_014784	NP_055599	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	1177					actin cytoskeleton organization|apoptosis|axon guidance|cellular component movement|cytokinesis|establishment of cell polarity|G-protein coupled receptor protein signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|positive regulation of transcription, DNA-dependent|regulation of cell growth|regulation of Rho protein signal transduction|Rho protein signal transduction|striated muscle contraction	cytosol|Golgi apparatus|plasma membrane	G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			ovary(3)|skin(2)|pleura(1)|lung(1)|kidney(1)|pancreas(1)	9	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)																	---	---	---	---
ETV3L	440695	broad.mit.edu	37	1	157067667	157067667	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157067667G>A	uc001fqq.1	-	4	885	c.600C>T	c.(598-600)AGC>AGT	p.S200S		NM_001004341	NP_001004341	Q6ZN32	ETV3L_HUMAN	ets variant 3-like	200						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4	Hepatocellular(266;0.158)	Prostate(1639;0.184)																---	---	---	---
FCRL5	83416	broad.mit.edu	37	1	157509140	157509140	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157509140G>A	uc001fqu.2	-	7	1296	c.1138C>T	c.(1138-1140)CCT>TCT	p.P380S	FCRL5_uc009wsm.2_Missense_Mutation_p.P380S|FCRL5_uc010phv.1_Missense_Mutation_p.P380S|FCRL5_uc010phw.1_Missense_Mutation_p.P295S|FCRL5_uc001fqv.1_Missense_Mutation_p.P380S|FCRL5_uc010phx.1_Missense_Mutation_p.P131S	NM_031281	NP_112571	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	380	Extracellular (Potential).|Ig-like C2-type 4.					integral to membrane|plasma membrane	receptor activity			ovary(3)|breast(2)|central_nervous_system(1)	6	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)																---	---	---	---
FCRL2	79368	broad.mit.edu	37	1	157739709	157739709	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157739709G>A	uc001fre.2	-	4	601	c.542C>T	c.(541-543)ACG>ATG	p.T181M	FCRL2_uc001frd.2_5'Flank|FCRL2_uc010phz.1_Missense_Mutation_p.T181M|FCRL2_uc009wsp.2_Intron|FCRL2_uc010pia.1_Missense_Mutation_p.T181M	NM_030764	NP_110391	Q96LA5	FCRL2_HUMAN	Fc receptor-like 2 precursor	181	Extracellular (Potential).|Ig-like C2-type 2.				cell-cell signaling	integral to membrane|plasma membrane|soluble fraction	receptor activity|SH3/SH2 adaptor activity			ovary(1)|pancreas(1)	2	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)															---	---	---	---
KIRREL	55243	broad.mit.edu	37	1	158061268	158061268	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158061268G>A	uc001frn.3	+	11	1797	c.1393G>A	c.(1393-1395)GAC>AAC	p.D465N	KIRREL_uc010pib.1_Missense_Mutation_p.D365N|KIRREL_uc009wsq.2_Missense_Mutation_p.D301N|KIRREL_uc001fro.3_Missense_Mutation_p.D279N	NM_018240	NP_060710	Q96J84	KIRR1_HUMAN	kin of IRRE like precursor	465	Ig-like C2-type 5.|Extracellular (Potential).					integral to membrane				ovary(1)	1	all_hematologic(112;0.0378)																	---	---	---	---
CD1B	910	broad.mit.edu	37	1	158299156	158299156	+	Intron	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158299156T>G	uc001frx.2	-						CD1B_uc001frw.2_Intron	NM_001764	NP_001755			CD1B antigen precursor						antigen processing and presentation|immune response	endosome membrane|integral to membrane|lysosomal membrane|plasma membrane	protein binding			ovary(2)	2	all_hematologic(112;0.0378)																	---	---	---	---
OR10Z1	128368	broad.mit.edu	37	1	158576987	158576987	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158576987C>T	uc010pio.1	+	1	759	c.759C>T	c.(757-759)GGC>GGT	p.G253G		NM_001004478	NP_001004478	Q8NGY1	O10Z1_HUMAN	olfactory receptor, family 10, subfamily Z,	253	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)|skin(1)	2	all_hematologic(112;0.0378)																	---	---	---	---
SPTA1	6708	broad.mit.edu	37	1	158650443	158650443	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158650443A>T	uc001fst.1	-	5	807	c.608T>A	c.(607-609)TTC>TAC	p.F203Y		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	203	Spectrin 3.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)																	---	---	---	---
OR6K3	391114	broad.mit.edu	37	1	158687848	158687848	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158687848G>C	uc010pip.1	-	1	106	c.106C>G	c.(106-108)CTT>GTT	p.L36V		NM_001005327	NP_001005327	Q8NGY3	OR6K3_HUMAN	olfactory receptor, family 6, subfamily K,	36	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|kidney(1)|central_nervous_system(1)	3	all_hematologic(112;0.0378)																	---	---	---	---
IFI16	3428	broad.mit.edu	37	1	158984683	158984683	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158984683T>G	uc001ftf.1	+	3	820	c.213T>G	c.(211-213)GAT>GAG	p.D71E	IFI16_uc001ftg.2_Missense_Mutation_p.D71E|IFI16_uc010pis.1_Missense_Mutation_p.D71E	NM_005531	NP_005522	Q16666	IF16_HUMAN	interferon, gamma-inducible protein 16	71	DAPIN.|Lys-rich.				cell proliferation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|monocyte differentiation|negative regulation of transcription, DNA-dependent|response to virus|transcription, DNA-dependent	cytoplasm|nuclear speck|nucleolus	double-stranded DNA binding|protein binding			ovary(1)	1	all_hematologic(112;0.0429)																	---	---	---	---
CRP	1401	broad.mit.edu	37	1	159683406	159683406	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159683406C>T	uc001ftw.2	-	2	688	c.584G>A	c.(583-585)GGC>GAC	p.G195D	CRP_uc001ftx.1_Intron|CRP_uc001fty.1_RNA	NM_000567	NP_000558	P02741	CRP_HUMAN	C-reactive protein, pentraxin-related precursor	195	Pentaxin.				acute-phase response|negative regulation of lipid storage|negative regulation of macrophage derived foam cell differentiation|opsonization		choline binding|Gram-positive bacterial cell surface binding|low-density lipoprotein particle binding|metal ion binding|protein binding			ovary(1)	1	all_hematologic(112;0.0429)				Atorvastatin(DB01076)|Bezafibrate(DB01393)													---	---	---	---
IGSF9	57549	broad.mit.edu	37	1	159900500	159900500	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159900500C>T	uc001fur.2	-	14	1993	c.1795G>A	c.(1795-1797)GTC>ATC	p.V599I	IGSF9_uc001fuq.2_Missense_Mutation_p.V583I|IGSF9_uc001fup.2_5'UTR	NM_001135050	NP_001128522	Q9P2J2	TUTLA_HUMAN	immunoglobulin superfamily, member 9 isoform a	599	Fibronectin type-III 1.|Extracellular (Potential).					cell junction|integral to membrane|synapse				ovary(2)|central_nervous_system(2)|large_intestine(1)	5	all_hematologic(112;0.0597)	Breast(1374;0.000126)	BRCA - Breast invasive adenocarcinoma(70;0.111)															---	---	---	---
KCNJ9	3765	broad.mit.edu	37	1	160054120	160054120	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160054120C>T	uc001fuy.1	+	2	542	c.300C>T	c.(298-300)TGC>TGT	p.C100C		NM_004983	NP_004974	Q92806	IRK9_HUMAN	potassium inwardly-rectifying channel subfamily	100	Extracellular (By similarity).				synaptic transmission	integral to membrane|plasma membrane	G-protein activated inward rectifier potassium channel activity|protein binding			ovary(1)|skin(1)	2	all_cancers(52;5.86e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)															---	---	---	---
IGSF8	93185	broad.mit.edu	37	1	160062798	160062798	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160062798C>T	uc001fva.2	-	4	1273	c.1228G>A	c.(1228-1230)GCC>ACC	p.A410T	IGSF8_uc001fuz.2_Missense_Mutation_p.A410T|IGSF8_uc009wtf.2_Missense_Mutation_p.A410T	NM_052868	NP_443100	Q969P0	IGSF8_HUMAN	immunoglobulin superfamily, member 8	410	Ig-like C2-type 3.|Extracellular (Potential).				cell proliferation|cellular component movement|nervous system development|single fertilization|skeletal muscle tissue development	integral to membrane	protein binding				0	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)															---	---	---	---
ATP1A2	477	broad.mit.edu	37	1	160099161	160099161	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160099161A>G	uc001fvc.2	+	11	1564	c.1432A>G	c.(1432-1434)ATT>GTT	p.I478V	ATP1A2_uc001fvb.2_Missense_Mutation_p.I478V|ATP1A2_uc001fvd.2_Missense_Mutation_p.I214V|ATP1A2_uc009wtg.1_Missense_Mutation_p.I166V	NM_000702	NP_000693	P50993	AT1A2_HUMAN	Na+/K+ -ATPase alpha 2 subunit proprotein	478	Cytoplasmic (Potential).				ATP biosynthetic process		ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity			central_nervous_system(3)|ovary(2)|skin(2)	7	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)															---	---	---	---
LY9	4063	broad.mit.edu	37	1	160771602	160771602	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160771602C>T	uc001fwu.2	+						LY9_uc001fwt.2_Silent_p.S159S|LY9_uc010pjs.1_Intron|LY9_uc001fwv.2_Intron|LY9_uc001fww.2_Intron|LY9_uc001fwx.2_Intron|LY9_uc001fwy.1_Intron	NM_002348	NP_002339			lymphocyte antigen 9 isoform a						cell adhesion|immunoglobulin mediated immune response	integral to membrane				ovary(1)	1	all_cancers(52;2.72e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)															---	---	---	---
LY9	4063	broad.mit.edu	37	1	160788066	160788066	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160788066C>T	uc001fwu.2	+	6	1451	c.1401C>T	c.(1399-1401)TGC>TGT	p.C467C	LY9_uc001fwv.2_Silent_p.C467C|LY9_uc001fww.2_Silent_p.C377C|LY9_uc001fwx.2_Silent_p.C377C|LY9_uc001fwy.1_Silent_p.C279C|LY9_uc001fwz.2_Silent_p.C119C	NM_002348	NP_002339	Q9HBG7	LY9_HUMAN	lymphocyte antigen 9 isoform a	467	Helical; (Potential).				cell adhesion|immunoglobulin mediated immune response	integral to membrane				ovary(1)	1	all_cancers(52;2.72e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)															---	---	---	---
ITLN2	142683	broad.mit.edu	37	1	160914976	160914976	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160914976C>T	uc001fxd.2	-	8	990	c.932G>A	c.(931-933)TGC>TAC	p.C311Y	ITLN2_uc009wts.2_Missense_Mutation_p.C310Y|ITLN2_uc010pju.1_Missense_Mutation_p.C228Y	NM_080878	NP_543154	Q8WWU7	ITLN2_HUMAN	intelectin 2 precursor	311					signal transduction	extracellular region	receptor binding|sugar binding			ovary(1)	1	all_cancers(52;2.99e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)															---	---	---	---
F11R	50848	broad.mit.edu	37	1	160968676	160968676	+	Silent	SNP	C	T	T	rs149044377	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160968676C>T	uc009wtt.2	-	10	1155	c.885G>A	c.(883-885)TCG>TCA	p.S295S	F11R_uc010pjv.1_Silent_p.S246S|F11R_uc001fxe.3_Silent_p.S292S|F11R_uc009wtu.2_Missense_Mutation_p.R276H|F11R_uc010pjw.1_Silent_p.S299S|F11R_uc001fxf.3_Silent_p.S295S	NM_016946	NP_058642	Q9Y624	JAM1_HUMAN	F11 receptor precursor	295	Cytoplasmic (Potential).				blood coagulation|inflammatory response|interspecies interaction between organisms|leukocyte migration|tight junction assembly	integral to membrane|tight junction				ovary(2)	2	all_cancers(52;6.73e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00207)															---	---	---	---
PPOX	5498	broad.mit.edu	37	1	161140705	161140705	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161140705T>C	uc001fyj.2	+	12	1547	c.1257T>C	c.(1255-1257)ATT>ATC	p.I419I	PPOX_uc001fyn.2_Silent_p.I127I|PPOX_uc001fyg.2_Silent_p.I419I|PPOX_uc001fyl.2_Silent_p.I385I|PPOX_uc001fym.2_RNA|PPOX_uc001fyk.2_Silent_p.I257I|PPOX_uc001fyh.2_Silent_p.I257I|PPOX_uc010pkg.1_Silent_p.I257I|PPOX_uc009wuc.1_Silent_p.I220I|PPOX_uc010pkh.1_Intron|PPOX_uc001fyi.2_Intron	NM_001122764	NP_001116236	P50336	PPOX_HUMAN	protoporphyrinogen oxidase	419					heme biosynthetic process	intrinsic to mitochondrial inner membrane|mitochondrial intermembrane space	flavin adenine dinucleotide binding|oxygen-dependent protoporphyrinogen oxidase activity			ovary(1)	1	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)											Porphyria_Variegata				---	---	---	---
B4GALT3	8703	broad.mit.edu	37	1	161144925	161144925	+	Missense_Mutation	SNP	G	T	T	rs148765132		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161144925G>T	uc001fyq.1	-	4	609	c.347C>A	c.(346-348)CCT>CAT	p.P116H	PPOX_uc010pkh.1_Intron|PPOX_uc001fyi.2_Intron|B4GALT3_uc001fyo.1_5'Flank|B4GALT3_uc001fyp.1_RNA|B4GALT3_uc001fyr.1_Missense_Mutation_p.P116H|B4GALT3_uc001fys.1_Missense_Mutation_p.P116H|B4GALT3_uc009wud.1_Missense_Mutation_p.P116H	NM_003779	NP_003770	O60512	B4GT3_HUMAN	UDP-Gal:betaGlcNAc beta 1,4-	116	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi cisterna membrane|integral to membrane	beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity|metal ion binding|N-acetyllactosamine synthase activity				0	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		N-Acetyl-D-glucosamine(DB00141)													---	---	---	---
HSPA6	3310	broad.mit.edu	37	1	161494877	161494877	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161494877C>T	uc001gap.2	+	2	1089	c.429C>T	c.(427-429)CAC>CAT	p.H143H	HSPA6_uc001gaq.2_Silent_p.H143H	NM_002155	NP_002146	P17066	HSP76_HUMAN	heat shock 70kDa protein 6 (HSP70B')	143					response to unfolded protein		ATP binding			skin(1)	1	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)															---	---	---	---
FCGR2C	9103	broad.mit.edu	37	1	161569442	161569442	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161569442C>T	uc001gav.2	+	8	920	c.821C>T	c.(820-822)GCC>GTC	p.A274V		NM_201563	NP_963857			Fc fragment of IgG, low affinity IIc, receptor												0	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)															---	---	---	---
OLFML2B	25903	broad.mit.edu	37	1	161993101	161993101	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161993101C>T	uc001gbu.2	-	1	544	c.120G>A	c.(118-120)GCG>GCA	p.A40A	OLFML2B_uc010pkq.1_Silent_p.A40A	NM_015441	NP_056256	Q68BL8	OLM2B_HUMAN	olfactomedin-like 2B precursor	40	Potential.									skin(1)	1	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.0172)															---	---	---	---
POGK	57645	broad.mit.edu	37	1	166818405	166818405	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166818405C>T	uc001gdt.1	+	5	709	c.589C>T	c.(589-591)CGC>TGC	p.R197C	POGK_uc010ple.1_Missense_Mutation_p.R112C|POGK_uc010plf.1_Missense_Mutation_p.R79C	NM_017542	NP_060012	Q9P215	POGK_HUMAN	pogo transposable element with KRAB domain	197					multicellular organismal development|regulation of transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1																		---	---	---	---
DUSP27	92235	broad.mit.edu	37	1	167095107	167095107	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167095107G>A	uc001geb.1	+	5	739	c.739G>A	c.(739-741)GCC>ACC	p.A247T		NM_001080426	NP_001073895	Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27	247	Tyrosine-protein phosphatase.				protein dephosphorylation		protein tyrosine/serine/threonine phosphatase activity			ovary(3)	3																		---	---	---	---
DUSP27	92235	broad.mit.edu	37	1	167096440	167096440	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167096440C>T	uc001geb.1	+	5	2072	c.2072C>T	c.(2071-2073)GCT>GTT	p.A691V		NM_001080426	NP_001073895	Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27	691					protein dephosphorylation		protein tyrosine/serine/threonine phosphatase activity			ovary(3)	3																		---	---	---	---
BRP44	25874	broad.mit.edu	37	1	167887567	167887567	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:167887567G>A	uc001ges.2	-	5	679	c.378C>T	c.(376-378)CAC>CAT	p.H126H	BRP44_uc001get.2_Silent_p.H126H|BRP44_uc001geu.2_Silent_p.H126H	NM_015415	NP_056230	O95563	BR44_HUMAN	brain protein 44	126						mitochondrion					0	all_hematologic(923;0.215)			KIRC - Kidney renal clear cell carcinoma(1967;0.247)														---	---	---	---
DCAF6	55827	broad.mit.edu	37	1	168037611	168037611	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168037611G>A	uc001gew.2	+	18	2670	c.2428G>A	c.(2428-2430)GAA>AAA	p.E810K	DCAF6_uc001gev.2_Missense_Mutation_p.E830K|DCAF6_uc001gex.2_Missense_Mutation_p.E901K|DCAF6_uc010plk.1_Missense_Mutation_p.E870K|DCAF6_uc001gey.2_Missense_Mutation_p.E683K|DCAF6_uc001gez.2_Missense_Mutation_p.E113K	NM_001017977	NP_001017977	Q58WW2	DCAF6_HUMAN	IQ motif and WD repeats 1 isoform b	810					positive regulation of transcription from RNA polymerase II promoter	CUL4 RING ubiquitin ligase complex|nucleus	ligand-dependent nuclear receptor transcription coactivator activity			ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
ATP1B1	481	broad.mit.edu	37	1	169094243	169094243	+	RNA	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169094243C>A	uc001gfs.1	+	3		c.469C>A			uc010plp.1_5'Flank					Synthetic construct DNA, clone: pF1KB8186, Homo sapiens ATP1B1 gene for ATPase, Na+/K+ transporting, beta 1 polypeptide, without stop codon, in Flexi system.						ATP biosynthetic process|blood coagulation|leukocyte migration	sodium:potassium-exchanging ATPase complex	protein binding|sodium:potassium-exchanging ATPase activity			ovary(1)	1	all_hematologic(923;0.208)																	---	---	---	---
F5	2153	broad.mit.edu	37	1	169489825	169489825	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169489825C>G	uc001ggg.1	-	22	6271	c.6126G>C	c.(6124-6126)AGG>AGC	p.R2042S		NM_000130	NP_000121	P12259	FA5_HUMAN	coagulation factor V precursor	2042	F5/8 type C 1.				cell adhesion|platelet activation|platelet degranulation	plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	all_hematologic(923;0.208)				Drotrecogin alfa(DB00055)													---	---	---	---
FMO2	2327	broad.mit.edu	37	1	171177951	171177951	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171177951C>A	uc001ghk.1	+	9	1392	c.1275C>A	c.(1273-1275)AGC>AGA	p.S425R	FMO2_uc010pmd.1_Missense_Mutation_p.S205R	NM_001460	NP_001451	Q99518	FMO2_HUMAN	flavin containing monooxygenase 2	425					drug metabolic process|NADPH oxidation|organic acid metabolic process|toxin metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|host cell microsome|integral to membrane|microsome	flavin adenine dinucleotide binding|flavin-containing monooxygenase activity|NADP binding			skin(1)	1	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)																	---	---	---	---
BAT2L2	23215	broad.mit.edu	37	1	171556853	171556853	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171556853G>A	uc010pmg.1	+	32	8295	c.8029G>A	c.(8029-8031)GCT>ACT	p.A2677T	BAT2L2_uc010pmh.1_Missense_Mutation_p.A1589T|BAT2L2_uc010pmi.1_Missense_Mutation_p.A514T|BAT2L2_uc010pmj.1_Missense_Mutation_p.A209T	NM_015172	NP_055987	Q9Y520	PRC2C_HUMAN	HBxAg transactivated protein 2	2677							protein C-terminus binding				0																		---	---	---	---
DNM3	26052	broad.mit.edu	37	1	171958232	171958232	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:171958232A>C	uc001gie.2	+	4	709	c.533A>C	c.(532-534)AAC>ACC	p.N178T	DNM3_uc001gid.3_Missense_Mutation_p.N178T|DNM3_uc009wwb.2_Missense_Mutation_p.N178T|DNM3_uc001gif.2_Missense_Mutation_p.N178T	NM_015569	NP_056384	Q9UQ16	DYN3_HUMAN	dynamin 3 isoform a	178					endocytosis|filopodium assembly|synapse assembly	dendritic spine|microtubule|perinuclear region of cytoplasm|postsynaptic density	GTP binding|GTPase activity|protein binding			breast(1)	1																		---	---	---	---
SLC9A11	284525	broad.mit.edu	37	1	173486701	173486701	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173486701G>A	uc001giz.2	-	23	3305	c.2882C>T	c.(2881-2883)ACC>ATC	p.T961I	SLC9A11_uc009wwe.2_Missense_Mutation_p.T519I	NM_178527	NP_848622	Q5TAH2	S9A11_HUMAN	solute carrier family 9, member 11	961	cNMP.				sodium ion transport	integral to membrane	ion channel activity|solute:hydrogen antiporter activity			ovary(2)	2																		---	---	---	---
SLC9A11	284525	broad.mit.edu	37	1	173486805	173486805	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173486805A>C	uc001giz.2	-	23	3201	c.2778T>G	c.(2776-2778)AAT>AAG	p.N926K	SLC9A11_uc009wwe.2_Missense_Mutation_p.N484K	NM_178527	NP_848622	Q5TAH2	S9A11_HUMAN	solute carrier family 9, member 11	926	cNMP.				sodium ion transport	integral to membrane	ion channel activity|solute:hydrogen antiporter activity			ovary(2)	2																		---	---	---	---
CENPL	91687	broad.mit.edu	37	1	173780301	173780301	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173780301C>T	uc001gje.3	-	2	351	c.137G>A	c.(136-138)CGA>CAA	p.R46Q	CENPL_uc009wwg.2_5'UTR|CENPL_uc001gjg.3_Missense_Mutation_p.R46Q|CENPL_uc001gjf.3_Missense_Mutation_p.R46Q	NM_033319	NP_201576	Q8N0S6	CENPL_HUMAN	centromere protein L isoform 2	46					mitotic prometaphase	chromosome, centromeric region|cytosol|nucleus					0																		---	---	---	---
GAS5	60674	broad.mit.edu	37	1	173836024	173836024	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173836024G>A	uc001gji.2	-						GAS5_uc001gjj.2_Intron|GAS5_uc001gjk.2_Intron|SNORD81_uc009wwi.1_5'Flank|SNORD47_uc001gjl.2_5'Flank|SNORD80_uc009wwj.1_5'Flank|SNORD79_uc009wwk.1_5'Flank|SNORD78_uc009wwl.2_5'Flank|SNORD44_uc001gjn.1_5'Flank|SNORD77_uc009wwm.1_5'Flank|SNORD76_uc009wwn.1_5'Flank|SNORD75_uc009wwo.1_RNA|ZBTB37_uc001gjp.1_5'Flank|ZBTB37_uc001gjq.3_5'Flank|ZBTB37_uc009wwp.1_5'Flank|ZBTB37_uc001gjr.2_5'Flank					Homo sapiens mRNA; cDNA DKFZp564D0164 (from clone DKFZp564D0164).												0																		---	---	---	---
ZBTB37	84614	broad.mit.edu	37	1	173839472	173839472	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:173839472A>G	uc009wwp.1	+	3	385	c.109A>G	c.(109-111)AAT>GAT	p.N37D	GAS5_uc001gjj.2_5'Flank|GAS5_uc001gjk.2_5'Flank|SNORD74_uc001gjo.1_5'Flank|ZBTB37_uc001gjp.1_Missense_Mutation_p.N37D|ZBTB37_uc001gjq.3_Missense_Mutation_p.N37D|ZBTB37_uc001gjr.2_Missense_Mutation_p.N37D	NM_001122770	NP_001116242	Q5TC79	ZBT37_HUMAN	zinc finger and BTB domain containing 37 isoform	37	BTB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
FAM5B	57795	broad.mit.edu	37	1	177250555	177250555	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177250555G>T	uc001glf.2	+	8	2555	c.2243G>T	c.(2242-2244)CGG>CTG	p.R748L	FAM5B_uc001glg.2_Missense_Mutation_p.R643L	NM_021165	NP_066988	Q9C0B6	FAM5B_HUMAN	family with sequence similarity 5, member B	748						extracellular region				skin(3)|ovary(2)|upper_aerodigestive_tract(1)	6																		---	---	---	---
SEC16B	89866	broad.mit.edu	37	1	177902643	177902643	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:177902643G>A	uc001gli.1	-	21	2790	c.2700C>T	c.(2698-2700)CTC>CTT	p.L900L	SEC16B_uc001glk.1_Silent_p.L577L|SEC16B_uc009wwy.1_Silent_p.L455L|SEC16B_uc001glh.1_Silent_p.L559L|SEC16B_uc009wwz.1_Silent_p.L559L|SEC16B_uc001glj.1_Silent_p.L901L	NM_033127	NP_149118	Q96JE7	SC16B_HUMAN	leucine zipper transcription regulator 2	900					protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|Golgi membrane				ovary(3)|central_nervous_system(1)	4																		---	---	---	---
RASAL2	9462	broad.mit.edu	37	1	178412334	178412334	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178412334G>A	uc001glr.2	+	6	1133	c.1008G>A	c.(1006-1008)GTG>GTA	p.V336V	RASAL2_uc001glq.2_Silent_p.V484V	NM_004841	NP_004832	Q9UJF2	NGAP_HUMAN	RAS protein activator like 2 isoform 1	336	Ras-GAP.				negative regulation of Ras protein signal transduction|signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	Ras GTPase activator activity			ovary(2)|breast(2)|large_intestine(1)	5																		---	---	---	---
ANGPTL1	9068	broad.mit.edu	37	1	178834855	178834855	+	Silent	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:178834855T>A	uc001gma.2	-	3	533	c.57A>T	c.(55-57)GGA>GGT	p.G19G	RALGPS2_uc001gly.1_Intron|RALGPS2_uc001glz.2_Intron|RALGPS2_uc010pnb.1_Intron|ANGPTL1_uc001gmb.2_Silent_p.G19G|ANGPTL1_uc010pnc.1_5'UTR	NM_004673	NP_004664	O95841	ANGL1_HUMAN	angiopoietin-like 1 precursor	19						extracellular space	receptor binding				0																		---	---	---	---
TOR3A	64222	broad.mit.edu	37	1	179054880	179054880	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179054880C>T	uc001gmd.2	+	3	643	c.491C>T	c.(490-492)TCG>TTG	p.S164L	TOR3A_uc010pnd.1_Intron	NM_022371	NP_071766	Q9H497	TOR3A_HUMAN	torsin family 3, member A precursor	164					chaperone mediated protein folding requiring cofactor	endoplasmic reticulum	ATP binding			pancreas(1)	1																		---	---	---	---
SOAT1	6646	broad.mit.edu	37	1	179317997	179317997	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179317997T>C	uc001gml.2	+	13	1297	c.1234T>C	c.(1234-1236)TCA>CCA	p.S412P	SOAT1_uc010pni.1_Missense_Mutation_p.S347P|SOAT1_uc001gmm.2_Missense_Mutation_p.S354P|SOAT1_uc010pnj.1_Missense_Mutation_p.S148P|SOAT1_uc010pnk.1_Missense_Mutation_p.S347P	NM_003101	NP_003092	P35610	SOAT1_HUMAN	sterol O-acyltransferase 1	412					cholesterol efflux|cholesterol esterification|cholesterol homeostasis|cholesterol metabolic process|cholesterol storage|macrophage derived foam cell differentiation|positive regulation of amyloid precursor protein biosynthetic process|very-low-density lipoprotein particle assembly	endoplasmic reticulum membrane|integral to membrane|microsome	cholesterol binding|cholesterol O-acyltransferase activity|fatty-acyl-CoA binding			central_nervous_system(1)|skin(1)	2					Ezetimibe(DB00973)|Hesperetin(DB01094)													---	---	---	---
NPHS2	7827	broad.mit.edu	37	1	179520480	179520480	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179520480A>C	uc001gmq.3	-	8	1065	c.980T>G	c.(979-981)CTT>CGT	p.L327R	C1orf125_uc009wxg.2_Intron|C1orf125_uc001gmo.2_Intron|C1orf125_uc001gmp.2_Intron|C1orf125_uc009wxh.2_Intron|NPHS2_uc009wxi.2_Missense_Mutation_p.L259R|C1orf125_uc001gmr.2_RNA	NM_014625	NP_055440	Q9NP85	PODO_HUMAN	podocin	327	Cytoplasmic (Potential).				excretion	integral to plasma membrane	protein binding				0																		---	---	---	---
TDRD5	163589	broad.mit.edu	37	1	179609073	179609073	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179609073G>A	uc001gnf.1	+	10	1870	c.1620G>A	c.(1618-1620)AAG>AAA	p.K540K	TDRD5_uc010pnp.1_Silent_p.K540K|TDRD5_uc001gnh.1_Silent_p.K95K	NM_173533	NP_775804	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	540	Tudor.				DNA methylation involved in gamete generation|P granule organization|spermatid development	chromatoid body|pi-body	nucleic acid binding			ovary(2)|skin(2)|central_nervous_system(1)	5																		---	---	---	---
TOR1AIP1	26092	broad.mit.edu	37	1	179886597	179886597	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:179886597A>G	uc001gnq.2	+	10	1193	c.975A>G	c.(973-975)GGA>GGG	p.G325G		NM_015602	NP_056417	Q5JTV8	TOIP1_HUMAN	lamina-associated polypeptide 1B	325	Nuclear (Potential).					integral to membrane|nuclear inner membrane				breast(1)|central_nervous_system(1)	2																		---	---	---	---
CEP350	9857	broad.mit.edu	37	1	180068121	180068121	+	Splice_Site	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180068121G>T	uc001gnt.2	+	37	9572	c.9189_splice	c.e37+1	p.L3063_splice	CEP350_uc009wxl.2_Splice_Site_p.L3062_splice|CEP350_uc001gnv.2_Splice_Site_p.L1198_splice|CEP350_uc001gnw.1_Splice_Site_p.L820_splice|CEP350_uc001gnx.1_Splice_Site_p.L820_splice	NM_014810	NP_055625			centrosome-associated protein 350							centrosome|nucleus|spindle				ovary(4)	4																		---	---	---	---
KIAA1614	57710	broad.mit.edu	37	1	180914543	180914543	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:180914543C>T	uc001gok.2	+	9	3459	c.3392C>T	c.(3391-3393)ACC>ATC	p.T1131I	KIAA1614_uc001gol.1_Missense_Mutation_p.T752I|KIAA1614_uc001gom.1_Missense_Mutation_p.T222I|STX6_uc009wxo.1_RNA	NM_020950	NP_066001	Q5VZ46	K1614_HUMAN	hypothetical protein LOC57710	1131										ovary(3)|skin(1)	4																		---	---	---	---
CACNA1E	777	broad.mit.edu	37	1	181549812	181549812	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181549812G>A	uc001gow.2	+	6	1016	c.851G>A	c.(850-852)GGC>GAC	p.G284D	CACNA1E_uc009wxr.2_Missense_Mutation_p.G191D|CACNA1E_uc009wxs.2_Missense_Mutation_p.G191D	NM_000721	NP_000712	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type,	284	I.|Extracellular (Potential).				energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6																		---	---	---	---
CACNA1E	777	broad.mit.edu	37	1	181680149	181680149	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181680149G>A	uc001gow.2	+	8	1280	c.1115G>A	c.(1114-1116)CGC>CAC	p.R372H	CACNA1E_uc009wxs.2_Missense_Mutation_p.R279H	NM_000721	NP_000712	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type,	372	Cytoplasmic (Potential).				energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6																		---	---	---	---
CACNA1E	777	broad.mit.edu	37	1	181706777	181706777	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181706777C>T	uc001gow.2	+	23	3704	c.3539C>T	c.(3538-3540)TCG>TTG	p.S1180L	CACNA1E_uc009wxs.2_Missense_Mutation_p.S1068L|CACNA1E_uc001gox.1_Missense_Mutation_p.S406L|CACNA1E_uc009wxt.2_Missense_Mutation_p.S406L	NM_000721	NP_000712	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type,	1180	Extracellular (Potential).|III.				energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6																		---	---	---	---
CACNA1E	777	broad.mit.edu	37	1	181732589	181732589	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181732589A>G	uc001gow.2	+	34	4902	c.4737A>G	c.(4735-4737)CGA>CGG	p.R1579R	CACNA1E_uc009wxs.2_Silent_p.R1467R|CACNA1E_uc001gox.1_Silent_p.R805R|CACNA1E_uc009wxt.2_Silent_p.R805R	NM_000721	NP_000712	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type,	1579	Helical; Name=S4 of repeat IV.|IV.				energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6																		---	---	---	---
RNASEL	6041	broad.mit.edu	37	1	182555353	182555353	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182555353C>T	uc001gpj.1	-	1	756	c.589G>A	c.(589-591)GCC>ACC	p.A197T	RNASEL_uc009wxz.1_Missense_Mutation_p.A197T|RNASEL_uc001gpk.2_Missense_Mutation_p.A197T|RNASEL_uc009wya.1_Missense_Mutation_p.A197T	NM_021133	NP_066956	Q05823	RN5A_HUMAN	ribonuclease L	197	ANK 5.				mRNA processing|response to virus|type I interferon-mediated signaling pathway	mitochondrion	ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|metal ion binding|protein kinase activity|RNA binding			ovary(4)|stomach(1)	5														Hereditary_Prostate_Cancer				---	---	---	---
DHX9	1660	broad.mit.edu	37	1	182850519	182850519	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182850519C>T	uc001gpr.2	+	23	2908	c.2745C>T	c.(2743-2745)CAC>CAT	p.H915H	DHX9_uc001gps.2_Silent_p.H701H|DHX9_uc001gpt.2_Silent_p.H194H|DHX9_uc009wyd.2_Translation_Start_Site	NM_001357	NP_001348	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 9	915					CRD-mediated mRNA stabilization|nuclear mRNA splicing, via spliceosome	centrosome|CRD-mediated mRNA stability complex|nucleolus|nucleoplasm|ribonucleoprotein complex	ATP binding|ATP-dependent DNA helicase activity|ATP-dependent RNA helicase activity|DNA binding|double-stranded RNA binding|protein binding			ovary(2)	2																		---	---	---	---
LAMC1	3915	broad.mit.edu	37	1	183072544	183072544	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183072544G>A	uc001gpy.3	+	2	757	c.500G>A	c.(499-501)CGG>CAG	p.R167Q	LAMC1_uc001gpx.2_Missense_Mutation_p.R167Q	NM_002293	NP_002284	P11047	LAMC1_HUMAN	laminin, gamma 1 precursor	167	Laminin N-terminal.				axon guidance|cell migration|endoderm development|extracellular matrix disassembly|hemidesmosome assembly|positive regulation of epithelial cell proliferation|protein complex assembly|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	extracellular matrix structural constituent			ovary(3)|large_intestine(1)|kidney(1)	5					Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
LAMC1	3915	broad.mit.edu	37	1	183099625	183099625	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183099625C>T	uc001gpy.3	+	19	3684	c.3427C>T	c.(3427-3429)CGG>TGG	p.R1143W		NM_002293	NP_002284	P11047	LAMC1_HUMAN	laminin, gamma 1 precursor	1143	Potential.|Domain II and I.				axon guidance|cell migration|endoderm development|extracellular matrix disassembly|hemidesmosome assembly|positive regulation of epithelial cell proliferation|protein complex assembly|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	extracellular matrix structural constituent			ovary(3)|large_intestine(1)|kidney(1)	5					Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
LAMC2	3918	broad.mit.edu	37	1	183197680	183197680	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:183197680G>A	uc001gqa.2	+	11	1954	c.1640G>A	c.(1639-1641)GGC>GAC	p.G547D	LAMC2_uc001gpz.3_Missense_Mutation_p.G547D|LAMC2_uc010poa.1_Missense_Mutation_p.G247D	NM_005562	NP_005553	Q13753	LAMC2_HUMAN	laminin, gamma 2 isoform a precursor	547	Laminin EGF-like 7.				cell adhesion|epidermis development|hemidesmosome assembly		heparin binding			skin(2)|ovary(1)	3																OREG0014041	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
C1orf21	81563	broad.mit.edu	37	1	184476827	184476827	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:184476827A>G	uc001gqv.1	+							NM_030806	NP_110433			chromosome 1 open reading frame 21												0		Breast(1374;0.00262)		Colorectal(1306;4.8e-08)|KIRC - Kidney renal clear cell carcinoma(1967;0.00314)														---	---	---	---
C1orf26	54823	broad.mit.edu	37	1	185143556	185143556	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185143556T>C	uc001grg.3	+	5	391	c.277T>C	c.(277-279)TCC>CCC	p.S93P	C1orf26_uc001grh.3_Missense_Mutation_p.S93P	NM_001105518	NP_001098988	Q5T5J6	SWT1_HUMAN	hypothetical protein LOC54823	93											0																		---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	185939509	185939509	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185939509C>A	uc001grq.1	+	15	2484	c.2255C>A	c.(2254-2256)CCT>CAT	p.P752H	HMCN1_uc001grr.1_Missense_Mutation_p.P93H	NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	752	Ig-like C2-type 4.				response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23																		---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	185985147	185985147	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:185985147C>T	uc001grq.1	+	32	5196	c.4967C>T	c.(4966-4968)GCT>GTT	p.A1656V		NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	1656	Ig-like C2-type 14.				response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23																		---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	186084476	186084476	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186084476C>A	uc001grq.1	+	75	11720	c.11491C>A	c.(11491-11493)CCA>ACA	p.P3831T		NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	3831	Ig-like C2-type 37.				response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23																		---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	186092281	186092281	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186092281C>T	uc001grq.1	+	81	12657	c.12428C>T	c.(12427-12429)GCT>GTT	p.A4143V		NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	4143	Ig-like C2-type 40.				response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23																		---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	186099812	186099812	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186099812G>A	uc001grq.1	+	85	13442	c.13213G>A	c.(13213-13215)GCC>ACC	p.A4405T	HMCN1_uc001grs.1_5'UTR	NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	4405	Ig-like C2-type 43.				response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23																		---	---	---	---
HMCN1	83872	broad.mit.edu	37	1	186143721	186143721	+	Missense_Mutation	SNP	G	A	A	rs138984150		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186143721G>A	uc001grq.1	+	103	16119	c.15890G>A	c.(15889-15891)CGT>CAT	p.R5297H	HMCN1_uc001grs.1_Missense_Mutation_p.R866H	NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	5297	EGF-like 5; calcium-binding (Potential).				response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23																		---	---	---	---
PRG4	10216	broad.mit.edu	37	1	186270782	186270782	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186270782C>T	uc001gru.3	+	4	309	c.258C>T	c.(256-258)TGC>TGT	p.C86C	PRG4_uc001grt.3_Silent_p.C45C|PRG4_uc009wyl.2_Silent_p.C86C|PRG4_uc009wym.2_Silent_p.C45C|PRG4_uc010poo.1_RNA	NM_005807	NP_005798	Q92954	PRG4_HUMAN	proteoglycan 4 isoform A	86	SMB 2.				cell proliferation|immune response	extracellular region	polysaccharide binding|protein binding|scavenger receptor activity			skin(1)	1																		---	---	---	---
PRG4	10216	broad.mit.edu	37	1	186275899	186275899	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186275899C>A	uc001gru.3	+	7	1099	c.1048C>A	c.(1048-1050)CCC>ACC	p.P350T	PRG4_uc001grt.3_Missense_Mutation_p.P309T|PRG4_uc009wyl.2_Missense_Mutation_p.P257T|PRG4_uc009wym.2_Missense_Mutation_p.P216T|PRG4_uc010poo.1_RNA	NM_005807	NP_005798	Q92954	PRG4_HUMAN	proteoglycan 4 isoform A	350	59 X 8 AA repeats of K-X-P-X-P-T-T-X.|1.				cell proliferation|immune response	extracellular region	polysaccharide binding|protein binding|scavenger receptor activity			skin(1)	1																		---	---	---	---
PTGS2	5743	broad.mit.edu	37	1	186648497	186648497	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186648497G>A	uc001gsb.2	-	2	263	c.126C>T	c.(124-126)TGC>TGT	p.C42C	PTGS2_uc009wyo.2_5'UTR	NM_000963	NP_000954	P35354	PGH2_HUMAN	prostaglandin-endoperoxide synthase 2 precursor	42	EGF-like.				cellular component movement|cyclooxygenase pathway|hormone biosynthetic process|positive regulation of brown fat cell differentiation|positive regulation of cell migration involved in sprouting angiogenesis|positive regulation of fever generation|positive regulation of fibroblast growth factor production|positive regulation of nitric oxide biosynthetic process|positive regulation of platelet-derived growth factor production|positive regulation of prostaglandin biosynthetic process|positive regulation of transforming growth factor-beta production|positive regulation vascular endothelial growth factor production|regulation of blood pressure|response to oxidative stress|xenobiotic metabolic process	endoplasmic reticulum lumen|endoplasmic reticulum membrane|microsome|neuron projection|nucleus	enzyme binding|heme binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peroxidase activity|prostaglandin-endoperoxide synthase activity			ovary(1)|central_nervous_system(1)	2					Acetaminophen(DB00316)|Aspirin(DB00945)|Balsalazide(DB01014)|Bromfenac(DB00963)|Carprofen(DB00821)|Celecoxib(DB00482)|Ciclopirox(DB01188)|Diclofenac(DB00586)|Diflunisal(DB00861)|Epoprostenol(DB01240)|Etodolac(DB00749)|Etoricoxib(DB01628)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|gamma-Homolinolenic acid(DB00154)|Ginseng(DB01404)|Ibuprofen(DB01050)|Icosapent(DB00159)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lenalidomide(DB00480)|Lumiracoxib(DB01283)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mesalazine(DB00244)|Nabumetone(DB00461)|Naproxen(DB00788)|Oxaprozin(DB00991)|Phenylbutazone(DB00812)|Rofecoxib(DB00533)|Salicyclic acid(DB00936)|Salsalate(DB01399)|Sulindac(DB00605)|Suprofen(DB00870)|Tenoxicam(DB00469)|Thalidomide(DB01041)|Tiaprofenic acid(DB01600)|Tolmetin(DB00500)|Valdecoxib(DB00580)													---	---	---	---
FAM5C	339479	broad.mit.edu	37	1	190068013	190068013	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:190068013G>A	uc001gse.1	-	8	1668	c.1436C>T	c.(1435-1437)GCC>GTC	p.A479V	FAM5C_uc010pot.1_Missense_Mutation_p.A377V	NM_199051	NP_950252	Q76B58	FAM5C_HUMAN	family with sequence similarity 5, member C	479						extracellular region				lung(2)|ovary(1)|kidney(1)|skin(1)	5	Prostate(682;0.198)																	---	---	---	---
TROVE2	6738	broad.mit.edu	37	1	193038232	193038232	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:193038232A>G	uc001gss.2	+	2	223	c.48A>G	c.(46-48)ATA>ATG	p.I16M	TROVE2_uc001gst.1_Intron|TROVE2_uc001gsu.1_Intron|TROVE2_uc001gsv.1_Missense_Mutation_p.I16M|TROVE2_uc001gsw.2_Missense_Mutation_p.I16M|TROVE2_uc009wyp.2_Missense_Mutation_p.I16M|TROVE2_uc009wyq.2_Missense_Mutation_p.I16M|TROVE2_uc001gsx.1_Missense_Mutation_p.I16M	NM_004600	NP_004591	P10155	RO60_HUMAN	TROVE domain family, member 2 isoform 2	16	TROVE.				transcription from RNA polymerase III promoter	cytoplasm|nucleus|ribonucleoprotein complex	protein binding|RNA binding				0																		---	---	---	---
CFH	3075	broad.mit.edu	37	1	196711077	196711077	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:196711077C>T	uc001gtj.3	+	19	3269	c.3029C>T	c.(3028-3030)GCG>GTG	p.A1010V		NM_000186	NP_000177	P08603	CFAH_HUMAN	complement factor H isoform a precursor	1010	Sushi 17.				complement activation, alternative pathway	extracellular space				skin(4)|ovary(1)|breast(1)	6																		---	---	---	---
ASPM	259266	broad.mit.edu	37	1	197072532	197072532	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197072532G>A	uc001gtu.2	-	18	6106	c.5849C>T	c.(5848-5850)GCG>GTG	p.A1950V	ASPM_uc001gtv.2_Intron|ASPM_uc001gtw.3_Intron	NM_018136	NP_060606	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle)-like, microcephaly	1950	IQ 12.				mitosis	cytoplasm|nucleus	calmodulin binding			ovary(4)|central_nervous_system(2)	6																		---	---	---	---
ZBTB41	360023	broad.mit.edu	37	1	197150225	197150225	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197150225A>G	uc001gtx.1	-	5	1638	c.1569T>C	c.(1567-1569)TGT>TGC	p.C523C	ZBTB41_uc009wyz.1_RNA	NM_194314	NP_919290	Q5SVQ8	ZBT41_HUMAN	zinc finger and BTB domain containing 41	523	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
CRB1	23418	broad.mit.edu	37	1	197390520	197390520	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:197390520C>T	uc001gtz.2	+	6	1697	c.1562C>T	c.(1561-1563)GCT>GTT	p.A521V	CRB1_uc010poz.1_Missense_Mutation_p.A452V|CRB1_uc010ppa.1_RNA|CRB1_uc009wza.2_Missense_Mutation_p.A409V|CRB1_uc010ppb.1_Missense_Mutation_p.A521V|CRB1_uc010ppc.1_RNA|CRB1_uc010ppd.1_Missense_Mutation_p.A2V|CRB1_uc001gub.1_Missense_Mutation_p.A170V	NM_201253	NP_957705	P82279	CRUM1_HUMAN	crumbs homolog 1 precursor	521	Extracellular (Potential).|Laminin G-like 1.				cell-cell signaling|establishment or maintenance of cell polarity	apical plasma membrane|extracellular region|integral to membrane	calcium ion binding|protein binding			ovary(5)|skin(3)|large_intestine(1)	9																		---	---	---	---
PTPRC	5788	broad.mit.edu	37	1	198668745	198668745	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198668745G>A	uc001gur.1	+	5	525	c.345G>A	c.(343-345)ACG>ACA	p.T115T	PTPRC_uc001gus.1_Silent_p.T115T|PTPRC_uc001gut.1_Intron|PTPRC_uc009wze.1_Silent_p.T51T|PTPRC_uc009wzf.1_Silent_p.T51T|PTPRC_uc010ppg.1_Silent_p.T51T|PTPRC_uc001guu.1_Silent_p.T158T|PTPRC_uc001guv.1_RNA|PTPRC_uc001guw.1_RNA	NM_002838	NP_002829	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	115	Extracellular (Potential).				axon guidance|B cell proliferation|B cell receptor signaling pathway|defense response to virus|immunoglobulin biosynthetic process|negative regulation of cytokine-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of T cell mediated cytotoxicity|positive regulation of antigen receptor-mediated signaling pathway|positive regulation of B cell proliferation|positive regulation of protein kinase activity|positive regulation of T cell proliferation|regulation of S phase|release of sequestered calcium ion into cytosol|T cell differentiation|T cell receptor signaling pathway	focal adhesion|integral to plasma membrane|membrane raft	protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			breast(4)|skin(3)|ovary(2)|lung(1)|kidney(1)|pancreas(1)	12																OREG0014061	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
KIF14	9928	broad.mit.edu	37	1	200584728	200584728	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200584728A>G	uc010ppk.1	-	3	1561	c.1122T>C	c.(1120-1122)ATT>ATC	p.I374I	KIF14_uc010ppj.1_5'UTR	NM_014875	NP_055690	Q15058	KIF14_HUMAN	kinesin family member 14	374	Kinesin-motor.				microtubule-based movement	cytoplasm|microtubule|nucleus|spindle	ATP binding|microtubule motor activity|protein binding			breast(3)|ovary(2)|skin(2)	7																		---	---	---	---
KIF21B	23046	broad.mit.edu	37	1	200960099	200960099	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:200960099T>G	uc001gvs.1	-	18	2950	c.2633A>C	c.(2632-2634)AAC>ACC	p.N878T	KIF21B_uc001gvr.1_Missense_Mutation_p.N878T|KIF21B_uc009wzl.1_Missense_Mutation_p.N878T|KIF21B_uc010ppn.1_Missense_Mutation_p.N878T	NM_017596	NP_060066	O75037	KI21B_HUMAN	kinesin family member 21B	878					microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)|skin(3)	6																		---	---	---	---
IGFN1	91156	broad.mit.edu	37	1	201195043	201195043	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201195043G>T	uc001gwc.2	+	11	2830	c.2058G>T	c.(2056-2058)CAG>CAT	p.Q686H	IGFN1_uc001gwb.2_RNA	NM_178275	NP_840059			RecName: Full=Immunoglobulin-like and fibronectin type III domain-containing protein 1; AltName: Full=EEF1A2-binding protein 1; AltName: Full=KY-interacting protein 1;											ovary(2)|pancreas(1)	3																		---	---	---	---
PKP1	5317	broad.mit.edu	37	1	201286876	201286876	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201286876C>T	uc001gwd.2	+	5	1274	c.1023C>T	c.(1021-1023)ACC>ACT	p.T341T	PKP1_uc001gwe.2_Silent_p.T341T|PKP1_uc009wzm.2_5'UTR	NM_000299	NP_000290	Q13835	PKP1_HUMAN	plakophilin 1 isoform 1b	341	ARM 3.				cell adhesion|cellular component disassembly involved in apoptosis|multicellular organismal development	desmosome|intermediate filament|nucleus	intermediate filament binding|signal transducer activity|structural constituent of epidermis			ovary(2)	2																		---	---	---	---
NAV1	89796	broad.mit.edu	37	1	201618360	201618360	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201618360G>A	uc001gwu.2	+	1	911	c.564G>A	c.(562-564)GCG>GCA	p.A188A		NM_020443	NP_065176	Q8NEY1	NAV1_HUMAN	neuron navigator 1	188					cell differentiation|nervous system development	cytoplasm|microtubule	nucleoside-triphosphatase activity|nucleotide binding			central_nervous_system(3)|ovary(1)	4																		---	---	---	---
LMOD1	25802	broad.mit.edu	37	1	201869880	201869880	+	Splice_Site	SNP	C	T	T	rs113789040		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:201869880C>T	uc001gxb.2	-	2	510	c.262_splice	c.e2-1	p.E88_splice	LMOD1_uc010ppu.1_Splice_Site_p.E88_splice	NM_012134	NP_036266			leiomodin 1 (smooth muscle)						muscle contraction	cytoskeleton|cytosol|membrane fraction	tropomyosin binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
GPR37L1	9283	broad.mit.edu	37	1	202092141	202092141	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202092141T>C	uc001gxj.2	+	1	113	c.50T>C	c.(49-51)GTG>GCG	p.V17A		NM_004767	NP_004758	O60883	ETBR2_HUMAN	G-protein coupled receptor 37 like 1 precursor	17						integral to membrane|plasma membrane	G-protein coupled receptor activity|protein binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
GPR37L1	9283	broad.mit.edu	37	1	202092502	202092502	+	Silent	SNP	G	A	A	rs114153525	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202092502G>A	uc001gxj.2	+	1	474	c.411G>A	c.(409-411)GCG>GCA	p.A137A		NM_004767	NP_004758	O60883	ETBR2_HUMAN	G-protein coupled receptor 37 like 1 precursor	137	Helical; Name=1; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity|protein binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
PPP1R12B	4660	broad.mit.edu	37	1	202406937	202406937	+	Intron	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202406937C>A	uc001gya.1	+						PPP1R12B_uc001gxy.2_Intron|PPP1R12B_uc009xad.1_Intron|PPP1R12B_uc009xae.1_Intron|PPP1R12B_uc001gxz.1_Intron	NM_002481	NP_002472			protein phosphatase 1, regulatory (inhibitor)						regulation of muscle contraction|signal transduction	cytoplasm	enzyme activator activity			ovary(3)	3			BRCA - Breast invasive adenocarcinoma(75;0.166)															---	---	---	---
PRELP	5549	broad.mit.edu	37	1	203453207	203453207	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203453207T>C	uc001gzs.2	+	2	1095	c.895T>C	c.(895-897)TCC>CCC	p.S299P	PRELP_uc001gzt.2_Missense_Mutation_p.S299P	NM_002725	NP_002716	P51888	PRELP_HUMAN	proline arginine-rich end leucine-rich repeat	299	LRR 9.				skeletal system development	proteinaceous extracellular matrix	extracellular matrix structural constituent			ovary(1)|central_nervous_system(1)|pancreas(1)	3			BRCA - Breast invasive adenocarcinoma(75;0.109)															---	---	---	---
ATP2B4	493	broad.mit.edu	37	1	203693125	203693125	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203693125C>T	uc001gzw.2	+						ATP2B4_uc001gzv.2_Intron|ATP2B4_uc009xaq.2_Intron|ATP2B4_uc001gzx.2_Intron|ATP2B4_uc009xar.2_Intron	NM_001684	NP_001675			plasma membrane calcium ATPase 4 isoform 4b						ATP biosynthetic process|platelet activation	integral to plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding|protein binding			ovary(2)|skin(1)	3	all_cancers(21;0.071)|all_epithelial(62;0.228)		BRCA - Breast invasive adenocarcinoma(75;0.109)															---	---	---	---
ZC3H11A	9877	broad.mit.edu	37	1	203787717	203787717	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203787717G>A	uc001hac.2	+	6	690	c.74G>A	c.(73-75)CGT>CAT	p.R25H	ZC3H11A_uc001had.2_Missense_Mutation_p.R25H|ZC3H11A_uc001hae.2_Missense_Mutation_p.R25H|ZC3H11A_uc001haf.2_Missense_Mutation_p.R25H|ZC3H11A_uc010pqm.1_5'UTR|ZC3H11A_uc001hag.1_Missense_Mutation_p.R25H	NM_014827	NP_055642	O75152	ZC11A_HUMAN	zinc finger CCCH-type containing 11A	25	C3H1-type 1.						nucleic acid binding|protein binding|zinc ion binding			lung(1)|central_nervous_system(1)	2	all_cancers(21;0.0904)|all_epithelial(62;0.234)		BRCA - Breast invasive adenocarcinoma(75;0.109)															---	---	---	---
ZC3H11A	9877	broad.mit.edu	37	1	203816757	203816757	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203816757G>A	uc001hac.2	+	15	2104	c.1488G>A	c.(1486-1488)CCG>CCA	p.P496P	ZC3H11A_uc001had.2_Silent_p.P496P|ZC3H11A_uc001hae.2_Silent_p.P496P|ZC3H11A_uc001haf.2_Silent_p.P496P|ZC3H11A_uc010pqm.1_Silent_p.P442P|ZC3H11A_uc001hag.1_Silent_p.P496P	NM_014827	NP_055642	O75152	ZC11A_HUMAN	zinc finger CCCH-type containing 11A	496							nucleic acid binding|protein binding|zinc ion binding			lung(1)|central_nervous_system(1)	2	all_cancers(21;0.0904)|all_epithelial(62;0.234)		BRCA - Breast invasive adenocarcinoma(75;0.109)															---	---	---	---
PLEKHA6	22874	broad.mit.edu	37	1	204214755	204214755	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204214755C>T	uc001hau.2	-	14	2337	c.2020G>A	c.(2020-2022)GCC>ACC	p.A674T	PLEKHA6_uc009xau.1_5'Flank|PLEKHA6_uc009xav.1_5'Flank	NM_014935	NP_055750	Q9Y2H5	PKHA6_HUMAN	phosphoinositol 3-phosphate-binding protein-3	674										ovary(3)|pancreas(1)	4	all_cancers(21;0.0222)|Breast(84;0.179)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.229)															---	---	---	---
PIK3C2B	5287	broad.mit.edu	37	1	204403694	204403694	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204403694C>A	uc001haw.2	-	25	4038	c.3559G>T	c.(3559-3561)GCC>TCC	p.A1187S	PIK3C2B_uc010pqv.1_Missense_Mutation_p.A1159S	NM_002646	NP_002637	O00750	P3C2B_HUMAN	phosphoinositide-3-kinase, class 2 beta	1187	PI3K/PI4K.				cell communication|phosphatidylinositol-mediated signaling	endoplasmic reticulum|microsome|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity|protein binding			lung(2)|breast(2)|stomach(1)|prostate(1)|central_nervous_system(1)	7	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)															---	---	---	---
PIK3C2B	5287	broad.mit.edu	37	1	204434433	204434433	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204434433G>T	uc001haw.2	-	4	1427	c.948C>A	c.(946-948)CCC>CCA	p.P316P	PIK3C2B_uc010pqv.1_Silent_p.P316P|PIK3C2B_uc001hax.1_Silent_p.P316P|PIK3C2B_uc009xbd.1_RNA	NM_002646	NP_002637	O00750	P3C2B_HUMAN	phosphoinositide-3-kinase, class 2 beta	316					cell communication|phosphatidylinositol-mediated signaling	endoplasmic reticulum|microsome|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity|protein binding			lung(2)|breast(2)|stomach(1)|prostate(1)|central_nervous_system(1)	7	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)															---	---	---	---
LRRN2	10446	broad.mit.edu	37	1	204587709	204587709	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204587709C>T	uc001hbe.1	-	3	1800	c.1412G>A	c.(1411-1413)GGC>GAC	p.G471D	MDM4_uc001hbd.1_Intron|LRRN2_uc001hbf.1_Missense_Mutation_p.G471D|LRRN2_uc009xbf.1_Missense_Mutation_p.G471D|MDM4_uc001hbc.2_Intron	NM_006338	NP_006329	O75325	LRRN2_HUMAN	leucine rich repeat neuronal 2 precursor	471	Ig-like C2-type.|Extracellular (Potential).				cell adhesion	integral to membrane	receptor activity			central_nervous_system(2)	2	all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)															---	---	---	---
LRRN2	10446	broad.mit.edu	37	1	204587983	204587983	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204587983C>T	uc001hbe.1	-	3	1526	c.1138G>A	c.(1138-1140)GCC>ACC	p.A380T	MDM4_uc001hbd.1_Intron|LRRN2_uc001hbf.1_Missense_Mutation_p.A380T|LRRN2_uc009xbf.1_Missense_Mutation_p.A380T|MDM4_uc001hbc.2_Intron	NM_006338	NP_006329	O75325	LRRN2_HUMAN	leucine rich repeat neuronal 2 precursor	380	Extracellular (Potential).|LRRCT.				cell adhesion	integral to membrane	receptor activity			central_nervous_system(2)	2	all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)															---	---	---	---
NFASC	23114	broad.mit.edu	37	1	204943372	204943372	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204943372C>T	uc001hbj.2	+	13	1673	c.1345C>T	c.(1345-1347)CGG>TGG	p.R449W	NFASC_uc001hbh.2_Missense_Mutation_p.R449W|NFASC_uc010pqz.1_Missense_Mutation_p.R443W|NFASC_uc010pra.1_Missense_Mutation_p.R460W|NFASC_uc001hbi.2_Missense_Mutation_p.R460W|NFASC_uc009xbg.1_Missense_Mutation_p.R533W|NFASC_uc010prb.1_Missense_Mutation_p.R460W|NFASC_uc010prc.1_5'UTR|NFASC_uc001hbk.1_Missense_Mutation_p.R270W	NM_001005388	NP_001005388	O94856	NFASC_HUMAN	neurofascin isoform 1 precursor	449	Extracellular (Potential).|Ig-like C2-type 5.				axon guidance|cell adhesion|myelination|peripheral nervous system development	integral to membrane|node of Ranvier|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)															---	---	---	---
NFASC	23114	broad.mit.edu	37	1	204971842	204971842	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204971842C>T	uc001hbj.2	+	27	3583	c.3255C>T	c.(3253-3255)ATC>ATT	p.I1085I	NFASC_uc010pra.1_Intron|NFASC_uc001hbi.2_Intron|NFASC_uc010prb.1_Intron|NFASC_uc010prc.1_Intron|NFASC_uc001hbl.1_Intron|NFASC_uc001hbm.1_Silent_p.I108I|NFASC_uc009xbh.1_Intron	NM_001005388	NP_001005388	O94856	NFASC_HUMAN	neurofascin isoform 1 precursor	1192	Extracellular (Potential).|Fibronectin type-III 5.				axon guidance|cell adhesion|myelination|peripheral nervous system development	integral to membrane|node of Ranvier|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)															---	---	---	---
NFASC	23114	broad.mit.edu	37	1	204985482	204985482	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:204985482G>T	uc001hbj.2	+	30	3866	c.3538G>T	c.(3538-3540)GGC>TGC	p.G1180C	NFASC_uc010pra.1_Missense_Mutation_p.G1114C|NFASC_uc001hbi.2_Missense_Mutation_p.G1109C|NFASC_uc010prb.1_Missense_Mutation_p.G1129C|NFASC_uc010prc.1_Missense_Mutation_p.G680C|NFASC_uc001hbl.1_Missense_Mutation_p.G256C|NFASC_uc001hbm.1_Missense_Mutation_p.G203C|NFASC_uc009xbh.1_Silent_p.T34T|NFASC_uc001hbo.1_Silent_p.T55T	NM_001005388	NP_001005388	O94856	NFASC_HUMAN	neurofascin isoform 1 precursor	1287	Cytoplasmic (Potential).				axon guidance|cell adhesion|myelination|peripheral nervous system development	integral to membrane|node of Ranvier|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)															---	---	---	---
DSTYK	25778	broad.mit.edu	37	1	205126424	205126424	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205126424C>T	uc001hbw.2	-	10	2393	c.2329G>A	c.(2329-2331)GAT>AAT	p.D777N	DSTYK_uc001hbx.2_Missense_Mutation_p.D777N	NM_015375	NP_056190	Q6XUX3	DUSTY_HUMAN	receptor interacting protein kinase 5 isoform 1	777	Protein kinase.	Proton acceptor (By similarity).				cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(1)	1																		---	---	---	---
NUAK2	81788	broad.mit.edu	37	1	205272901	205272901	+	Missense_Mutation	SNP	C	T	T	rs116631538	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205272901C>T	uc001hce.2	-	7	1691	c.1564G>A	c.(1564-1566)GGC>AGC	p.G522S		NM_030952	NP_112214	Q9H093	NUAK2_HUMAN	NUAK family, SNF1-like kinase, 2	522					actin cytoskeleton organization|apoptosis|cellular response to glucose starvation|negative regulation of apoptosis		ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(3)|stomach(1)|breast(1)	5	Breast(84;0.186)		BRCA - Breast invasive adenocarcinoma(75;0.117)															---	---	---	---
KLHDC8A	55220	broad.mit.edu	37	1	205306634	205306634	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205306634G>A	uc001hcf.1	-	6	1514	c.946C>T	c.(946-948)CGC>TGC	p.R316C	KLHDC8A_uc010prg.1_Missense_Mutation_p.R203C|KLHDC8A_uc001hcg.1_Missense_Mutation_p.R316C	NM_018203	NP_060673	Q8IYD2	KLD8A_HUMAN	kelch domain containing 8A	316	Kelch 7.									ovary(1)	1	Breast(84;0.23)		BRCA - Breast invasive adenocarcinoma(75;0.117)															---	---	---	---
ELK4	2005	broad.mit.edu	37	1	205589425	205589425	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205589425G>A	uc001hcy.1	-	3	1999	c.749C>T	c.(748-750)GCC>GTC	p.A250V	ELK4_uc001hcz.2_Missense_Mutation_p.A250V	NM_001973	NP_001964	P28324	ELK4_HUMAN	ELK4 protein isoform a	250						cytoplasm|nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity				0	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0908)					T	SLC45A3	prostate								---	---	---	---
C1orf186	440712	broad.mit.edu	37	1	206239446	206239446	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206239446G>T	uc001hdt.1	-	6	1091	c.452C>A	c.(451-453)CCC>CAC	p.P151H		NM_001007544	NP_001007545	Q6ZWK4	CA186_HUMAN	hypothetical protein LOC440712	151						integral to membrane					0			BRCA - Breast invasive adenocarcinoma(75;0.0754)															---	---	---	---
CTSE	1510	broad.mit.edu	37	1	206318339	206318339	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206318339A>G	uc001hdu.2	+	2	215	c.97A>G	c.(97-99)AAG>GAG	p.K33E	CTSE_uc001hdv.2_Missense_Mutation_p.K33E|CTSE_uc010prs.1_Intron	NM_001910	NP_001901	P14091	CATE_HUMAN	cathepsin E isoform a preproprotein	33					antigen processing and presentation of exogenous peptide antigen via MHC class II|digestion|proteolysis	endosome	aspartic-type endopeptidase activity			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(75;0.0754)															---	---	---	---
IL19	29949	broad.mit.edu	37	1	207010317	207010317	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207010317C>A	uc001hep.2	+	4	1098	c.159C>A	c.(157-159)ACC>ACA	p.T53T	IL19_uc001heo.2_Silent_p.T91T|IL19_uc010prx.1_Silent_p.T53T	NM_013371	NP_037503	Q9UHD0	IL19_HUMAN	interleukin 19 isoform 2 precursor	53					apoptosis|immune response|signal transduction	extracellular space	cytokine activity			ovary(1)|central_nervous_system(1)	2			BRCA - Breast invasive adenocarcinoma(75;0.211)															---	---	---	---
MIR29B2	407025	broad.mit.edu	37	1	207975799	207975799	+	RNA	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:207975799C>T	hsa-mir-29b-2|MI0000107	-			c.70C>T			uc001hgr.2_RNA|uc009xcm.1_RNA|MIR29C_hsa-mir-29c|MI0000735_5'Flank																	0																		---	---	---	---
CAMK1G	57172	broad.mit.edu	37	1	209785375	209785375	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209785375G>T	uc001hhd.2	+	11	1256	c.1154G>T	c.(1153-1155)GGT>GTT	p.G385V	CAMK1G_uc001hhf.3_Missense_Mutation_p.G385V|CAMK1G_uc001hhe.2_Missense_Mutation_p.G385V	NM_020439	NP_065172	Q96NX5	KCC1G_HUMAN	calcium/calmodulin-dependent protein kinase IG	385						Golgi membrane|plasma membrane	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			breast(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.0475)														---	---	---	---
LAMB3	3914	broad.mit.edu	37	1	209800865	209800865	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209800865G>A	uc001hhg.2	-	11	1738	c.1348C>T	c.(1348-1350)CGC>TGC	p.R450C	LAMB3_uc009xco.2_Missense_Mutation_p.R450C|LAMB3_uc001hhh.2_Missense_Mutation_p.R450C|LAMB3_uc010psl.1_RNA	NM_001017402	NP_001017402	Q13751	LAMB3_HUMAN	laminin, beta 3 precursor	450	Laminin EGF-like 4.		R -> C (in a colorectal cancer sample; somatic mutation).		cell adhesion|epidermis development|hemidesmosome assembly		structural molecule activity	p.R450C(1)		central_nervous_system(2)|skin(2)|large_intestine(1)|ovary(1)	6				OV - Ovarian serous cystadenocarcinoma(81;0.0519)												OREG0014217	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
C1orf107	27042	broad.mit.edu	37	1	210010156	210010156	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210010156T>C	uc001hhr.1	+	6	738	c.662T>C	c.(661-663)CTG>CCG	p.L221P	C1orf107_uc009xcu.1_5'UTR	NM_014388	NP_055203	Q68CQ4	DIEXF_HUMAN	digestive-organ expansion factor homolog	221					multicellular organismal development	nucleus					0				OV - Ovarian serous cystadenocarcinoma(81;0.0367)														---	---	---	---
SYT14	255928	broad.mit.edu	37	1	210273673	210273673	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210273673G>A	uc009xcv.2	+	6	1103	c.1031G>A	c.(1030-1032)CGG>CAG	p.R344Q	SYT14_uc001hhs.3_Missense_Mutation_p.R389Q|SYT14_uc001hht.3_Missense_Mutation_p.R344Q|SYT14_uc001hhu.3_Intron|SYT14_uc010psn.1_Missense_Mutation_p.R389Q|SYT14_uc010pso.1_Missense_Mutation_p.R306Q	NM_153262	NP_694994	Q8NB59	SYT14_HUMAN	synaptotagmin XIV isoform 4	344	Cytoplasmic (Potential).|C2 1.					integral to membrane				ovary(1)|skin(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.085)														---	---	---	---
KCNH1	3756	broad.mit.edu	37	1	210857128	210857128	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:210857128A>G	uc001hib.2	-	11	2635	c.2465T>C	c.(2464-2466)CTG>CCG	p.L822P	KCNH1_uc001hic.2_Missense_Mutation_p.L795P	NM_172362	NP_758872	O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H,	822	Cytoplasmic (Potential).				myoblast fusion|regulation of transcription, DNA-dependent	voltage-gated potassium channel complex	calmodulin binding|delayed rectifier potassium channel activity|two-component sensor activity			ovary(4)|central_nervous_system(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)														---	---	---	---
RCOR3	55758	broad.mit.edu	37	1	211451496	211451496	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211451496A>G	uc001hig.2	+	5	549	c.380A>G	c.(379-381)TAC>TGC	p.Y127C	RCOR3_uc010psv.1_RNA|RCOR3_uc001hie.2_Missense_Mutation_p.Y185C|RCOR3_uc010psw.1_Missense_Mutation_p.Y185C|RCOR3_uc001hif.2_Missense_Mutation_p.Y185C	NM_018254	NP_060724	Q9P2K3	RCOR3_HUMAN	REST corepressor 3 isoform d	127	SANT 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(81;0.00961)|all cancers(67;0.0999)|Epithelial(68;0.171)														---	---	---	---
INTS7	25896	broad.mit.edu	37	1	212161258	212161258	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212161258C>T	uc001hiw.1	-	8	1072	c.967G>A	c.(967-969)GCC>ACC	p.A323T	INTS7_uc009xdb.1_Missense_Mutation_p.A323T|INTS7_uc001hix.1_Missense_Mutation_p.A199T|INTS7_uc001hiy.1_Missense_Mutation_p.A323T|INTS7_uc010pta.1_Missense_Mutation_p.A274T	NM_015434	NP_056249	Q9NVH2	INT7_HUMAN	integrator complex subunit 7	323					snRNA processing	integrator complex	protein binding				0				OV - Ovarian serous cystadenocarcinoma(81;0.00584)|all cancers(67;0.0318)|Epithelial(68;0.0852)														---	---	---	---
BATF3	55509	broad.mit.edu	37	1	212860138	212860138	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212860138G>A	uc001hjl.1	-	3	602	c.379C>T	c.(379-381)CGA>TGA	p.R127*		NM_018664	NP_061134	Q9NR55	BATF3_HUMAN	basic leucine zipper transcription factor,	127					transcription from RNA polymerase II promoter	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity				0				OV - Ovarian serous cystadenocarcinoma(81;0.0046)|all cancers(67;0.00785)|GBM - Glioblastoma multiforme(131;0.0731)|Epithelial(68;0.0781)														---	---	---	---
TATDN3	128387	broad.mit.edu	37	1	212977715	212977715	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:212977715G>A	uc001hjo.2	+	6	469	c.375G>A	c.(373-375)GAG>GAA	p.E125E	TATDN3_uc010ptj.1_Silent_p.E125E|TATDN3_uc010ptk.1_Silent_p.E125E|TATDN3_uc001hjp.2_Silent_p.E125E|TATDN3_uc010ptl.1_Silent_p.E104E|TATDN3_uc010ptm.1_Silent_p.E73E	NM_001042552	NP_001036017	Q17R31	TATD3_HUMAN	TatD DNase domain containing 3 isoform 1	125						nucleus	endodeoxyribonuclease activity, producing 5'-phosphomonoesters|metal ion binding				0				OV - Ovarian serous cystadenocarcinoma(81;0.00699)|all cancers(67;0.0118)|GBM - Glioblastoma multiforme(131;0.0801)|Epithelial(68;0.104)														---	---	---	---
RPS6KC1	26750	broad.mit.edu	37	1	213436144	213436144	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:213436144C>A	uc010ptr.1	+	14	3234	c.3075C>A	c.(3073-3075)CGC>CGA	p.R1025R	RPS6KC1_uc001hkd.2_Silent_p.R1013R|RPS6KC1_uc010pts.1_Silent_p.R813R|RPS6KC1_uc010ptt.1_Silent_p.R813R|RPS6KC1_uc010ptu.1_Silent_p.R844R|RPS6KC1_uc010ptv.1_Silent_p.R560R|RPS6KC1_uc001hke.2_Silent_p.R844R	NM_012424	NP_036556	Q96S38	KS6C1_HUMAN	ribosomal protein S6 kinase, 52kDa, polypeptide	1025	Protein kinase 2.				cell communication|signal transduction	early endosome|membrane	ATP binding|phosphatidylinositol binding|protein binding|protein serine/threonine kinase activity			lung(4)|ovary(3)|breast(1)	8				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)														---	---	---	---
USH2A	7399	broad.mit.edu	37	1	216052239	216052239	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216052239T>G	uc001hku.1	-	42	8812	c.8425A>C	c.(8425-8427)AGT>CGT	p.S2809R		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	2809	Fibronectin type-III 14.|Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)											HNSCC(13;0.011)			---	---	---	---
USH2A	7399	broad.mit.edu	37	1	216260091	216260091	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:216260091G>A	uc001hku.1	-	24	5344	c.4957C>T	c.(4957-4959)CGA>TGA	p.R1653*		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	1653	Laminin G-like 1.|Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)											HNSCC(13;0.011)			---	---	---	---
SLC30A10	55532	broad.mit.edu	37	1	220101406	220101406	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220101406A>C	uc001hlw.2	-	1	588	c.377T>G	c.(376-378)GTC>GGC	p.V126G	SLC30A10_uc001hlu.1_Intron|SLC30A10_uc001hlx.2_5'UTR	NM_018713	NP_061183	Q6XR72	ZNT10_HUMAN	solute carrier family 30 (zinc transporter),	126	Helical; (Potential).				zinc ion transport	integral to membrane|plasma membrane	cation transmembrane transporter activity				0				GBM - Glioblastoma multiforme(131;0.051)|all cancers(67;0.209)														---	---	---	---
BPNT1	10380	broad.mit.edu	37	1	220253154	220253154	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220253154A>G	uc001hma.2	-	2	207	c.35T>C	c.(34-36)GTA>GCA	p.V12A	BPNT1_uc010pug.1_Intron|BPNT1_uc010puh.1_Missense_Mutation_p.V12A|BPNT1_uc001hmb.3_Missense_Mutation_p.V12A	NM_006085	NP_006076	O95861	BPNT1_HUMAN	3'(2'), 5'-bisphosphate nucleotidase 1	12					3'-phosphoadenosine 5'-phosphosulfate metabolic process|nervous system development|xenobiotic metabolic process	cytosol	3'(2'),5'-bisphosphate nucleotidase activity			ovary(1)	1				GBM - Glioblastoma multiforme(131;0.0558)														---	---	---	---
MARK1	4139	broad.mit.edu	37	1	220752789	220752789	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220752789T>C	uc001hmn.3	+	2	742	c.145T>C	c.(145-147)TCA>CCA	p.S49P	MARK1_uc001hml.2_Missense_Mutation_p.S49P|MARK1_uc009xdw.2_Missense_Mutation_p.S49P|MARK1_uc010pun.1_Missense_Mutation_p.S49P|MARK1_uc001hmm.3_Missense_Mutation_p.S49P	NM_018650	NP_061120	Q9P0L2	MARK1_HUMAN	MAP/microtubule affinity-regulating kinase 1	49					intracellular protein kinase cascade	cytoplasm|microtubule cytoskeleton	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(4)|central_nervous_system(2)|skin(2)|stomach(1)|lung(1)	10				GBM - Glioblastoma multiforme(131;0.0407)														---	---	---	---
MARK1	4139	broad.mit.edu	37	1	220773168	220773168	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220773168G>T	uc001hmn.3	+	5	984	c.387G>T	c.(385-387)GAG>GAT	p.E129D	MARK1_uc009xdw.2_Missense_Mutation_p.E129D|MARK1_uc010pun.1_Missense_Mutation_p.E129D|MARK1_uc001hmm.3_Intron	NM_018650	NP_061120	Q9P0L2	MARK1_HUMAN	MAP/microtubule affinity-regulating kinase 1	129	Protein kinase.				intracellular protein kinase cascade	cytoplasm|microtubule cytoskeleton	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(4)|central_nervous_system(2)|skin(2)|stomach(1)|lung(1)	10				GBM - Glioblastoma multiforme(131;0.0407)														---	---	---	---
MARK1	4139	broad.mit.edu	37	1	220835175	220835175	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220835175A>C	uc001hmn.3	+	18	2652	c.2055A>C	c.(2053-2055)AAA>AAC	p.K685N	MARK1_uc009xdw.2_Missense_Mutation_p.K686N|MARK1_uc010pun.1_Missense_Mutation_p.K670N|MARK1_uc001hmm.3_Missense_Mutation_p.K648N	NM_018650	NP_061120	Q9P0L2	MARK1_HUMAN	MAP/microtubule affinity-regulating kinase 1	685					intracellular protein kinase cascade	cytoplasm|microtubule cytoskeleton	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(4)|central_nervous_system(2)|skin(2)|stomach(1)|lung(1)	10				GBM - Glioblastoma multiforme(131;0.0407)														---	---	---	---
MOSC2	54996	broad.mit.edu	37	1	220935141	220935141	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:220935141C>A	uc001hmq.2	+	3	786	c.588C>A	c.(586-588)CCC>CCA	p.P196P	MOSC2_uc001hmr.2_Silent_p.P196P|MOSC2_uc009xdx.2_Silent_p.P196P	NM_017898	NP_060368	Q969Z3	MOSC2_HUMAN	MOCO sulphurase C-terminal domain containing 2	196	MOSC.					mitochondrial outer membrane|peroxisome	molybdenum ion binding|oxidoreductase activity|pyridoxal phosphate binding				0				GBM - Glioblastoma multiforme(131;0.00499)|all cancers(67;0.204)														---	---	---	---
HLX	3142	broad.mit.edu	37	1	221057756	221057756	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:221057756C>T	uc001hmv.3	+	4	1634	c.1177C>T	c.(1177-1179)CGG>TGG	p.R393W		NM_021958	NP_068777	Q14774	HLX_HUMAN	H2.0-like homeobox	393	Ser-rich.				cell differentiation	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2				GBM - Glioblastoma multiforme(131;0.00914)														---	---	---	---
HHIPL2	79802	broad.mit.edu	37	1	222717516	222717516	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:222717516C>T	uc001hnh.1	-	2	395	c.337G>A	c.(337-339)GCA>ACA	p.A113T		NM_024746	NP_079022	Q6UWX4	HIPL2_HUMAN	HHIP-like 2 precursor	113					carbohydrate metabolic process	extracellular region	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor|quinone binding			ovary(1)	1				GBM - Glioblastoma multiforme(131;0.0185)														---	---	---	---
DISP1	84976	broad.mit.edu	37	1	223177973	223177973	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223177973C>T	uc001hnu.1	+	8	3381	c.3234C>T	c.(3232-3234)CGC>CGT	p.R1078R		NM_032890	NP_116279	Q96F81	DISP1_HUMAN	dispatched A	1078					diaphragm development|protein homotrimerization|regulation of protein secretion|smoothened signaling pathway	basolateral plasma membrane|integral to membrane	hedgehog receptor activity|peptide transporter activity				0				GBM - Glioblastoma multiforme(131;0.102)														---	---	---	---
SUSD4	55061	broad.mit.edu	37	1	223396820	223396820	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223396820G>A	uc001hnx.2	-	7	1849	c.1215C>T	c.(1213-1215)CCC>CCT	p.P405P	SUSD4_uc001hny.3_Silent_p.P405P|SUSD4_uc010puw.1_Silent_p.P245P	NM_017982	NP_060452	Q5VX71	SUSD4_HUMAN	sushi domain containing 4 isoform a	405	Cytoplasmic (Potential).					integral to membrane					0				GBM - Glioblastoma multiforme(131;0.0611)														---	---	---	---
CAPN2	824	broad.mit.edu	37	1	223905528	223905528	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223905528C>T	uc001hob.3	+	2	526	c.302C>T	c.(301-303)GCC>GTC	p.A101V	CAPN2_uc010puy.1_Missense_Mutation_p.A23V	NM_001748	NP_001739	P17655	CAN2_HUMAN	calpain 2 isoform 1	101	Calpain catalytic.				proteolysis	cytoplasm|plasma membrane				lung(3)|breast(1)|skin(1)	5				GBM - Glioblastoma multiforme(131;0.109)														---	---	---	---
NVL	4931	broad.mit.edu	37	1	224505618	224505618	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224505618C>T	uc001hok.2	-	3	189	c.146G>A	c.(145-147)CGA>CAA	p.R49Q	NVL_uc001hol.2_5'UTR|NVL_uc010pvd.1_Missense_Mutation_p.R49Q|NVL_uc010pve.1_5'UTR|NVL_uc010pvf.1_RNA|NVL_uc010pvg.1_Missense_Mutation_p.R49Q	NM_002533	NP_002524	O15381	NVL_HUMAN	nuclear VCP-like isoform 1	49						aggresome|cytoplasm|nucleolus	ATP binding|nucleoside-triphosphatase activity			skin(2)	2				GBM - Glioblastoma multiforme(131;0.00501)														---	---	---	---
EPHX1	2052	broad.mit.edu	37	1	226016544	226016544	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:226016544G>A	uc001hpk.2	+	2	194	c.114G>A	c.(112-114)ACG>ACA	p.T38T	EPHX1_uc001hpl.2_Silent_p.T38T	NM_001136018	NP_001129490	P07099	HYEP_HUMAN	epoxide hydrolase 1	38					aromatic compound catabolic process|response to toxin	endoplasmic reticulum membrane|integral to membrane|microsome	cis-stilbene-oxide hydrolase activity|epoxide hydrolase activity			ovary(3)|lung(1)	4	Breast(184;0.197)																	---	---	---	---
CABC1	56997	broad.mit.edu	37	1	227172344	227172344	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227172344C>A	uc001hqm.1	+	17	4913	c.1494C>A	c.(1492-1494)CCC>CCA	p.P498P	CABC1_uc001hqn.1_Silent_p.P498P|CABC1_uc009xeq.1_Silent_p.P446P|CABC1_uc010pvq.1_Silent_p.P219P|CABC1_uc010pvr.1_Silent_p.P172P|CABC1_uc001hqo.1_Silent_p.P219P|CABC1_uc009xer.1_Silent_p.P14P	NM_020247	NP_064632	Q8NI60	ADCK3_HUMAN	chaperone, ABC1 activity of bc1 complex like	498	Protein kinase.				cell death	mitochondrion	ATP binding|protein serine/threonine kinase activity				0		Prostate(94;0.0771)																---	---	---	---
CDC42BPA	8476	broad.mit.edu	37	1	227218993	227218993	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227218993T>C	uc001hqr.2	-						CDC42BPA_uc001hqq.2_Intron|CDC42BPA_uc001hqs.2_Intron|CDC42BPA_uc009xes.2_Intron|CDC42BPA_uc010pvs.1_Intron|CDC42BPA_uc001hqp.2_Intron|CDC42BPA_uc001hqt.2_Intron|CDC42BPA_uc001hqu.1_Intron	NM_003607	NP_003598			CDC42-binding protein kinase alpha isoform B						actin cytoskeleton reorganization|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm	ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1)	11		all_cancers(173;0.156)|Prostate(94;0.0792)																---	---	---	---
CDC42BPA	8476	broad.mit.edu	37	1	227300469	227300469	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227300469C>T	uc001hqr.2	-	13	2736	c.1793G>A	c.(1792-1794)CGC>CAC	p.R598H	CDC42BPA_uc001hqs.2_Intron|CDC42BPA_uc009xes.2_Missense_Mutation_p.R598H|CDC42BPA_uc010pvs.1_Missense_Mutation_p.R598H	NM_003607	NP_003598	Q5VT25	MRCKA_HUMAN	CDC42-binding protein kinase alpha isoform B	598	Potential.				actin cytoskeleton reorganization|intracellular signal transduction	cell leading edge|cell-cell junction|cytoplasm	ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			lung(6)|breast(2)|stomach(1)|ovary(1)|pancreas(1)	11		all_cancers(173;0.156)|Prostate(94;0.0792)																---	---	---	---
SNAP47	116841	broad.mit.edu	37	1	227947003	227947003	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:227947003C>T	uc001hrf.2	+	3	1354	c.940C>T	c.(940-942)CGC>TGC	p.R314C	SNAP47_uc001hqz.2_Missense_Mutation_p.R269C|SNAP47_uc001hra.2_Missense_Mutation_p.R72C|SNAP47_uc001hrd.2_Missense_Mutation_p.R314C|SNAP47_uc001hre.2_Missense_Mutation_p.R72C|SNAP47_uc001hrg.1_Missense_Mutation_p.R269C	NM_053052	NP_444280	Q5SQN1	SNP47_HUMAN	synaptosomal-associated protein, 47kDa	314						endomembrane system|membrane|perinuclear region of cytoplasm				ovary(1)	1																		---	---	---	---
OBSCN	84033	broad.mit.edu	37	1	228447314	228447314	+	Intron	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228447314T>G	uc009xez.1	+						OBSCN_uc001hsn.2_Intron	NM_001098623	NP_001092093			obscurin, cytoskeletal calmodulin and						apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1)	28		Prostate(94;0.0405)																---	---	---	---
OBSCN	84033	broad.mit.edu	37	1	228466474	228466474	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228466474G>A	uc009xez.1	+	26	6988	c.6944G>A	c.(6943-6945)CGG>CAG	p.R2315Q	OBSCN_uc001hsn.2_Missense_Mutation_p.R2315Q|OBSCN_uc001hsp.1_Missense_Mutation_p.R14Q|OBSCN_uc001hsq.1_5'Flank	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	2315	Ig-like 23.				apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1)	28		Prostate(94;0.0405)																---	---	---	---
OBSCN	84033	broad.mit.edu	37	1	228495030	228495030	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228495030C>T	uc009xez.1	+	46	12308	c.12264C>T	c.(12262-12264)TGC>TGT	p.C4088C	OBSCN_uc001hsn.2_Silent_p.C4088C	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	4088	Ig-like 42.				apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1)	28		Prostate(94;0.0405)																---	---	---	---
OBSCN	84033	broad.mit.edu	37	1	228509612	228509612	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228509612G>A	uc009xez.1	+	55	15114	c.15070G>A	c.(15070-15072)GCT>ACT	p.A5024T	OBSCN_uc001hsn.2_Missense_Mutation_p.A5024T	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	5024					apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1)	28		Prostate(94;0.0405)																---	---	---	---
OBSCN	84033	broad.mit.edu	37	1	228547795	228547795	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228547795G>A	uc009xez.1	+						OBSCN_uc001hsn.2_Missense_Mutation_p.R6401H|OBSCN_uc001hsr.1_Intron|OBSCN_uc009xfa.2_Missense_Mutation_p.R63H	NM_001098623	NP_001092093			obscurin, cytoskeletal calmodulin and						apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1)	28		Prostate(94;0.0405)																---	---	---	---
RHOU	58480	broad.mit.edu	37	1	228879157	228879157	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228879157C>T	uc001htf.2	+	3	1068	c.447C>T	c.(445-447)TGC>TGT	p.C149C		NM_021205	NP_067028	Q7L0Q8	RHOU_HUMAN	ras homolog gene family, member U	149					regulation of small GTPase mediated signal transduction	cell projection|cytosol|focal adhesion|Golgi membrane|podosome	GTP binding|metal ion binding|protein binding				0	Breast(184;0.162)	Prostate(94;0.183)																---	---	---	---
ACTA1	58	broad.mit.edu	37	1	229568532	229568532	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229568532G>A	uc001htm.2	-	3	330	c.225C>T	c.(223-225)CAC>CAT	p.H75H		NM_001100	NP_001091	P68133	ACTS_HUMAN	actin, alpha 1, skeletal muscle	75			H -> L (in NEM3).|H -> R (in NEM3).		muscle filament sliding|skeletal muscle fiber development|skeletal muscle thin filament assembly	actin filament|cytosol|stress fiber|striated muscle thin filament	ADP binding|ATP binding|myosin binding|structural constituent of cytoskeleton				0	Breast(184;0.0858)|Ovarian(103;0.103)	Prostate(94;0.167)			Dornase Alfa(DB00003)													---	---	---	---
URB2	9816	broad.mit.edu	37	1	229774000	229774000	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:229774000A>G	uc001hts.1	+						URB2_uc009xfd.1_Intron	NM_014777	NP_055592			URB2 ribosome biogenesis 2 homolog							nucleolus				central_nervous_system(2)|ovary(1)	3																		---	---	---	---
AGT	183	broad.mit.edu	37	1	230845731	230845731	+	Intron	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230845731T>G	uc001hty.3	-						AGT_uc009xfe.2_Intron|AGT_uc009xff.2_Intron	NM_000029	NP_000020			angiotensinogen preproprotein						activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|blood vessel remodeling|cell-cell signaling|cellular lipid metabolic process|G-protein signaling, coupled to cGMP nucleotide second messenger|kidney development|low-density lipoprotein particle remodeling|negative regulation of nerve growth factor receptor signaling pathway|nitric oxide mediated signal transduction|positive regulation of activation of JAK2 kinase activity|positive regulation of apoptosis|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of cardiac muscle hypertrophy|positive regulation of cholesterol esterification|positive regulation of cytokine production|positive regulation of endothelial cell migration|positive regulation of epidermal growth factor receptor signaling pathway|positive regulation of fibroblast proliferation|positive regulation of inflammatory response|positive regulation of NAD(P)H oxidase activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein tyrosine kinase activity|positive regulation of reactive oxygen species metabolic process|positive regulation of transcription, DNA-dependent|regulation of proteolysis|regulation of renal output by angiotensin|regulation of renal sodium excretion|regulation of vasoconstriction|renin-angiotensin regulation of aldosterone production|response to muscle activity involved in regulation of muscle adaptation	extracellular space|soluble fraction	acetyltransferase activator activity|growth factor activity|hormone activity|serine-type endopeptidase inhibitor activity|type 1 angiotensin receptor binding|type 2 angiotensin receptor binding				0	Breast(184;0.0735)|Ovarian(103;0.183)	all_cancers(173;4.64e-23)|all_epithelial(177;3.61e-18)|Breast(1374;0.00093)|all_neural(198;0.0604)|Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;4.4e-06)|Colorectal(1306;5.46e-06)|COAD - Colon adenocarcinoma(196;0.000256)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)	Aliskiren(DB01258)|Atorvastatin(DB01076)|Cilazapril(DB01340)|Irbesartan(DB01029)|Lisinopril(DB00722)|Ouabain(DB01092)|Simvastatin(DB00641)													---	---	---	---
CAPN9	10753	broad.mit.edu	37	1	230883378	230883378	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230883378G>A	uc001htz.1	+	1	249	c.136G>A	c.(136-138)GCA>ACA	p.A46T	CAPN9_uc009xfg.1_Missense_Mutation_p.A46T|CAPN9_uc001hua.1_Missense_Mutation_p.A46T	NM_006615	NP_006606	O14815	CAN9_HUMAN	calpain 9 isoform 1	46	Calpain catalytic.				digestion|proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			ovary(1)	1	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)																---	---	---	---
ARV1	64801	broad.mit.edu	37	1	231125991	231125991	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231125991T>G	uc009xfl.1	+	3	459	c.430T>G	c.(430-432)TTT>GTT	p.F144V	ARV1_uc001huh.2_Missense_Mutation_p.F144V	NM_022786	NP_073623	Q9H2C2	ARV1_HUMAN	ARV1 homolog	144	Helical; (Potential).				sphingolipid metabolic process	integral to membrane				breast(2)	2	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)		COAD - Colon adenocarcinoma(196;0.211)|Colorectal(1306;0.233)														---	---	---	---
TRIM67	440730	broad.mit.edu	37	1	231299704	231299704	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:231299704G>A	uc009xfn.1	+	1	1031	c.989G>A	c.(988-990)GGC>GAC	p.G330D		NM_001004342	NP_001004342	Q6ZTA4	TRI67_HUMAN	tripartite motif-containing 67	330	B box-type 2.					cytoplasm|cytoskeleton	zinc ion binding			ovary(2)|breast(1)|kidney(1)	4	Breast(184;0.0871)	all_cancers(173;0.189)|Prostate(94;0.167)																---	---	---	---
PCNXL2	80003	broad.mit.edu	37	1	233231607	233231607	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:233231607G>A	uc001hvl.2	-	22	4075	c.3840C>T	c.(3838-3840)CTC>CTT	p.L1280L	PCNXL2_uc001hvm.1_RNA|PCNXL2_uc009xfu.2_Intron|PCNXL2_uc001hvp.1_RNA|PCNXL2_uc009xfv.1_RNA	NM_014801	NP_055616	A6NKB5	PCX2_HUMAN	pecanex-like 2	1280	Helical; (Potential).					integral to membrane				central_nervous_system(1)|pancreas(1)	2		all_cancers(173;0.0347)|Prostate(94;0.137)																---	---	---	---
SLC35F3	148641	broad.mit.edu	37	1	234455888	234455888	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234455888A>G	uc001hwa.1	+	6	1213	c.985A>G	c.(985-987)ACT>GCT	p.T329A	SLC35F3_uc001hvy.1_Missense_Mutation_p.T398A	NM_173508	NP_775779	Q8IY50	S35F3_HUMAN	solute carrier family 35, member F3	329	Helical; (Potential).				transport	integral to membrane				ovary(2)	2	Ovarian(103;0.0454)	all_cancers(173;0.145)|Prostate(94;0.0885)	OV - Ovarian serous cystadenocarcinoma(106;0.00531)															---	---	---	---
TARBP1	6894	broad.mit.edu	37	1	234529420	234529420	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:234529420C>T	uc001hwd.2	-	27	4407	c.4407G>A	c.(4405-4407)TCG>TCA	p.S1469S		NM_005646	NP_005637	Q13395	TARB1_HUMAN	TAR RNA binding protein 1	1469					regulation of transcription from RNA polymerase II promoter|RNA processing	nucleus	RNA binding|RNA methyltransferase activity			ovary(2)|skin(1)	3	Ovarian(103;0.0339)	all_cancers(173;0.00995)|Prostate(94;0.0115)|all_epithelial(177;0.172)	OV - Ovarian serous cystadenocarcinoma(106;0.000263)															---	---	---	---
RBM34	23029	broad.mit.edu	37	1	235301226	235301226	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235301226C>T	uc001hwn.2	-	8	845	c.815G>A	c.(814-816)CGT>CAT	p.R272H	RBM34_uc001hwo.2_RNA|ARID4B_uc001hwp.2_RNA	NM_015014	NP_055829	P42696	RBM34_HUMAN	RNA binding motif protein 34 isoform 1	272	RRM 1.					nucleolus	nucleotide binding|RNA binding			central_nervous_system(1)	1	Ovarian(103;0.0398)	all_cancers(173;0.177)|Prostate(94;0.0166)	OV - Ovarian serous cystadenocarcinoma(106;5.43e-05)|Epithelial(3;0.000121)															---	---	---	---
ARID4B	51742	broad.mit.edu	37	1	235338539	235338539	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:235338539A>G	uc001hwq.2	-	22	4122	c.3624T>C	c.(3622-3624)AGT>AGC	p.S1208S	ARID4B_uc001hwr.2_Silent_p.S1122S|ARID4B_uc001hwp.2_RNA	NM_016374	NP_057458	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B isoform 1	1208					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding			ovary(2)|lung(1)	3	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)															---	---	---	---
HEATR1	55127	broad.mit.edu	37	1	236727846	236727846	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236727846T>C	uc001hyd.1	-	32	4676	c.4551A>G	c.(4549-4551)TCA>TCG	p.S1517S	HEATR1_uc009xgh.1_Silent_p.S679S	NM_018072	NP_060542	Q9H583	HEAT1_HUMAN	protein BAP28	1517					rRNA processing	nucleolus|ribonucleoprotein complex	protein binding			ovary(2)|skin(1)	3	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)															---	---	---	---
HEATR1	55127	broad.mit.edu	37	1	236760162	236760162	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236760162C>T	uc001hyd.1	-	6	843	c.718G>A	c.(718-720)GCC>ACC	p.A240T		NM_018072	NP_060542	Q9H583	HEAT1_HUMAN	protein BAP28	240					rRNA processing	nucleolus|ribonucleoprotein complex	protein binding			ovary(2)|skin(1)	3	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)															---	---	---	---
MTR	4548	broad.mit.edu	37	1	236988672	236988672	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:236988672G>A	uc001hyi.3	+	10	1323	c.900G>A	c.(898-900)ACG>ACA	p.T300T	MTR_uc010pxw.1_5'UTR|MTR_uc010pxx.1_Silent_p.T300T|MTR_uc010pxy.1_Silent_p.T300T|MTR_uc009xgj.1_Intron	NM_000254	NP_000245	Q99707	METH_HUMAN	5-methyltetrahydrofolate-homocysteine	300	Hcy-binding.				nervous system development|xenobiotic metabolic process	cytosol	cobalamin binding|homocysteine S-methyltransferase activity|methionine synthase activity|protein binding|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)													---	---	---	---
RYR2	6262	broad.mit.edu	37	1	237753160	237753160	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237753160C>T	uc001hyl.1	+	30	3786	c.3666C>T	c.(3664-3666)AGC>AGT	p.S1222S		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	1222	Cytoplasmic (By similarity).|4 X approximate repeats.|B30.2/SPRY 2.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)															---	---	---	---
RYR2	6262	broad.mit.edu	37	1	237777845	237777845	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237777845C>T	uc001hyl.1	+	37	5537	c.5417C>T	c.(5416-5418)GCC>GTC	p.A1806V		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	1806	Cytoplasmic (By similarity).|4 X approximate repeats.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)															---	---	---	---
RYR2	6262	broad.mit.edu	37	1	237919646	237919646	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237919646G>A	uc001hyl.1	+	81	11324	c.11204G>A	c.(11203-11205)GGC>GAC	p.G3735D	RYR2_uc010pya.1_Missense_Mutation_p.G150D	NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	3735					cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)															---	---	---	---
RYR2	6262	broad.mit.edu	37	1	237919647	237919647	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237919647C>T	uc001hyl.1	+	81	11325	c.11205C>T	c.(11203-11205)GGC>GGT	p.G3735G	RYR2_uc010pya.1_Silent_p.G150G	NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	3735					cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)															---	---	---	---
ZP4	57829	broad.mit.edu	37	1	238050775	238050775	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:238050775G>A	uc001hym.2	-	5	640	c.640C>T	c.(640-642)CGC>TGC	p.R214C	LOC100130331_uc010pyc.1_Intron	NM_021186	NP_067009	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4 preproprotein	214	ZP.|Extracellular (Potential).				acrosomal vesicle exocytosis|negative regulation of binding of sperm to zona pellucida|positive regulation of acrosome reaction|positive regulation of humoral immune response|positive regulation of protein kinase activity|positive regulation of T cell proliferation|protein kinase A signaling cascade|protein kinase C signaling cascade	integral to membrane|intracellular|plasma membrane|proteinaceous extracellular matrix	acrosin binding|receptor activity			ovary(2)|skin(1)	3	Ovarian(103;0.103)	all_cancers(173;0.00175)|all_epithelial(177;0.162)|all_neural(198;0.164)|Melanoma(53;0.211)|Prostate(94;0.214)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)															---	---	---	---
FMN2	56776	broad.mit.edu	37	1	240370761	240370761	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240370761C>A	uc010pyd.1	+	5	2874	c.2649C>A	c.(2647-2649)CTC>CTA	p.L883L	FMN2_uc010pye.1_Silent_p.L887L	NM_020066	NP_064450	Q9NZ56	FMN2_HUMAN	formin 2	883	Pro-rich.|FH1.				actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1)	12	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)															---	---	---	---
FMN2	56776	broad.mit.edu	37	1	240370847	240370847	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:240370847C>A	uc010pyd.1	+	5	2960	c.2735C>A	c.(2734-2736)CCC>CAC	p.P912H	FMN2_uc010pye.1_Missense_Mutation_p.P916H	NM_020066	NP_064450	Q9NZ56	FMN2_HUMAN	formin 2	912	Pro-rich.|FH1.				actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1)	12	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)															---	---	---	---
WDR64	128025	broad.mit.edu	37	1	241946570	241946570	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241946570C>T	uc001hzf.1	+						WDR64_uc001hzg.1_Intron	NM_144625	NP_653226			WD repeat domain 64											skin(1)	1	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)															---	---	---	---
WDR64	128025	broad.mit.edu	37	1	241959600	241959600	+	Silent	SNP	C	T	T	rs145395572		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:241959600C>T	uc001hzf.1	+	16	1902	c.1749C>T	c.(1747-1749)GGC>GGT	p.G583G	WDR64_uc001hzg.1_Silent_p.G496G	NM_144625	NP_653226	B1ANS9	WDR64_HUMAN	WD repeat domain 64	1030										skin(1)	1	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)															---	---	---	---
SDCCAG8	10806	broad.mit.edu	37	1	243480168	243480168	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:243480168T>C	uc001hzw.2	+	9	1197	c.1041T>C	c.(1039-1041)TCT>TCC	p.S347S	SDCCAG8_uc010pyk.1_Silent_p.S202S|SDCCAG8_uc010pyl.1_Silent_p.S159S|SDCCAG8_uc001hzx.2_Silent_p.S159S	NM_006642	NP_006633	Q86SQ7	SDCG8_HUMAN	serologically defined colon cancer antigen 8	347	Sufficient for homodimerization (By similarity).				establishment of cell polarity|G2/M transition of mitotic cell cycle|tube formation	cell-cell junction|centriole|cytosol	protein binding				0	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)	COAD - Colon adenocarcinoma(196;0.145)														---	---	---	---
KIF26B	55083	broad.mit.edu	37	1	245849533	245849533	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245849533G>A	uc001ibf.1	+	12	3688	c.3248G>A	c.(3247-3249)AGC>AAC	p.S1083N	KIF26B_uc001ibg.1_Missense_Mutation_p.S701N|KIF26B_uc001ibh.1_Missense_Mutation_p.S325N	NM_018012	NP_060482	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	1083					microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)															---	---	---	---
CNST	163882	broad.mit.edu	37	1	246797797	246797797	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:246797797A>G	uc001ibp.2	+	6	1104	c.726A>G	c.(724-726)CAA>CAG	p.Q242Q	CNST_uc001ibo.3_Silent_p.Q242Q	NM_152609	NP_689822	Q6PJW8	CNST_HUMAN	hypothetical protein LOC163882 isoform 1	242					positive regulation of Golgi to plasma membrane protein transport	integral to membrane|plasma membrane|protein complex|trans-Golgi network|transport vesicle	connexin binding				0																		---	---	---	---
AHCTF1	25909	broad.mit.edu	37	1	247058023	247058023	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247058023C>T	uc001ibu.1	-	13	1749	c.1742G>A	c.(1741-1743)CGC>CAC	p.R581H	AHCTF1_uc001ibv.1_Missense_Mutation_p.R590H|AHCTF1_uc009xgs.1_5'UTR	NM_015446	NP_056261	Q8WYP5	ELYS_HUMAN	transcription factor ELYS	581	Necessary for cytoplasmic localization (By similarity).				cytokinesis|mitotic prometaphase|mRNA transport|nuclear pore complex assembly|protein transport|transmembrane transport	condensed chromosome kinetochore|cytosol|nuclear matrix|nuclear membrane|nuclear pore|nucleoplasm	DNA binding			ovary(5)|skin(2)	7	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)															---	---	---	---
ZNF695	57116	broad.mit.edu	37	1	247150263	247150263	+	3'UTR	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247150263T>G	uc009xgu.2	-	4					ZNF695_uc001ica.2_Intron|ZNF695_uc001icb.1_Intron|ZNF695_uc009xgt.1_Intron|ZNF695_uc001ibx.2_Intron|ZNF695_uc001iby.2_Intron	NM_020394	NP_065127			zinc finger protein SBZF3						regulation of transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding				0	all_cancers(71;4.01e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)															---	---	---	---
ZNF496	84838	broad.mit.edu	37	1	247486456	247486456	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247486456C>T	uc001ico.2	-	5	1116	c.651G>A	c.(649-651)CCG>CCA	p.P217P	ZNF496_uc009xgv.2_Silent_p.P217P|ZNF496_uc001icp.2_Silent_p.P217P|ZNF496_uc010pyv.1_Silent_p.P217P	NM_032752	NP_116141	Q96IT1	ZN496_HUMAN	zinc finger protein 496	217					positive regulation of transcription, DNA-dependent|viral reproduction		DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	all_cancers(71;0.000136)|all_epithelial(71;2.62e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0607)|Lung NSC(105;0.0661)		OV - Ovarian serous cystadenocarcinoma(106;0.00703)															---	---	---	---
NLRP3	114548	broad.mit.edu	37	1	247587653	247587653	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247587653G>A	uc001icr.2	+	5	1046	c.908G>A	c.(907-909)GGC>GAC	p.G303D	NLRP3_uc001ics.2_Missense_Mutation_p.G303D|NLRP3_uc001icu.2_Missense_Mutation_p.G303D|NLRP3_uc001icw.2_Missense_Mutation_p.G303D|NLRP3_uc001icv.2_Missense_Mutation_p.G303D|NLRP3_uc010pyw.1_Missense_Mutation_p.G301D|NLRP3_uc001ict.1_Missense_Mutation_p.G301D	NM_001079821	NP_001073289	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3 isoform a	303	NACHT.				detection of biotic stimulus|induction of apoptosis|inflammatory response|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|positive regulation of interleukin-1 beta secretion|protein oligomerization|signal transduction	cytoplasm	ATP binding|peptidoglycan binding|protein binding			lung(8)|skin(8)|ovary(7)|upper_aerodigestive_tract(1)|breast(1)|pancreas(1)	26	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)															---	---	---	---
NLRP3	114548	broad.mit.edu	37	1	247587661	247587661	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247587661G>T	uc001icr.2	+	5	1054	c.916G>T	c.(916-918)GAG>TAG	p.E306*	NLRP3_uc001ics.2_Nonsense_Mutation_p.E306*|NLRP3_uc001icu.2_Nonsense_Mutation_p.E306*|NLRP3_uc001icw.2_Nonsense_Mutation_p.E306*|NLRP3_uc001icv.2_Nonsense_Mutation_p.E306*|NLRP3_uc010pyw.1_Nonsense_Mutation_p.E304*|NLRP3_uc001ict.1_Nonsense_Mutation_p.E304*	NM_001079821	NP_001073289	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3 isoform a	306	NACHT.				detection of biotic stimulus|induction of apoptosis|inflammatory response|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|positive regulation of interleukin-1 beta secretion|protein oligomerization|signal transduction	cytoplasm	ATP binding|peptidoglycan binding|protein binding			lung(8)|skin(8)|ovary(7)|upper_aerodigestive_tract(1)|breast(1)|pancreas(1)	26	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)															---	---	---	---
OR2L8	391190	broad.mit.edu	37	1	248112371	248112371	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248112371A>G	uc001idt.1	+	1	212	c.212A>G	c.(211-213)AAT>AGT	p.N71S	OR2L13_uc001ids.2_Intron	NM_001001963	NP_001001963	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L,	71	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)															---	---	---	---
OR2L3	391192	broad.mit.edu	37	1	248224093	248224093	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248224093C>T	uc001idx.1	+	1	110	c.110C>T	c.(109-111)GCT>GTT	p.A37V	OR2L13_uc001ids.2_Intron	NM_001004687	NP_001004687	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L,	37	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)															---	---	---	---
OR2L3	391192	broad.mit.edu	37	1	248224716	248224716	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248224716A>C	uc001idx.1	+	1	733	c.733A>C	c.(733-735)ACT>CCT	p.T245P	OR2L13_uc001ids.2_Intron	NM_001004687	NP_001004687	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L,	245	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)															---	---	---	---
OR2L13	284521	broad.mit.edu	37	1	248263029	248263029	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248263029G>A	uc001ids.2	+	3	689	c.352G>A	c.(352-354)GCC>ACC	p.A118T		NM_175911	NP_787107	Q8N349	OR2LD_HUMAN	olfactory receptor, family 2, subfamily L,	118	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity|protein binding			central_nervous_system(2)|ovary(1)|skin(1)	4	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0132)															---	---	---	---
OR2M5	127059	broad.mit.edu	37	1	248308528	248308528	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248308528C>T	uc010pze.1	+	1	79	c.79C>T	c.(79-81)CTC>TTC	p.L27F		NM_001004690	NP_001004690	A3KFT3	OR2M5_HUMAN	olfactory receptor, family 2, subfamily M,	27	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|kidney(1)	3	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0388)															---	---	---	---
OR2T12	127064	broad.mit.edu	37	1	248458150	248458150	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248458150G>A	uc010pzj.1	-	1	731	c.731C>T	c.(730-732)GCT>GTT	p.A244V		NM_001004692	NP_001004692	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T,	244	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)	3	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0201)															---	---	---	---
OR2M7	391196	broad.mit.edu	37	1	248487569	248487569	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248487569A>T	uc010pzk.1	-	1	302	c.302T>A	c.(301-303)ATT>AAT	p.I101N		NM_001004691	NP_001004691	Q8NG81	OR2M7_HUMAN	olfactory receptor, family 2, subfamily M,	101	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)															---	---	---	---
SH3BP5L	80851	broad.mit.edu	37	1	249106457	249106457	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:249106457C>T	uc001iew.1	-	7	1376	c.824G>A	c.(823-825)CGC>CAC	p.R275H	SH3BP5L_uc010pzp.1_Missense_Mutation_p.R168H|SH3BP5L_uc010pzq.1_Missense_Mutation_p.R243H|SH3BP5L_uc001iev.1_Missense_Mutation_p.R156H	NM_030645	NP_085148	Q7L8J4	3BP5L_HUMAN	SH3-binding domain protein 5-like	275											0	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)															---	---	---	---
ZNF672	79894	broad.mit.edu	37	1	249142605	249142605	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:249142605G>A	uc001iex.2	+	4	1827	c.1132G>A	c.(1132-1134)GTC>ATC	p.V378I		NM_024836	NP_079112	Q499Z4	ZN672_HUMAN	zinc finger protein 672	378	C2H2-type 13.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)															---	---	---	---
PXDN	7837	broad.mit.edu	37	2	1648407	1648407	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1648407G>A	uc002qxa.2	-	18	3790	c.3726C>T	c.(3724-3726)CGC>CGT	p.R1242R		NM_012293	NP_036425	Q92626	PXDN_HUMAN	peroxidasin precursor	1242					extracellular matrix organization|hydrogen peroxide catabolic process|immune response	endoplasmic reticulum|extracellular space|proteinaceous extracellular matrix	extracellular matrix structural constituent|heme binding|interleukin-1 receptor antagonist activity|peroxidase activity			pancreas(6)|ovary(2)	8	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)														---	---	---	---
PXDN	7837	broad.mit.edu	37	2	1670197	1670197	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1670197C>T	uc002qxa.2	-	10	1144	c.1080G>A	c.(1078-1080)ACG>ACA	p.T360T	PXDN_uc002qxb.1_Silent_p.T360T|PXDN_uc002qxc.1_Silent_p.T177T	NM_012293	NP_036425	Q92626	PXDN_HUMAN	peroxidasin precursor	360	Ig-like C2-type 2.				extracellular matrix organization|hydrogen peroxide catabolic process|immune response	endoplasmic reticulum|extracellular space|proteinaceous extracellular matrix	extracellular matrix structural constituent|heme binding|interleukin-1 receptor antagonist activity|peroxidase activity			pancreas(6)|ovary(2)	8	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)														---	---	---	---
PXDN	7837	broad.mit.edu	37	2	1691459	1691459	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1691459C>T	uc002qxa.2	-	4	425	c.361G>A	c.(361-363)GAG>AAG	p.E121K	PXDN_uc002qxb.1_Missense_Mutation_p.E121K|PXDN_uc002qxc.1_Intron	NM_012293	NP_036425	Q92626	PXDN_HUMAN	peroxidasin precursor	121	LRR 2.				extracellular matrix organization|hydrogen peroxide catabolic process|immune response	endoplasmic reticulum|extracellular space|proteinaceous extracellular matrix	extracellular matrix structural constituent|heme binding|interleukin-1 receptor antagonist activity|peroxidase activity			pancreas(6)|ovary(2)	8	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)														---	---	---	---
MYT1L	23040	broad.mit.edu	37	2	1983487	1983487	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1983487G>A	uc002qxe.2	-						MYT1L_uc002qxd.2_Intron|MYT1L_uc002qxf.1_RNA	NM_015025	NP_055840			myelin transcription factor 1-like						cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)														---	---	---	---
RNASEH1	246243	broad.mit.edu	37	2	3596657	3596657	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3596657C>T	uc002qxt.2	-	5	645	c.555G>A	c.(553-555)GCG>GCA	p.A185A	RNASEH1_uc002qxs.2_Silent_p.A68A	NM_002936	NP_002927	O60930	RNH1_HUMAN	ribonuclease H1	185	RNase H.				RNA catabolic process	cytoplasm	magnesium ion binding|ribonuclease H activity|RNA binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.0713)|Epithelial(75;0.167)|all cancers(51;0.22)														---	---	---	---
RNASEH1	246243	broad.mit.edu	37	2	3599804	3599804	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3599804C>T	uc002qxt.2	-	3	429	c.339G>A	c.(337-339)CCG>CCA	p.P113P	RNASEH1_uc002qxs.2_5'UTR	NM_002936	NP_002927	O60930	RNH1_HUMAN	ribonuclease H1	113					RNA catabolic process	cytoplasm	magnesium ion binding|ribonuclease H activity|RNA binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.0713)|Epithelial(75;0.167)|all cancers(51;0.22)														---	---	---	---
RNASEH1	246243	broad.mit.edu	37	2	3604468	3604468	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3604468C>T	uc002qxt.2	-	2	245	c.155G>A	c.(154-156)CGG>CAG	p.R52Q	RNASEH1_uc002qxs.2_5'UTR|uc002qxu.2_5'Flank|uc002qxv.2_5'Flank	NM_002936	NP_002927	O60930	RNH1_HUMAN	ribonuclease H1	52					RNA catabolic process	cytoplasm	magnesium ion binding|ribonuclease H activity|RNA binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.0713)|Epithelial(75;0.167)|all cancers(51;0.22)														---	---	---	---
COLEC11	78989	broad.mit.edu	37	2	3691529	3691529	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:3691529G>A	uc002qya.2	+	7	785	c.637G>A	c.(637-639)GCC>ACC	p.A213T	COLEC11_uc002qxz.2_Missense_Mutation_p.A210T|COLEC11_uc002qyb.2_Missense_Mutation_p.A189T|COLEC11_uc002qyc.2_Missense_Mutation_p.A189T|COLEC11_uc010ewo.2_Missense_Mutation_p.A165T|COLEC11_uc010ewp.2_Missense_Mutation_p.A187T|COLEC11_uc010ewq.2_Missense_Mutation_p.A163T|COLEC11_uc010ewr.2_Missense_Mutation_p.A163T|COLEC11_uc010ews.2_Missense_Mutation_p.A139T	NM_024027	NP_076932	Q9BWP8	COL11_HUMAN	collectin sub-family member 11 isoform a	213	C-type lectin.					collagen	mannose binding				0	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.127)														---	---	---	---
SOX11	6664	broad.mit.edu	37	2	5833110	5833110	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:5833110G>A	uc002qyj.2	+	1	312	c.257G>A	c.(256-258)CGC>CAC	p.R86H		NM_003108	NP_003099	P35716	SOX11_HUMAN	SRY-box 11	86	HMG box.				cardiac ventricle formation|closure of optic fissure|cornea development in camera-type eye|embryonic digestive tract morphogenesis|embryonic skeletal system morphogenesis|eyelid development in camera-type eye|glial cell proliferation|hard palate development|lens morphogenesis in camera-type eye|limb bud formation|lung morphogenesis|negative regulation of cell death|negative regulation of glial cell proliferation|negative regulation of lymphocyte proliferation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription regulatory region DNA binding|neural crest cell development|neural tube formation|neuroepithelial cell differentiation|noradrenergic neuron differentiation|outflow tract morphogenesis|positive regulation of BMP signaling pathway|positive regulation of hippo signaling cascade|positive regulation of hormone secretion|positive regulation of neurogenesis|positive regulation of neuron differentiation|positive regulation of ossification|positive regulation of osteoblast differentiation|positive regulation of stem cell proliferation|regulation of transforming growth factor beta receptor signaling pathway|signal transduction involved in G1/S transition checkpoint|soft palate development|somite development|spinal cord development|sympathetic nervous system development|ventricular septum morphogenesis	cytoplasm|nucleolus	enhancer sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|RNA polymerase II transcription coactivator activity|translation factor activity, nucleic acid binding			central_nervous_system(3)	3	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			OV - Ovarian serous cystadenocarcinoma(76;0.132)														---	---	---	---
RSAD2	91543	broad.mit.edu	37	2	7027236	7027236	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:7027236T>G	uc002qyp.1	+	3	815	c.679T>G	c.(679-681)TTC>GTC	p.F227V		NM_080657	NP_542388	Q8WXG1	RSAD2_HUMAN	radical S-adenosyl methionine domain containing	227					defense response to virus	endoplasmic reticulum membrane|Golgi apparatus	catalytic activity|iron-sulfur cluster binding|metal ion binding				0	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			OV - Ovarian serous cystadenocarcinoma(76;0.191)														---	---	---	---
KIDINS220	57498	broad.mit.edu	37	2	8871821	8871821	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:8871821A>G	uc002qzc.2	-	30	4527	c.4345T>C	c.(4345-4347)TCC>CCC	p.S1449P	KIDINS220_uc010yiv.1_Intron|KIDINS220_uc002qzd.2_Missense_Mutation_p.S1350P|KIDINS220_uc002qzb.2_Missense_Mutation_p.S303P	NM_020738	NP_065789	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate of 220 kDa	1449	Cytoplasmic (Potential).				activation of MAPKK activity|nerve growth factor receptor signaling pathway	cytosol|integral to membrane				ovary(3)|central_nervous_system(1)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
CPSF3	51692	broad.mit.edu	37	2	9582107	9582107	+	Splice_Site	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:9582107T>C	uc002qzo.1	+	9	1130	c.1095_splice	c.e9+2	p.K365_splice	CPSF3_uc010ewx.1_Splice_Site_p.K365_splice|CPSF3_uc002qzp.1_Splice_Site_p.K328_splice	NM_016207	NP_057291			cleavage and polyadenylation specific factor 3,						histone mRNA 3'-end processing|mRNA cleavage|mRNA export from nucleus|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex|ribonucleoprotein complex	5'-3' exonuclease activity|endoribonuclease activity|metal ion binding|protein binding|RNA binding			breast(2)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;2.39e-25)|all_epithelial(98;8.75e-19)|Lung NSC(108;2.38e-06)|Ovarian(717;0.0308)		all cancers(51;2.2e-40)|Epithelial(75;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(76;4.35e-21)|STAD - Stomach adenocarcinoma(1183;0.00644)														---	---	---	---
TAF1B	9014	broad.mit.edu	37	2	10008471	10008471	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10008471T>C	uc002qzz.2	+	6	566	c.466T>C	c.(466-468)TGT>CGT	p.C156R	TAF1B_uc010exc.2_Missense_Mutation_p.C156R|TAF1B_uc002qzy.3_Missense_Mutation_p.C156R|TAF1B_uc010yja.1_5'UTR|TAF1B_uc010exd.2_5'UTR	NM_005680	NP_005671	Q53T94	TAF1B_HUMAN	TBP-associated factor 1B	156					termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|breast(1)|pancreas(1)	3	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
KLF11	8462	broad.mit.edu	37	2	10188012	10188012	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10188012C>A	uc002raf.1	+	3	710	c.548C>A	c.(547-549)CCT>CAT	p.P183H	KLF11_uc010yjc.1_Missense_Mutation_p.P166H	NM_003597	NP_003588	O14901	KLF11_HUMAN	Kruppel-like factor 11	183					apoptosis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of apoptosis|regulation of transcription involved in S phase of mitotic cell cycle	nucleus	sequence-specific DNA binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(2)	2	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.133)|OV - Ovarian serous cystadenocarcinoma(76;0.228)														---	---	---	---
NOL10	79954	broad.mit.edu	37	2	10729400	10729400	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10729400G>A	uc002raq.2	-	19	1738	c.1613C>T	c.(1612-1614)CCG>CTG	p.P538L	NOL10_uc010yje.1_Missense_Mutation_p.P512L|NOL10_uc010yjf.1_Missense_Mutation_p.P488L|NOL10_uc002rap.2_Missense_Mutation_p.P488L	NM_024894	NP_079170	Q9BSC4	NOL10_HUMAN	nucleolar protein 10	538	Potential.					nucleolus					0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.207)														---	---	---	---
NOL10	79954	broad.mit.edu	37	2	10808789	10808789	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:10808789A>G	uc002raq.2	-	7	650	c.525T>C	c.(523-525)GAT>GAC	p.D175D	NOL10_uc010yje.1_Silent_p.D149D|NOL10_uc010yjf.1_Silent_p.D125D|NOL10_uc002rap.2_Silent_p.D175D|NOL10_uc002rar.2_Silent_p.D25D	NM_024894	NP_079170	Q9BSC4	NOL10_HUMAN	nucleolar protein 10	175	WD 2.					nucleolus					0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.207)														---	---	---	---
KCNF1	3754	broad.mit.edu	37	2	11052843	11052843	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11052843G>A	uc002rax.2	+	1	781	c.291G>A	c.(289-291)GAG>GAA	p.E97E		NM_002236	NP_002227	Q9H3M0	KCNF1_HUMAN	potassium voltage-gated channel, subfamily F,	97	Cytoplasmic (Potential).					voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.128)														---	---	---	---
KCNF1	3754	broad.mit.edu	37	2	11053304	11053304	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11053304C>T	uc002rax.2	+	1	1242	c.752C>T	c.(751-753)GCG>GTG	p.A251V		NM_002236	NP_002227	Q9H3M0	KCNF1_HUMAN	potassium voltage-gated channel, subfamily F,	251	Helical; Name=Segment S3; (Potential).					voltage-gated potassium channel complex	voltage-gated potassium channel activity	p.A251A(1)		ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.128)														---	---	---	---
ROCK2	9475	broad.mit.edu	37	2	11332359	11332359	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11332359G>A	uc002rbd.1	-	32	4527	c.4078C>T	c.(4078-4080)CGA>TGA	p.R1360*		NM_004850	NP_004841	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein	1360					axon guidance|cytokinesis|intracellular signal transduction	cytosol|plasma membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|structural molecule activity			stomach(2)|skin(2)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)														---	---	---	---
E2F6	1876	broad.mit.edu	37	2	11597324	11597324	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11597324T>C	uc002rbh.2	-	2	436	c.144A>G	c.(142-144)GTA>GTG	p.V48V	E2F6_uc002rbe.2_5'UTR|E2F6_uc002rbf.2_Silent_p.V16V|E2F6_uc002rbg.2_5'UTR|E2F6_uc002rbi.2_Intron|E2F6_uc010yjl.1_RNA|E2F6_uc002rbj.1_RNA	NM_198256	NP_937987	O75461	E2F6_HUMAN	E2F transcription factor 6	48					negative regulation of transcription from RNA polymerase II promoter	MLL1 complex|transcription factor complex	DNA binding|transcription corepressor activity			skin(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.114)|OV - Ovarian serous cystadenocarcinoma(76;0.168)														---	---	---	---
GREB1	9687	broad.mit.edu	37	2	11733157	11733157	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11733157G>T	uc002rbk.1	+	11	1901	c.1601G>T	c.(1600-1602)CGG>CTG	p.R534L	GREB1_uc002rbo.1_Missense_Mutation_p.R168L	NM_014668	NP_055483	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	534						integral to membrane				ovary(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)														---	---	---	---
GREB1	9687	broad.mit.edu	37	2	11741046	11741046	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11741046C>A	uc002rbk.1	+	16	2754	c.2454C>A	c.(2452-2454)TTC>TTA	p.F818L	GREB1_uc002rbo.1_Missense_Mutation_p.F452L	NM_014668	NP_055483	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	818						integral to membrane				ovary(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)														---	---	---	---
LPIN1	23175	broad.mit.edu	37	2	11913738	11913738	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11913738T>C	uc010yjn.1	+						LPIN1_uc010yjm.1_Intron|LPIN1_uc002rbt.2_Intron|LPIN1_uc002rbs.2_Intron	NM_145693	NP_663731			lipin 1						fatty acid catabolic process|transcription, DNA-dependent|triglyceride biosynthetic process|triglyceride mobilization	cytosol|endoplasmic reticulum membrane	phosphatidate phosphatase activity			ovary(2)|large_intestine(1)|skin(1)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)														---	---	---	---
LPIN1	23175	broad.mit.edu	37	2	11944613	11944613	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11944613G>A	uc010yjn.1	+	16	2244	c.1970G>A	c.(1969-1971)GGC>GAC	p.G657D	LPIN1_uc010yjm.1_Missense_Mutation_p.G742D|LPIN1_uc002rbt.2_Missense_Mutation_p.G657D|LPIN1_uc010yjo.1_Missense_Mutation_p.G158D	NM_145693	NP_663731	Q14693	LPIN1_HUMAN	lipin 1	657	C-LIP.				fatty acid catabolic process|transcription, DNA-dependent|triglyceride biosynthetic process|triglyceride mobilization	cytosol|endoplasmic reticulum membrane	phosphatidate phosphatase activity			ovary(2)|large_intestine(1)|skin(1)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)														---	---	---	---
NBAS	51594	broad.mit.edu	37	2	15523328	15523328	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:15523328T>C	uc002rcc.1	-						NBAS_uc010exl.1_Intron|NBAS_uc002rcd.1_Intron	NM_015909	NP_056993			neuroblastoma-amplified protein											ovary(2)|liver(1)|skin(1)	4																		---	---	---	---
MYCN	4613	broad.mit.edu	37	2	16085885	16085885	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16085885C>T	uc002rci.2	+	3	1361	c.1061C>T	c.(1060-1062)GCG>GTG	p.A354V	MYCN_uc010yjr.1_Missense_Mutation_p.A346V	NM_005378	NP_005369	P04198	MYCN_HUMAN	v-myc myelocytomatosis viral related oncogene,	354					regulation of transcription from RNA polymerase II promoter	chromatin|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|ovary(1)|lung(1)|skin(1)	5	all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197)		GBM - Glioblastoma multiforme(3;0.000332)					A		neuroblastoma								---	---	---	---
NT5C1B	93034	broad.mit.edu	37	2	18765480	18765480	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:18765480G>A	uc002rcz.2	-	6	1049	c.945C>T	c.(943-945)TGC>TGT	p.C315C	NT5C1B_uc002rcy.2_Silent_p.C315C|NT5C1B_uc010exr.2_Silent_p.C257C|NT5C1B_uc010yju.1_Silent_p.C255C|NT5C1B_uc002rda.2_Silent_p.C255C|NT5C1B_uc010yjv.1_Silent_p.C332C|NT5C1B_uc010yjw.1_Silent_p.C298C|NT5C1B_uc010exs.2_Silent_p.C317C|NT5C1B_uc002rdb.1_Silent_p.C107C	NM_001002006	NP_001002006	Q96P26	5NT1B_HUMAN	5' nucleotidase, cytosolic IB isoform 1	315					purine base metabolic process|purine nucleotide catabolic process	cytosol	5'-nucleotidase activity|magnesium ion binding|nucleotide binding			skin(2)|ovary(1)	3	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.177)	Ovarian(717;0.208)																---	---	---	---
WDR35	57539	broad.mit.edu	37	2	20174364	20174364	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20174364C>T	uc002rdi.2	-	7	709	c.601G>A	c.(601-603)GTC>ATC	p.V201I	WDR35_uc002rdj.2_Missense_Mutation_p.V201I|WDR35_uc010ext.2_RNA|WDR35_uc002rdh.2_5'UTR	NM_001006657	NP_001006658	Q9P2L0	WDR35_HUMAN	WD repeat domain 35 isoform 1	201										ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
APOB	338	broad.mit.edu	37	2	21228798	21228798	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21228798C>T	uc002red.2	-	26	11070	c.10942G>A	c.(10942-10944)GTC>ATC	p.V3648I		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	3648					cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus	chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle	cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity			ovary(11)|skin(9)|central_nervous_system(3)|large_intestine(2)|upper_aerodigestive_tract(1)|pancreas(1)	27	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Atorvastatin(DB01076)													---	---	---	---
APOB	338	broad.mit.edu	37	2	21252504	21252504	+	Intron	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:21252504A>T	uc002red.2	-							NM_000384	NP_000375			apolipoprotein B precursor						cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus	chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle	cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity			ovary(11)|skin(9)|central_nervous_system(3)|large_intestine(2)|upper_aerodigestive_tract(1)|pancreas(1)	27	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Atorvastatin(DB01076)													---	---	---	---
ITSN2	50618	broad.mit.edu	37	2	24443879	24443879	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24443879C>A	uc002rfe.2	-	30	3892	c.3634G>T	c.(3634-3636)GGC>TGC	p.G1212C	ITSN2_uc002rff.2_Missense_Mutation_p.G1185C|ITSN2_uc002rfg.2_Missense_Mutation_p.G1212C	NM_006277	NP_006268	Q9NZM3	ITSN2_HUMAN	intersectin 2 isoform 1	1212	DH.				endocytosis|regulation of Rho protein signal transduction	cytoplasm	calcium ion binding|Rho guanyl-nucleotide exchange factor activity|SH3/SH2 adaptor activity			kidney(2)|ovary(1)|central_nervous_system(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
ADCY3	109	broad.mit.edu	37	2	25044488	25044488	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25044488G>A	uc002rfs.3	-	19	3224	c.3025C>T	c.(3025-3027)CGC>TGC	p.R1009C	ADCY3_uc002rfr.3_Missense_Mutation_p.R596C|ADCY3_uc010ykm.1_Missense_Mutation_p.R1010C	NM_004036	NP_004027	O60266	ADCY3_HUMAN	adenylate cyclase 3	1009	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|sensory perception of smell|synaptic transmission|transmembrane transport|water transport	cytoplasm|integral to plasma membrane	ATP binding|calmodulin binding|metal ion binding			breast(3)|ovary(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)																	---	---	---	---
DNMT3A	1788	broad.mit.edu	37	2	25462047	25462047	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25462047G>A	uc002rgc.2	-	20	2617	c.2360C>T	c.(2359-2361)GCT>GTT	p.A787V	DNMT3A_uc002rgd.2_Missense_Mutation_p.A787V|DNMT3A_uc010eyi.2_RNA|DNMT3A_uc002rgb.2_Missense_Mutation_p.A598V	NM_022552	NP_072046	Q9Y6K1	DNM3A_HUMAN	DNA cytosine methyltransferase 3 alpha isoform	787					regulation of gene expression by genetic imprinting	cytoplasm|euchromatin|nuclear matrix	DNA (cytosine-5-)-methyltransferase activity|DNA binding|metal ion binding|protein binding			haematopoietic_and_lymphoid_tissue(133)|lung(4)|ovary(3)	140	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)							Mis|F|N|S		AML								---	---	---	---
DNMT3A	1788	broad.mit.edu	37	2	25463523	25463523	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25463523C>T	uc002rgc.2	-	18	2416	c.2159G>A	c.(2158-2160)CGC>CAC	p.R720H	DNMT3A_uc002rgd.2_Missense_Mutation_p.R720H|DNMT3A_uc010eyi.2_RNA|DNMT3A_uc002rgb.2_Missense_Mutation_p.R531H	NM_022552	NP_072046	Q9Y6K1	DNM3A_HUMAN	DNA cytosine methyltransferase 3 alpha isoform	720					regulation of gene expression by genetic imprinting	cytoplasm|euchromatin|nuclear matrix	DNA (cytosine-5-)-methyltransferase activity|DNA binding|metal ion binding|protein binding			haematopoietic_and_lymphoid_tissue(133)|lung(4)|ovary(3)	140	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)							Mis|F|N|S		AML								---	---	---	---
DNMT3A	1788	broad.mit.edu	37	2	25523073	25523073	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25523073G>A	uc002rgc.2	-	3	369	c.112C>T	c.(112-114)CGC>TGC	p.R38C	DNMT3A_uc002rgd.2_Missense_Mutation_p.R38C|DNMT3A_uc010eyi.2_RNA|DNMT3A_uc002rge.2_Missense_Mutation_p.R35C|DNMT3A_uc002rgf.2_Missense_Mutation_p.R38C	NM_022552	NP_072046	Q9Y6K1	DNM3A_HUMAN	DNA cytosine methyltransferase 3 alpha isoform	38					regulation of gene expression by genetic imprinting	cytoplasm|euchromatin|nuclear matrix	DNA (cytosine-5-)-methyltransferase activity|DNA binding|metal ion binding|protein binding	p.R38H(1)		haematopoietic_and_lymphoid_tissue(133)|lung(4)|ovary(3)	140	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)							Mis|F|N|S		AML								---	---	---	---
ASXL2	55252	broad.mit.edu	37	2	25965518	25965518	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:25965518T>G	uc002rgs.2	-	12	3909	c.3688A>C	c.(3688-3690)AAT>CAT	p.N1230H	ASXL2_uc002rgt.1_Missense_Mutation_p.N713H	NM_018263	NP_060733	Q76L83	ASXL2_HUMAN	additional sex combs like 2	1230					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|protein binding			pancreas(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
KIF3C	3797	broad.mit.edu	37	2	26203459	26203459	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26203459C>T	uc002rgu.2	-	1	1985	c.1328G>A	c.(1327-1329)CGC>CAC	p.R443H	KIF3C_uc010eyj.1_RNA|KIF3C_uc010ykr.1_Missense_Mutation_p.R443H	NM_002254	NP_002245	O14782	KIF3C_HUMAN	kinesin family member 3C	443	Potential.				blood coagulation|microtubule-based movement	cytosol|kinesin complex|microtubule	ATP binding|microtubule motor activity			ovary(3)|skin(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
GPR113	165082	broad.mit.edu	37	2	26534540	26534540	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:26534540G>T	uc002rhe.3	-	11	2056	c.2056C>A	c.(2056-2058)CTT>ATT	p.L686I	GPR113_uc010yky.1_Missense_Mutation_p.L617I|GPR113_uc002rhb.1_Missense_Mutation_p.L289I|GPR113_uc010eyk.1_Missense_Mutation_p.L487I|GPR113_uc002rhc.1_Missense_Mutation_p.L289I|GPR113_uc002rhd.1_RNA	NM_001145168	NP_001138640	Q8IZF5	GP113_HUMAN	G-protein coupled receptor 113 isoform 1	686	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(4)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
ABHD1	84696	broad.mit.edu	37	2	27353288	27353288	+	Intron	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27353288A>T	uc002rit.2	+						ABHD1_uc002riu.2_Intron|ABHD1_uc002riv.2_Intron	NM_032604	NP_115993			abhydrolase domain-containing protein 1							integral to membrane	carboxylesterase activity				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
PREB	10113	broad.mit.edu	37	2	27354610	27354610	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27354610C>T	uc002rix.1	-	8	1342	c.1089G>A	c.(1087-1089)GGG>GGA	p.G363G	PREB_uc002riy.1_Silent_p.G291G|PREB_uc002riz.1_RNA|PREB_uc002rja.1_Silent_p.G305G	NM_013388	NP_037520	Q9HCU5	PREB_HUMAN	prolactin regulatory element binding protein	363	Cytoplasmic (Potential).				COPII vesicle coating|post-translational protein modification|protein N-linked glycosylation via asparagine|protein transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	endoplasmic reticulum membrane|integral to membrane|nucleus	DNA binding|guanyl-nucleotide exchange factor activity|protein binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
SLC5A6	8884	broad.mit.edu	37	2	27427681	27427681	+	Missense_Mutation	SNP	G	A	A	rs151071040		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27427681G>A	uc002rjd.2	-	8	1244	c.853C>T	c.(853-855)CGC>TGC	p.R285C	SLC5A6_uc010eyv.1_Missense_Mutation_p.R285C	NM_021095	NP_066918	Q9Y289	SC5A6_HUMAN	solute carrier family 5 (sodium-dependent	285					biotin metabolic process|pantothenate metabolic process	integral to plasma membrane|membrane fraction	sodium-dependent multivitamin transmembrane transporter activity			ovary(2)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Biotin(DB00121)|Lipoic Acid(DB00166)													---	---	---	---
GTF3C2	2976	broad.mit.edu	37	2	27551413	27551413	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27551413G>A	uc002rjv.1	-	17	2541	c.2178C>T	c.(2176-2178)TCC>TCT	p.S726S	MPV17_uc002rjt.2_5'Flank|GTF3C2_uc010eyy.1_Silent_p.S181S|GTF3C2_uc002rju.1_Silent_p.S737S|GTF3C2_uc002rjw.1_Silent_p.S726S	NM_001521	NP_001512	Q8WUA4	TF3C2_HUMAN	general transcription factor IIIC, polypeptide	726						transcription factor TFIIIC complex				ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
EIF2B4	8890	broad.mit.edu	37	2	27587673	27587673	+	Silent	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27587673T>G	uc002rkb.2	-	12	1427	c.1284A>C	c.(1282-1284)CGA>CGC	p.R428R	EIF2B4_uc002rjz.2_Silent_p.R448R|EIF2B4_uc002rka.2_Silent_p.R413R|EIF2B4_uc002rkc.2_Silent_p.R427R|EIF2B4_uc002rkd.2_Silent_p.R222R|EIF2B4_uc002rke.2_Silent_p.R397R	NM_001034116	NP_001029288	Q9UI10	EI2BD_HUMAN	eukaryotic translation initiation factor 2B,	428					myelination|negative regulation of translational initiation in response to stress|oligodendrocyte development|ovarian follicle development|response to glucose stimulus|response to heat|response to peptide hormone stimulus	cytosol|eukaryotic translation initiation factor 2B complex	translation initiation factor activity|translation initiation factor binding				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
EIF2B4	8890	broad.mit.edu	37	2	27590906	27590906	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27590906G>A	uc002rkb.2	-	7	834	c.691C>T	c.(691-693)CGT>TGT	p.R231C	EIF2B4_uc002rjz.2_Missense_Mutation_p.R251C|EIF2B4_uc002rka.2_Missense_Mutation_p.R216C|EIF2B4_uc002rkc.2_Missense_Mutation_p.R230C|EIF2B4_uc002rkd.2_Missense_Mutation_p.R25C|EIF2B4_uc002rke.2_Missense_Mutation_p.R200C|EIF2B4_uc002rkf.1_3'UTR|SNX17_uc010ylj.1_5'Flank|SNX17_uc002rkg.1_5'Flank|SNX17_uc010ylk.1_5'Flank|SNX17_uc010eza.1_5'Flank|SNX17_uc002rki.1_5'Flank|SNX17_uc002rkh.1_5'Flank|SNX17_uc010yll.1_5'Flank|SNX17_uc010ylm.1_5'Flank|SNX17_uc010yln.1_5'Flank|SNX17_uc010ylo.1_5'Flank|SNX17_uc010ylp.1_5'Flank	NM_001034116	NP_001029288	Q9UI10	EI2BD_HUMAN	eukaryotic translation initiation factor 2B,	231					myelination|negative regulation of translational initiation in response to stress|oligodendrocyte development|ovarian follicle development|response to glucose stimulus|response to heat|response to peptide hormone stimulus	cytosol|eukaryotic translation initiation factor 2B complex	translation initiation factor activity|translation initiation factor binding				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)																	---	---	---	---
GCKR	2646	broad.mit.edu	37	2	27730133	27730133	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27730133T>C	uc002rky.2	+	13	1164	c.1098T>C	c.(1096-1098)GGT>GGC	p.G366G	GCKR_uc010ezd.2_Silent_p.G364G|GCKR_uc010ylu.1_Silent_p.G176G	NM_001486	NP_001477	Q14397	GCKR_HUMAN	glucokinase regulatory protein	366	SIS 2.				carbohydrate metabolic process|glucose transport|negative regulation of glucokinase activity|positive regulation of gene expression|protein import into nucleus, translocation|regulation of glucose transport|response to fructose stimulus|transmembrane transport|triglyceride homeostasis|urate metabolic process	cytosol|nucleoplasm	fructose-6-phosphate binding|protein binding			ovary(2)	2	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
C2orf16	84226	broad.mit.edu	37	2	27800465	27800465	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27800465C>T	uc002rkz.3	+	1	1077	c.1026C>T	c.(1024-1026)CAC>CAT	p.H342H		NM_032266	NP_115642	Q68DN1	CB016_HUMAN	hypothetical protein LOC84226	342										large_intestine(1)	1	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
ZNF512	84450	broad.mit.edu	37	2	27806535	27806535	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27806535C>T	uc002rla.2	+	2	128	c.41C>T	c.(40-42)CCC>CTC	p.P14L	ZNF512_uc010ylv.1_5'UTR|ZNF512_uc010ylw.1_Missense_Mutation_p.P14L|ZNF512_uc002rlb.2_Intron|ZNF512_uc010ylx.1_5'UTR|ZNF512_uc002rlc.2_Intron|ZNF512_uc010yly.1_Intron|ZNF512_uc010ylz.1_5'UTR	NM_032434	NP_115810	Q96ME7	ZN512_HUMAN	zinc finger protein 512	14					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
SLC4A1AP	22950	broad.mit.edu	37	2	27888071	27888071	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27888071A>G	uc002rlk.3	+	2	1212	c.930A>G	c.(928-930)GAA>GAG	p.E310E	SUPT7L_uc002rlh.1_5'Flank|SUPT7L_uc002rli.1_5'Flank|SUPT7L_uc010ymf.1_5'Flank|SUPT7L_uc002rlj.1_5'Flank|SUPT7L_uc010ezh.1_5'Flank	NM_018158	NP_060628	Q9BWU0	NADAP_HUMAN	solute carrier family 4 (anion exchanger),	310						cytoplasm|nucleus	double-stranded RNA binding|protein binding				0	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
MRPL33	9553	broad.mit.edu	37	2	28002338	28002338	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28002338C>T	uc002rlm.1	+	4	248	c.187C>T	c.(187-189)CGC>TGC	p.R63C	MRPL33_uc002rln.1_Missense_Mutation_p.T27M	NM_004891	NP_004882	O75394	RM33_HUMAN	mitochondrial ribosomal protein L33 isoform a	63					translation	mitochondrion|ribosome	structural constituent of ribosome				0	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
PLB1	151056	broad.mit.edu	37	2	28804935	28804935	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28804935G>A	uc002rmb.1	+	24	1567	c.1567G>A	c.(1567-1569)GTC>ATC	p.V523I	PLB1_uc010ezj.1_Intron|PLB1_uc002rmc.2_Missense_Mutation_p.V211I|PLB1_uc002rmd.1_Missense_Mutation_p.V33I	NM_153021	NP_694566	Q6P1J6	PLB1_HUMAN	phospholipase B1 precursor	523	4 X 308-326 AA approximate repeats.|2.|Extracellular (Potential).				lipid catabolic process|retinoid metabolic process|steroid metabolic process	apical plasma membrane|integral to membrane	lysophospholipase activity|phospholipase A2 activity|retinyl-palmitate esterase activity			ovary(4)|large_intestine(2)|skin(2)|breast(1)	9	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
PLB1	151056	broad.mit.edu	37	2	28865882	28865882	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:28865882C>T	uc002rmb.1	+	58	4332	c.4332C>T	c.(4330-4332)GGC>GGT	p.G1444G	PLB1_uc010ezj.1_Silent_p.G1433G|PLB1_uc002rme.1_Silent_p.G409G|PLB1_uc002rmf.1_RNA	NM_153021	NP_694566	Q6P1J6	PLB1_HUMAN	phospholipase B1 precursor	1444	Necessary for membrane localization (By similarity).|Cytoplasmic (Potential).				lipid catabolic process|retinoid metabolic process|steroid metabolic process	apical plasma membrane|integral to membrane	lysophospholipase activity|phospholipase A2 activity|retinyl-palmitate esterase activity			ovary(4)|large_intestine(2)|skin(2)|breast(1)	9	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
FAM179A	165186	broad.mit.edu	37	2	29222126	29222126	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29222126T>C	uc010ezl.2	+	4	570	c.219T>C	c.(217-219)GGT>GGC	p.G73G	FAM179A_uc010ymm.1_Silent_p.G73G	NM_199280	NP_954974	Q6ZUX3	F179A_HUMAN	hypothetical protein LOC165186	73							binding			ovary(3)|skin(1)	4																		---	---	---	---
C2orf71	388939	broad.mit.edu	37	2	29295833	29295833	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29295833C>A	uc002rmt.1	-	1	1295	c.1295G>T	c.(1294-1296)AGC>ATC	p.S432I		NM_001029883	NP_001025054	A6NGG8	CB071_HUMAN	hypothetical protein LOC388939	432					response to stimulus|visual perception	photoreceptor outer segment				skin(1)	1																		---	---	---	---
CAPN13	92291	broad.mit.edu	37	2	30977174	30977174	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:30977174C>T	uc002rnn.2	-	9	1099	c.923G>A	c.(922-924)CGG>CAG	p.R308Q	CAPN13_uc002rnp.1_Missense_Mutation_p.R308Q	NM_144575	NP_653176	Q6MZZ7	CAN13_HUMAN	calpain 13	308	Calpain catalytic.				proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			large_intestine(1)|ovary(1)	2	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
XDH	7498	broad.mit.edu	37	2	31560669	31560669	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31560669C>T	uc002rnv.1	-	35	3868	c.3789G>A	c.(3787-3789)CCG>CCA	p.P1263P		NM_000379	NP_000370	P47989	XDH_HUMAN	xanthine dehydrogenase	1263					purine nucleotide catabolic process|xanthine catabolic process	cytosol|extracellular region|peroxisome	2 iron, 2 sulfur cluster binding|electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|molybdopterin cofactor binding|protein homodimerization activity|xanthine dehydrogenase activity|xanthine oxidase activity			skin(4)|breast(2)|ovary(1)|central_nervous_system(1)	8	Acute lymphoblastic leukemia(172;0.155)				Allopurinol(DB00437)|Carvedilol(DB01136)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Desflurane(DB01189)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|NADH(DB00157)|Nitrofurazone(DB00336)|Papaverine(DB01113)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Rasburicase(DB00049)|Spermine(DB00127)|Trifluoperazine(DB00831)|Vitamin E(DB00163)													---	---	---	---
SRD5A2	6716	broad.mit.edu	37	2	31805963	31805963	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:31805963C>T	uc002rnw.1	-	1	78	c.7G>A	c.(7-9)GTT>ATT	p.V3I		NM_000348	NP_000339	P31213	S5A2_HUMAN	3-oxo-5 alpha-steroid 4-dehydrogenase 2	3					androgen biosynthetic process|cell differentiation|cell-cell signaling|male gonad development	endoplasmic reticulum membrane|integral to membrane|microsome	3-oxo-5-alpha-steroid 4-dehydrogenase activity|sterol 5-alpha reductase activity				0	Acute lymphoblastic leukemia(172;0.155)				Azelaic Acid(DB00548)|Dutasteride(DB01126)													---	---	---	---
BIRC6	57448	broad.mit.edu	37	2	32689786	32689786	+	Silent	SNP	C	T	T	rs147771042		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32689786C>T	uc010ezu.2	+	25	5285	c.5151C>T	c.(5149-5151)TCC>TCT	p.S1717S		NM_016252	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat-containing 6	1717					anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
BIRC6	57448	broad.mit.edu	37	2	32718730	32718730	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32718730G>C	uc010ezu.2	+	45	8598	c.8464G>C	c.(8464-8466)GAA>CAA	p.E2822Q		NM_016252	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat-containing 6	2822					anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
BIRC6	57448	broad.mit.edu	37	2	32724832	32724832	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32724832T>G	uc010ezu.2	+	46	8821	c.8687T>G	c.(8686-8688)CTC>CGC	p.L2896R		NM_016252	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat-containing 6	2896					anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)																	---	---	---	---
LTBP1	4052	broad.mit.edu	37	2	33505228	33505228	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33505228A>G	uc002ros.2	+						LTBP1_uc002rot.2_Intron|LTBP1_uc002rou.2_Intron|LTBP1_uc002rov.2_Intron|LTBP1_uc010ymz.1_Intron|LTBP1_uc010yna.1_Intron	NM_206943	NP_996826			latent transforming growth factor beta binding						negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta	proteinaceous extracellular matrix	calcium ion binding|growth factor binding|transforming growth factor beta receptor activity			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)	8	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)																---	---	---	---
LTBP1	4052	broad.mit.edu	37	2	33526602	33526602	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33526602C>T	uc002ros.2	+	22	3375	c.3375C>T	c.(3373-3375)TGC>TGT	p.C1125C	LTBP1_uc002rot.2_Silent_p.C799C|LTBP1_uc002rou.2_Silent_p.C798C|LTBP1_uc002rov.2_Silent_p.C745C|LTBP1_uc010ymz.1_Silent_p.C798C|LTBP1_uc010yna.1_Silent_p.C745C|LTBP1_uc010ynb.1_Silent_p.C64C	NM_206943	NP_996826	Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding	1124	EGF-like 10; calcium-binding (Potential).				negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta	proteinaceous extracellular matrix	calcium ion binding|growth factor binding|transforming growth factor beta receptor activity			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)	8	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)																---	---	---	---
LTBP1	4052	broad.mit.edu	37	2	33526610	33526610	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:33526610G>A	uc002ros.2	+	22	3383	c.3383G>A	c.(3382-3384)CGT>CAT	p.R1128H	LTBP1_uc002rot.2_Missense_Mutation_p.R802H|LTBP1_uc002rou.2_Missense_Mutation_p.R801H|LTBP1_uc002rov.2_Missense_Mutation_p.R748H|LTBP1_uc010ymz.1_Missense_Mutation_p.R801H|LTBP1_uc010yna.1_Missense_Mutation_p.R748H|LTBP1_uc010ynb.1_Missense_Mutation_p.R67H	NM_206943	NP_996826	Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding	1127	EGF-like 10; calcium-binding (Potential).				negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta	proteinaceous extracellular matrix	calcium ion binding|growth factor binding|transforming growth factor beta receptor activity			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)	8	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)																---	---	---	---
HEATR5B	54497	broad.mit.edu	37	2	37255938	37255938	+	Silent	SNP	G	T	T	rs147083195		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37255938G>T	uc002rpp.1	-	23	3583	c.3487C>A	c.(3487-3489)CGA>AGA	p.R1163R		NM_019024	NP_061897	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	1163							binding			ovary(5)|skin(2)|breast(1)	8		all_hematologic(82;0.21)																---	---	---	---
CCDC75	253635	broad.mit.edu	37	2	37321339	37321339	+	Splice_Site	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37321339G>A	uc010ezz.2	+	7	787	c.642_splice	c.e7+1	p.S214_splice	CCDC75_uc002rpr.3_Splice_Site_p.S111_splice	NM_174931	NP_777591			coiled-coil domain containing 75							intracellular	nucleic acid binding				0		all_hematologic(82;0.21)																---	---	---	---
SULT6B1	391365	broad.mit.edu	37	2	37395116	37395116	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:37395116C>A	uc002rpu.2	-	7	781	c.760G>T	c.(760-762)GGA>TGA	p.G254*	SULT6B1_uc010yni.1_RNA	NM_001032377	NP_001027549	Q6IMI4	ST6B1_HUMAN	sulfotransferase family, cytosolic, 6B, member	292						cytoplasm	sulfotransferase activity			ovary(1)|breast(1)|central_nervous_system(1)	3		all_hematologic(82;0.248)																---	---	---	---
SOS1	6654	broad.mit.edu	37	2	39222483	39222483	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:39222483A>G	uc002rrk.3	-	20	3168	c.3127T>C	c.(3127-3129)TCA>CCA	p.S1043P	SOS1_uc002rrj.3_Missense_Mutation_p.S657P	NM_005633	NP_005624	Q07889	SOS1_HUMAN	son of sevenless homolog 1	1043					apoptosis|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	cytosol	DNA binding|protein binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			ovary(4)|breast(3)|lung(2)|central_nervous_system(1)	10		all_hematologic(82;0.21)												Noonan_syndrome				---	---	---	---
SLC8A1	6546	broad.mit.edu	37	2	40366664	40366664	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:40366664T>C	uc002rrx.2	-	9	2446	c.2422A>G	c.(2422-2424)ATC>GTC	p.I808V	uc002rrw.2_Intron|SLC8A1_uc002rry.2_Missense_Mutation_p.I803V|SLC8A1_uc002rrz.2_Missense_Mutation_p.I795V|SLC8A1_uc002rsa.2_Missense_Mutation_p.I772V|SLC8A1_uc002rsd.3_Missense_Mutation_p.I772V	NM_021097	NP_066920	P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium	808	Helical; (Potential).				cell communication|muscle contraction|platelet activation	integral to plasma membrane	calcium:sodium antiporter activity|calmodulin binding|heat shock protein binding			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)													---	---	---	---
KCNG3	170850	broad.mit.edu	37	2	42720328	42720328	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:42720328C>T	uc002rsn.2	-	1	910	c.314G>A	c.(313-315)GGC>GAC	p.G105D	MTA3_uc002rso.1_5'Flank|KCNG3_uc002rsm.2_Missense_Mutation_p.G105D	NM_133329	NP_579875	Q8TAE7	KCNG3_HUMAN	potassium voltage-gated channel, subfamily G,	105	Cytoplasmic (Potential).					endoplasmic reticulum|voltage-gated potassium channel complex	protein binding			central_nervous_system(1)	1																		---	---	---	---
THADA	63892	broad.mit.edu	37	2	43735796	43735796	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:43735796G>A	uc002rsw.3	-	23	3850	c.3498C>T	c.(3496-3498)TTC>TTT	p.F1166F	THADA_uc010far.2_Silent_p.F435F|THADA_uc002rsx.3_Silent_p.F1166F|THADA_uc002rsy.3_RNA|THADA_uc010fas.1_RNA|THADA_uc002rsz.2_Silent_p.F875F|THADA_uc010fat.1_Silent_p.F313F|THADA_uc002rta.2_Silent_p.F876F	NM_001083953	NP_001077422	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	1166							binding			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)																---	---	---	---
ABCG5	64240	broad.mit.edu	37	2	44053641	44053641	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44053641C>T	uc002rtn.2	-	6	794	c.654G>A	c.(652-654)GAG>GAA	p.E218E	ABCG5_uc002rtm.2_Intron|ABCG5_uc002rto.2_Intron|ABCG5_uc002rtp.2_Intron	NM_022436	NP_071881	Q9H222	ABCG5_HUMAN	ATP-binding cassette sub-family G member 5	218	ABC transporter.|Cytoplasmic (Potential).				cholesterol efflux|cholesterol homeostasis|excretion|lipid metabolic process|negative regulation of intestinal cholesterol absorption|negative regulation of intestinal phytosterol absorption	apical plasma membrane|integral to membrane	ATP binding|ATPase activity|protein heterodimerization activity			ovary(1)|skin(1)	2		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)																---	---	---	---
LRPPRC	10128	broad.mit.edu	37	2	44145525	44145525	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44145525T>C	uc002rtr.2	-	28	2967	c.2909A>G	c.(2908-2910)GAC>GGC	p.D970G	LRPPRC_uc010yob.1_Missense_Mutation_p.D870G	NM_133259	NP_573566	P42704	LPPRC_HUMAN	leucine-rich PPR motif-containing protein	970	PPR 14.				mitochondrion transport along microtubule|mRNA transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	condensed nuclear chromosome|cytoskeleton|mitochondrial nucleoid|nuclear inner membrane|nuclear outer membrane|nucleoplasm|perinuclear region of cytoplasm	beta-tubulin binding|microtubule binding|RNA binding			ovary(2)|skin(1)	3		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)																---	---	---	---
SRBD1	55133	broad.mit.edu	37	2	45800393	45800393	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:45800393G>A	uc002rus.2	-	9	1334	c.1258C>T	c.(1258-1260)CTC>TTC	p.L420F		NM_018079	NP_060549	Q8N5C6	SRBD1_HUMAN	S1 RNA binding domain 1	420					nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		hydrolase activity, acting on ester bonds|RNA binding			central_nervous_system(1)	1		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	LUSC - Lung squamous cell carcinoma(58;0.0917)|Lung(47;0.154)															---	---	---	---
C2orf61	285051	broad.mit.edu	37	2	47378549	47378549	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:47378549G>A	uc002rvs.2	-	3	374	c.247C>T	c.(247-249)CCA>TCA	p.P83S	C2orf61_uc010fbd.2_RNA|C2orf61_uc010yog.1_Missense_Mutation_p.P83S	NM_173649	NP_775920	Q8N801	CB061_HUMAN	hypothetical protein LOC285051 isoform 2	83								p.0?(2)			0		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)															---	---	---	---
FSHR	2492	broad.mit.edu	37	2	49190419	49190419	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:49190419A>G	uc002rww.2	-	10	1615	c.1541T>C	c.(1540-1542)GTG>GCG	p.V514A	FSHR_uc002rwx.2_Missense_Mutation_p.V452A|FSHR_uc010fbn.2_Missense_Mutation_p.V488A	NM_000145	NP_000136	P23945	FSHR_HUMAN	follicle stimulating hormone receptor isoform 1	514	Extracellular (Potential).				female gamete generation|male gonad development|spermatogenesis	integral to membrane|plasma membrane	follicle-stimulating hormone receptor activity|protein binding			ovary(4)|lung(2)|central_nervous_system(1)|skin(1)	8		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Urofollitropin(DB00094)									Gonadal_Dysgenesis_46_XX				---	---	---	---
NRXN1	9378	broad.mit.edu	37	2	50464108	50464108	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:50464108G>A	uc010fbp.2	-	2	1067	c.260C>T	c.(259-261)GCT>GTT	p.A87V	NRXN1_uc002rxb.3_Missense_Mutation_p.P794L|NRXN1_uc010fbq.2_Missense_Mutation_p.P1162L|NRXN1_uc002rxe.3_Missense_Mutation_p.P1122L|NRXN1_uc002rxc.1_RNA	NM_138735	NP_620072	P58400	NRX1B_HUMAN	neurexin 1 isoform beta precursor	87	Extracellular (Potential).				angiogenesis|neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)															---	---	---	---
PSME4	23198	broad.mit.edu	37	2	54120000	54120000	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54120000A>C	uc002rxp.2	-	36	4192	c.4136T>G	c.(4135-4137)GTT>GGT	p.V1379G	PSME4_uc010yop.1_Missense_Mutation_p.V1265G|PSME4_uc010yoq.1_RNA|PSME4_uc010fbu.1_Missense_Mutation_p.V754G|PSME4_uc010fbv.1_Missense_Mutation_p.V523G	NM_014614	NP_055429	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator	1379	HEAT 4.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|M/G1 transition of mitotic cell cycle|mRNA metabolic process|multicellular organismal development|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|spermatogenesis|viral reproduction	nuclear speck|proteasome complex	binding			ovary(2)|breast(2)|pancreas(1)	5			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)															---	---	---	---
PSME4	23198	broad.mit.edu	37	2	54147328	54147328	+	Splice_Site	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54147328A>G	uc002rxp.2	-	19	2476	c.2420_splice	c.e19+1	p.R807_splice	PSME4_uc010yop.1_Splice_Site_p.R693_splice|PSME4_uc010yoq.1_Splice_Site|PSME4_uc010fbu.1_Splice_Site_p.R182_splice|PSME4_uc010fbv.1_Intron	NM_014614	NP_055429			proteasome (prosome, macropain) activator						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|M/G1 transition of mitotic cell cycle|mRNA metabolic process|multicellular organismal development|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|spermatogenesis|viral reproduction	nuclear speck|proteasome complex	binding			ovary(2)|breast(2)|pancreas(1)	5			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)															---	---	---	---
SPTBN1	6711	broad.mit.edu	37	2	54856717	54856717	+	Missense_Mutation	SNP	G	A	A	rs141532384		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54856717G>A	uc002rxu.2	+	14	2695	c.2446G>A	c.(2446-2448)GAG>AAG	p.E816K	SPTBN1_uc002rxv.1_Missense_Mutation_p.E816K|SPTBN1_uc002rxx.2_Missense_Mutation_p.E803K	NM_003128	NP_003119	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1 isoform 1	816	Spectrin 5.				actin filament capping|axon guidance	cytosol|nucleolus|plasma membrane|sarcomere|spectrin	actin binding|calmodulin binding|protein binding|structural constituent of cytoskeleton			ovary(3)|breast(2)|central_nervous_system(2)|skin(1)	8			Lung(47;0.24)															---	---	---	---
SPTBN1	6711	broad.mit.edu	37	2	54872389	54872389	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:54872389G>A	uc002rxu.2	+	21	4542	c.4293G>A	c.(4291-4293)GTG>GTA	p.V1431V	SPTBN1_uc002rxx.2_Silent_p.V1418V	NM_003128	NP_003119	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1 isoform 1	1431	Spectrin 11.				actin filament capping|axon guidance	cytosol|nucleolus|plasma membrane|sarcomere|spectrin	actin binding|calmodulin binding|protein binding|structural constituent of cytoskeleton			ovary(3)|breast(2)|central_nervous_system(2)|skin(1)	8			Lung(47;0.24)															---	---	---	---
PNPT1	87178	broad.mit.edu	37	2	55907991	55907991	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55907991G>A	uc002rzf.2	-	6	569	c.516C>T	c.(514-516)GGC>GGT	p.G172G	PNPT1_uc002rzg.2_RNA	NM_033109	NP_149100	Q8TCS8	PNPT1_HUMAN	polyribonucleotide nucleotidyltransferase 1	172					mRNA catabolic process|RNA processing	plasma membrane	3'-5'-exoribonuclease activity|polyribonucleotide nucleotidyltransferase activity|RNA binding				0			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)															---	---	---	---
BCL11A	53335	broad.mit.edu	37	2	60688057	60688057	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:60688057C>T	uc002sae.1	-	4	2218	c.1990G>A	c.(1990-1992)GCG>ACG	p.A664T	BCL11A_uc002sab.2_Missense_Mutation_p.A664T|BCL11A_uc002sac.2_Intron|BCL11A_uc010ypi.1_Missense_Mutation_p.A333T|BCL11A_uc010ypj.1_Missense_Mutation_p.A630T|BCL11A_uc002sad.1_Missense_Mutation_p.A512T|BCL11A_uc002saf.1_Missense_Mutation_p.A630T	NM_022893	NP_075044	Q9H165	BC11A_HUMAN	B-cell CLL/lymphoma 11A isoform 1	664					negative regulation of axon extension|negative regulation of collateral sprouting|negative regulation of dendrite development|positive regulation of collateral sprouting|positive regulation of neuron projection development|positive regulation of transcription from RNA polymerase II promoter|protein sumoylation|regulation of dendrite development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|cytoplasm|nucleus|nucleus	nucleic acid binding|protein heterodimerization activity|protein homodimerization activity|zinc ion binding			central_nervous_system(6)|breast(3)|ovary(2)|skin(2)	13			LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199)					T	IGH@	B-CLL								---	---	---	---
PAPOLG	64895	broad.mit.edu	37	2	61019430	61019430	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61019430T>C	uc002sai.2	+						PAPOLG_uc002saj.2_Intron|PAPOLG_uc002sak.2_Intron|PAPOLG_uc010fch.2_Intron	NM_022894	NP_075045			poly(A) polymerase gamma						mRNA processing|RNA polyadenylation|transcription, DNA-dependent	nucleus	ATP binding|metal ion binding|polynucleotide adenylyltransferase activity|RNA binding			ovary(1)|central_nervous_system(1)	2	all_hematologic(2;0.0797)		LUSC - Lung squamous cell carcinoma(5;1.19e-07)|Lung(5;2.86e-06)|Epithelial(17;0.0768)															---	---	---	---
PEX13	5194	broad.mit.edu	37	2	61258940	61258940	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61258940C>A	uc002sau.3	+	2	562	c.479C>A	c.(478-480)GCT>GAT	p.A160D		NM_002618	NP_002609	Q92968	PEX13_HUMAN	peroxisomal biogenesis factor 13	160	Targeting to peroxisomes.|Lumenal (Potential).				cerebral cortex cell migration|fatty acid alpha-oxidation|locomotory behavior|microtubule-based peroxisome localization|neuron migration|protein import into peroxisome matrix, docking|suckling behavior	integral to peroxisomal membrane|membrane fraction	protein binding			skin(1)	1			LUSC - Lung squamous cell carcinoma(5;2.05e-06)|Lung(5;3.13e-05)|Epithelial(17;0.114)															---	---	---	---
USP34	9736	broad.mit.edu	37	2	61433981	61433981	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61433981G>T	uc002sbe.2	-	71	8982	c.8960C>A	c.(8959-8961)GCT>GAT	p.A2987D	USP34_uc002sbd.2_5'Flank	NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34	2987					positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)															---	---	---	---
VPS54	51542	broad.mit.edu	37	2	64196098	64196098	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64196098A>G	uc002scq.2	-	5	648	c.485T>C	c.(484-486)GTA>GCA	p.V162A	VPS54_uc002scp.2_Missense_Mutation_p.V150A|VPS54_uc010fct.2_Missense_Mutation_p.V45A	NM_016516	NP_057600	Q9P1Q0	VPS54_HUMAN	vacuolar protein sorting 54 isoform 1	162					protein transport|retrograde transport, endosome to Golgi						0																		---	---	---	---
ARHGAP25	9938	broad.mit.edu	37	2	68962343	68962343	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68962343A>T	uc002seu.2	+	1	376	c.12A>T	c.(10-12)AAA>AAT	p.K4N	ARHGAP25_uc010yqk.1_Intron|ARHGAP25_uc010fdg.2_Missense_Mutation_p.K4N|ARHGAP25_uc010yql.1_Missense_Mutation_p.K4N	NM_001007231	NP_001007232	P42331	RHG25_HUMAN	Rho GTPase activating protein 25 isoform a	4					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(2)|breast(2)	4																		---	---	---	---
ANTXR1	84168	broad.mit.edu	37	2	69409754	69409754	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69409754C>T	uc002sfg.2	+	16	1671	c.1315C>T	c.(1315-1317)CGG>TGG	p.R439W		NM_032208	NP_115584	Q9H6X2	ANTR1_HUMAN	anthrax toxin receptor 1 isoform 1 precursor	439	Cytoplasmic (Potential).				actin cytoskeleton reorganization|substrate adhesion-dependent cell spreading	filopodium membrane|integral to membrane|lamellipodium membrane	actin filament binding|collagen binding|metal ion binding|protein binding|transmembrane receptor activity			ovary(2)|skin(2)	4														Familial_Infantile_Hemangioma				---	---	---	---
NFU1	27247	broad.mit.edu	37	2	69627579	69627579	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:69627579A>C	uc002sfk.2	-	7	836	c.637T>G	c.(637-639)TGC>GGC	p.C213G	NFU1_uc002sfj.2_Missense_Mutation_p.C189G|NFU1_uc002sfl.2_Missense_Mutation_p.C72G|NFU1_uc002sfm.2_Missense_Mutation_p.C72G|NFU1_uc010fdi.2_Intron|NFU1_uc002sfn.1_Missense_Mutation_p.C213G	NM_001002755	NP_001002755	Q9UMS0	NFU1_HUMAN	HIRA interacting protein 5 isoform 2	213	NifU.				iron-sulfur cluster assembly	cytosol|mitochondrion|nucleus	4 iron, 4 sulfur cluster binding|iron ion binding|protein binding				0																		---	---	---	---
C2orf42	54980	broad.mit.edu	37	2	70377554	70377554	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70377554T>C	uc002sgh.2	-	10	1987	c.1659A>G	c.(1657-1659)CAA>CAG	p.Q553Q		NM_017880	NP_060350	Q9NWW7	CB042_HUMAN	hypothetical protein LOC54980	553											0																		---	---	---	---
C2orf42	54980	broad.mit.edu	37	2	70377579	70377579	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70377579C>T	uc002sgh.2	-	10	1962	c.1634G>A	c.(1633-1635)CGG>CAG	p.R545Q		NM_017880	NP_060350	Q9NWW7	CB042_HUMAN	hypothetical protein LOC54980	545											0																		---	---	---	---
ADD2	119	broad.mit.edu	37	2	70901878	70901878	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70901878C>A	uc002sgz.2	-	14	2138	c.1673G>T	c.(1672-1674)AGC>ATC	p.S558I	ADD2_uc010fds.1_RNA|ADD2_uc002sgy.2_Missense_Mutation_p.S558I|ADD2_uc002sha.2_Missense_Mutation_p.S252I|ADD2_uc002sgx.2_Missense_Mutation_p.S558I|ADD2_uc010fdt.1_Missense_Mutation_p.S558I	NM_001617	NP_001608	P35612	ADDB_HUMAN	adducin 2 isoform a	558					actin filament bundle assembly|barbed-end actin filament capping|positive regulation of protein binding	cytoplasm|F-actin capping protein complex|plasma membrane	actin filament binding|calmodulin binding|metal ion binding|protein heterodimerization activity|protein homodimerization activity|spectrin binding			ovary(2)|pancreas(1)	3																		---	---	---	---
ANKRD53	79998	broad.mit.edu	37	2	71206914	71206914	+	Missense_Mutation	SNP	G	A	A	rs141661790		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71206914G>A	uc002shl.3	+	3	742	c.541G>A	c.(541-543)GTC>ATC	p.V181I	ANKRD53_uc002shk.3_Missense_Mutation_p.V181I|ANKRD53_uc002shm.3_Missense_Mutation_p.V147I	NM_001115116	NP_001108588	Q8N9V6	ANR53_HUMAN	ankyrin repeat domain 53 isoform a	181	ANK 2.										0																		---	---	---	---
NAGK	55577	broad.mit.edu	37	2	71300632	71300632	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:71300632G>A	uc002shp.3	+	6	893	c.487G>A	c.(487-489)GCA>ACA	p.A163T	NAGK_uc010fea.2_RNA|NAGK_uc002shq.3_Missense_Mutation_p.A14T|NAGK_uc002shr.2_Missense_Mutation_p.A112T	NM_017567	NP_060037	Q9UJ70	NAGK_HUMAN	N-Acetylglucosamine kinase	163					N-acetylglucosamine metabolic process|N-acetylmannosamine metabolic process		ATP binding|N-acetylglucosamine kinase activity|protein binding				0					N-Acetyl-D-glucosamine(DB00141)													---	---	---	---
RAB11FIP5	26056	broad.mit.edu	37	2	73315385	73315385	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73315385C>T	uc002siu.3	-	3	1602	c.1361G>A	c.(1360-1362)CGG>CAG	p.R454Q	RAB11FIP5_uc002sit.3_Missense_Mutation_p.R376Q	NM_015470	NP_056285	Q9BXF6	RFIP5_HUMAN	RAB11 family interacting protein 5 (class I)	454					protein transport	mitochondrial outer membrane|recycling endosome membrane	gamma-tubulin binding				0																		---	---	---	---
CCT7	10574	broad.mit.edu	37	2	73471709	73471709	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73471709G>A	uc002siz.2	+	6	586	c.484G>A	c.(484-486)GCT>ACT	p.A162T	CCT7_uc002sja.2_Intron|CCT7_uc010yrf.1_Missense_Mutation_p.A118T|CCT7_uc010feu.2_Missense_Mutation_p.A120T|CCT7_uc010yrg.1_Missense_Mutation_p.A62T|CCT7_uc010yrh.1_Missense_Mutation_p.A34T|CCT7_uc010yri.1_Missense_Mutation_p.A75T	NM_006429	NP_006420	Q99832	TCPH_HUMAN	chaperonin containing TCP1, subunit 7 isoform a	162					'de novo' posttranslational protein folding		ATP binding|unfolded protein binding				0																		---	---	---	---
ALMS1	7840	broad.mit.edu	37	2	73717319	73717319	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73717319G>A	uc002sje.1	+	12	8347	c.8236G>A	c.(8236-8238)GCA>ACA	p.A2746T	ALMS1_uc002sjf.1_Missense_Mutation_p.A2702T|ALMS1_uc002sjg.2_Missense_Mutation_p.A2132T|ALMS1_uc002sjh.1_Missense_Mutation_p.A2132T	NM_015120	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2744					G2/M transition of mitotic cell cycle	centrosome|cilium|cytosol|microtubule basal body|spindle pole				skin(3)|ovary(2)|breast(2)|pancreas(1)|lung(1)	9																		---	---	---	---
ALMS1	7840	broad.mit.edu	37	2	73800209	73800209	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73800209G>A	uc002sje.1	+	18	11319	c.11208G>A	c.(11206-11208)TCG>TCA	p.S3736S	ALMS1_uc002sjf.1_Silent_p.S3692S|ALMS1_uc002sjg.2_Silent_p.S3122S|ALMS1_uc002sjh.1_Silent_p.S3122S	NM_015120	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	3734					G2/M transition of mitotic cell cycle	centrosome|cilium|cytosol|microtubule basal body|spindle pole				skin(3)|ovary(2)|breast(2)|pancreas(1)|lung(1)	9																		---	---	---	---
DCTN1	1639	broad.mit.edu	37	2	74593384	74593384	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74593384C>T	uc002skx.2	-	23	3058	c.2747G>A	c.(2746-2748)CGG>CAG	p.R916Q	SLC4A5_uc002skl.2_5'Flank|DCTN1_uc002skt.1_5'Flank|DCTN1_uc002skv.2_Missense_Mutation_p.R782Q|DCTN1_uc002sku.2_Missense_Mutation_p.R782Q|DCTN1_uc002skw.1_Missense_Mutation_p.R892Q|DCTN1_uc010ffd.2_Missense_Mutation_p.R896Q|DCTN1_uc002sky.2_Missense_Mutation_p.R879Q	NM_004082	NP_004073	Q14203	DCTN1_HUMAN	dynactin 1 isoform 1	916					cell death|G2/M transition of mitotic cell cycle|mitosis|nervous system development	centrosome|cytosol|kinetochore|microtubule|spindle pole	motor activity|protein binding			ovary(3)|skin(2)	5																		---	---	---	---
MOGS	7841	broad.mit.edu	37	2	74689839	74689839	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74689839C>A	uc010ffj.2	-	4	1240	c.1077G>T	c.(1075-1077)CAG>CAT	p.Q359H	MOGS_uc010ffh.2_Missense_Mutation_p.Q84H|MOGS_uc010yrt.1_Missense_Mutation_p.Q240H|MOGS_uc010ffi.2_Missense_Mutation_p.Q253H	NM_006302	NP_006293	Q13724	MOGS_HUMAN	mannosyl-oligosaccharide glucosidase isoform 1	359	Lumenal (Potential).				oligosaccharide metabolic process|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane|membrane fraction	mannosyl-oligosaccharide glucosidase activity				0																		---	---	---	---
PCGF1	84759	broad.mit.edu	37	2	74733177	74733177	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74733177T>C	uc002slz.2	-	5	458	c.432A>G	c.(430-432)GCA>GCG	p.A144A	LBX2_uc002slw.2_5'Flank|PCGF1_uc002sly.2_Silent_p.A61A	NM_032673	NP_116062	Q9BSM1	PCGF1_HUMAN	polycomb group ring finger 1	144					histone H2A monoubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	PcG protein complex	protein C-terminus binding|zinc ion binding			ovary(1)	1																		---	---	---	---
LOXL3	84695	broad.mit.edu	37	2	74760730	74760730	+	3'UTR	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74760730C>T	uc002smp.1	-	14					LOXL3_uc002smo.1_3'UTR|LOXL3_uc010ffm.1_3'UTR|LOXL3_uc002smq.1_3'UTR	NM_032603	NP_115992			lysyl oxidase-like 3 precursor							extracellular space|membrane	copper ion binding|protein-lysine 6-oxidase activity|scavenger receptor activity				0																		---	---	---	---
SEMA4F	10505	broad.mit.edu	37	2	74900921	74900921	+	Missense_Mutation	SNP	G	A	A	rs141100984		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74900921G>A	uc002sna.1	+	7	899	c.788G>A	c.(787-789)CGC>CAC	p.R263H	SEMA4F_uc010ysb.1_3'UTR|SEMA4F_uc010ffq.1_Missense_Mutation_p.R230H|SEMA4F_uc010ffr.1_Intron|SEMA4F_uc002snb.1_5'UTR|SEMA4F_uc002snc.1_Intron	NM_004263	NP_004254	O95754	SEM4F_HUMAN	semaphorin W precursor	263	Sema.|Extracellular (Potential).				cell-cell signaling	endoplasmic reticulum|integral to plasma membrane	receptor activity			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
TACR1	6869	broad.mit.edu	37	2	75276802	75276802	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:75276802G>A	uc002sng.2	-	5	1566	c.981C>T	c.(979-981)AGC>AGT	p.S327S		NM_001058	NP_001049	P25103	NK1R_HUMAN	tachykinin receptor 1 isoform long	327	Cytoplasmic (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|detection of abiotic stimulus|mechanosensory behavior	integral to plasma membrane	protein binding			ovary(1)	1					Aprepitant(DB00673)|Ketamine(DB01221)|Vapreotide(DB04894)													---	---	---	---
SUCLG1	8802	broad.mit.edu	37	2	84668483	84668483	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:84668483A>C	uc002son.2	-	4	612	c.419T>G	c.(418-420)GTT>GGT	p.V140G	SUCLG1_uc010ysk.1_Missense_Mutation_p.V127G	NM_003849	NP_003840	P53597	SUCA_HUMAN	succinate-CoA ligase, GDP-forming alpha subunit	140					tricarboxylic acid cycle		ATP citrate synthase activity|GTP binding|succinate-CoA ligase (GDP-forming) activity				0					Succinic acid(DB00139)													---	---	---	---
C2orf89	129293	broad.mit.edu	37	2	85051281	85051281	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85051281A>G	uc010ysl.1	-	6	1219	c.1130T>C	c.(1129-1131)TTT>TCT	p.F377S	C2orf89_uc002sou.3_Missense_Mutation_p.F328S	NM_001080824	NP_001074293	Q86V40	CB089_HUMAN	hypothetical protein LOC129293 precursor	377	Extracellular (Potential).					integral to membrane				ovary(1)	1																		---	---	---	---
TGOLN2	10618	broad.mit.edu	37	2	85554616	85554616	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85554616G>C	uc010fgd.1	-	2	528	c.239C>G	c.(238-240)ACC>AGC	p.T80S	TGOLN2_uc002soz.2_Missense_Mutation_p.T80S|TGOLN2_uc002spa.2_Intron|TGOLN2_uc002spb.2_Missense_Mutation_p.T80S|TGOLN2_uc002spc.1_Missense_Mutation_p.T80S	NM_006464	NP_006455	O43493	TGON2_HUMAN	trans-golgi network protein 2	80	Extracellular (Potential).|14 X 14 AA tandem repeats.|2.					integral to membrane|nucleus|plasma membrane|trans-Golgi network|transport vesicle	protein binding				0																		---	---	---	---
GGCX	2677	broad.mit.edu	37	2	85778977	85778977	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85778977G>T	uc002sps.2	-	11	1673	c.1567C>A	c.(1567-1569)CTA>ATA	p.L523I	GGCX_uc010yss.1_Missense_Mutation_p.L339I|GGCX_uc010yst.1_Missense_Mutation_p.L466I	NM_000821	NP_000812	P38435	VKGC_HUMAN	gamma-glutamyl carboxylase isoform 1	523	Lumenal (Potential).				blood coagulation|peptidyl-glutamic acid carboxylation|post-translational protein modification	endoplasmic reticulum membrane|integral to membrane|membrane fraction	gamma-glutamyl carboxylase activity			ovary(1)	1					Anisindione(DB01125)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Drotrecogin alfa(DB00055)|L-Glutamic Acid(DB00142)|Menadione(DB00170)|Phytonadione(DB01022)											OREG0014747	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ATOH8	84913	broad.mit.edu	37	2	85991288	85991288	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85991288C>T	uc002sqn.2	+	2	1347	c.943C>T	c.(943-945)CGT>TGT	p.R315C	ATOH8_uc002sqm.3_Missense_Mutation_p.R315C	NM_032827	NP_116216	Q96SQ7	ATOH8_HUMAN	atonal homolog 8	315					cell differentiation|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0																		---	---	---	---
POLR1A	25885	broad.mit.edu	37	2	86327093	86327093	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86327093C>T	uc002sqs.2	-	2	659	c.280G>A	c.(280-282)GAT>AAT	p.D94N	POLR1A_uc002sqv.2_Missense_Mutation_p.D94N	NM_015425	NP_056240	O95602	RPA1_HUMAN	DNA-directed RNA polymerase I A	94					termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	DNA-directed RNA polymerase I complex|nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|protein binding|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
KDM3A	55818	broad.mit.edu	37	2	86705771	86705771	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:86705771G>A	uc002sri.3	+	15	2556	c.2229G>A	c.(2227-2229)GCG>GCA	p.A743A	KDM3A_uc010ytj.1_Silent_p.A743A|KDM3A_uc010ytk.1_Silent_p.A691A	NM_018433	NP_060903	Q9Y4C1	KDM3A_HUMAN	jumonji domain containing 1A	743					androgen receptor signaling pathway|cell differentiation|formaldehyde biosynthetic process|histone H3-K9 demethylation|hormone-mediated signaling pathway|positive regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	cytoplasm|nucleus	androgen receptor binding|iron ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			breast(2)|ovary(1)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
SMYD1	150572	broad.mit.edu	37	2	88387450	88387450	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88387450C>A	uc002ssr.2	+	3	386	c.384C>A	c.(382-384)TCC>TCA	p.S128S	SMYD1_uc002ssq.1_Intron	NM_198274	NP_938015	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1	128	SET.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			ovary(2)|lung(1)|skin(1)	4																		---	---	---	---
SMYD1	150572	broad.mit.edu	37	2	88387591	88387591	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88387591A>G	uc002ssr.2	+	3	527	c.525A>G	c.(523-525)GGA>GGG	p.G175G	SMYD1_uc002ssq.1_Intron|SMYD1_uc002sss.2_5'Flank	NM_198274	NP_938015	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1	175	SET.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			ovary(2)|lung(1)|skin(1)	4																		---	---	---	---
EIF2AK3	9451	broad.mit.edu	37	2	88874511	88874511	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:88874511G>A	uc002stc.3	-	13	2692	c.2490C>T	c.(2488-2490)GGC>GGT	p.G830G		NM_004836	NP_004827	Q9NZJ5	E2AK3_HUMAN	eukaryotic translation initiation factor 2-alpha	830	Cytoplasmic (Potential).|Protein kinase.				activation of caspase activity|bone mineralization|calcium-mediated signaling|chondrocyte development|endocrine pancreas development|endoplasmic reticulum organization|endoplasmic reticulum unfolded protein response|ER overload response|insulin secretion|insulin-like growth factor receptor signaling pathway|negative regulation of myelination|negative regulation of translational initiation in response to stress|protein autophosphorylation|protein homooligomerization	endoplasmic reticulum membrane|integral to membrane	ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|identical protein binding			ovary(3)	3																		---	---	---	---
Unknown	0	broad.mit.edu	37	2	90212065	90212065	+	RNA	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90212065T>G	uc010fhm.2	+	26		c.3489T>G								Parts of antibodies, mostly variable regions.																														---	---	---	---
Unknown	0	broad.mit.edu	37	2	90229304	90229304	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90229304A>G	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																														---	---	---	---
MRPS5	64969	broad.mit.edu	37	2	95775709	95775709	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95775709T>C	uc002sub.2	-	4	573	c.355A>G	c.(355-357)AAA>GAA	p.K119E	MRPS5_uc002suc.2_RNA|MRPS5_uc010yud.1_Missense_Mutation_p.K119E	NM_031902	NP_114108	P82675	RT05_HUMAN	mitochondrial ribosomal protein S5	119					translation	mitochondrion|ribosome	protein binding|RNA binding|structural constituent of ribosome			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
ZNF514	84874	broad.mit.edu	37	2	95815517	95815517	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:95815517C>T	uc002sue.1	-	5	1087	c.713G>A	c.(712-714)GGA>GAA	p.G238E	ZNF514_uc002sud.1_Missense_Mutation_p.G311E	NM_032788	NP_116177	Q96K75	ZN514_HUMAN	zinc finger protein 514	238	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ASTL	431705	broad.mit.edu	37	2	96789953	96789953	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96789953C>T	uc010yui.1	-	9	932	c.932G>A	c.(931-933)CGG>CAG	p.R311Q		NM_001002036	NP_001002036	Q6HA08	ASTL_HUMAN	astacin-like metalloendopeptidase precursor	311					proteolysis		metalloendopeptidase activity|zinc ion binding				0																		---	---	---	---
SNRNP200	23020	broad.mit.edu	37	2	96944582	96944582	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96944582C>T	uc002svu.2	-	37	5374	c.5288G>A	c.(5287-5289)CGC>CAC	p.R1763H	SNRNP200_uc002svt.2_Missense_Mutation_p.R373H|SNRNP200_uc010yuj.1_RNA	NM_014014	NP_054733	O75643	U520_HUMAN	activating signal cointegrator 1 complex subunit	1763						catalytic step 2 spliceosome|nucleoplasm|U5 snRNP	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			ovary(5)|skin(4)|large_intestine(1)	10																		---	---	---	---
KIAA1310	55683	broad.mit.edu	37	2	97270111	97270111	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97270111A>G	uc002swn.3	-	17	2171	c.2025T>C	c.(2023-2025)AGT>AGC	p.S675S	KIAA1310_uc002swh.3_Silent_p.S561S|KIAA1310_uc002swi.3_Silent_p.S602S|KIAA1310_uc002swj.3_RNA|KIAA1310_uc002swk.3_Silent_p.S588S|KIAA1310_uc010fhz.2_Silent_p.S495S|KIAA1310_uc002swl.3_Silent_p.S574S|KIAA1310_uc002swm.3_RNA|KIAA1310_uc010yur.1_Silent_p.S469S|KIAA1310_uc002swo.2_Silent_p.S23S	NM_001115016	NP_001108488	Q9P2N6	K1310_HUMAN	hypothetical protein LOC55683 isoform a	701	Ser-rich.										0																		---	---	---	---
FER1L5	90342	broad.mit.edu	37	2	97366114	97366114	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97366114G>A	uc010fia.2	+	44	5057	c.5057G>A	c.(5056-5058)CGC>CAC	p.R1686H	FER1L5_uc002sws.3_Missense_Mutation_p.R404H|FER1L5_uc002swt.3_Missense_Mutation_p.R404H|FER1L5_uc010yus.1_Missense_Mutation_p.R403H	NM_001113382	NP_001106853	A0AVI2	FR1L5_HUMAN	fer-1-like 5 isoform 2	1686						integral to membrane				ovary(1)	1																		---	---	---	---
CNNM4	26504	broad.mit.edu	37	2	97428140	97428140	+	Splice_Site	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97428140T>C	uc002swx.2	+	1	1500	c.1402_splice	c.e1+2	p.G468_splice		NM_020184	NP_064569			cyclin M4						biomineral tissue development|ion transport|response to stimulus|visual perception	integral to membrane|plasma membrane				breast(2)|ovary(1)	3																		---	---	---	---
CNNM3	26505	broad.mit.edu	37	2	97494326	97494326	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97494326G>A	uc002swy.2	+	6	1833	c.1809G>A	c.(1807-1809)TCG>TCA	p.S603S	CNNM3_uc002swz.2_Silent_p.S555S	NM_017623	NP_060093	Q8NE01	CNNM3_HUMAN	cyclin M3 isoform 1	603					ion transport	integral to membrane|plasma membrane	protein binding			ovary(1)	1																		---	---	---	---
ANKRD23	200539	broad.mit.edu	37	2	97506176	97506176	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97506176C>T	uc002sxa.2	-	5	531	c.502G>A	c.(502-504)GCC>ACC	p.A168T	ANKRD23_uc002sxb.2_RNA|ANKRD23_uc002sxc.2_Missense_Mutation_p.A126T	NM_144994	NP_659431	Q86SG2	ANR23_HUMAN	diabetes related ankyrin repeat protein	168	ANK 1.					nucleus				ovary(1)	1																		---	---	---	---
SEMA4C	54910	broad.mit.edu	37	2	97530457	97530457	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97530457A>C	uc002sxh.3	-	9	1107	c.947T>G	c.(946-948)GTT>GGT	p.V316G	SEMA4C_uc002sxf.3_5'Flank|SEMA4C_uc002sxe.2_5'Flank|SEMA4C_uc002sxg.3_Missense_Mutation_p.V369G	NM_017789	NP_060259	Q9C0C4	SEM4C_HUMAN	semaphorin 4C precursor	316	Extracellular (Potential).|Dominant negative effect on myogenic differentiation (By similarity).|Sema.				muscle cell differentiation|nervous system development|positive regulation of stress-activated MAPK cascade	cell junction|integral to membrane|postsynaptic density|postsynaptic membrane|synaptic vesicle membrane	receptor activity			skin(2)	2																		---	---	---	---
ANKRD36B	57730	broad.mit.edu	37	2	98175437	98175437	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98175437C>T	uc010yvc.1	-	9	1166	c.886G>A	c.(886-888)GCT>ACT	p.A296T	ANKRD36B_uc010yve.1_RNA|ANKRD36B_uc010fif.2_RNA	NM_025190	NP_079466	Q8N2N9	AN36B_HUMAN	ankyrin repeat domain 36B	296											0																		---	---	---	---
ACTR1B	10120	broad.mit.edu	37	2	98277069	98277069	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98277069G>T	uc002syb.2	-	3	362	c.154C>A	c.(154-156)CTG>ATG	p.L52M		NM_005735	NP_005726	P42025	ACTY_HUMAN	ARP1 actin-related protein 1 homolog B,	52						centrosome|dynactin complex	ATP binding|protein binding			skin(1)	1																		---	---	---	---
ZAP70	7535	broad.mit.edu	37	2	98353926	98353926	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98353926G>A	uc002syd.1	+						ZAP70_uc002sye.1_Intron|ZAP70_uc002syf.1_Intron	NM_001079	NP_001070			zeta-chain associated protein kinase 70kDa						immune response|intracellular protein kinase cascade|positive thymic T cell selection|T cell receptor signaling pathway	cytosol|T cell receptor complex	ATP binding|non-membrane spanning protein tyrosine kinase activity			lung(4)|upper_aerodigestive_tract(1)|ovary(1)	6																		---	---	---	---
TMEM131	23505	broad.mit.edu	37	2	98392471	98392471	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98392471T>G	uc002syh.3	-	32	4384	c.4155A>C	c.(4153-4155)AAA>AAC	p.K1385N		NM_015348	NP_056163	Q92545	TM131_HUMAN	RW1 protein	1385	Lys-rich.					integral to membrane		p.K1272K(1)		ovary(4)|central_nervous_system(2)	6																		---	---	---	---
TMEM131	23505	broad.mit.edu	37	2	98426152	98426152	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:98426152G>T	uc002syh.3	-	19	2283	c.2054C>A	c.(2053-2055)CCA>CAA	p.P685Q		NM_015348	NP_056163	Q92545	TM131_HUMAN	RW1 protein	685						integral to membrane				ovary(4)|central_nervous_system(2)	6																		---	---	---	---
INPP4A	3631	broad.mit.edu	37	2	99154342	99154342	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99154342C>A	uc002syy.2	+	8	877	c.484C>A	c.(484-486)CGT>AGT	p.R162S	INPP4A_uc010yvj.1_Missense_Mutation_p.R162S|INPP4A_uc010yvk.1_Missense_Mutation_p.R162S|INPP4A_uc002syx.2_Missense_Mutation_p.R162S|INPP4A_uc010fik.2_Intron	NM_001134224	NP_001127696	Q96PE3	INP4A_HUMAN	inositol polyphosphate-4-phosphatase, type 1	162					signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			kidney(1)	1																		---	---	---	---
C2orf55	343990	broad.mit.edu	37	2	99448930	99448930	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99448930C>A	uc002szf.1	-	5	715	c.421G>T	c.(421-423)GGG>TGG	p.G141W		NM_207362	NP_997245	Q6NV74	CB055_HUMAN	hypothetical protein LOC343990	141											0																		---	---	---	---
C2orf15	150590	broad.mit.edu	37	2	99767217	99767217	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99767217G>T	uc002szk.2	+	4	697	c.298G>T	c.(298-300)GGA>TGA	p.G100*	TSGA10_uc002szi.3_Intron|MRPL30_uc002szl.1_Intron	NM_144706	NP_653307	Q8WU43	CB015_HUMAN	hypothetical protein LOC150590	100											0																		---	---	---	---
REV1	51455	broad.mit.edu	37	2	100022385	100022385	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100022385G>A	uc002tad.2	-	17	3010	c.2798C>T	c.(2797-2799)CCG>CTG	p.P933L	REV1_uc002tac.2_Missense_Mutation_p.P932L	NM_016316	NP_057400	Q9UBZ9	REV1_HUMAN	REV1-like isoform 1	933					DNA replication|error-prone translesion synthesis|response to UV	nucleoplasm	damaged DNA binding|DNA-directed DNA polymerase activity|magnesium ion binding|protein binding			ovary(2)	2													DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
AFF3	3899	broad.mit.edu	37	2	100209963	100209963	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100209963C>A	uc002tag.2	-	14	2396	c.2160G>T	c.(2158-2160)AGG>AGT	p.R720S	AFF3_uc002taf.2_Missense_Mutation_p.R745S|AFF3_uc010fiq.1_Missense_Mutation_p.R720S|AFF3_uc010yvr.1_Missense_Mutation_p.R873S|AFF3_uc002tah.1_Missense_Mutation_p.R745S	NM_002285	NP_002276	P51826	AFF3_HUMAN	AF4/FMR2 family, member 3 isoform 1	720					multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6																		---	---	---	---
AFF3	3899	broad.mit.edu	37	2	100623325	100623325	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:100623325C>T	uc002tag.2	-	6	878	c.642G>A	c.(640-642)CAG>CAA	p.Q214Q	AFF3_uc002taf.2_Silent_p.Q239Q|AFF3_uc010fiq.1_Silent_p.Q214Q|AFF3_uc010yvr.1_Silent_p.Q368Q|AFF3_uc002tah.1_Silent_p.Q239Q|AFF3_uc010fir.1_Silent_p.Q291Q|AFF3_uc002tai.2_Silent_p.Q136Q	NM_002285	NP_002276	P51826	AFF3_HUMAN	AF4/FMR2 family, member 3 isoform 1	214					multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6																		---	---	---	---
CHST10	9486	broad.mit.edu	37	2	101012016	101012016	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101012016C>T	uc002tam.2	-	6	847	c.488G>A	c.(487-489)GGC>GAC	p.G163D		NM_004854	NP_004845	O43529	CHSTA_HUMAN	HNK-1 sulfotransferase	163	Lumenal (Potential).				carbohydrate biosynthetic process|cell adhesion	Golgi membrane|integral to membrane|membrane fraction				ovary(1)	1																		---	---	---	---
NMS	129521	broad.mit.edu	37	2	101086941	101086941	+	5'Flank	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101086941G>A	uc002tan.1	+							NM_001011717	NP_001011717			neuromedin S precursor						neuropeptide signaling pathway|regulation of smooth muscle contraction	extracellular region				ovary(1)	1																		---	---	---	---
PDCL3	79031	broad.mit.edu	37	2	101192854	101192854	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101192854A>G	uc002tao.2	+	6	728	c.616A>G	c.(616-618)ACA>GCA	p.T206A		NM_024065	NP_076970	Q9H2J4	PDCL3_HUMAN	phosducin-like 3	206					apoptosis|interspecies interaction between organisms	cytoplasm	protein binding				0																		---	---	---	---
IL1RL2	8808	broad.mit.edu	37	2	102851688	102851688	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:102851688G>A	uc002tbs.2	+	11	1755	c.1629G>A	c.(1627-1629)CCG>CCA	p.P543P	IL1RL2_uc002tbt.2_Silent_p.P425P	NM_003854	NP_003845	Q9HB29	ILRL2_HUMAN	interleukin 1 receptor-like 2 precursor	543	Cytoplasmic (Potential).				cellular defense response|innate immune response	integral to plasma membrane	interleukin-1, Type I, activating receptor activity			ovary(2)	2																OREG0014848	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
TGFBRAP1	9392	broad.mit.edu	37	2	105924170	105924170	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:105924170C>T	uc002tcq.2	-	2	673	c.589G>A	c.(589-591)GTC>ATC	p.V197I	TGFBRAP1_uc002tcr.3_Missense_Mutation_p.V197I	NM_004257	NP_004248	Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor	197	CNH.				regulation of transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway	cytoplasm|membrane	SMAD binding|small GTPase regulator activity|transforming growth factor beta receptor binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
C2orf40	84417	broad.mit.edu	37	2	106694296	106694296	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:106694296C>T	uc010fjf.2	+	4	469	c.361C>T	c.(361-363)CGT>TGT	p.R121C		NM_032411	NP_115787	Q9H1Z8	AUGN_HUMAN	esophageal cancer related gene 4 protein	121						extracellular region|transport vesicle					0																		---	---	---	---
ST6GAL2	84620	broad.mit.edu	37	2	107460259	107460259	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107460259G>A	uc002tdq.2	-	2	294	c.175C>T	c.(175-177)CGG>TGG	p.R59W	ST6GAL2_uc002tdr.2_Missense_Mutation_p.R59W|ST6GAL2_uc002tds.3_Missense_Mutation_p.R59W	NM_001142351	NP_001135823	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide	59	Lumenal (Potential).				growth|multicellular organismal development|oligosaccharide metabolic process|protein glycosylation	Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,6-sialyltransferase activity			pancreas(6)|ovary(4)|skin(1)	11																		---	---	---	---
RANBP2	5903	broad.mit.edu	37	2	109367844	109367844	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109367844T>G	uc002tem.3	+	10	1524	c.1398T>G	c.(1396-1398)CAT>CAG	p.H466Q		NM_006267	NP_006258	P49792	RBP2_HUMAN	RAN binding protein 2	466					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein folding|protein import into nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	peptidyl-prolyl cis-trans isomerase activity|Ran GTPase binding|zinc ion binding		RANBP2/ALK(16)	soft_tissue(16)|lung(1)|pancreas(1)	18																		---	---	---	---
RANBP2	5903	broad.mit.edu	37	2	109371681	109371681	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109371681T>G	uc002tem.3	+	17	2558	c.2432T>G	c.(2431-2433)CTG>CGG	p.L811R		NM_006267	NP_006258	P49792	RBP2_HUMAN	RAN binding protein 2	811					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein folding|protein import into nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	peptidyl-prolyl cis-trans isomerase activity|Ran GTPase binding|zinc ion binding		RANBP2/ALK(16)	soft_tissue(16)|lung(1)|pancreas(1)	18																		---	---	---	---
RANBP2	5903	broad.mit.edu	37	2	109371714	109371714	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109371714A>C	uc002tem.3	+	17	2591	c.2465A>C	c.(2464-2466)AAG>ACG	p.K822T		NM_006267	NP_006258	P49792	RBP2_HUMAN	RAN binding protein 2	822					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein folding|protein import into nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	peptidyl-prolyl cis-trans isomerase activity|Ran GTPase binding|zinc ion binding		RANBP2/ALK(16)	soft_tissue(16)|lung(1)|pancreas(1)	18																		---	---	---	---
ANKRD57	65124	broad.mit.edu	37	2	110373605	110373605	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110373605G>A	uc002tfb.2	+	1	1695	c.1539G>A	c.(1537-1539)TCG>TCA	p.S513S	SEPT10_uc010ywu.1_5'Flank|SEPT10_uc002tew.2_5'Flank|SEPT10_uc002tex.2_5'Flank|SEPT10_uc002tey.2_5'Flank|SEPT10_uc010ywv.1_5'Flank	NM_023016	NP_075392	Q53LP3	ANR57_HUMAN	ankyrin repeat domain 57	513											0																		---	---	---	---
ACOXL	55289	broad.mit.edu	37	2	111562913	111562913	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:111562913C>A	uc002tgr.3	+	9	918	c.694C>A	c.(694-696)CTG>ATG	p.L232M	ACOXL_uc010fkc.2_Missense_Mutation_p.L232M|ACOXL_uc010yxk.1_Missense_Mutation_p.L232M	NM_001105516	NP_001098986	Q9NUZ1	ACOXL_HUMAN	acyl-Coenzyme A oxidase-like 2	232					fatty acid beta-oxidation	peroxisome	acyl-CoA dehydrogenase activity|acyl-CoA oxidase activity				0																		---	---	---	---
ANAPC1	64682	broad.mit.edu	37	2	112608394	112608394	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112608394T>C	uc002thi.2	-	14	1856	c.1609A>G	c.(1609-1611)ACT>GCT	p.T537A		NM_022662	NP_073153	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1	537					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm				skin(2)	2																		---	---	---	---
ANAPC1	64682	broad.mit.edu	37	2	112608407	112608407	+	Silent	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112608407T>A	uc002thi.2	-	14	1843	c.1596A>T	c.(1594-1596)CTA>CTT	p.L532L		NM_022662	NP_073153	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1	532					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm				skin(2)	2																		---	---	---	---
ANAPC1	64682	broad.mit.edu	37	2	112614266	112614266	+	Intron	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112614266C>A	uc002thi.2	-							NM_022662	NP_073153			anaphase promoting complex subunit 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm				skin(2)	2																		---	---	---	---
MERTK	10461	broad.mit.edu	37	2	112687108	112687108	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112687108C>A	uc002thk.1	+	2	595	c.473C>A	c.(472-474)GCT>GAT	p.A158D	MERTK_uc002thl.1_Intron	NM_006343	NP_006334	Q12866	MERTK_HUMAN	MER receptor tyrosine kinase precursor	158	Extracellular (Potential).|Ig-like C2-type 1.				cell surface receptor linked signaling pathway|cell-cell signaling|leukocyte migration	integral to plasma membrane|soluble fraction	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(6)|upper_aerodigestive_tract(1)|stomach(1)|kidney(1)	9																		---	---	---	---
FBLN7	129804	broad.mit.edu	37	2	112940375	112940375	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:112940375C>T	uc002tho.1	+	6	949	c.678C>T	c.(676-678)AAC>AAT	p.N226N	FBLN7_uc002thn.2_Silent_p.N226N|FBLN7_uc010fki.1_Silent_p.N180N|FBLN7_uc010fkj.1_Intron	NM_153214	NP_694946	Q53RD9	FBLN7_HUMAN	fibulin 7 isoform 1	226	EGF-like 2; calcium-binding (Potential).				cell adhesion	proteinaceous extracellular matrix	calcium ion binding|heparin binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
ZC3H6	376940	broad.mit.edu	37	2	113069433	113069433	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113069433G>A	uc002thq.1	+	5	1060	c.666G>A	c.(664-666)CCG>CCA	p.P222P		NM_198581	NP_940983	P61129	ZC3H6_HUMAN	zinc finger CCCH-type domain containing 6	222							nucleic acid binding|zinc ion binding			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
SLC20A1	6574	broad.mit.edu	37	2	113417057	113417057	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113417057G>A	uc002tib.2	+	8	1771	c.1325G>A	c.(1324-1326)GGC>GAC	p.G442D	SLC20A1_uc002tic.1_Missense_Mutation_p.G254D	NM_005415	NP_005406	Q8WUM9	S20A1_HUMAN	solute carrier family 20 (phosphate	442	Cytoplasmic (Potential).				phosphate metabolic process|positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to plasma membrane	inorganic phosphate transmembrane transporter activity|receptor activity|sodium-dependent phosphate transmembrane transporter activity			ovary(2)	2																		---	---	---	---
FOXD4L1	200350	broad.mit.edu	37	2	114256862	114256862	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114256862G>A	uc002tjw.3	+	1	202	c.29G>A	c.(28-30)CGC>CAC	p.R10H		NM_012184	NP_036316	Q9NU39	FX4L1_HUMAN	forkhead box D4-like 1	10					axon extension involved in axon guidance|cartilage development|dichotomous subdivision of terminal units involved in ureteric bud branching|embryo development|enteric nervous system development|iridophore differentiation|lateral line nerve glial cell development|melanocyte differentiation|neural crest cell migration|pattern specification process|peripheral nervous system development|positive regulation of BMP signaling pathway|positive regulation of kidney development|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|sympathetic nervous system development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding				0																		---	---	---	---
FOXD4L1	200350	broad.mit.edu	37	2	114257149	114257149	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114257149G>A	uc002tjw.3	+	1	489	c.316G>A	c.(316-318)GCA>ACA	p.A106T		NM_012184	NP_036316	Q9NU39	FX4L1_HUMAN	forkhead box D4-like 1	106					axon extension involved in axon guidance|cartilage development|dichotomous subdivision of terminal units involved in ureteric bud branching|embryo development|enteric nervous system development|iridophore differentiation|lateral line nerve glial cell development|melanocyte differentiation|neural crest cell migration|pattern specification process|peripheral nervous system development|positive regulation of BMP signaling pathway|positive regulation of kidney development|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|sympathetic nervous system development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding				0																		---	---	---	---
DPP10	57628	broad.mit.edu	37	2	116525904	116525904	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116525904G>A	uc002tla.1	+	13	1602	c.1145G>A	c.(1144-1146)AGC>AAC	p.S382N	DPP10_uc002tlb.1_Missense_Mutation_p.S332N|DPP10_uc002tlc.1_Missense_Mutation_p.S378N|DPP10_uc002tle.2_Missense_Mutation_p.S386N|DPP10_uc002tlf.1_Missense_Mutation_p.S375N	NM_020868	NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl peptidase 10 isoform long	382	Extracellular (Potential).				proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10																		---	---	---	---
DPP10	57628	broad.mit.edu	37	2	116598367	116598367	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:116598367C>A	uc002tla.1	+	25	2681	c.2224C>A	c.(2224-2226)CTA>ATA	p.L742I	DPP10_uc002tlb.1_Missense_Mutation_p.L692I|DPP10_uc002tlc.1_Missense_Mutation_p.L738I|DPP10_uc002tle.2_Missense_Mutation_p.L746I|DPP10_uc002tlf.1_Missense_Mutation_p.L735I	NM_020868	NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl peptidase 10 isoform long	742	Extracellular (Potential).				proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|skin(2)|breast(1)	10																		---	---	---	---
STEAP3	55240	broad.mit.edu	37	2	120020759	120020759	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120020759G>A	uc002tlp.2	+	6	1469	c.1312G>A	c.(1312-1314)GTG>ATG	p.V438M	STEAP3_uc002tlq.2_Missense_Mutation_p.V448M|STEAP3_uc002tlr.2_Missense_Mutation_p.V438M|STEAP3_uc010fle.2_3'UTR	NM_018234	NP_060704	Q658P3	STEA3_HUMAN	dudulin 2 isoform b	438	Helical; (Potential).				apoptosis|cell cycle|cellular iron ion homeostasis|protein secretion|transferrin transport|transmembrane transport	endosome membrane|integral to membrane|multivesicular body	electron carrier activity|flavin adenine dinucleotide binding|iron ion binding			central_nervous_system(2)|skin(1)	3																		---	---	---	---
DBI	1622	broad.mit.edu	37	2	120125892	120125892	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120125892C>T	uc002tlv.2	+						C2orf76_uc002tls.2_5'Flank|C2orf76_uc010flf.1_5'Flank|C2orf76_uc010yyg.1_5'Flank|C2orf76_uc002tlt.2_5'Flank|C2orf76_uc002tlu.2_5'Flank|DBI_uc010yyh.1_Intron|DBI_uc010yyi.1_Intron|DBI_uc010yyj.1_Intron|DBI_uc010yyk.1_Intron|DBI_uc010yyl.1_Intron|DBI_uc010yym.1_Intron|DBI_uc010yyn.1_Intron|DBI_uc002tlw.2_Intron|DBI_uc010yyo.1_Intron|DBI_uc002tlx.2_Intron|DBI_uc010yyp.1_RNA	NM_001079862	NP_001073331			diazepam binding inhibitor isoform 3						transport		benzodiazepine receptor binding|fatty-acyl-CoA binding				0																		---	---	---	---
PCDP1	200373	broad.mit.edu	37	2	120397458	120397458	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:120397458G>A	uc002tmb.2	+							NM_001029996	NP_001025167			primary ciliary dyskinesia protein 1							cilium	calmodulin binding				0	Colorectal(110;0.196)																	---	---	---	---
TSN	7247	broad.mit.edu	37	2	122519016	122519016	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:122519016C>T	uc002tnl.2	+	4	524	c.289C>T	c.(289-291)CGC>TGC	p.R97C	TSN_uc002tnm.2_Missense_Mutation_p.R50C|TSN_uc010yze.1_Missense_Mutation_p.R97C|TSN_uc010flt.2_Intron	NM_004622	NP_004613	Q15631	TSN_HUMAN	translin	97					DNA recombination	cytoplasm|nucleus	sequence-specific DNA binding			breast(2)|large_intestine(1)	3		Ovarian(717;0.0563)|Prostate(154;0.116)																---	---	---	---
CYP27C1	339761	broad.mit.edu	37	2	127953032	127953032	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:127953032G>T	uc002tod.2	-	5	729	c.598C>A	c.(598-600)CCA>ACA	p.P200T		NM_001001665	NP_001001665	Q4G0S4	C27C1_HUMAN	cytochrome P450, family 27, subfamily C,	200						membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen				0	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.071)														---	---	---	---
MYO7B	4648	broad.mit.edu	37	2	128339966	128339966	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128339966C>T	uc002top.2	+	12	1341	c.1288C>T	c.(1288-1290)CGG>TGG	p.R430W		NM_001080527	NP_001073996	Q6PIF6	MYO7B_HUMAN	myosin VIIB	430	Myosin head-like.					apical plasma membrane|myosin complex	actin binding|ATP binding|motor activity			ovary(1)|pancreas(1)	2	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)														---	---	---	---
MYO7B	4648	broad.mit.edu	37	2	128342430	128342430	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128342430C>T	uc002top.2	+	14	1685	c.1632C>T	c.(1630-1632)ATC>ATT	p.I544I		NM_001080527	NP_001073996	Q6PIF6	MYO7B_HUMAN	myosin VIIB	544	Myosin head-like.					apical plasma membrane|myosin complex	actin binding|ATP binding|motor activity			ovary(1)|pancreas(1)	2	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)														---	---	---	---
MYO7B	4648	broad.mit.edu	37	2	128351172	128351172	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128351172C>T	uc002top.2	+	18	2250	c.2197C>T	c.(2197-2199)CGG>TGG	p.R733W		NM_001080527	NP_001073996	Q6PIF6	MYO7B_HUMAN	myosin VIIB	733						apical plasma membrane|myosin complex	actin binding|ATP binding|motor activity			ovary(1)|pancreas(1)	2	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)														---	---	---	---
MYO7B	4648	broad.mit.edu	37	2	128394168	128394168	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128394168C>T	uc002top.2	+	45	6147	c.6094C>T	c.(6094-6096)CGA>TGA	p.R2032*	MYO7B_uc002tos.1_Nonsense_Mutation_p.R142*|MYO7B_uc002tot.2_Nonsense_Mutation_p.R142*	NM_001080527	NP_001073996	Q6PIF6	MYO7B_HUMAN	myosin VIIB	2032	FERM 2.					apical plasma membrane|myosin complex	actin binding|ATP binding|motor activity			ovary(1)|pancreas(1)	2	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)														---	---	---	---
LIMS2	55679	broad.mit.edu	37	2	128412428	128412428	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128412428A>C	uc002tpa.2	-	3	380	c.214T>G	c.(214-216)TTT>GTT	p.F72V	LIMS2_uc002tox.2_Missense_Mutation_p.F96V|LIMS2_uc010fmb.2_5'UTR|LIMS2_uc002toy.2_Missense_Mutation_p.F67V|LIMS2_uc010yzm.1_Missense_Mutation_p.F94V|LIMS2_uc002toz.2_Missense_Mutation_p.F67V|LIMS2_uc002tpb.2_Missense_Mutation_p.F67V	NM_001161403	NP_001154875	Q7Z4I7	LIMS2_HUMAN	LIM and senescent cell antigen-like domains 2	72	LIM zinc-binding 1.				cell junction assembly	cytosol|focal adhesion|nucleus	zinc ion binding				0	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0681)														---	---	---	---
WDR33	55339	broad.mit.edu	37	2	128466335	128466335	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128466335G>A	uc002tpg.1	-	21	3880	c.3697C>T	c.(3697-3699)CGC>TGC	p.R1233C		NM_018383	NP_060853	Q9C0J8	WDR33_HUMAN	WD repeat domain 33 isoform 1	1233					postreplication repair|spermatogenesis	collagen|nucleus	protein binding				0	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)														---	---	---	---
WDR33	55339	broad.mit.edu	37	2	128522444	128522444	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128522444A>G	uc002tpg.1	-	6	767	c.584T>C	c.(583-585)GTC>GCC	p.V195A	WDR33_uc002tph.1_Missense_Mutation_p.V195A|WDR33_uc002tpi.1_Missense_Mutation_p.V195A	NM_018383	NP_060853	Q9C0J8	WDR33_HUMAN	WD repeat domain 33 isoform 1	195	WD 2.				postreplication repair|spermatogenesis	collagen|nucleus	protein binding				0	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)														---	---	---	---
UGGT1	56886	broad.mit.edu	37	2	128873875	128873875	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128873875A>T	uc002tps.2	+	8	1008	c.830A>T	c.(829-831)GAT>GTT	p.D277V	UGGT1_uc010fme.1_Missense_Mutation_p.D152V|UGGT1_uc002tpr.2_Missense_Mutation_p.D253V	NM_020120	NP_064505	Q9NYU2	UGGG1_HUMAN	UDP-glucose ceramide glucosyltransferase-like 1	277					'de novo' posttranslational protein folding|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity|unfolded protein binding			ovary(1)	1																		---	---	---	---
HS6ST1	9394	broad.mit.edu	37	2	129026288	129026288	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129026288C>T	uc002tpt.3	-	2	718	c.684G>A	c.(682-684)ACG>ACA	p.T228T		NM_004807	NP_004798	O60243	H6ST1_HUMAN	heparan sulfate 6-O-sulfotransferase 1	228	Lumenal (Potential).				heparan sulfate proteoglycan biosynthetic process, enzymatic modification	integral to plasma membrane	sulfotransferase activity			pancreas(1)	1	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.117)														---	---	---	---
HS6ST1	9394	broad.mit.edu	37	2	129026297	129026297	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129026297G>A	uc002tpt.3	-	2	709	c.675C>T	c.(673-675)TAC>TAT	p.Y225Y		NM_004807	NP_004798	O60243	H6ST1_HUMAN	heparan sulfate 6-O-sulfotransferase 1	225	Lumenal (Potential).				heparan sulfate proteoglycan biosynthetic process, enzymatic modification	integral to plasma membrane	sulfotransferase activity			pancreas(1)	1	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.117)														---	---	---	---
POTEF	728378	broad.mit.edu	37	2	130832333	130832333	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130832333G>A	uc010fmh.2	-	17	3112	c.2712C>T	c.(2710-2712)GCC>GCT	p.A904A		NM_001099771	NP_001093241	A5A3E0	POTEF_HUMAN	prostate, ovary, testis expressed protein on	904	Actin-like.					cell cortex	ATP binding			skin(3)|ovary(2)	5																		---	---	---	---
TUBA3E	112714	broad.mit.edu	37	2	130949696	130949696	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:130949696C>T	uc002tqv.2	-	5	1162	c.1061G>A	c.(1060-1062)GGC>GAC	p.G354D		NM_207312	NP_997195	Q6PEY2	TBA3E_HUMAN	tubulin, alpha 3e	354					microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|structural molecule activity			skin(1)	1	Colorectal(110;0.1)																	---	---	---	---
IMP4	92856	broad.mit.edu	37	2	131103414	131103414	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131103414G>A	uc002tra.1	+	6	519	c.502G>A	c.(502-504)GTC>ATC	p.V168I		NM_033416	NP_219484	Q96G21	IMP4_HUMAN	IMP4, U3 small nucleolar ribonucleoprotein,	168	Brix.				rRNA processing|translation	nucleolus|ribonucleoprotein complex	aminoacyl-tRNA ligase activity|ATP binding|protein binding			central_nervous_system(2)	2	Colorectal(110;0.1)																	---	---	---	---
GPR148	344561	broad.mit.edu	37	2	131486984	131486984	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131486984T>C	uc002trv.1	+	1	262	c.260T>C	c.(259-261)CTG>CCG	p.L87P		NM_207364	NP_997247	Q8TDV2	GP148_HUMAN	G protein-coupled receptor 148	87	Helical; Name=2; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			skin(1)	1	Colorectal(110;0.1)																	---	---	---	---
ARHGEF4	50649	broad.mit.edu	37	2	131797836	131797836	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131797836C>T	uc002tsa.1	+	8	1447	c.927C>T	c.(925-927)GGC>GGT	p.G309G	ARHGEF4_uc010fmw.1_Intron|ARHGEF4_uc002tsb.1_Silent_p.G309G|ARHGEF4_uc010fmx.1_Intron|ARHGEF4_uc002tsc.1_5'UTR	NM_015320	NP_056135	Q9NR80	ARHG4_HUMAN	Rho guanine nucleotide exchange factor 4 isoform	309	DH.				apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|lamellipodium assembly|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|ruffle membrane	protein domain specific binding|Rac guanyl-nucleotide exchange factor activity			breast(3)|ovary(2)|skin(1)	6		Prostate(154;0.055)		BRCA - Breast invasive adenocarcinoma(221;0.097)														---	---	---	---
ARHGEF4	50649	broad.mit.edu	37	2	131803619	131803619	+	Missense_Mutation	SNP	C	T	T	rs146423704	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:131803619C>T	uc002tsa.1	+	14	2450	c.1930C>T	c.(1930-1932)CGG>TGG	p.R644W	ARHGEF4_uc010fmw.1_Missense_Mutation_p.R792W|ARHGEF4_uc002tsb.1_3'UTR|ARHGEF4_uc010fmx.1_Missense_Mutation_p.R584W|ARHGEF4_uc002tsc.1_Missense_Mutation_p.R187W	NM_015320	NP_056135	Q9NR80	ARHG4_HUMAN	Rho guanine nucleotide exchange factor 4 isoform	644					apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|lamellipodium assembly|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|ruffle membrane	protein domain specific binding|Rac guanyl-nucleotide exchange factor activity			breast(3)|ovary(2)|skin(1)	6		Prostate(154;0.055)		BRCA - Breast invasive adenocarcinoma(221;0.097)														---	---	---	---
GPR39	2863	broad.mit.edu	37	2	133174931	133174931	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133174931C>A	uc002ttl.2	+	1	785	c.316C>A	c.(316-318)CTG>ATG	p.L106M		NM_001508	NP_001499	O43194	GPR39_HUMAN	G protein-coupled receptor 39	106	Extracellular (Potential).					integral to plasma membrane	G-protein coupled receptor activity|metal ion binding				0																		---	---	---	---
GPR39	2863	broad.mit.edu	37	2	133402903	133402903	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133402903C>T	uc002ttl.2	+	2	1555	c.1086C>T	c.(1084-1086)CGC>CGT	p.R362R	LYPD1_uc002ttm.3_3'UTR|LYPD1_uc002ttn.2_3'UTR|LYPD1_uc002tto.2_3'UTR	NM_001508	NP_001499	O43194	GPR39_HUMAN	G protein-coupled receptor 39	362	Cytoplasmic (Potential).					integral to plasma membrane	G-protein coupled receptor activity|metal ion binding				0																		---	---	---	---
YSK4	80122	broad.mit.edu	37	2	135738394	135738394	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135738394G>A	uc002tue.1	-	9	3948	c.3917C>T	c.(3916-3918)ACC>ATC	p.T1306I	YSK4_uc002tuf.1_Missense_Mutation_p.T488I|YSK4_uc010fnc.1_Missense_Mutation_p.T440I|YSK4_uc010fnd.1_Missense_Mutation_p.T1193I|YSK4_uc010zbg.1_Missense_Mutation_p.T438I|YSK4_uc002tuh.3_Missense_Mutation_p.T1034I|YSK4_uc002tui.3_3'UTR	NM_025052	NP_079328	Q56UN5	YSK4_HUMAN	Yeast Sps1/Ste20-related kinase 4 isoform 1	1306	Protein kinase.						ATP binding|protein serine/threonine kinase activity			stomach(2)|urinary_tract(1)|ovary(1)|breast(1)	5				BRCA - Breast invasive adenocarcinoma(221;0.112)														---	---	---	---
YSK4	80122	broad.mit.edu	37	2	135744190	135744190	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135744190C>T	uc002tue.1	-	7	2283	c.2252G>A	c.(2251-2253)AGC>AAC	p.S751N	YSK4_uc002tuf.1_Intron|YSK4_uc010fnc.1_Intron|YSK4_uc010fnd.1_Missense_Mutation_p.S638N|YSK4_uc010zbg.1_Intron|YSK4_uc002tuh.3_Missense_Mutation_p.S479N|YSK4_uc002tui.3_Missense_Mutation_p.S768N	NM_025052	NP_079328	Q56UN5	YSK4_HUMAN	Yeast Sps1/Ste20-related kinase 4 isoform 1	751							ATP binding|protein serine/threonine kinase activity			stomach(2)|urinary_tract(1)|ovary(1)|breast(1)	5				BRCA - Breast invasive adenocarcinoma(221;0.112)														---	---	---	---
ZRANB3	84083	broad.mit.edu	37	2	135957932	135957932	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:135957932G>A	uc002tum.2	-	21	3337	c.3220C>T	c.(3220-3222)CGA>TGA	p.R1074*	ZRANB3_uc002tuk.2_Nonsense_Mutation_p.R617*|ZRANB3_uc002tul.2_Nonsense_Mutation_p.R1072*	NM_032143	NP_115519	Q5FWF4	ZRAB3_HUMAN	zinc finger, RAN-binding domain containing 3	1074						intracellular	ATP binding|DNA binding|endonuclease activity|helicase activity|zinc ion binding			lung(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.135)														---	---	---	---
R3HDM1	23518	broad.mit.edu	37	2	136393757	136393757	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136393757C>T	uc002tuo.2	+						R3HDM1_uc010fni.2_Intron|R3HDM1_uc002tup.2_Intron|R3HDM1_uc010zbh.1_Intron	NM_015361	NP_056176			R3H domain containing 1								nucleic acid binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.127)														---	---	---	---
R3HDM1	23518	broad.mit.edu	37	2	136396700	136396700	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136396700T>C	uc002tuo.2	+						R3HDM1_uc010fni.2_Intron|R3HDM1_uc002tup.2_Intron|R3HDM1_uc010zbh.1_Intron	NM_015361	NP_056176			R3H domain containing 1								nucleic acid binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.127)														---	---	---	---
MIR128-1	406915	broad.mit.edu	37	2	136422986	136422986	+	RNA	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136422986C>T	hsa-mir-128-1|MI0000447	+			c.20C>T			R3HDM1_uc002tuo.2_Intron|R3HDM1_uc010fni.2_Intron|R3HDM1_uc002tup.2_Intron|R3HDM1_uc010zbh.1_Intron|uc010zbi.1_RNA																	0																		---	---	---	---
UBXN4	23190	broad.mit.edu	37	2	136540349	136540349	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136540349A>C	uc002tur.2	+	13	1730	c.1419A>C	c.(1417-1419)AAA>AAC	p.K473N	UBXN4_uc002tus.2_Missense_Mutation_p.K239N|UBXN4_uc002tut.2_Missense_Mutation_p.K109N	NM_014607	NP_055422	Q92575	UBXN4_HUMAN	UBX domain containing 2	473	Cytoplasmic (Potential).				response to unfolded protein	endoplasmic reticulum membrane|nuclear envelope	protein binding			skin(2)	2																		---	---	---	---
LCT	3938	broad.mit.edu	37	2	136570154	136570154	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136570154C>T	uc002tuu.1	-	7	2091	c.2080G>A	c.(2080-2082)GCC>ACC	p.A694T		NM_002299	NP_002290	P09848	LPH_HUMAN	lactase-phlorizin hydrolase preproprotein	694	Extracellular (Potential).|4 X approximate repeats.|2.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|integral to plasma membrane|membrane fraction	cation binding|glycosylceramidase activity|lactase activity			ovary(7)|central_nervous_system(2)|skin(2)|pancreas(1)|lung(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.169)														---	---	---	---
CXCR4	7852	broad.mit.edu	37	2	136872857	136872857	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:136872857A>T	uc002tuz.2	-	2	736	c.641T>A	c.(640-642)GTC>GAC	p.V214D	CXCR4_uc002tuy.2_Missense_Mutation_p.V218D|CXCR4_uc010fnk.2_Missense_Mutation_p.V199D	NM_003467	NP_003458	P61073	CXCR4_HUMAN	chemokine (C-X-C motif) receptor 4 isoform b	214	Helical; Name=5.				activation of MAPK activity|apoptosis|dendritic cell chemotaxis|elevation of cytosolic calcium ion concentration|entry into host cell|inflammatory response|initiation of viral infection|regulation of chemotaxis|response to hypoxia|response to virus	cell leading edge|cell surface|cytoplasmic membrane-bounded vesicle|integral to membrane|plasma membrane	actin binding|C-X-C chemokine receptor activity|coreceptor activity|myosin light chain binding|ubiquitin binding|ubiquitin protein ligase binding			upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.155)	Framycetin(DB00452)													---	---	---	---
THSD7B	80731	broad.mit.edu	37	2	137814249	137814249	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:137814249G>A	uc002tva.1	+	2	306	c.306G>A	c.(304-306)ACG>ACA	p.T102T	THSD7B_uc010zbj.1_RNA|THSD7B_uc002tvb.2_5'UTR	NM_001080427	NP_001073896			thrombospondin, type I, domain containing 7B											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)														---	---	---	---
SPOPL	339745	broad.mit.edu	37	2	139326632	139326632	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:139326632A>G	uc002tvh.2	+	11	1561	c.1161A>G	c.(1159-1161)AAA>AAG	p.K387K		NM_001001664	NP_001001664	Q6IQ16	SPOPL_HUMAN	speckle-type POZ protein-like	387						nucleus				skin(2)|breast(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.0296)														---	---	---	---
LRP1B	53353	broad.mit.edu	37	2	142004837	142004837	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:142004837A>G	uc002tvj.1	-	5	1522	c.550T>C	c.(550-552)TAC>CAC	p.Y184H	LRP1B_uc010fnl.1_Intron	NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	184	Extracellular (Potential).|EGF-like 2; calcium-binding (Potential).				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)											TSP Lung(27;0.18)			---	---	---	---
MBD5	55777	broad.mit.edu	37	2	149221443	149221443	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149221443G>T	uc002twm.3	+	8	1340	c.352G>T	c.(352-354)GCC>TCC	p.A118S	MBD5_uc010zbs.1_RNA|MBD5_uc010fns.2_Missense_Mutation_p.A118S	NM_018328	NP_060798	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5	118						chromosome|nucleus	chromatin binding|DNA binding			skin(3)|ovary(2)	5				BRCA - Breast invasive adenocarcinoma(221;0.0569)														---	---	---	---
MBD5	55777	broad.mit.edu	37	2	149226485	149226485	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149226485C>T	uc002twm.3	+	9	1961	c.973C>T	c.(973-975)CGA>TGA	p.R325*	MBD5_uc010zbs.1_RNA|MBD5_uc010fns.2_Nonsense_Mutation_p.R325*|MBD5_uc002twn.1_5'Flank	NM_018328	NP_060798	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5	325						chromosome|nucleus	chromatin binding|DNA binding			skin(3)|ovary(2)	5				BRCA - Breast invasive adenocarcinoma(221;0.0569)														---	---	---	---
NEB	4703	broad.mit.edu	37	2	152390826	152390826	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152390826T>C	uc010fnx.2	-	115	16408	c.16217A>G	c.(16216-16218)TAC>TGC	p.Y5406C	NEB_uc002txr.2_Missense_Mutation_p.Y1829C|NEB_uc002txt.3_5'Flank	NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	5406	Nebulin 147.				muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)														---	---	---	---
NEB	4703	broad.mit.edu	37	2	152393734	152393734	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152393734T>A	uc010fnx.2	-	113	16207	c.16016A>T	c.(16015-16017)GAC>GTC	p.D5339V	NEB_uc002txr.2_Missense_Mutation_p.D1762V	NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	5339	Nebulin 145.				muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)														---	---	---	---
NEB	4703	broad.mit.edu	37	2	152432749	152432749	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152432749C>T	uc010fnx.2	-	78	11912	c.11721G>A	c.(11719-11721)ACG>ACA	p.T3907T	NEB_uc002txr.2_Silent_p.T330T	NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	3907					muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)														---	---	---	---
NEB	4703	broad.mit.edu	37	2	152487228	152487228	+	Splice_Site	SNP	C	T	T	rs113803601		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152487228C>T	uc010fnx.2	-	63	9185	c.8994_splice	c.e63+1	p.E2998_splice	NEB_uc002txu.2_Splice_Site_p.E345_splice	NM_004543	NP_004534			nebulin isoform 3						muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)														---	---	---	---
NEB	4703	broad.mit.edu	37	2	152527650	152527650	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152527650C>T	uc010fnx.2	-	38	4584	c.4393G>A	c.(4393-4395)GAT>AAT	p.D1465N		NM_004543	NP_004534	P20929	NEBU_HUMAN	nebulin isoform 3	1465	Nebulin 37.				muscle filament sliding|muscle organ development|regulation of actin filament length|somatic muscle development	actin cytoskeleton|cytosol|Z disc	actin binding|structural constituent of muscle			ovary(8)|large_intestine(5)|breast(3)|central_nervous_system(2)|skin(1)|pancreas(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.219)														---	---	---	---
FMNL2	114793	broad.mit.edu	37	2	153192164	153192164	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:153192164C>T	uc002tye.2	+	1	414	c.47C>T	c.(46-48)GCG>GTG	p.A16V		NM_052905	NP_443137	Q96PY5	FMNL2_HUMAN	formin-like 2	16					actin cytoskeleton organization	cytoplasm	actin binding|Rho GTPase binding			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
NR4A2	4929	broad.mit.edu	37	2	157183323	157183323	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:157183323T>G	uc002tyz.3	-	6	1690	c.1268A>C	c.(1267-1269)AAG>ACG	p.K423T	NR4A2_uc002tyx.3_Missense_Mutation_p.K360T|NR4A2_uc010zcf.1_Missense_Mutation_p.K423T|NR4A2_uc010zcg.1_Missense_Mutation_p.K45T	NM_006186	NP_006177	P43354	NR4A2_HUMAN	nuclear receptor subfamily 4, group A, member 2	423	Ligand-binding (Potential).				cellular response to extracellular stimulus|dopaminergic neuron differentiation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to protein stimulus	nucleoplasm	sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(3)	3																		---	---	---	---
TANC1	85461	broad.mit.edu	37	2	160035217	160035217	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160035217G>A	uc002uag.2	+	14	2327	c.2053G>A	c.(2053-2055)GAT>AAT	p.D685N	TANC1_uc010fol.1_Missense_Mutation_p.D579N|TANC1_uc010zcm.1_Missense_Mutation_p.D677N|TANC1_uc010fom.1_Missense_Mutation_p.D491N|TANC1_uc002uai.1_RNA	NM_033394	NP_203752	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and	685						cell junction|postsynaptic density|postsynaptic membrane	binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
TANC1	85461	broad.mit.edu	37	2	160075881	160075881	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160075881G>A	uc002uag.2	+						TANC1_uc010zcm.1_Intron|TANC1_uc010fom.1_Intron|TANC1_uc010fon.2_Translation_Start_Site	NM_033394	NP_203752			tetratricopeptide repeat, ankyrin repeat and							cell junction|postsynaptic density|postsynaptic membrane	binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
PLA2R1	22925	broad.mit.edu	37	2	160869860	160869860	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:160869860A>G	uc002ube.1	-	10	1785	c.1578T>C	c.(1576-1578)TGT>TGC	p.C526C	PLA2R1_uc010zcp.1_Silent_p.C526C|PLA2R1_uc002ubf.2_Silent_p.C526C	NM_007366	NP_031392	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1 isoform 1 precursor	526	Extracellular (Potential).|C-type lectin 3.				endocytosis	extracellular space|integral to plasma membrane	receptor activity|sugar binding			skin(2)|ovary(1)	3																		---	---	---	---
TBR1	10716	broad.mit.edu	37	2	162273320	162273320	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162273320G>A	uc002ubw.1	+	1	701	c.399G>A	c.(397-399)GCG>GCA	p.A133A	TBR1_uc010foy.2_5'Flank	NM_006593	NP_006584	Q16650	TBR1_HUMAN	T-box, brain, 1	133						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
DPP4	1803	broad.mit.edu	37	2	162865086	162865086	+	Missense_Mutation	SNP	C	T	T	rs138430103	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:162865086C>T	uc002ubz.2	-	22	2534	c.1973G>A	c.(1972-1974)CGG>CAG	p.R658Q	DPP4_uc010fpb.2_Missense_Mutation_p.R334Q	NM_001935	NP_001926	P27487	DPP4_HUMAN	dipeptidylpeptidase IV	658	Extracellular (Potential).				cell adhesion|endothelial cell migration|negative regulation of extracellular matrix disassembly|positive regulation of cell proliferation|proteolysis|regulation of cell-cell adhesion mediated by integrin|response to hypoxia|T cell activation|T cell costimulation	apical plasma membrane|cell surface|endocytic vesicle|extracellular region|integral to membrane|invadopodium membrane|lamellipodium membrane|membrane raft	aminopeptidase activity|dipeptidyl-peptidase activity|protease binding|protein homodimerization activity|receptor activity|receptor binding|serine-type endopeptidase activity			ovary(3)	3					Sitagliptin(DB01261)													---	---	---	---
GCA	25801	broad.mit.edu	37	2	163216735	163216735	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163216735G>T	uc002ucg.2	+	8	812	c.636G>T	c.(634-636)CAG>CAT	p.Q212H	GCA_uc010zcu.1_Missense_Mutation_p.Q193H	NM_012198	NP_036330	P28676	GRAN_HUMAN	grancalcin, EF-hand calcium binding protein	212					cellular membrane fusion	cytoplasm|plasma membrane	calcium ion binding|protein homodimerization activity				0																		---	---	---	---
COBLL1	22837	broad.mit.edu	37	2	165578976	165578976	+	Missense_Mutation	SNP	A	C	C	rs35945844		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:165578976A>C	uc010zcw.1	-	8	1040	c.916T>G	c.(916-918)TTT>GTT	p.F306V	COBLL1_uc002ucp.2_Missense_Mutation_p.F240V|COBLL1_uc002ucq.2_Missense_Mutation_p.F240V|COBLL1_uc010zcx.1_Missense_Mutation_p.F286V|COBLL1_uc002ucs.1_RNA|COBLL1_uc002uco.2_Missense_Mutation_p.F9V	NM_014900	NP_055715	Q53SF7	COBL1_HUMAN	COBL-like 1	278										ovary(2)|pancreas(1)	3																		---	---	---	---
SCN2A	6326	broad.mit.edu	37	2	166165185	166165185	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166165185T>C	uc002udc.2	+	5	776	c.486T>C	c.(484-486)TTT>TTC	p.F162F	SCN2A_uc002udd.2_Silent_p.F162F|SCN2A_uc002ude.2_Silent_p.F162F	NM_001040142	NP_001035232	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha	162	I.|Helical; Name=S2 of repeat I; (Potential).				myelination	node of Ranvier|voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|breast(1)|pancreas(1)	8					Lamotrigine(DB00555)													---	---	---	---
CSRNP3	80034	broad.mit.edu	37	2	166451688	166451688	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166451688A>G	uc002udf.2	+	4	489	c.113A>G	c.(112-114)GAC>GGC	p.D38G	CSRNP3_uc002udg.2_Missense_Mutation_p.D38G	NM_024969	NP_079245	Q8WYN3	CSRN3_HUMAN	cysteine-serine-rich nuclear protein 3	38	Ser-rich.				apoptosis|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|large_intestine(1)|skin(1)	5																		---	---	---	---
SCN1A	6323	broad.mit.edu	37	2	166901597	166901597	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166901597C>A	uc010zcz.1	-	10	1636	c.1618G>T	c.(1618-1620)GGG>TGG	p.G540W	SCN1A_uc002udo.3_Missense_Mutation_p.G409W|SCN1A_uc010fpk.2_Missense_Mutation_p.G409W	NM_006920	NP_008851	P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha	540						voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|skin(6)|large_intestine(1)	13					Lamotrigine(DB00555)|Levetiracetam(DB01202)|Phenacemide(DB01121)|Phenytoin(DB00252)|Topiramate(DB00273)|Zonisamide(DB00909)													---	---	---	---
SCN9A	6335	broad.mit.edu	37	2	167060728	167060728	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:167060728A>T	uc010fpl.2	-	26	4819	c.4478T>A	c.(4477-4479)ATC>AAC	p.I1493N	uc002udp.2_Intron	NM_002977	NP_002968	Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha	1504						voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|central_nervous_system(5)|skin(2)	13					Lamotrigine(DB00555)|Lidocaine(DB00281)													---	---	---	---
XIRP2	129446	broad.mit.edu	37	2	168098408	168098408	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:168098408C>A	uc002udx.2	+	7	1182	c.1164C>A	c.(1162-1164)GCC>GCA	p.A388A	XIRP2_uc010fpn.2_Silent_p.A421A|XIRP2_uc010fpo.2_Silent_p.A388A|XIRP2_uc010fpp.2_Silent_p.A388A|XIRP2_uc002udy.2_Silent_p.A213A|XIRP2_uc010fpq.2_Silent_p.A166A|XIRP2_uc010fpr.2_Silent_p.A166A	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	213					actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14																		---	---	---	---
NOSTRIN	115677	broad.mit.edu	37	2	169659146	169659146	+	5'Flank	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169659146C>T	uc002ueg.2	+						NOSTRIN_uc002uef.2_5'UTR|NOSTRIN_uc002uei.2_5'UTR|NOSTRIN_uc010fpu.2_5'UTR|NOSTRIN_uc002ueh.2_5'UTR	NM_001039724	NP_001034813			nitric oxide synthase trafficker isoform 2						endocytosis|nitric oxide metabolic process|regulation of nitric-oxide synthase activity	cytoplasmic membrane-bounded vesicle|cytoskeleton|plasma membrane	protein binding				0																		---	---	---	---
ABCB11	8647	broad.mit.edu	37	2	169781238	169781238	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169781238C>T	uc002ueo.1	-	27	3820	c.3694G>A	c.(3694-3696)GCC>ACC	p.A1232T	ABCB11_uc010zda.1_Missense_Mutation_p.A650T|ABCB11_uc010zdb.1_Missense_Mutation_p.A708T	NM_003742	NP_003733	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP),	1232	Cytoplasmic (Potential).|ABC transporter 2.				bile acid biosynthetic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|bile acid-exporting ATPase activity|canalicular bile acid transmembrane transporter activity|sodium-exporting ATPase activity, phosphorylative mechanism			ovary(2)|large_intestine(2)|breast(1)	5					Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Glibenclamide(DB01016)													---	---	---	---
LRP2	4036	broad.mit.edu	37	2	169995867	169995867	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:169995867G>T	uc002ues.2	-	74	13495	c.13282C>A	c.(13282-13284)CTG>ATG	p.L4428M		NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2	4428	Helical; (Potential).				hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)													---	---	---	---
LRP2	4036	broad.mit.edu	37	2	170044552	170044552	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170044552G>A	uc002ues.2	-	49	9469	c.9256C>T	c.(9256-9258)CGC>TGC	p.R3086C		NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2	3086	Extracellular (Potential).|LDL-receptor class A 25.				hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)													---	---	---	---
TLK1	9874	broad.mit.edu	37	2	171917662	171917662	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:171917662G>A	uc002ugn.2	-	4	807	c.335C>T	c.(334-336)CCG>CTG	p.P112L	TLK1_uc002ugo.2_Missense_Mutation_p.P112L|TLK1_uc002ugp.2_Missense_Mutation_p.P64L|TLK1_uc002ugq.2_RNA|TLK1_uc010zdn.1_Missense_Mutation_p.P16L	NM_012290	NP_036422	Q9UKI8	TLK1_HUMAN	tousled-like kinase 1 isoform 1	112					cell cycle|chromatin modification|intracellular protein transport|intracellular signal transduction|regulation of chromatin assembly or disassembly|response to DNA damage stimulus	nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(1)	1																		---	---	---	---
MAP1D	254042	broad.mit.edu	37	2	172931021	172931021	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:172931021A>G	uc002uhk.2	+	5	600	c.527A>G	c.(526-528)AAC>AGC	p.N176S	MAP1D_uc010zdw.1_Missense_Mutation_p.N58S	NM_199227	NP_954697	Q6UB28	AMP1D_HUMAN	methionine aminopeptidase 1D precursor	176					N-terminal protein amino acid modification|peptidyl-methionine modification|proteolysis	mitochondrion	aminopeptidase activity|metal ion binding|metalloexopeptidase activity				0			OV - Ovarian serous cystadenocarcinoma(117;0.216)															---	---	---	---
RAPGEF4	11069	broad.mit.edu	37	2	173787028	173787028	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173787028C>T	uc002uhv.3	+	6	724	c.537C>T	c.(535-537)AAC>AAT	p.N179N	RAPGEF4_uc002uhu.2_Silent_p.N179N|RAPGEF4_uc002uhw.3_Silent_p.N35N|RAPGEF4_uc010zec.1_Silent_p.N26N|RAPGEF4_uc010zed.1_Silent_p.N26N|RAPGEF4_uc010zee.1_Silent_p.N26N|RAPGEF4_uc010fqo.2_Silent_p.N26N|RAPGEF4_uc010zef.1_Translation_Start_Site	NM_007023	NP_008954	Q8WZA2	RPGF4_HUMAN	Rap guanine nucleotide exchange factor (GEF) 4	179					blood coagulation|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|regulation of insulin secretion|regulation of protein phosphorylation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cAMP-dependent protein kinase complex|membrane fraction|plasma membrane	cAMP binding|cAMP-dependent protein kinase regulator activity|Ras GTPase binding|Ras guanyl-nucleotide exchange factor activity			large_intestine(2)|skin(2)|kidney(1)|central_nervous_system(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.194)															---	---	---	---
GPR155	151556	broad.mit.edu	37	2	175301042	175301042	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175301042G>A	uc002uit.2	-	17	2806	c.2415C>T	c.(2413-2415)TAC>TAT	p.Y805Y	GPR155_uc002uiu.2_Silent_p.Y805Y|GPR155_uc002uiv.2_Silent_p.Y805Y|GPR155_uc010fqs.2_Silent_p.Y777Y	NM_001033045	NP_001028217	Q7Z3F1	GP155_HUMAN	G protein-coupled receptor 155 isoform 9	805	DEP.				intracellular signal transduction|transmembrane transport	integral to membrane				ovary(1)	1																		---	---	---	---
WIPF1	7456	broad.mit.edu	37	2	175436392	175436392	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175436392G>A	uc002uiy.2	-						uc002uiw.2_Intron|uc002uix.1_Intron|WIPF1_uc002uja.2_Intron|WIPF1_uc010fqt.1_Intron|WIPF1_uc002ujc.1_Missense_Mutation_p.R381C|WIPF1_uc002uiz.2_Intron|WIPF1_uc002ujb.1_Intron|WIPF1_uc010zep.1_Missense_Mutation_p.R381C	NM_003387	NP_003378			WAS/WASL interacting protein family, member 1						actin polymerization or depolymerization|protein complex assembly	cytoplasmic membrane-bounded vesicle	actin binding|profilin binding			ovary(1)|skin(1)	2																		---	---	---	---
ATP5G3	518	broad.mit.edu	37	2	176046082	176046082	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:176046082C>T	uc002ujz.3	-						ATP5G3_uc002uka.3_Splice_Site_p.L13_splice|ATP5G3_uc002ukb.1_Intron	NM_001002258	NP_001002258			ATP synthase, H+ transporting, mitochondrial F0						ATP hydrolysis coupled proton transport|ATP synthesis coupled proton transport	integral to membrane|mitochondrial proton-transporting ATP synthase complex|proton-transporting ATP synthase complex, coupling factor F(o)	hydrogen ion transmembrane transporter activity|lipid binding|protein binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.147)															---	---	---	---
AGPS	8540	broad.mit.edu	37	2	178357897	178357897	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178357897C>T	uc002ull.2	+	12	1302	c.1255C>T	c.(1255-1257)CGC>TGC	p.R419C	AGPS_uc010zfb.1_Missense_Mutation_p.R329C	NM_003659	NP_003650	O00116	ADAS_HUMAN	alkyldihydroxyacetone phosphate synthase	419			R -> H (in RCDP3).		ether lipid biosynthetic process	peroxisomal matrix|peroxisomal membrane|plasma membrane	alkylglycerone-phosphate synthase activity|flavin adenine dinucleotide binding|oxidoreductase activity			ovary(2)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.0018)|Epithelial(96;0.00919)|all cancers(119;0.0358)															---	---	---	---
TTC30B	150737	broad.mit.edu	37	2	178416126	178416126	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178416126C>T	uc002uln.2	-	1	1399	c.1366G>A	c.(1366-1368)GAC>AAC	p.D456N	TTC30B_uc010zfc.1_Missense_Mutation_p.D228N	NM_152517	NP_689730	Q8N4P2	TT30B_HUMAN	tetratricopeptide repeat domain 30B	456	TPR 6.				cell projection organization	cilium	binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.00151)|Epithelial(96;0.00931)|all cancers(119;0.0362)															---	---	---	---
OSBPL6	114880	broad.mit.edu	37	2	179170990	179170990	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179170990T>C	uc002ulx.2	+	3	457	c.79T>C	c.(79-81)TCC>CCC	p.S27P	OSBPL6_uc002ulw.2_Missense_Mutation_p.S27P|OSBPL6_uc002uly.2_Missense_Mutation_p.S27P|OSBPL6_uc010zfe.1_Missense_Mutation_p.S27P|OSBPL6_uc002ulz.2_Missense_Mutation_p.S27P	NM_032523	NP_115912	Q9BZF3	OSBL6_HUMAN	oxysterol-binding protein-like protein 6 isoform	27					lipid transport		lipid binding			pancreas(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)															---	---	---	---
OSBPL6	114880	broad.mit.edu	37	2	179185131	179185131	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179185131T>C	uc002ulx.2	+						OSBPL6_uc002ulw.2_Intron|OSBPL6_uc002uly.2_Intron|OSBPL6_uc010zfe.1_Intron|OSBPL6_uc002ulz.2_Intron|OSBPL6_uc002uma.2_Splice_Site_p.R13_splice	NM_032523	NP_115912			oxysterol-binding protein-like protein 6 isoform						lipid transport		lipid binding			pancreas(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179392191	179392191	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179392191G>T	uc010zfg.1	-	311	100182	c.99958C>A	c.(99958-99960)CTT>ATT	p.L33320I	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.L27015I|TTN_uc010zfi.1_Missense_Mutation_p.L26948I|TTN_uc010zfj.1_Missense_Mutation_p.L26823I|TTN_uc002umq.2_Intron	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	34247							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179392409	179392409	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179392409C>A	uc010zfg.1	-	311	99964	c.99740G>T	c.(99739-99741)AGC>ATC	p.S33247I	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.S26942I|TTN_uc010zfi.1_Missense_Mutation_p.S26875I|TTN_uc010zfj.1_Missense_Mutation_p.S26750I|TTN_uc002umq.2_Intron	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	34174							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179411328	179411328	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179411328G>A	uc010zfg.1	-	290	87347	c.87123C>T	c.(87121-87123)TAC>TAT	p.Y29041Y	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Silent_p.Y22736Y|TTN_uc010zfi.1_Silent_p.Y22669Y|TTN_uc010zfj.1_Silent_p.Y22544Y	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	29968							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179418837	179418837	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179418837G>T	uc010zfg.1	-	282	81521	c.81297C>A	c.(81295-81297)GGC>GGA	p.G27099G	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Silent_p.G20794G|TTN_uc010zfi.1_Silent_p.G20727G|TTN_uc010zfj.1_Silent_p.G20602G	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	28026							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179422483	179422483	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179422483T>C	uc010zfg.1	-	277	80118	c.79894A>G	c.(79894-79896)ATG>GTG	p.M26632V	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.M20327V|TTN_uc010zfi.1_Missense_Mutation_p.M20260V|TTN_uc010zfj.1_Missense_Mutation_p.M20135V	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	27559							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179422614	179422614	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179422614G>A	uc010zfg.1	-	277	79987	c.79763C>T	c.(79762-79764)ACT>ATT	p.T26588I	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.T20283I|TTN_uc010zfi.1_Missense_Mutation_p.T20216I|TTN_uc010zfj.1_Missense_Mutation_p.T20091I	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	27515							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179423276	179423276	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179423276G>A	uc010zfg.1	-	276	79430	c.79206C>T	c.(79204-79206)GGC>GGT	p.G26402G	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Silent_p.G20097G|TTN_uc010zfi.1_Silent_p.G20030G|TTN_uc010zfj.1_Silent_p.G19905G	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	27329							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179432626	179432626	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179432626T>G	uc010zfg.1	-	275	70753	c.70529A>C	c.(70528-70530)AAG>ACG	p.K23510T	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.K17205T|TTN_uc010zfi.1_Missense_Mutation_p.K17138T|TTN_uc010zfj.1_Missense_Mutation_p.K17013T	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	24437							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179432858	179432858	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179432858C>A	uc010zfg.1	-	275	70521	c.70297G>T	c.(70297-70299)GCC>TCC	p.A23433S	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.A17128S|TTN_uc010zfi.1_Missense_Mutation_p.A17061S|TTN_uc010zfj.1_Missense_Mutation_p.A16936S	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	24360							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179449052	179449052	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179449052G>A	uc010zfg.1	-	260	57746	c.57522C>T	c.(57520-57522)TCC>TCT	p.S19174S	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Silent_p.S12869S|TTN_uc010zfi.1_Silent_p.S12802S|TTN_uc010zfj.1_Silent_p.S12677S	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	20101							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179452132	179452132	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179452132G>T	uc010zfg.1	-	256	56326	c.56102C>A	c.(56101-56103)CCT>CAT	p.P18701H	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.P12396H|TTN_uc010zfi.1_Missense_Mutation_p.P12329H|TTN_uc010zfj.1_Missense_Mutation_p.P12204H	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	19628							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179456900	179456900	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179456900T>C	uc010zfg.1	-	251	52251	c.52027A>G	c.(52027-52029)AAT>GAT	p.N17343D	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.N11038D|TTN_uc010zfi.1_Missense_Mutation_p.N10971D|TTN_uc010zfj.1_Missense_Mutation_p.N10846D	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	18270							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179463511	179463511	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179463511G>A	uc010zfg.1	-	240	49446	c.49222C>T	c.(49222-49224)CTG>TTG	p.L16408L	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Silent_p.L10103L|TTN_uc010zfi.1_Silent_p.L10036L|TTN_uc010zfj.1_Silent_p.L9911L	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	17335							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179466784	179466784	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179466784C>T	uc010zfg.1	-	233	47734	c.47510G>A	c.(47509-47511)CGC>CAC	p.R15837H	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.R9532H|TTN_uc010zfi.1_Missense_Mutation_p.R9465H|TTN_uc010zfj.1_Missense_Mutation_p.R9340H	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	16764							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179472351	179472351	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179472351C>A	uc010zfg.1	-	226	45584	c.45360G>T	c.(45358-45360)AAG>AAT	p.K15120N	uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.K8815N|TTN_uc010zfi.1_Missense_Mutation_p.K8748N|TTN_uc010zfj.1_Missense_Mutation_p.K8623N	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	16047							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179498235	179498235	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179498235C>T	uc010zfg.1	-	181	35371	c.35147G>A	c.(35146-35148)CGC>CAC	p.R11716H	TTN_uc010zfh.1_Missense_Mutation_p.R5411H|TTN_uc010zfi.1_Missense_Mutation_p.R5344H|TTN_uc010zfj.1_Missense_Mutation_p.R5219H	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	12643							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179590609	179590609	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179590609A>C	uc010zfg.1	-	67	16932	c.16708T>G	c.(16708-16710)TTC>GTC	p.F5570V	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.F2231V	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	6497							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179590622	179590622	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179590622A>C	uc010zfg.1	-	67	16919	c.16695T>G	c.(16693-16695)ATT>ATG	p.I5565M	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.I2226M	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	6492							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
TTN	7273	broad.mit.edu	37	2	179638234	179638234	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179638234G>A	uc010zfg.1	-	32	7773	c.7549C>T	c.(7549-7551)CTG>TTG	p.L2517L	TTN_uc010zfh.1_Silent_p.L2471L|TTN_uc010zfi.1_Silent_p.L2471L|TTN_uc010zfj.1_Silent_p.L2471L|TTN_uc002unb.2_Silent_p.L2517L	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	2517							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)															---	---	---	---
CCDC141	285025	broad.mit.edu	37	2	179734043	179734043	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179734043G>A	uc002unf.1	-							NM_173648	NP_775919			coiled-coil domain containing 141								protein binding			ovary(7)|pancreas(2)|skin(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147)															---	---	---	---
CWC22	57703	broad.mit.edu	37	2	180818988	180818988	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:180818988G>A	uc010frh.1	-	16	1933	c.1633C>T	c.(1633-1635)CGA>TGA	p.R545*	CWC22_uc002uno.2_Nonsense_Mutation_p.R67*|CWC22_uc002unp.2_Nonsense_Mutation_p.R545*	NM_020943	NP_065994	Q9HCG8	CWC22_HUMAN	CWC22 spliceosome-associated protein homolog	545	MI.					catalytic step 2 spliceosome	protein binding|RNA binding				0																		---	---	---	---
DNAJC10	54431	broad.mit.edu	37	2	183640091	183640091	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183640091G>A	uc002uow.1	+	23	2729	c.2314G>A	c.(2314-2316)GCT>ACT	p.A772T	DNAJC10_uc002uox.1_RNA|DNAJC10_uc002uoy.1_RNA|DNAJC10_uc002uoz.1_Missense_Mutation_p.A726T|DNAJC10_uc010fro.1_RNA	NM_018981	NP_061854	Q8IXB1	DJC10_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 10	772	Thioredoxin 4.				apoptosis in response to endoplasmic reticulum stress|cell redox homeostasis|ER-associated protein catabolic process|glycerol ether metabolic process|negative regulation of protein phosphorylation|protein folding|response to endoplasmic reticulum stress	endoplasmic reticulum chaperone complex|endoplasmic reticulum lumen|extracellular region	ATPase activator activity|ATPase binding|chaperone binding|electron carrier activity|heat shock protein binding|misfolded protein binding|protein disulfide oxidoreductase activity|unfolded protein binding			ovary(1)|large_intestine(1)|breast(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)															---	---	---	---
FRZB	2487	broad.mit.edu	37	2	183699593	183699593	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183699593G>A	uc002upa.1	-	6	1179	c.961C>T	c.(961-963)CGG>TGG	p.R321W		NM_001463	NP_001454	Q92765	SFRP3_HUMAN	frizzled-related protein precursor	321					brain development|cochlea morphogenesis|gonad development|mammary gland involution|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cartilage development|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of hepatocyte differentiation|positive regulation of apoptosis|positive regulation of fat cell differentiation|skeletal system development|vasculature development|Wnt receptor signaling pathway	cytoplasm|extracellular space|membrane	PDZ domain binding|Wnt receptor activity|Wnt-protein binding			ovary(2)|lung(1)|central_nervous_system(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.109)|Epithelial(96;0.231)															---	---	---	---
NCKAP1	10787	broad.mit.edu	37	2	183848055	183848055	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:183848055C>A	uc002upc.2	-	11	1462	c.1060G>T	c.(1060-1062)GCT>TCT	p.A354S	NCKAP1_uc002upb.2_Missense_Mutation_p.A360S	NM_013436	NP_038464	Q9Y2A7	NCKP1_HUMAN	NCK-associated protein 1 isoform 1	354					apoptosis|central nervous system development	integral to membrane|lamellipodium membrane	protein binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)															---	---	---	---
Unknown	0	broad.mit.edu	37	2	186670252	186670252	+	Intron	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:186670252T>G	uc002upm.2	+						uc010zfu.1_5'Flank					Homo sapiens cDNA FLJ44048 fis, clone TESTI4030669.																														---	---	---	---
ITGAV	3685	broad.mit.edu	37	2	187523881	187523881	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187523881G>A	uc002upq.2	+	18	2112	c.1836G>A	c.(1834-1836)ACG>ACA	p.T612T	ITGAV_uc010frs.2_Silent_p.T576T|ITGAV_uc010zfv.1_Silent_p.T566T	NM_002210	NP_002201	P06756	ITAV_HUMAN	integrin alpha-V isoform 1 precursor	612	Extracellular (Potential).				angiogenesis|axon guidance|blood coagulation|cell-matrix adhesion|entry of bacterium into host cell|entry of symbiont into host cell by promotion of host phagocytosis|entry of virus into host cell|ERK1 and ERK2 cascade|integrin-mediated signaling pathway|leukocyte migration|negative regulation of apoptosis|negative regulation of lipid storage|negative regulation of lipid transport|negative regulation of lipoprotein metabolic process|negative regulation of low-density lipoprotein particle receptor biosynthetic process|negative regulation of macrophage derived foam cell differentiation|positive regulation of cell adhesion|positive regulation of cell proliferation|regulation of apoptotic cell clearance	integrin complex	receptor activity|transforming growth factor beta binding			ovary(2)|kidney(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0185)|Epithelial(96;0.072)|all cancers(119;0.189)	STAD - Stomach adenocarcinoma(3;0.106)|COAD - Colon adenocarcinoma(31;0.108)														---	---	---	---
ZSWIM2	151112	broad.mit.edu	37	2	187693502	187693502	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:187693502T>C	uc002upu.1	-	9	1151	c.1111A>G	c.(1111-1113)ATT>GTT	p.I371V		NM_182521	NP_872327	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM domain containing 2	371	RING-type 2.				apoptosis		zinc ion binding			ovary(2)|skin(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)															---	---	---	---
COL3A1	1281	broad.mit.edu	37	2	189855035	189855035	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189855035T>C	uc002uqj.1	+	10	864	c.747T>C	c.(745-747)GGT>GGC	p.G249G	COL3A1_uc010frw.1_5'Flank	NM_000090	NP_000081	P02461	CO3A1_HUMAN	collagen type III alpha 1 preproprotein	249	Triple-helical region.		G -> D (in EDS4).|G -> V (in EDS4).		axon guidance|cell-matrix adhesion|collagen biosynthetic process|collagen fibril organization|fibril organization|heart development|integrin-mediated signaling pathway|negative regulation of immune response|peptide cross-linking|platelet activation|response to cytokine stimulus|response to radiation|skin development|transforming growth factor beta receptor signaling pathway	collagen type III|extracellular space	extracellular matrix structural constituent|integrin binding|platelet-derived growth factor binding			central_nervous_system(7)|ovary(4)|large_intestine(2)	13			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)|Palifermin(DB00039)													---	---	---	---
MSTN	2660	broad.mit.edu	37	2	190927299	190927299	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:190927299A>G	uc002urp.2	-	1	157	c.24T>C	c.(22-24)GTT>GTC	p.V8V		NM_005259	NP_005250	O14793	GDF8_HUMAN	myostatin precursor	8					muscle organ development|positive regulation of transcription, DNA-dependent	extracellular space	cytokine activity|growth factor activity			lung(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.000742)|Epithelial(96;0.0121)|all cancers(119;0.0395)															---	---	---	---
STAT1	6772	broad.mit.edu	37	2	191865867	191865867	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191865867C>T	uc002usj.2	-	6	783	c.395G>A	c.(394-396)AGC>AAC	p.S132N	STAT1_uc010fse.1_Missense_Mutation_p.S132N|STAT1_uc002usk.2_Missense_Mutation_p.S132N|STAT1_uc002usl.2_Missense_Mutation_p.S134N|STAT1_uc010fsf.1_5'UTR	NM_007315	NP_009330	P42224	STAT1_HUMAN	signal transducer and activator of transcription	132					activation of caspase activity|I-kappaB kinase/NF-kappaB cascade|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway|tyrosine phosphorylation of STAT protein	cytosol|nucleolus|nucleoplasm	calcium ion binding|protein binding|RNA polymerase II core promoter sequence-specific DNA binding|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity|signal transducer activity			lung(3)|breast(3)|central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.00434)|Epithelial(96;0.0555)|all cancers(119;0.141)		Fludarabine(DB01073)													---	---	---	---
STAT4	6775	broad.mit.edu	37	2	191934417	191934417	+	Splice_Site	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:191934417A>C	uc002usm.1	-	6	798	c.544_splice	c.e6+1	p.D182_splice	STAT4_uc002usn.1_Splice_Site_p.D182_splice|STAT4_uc010zgk.1_Intron|STAT4_uc002uso.2_Splice_Site_p.D182_splice	NM_003151	NP_003142			signal transducer and activator of transcription						JAK-STAT cascade	cytoplasm|nucleus	calcium ion binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			breast(3)|skin(2)|lung(1)|ovary(1)|prostate(1)|pancreas(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.0864)|all cancers(119;0.204)															---	---	---	---
DNAH7	56171	broad.mit.edu	37	2	196729068	196729068	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196729068C>T	uc002utj.3	-	41	7412	c.7311G>A	c.(7309-7311)ATG>ATA	p.M2437I		NM_018897	NP_061720	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	2437	AAA 4 (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12																		---	---	---	---
DNAH7	56171	broad.mit.edu	37	2	196751006	196751006	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:196751006C>T	uc002utj.3	-							NM_018897	NP_061720			dynein, axonemal, heavy chain 7						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			skin(10)|ovary(2)	12																		---	---	---	---
HECW2	57520	broad.mit.edu	37	2	197143240	197143240	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197143240C>T	uc002utm.1	-						HECW2_uc002utl.1_Intron	NM_020760	NP_065811			HECT, C2 and WW domain containing E3 ubiquitin						protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm	ubiquitin-protein ligase activity			skin(5)|ovary(5)|lung(4)|pancreas(2)|central_nervous_system(1)|kidney(1)	18																		---	---	---	---
ANKRD44	91526	broad.mit.edu	37	2	198051753	198051753	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198051753A>G	uc002uuc.2	-	2	272	c.105T>C	c.(103-105)AAT>AAC	p.N35N	ANKRD44_uc002uua.1_Silent_p.N10N|ANKRD44_uc002uub.2_Silent_p.N35N|ANKRD44_uc010zgw.1_5'UTR|ANKRD44_uc002uud.1_Silent_p.N35N	NM_153697	NP_710181	Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	35	ANK 1.						protein binding			ovary(4)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(117;0.246)															---	---	---	---
PLCL1	5334	broad.mit.edu	37	2	198950721	198950721	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:198950721C>T	uc010fsp.2	+	2	2771	c.2480C>T	c.(2479-2481)CCC>CTC	p.P827L	PLCL1_uc002uuv.3_Missense_Mutation_p.P748L	NM_001114661	NP_001108133	Q15111	PLCL1_HUMAN	RecName: Full=Inactive phospholipase C-like protein 1;          Short=PLC-L1; AltName: Full=Phospholipase C-deleted in lung carcinoma; AltName: Full=Phospholipase C-related but catalytically inactive protein;          Short=PRIP;	827					intracellular signal transduction|lipid metabolic process	cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|skin(1)	2					Quinacrine(DB01103)													---	---	---	---
KCTD18	130535	broad.mit.edu	37	2	201369584	201369584	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201369584C>T	uc002uvs.2	-	3	776	c.259G>A	c.(259-261)GCC>ACC	p.A87T	KCTD18_uc002uvt.2_Missense_Mutation_p.A87T|KCTD18_uc002uvu.1_Missense_Mutation_p.A87T	NM_152387	NP_689600	Q6PI47	KCD18_HUMAN	potassium channel tetramerization domain	87						voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)	1																		---	---	---	---
SGOL2	151246	broad.mit.edu	37	2	201437602	201437602	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201437602A>C	uc002uvw.2	+	7	2646	c.2533A>C	c.(2533-2535)ACC>CCC	p.T845P	SGOL2_uc010zhd.1_Missense_Mutation_p.T845P|SGOL2_uc010zhe.1_Missense_Mutation_p.T845P	NM_152524	NP_689737	Q562F6	SGOL2_HUMAN	shugoshin-like 2 isoform 1	845					cell division|mitotic prometaphase	condensed chromosome kinetochore|cytosol|mitotic cohesin complex	protein binding			ovary(2)|skin(2)	4																		---	---	---	---
AOX1	316	broad.mit.edu	37	2	201485449	201485449	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201485449C>T	uc002uvx.2	+	17	1882	c.1781C>T	c.(1780-1782)ACG>ATG	p.T594M	AOX1_uc010zhf.1_Missense_Mutation_p.T150M|AOX1_uc010fsu.2_Intron	NM_001159	NP_001150	Q06278	ADO_HUMAN	aldehyde oxidase 1	594					inflammatory response|reactive oxygen species metabolic process	cytoplasm	2 iron, 2 sulfur cluster binding|aldehyde oxidase activity|flavin adenine dinucleotide binding|iron ion binding|NAD binding|xanthine dehydrogenase activity			ovary(4)|pancreas(1)|skin(1)	6					Brimonidine(DB00484)|Chlorpromazine(DB00477)|Famciclovir(DB00426)|Menadione(DB00170)|Methotrexate(DB00563)|NADH(DB00157)|Palonosetron(DB00377)|Penciclovir(DB00299)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)													---	---	---	---
AOX1	316	broad.mit.edu	37	2	201501759	201501759	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201501759C>T	uc002uvx.2	+	22	2573	c.2472C>T	c.(2470-2472)GCC>GCT	p.A824A	AOX1_uc010zhf.1_Silent_p.A380A|AOX1_uc010fsu.2_Silent_p.A190A	NM_001159	NP_001150	Q06278	ADO_HUMAN	aldehyde oxidase 1	824					inflammatory response|reactive oxygen species metabolic process	cytoplasm	2 iron, 2 sulfur cluster binding|aldehyde oxidase activity|flavin adenine dinucleotide binding|iron ion binding|NAD binding|xanthine dehydrogenase activity			ovary(4)|pancreas(1)|skin(1)	6					Brimonidine(DB00484)|Chlorpromazine(DB00477)|Famciclovir(DB00426)|Menadione(DB00170)|Methotrexate(DB00563)|NADH(DB00157)|Palonosetron(DB00377)|Penciclovir(DB00299)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)													---	---	---	---
MPP4	58538	broad.mit.edu	37	2	202550655	202550655	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202550655T>G	uc002uyk.3	-	6	687	c.479A>C	c.(478-480)AAC>ACC	p.N160T	MPP4_uc010ftj.2_Missense_Mutation_p.N160T|MPP4_uc010zhq.1_Missense_Mutation_p.N160T|MPP4_uc010zhr.1_Missense_Mutation_p.N160T|MPP4_uc010zhs.1_Intron|MPP4_uc002uyj.3_Intron|MPP4_uc010zht.1_Missense_Mutation_p.N133T|MPP4_uc002uyl.3_RNA|MPP4_uc010ftk.2_Missense_Mutation_p.N160T|MPP4_uc002uym.1_Intron|MPP4_uc002uyn.2_Intron	NM_033066	NP_149055	Q96JB8	MPP4_HUMAN	membrane protein, palmitoylated 4	160	PDZ.					cytoplasm	protein binding				0																		---	---	---	---
NOP58	51602	broad.mit.edu	37	2	203160491	203160491	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203160491T>C	uc002uzb.2	+	10	1152	c.1002T>C	c.(1000-1002)GAT>GAC	p.D334D		NM_015934	NP_057018	Q9Y2X3	NOP58_HUMAN	NOP58 ribonucleoprotein homolog	334	Nop.				cell growth|rRNA processing|snRNP protein import into nucleus	box C/D snoRNP complex|Cajal body|cytoplasm|pre-snoRNP complex	protein binding|snoRNA binding				0																		---	---	---	---
PARD3B	117583	broad.mit.edu	37	2	205978249	205978249	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:205978249G>T	uc002var.1	+	6	835	c.628G>T	c.(628-630)GGA>TGA	p.G210*	PARD3B_uc010fub.1_Nonsense_Mutation_p.G210*|PARD3B_uc002vao.1_Nonsense_Mutation_p.G210*|PARD3B_uc002vap.1_Nonsense_Mutation_p.G210*|PARD3B_uc002vaq.1_Nonsense_Mutation_p.G210*	NM_152526	NP_689739	Q8TEW8	PAR3L_HUMAN	par-3 partitioning defective 3 homolog B isoform	210	PDZ 1.				cell cycle|cell division	endomembrane system|tight junction				skin(2)|ovary(1)|breast(1)	4		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)														---	---	---	---
INO80D	54891	broad.mit.edu	37	2	206869855	206869855	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:206869855G>A	uc002vaz.3	-	11	2726	c.2321C>T	c.(2320-2322)GCA>GTA	p.A774V		NM_017759	NP_060229	Q53TQ3	IN80D_HUMAN	INO80 complex subunit D	774					DNA recombination|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(1)	1																		---	---	---	---
NDUFS1	4719	broad.mit.edu	37	2	207007491	207007491	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207007491A>G	uc002vbe.2	-	11	1179	c.1052T>C	c.(1051-1053)CTG>CCG	p.L351P	NDUFS1_uc010ziq.1_Missense_Mutation_p.L365P|NDUFS1_uc010zir.1_Missense_Mutation_p.L315P|NDUFS1_uc010zis.1_Missense_Mutation_p.L294P|NDUFS1_uc010zit.1_Missense_Mutation_p.L240P|NDUFS1_uc010ziu.1_Missense_Mutation_p.L235P	NM_005006	NP_004997	P28331	NDUS1_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 1,	351					apoptosis|ATP metabolic process|mitochondrial electron transport, NADH to ubiquinone|reactive oxygen species metabolic process|regulation of mitochondrial membrane potential|transport	mitochondrial intermembrane space|mitochondrial respiratory chain complex I	2 iron, 2 sulfur cluster binding|4 iron, 4 sulfur cluster binding|electron carrier activity|metal ion binding|NADH dehydrogenase (ubiquinone) activity|protein binding			ovary(1)	1					NADH(DB00157)													---	---	---	---
ZDBF2	57683	broad.mit.edu	37	2	207175714	207175714	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207175714T>C	uc002vbp.2	+	5	6712	c.6462T>C	c.(6460-6462)GAT>GAC	p.D2154D		NM_020923	NP_065974	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	2154							nucleic acid binding|zinc ion binding			ovary(3)	3																		---	---	---	---
ADAM23	8745	broad.mit.edu	37	2	207436522	207436522	+	Nonsense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:207436522T>A	uc002vbq.2	+	17	1861	c.1638T>A	c.(1636-1638)TGT>TGA	p.C546*	ADAM23_uc010ziv.1_RNA	NM_003812	NP_003803	O75077	ADA23_HUMAN	ADAM metallopeptidase domain 23 preproprotein	546	Disintegrin.|Extracellular (Potential).				cell adhesion|central nervous system development|proteolysis	extracellular region|integral to plasma membrane	integrin binding|metalloendopeptidase activity|zinc ion binding			skin(2)|ovary(1)	3				LUSC - Lung squamous cell carcinoma(261;0.0961)|Lung(261;0.182)|Epithelial(149;0.205)														---	---	---	---
CRYGC	1420	broad.mit.edu	37	2	208993028	208993028	+	Missense_Mutation	SNP	G	A	A	rs141474796		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208993028G>A	uc002vco.3	-	3	462	c.424C>T	c.(424-426)CGG>TGG	p.R142W		NM_020989	NP_066269	P07315	CRGC_HUMAN	crystallin, gamma C	142	Beta/gamma crystallin 'Greek key' 4.				visual perception	cytoplasm|nucleus	protein binding|structural constituent of eye lens				0				LUSC - Lung squamous cell carcinoma(261;0.0703)|Epithelial(149;0.0858)|Lung(261;0.133)														---	---	---	---
CRYGA	1418	broad.mit.edu	37	2	209025629	209025629	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209025629G>A	uc002vcq.3	-	3	441	c.424C>T	c.(424-426)CGG>TGG	p.R142W		NM_014617	NP_055432	P11844	CRGA_HUMAN	crystallin, gamma A	142	Beta/gamma crystallin 'Greek key' 4.				visual perception		structural constituent of eye lens				0				Epithelial(149;0.067)|LUSC - Lung squamous cell carcinoma(261;0.0708)|Lung(261;0.135)														---	---	---	---
MAP2	4133	broad.mit.edu	37	2	210557682	210557682	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210557682A>C	uc002vde.1	+	7	1036	c.788A>C	c.(787-789)AAG>ACG	p.K263T	MAP2_uc002vdc.1_Missense_Mutation_p.K263T|MAP2_uc002vdd.1_Intron|MAP2_uc002vdf.1_Intron|MAP2_uc002vdg.1_Intron|MAP2_uc002vdh.1_Intron|MAP2_uc002vdi.1_Missense_Mutation_p.K259T	NM_002374	NP_002365	P11137	MAP2_HUMAN	microtubule-associated protein 2 isoform 1	263					central nervous system neuron development|dendrite morphogenesis|negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	beta-dystroglycan binding|calmodulin binding|structural molecule activity			ovary(9)|upper_aerodigestive_tract(2)|large_intestine(2)|pancreas(2)|central_nervous_system(1)|skin(1)	17		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Estramustine(DB01196)													---	---	---	---
MAP2	4133	broad.mit.edu	37	2	210559702	210559702	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210559702C>T	uc002vde.1	+	7	3056	c.2808C>T	c.(2806-2808)TCC>TCT	p.S936S	MAP2_uc002vdc.1_Silent_p.S936S|MAP2_uc002vdd.1_Intron|MAP2_uc002vdf.1_Intron|MAP2_uc002vdg.1_Intron|MAP2_uc002vdh.1_Intron|MAP2_uc002vdi.1_Silent_p.S932S	NM_002374	NP_002365	P11137	MAP2_HUMAN	microtubule-associated protein 2 isoform 1	936					central nervous system neuron development|dendrite morphogenesis|negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	beta-dystroglycan binding|calmodulin binding|structural molecule activity			ovary(9)|upper_aerodigestive_tract(2)|large_intestine(2)|pancreas(2)|central_nervous_system(1)|skin(1)	17		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Estramustine(DB01196)													---	---	---	---
MAP2	4133	broad.mit.edu	37	2	210560646	210560646	+	Missense_Mutation	SNP	G	A	A	rs142649637	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:210560646G>A	uc002vde.1	+	7	4000	c.3752G>A	c.(3751-3753)CGC>CAC	p.R1251H	MAP2_uc002vdc.1_Missense_Mutation_p.R1251H|MAP2_uc002vdd.1_Intron|MAP2_uc002vdf.1_Intron|MAP2_uc002vdg.1_Intron|MAP2_uc002vdh.1_Intron|MAP2_uc002vdi.1_Missense_Mutation_p.R1247H	NM_002374	NP_002365	P11137	MAP2_HUMAN	microtubule-associated protein 2 isoform 1	1251					central nervous system neuron development|dendrite morphogenesis|negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	beta-dystroglycan binding|calmodulin binding|structural molecule activity			ovary(9)|upper_aerodigestive_tract(2)|large_intestine(2)|pancreas(2)|central_nervous_system(1)|skin(1)	17		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Estramustine(DB01196)													---	---	---	---
CPS1	1373	broad.mit.edu	37	2	211523344	211523344	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:211523344A>G	uc002vee.3	+	31	3820	c.3688A>G	c.(3688-3690)ATT>GTT	p.I1230V	CPS1_uc010fur.2_Missense_Mutation_p.I1236V|CPS1_uc010fus.2_Missense_Mutation_p.I779V	NM_001875	NP_001866	P31327	CPSM_HUMAN	carbamoyl-phosphate synthetase 1 isoform b	1230	ATP-grasp 2.				carbamoyl phosphate biosynthetic process|citrulline biosynthetic process|glutamine metabolic process|glycogen catabolic process|nitric oxide metabolic process|positive regulation of vasodilation|response to lipopolysaccharide|triglyceride catabolic process|urea cycle	mitochondrial nucleoid	ATP binding|carbamoyl-phosphate synthase (ammonia) activity			ovary(8)|central_nervous_system(3)|breast(1)|skin(1)	13				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)														---	---	---	---
ERBB4	2066	broad.mit.edu	37	2	212426711	212426711	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:212426711C>A	uc002veg.1	-	20	2502	c.2404G>T	c.(2404-2406)GGC>TGC	p.G802C	ERBB4_uc002veh.1_Missense_Mutation_p.G802C|ERBB4_uc010zji.1_Missense_Mutation_p.G792C|ERBB4_uc010zjj.1_Missense_Mutation_p.G792C|ERBB4_uc010fut.1_Missense_Mutation_p.G802C	NM_005235	NP_005226	Q15303	ERBB4_HUMAN	v-erb-a erythroblastic leukemia viral oncogene	802	Protein kinase.|Cytoplasmic (Potential).				cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent|transmembrane receptor protein tyrosine kinase signaling pathway	basolateral plasma membrane|cytoplasm|integral to membrane|nucleus	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(21)|skin(5)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	33		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)											TSP Lung(8;0.080)			---	---	---	---
SPAG16	79582	broad.mit.edu	37	2	214794725	214794725	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:214794725A>G	uc002veq.2	+	12	1348	c.1256A>G	c.(1255-1257)AAA>AGA	p.K419R	SPAG16_uc010fuz.1_Missense_Mutation_p.K270R|SPAG16_uc002ver.2_Missense_Mutation_p.K365R|SPAG16_uc010zjk.1_Missense_Mutation_p.K325R	NM_024532	NP_078808	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16 isoform 1	419	WD 2.				cilium assembly	cilium axoneme|flagellar axoneme				ovary(1)|skin(1)	2		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)														---	---	---	---
BARD1	580	broad.mit.edu	37	2	215593642	215593642	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215593642C>A	uc002veu.2	-	11	2227	c.2092G>T	c.(2092-2094)GGT>TGT	p.G698C	BARD1_uc010zjm.1_Missense_Mutation_p.Q552H	NM_000465	NP_000456	Q99728	BARD1_HUMAN	BRCA1 associated RING domain 1	698	BRCT 2.				cell cycle arrest|DNA repair|negative regulation of apoptosis|negative regulation of mRNA 3'-end processing|negative regulation of protein export from nucleus|positive regulation of apoptosis|positive regulation of protein catabolic process|protein K6-linked ubiquitination|regulation of phosphorylation|tissue homeostasis	BRCA1-A complex|BRCA1-BARD1 complex|cytoplasm	kinase binding|protein heterodimerization activity|protein homodimerization activity|RNA binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)	2		Renal(323;0.0243)		Epithelial(149;3.2e-06)|all cancers(144;0.000461)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)										Neuroblastoma_Familial_Clustering_of|Congenital_Central_Hypoventilation_Syndrome				---	---	---	---
ABCA12	26154	broad.mit.edu	37	2	215855530	215855530	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215855530T>C	uc002vew.2	-	24	3740	c.3520A>G	c.(3520-3522)ATT>GTT	p.I1174V	ABCA12_uc002vev.2_Missense_Mutation_p.I856V|ABCA12_uc010zjn.1_Missense_Mutation_p.I101V	NM_173076	NP_775099	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A, member 12	1174	Helical; (Potential).				cellular homeostasis|lipid transport	integral to membrane	ATP binding|ATPase activity			ovary(6)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	11		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)														---	---	---	---
ABCA12	26154	broad.mit.edu	37	2	215884116	215884116	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:215884116G>A	uc002vew.2	-	13	1821	c.1601C>T	c.(1600-1602)CCG>CTG	p.P534L	ABCA12_uc002vev.2_Missense_Mutation_p.P216L|ABCA12_uc010zjn.1_5'UTR	NM_173076	NP_775099	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A, member 12	534					cellular homeostasis|lipid transport	integral to membrane	ATP binding|ATPase activity			ovary(6)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	11		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)														---	---	---	---
ATIC	471	broad.mit.edu	37	2	216214327	216214327	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216214327C>T	uc002vex.3	+	16	1902	c.1728C>T	c.(1726-1728)GAC>GAT	p.D576D	ATIC_uc010zjo.1_Silent_p.D517D|ATIC_uc002vey.3_Silent_p.D575D	NM_004044	NP_004035	P31939	PUR9_HUMAN	5-aminoimidazole-4-carboxamide ribonucleotide	576					IMP biosynthetic process|purine base metabolic process	cytosol	IMP cyclohydrolase activity|phosphoribosylaminoimidazolecarboxamide formyltransferase activity|protein homodimerization activity		ATIC/ALK(24)	haematopoietic_and_lymphoid_tissue(22)|ovary(2)|lung(2)|soft_tissue(2)|skin(1)	29		Renal(323;0.229)		Epithelial(149;2.02e-06)|all cancers(144;0.000316)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.0097)	Tetrahydrofolic acid(DB00116)			T	ALK	ALCL								---	---	---	---
FN1	2335	broad.mit.edu	37	2	216257857	216257857	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216257857G>A	uc002vfa.2	-	25	4132	c.3866C>T	c.(3865-3867)CCG>CTG	p.P1289L	FN1_uc002vfb.2_Intron|FN1_uc002vfc.2_Intron|FN1_uc002vfd.2_Missense_Mutation_p.P1289L|FN1_uc002vfe.2_Intron|FN1_uc002vff.2_Intron|FN1_uc002vfg.2_Intron|FN1_uc002vfh.2_Intron|FN1_uc002vfi.2_Missense_Mutation_p.P1289L|FN1_uc002vfj.2_Missense_Mutation_p.P1289L|FN1_uc002vez.2_5'Flank|FN1_uc010zjp.1_5'UTR	NM_212482	NP_997647	P02751	FINC_HUMAN	fibronectin 1 isoform 1 preproprotein	1289	Fibronectin type-III 8.|Cell-attachment.				acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading	ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix	collagen binding|extracellular matrix structural constituent|heparin binding			central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1)	13		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
FN1	2335	broad.mit.edu	37	2	216269250	216269250	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216269250G>A	uc002vfa.2	-	20	3381	c.3115C>T	c.(3115-3117)CCC>TCC	p.P1039S	FN1_uc002vfb.2_Missense_Mutation_p.P1039S|FN1_uc002vfc.2_Missense_Mutation_p.P1039S|FN1_uc002vfd.2_Missense_Mutation_p.P1039S|FN1_uc002vfe.2_Missense_Mutation_p.P1039S|FN1_uc002vff.2_Missense_Mutation_p.P1039S|FN1_uc002vfg.2_Missense_Mutation_p.P1039S|FN1_uc002vfh.2_Missense_Mutation_p.P1039S|FN1_uc002vfi.2_Missense_Mutation_p.P1039S|FN1_uc002vfj.2_Missense_Mutation_p.P1039S	NM_212482	NP_997647	P02751	FINC_HUMAN	fibronectin 1 isoform 1 preproprotein	1039	|Fibronectin type-III 5.				acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading	ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix	collagen binding|extracellular matrix structural constituent|heparin binding			central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1)	13		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
FN1	2335	broad.mit.edu	37	2	216271097	216271097	+	Silent	SNP	G	A	A	rs138522820	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216271097G>A	uc002vfa.2	-	19	3116	c.2850C>T	c.(2848-2850)CAC>CAT	p.H950H	FN1_uc002vfb.2_Silent_p.H950H|FN1_uc002vfc.2_Silent_p.H950H|FN1_uc002vfd.2_Silent_p.H950H|FN1_uc002vfe.2_Silent_p.H950H|FN1_uc002vff.2_Silent_p.H950H|FN1_uc002vfg.2_Silent_p.H950H|FN1_uc002vfh.2_Silent_p.H950H|FN1_uc002vfi.2_Silent_p.H950H|FN1_uc002vfj.2_Silent_p.H950H	NM_212482	NP_997647	P02751	FINC_HUMAN	fibronectin 1 isoform 1 preproprotein	950	|Fibronectin type-III 4.				acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading	ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix	collagen binding|extracellular matrix structural constituent|heparin binding			central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1)	13		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
AAMP	14	broad.mit.edu	37	2	219130815	219130815	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219130815C>T	uc002vhk.2	-	6	819	c.735G>A	c.(733-735)AAG>AAA	p.K245K	AAMP_uc002vhj.2_Silent_p.K226K|AAMP_uc010fvo.2_Silent_p.K245K|AAMP_uc002vhl.2_Silent_p.K246K	NM_001087	NP_001078	Q13685	AAMP_HUMAN	angio-associated, migratory cell protein	245	WD 4.				angiogenesis|cell differentiation|positive regulation of endothelial cell migration|smooth muscle cell migration	cell surface|cytoplasm|plasma membrane	heparin binding			ovary(1)	1		Renal(207;0.0474)		Epithelial(149;7.19e-07)|all cancers(144;0.000131)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
STK36	27148	broad.mit.edu	37	2	219549863	219549863	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219549863C>A	uc002viu.2	+	11	1558	c.1292C>A	c.(1291-1293)CCT>CAT	p.P431H	STK36_uc002viv.2_Missense_Mutation_p.P431H	NM_015690	NP_056505	Q9NRP7	STK36_HUMAN	serine/threonine kinase 36	431					cilium assembly|positive regulation of hh target transcription factor activity|positive regulation of smoothened signaling pathway|post-embryonic development	aggresome|cytoplasm|focal adhesion|intermediate filament cytoskeleton|nucleus	ATP binding|protein serine/threonine kinase activity|transcription factor binding			ovary(4)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)	11		Renal(207;0.0915)		Epithelial(149;9.65e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00984)														---	---	---	---
CCDC108	255101	broad.mit.edu	37	2	219869090	219869090	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219869090C>T	uc002vjl.1	-	33	5223	c.5139G>A	c.(5137-5139)GAG>GAA	p.E1713E	uc010fvz.1_5'Flank|MIR375_hsa-mir-375|MI0000783_5'Flank	NM_194302	NP_919278	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108 isoform 1	1713						integral to membrane	structural molecule activity			ovary(2)|upper_aerodigestive_tract(1)|pancreas(1)	4		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
ATG9A	79065	broad.mit.edu	37	2	220086030	220086030	+	Intron	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220086030G>T	uc002vke.1	-						ABCB6_uc002vkc.1_5'Flank|ABCB6_uc010fwe.1_5'Flank|ABCB6_uc010zku.1_5'Flank|ATG9A_uc002vkd.1_Intron|ATG9A_uc002vkf.1_Intron	NM_001077198	NP_001070666			APG9 autophagy 9-like 1						autophagic vacuole assembly|protein transport	autophagic vacuole membrane|cytoplasmic vesicle|Golgi apparatus|integral to membrane|late endosome membrane				skin(1)	1		Renal(207;0.0474)		Epithelial(149;1.37e-06)|all cancers(144;0.000222)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)														---	---	---	---
SPEG	10290	broad.mit.edu	37	2	220331981	220331981	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220331981C>T	uc010fwg.2	+	10	2967	c.2967C>T	c.(2965-2967)TGC>TGT	p.C989C		NM_005876	NP_005867	Q15772	SPEG_HUMAN	SPEG complex locus	989	Ig-like 4.				muscle organ development|negative regulation of cell proliferation	nucleus	ATP binding|protein serine/threonine kinase activity			stomach(9)|ovary(4)|central_nervous_system(1)	14		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)														---	---	---	---
SPEG	10290	broad.mit.edu	37	2	220332163	220332163	+	Intron	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220332163C>A	uc010fwg.2	+							NM_005876	NP_005867			SPEG complex locus						muscle organ development|negative regulation of cell proliferation	nucleus	ATP binding|protein serine/threonine kinase activity			stomach(9)|ovary(4)|central_nervous_system(1)	14		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)														---	---	---	---
SPEG	10290	broad.mit.edu	37	2	220345415	220345415	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220345415C>A	uc010fwg.2	+	26	5365	c.5365C>A	c.(5365-5367)CTC>ATC	p.L1789I		NM_005876	NP_005867	Q15772	SPEG_HUMAN	SPEG complex locus	1789	Protein kinase 1.				muscle organ development|negative regulation of cell proliferation	nucleus	ATP binding|protein serine/threonine kinase activity			stomach(9)|ovary(4)|central_nervous_system(1)	14		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)														---	---	---	---
GMPPA	29926	broad.mit.edu	37	2	220366649	220366649	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220366649C>A	uc002vlr.2	+	5	387	c.319C>A	c.(319-321)CCC>ACC	p.P107T	GMPPA_uc002vls.2_Missense_Mutation_p.P107T|GMPPA_uc002vlt.2_Missense_Mutation_p.P107T|GMPPA_uc002vlu.2_Missense_Mutation_p.P107T|GMPPA_uc002vlv.2_Missense_Mutation_p.P107T|GMPPA_uc002vlw.2_RNA|GMPPA_uc002vlx.2_Missense_Mutation_p.P107T	NM_013335	NP_037467	Q96IJ6	GMPPA_HUMAN	GDP-mannose pyrophosphorylase A	107					dolichol-linked oligosaccharide biosynthetic process|GDP-mannose biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine		GTP binding|mannose-1-phosphate guanylyltransferase activity				0		Renal(207;0.0183)		Epithelial(149;3.82e-10)|all cancers(144;6.25e-08)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00807)|READ - Rectum adenocarcinoma(5;0.148)														---	---	---	---
GMPPA	29926	broad.mit.edu	37	2	220370079	220370079	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220370079C>T	uc002vlr.2	+	8	818	c.750C>T	c.(748-750)TCC>TCT	p.S250S	GMPPA_uc002vls.2_Silent_p.S250S|GMPPA_uc002vlt.2_Silent_p.S250S|GMPPA_uc002vlu.2_Silent_p.S250S|GMPPA_uc002vlv.2_Silent_p.S250S|GMPPA_uc002vlw.2_RNA|GMPPA_uc002vlx.2_Silent_p.S250S	NM_013335	NP_037467	Q96IJ6	GMPPA_HUMAN	GDP-mannose pyrophosphorylase A	250					dolichol-linked oligosaccharide biosynthetic process|GDP-mannose biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine		GTP binding|mannose-1-phosphate guanylyltransferase activity				0		Renal(207;0.0183)		Epithelial(149;3.82e-10)|all cancers(144;6.25e-08)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00807)|READ - Rectum adenocarcinoma(5;0.148)														---	---	---	---
MOGAT1	116255	broad.mit.edu	37	2	223554036	223554036	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223554036A>G	uc010fws.1	+	3	374	c.326A>G	c.(325-327)CAC>CGC	p.H109R	MOGAT1_uc010fwt.1_Missense_Mutation_p.H69R	NM_058165	NP_477513	Q96PD6	MOGT1_HUMAN	monoacylglycerol O-acyltransferase 1	109					glycerol metabolic process	endoplasmic reticulum membrane|integral to membrane	2-acylglycerol O-acyltransferase activity			breast(1)	1		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;2.06e-07)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0105)														---	---	---	---
ACSL3	2181	broad.mit.edu	37	2	223783922	223783922	+	Splice_Site	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:223783922T>C	uc002vni.2	+	7	1256	c.805_splice	c.e7+2	p.E269_splice	ACSL3_uc002vnj.2_Splice_Site_p.E269_splice	NM_004457	NP_004448			acyl-CoA synthetase long-chain family member 3						long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane|peroxisomal membrane	ATP binding|fatty-acyl-CoA synthase activity|long-chain fatty acid-CoA ligase activity|protein binding			ovary(2)	2		Renal(207;0.0183)		Epithelial(121;1.28e-10)|all cancers(144;8.06e-08)|Lung(261;0.00834)|LUSC - Lung squamous cell carcinoma(224;0.00864)	Icosapent(DB00159)			T	ETV1	prostate								---	---	---	---
SCG2	7857	broad.mit.edu	37	2	224463699	224463699	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224463699T>C	uc002vnm.2	-	2	435	c.302A>G	c.(301-303)GAG>GGG	p.E101G		NM_003469	NP_003460	P13521	SCG2_HUMAN	secretogranin II precursor	101					angiogenesis|endothelial cell migration|eosinophil chemotaxis|induction of positive chemotaxis|inflammatory response|MAPKKK cascade|negative regulation of apoptosis|negative regulation of endothelial cell proliferation|positive regulation of endothelial cell proliferation|protein secretion	extracellular space|stored secretory granule	chemoattractant activity|cytokine activity			ovary(1)	1		Renal(207;0.0112)|Lung NSC(271;0.0185)|all_lung(227;0.0271)		Epithelial(121;8.16e-11)|all cancers(144;4.66e-08)|Lung(261;0.00714)|LUSC - Lung squamous cell carcinoma(224;0.008)														---	---	---	---
WDFY1	57590	broad.mit.edu	37	2	224770709	224770709	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:224770709C>T	uc002vnq.2	-	4	340	c.289G>A	c.(289-291)GTT>ATT	p.V97I		NM_020830	NP_065881	Q8IWB7	WDFY1_HUMAN	WD repeat and FYVE domain containing 1	97	WD 2.					cytosol|early endosome|nucleus	1-phosphatidylinositol binding|zinc ion binding			lung(1)	1		all_lung(227;0.00682)|Lung NSC(271;0.00859)|Renal(207;0.0112)|all_hematologic(139;0.189)		Epithelial(121;5.34e-10)|all cancers(144;1.67e-07)|Lung(261;0.00807)|LUSC - Lung squamous cell carcinoma(224;0.00843)														---	---	---	---
DOCK10	55619	broad.mit.edu	37	2	225695290	225695290	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225695290C>T	uc010fwz.1	-	27	3243	c.3004G>A	c.(3004-3006)GCA>ACA	p.A1002T	DOCK10_uc002vob.2_Missense_Mutation_p.A996T	NM_014689	NP_055504	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	1002							GTP binding			ovary(2)	2		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)														---	---	---	---
DOCK10	55619	broad.mit.edu	37	2	225709925	225709925	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225709925C>T	uc010fwz.1	-	21	2715	c.2476G>A	c.(2476-2478)GGA>AGA	p.G826R	DOCK10_uc002vob.2_Missense_Mutation_p.G820R	NM_014689	NP_055504	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	826	DHR-1.						GTP binding			ovary(2)	2		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)														---	---	---	---
COL4A4	1286	broad.mit.edu	37	2	227985764	227985764	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:227985764C>T	uc010zlt.1	-	5	947	c.293G>A	c.(292-294)GGC>GAC	p.G98D		NM_000092	NP_000083	P53420	CO4A4_HUMAN	alpha 4 type IV collagen precursor	98	Triple-helical region.				axon guidance|glomerular basement membrane development	basal lamina|collagen type IV	extracellular matrix structural constituent|protein binding			ovary(5)|central_nervous_system(3)|pancreas(1)|breast(1)|skin(1)	11		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)														---	---	---	---
MFF	56947	broad.mit.edu	37	2	228221792	228221792	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228221792G>T	uc002vos.2	+	11	1406	c.988G>T	c.(988-990)GCT>TCT	p.A330S	MFF_uc002vot.2_Missense_Mutation_p.A279S|MFF_uc002vou.2_Missense_Mutation_p.A252S|MFF_uc002vov.2_Missense_Mutation_p.A226S|MFF_uc002vow.2_Missense_Mutation_p.A231S|MFF_uc002vox.2_Missense_Mutation_p.A206S|MFF_uc002voy.2_Missense_Mutation_p.A330S|MFF_uc002voz.2_Missense_Mutation_p.A206S|MFF_uc002vpa.2_Missense_Mutation_p.A118S	NM_020194	NP_064579	Q9GZY8	MFF_HUMAN	mitochondrial fission factor	330	Helical; Anchor for type IV membrane protein; (Potential).					integral to membrane|mitochondrial outer membrane				large_intestine(1)	1																		---	---	---	---
C2orf83	56918	broad.mit.edu	37	2	228497769	228497769	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228497769A>T	uc002vph.2	-	1	268	c.33T>A	c.(31-33)AAT>AAA	p.N11K	C2orf83_uc010zlu.1_Missense_Mutation_p.N11K	NM_020161	NP_064546	Q53S99	CB083_HUMAN	hypothetical protein LOC56918 isoform 1	11						membrane	folic acid binding|reduced folate carrier activity				0																		---	---	---	---
SLC19A3	80704	broad.mit.edu	37	2	228560653	228560653	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228560653C>T	uc002vpi.2	-	4	1213	c.1124G>A	c.(1123-1125)GGC>GAC	p.G375D	SLC19A3_uc002vpj.2_RNA|SLC19A3_uc010zlv.1_Missense_Mutation_p.G371D	NM_025243	NP_079519	Q9BZV2	S19A3_HUMAN	solute carrier family 19, member 3	375	Extracellular (Potential).				thiamine-containing compound metabolic process	integral to membrane|plasma membrane	folic acid binding|reduced folate carrier activity|thiamine uptake transmembrane transporter activity			ovary(2)	2		Renal(207;0.0112)|all_lung(227;0.0335)|Lung NSC(271;0.142)|all_hematologic(139;0.21)|Esophageal squamous(248;0.236)		Epithelial(121;1.58e-10)|all cancers(144;8.55e-08)|Lung(261;0.00948)|LUSC - Lung squamous cell carcinoma(224;0.0125)	L-Cysteine(DB00151)													---	---	---	---
SPHKAP	80309	broad.mit.edu	37	2	228881548	228881548	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:228881548G>A	uc002vpq.2	-	7	4069	c.4022C>T	c.(4021-4023)CCC>CTC	p.P1341L	SPHKAP_uc002vpp.2_Missense_Mutation_p.P1341L|SPHKAP_uc010zlx.1_Missense_Mutation_p.P1341L	NM_001142644	NP_001136116	Q2M3C7	SPKAP_HUMAN	sphingosine kinase type 1-interacting protein	1341						cytoplasm	protein binding			skin(5)|ovary(4)|lung(1)	10		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)														---	---	---	---
DNER	92737	broad.mit.edu	37	2	230231605	230231605	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230231605A>T	uc002vpv.2	-	12	2233	c.2086T>A	c.(2086-2088)TCC>ACC	p.S696T		NM_139072	NP_620711	Q8NFT8	DNER_HUMAN	delta-notch-like EGF repeat-containing	696	Cytoplasmic (Potential).				central nervous system development|endocytosis|neuron migration|Notch signaling pathway|synapse assembly	dendrite|early endosome|integral to membrane|plasma membrane	calcium ion binding|clathrin binding|transmembrane receptor activity			lung(5)|ovary(2)|skin(1)	8		all_lung(227;0.00413)|Renal(207;0.0113)|Lung NSC(271;0.0211)|all_hematologic(139;0.105)|Acute lymphoblastic leukemia(138;0.175)		Epithelial(121;1.4e-11)|all cancers(144;7.7e-09)|LUSC - Lung squamous cell carcinoma(224;0.034)|Lung(119;0.0375)														---	---	---	---
DNER	92737	broad.mit.edu	37	2	230231839	230231839	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230231839C>T	uc002vpv.2	-							NM_139072	NP_620711			delta-notch-like EGF repeat-containing						central nervous system development|endocytosis|neuron migration|Notch signaling pathway|synapse assembly	dendrite|early endosome|integral to membrane|plasma membrane	calcium ion binding|clathrin binding|transmembrane receptor activity			lung(5)|ovary(2)|skin(1)	8		all_lung(227;0.00413)|Renal(207;0.0113)|Lung NSC(271;0.0211)|all_hematologic(139;0.105)|Acute lymphoblastic leukemia(138;0.175)		Epithelial(121;1.4e-11)|all cancers(144;7.7e-09)|LUSC - Lung squamous cell carcinoma(224;0.034)|Lung(119;0.0375)														---	---	---	---
TRIP12	9320	broad.mit.edu	37	2	230683109	230683109	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230683109A>C	uc002vpw.1	-	8	1535	c.1426T>G	c.(1426-1428)TTT>GTT	p.F476V	TRIP12_uc002vpx.1_Missense_Mutation_p.F524V|TRIP12_uc002vpy.1_Missense_Mutation_p.F179V|TRIP12_uc010zlz.1_Intron|TRIP12_uc010fxh.1_Missense_Mutation_p.F482V	NM_004238	NP_004229	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	476					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	proteasome complex	thyroid hormone receptor binding|ubiquitin-protein ligase activity			ovary(4)|lung(2)|breast(1)|central_nervous_system(1)|skin(1)	9		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)														---	---	---	---
SLC16A14	151473	broad.mit.edu	37	2	230910593	230910593	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:230910593A>C	uc002vqd.1	-	4	1612	c.1249T>G	c.(1249-1251)TTT>GTT	p.F417V	FBXO36_uc010fxi.1_Intron|SLC16A14_uc002vqe.2_Missense_Mutation_p.F417V|SLC16A14_uc002vqf.2_Missense_Mutation_p.F417V	NM_152527	NP_689740	Q7RTX9	MOT14_HUMAN	solute carrier family 16 (monocarboxylic acid	417	Helical; (Potential).					integral to membrane|plasma membrane	symporter activity			ovary(4)|skin(2)	6		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.149)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;7.31e-13)|all cancers(144;5.1e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00948)														---	---	---	---
SP140L	93349	broad.mit.edu	37	2	231256909	231256909	+	Missense_Mutation	SNP	C	T	T	rs61750011		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231256909C>T	uc010fxm.1	+	12	1163	c.1072C>T	c.(1072-1074)CGC>TGC	p.R358C	SP140L_uc010fxo.1_Missense_Mutation_p.R130C	NM_138402	NP_612411	Q9H930	LY10L_HUMAN	SP140 nuclear body protein-like	358	SAND.					nucleus	DNA binding|metal ion binding	p.R358H(1)		central_nervous_system(1)	1																		---	---	---	---
ITM2C	81618	broad.mit.edu	37	2	231742734	231742734	+	Missense_Mutation	SNP	C	T	T	rs145202961		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231742734C>T	uc002vqz.2	+	6	844	c.724C>T	c.(724-726)CGT>TGT	p.R242C	ITM2C_uc002vra.2_Missense_Mutation_p.R195C|ITM2C_uc002vrb.2_Missense_Mutation_p.R205C|ITM2C_uc002vrc.2_Missense_Mutation_p.R131C|ITM2C_uc002vrd.2_Missense_Mutation_p.R94C	NM_030926	NP_112188	Q9NQX7	ITM2C_HUMAN	integral membrane protein 2C isoform 1	242		Cleavage; by furin.		KR->AA: Completely abrogates proteolytic processing.	negative regulation of neuron projection development|neuron differentiation	Golgi apparatus|integral to membrane|lysosomal membrane|perinuclear region of cytoplasm	beta-amyloid binding				0		Renal(207;0.0112)|all_lung(227;0.0741)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)|Lung NSC(271;0.204)		Epithelial(121;8.47e-12)|all cancers(144;3.44e-09)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0142)														---	---	---	---
PSMD1	5707	broad.mit.edu	37	2	231937099	231937099	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231937099C>T	uc002vrn.1	+	7	982	c.851C>T	c.(850-852)ACG>ATG	p.T284M	PSMD1_uc002vrm.1_Missense_Mutation_p.T284M|PSMD1_uc010fxu.1_Missense_Mutation_p.T148M	NM_002807	NP_002798	Q99460	PSMD1_HUMAN	proteasome 26S non-ATPase subunit 1	284					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|regulation of protein catabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome regulatory particle	enzyme regulator activity|protein binding			ovary(1)|skin(1)	2		Ovarian(221;0.000626)|Medulloblastoma(418;0.0109)|Renal(207;0.0112)|Lung NSC(271;0.0538)|all_lung(227;0.0713)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;4e-26)|LUSC - Lung squamous cell carcinoma(224;0.0138)|Lung(119;0.0168)	Bortezomib(DB00188)													---	---	---	---
HTR2B	3357	broad.mit.edu	37	2	231973842	231973842	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:231973842C>T	uc002vro.2	-	4	1340	c.835G>A	c.(835-837)GAA>AAA	p.E279K	PSMD1_uc002vrm.1_Intron|PSMD1_uc010fxu.1_Intron|PSMD1_uc002vrn.1_Intron|HTR2B_uc010fxv.2_Missense_Mutation_p.E212K	NM_000867	NP_000858	P41595	5HT2B_HUMAN	5-hydroxytryptamine (serotonin) receptor 2B	279	Cytoplasmic (By similarity).				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|calcium-mediated signaling|cardiac muscle hypertrophy|cellular response to calcium ion|cellular response to temperature stimulus|cGMP biosynthetic process|embryonic morphogenesis|ERK1 and ERK2 cascade|G-protein coupled receptor internalization|heart morphogenesis|intestine smooth muscle contraction|negative regulation of apoptosis|negative regulation of autophagy|neural crest cell migration|phosphatidylinositol 3-kinase cascade|phosphatidylinositol biosynthetic process|phosphorylation|positive regulation of cell division|positive regulation of cytokine production|positive regulation of cytokine secretion|positive regulation of endothelial cell proliferation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of MAP kinase activity|positive regulation of nitric-oxide synthase activity|protein kinase C signaling cascade|regulation of behavior|release of sequestered calcium ion into cytosol|response to drug|vasoconstriction	cytoplasm|integral to membrane|plasma membrane	calcium channel activity|drug binding|G-protein alpha-subunit binding|phosphatidylinositol phospholipase C activity|Ras GTPase activator activity|serotonin binding|serotonin receptor activity				0		Renal(207;0.025)|all_hematologic(139;0.094)|Acute lymphoblastic leukemia(138;0.164)|Medulloblastoma(418;0.232)		Epithelial(121;4.48e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0141)	Chlorprothixene(DB01239)|Eletriptan(DB00216)|Fenfluramine(DB00574)|Methotrimeprazine(DB01403)|Minaprine(DB00805)|Quetiapine(DB01224)|Sumatriptan(DB00669)|Tegaserod(DB01079)|Triflupromazine(DB00508)													---	---	---	---
C2orf57	165100	broad.mit.edu	37	2	232457703	232457703	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232457703G>T	uc002vrz.2	+	1	92	c.41G>T	c.(40-42)AGC>ATC	p.S14I		NM_152614	NP_689827	Q53QW1	CB057_HUMAN	hypothetical protein LOC165100	14										ovary(1)	1		Renal(207;0.025)|all_hematologic(139;0.0735)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;1.33e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)														---	---	---	---
C2orf57	165100	broad.mit.edu	37	2	232458169	232458169	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:232458169T>C	uc002vrz.2	+	1	558	c.507T>C	c.(505-507)AGT>AGC	p.S169S		NM_152614	NP_689827	Q53QW1	CB057_HUMAN	hypothetical protein LOC165100	169										ovary(1)	1		Renal(207;0.025)|all_hematologic(139;0.0735)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;1.33e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)														---	---	---	---
DIS3L2	129563	broad.mit.edu	37	2	233001275	233001275	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233001275G>A	uc010fxz.2	+	8	1072	c.796G>A	c.(796-798)GCC>ACC	p.A266T	DIS3L2_uc002vsm.3_RNA|DIS3L2_uc002vso.2_RNA	NM_152383	NP_689596	Q8IYB7	DI3L2_HUMAN	DIS3 mitotic control homolog (S.	266							exonuclease activity|ribonuclease activity|RNA binding			ovary(1)|breast(1)|central_nervous_system(1)	3		all_hematologic(139;0.00809)|Renal(207;0.0113)|Acute lymphoblastic leukemia(138;0.0195)|all_lung(227;0.0465)|Lung NSC(271;0.136)		Epithelial(121;1.6e-13)|BRCA - Breast invasive adenocarcinoma(100;0.00104)|LUSC - Lung squamous cell carcinoma(224;0.0109)|Lung(119;0.0149)														---	---	---	---
DIS3L2	129563	broad.mit.edu	37	2	233075027	233075027	+	Intron	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233075027C>A	uc010fxz.2	+						DIS3L2_uc002vsm.3_Intron|DIS3L2_uc002vso.2_Intron	NM_152383	NP_689596			DIS3 mitotic control homolog (S.								exonuclease activity|ribonuclease activity|RNA binding			ovary(1)|breast(1)|central_nervous_system(1)	3		all_hematologic(139;0.00809)|Renal(207;0.0113)|Acute lymphoblastic leukemia(138;0.0195)|all_lung(227;0.0465)|Lung NSC(271;0.136)		Epithelial(121;1.6e-13)|BRCA - Breast invasive adenocarcinoma(100;0.00104)|LUSC - Lung squamous cell carcinoma(224;0.0109)|Lung(119;0.0149)														---	---	---	---
EIF4E2	9470	broad.mit.edu	37	2	233431565	233431565	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:233431565G>T	uc002vta.2	+	5	480	c.402G>T	c.(400-402)AAG>AAT	p.K134N	EIF4E2_uc002vtb.1_Missense_Mutation_p.K134N|EIF4E2_uc010zmi.1_Missense_Mutation_p.K89N	NM_004846	NP_004837	O60573	IF4E2_HUMAN	eukaryotic translation initiation factor 4E	134					regulation of translation	cytoplasm|mRNA cap binding complex	RNA cap binding|translation initiation factor activity|ubiquitin protein ligase binding				0		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;2.3e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000912)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)														---	---	---	---
INPP5D	3635	broad.mit.edu	37	2	234112925	234112925	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234112925G>A	uc010zmo.1	+	25	3282	c.3129G>A	c.(3127-3129)CCG>CCA	p.P1043P	INPP5D_uc010zmp.1_Silent_p.P1042P	NM_001017915	NP_001017915	Q92835	SHIP1_HUMAN	SH2 containing inositol phosphatase isoform a	1043	SH3-binding 3.|Pro-rich.				apoptosis|blood coagulation|leukocyte migration|T cell receptor signaling pathway	cytosol	inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|SH3 domain binding			ovary(1)|central_nervous_system(1)	2		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0273)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0843)		Epithelial(121;1.16e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000479)|LUSC - Lung squamous cell carcinoma(224;0.00655)|Lung(119;0.00802)|GBM - Glioblastoma multiforme(43;0.0185)														---	---	---	---
DGKD	8527	broad.mit.edu	37	2	234359704	234359704	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234359704G>A	uc002vui.1	+						DGKD_uc002vuj.1_Intron|DGKD_uc010fyh.1_Intron|DGKD_uc010fyi.1_Intron	NM_152879	NP_690618			diacylglycerol kinase, delta 130kDa isoform 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell growth|diacylglycerol metabolic process|endocytosis|epidermal growth factor receptor signaling pathway|multicellular organismal development|platelet activation|protein homooligomerization|protein transport|response to organic substance|second-messenger-mediated signaling	cytoplasm|cytoplasmic membrane-bounded vesicle|plasma membrane|plasma membrane	ATP binding|diacylglycerol binding|diacylglycerol kinase activity|metal ion binding|protein heterodimerization activity|protein homodimerization activity			central_nervous_system(2)|pancreas(1)|lung(1)|skin(1)	5		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0538)		Epithelial(121;1.31e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000416)|Lung(119;0.00285)|LUSC - Lung squamous cell carcinoma(224;0.00655)	Phosphatidylserine(DB00144)													---	---	---	---
DGKD	8527	broad.mit.edu	37	2	234368837	234368837	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234368837T>C	uc002vui.1	+						DGKD_uc002vuj.1_Intron|DGKD_uc010fyi.1_Intron	NM_152879	NP_690618			diacylglycerol kinase, delta 130kDa isoform 2						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell growth|diacylglycerol metabolic process|endocytosis|epidermal growth factor receptor signaling pathway|multicellular organismal development|platelet activation|protein homooligomerization|protein transport|response to organic substance|second-messenger-mediated signaling	cytoplasm|cytoplasmic membrane-bounded vesicle|plasma membrane|plasma membrane	ATP binding|diacylglycerol binding|diacylglycerol kinase activity|metal ion binding|protein heterodimerization activity|protein homodimerization activity			central_nervous_system(2)|pancreas(1)|lung(1)|skin(1)	5		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0538)		Epithelial(121;1.31e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000416)|Lung(119;0.00285)|LUSC - Lung squamous cell carcinoma(224;0.00655)	Phosphatidylserine(DB00144)													---	---	---	---
UGT1A7	54577	broad.mit.edu	37	2	234591152	234591152	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234591152T>C	uc002vut.2	+	1	569	c.569T>C	c.(568-570)GTC>GCC	p.V190A	UGT1A8_uc010zmv.1_Intron|UGT1A8_uc002vup.2_Intron|UGT1A10_uc002vuq.3_Intron|UGT1A10_uc002vur.2_Intron|UGT1A9_uc010zmw.1_Intron|UGT1A9_uc002vus.2_Intron|UGT1A7_uc010zmx.1_Missense_Mutation_p.V190A	NM_019077	NP_061950	Q9HAW7	UD17_HUMAN	UDP glycosyltransferase 1 family, polypeptide A7	190					drug metabolic process|negative regulation of fatty acid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	drug binding|enzyme inhibitor activity|glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity|protein kinase C binding|retinoic acid binding			ovary(1)	1		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;8.93e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000412)|Lung(119;0.00333)|LUSC - Lung squamous cell carcinoma(224;0.00746)														---	---	---	---
UGT1A5	54579	broad.mit.edu	37	2	234622114	234622114	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:234622114G>A	uc002vuw.2	+	1	477	c.477G>A	c.(475-477)GCG>GCA	p.A159A	UGT1A8_uc010zmv.1_Intron|UGT1A8_uc002vup.2_Intron|UGT1A10_uc002vuq.3_Intron|UGT1A10_uc002vur.2_Intron|UGT1A9_uc010zmw.1_Intron|UGT1A9_uc002vus.2_Intron|UGT1A7_uc010zmx.1_Intron|UGT1A7_uc002vut.2_Intron|UGT1A6_uc002vuu.2_Intron|UGT1A6_uc010zmy.1_Intron|UGT1A6_uc002vuv.3_Intron|UGT1A5_uc010zmz.1_Silent_p.A159A	NM_019078	NP_061951	P35504	UD15_HUMAN	UDP glycosyltransferase 1 family, polypeptide A5	159					xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			skin(1)	1		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;4.51e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000523)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.00645)														---	---	---	---
ARL4C	10123	broad.mit.edu	37	2	235404755	235404755	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235404755G>A	uc002vvn.2	-	1	939	c.476C>T	c.(475-477)CCG>CTG	p.P159L	ARL4C_uc002vvm.3_Missense_Mutation_p.P159L	NM_005737	NP_005728	P56559	ARL4C_HUMAN	ADP-ribosylation factor-like 4C	159					endocytic recycling|small GTPase mediated signal transduction	cytoplasm|filopodium|nucleus|plasma membrane	alpha-tubulin binding|GTP binding|GTPase activity			skin(1)	1		Breast(86;0.000596)|Renal(207;0.00339)|all_lung(227;0.00354)|all_hematologic(139;0.0494)|Lung NSC(271;0.0496)|Lung SC(224;0.164)|all_neural(83;0.173)		Epithelial(121;2.6e-19)|BRCA - Breast invasive adenocarcinoma(100;0.000296)|Lung(119;0.002)|LUSC - Lung squamous cell carcinoma(224;0.0048)														---	---	---	---
SH3BP4	23677	broad.mit.edu	37	2	235951412	235951412	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:235951412C>A	uc002vvp.2	+	4	2392	c.1999C>A	c.(1999-2001)CGG>AGG	p.R667R	SH3BP4_uc010fym.2_Silent_p.R667R|SH3BP4_uc002vvq.2_Silent_p.R667R	NM_014521	NP_055336	Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	667					endocytosis	clathrin-coated vesicle|coated pit|nucleus	protein binding			skin(3)|ovary(1)	4		Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419)		Epithelial(121;7.66e-20)|BRCA - Breast invasive adenocarcinoma(100;0.000402)|Lung(119;0.00299)|LUSC - Lung squamous cell carcinoma(224;0.00645)|GBM - Glioblastoma multiforme(43;0.237)														---	---	---	---
AGAP1	116987	broad.mit.edu	37	2	236649607	236649607	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236649607G>A	uc002vvs.2	+	4	906	c.311G>A	c.(310-312)GGT>GAT	p.G104D	AGAP1_uc002vvt.2_Missense_Mutation_p.G104D	NM_001037131	NP_001032208	Q9UPQ3	AGAP1_HUMAN	centaurin, gamma 2 isoform 1	104	Small GTPase-like.				protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm	ARF GTPase activator activity|GTP binding|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
AGAP1	116987	broad.mit.edu	37	2	236877267	236877267	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:236877267G>T	uc002vvs.2	+	13	2240	c.1645G>T	c.(1645-1647)GAA>TAA	p.E549*	AGAP1_uc002vvt.2_Nonsense_Mutation_p.E496*	NM_001037131	NP_001032208	Q9UPQ3	AGAP1_HUMAN	centaurin, gamma 2 isoform 1	549	PH.				protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm	ARF GTPase activator activity|GTP binding|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
ASB18	401036	broad.mit.edu	37	2	237172995	237172995	+	5'Flank	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:237172995G>A	uc010znh.1	-							NM_212556	NP_997721			ankyrin repeat and SOCS box-containing 18						intracellular signal transduction					ovary(1)	1		all_hematologic(139;0.00615)|Renal(207;0.00963)|Breast(86;0.0126)|Acute lymphoblastic leukemia(138;0.0815)		Epithelial(121;2.04e-26)|OV - Ovarian serous cystadenocarcinoma(60;1.47e-11)|BRCA - Breast invasive adenocarcinoma(100;2.88e-05)|Lung(119;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00644)|GBM - Glioblastoma multiforme(43;0.244)														---	---	---	---
COL6A3	1293	broad.mit.edu	37	2	238233419	238233419	+	Nonstop_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238233419A>G	uc002vwl.2	-	44	9817	c.9532T>C	c.(9532-9534)TAA>CAA	p.*3178Q	COL6A3_uc002vwo.2_Nonstop_Mutation_p.*2972Q|COL6A3_uc010znj.1_Nonstop_Mutation_p.*2571Q|COL6A3_uc002vwj.2_Nonstop_Mutation_p.*559Q	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	3178					axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	18		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)														---	---	---	---
COL6A3	1293	broad.mit.edu	37	2	238275562	238275562	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238275562C>T	uc002vwl.2	-	11	5553	c.5268G>A	c.(5266-5268)GTG>GTA	p.V1756V	COL6A3_uc002vwo.2_Silent_p.V1550V|COL6A3_uc010znj.1_Silent_p.V1149V	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	1756	VWFA 9.|Nonhelical region.				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	18		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)														---	---	---	---
KLHL30	377007	broad.mit.edu	37	2	239049665	239049665	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239049665C>T	uc002vxr.1	+	1	249	c.216C>T	c.(214-216)TTC>TTT	p.F72F		NM_198582	NP_940984	Q0D2K2	KLH30_HUMAN	kelch-like 30	90	BTB.										0		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)														---	---	---	---
HDAC4	9759	broad.mit.edu	37	2	240111598	240111598	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240111598G>A	uc002vyk.3	-	4	1062	c.270C>T	c.(268-270)ATC>ATT	p.I90I	HDAC4_uc010fyz.1_Silent_p.I85I|HDAC4_uc010zoa.1_Silent_p.I85I|HDAC4_uc010fza.2_Silent_p.I90I|HDAC4_uc002vyl.1_RNA|HDAC4_uc010fyy.2_Silent_p.I42I	NM_006037	NP_006028	P56524	HDAC4_HUMAN	histone deacetylase 4	90	Potential.				B cell differentiation|cardiac muscle hypertrophy in response to stress|chromatin remodeling|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of glycolysis|negative regulation of myotube differentiation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nervous system development|peptidyl-lysine deacetylation|positive regulation of cell proliferation|positive regulation of protein sumoylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|response to denervation involved in regulation of muscle adaptation|response to interleukin-1|transcription, DNA-dependent	histone deacetylase complex|transcriptional repressor complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|potassium ion binding|repressing transcription factor binding|zinc ion binding			breast(3)|skin(2)|ovary(1)	6		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)														---	---	---	---
NDUFA10	4705	broad.mit.edu	37	2	240957961	240957961	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240957961C>T	uc002vyn.2	-						NDUFA10_uc010fzc.1_Missense_Mutation_p.A186T|NDUFA10_uc002vyo.1_Intron|NDUFA10_uc002vyp.2_Missense_Mutation_p.A186T	NM_004544	NP_004535			NADH dehydrogenase (ubiquinone) 1 alpha						mitochondrial electron transport, NADH to ubiquinone|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|transport	mitochondrial matrix|mitochondrial respiratory chain complex I	ATP binding|NADH dehydrogenase (ubiquinone) activity|phosphotransferase activity, alcohol group as acceptor			central_nervous_system(1)	1		all_epithelial(40;4.26e-15)|Breast(86;4.4e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0396)|Lung NSC(271;0.128)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(121;7.82e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.5e-13)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;2.39e-05)|Lung(119;0.00519)|LUSC - Lung squamous cell carcinoma(224;0.0202)	NADH(DB00157)													---	---	---	---
OR6B3	150681	broad.mit.edu	37	2	240984687	240984687	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:240984687C>T	uc010zoe.1	-	1	803	c.803G>A	c.(802-804)CGG>CAG	p.R268Q	PRR21_uc010zod.1_5'Flank	NM_173351	NP_775486	Q8NGW1	OR6B3_HUMAN	olfactory receptor, family 6, subfamily B,	268	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		all_epithelial(40;1.64e-11)|Breast(86;0.000327)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.229)|Melanoma(123;0.238)		Epithelial(121;1.05e-29)|all cancers(36;3.52e-28)|OV - Ovarian serous cystadenocarcinoma(60;4.63e-14)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.56e-05)|Lung(119;0.00344)|LUSC - Lung squamous cell carcinoma(224;0.0148)|Colorectal(34;0.019)|COAD - Colon adenocarcinoma(134;0.141)														---	---	---	---
AQP12A	375318	broad.mit.edu	37	2	241631426	241631426	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241631426C>T	uc002vzu.2	+	1	165	c.96C>T	c.(94-96)GGC>GGT	p.G32G	AQP12A_uc002vzv.2_Intron	NM_198998	NP_945349	Q8IXF9	AQ12A_HUMAN	aquaporin 12A	32						integral to membrane	transporter activity				0		all_epithelial(40;7.49e-12)|Breast(86;0.000148)|Renal(207;0.00571)|Ovarian(221;0.104)|all_neural(83;0.107)|all_hematologic(139;0.182)|all_lung(227;0.186)|Melanoma(123;0.238)		Epithelial(32;2.2e-31)|all cancers(36;1.08e-28)|OV - Ovarian serous cystadenocarcinoma(60;2.13e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.52e-06)|Lung(119;0.00163)|LUSC - Lung squamous cell carcinoma(224;0.008)|Colorectal(34;0.0124)|COAD - Colon adenocarcinoma(134;0.0757)														---	---	---	---
KIF1A	547	broad.mit.edu	37	2	241725858	241725858	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241725858C>T	uc002vzy.2	-	6	648	c.502G>A	c.(502-504)GTG>ATG	p.V168M	KIF1A_uc010fzk.2_Missense_Mutation_p.V168M|KIF1A_uc002vzz.1_Missense_Mutation_p.V168M	NM_004321	NP_004312	Q12756	KIF1A_HUMAN	axonal transport of synaptic vesicles	168	Kinesin-motor.				anterograde axon cargo transport	cytoplasm|microtubule|nucleus	ATP binding|microtubule motor activity			lung(1)	1		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)														---	---	---	---
KIF1A	547	broad.mit.edu	37	2	241727548	241727548	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241727548C>T	uc002vzy.2	-	4	429	c.283G>A	c.(283-285)GCC>ACC	p.A95T	KIF1A_uc010fzk.2_Missense_Mutation_p.A95T|KIF1A_uc002vzz.1_Missense_Mutation_p.A95T	NM_004321	NP_004312	Q12756	KIF1A_HUMAN	axonal transport of synaptic vesicles	95	Kinesin-motor.				anterograde axon cargo transport	cytoplasm|microtubule|nucleus	ATP binding|microtubule motor activity			lung(1)	1		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)														---	---	---	---
SNED1	25992	broad.mit.edu	37	2	241991870	241991870	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241991870C>T	uc002wah.1	+	15	2068	c.2068C>T	c.(2068-2070)CGC>TGC	p.R690C		NM_001080437	NP_001073906	Q8TER0	SNED1_HUMAN	6720455I24Rik homolog precursor	690	EGF-like 10.				cell-matrix adhesion	extracellular region	calcium ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)														---	---	---	---
MTERFD2	130916	broad.mit.edu	37	2	242035468	242035468	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242035468T>C	uc002wan.1	-	3	1671	c.1178A>G	c.(1177-1179)GAC>GGC	p.D393G	MTERFD2_uc010zoj.1_Missense_Mutation_p.D176G	NM_182501	NP_872307	Q7Z6M4	MTER2_HUMAN	MTERF domain containing 2	364										ovary(1)	1		all_cancers(19;4.67e-31)|all_epithelial(40;8.67e-13)|Breast(86;0.000141)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;2.47e-32)|all cancers(36;1.79e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.59e-14)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;2.81e-06)|Lung(119;0.000509)|LUSC - Lung squamous cell carcinoma(224;0.00442)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0886)														---	---	---	---
PASK	23178	broad.mit.edu	37	2	242046868	242046868	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242046868T>C	uc002wao.1	-	17	3806	c.3714A>G	c.(3712-3714)AGA>AGG	p.R1238R	PASK_uc010zol.1_Silent_p.R1052R|PASK_uc010zom.1_Silent_p.R1203R|PASK_uc010fzl.1_Silent_p.R1245R|PASK_uc010zon.1_Silent_p.R1019R	NM_015148	NP_055963	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	1238	Protein kinase.				regulation of transcription, DNA-dependent	Golgi apparatus	ATP binding|identical protein binding|protein serine/threonine kinase activity|signal transducer activity			ovary(4)|lung(1)|skin(1)	6		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)														---	---	---	---
PASK	23178	broad.mit.edu	37	2	242079304	242079304	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242079304G>A	uc002wao.1	-	4	688	c.596C>T	c.(595-597)ACG>ATG	p.T199M	PASK_uc010zol.1_Intron|PASK_uc010zom.1_Missense_Mutation_p.T199M|PASK_uc010fzl.1_Missense_Mutation_p.T199M|PASK_uc010zon.1_Intron|PASK_uc002waq.2_Missense_Mutation_p.T199M	NM_015148	NP_055963	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	199					regulation of transcription, DNA-dependent	Golgi apparatus	ATP binding|identical protein binding|protein serine/threonine kinase activity|signal transducer activity			ovary(4)|lung(1)|skin(1)	6		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)														---	---	---	---
PASK	23178	broad.mit.edu	37	2	242079357	242079357	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242079357G>T	uc002wao.1	-	4	635	c.543C>A	c.(541-543)GCC>GCA	p.A181A	PASK_uc010zol.1_Intron|PASK_uc010zom.1_Silent_p.A181A|PASK_uc010fzl.1_Silent_p.A181A|PASK_uc010zon.1_Intron|PASK_uc002waq.2_Silent_p.A181A	NM_015148	NP_055963	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	181	PAS 1.				regulation of transcription, DNA-dependent	Golgi apparatus	ATP binding|identical protein binding|protein serine/threonine kinase activity|signal transducer activity			ovary(4)|lung(1)|skin(1)	6		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)														---	---	---	---
ANO7	50636	broad.mit.edu	37	2	242128141	242128141	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242128141G>A	uc002wax.2	+	1	218	c.115G>A	c.(115-117)GCC>ACC	p.A39T	ANO7_uc002waw.2_Missense_Mutation_p.A39T	NM_001001891	NP_001001891	Q6IWH7	ANO7_HUMAN	transmembrane protein 16G isoform NGEP long	39	Cytoplasmic (Potential).					cell junction|chloride channel complex|cytosol	chloride channel activity			pancreas(2)|central_nervous_system(1)	3																		---	---	---	---
ANO7	50636	broad.mit.edu	37	2	242163179	242163179	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242163179G>A	uc002wax.2	+	23	2780	c.2677G>A	c.(2677-2679)GCA>ACA	p.A893T		NM_001001891	NP_001001891	Q6IWH7	ANO7_HUMAN	transmembrane protein 16G isoform NGEP long	893	Cytoplasmic (Potential).					cell junction|chloride channel complex|cytosol	chloride channel activity			pancreas(2)|central_nervous_system(1)	3																		---	---	---	---
HDLBP	3069	broad.mit.edu	37	2	242169278	242169278	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242169278G>A	uc002waz.2	-	27	3918	c.3690C>T	c.(3688-3690)GAC>GAT	p.D1230D	HDLBP_uc002wba.2_Silent_p.D1230D|HDLBP_uc002wbb.2_Silent_p.D1182D	NM_203346	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	1230					cholesterol metabolic process|lipid transport	cytoplasm|high-density lipoprotein particle|nucleus|plasma membrane	lipid binding|protein binding|RNA binding			breast(3)|skin(1)	4		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)														---	---	---	---
HDLBP	3069	broad.mit.edu	37	2	242179334	242179334	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242179334C>A	uc002waz.2	-	18	2601	c.2373G>T	c.(2371-2373)GAG>GAT	p.E791D	HDLBP_uc002wba.2_Missense_Mutation_p.E791D|HDLBP_uc002wbb.2_Missense_Mutation_p.E743D	NM_203346	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	791	KH 9.				cholesterol metabolic process|lipid transport	cytoplasm|high-density lipoprotein particle|nucleus|plasma membrane	lipid binding|protein binding|RNA binding			breast(3)|skin(1)	4		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)														---	---	---	---
HDLBP	3069	broad.mit.edu	37	2	242194543	242194543	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242194543C>T	uc002waz.2	-	9	1339	c.1111G>A	c.(1111-1113)GCC>ACC	p.A371T	HDLBP_uc002wba.2_Missense_Mutation_p.A371T|HDLBP_uc002wbb.2_Missense_Mutation_p.A323T|HDLBP_uc010fzn.1_Missense_Mutation_p.A100T	NM_203346	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	371	KH 3.				cholesterol metabolic process|lipid transport	cytoplasm|high-density lipoprotein particle|nucleus|plasma membrane	lipid binding|protein binding|RNA binding			breast(3)|skin(1)	4		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)														---	---	---	---
FARP2	9855	broad.mit.edu	37	2	242431102	242431102	+	Intron	SNP	C	T	T	rs148100094	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242431102C>T	uc002wbi.1	+							NM_014808	NP_055623			FERM, RhoGEF and pleckstrin domain protein 2						axon guidance|neuron remodeling|Rac protein signal transduction|regulation of Rho protein signal transduction	cytoskeleton|cytosol|extrinsic to membrane	cytoskeletal protein binding|Rho guanyl-nucleotide exchange factor activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)														---	---	---	---
THAP4	51078	broad.mit.edu	37	2	242572945	242572945	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242572945G>A	uc002wbt.2	-	2	850	c.627C>T	c.(625-627)GGC>GGT	p.G209G		NM_015963	NP_057047	Q8WY91	THAP4_HUMAN	THAP domain containing 4 isoform 1	209							DNA binding|metal ion binding				0		all_cancers(19;2.09e-34)|all_epithelial(40;2.09e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Ovarian(221;0.069)|Lung NSC(271;0.0886)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.2)		Epithelial(32;2.3e-33)|all cancers(36;8.99e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.68e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0844)														---	---	---	---
D2HGDH	728294	broad.mit.edu	37	2	242681983	242681983	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242681983G>A	uc002wce.1	+	4	657	c.484G>A	c.(484-486)GTG>ATG	p.V162M	D2HGDH_uc010zpc.1_RNA|D2HGDH_uc010fzq.1_Missense_Mutation_p.V28M|D2HGDH_uc002wcg.1_RNA	NM_152783	NP_689996	Q8N465	D2HDH_HUMAN	D-2-hydroxyglutarate dehydrogenase precursor	162	FAD-binding PCMH-type.				2-oxoglutarate metabolic process|cellular protein metabolic process|response to cobalt ion|response to manganese ion|response to zinc ion	mitochondrial matrix	(R)-2-hydroxyglutarate dehydrogenase activity|flavin adenine dinucleotide binding|protein binding				0		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;4.59e-33)|all cancers(36;9.89e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.89e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0833)														---	---	---	---
NEU4	129807	broad.mit.edu	37	2	242757793	242757793	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242757793C>T	uc010fzr.2	+	4	960	c.874C>T	c.(874-876)CGG>TGG	p.R292W	NEU4_uc002wcl.2_RNA|NEU4_uc002wcm.2_Missense_Mutation_p.R292W|NEU4_uc002wcn.1_Missense_Mutation_p.R304W|NEU4_uc002wco.1_Missense_Mutation_p.R292W|NEU4_uc002wcp.1_Missense_Mutation_p.R304W	NM_080741	NP_542779	Q8WWR8	NEUR4_HUMAN	sialidase 4	292	Pro-rich.					lysosomal lumen|organelle inner membrane	exo-alpha-sialidase activity|protein binding				0		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;3.84e-33)|all cancers(36;8.08e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.41e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0825)														---	---	---	---
CNTN6	27255	broad.mit.edu	37	3	1427439	1427439	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:1427439G>T	uc003boz.2	+	20	2929	c.2662G>T	c.(2662-2664)GGG>TGG	p.G888W	CNTN6_uc011asj.1_Missense_Mutation_p.G816W|CNTN6_uc003bpa.2_Missense_Mutation_p.G888W	NM_014461	NP_055276	Q9UQ52	CNTN6_HUMAN	contactin 6 precursor	888	Fibronectin type-III 3.				axon guidance|cell adhesion|central nervous system development|Notch signaling pathway	anchored to membrane|plasma membrane				skin(3)|lung(2)|breast(2)|pancreas(1)	8		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)														---	---	---	---
CNTN4	152330	broad.mit.edu	37	3	2924899	2924899	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:2924899A>G	uc003bpc.2	+	8	944	c.723A>G	c.(721-723)GCA>GCG	p.A241A	CNTN4_uc003bpb.1_Intron|CNTN4_uc003bpd.1_Silent_p.A241A	NM_175607	NP_783200	Q8IWV2	CNTN4_HUMAN	contactin 4 isoform a precursor	241	Ig-like C2-type 3.				axon guidance|axonal fasciculation|brain development|negative regulation of neuron differentiation|neuron cell-cell adhesion|regulation of synaptic plasticity	anchored to membrane|axon|extracellular region|plasma membrane	protein binding			large_intestine(2)|ovary(2)|lung(1)|central_nervous_system(1)|pancreas(1)	7		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)														---	---	---	---
LRRN1	57633	broad.mit.edu	37	3	3886560	3886560	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:3886560T>C	uc003bpt.3	+	2	996	c.235T>C	c.(235-237)TTA>CTA	p.L79L	SUMF1_uc003bps.1_Intron	NM_020873	NP_065924	Q6UXK5	LRRN1_HUMAN	leucine rich repeat neuronal 1 precursor	79	Extracellular (Potential).|LRR 1.					integral to membrane				central_nervous_system(1)	1				Epithelial(13;0.000886)|all cancers(10;0.0032)|OV - Ovarian serous cystadenocarcinoma(96;0.00608)|STAD - Stomach adenocarcinoma(44;0.0617)														---	---	---	---
SUMF1	285362	broad.mit.edu	37	3	4452558	4452558	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4452558C>T	uc003bpz.1	-	7	970	c.945G>A	c.(943-945)ACG>ACA	p.T315T	SUMF1_uc003bps.1_RNA|SUMF1_uc011ass.1_Silent_p.T290T|SUMF1_uc010hby.1_Silent_p.T315T|SUMF1_uc011ast.1_Silent_p.T183T	NM_182760	NP_877437	Q8NBK3	SUMF1_HUMAN	sulfatase modifying factor 1 isoform 1	315						endoplasmic reticulum lumen	metal ion binding|oxidoreductase activity			upper_aerodigestive_tract(1)	1		Melanoma(143;0.068)|Colorectal(144;0.233)		Epithelial(13;0.0147)|OV - Ovarian serous cystadenocarcinoma(96;0.0444)|all cancers(10;0.0549)														---	---	---	---
SUMF1	285362	broad.mit.edu	37	3	4494739	4494739	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:4494739A>G	uc003bpz.1	-						SUMF1_uc003bps.1_Intron|SUMF1_uc011ass.1_Intron|SUMF1_uc010hby.1_Intron|SUMF1_uc011ast.1_Intron	NM_182760	NP_877437			sulfatase modifying factor 1 isoform 1							endoplasmic reticulum lumen	metal ion binding|oxidoreductase activity			upper_aerodigestive_tract(1)	1		Melanoma(143;0.068)|Colorectal(144;0.233)		Epithelial(13;0.0147)|OV - Ovarian serous cystadenocarcinoma(96;0.0444)|all cancers(10;0.0549)														---	---	---	---
GRM7	2917	broad.mit.edu	37	3	7348224	7348224	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:7348224C>T	uc003bqm.2	+	4	1192	c.918C>T	c.(916-918)GGC>GGT	p.G306G	GRM7_uc011ata.1_RNA|GRM7_uc011atb.1_RNA|GRM7_uc010hcf.2_RNA|GRM7_uc011atc.1_RNA|GRM7_uc010hcg.2_Silent_p.G306G|GRM7_uc003bql.2_Silent_p.G306G|GRM7_uc003bqn.1_5'UTR	NM_000844	NP_000835	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7 isoform a	306	Extracellular (Potential).				negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission	asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone	adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding			ovary(4)|lung(3)	7					L-Glutamic Acid(DB00142)													---	---	---	---
RAD18	56852	broad.mit.edu	37	3	8977685	8977685	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:8977685A>G	uc003brd.2	-	7	836	c.759T>C	c.(757-759)GAT>GAC	p.D253D	RAD18_uc003bre.2_RNA	NM_020165	NP_064550	Q9NS91	RAD18_HUMAN	postreplication repair protein hRAD18p	253	SAP.				DNA repair	nucleus|replication fork	damaged DNA binding|ligase activity|ubiquitin protein ligase binding|Y-form DNA binding|zinc ion binding			skin(3)|ovary(2)	5				OV - Ovarian serous cystadenocarcinoma(96;0.0552)									Rad6_pathway					---	---	---	---
SRGAP3	9901	broad.mit.edu	37	3	9098004	9098004	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9098004G>A	uc003brf.1	-	8	1714	c.1038C>T	c.(1036-1038)AGC>AGT	p.S346S	SRGAP3_uc003brg.1_Silent_p.S346S|SRGAP3_uc003bri.1_RNA|SRGAP3_uc003brj.1_Silent_p.S206S	NM_014850	NP_055665	O43295	SRGP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 3	346					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding		SRGAP3/RAF1(4)	central_nervous_system(4)|skin(3)|urinary_tract(1)|breast(1)	9				OV - Ovarian serous cystadenocarcinoma(96;0.0563)				T	RAF1	pilocytic astrocytoma								---	---	---	---
THUMPD3	25917	broad.mit.edu	37	3	9426297	9426297	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9426297A>G	uc003bro.3	+	10	1597	c.1449A>G	c.(1447-1449)ATA>ATG	p.I483M	LOC440944_uc003brm.2_Intron|THUMPD3_uc003brn.3_Missense_Mutation_p.I483M	NM_001114092	NP_001107564	Q9BV44	THUM3_HUMAN	THUMP domain containing 3	483							methyltransferase activity|protein binding|RNA binding			ovary(1)	1	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.101)														---	---	---	---
BRPF1	7862	broad.mit.edu	37	3	9785487	9785487	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:9785487C>T	uc003bse.2	+	8	2918	c.2519C>T	c.(2518-2520)TCG>TTG	p.S840L	BRPF1_uc003bsf.2_Missense_Mutation_p.S846L|BRPF1_uc003bsg.2_Missense_Mutation_p.S839L|BRPF1_uc011ati.1_Missense_Mutation_p.S840L	NM_004634	NP_004625	P55201	BRPF1_HUMAN	bromodomain and PHD finger-containing protein 1	840	Required for RUNX1 and RUNX2 transcriptional activation.				histone H3 acetylation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|MOZ/MORF histone acetyltransferase complex|plasma membrane	DNA binding|zinc ion binding			ovary(2)|central_nervous_system(1)	3	Medulloblastoma(99;0.227)																	---	---	---	---
FANCD2	2177	broad.mit.edu	37	3	10127618	10127618	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10127618C>T	uc003buw.2	+						FANCD2_uc003bux.1_Intron|FANCD2_uc003buy.1_Intron|FANCD2_uc010hcw.1_Intron|C3orf24_uc003buz.2_Intron	NM_033084	NP_149075			Fanconi anemia complementation group D2 isoform						DNA repair|response to gamma radiation	nucleoplasm	protein binding|protein binding			central_nervous_system(2)|ovary(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(96;0.148)				D|Mis|N|F			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
IRAK2	3656	broad.mit.edu	37	3	10219682	10219682	+	Silent	SNP	G	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10219682G>C	uc003bve.1	+	2	331	c.255G>C	c.(253-255)CGG>CGC	p.R85R		NM_001570	NP_001561	O43187	IRAK2_HUMAN	interleukin-1 receptor-associated kinase 2	85	Death.				activation of MAPK activity|I-kappaB kinase/NF-kappaB cascade|inflammatory response|innate immune response|interleukin-1-mediated signaling pathway|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of NF-kappaB transcription factor activity|positive regulation of NF-kappaB transcription factor activity|regulation of cytokine-mediated signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cell surface|cytosol|endosome membrane|plasma membrane	ATP binding|NF-kappaB-inducing kinase activity|protein heterodimerization activity|protein homodimerization activity			lung(5)|breast(3)	8																		---	---	---	---
IRAK2	3656	broad.mit.edu	37	3	10254926	10254926	+	Silent	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10254926T>G	uc003bve.1	+	5	640	c.564T>G	c.(562-564)CTT>CTG	p.L188L		NM_001570	NP_001561	O43187	IRAK2_HUMAN	interleukin-1 receptor-associated kinase 2	188					activation of MAPK activity|I-kappaB kinase/NF-kappaB cascade|inflammatory response|innate immune response|interleukin-1-mediated signaling pathway|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of NF-kappaB transcription factor activity|positive regulation of NF-kappaB transcription factor activity|regulation of cytokine-mediated signaling pathway|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cell surface|cytosol|endosome membrane|plasma membrane	ATP binding|NF-kappaB-inducing kinase activity|protein heterodimerization activity|protein homodimerization activity			lung(5)|breast(3)	8																		---	---	---	---
SLC6A11	6538	broad.mit.edu	37	3	10970945	10970945	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10970945C>T	uc003bvz.2	+	10	1325	c.1291C>T	c.(1291-1293)CGG>TGG	p.R431W		NM_014229	NP_055044	P48066	S6A11_HUMAN	solute carrier family 6 (neurotransmitter	431					neurotransmitter secretion	integral to plasma membrane	gamma-aminobutyric acid:sodium symporter activity|neurotransmitter:sodium symporter activity			skin(3)|ovary(1)	4				OV - Ovarian serous cystadenocarcinoma(96;0.229)														---	---	---	---
CAND2	23066	broad.mit.edu	37	3	12858533	12858533	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12858533C>T	uc003bxk.2	+	10	2151	c.2102C>T	c.(2101-2103)GCC>GTC	p.A701V	CAND2_uc003bxj.2_Missense_Mutation_p.A608V	NM_001162499	NP_001155971	O75155	CAND2_HUMAN	TBP-interacting protein isoform 1	701	HEAT 15.				positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			skin(3)|pancreas(1)	4																		---	---	---	---
XPC	7508	broad.mit.edu	37	3	14199699	14199699	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14199699C>T	uc011ave.1	-	9	1788	c.1684G>A	c.(1684-1686)GCC>ACC	p.A562T	XPC_uc011avf.1_Missense_Mutation_p.A369T|XPC_uc011avg.1_Missense_Mutation_p.A525T	NM_004628	NP_004619	Q01831	XPC_HUMAN	xeroderma pigmentosum, complementation group C	562	Interaction with RAD23B.				nucleotide-excision repair, DNA damage recognition|nucleotide-excision repair, DNA damage removal	cytoplasm|nucleoplasm|XPC complex	bubble DNA binding|damaged DNA binding|loop DNA binding|protein binding|single-stranded DNA binding			ovary(2)|breast(1)	3								Mis|N|F|S			skin basal cell|skin squamous cell|melanoma		NER	Xeroderma_Pigmentosum				---	---	---	---
SLC6A6	6533	broad.mit.edu	37	3	14526471	14526471	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14526471G>A	uc010heg.2	+	22	2110	c.1819G>A	c.(1819-1821)GCT>ACT	p.A607T	SLC6A6_uc003byq.2_Missense_Mutation_p.A607T|SLC6A6_uc003byr.2_RNA	NM_001134367	NP_001127839	P31641	SC6A6_HUMAN	solute carrier family 6 (neurotransmitter	607	Cytoplasmic (Potential).				cellular amino acid metabolic process	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity|taurine:sodium symporter activity			ovary(1)	1																		---	---	---	---
C3orf19	51244	broad.mit.edu	37	3	14711480	14711480	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14711480C>T	uc003byw.2	+	10	1083	c.992C>T	c.(991-993)GCT>GTT	p.A331V	C3orf19_uc010hej.2_Missense_Mutation_p.A160V	NM_016474	NP_057558	Q6PII3	CC019_HUMAN	hypothetical protein LOC51244	331											0																		---	---	---	---
C3orf20	84077	broad.mit.edu	37	3	14744749	14744749	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14744749G>A	uc003byy.2	+	6	1262	c.858G>A	c.(856-858)CTG>CTA	p.L286L	C3orf20_uc003byz.2_Silent_p.L164L|C3orf20_uc003bza.2_Silent_p.L164L|C3orf20_uc003byx.1_Silent_p.L286L	NM_032137	NP_115513	Q8ND61	CC020_HUMAN	hypothetical protein LOC84077	286						cytoplasm|integral to membrane				ovary(3)|skin(1)	4																		---	---	---	---
FGD5	152273	broad.mit.edu	37	3	14863033	14863033	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14863033G>T	uc003bzc.2	+	1	2565	c.2455G>T	c.(2455-2457)GGC>TGC	p.G819C	FGD5_uc011avk.1_Missense_Mutation_p.G819C	NM_152536	NP_689749	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	819					actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(3)|kidney(1)|pancreas(1)	5																		---	---	---	---
ZFYVE20	64145	broad.mit.edu	37	3	15116318	15116318	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15116318G>A	uc003bzm.1	-	14	1940	c.1326C>T	c.(1324-1326)GGC>GGT	p.G442G	ZFYVE20_uc010hek.1_Silent_p.G442G	NM_022340	NP_071735	Q9H1K0	RBNS5_HUMAN	FYVE-finger-containing Rab5 effector protein	442	Necessary for the interaction with RAB4A.|Necessary for the interaction with EHD1.				blood coagulation|endosome transport|protein transport	early endosome membrane|plasma membrane	protein binding|zinc ion binding			skin(2)	2																		---	---	---	---
CAPN7	23473	broad.mit.edu	37	3	15282285	15282285	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:15282285A>T	uc003bzn.2	+	14	1847	c.1577A>T	c.(1576-1578)GAT>GTT	p.D526V		NM_014296	NP_055111	Q9Y6W3	CAN7_HUMAN	calpain 7	526	Calpain catalytic.				proteolysis	nucleus	calcium-dependent cysteine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
RFTN1	23180	broad.mit.edu	37	3	16475457	16475457	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:16475457G>A	uc003cay.2	-	3	515	c.233C>T	c.(232-234)TCG>TTG	p.S78L	RFTN1_uc010hes.2_Missense_Mutation_p.S42L	NM_015150	NP_055965	Q14699	RFTN1_HUMAN	raft-linking protein	78						plasma membrane				ovary(3)|central_nervous_system(1)	4																		---	---	---	---
PLCL2	23228	broad.mit.edu	37	3	17056315	17056315	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17056315T>G	uc011awc.1	+	6	3011	c.2906T>G	c.(2905-2907)GTC>GGC	p.V969G	PLCL2_uc011awd.1_Missense_Mutation_p.V851G	NM_001144382	NP_001137854	Q9UPR0	PLCL2_HUMAN	phospholipase C-like 2 isoform 1	977					intracellular signal transduction|lipid metabolic process	cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			skin(2)|ovary(1)|lung(1)	4																		---	---	---	---
TBC1D5	9779	broad.mit.edu	37	3	17413686	17413686	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17413686C>T	uc003cbf.2	-	13	2541	c.876G>A	c.(874-876)GGG>GGA	p.G292G	TBC1D5_uc010hev.2_Silent_p.G292G|TBC1D5_uc003cbe.2_Silent_p.G292G|TBC1D5_uc010hew.1_Silent_p.G244G	NM_014744	NP_055559	Q92609	TBCD5_HUMAN	TBC1 domain family, member 5 isoform b	292	Rab-GAP TBC.					intracellular	protein binding|Rab GTPase activator activity			ovary(1)	1																		---	---	---	---
SATB1	6304	broad.mit.edu	37	3	18391127	18391127	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:18391127C>T	uc003cbh.2	-	11	3562	c.1827G>A	c.(1825-1827)CCG>CCA	p.P609P	SATB1_uc003cbi.2_Silent_p.P641P|SATB1_uc003cbj.2_Silent_p.P609P	NM_002971	NP_002962	Q01826	SATB1_HUMAN	special AT-rich sequence binding protein 1	609	Poly-Pro.				cellular component disassembly involved in apoptosis|interspecies interaction between organisms|negative regulation of transcription from RNA polymerase II promoter	nuclear matrix|PML body	double-stranded DNA binding|sequence-specific DNA binding			skin(2)|ovary(1)|lung(1)	4																		---	---	---	---
KCNH8	131096	broad.mit.edu	37	3	19492829	19492829	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:19492829G>T	uc003cbk.1	+	10	1953	c.1758G>T	c.(1756-1758)CAG>CAT	p.Q586H	KCNH8_uc011awe.1_3'UTR|KCNH8_uc010hex.1_Missense_Mutation_p.Q47H|KCNH8_uc011awf.1_3'UTR	NM_144633	NP_653234	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H,	586	cNMP.|Cytoplasmic (Potential).					integral to membrane	two-component sensor activity			lung(4)|ovary(1)	5																		---	---	---	---
SGOL1	151648	broad.mit.edu	37	3	20215995	20215995	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:20215995A>G	uc003cbs.2	-	6	1215	c.1028T>C	c.(1027-1029)GTT>GCT	p.V343A	SGOL1_uc003cbr.2_Intron|SGOL1_uc010hfa.2_Intron|SGOL1_uc003cbt.2_Intron|SGOL1_uc003cbu.2_Missense_Mutation_p.V343A|SGOL1_uc003cbv.2_Intron|SGOL1_uc003cbw.2_Intron|SGOL1_uc003cbx.2_Intron|SGOL1_uc003cby.2_Intron|SGOL1_uc003cbz.2_Missense_Mutation_p.V343A|SGOL1_uc003cca.2_Missense_Mutation_p.V343A|SGOL1_uc003ccb.2_Intron|SGOL1_uc003ccc.2_Intron	NM_001012410	NP_001012410	Q5FBB7	SGOL1_HUMAN	shugoshin-like 1 isoform A2	343					attachment of spindle microtubules to kinetochore|cell division|centriole-centriole cohesion|meiotic chromosome segregation|mitotic prometaphase	centrosome|condensed chromosome kinetochore|cytosol|mitotic cohesin complex|spindle pole	protein binding				0																		---	---	---	---
ZNF385D	79750	broad.mit.edu	37	3	21467150	21467150	+	Missense_Mutation	SNP	T	C	C	rs149202584	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:21467150T>C	uc003cce.2	-	6	1094	c.686A>G	c.(685-687)AAA>AGA	p.K229R		NM_024697	NP_078973	Q9H6B1	Z385D_HUMAN	zinc finger protein 385D	229	Matrin-type 2.					nucleus	nucleic acid binding|zinc ion binding			large_intestine(2)|skin(2)|ovary(1)	5																		---	---	---	---
ZNF385D	79750	broad.mit.edu	37	3	21552371	21552371	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:21552371T>C	uc003cce.2	-	4	829	c.421A>G	c.(421-423)ACC>GCC	p.T141A	ZNF385D_uc010hfb.1_RNA	NM_024697	NP_078973	Q9H6B1	Z385D_HUMAN	zinc finger protein 385D	141	Thr-rich.					nucleus	nucleic acid binding|zinc ion binding			large_intestine(2)|skin(2)|ovary(1)	5																		---	---	---	---
THRB	7068	broad.mit.edu	37	3	24174948	24174948	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:24174948T>G	uc003ccx.3	-	9	1093	c.744A>C	c.(742-744)GAA>GAC	p.E248D	THRB_uc010hfe.2_Missense_Mutation_p.E248D|THRB_uc003ccy.3_Missense_Mutation_p.E248D|THRB_uc003ccz.3_Missense_Mutation_p.E243D	NM_001128176	NP_001121648	P10828	THB_HUMAN	thyroid hormone receptor, beta	248	Ligand-binding.|Interaction with NR2F6.				regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	enzyme binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|thyroid hormone receptor activity|transcription corepressor activity|zinc ion binding			skin(2)|pancreas(1)	3					Levothyroxine(DB00451)|Liothyronine(DB00279)													---	---	---	---
NEK10	152110	broad.mit.edu	37	3	27216288	27216288	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27216288T>G	uc010hfk.2	-	6	707	c.478A>C	c.(478-480)AGT>CGT	p.S160R	NEK10_uc003cds.1_Missense_Mutation_p.S245R|NEK10_uc010hfj.2_Missense_Mutation_p.S160R			Q6ZWH5	NEK10_HUMAN	RecName: Full=Serine/threonine-protein kinase Nek10;          EC=2.7.11.1; AltName: Full=NimA-related protein kinase 10;	848							ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(5)|stomach(2)|central_nervous_system(2)|lung(2)|skin(1)|pancreas(1)	13																		---	---	---	---
SLC4A7	9497	broad.mit.edu	37	3	27472884	27472884	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:27472884A>G	uc003cdv.2	-	7	1099	c.1028T>C	c.(1027-1029)ATT>ACT	p.I343T	SLC4A7_uc011awu.1_RNA|SLC4A7_uc011awv.1_Intron|SLC4A7_uc003cdu.3_Intron|SLC4A7_uc011aww.1_Missense_Mutation_p.I352T|SLC4A7_uc011awx.1_Missense_Mutation_p.I339T|SLC4A7_uc011awy.1_Missense_Mutation_p.I335T|SLC4A7_uc011awz.1_Intron|SLC4A7_uc011axa.1_Intron|SLC4A7_uc011axb.1_Missense_Mutation_p.I339T|SLC4A7_uc010hfm.2_Intron|SLC4A7_uc003cdw.2_Intron	NM_003615	NP_003606	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate	343	Extracellular (Potential).					apical plasma membrane|basolateral plasma membrane|integral to membrane|stereocilium	inorganic anion exchanger activity|protein binding|sodium:bicarbonate symporter activity			ovary(3)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
OSBPL10	114884	broad.mit.edu	37	3	31725400	31725400	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:31725400G>A	uc003cev.2	-	9	1833	c.1452C>T	c.(1450-1452)GGC>GGT	p.G484G	OSBPL10_uc003ceu.1_Silent_p.G241G|OSBPL10_uc011axf.1_Silent_p.G420G	NM_017784	NP_060254	Q9BXB5	OSB10_HUMAN	oxysterol-binding protein-like protein 10	484					lipid transport		lipid binding			skin(1)	1				STAD - Stomach adenocarcinoma(1;0.00406)														---	---	---	---
OSBPL10	114884	broad.mit.edu	37	3	31774776	31774776	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:31774776G>A	uc003cev.2	-	7	1449	c.1068C>T	c.(1066-1068)GAC>GAT	p.D356D	OSBPL10_uc003ceu.1_Silent_p.D113D|OSBPL10_uc011axf.1_Silent_p.D292D	NM_017784	NP_060254	Q9BXB5	OSB10_HUMAN	oxysterol-binding protein-like protein 10	356					lipid transport		lipid binding			skin(1)	1				STAD - Stomach adenocarcinoma(1;0.00406)														---	---	---	---
CMTM8	152189	broad.mit.edu	37	3	32409470	32409470	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32409470C>T	uc003cex.2	+	3	722	c.428C>T	c.(427-429)GCG>GTG	p.A143V	CMTM8_uc010hfu.2_Missense_Mutation_p.A85V	NM_178868	NP_849199	Q8IZV2	CKLF8_HUMAN	CKLF-like MARVEL transmembrane domain containing	143	MARVEL.				chemotaxis	extracellular space|integral to membrane	cytokine activity				0																		---	---	---	---
TRIM71	131405	broad.mit.edu	37	3	32933115	32933115	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:32933115C>T	uc003cff.2	+	4	2482	c.2419C>T	c.(2419-2421)CGC>TGC	p.R807C		NM_001039111	NP_001034200	Q2Q1W2	LIN41_HUMAN	tripartite motif-containing 71	807	NHL 5.				multicellular organismal development	cytoplasm	zinc ion binding			ovary(2)|large_intestine(1)	3																		---	---	---	---
CRTAP	10491	broad.mit.edu	37	3	33175724	33175724	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33175724C>T	uc003cfl.3	+	6	1239	c.1119C>T	c.(1117-1119)GAC>GAT	p.D373D	CRTAP_uc010hfz.2_Silent_p.D330D|CRTAP_uc003cfm.2_Silent_p.D194D|CRTAP_uc003cfn.2_Silent_p.D194D	NM_006371	NP_006362	O75718	CRTAP_HUMAN	cartilage associated protein precursor	373						proteinaceous extracellular matrix	binding				0																		---	---	---	---
ARPP21	10777	broad.mit.edu	37	3	35778816	35778816	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:35778816C>T	uc003cgb.2	+	16	1870	c.1606C>T	c.(1606-1608)CCA>TCA	p.P536S	ARPP21_uc003cga.2_Missense_Mutation_p.P482S|ARPP21_uc011axy.1_Missense_Mutation_p.P502S|ARPP21_uc003cgf.2_Missense_Mutation_p.P337S|ARPP21_uc003cgg.2_Missense_Mutation_p.P24S	NM_016300	NP_057384	Q9UBL0	ARP21_HUMAN	cyclic AMP-regulated phosphoprotein, 21 kD	536	Gln-rich.					cytoplasm	nucleic acid binding			ovary(2)|skin(1)	3																		---	---	---	---
TRANK1	9881	broad.mit.edu	37	3	36898104	36898104	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36898104C>T	uc003cgj.2	-	3	1629	c.1327G>A	c.(1327-1329)GCC>ACC	p.A443T		NM_014831	NP_055646	O15050	TRNK1_HUMAN	lupus brain antigen 1	993					DNA repair		ATP binding|ATP-dependent DNA helicase activity|DNA binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
ITGA9	3680	broad.mit.edu	37	3	37574853	37574853	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37574853C>A	uc003chd.2	+	14	1475	c.1422C>A	c.(1420-1422)TCC>TCA	p.S474S	ITGA9_uc003chc.2_Silent_p.S474S	NM_002207	NP_002198	Q13797	ITA9_HUMAN	integrin, alpha 9 precursor	474	Extracellular (Potential).|FG-GAP 7.				axon guidance|cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			breast(3)|pancreas(1)|lung(1)|skin(1)	6				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)														---	---	---	---
ITGA9	3680	broad.mit.edu	37	3	37783223	37783223	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:37783223G>A	uc003chd.2	+	21	2290	c.2237G>A	c.(2236-2238)GGC>GAC	p.G746D		NM_002207	NP_002198	Q13797	ITA9_HUMAN	integrin, alpha 9 precursor	746	Extracellular (Potential).				axon guidance|cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			breast(3)|pancreas(1)|lung(1)|skin(1)	6				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)														---	---	---	---
MYD88	4615	broad.mit.edu	37	3	38182256	38182256	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38182256G>A	uc003chx.2	+	4	900	c.716G>A	c.(715-717)CGG>CAG	p.R239Q	MYD88_uc011ayi.1_Missense_Mutation_p.R231Q|MYD88_uc011ayj.1_Missense_Mutation_p.G171R|MYD88_uc011ayk.1_Missense_Mutation_p.G126R|MYD88_uc011ayl.1_Missense_Mutation_p.R186Q	NM_002468	NP_002459	Q99836	MYD88_HUMAN	myeloid differentiation primary response gene	218	TIR.				3'-UTR-mediated mRNA stabilization|anti-apoptosis|cellular response to mechanical stimulus|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-17 production|positive regulation of interleukin-23 production|positive regulation of interleukin-6 production|regulation of inflammatory response|response to interleukin-1|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane|intrinsic to membrane|plasma membrane	death receptor binding|TIR domain binding|transmembrane receptor activity			haematopoietic_and_lymphoid_tissue(93)|breast(1)	94				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)				Mis 		ABC-DLBCL								---	---	---	---
SLC22A13	9390	broad.mit.edu	37	3	38307726	38307726	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38307726T>C	uc003chz.3	+	1	429	c.375T>C	c.(373-375)AAT>AAC	p.N125N	SLC22A13_uc011aym.1_RNA|SLC22A13_uc011ayn.1_Silent_p.N125N	NM_004256	NP_004247	Q9Y226	S22AD_HUMAN	solute carrier family 22 (organic anion	125	Extracellular (Potential).					integral to plasma membrane	organic cation transmembrane transporter activity			skin(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0533)|Kidney(284;0.067)														---	---	---	---
XYLB	9942	broad.mit.edu	37	3	38417720	38417720	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38417720C>A	uc003cic.2	+	13	1226	c.1117C>A	c.(1117-1119)CTG>ATG	p.L373M	XYLB_uc011ayp.1_Missense_Mutation_p.L236M|XYLB_uc003cid.1_Missense_Mutation_p.L295M	NM_005108	NP_005099	O75191	XYLB_HUMAN	xylulokinase	373					D-xylose metabolic process|generation of precursor metabolites and energy|xylulose catabolic process		ATP binding|xylulokinase activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.00372)|Kidney(284;0.00405)														---	---	---	---
SCN10A	6336	broad.mit.edu	37	3	38770389	38770389	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38770389G>A	uc003ciq.2	-	15	2284	c.2284C>T	c.(2284-2286)CGC>TGC	p.R762C		NM_006514	NP_006505	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha	762	Helical; Voltage-sensor; Name=S4 of repeat II; (Potential).|II.				sensory perception	voltage-gated sodium channel complex				ovary(5)|skin(3)|large_intestine(1)|kidney(1)	10				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cocaine(DB00907)|Dibucaine(DB00527)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)													---	---	---	---
SCN11A	11280	broad.mit.edu	37	3	38938500	38938500	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38938500G>A	uc011ays.1	-	14	2438	c.2239C>T	c.(2239-2241)CGG>TGG	p.R747W	SCN11A_uc010hhn.1_5'Flank	NM_014139	NP_054858	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha	747	II.				response to drug	voltage-gated sodium channel complex	voltage-gated sodium channel activity			skin(6)|ovary(1)|haematopoietic_and_lymphoid_tissue(1)|pancreas(1)	9				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)													---	---	---	---
GORASP1	64689	broad.mit.edu	37	3	39142351	39142351	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39142351C>T	uc003ciw.1	-	5	551	c.453G>A	c.(451-453)ACG>ACA	p.T151T	GORASP1_uc003civ.1_RNA|GORASP1_uc003cix.1_RNA|GORASP1_uc003ciy.1_RNA|GORASP1_uc011ayw.1_Silent_p.T56T|GORASP1_uc003ciz.1_Intron	NM_031899	NP_114105	Q9BQQ3	GORS1_HUMAN	Golgi reassembly stacking protein 1	151					mitotic prophase|protein transport	cytosol|Golgi apparatus|membrane				ovary(2)|central_nervous_system(1)	3				KIRC - Kidney renal clear cell carcinoma(284;0.0519)|Kidney(284;0.0653)												OREG0015486	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
TTC21A	199223	broad.mit.edu	37	3	39170216	39170216	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39170216T>C	uc003cjc.2	+	14	1887	c.1710T>C	c.(1708-1710)GAT>GAC	p.D570D	TTC21A_uc003cje.2_Silent_p.D571D|TTC21A_uc003cjd.2_RNA|TTC21A_uc011ayx.1_Silent_p.D522D	NM_145755	NP_665698	Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A isoform 2	570							binding			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)														---	---	---	---
CCR8	1237	broad.mit.edu	37	3	39374858	39374858	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39374858T>A	uc010hhr.2	+	2	1174	c.1036T>A	c.(1036-1038)TCC>ACC	p.S346T	CCR8_uc003cjm.2_Missense_Mutation_p.S263T	NM_005201	NP_005192	P51685	CCR8_HUMAN	chemokine (C-C motif) receptor 8	346	Cytoplasmic (Potential).				cell adhesion|chemotaxis|elevation of cytosolic calcium ion concentration|immune response	integral to plasma membrane	coreceptor activity			ovary(1)|lung(1)	2				KIRC - Kidney renal clear cell carcinoma(284;0.0504)|Kidney(284;0.0635)														---	---	---	---
ZNF621	285268	broad.mit.edu	37	3	40573743	40573743	+	Missense_Mutation	SNP	G	A	A	rs150435196		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40573743G>A	uc003ckm.2	+	5	698	c.482G>A	c.(481-483)CGA>CAA	p.R161Q	ZNF621_uc003ckn.2_Missense_Mutation_p.R161Q|ZNF621_uc003cko.2_Missense_Mutation_p.R126Q|ZNF621_uc011aze.1_Missense_Mutation_p.R153Q	NM_001098414	NP_001091884	Q6ZSS3	ZN621_HUMAN	zinc finger protein 621	161	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0515)|Kidney(284;0.0648)														---	---	---	---
VIPR1	7433	broad.mit.edu	37	3	42572370	42572370	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42572370G>A	uc003clf.2	+	7	860	c.736G>A	c.(736-738)GTC>ATC	p.V246I	VIPR1_uc011azl.1_Missense_Mutation_p.V198I|VIPR1_uc011azm.1_Silent_p.P42P|VIPR1_uc011azn.1_Missense_Mutation_p.V219I|VIPR1_uc003clg.2_5'Flank	NM_004624	NP_004615	P32241	VIPR1_HUMAN	vasoactive intestinal peptide receptor 1	246	Cytoplasmic (Potential).				digestion|G-protein signaling, coupled to cyclic nucleotide second messenger|immune response|muscle contraction|positive regulation of cell proliferation|synaptic transmission	integral to plasma membrane	vasoactive intestinal polypeptide receptor activity			skin(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.241)														---	---	---	---
NKTR	4820	broad.mit.edu	37	3	42684055	42684055	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42684055G>A	uc003clo.2	+	14	4256	c.4109G>A	c.(4108-4110)CGG>CAG	p.R1370Q	NKTR_uc003clp.2_Missense_Mutation_p.R1117Q|NKTR_uc011azp.1_Missense_Mutation_p.R169Q|NKTR_uc003cls.2_Missense_Mutation_p.R1070Q	NM_005385	NP_005376	P30414	NKTR_HUMAN	natural killer-tumor recognition sequence	1370					protein folding	membrane	cyclosporin A binding|peptidyl-prolyl cis-trans isomerase activity			ovary(2)|skin(1)	3				KIRC - Kidney renal clear cell carcinoma(284;0.24)														---	---	---	---
KBTBD5	131377	broad.mit.edu	37	3	42730091	42730091	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42730091G>A	uc003clv.1	+							NM_152393	NP_689606			kelch repeat and BTB (POZ) domain containing 5											ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.214)														---	---	---	---
CCBP2	1238	broad.mit.edu	37	3	42906895	42906895	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:42906895G>A	uc003cme.2	+	3	1080	c.901G>A	c.(901-903)GCC>ACC	p.A301T	CCBP2_uc003cmd.1_Intron|CCBP2_uc003cmf.2_Missense_Mutation_p.A301T|CCBP2_uc003cmg.2_Intron|CYP8B1_uc010hif.2_Intron	NM_001296	NP_001287	O00590	CCBP2_HUMAN	chemokine binding protein 2	301	Helical; Name=7; (Potential).				chemotaxis|immune response|multicellular organismal development	integral to plasma membrane	C-X-C chemokine receptor activity			lung(4)|skin(1)	5				KIRC - Kidney renal clear cell carcinoma(284;0.241)														---	---	---	---
SNRK	54861	broad.mit.edu	37	3	43345155	43345155	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43345155G>A	uc003cms.3	+	3	792	c.460G>A	c.(460-462)GTA>ATA	p.V154I	SNRK_uc003cmt.3_Missense_Mutation_p.V154I|SNRK_uc010hik.2_Missense_Mutation_p.V154I|SNRK_uc011azr.1_Intron|SNRK_uc003cmu.2_Missense_Mutation_p.V154I	NM_017719	NP_060189	Q9NRH2	SNRK_HUMAN	SNF related kinase	154	Protein kinase.				myeloid cell differentiation	nucleus	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(3)|stomach(1)|breast(1)|skin(1)	6				KIRC - Kidney renal clear cell carcinoma(284;0.0636)|Kidney(284;0.0792)														---	---	---	---
SNRK	54861	broad.mit.edu	37	3	43389842	43389842	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:43389842G>A	uc003cms.3	+	7	2423	c.2091G>A	c.(2089-2091)CAG>CAA	p.Q697Q	SNRK_uc003cmt.3_Silent_p.Q697Q|SNRK_uc010hik.2_Silent_p.Q697Q|SNRK_uc011azr.1_Silent_p.Q491Q	NM_017719	NP_060189	Q9NRH2	SNRK_HUMAN	SNF related kinase	697					myeloid cell differentiation	nucleus	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(3)|stomach(1)|breast(1)|skin(1)	6				KIRC - Kidney renal clear cell carcinoma(284;0.0636)|Kidney(284;0.0792)														---	---	---	---
ZNF197	10168	broad.mit.edu	37	3	44672647	44672647	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44672647G>A	uc003cnm.2	+	3	690	c.484G>A	c.(484-486)GCA>ACA	p.A162T	ZNF197_uc003cnn.2_Missense_Mutation_p.A162T|ZNF197_uc003cno.2_RNA|ZNF197_uc003cnp.2_Missense_Mutation_p.A162T	NM_006991	NP_008922	O14709	ZN197_HUMAN	zinc finger protein 197 isoform 1	162					viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)|skin(1)	4				KIRC - Kidney renal clear cell carcinoma(197;0.0478)|Kidney(197;0.0598)														---	---	---	---
ZNF502	91392	broad.mit.edu	37	3	44763268	44763268	+	Missense_Mutation	SNP	A	G	G	rs145256884		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44763268A>G	uc011baa.1	+	4	1214	c.959A>G	c.(958-960)GAA>GGA	p.E320G	ZNF502_uc003cns.2_Missense_Mutation_p.E320G|ZNF502_uc011bab.1_Missense_Mutation_p.E320G|ZNF502_uc003cnt.2_Missense_Mutation_p.E320G	NM_001134440	NP_001127912	Q8TBZ5	ZN502_HUMAN	zinc finger protein 502	320					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				BRCA - Breast invasive adenocarcinoma(193;0.00855)|KIRC - Kidney renal clear cell carcinoma(197;0.0471)|Kidney(197;0.0589)														---	---	---	---
KIF15	56992	broad.mit.edu	37	3	44841886	44841886	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44841886G>A	uc003cnx.3	+	11	1328	c.1179G>A	c.(1177-1179)GAG>GAA	p.E393E	KIF15_uc010hiq.2_Silent_p.E296E|KIF15_uc003cny.1_Silent_p.E28E	NM_020242	NP_064627	Q9NS87	KIF15_HUMAN	kinesin family member 15	393	Potential.				blood coagulation|cell proliferation|microtubule-based movement|mitosis	centrosome|cytosol|microtubule|plus-end kinesin complex|spindle	ATP binding|DNA binding|microtubule motor activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)														---	---	---	---
EXOSC7	23016	broad.mit.edu	37	3	45031080	45031080	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45031080G>A	uc003coi.2	+	3	227	c.198G>A	c.(196-198)ATG>ATA	p.M66I	EXOSC7_uc003coh.1_Missense_Mutation_p.M1I|EXOSC7_uc011bae.1_Missense_Mutation_p.M66I|EXOSC7_uc010his.1_Intron|EXOSC7_uc003coj.2_Missense_Mutation_p.M66I	NM_015004	NP_055819	Q15024	EXOS7_HUMAN	exosome component 7	66					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|rRNA processing	cytosol|exosome (RNase complex)|nucleolus	3'-5'-exoribonuclease activity|protein binding|RNA binding				0				BRCA - Breast invasive adenocarcinoma(193;0.00911)|KIRC - Kidney renal clear cell carcinoma(197;0.0509)|Kidney(197;0.064)														---	---	---	---
LARS2	23395	broad.mit.edu	37	3	45515746	45515746	+	Silent	SNP	C	T	T	rs144694969		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45515746C>T	uc003cop.1	+	9	947	c.762C>T	c.(760-762)GAC>GAT	p.D254D	LARS2_uc010hit.1_Silent_p.D211D	NM_015340	NP_056155	Q15031	SYLM_HUMAN	leucyl-tRNA synthetase 2, mitochondrial	254					leucyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|leucine-tRNA ligase activity			upper_aerodigestive_tract(1)|ovary(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.0122)|KIRC - Kidney renal clear cell carcinoma(197;0.0313)|Kidney(197;0.0372)	L-Leucine(DB00149)													---	---	---	---
LIMD1	8994	broad.mit.edu	37	3	45709807	45709807	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45709807G>A	uc003coq.2	+	4	1649	c.1600G>A	c.(1600-1602)GCT>ACT	p.A534T		NM_014240	NP_055055	Q9UGP4	LIMD1_HUMAN	LIM domains containing 1	534	Necessary for nuclear localization.				cytoplasmic mRNA processing body assembly|gene silencing by miRNA|multicellular organismal development|negative regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	cytoplasmic mRNA processing body|nucleus|RNA-induced silencing complex	protein binding|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.011)|KIRC - Kidney renal clear cell carcinoma(197;0.0264)|Kidney(197;0.0315)														---	---	---	---
CXCR6	10663	broad.mit.edu	37	3	45988216	45988216	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:45988216C>T	uc003cpc.1	+	2	324	c.243C>T	c.(241-243)GTC>GTT	p.V81V	FYCO1_uc003cpb.3_Intron|FYCO1_uc011bal.1_Intron|CXCR6_uc010hix.1_Silent_p.V81V	NM_006564	NP_006555	O00574	CXCR6_HUMAN	G protein-coupled receptor TYMSTR	81	Helical; Name=2; (Potential).				viral genome replication	integral to plasma membrane	coreceptor activity			skin(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.00113)|KIRC - Kidney renal clear cell carcinoma(197;0.0172)|Kidney(197;0.0203)														---	---	---	---
TMIE	259236	broad.mit.edu	37	3	46750774	46750774	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46750774G>A	uc010hjk.1	+						TMIE_uc010hjj.1_Intron	NM_147196	NP_671729			transmembrane inner ear protein precursor							integral to membrane					0				BRCA - Breast invasive adenocarcinoma(193;0.000688)|KIRC - Kidney renal clear cell carcinoma(197;0.0177)|Kidney(197;0.0208)														---	---	---	---
PRSS50	29122	broad.mit.edu	37	3	46753883	46753883	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46753883G>A	uc003cqe.1	-	6	1070	c.1011C>T	c.(1009-1011)AGC>AGT	p.S337S	PRSS50_uc003cqf.1_Silent_p.S251S	NM_013270	NP_037402	Q9UI38	TSP50_HUMAN	testes-specific protease 50 precursor	337	Peptidase S1.				proteolysis	endoplasmic reticulum	serine-type endopeptidase activity|threonine-type endopeptidase activity				0																		---	---	---	---
PTH1R	5745	broad.mit.edu	37	3	46940148	46940148	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:46940148G>A	uc003cqm.2	+						PTH1R_uc003cqn.2_Intron	NM_000316	NP_000307			parathyroid hormone receptor 1 precursor							cytoplasm|integral to plasma membrane|nucleus	parathyroid hormone receptor activity|peptide hormone binding|protein self-association			breast(1)	1														Ollier_disease_/_Maffuci_syndrome				---	---	---	---
NBEAL2	23218	broad.mit.edu	37	3	47045624	47045624	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47045624G>A	uc003cqp.2	+	37	6118	c.5939G>A	c.(5938-5940)CGT>CAT	p.R1980H	NBEAL2_uc010hjm.1_Missense_Mutation_p.R1357H|NBEAL2_uc010hjn.1_Missense_Mutation_p.R376H|NBEAL2_uc010hjo.1_5'Flank	NM_015175	NP_055990	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	1980							binding			ovary(1)	1		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)														---	---	---	---
CSPG5	10675	broad.mit.edu	37	3	47618363	47618363	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47618363C>A	uc003crp.3	-	2	1329	c.1153G>T	c.(1153-1155)GGC>TGC	p.G385C	CSPG5_uc003crn.2_Missense_Mutation_p.G247C|CSPG5_uc003cro.3_Missense_Mutation_p.G385C|CSPG5_uc011bbb.1_Missense_Mutation_p.G247C	NM_006574	NP_006565	O95196	CSPG5_HUMAN	chondroitin sulfate proteoglycan 5 (neuroglycan	385	EGF-like.|Extracellular (Potential).				cell differentiation|intracellular transport|nervous system development|regulation of growth	endoplasmic reticulum membrane|Golgi-associated vesicle membrane|integral to plasma membrane|membrane fraction	growth factor activity			ovary(1)|central_nervous_system(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.000266)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)														---	---	---	---
CSPG5	10675	broad.mit.edu	37	3	47618653	47618653	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:47618653G>A	uc003crp.3	-	2	1039	c.863C>T	c.(862-864)GCA>GTA	p.A288V	CSPG5_uc003crn.2_Missense_Mutation_p.A150V|CSPG5_uc003cro.3_Missense_Mutation_p.A288V|CSPG5_uc011bbb.1_Missense_Mutation_p.A150V	NM_006574	NP_006565	O95196	CSPG5_HUMAN	chondroitin sulfate proteoglycan 5 (neuroglycan	288	Interaction with TNC and TNR (By similarity).|Extracellular (Potential).				cell differentiation|intracellular transport|nervous system development|regulation of growth	endoplasmic reticulum membrane|Golgi-associated vesicle membrane|integral to plasma membrane|membrane fraction	growth factor activity			ovary(1)|central_nervous_system(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.000266)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)														---	---	---	---
NME6	10201	broad.mit.edu	37	3	48336687	48336687	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48336687G>A	uc003csp.3	-	5	323	c.272C>T	c.(271-273)GCC>GTC	p.A91V	NME6_uc003cso.2_Missense_Mutation_p.A99V|NME6_uc011bbh.1_Missense_Mutation_p.P78S|NME6_uc010hju.2_5'UTR|NME6_uc011bbi.1_Intron	NM_005793	NP_005784	O75414	NDK6_HUMAN	nucleoside diphosphate kinase type 6	91					anti-apoptosis|apoptosis|CTP biosynthetic process|GTP biosynthetic process|negative regulation of cell growth|negative regulation of mitosis|UTP biosynthetic process	mitochondrion	ATP binding|metal ion binding|nucleoside diphosphate kinase activity				0				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00609)														---	---	---	---
PLXNB1	5364	broad.mit.edu	37	3	48452394	48452394	+	Missense_Mutation	SNP	C	T	T	rs149655601		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48452394C>T	uc003csw.2	-	29	5569	c.5299G>A	c.(5299-5301)GTG>ATG	p.V1767M	PLXNB1_uc003cst.2_Missense_Mutation_p.V217M|PLXNB1_uc003csu.2_Missense_Mutation_p.V1584M|PLXNB1_uc003csx.2_Missense_Mutation_p.V1767M	NM_002673	NP_002664	O43157	PLXB1_HUMAN	plexin B1 precursor	1767	Cytoplasmic (Potential).				axon guidance|cell migration|intracellular signal transduction|regulation of cell shape|regulation of cytoskeleton organization|regulation of small GTPase mediated signal transduction|semaphorin-plexin signaling pathway	extracellular region|integral to plasma membrane|intracellular|semaphorin receptor complex	GTPase activator activity|semaphorin receptor activity|semaphorin receptor binding			ovary(2)|pancreas(1)|breast(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)														---	---	---	---
TMEM89	440955	broad.mit.edu	37	3	48659174	48659174	+	Missense_Mutation	SNP	C	T	T	rs149562791		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48659174C>T	uc011bbo.1	-	1	16	c.16G>A	c.(16-18)GCC>ACC	p.A6T		NM_001008269	NP_001008270	A2RUT3	TMM89_HUMAN	transmembrane protein 89 precursor	6						integral to membrane					0				BRCA - Breast invasive adenocarcinoma(193;0.000286)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)														---	---	---	---
CELSR3	1951	broad.mit.edu	37	3	48686226	48686226	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48686226C>T	uc003cul.2	-	18	6984	c.6703G>A	c.(6703-6705)GCC>ACC	p.A2235T	CELSR3_uc003cuf.1_Missense_Mutation_p.A2305T|CELSR3_uc010hkg.2_Missense_Mutation_p.A218T	NM_001407	NP_001398	Q9NYQ7	CELR3_HUMAN	cadherin EGF LAG seven-pass G-type receptor 3	2235	Extracellular (Potential).				homophilic cell adhesion|multicellular organismal development|neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(5)|upper_aerodigestive_tract(2)|central_nervous_system(2)|skin(2)	11				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)														---	---	---	---
CELSR3	1951	broad.mit.edu	37	3	48699134	48699134	+	Missense_Mutation	SNP	G	A	A	rs76423828	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48699134G>A	uc003cul.2	-	1	1215	c.934C>T	c.(934-936)CGG>TGG	p.R312W	CELSR3_uc003cuf.1_Missense_Mutation_p.R382W	NM_001407	NP_001398	Q9NYQ7	CELR3_HUMAN	cadherin EGF LAG seven-pass G-type receptor 3	312	Extracellular (Potential).				homophilic cell adhesion|multicellular organismal development|neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(5)|upper_aerodigestive_tract(2)|central_nervous_system(2)|skin(2)	11				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)														---	---	---	---
SLC25A20	788	broad.mit.edu	37	3	48921538	48921538	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48921538C>T	uc003cva.3	-	3	393	c.218G>A	c.(217-219)CGG>CAG	p.R73Q	SLC25A20_uc011bbw.1_Missense_Mutation_p.R23Q|SLC25A20_uc010hkj.2_Intron	NM_000387	NP_000378	O43772	MCAT_HUMAN	carnitine/acylcarnitine translocase	73	Solcar 1.|Mitochondrial matrix (Potential).				carnitine shuttle|cellular lipid metabolic process|regulation of fatty acid oxidation	integral to membrane|mitochondrial inner membrane	acyl carnitine transporter activity				0				BRCA - Breast invasive adenocarcinoma(193;0.000168)|Kidney(197;0.00231)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)	L-Carnitine(DB00583)													---	---	---	---
WDR6	11180	broad.mit.edu	37	3	49049554	49049554	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49049554A>C	uc003cvj.2	+	2	815	c.677A>C	c.(676-678)AAC>ACC	p.N226T	WDR6_uc011bbx.1_Missense_Mutation_p.N97T|WDR6_uc011bby.1_Intron|WDR6_uc010hkn.2_Missense_Mutation_p.N170T|WDR6_uc011bbz.1_Missense_Mutation_p.N145T	NM_018031	NP_060501	Q9NNW5	WDR6_HUMAN	WD repeat domain 6 protein	196	WD 2.				cell cycle arrest|negative regulation of cell proliferation	cytoplasm				central_nervous_system(1)	1				Kidney(197;9.12e-07)|KIRC - Kidney renal clear cell carcinoma(197;1.32e-05)|BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000155)														---	---	---	---
LAMB2	3913	broad.mit.edu	37	3	49161698	49161698	+	Missense_Mutation	SNP	G	A	A	rs149719225		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49161698G>A	uc003cwe.2	-	23	3648	c.3349C>T	c.(3349-3351)CGT>TGT	p.R1117C		NM_002292	NP_002283	P55268	LAMB2_HUMAN	laminin, beta 2 precursor	1117	Laminin EGF-like 12.				cell adhesion	laminin-11 complex|laminin-3 complex	structural molecule activity			ovary(3)	3				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)														---	---	---	---
LAMB2	3913	broad.mit.edu	37	3	49163306	49163306	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49163306G>T	uc003cwe.2	-	18	2661	c.2362C>A	c.(2362-2364)CAA>AAA	p.Q788K	LAMB2_uc003cwf.1_Missense_Mutation_p.Q788K	NM_002292	NP_002283	P55268	LAMB2_HUMAN	laminin, beta 2 precursor	788	Laminin EGF-like 6.				cell adhesion	laminin-11 complex|laminin-3 complex	structural molecule activity			ovary(3)	3				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)														---	---	---	---
DAG1	1605	broad.mit.edu	37	3	49569450	49569450	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49569450T>A	uc003cxc.3	+	3	1924	c.1506T>A	c.(1504-1506)CAT>CAA	p.H502Q		NM_004393	NP_004384	Q14118	DAG1_HUMAN	dystroglycan 1 preproprotein	502	Peptidase S72.				cytoskeletal anchoring at plasma membrane|interspecies interaction between organisms|microtubule anchoring|negative regulation of cell migration|negative regulation of MAPKKK cascade|negative regulation of protein kinase B signaling cascade	basement membrane|contractile ring|cytoplasm|cytoskeleton|dystrophin-associated glycoprotein complex|extracellular space|filopodium|integral to membrane|integral to membrane of membrane fraction|lamellipodium|nucleoplasm	actin binding|alpha-actinin binding|calcium ion binding|laminin-1 binding|receptor activity|structural constituent of muscle|tubulin binding|vinculin binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.00241)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)														---	---	---	---
MST1	4485	broad.mit.edu	37	3	49723502	49723502	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49723502C>T	uc003cxg.2	-	9	1212	c.1140G>A	c.(1138-1140)CGG>CGA	p.R380R	MST1_uc011bcs.1_Missense_Mutation_p.G419D|MST1_uc010hkx.2_3'UTR|MST1_uc011bct.1_3'UTR	NM_020998	NP_066278	P26927	HGFL_HUMAN	macrophage stimulating 1 (hepatocyte growth	366					proteolysis	extracellular region	serine-type endopeptidase activity			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;4.47e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)														---	---	---	---
TRAIP	10293	broad.mit.edu	37	3	49879298	49879298	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49879298G>A	uc003cxs.1	-	7	684	c.578C>T	c.(577-579)GCG>GTG	p.A193V	TRAIP_uc010hla.1_Intron	NM_005879	NP_005870	Q9BWF2	TRAIP_HUMAN	TRAF interacting protein	193					cell proliferation|induction of apoptosis	perinuclear region of cytoplasm	protein binding|zinc ion binding			lung(4)|upper_aerodigestive_tract(1)|ovary(1)	6				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)														---	---	---	---
MON1A	84315	broad.mit.edu	37	3	49949356	49949356	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:49949356G>A	uc003cxz.2	-	3	633	c.507C>T	c.(505-507)AGC>AGT	p.S169S	MON1A_uc003cya.2_Intron|MON1A_uc003cyb.2_Intron	NM_032355	NP_115731	Q86VX9	MON1A_HUMAN	MON1 homolog A isoform a	72							protein binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(193;4.62e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)														---	---	---	---
SEMA3F	6405	broad.mit.edu	37	3	50220161	50220161	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50220161C>T	uc003cyj.2	+	9	1046	c.848C>T	c.(847-849)TCG>TTG	p.S283L	SEMA3F_uc003cyk.2_Missense_Mutation_p.S252L	NM_004186	NP_004177	Q13275	SEM3F_HUMAN	semaphorin 3F precursor	283	Sema.				axon guidance	extracellular space|membrane	chemorepellent activity|receptor activity			lung(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.00013)|KIRC - Kidney renal clear cell carcinoma(197;0.00599)|Kidney(197;0.00688)														---	---	---	---
SEMA3F	6405	broad.mit.edu	37	3	50222044	50222044	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50222044C>T	uc003cyj.2	+	13	1451	c.1253C>T	c.(1252-1254)ACG>ATG	p.T418M	SEMA3F_uc003cyk.2_Missense_Mutation_p.T387M	NM_004186	NP_004177	Q13275	SEM3F_HUMAN	semaphorin 3F precursor	418	Sema.				axon guidance	extracellular space|membrane	chemorepellent activity|receptor activity			lung(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.00013)|KIRC - Kidney renal clear cell carcinoma(197;0.00599)|Kidney(197;0.00688)														---	---	---	---
SEMA3F	6405	broad.mit.edu	37	3	50222148	50222148	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50222148C>A	uc003cyj.2	+	13	1555	c.1357C>A	c.(1357-1359)CTG>ATG	p.L453M	SEMA3F_uc003cyk.2_Missense_Mutation_p.L422M	NM_004186	NP_004177	Q13275	SEM3F_HUMAN	semaphorin 3F precursor	453	Sema.				axon guidance	extracellular space|membrane	chemorepellent activity|receptor activity			lung(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.00013)|KIRC - Kidney renal clear cell carcinoma(197;0.00599)|Kidney(197;0.00688)														---	---	---	---
GNAI2	2771	broad.mit.edu	37	3	50289578	50289578	+	Intron	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50289578A>C	uc003cyq.1	+						GNAI2_uc003cyo.1_Intron|GNAI2_uc003cyp.1_Intron|GNAI2_uc010hlg.1_Intron|GNAI2_uc011bdn.1_Intron|GNAI2_uc003cyr.1_5'UTR	NM_002070	NP_002061			guanine nucleotide binding protein (G protein),						adenosine receptor signaling pathway|cell cycle|cell division|gamma-aminobutyric acid signaling pathway|inhibition of adenylate cyclase activity by G-protein signaling pathway|negative regulation of calcium ion transport via voltage-gated calcium channel activity|platelet activation|response to nutrient|synaptic transmission	centrosome|heterotrimeric G-protein complex|midbody	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity			ovary(1)|central_nervous_system(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000288)|KIRC - Kidney renal clear cell carcinoma(197;0.00571)|Kidney(197;0.00651)														---	---	---	---
TMEM115	11070	broad.mit.edu	37	3	50396092	50396092	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50396092T>C	uc003dan.1	-	1	848	c.403A>G	c.(403-405)ATC>GTC	p.I135V		NM_007024	NP_008955	Q12893	TM115_HUMAN	PL6 protein	135	Helical; (Potential).				negative regulation of cell proliferation	Golgi apparatus|integral to membrane|nucleus					0				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)														---	---	---	---
TMEM115	11070	broad.mit.edu	37	3	50396212	50396212	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50396212C>T	uc003dan.1	-	1	728	c.283G>A	c.(283-285)GCC>ACC	p.A95T		NM_007024	NP_008955	Q12893	TM115_HUMAN	PL6 protein	95					negative regulation of cell proliferation	Golgi apparatus|integral to membrane|nucleus					0				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)														---	---	---	---
CISH	1154	broad.mit.edu	37	3	50645055	50645055	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:50645055A>C	uc003dax.2	-	3	941	c.760T>G	c.(760-762)TAC>GAC	p.Y254D	CISH_uc010hlq.2_Missense_Mutation_p.Y271D	NM_145071	NP_659508	Q9NSE2	CISH_HUMAN	cytokine-inducible SH2-containing protein	254	SOCS box.				intracellular signal transduction|negative regulation of signal transduction|regulation of cell growth	intracellular					0				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)														---	---	---	---
DOCK3	1795	broad.mit.edu	37	3	51378785	51378785	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51378785G>A	uc011bds.1	+	38	3907	c.3884G>A	c.(3883-3885)CGG>CAG	p.R1295Q		NM_004947	NP_004938	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	1295	DHR-2.					cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding				0				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)														---	---	---	---
RAD54L2	23132	broad.mit.edu	37	3	51696908	51696908	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:51696908C>T	uc011bdt.1	+	22	4001	c.3876C>T	c.(3874-3876)GGC>GGT	p.G1292G	RAD54L2_uc003dbh.2_Silent_p.G881G|RAD54L2_uc011bdu.1_Silent_p.G986G|RAD54L2_uc003dbj.2_Silent_p.G618G	NM_015106	NP_055921	Q9Y4B4	ARIP4_HUMAN	RAD54-like 2	1292						nucleus	ATP binding|DNA binding|helicase activity			ovary(3)	3				BRCA - Breast invasive adenocarcinoma(193;0.000102)|Kidney(197;0.000758)|KIRC - Kidney renal clear cell carcinoma(197;0.000896)														---	---	---	---
DNAH1	25981	broad.mit.edu	37	3	52407046	52407046	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52407046G>A	uc011bef.1	+	44	7223	c.6962G>A	c.(6961-6963)GGC>GAC	p.G2321D		NM_015512	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	2321	AAA 3 (By similarity).				ciliary or flagellar motility|microtubule-based movement|response to mechanical stimulus	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			large_intestine(3)	3				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)														---	---	---	---
STAB1	23166	broad.mit.edu	37	3	52535322	52535322	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52535322C>T	uc003dej.2	+						STAB1_uc003dei.1_Intron	NM_015136	NP_055951			stabilin 1 precursor						cell adhesion|cell-cell signaling|defense response to bacterium|inflammatory response|negative regulation of angiogenesis|receptor-mediated endocytosis	integral to plasma membrane	bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			large_intestine(3)|upper_aerodigestive_tract(2)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	9				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)														---	---	---	---
STAB1	23166	broad.mit.edu	37	3	52543996	52543996	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52543996G>T	uc003dej.2	+	23	2532	c.2458G>T	c.(2458-2460)GGG>TGG	p.G820W		NM_015136	NP_055951	Q9NY15	STAB1_HUMAN	stabilin 1 precursor	820	EGF-like 6.|Extracellular (Potential).				cell adhesion|cell-cell signaling|defense response to bacterium|inflammatory response|negative regulation of angiogenesis|receptor-mediated endocytosis	integral to plasma membrane	bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			large_intestine(3)|upper_aerodigestive_tract(2)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	9				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)														---	---	---	---
STAB1	23166	broad.mit.edu	37	3	52548207	52548207	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52548207C>T	uc003dej.2	+	33	3598	c.3524C>T	c.(3523-3525)GCC>GTC	p.A1175V		NM_015136	NP_055951	Q9NY15	STAB1_HUMAN	stabilin 1 precursor	1175	FAS1 4.|Extracellular (Potential).				cell adhesion|cell-cell signaling|defense response to bacterium|inflammatory response|negative regulation of angiogenesis|receptor-mediated endocytosis	integral to plasma membrane	bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			large_intestine(3)|upper_aerodigestive_tract(2)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	9				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)														---	---	---	---
NT5DC2	64943	broad.mit.edu	37	3	52568582	52568582	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52568582C>T	uc003deo.2	-	1	512	c.88G>A	c.(88-90)GAG>AAG	p.E30K	NT5DC2_uc003den.2_5'Flank|NT5DC2_uc010hmi.2_5'Flank|NT5DC2_uc010hmj.2_5'UTR|LOC440957_uc003dep.2_5'Flank	NM_022908	NP_075059	Q9H857	NT5D2_HUMAN	5'-nucleotidase domain containing 2 isoform 2	30							hydrolase activity|metal ion binding				0				BRCA - Breast invasive adenocarcinoma(193;1.7e-05)|Kidney(197;0.00177)|KIRC - Kidney renal clear cell carcinoma(197;0.002)|OV - Ovarian serous cystadenocarcinoma(275;0.0476)														---	---	---	---
PBRM1	55193	broad.mit.edu	37	3	52582241	52582241	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52582241G>A	uc003des.2	-	30	4920	c.4908C>T	c.(4906-4908)CGC>CGT	p.R1636R	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Silent_p.R1529R|PBRM1_uc003der.2_Silent_p.R1549R|PBRM1_uc003det.2_Silent_p.R1544R|PBRM1_uc003deu.2_Silent_p.R1599R|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Silent_p.R1581R|PBRM1_uc010hmk.1_Silent_p.R1556R|PBRM1_uc003dey.2_Silent_p.R1529R	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	1636					chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)				Mis|N|F|S|D|O		clear cell renal carcinoma|breast								---	---	---	---
PBRM1	55193	broad.mit.edu	37	3	52643650	52643650	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52643650G>T	uc003des.2	-	16	2258	c.2246C>A	c.(2245-2247)GCT>GAT	p.A749D	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Missense_Mutation_p.A749D|PBRM1_uc003der.2_Missense_Mutation_p.A717D|PBRM1_uc003det.2_Missense_Mutation_p.A764D|PBRM1_uc003deu.2_Missense_Mutation_p.A764D|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Missense_Mutation_p.A749D|PBRM1_uc010hmk.1_Missense_Mutation_p.A749D|PBRM1_uc003dey.2_Missense_Mutation_p.A749D|PBRM1_uc003dez.1_Missense_Mutation_p.A749D|PBRM1_uc003dfb.1_Missense_Mutation_p.A662D|PBRM1_uc003dfa.1_Missense_Mutation_p.A95D|PBRM1_uc003dfc.2_Missense_Mutation_p.A116D	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	749					chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)				Mis|N|F|S|D|O		clear cell renal carcinoma|breast								---	---	---	---
PBRM1	55193	broad.mit.edu	37	3	52682382	52682382	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52682382T>C	uc003des.2	-	7	803	c.791A>G	c.(790-792)GAG>GGG	p.E264G	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Missense_Mutation_p.E264G|PBRM1_uc003der.2_Missense_Mutation_p.E264G|PBRM1_uc003det.2_Missense_Mutation_p.E264G|PBRM1_uc003deu.2_Missense_Mutation_p.E264G|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Missense_Mutation_p.E264G|PBRM1_uc010hmk.1_Missense_Mutation_p.E264G|PBRM1_uc003dey.2_Missense_Mutation_p.E264G|PBRM1_uc003dez.1_Missense_Mutation_p.E264G|PBRM1_uc003dfb.1_Missense_Mutation_p.E162G	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	264	Bromo 2.				chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)				Mis|N|F|S|D|O		clear cell renal carcinoma|breast								---	---	---	---
GNL3	26354	broad.mit.edu	37	3	52721260	52721260	+	Splice_Site	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52721260A>G	uc003dfd.2	+	3	246	c.73_splice	c.e3-2	p.V25_splice	PBRM1_uc003dey.2_5'Flank|GNL3_uc011beh.1_Splice_Site|GNL3_uc003dfe.2_Splice_Site_p.V13_splice|GNL3_uc003dff.2_Splice_Site_p.V13_splice|SNORD19_uc003dfg.1_5'Flank	NM_014366	NP_055181			guanine nucleotide binding protein-like 3						regulation of cell proliferation	nucleolus	GTP binding|protein binding				0				BRCA - Breast invasive adenocarcinoma(193;6.75e-05)|Kidney(197;0.000611)|KIRC - Kidney renal clear cell carcinoma(197;0.000773)|OV - Ovarian serous cystadenocarcinoma(275;0.048)														---	---	---	---
GLT8D1	55830	broad.mit.edu	37	3	52729250	52729250	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52729250T>C	uc003dfi.3	-	9	1020	c.881A>G	c.(880-882)CAA>CGA	p.Q294R	GLT8D1_uc003dfj.2_Missense_Mutation_p.Q294R|GLT8D1_uc003dfk.2_Missense_Mutation_p.Q294R|GLT8D1_uc003dfl.2_Missense_Mutation_p.Q294R|GLT8D1_uc003dfm.2_Missense_Mutation_p.Q294R|GLT8D1_uc003dfn.2_Missense_Mutation_p.Q294R|GLT8D1_uc003dfo.1_Missense_Mutation_p.Q294R	NM_152932	NP_690909	Q68CQ7	GL8D1_HUMAN	glycosyltransferase 8 domain containing 1	294	Lumenal (Potential).					integral to membrane|mitochondrion	transferase activity, transferring glycosyl groups				0				BRCA - Breast invasive adenocarcinoma(193;6.78e-05)|Kidney(197;0.000618)|KIRC - Kidney renal clear cell carcinoma(197;0.000779)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)														---	---	---	---
GLT8D1	55830	broad.mit.edu	37	3	52731855	52731855	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52731855C>T	uc003dfi.3	-	4	350	c.211G>A	c.(211-213)GCT>ACT	p.A71T	GLT8D1_uc003dfj.2_Missense_Mutation_p.A71T|GLT8D1_uc003dfk.2_Missense_Mutation_p.A71T|GLT8D1_uc003dfl.2_Missense_Mutation_p.A71T|GLT8D1_uc003dfm.2_Missense_Mutation_p.A71T|GLT8D1_uc003dfn.2_Missense_Mutation_p.A71T|GLT8D1_uc003dfo.1_Missense_Mutation_p.A71T	NM_152932	NP_690909	Q68CQ7	GL8D1_HUMAN	glycosyltransferase 8 domain containing 1	71	Lumenal (Potential).					integral to membrane|mitochondrion	transferase activity, transferring glycosyl groups				0				BRCA - Breast invasive adenocarcinoma(193;6.78e-05)|Kidney(197;0.000618)|KIRC - Kidney renal clear cell carcinoma(197;0.000779)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)														---	---	---	---
NEK4	6787	broad.mit.edu	37	3	52794870	52794870	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52794870T>G	uc003dfq.3	-	6	1093	c.904A>C	c.(904-906)AAT>CAT	p.N302H	NEK4_uc011bej.1_Missense_Mutation_p.N213H|NEK4_uc003dfr.2_Missense_Mutation_p.N302H	NM_003157	NP_003148	P51957	NEK4_HUMAN	NIMA-related kinase 4	302					cell division|mitosis	nucleus	ATP binding|metal ion binding|protein serine/threonine kinase activity			large_intestine(1)	1				BRCA - Breast invasive adenocarcinoma(193;7.44e-05)|Kidney(197;0.000711)|KIRC - Kidney renal clear cell carcinoma(197;0.00086)|OV - Ovarian serous cystadenocarcinoma(275;0.0513)														---	---	---	---
ITIH4	3700	broad.mit.edu	37	3	52857889	52857889	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52857889C>T	uc003dfz.2	-	10	1339	c.1303G>A	c.(1303-1305)GGC>AGC	p.G435S	ITIH4_uc011bel.1_Missense_Mutation_p.G165S|ITIH4_uc003dfy.2_Missense_Mutation_p.G299S|ITIH4_uc011bem.1_Missense_Mutation_p.G435S|ITIH4_uc011ben.1_Missense_Mutation_p.G435S	NM_002218	NP_002209	Q14624	ITIH4_HUMAN	inter-alpha (globulin) inhibitor H4	435					acute-phase response|hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(1)	3				BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)														---	---	---	---
RFT1	91869	broad.mit.edu	37	3	53133401	53133401	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53133401C>T	uc003dgj.2	-	11	1258	c.1204G>A	c.(1204-1206)GAC>AAC	p.D402N	RFT1_uc003dgk.2_Missense_Mutation_p.D363N	NM_052859	NP_443091	Q96AA3	RFT1_HUMAN	RFT1 homolog	402					carbohydrate transport|dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane	lipid transporter activity			skin(1)	1				BRCA - Breast invasive adenocarcinoma(193;6.98e-05)|Kidney(197;0.0017)|KIRC - Kidney renal clear cell carcinoma(197;0.00192)|OV - Ovarian serous cystadenocarcinoma(275;0.104)														---	---	---	---
DCP1A	55802	broad.mit.edu	37	3	53326255	53326255	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53326255T>C	uc003dgs.3	-	7	1320	c.1227A>G	c.(1225-1227)ACA>ACG	p.T409T	DCP1A_uc003dgt.3_RNA	NM_018403	NP_060873	Q9NPI6	DCP1A_HUMAN	DCP1 decapping enzyme homolog A	409					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytoplasmic mRNA processing body|cytosol|nucleus	hydrolase activity|protein binding				0				BRCA - Breast invasive adenocarcinoma(193;0.000164)|KIRC - Kidney renal clear cell carcinoma(197;0.00525)|Kidney(197;0.00579)|OV - Ovarian serous cystadenocarcinoma(275;0.0647)														---	---	---	---
CACNA1D	776	broad.mit.edu	37	3	53531424	53531424	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53531424G>A	uc003dgv.3	+	2	476	c.313G>A	c.(313-315)GCC>ACC	p.A105T	CACNA1D_uc003dgu.3_Missense_Mutation_p.A105T|CACNA1D_uc003dgy.3_Missense_Mutation_p.A105T	NM_001128840	NP_001122312	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type,	105	Cytoplasmic (Potential).				axon guidance|energy reserve metabolic process|regulation of insulin secretion	voltage-gated calcium channel complex	voltage-gated calcium channel activity	p.A105T(1)		ovary(6)|upper_aerodigestive_tract(2)|liver(1)|central_nervous_system(1)|skin(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Verapamil(DB00661)													---	---	---	---
CACNA1D	776	broad.mit.edu	37	3	53835233	53835233	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53835233C>T	uc003dgv.3	+	42	5352	c.5189C>T	c.(5188-5190)CCT>CTT	p.P1730L	CACNA1D_uc003dgu.3_Missense_Mutation_p.P1750L|CACNA1D_uc003dgy.3_Missense_Mutation_p.P1715L|CACNA1D_uc003dgw.3_Missense_Mutation_p.P1397L|CACNA1D_uc011bes.1_RNA	NM_001128840	NP_001122312	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type,	1730	Cytoplasmic (Potential).				axon guidance|energy reserve metabolic process|regulation of insulin secretion	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(6)|upper_aerodigestive_tract(2)|liver(1)|central_nervous_system(1)|skin(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Verapamil(DB00661)													---	---	---	---
LRTM1	57408	broad.mit.edu	37	3	54952782	54952782	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:54952782C>T	uc003dhl.2	-	3	876	c.742G>A	c.(742-744)GGC>AGC	p.G248S	CACNA2D3_uc003dhf.2_Intron|CACNA2D3_uc003dhg.1_Intron|CACNA2D3_uc003dhh.1_Intron	NM_020678	NP_065729	Q9HBL6	LRTM1_HUMAN	leucine-rich repeats and transmembrane domains 1	248	Extracellular (Potential).					integral to membrane					0				KIRC - Kidney renal clear cell carcinoma(284;0.00975)|Kidney(284;0.0112)|OV - Ovarian serous cystadenocarcinoma(275;0.0502)														---	---	---	---
ARHGEF3	50650	broad.mit.edu	37	3	56789096	56789096	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:56789096C>T	uc003dig.2	-	3	457	c.288G>A	c.(286-288)ACG>ACA	p.T96T	ARHGEF3_uc011bew.1_Silent_p.T96T|ARHGEF3_uc003dih.2_Silent_p.T128T|ARHGEF3_uc011bev.1_Silent_p.T67T|ARHGEF3_uc003dif.2_Silent_p.T102T|ARHGEF3_uc010hmy.1_5'UTR|ARHGEF3_uc003dii.2_Silent_p.T96T	NM_019555	NP_062455	Q9NR81	ARHG3_HUMAN	Rho guanine nucleotide exchange factor 3 isoform	96					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|Rho protein signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0161)|Kidney(284;0.019)|OV - Ovarian serous cystadenocarcinoma(275;0.193)														---	---	---	---
FLNB	2317	broad.mit.edu	37	3	58097921	58097921	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58097921G>T	uc003djj.2	+	18	2786	c.2621G>T	c.(2620-2622)GGG>GTG	p.G874V	FLNB_uc010hne.2_Missense_Mutation_p.G874V|FLNB_uc003djk.2_Missense_Mutation_p.G874V|FLNB_uc010hnf.2_Missense_Mutation_p.G874V|FLNB_uc003djl.2_Missense_Mutation_p.G705V|FLNB_uc003djm.2_Missense_Mutation_p.G705V	NM_001457	NP_001448	O75369	FLNB_HUMAN	filamin B isoform 2	874	Filamin 7.				actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction	cell cortex|integral to membrane|nucleus|sarcomere	actin binding			breast(8)|ovary(5)|lung(3)|skin(2)|central_nervous_system(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)														---	---	---	---
FLNB	2317	broad.mit.edu	37	3	58124099	58124099	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58124099C>T	uc003djj.2	+	29	5117	c.4952C>T	c.(4951-4953)ACG>ATG	p.T1651M	FLNB_uc010hne.2_Missense_Mutation_p.T1682M|FLNB_uc003djk.2_Missense_Mutation_p.T1651M|FLNB_uc010hnf.2_Missense_Mutation_p.T1651M|FLNB_uc003djl.2_Missense_Mutation_p.T1482M|FLNB_uc003djm.2_Missense_Mutation_p.T1482M	NM_001457	NP_001448	O75369	FLNB_HUMAN	filamin B isoform 2	1651	Filamin 15.				actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction	cell cortex|integral to membrane|nucleus|sarcomere	actin binding			breast(8)|ovary(5)|lung(3)|skin(2)|central_nervous_system(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)														---	---	---	---
FLNB	2317	broad.mit.edu	37	3	58155309	58155309	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58155309T>C	uc003djj.2	+						FLNB_uc010hne.2_Intron|FLNB_uc003djk.2_Intron|FLNB_uc010hnf.2_Intron|FLNB_uc003djl.2_Intron|FLNB_uc003djm.2_Intron|uc003djn.2_Intron	NM_001457	NP_001448			filamin B isoform 2						actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction	cell cortex|integral to membrane|nucleus|sarcomere	actin binding			breast(8)|ovary(5)|lung(3)|skin(2)|central_nervous_system(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)														---	---	---	---
DNASE1L3	1776	broad.mit.edu	37	3	58186738	58186738	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:58186738G>A	uc003djo.1	-	5	629	c.532C>T	c.(532-534)CGC>TGC	p.R178C	DNASE1L3_uc011bfd.1_Missense_Mutation_p.R148C|DNASE1L3_uc003djp.1_Missense_Mutation_p.R178C|DNASE1L3_uc003djq.1_Missense_Mutation_p.R178C	NM_004944	NP_004935	Q13609	DNSL3_HUMAN	deoxyribonuclease I-like 3 precursor	178					apoptosis|DNA catabolic process	nucleus	calcium ion binding|DNA binding|endodeoxyribonuclease activity, producing 5'-phosphomonoesters			breast(2)|large_intestine(1)	3				BRCA - Breast invasive adenocarcinoma(55;0.00021)|KIRC - Kidney renal clear cell carcinoma(284;0.0445)|Kidney(284;0.0556)|OV - Ovarian serous cystadenocarcinoma(275;0.202)														---	---	---	---
PTPRG	5793	broad.mit.edu	37	3	62248567	62248567	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:62248567C>T	uc003dlb.2	+	17	3373	c.2654C>T	c.(2653-2655)GCA>GTA	p.A885V	PTPRG_uc003dlc.2_Missense_Mutation_p.A856V|PTPRG_uc011bfi.1_Missense_Mutation_p.A131V|uc010hno.2_RNA|uc003dld.3_RNA|uc010hnp.2_RNA|uc003dle.3_RNA	NM_002841	NP_002832	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	885	Cytoplasmic (Potential).|Tyrosine-protein phosphatase 1.				transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	identical protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(5)|lung(2)	7				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)														---	---	---	---
ADAMTS9	56999	broad.mit.edu	37	3	64601793	64601793	+	Missense_Mutation	SNP	C	T	T	rs113699218	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:64601793C>T	uc003dmg.2	-	20	2899	c.2867G>A	c.(2866-2868)CGC>CAC	p.R956H	ADAMTS9_uc011bfo.1_Missense_Mutation_p.R928H|ADAMTS9_uc003dmh.1_Missense_Mutation_p.R785H|ADAMTS9_uc003dmk.1_Missense_Mutation_p.R956H|ADAMTS9_uc011bfp.1_5'UTR	NM_182920	NP_891550	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1	956	TSP type-1 3.				glycoprotein catabolic process|multicellular organismal development|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|urinary_tract(1)|skin(1)	4		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)														---	---	---	---
MAGI1	9223	broad.mit.edu	37	3	65344795	65344795	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:65344795T>C	uc003dmn.2	-						MAGI1_uc003dmm.2_Missense_Mutation_p.R1251G	NM_001033057	NP_001028229			membrane associated guanylate kinase, WW and PDZ						cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly	tight junction	ATP binding|protein C-terminus binding			lung(2)|skin(1)|breast(1)|kidney(1)|pancreas(1)	6		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)														---	---	---	---
TMF1	7110	broad.mit.edu	37	3	69097211	69097211	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69097211C>T	uc003dnn.2	-	2	892	c.645G>A	c.(643-645)ACG>ACA	p.T215T	TMF1_uc011bfx.1_Silent_p.T215T	NM_007114	NP_009045	P82094	TMF1_HUMAN	TATA element modulatory factor 1	215					regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	Golgi membrane|nucleus	DNA binding|protein binding|transcription cofactor activity				0		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;4.48e-05)|Epithelial(33;0.000274)|LUSC - Lung squamous cell carcinoma(21;0.0123)|KIRC - Kidney renal clear cell carcinoma(39;0.211)|Kidney(39;0.247)														---	---	---	---
FRMD4B	23150	broad.mit.edu	37	3	69231758	69231758	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69231758C>A	uc003dnv.2	-	20	2320	c.2030G>T	c.(2029-2031)AGC>ATC	p.S677I	FRMD4B_uc003dnw.2_Intron|FRMD4B_uc003dnu.2_Missense_Mutation_p.S329I|FRMD4B_uc011bga.1_Missense_Mutation_p.S521I	NM_015123	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B	677						cytoplasm|cytoskeleton	binding			ovary(3)|central_nervous_system(1)	4		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)														---	---	---	---
FOXP1	27086	broad.mit.edu	37	3	71247446	71247446	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:71247446G>A	uc003dol.2	-	2	410	c.87C>T	c.(85-87)TGC>TGT	p.C29C	FOXP1_uc003dom.2_Silent_p.C29C|FOXP1_uc003don.2_RNA|FOXP1_uc003doo.2_Silent_p.C29C|FOXP1_uc003dop.2_Silent_p.C29C|FOXP1_uc003doq.1_Silent_p.C29C|FOXP1_uc003dos.2_Silent_p.C29C	NM_032682	NP_116071	Q9H334	FOXP1_HUMAN	forkhead box P1 isoform 1	29					cardiac muscle cell differentiation|embryo development|immunoglobulin V(D)J recombination|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of immunoglobulin production|positive regulation of mesenchymal cell proliferation|pre-B cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|skeletal muscle tissue development|smooth muscle tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)				T	PAX5	ALL								---	---	---	---
CNTN3	5067	broad.mit.edu	37	3	74414809	74414809	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:74414809C>T	uc003dpm.1	-	8	1071	c.991G>A	c.(991-993)GTG>ATG	p.V331M		NM_020872	NP_065923	Q9P232	CNTN3_HUMAN	contactin 3 precursor	331	Ig-like C2-type 4.				cell adhesion	anchored to membrane|plasma membrane	protein binding			breast(3)|ovary(1)|skin(1)	5		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)														---	---	---	---
ROBO2	6092	broad.mit.edu	37	3	77607109	77607109	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:77607109C>T	uc003dpy.3	+	9	1889	c.1246C>T	c.(1246-1248)CCT>TCT	p.P416S	ROBO2_uc003dpz.2_Missense_Mutation_p.P420S|ROBO2_uc011bgj.1_RNA|ROBO2_uc011bgk.1_Missense_Mutation_p.P420S	NM_002942	NP_002933	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2	416	Extracellular (Potential).				apoptosis involved in luteolysis|axon midline choice point recognition|cellular response to hormone stimulus|homophilic cell adhesion|metanephros development|negative regulation of negative chemotaxis|negative regulation of synaptogenesis|olfactory bulb interneuron development|positive regulation of axonogenesis|retinal ganglion cell axon guidance|ureteric bud development	axolemma|cell surface|integral to membrane	axon guidance receptor activity|identical protein binding			lung(5)|skin(3)|ovary(1)|large_intestine(1)|liver(1)	11				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)														---	---	---	---
ROBO2	6092	broad.mit.edu	37	3	77644344	77644344	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:77644344C>T	uc003dpy.3	+						ROBO2_uc003dpz.2_Intron|ROBO2_uc011bgj.1_Intron|ROBO2_uc011bgk.1_Intron|ROBO2_uc003dqa.2_Intron	NM_002942	NP_002933			roundabout, axon guidance receptor, homolog 2						apoptosis involved in luteolysis|axon midline choice point recognition|cellular response to hormone stimulus|homophilic cell adhesion|metanephros development|negative regulation of negative chemotaxis|negative regulation of synaptogenesis|olfactory bulb interneuron development|positive regulation of axonogenesis|retinal ganglion cell axon guidance|ureteric bud development	axolemma|cell surface|integral to membrane	axon guidance receptor activity|identical protein binding			lung(5)|skin(3)|ovary(1)|large_intestine(1)|liver(1)	11				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)														---	---	---	---
GBE1	2632	broad.mit.edu	37	3	81630359	81630359	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:81630359C>T	uc003dqg.2	-	12	1686	c.1403G>A	c.(1402-1404)CGC>CAC	p.R468H	GBE1_uc011bgm.1_Missense_Mutation_p.R427H	NM_000158	NP_000149	Q04446	GLGB_HUMAN	glucan (1,4-alpha-), branching enzyme 1	468					glucose metabolic process|glycogen biosynthetic process	cytosol	1,4-alpha-glucan branching enzyme activity|cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			ovary(3)	3		Lung NSC(201;0.0117)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0654)|Epithelial(33;0.00305)|LUSC - Lung squamous cell carcinoma(29;0.00646)|BRCA - Breast invasive adenocarcinoma(55;0.00813)|Lung(72;0.0129)|KIRC - Kidney renal clear cell carcinoma(39;0.212)|Kidney(39;0.247)										Glycogen_Storage_Disease_type_IV				---	---	---	---
CADM2	253559	broad.mit.edu	37	3	86115859	86115859	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:86115859G>A	uc003dqj.2	+	10	1860	c.1234G>A	c.(1234-1236)GAT>AAT	p.D412N	CADM2_uc003dqk.2_Missense_Mutation_p.D381N|CADM2_uc003dql.2_Missense_Mutation_p.D414N|uc003dqm.1_5'Flank	NM_153184	NP_694854	Q8N3J6	CADM2_HUMAN	immunoglobulin superfamily, member 4D	412	Cytoplasmic (Potential).				adherens junction organization|cell junction assembly	integral to membrane|plasma membrane				ovary(1)|lung(1)|kidney(1)|skin(1)	4		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)														---	---	---	---
EPHA3	2042	broad.mit.edu	37	3	89498424	89498424	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:89498424G>A	uc003dqy.2	+	14	2621	c.2396G>A	c.(2395-2397)CGC>CAC	p.R799H	EPHA3_uc010hon.1_RNA	NM_005233	NP_005224	P29320	EPHA3_HUMAN	ephrin receptor EphA3 isoform a precursor	799	Cytoplasmic (Potential).|Protein kinase.					extracellular region|integral to plasma membrane	ATP binding			lung(17)|ovary(7)|large_intestine(4)|central_nervous_system(2)|stomach(1)|skin(1)|pancreas(1)	33	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)											TSP Lung(6;0.00050)			---	---	---	---
EPHA6	285220	broad.mit.edu	37	3	96706499	96706499	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:96706499G>A	uc010how.1	+	3	819	c.776G>A	c.(775-777)CGC>CAC	p.R259H	EPHA6_uc003drp.1_Missense_Mutation_p.R259H	NM_001080448	NP_001073917	Q9UF33	EPHA6_HUMAN	EPH receptor A6 isoform a	164	Ephrin-binding.|Extracellular (Potential).					integral to plasma membrane	ATP binding|ephrin receptor activity			stomach(5)|lung(4)|central_nervous_system(3)|breast(1)|skin(1)|ovary(1)|kidney(1)	16																		---	---	---	---
MINA	84864	broad.mit.edu	37	3	97677938	97677938	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97677938G>A	uc003drz.1	-	4	1144	c.638C>T	c.(637-639)GCC>GTC	p.A213V	MINA_uc003dsa.1_Missense_Mutation_p.A213V|MINA_uc003dsb.1_Missense_Mutation_p.A213V|MINA_uc003dsc.1_Missense_Mutation_p.A213V|MINA_uc010hpa.1_RNA|MINA_uc010hpb.1_RNA	NM_001042533	NP_001035998	Q8IUF8	MINA_HUMAN	MYC induced nuclear antigen isoform a	213	JmjC.				ribosome biogenesis	cytoplasm|nucleolus				ovary(1)	1																		---	---	---	---
MINA	84864	broad.mit.edu	37	3	97680454	97680454	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97680454C>T	uc003drz.1	-	3	1037	c.531G>A	c.(529-531)CCG>CCA	p.P177P	MINA_uc003dsa.1_Silent_p.P177P|MINA_uc003dsb.1_Silent_p.P177P|MINA_uc003dsc.1_Silent_p.P177P|MINA_uc010hpa.1_RNA|MINA_uc010hpb.1_RNA	NM_001042533	NP_001035998	Q8IUF8	MINA_HUMAN	MYC induced nuclear antigen isoform a	177	JmjC.				ribosome biogenesis	cytoplasm|nucleolus				ovary(1)	1																		---	---	---	---
OR5AC2	81050	broad.mit.edu	37	3	97806217	97806217	+	Silent	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:97806217T>G	uc011bgs.1	+	1	201	c.201T>G	c.(199-201)GGT>GGG	p.G67G		NM_054106	NP_473447	Q9NZP5	O5AC2_HUMAN	olfactory receptor, family 5, subfamily AC,	67	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1																		---	---	---	---
OR5K3	403277	broad.mit.edu	37	3	98110010	98110010	+	Silent	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:98110010T>G	uc011bgw.1	+	1	501	c.501T>G	c.(499-501)ACT>ACG	p.T167T		NM_001005516	NP_001005516	A6NET4	OR5K3_HUMAN	olfactory receptor, family 5, subfamily K,	167	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0																		---	---	---	---
IMPG2	50939	broad.mit.edu	37	3	100948378	100948378	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:100948378T>C	uc003duq.1	-	17	3682	c.3479A>G	c.(3478-3480)AAC>AGC	p.N1160S	IMPG2_uc011bhe.1_Missense_Mutation_p.N1023S|IMPG2_uc010hpj.1_RNA	NM_016247	NP_057331	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2	1160	Cytoplasmic (Potential).				visual perception	integral to membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|heparin binding|hyaluronic acid binding|receptor activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3																		---	---	---	---
BBX	56987	broad.mit.edu	37	3	107466825	107466825	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:107466825C>T	uc010hpr.2	+	9	1091	c.764C>T	c.(763-765)ACG>ATG	p.T255M	BBX_uc003dwk.3_Missense_Mutation_p.T255M|BBX_uc003dwl.3_Missense_Mutation_p.T255M|BBX_uc010hps.1_Missense_Mutation_p.T276M|BBX_uc003dwm.3_Missense_Mutation_p.T255M	NM_001142568	NP_001136040	Q8WY36	BBX_HUMAN	HMG-BOX transcription factor BBX isoform 1	255					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(3)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(3;0.112)															---	---	---	---
MYH15	22989	broad.mit.edu	37	3	108156511	108156511	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108156511T>C	uc003dxa.1	-	26	3228	c.3171A>G	c.(3169-3171)AGA>AGG	p.R1057R		NM_014981	NP_055796	Q9Y2K3	MYH15_HUMAN	myosin, heavy polypeptide 15	1057	Potential.					myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(5)|central_nervous_system(2)	7																		---	---	---	---
DZIP3	9666	broad.mit.edu	37	3	108373155	108373155	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:108373155C>A	uc003dxd.2	+	19	2619	c.2197C>A	c.(2197-2199)CAG>AAG	p.Q733K	DZIP3_uc003dxf.1_Missense_Mutation_p.Q733K|DZIP3_uc011bhm.1_Missense_Mutation_p.Q184K|DZIP3_uc003dxg.1_Missense_Mutation_p.Q456K	NM_014648	NP_055463	Q86Y13	DZIP3_HUMAN	DAZ interacting protein 3, zinc finger	733					protein polyubiquitination	cytoplasm	polyubiquitin binding|RNA binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
CD96	10225	broad.mit.edu	37	3	111366423	111366423	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111366423C>T	uc003dxw.2	+	14	1729	c.1559C>T	c.(1558-1560)TCC>TTC	p.S520F	CD96_uc003dxx.2_Missense_Mutation_p.S504F|CD96_uc010hpy.1_Missense_Mutation_p.S503F	NM_198196	NP_937839	P40200	TACT_HUMAN	CD96 antigen isoform 1 precursor	520	Helical; (Potential).				cell adhesion|immune response|regulation of immune response	integral to plasma membrane				skin(2)|central_nervous_system(1)	3														Opitz_Trigonocephaly_syndrome				---	---	---	---
PHLDB2	90102	broad.mit.edu	37	3	111632332	111632332	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:111632332G>A	uc010hqa.2	+	3	1913	c.1502G>A	c.(1501-1503)AGC>AAC	p.S501N	PHLDB2_uc003dyc.2_Missense_Mutation_p.S528N|PHLDB2_uc003dyd.2_Missense_Mutation_p.S501N|PHLDB2_uc003dyg.2_Missense_Mutation_p.S501N|PHLDB2_uc003dyh.2_Missense_Mutation_p.S501N|PHLDB2_uc003dyi.2_Missense_Mutation_p.S87N|PHLDB2_uc003dyf.3_Missense_Mutation_p.S501N	NM_001134438	NP_001127910	Q86SQ0	PHLB2_HUMAN	pleckstrin homology-like domain, family B,	501						cytoplasm|intermediate filament cytoskeleton|plasma membrane				ovary(4)|skin(2)	6																		---	---	---	---
BTLA	151888	broad.mit.edu	37	3	112198473	112198473	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112198473T>C	uc003dza.3	-	2	435	c.232A>G	c.(232-234)ACA>GCA	p.T78A	BTLA_uc003dzb.3_Missense_Mutation_p.T78A	NM_181780	NP_861445	Q7Z6A9	BTLA_HUMAN	B and T lymphocyte associated isoform 1	78	Ig-like V-type.|Extracellular (Potential).				T cell costimulation		receptor activity				0		Acute lymphoblastic leukemia(4;1.34e-07)|all_hematologic(4;0.000361)																---	---	---	---
CD200R1L	344807	broad.mit.edu	37	3	112546512	112546512	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112546512T>C	uc003dzi.1	-	3	358	c.132A>G	c.(130-132)GTA>GTG	p.V44V	CD200R1L_uc011bhw.1_Silent_p.V23V|CD200R1L_uc010hqf.1_Silent_p.V23V	NM_001008784	NP_001008784	Q6Q8B3	MO2R2_HUMAN	CD200 cell surface glycoprotein receptor 2	44	Extracellular (Potential).					integral to membrane	receptor activity			ovary(1)	1																		---	---	---	---
CD200R1	131450	broad.mit.edu	37	3	112647777	112647777	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112647777C>A	uc003dzk.1	-	4	819	c.586G>T	c.(586-588)GGC>TGC	p.G196C	CD200R1_uc003dzj.1_Missense_Mutation_p.G219C|CD200R1_uc011bhx.1_Missense_Mutation_p.G174C|CD200R1_uc003dzl.1_3'UTR|CD200R1_uc003dzm.1_3'UTR	NM_170780	NP_740750	Q8TD46	MO2R1_HUMAN	CD200 receptor 1 isoform d	196	Ig-like C2-type.|Extracellular (Potential).				interspecies interaction between organisms|regulation of immune response	extracellular region|integral to membrane|plasma membrane	receptor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
BOC	91653	broad.mit.edu	37	3	112999891	112999891	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:112999891G>A	uc003dzx.2	+	15	2943	c.2322G>A	c.(2320-2322)TGG>TGA	p.W774*	BOC_uc003dzy.2_Nonsense_Mutation_p.W774*|BOC_uc003dzz.2_Nonsense_Mutation_p.W775*|BOC_uc003eab.2_Nonsense_Mutation_p.W475*|BOC_uc003eac.2_Nonsense_Mutation_p.W89*	NM_033254	NP_150279	Q9BWV1	BOC_HUMAN	brother of CDO precursor	774	Fibronectin type-III 3.|Extracellular (Potential).				cell adhesion|muscle cell differentiation|positive regulation of myoblast differentiation	integral to membrane|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|pancreas(1)	6			Epithelial(53;0.227)															---	---	---	---
BOC	91653	broad.mit.edu	37	3	113005674	113005674	+	Missense_Mutation	SNP	C	T	T	rs145326895		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113005674C>T	uc003dzx.2	+	20	3931	c.3310C>T	c.(3310-3312)CGT>TGT	p.R1104C	BOC_uc003dzy.2_Missense_Mutation_p.R1104C|BOC_uc003dzz.2_Missense_Mutation_p.R1105C|BOC_uc003eab.2_Missense_Mutation_p.R805C|BOC_uc003eac.2_Intron	NM_033254	NP_150279	Q9BWV1	BOC_HUMAN	brother of CDO precursor	1104	Cytoplasmic (Potential).				cell adhesion|muscle cell differentiation|positive regulation of myoblast differentiation	integral to membrane|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|pancreas(1)	6			Epithelial(53;0.227)															---	---	---	---
CCDC52	152185	broad.mit.edu	37	3	113179611	113179611	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113179611C>T	uc003eag.3	-	12	1579	c.1288G>A	c.(1288-1290)GCA>ACA	p.A430T	CCDC52_uc003eaf.3_RNA|CCDC52_uc003eah.1_Missense_Mutation_p.A326T	NM_144718	NP_653319	Q8N0Z3	SPICE_HUMAN	coiled-coil domain containing 52	430	Potential.				cell division|mitosis	centriole|spindle	protein binding				0																		---	---	---	---
KIAA2018	205717	broad.mit.edu	37	3	113374769	113374769	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113374769G>T	uc003eam.2	-	7	6171	c.5760C>A	c.(5758-5760)TCC>TCA	p.S1920S	KIAA2018_uc003eal.2_Silent_p.S1864S	NM_001009899	NP_001009899	Q68DE3	K2018_HUMAN	hypothetical protein LOC205717	1920					regulation of transcription, DNA-dependent	membrane|nucleus	calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity			skin(2)|ovary(1)	3																		---	---	---	---
GRAMD1C	54762	broad.mit.edu	37	3	113563441	113563441	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113563441T>C	uc003eaq.3	+	2	195	c.119T>C	c.(118-120)GTA>GCA	p.V40A	GRAMD1C_uc011bil.1_RNA|GRAMD1C_uc011bim.1_RNA	NM_017577	NP_060047	Q8IYS0	GRM1C_HUMAN	GRAM domain containing 1C	40						integral to membrane				ovary(2)|skin(1)	3																		---	---	---	---
GRAMD1C	54762	broad.mit.edu	37	3	113653365	113653365	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113653365A>G	uc003eaq.3	+	13	1515	c.1439A>G	c.(1438-1440)GAC>GGC	p.D480G	GRAMD1C_uc011bil.1_RNA|GRAMD1C_uc011bim.1_RNA|GRAMD1C_uc003ear.2_Missense_Mutation_p.D313G|GRAMD1C_uc003eas.2_Missense_Mutation_p.D275G|GRAMD1C_uc003eat.2_Missense_Mutation_p.D139G	NM_017577	NP_060047	Q8IYS0	GRM1C_HUMAN	GRAM domain containing 1C	480						integral to membrane				ovary(2)|skin(1)	3																		---	---	---	---
ZDHHC23	254887	broad.mit.edu	37	3	113677337	113677337	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113677337C>T	uc003eau.2	+	5	1467	c.1168C>T	c.(1168-1170)CGA>TGA	p.R390*	ZDHHC23_uc003eav.2_Nonsense_Mutation_p.R384*|ZDHHC23_uc003eaw.1_Nonsense_Mutation_p.R84*	NM_173570	NP_775841	Q8IYP9	ZDH23_HUMAN	zinc finger, DHHC domain containing 23	390						integral to membrane	acyltransferase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
KIAA1407	57577	broad.mit.edu	37	3	113729805	113729805	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:113729805C>T	uc003eax.2	-	9	1374	c.1227G>A	c.(1225-1227)TGG>TGA	p.W409*	KIAA1407_uc011bin.1_RNA|KIAA1407_uc011bio.1_Nonsense_Mutation_p.W387*|KIAA1407_uc011bip.1_Nonsense_Mutation_p.W396*	NM_020817	NP_065868	Q8NCU4	K1407_HUMAN	hypothetical protein LOC57577	409	Potential.									ovary(2)	2																		---	---	---	---
ZBTB20	26137	broad.mit.edu	37	3	114069533	114069533	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:114069533C>T	uc003ebi.2	-	4	1572	c.1392G>A	c.(1390-1392)ACG>ACA	p.T464T	ZBTB20_uc003ebj.2_Silent_p.T391T|ZBTB20_uc010hqp.2_Silent_p.T391T|ZBTB20_uc003ebk.2_Silent_p.T391T|ZBTB20_uc003ebl.2_Silent_p.T391T|ZBTB20_uc003ebm.2_Silent_p.T391T|ZBTB20_uc003ebn.2_Silent_p.T391T|uc003ebo.1_5'Flank	NM_015642	NP_056457	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20 isoform	464					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)														---	---	---	---
ARHGAP31	57514	broad.mit.edu	37	3	119112364	119112364	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119112364G>T	uc003ecj.3	+	8	1464	c.932G>T	c.(931-933)GGA>GTA	p.G311V		NM_020754	NP_065805	Q2M1Z3	RHG31_HUMAN	Cdc42 GTPase-activating protein	311					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|focal adhesion|lamellipodium	GTPase activator activity			ovary(2)	2																		---	---	---	---
C3orf15	89876	broad.mit.edu	37	3	119452254	119452254	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119452254A>C	uc003ede.3	+	10	1322	c.1245A>C	c.(1243-1245)CAA>CAC	p.Q415H	C3orf15_uc010hqy.1_Missense_Mutation_p.Q415H|C3orf15_uc010hqz.2_Missense_Mutation_p.Q353H|C3orf15_uc011bjd.1_Missense_Mutation_p.Q289H|C3orf15_uc011bje.1_Missense_Mutation_p.Q395H|C3orf15_uc010hra.1_Missense_Mutation_p.Q176H	NM_033364	NP_203528	Q7Z4T9	AAT1_HUMAN	AAT1-alpha	Error:Variant_position_missing_in_Q7Z4T9_after_alignment						mitochondrion	protein binding			ovary(2)|pancreas(1)	3				GBM - Glioblastoma multiforme(114;0.186)														---	---	---	---
HGD	3081	broad.mit.edu	37	3	120363214	120363214	+	Silent	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120363214A>C	uc003edw.2	-	10	1096	c.726T>G	c.(724-726)GGT>GGG	p.G242G	HGD_uc003edv.2_Silent_p.G101G	NM_000187	NP_000178	Q93099	HGD_HUMAN	homogentisate 1,2-dioxygenase	242					L-phenylalanine catabolic process|tyrosine catabolic process	cytosol	homogentisate 1,2-dioxygenase activity|metal ion binding				0				GBM - Glioblastoma multiforme(114;0.158)														---	---	---	---
STXBP5L	9515	broad.mit.edu	37	3	120973872	120973872	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:120973872A>G	uc003eec.3	+	16	1712	c.1572A>G	c.(1570-1572)CCA>CCG	p.P524P	STXBP5L_uc011bji.1_Silent_p.P524P	NM_014980	NP_055795	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	524	WD 9.				exocytosis|protein transport	cytoplasm|integral to membrane|plasma membrane				ovary(7)|skin(2)	9				GBM - Glioblastoma multiforme(114;0.0694)														---	---	---	---
GOLGB1	2804	broad.mit.edu	37	3	121383825	121383825	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121383825C>T	uc003eei.3	-	21	9719	c.9593G>A	c.(9592-9594)GGC>GAC	p.G3198D	GOLGB1_uc010hrc.2_Missense_Mutation_p.G3208D|GOLGB1_uc003eej.3_Missense_Mutation_p.G3164D	NM_004487	NP_004478	Q14789	GOGB1_HUMAN	golgi autoantigen, golgin subfamily b,	3198	Cytoplasmic (Potential).				Golgi organization	ER-Golgi intermediate compartment|Golgi membrane|Golgi stack|integral to membrane	protein binding			ovary(6)|breast(2)|skin(2)	10				GBM - Glioblastoma multiforme(114;0.0989)														---	---	---	---
GOLGB1	2804	broad.mit.edu	37	3	121415587	121415587	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121415587C>T	uc003eei.3	-	13	3894	c.3768G>A	c.(3766-3768)TCG>TCA	p.S1256S	GOLGB1_uc010hrc.2_Silent_p.S1261S|GOLGB1_uc003eej.3_Silent_p.S1222S|GOLGB1_uc011bjm.1_Silent_p.S1142S|GOLGB1_uc010hrd.1_Silent_p.S1220S	NM_004487	NP_004478	Q14789	GOGB1_HUMAN	golgi autoantigen, golgin subfamily b,	1256	Cytoplasmic (Potential).				Golgi organization	ER-Golgi intermediate compartment|Golgi membrane|Golgi stack|integral to membrane	protein binding			ovary(6)|breast(2)|skin(2)	10				GBM - Glioblastoma multiforme(114;0.0989)														---	---	---	---
PARP15	165631	broad.mit.edu	37	3	122354874	122354874	+	Missense_Mutation	SNP	G	A	A	rs146577543	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122354874G>A	uc003efm.2	+	12	2030	c.1964G>A	c.(1963-1965)CGA>CAA	p.R655Q	PARP15_uc003efn.2_Missense_Mutation_p.R460Q|PARP15_uc003efo.1_Missense_Mutation_p.R402Q|PARP15_uc003efp.1_Missense_Mutation_p.R421Q|PARP15_uc011bjt.1_Missense_Mutation_p.R352Q	NM_001113523	NP_001106995	Q460N3	PAR15_HUMAN	poly (ADP-ribose) polymerase family, member 15	633	PARP catalytic.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	NAD+ ADP-ribosyltransferase activity			lung(3)|upper_aerodigestive_tract(1)|ovary(1)	5				GBM - Glioblastoma multiforme(114;0.0531)														---	---	---	---
PARP14	54625	broad.mit.edu	37	3	122419980	122419980	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:122419980T>C	uc003efq.3	+	6	2638	c.2579T>C	c.(2578-2580)CTA>CCA	p.L860P	PARP14_uc010hrk.2_RNA|PARP14_uc003efr.2_Missense_Mutation_p.L577P|PARP14_uc003efs.1_Missense_Mutation_p.L577P	NM_017554	NP_060024	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	860	Macro 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	NAD+ ADP-ribosyltransferase activity			ovary(2)|breast(2)|lung(1)|pancreas(1)	6				GBM - Glioblastoma multiforme(114;0.0531)														---	---	---	---
MYLK	4638	broad.mit.edu	37	3	123345699	123345699	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123345699C>T	uc003ego.2	-	31	5486	c.5204G>A	c.(5203-5205)CGG>CAG	p.R1735Q	uc003egk.2_Intron|MYLK_uc010hrr.2_Missense_Mutation_p.R170Q|MYLK_uc011bjv.1_Missense_Mutation_p.R535Q|MYLK_uc011bjw.1_Missense_Mutation_p.R1735Q|MYLK_uc003egp.2_Missense_Mutation_p.R1666Q|MYLK_uc003egq.2_Missense_Mutation_p.R1684Q|MYLK_uc003egr.2_Missense_Mutation_p.R1615Q|MYLK_uc003egs.2_Missense_Mutation_p.R1559Q	NM_053025	NP_444253	Q15746	MYLK_HUMAN	myosin light chain kinase isoform 1	1735	Calmodulin-binding.				aorta smooth muscle tissue morphogenesis|muscle contraction	cytosol	actin binding|ATP binding|calmodulin binding|metal ion binding|myosin light chain kinase activity			ovary(6)|skin(2)|stomach(1)	9		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)														---	---	---	---
MYLK	4638	broad.mit.edu	37	3	123419357	123419357	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123419357A>G	uc003ego.2	-	18	3240	c.2958T>C	c.(2956-2958)GGT>GGC	p.G986G	MYLK_uc011bjw.1_Silent_p.G986G|MYLK_uc003egp.2_Silent_p.G917G|MYLK_uc003egq.2_Silent_p.G986G|MYLK_uc003egr.2_Silent_p.G917G|MYLK_uc003egs.2_Silent_p.G810G|MYLK_uc003egt.2_Silent_p.G177G	NM_053025	NP_444253	Q15746	MYLK_HUMAN	myosin light chain kinase isoform 1	986	1-5; truncated.|5 X 28 AA approximate tandem repeats.				aorta smooth muscle tissue morphogenesis|muscle contraction	cytosol	actin binding|ATP binding|calmodulin binding|metal ion binding|myosin light chain kinase activity			ovary(6)|skin(2)|stomach(1)	9		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)														---	---	---	---
MYLK	4638	broad.mit.edu	37	3	123452995	123452995	+	Missense_Mutation	SNP	G	A	A	rs150096018		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123452995G>A	uc003ego.2	-	10	1130	c.848C>T	c.(847-849)TCG>TTG	p.S283L	MYLK_uc011bjw.1_Missense_Mutation_p.S283L|MYLK_uc003egp.2_Missense_Mutation_p.S283L|MYLK_uc003egq.2_Missense_Mutation_p.S283L|MYLK_uc003egr.2_Missense_Mutation_p.S283L|MYLK_uc003egs.2_Missense_Mutation_p.S107L	NM_053025	NP_444253	Q15746	MYLK_HUMAN	myosin light chain kinase isoform 1	283					aorta smooth muscle tissue morphogenesis|muscle contraction	cytosol	actin binding|ATP binding|calmodulin binding|metal ion binding|myosin light chain kinase activity			ovary(6)|skin(2)|stomach(1)	9		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)														---	---	---	---
KALRN	8997	broad.mit.edu	37	3	123983454	123983454	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:123983454A>G	uc003ehg.2	+	4	494	c.367A>G	c.(367-369)ATC>GTC	p.I123V	KALRN_uc010hrv.1_Missense_Mutation_p.I123V|KALRN_uc003ehf.1_Missense_Mutation_p.I123V|KALRN_uc011bjy.1_Missense_Mutation_p.I123V	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1	123	CRAL-TRIO.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
KALRN	8997	broad.mit.edu	37	3	124053259	124053259	+	Missense_Mutation	SNP	C	T	T	rs147539685		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124053259C>T	uc003ehg.2	+	9	1685	c.1558C>T	c.(1558-1560)CGG>TGG	p.R520W	KALRN_uc010hrv.1_Missense_Mutation_p.R520W|KALRN_uc003ehf.1_Missense_Mutation_p.R520W|KALRN_uc011bjy.1_Missense_Mutation_p.R520W	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1	520					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
KALRN	8997	broad.mit.edu	37	3	124351409	124351409	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124351409T>C	uc003ehg.2	+	35	5446	c.5319T>C	c.(5317-5319)AGT>AGC	p.S1773S	KALRN_uc003ehi.2_Silent_p.S146S|KALRN_uc003ehk.2_Silent_p.S76S|KALRN_uc003ehj.2_Silent_p.S76S	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1	1773					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
ITGB5	3693	broad.mit.edu	37	3	124536564	124536564	+	Intron	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124536564A>T	uc003eho.2	-						ITGB5_uc010hrx.2_5'Flank	NM_002213	NP_002204			integrin, beta 5 precursor						cell-matrix adhesion|integrin-mediated signaling pathway|multicellular organismal development|muscle contraction	integrin complex	receptor activity			skin(2)	2				GBM - Glioblastoma multiforme(114;0.163)														---	---	---	---
SLC12A8	84561	broad.mit.edu	37	3	124810303	124810303	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124810303G>A	uc003ehv.3	-	12	2012	c.1901C>T	c.(1900-1902)GCC>GTC	p.A634V	SLC12A8_uc003ehw.3_Missense_Mutation_p.A663V|SLC12A8_uc003eht.3_Missense_Mutation_p.A435V|SLC12A8_uc003ehu.3_Missense_Mutation_p.A387V|SLC12A8_uc010hry.2_Intron	NM_024628	NP_078904	A0AV02	S12A8_HUMAN	solute carrier family 12, member 8	634	Helical; (Potential).				potassium ion transport	integral to membrane	symporter activity				0																		---	---	---	---
SLC12A8	84561	broad.mit.edu	37	3	124896650	124896650	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124896650G>A	uc003ehv.3	-	5	670	c.559C>T	c.(559-561)CTG>TTG	p.L187L	SLC12A8_uc003ehw.3_Silent_p.L216L|SLC12A8_uc010hrz.1_Silent_p.L52L	NM_024628	NP_078904	A0AV02	S12A8_HUMAN	solute carrier family 12, member 8	187	Helical; (Potential).				potassium ion transport	integral to membrane	symporter activity				0																		---	---	---	---
SLC12A8	84561	broad.mit.edu	37	3	124909310	124909310	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:124909310G>T	uc003ehv.3	-	3	218	c.107C>A	c.(106-108)CCT>CAT	p.P36H	SLC12A8_uc003ehw.3_Missense_Mutation_p.P65H|SLC12A8_uc010hrz.1_Translation_Start_Site	NM_024628	NP_078904	A0AV02	S12A8_HUMAN	solute carrier family 12, member 8	36					potassium ion transport	integral to membrane	symporter activity				0																		---	---	---	---
ALDH1L1	10840	broad.mit.edu	37	3	125874283	125874283	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:125874283C>T	uc003eim.1	-	5	782	c.592G>A	c.(592-594)GCC>ACC	p.A198T	ALDH1L1_uc010hse.1_RNA|ALDH1L1_uc011bki.1_Intron|ALDH1L1_uc003eio.2_5'UTR|ALDH1L1_uc010hsf.1_Missense_Mutation_p.A224T|ALDH1L1_uc003eip.1_Missense_Mutation_p.A105T|ALDH1L1_uc011bkj.1_Missense_Mutation_p.A23T	NM_012190	NP_036322	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	198	GART.				10-formyltetrahydrofolate catabolic process|biosynthetic process		acyl carrier activity|cofactor binding|formyltetrahydrofolate dehydrogenase activity|hydroxymethyl-, formyl- and related transferase activity|methyltransferase activity			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4				GBM - Glioblastoma multiforme(114;0.0462)	Tetrahydrofolic acid(DB00116)													---	---	---	---
ZXDC	79364	broad.mit.edu	37	3	126180639	126180639	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126180639G>A	uc003eiv.2	-	6	1920	c.1866C>T	c.(1864-1866)GAC>GAT	p.D622D	ZXDC_uc010hsh.2_RNA|ZXDC_uc003eix.2_Silent_p.D622D	NM_025112	NP_079388	Q2QGD7	ZXDC_HUMAN	ZXD family zinc finger C isoform 1	622	Required for transcriptional activation.				positive regulation of transcription, DNA-dependent	nucleus	C2H2 zinc finger domain binding|identical protein binding|LRR domain binding|nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.155)														---	---	---	---
ZXDC	79364	broad.mit.edu	37	3	126180739	126180739	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126180739G>A	uc003eiv.2	-	6	1820	c.1766C>T	c.(1765-1767)ACG>ATG	p.T589M	ZXDC_uc010hsh.2_RNA|ZXDC_uc003eix.2_Missense_Mutation_p.T589M	NM_025112	NP_079388	Q2QGD7	ZXDC_HUMAN	ZXD family zinc finger C isoform 1	589	Required for transcriptional activation.				positive regulation of transcription, DNA-dependent	nucleus	C2H2 zinc finger domain binding|identical protein binding|LRR domain binding|nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.155)														---	---	---	---
PLXNA1	5361	broad.mit.edu	37	3	126751643	126751643	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126751643C>T	uc003ejg.2	+	30	5494	c.5490C>T	c.(5488-5490)CAC>CAT	p.H1830H	PLXNA1_uc003ejh.2_Silent_p.H498H	NM_032242	NP_115618	Q9UIW2	PLXA1_HUMAN	plexin A1	1853	Cytoplasmic (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane	semaphorin receptor activity			ovary(1)|pancreas(1)|skin(1)	3				GBM - Glioblastoma multiforme(114;0.155)														---	---	---	---
MCM2	4171	broad.mit.edu	37	3	127323937	127323937	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127323937G>A	uc003ejp.2	+	4	668	c.611G>A	c.(610-612)CGC>CAC	p.R204H	MCM2_uc011bkm.1_Missense_Mutation_p.R74H|MCM2_uc010hsl.2_RNA|MCM2_uc011bkn.1_Missense_Mutation_p.R88H	NM_004526	NP_004517	P49736	MCM2_HUMAN	minichromosome maintenance complex component 2	204	Interaction with MYST2 (By similarity).				cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	chromatin|MCM complex	ATP binding|helicase activity|metal ion binding			ovary(3)|skin(1)	4																		---	---	---	---
ABTB1	80325	broad.mit.edu	37	3	127396022	127396022	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127396022C>T	uc003ejt.2	+	8	743	c.655C>T	c.(655-657)CCA>TCA	p.P219S	ABTB1_uc003ejr.2_Missense_Mutation_p.P77S|ABTB1_uc003ejs.2_Missense_Mutation_p.P194S|ABTB1_uc003eju.2_Missense_Mutation_p.P77S|ABTB1_uc010hsm.2_5'UTR	NM_172027	NP_742024	Q969K4	ABTB1_HUMAN	ankyrin repeat and BTB (POZ) domain containing 1	219						cytoplasm|nucleolus|plasma membrane	translation elongation factor activity				0																		---	---	---	---
SEC61A1	29927	broad.mit.edu	37	3	127783794	127783794	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127783794C>A	uc003ekb.2	+	8	875	c.691C>A	c.(691-693)CGG>AGG	p.R231R	RUVBL1_uc003eke.2_3'UTR|RUVBL1_uc003ekf.2_3'UTR|SEC61A1_uc003ekc.2_Silent_p.R178R|SEC61A1_uc003ekd.2_Silent_p.R111R|SEC61A1_uc003ekg.2_Intron	NM_013336	NP_037468	P61619	S61A1_HUMAN	Sec61 alpha 1 subunit	231	Lumenal (Potential).				protein targeting to ER	integral to endoplasmic reticulum membrane	P-P-bond-hydrolysis-driven protein transmembrane transporter activity|protein binding|ribosome binding			ovary(1)	1																		---	---	---	---
RUVBL1	8607	broad.mit.edu	37	3	127806624	127806624	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127806624G>A	uc003ekh.2	-	9	1148	c.1044C>T	c.(1042-1044)CAC>CAT	p.H348H	RUVBL1_uc003eke.2_Intron|RUVBL1_uc003ekf.2_Silent_p.H288H|RUVBL1_uc010hss.2_Silent_p.H348H	NM_003707	NP_003698	Q9Y265	RUVB1_HUMAN	RuvB-like 1	348					cell division|CenH3-containing nucleosome assembly at centromere|DNA recombination|DNA repair|histone H2A acetylation|histone H4 acetylation|mitosis|regulation of growth|regulation of transcription from RNA polymerase II promoter|spermatogenesis|transcription, DNA-dependent	Golgi apparatus|Ino80 complex|membrane|microtubule organizing center|MLL1 complex|NuA4 histone acetyltransferase complex|nuclear matrix	ATP binding|DNA helicase activity|protein binding			skin(1)	1				GBM - Glioblastoma multiforme(114;0.181)														---	---	---	---
COPG	22820	broad.mit.edu	37	3	128990638	128990638	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128990638C>T	uc003els.2	+	19	1972	c.1872C>T	c.(1870-1872)CGC>CGT	p.R624R	COPG_uc010htb.2_Silent_p.R530R	NM_016128	NP_057212	Q9Y678	COPG_HUMAN	coatomer protein complex, subunit gamma 1	624	Interaction with ZNF289/ARFGAP2.				COPI coating of Golgi vesicle|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol	protein binding|structural molecule activity			ovary(3)|breast(1)	4																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	129137214	129137214	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129137214C>T	uc003emg.2	-	3	727	c.564G>A	c.(562-564)TCG>TCA	p.S188S		NM_207307	NP_997190			hypothetical protein LOC90288																														---	---	---	---
PLXND1	23129	broad.mit.edu	37	3	129290078	129290078	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129290078C>T	uc003emx.2	-	18	3505	c.3405G>A	c.(3403-3405)GCG>GCA	p.A1135A		NM_015103	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1 precursor	1135	Extracellular (Potential).|IPT/TIG 3.				axon guidance	integral to membrane|intracellular|plasma membrane				large_intestine(1)	1																		---	---	---	---
PLXND1	23129	broad.mit.edu	37	3	129290376	129290376	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:129290376G>A	uc003emx.2	-	17	3412	c.3312C>T	c.(3310-3312)GTC>GTT	p.V1104V		NM_015103	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1 precursor	1104	Extracellular (Potential).|IPT/TIG 3.				axon guidance	integral to membrane|intracellular|plasma membrane				large_intestine(1)	1																		---	---	---	---
COL6A6	131873	broad.mit.edu	37	3	130300549	130300549	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130300549T>A	uc010htl.2	+	8	3723	c.3692T>A	c.(3691-3693)GTG>GAG	p.V1231E	COL6A6_uc003eni.3_5'Flank	NM_001102608	NP_001096078	A6NMZ7	CO6A6_HUMAN	collagen type VI alpha 6 precursor	1231	VWFA 7.|Nonhelical region.				axon guidance|cell adhesion	collagen				ovary(6)|central_nervous_system(1)|pancreas(1)	8																		---	---	---	---
COL6A6	131873	broad.mit.edu	37	3	130329502	130329502	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130329502G>T	uc010htl.2	+	22	4793	c.4762G>T	c.(4762-4764)GGA>TGA	p.G1588*	COL6A6_uc003eni.3_Translation_Start_Site	NM_001102608	NP_001096078	A6NMZ7	CO6A6_HUMAN	collagen type VI alpha 6 precursor	1588	Triple-helical region.				axon guidance|cell adhesion	collagen				ovary(6)|central_nervous_system(1)|pancreas(1)	8																		---	---	---	---
PIK3R4	30849	broad.mit.edu	37	3	130399498	130399498	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130399498A>G	uc003enj.2	-	19	4446	c.3865T>C	c.(3865-3867)TCC>CCC	p.S1289P		NM_014602	NP_055417	Q99570	PI3R4_HUMAN	phosphoinositide-3-kinase, regulatory subunit 4	1289					fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway	cytosol	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1)	12																		---	---	---	---
PIK3R4	30849	broad.mit.edu	37	3	130452624	130452624	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:130452624A>G	uc003enj.2	-	4	1799	c.1218T>C	c.(1216-1218)GCT>GCC	p.A406A		NM_014602	NP_055417	Q99570	PI3R4_HUMAN	phosphoinositide-3-kinase, regulatory subunit 4	406					fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway	cytosol	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1)	12																		---	---	---	---
ACAD11	84129	broad.mit.edu	37	3	132297691	132297691	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132297691T>G	uc003eov.3	-	15	2103	c.1723A>C	c.(1723-1725)AAC>CAC	p.N575H	ACAD11_uc011blr.1_3'UTR	NM_032169	NP_115545	Q709F0	ACD11_HUMAN	putative acyl-CoA dehydrogenase	575						peroxisome	acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding|transferase activity, transferring phosphorus-containing groups			ovary(1)	1																		---	---	---	---
CCRL1	51554	broad.mit.edu	37	3	132320115	132320115	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:132320115G>A	uc003eow.2	+	2	957	c.874G>A	c.(874-876)GCA>ACA	p.A292T	ACAD11_uc003eov.3_Intron|ACAD11_uc011blr.1_Intron|CCRL1_uc003eox.2_Missense_Mutation_p.A292T	NM_016557	NP_057641	Q9NPB9	CCRL1_HUMAN	chemokine (C-C motif) receptor-like 1	292	Helical; Name=7; (Potential).				chemotaxis|immune response	integral to plasma membrane	C-C chemokine receptor activity				0																		---	---	---	---
TOPBP1	11073	broad.mit.edu	37	3	133363182	133363182	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133363182C>T	uc003eps.2	-	11	1662	c.1530G>A	c.(1528-1530)AGG>AGA	p.R510R		NM_007027	NP_008958	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1	510					DNA repair|response to ionizing radiation	microtubule organizing center|PML body|spindle pole	DNA binding|protein C-terminus binding			ovary(2)|kidney(2)|skin(1)|lung(1)|pancreas(1)	7													Other_conserved_DNA_damage_response_genes					---	---	---	---
C3orf36	80111	broad.mit.edu	37	3	133647205	133647205	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133647205A>G	uc003epz.1	-	1	1452	c.443T>C	c.(442-444)GTG>GCG	p.V148A		NM_025041	NP_079317	Q3SXR2	CC036_HUMAN	hypothetical protein LOC80111	148										ovary(1)	1																		---	---	---	---
Unknown	0	broad.mit.edu	37	3	133941334	133941334	+	IGR	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133941334G>A								RYK (-28252 upstream) : RYK (-65356 downstream)																																			---	---	---	---
AMOTL2	51421	broad.mit.edu	37	3	134086440	134086440	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134086440T>G	uc003eqf.2	-	3	1231	c.1114A>C	c.(1114-1116)ATG>CTG	p.M372L	AMOTL2_uc003eqg.1_Missense_Mutation_p.M314L|AMOTL2_uc003eqh.1_Missense_Mutation_p.M314L|AMOTL2_uc003eqe.1_5'Flank	NM_016201	NP_057285	Q9Y2J4	AMOL2_HUMAN	angiomotin like 2	314	Potential.									large_intestine(1)	1																		---	---	---	---
AMOTL2	51421	broad.mit.edu	37	3	134089566	134089566	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134089566G>A	uc003eqf.2	-	2	1001	c.884C>T	c.(883-885)CCG>CTG	p.P295L	AMOTL2_uc003eqg.1_Missense_Mutation_p.P237L|AMOTL2_uc003eqh.1_Missense_Mutation_p.P237L	NM_016201	NP_057285	Q9Y2J4	AMOL2_HUMAN	angiomotin like 2	237										large_intestine(1)	1																		---	---	---	---
KY	339855	broad.mit.edu	37	3	134348501	134348501	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:134348501G>A	uc010hty.2	-	4	361	c.299C>T	c.(298-300)GCC>GTC	p.A100V	KY_uc011blw.1_Missense_Mutation_p.A100V|KY_uc011blx.1_Missense_Mutation_p.A79V|KY_uc003eqs.1_Missense_Mutation_p.A120V	NM_178554	NP_848649	Q8NBH2	KY_HUMAN	kyphoscoliosis peptidase	100						cytoskeleton|Z disc	peptidase activity			ovary(2)	2																		---	---	---	---
STAG1	10274	broad.mit.edu	37	3	136141794	136141794	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136141794C>A	uc003era.1	-	17	2035	c.1743G>T	c.(1741-1743)AAG>AAT	p.K581N	STAG1_uc003erb.1_Missense_Mutation_p.K581N|STAG1_uc003erc.1_Missense_Mutation_p.K355N|STAG1_uc010hua.1_Missense_Mutation_p.K444N	NM_005862	NP_005853	Q8WVM7	STAG1_HUMAN	stromal antigen 1	581					cell division|chromosome segregation|mitotic metaphase/anaphase transition|mitotic prometaphase	cell junction|chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(2)	2																		---	---	---	---
TMEM22	80723	broad.mit.edu	37	3	136574067	136574067	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136574067C>A	uc003erf.3	+	2	979	c.765C>A	c.(763-765)GCC>GCA	p.A255A	TMEM22_uc003erg.3_Silent_p.A255A|TMEM22_uc010hub.2_Silent_p.A255A	NM_001097600	NP_001091069	Q8TBE7	TMM22_HUMAN	transmembrane protein 22	255	Helical; (Potential).					Golgi apparatus|integral to membrane				ovary(1)	1																		---	---	---	---
ARMC8	25852	broad.mit.edu	37	3	137963964	137963964	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137963964G>A	uc003esa.1	+	13	1398	c.1031G>A	c.(1030-1032)CGC>CAC	p.R344H	ARMC8_uc003erw.2_Missense_Mutation_p.R344H|ARMC8_uc003erx.2_Missense_Mutation_p.R344H|ARMC8_uc003ery.2_Missense_Mutation_p.R316H|ARMC8_uc003erz.2_Missense_Mutation_p.R316H|ARMC8_uc011bmf.1_Missense_Mutation_p.R327H|ARMC8_uc011bmg.1_Missense_Mutation_p.R291H|ARMC8_uc011bmh.1_Missense_Mutation_p.R285H|ARMC8_uc003esb.1_Missense_Mutation_p.R316H|ARMC8_uc003esc.1_Missense_Mutation_p.R116H	NM_015396	NP_056211	Q8IUR7	ARMC8_HUMAN	armadillo repeat containing 8 isoform 2	358							binding				0																		---	---	---	---
ARMC8	25852	broad.mit.edu	37	3	137964082	137964082	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:137964082G>A	uc003esa.1	+						ARMC8_uc003erw.2_Silent_p.T383T|ARMC8_uc003erx.2_Silent_p.T383T|ARMC8_uc003ery.2_Silent_p.T355T|ARMC8_uc003erz.2_Silent_p.T355T|ARMC8_uc011bmf.1_Intron|ARMC8_uc011bmg.1_Intron|ARMC8_uc011bmh.1_Intron|ARMC8_uc003esb.1_Intron|ARMC8_uc003esc.1_Intron	NM_015396	NP_056211			armadillo repeat containing 8 isoform 2								binding				0																		---	---	---	---
CLSTN2	64084	broad.mit.edu	37	3	140122554	140122554	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140122554C>A	uc003etn.2	+	3	506	c.316C>A	c.(316-318)CTC>ATC	p.L106I	CLSTN2_uc003etm.2_Missense_Mutation_p.L106I	NM_022131	NP_071414	Q9H4D0	CSTN2_HUMAN	calsyntenin 2 precursor	106	Extracellular (Potential).|Cadherin 1.				homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			skin(3)|large_intestine(2)|pancreas(1)|central_nervous_system(1)	7															HNSCC(16;0.037)			---	---	---	---
TRIM42	287015	broad.mit.edu	37	3	140401421	140401421	+	Silent	SNP	C	T	T	rs114532663	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140401421C>T	uc003eto.1	+	2	650	c.459C>T	c.(457-459)CGC>CGT	p.R153R		NM_152616	NP_689829	Q8IWZ5	TRI42_HUMAN	tripartite motif-containing 42	153	RING-type.					intracellular	zinc ion binding			lung(2)|skin(2)|upper_aerodigestive_tract(1)|breast(1)|central_nervous_system(1)	7																		---	---	---	---
TRIM42	287015	broad.mit.edu	37	3	140406909	140406909	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:140406909G>T	uc003eto.1	+	3	1576	c.1385G>T	c.(1384-1386)AGG>ATG	p.R462M		NM_152616	NP_689829	Q8IWZ5	TRI42_HUMAN	tripartite motif-containing 42	462	COS.					intracellular	zinc ion binding			lung(2)|skin(2)|upper_aerodigestive_tract(1)|breast(1)|central_nervous_system(1)	7																		---	---	---	---
PLOD2	5352	broad.mit.edu	37	3	145809605	145809605	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:145809605G>A	uc003evs.1	-	8	1367	c.861C>T	c.(859-861)GTC>GTT	p.V287V	PLOD2_uc011bnm.1_Silent_p.V232V|PLOD2_uc003evr.1_Silent_p.V287V	NM_000935	NP_000926	O00469	PLOD2_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase	287					protein modification process|response to hypoxia	rough endoplasmic reticulum membrane	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-lysine 5-dioxygenase activity|protein binding			ovary(1)|skin(1)	2					Vitamin C(DB00126)													---	---	---	---
PLSCR2	57047	broad.mit.edu	37	3	146167085	146167085	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:146167085C>T	uc003evv.1	-	7	886	c.553G>A	c.(553-555)GCA>ACA	p.A185T	PLSCR2_uc003evw.1_Missense_Mutation_p.A254T	NM_020359	NP_065092	Q9NRY7	PLS2_HUMAN	phospholipid scramblase 2	185	Cytoplasmic (By similarity).				phospholipid scrambling	integral to membrane|plasma membrane	calcium ion binding|phospholipid scramblase activity				0																		---	---	---	---
PLSCR2	57047	broad.mit.edu	37	3	146171822	146171822	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:146171822G>A	uc003evv.1	-	6	783	c.450C>T	c.(448-450)ATC>ATT	p.I150I	PLSCR2_uc003evw.1_Silent_p.I219I	NM_020359	NP_065092	Q9NRY7	PLS2_HUMAN	phospholipid scramblase 2	150	Cytoplasmic (By similarity).				phospholipid scrambling	integral to membrane|plasma membrane	calcium ion binding|phospholipid scramblase activity				0																		---	---	---	---
GPR87	53836	broad.mit.edu	37	3	151012504	151012504	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151012504A>G	uc003eyt.2	-	3	891	c.530T>C	c.(529-531)ATC>ACC	p.I177T	MED12L_uc011bnz.1_Intron|MED12L_uc003eyp.2_Intron	NM_023915	NP_076404	Q9BY21	GPR87_HUMAN	G protein-coupled receptor 87	177	Helical; Name=4; (Potential).					integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			large_intestine(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)															---	---	---	---
P2RY13	53829	broad.mit.edu	37	3	151046310	151046310	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151046310A>T	uc003eyv.2	-	2	555	c.534T>A	c.(532-534)AAT>AAA	p.N178K	MED12L_uc011bnz.1_Intron|MED12L_uc003eyp.2_Intron	NM_176894	NP_795713	Q9BPV8	P2Y13_HUMAN	purinergic receptor P2Y, G-protein coupled, 13	178	Helical; Name=4; (Potential).					integral to membrane|plasma membrane				ovary(3)|lung(1)	4			LUSC - Lung squamous cell carcinoma(72;0.0189)|Lung(72;0.0278)															---	---	---	---
MED12L	116931	broad.mit.edu	37	3	151085530	151085530	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151085530G>A	uc003eyp.2	+	22	3357	c.3319G>A	c.(3319-3321)GCA>ACA	p.A1107T	MED12L_uc011bnz.1_Missense_Mutation_p.A967T|P2RY12_uc011boa.1_Intron|P2RY12_uc003eyx.1_Intron|MED12L_uc003eyy.1_Missense_Mutation_p.A270T	NM_053002	NP_443728	Q86YW9	MD12L_HUMAN	mediator of RNA polymerase II transcription,	1107					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)															---	---	---	---
MED12L	116931	broad.mit.edu	37	3	151085967	151085967	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151085967G>A	uc003eyp.2	+	23	3411	c.3373G>A	c.(3373-3375)GCG>ACG	p.A1125T	MED12L_uc011bnz.1_Missense_Mutation_p.A985T|P2RY12_uc011boa.1_Intron|P2RY12_uc003eyx.1_Intron|MED12L_uc003eyy.1_Missense_Mutation_p.A288T	NM_053002	NP_443728	Q86YW9	MD12L_HUMAN	mediator of RNA polymerase II transcription,	1125					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)															---	---	---	---
IGSF10	285313	broad.mit.edu	37	3	151161258	151161258	+	Missense_Mutation	SNP	C	T	T	rs147801336	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151161258C>T	uc011bod.1	-	5	5477	c.5477G>A	c.(5476-5478)GGT>GAT	p.G1826D	IGSF10_uc011bob.1_5'Flank|IGSF10_uc011boc.1_5'Flank	NM_178822	NP_849144	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10 precursor	1826	Ig-like C2-type 4.				cell differentiation|multicellular organismal development|ossification	extracellular region				skin(7)|ovary(5)|central_nervous_system(1)	13			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)															---	---	---	---
IGSF10	285313	broad.mit.edu	37	3	151165823	151165823	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151165823T>G	uc011bod.1	-	4	1946	c.1946A>C	c.(1945-1947)AAC>ACC	p.N649T		NM_178822	NP_849144	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10 precursor	649	Ig-like C2-type 2.				cell differentiation|multicellular organismal development|ossification	extracellular region				skin(7)|ovary(5)|central_nervous_system(1)	13			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)															---	---	---	---
AADACL2	344752	broad.mit.edu	37	3	151474924	151474924	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151474924G>A	uc003ezc.2	+	5	868	c.748G>A	c.(748-750)GTG>ATG	p.V250M	AADACL2_uc010hvn.2_Missense_Mutation_p.V37M	NM_207365	NP_997248	Q6P093	ADCL2_HUMAN	arylacetamide deacetylase-like 2 precursor	250						extracellular region|integral to membrane	carboxylesterase activity				0			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)															---	---	---	---
GPR149	344758	broad.mit.edu	37	3	154146910	154146910	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154146910C>T	uc003faa.2	-	1	595	c.495G>A	c.(493-495)TCG>TCA	p.S165S		NM_001038705	NP_001033794	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	165	Helical; Name=4; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(6)	6			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)															---	---	---	---
GPR149	344758	broad.mit.edu	37	3	154147409	154147409	+	Translation_Start_Site	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154147409C>A	uc003faa.2	-	1	96	c.-4G>T	c.(-6--2)AAGGA>AATGA			NM_001038705	NP_001033794			G protein-coupled receptor 149							integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(6)	6			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)															---	---	---	---
MME	4311	broad.mit.edu	37	3	154801960	154801960	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154801960G>A	uc010hvr.1	+	2	215	c.4G>A	c.(4-6)GGC>AGC	p.G2S	MME_uc003fab.1_Missense_Mutation_p.G2S|MME_uc003fac.1_Missense_Mutation_p.G2S|MME_uc003fad.1_Missense_Mutation_p.G2S|MME_uc003fae.1_Missense_Mutation_p.G2S	NM_007289	NP_009220	P08473	NEP_HUMAN	membrane metallo-endopeptidase	2	Cytoplasmic (Potential).				cell-cell signaling|proteolysis	integral to plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			ovary(2)|central_nervous_system(1)	3		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)													---	---	---	---
MME	4311	broad.mit.edu	37	3	154864927	154864927	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:154864927T>C	uc010hvr.1	+						MME_uc003fab.1_Intron|MME_uc003fac.1_Intron|MME_uc003fad.1_Intron|MME_uc003fae.1_Intron	NM_007289	NP_009220			membrane metallo-endopeptidase						cell-cell signaling|proteolysis	integral to plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			ovary(2)|central_nervous_system(1)	3		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)													---	---	---	---
KCNAB1	7881	broad.mit.edu	37	3	155861002	155861002	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155861002C>T	uc003far.2	+						KCNAB1_uc011bon.1_Intron|KCNAB1_uc003fas.2_Missense_Mutation_p.P12L	NM_172160	NP_751892			potassium voltage-gated channel, shaker-related							cytoplasm|integral to membrane	oxidoreductase activity|potassium channel regulator activity|voltage-gated potassium channel activity			ovary(3)|skin(1)	4			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)															---	---	---	---
VEPH1	79674	broad.mit.edu	37	3	156978979	156978979	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:156978979C>T	uc003fbj.1	-	14	2763	c.2446G>A	c.(2446-2448)GTG>ATG	p.V816M	VEPH1_uc003fbk.1_Missense_Mutation_p.V816M|VEPH1_uc010hvu.1_Missense_Mutation_p.V771M	NM_024621	NP_078897	Q14D04	MELT_HUMAN	ventricular zone expressed PH domain homolog 1	816	PH.					plasma membrane				breast(3)|ovary(1)|lung(1)	5			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)															---	---	---	---
RSRC1	51319	broad.mit.edu	37	3	157920885	157920885	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:157920885T>C	uc003fbt.2	+	4	456	c.345T>C	c.(343-345)CGT>CGC	p.R115R	RSRC1_uc011bou.1_Intron|RSRC1_uc003fbu.1_Silent_p.R115R|RSRC1_uc003fbv.2_Intron	NM_016625	NP_057709	Q96IZ7	RSRC1_HUMAN	arginine/serine-rich coiled-coil 1	115	Arg/Ser-rich.				nucleocytoplasmic transport	cytoplasm|nuclear speck	protein binding				0			Lung(72;0.00416)|LUSC - Lung squamous cell carcinoma(72;0.00575)															---	---	---	---
GFM1	85476	broad.mit.edu	37	3	158364643	158364643	+	Missense_Mutation	SNP	G	A	A	rs138103784		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:158364643G>A	uc003fce.2	+	4	586	c.479G>A	c.(478-480)CGT>CAT	p.R160H	GFM1_uc003fcd.2_Missense_Mutation_p.R160H|GFM1_uc003fcf.2_RNA|GFM1_uc003fcg.2_Missense_Mutation_p.R72H	NM_024996	NP_079272	Q96RP9	EFGM_HUMAN	G elongation factor, mitochondrial 1 precursor	160					mitochondrial translational elongation	mitochondrion	GTP binding|GTPase activity|translation elongation factor activity			ovary(3)|central_nervous_system(1)	4			Lung(72;0.00309)|LUSC - Lung squamous cell carcinoma(72;0.0043)															---	---	---	---
SMC4	10051	broad.mit.edu	37	3	160143931	160143931	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160143931G>A	uc003fdh.2	+	17	2661	c.2548G>A	c.(2548-2550)GCC>ACC	p.A850T	IFT80_uc003fda.2_Intron|SMC4_uc003fdi.2_Missense_Mutation_p.A825T|SMC4_uc003fdj.2_Missense_Mutation_p.A850T|SMC4_uc010hwd.2_Missense_Mutation_p.A850T|SMC4_uc003fdl.2_Missense_Mutation_p.A553T	NM_001002800	NP_001002800	Q9NTJ3	SMC4_HUMAN	SMC4 structural maintenance of chromosomes	850	Potential.				cell division|mitotic chromosome condensation	condensin complex|cytoplasm|nucleus	ATP binding|protein heterodimerization activity			ovary(1)|breast(1)	2			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)															---	---	---	---
TRIM59	286827	broad.mit.edu	37	3	160156340	160156340	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160156340C>A	uc003fdm.2	-	3	827	c.632G>T	c.(631-633)GGC>GTC	p.G211V	IFT80_uc003fda.2_RNA	NM_173084	NP_775107	Q8IWR1	TRI59_HUMAN	tripartite motif-containing 59	211	Potential.					integral to membrane|intracellular	zinc ion binding				0			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)															---	---	---	---
Unknown	0	broad.mit.edu	37	3	161147285	161147285	+	IGR	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:161147285C>T								C3orf57 (57414 upstream) : OTOL1 (67311 downstream)																																			---	---	---	---
ZBBX	79740	broad.mit.edu	37	3	167045903	167045903	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:167045903A>G	uc003fep.2	-	11	1012	c.689T>C	c.(688-690)GTA>GCA	p.V230A	ZBBX_uc011bpc.1_Missense_Mutation_p.V230A|ZBBX_uc003feq.2_Missense_Mutation_p.V201A	NM_024687	NP_078963	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	230						intracellular	zinc ion binding			ovary(2)	2																		---	---	---	---
MYNN	55892	broad.mit.edu	37	3	169496801	169496801	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169496801C>T	uc003fft.2	+	3	941	c.512C>T	c.(511-513)GCG>GTG	p.A171V	MYNN_uc011bpm.1_Missense_Mutation_p.A57V|MYNN_uc003ffu.2_Missense_Mutation_p.A171V|MYNN_uc003ffv.2_5'UTR|MYNN_uc010hwo.2_Missense_Mutation_p.A171V|MYNN_uc003ffw.1_RNA	NM_018657	NP_061127	Q9NPC7	MYNN_HUMAN	myoneurin	171						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(1)	1	all_cancers(22;9.55e-22)|all_epithelial(15;2.04e-26)|all_lung(20;5.05e-16)|Lung NSC(18;2.19e-15)|Ovarian(172;0.000223)|Breast(254;0.197)		Epithelial(2;4.03e-64)|all cancers(2;2.19e-58)|Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00676)															---	---	---	---
SEC62	7095	broad.mit.edu	37	3	169710720	169710720	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169710720A>G	uc003fgg.2	+	8	1100	c.1069A>G	c.(1069-1071)AGT>GGT	p.S357G	SEC62_uc003fgh.2_Missense_Mutation_p.S357G	NM_003262	NP_003253	Q99442	SEC62_HUMAN	translocation protein 1	357	Cytoplasmic (Potential).				cotranslational protein targeting to membrane|transmembrane transport	aggresome|endoplasmic reticulum membrane|integral to membrane|intermediate filament cytoskeleton|rough endoplasmic reticulum	protein transporter activity|receptor activity			ovary(1)	1																		---	---	---	---
PHC3	80012	broad.mit.edu	37	3	169896699	169896699	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169896699A>G	uc010hws.1	-	2	70	c.6T>C	c.(4-6)GAT>GAC	p.D2D	PHC3_uc003fgl.2_Silent_p.D14D|PHC3_uc011bpq.1_Silent_p.D14D|PHC3_uc011bpr.1_Silent_p.D14D|PHC3_uc003fgm.2_Silent_p.D14D|PHC3_uc003fgo.1_Silent_p.D2D|PHC3_uc003fgp.3_Silent_p.D14D|PHC3_uc003fgq.3_Silent_p.D14D|PHC3_uc003fgr.1_RNA	NM_024947	NP_079223	Q8NDX5	PHC3_HUMAN	polyhomeotic like 3	2					multicellular organismal development	PcG protein complex	DNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2	all_cancers(22;2.67e-22)|all_epithelial(15;4.73e-27)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)															---	---	---	---
PLD1	5337	broad.mit.edu	37	3	171360649	171360649	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171360649A>G	uc003fhs.2	-	23	2690	c.2574T>C	c.(2572-2574)CTT>CTC	p.L858L	PLD1_uc003fht.2_Silent_p.L820L|PLD1_uc003fhu.3_Silent_p.L152L	NM_002662	NP_002653	Q13393	PLD1_HUMAN	phospholipase D1 isoform a	858	Catalytic.				cell communication|chemotaxis|Ras protein signal transduction	endoplasmic reticulum membrane|Golgi membrane|late endosome membrane|perinuclear region of cytoplasm	NAPE-specific phospholipase D activity|phosphatidylinositol binding|phospholipase D activity			ovary(2)|lung(1)	3	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)													---	---	---	---
FNDC3B	64778	broad.mit.edu	37	3	172058924	172058924	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:172058924A>G	uc003fhy.2	+	17	2046	c.1874A>G	c.(1873-1875)TAC>TGC	p.Y625C	FNDC3B_uc003fhz.3_Missense_Mutation_p.Y625C	NM_022763	NP_073600	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	625	Fibronectin type-III 4.					endoplasmic reticulum|integral to membrane				ovary(2)|breast(1)	3	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)														---	---	---	---
PIK3CA	5290	broad.mit.edu	37	3	178917575	178917575	+	Silent	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178917575T>G	uc003fjk.2	+	3	607	c.450T>G	c.(448-450)GCT>GCG	p.A150A		NM_006218	NP_006209	P42336	PK3CA_HUMAN	phosphoinositide-3-kinase, catalytic, alpha	150					epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway		1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity			breast(1564)|large_intestine(776)|endometrium(246)|urinary_tract(195)|ovary(141)|skin(112)|stomach(98)|thyroid(77)|central_nervous_system(69)|lung(65)|upper_aerodigestive_tract(58)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|prostate(3)|kidney(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1)	3553	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)				57	Mis		colorectal|gastric|gliobastoma|breast					HNSCC(19;0.045)|TSP Lung(28;0.18)			---	---	---	---
KCNMB3	27094	broad.mit.edu	37	3	178968532	178968532	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178968532T>C	uc003fjm.2	-	2	771	c.259A>G	c.(259-261)AGC>GGC	p.S87G	KCNMB3_uc003fjl.3_RNA|KCNMB3_uc011bqc.1_Missense_Mutation_p.S85G|KCNMB3_uc003fjn.2_Missense_Mutation_p.S83G|KCNMB3_uc003fjo.2_Missense_Mutation_p.S65G|KCNMB3_uc003fjp.1_Missense_Mutation_p.S85G	NM_014407	NP_055222	Q9NPA1	KCMB3_HUMAN	calcium-activated potassium channel beta 3	87	Extracellular (Potential).				detection of calcium ion|platelet activation|regulation of action potential in neuron	voltage-gated potassium channel complex	calcium-activated potassium channel activity|potassium channel regulator activity				0	all_cancers(143;5.6e-17)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;2.41e-27)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.03)															---	---	---	---
GNB4	59345	broad.mit.edu	37	3	179119111	179119111	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:179119111A>G	uc003fjv.3	-						GNB4_uc003fju.3_Intron	NM_021629	NP_067642			guanine nucleotide-binding protein, beta-4						cellular response to glucagon stimulus|energy reserve metabolic process	plasma membrane	signal transducer activity			skin(2)	2	all_cancers(143;2.01e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.237)															---	---	---	---
ATP11B	23200	broad.mit.edu	37	3	182583252	182583252	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182583252C>T	uc003flb.2	+	13	1466	c.1209C>T	c.(1207-1209)TAC>TAT	p.Y403Y	ATP11B_uc003flc.2_Translation_Start_Site	NM_014616	NP_055431	Q9Y2G3	AT11B_HUMAN	ATPase, class VI, type 11B	403	Cytoplasmic (Potential).				aminophospholipid transport|ATP biosynthetic process	integral to membrane|nuclear inner membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|pancreas(1)	3	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;1.2e-42)|Epithelial(37;2.77e-36)|LUSC - Lung squamous cell carcinoma(7;7.58e-24)|Lung(8;4.66e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.35e-20)															---	---	---	---
MCCC1	56922	broad.mit.edu	37	3	182740260	182740260	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182740260A>G	uc003fle.2	-	16	1951	c.1814T>C	c.(1813-1815)GTT>GCT	p.V605A	MCCC1_uc010hxi.2_RNA|MCCC1_uc011bqo.1_RNA|MCCC1_uc003flf.2_Missense_Mutation_p.V488A|MCCC1_uc003flg.2_Missense_Mutation_p.V496A|MCCC1_uc011bqp.1_Missense_Mutation_p.V558A	NM_020166	NP_064551	Q96RQ3	MCCA_HUMAN	methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)	605					biotin metabolic process|leucine catabolic process	mitochondrial inner membrane|mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|metal ion binding|methylcrotonoyl-CoA carboxylase activity			ovary(1)|central_nervous_system(1)|skin(1)	3	all_cancers(143;1.84e-14)|Ovarian(172;0.0355)		all cancers(12;1.8e-44)|Epithelial(37;3.23e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;5.07e-21)		Biotin(DB00121)													---	---	---	---
KLHL6	89857	broad.mit.edu	37	3	183209714	183209714	+	3'UTR	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183209714G>A	uc003flr.2	-	7					KLHL6_uc003fls.1_RNA|KLHL6_uc003flt.1_3'UTR|KLHL6_uc010hxk.1_RNA	NM_130446	NP_569713			kelch-like 6											haematopoietic_and_lymphoid_tissue(2)|ovary(1)	3	all_cancers(143;9.2e-12)|Ovarian(172;0.0172)		all cancers(12;1.29e-44)|Epithelial(37;1.24e-38)|LUSC - Lung squamous cell carcinoma(7;2.58e-24)|Lung(8;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.32e-22)															---	---	---	---
YEATS2	55689	broad.mit.edu	37	3	183495351	183495351	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183495351C>T	uc003fly.2	+	19	2794	c.2599C>T	c.(2599-2601)CCA>TCA	p.P867S	YEATS2_uc003flz.2_5'UTR	NM_018023	NP_060493	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2	867					histone H3 acetylation|negative regulation of transcription from RNA polymerase II promoter	Ada2/Gcn5/Ada3 transcription activator complex	TBP-class protein binding			ovary(3)|large_intestine(1)	4	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)															---	---	---	---
YEATS2	55689	broad.mit.edu	37	3	183515771	183515771	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183515771G>A	uc003fly.2	+	22	3353	c.3158G>A	c.(3157-3159)AGC>AAC	p.S1053N		NM_018023	NP_060493	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2	1053					histone H3 acetylation|negative regulation of transcription from RNA polymerase II promoter	Ada2/Gcn5/Ada3 transcription activator complex	TBP-class protein binding			ovary(3)|large_intestine(1)	4	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)															---	---	---	---
YEATS2	55689	broad.mit.edu	37	3	183524800	183524800	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183524800C>T	uc003fly.2	+	28	4126	c.3931C>T	c.(3931-3933)CAG>TAG	p.Q1311*	uc003fma.1_5'Flank	NM_018023	NP_060493	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2	1311					histone H3 acetylation|negative regulation of transcription from RNA polymerase II promoter	Ada2/Gcn5/Ada3 transcription activator complex	TBP-class protein binding			ovary(3)|large_intestine(1)	4	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)															---	---	---	---
AP2M1	1173	broad.mit.edu	37	3	183896725	183896725	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183896725G>A	uc011bqx.1	+	3	312	c.155G>A	c.(154-156)CGC>CAC	p.R52H	AP2M1_uc003fmw.2_Missense_Mutation_p.R52H|AP2M1_uc003fmx.2_Missense_Mutation_p.R52H|AP2M1_uc003fmy.2_Missense_Mutation_p.R52H|AP2M1_uc011bqy.1_5'Flank|AP2M1_uc011bqz.1_5'Flank	NM_004068	NP_004059	Q96CW1	AP2M1_HUMAN	adaptor-related protein complex 2, mu 1 subunit	52					axon guidance|cellular membrane organization|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of defense response to virus by virus|synaptic transmission|vesicle-mediated transport|viral reproduction	clathrin adaptor complex|clathrin coat of coated pit|cytosol|endocytic vesicle membrane|peroxisomal membrane	lipid binding|protein binding|transporter activity				0	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.92e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)															---	---	---	---
AP2M1	1173	broad.mit.edu	37	3	183896839	183896839	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183896839C>T	uc011bqx.1	+	3	426	c.269C>T	c.(268-270)GCT>GTT	p.A90V	AP2M1_uc003fmw.2_Missense_Mutation_p.A90V|AP2M1_uc003fmx.2_Missense_Mutation_p.A90V|AP2M1_uc003fmy.2_Missense_Mutation_p.A90V|AP2M1_uc011bqy.1_5'Flank|AP2M1_uc011bqz.1_5'Flank	NM_004068	NP_004059	Q96CW1	AP2M1_HUMAN	adaptor-related protein complex 2, mu 1 subunit	90					axon guidance|cellular membrane organization|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of defense response to virus by virus|synaptic transmission|vesicle-mediated transport|viral reproduction	clathrin adaptor complex|clathrin coat of coated pit|cytosol|endocytic vesicle membrane|peroxisomal membrane	lipid binding|protein binding|transporter activity				0	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.92e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)															---	---	---	---
AP2M1	1173	broad.mit.edu	37	3	183901311	183901311	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183901311G>T	uc011bqx.1	+	12	1372	c.1215G>T	c.(1213-1215)AAG>AAT	p.K405N	AP2M1_uc003fmw.2_Missense_Mutation_p.K403N|AP2M1_uc003fmx.2_Missense_Mutation_p.K333N|AP2M1_uc003fmy.2_Missense_Mutation_p.K403N|AP2M1_uc011bqy.1_Missense_Mutation_p.K275N|ABCF3_uc003fmz.2_5'Flank|ABCF3_uc003fna.2_5'Flank	NM_004068	NP_004059	Q96CW1	AP2M1_HUMAN	adaptor-related protein complex 2, mu 1 subunit	405	MHD.				axon guidance|cellular membrane organization|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of defense response to virus by virus|synaptic transmission|vesicle-mediated transport|viral reproduction	clathrin adaptor complex|clathrin coat of coated pit|cytosol|endocytic vesicle membrane|peroxisomal membrane	lipid binding|protein binding|transporter activity				0	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.92e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)															---	---	---	---
ECE2	9718	broad.mit.edu	37	3	183975299	183975299	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183975299G>A	uc003fni.3	+	2	273	c.235G>A	c.(235-237)GGA>AGA	p.G79R	ECE2_uc003fnh.3_Missense_Mutation_p.G79R	NM_014693	NP_055508	O60344	ECE2_HUMAN	endothelin converting enzyme 2 isoform A	79	Cytoplasmic (Potential).|Methyltransferase-like region.				brain development|cardioblast differentiation|cell-cell signaling|peptide hormone processing	cytoplasmic vesicle membrane|Golgi membrane|integral to membrane	metal ion binding|metalloendopeptidase activity|methyltransferase activity			ovary(2)|skin(2)	4	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)															---	---	---	---
ECE2	9718	broad.mit.edu	37	3	183975407	183975407	+	Missense_Mutation	SNP	C	T	T	rs146338541		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:183975407C>T	uc003fni.3	+	2	381	c.343C>T	c.(343-345)CGG>TGG	p.R115W	ECE2_uc003fnh.3_Missense_Mutation_p.R115W	NM_014693	NP_055508	O60344	ECE2_HUMAN	endothelin converting enzyme 2 isoform A	115	Cytoplasmic (Potential).|Methyltransferase-like region.				brain development|cardioblast differentiation|cell-cell signaling|peptide hormone processing	cytoplasmic vesicle membrane|Golgi membrane|integral to membrane	metal ion binding|metalloendopeptidase activity|methyltransferase activity			ovary(2)|skin(2)	4	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)															---	---	---	---
ECE2	9718	broad.mit.edu	37	3	184003292	184003292	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184003292A>T	uc003fni.3	+	10	1567	c.1529A>T	c.(1528-1530)AAC>ATC	p.N510I	ECE2_uc011brh.1_Missense_Mutation_p.N363I|ECE2_uc003fnl.3_Missense_Mutation_p.N438I|ECE2_uc003fnm.3_Missense_Mutation_p.N392I|ECE2_uc003fnk.3_Missense_Mutation_p.N363I|ECE2_uc011bri.1_Missense_Mutation_p.N425I|ECE2_uc010hxv.2_Missense_Mutation_p.N154I	NM_014693	NP_055508	O60344	ECE2_HUMAN	endothelin converting enzyme 2 isoform A	510	Lumenal (Potential).|Endothelin-converting enzyme 2 region.				brain development|cardioblast differentiation|cell-cell signaling|peptide hormone processing	cytoplasmic vesicle membrane|Golgi membrane|integral to membrane	metal ion binding|metalloendopeptidase activity|methyltransferase activity			ovary(2)|skin(2)	4	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)													OREG0015945	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
ECE2	9718	broad.mit.edu	37	3	184007457	184007457	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184007457T>C	uc003fni.3	+	13	1894	c.1856T>C	c.(1855-1857)TTC>TCC	p.F619S	ECE2_uc011brh.1_Missense_Mutation_p.F472S|ECE2_uc003fnl.3_Missense_Mutation_p.F547S|ECE2_uc003fnm.3_Missense_Mutation_p.F501S|ECE2_uc003fnk.3_Missense_Mutation_p.F472S|ECE2_uc011bri.1_Missense_Mutation_p.F534S|ECE2_uc010hxv.2_Missense_Mutation_p.F263S	NM_014693	NP_055508	O60344	ECE2_HUMAN	endothelin converting enzyme 2 isoform A	619	Lumenal (Potential).|Endothelin-converting enzyme 2 region.				brain development|cardioblast differentiation|cell-cell signaling|peptide hormone processing	cytoplasmic vesicle membrane|Golgi membrane|integral to membrane	metal ion binding|metalloendopeptidase activity|methyltransferase activity			ovary(2)|skin(2)	4	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)													OREG0015946	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
PSMD2	5708	broad.mit.edu	37	3	184023853	184023853	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184023853G>T	uc003fnn.1	+	14	1747	c.1714G>T	c.(1714-1716)GCC>TCC	p.A572S	PSMD2_uc011brj.1_Missense_Mutation_p.A413S|PSMD2_uc011brk.1_Missense_Mutation_p.A442S	NM_002808	NP_002799	Q13200	PSMD2_HUMAN	proteasome 26S non-ATPase subunit 2	572	PC 5.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|regulation of protein catabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome regulatory particle	enzyme regulator activity|protein binding				0	all_cancers(143;1.54e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		Bortezomib(DB00188)											OREG0015947	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
EIF4G1	1981	broad.mit.edu	37	3	184041329	184041329	+	Missense_Mutation	SNP	C	T	T	rs147678593	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184041329C>T	uc003fnp.2	+	15	2420	c.2222C>T	c.(2221-2223)ACG>ATG	p.T741M	EIF4G1_uc003fno.1_Missense_Mutation_p.T682M|EIF4G1_uc010hxw.1_Missense_Mutation_p.T577M|EIF4G1_uc003fnt.2_Missense_Mutation_p.T452M|EIF4G1_uc003fnq.2_Missense_Mutation_p.T654M|EIF4G1_uc003fnr.2_Missense_Mutation_p.T577M|EIF4G1_uc010hxx.2_Missense_Mutation_p.T748M|EIF4G1_uc003fns.2_Missense_Mutation_p.T701M|EIF4G1_uc010hxy.2_Missense_Mutation_p.T748M|EIF4G1_uc003fnv.3_Missense_Mutation_p.T742M|EIF4G1_uc003fnu.3_Missense_Mutation_p.T741M|EIF4G1_uc003fnw.2_Missense_Mutation_p.T748M|EIF4G1_uc003fnx.2_Missense_Mutation_p.T546M|EIF4G1_uc003fny.3_Missense_Mutation_p.T545M|SNORD66_uc003fnz.2_5'Flank	NM_198241	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4	741	eIF3/EIF4A-binding.|MIF4G.				insulin receptor signaling pathway|interspecies interaction between organisms|nuclear-transcribed mRNA poly(A) tail shortening|regulation of translational initiation	cytosol|eukaryotic translation initiation factor 4F complex	protein binding|translation initiation factor activity			lung(2)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)															---	---	---	---
FAM131A	131408	broad.mit.edu	37	3	184062488	184062488	+	Silent	SNP	C	T	T	rs150189351	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184062488C>T	uc003fog.2	+	3	2102	c.738C>T	c.(736-738)GGC>GGT	p.G246G	FAM131A_uc003fob.1_Silent_p.G154G|FAM131A_uc003foc.2_Silent_p.G192G|FAM131A_uc003foe.2_Silent_p.G192G	NM_144635	NP_653236	Q6UXB0	F131A_HUMAN	hypothetical protein LOC131408 precursor	246						extracellular region				breast(1)	1	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)															---	---	---	---
CHRD	8646	broad.mit.edu	37	3	184104831	184104831	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184104831C>T	uc003fov.2	+						CHRD_uc003fow.2_Intron|CHRD_uc003fox.2_Intron|CHRD_uc003foy.2_Intron|CHRD_uc010hyc.2_Intron|CHRD_uc011brr.1_Intron	NM_003741	NP_003732			chordin precursor						BMP signaling pathway involved in spinal cord dorsal/ventral patterning|floor plate development|negative regulation of BMP signaling pathway|negative regulation of cell migration|positive regulation of cell adhesion|skeletal system development	extracellular space	cytokine binding			skin(2)|ovary(1)	3	all_cancers(143;6.33e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)															---	---	---	---
VPS8	23355	broad.mit.edu	37	3	184603925	184603925	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184603925T>C	uc003fpb.1	+	21	1927	c.1756T>C	c.(1756-1758)TGC>CGC	p.C586R	VPS8_uc010hyd.1_Intron|VPS8_uc010hye.1_Missense_Mutation_p.C15R	NM_015303	NP_056118	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog isoform b	588							zinc ion binding			ovary(1)	1	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)															---	---	---	---
SENP2	59343	broad.mit.edu	37	3	185331146	185331146	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185331146A>G	uc003fpn.2	+	10	1054	c.883A>G	c.(883-885)AAA>GAA	p.K295E	SENP2_uc011brv.1_Missense_Mutation_p.K285E|SENP2_uc011brw.1_Missense_Mutation_p.K108E	NM_021627	NP_067640	Q9HC62	SENP2_HUMAN	SUMO1/sentrin/SMT3 specific protease 2	295					mRNA transport|protein desumoylation|protein transport|proteolysis|regulation of Wnt receptor signaling pathway|transmembrane transport|Wnt receptor signaling pathway	cytoplasm|nuclear membrane|nuclear pore	protein binding|SUMO-specific protease activity				0	all_cancers(143;1.28e-10)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;1.31e-21)															---	---	---	---
TRA2B	6434	broad.mit.edu	37	3	185641599	185641599	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:185641599T>C	uc003fpv.2	-	4	783	c.507A>G	c.(505-507)GTA>GTG	p.V169V	TRA2B_uc003fpt.2_RNA|TRA2B_uc003fpu.2_RNA|TRA2B_uc010hym.2_Silent_p.V69V|TRA2B_uc003fpw.2_Silent_p.V169V	NM_004593	NP_004584	P62995	TRA2B_HUMAN	splicing factor, arginine/serine-rich 10	169	RRM.				nuclear mRNA splicing, via spliceosome	nucleus	nucleotide binding|protein binding|RNA binding			ovary(2)	2																		---	---	---	---
HRG	3273	broad.mit.edu	37	3	186395147	186395147	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186395147C>A	uc003fqq.2	+	7	1076	c.1053C>A	c.(1051-1053)CCC>CCA	p.P351P		NM_000412	NP_000403	P04196	HRG_HUMAN	histidine-rich glycoprotein precursor	351	His/Pro-rich (HRR).				fibrinolysis|platelet activation|platelet degranulation	extracellular region|plasma membrane|platelet alpha granule lumen	cysteine-type endopeptidase inhibitor activity|heparin binding			ovary(1)|central_nervous_system(1)	2	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0683)														---	---	---	---
RTP1	132112	broad.mit.edu	37	3	186915478	186915478	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186915478C>T	uc003frg.2	+	1	205	c.175C>T	c.(175-177)CCG>TCG	p.P59S		NM_153708	NP_714919	P59025	RTP1_HUMAN	receptor transporting protein 1	59	Cytoplasmic (Potential).				protein insertion into membrane	cell surface|integral to membrane|plasma membrane	olfactory receptor binding			ovary(2)|breast(1)	3	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.56e-18)	GBM - Glioblastoma multiforme(93;0.0269)														---	---	---	---
MASP1	5648	broad.mit.edu	37	3	186944285	186944285	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186944285C>T	uc003frh.1	-	12	1797	c.1465G>A	c.(1465-1467)GCA>ACA	p.A489T		NM_001879	NP_001870	P48740	MASP1_HUMAN	mannan-binding lectin serine protease 1 isoform	489	Peptidase S1.				complement activation, lectin pathway|negative regulation of complement activation|proteolysis	extracellular space	calcium ion binding|calcium-dependent protein binding|protein binding|protein homodimerization activity|serine-type endopeptidase activity			ovary(2)|breast(1)|liver(1)	4	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.49e-18)	GBM - Glioblastoma multiforme(93;0.0366)														---	---	---	---
TP63	8626	broad.mit.edu	37	3	189526177	189526177	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189526177G>A	uc003fry.2	+	4	530	c.441G>A	c.(439-441)TCG>TCA	p.S147S	TP63_uc003frx.2_Silent_p.S147S|TP63_uc003frz.2_Silent_p.S147S|TP63_uc010hzc.1_Silent_p.S147S|TP63_uc003fsa.2_Silent_p.S53S|TP63_uc003fsb.2_Silent_p.S53S|TP63_uc003fsc.2_Silent_p.S53S|TP63_uc003fsd.2_Silent_p.S53S|TP63_uc010hzd.1_Intron|TP63_uc003fse.1_Silent_p.S28S	NM_003722	NP_003713	Q9H3D4	P63_HUMAN	tumor protein p63 isoform 1	147					anti-apoptosis|cellular response to UV|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of transcription from RNA polymerase II promoter|Notch signaling pathway|positive regulation of Notch signaling pathway|protein homotetramerization|regulation of neuron apoptosis|response to gamma radiation|response to X-ray	chromatin|cytosol|dendrite|Golgi apparatus|transcription factor complex	chromatin binding|damaged DNA binding|double-stranded DNA binding|identical protein binding|metal ion binding|p53 binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(5)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	12	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)										Hay-Wells_syndrome	HNSCC(45;0.13)			---	---	---	---
TP63	8626	broad.mit.edu	37	3	189590696	189590696	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189590696C>A	uc003fry.2	+	10	1350	c.1261C>A	c.(1261-1263)CTG>ATG	p.L421M	TP63_uc003frx.2_Missense_Mutation_p.L421M|TP63_uc003frz.2_Missense_Mutation_p.L421M|TP63_uc010hzc.1_Missense_Mutation_p.L421M|TP63_uc003fsa.2_Missense_Mutation_p.L327M|TP63_uc003fsb.2_Missense_Mutation_p.L327M|TP63_uc003fsc.2_Missense_Mutation_p.L327M|TP63_uc003fsd.2_Missense_Mutation_p.L327M|TP63_uc010hzd.1_Missense_Mutation_p.L242M	NM_003722	NP_003713	Q9H3D4	P63_HUMAN	tumor protein p63 isoform 1	421	Oligomerization.				anti-apoptosis|cellular response to UV|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of transcription from RNA polymerase II promoter|Notch signaling pathway|positive regulation of Notch signaling pathway|protein homotetramerization|regulation of neuron apoptosis|response to gamma radiation|response to X-ray	chromatin|cytosol|dendrite|Golgi apparatus|transcription factor complex	chromatin binding|damaged DNA binding|double-stranded DNA binding|identical protein binding|metal ion binding|p53 binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(5)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	12	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)										Hay-Wells_syndrome	HNSCC(45;0.13)			---	---	---	---
Unknown	0	broad.mit.edu	37	3	190967915	190967915	+	IGR	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:190967915T>A								OSTN (7 upstream) : UTS2D (17030 downstream)																																			---	---	---	---
ATP13A5	344905	broad.mit.edu	37	3	193019019	193019019	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193019019C>T	uc011bsq.1	-	24	2756	c.2756G>A	c.(2755-2757)AGT>AAT	p.S919N		NM_198505	NP_940907	Q4VNC0	AT135_HUMAN	ATPase type 13A5	919	Helical; (Potential).				ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(5)|skin(4)|large_intestine(2)	11	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)														---	---	---	---
ATP13A4	84239	broad.mit.edu	37	3	193180617	193180617	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:193180617A>G	uc003ftd.2	-						ATP13A4_uc003fte.1_Intron|ATP13A4_uc011bsr.1_Intron|ATP13A4_uc010hzi.2_Intron|ATP13A4_uc003ftf.3_Intron	NM_032279	NP_115655			ATPase type 13A4						ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(2)	2	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)														---	---	---	---
ATP13A3	79572	broad.mit.edu	37	3	194126693	194126693	+	Silent	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194126693A>C	uc003fty.3	-	32	4038	c.3636T>G	c.(3634-3636)GCT>GCG	p.A1212A	ATP13A3_uc003ftx.3_Silent_p.A121A	NM_024524	NP_078800	Q9H7F0	AT133_HUMAN	ATPase type 13A3	1212					ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(1)	1	all_cancers(143;6.01e-09)|Ovarian(172;0.0634)	Melanoma(1037;0.211)	OV - Ovarian serous cystadenocarcinoma(49;3.83e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;5.98e-05)														---	---	---	---
ATP13A3	79572	broad.mit.edu	37	3	194150497	194150497	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:194150497G>A	uc003fty.3	-	26	3186	c.2784C>T	c.(2782-2784)GGC>GGT	p.G928G	ATP13A3_uc003ftz.1_Silent_p.G634G	NM_024524	NP_078800	Q9H7F0	AT133_HUMAN	ATPase type 13A3	928					ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(1)	1	all_cancers(143;6.01e-09)|Ovarian(172;0.0634)	Melanoma(1037;0.211)	OV - Ovarian serous cystadenocarcinoma(49;3.83e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;5.98e-05)														---	---	---	---
MUC20	200958	broad.mit.edu	37	3	195453104	195453104	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195453104G>A	uc010hzo.2	+	3	1243	c.1117G>A	c.(1117-1119)GTC>ATC	p.V373I	MUC20_uc010hzp.2_Missense_Mutation_p.V338I|MUC20_uc011bte.1_RNA	NM_152673	NP_689886	Q8N307	MUC20_HUMAN	mucin 20 isoform L	544	Involved in oligomerization.				protein homooligomerization	apical plasma membrane|basal plasma membrane|extracellular region|microvillus membrane					0	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)														---	---	---	---
MUC4	4585	broad.mit.edu	37	3	195477912	195477912	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195477912G>T	uc011bto.1	-	24	15795	c.15335C>A	c.(15334-15336)CCT>CAT	p.P5112H	MUC4_uc010hzq.2_Missense_Mutation_p.P97H|MUC4_uc003fuz.2_Missense_Mutation_p.P838H|MUC4_uc003fva.2_Missense_Mutation_p.P720H|MUC4_uc003fvb.2_Missense_Mutation_p.P756H|MUC4_uc003fvc.2_RNA|MUC4_uc003fvd.2_RNA|MUC4_uc003fve.2_Missense_Mutation_p.P756H|MUC4_uc010hzr.2_RNA|MUC4_uc011btf.1_Missense_Mutation_p.P720H|MUC4_uc011btg.1_RNA|MUC4_uc011bth.1_Missense_Mutation_p.P804H|MUC4_uc011bti.1_Missense_Mutation_p.P804H|MUC4_uc011btj.1_Missense_Mutation_p.P981H|MUC4_uc011btk.1_Missense_Mutation_p.P720H|MUC4_uc011btl.1_Missense_Mutation_p.P749H|MUC4_uc011btm.1_Missense_Mutation_p.P929H|MUC4_uc011btn.1_Missense_Mutation_p.P720H|MUC4_uc003fvo.2_Missense_Mutation_p.P1004H|MUC4_uc003fvp.2_Missense_Mutation_p.P953H	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	1997					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)														---	---	---	---
MUC4	4585	broad.mit.edu	37	3	195538663	195538663	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195538663A>G	uc011bto.1	-	1	486	c.26T>C	c.(25-27)GTC>GCC	p.V9A	MUC4_uc003fvo.2_Missense_Mutation_p.V9A|MUC4_uc003fvp.2_Missense_Mutation_p.V9A|MUC4_uc010hzv.2_RNA	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	9					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)														---	---	---	---
OSTalpha	200931	broad.mit.edu	37	3	195954002	195954002	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195954002G>A	uc003fwd.2	+						OSTalpha_uc011btu.1_Silent_p.P100P|OSTalpha_uc010iac.1_5'Flank|OSTalpha_uc003fwe.2_5'Flank	NM_152672	NP_689885			organic solute transporter alpha							integral to membrane|plasma membrane	transporter activity			ovary(1)	1	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;8.83e-25)|all cancers(36;8.38e-23)|OV - Ovarian serous cystadenocarcinoma(49;7.08e-19)|LUSC - Lung squamous cell carcinoma(58;7.51e-07)|Lung(62;1.06e-06)	GBM - Glioblastoma multiforme(46;0.00202)														---	---	---	---
LRRC33	375387	broad.mit.edu	37	3	196387058	196387058	+	Missense_Mutation	SNP	C	T	T	rs140233771	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:196387058C>T	uc003fwv.2	+	3	648	c.544C>T	c.(544-546)CGT>TGT	p.R182C		NM_198565	NP_940967	Q86YC3	LRC33_HUMAN	leucine rich repeat containing 33 precursor	182	Extracellular (Potential).|LRR 6.					integral to membrane				ovary(2)|central_nervous_system(1)	3	all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.9e-23)|all cancers(36;1.76e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00326)														---	---	---	---
ZNF141	7700	broad.mit.edu	37	4	367091	367091	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:367091A>G	uc003gaa.2	+	5	1043	c.865A>G	c.(865-867)AGG>GGG	p.R289G	ZNF141_uc003gab.2_Intron	NM_003441	NP_003432	Q15928	ZN141_HUMAN	zinc finger protein 141	289	C2H2-type 5.				anatomical structure morphogenesis|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ZNF721	170960	broad.mit.edu	37	4	436350	436350	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:436350T>C	uc003gag.2	-	3	2597	c.1906A>G	c.(1906-1908)ACT>GCT	p.T636A	ABCA11P_uc003gac.2_Intron|ABCA11P_uc003gad.2_Intron|ABCA11P_uc011buv.1_Intron|ABCA11P_uc003gae.2_Intron|ABCA11P_uc010ibd.1_Intron|ZNF721_uc003gaf.3_Missense_Mutation_p.T668A|ZNF721_uc010ibe.2_Missense_Mutation_p.T624A	NM_133474	NP_597731	D9N162	D9N162_HUMAN	zinc finger protein 721	636						intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1																		---	---	---	---
PDE6B	5158	broad.mit.edu	37	4	651219	651219	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:651219A>G	uc003gap.2	+	10	1390	c.1337A>G	c.(1336-1338)GAC>GGC	p.D446G	PDE6B_uc003gao.3_Missense_Mutation_p.D446G|PDE6B_uc011buy.1_Missense_Mutation_p.D167G|uc003gaq.1_5'Flank	NM_000283	NP_000274	P35913	PDE6B_HUMAN	phosphodiesterase 6B isoform 1	446					cytosolic calcium ion homeostasis|GMP metabolic process|phototransduction, visible light|platelet activation|visual perception	cytosol|membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding				0																		---	---	---	---
PDE6B	5158	broad.mit.edu	37	4	657558	657558	+	Splice_Site	SNP	G	T	T	rs150108615		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:657558G>T	uc003gap.2	+	16	1974	c.1921_splice	c.e16-1	p.T641_splice	PDE6B_uc003gao.3_Splice_Site_p.T641_splice|PDE6B_uc011buy.1_Splice_Site_p.T362_splice|PDE6B_uc011buz.1_Splice_Site_p.T73_splice	NM_000283	NP_000274			phosphodiesterase 6B isoform 1						cytosolic calcium ion homeostasis|GMP metabolic process|phototransduction, visible light|platelet activation|visual perception	cytosol|membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding				0																		---	---	---	---
PDE6B	5158	broad.mit.edu	37	4	658667	658667	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:658667C>T	uc003gap.2	+						PDE6B_uc003gao.3_Intron|PDE6B_uc011buy.1_Intron|PDE6B_uc011buz.1_Intron	NM_000283	NP_000274			phosphodiesterase 6B isoform 1						cytosolic calcium ion homeostasis|GMP metabolic process|phototransduction, visible light|platelet activation|visual perception	cytosol|membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding				0																		---	---	---	---
GAK	2580	broad.mit.edu	37	4	860943	860943	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:860943G>A	uc003gbm.3	-	21	2872	c.2673C>T	c.(2671-2673)GGC>GGT	p.G891G	GAK_uc003gbn.3_Silent_p.G812G|GAK_uc010ibk.1_Silent_p.G785G|GAK_uc010ibi.2_Silent_p.G72G|GAK_uc010ibj.2_RNA|GAK_uc003gbl.3_Silent_p.G755G	NM_005255	NP_005246	O14976	GAK_HUMAN	cyclin G associated kinase	891					cell cycle	focal adhesion|Golgi apparatus|perinuclear region of cytoplasm	ATP binding|heat shock protein binding|protein serine/threonine kinase activity			lung(2)|central_nervous_system(1)|skin(1)	4				Colorectal(103;0.219)														---	---	---	---
GAK	2580	broad.mit.edu	37	4	860995	860995	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:860995G>T	uc003gbm.3	-	21	2820	c.2621C>A	c.(2620-2622)CCT>CAT	p.P874H	GAK_uc003gbn.3_Missense_Mutation_p.P795H|GAK_uc010ibk.1_Missense_Mutation_p.P768H|GAK_uc010ibi.2_Missense_Mutation_p.P55H|GAK_uc010ibj.2_RNA|GAK_uc003gbl.3_Missense_Mutation_p.P738H	NM_005255	NP_005246	O14976	GAK_HUMAN	cyclin G associated kinase	874					cell cycle	focal adhesion|Golgi apparatus|perinuclear region of cytoplasm	ATP binding|heat shock protein binding|protein serine/threonine kinase activity			lung(2)|central_nervous_system(1)|skin(1)	4				Colorectal(103;0.219)														---	---	---	---
DGKQ	1609	broad.mit.edu	37	4	955561	955561	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:955561G>T	uc003gbw.2	-	20	2451	c.2377C>A	c.(2377-2379)CTG>ATG	p.L793M	DGKQ_uc010ibn.2_Missense_Mutation_p.L780M	NM_001347	NP_001338	P52824	DGKQ_HUMAN	diacylglycerol kinase, theta	793					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|platelet activation|protein kinase C signaling cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to ATP|thrombin receptor signaling pathway	cytoskeleton|cytosol|nuclear speck|plasma membrane	activating transcription factor binding|ATP binding|diacylglycerol kinase activity|kinase binding|metal ion binding|phospholipase binding			kidney(1)	1			OV - Ovarian serous cystadenocarcinoma(23;0.0158)															---	---	---	---
TACC3	10460	broad.mit.edu	37	4	1746710	1746710	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1746710C>T	uc003gdo.2	+	16	2595	c.2487C>T	c.(2485-2487)GAC>GAT	p.D829D	TACC3_uc003gdp.2_Silent_p.D469D|TACC3_uc010ica.2_Silent_p.D250D	NM_006342	NP_006333	Q9Y6A5	TACC3_HUMAN	transforming, acidic coiled-coil containing	829	Potential.					centrosome				ovary(1)|central_nervous_system(1)	2		Breast(71;0.212)|all_epithelial(65;0.241)	OV - Ovarian serous cystadenocarcinoma(23;0.00765)|Epithelial(3;0.0126)															---	---	---	---
WHSC1	7468	broad.mit.edu	37	4	1976365	1976365	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:1976365G>A	uc003gdz.3	+						WHSC1_uc003geb.3_Intron|WHSC1_uc003gec.3_Intron|WHSC1_uc003ged.3_Intron|WHSC1_uc003gee.3_Intron|WHSC1_uc003gef.3_Intron|WHSC1_uc003gei.3_Intron|WHSC1_uc011bvh.1_Intron|WHSC1_uc010icf.2_Intron|SCARNA22_uc003gej.2_RNA	NM_001042424	NP_001035889			Wolf-Hirschhorn syndrome candidate 1 protein						anatomical structure morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|cytoplasm|nuclear membrane|nucleolus	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			ovary(3)|lung(3)|skin(2)|pancreas(1)	9		all_epithelial(65;1.34e-05)	OV - Ovarian serous cystadenocarcinoma(23;0.00606)	STAD - Stomach adenocarcinoma(129;0.232)				T	IGH@	MM								---	---	---	---
POLN	353497	broad.mit.edu	37	4	2209771	2209771	+	Silent	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2209771T>G	uc003ger.2	-	3	657	c.657A>C	c.(655-657)GCA>GCC	p.A219A	POLN_uc010ich.1_5'UTR|POLN_uc011bvi.1_Silent_p.A219A	NM_181808	NP_861524	Q7Z5Q5	DPOLN_HUMAN	DNA-directed DNA polymerase nu	219					DNA repair|DNA replication	nucleus	DNA binding|DNA-directed DNA polymerase activity			kidney(2)|ovary(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(23;0.0955)										DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
ZFYVE28	57732	broad.mit.edu	37	4	2275887	2275887	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:2275887G>A	uc003gex.1	-	9	2427	c.2108C>T	c.(2107-2109)GCA>GTA	p.A703V	ZFYVE28_uc011bvk.1_Missense_Mutation_p.A633V|ZFYVE28_uc011bvl.1_Missense_Mutation_p.A673V|ZFYVE28_uc003gew.1_Missense_Mutation_p.A589V	NM_020972	NP_066023	Q9HCC9	LST2_HUMAN	zinc finger, FYVE domain containing 28	703					negative regulation of epidermal growth factor receptor activity	cytosol|early endosome membrane	metal ion binding|phosphatidylinositol-3-phosphate binding|protein binding			skin(2)|ovary(1)	3																		---	---	---	---
RGS12	6002	broad.mit.edu	37	4	3319188	3319188	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3319188C>T	uc003ggw.2	+	2	2195	c.1291C>T	c.(1291-1293)CAG>TAG	p.Q431*	RGS12_uc003ggu.2_Nonsense_Mutation_p.Q431*|RGS12_uc010ics.1_Intron|RGS12_uc011bvr.1_RNA|RGS12_uc003ggv.2_Nonsense_Mutation_p.Q431*|RGS12_uc003ggx.1_Nonsense_Mutation_p.Q431*	NM_198229	NP_937872	O14924	RGS12_HUMAN	regulator of G-protein signalling 12 isoform 1	431						condensed nuclear chromosome|cytoplasm|plasma membrane	GTPase activator activity|receptor signaling protein activity			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)														---	---	---	---
DOK7	285489	broad.mit.edu	37	4	3475160	3475160	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3475160A>T	uc003ghd.2	+	3	198	c.128A>T	c.(127-129)GAC>GTC	p.D43V	DOK7_uc003ghe.2_5'UTR	NM_173660	NP_775931	Q18PE1	DOK7_HUMAN	downstream of tyrosine kinase 7 isoform 1	43	PH.				positive regulation of protein tyrosine kinase activity	cell junction|synapse	insulin receptor binding|protein kinase binding			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)														---	---	---	---
DOK7	285489	broad.mit.edu	37	4	3494492	3494492	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3494492A>G	uc003ghd.2	+	7	849	c.779A>G	c.(778-780)GAC>GGC	p.D260G	DOK7_uc003ghe.2_Missense_Mutation_p.D122G|DOK7_uc003ghf.2_Missense_Mutation_p.T2A|DOK7_uc003ghg.1_5'Flank	NM_173660	NP_775931	Q18PE1	DOK7_HUMAN	downstream of tyrosine kinase 7 isoform 1	260					positive regulation of protein tyrosine kinase activity	cell junction|synapse	insulin receptor binding|protein kinase binding			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)														---	---	---	---
ADRA2C	152	broad.mit.edu	37	4	3768705	3768705	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3768705C>T	uc003ghm.2	+	1	410	c.372C>T	c.(370-372)TGC>TGT	p.C124C	ADRA2C_uc010icx.2_Silent_p.C124C	NM_000683	NP_000674	P18825	ADA2C_HUMAN	alpha-2C-adrenergic receptor	124	Extracellular (By similarity).				activation of MAPK activity by adrenergic receptor signaling pathway|activation of protein kinase B activity|blood coagulation|cell-cell signaling|energy reserve metabolic process|epidermal growth factor receptor transactivation by G-protein coupled receptor signaling pathway|negative regulation of epinephrine secretion|negative regulation of norepinephrine secretion|positive regulation of neuron differentiation|regulation of insulin secretion	endosome|integral to plasma membrane	alpha-2A adrenergic receptor binding|alpha2-adrenergic receptor activity|epinephrine binding|protein heterodimerization activity|protein homodimerization activity				0				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)	Bethanidine(DB00217)|Brimonidine(DB00484)|Debrisoquin(DB04840)|Fenoldopam(DB00800)|Guanadrel Sulfate(DB00226)|Guanethidine(DB01170)|Lofexidine(DB04948)|Norepinephrine(DB00368)|Yohimbine(DB01392)													---	---	---	---
STK32B	55351	broad.mit.edu	37	4	5461914	5461914	+	Missense_Mutation	SNP	G	A	A	rs144030427		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5461914G>A	uc003gih.1	+	9	932	c.868G>A	c.(868-870)GCG>ACG	p.A290T	STK32B_uc010ida.1_Missense_Mutation_p.A243T	NM_018401	NP_060871	Q9NY57	ST32B_HUMAN	serine/threonine kinase 32B	290							ATP binding|metal ion binding|protein serine/threonine kinase activity			breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5																OREG0016061	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
JAKMIP1	152789	broad.mit.edu	37	4	6087218	6087218	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6087218G>A	uc003giu.3	-	4	1039	c.763C>T	c.(763-765)CGG>TGG	p.R255W	JAKMIP1_uc010idb.1_Missense_Mutation_p.R255W|JAKMIP1_uc010idc.1_Missense_Mutation_p.R90W|JAKMIP1_uc010idd.1_Missense_Mutation_p.R255W|JAKMIP1_uc011bwc.1_Missense_Mutation_p.R90W|JAKMIP1_uc003giv.3_Missense_Mutation_p.R255W|JAKMIP1_uc010ide.2_Missense_Mutation_p.R255W	NM_144720	NP_653321	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein	255	Potential.|Mediates association with microtubules.				protein transport	cytoplasm|membrane|microtubule|peripheral to membrane of membrane fraction|ribonucleoprotein complex	GABA receptor binding|RNA binding			large_intestine(1)|pancreas(1)|ovary(1)|skin(1)	4																		---	---	---	---
KIAA0232	9778	broad.mit.edu	37	4	6864748	6864748	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:6864748G>T	uc003gjr.3	+	7	3102	c.2639G>T	c.(2638-2640)AGG>ATG	p.R880M	KIAA0232_uc003gjq.3_Missense_Mutation_p.R880M	NM_014743	NP_055558	Q92628	K0232_HUMAN	hypothetical protein LOC9778	880							ATP binding			ovary(2)	2																		---	---	---	---
TBC1D14	57533	broad.mit.edu	37	4	7026888	7026888	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7026888G>A	uc011bwg.1	+	13	1994	c.1915G>A	c.(1915-1917)GCC>ACC	p.A639T	TBC1D14_uc003gjs.3_Missense_Mutation_p.A639T|TBC1D14_uc010idh.2_Missense_Mutation_p.A359T|TBC1D14_uc011bwh.1_Missense_Mutation_p.A286T|TBC1D14_uc003gju.3_Missense_Mutation_p.A130T	NM_001113361	NP_001106832	Q9P2M4	TBC14_HUMAN	TBC1 domain family, member 14 isoform a	639						intracellular	Rab GTPase activator activity			ovary(1)|pancreas(1)	2																		---	---	---	---
AFAP1	60312	broad.mit.edu	37	4	7820794	7820794	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7820794C>T	uc003gkg.1	-						AFAP1_uc011bwk.1_Intron	NM_198595	NP_940997			actin filament associated protein 1							actin cytoskeleton|cytoplasm|focal adhesion	actin binding				0																		---	---	---	---
AFAP1	60312	broad.mit.edu	37	4	7840365	7840365	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7840365C>T	uc003gkg.1	-	6	885	c.612G>A	c.(610-612)ACG>ACA	p.T204T	AFAP1_uc011bwk.1_Silent_p.T204T	NM_198595	NP_940997	Q8N556	AFAP1_HUMAN	actin filament associated protein 1	204	PH 1.					actin cytoskeleton|cytoplasm|focal adhesion	actin binding				0																		---	---	---	---
ABLIM2	84448	broad.mit.edu	37	4	8089918	8089918	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8089918C>T	uc003gko.2	-	4	575	c.432G>A	c.(430-432)GCG>GCA	p.A144A	ABLIM2_uc003gkj.3_Silent_p.A144A|ABLIM2_uc003gkm.3_Silent_p.A144A|ABLIM2_uc003gkp.2_Silent_p.A144A|ABLIM2_uc003gkq.2_Silent_p.A144A|ABLIM2_uc003gkr.2_Silent_p.A144A|ABLIM2_uc003gks.3_Silent_p.A144A|ABLIM2_uc011bwl.1_Silent_p.A149A	NM_001130084	NP_001123556	Q6H8Q1	ABLM2_HUMAN	actin binding LIM protein family, member 2	144					axon guidance|cytoskeleton organization	actin cytoskeleton|cytoplasm|intermediate filament cytoskeleton|nucleus	actin binding|zinc ion binding			pancreas(3)	3																		---	---	---	---
ACOX3	8310	broad.mit.edu	37	4	8401375	8401375	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:8401375C>T	uc010idk.2	-	8	926	c.781G>A	c.(781-783)GCC>ACC	p.A261T	ACOX3_uc003glc.3_Missense_Mutation_p.A261T|ACOX3_uc003gld.3_Missense_Mutation_p.A261T|ACOX3_uc003gle.1_Missense_Mutation_p.A166T	NM_003501	NP_003492	O15254	ACOX3_HUMAN	acyl-Coenzyme A oxidase 3 isoform a	261					bile acid metabolic process|fatty acid beta-oxidation using acyl-CoA oxidase	peroxisomal matrix	acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding|pristanoyl-CoA oxidase activity			central_nervous_system(1)	1																		---	---	---	---
DRD5	1816	broad.mit.edu	37	4	9783954	9783954	+	Missense_Mutation	SNP	G	A	A	rs147038465		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9783954G>A	uc003gmb.3	+	1	697	c.301G>A	c.(301-303)GCC>ACC	p.A101T		NM_000798	NP_000789	P21918	DRD5_HUMAN	dopamine receptor D5	101	Helical; Name=2; (Potential).				activation of adenylate cyclase activity by dopamine receptor signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|cellular calcium ion homeostasis|negative regulation of NAD(P)H oxidase activity|reactive oxygen species metabolic process|synaptic transmission, dopaminergic	integral to plasma membrane				skin(1)	1					Apomorphine(DB00714)|Carphenazine(DB01038)|Fenoldopam(DB00800)|Zuclopenthixol(DB01624)													---	---	---	---
DRD5	1816	broad.mit.edu	37	4	9784407	9784407	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:9784407G>A	uc003gmb.3	+	1	1150	c.754G>A	c.(754-756)GCC>ACC	p.A252T		NM_000798	NP_000789	P21918	DRD5_HUMAN	dopamine receptor D5	252	Cytoplasmic (Potential).				activation of adenylate cyclase activity by dopamine receptor signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|cellular calcium ion homeostasis|negative regulation of NAD(P)H oxidase activity|reactive oxygen species metabolic process|synaptic transmission, dopaminergic	integral to plasma membrane				skin(1)	1					Apomorphine(DB00714)|Carphenazine(DB01038)|Fenoldopam(DB00800)|Zuclopenthixol(DB01624)													---	---	---	---
ZNF518B	85460	broad.mit.edu	37	4	10445653	10445653	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:10445653G>A	uc003gmn.2	-	3	2787	c.2300C>T	c.(2299-2301)GCC>GTC	p.A767V		NM_053042	NP_444270	Q9C0D4	Z518B_HUMAN	zinc finger protein 518B	767					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)	4																		---	---	---	---
FBXL5	26234	broad.mit.edu	37	4	15627107	15627107	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15627107A>G	uc003goc.1	-	9	1721	c.1618T>C	c.(1618-1620)TCT>CCT	p.S540P	FBXL5_uc010idw.1_Missense_Mutation_p.S453P|FBXL5_uc003gob.1_Missense_Mutation_p.S414P|FBXL5_uc010idx.1_Missense_Mutation_p.S539P|FBXL5_uc003god.1_Missense_Mutation_p.S523P|FBXL5_uc010idy.1_Missense_Mutation_p.S540P	NM_012161	NP_036293	Q9UKA1	FBXL5_HUMAN	F-box and leucine-rich repeat protein 5 isoform	540					iron ion homeostasis|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	perinuclear region of cytoplasm|SCF ubiquitin ligase complex	iron ion binding|protein binding|ubiquitin-protein ligase activity				0																		---	---	---	---
CD38	952	broad.mit.edu	37	4	15826517	15826517	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:15826517G>A	uc011bxc.1	+	3	484	c.377G>A	c.(376-378)AGC>AAC	p.S126N	CD38_uc003goj.1_Missense_Mutation_p.S126N|CD38_uc003gol.1_Missense_Mutation_p.S126N	NM_001775	NP_001766	P28907	CD38_HUMAN	CD38 antigen	126	Extracellular (Potential).				B cell receptor signaling pathway|induction of apoptosis by extracellular signals|negative regulation of apoptosis|negative regulation of transcription, DNA-dependent|positive regulation of B cell proliferation|positive regulation of transcription, DNA-dependent|response to drug	integral to membrane|plasma membrane	binding|NAD+ nucleosidase activity|receptor activity			ovary(2)	2																		---	---	---	---
DCAF16	54876	broad.mit.edu	37	4	17805578	17805578	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:17805578A>G	uc003gpn.2	-	3	1248	c.187T>C	c.(187-189)TCC>CCC	p.S63P	DCAF16_uc003gpo.2_RNA	NM_017741	NP_060211	Q9NXF7	DCA16_HUMAN	DDB1 and CUL4 associated factor 16	63						CUL4 RING ubiquitin ligase complex				ovary(1)	1																		---	---	---	---
SLIT2	9353	broad.mit.edu	37	4	20544140	20544140	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20544140C>A	uc003gpr.1	+	21	2371	c.2167C>A	c.(2167-2169)CCA>ACA	p.P723T	SLIT2_uc003gps.1_Missense_Mutation_p.P715T	NM_004787	NP_004778	O94813	SLIT2_HUMAN	slit homolog 2 precursor	723	LRRNT 4.				apoptosis involved in luteolysis|axon extension involved in axon guidance|branching morphogenesis of a tube|cell migration involved in sprouting angiogenesis|cellular response to heparin|cellular response to hormone stimulus|chemorepulsion involved in postnatal olfactory bulb interneuron migration|corticospinal neuron axon guidance through spinal cord|induction of negative chemotaxis|motor axon guidance|negative regulation of actin filament polymerization|negative regulation of cell growth|negative regulation of cellular response to growth factor stimulus|negative regulation of chemokine-mediated signaling pathway|negative regulation of endothelial cell migration|negative regulation of lamellipodium assembly|negative regulation of mononuclear cell migration|negative regulation of neutrophil chemotaxis|negative regulation of protein phosphorylation|negative regulation of retinal ganglion cell axon guidance|negative regulation of small GTPase mediated signal transduction|negative regulation of smooth muscle cell chemotaxis|negative regulation of vascular permeability|positive regulation of apoptosis|positive regulation of axonogenesis|response to cortisol stimulus|retinal ganglion cell axon guidance|Roundabout signaling pathway|ureteric bud development	cell surface|cytoplasm|extracellular space|plasma membrane	calcium ion binding|GTPase inhibitor activity|heparin binding|laminin-1 binding|protein homodimerization activity|proteoglycan binding|Roundabout binding			central_nervous_system(4)|skin(4)|ovary(3)	11																		---	---	---	---
KCNIP4	80333	broad.mit.edu	37	4	20884266	20884266	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:20884266C>T	uc003gqe.2	-						KCNIP4_uc003gqf.1_Intron|KCNIP4_uc003gqg.1_Intron|KCNIP4_uc003gqh.1_Intron|KCNIP4_uc003gqi.1_Intron|KCNIP4_uc010iel.2_Missense_Mutation_p.C23Y|KCNIP4_uc003gqd.3_Missense_Mutation_p.C6Y	NM_147182	NP_671711			Kv channel interacting protein 4 isoform 3							plasma membrane	calcium ion binding|potassium channel activity|protein binding|voltage-gated ion channel activity				0		Breast(46;0.134)																---	---	---	---
GPR125	166647	broad.mit.edu	37	4	22389385	22389385	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22389385A>G	uc003gqm.1	-	19	4174	c.3909T>C	c.(3907-3909)GGT>GGC	p.G1303G	GPR125_uc010ieo.1_Silent_p.G1159G|GPR125_uc003gql.1_Silent_p.G430G	NM_145290	NP_660333	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125 precursor	1303	Cytoplasmic (Potential).				neuropeptide signaling pathway	integral to membrane	G-protein coupled receptor activity			skin(1)	1		Breast(46;0.198)																---	---	---	---
GPR125	166647	broad.mit.edu	37	4	22390718	22390718	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:22390718C>T	uc003gqm.1	-	18	2981	c.2716G>A	c.(2716-2718)GCA>ACA	p.A906T	GPR125_uc010ieo.1_Missense_Mutation_p.A762T|GPR125_uc003gql.1_Missense_Mutation_p.A33T	NM_145290	NP_660333	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125 precursor	906	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane	G-protein coupled receptor activity			skin(1)	1		Breast(46;0.198)																---	---	---	---
PPARGC1A	10891	broad.mit.edu	37	4	23803876	23803876	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:23803876C>A	uc003gqs.2	-	11	2232	c.2112G>T	c.(2110-2112)GAG>GAT	p.E704D	PPARGC1A_uc003gqt.2_RNA	NM_013261	NP_037393	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor	704	RRM.				androgen receptor signaling pathway|brown fat cell differentiation|cellular glucose homeostasis|digestion|fatty acid oxidation|gluconeogenesis|mitochondrion organization|mRNA processing|neuron death|positive regulation of fatty acid oxidation|positive regulation of gluconeogenesis|positive regulation of histone acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|protein complex assembly|protein stabilization|response to muscle activity|response to starvation|RNA splicing|temperature homeostasis|transcription initiation from RNA polymerase II promoter	DNA-directed RNA polymerase II, core complex	androgen receptor binding|DNA binding|ligand-dependent nuclear receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|nucleotide binding|RNA binding|RNA polymerase II transcription cofactor activity|transcription factor binding			ovary(2)|lung(2)|kidney(2)|skin(2)	8		Breast(46;0.0503)																---	---	---	---
DHX15	1665	broad.mit.edu	37	4	24531405	24531405	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24531405A>G	uc003gqx.2	-						DHX15_uc003gqv.2_Intron|DHX15_uc003gqw.2_Intron	NM_001358	NP_001349			DEAH (Asp-Glu-Ala-His) box polypeptide 15						mRNA processing	U12-type spliceosomal complex	ATP binding|ATP-dependent helicase activity|nucleic acid binding|RNA helicase activity			ovary(1)	1		Breast(46;0.0503)																---	---	---	---
CCDC149	91050	broad.mit.edu	37	4	24836620	24836620	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24836620T>C	uc011bxr.1	-	9	914	c.770A>G	c.(769-771)CAG>CGG	p.Q257R	CCDC149_uc003grc.2_Missense_Mutation_p.Q257R|CCDC149_uc003grb.2_RNA|CCDC149_uc003grd.2_Intron|CCDC149_uc003gre.2_Missense_Mutation_p.Q202R|CCDC149_uc011bxq.1_Missense_Mutation_p.Q130R	NM_173463	NP_775734	B4DZG3	B4DZG3_HUMAN	coiled-coil domain containing 149 isoform 1	257											0		Breast(46;0.173)																---	---	---	---
LGI2	55203	broad.mit.edu	37	4	25005320	25005320	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25005320G>A	uc003grf.2	-	8	1490	c.1391C>T	c.(1390-1392)GCC>GTC	p.A464V		NM_018176	NP_060646	Q8N0V4	LGI2_HUMAN	leucine-rich repeat LGI family, member 2	464	EAR 6.					extracellular region					0		Breast(46;0.173)																---	---	---	---
PI4K2B	55300	broad.mit.edu	37	4	25256832	25256832	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25256832C>T	uc003grk.2	+	3	702	c.569C>T	c.(568-570)GCG>GTG	p.A190V	PI4K2B_uc011bxs.1_Missense_Mutation_p.A94V	NM_018323	NP_060793	Q8TCG2	P4K2B_HUMAN	phosphatidylinositol 4-kinase type 2 beta	190	PI3K/PI4K.					cytoplasm|membrane	1-phosphatidylinositol 4-kinase activity|ATP binding			ovary(2)|skin(2)	4		Breast(46;0.173)																---	---	---	---
ANAPC4	29945	broad.mit.edu	37	4	25419360	25419360	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25419360T>C	uc003gro.2	+	28	2327	c.2198T>C	c.(2197-2199)GTG>GCG	p.V733A	ANAPC4_uc003grp.2_Missense_Mutation_p.V619A|ANAPC4_uc003grq.2_Missense_Mutation_p.V186A	NM_013367	NP_037499	Q9UJX5	APC4_HUMAN	anaphase-promoting complex subunit 4	733					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|G2/M transition of mitotic cell cycle|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm	protein phosphatase binding|ubiquitin-protein ligase activity			ovary(2)|large_intestine(1)|pancreas(1)|skin(1)	5		Breast(46;0.0503)																---	---	---	---
RBPJ	3516	broad.mit.edu	37	4	26417169	26417169	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26417169C>A	uc003grx.1	+	5	503	c.267C>A	c.(265-267)CGC>CGA	p.R89R	RBPJ_uc003gry.1_Silent_p.R74R|RBPJ_uc003grz.1_Silent_p.R89R|RBPJ_uc011bxt.1_Silent_p.R89R|RBPJ_uc003gsa.1_Silent_p.R75R|RBPJ_uc003gsb.1_Silent_p.R76R|RBPJ_uc003gsc.1_Silent_p.R75R	NM_005349	NP_005340	Q06330	SUH_HUMAN	recombining binding protein suppressor of	89					DNA recombination|negative regulation of transcription, DNA-dependent|positive regulation of transcription of Notch receptor target	cytoplasm|nucleolus|nucleoplasm	DNA binding|protein binding|recombinase activity|sequence-specific DNA binding transcription factor activity			ovary(1)|lung(1)|central_nervous_system(1)	3		Breast(46;0.0503)																---	---	---	---
CCKAR	886	broad.mit.edu	37	4	26483510	26483510	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26483510C>T	uc003gse.1	-	5	1190	c.1037G>A	c.(1036-1038)CGC>CAC	p.R346H		NM_000730	NP_000721	P32238	CCKAR_HUMAN	cholecystokinin A receptor	346	Extracellular (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|elevation of cytosolic calcium ion concentration|response to nutrient	integral to plasma membrane	cholecystokinin receptor activity			lung(3)|pancreas(1)	4		Breast(46;0.0503)			Ceruletide(DB00403)													---	---	---	---
TBC1D19	55296	broad.mit.edu	37	4	26638909	26638909	+	Splice_Site	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26638909T>C	uc003gsf.3	+	5	639	c.369_splice	c.e5+2	p.K123_splice	TBC1D19_uc010iew.2_Splice_Site_p.K123_splice|TBC1D19_uc011bxu.1_Splice_Site_p.K58_splice	NM_018317	NP_060787			TBC1 domain family, member 19							intracellular	Rab GTPase activator activity			breast(1)	1		Breast(46;0.0503)																---	---	---	---
STIM2	57620	broad.mit.edu	37	4	26921207	26921207	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:26921207A>C	uc003gsh.3	+	2	710	c.494A>C	c.(493-495)CAA>CCA	p.Q165P	STIM2_uc003gsg.3_Missense_Mutation_p.Q165P|STIM2_uc010iex.2_Missense_Mutation_p.Q165P	NM_020860	NP_065911	Q9P246	STIM2_HUMAN	stromal interaction molecule 2	78	EF-hand.|Extracellular (Potential).				activation of store-operated calcium channel activity|calcium ion transport|cellular calcium ion homeostasis|negative regulation of calcium ion transport via store-operated calcium channel activity	endoplasmic reticulum membrane|integral to membrane|plasma membrane	calcium channel regulator activity|calcium ion binding|protein binding			central_nervous_system(1)|skin(1)	2		Breast(46;0.0503)																---	---	---	---
STIM2	57620	broad.mit.edu	37	4	27010471	27010471	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27010471G>A	uc003gsh.3	+	11	1837	c.1621G>A	c.(1621-1623)GCC>ACC	p.A541T	STIM2_uc003gsg.3_Missense_Mutation_p.A533T|STIM2_uc010iex.2_Missense_Mutation_p.A533T|STIM2_uc010iey.2_Missense_Mutation_p.A157T	NM_020860	NP_065911	Q9P246	STIM2_HUMAN	stromal interaction molecule 2	446	Cytoplasmic (Potential).				activation of store-operated calcium channel activity|calcium ion transport|cellular calcium ion homeostasis|negative regulation of calcium ion transport via store-operated calcium channel activity	endoplasmic reticulum membrane|integral to membrane|plasma membrane	calcium channel regulator activity|calcium ion binding|protein binding			central_nervous_system(1)|skin(1)	2		Breast(46;0.0503)																---	---	---	---
STIM2	57620	broad.mit.edu	37	4	27019446	27019446	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:27019446G>A	uc003gsh.3	+	12	2104	c.1888G>A	c.(1888-1890)GCC>ACC	p.A630T	STIM2_uc003gsg.3_Missense_Mutation_p.A622T|STIM2_uc010iex.2_Missense_Mutation_p.A622T|STIM2_uc010iey.2_Missense_Mutation_p.A246T	NM_020860	NP_065911	Q9P246	STIM2_HUMAN	stromal interaction molecule 2	535	Cytoplasmic (Potential).|His/Pro-rich.				activation of store-operated calcium channel activity|calcium ion transport|cellular calcium ion homeostasis|negative regulation of calcium ion transport via store-operated calcium channel activity	endoplasmic reticulum membrane|integral to membrane|plasma membrane	calcium channel regulator activity|calcium ion binding|protein binding			central_nervous_system(1)|skin(1)	2		Breast(46;0.0503)																---	---	---	---
ARAP2	116984	broad.mit.edu	37	4	36150025	36150025	+	Splice_Site	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:36150025A>G	uc003gsq.1	-	17	3338	c.3000_splice	c.e17+1	p.K1000_splice		NM_015230	NP_056045			ArfGAP with RhoGAP domain, ankyrin repeat and PH						regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytosol	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
ARAP2	116984	broad.mit.edu	37	4	36163159	36163159	+	Silent	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:36163159A>C	uc003gsq.1	-	12	2525	c.2187T>G	c.(2185-2187)TCT>TCG	p.S729S	ARAP2_uc003gsr.1_Silent_p.S729S	NM_015230	NP_056045	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH	729	Arf-GAP.				regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytosol	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
PGM2	55276	broad.mit.edu	37	4	37848697	37848697	+	Missense_Mutation	SNP	C	T	T	rs147924614		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:37848697C>T	uc011byb.1	+	9	1226	c.1153C>T	c.(1153-1155)CGG>TGG	p.R385W	PGM2_uc011bya.1_Missense_Mutation_p.R246W|PGM2_uc011byc.1_Missense_Mutation_p.R225W	NM_018290	NP_060760	Q96G03	PGM2_HUMAN	phosphoglucomutase 2	385					glucose 1-phosphate metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol	magnesium ion binding|phosphoglucomutase activity|phosphopentomutase activity			ovary(1)	1																		---	---	---	---
TLR6	10333	broad.mit.edu	37	4	38829386	38829386	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:38829386C>A	uc003gtm.2	-	1	1775	c.1709G>T	c.(1708-1710)AGC>ATC	p.S570I	TLR6_uc010ifg.1_Missense_Mutation_p.S570I	NM_006068	NP_006059	Q9Y2C9	TLR6_HUMAN	toll-like receptor 6 precursor	570	LRRCT.|Extracellular (Potential).				activation of NF-kappaB-inducing kinase activity|cellular response to diacyl bacterial lipopeptide|defense response to bacterium|detection of diacyl bacterial lipopeptide|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-6 biosynthetic process|positive regulation of JUN kinase activity|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	integral to plasma membrane|phagocytic vesicle membrane	lipopeptide binding|transmembrane receptor activity			ovary(2)	2																		---	---	---	---
KLB	152831	broad.mit.edu	37	4	39436296	39436296	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39436296C>T	uc003gua.2	+	2	1389	c.1292C>T	c.(1291-1293)ACG>ATG	p.T431M	KLB_uc011byj.1_Missense_Mutation_p.T431M	NM_175737	NP_783864	Q86Z14	KLOTB_HUMAN	klotho beta	431	Extracellular (Potential).|Glycosyl hydrolase-1 1.				carbohydrate metabolic process	integral to membrane|plasma membrane	cation binding|fibroblast growth factor binding|hydrolase activity, hydrolyzing O-glycosyl compounds			skin(1)	1																		---	---	---	---
CHRNA9	55584	broad.mit.edu	37	4	40351213	40351213	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40351213T>C	uc003gva.1	+	4	696	c.680T>C	c.(679-681)GTC>GCC	p.V227A		NM_017581	NP_060051	Q9UGM1	ACHA9_HUMAN	cholinergic receptor, nicotinic, alpha 9	227	Extracellular (Potential).				elevation of cytosolic calcium ion concentration|synaptic transmission	cell junction|postsynaptic membrane	calcium channel activity|receptor activity			breast(3)|skin(3)|central_nervous_system(1)	7					Nicotine(DB00184)													---	---	---	---
RBM47	54502	broad.mit.edu	37	4	40439840	40439840	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40439840G>A	uc003gvc.2	-	4	1781	c.1071C>T	c.(1069-1071)TAC>TAT	p.Y357Y	RBM47_uc003gvd.2_Silent_p.Y357Y|RBM47_uc003gve.2_RNA|RBM47_uc011bys.1_Silent_p.Y319Y|RBM47_uc003gvg.1_Silent_p.Y357Y	NM_001098634	NP_001092104	A0AV96	RBM47_HUMAN	RNA binding motif protein 47 isoform a	357						nucleus	nucleotide binding|RNA binding			breast(3)	3																		---	---	---	---
RBM47	54502	broad.mit.edu	37	4	40440371	40440371	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:40440371G>A	uc003gvc.2	-	4	1250	c.540C>T	c.(538-540)GAC>GAT	p.D180D	RBM47_uc003gvd.2_Silent_p.D180D|RBM47_uc003gve.2_RNA|RBM47_uc011bys.1_Silent_p.D142D|RBM47_uc003gvg.1_Silent_p.D180D	NM_001098634	NP_001092104	A0AV96	RBM47_HUMAN	RNA binding motif protein 47 isoform a	180	RRM 2.					nucleus	nucleotide binding|RNA binding			breast(3)	3																		---	---	---	---
SLC30A9	10463	broad.mit.edu	37	4	42025392	42025392	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42025392T>C	uc003gwl.2	+	6	747	c.601T>C	c.(601-603)TAC>CAC	p.Y201H	SLC30A9_uc011byx.1_5'UTR	NM_006345	NP_006336	Q6PML9	ZNT9_HUMAN	solute carrier family 30 (zinc transporter),	201					nucleotide-excision repair|zinc ion transport	cytoskeleton|integral to membrane|nucleus	cation transmembrane transporter activity|nucleotide binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
ATP8A1	10396	broad.mit.edu	37	4	42448638	42448638	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42448638T>G	uc003gwr.2	-	31	3152	c.2920A>C	c.(2920-2922)ACC>CCC	p.T974P	ATP8A1_uc003gwq.2_Missense_Mutation_p.T200P|ATP8A1_uc003gws.2_Missense_Mutation_p.T959P	NM_006095	NP_006086	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT),	974	Extracellular (Potential).				ATP biosynthetic process	chromaffin granule membrane|integral to membrane|plasma membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			skin(2)|central_nervous_system(1)	3					Phosphatidylserine(DB00144)													---	---	---	---
SLAIN2	57606	broad.mit.edu	37	4	48422238	48422238	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48422238C>A	uc003gya.3	+	7	1601	c.1457C>A	c.(1456-1458)CCT>CAT	p.P486H		NM_020846	NP_065897	Q9P270	SLAI2_HUMAN	SLAIN motif family, member 2	486						centrosome					0																		---	---	---	---
SLC10A4	201780	broad.mit.edu	37	4	48487028	48487028	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48487028A>T	uc003gyc.2	+	2	889	c.670A>T	c.(670-672)ATC>TTC	p.I224F		NM_152679	NP_689892	Q96EP9	NTCP4_HUMAN	solute carrier family 10, member 4	224	Extracellular (Potential).					integral to membrane	bile acid:sodium symporter activity			central_nervous_system(1)	1																		---	---	---	---
ZAR1	326340	broad.mit.edu	37	4	48496198	48496198	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48496198C>T	uc003gyd.2	+	4	1212	c.1212C>T	c.(1210-1212)TGC>TGT	p.C404C		NM_175619	NP_783318	Q86SH2	ZAR1_HUMAN	zygote arrest 1	404					multicellular organismal development	cytoplasm|membrane	bile acid:sodium symporter activity				0																		---	---	---	---
FRYL	285527	broad.mit.edu	37	4	48563495	48563495	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:48563495G>A	uc003gyh.1	-	33	4460	c.3855C>T	c.(3853-3855)GCC>GCT	p.A1285A	FRYL_uc003gyk.2_Silent_p.A1285A|FRYL_uc003gyi.1_Silent_p.A174A	NM_015030	NP_055845	O94915	FRYL_HUMAN	furry-like	1285					regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			skin(1)	1																		---	---	---	---
LRRC66	339977	broad.mit.edu	37	4	52861921	52861921	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:52861921C>T	uc003gzi.2	-	4	1280	c.1267G>A	c.(1267-1269)GAG>AAG	p.E423K		NM_001024611	NP_001019782	Q68CR7	LRC66_HUMAN	leucine rich repeat containing 66	423						integral to membrane				ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
LRRC66	339977	broad.mit.edu	37	4	52863906	52863906	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:52863906T>C	uc003gzi.2	-							NM_001024611	NP_001019782			leucine rich repeat containing 66							integral to membrane				ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
SPATA18	132671	broad.mit.edu	37	4	52945920	52945920	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:52945920G>A	uc003gzl.2	+	9	1468	c.1190G>A	c.(1189-1191)CGA>CAA	p.R397Q	SPATA18_uc010igl.1_RNA|SPATA18_uc011bzq.1_Missense_Mutation_p.R365Q|SPATA18_uc003gzk.1_Missense_Mutation_p.R397Q	NM_145263	NP_660306	Q8TC71	MIEAP_HUMAN	spermatogenesis associated 18 homolog	397					mitochondrial protein catabolic process|mitochondrion degradation by induced vacuole formation|response to DNA damage stimulus	mitochondrial outer membrane	protein binding			ovary(2)|skin(2)	4			GBM - Glioblastoma multiforme(4;1.77e-13)|LUSC - Lung squamous cell carcinoma(32;0.00204)															---	---	---	---
KDR	3791	broad.mit.edu	37	4	55984950	55984950	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:55984950T>C	uc003has.2	-	3	481	c.179A>G	c.(178-180)GAC>GGC	p.D60G	KDR_uc003hat.1_Missense_Mutation_p.D60G|KDR_uc011bzx.1_Missense_Mutation_p.D60G	NM_002253	NP_002244	P35968	VGFR2_HUMAN	kinase insert domain receptor precursor	60	Ig-like C2-type 1.|Extracellular (Potential).				angiogenesis|cell differentiation|interspecies interaction between organisms|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of focal adhesion assembly|positive regulation of positive chemotaxis|regulation of cell shape	integral to plasma membrane	ATP binding|growth factor binding|Hsp90 protein binding|integrin binding|receptor signaling protein tyrosine kinase activity|vascular endothelial growth factor receptor activity			lung(16)|soft_tissue(4)|central_nervous_system(4)|large_intestine(2)|stomach(2)|skin(2)|ovary(2)|kidney(1)	33	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Sorafenib(DB00398)|Sunitinib(DB01268)			Mis		NSCLC|angiosarcoma				Familial_Infantile_Hemangioma	TSP Lung(20;0.16)			---	---	---	---
KIAA1211	57482	broad.mit.edu	37	4	57164425	57164425	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57164425T>C	uc003hbk.2	+	4	421	c.30T>C	c.(28-30)AGT>AGC	p.S10S	KIAA1211_uc010iha.2_5'UTR	NM_020722	NP_065773	Q6ZU35	K1211_HUMAN	hypothetical protein LOC57482	10										ovary(1)|skin(1)	2	Glioma(25;0.08)|all_neural(26;0.101)																	---	---	---	---
KIAA1211	57482	broad.mit.edu	37	4	57181601	57181601	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57181601G>A	uc003hbk.2	+	8	2324	c.1933G>A	c.(1933-1935)GCG>ACG	p.A645T	KIAA1211_uc010iha.2_Missense_Mutation_p.A638T|KIAA1211_uc011bzz.1_Missense_Mutation_p.A555T|KIAA1211_uc003hbm.1_Missense_Mutation_p.A531T	NM_020722	NP_065773	Q6ZU35	K1211_HUMAN	hypothetical protein LOC57482	645										ovary(1)|skin(1)	2	Glioma(25;0.08)|all_neural(26;0.101)																	---	---	---	---
KIAA1211	57482	broad.mit.edu	37	4	57182238	57182238	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57182238G>A	uc003hbk.2	+	8	2961	c.2570G>A	c.(2569-2571)CGC>CAC	p.R857H	KIAA1211_uc010iha.2_Missense_Mutation_p.R850H|KIAA1211_uc011bzz.1_Missense_Mutation_p.R767H|KIAA1211_uc003hbm.1_Missense_Mutation_p.R743H	NM_020722	NP_065773	Q6ZU35	K1211_HUMAN	hypothetical protein LOC57482	857										ovary(1)|skin(1)	2	Glioma(25;0.08)|all_neural(26;0.101)																	---	---	---	---
AASDH	132949	broad.mit.edu	37	4	57215607	57215607	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57215607T>C	uc003hbn.2	-	11	2463	c.2310A>G	c.(2308-2310)TCA>TCG	p.S770S	AASDH_uc010ihb.2_Silent_p.S285S|AASDH_uc011caa.1_Silent_p.S617S|AASDH_uc003hbo.2_Silent_p.S670S|AASDH_uc011cab.1_Silent_p.S285S|AASDH_uc010ihc.2_Silent_p.S770S|AASDH_uc003hbp.2_Silent_p.S770S	NM_181806	NP_861522	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	770					fatty acid metabolic process		acid-thiol ligase activity|acyl carrier activity|ATP binding|cofactor binding			ovary(4)	4	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)																---	---	---	---
C4orf14	84273	broad.mit.edu	37	4	57829625	57829625	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:57829625T>C	uc003hck.2	-	7	2163	c.2088A>G	c.(2086-2088)ATA>ATG	p.I696M		NM_032313	NP_115689	Q8NC60	CD014_HUMAN	hypothetical protein LOC84273	696							GTP binding			ovary(1)|breast(1)	2	Glioma(25;0.08)|all_neural(26;0.181)																	---	---	---	---
LPHN3	23284	broad.mit.edu	37	4	62449405	62449405	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:62449405T>C	uc010ihh.2	+						LPHN3_uc003hcq.3_Intron|LPHN3_uc010ihg.1_Intron	NM_015236	NP_056051			latrophilin 3 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			lung(15)|ovary(1)|central_nervous_system(1)|pancreas(1)	18																		---	---	---	---
TMPRSS11B	132724	broad.mit.edu	37	4	69107481	69107481	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69107481G>A	uc003hdw.3	-	2	186	c.50C>T	c.(49-51)ACG>ATG	p.T17M		NM_182502	NP_872308	Q86T26	TM11B_HUMAN	transmembrane protease, serine 11B	17	Cytoplasmic (Potential).				proteolysis	extracellular region|integral to plasma membrane	serine-type endopeptidase activity			ovary(1)	1																		---	---	---	---
YTHDC1	91746	broad.mit.edu	37	4	69182103	69182103	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69182103G>A	uc003hdx.2	-	16	2241	c.1888C>T	c.(1888-1890)CCT>TCT	p.P630S	YTHDC1_uc003hdy.2_Missense_Mutation_p.P612S	NM_001031732	NP_001026902	Q96MU7	YTDC1_HUMAN	splicing factor YT521-B isoform 1	630	Pro-rich.									upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
YTHDC1	91746	broad.mit.edu	37	4	69202941	69202941	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69202941T>C	uc003hdx.2	-	4	1040	c.687A>G	c.(685-687)GGA>GGG	p.G229G	YTHDC1_uc003hdy.2_Silent_p.G229G	NM_001031732	NP_001026902	Q96MU7	YTDC1_HUMAN	splicing factor YT521-B isoform 1	229	Glu-rich.									upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
UGT2A3	79799	broad.mit.edu	37	4	69817244	69817244	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:69817244T>C	uc003hef.2	-	1	266	c.235A>G	c.(235-237)ATG>GTG	p.M79V	UGT2A3_uc010ihp.1_RNA	NM_024743	NP_079019	Q6UWM9	UD2A3_HUMAN	UDP glucuronosyltransferase 2 family,	79	Extracellular (Potential).					integral to membrane	glucuronosyltransferase activity			ovary(1)|skin(1)	2																		---	---	---	---
CSN2	1447	broad.mit.edu	37	4	70825768	70825768	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:70825768T>C	uc003hes.3	-						CSN2_uc003het.3_Intron	NM_001891	NP_001882			casein beta precursor						calcium ion transport	extracellular region	calcium ion binding|enzyme inhibitor activity|transporter activity				0																		---	---	---	---
CSN3	1448	broad.mit.edu	37	4	71114734	71114734	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71114734G>A	uc003hfe.3	+	4	165	c.107G>A	c.(106-108)AGA>AAA	p.R36K		NM_005212	NP_005203	P07498	CASK_HUMAN	casein kappa precursor	36						extracellular region	protein binding			ovary(2)|kidney(1)|central_nervous_system(1)	4																		---	---	---	---
C4orf35	85438	broad.mit.edu	37	4	71201810	71201810	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71201810G>A	uc003hff.2	+	1	1140	c.1054G>A	c.(1054-1056)GTA>ATA	p.V352I		NM_033122	NP_149113	Q96KC9	CABS1_HUMAN	testis development protein NYD-SP26	352						flagellum	calcium ion binding				0		all_hematologic(202;0.196)																---	---	---	---
SMR3B	10879	broad.mit.edu	37	4	71255373	71255373	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71255373T>C	uc011cas.1	+						SMR3B_uc003hfh.2_Intron	NM_006685	NP_006676			submaxillary gland androgen regulated protein 3							extracellular space				skin(1)	1		all_hematologic(202;0.196)																---	---	---	---
RUFY3	22902	broad.mit.edu	37	4	71630237	71630237	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:71630237G>A	uc003hfq.2	+	4	1111	c.516G>A	c.(514-516)ATG>ATA	p.M172I	RUFY3_uc003hfp.3_Missense_Mutation_p.M232I|RUFY3_uc011cax.1_Missense_Mutation_p.M190I|RUFY3_uc003hfr.2_Missense_Mutation_p.M172I|RUFY3_uc011cay.1_Missense_Mutation_p.M108I	NM_014961	NP_055776	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3 isoform 2	172	RUN.				negative regulation of axonogenesis	filopodium|growth cone					0		all_hematologic(202;0.248)	Lung(101;0.235)															---	---	---	---
ANKRD17	26057	broad.mit.edu	37	4	73942778	73942778	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73942778A>G	uc003hgp.2	-	33	7748	c.7631T>C	c.(7630-7632)GTA>GCA	p.V2544A	ANKRD17_uc003hgo.2_Missense_Mutation_p.V2431A|ANKRD17_uc003hgq.2_Missense_Mutation_p.V2293A|ANKRD17_uc003hgr.2_Missense_Mutation_p.V2543A	NM_032217	NP_115593	O75179	ANR17_HUMAN	ankyrin repeat domain protein 17 isoform a	2544					interspecies interaction between organisms	cytoplasm|nucleus	RNA binding			ovary(5)|skin(3)|upper_aerodigestive_tract(1)|lung(1)	10	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)															---	---	---	---
ALB	213	broad.mit.edu	37	4	74279208	74279208	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74279208A>C	uc003hgs.3	+	8	988	c.915A>C	c.(913-915)AAA>AAC	p.K305N	ALB_uc003hgw.3_Missense_Mutation_p.K113N|ALB_uc011cbe.1_5'UTR|ALB_uc003hgt.3_Missense_Mutation_p.K305N|ALB_uc010iii.2_Missense_Mutation_p.K190N|ALB_uc003hgu.3_Missense_Mutation_p.K155N|ALB_uc003hgv.3_5'UTR|ALB_uc011cbf.1_Missense_Mutation_p.K195N|ALB_uc010iij.2_RNA|ALB_uc003hgx.3_5'UTR	NM_000477	NP_000468	P02768	ALBU_HUMAN	albumin preproprotein	305	Albumin 2.				bile acid and bile salt transport|bile acid metabolic process|cellular response to starvation|hemolysis by symbiont of host erythrocytes|lipoprotein metabolic process|maintenance of mitochondrion location|negative regulation of apoptosis|platelet activation|platelet degranulation|sodium-independent organic anion transport|transmembrane transport	extracellular space|platelet alpha granule lumen|protein complex	antioxidant activity|chaperone binding|copper ion binding|DNA binding|drug binding|fatty acid binding|pyridoxal phosphate binding|toxin binding			ovary(3)|skin(3)	6	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)		Acenocoumarol(DB01418)|Acitretin(DB00459)|Alfentanil(DB00802)|Aluminium(DB01370)|Auranofin(DB00995)|Bismuth(DB01402)|Captopril(DB01197)|Carboplatin(DB00958)|Cefalotin(DB00456)|Cefazolin(DB01327)|Cefonicid(DB01328)|Cefoperazone(DB01329)|Chlorpheniramine(DB01114)|Chlorpromazine(DB00477)|Ciprofloxacin(DB00537)|Clonazepam(DB01068)|Cloxacillin(DB01147)|Cytarabine(DB00987)|Dantrolene(DB01219)|Diclofenac(DB00586)|Diflunisal(DB00861)|Digitoxin(DB01396)|Estrone(DB00655)|Ethacrynic acid(DB00903)|Etodolac(DB00749)|Flurbiprofen(DB00712)|Gadobenate Dimeglumine(DB00743)|Gatifloxacin(DB01044)|Gliclazide(DB01120)|Halothane(DB01159)|Human Serum Albumin(DB00062)|Hyaluronidase(DB00070)|Ibuprofen(DB01050)|Insulin-detemir(DB01307)|Insulin-glargine(DB01308)|Iodipamide(DB04711)|Ketoprofen(DB01009)|Levamisole(DB00848)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Mefenamic acid(DB00784)|Mephenytoin(DB00532)|Methotrexate(DB00563)|Nortriptyline(DB00540)|Oxazepam(DB00842)|Paclitaxel(DB01229)|Phenprocoumon(DB00946)|Probenecid(DB01032)|Propofol(DB00818)|Pyridoxine(DB00165)|Salicyclic acid(DB00936)|Saquinavir(DB01232)|Serum albumin(DB00096)|Serum albumin iodonated(DB00064)|Sodium lauryl sulfate(DB00815)|Sucralfate(DB00364)|Sulfamethizole(DB00576)|Sulindac(DB00605)|Suprofen(DB00870)|Testosterone(DB00624)|Xanthophyll(DB00137)													---	---	---	---
AFP	174	broad.mit.edu	37	4	74316322	74316322	+	Intron	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:74316322C>A	uc003hgz.1	+						AFP_uc003hha.1_Intron|AFP_uc011cbg.1_Intron	NM_001134	NP_001125			alpha-fetoprotein precursor						transport		metal ion binding			ovary(1)	1	Breast(15;0.00102)		Epithelial(6;2.42e-05)|all cancers(17;0.000268)|OV - Ovarian serous cystadenocarcinoma(6;0.000324)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)											Alpha-Fetoprotein_Hereditary_Persistence_of				---	---	---	---
USO1	8615	broad.mit.edu	37	4	76695844	76695844	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76695844C>T	uc003hiu.2	+	7	746	c.571C>T	c.(571-573)CAG>TAG	p.Q191*	USO1_uc003hiv.2_Nonsense_Mutation_p.Q26*|USO1_uc003hiw.2_Nonsense_Mutation_p.Q26*	NM_003715	NP_003706	O60763	USO1_HUMAN	USO1 homolog, vesicle docking protein	191	Globular head.|ARM 3.				intracellular protein transport|vesicle fusion with Golgi apparatus	cytosol|Golgi membrane	protein binding|protein transporter activity			ovary(2)|central_nervous_system(1)	3			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)															---	---	---	---
PPEF2	5470	broad.mit.edu	37	4	76785646	76785646	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76785646C>T	uc003hix.2	-	16	2312	c.1955G>A	c.(1954-1956)CGA>CAA	p.R652Q	PPEF2_uc003hiy.2_RNA	NM_006239	NP_006230	O14830	PPE2_HUMAN	serine/threonine protein phosphatase with	652	EF-hand 2.				detection of stimulus involved in sensory perception|negative regulation of MAPKKK cascade|negative regulation of peptidyl-threonine phosphorylation|protein dephosphorylation|visual perception	cytoplasm|photoreceptor inner segment|photoreceptor outer segment	calcium ion binding|Hsp70 protein binding|Hsp90 protein binding|iron ion binding|manganese ion binding|mitogen-activated protein kinase kinase kinase binding|protein serine/threonine phosphatase activity			ovary(2)|lung(1)|central_nervous_system(1)	4			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)															---	---	---	---
SDAD1	55153	broad.mit.edu	37	4	76878827	76878827	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:76878827C>T	uc003hje.3	-	19	1732	c.1613G>A	c.(1612-1614)CGG>CAG	p.R538Q	SDAD1_uc003hjf.3_Missense_Mutation_p.R441Q|SDAD1_uc011cbr.1_Missense_Mutation_p.R501Q	NM_018115	NP_060585	Q9NVU7	SDA1_HUMAN	SDA1 domain containing 1	538					protein transport|ribosomal large subunit biogenesis	nucleolus	protein binding			ovary(1)	1			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)															---	---	---	---
CCDC158	339965	broad.mit.edu	37	4	77303773	77303773	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77303773C>A	uc003hkb.3	-	7	1057	c.904G>T	c.(904-906)GAA>TAA	p.E302*	CCDC158_uc003hkd.2_Nonsense_Mutation_p.E302*	NM_001042784	NP_001036249	Q5M9N0	CD158_HUMAN	coiled-coil domain containing 158	302	Potential.									skin(3)|ovary(2)|pancreas(1)	6																		---	---	---	---
FRAS1	80144	broad.mit.edu	37	4	79238582	79238582	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79238582G>T	uc003hlb.2	+	17	2320	c.1880G>T	c.(1879-1881)AGC>ATC	p.S627I	FRAS1_uc003hkw.2_Missense_Mutation_p.S627I|FRAS1_uc003hky.1_Missense_Mutation_p.S331I|FRAS1_uc003hkz.2_Missense_Mutation_p.S331I|FRAS1_uc003hla.1_Missense_Mutation_p.S138I	NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1	627	FU 5.|Extracellular (Potential).				cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5																		---	---	---	---
BMP2K	55589	broad.mit.edu	37	4	79781221	79781221	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79781221C>T	uc003hlk.2	+						BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_Intron	NM_198892	NP_942595			BMP-2 inducible kinase isoform a							nucleus	ATP binding|protein serine/threonine kinase activity			lung(1)	1																		---	---	---	---
BMP2K	55589	broad.mit.edu	37	4	79832781	79832781	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79832781G>A	uc003hlk.2	+	16	3246	c.3080G>A	c.(3079-3081)CGA>CAA	p.R1027Q	PAQR3_uc003hlm.2_Intron|PAQR3_uc003hln.2_Intron|uc010ijm.1_5'Flank	NM_198892	NP_942595	Q9NSY1	BMP2K_HUMAN	BMP-2 inducible kinase isoform a	1027						nucleus	ATP binding|protein serine/threonine kinase activity			lung(1)	1																		---	---	---	---
NAA11	84779	broad.mit.edu	37	4	80246701	80246701	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:80246701C>T	uc003hlt.3	-	1	471	c.331G>A	c.(331-333)GTC>ATC	p.V111I		NM_032693	NP_116082	Q9BSU3	NAA11_HUMAN	alpha-N-acetyltransferase 1B	111	N-acetyltransferase.					cytoplasm|nucleus	peptide alpha-N-acetyltransferase activity|protein binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
SEC31A	22872	broad.mit.edu	37	4	83801963	83801963	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:83801963G>T	uc003hnf.2	-	3	356	c.192C>A	c.(190-192)TCC>TCA	p.S64S	SEC31A_uc011ccl.1_Silent_p.S64S|SEC31A_uc003hnl.2_Silent_p.S64S|SEC31A_uc003hng.2_Silent_p.S64S|SEC31A_uc003hnh.2_Silent_p.S64S|SEC31A_uc003hni.2_Silent_p.S64S|SEC31A_uc003hnj.2_Silent_p.S64S|SEC31A_uc011ccm.1_Silent_p.S59S|SEC31A_uc011ccn.1_Silent_p.S64S|SEC31A_uc003hnk.2_Silent_p.S64S|SEC31A_uc003hnm.2_Silent_p.S64S|SEC31A_uc003hnn.1_Silent_p.S64S|SEC31A_uc003hno.2_Silent_p.S64S	NM_001077207	NP_001070675	O94979	SC31A_HUMAN	SEC31 homolog A isoform 1	64					COPII vesicle coating|post-translational protein modification|protein N-linked glycosylation via asparagine|protein transport|response to calcium ion	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|perinuclear region of cytoplasm	calcium-dependent protein binding		SEC31A/JAK2(4)|SEC31A/ALK(3)	haematopoietic_and_lymphoid_tissue(4)|soft_tissue(3)|breast(1)	8		Hepatocellular(203;0.114)																---	---	---	---
FAM175A	84142	broad.mit.edu	37	4	84403340	84403340	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:84403340G>T	uc003hou.2	-	2	210	c.145C>A	c.(145-147)CAA>AAA	p.Q49K	FAM175A_uc003hov.2_5'UTR	NM_139076	NP_620775	Q6UWZ7	F175A_HUMAN	coiled-coil domain containing 98	49	MPN-like.				chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of DNA repair|response to ionizing radiation	BRCA1-A complex	polyubiquitin binding			kidney(1)	1																		---	---	---	---
MAPK10	5602	broad.mit.edu	37	4	87022210	87022210	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87022210T>G	uc003hpq.2	-	7	792	c.725A>C	c.(724-726)GAG>GCG	p.E242A	MAPK10_uc010ikg.2_Missense_Mutation_p.E204A|MAPK10_uc003hpr.2_Missense_Mutation_p.E204A|MAPK10_uc003hps.2_Missense_Mutation_p.E242A|MAPK10_uc003hpt.2_Missense_Mutation_p.E242A|MAPK10_uc003hpu.2_Missense_Mutation_p.E242A|MAPK10_uc003hpv.2_Missense_Mutation_p.E97A|MAPK10_uc003hpn.2_5'Flank|MAPK10_uc003hpo.2_Missense_Mutation_p.E97A|MAPK10_uc011ccw.1_Missense_Mutation_p.E128A|MAPK10_uc003hpp.2_Missense_Mutation_p.E97A	NM_138982	NP_620448	P53779	MK10_HUMAN	mitogen-activated protein kinase 10 isoform 2	242	Protein kinase.				innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|regulation of sequence-specific DNA binding transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|JUN kinase activity|MAP kinase kinase activity|protein binding			stomach(1)|breast(1)|central_nervous_system(1)	3		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.243)		OV - Ovarian serous cystadenocarcinoma(123;0.002)														---	---	---	---
MAPK10	5602	broad.mit.edu	37	4	87028471	87028471	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87028471C>T	uc003hpq.2	-	4	338	c.271G>A	c.(271-273)GCC>ACC	p.A91T	MAPK10_uc010ikg.2_Missense_Mutation_p.A53T|MAPK10_uc003hpr.2_Missense_Mutation_p.A53T|MAPK10_uc003hps.2_Missense_Mutation_p.A91T|MAPK10_uc003hpt.2_Missense_Mutation_p.A91T|MAPK10_uc003hpu.2_Missense_Mutation_p.A91T|MAPK10_uc003hpv.2_5'UTR|MAPK10_uc010ikh.1_RNA|MAPK10_uc003hpo.2_5'UTR|MAPK10_uc011ccw.1_5'UTR|MAPK10_uc003hpp.2_5'UTR	NM_138982	NP_620448	P53779	MK10_HUMAN	mitogen-activated protein kinase 10 isoform 2	91	Protein kinase.				innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|regulation of sequence-specific DNA binding transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|JUN kinase activity|MAP kinase kinase activity|protein binding			stomach(1)|breast(1)|central_nervous_system(1)	3		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.243)		OV - Ovarian serous cystadenocarcinoma(123;0.002)														---	---	---	---
HSD17B11	51170	broad.mit.edu	37	4	88261752	88261752	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:88261752T>C	uc003hqp.2	-	6	935	c.702A>G	c.(700-702)GGA>GGG	p.G234G		NM_016245	NP_057329	Q8NBQ5	DHB11_HUMAN	estradiol 17-beta-dehydrogenase 11	234					androgen catabolic process|steroid biosynthetic process	cytoplasm|extracellular region	binding|estradiol 17-beta-dehydrogenase activity			ovary(2)	2		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000339)														---	---	---	---
HERC6	55008	broad.mit.edu	37	4	89311938	89311938	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:89311938G>T	uc011cdi.1	+	4	754	c.571G>T	c.(571-573)GCT>TCT	p.A191S	HERC6_uc003hrp.1_RNA|HERC6_uc011cdj.1_Missense_Mutation_p.A191S|HERC6_uc011cdk.1_RNA|HERC6_uc011cdl.1_RNA	NM_017912	NP_060382	Q8IVU3	HERC6_HUMAN	hect domain and RLD 6 isoform 1	191	RCC1 3.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytosol	ubiquitin-protein ligase activity			lung(3)|ovary(1)|kidney(1)	5		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000222)														---	---	---	---
MMRN1	22915	broad.mit.edu	37	4	90833107	90833107	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:90833107A>G	uc003hst.2	+	3	827	c.756A>G	c.(754-756)ATA>ATG	p.I252M	MMRN1_uc010iku.2_Missense_Mutation_p.I218M|MMRN1_uc011cds.1_Translation_Start_Site	NM_007351	NP_031377	Q13201	MMRN1_HUMAN	multimerin 1	252	EMI.				cell adhesion|platelet activation|platelet degranulation	extracellular region|platelet alpha granule lumen				ovary(4)	4		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)														---	---	---	---
GRID2	2895	broad.mit.edu	37	4	93511442	93511442	+	Intron	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:93511442G>T	uc011cdt.1	+						GRID2_uc010ikx.2_Intron|GRID2_uc011cdu.1_Intron	NM_001510	NP_001501			glutamate receptor, ionotropic, delta 2						glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)													---	---	---	---
GRID2	2895	broad.mit.edu	37	4	94137973	94137973	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:94137973C>A	uc011cdt.1	+	6	1132	c.874C>A	c.(874-876)CAG>AAG	p.Q292K	GRID2_uc010ikx.2_Missense_Mutation_p.Q292K|GRID2_uc011cdu.1_Missense_Mutation_p.Q197K|GRID2_uc010ikz.1_5'UTR	NM_001510	NP_001501	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	292	Extracellular (Potential).				glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)													---	---	---	---
PDLIM5	10611	broad.mit.edu	37	4	95561510	95561510	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95561510C>T	uc003hti.2	+	9	1343	c.1192C>T	c.(1192-1194)CCA>TCA	p.P398S	PDLIM5_uc011cdx.1_Missense_Mutation_p.P295S|PDLIM5_uc003hth.2_Missense_Mutation_p.P289S|PDLIM5_uc003htj.2_Missense_Mutation_p.P73S|PDLIM5_uc003htk.2_Missense_Mutation_p.P427S|PDLIM5_uc011cdy.1_Missense_Mutation_p.P276S|PDLIM5_uc003htl.2_Missense_Mutation_p.P73S	NM_006457	NP_006448	Q96HC4	PDLI5_HUMAN	PDZ and LIM domain 5 isoform a	398					regulation of dendritic spine morphogenesis|regulation of synaptogenesis	actin cytoskeleton|cell junction|cytosol|postsynaptic density|postsynaptic membrane|synaptosome	actin binding|actinin binding|protein kinase C binding|zinc ion binding			ovary(1)|skin(1)	2		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.84e-09)														---	---	---	---
BMPR1B	658	broad.mit.edu	37	4	96051185	96051185	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:96051185T>C	uc003htm.3	+	9	1032	c.758T>C	c.(757-759)ATG>ACG	p.M253T	BMPR1B_uc010ilb.2_Missense_Mutation_p.M253T|BMPR1B_uc003htn.3_Missense_Mutation_p.M253T	NM_001203	NP_001194	O00238	BMR1B_HUMAN	bone morphogenetic protein receptor, type IB	253	Cytoplasmic (Potential).|Protein kinase.				BMP signaling pathway|cartilage condensation|eye development|limb morphogenesis|ovarian cumulus expansion|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	receptor complex	ATP binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta receptor activity			lung(4)|skin(2)|stomach(1)|breast(1)	8		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.51e-07)														---	---	---	---
ADH6	130	broad.mit.edu	37	4	100129906	100129906	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100129906T>G	uc003hup.3	-	6	841	c.747A>C	c.(745-747)AAA>AAC	p.K249N	uc003hum.1_Intron|ADH6_uc003huo.2_Missense_Mutation_p.K249N|ADH6_uc011cef.1_Missense_Mutation_p.K40N|ADH6_uc010ile.2_Missense_Mutation_p.K249N	NM_000672	NP_000663	P28332	ADH6_HUMAN	class V alcohol dehydrogenase isoform 2	249					ethanol oxidation|response to ethanol|xenobiotic metabolic process	cytosol	alcohol dehydrogenase (NAD) activity|electron carrier activity|zinc ion binding			ovary(1)|kidney(1)|skin(1)	3				OV - Ovarian serous cystadenocarcinoma(123;3.58e-08)	Abacavir(DB01048)|NADH(DB00157)													---	---	---	---
ADH1A	124	broad.mit.edu	37	4	100200649	100200649	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100200649A>G	uc003hur.1	-	8	1108	c.1037T>C	c.(1036-1038)TTA>TCA	p.L346S	uc003hum.1_Intron|ADH1A_uc011ceg.1_Missense_Mutation_p.L346S	NM_000667	NP_000658	P07327	ADH1A_HUMAN	class I alcohol dehydrogenase, alpha subunit	346					ethanol oxidation|transcription, DNA-dependent|xenobiotic metabolic process	cytosol	alcohol dehydrogenase activity, zinc-dependent|protein binding|zinc ion binding			large_intestine(1)|ovary(1)	2				OV - Ovarian serous cystadenocarcinoma(123;9.56e-08)	Fomepizole(DB01213)|NADH(DB00157)													---	---	---	---
ADH1A	124	broad.mit.edu	37	4	100205961	100205961	+	Splice_Site	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100205961C>A	uc003hur.1	-	4	331	c.260_splice	c.e4-1	p.G87_splice	uc003hum.1_Intron|ADH1A_uc011ceg.1_Splice_Site_p.G87_splice|ADH1A_uc010ilf.1_5'Flank|ADH1A_uc010ilg.1_Intron	NM_000667	NP_000658			class I alcohol dehydrogenase, alpha subunit						ethanol oxidation|transcription, DNA-dependent|xenobiotic metabolic process	cytosol	alcohol dehydrogenase activity, zinc-dependent|protein binding|zinc ion binding			large_intestine(1)|ovary(1)	2				OV - Ovarian serous cystadenocarcinoma(123;9.56e-08)	Fomepizole(DB01213)|NADH(DB00157)													---	---	---	---
ADH7	131	broad.mit.edu	37	4	100336635	100336635	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100336635C>A	uc003huv.1	-	8	1235	c.1136G>T	c.(1135-1137)AGC>ATC	p.S379I		NM_000673	NP_000664	P40394	ADH7_HUMAN	class IV alcohol dehydrogenase, mu or sigma	379					ethanol oxidation|fatty acid omega-oxidation|response to bacterium|response to ethanol|xenobiotic metabolic process	cytosol|soluble fraction	alcohol dehydrogenase activity, zinc-dependent|aldehyde oxidase activity|ethanol binding|receptor antagonist activity|retinol binding|retinol dehydrogenase activity			lung(2)|skin(1)	3				OV - Ovarian serous cystadenocarcinoma(123;1.75e-08)	NADH(DB00157)													---	---	---	---
C4orf17	84103	broad.mit.edu	37	4	100463083	100463083	+	Silent	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100463083T>G	uc003huw.2	+	9	1220	c.897T>G	c.(895-897)CCT>CCG	p.P299P	C4orf17_uc003hux.2_RNA	NM_032149	NP_115525	Q53FE4	CD017_HUMAN	hypothetical protein LOC84103	299											0				OV - Ovarian serous cystadenocarcinoma(123;2.08e-08)														---	---	---	---
DAPP1	27071	broad.mit.edu	37	4	100756845	100756845	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:100756845G>A	uc003hvf.3	+	2	257	c.167G>A	c.(166-168)GGC>GAC	p.G56D	DAPP1_uc011cek.1_Missense_Mutation_p.G56D|DAPP1_uc010ilh.2_Missense_Mutation_p.G56D	NM_014395	NP_055210	Q9UN19	DAPP1_HUMAN	dual adaptor of phosphotyrosine and	56	SH2.				signal transduction	cytoplasm|plasma membrane	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|protein tyrosine phosphatase activity				0				OV - Ovarian serous cystadenocarcinoma(123;7.04e-09)														---	---	---	---
CENPE	1062	broad.mit.edu	37	4	104057479	104057479	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104057479T>C	uc003hxb.1	-	40	6431	c.6341A>G	c.(6340-6342)TAT>TGT	p.Y2114C	CENPE_uc003hxc.1_Missense_Mutation_p.Y1993C	NM_001813	NP_001804	Q02224	CENPE_HUMAN	centromere protein E	2114	Potential.				blood coagulation|cell division|kinetochore assembly|microtubule-based movement|mitotic chromosome movement towards spindle pole|mitotic metaphase|mitotic metaphase plate congression|mitotic prometaphase|multicellular organismal development|positive regulation of protein kinase activity	condensed chromosome kinetochore|cytosol|microtubule|nucleus|spindle	ATP binding|kinetochore binding|microtubule motor activity			ovary(5)|breast(4)	9				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)														---	---	---	---
CENPE	1062	broad.mit.edu	37	4	104061201	104061201	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104061201A>G	uc003hxb.1	-	38	6039	c.5949T>C	c.(5947-5949)CTT>CTC	p.L1983L	CENPE_uc003hxc.1_Intron|CENPE_uc003hxd.1_Intron	NM_001813	NP_001804	Q02224	CENPE_HUMAN	centromere protein E	1983	Potential.				blood coagulation|cell division|kinetochore assembly|microtubule-based movement|mitotic chromosome movement towards spindle pole|mitotic metaphase|mitotic metaphase plate congression|mitotic prometaphase|multicellular organismal development|positive regulation of protein kinase activity	condensed chromosome kinetochore|cytosol|microtubule|nucleus|spindle	ATP binding|kinetochore binding|microtubule motor activity			ovary(5)|breast(4)	9				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)														---	---	---	---
CENPE	1062	broad.mit.edu	37	4	104074273	104074273	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104074273T>C	uc003hxb.1	-	25	3258	c.3168A>G	c.(3166-3168)CAA>CAG	p.Q1056Q	CENPE_uc003hxc.1_Silent_p.Q1031Q	NM_001813	NP_001804	Q02224	CENPE_HUMAN	centromere protein E	1056	Potential.				blood coagulation|cell division|kinetochore assembly|microtubule-based movement|mitotic chromosome movement towards spindle pole|mitotic metaphase|mitotic metaphase plate congression|mitotic prometaphase|multicellular organismal development|positive regulation of protein kinase activity	condensed chromosome kinetochore|cytosol|microtubule|nucleus|spindle	ATP binding|kinetochore binding|microtubule motor activity			ovary(5)|breast(4)	9				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)														---	---	---	---
PPA2	27068	broad.mit.edu	37	4	106367644	106367644	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106367644G>T	uc003hxl.2	-	5	357	c.337C>A	c.(337-339)CCA>ACA	p.P113T	PPA2_uc003hxm.2_Missense_Mutation_p.P95T|PPA2_uc003hxn.2_Missense_Mutation_p.P113T|PPA2_uc003hxo.2_Intron|PPA2_uc003hxp.2_Intron|PPA2_uc003hxq.2_Missense_Mutation_p.P20T|PPA2_uc003hxr.2_Missense_Mutation_p.P20T|PPA2_uc011cfa.1_Missense_Mutation_p.P20T	NM_176869	NP_789845	Q9H2U2	IPYR2_HUMAN	inorganic pyrophosphatase 2 isoform 1 precursor	113					diphosphate metabolic process|tRNA aminoacylation for protein translation	mitochondrial matrix	inorganic diphosphatase activity|magnesium ion binding			pancreas(1)	1		Myeloproliferative disorder(5;0.0255)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.03e-07)														---	---	---	---
GSTCD	79807	broad.mit.edu	37	4	106763277	106763277	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:106763277A>G	uc003hxz.3	+	11	1823	c.1751A>G	c.(1750-1752)CAA>CGA	p.Q584R	GSTCD_uc003hxy.3_Missense_Mutation_p.Q497R|GSTCD_uc011cfb.1_Missense_Mutation_p.Q207R	NM_001031720	NP_001026890	Q8NEC7	GSTCD_HUMAN	glutathione S-transferase, C-terminal domain	584						cytoplasm	rRNA methyltransferase activity			breast(1)|central_nervous_system(1)	2		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;3.15e-07)|READ - Rectum adenocarcinoma(30;0.139)														---	---	---	---
LEF1	51176	broad.mit.edu	37	4	109088897	109088897	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109088897G>A	uc003hyt.1	-	1	682	c.27C>T	c.(25-27)GGC>GGT	p.G9G	LEF1_uc011cfj.1_5'Flank|LEF1_uc011cfk.1_5'Flank|LEF1_uc003hyu.1_Silent_p.G9G|LEF1_uc003hyv.1_Silent_p.G9G|LEF1_uc010imb.1_RNA	NM_016269	NP_057353	Q9UJU2	LEF1_HUMAN	lymphoid enhancer-binding factor 1 isoform 1	9	Poly-Gly.|CTNNB1-binding (By similarity).				canonical Wnt receptor signaling pathway|cell chemotaxis|cellular response to interleukin-4|epithelial to mesenchymal transition|histone H3 acetylation|histone H4 acetylation|negative regulation of apoptosis in bone marrow|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cell-cell adhesion|negative regulation of DNA binding|negative regulation of estrogen receptor binding|negative regulation of interleukin-13 production|negative regulation of interleukin-4 production|negative regulation of interleukin-5 production|negative regulation of transcription, DNA-dependent|neutrophil differentiation|osteoblast differentiation|palate development|positive regulation by host of viral transcription|positive regulation of cell cycle process|positive regulation of cell growth|positive regulation of cell migration|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of cell proliferation in bone marrow|positive regulation of cell-cell adhesion|positive regulation of epithelial to mesenchymal transition|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|T-helper 1 cell differentiation	cytoplasm|protein-DNA complex|transcription factor complex	armadillo repeat domain binding|beta-catenin binding|C2H2 zinc finger domain binding|caspase inhibitor activity|DNA bending activity|enhancer binding|estrogen receptor activity|estrogen receptor binding|gamma-catenin binding|histone binding|sequence-specific DNA binding|transcription regulatory region DNA binding			large_intestine(1)	1				OV - Ovarian serous cystadenocarcinoma(123;0.000224)														---	---	---	---
LEF1	51176	broad.mit.edu	37	4	109088900	109088900	+	Silent	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:109088900A>T	uc003hyt.1	-	1	679	c.24T>A	c.(22-24)GGT>GGA	p.G8G	LEF1_uc011cfj.1_5'Flank|LEF1_uc011cfk.1_5'Flank|LEF1_uc003hyu.1_Silent_p.G8G|LEF1_uc003hyv.1_Silent_p.G8G|LEF1_uc010imb.1_RNA	NM_016269	NP_057353	Q9UJU2	LEF1_HUMAN	lymphoid enhancer-binding factor 1 isoform 1	8	Poly-Gly.|CTNNB1-binding (By similarity).				canonical Wnt receptor signaling pathway|cell chemotaxis|cellular response to interleukin-4|epithelial to mesenchymal transition|histone H3 acetylation|histone H4 acetylation|negative regulation of apoptosis in bone marrow|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cell-cell adhesion|negative regulation of DNA binding|negative regulation of estrogen receptor binding|negative regulation of interleukin-13 production|negative regulation of interleukin-4 production|negative regulation of interleukin-5 production|negative regulation of transcription, DNA-dependent|neutrophil differentiation|osteoblast differentiation|palate development|positive regulation by host of viral transcription|positive regulation of cell cycle process|positive regulation of cell growth|positive regulation of cell migration|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of cell proliferation in bone marrow|positive regulation of cell-cell adhesion|positive regulation of epithelial to mesenchymal transition|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|T-helper 1 cell differentiation	cytoplasm|protein-DNA complex|transcription factor complex	armadillo repeat domain binding|beta-catenin binding|C2H2 zinc finger domain binding|caspase inhibitor activity|DNA bending activity|enhancer binding|estrogen receptor activity|estrogen receptor binding|gamma-catenin binding|histone binding|sequence-specific DNA binding|transcription regulatory region DNA binding			large_intestine(1)	1				OV - Ovarian serous cystadenocarcinoma(123;0.000224)														---	---	---	---
EGF	1950	broad.mit.edu	37	4	110882013	110882013	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:110882013C>T	uc003hzy.3	+						EGF_uc011cfu.1_Intron|EGF_uc011cfv.1_Intron	NM_001963	NP_001954			epidermal growth factor precursor						angiogenesis|DNA replication|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of secretion|platelet activation|platelet degranulation|positive regulation of catenin import into nucleus|positive regulation of epidermal growth factor receptor activity|positive regulation of MAP kinase activity|positive regulation of mitosis|regulation of calcium ion import|regulation of protein localization at cell surface	integral to membrane|plasma membrane|platelet alpha granule lumen	calcium ion binding|epidermal growth factor receptor binding|growth factor activity|transmembrane receptor protein tyrosine kinase activator activity			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4		Hepatocellular(203;0.0893)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Sulindac(DB00605)													---	---	---	---
C4orf21	55345	broad.mit.edu	37	4	113506818	113506818	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113506818T>C	uc003iau.2	-	14	4191	c.3980A>G	c.(3979-3981)GAC>GGC	p.D1327G	C4orf21_uc003iav.2_RNA	NM_018392	NP_060862	Q6ZU11	YD002_HUMAN	prematurely terminated mRNA decay factor-like	149						integral to membrane	zinc ion binding				0		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)														---	---	---	---
C4orf21	55345	broad.mit.edu	37	4	113541168	113541168	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:113541168C>A	uc003iau.2	-	5	552	c.341G>T	c.(340-342)AGG>ATG	p.R114M	C4orf21_uc003iaw.2_Missense_Mutation_p.R114M	NM_018392	NP_060862	Q6ZU11	YD002_HUMAN	prematurely terminated mRNA decay factor-like	Error:Variant_position_missing_in_Q6ZU11_after_alignment						integral to membrane	zinc ion binding				0		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)														---	---	---	---
ANK2	287	broad.mit.edu	37	4	114251533	114251533	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114251533G>A	uc003ibe.3	+	27	3132	c.3032G>A	c.(3031-3033)CGC>CAC	p.R1011H	ANK2_uc003ibd.3_Missense_Mutation_p.R1002H|ANK2_uc003ibf.3_Missense_Mutation_p.R1011H|ANK2_uc011cgc.1_Missense_Mutation_p.R220H|ANK2_uc003ibg.3_Missense_Mutation_p.R39H|ANK2_uc003ibc.2_Missense_Mutation_p.R987H|ANK2_uc011cgb.1_Missense_Mutation_p.R1026H	NM_001148	NP_001139	Q01484	ANK2_HUMAN	ankyrin 2 isoform 1	1011	ZU5.|Interaction with SPTBN1.				axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)|skin(1)	14		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)														---	---	---	---
ANK2	287	broad.mit.edu	37	4	114275283	114275283	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:114275283G>A	uc003ibe.3	+	38	5609	c.5509G>A	c.(5509-5511)GCA>ACA	p.A1837T	ANK2_uc003ibd.3_Intron|ANK2_uc003ibf.3_Intron|ANK2_uc011cgc.1_Intron|ANK2_uc003ibg.3_Intron|ANK2_uc003ibh.3_Intron|ANK2_uc011cgd.1_5'Flank|ANK2_uc011cgb.1_Missense_Mutation_p.A1852T	NM_001148	NP_001139	Q01484	ANK2_HUMAN	ankyrin 2 isoform 1	1804	Repeat A.|Repeat-rich region.				axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)|skin(1)	14		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)														---	---	---	---
NDST4	64579	broad.mit.edu	37	4	115997963	115997963	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:115997963T>C	uc003ibu.2	-	2	909	c.230A>G	c.(229-231)GAC>GGC	p.D77G	NDST4_uc010imw.2_Intron	NM_022569	NP_072091	Q9H3R1	NDST4_HUMAN	heparan sulfate N-deacetylase/N-sulfotransferase	77	Lumenal (Potential).|Heparan sulfate N-deacetylase 4.					Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			skin(3)|ovary(1)	4		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000562)														---	---	---	---
SEC24D	9871	broad.mit.edu	37	4	119661871	119661871	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119661871C>T	uc003ici.3	-	17	2457	c.2185G>A	c.(2185-2187)GTG>ATG	p.V729M	SEC24D_uc003ich.3_RNA|SEC24D_uc003icj.3_Missense_Mutation_p.V730M|SEC24D_uc003icl.2_RNA	NM_014822	NP_055637	O94855	SC24D_HUMAN	Sec24-related protein D	729					COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|Golgi membrane|perinuclear region of cytoplasm	zinc ion binding				0																		---	---	---	---
SEC24D	9871	broad.mit.edu	37	4	119754820	119754820	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119754820G>A	uc003ici.3	-	2	304	c.32C>T	c.(31-33)CCG>CTG	p.P11L	SEC24D_uc003icj.3_Missense_Mutation_p.P11L|SEC24D_uc003icl.2_RNA|SEC24D_uc010imz.1_RNA|SEC24D_uc011cgg.1_RNA	NM_014822	NP_055637	O94855	SC24D_HUMAN	Sec24-related protein D	11	Pro-rich.				COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|Golgi membrane|perinuclear region of cytoplasm	zinc ion binding				0																		---	---	---	---
SYNPO2	171024	broad.mit.edu	37	4	119951837	119951837	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:119951837T>G	uc003icm.3	+	4	2103	c.1907T>G	c.(1906-1908)GTT>GGT	p.V636G	SYNPO2_uc010ina.2_Missense_Mutation_p.V636G|SYNPO2_uc010inb.2_Missense_Mutation_p.V636G|SYNPO2_uc011cgh.1_Intron|SYNPO2_uc010inc.2_Missense_Mutation_p.V564G	NM_001128933	NP_001122405	Q9UMS6	SYNP2_HUMAN	synaptopodin 2 isoform b	636	Pro-rich.					nucleus|Z disc	14-3-3 protein binding|actin binding|muscle alpha-actinin binding			ovary(2)	2																		---	---	---	---
PDE5A	8654	broad.mit.edu	37	4	120528342	120528342	+	Missense_Mutation	SNP	C	T	T	rs150282561	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120528342C>T	uc003idh.2	-	2	418	c.263G>A	c.(262-264)CGT>CAT	p.R88H	PDE5A_uc003idf.2_Missense_Mutation_p.R46H|PDE5A_uc003idg.2_Missense_Mutation_p.R36H	NM_001083	NP_001074	O76074	PDE5A_HUMAN	phosphodiesterase 5A isoform 1	88					platelet activation|signal transduction	cytosol	3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|zinc ion binding				0					Dipyridamole(DB00975)|Pentoxifylline(DB00806)|Sildenafil(DB00203)|Tadalafil(DB00820)|Theophylline(DB00277)|Vardenafil(DB00862)													---	---	---	---
BBS7	55212	broad.mit.edu	37	4	122780191	122780191	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:122780191T>C	uc003ied.2	-	5	658	c.484A>G	c.(484-486)ACA>GCA	p.T162A	BBS7_uc003iee.1_Missense_Mutation_p.T162A	NM_176824	NP_789794	Q8IWZ6	BBS7_HUMAN	Bardet-Biedl syndrome 7 protein isoform a	162					cilium morphogenesis|digestive tract morphogenesis|fat cell differentiation|heart looping|melanosome transport|pigment granule aggregation in cell center|response to stimulus|visual perception	BBSome|centrosome|cilium membrane	protein binding			ovary(1)	1														Bardet-Biedl_syndrome				---	---	---	---
KIAA1109	84162	broad.mit.edu	37	4	123095771	123095771	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123095771G>A	uc003ieh.2	+	3	302	c.257G>A	c.(256-258)CGT>CAT	p.R86H		NM_015312	NP_056127	Q2LD37	K1109_HUMAN	fragile site-associated protein	86					regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12																		---	---	---	---
KIAA1109	84162	broad.mit.edu	37	4	123276966	123276966	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123276966G>A	uc003ieh.2	+	81	14366	c.14321G>A	c.(14320-14322)CGT>CAT	p.R4774H	KIAA1109_uc003iem.2_Missense_Mutation_p.R1130H	NM_015312	NP_056127	Q2LD37	K1109_HUMAN	fragile site-associated protein	4774					regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12																		---	---	---	---
ANKRD50	57182	broad.mit.edu	37	4	125592216	125592216	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:125592216G>A	uc003ifg.3	-	3	2482	c.2216C>T	c.(2215-2217)GCT>GTT	p.A739V	ANKRD50_uc011cgo.1_Missense_Mutation_p.A560V|ANKRD50_uc010inw.2_Missense_Mutation_p.A739V	NM_020337	NP_065070	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	739	ANK 8.									central_nervous_system(1)	1																		---	---	---	---
FAT4	79633	broad.mit.edu	37	4	126373932	126373932	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:126373932A>C	uc003ifj.3	+	9	11761	c.11761A>C	c.(11761-11763)AGC>CGC	p.S3921R	FAT4_uc011cgp.1_Missense_Mutation_p.S2219R|FAT4_uc003ifi.1_Missense_Mutation_p.S1399R	NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	3921	EGF-like 3; calcium-binding (Potential).|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18																		---	---	---	---
INTU	27152	broad.mit.edu	37	4	128584578	128584578	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:128584578A>G	uc003ifk.1	+	4	881	c.811A>G	c.(811-813)ACA>GCA	p.T271A	INTU_uc011cgq.1_RNA	NM_015693	NP_056508	Q9ULD6	PDZD6_HUMAN	PDZ domain containing 6	271										ovary(1)	1																		---	---	---	---
PHF17	79960	broad.mit.edu	37	4	129792870	129792870	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:129792870A>G	uc003igk.2	+	11	2262	c.1982A>G	c.(1981-1983)GAC>GGC	p.D661G	PHF17_uc003igl.2_Missense_Mutation_p.D649G|PHF17_uc011cgy.1_Missense_Mutation_p.D661G	NM_199320	NP_955352	Q6IE81	JADE1_HUMAN	PHD finger protein 17 long isoform	661					apoptosis|histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation|negative regulation of cell growth|regulation of transcription, DNA-dependent|response to stress|transcription, DNA-dependent	histone acetyltransferase complex|mitochondrion	protein binding|zinc ion binding				0																		---	---	---	---
PCDH10	57575	broad.mit.edu	37	4	134072680	134072680	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:134072680G>A	uc003iha.2	+	1	2211	c.1385G>A	c.(1384-1386)CGT>CAT	p.R462H	uc003igy.2_5'Flank|PCDH10_uc003igz.2_Missense_Mutation_p.R462H	NM_032961	NP_116586	Q9P2E7	PCD10_HUMAN	protocadherin 10 isoform 1 precursor	462	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2				LUSC - Lung squamous cell carcinoma(193;0.227)														---	---	---	---
C4orf49	84709	broad.mit.edu	37	4	140196447	140196447	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140196447T>C	uc003ihr.1	-	2	362	c.182A>G	c.(181-183)TAT>TGT	p.Y61C		NM_032623	NP_116012	Q8TDB4	CD049_HUMAN	ovary-specific acidic protein	61	Helical; (Potential).					integral to membrane				central_nervous_system(1)|skin(1)	2																		---	---	---	---
MGST2	4258	broad.mit.edu	37	4	140625225	140625225	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:140625225G>A	uc003ihy.2	+	5	619	c.367G>A	c.(367-369)GCC>ACC	p.A123T	MGST2_uc010ioi.1_RNA	NM_002413	NP_002404	Q99735	MGST2_HUMAN	microsomal glutathione S-transferase 2	123	Helical; (Potential).				glutathione biosynthetic process|leukotriene biosynthetic process|leukotriene production involved in inflammatory response|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome|nuclear membrane|plasma membrane	enzyme activator activity|glutathione peroxidase activity|glutathione transferase activity|leukotriene-C4 synthase activity			ovary(1)	1	all_hematologic(180;0.162)				Glutathione(DB00143)													---	---	---	---
CLGN	1047	broad.mit.edu	37	4	141323173	141323173	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141323173A>C	uc011chi.1	-	7	685	c.467T>G	c.(466-468)ATT>AGT	p.I156S	CLGN_uc003iii.2_Missense_Mutation_p.I156S	NM_001130675	NP_001124147	O14967	CLGN_HUMAN	calmegin precursor	156	Lumenal (Potential).				protein folding	endoplasmic reticulum membrane|integral to membrane	calcium ion binding|unfolded protein binding			ovary(2)|skin(1)	3	all_hematologic(180;0.162)																	---	---	---	---
RNF150	57484	broad.mit.edu	37	4	142053518	142053518	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:142053518C>A	uc003iio.1	-	1	1099	c.445G>T	c.(445-447)GGC>TGC	p.G149C	RNF150_uc010iok.1_Missense_Mutation_p.G149C|RNF150_uc003iip.1_Missense_Mutation_p.G149C	NM_020724	NP_065775	Q9ULK6	RN150_HUMAN	ring finger protein 150 precursor	149	Extracellular (Potential).|PA.					integral to membrane	zinc ion binding			ovary(1)	1	all_hematologic(180;0.162)																	---	---	---	---
INPP4B	8821	broad.mit.edu	37	4	143043380	143043380	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:143043380A>G	uc003iix.3	-	22	2631	c.2036T>C	c.(2035-2037)CTA>CCA	p.L679P	INPP4B_uc003iiw.3_Missense_Mutation_p.L679P|INPP4B_uc011chm.1_RNA|INPP4B_uc011chn.1_Missense_Mutation_p.L494P|INPP4B_uc011cho.1_RNA	NM_003866	NP_003857	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II,	679					signal transduction		phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity			ovary(1)|lung(1)	2	all_hematologic(180;0.158)																	---	---	---	---
OTUD4	54726	broad.mit.edu	37	4	146063379	146063379	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146063379C>T	uc003ika.3	-	18	1734	c.1596G>A	c.(1594-1596)TGG>TGA	p.W532*	OTUD4_uc003ijz.3_Nonsense_Mutation_p.W531*	NM_001102653	NP_001096123	Q01804	OTUD4_HUMAN	OTU domain containing 4 protein isoform 3	596							protein binding			ovary(2)|breast(1)	3	all_hematologic(180;0.151)																	---	---	---	---
MMAA	166785	broad.mit.edu	37	4	146560499	146560499	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146560499A>G	uc003ikh.3	+	2	293	c.208A>G	c.(208-210)ACC>GCC	p.T70A	MMAA_uc003ikg.2_Missense_Mutation_p.T70A|MMAA_uc003iki.1_RNA|MMAA_uc010iow.2_RNA	NM_172250	NP_758454	Q8IVH4	MMAA_HUMAN	methylmalonic aciduria type A precursor	70						mitochondrion	GTP binding|nucleoside-triphosphatase activity			ovary(1)	1	all_hematologic(180;0.151)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)													---	---	---	---
ZNF827	152485	broad.mit.edu	37	4	146770653	146770653	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146770653A>G	uc003ikn.2	-	6	2090	c.2042T>C	c.(2041-2043)ATC>ACC	p.I681T	ZNF827_uc003ikm.2_Missense_Mutation_p.I681T|ZNF827_uc010iox.2_Missense_Mutation_p.I331T	NM_178835	NP_849157	Q17R98	ZN827_HUMAN	zinc finger protein 827	681					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_hematologic(180;0.151)																	---	---	---	---
POU4F2	5458	broad.mit.edu	37	4	147561576	147561576	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147561576G>A	uc003ikv.2	+	2	1094	c.846G>A	c.(844-846)GCG>GCA	p.A282A		NM_004575	NP_004566	Q12837	PO4F2_HUMAN	Brn3b POU domain transcription factor	282	POU-specific.				estrogen receptor signaling pathway|MAPKKK cascade|negative regulation of transcription from RNA polymerase II promoter	nuclear speck	RNA polymerase II core promoter proximal region sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription			breast(1)	1	all_hematologic(180;0.151)																	---	---	---	---
TTC29	83894	broad.mit.edu	37	4	147824728	147824728	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:147824728T>C	uc003ikw.3	-	6	781	c.554A>G	c.(553-555)CAC>CGC	p.H185R	TTC29_uc010ipc.2_RNA|TTC29_uc003ikx.3_Missense_Mutation_p.H211R|TTC29_uc010ipd.1_Missense_Mutation_p.H185R	NM_031956	NP_114162	Q8NA56	TTC29_HUMAN	tetratricopeptide repeat domain 29	185	TPR 1.						binding				0	all_hematologic(180;0.151)																	---	---	---	---
EDNRA	1909	broad.mit.edu	37	4	148406910	148406910	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148406910A>G	uc003iky.2	+	2	769	c.77A>G	c.(76-78)TAC>TGC	p.Y26C	EDNRA_uc011cid.1_Intron|EDNRA_uc010ipe.1_Missense_Mutation_p.Y26C|EDNRA_uc010ipf.1_RNA|EDNRA_uc010ipg.1_Missense_Mutation_p.Y26C	NM_001957	NP_001948	P25101	EDNRA_HUMAN	endothelin receptor type A isoform a precursor	26	Extracellular (Potential).				activation of adenylate cyclase activity|artery smooth muscle contraction|cell proliferation|glucose transport|respiratory gaseous exchange	integral to plasma membrane	endothelin-A receptor activity|phosphatidylinositol phospholipase C activity			ovary(1)|breast(1)	2	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.154)	Bosentan(DB00559)													---	---	---	---
EDNRA	1909	broad.mit.edu	37	4	148461554	148461554	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148461554G>A	uc003iky.2	+	7	1752	c.1060G>A	c.(1060-1062)GGT>AGT	p.G354S	EDNRA_uc011cid.1_Missense_Mutation_p.G129S|EDNRA_uc010ipf.1_RNA|EDNRA_uc010ipg.1_Missense_Mutation_p.G245S	NM_001957	NP_001948	P25101	EDNRA_HUMAN	endothelin receptor type A isoform a precursor	354	Helical; Name=7; (Potential).				activation of adenylate cyclase activity|artery smooth muscle contraction|cell proliferation|glucose transport|respiratory gaseous exchange	integral to plasma membrane	endothelin-A receptor activity|phosphatidylinositol phospholipase C activity			ovary(1)|breast(1)	2	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.154)	Bosentan(DB00559)													---	---	---	---
ARHGAP10	79658	broad.mit.edu	37	4	148867816	148867816	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:148867816A>G	uc003ilf.2	+	15	1352	c.1352A>G	c.(1351-1353)GAA>GGA	p.E451G	ARHGAP10_uc003ilg.2_Missense_Mutation_p.E100G|ARHGAP10_uc003ilh.2_Missense_Mutation_p.E32G	NM_024605	NP_078881	A1A4S6	RHG10_HUMAN	Rho GTPase activating protein 10	451	Rho-GAP.				apoptosis|filopodium assembly|regulation of apoptosis|small GTPase mediated signal transduction	cytosol|perinuclear region of cytoplasm|plasma membrane	cytoskeletal adaptor activity|SH3 domain binding			skin(2)|pancreas(1)|lung(1)	4	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)														---	---	---	---
DCLK2	166614	broad.mit.edu	37	4	151023905	151023905	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151023905G>A	uc003ilm.3	+	2	797	c.697G>A	c.(697-699)GAA>AAA	p.E233K	DCLK2_uc003iln.3_Missense_Mutation_p.E233K|DCLK2_uc003ilo.3_Missense_Mutation_p.E233K|DCLK2_uc003ilp.3_RNA	NM_001040260	NP_001035350	Q8N568	DCLK2_HUMAN	doublecortin-like kinase 2 isoform a	233	Doublecortin 2.				intracellular signal transduction	cytoplasm|cytoskeleton	ATP binding|protein serine/threonine kinase activity			ovary(3)	3	all_hematologic(180;0.151)																	---	---	---	---
DCLK2	166614	broad.mit.edu	37	4	151153525	151153525	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151153525C>T	uc003ilm.3	+	9	1436	c.1336C>T	c.(1336-1338)CGA>TGA	p.R446*	DCLK2_uc003iln.3_Nonsense_Mutation_p.R445*|DCLK2_uc003ilo.3_Nonsense_Mutation_p.R463*|DCLK2_uc003ilp.3_RNA	NM_001040260	NP_001035350	Q8N568	DCLK2_HUMAN	doublecortin-like kinase 2 isoform a	446	Protein kinase.				intracellular signal transduction	cytoplasm|cytoskeleton	ATP binding|protein serine/threonine kinase activity			ovary(3)	3	all_hematologic(180;0.151)																	---	---	---	---
LRBA	987	broad.mit.edu	37	4	151199060	151199060	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151199060C>T	uc010ipj.2	-	57	8920	c.8446G>A	c.(8446-8448)GCC>ACC	p.A2816T	LRBA_uc010ipi.2_Missense_Mutation_p.A338T|LRBA_uc003ils.3_Missense_Mutation_p.A711T|LRBA_uc003ilt.3_Missense_Mutation_p.A1464T|LRBA_uc003ilu.3_Missense_Mutation_p.A2804T|LRBA_uc003ilr.3_Missense_Mutation_p.A236T	NM_006726	NP_006717	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and	2816	WD 5.					endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)|skin(1)	7	all_hematologic(180;0.151)																	---	---	---	---
MAB21L2	10586	broad.mit.edu	37	4	151504433	151504433	+	Silent	SNP	C	T	T	rs139360189		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151504433C>T	uc003ilw.2	+	1	1357	c.252C>T	c.(250-252)GGC>GGT	p.G84G	LRBA_uc003ils.3_5'Flank|LRBA_uc003ilt.3_Intron|LRBA_uc003ilu.3_Intron|LRBA_uc010ipj.2_Intron	NM_006439	NP_006430	Q9Y586	MB212_HUMAN	mab-21-like protein 2	84					nervous system development	nucleus				ovary(1)	1	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.159)														---	---	---	---
LRBA	987	broad.mit.edu	37	4	151765281	151765281	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151765281G>A	uc010ipj.2	-	28	5014	c.4540C>T	c.(4540-4542)CGG>TGG	p.R1514W	LRBA_uc003ilt.3_Missense_Mutation_p.R173W|LRBA_uc003ilu.3_Missense_Mutation_p.R1514W	NM_006726	NP_006717	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and	1514						endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)|skin(1)	7	all_hematologic(180;0.151)																	---	---	---	---
RPS3A	6189	broad.mit.edu	37	4	152025025	152025025	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152025025A>G	uc003ilz.2	+						RPS3A_uc011cie.1_3'UTR|SNORD73A_uc003ima.1_RNA	NM_001006	NP_000997			ribosomal protein S3a						cell differentiation|endocrine pancreas development|induction of apoptosis|translational elongation|translational initiation|translational termination|viral transcription	cytosolic small ribosomal subunit|nucleolus	protein binding|RNA binding|structural constituent of ribosome			ovary(1)	1	all_hematologic(180;0.093)																	---	---	---	---
FBXW7	55294	broad.mit.edu	37	4	153253775	153253775	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153253775G>A	uc003ims.2	-	6	1107	c.958C>T	c.(958-960)CTC>TTC	p.L320F	FBXW7_uc011cii.1_Missense_Mutation_p.L320F|FBXW7_uc003imt.2_Missense_Mutation_p.L320F|FBXW7_uc011cih.1_Missense_Mutation_p.L144F|FBXW7_uc003imq.2_Missense_Mutation_p.L240F|FBXW7_uc003imr.2_Missense_Mutation_p.L202F	NM_033632	NP_361014	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7 isoform	320	F-box.				interspecies interaction between organisms|lipid homeostasis|negative regulation of DNA endoreduplication|negative regulation of hepatocyte proliferation|negative regulation of Notch signaling pathway|negative regulation of triglyceride biosynthetic process|positive regulation of epidermal growth factor receptor activity|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|protein stabilization|protein ubiquitination|regulation of lipid storage|regulation of protein localization|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|sister chromatid cohesion|vasculature development	nucleolus|nucleolus|nucleoplasm|nucleoplasm|SCF ubiquitin ligase complex	protein binding|protein binding			haematopoietic_and_lymphoid_tissue(125)|large_intestine(99)|stomach(16)|lung(14)|endometrium(13)|ovary(9)|biliary_tract(8)|upper_aerodigestive_tract(5)|central_nervous_system(3)|kidney(3)|skin(3)|pancreas(3)|breast(2)|prostate(2)|cervix(1)|NS(1)|bone(1)	308	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)						Mis|N|D|F		colorectal|endometrial|T-ALL								---	---	---	---
FBXW7	55294	broad.mit.edu	37	4	153253824	153253824	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153253824T>G	uc003ims.2	-	6	1058	c.909A>C	c.(907-909)CAA>CAC	p.Q303H	FBXW7_uc011cii.1_Missense_Mutation_p.Q303H|FBXW7_uc003imt.2_Missense_Mutation_p.Q303H|FBXW7_uc011cih.1_Missense_Mutation_p.Q127H|FBXW7_uc003imq.2_Missense_Mutation_p.Q223H|FBXW7_uc003imr.2_Missense_Mutation_p.Q185H	NM_033632	NP_361014	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7 isoform	303	F-box.				interspecies interaction between organisms|lipid homeostasis|negative regulation of DNA endoreduplication|negative regulation of hepatocyte proliferation|negative regulation of Notch signaling pathway|negative regulation of triglyceride biosynthetic process|positive regulation of epidermal growth factor receptor activity|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|protein stabilization|protein ubiquitination|regulation of lipid storage|regulation of protein localization|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|sister chromatid cohesion|vasculature development	nucleolus|nucleolus|nucleoplasm|nucleoplasm|SCF ubiquitin ligase complex	protein binding|protein binding	p.Q303*(1)		haematopoietic_and_lymphoid_tissue(125)|large_intestine(99)|stomach(16)|lung(14)|endometrium(13)|ovary(9)|biliary_tract(8)|upper_aerodigestive_tract(5)|central_nervous_system(3)|kidney(3)|skin(3)|pancreas(3)|breast(2)|prostate(2)|cervix(1)|NS(1)|bone(1)	308	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)						Mis|N|D|F		colorectal|endometrial|T-ALL								---	---	---	---
FBXW7	55294	broad.mit.edu	37	4	153303371	153303371	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:153303371A>G	uc003ims.2	-						FBXW7_uc011cii.1_Intron|FBXW7_uc003imt.2_Intron|FBXW7_uc003imr.2_Silent_p.I39I	NM_033632	NP_361014			F-box and WD repeat domain containing 7 isoform						interspecies interaction between organisms|lipid homeostasis|negative regulation of DNA endoreduplication|negative regulation of hepatocyte proliferation|negative regulation of Notch signaling pathway|negative regulation of triglyceride biosynthetic process|positive regulation of epidermal growth factor receptor activity|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|protein stabilization|protein ubiquitination|regulation of lipid storage|regulation of protein localization|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|sister chromatid cohesion|vasculature development	nucleolus|nucleolus|nucleoplasm|nucleoplasm|SCF ubiquitin ligase complex	protein binding|protein binding			haematopoietic_and_lymphoid_tissue(125)|large_intestine(99)|stomach(16)|lung(14)|endometrium(13)|ovary(9)|biliary_tract(8)|upper_aerodigestive_tract(5)|central_nervous_system(3)|kidney(3)|skin(3)|pancreas(3)|breast(2)|prostate(2)|cervix(1)|NS(1)|bone(1)	308	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)						Mis|N|D|F		colorectal|endometrial|T-ALL								---	---	---	---
TRIM2	23321	broad.mit.edu	37	4	154197136	154197136	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154197136G>A	uc003ing.2	+	3	427	c.226G>A	c.(226-228)GCG>ACG	p.A76T	TRIM2_uc003inh.2_Missense_Mutation_p.A103T|TRIM2_uc003ini.1_Missense_Mutation_p.A94T	NM_001130067	NP_001123539	Q9C040	TRIM2_HUMAN	tripartite motif-containing 2 isoform 2	76						cytoplasm	zinc ion binding			central_nervous_system(1)	1	all_hematologic(180;0.093)	Medulloblastoma(177;0.00225)		GBM - Glioblastoma multiforme(119;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0703)														---	---	---	---
TLR2	7097	broad.mit.edu	37	4	154625998	154625998	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154625998T>C	uc003inq.2	+	3	2158	c.1939T>C	c.(1939-1941)TAC>CAC	p.Y647H	TLR2_uc003inr.2_Missense_Mutation_p.Y647H|TLR2_uc003ins.2_Missense_Mutation_p.Y647H	NM_003264	NP_003255	O60603	TLR2_HUMAN	toll-like receptor 2 precursor	647	TIR.|Cytoplasmic (Potential).				cellular response to diacyl bacterial lipopeptide|cellular response to lipoteichoic acid|cellular response to triacyl bacterial lipopeptide|detection of diacyl bacterial lipopeptide|detection of triacyl bacterial lipopeptide|I-kappaB phosphorylation|induction of apoptosis|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of chemokine production|positive regulation of interferon-beta production|positive regulation of interleukin-12 production|positive regulation of interleukin-18 production|positive regulation of interleukin-6 production|positive regulation of interleukin-8 production|positive regulation of NF-kappaB import into nucleus|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of toll-like receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tumor necrosis factor production|positive regulation of Wnt receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytoplasm|integral to plasma membrane|Toll-like receptor 1-Toll-like receptor 2 protein complex	Gram-positive bacterial cell surface binding|lipopolysaccharide receptor activity|peptidoglycan binding|protein heterodimerization activity|transmembrane receptor activity|triacyl lipopeptide binding			ovary(1)|lung(1)|breast(1)	3	all_hematologic(180;0.093)	Renal(120;0.117)																---	---	---	---
RNF175	285533	broad.mit.edu	37	4	154631578	154631578	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154631578C>T	uc003int.2	-	9	1303	c.930G>A	c.(928-930)TGG>TGA	p.W310*		NM_173662	NP_775933	Q8N4F7	RN175_HUMAN	ring finger protein 175	310						integral to membrane	zinc ion binding			ovary(1)|pancreas(1)	2	all_hematologic(180;0.093)	Renal(120;0.118)																---	---	---	---
DCHS2	54798	broad.mit.edu	37	4	155250767	155250767	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155250767C>T	uc003inw.2	-	11	2461	c.2461G>A	c.(2461-2463)GCC>ACC	p.A821T	DCHS2_uc003inx.2_Missense_Mutation_p.A1276T	NM_017639	NP_060109	Q6V1P9	PCD23_HUMAN	dachsous 2 isoform 1	821	Cadherin 6.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|pancreas(1)	4	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)														---	---	---	---
PLRG1	5356	broad.mit.edu	37	4	155467298	155467298	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:155467298C>T	uc003iny.2	-	5	444	c.381G>A	c.(379-381)GCG>GCA	p.A127A	PLRG1_uc003inz.2_Silent_p.A118A|PLRG1_uc011cil.1_Intron	NM_002669	NP_002660	O43660	PLRG1_HUMAN	pleiotropic regulator 1 (PRL1 homolog,	127						catalytic step 2 spliceosome|nuclear speck	protein binding|signal transducer activity|transcription corepressor activity				0	all_hematologic(180;0.215)	Renal(120;0.0854)																---	---	---	---
GUCY1A3	2982	broad.mit.edu	37	4	156643320	156643320	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156643320T>A	uc003iov.2	+	10	2383	c.1847T>A	c.(1846-1848)ATC>AAC	p.I616N	GUCY1A3_uc010iqc.2_Missense_Mutation_p.I616N|GUCY1A3_uc003iow.2_Missense_Mutation_p.I616N|GUCY1A3_uc010iqd.2_Missense_Mutation_p.I615N|GUCY1A3_uc003iox.2_Missense_Mutation_p.I616N|GUCY1A3_uc003ioz.2_Missense_Mutation_p.I381N|GUCY1A3_uc003ioy.2_Missense_Mutation_p.I616N|GUCY1A3_uc010iqe.2_Missense_Mutation_p.I381N|GUCY1A3_uc003ipa.2_RNA|GUCY1A3_uc003ipb.2_Missense_Mutation_p.I616N	NM_000856	NP_000847	Q02108	GCYA3_HUMAN	guanylate cyclase 1, soluble, alpha 3 isoform A	616					blood circulation|intracellular signal transduction|nitric oxide mediated signal transduction|platelet activation	guanylate cyclase complex, soluble	GTP binding|guanylate cyclase activity|heme binding|receptor activity			central_nervous_system(2)|ovary(1)|skin(1)	4	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.17)														---	---	---	---
TDO2	6999	broad.mit.edu	37	4	156825226	156825226	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156825226G>A	uc003ipf.1	+	2	156	c.92G>A	c.(91-93)GGT>GAT	p.G31D		NM_005651	NP_005642	P48775	T23O_HUMAN	tryptophan 2,3-dioxygenase	31					tryptophan catabolic process to kynurenine	cytosol	tryptophan 2,3-dioxygenase activity				0	all_hematologic(180;0.24)	Renal(120;0.0854)		KIRC - Kidney renal clear cell carcinoma(143;0.0455)|Kidney(143;0.0568)|COAD - Colon adenocarcinoma(41;0.141)	L-Tryptophan(DB00150)													---	---	---	---
FAM198B	51313	broad.mit.edu	37	4	159048603	159048603	+	Missense_Mutation	SNP	A	G	G	rs138391669	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159048603A>G	uc003ipp.3	-	5	1968	c.1516T>C	c.(1516-1518)TAT>CAT	p.Y506H	FAM198B_uc003ipq.3_Missense_Mutation_p.Y514H|FAM198B_uc003ipr.3_Missense_Mutation_p.Y506H	NM_016613	NP_057697	Q6UWH4	F198B_HUMAN	hypothetical protein LOC51313 isoform 2	506	Extracellular (Potential).					Golgi membrane|integral to membrane					0																		---	---	---	---
FAM198B	51313	broad.mit.edu	37	4	159091842	159091842	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159091842T>C	uc003ipp.3	-	2	1138	c.686A>G	c.(685-687)GAC>GGC	p.D229G	uc003ipu.1_5'Flank|FAM198B_uc003ipq.3_Missense_Mutation_p.D229G|FAM198B_uc003ipr.3_Missense_Mutation_p.D229G|FAM198B_uc003ips.2_Missense_Mutation_p.D229G|uc003ipt.1_5'Flank	NM_016613	NP_057697	Q6UWH4	F198B_HUMAN	hypothetical protein LOC51313 isoform 2	229	Extracellular (Potential).					Golgi membrane|integral to membrane					0																OREG0016378	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
RXFP1	59350	broad.mit.edu	37	4	159559150	159559150	+	Intron	SNP	T	A	A	rs35818367		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159559150T>A	uc003ipz.2	+						RXFP1_uc010iqj.1_Intron|RXFP1_uc011cja.1_Intron|RXFP1_uc010iqo.2_Intron|RXFP1_uc011cjb.1_Intron|RXFP1_uc010iqk.2_Intron|RXFP1_uc011cjc.1_Intron|RXFP1_uc011cjd.1_Intron|RXFP1_uc010iql.2_Intron|RXFP1_uc011cje.1_Intron|RXFP1_uc010iqm.2_Intron|RXFP1_uc011cjf.1_Intron|RXFP1_uc010iqn.2_Intron	NM_021634	NP_067647			relaxin/insulin-like family peptide receptor 1							integral to membrane|plasma membrane	G-protein coupled receptor activity|metal ion binding				0	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0219)														---	---	---	---
C4orf46	201725	broad.mit.edu	37	4	159590896	159590896	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159590896G>T	uc003iqa.2	-	2	460	c.211C>A	c.(211-213)CTT>ATT	p.L71I	C4orf46_uc010iqp.1_RNA|ETFDH_uc010iqq.2_5'Flank|ETFDH_uc003iqb.2_5'Flank|ETFDH_uc011cjg.1_5'Flank|ETFDH_uc010iqr.2_5'Flank	NM_001008393	NP_001008394	Q504U0	CD046_HUMAN	hypothetical protein LOC201725	71										skin(1)	1																		---	---	---	---
FNIP2	57600	broad.mit.edu	37	4	159791528	159791528	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:159791528C>T	uc003iqe.3	+	14	3039	c.2856C>T	c.(2854-2856)TGC>TGT	p.C952C		NM_020840	NP_065891	Q9P278	FNIP2_HUMAN	folliculin interacting protein 2	952					DNA damage response, signal transduction resulting in induction of apoptosis|protein phosphorylation|regulation of protein phosphorylation	cytoplasm	protein binding				0	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.00936)														---	---	---	---
RAPGEF2	9693	broad.mit.edu	37	4	160275189	160275189	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:160275189G>T	uc003iqg.3	+	22	4469	c.4159G>T	c.(4159-4161)GGG>TGG	p.G1387W		NM_014247	NP_055062	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor 2	1387					cAMP-mediated signaling|MAPKKK cascade|small GTPase mediated signal transduction	integral to plasma membrane|intracellular	calcium ion binding|diacylglycerol binding|Rap GTPase activator activity|Rap guanyl-nucleotide exchange factor activity|signal transducer activity			lung(2)|upper_aerodigestive_tract(1)|skin(1)	4	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)														---	---	---	---
NPY5R	4889	broad.mit.edu	37	4	164271614	164271614	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164271614A>G	uc003iqn.2	+	4	371	c.189A>G	c.(187-189)TTA>TTG	p.L63L		NM_006174	NP_006165	Q15761	NPY5R_HUMAN	neuropeptide Y receptor Y5	63	Helical; Name=1; (Potential).				cardiac left ventricle morphogenesis|outflow tract morphogenesis	integral to plasma membrane				lung(6)|skin(1)	7	all_hematologic(180;0.166)	Prostate(90;0.109)																---	---	---	---
TKTL2	84076	broad.mit.edu	37	4	164393287	164393287	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164393287G>A	uc003iqp.3	-	1	1761	c.1600C>T	c.(1600-1602)CGT>TGT	p.R534C		NM_032136	NP_115512	Q9H0I9	TKTL2_HUMAN	transketolase-like 2	534						cytoplasm	metal ion binding|transketolase activity			ovary(2)|skin(2)|pancreas(1)	5	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)																---	---	---	---
MARCH1	55016	broad.mit.edu	37	4	164450069	164450069	+	Missense_Mutation	SNP	C	T	T	rs138795587		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164450069C>T	uc003iqs.1	-	8	1678	c.701G>A	c.(700-702)CGT>CAT	p.R234H	MARCH1_uc003iqr.1_Missense_Mutation_p.R217H	NM_017923	NP_060393	Q8TCQ1	MARH1_HUMAN	membrane-associated RING-CH protein I	234	Responsible for down-regulation of CD86 and MHC class II cell surface expression (By similarity).				antigen processing and presentation of peptide antigen via MHC class II|immune response	cytoplasmic vesicle membrane|early endosome membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|plasma membrane	MHC protein binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)	2	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)																---	---	---	---
KLHL2	11275	broad.mit.edu	37	4	166160009	166160009	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166160009T>C	uc003irb.2	+	4	598	c.339T>C	c.(337-339)TAT>TAC	p.Y113Y	KLHL2_uc011cjm.1_Silent_p.Y117Y|KLHL2_uc003irc.2_Silent_p.Y25Y	NM_007246	NP_009177	O95198	KLHL2_HUMAN	kelch-like 2, Mayven isoform 1	113	BTB.				intracellular protein transport	actin cytoskeleton|cytoplasm	actin binding|transporter activity				0	all_hematologic(180;0.221)			GBM - Glioblastoma multiforme(119;2.94e-27)|COAD - Colon adenocarcinoma(41;1.4e-05)|Kidney(143;4.95e-05)|KIRC - Kidney renal clear cell carcinoma(143;0.000927)														---	---	---	---
CPE	1363	broad.mit.edu	37	4	166405674	166405674	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166405674G>A	uc003irg.3	+	5	1168	c.891G>A	c.(889-891)CGG>CGA	p.R297R		NM_001873	NP_001864	P16870	CBPE_HUMAN	carboxypeptidase E preproprotein	297			R -> Q (in a colorectal cancer sample; somatic mutation).		cardiac left ventricle morphogenesis|neuropeptide signaling pathway|protein modification process	extracellular region|nucleus|plasma membrane	metallocarboxypeptidase activity|protein binding|zinc ion binding	p.R297Q(1)		large_intestine(1)|ovary(1)|skin(1)	3	all_hematologic(180;0.221)	Prostate(90;0.0962)|Melanoma(52;0.18)		GBM - Glioblastoma multiforme(119;0.137)	Glucagon recombinant(DB00040)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
TLL1	7092	broad.mit.edu	37	4	166986929	166986929	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166986929T>C	uc003irh.1	+	16	2749	c.2102T>C	c.(2101-2103)ATC>ACC	p.I701T	TLL1_uc011cjn.1_Missense_Mutation_p.I724T|TLL1_uc011cjo.1_Missense_Mutation_p.I525T	NM_012464	NP_036596	O43897	TLL1_HUMAN	tolloid-like 1 precursor	701	CUB 3.				cell differentiation|proteolysis|skeletal system development	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)														---	---	---	---
DDX60	55601	broad.mit.edu	37	4	169142937	169142937	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169142937G>T	uc003irp.2	-	36	5212	c.4920C>A	c.(4918-4920)GCC>GCA	p.A1640A	DDX60_uc003iro.2_Silent_p.A111A	NM_017631	NP_060101	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	1640							ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0485)														---	---	---	---
PALLD	23022	broad.mit.edu	37	4	169611817	169611817	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169611817G>A	uc011cjx.1	+	7	1610	c.1399G>A	c.(1399-1401)GCA>ACA	p.A467T	PALLD_uc003iru.2_Missense_Mutation_p.A467T|PALLD_uc003irv.2_Missense_Mutation_p.A85T	NM_016081	NP_057165	Q8WX93	PALLD_HUMAN	palladin isoform 2	467	Ig-like C2-type 2.				cytoskeleton organization	actin filament|focal adhesion|lamellipodium|nucleus|ruffle|sarcomere	actin binding|muscle alpha-actinin binding			ovary(1)	1		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)										Pancreatic_Cancer_Familial_Clustering_of				---	---	---	---
CBR4	84869	broad.mit.edu	37	4	169923235	169923235	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:169923235A>G	uc003iry.2	-	4	704	c.522T>C	c.(520-522)AAT>AAC	p.N174N	CBR4_uc011cjy.1_RNA|CBR4_uc003irz.1_Silent_p.N174N	NM_032783	NP_116172	Q8N4T8	CBR4_HUMAN	carbonic reductase 4	174					fatty acid biosynthetic process|protein homotetramerization	mitochondrial matrix	NADPH binding|NADPH dehydrogenase (quinone) activity|protein binding|quinone binding				0		Prostate(90;0.00263)|Renal(120;0.0183)|Melanoma(52;0.123)		GBM - Glioblastoma multiforme(119;0.0321)														---	---	---	---
NEK1	4750	broad.mit.edu	37	4	170511930	170511930	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170511930C>G	uc003isb.1	-	5	835	c.343G>C	c.(343-345)GCC>CCC	p.A115P	NEK1_uc003isc.1_Missense_Mutation_p.A115P|NEK1_uc003isd.1_Missense_Mutation_p.A115P|NEK1_uc003ise.1_Missense_Mutation_p.A115P|NEK1_uc003isf.1_Missense_Mutation_p.A115P|NEK1_uc003isg.1_Missense_Mutation_p.A36P	NM_012224	NP_036356	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1	115	Protein kinase.				cell division|cilium assembly|mitosis	nucleus|pericentriolar material	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(3)|ovary(2)|large_intestine(1)	6		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)														---	---	---	---
CLCN3	1182	broad.mit.edu	37	4	170610266	170610266	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170610266C>T	uc003isi.2	+	5	1000	c.491C>T	c.(490-492)GCG>GTG	p.A164V	CLCN3_uc003ish.2_Missense_Mutation_p.A164V|CLCN3_uc011cjz.1_Missense_Mutation_p.A147V|CLCN3_uc011cka.1_Missense_Mutation_p.A164V|CLCN3_uc003isj.1_Missense_Mutation_p.A137V	NM_001829	NP_001820	P51790	CLCN3_HUMAN	chloride channel 3 isoform b	164					endosomal lumen acidification	cell surface|early endosome membrane|Golgi membrane|integral to membrane|late endosome membrane|transport vesicle membrane	antiporter activity|ATP binding|PDZ domain binding|protein heterodimerization activity|protein homodimerization activity|voltage-gated chloride channel activity			breast(2)|ovary(1)	3		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0233)|LUSC - Lung squamous cell carcinoma(193;0.131)														---	---	---	---
CLCN3	1182	broad.mit.edu	37	4	170628156	170628156	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170628156T>C	uc003isi.2	+	11	2397	c.1888T>C	c.(1888-1890)TAT>CAT	p.Y630H	CLCN3_uc003ish.2_Missense_Mutation_p.Y630H|CLCN3_uc011cjz.1_Missense_Mutation_p.Y613H|CLCN3_uc011cka.1_Missense_Mutation_p.Y603H|CLCN3_uc003isj.1_Missense_Mutation_p.Y603H	NM_001829	NP_001820	P51790	CLCN3_HUMAN	chloride channel 3 isoform b	630	Cytoplasmic (By similarity).	Chloride (By similarity).			endosomal lumen acidification	cell surface|early endosome membrane|Golgi membrane|integral to membrane|late endosome membrane|transport vesicle membrane	antiporter activity|ATP binding|PDZ domain binding|protein heterodimerization activity|protein homodimerization activity|voltage-gated chloride channel activity			breast(2)|ovary(1)	3		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0233)|LUSC - Lung squamous cell carcinoma(193;0.131)														---	---	---	---
CLCN3	1182	broad.mit.edu	37	4	170628259	170628259	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170628259A>T	uc003isi.2	+	11	2500	c.1991A>T	c.(1990-1992)GAT>GTT	p.D664V	CLCN3_uc003ish.2_Missense_Mutation_p.D664V|CLCN3_uc011cjz.1_Missense_Mutation_p.D647V|CLCN3_uc011cka.1_Missense_Mutation_p.D637V|CLCN3_uc003isj.1_Missense_Mutation_p.D637V	NM_001829	NP_001820	P51790	CLCN3_HUMAN	chloride channel 3 isoform b	664	CBS 1.|Cytoplasmic (By similarity).				endosomal lumen acidification	cell surface|early endosome membrane|Golgi membrane|integral to membrane|late endosome membrane|transport vesicle membrane	antiporter activity|ATP binding|PDZ domain binding|protein heterodimerization activity|protein homodimerization activity|voltage-gated chloride channel activity			breast(2)|ovary(1)	3		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0233)|LUSC - Lung squamous cell carcinoma(193;0.131)														---	---	---	---
C4orf27	54969	broad.mit.edu	37	4	170650841	170650841	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170650841C>T	uc003isl.3	-	8	994	c.929G>A	c.(928-930)GGC>GAC	p.G310D		NM_017867	NP_060337	Q9NWY4	CD027_HUMAN	hypothetical protein LOC54969	310						nucleus				ovary(1)|pancreas(1)	2		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.018)|LUSC - Lung squamous cell carcinoma(193;0.116)														---	---	---	---
AADAT	51166	broad.mit.edu	37	4	170987558	170987558	+	Intron	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:170987558C>A	uc003isr.2	-						AADAT_uc003iss.2_Intron|AADAT_uc003ist.2_Intron	NM_016228	NP_057312			kynurenine aminotransferase II						2-oxoglutarate metabolic process|biosynthetic process|glutamate metabolic process|lysine catabolic process	mitochondrial matrix	2-aminoadipate transaminase activity|kynurenine-oxoglutarate transaminase activity|protein homodimerization activity				0		Prostate(90;0.00601)|Renal(120;0.0183)|all_neural(102;0.122)|Melanoma(52;0.17)		GBM - Glioblastoma multiforme(119;0.0355)|LUSC - Lung squamous cell carcinoma(193;0.118)	L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)													---	---	---	---
GALNTL6	442117	broad.mit.edu	37	4	173730565	173730565	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:173730565A>T	uc003isv.2	+	6	1343	c.607A>T	c.(607-609)ATT>TTT	p.I203F		NM_001034845	NP_001030017	Q49A17	GLTL6_HUMAN	N-acetylgalactosaminyltransferase-like 6	203	Catalytic subdomain A.|Lumenal (Potential).					Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			breast(2)|ovary(1)|skin(1)	4																		---	---	---	---
HMGB2	3148	broad.mit.edu	37	4	174254704	174254704	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174254704C>T	uc011ckc.1	-	1	217	c.97G>A	c.(97-99)GAC>AAC	p.D33N	HMGB2_uc003ita.3_Missense_Mutation_p.D33N|HMGB2_uc003itb.2_Missense_Mutation_p.D33N|HMGB2_uc003itc.2_Missense_Mutation_p.D33N	NM_001130689	NP_001124161	P26583	HMGB2_HUMAN	high-mobility group box 2	33	HMG box 1.				base-excision repair, DNA ligation|cell chemotaxis|cellular response to lipopolysaccharide|DNA fragmentation involved in apoptotic nuclear change|DNA topological change|negative regulation of transcription, DNA-dependent|nucleosome assembly|phosphatidylinositol-mediated signaling|positive regulation of DNA binding|positive regulation of endothelial cell proliferation|positive regulation of erythrocyte differentiation|positive regulation of megakaryocyte differentiation|positive regulation of nuclease activity|positive regulation of transcription from RNA polymerase II promoter|V(D)J recombination	condensed chromosome|extracellular space|nucleolus|nucleoplasm|perinuclear region of cytoplasm|protein complex	chemoattractant activity|damaged DNA binding|DNA bending activity|double-stranded DNA binding|RAGE receptor binding|sequence-specific DNA binding transcription factor activity|single-stranded DNA binding|transcription regulatory region DNA binding				0		Prostate(90;0.0132)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_hematologic(60;0.107)|all_neural(102;0.122)		all cancers(43;9.58e-18)|Epithelial(43;3.75e-16)|OV - Ovarian serous cystadenocarcinoma(60;6.24e-09)|STAD - Stomach adenocarcinoma(60;0.00273)|GBM - Glioblastoma multiforme(59;0.0064)|LUSC - Lung squamous cell carcinoma(193;0.0903)|Kidney(143;0.249)														---	---	---	---
GPM6A	2823	broad.mit.edu	37	4	176594837	176594837	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:176594837G>A	uc003iuf.2	-	3	1185	c.381C>T	c.(379-381)AGC>AGT	p.S127S	GPM6A_uc011ckj.1_Silent_p.S120S|GPM6A_uc003iug.2_Silent_p.S127S|GPM6A_uc003iuh.2_Silent_p.S116S	NM_201591	NP_963885	P51674	GPM6A_HUMAN	glycoprotein M6A isoform 2	127	Cytoplasmic (Potential).					cell surface|integral to membrane					0		Breast(14;7.35e-05)|Melanoma(52;0.00909)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;9.21e-19)|Epithelial(43;3.01e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.02e-09)|STAD - Stomach adenocarcinoma(60;0.00083)|GBM - Glioblastoma multiforme(59;0.00168)|LUSC - Lung squamous cell carcinoma(193;0.0388)														---	---	---	---
AGA	175	broad.mit.edu	37	4	178358589	178358589	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:178358589T>C	uc003iuu.1	-	5	654	c.592A>G	c.(592-594)ACA>GCA	p.T198A	AGA_uc010irt.1_5'Flank|AGA_uc003iuv.1_Missense_Mutation_p.T102A|AGA_uc003iuw.2_Missense_Mutation_p.T102A	NM_000027	NP_000018	P20933	ASPG_HUMAN	aspartylglucosaminidase precursor	198					asparagine catabolic process via L-aspartate|protein deglycosylation|protein maturation	endoplasmic reticulum|intermediate filament cytoskeleton|lysosome|microtubule cytoskeleton	N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity				0		all_lung(41;1.27e-09)|Lung NSC(41;1.1e-08)|Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Hepatocellular(41;0.148)|all_neural(102;0.164)|Colorectal(36;0.245)		all cancers(43;1.37e-22)|Epithelial(43;3.86e-20)|OV - Ovarian serous cystadenocarcinoma(60;3.8e-11)|Colorectal(24;6.98e-05)|GBM - Glioblastoma multiforme(59;0.000362)|COAD - Colon adenocarcinoma(29;0.000462)|STAD - Stomach adenocarcinoma(60;0.0029)|LUSC - Lung squamous cell carcinoma(193;0.0328)|READ - Rectum adenocarcinoma(43;0.163)														---	---	---	---
ODZ3	55714	broad.mit.edu	37	4	183720979	183720979	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183720979G>A	uc003ivd.1	+	27	7612	c.7575G>A	c.(7573-7575)GCG>GCA	p.A2525A		NM_001080477	NP_001073946	Q9P273	TEN3_HUMAN	odz, odd Oz/ten-m homolog 3	2525	Extracellular (Potential).				signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)														---	---	---	---
WWC2	80014	broad.mit.edu	37	4	184186165	184186165	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184186165C>T	uc010irx.2	+	12	2126	c.1944C>T	c.(1942-1944)ATC>ATT	p.I648I	WWC2_uc003ivk.3_Silent_p.I443I|WWC2_uc003ivl.3_RNA|WWC2_uc010iry.2_Silent_p.I330I|WWC2_uc003ivn.3_Silent_p.I163I|WWC2_uc010irz.2_5'Flank	NM_024949	NP_079225	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2	648										ovary(2)|lung(1)	3		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)														---	---	---	---
MLF1IP	79682	broad.mit.edu	37	4	185652115	185652115	+	Missense_Mutation	SNP	G	A	A	rs148908002	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:185652115G>A	uc003iwq.2	-	2	125	c.55C>T	c.(55-57)CGT>TGT	p.R19C	MLF1IP_uc003iwp.2_RNA|MLF1IP_uc003iwr.1_Missense_Mutation_p.R19C	NM_024629	NP_078905	Q71F23	CENPU_HUMAN	MLF1 interacting protein	19	Nuclear localization signal (Potential).				CenH3-containing nucleosome assembly at centromere|interspecies interaction between organisms|mitotic prometaphase|regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|condensed chromosome kinetochore|cytosol|nucleoplasm					0		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Hepatocellular(41;0.000519)|Colorectal(36;0.00172)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.0299)|all_hematologic(60;0.0592)|Medulloblastoma(177;0.146)		all cancers(43;7.83e-28)|Epithelial(43;2.56e-24)|OV - Ovarian serous cystadenocarcinoma(60;4.5e-11)|Colorectal(24;3.27e-06)|STAD - Stomach adenocarcinoma(60;2.66e-05)|GBM - Glioblastoma multiforme(59;3.16e-05)|BRCA - Breast invasive adenocarcinoma(30;0.000252)|COAD - Colon adenocarcinoma(29;0.000512)|LUSC - Lung squamous cell carcinoma(40;0.01)|READ - Rectum adenocarcinoma(43;0.0419)														---	---	---	---
SNX25	83891	broad.mit.edu	37	4	186179999	186179999	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186179999T>C	uc003ixh.2	+							NM_031953	NP_114159			sorting nexin 25						cell communication|protein transport	endosome membrane	phosphatidylinositol binding|signal transducer activity			ovary(2)|breast(2)|pancreas(1)	5		all_lung(41;1.03e-13)|Lung NSC(41;2.5e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;2.13e-24)|Epithelial(43;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.6e-11)|BRCA - Breast invasive adenocarcinoma(30;0.00013)|Colorectal(24;0.000165)|GBM - Glioblastoma multiforme(59;0.000357)|COAD - Colon adenocarcinoma(29;0.000887)|STAD - Stomach adenocarcinoma(60;0.00118)|LUSC - Lung squamous cell carcinoma(40;0.0129)|READ - Rectum adenocarcinoma(43;0.228)														---	---	---	---
SNX25	83891	broad.mit.edu	37	4	186283085	186283085	+	Missense_Mutation	SNP	C	T	T	rs34637796		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186283085C>T	uc003ixh.2	+	17	2356	c.2167C>T	c.(2167-2169)CGG>TGG	p.R723W	SNX25_uc010ish.2_Missense_Mutation_p.R439W|SNX25_uc003ixi.2_Missense_Mutation_p.R227W	NM_031953	NP_114159	Q9H3E2	SNX25_HUMAN	sorting nexin 25	723					cell communication|protein transport	endosome membrane	phosphatidylinositol binding|signal transducer activity			ovary(2)|breast(2)|pancreas(1)	5		all_lung(41;1.03e-13)|Lung NSC(41;2.5e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;2.13e-24)|Epithelial(43;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.6e-11)|BRCA - Breast invasive adenocarcinoma(30;0.00013)|Colorectal(24;0.000165)|GBM - Glioblastoma multiforme(59;0.000357)|COAD - Colon adenocarcinoma(29;0.000887)|STAD - Stomach adenocarcinoma(60;0.00118)|LUSC - Lung squamous cell carcinoma(40;0.0129)|READ - Rectum adenocarcinoma(43;0.228)														---	---	---	---
LRP2BP	55805	broad.mit.edu	37	4	186291825	186291825	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:186291825T>A	uc003ixj.1	-	7	1759	c.947A>T	c.(946-948)GAT>GTT	p.D316V	LRP2BP_uc003ixk.1_Missense_Mutation_p.D290V|LRP2BP_uc011ckr.1_Missense_Mutation_p.D316V	NM_018409	NP_060879	Q9P2M1	LR2BP_HUMAN	LRP2 binding protein	316	Sel1-like 6.					cytoplasm	protein binding				0		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;0.00109)|Colorectal(36;0.0215)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;2.14e-25)|Epithelial(43;1.55e-22)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-11)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.000132)|STAD - Stomach adenocarcinoma(60;0.000766)|Colorectal(24;0.00116)|LUSC - Lung squamous cell carcinoma(40;0.00904)|COAD - Colon adenocarcinoma(29;0.0101)|READ - Rectum adenocarcinoma(43;0.161)														---	---	---	---
CYP4V2	285440	broad.mit.edu	37	4	187130304	187130304	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187130304G>T	uc003iyw.3	+	10	1587	c.1283G>T	c.(1282-1284)AGA>ATA	p.R428I	CYP4V2_uc010ism.2_RNA	NM_207352	NP_997235	Q6ZWL3	CP4V2_HUMAN	cytochrome P450, family 4, subfamily v,	428					response to stimulus|visual perception	endoplasmic reticulum membrane|integral to membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen				0		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.33e-10)|BRCA - Breast invasive adenocarcinoma(30;3.84e-05)|GBM - Glioblastoma multiforme(59;0.000132)|STAD - Stomach adenocarcinoma(60;0.000293)|LUSC - Lung squamous cell carcinoma(40;0.00242)|READ - Rectum adenocarcinoma(43;0.17)														---	---	---	---
KLKB1	3818	broad.mit.edu	37	4	187172448	187172448	+	Silent	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187172448A>T	uc003iyy.2	+	8	905	c.834A>T	c.(832-834)GGA>GGT	p.G278G	KLKB1_uc011clc.1_Silent_p.G76G|KLKB1_uc011cld.1_Silent_p.G240G	NM_000892	NP_000883	P03952	KLKB1_HUMAN	plasma kallikrein B1 precursor	278	Apple 3.				blood coagulation, intrinsic pathway|Factor XII activation|fibrinolysis|plasminogen activation|positive regulation of fibrinolysis	cytoplasm|extracellular space|plasma membrane	serine-type endopeptidase activity			ovary(1)	1		all_cancers(14;1.55e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00664)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.29e-10)|BRCA - Breast invasive adenocarcinoma(30;3.8e-05)|GBM - Glioblastoma multiforme(59;0.000131)|STAD - Stomach adenocarcinoma(60;0.000292)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.168)														---	---	---	---
FAT1	2195	broad.mit.edu	37	4	187530344	187530344	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187530344C>T	uc003izf.2	-	16	10387	c.10199G>A	c.(10198-10200)CGA>CAA	p.R3400Q		NM_005245	NP_005236	Q14517	FAT1_HUMAN	FAT tumor suppressor 1 precursor	3400	Extracellular (Potential).|Cadherin 31.				actin filament organization|anatomical structure morphogenesis|cell migration|cell-cell signaling|establishment or maintenance of cell polarity|homophilic cell adhesion	cell-cell junction|integral to plasma membrane|nucleus|perinuclear region of cytoplasm	calcium ion binding|protein binding			ovary(10)|central_nervous_system(1)|pancreas(1)	12															HNSCC(5;0.00058)			---	---	---	---
AHRR	57491	broad.mit.edu	37	5	422889	422889	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:422889G>A	uc003jav.2	+	6	543	c.499G>A	c.(499-501)GAC>AAC	p.D167N	AHRR_uc003jaw.2_Missense_Mutation_p.D163N|AHRR_uc010isy.2_Missense_Mutation_p.D13N|AHRR_uc010isz.2_Missense_Mutation_p.D163N|AHRR_uc003jax.2_5'UTR|AHRR_uc003jay.2_Missense_Mutation_p.D23N	NM_020731	NP_065782	A9YTQ3	AHRR_HUMAN	arylhydrocarbon receptor repressor	167	PAS.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			breast(2)	2			Epithelial(17;0.0011)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00354)|Lung(60;0.0863)															---	---	---	---
EXOC3	11336	broad.mit.edu	37	5	464489	464489	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:464489T>C	uc003jba.2	+	10	1866	c.1738T>C	c.(1738-1740)TTC>CTC	p.F580L		NM_007277	NP_009208	O60645	EXOC3_HUMAN	Sec6 protein	591					exocytosis|protein transport						0		Ovarian(839;0.0563)	Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)															---	---	---	---
SLC9A3	6550	broad.mit.edu	37	5	480029	480029	+	Silent	SNP	C	T	T	rs147340203		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:480029C>T	uc003jbe.2	-	10	1681	c.1569G>A	c.(1567-1569)TCG>TCA	p.S523S	SLC9A3_uc011clx.1_Silent_p.S514S|uc011cly.1_RNA	NM_004174	NP_004165	P48764	SL9A3_HUMAN	solute carrier family 9 (sodium/hydrogen	523	Cytoplasmic (Potential).					cell surface|integral to membrane	sodium:hydrogen antiporter activity				0			Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)															---	---	---	---
TPPP	11076	broad.mit.edu	37	5	677857	677857	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:677857G>A	uc003jbg.3	-						TPPP_uc003jbh.3_Intron	NM_007030	NP_008961			tubulin polymerization promoting protein						microtubule bundle formation|microtubule polymerization|positive regulation of protein polymerization	nucleus|perinuclear region of cytoplasm|soluble fraction	calcium ion binding|microtubule binding				0		Ovarian(839;0.0563)	Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)	GBM - Glioblastoma multiforme(108;0.0191)														---	---	---	---
TERT	7015	broad.mit.edu	37	5	1255505	1255505	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1255505C>A	uc003jcb.1	-	14	3112	c.3054G>T	c.(3052-3054)CAG>CAT	p.Q1018H	TERT_uc003jbz.1_Missense_Mutation_p.Q214H|TERT_uc003jca.1_Missense_Mutation_p.Q1006H|TERT_uc003jcc.1_Missense_Mutation_p.Q955H|TERT_uc003jcd.1_RNA|TERT_uc003jce.1_RNA	NM_198253	NP_937983	O14746	TERT_HUMAN	telomerase reverse transcriptase isoform 1	1018	CTE.				anti-apoptosis|DNA strand elongation|replicative senescence|telomere formation via telomerase|telomere maintenance via telomerase	cytoplasm|nucleolus|PML body|telomerase holoenzyme complex	protein homodimerization activity|telomeric DNA binding|telomeric RNA binding|telomeric template RNA reverse transcriptase activity			lung(7)|ovary(2)|central_nervous_system(2)|skin(1)	12	all_cancers(3;3.17e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.87e-10)		Epithelial(17;0.00105)|all cancers(22;0.00178)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)											TERT_Mutation-Associated_Haematological_Disorders|Congenital_Dyskeratosis|Pulmonary_Fibrosis_Idiopathic				---	---	---	---
LPCAT1	79888	broad.mit.edu	37	5	1474668	1474668	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1474668T>C	uc003jcm.2	-							NM_024830	NP_079106			lysophosphatidylcholine acyltransferase 1						phospholipid biosynthetic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane	1-acylglycerophosphocholine O-acyltransferase activity|1-alkylglycerophosphocholine O-acetyltransferase activity|calcium ion binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(19;0.0274)|all cancers(22;0.0534)	GBM - Glioblastoma multiforme(108;0.156)														---	---	---	---
ADAMTS16	170690	broad.mit.edu	37	5	5182409	5182409	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5182409C>T	uc003jdl.2	+	4	892	c.754C>T	c.(754-756)CGC>TGC	p.R252C	ADAMTS16_uc003jdk.1_Missense_Mutation_p.R252C|ADAMTS16_uc003jdj.1_Missense_Mutation_p.R252C	NM_139056	NP_620687	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1	252	Cysteine switch (By similarity).				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(3)|lung(2)|large_intestine(1)|breast(1)|pancreas(1)	8																		---	---	---	---
ADAMTS16	170690	broad.mit.edu	37	5	5242187	5242187	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5242187C>T	uc003jdl.2	+	17	2683	c.2545C>T	c.(2545-2547)CCG>TCG	p.P849S	ADAMTS16_uc003jdk.1_Missense_Mutation_p.P849S	NM_139056	NP_620687	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1	849	Spacer.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(3)|lung(2)|large_intestine(1)|breast(1)|pancreas(1)	8																		---	---	---	---
KIAA0947	23379	broad.mit.edu	37	5	5464054	5464054	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5464054C>T	uc003jdm.3	+	13	4829	c.4607C>T	c.(4606-4608)GCG>GTG	p.A1536V		NM_015325	NP_056140	Q9Y2F5	K0947_HUMAN	hypothetical protein LOC23379	1536										ovary(1)|central_nervous_system(1)	2																		---	---	---	---
KIAA0947	23379	broad.mit.edu	37	5	5473849	5473849	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:5473849A>T	uc003jdm.3	+	16	6623	c.6401A>T	c.(6400-6402)GAT>GTT	p.D2134V		NM_015325	NP_056140	Q9Y2F5	K0947_HUMAN	hypothetical protein LOC23379	2134										ovary(1)|central_nervous_system(1)	2																		---	---	---	---
NSUN2	54888	broad.mit.edu	37	5	6604742	6604742	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6604742G>T	uc003jdu.2	-	16	1859	c.1794C>A	c.(1792-1794)GAC>GAA	p.D598E	NSUN2_uc003jds.2_Missense_Mutation_p.D44E|NSUN2_uc003jdt.2_Missense_Mutation_p.D362E|NSUN2_uc011cmk.1_Missense_Mutation_p.D563E|NSUN2_uc003jdv.2_Missense_Mutation_p.D362E	NM_017755	NP_060225	Q08J23	NSUN2_HUMAN	NOL1/NOP2/Sun domain family, member 2	598						cytoplasm|nucleolus	tRNA (cytosine-5-)-methyltransferase activity|tRNA binding			ovary(1)	1																		---	---	---	---
PAPD7	11044	broad.mit.edu	37	5	6748696	6748696	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:6748696G>A	uc003jdx.1	+	8	958	c.829G>A	c.(829-831)GCC>ACC	p.A277T	PAPD7_uc011cmn.1_Missense_Mutation_p.A268T|PAPD7_uc010itl.1_Missense_Mutation_p.A97T	NM_006999	NP_008930	Q5XG87	PAPD7_HUMAN	DNA polymerase sigma	277					cell division|DNA replication|double-strand break repair|mitotic chromosome condensation|response to drug|sister chromatid cohesion	nucleus	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|SMC protein binding			ovary(1)	1																		---	---	---	---
ADCY2	108	broad.mit.edu	37	5	7724715	7724715	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:7724715A>G	uc003jdz.1	+	13	1828	c.1761A>G	c.(1759-1761)GTA>GTG	p.V587V	ADCY2_uc011cmo.1_Silent_p.V407V	NM_020546	NP_065433	Q08462	ADCY2_HUMAN	adenylate cyclase 2	587	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)|skin(1)	7																		---	---	---	---
CMBL	134147	broad.mit.edu	37	5	10288522	10288522	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10288522C>T	uc003jes.2	-							NM_138809	NP_620164			carboxymethylenebutenolidase							cytosol	hydrolase activity|protein binding			skin(1)	1																		---	---	---	---
CTNND2	1501	broad.mit.edu	37	5	11236855	11236855	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:11236855G>A	uc003jfa.1	-	10	1854	c.1709C>T	c.(1708-1710)GCG>GTG	p.A570V	CTNND2_uc010itt.2_Missense_Mutation_p.A479V|CTNND2_uc011cmy.1_Missense_Mutation_p.A233V|CTNND2_uc011cmz.1_Missense_Mutation_p.A137V|CTNND2_uc010itu.1_RNA|CTNND2_uc011cmx.1_Missense_Mutation_p.A137V	NM_001332	NP_001323	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	570	ARM 2.				multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8																		---	---	---	---
DNAH5	1767	broad.mit.edu	37	5	13719041	13719041	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13719041G>A	uc003jfd.2	-	72	12491	c.12449C>T	c.(12448-12450)GCC>GTC	p.A4150V	DNAH5_uc003jfc.2_Missense_Mutation_p.A318V	NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4150	AAA 6 (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)													Kartagener_syndrome				---	---	---	---
DNAH5	1767	broad.mit.edu	37	5	13737408	13737408	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13737408G>T	uc003jfd.2	-	66	11450	c.11408C>A	c.(11407-11409)GCT>GAT	p.A3803D	DNAH5_uc003jfc.2_Intron	NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3803	Potential.				microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)													Kartagener_syndrome				---	---	---	---
DNAH5	1767	broad.mit.edu	37	5	13737430	13737430	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13737430T>C	uc003jfd.2	-	66	11428	c.11386A>G	c.(11386-11388)ACA>GCA	p.T3796A	DNAH5_uc003jfc.2_Intron	NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3796	Potential.|AAA 5 (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)													Kartagener_syndrome				---	---	---	---
DNAH5	1767	broad.mit.edu	37	5	13823400	13823400	+	Missense_Mutation	SNP	G	T	T	rs144308691		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13823400G>T	uc003jfd.2	-	40	6701	c.6659C>A	c.(6658-6660)CCT>CAT	p.P2220H		NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2220					microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)													Kartagener_syndrome				---	---	---	---
DNAH5	1767	broad.mit.edu	37	5	13865820	13865820	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13865820T>C	uc003jfd.2	-	27	4354	c.4312A>G	c.(4312-4314)AAT>GAT	p.N1438D		NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1438	Potential.|Stem (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)													Kartagener_syndrome				---	---	---	---
DNAH5	1767	broad.mit.edu	37	5	13901387	13901387	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13901387G>T	uc003jfd.2	-	14	2068	c.2026C>A	c.(2026-2028)CTC>ATC	p.L676I		NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	676	Stem (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)													Kartagener_syndrome				---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14401169	14401169	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14401169T>G	uc003jff.2	+	31	4718	c.4712T>G	c.(4711-4713)CTT>CGT	p.L1571R	TRIO_uc003jfg.2_RNA|TRIO_uc003jfh.1_Missense_Mutation_p.L1220R	NM_007118	NP_009049	O75962	TRIO_HUMAN	triple functional domain (PTPRF interacting)	1571	PH 1.				apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)																	---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14462875	14462875	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14462875C>T	uc003jff.2	+	36	5514	c.5508C>T	c.(5506-5508)AAC>AAT	p.N1836N	TRIO_uc003jfg.2_RNA|TRIO_uc003jfh.1_Silent_p.N1485N|TRIO_uc003jfi.1_Silent_p.N139N	NM_007118	NP_009049	O75962	TRIO_HUMAN	triple functional domain (PTPRF interacting)	1836					apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)																	---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14462963	14462963	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14462963G>A	uc003jff.2	+	36	5602	c.5596G>A	c.(5596-5598)GCC>ACC	p.A1866T	TRIO_uc003jfg.2_RNA|TRIO_uc003jfh.1_Missense_Mutation_p.A1515T|TRIO_uc003jfi.1_Missense_Mutation_p.A169T	NM_007118	NP_009049	O75962	TRIO_HUMAN	triple functional domain (PTPRF interacting)	1866					apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)																	---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14482762	14482762	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14482762T>C	uc003jff.2	+	46	6543	c.6537T>C	c.(6535-6537)CTT>CTC	p.L2179L	TRIO_uc003jfg.2_RNA|TRIO_uc003jfh.1_Silent_p.L1828L	NM_007118	NP_009049	O75962	TRIO_HUMAN	triple functional domain (PTPRF interacting)	2179	PH 2.				apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)																	---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14498662	14498662	+	Missense_Mutation	SNP	G	A	A	rs143848658		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14498662G>A	uc003jff.2	+	53	8251	c.8245G>A	c.(8245-8247)GTG>ATG	p.V2749M	TRIO_uc003jfg.2_RNA	NM_007118	NP_009049	O75962	TRIO_HUMAN	triple functional domain (PTPRF interacting)	2749	Ig-like C2-type.				apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)																	---	---	---	---
TRIO	7204	broad.mit.edu	37	5	14508414	14508414	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14508414C>T	uc003jff.2	+	57	9183	c.9177C>T	c.(9175-9177)GGC>GGT	p.G3059G	TRIO_uc003jfg.2_RNA	NM_007118	NP_009049	O75962	TRIO_HUMAN	triple functional domain (PTPRF interacting)	3059					apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)																	---	---	---	---
ANKH	56172	broad.mit.edu	37	5	14755995	14755995	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:14755995G>T	uc003jfm.3	-	4	822	c.491C>A	c.(490-492)GCC>GAC	p.A164D		NM_054027	NP_473368	Q9HCJ1	ANKH_HUMAN	progressive ankylosis protein	164	Helical; (Potential).				locomotory behavior|regulation of bone mineralization|skeletal system development	integral to plasma membrane|outer membrane	inorganic diphosphate transmembrane transporter activity|inorganic phosphate transmembrane transporter activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
ZNF622	90441	broad.mit.edu	37	5	16465311	16465311	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:16465311G>A	uc003jfq.2	-	1	584	c.464C>T	c.(463-465)GCC>GTC	p.A155V		NM_033414	NP_219482	Q969S3	ZN622_HUMAN	zinc finger protein 622	155						cytoplasm|nucleus	nucleic acid binding|zinc ion binding			ovary(1)	1																		---	---	---	---
CDH18	1016	broad.mit.edu	37	5	19473675	19473675	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:19473675T>C	uc003jgc.2	-	12	2410	c.2033A>G	c.(2032-2034)AAT>AGT	p.N678S	CDH18_uc003jgd.2_Missense_Mutation_p.N678S|CDH18_uc011cnm.1_3'UTR	NM_004934	NP_004925	Q13634	CAD18_HUMAN	cadherin 18, type 2 preproprotein	678	Cytoplasmic (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)																	---	---	---	---
CDH12	1010	broad.mit.edu	37	5	21765175	21765175	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21765175A>G	uc010iuc.2	-	9	1885	c.1427T>C	c.(1426-1428)CTG>CCG	p.L476P	CDH12_uc011cno.1_Missense_Mutation_p.L436P|CDH12_uc003jgk.2_Missense_Mutation_p.L476P|uc003jgj.2_Intron	NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein	476	Extracellular (Potential).|Cadherin 4.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2															HNSCC(59;0.17)			---	---	---	---
CDH12	1010	broad.mit.edu	37	5	21783502	21783502	+	Missense_Mutation	SNP	G	A	A	rs143124599	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21783502G>A	uc010iuc.2	-	8	1816	c.1358C>T	c.(1357-1359)GCG>GTG	p.A453V	CDH12_uc011cno.1_Missense_Mutation_p.A413V|CDH12_uc003jgk.2_Missense_Mutation_p.A453V	NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein	453	Extracellular (Potential).|Cadherin 4.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2															HNSCC(59;0.17)			---	---	---	---
CDH10	1008	broad.mit.edu	37	5	24491795	24491795	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24491795C>T	uc003jgr.1	-	11	2098	c.1766G>A	c.(1765-1767)TGT>TAT	p.C589Y	CDH10_uc011cnu.1_RNA	NM_006727	NP_006718	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 preproprotein	589	Cadherin 5.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|pancreas(4)|breast(2)	12				STAD - Stomach adenocarcinoma(35;0.0556)											HNSCC(23;0.051)			---	---	---	---
CDH10	1008	broad.mit.edu	37	5	24537670	24537670	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:24537670C>T	uc003jgr.1	-	3	677	c.345G>A	c.(343-345)AGG>AGA	p.R115R	CDH10_uc011cnu.1_RNA	NM_006727	NP_006718	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 preproprotein	115	Cadherin 1.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|pancreas(4)|breast(2)	12				STAD - Stomach adenocarcinoma(35;0.0556)											HNSCC(23;0.051)			---	---	---	---
PDZD2	23037	broad.mit.edu	37	5	32077599	32077599	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32077599C>T	uc003jhl.2	+	19	3957	c.3569C>T	c.(3568-3570)GCT>GTT	p.A1190V	PDZD2_uc003jhm.2_Missense_Mutation_p.A1190V|PDZD2_uc011cnx.1_Missense_Mutation_p.A1016V	NM_178140	NP_835260	O15018	PDZD2_HUMAN	PDZ domain containing 2	1190					cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|skin(2)|large_intestine(1)	9																		---	---	---	---
MTMR12	54545	broad.mit.edu	37	5	32274208	32274208	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:32274208C>T	uc003jhq.2	-	3	333	c.163G>A	c.(163-165)GCC>ACC	p.A55T	MTMR12_uc010iuk.2_Missense_Mutation_p.A55T|MTMR12_uc010iul.2_Missense_Mutation_p.A55T	NM_001040446	NP_001035536	Q9C0I1	MTMRC_HUMAN	myotubularin related protein 12	55						cytoplasm	phosphatase activity			ovary(1)	1																		---	---	---	---
ADAMTS12	81792	broad.mit.edu	37	5	33549440	33549440	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33549440C>T	uc003jia.1	-	21	4337	c.4174G>A	c.(4174-4176)GTG>ATG	p.V1392M	ADAMTS12_uc010iuq.1_Missense_Mutation_p.V1307M	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1392	TSP type-1 6.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	9															HNSCC(64;0.19)			---	---	---	---
AMACR	23600	broad.mit.edu	37	5	33989470	33989470	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33989470A>G	uc003jig.2	-	5	959	c.877T>C	c.(877-879)TGT>CGT	p.C293R	AMACR_uc003jih.2_3'UTR|AMACR_uc003jii.2_Missense_Mutation_p.C278R|AMACR_uc003jij.2_Missense_Mutation_p.C293R	NM_014324	NP_055139	Q9UHK6	AMACR_HUMAN	alpha-methylacyl-CoA racemase isoform 1	293					bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase	mitochondrion|peroxisomal matrix	alpha-methylacyl-CoA racemase activity				0																		---	---	---	---
TTC23L	153657	broad.mit.edu	37	5	34863073	34863073	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34863073G>A	uc003jiu.2	+	5	553	c.450G>A	c.(448-450)ACG>ACA	p.T150T	TTC23L_uc003jiv.2_5'Flank|TTC23L_uc010iut.1_5'Flank	NM_144725	NP_653326	Q6PF05	TT23L_HUMAN	tetratricopeptide repeat domain 23-like	150							binding			central_nervous_system(1)	1																		---	---	---	---
DNAJC21	134218	broad.mit.edu	37	5	34937695	34937695	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:34937695G>A	uc003jjc.2	+	5	930	c.703G>A	c.(703-705)GCC>ACC	p.A235T	DNAJC21_uc003jjb.2_Missense_Mutation_p.A235T|DNAJC21_uc010iuu.1_Missense_Mutation_p.A119T	NM_001012339	NP_001012339	Q5F1R6	DJC21_HUMAN	DnaJ homology subfamily A member 5 isoform 2	235	Glu-rich.				protein folding	ribosome	heat shock protein binding|nucleic acid binding|unfolded protein binding|zinc ion binding			breast(1)|skin(1)	2	all_lung(31;7.08e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)															---	---	---	---
AGXT2	64902	broad.mit.edu	37	5	35026598	35026598	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:35026598C>A	uc003jjf.2	-	8	866	c.787G>T	c.(787-789)GAT>TAT	p.D263Y	AGXT2_uc003jje.1_5'Flank|AGXT2_uc011com.1_Missense_Mutation_p.D263Y	NM_031900	NP_114106	Q9BYV1	AGT2_HUMAN	alanine-glyoxylate aminotransferase 2 precursor	263					glyoxylate metabolic process|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process	mitochondrial matrix	(R)-3-amino-2-methylpropionate-pyruvate transaminase activity|alanine-glyoxylate transaminase activity|pyridoxal phosphate binding			ovary(3)|skin(1)	4	all_lung(31;4.52e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)	GBM - Glioblastoma multiforme(108;0.181)	Glycine(DB00145)|L-Alanine(DB00160)|Pyridoxal Phosphate(DB00114)|Pyruvic acid(DB00119)													---	---	---	---
SLC1A3	6507	broad.mit.edu	37	5	36679730	36679730	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36679730T>C	uc003jkj.3	+	7	1338	c.862T>C	c.(862-864)TAT>CAT	p.Y288H	SLC1A3_uc011cox.1_Missense_Mutation_p.Y181H|SLC1A3_uc010iuy.2_Missense_Mutation_p.Y288H	NM_004172	NP_004163	P43003	EAA1_HUMAN	solute carrier family 1 (glial high affinity	288	Helical; (Potential).				D-aspartate import|L-glutamate import|neurotransmitter uptake	integral to membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|sodium:dicarboxylate symporter activity				0	all_lung(31;0.000245)		Epithelial(62;0.0444)|Lung(74;0.111)|all cancers(62;0.128)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)		L-Glutamic Acid(DB00142)													---	---	---	---
SLC1A3	6507	broad.mit.edu	37	5	36684005	36684005	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36684005T>C	uc003jkj.3	+	9	1805	c.1329T>C	c.(1327-1329)ATT>ATC	p.I443I	SLC1A3_uc011cox.1_Silent_p.I336I|SLC1A3_uc010iuy.2_Intron	NM_004172	NP_004163	P43003	EAA1_HUMAN	solute carrier family 1 (glial high affinity	443					D-aspartate import|L-glutamate import|neurotransmitter uptake	integral to membrane|membrane fraction	high-affinity glutamate transmembrane transporter activity|sodium:dicarboxylate symporter activity				0	all_lung(31;0.000245)		Epithelial(62;0.0444)|Lung(74;0.111)|all cancers(62;0.128)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)		L-Glutamic Acid(DB00142)													---	---	---	---
NIPBL	25836	broad.mit.edu	37	5	36986090	36986090	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36986090C>T	uc003jkl.3	+	10	3307	c.2808C>T	c.(2806-2808)GAC>GAT	p.D936D	NIPBL_uc003jkk.3_Silent_p.D936D|NIPBL_uc003jkm.1_Silent_p.D815D	NM_133433	NP_597677	Q6KC79	NIPBL_HUMAN	delangin isoform A	936					brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis	SMC loading complex	chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding			ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1)	9	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)															---	---	---	---
NIPBL	25836	broad.mit.edu	37	5	37003421	37003421	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37003421G>A	uc003jkl.3	+	16	4326	c.3827G>A	c.(3826-3828)GGG>GAG	p.G1276E	NIPBL_uc003jkk.3_Missense_Mutation_p.G1276E	NM_133433	NP_597677	Q6KC79	NIPBL_HUMAN	delangin isoform A	1276					brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis	SMC loading complex	chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding			ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1)	9	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)															---	---	---	---
C5orf42	65250	broad.mit.edu	37	5	37174054	37174054	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37174054G>A	uc011cpa.1	-						C5orf42_uc011coy.1_Intron|C5orf42_uc003jks.2_Intron|C5orf42_uc011coz.1_Intron|C5orf42_uc003jkr.1_Intron	NM_023073	NP_075561			hypothetical protein LOC65250											ovary(4)|breast(2)|skin(1)	7	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)															---	---	---	---
WDR70	55100	broad.mit.edu	37	5	37703135	37703135	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37703135T>C	uc003jkv.2	+	13	1420	c.1362T>C	c.(1360-1362)GTT>GTC	p.V454V		NM_018034	NP_060504	Q9NW82	WDR70_HUMAN	WD repeat domain 70	454	WD 6.									ovary(1)|central_nervous_system(1)	2	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)															---	---	---	---
EGFLAM	133584	broad.mit.edu	37	5	38418352	38418352	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38418352A>G	uc003jlc.1	+	12	2003	c.1679A>G	c.(1678-1680)GAT>GGT	p.D560G	EGFLAM_uc003jlb.1_Missense_Mutation_p.D560G|EGFLAM_uc003jle.1_Missense_Mutation_p.D326G|EGFLAM_uc003jlf.1_Intron	NM_152403	NP_689616	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G	560	Laminin G-like 1.					cell junction|proteinaceous extracellular matrix|synapse				pancreas(3)|skin(3)|ovary(1)	7	all_lung(31;0.000385)																	---	---	---	---
LIFR	3977	broad.mit.edu	37	5	38482134	38482134	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38482134T>G	uc010ive.1	-	20	3189	c.2857A>C	c.(2857-2859)ATC>CTC	p.I953L	LIFR_uc003jli.2_Missense_Mutation_p.I953L	NM_001127671	NP_001121143	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor precursor	953	Cytoplasmic (Potential).				positive regulation of cell proliferation	extracellular region|integral to plasma membrane	ciliary neurotrophic factor receptor binding|growth factor binding|leukemia inhibitory factor receptor activity			ovary(3)|large_intestine(1)	4	all_lung(31;0.00021)							T	PLAG1	salivary adenoma								---	---	---	---
LIFR	3977	broad.mit.edu	37	5	38527405	38527405	+	Intron	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:38527405A>C	uc010ive.1	-						LIFR_uc003jli.2_Intron	NM_001127671	NP_001121143			leukemia inhibitory factor receptor precursor						positive regulation of cell proliferation	extracellular region|integral to plasma membrane	ciliary neurotrophic factor receptor binding|growth factor binding|leukemia inhibitory factor receptor activity			ovary(3)|large_intestine(1)	4	all_lung(31;0.00021)							T	PLAG1	salivary adenoma								---	---	---	---
DAB2	1601	broad.mit.edu	37	5	39377102	39377102	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:39377102C>T	uc003jlx.2	-	12	2318	c.1787G>A	c.(1786-1788)AGC>AAC	p.S596N	DAB2_uc003jlw.2_Missense_Mutation_p.S575N	NM_001343	NP_001334	P98082	DAB2_HUMAN	disabled homolog 2	596					cell proliferation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of protein binding|negative regulation of transcription, DNA-dependent|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|positive regulation of transcription, DNA-dependent|positive regulation of Wnt receptor signaling pathway, planar cell polarity pathway	clathrin coated vesicle membrane|coated pit	protein C-terminus binding			kidney(2)|skin(1)	3	all_lung(31;0.000197)		Epithelial(62;0.137)													OREG0016586	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CARD6	84674	broad.mit.edu	37	5	40853931	40853931	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40853931C>T	uc003jmg.2	+	3	2572	c.2497C>T	c.(2497-2499)CCA>TCA	p.P833S		NM_032587	NP_115976	Q9BX69	CARD6_HUMAN	caspase recruitment domain family, member 6	833					apoptosis|regulation of apoptosis	intracellular				ovary(2)|skin(2)|lung(1)	5																		---	---	---	---
HEATR7B2	133558	broad.mit.edu	37	5	41019023	41019023	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41019023T>G	uc003jmj.3	-	25	3029	c.2539A>C	c.(2539-2541)AGT>CGT	p.S847R	HEATR7B2_uc003jmi.3_Missense_Mutation_p.S402R	NM_173489	NP_775760	Q7Z745	HTRB2_HUMAN	HEAT repeat family member 7B2	847							binding			ovary(6)|central_nervous_system(2)	8																		---	---	---	---
C6	729	broad.mit.edu	37	5	41149415	41149415	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:41149415T>C	uc003jmk.2	-	17	2761	c.2551A>G	c.(2551-2553)AGA>GGA	p.R851G	C6_uc003jml.1_Missense_Mutation_p.R851G	NM_000065	NP_000056	P13671	CO6_HUMAN	complement component 6 precursor	851	C5b-binding domain.				complement activation, classical pathway|cytolysis|innate immune response	membrane attack complex	protein binding			ovary(3)|central_nervous_system(2)|skin(2)	7		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)																---	---	---	---
GZMA	3001	broad.mit.edu	37	5	54401446	54401446	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54401446T>C	uc003jpm.2	+	2	252	c.215T>C	c.(214-216)TTG>TCG	p.L72S		NM_006144	NP_006135	P12544	GRAA_HUMAN	granzyme A precursor	72	Peptidase S1.			NL -> IP (in Ref. 5; no nucleotide entry).	cleavage of lamin|cytolysis|immune response|negative regulation of DNA binding|negative regulation of endodeoxyribonuclease activity|negative regulation of oxidoreductase activity|positive regulation of apoptosis	extracellular region|immunological synapse|nucleus	protein homodimerization activity|serine-type endopeptidase activity			ovary(2)|pancreas(1)|skin(1)	4		Lung NSC(810;4.08e-05)|Breast(144;0.0433)|Prostate(74;0.183)																---	---	---	---
DHX29	54505	broad.mit.edu	37	5	54570772	54570772	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:54570772G>A	uc003jpx.2	-	15	2614	c.2494C>T	c.(2494-2496)CGC>TGC	p.R832C	DHX29_uc010ivw.2_RNA	NM_019030	NP_061903	Q7Z478	DHX29_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 29	832							ATP binding|ATP-dependent helicase activity|translation initiation factor activity			ovary(2)|central_nervous_system(1)|skin(1)	4		Lung NSC(810;4.08e-05)|Breast(144;0.0544)|Prostate(74;0.183)																---	---	---	---
MAP3K1	4214	broad.mit.edu	37	5	56161716	56161716	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:56161716C>T	uc003jqw.3	+	6	1714	c.1213C>T	c.(1213-1215)CGT>TGT	p.R405C		NM_005921	NP_005912	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase	405					cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	ATP binding|zinc ion binding			ovary(1)|skin(1)	2		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)														---	---	---	---
PLK2	10769	broad.mit.edu	37	5	57751356	57751356	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:57751356A>G	uc003jrn.2	-							NM_006622	NP_006613			polo-like kinase 2						positive regulation of I-kappaB kinase/NF-kappaB cascade		ATP binding|protein binding|protein serine/threonine kinase activity|signal transducer activity			ovary(2)|lung(1)|skin(1)	4		all_cancers(5;1.76e-12)|all_epithelial(5;2.09e-13)|all_lung(5;6.64e-05)|Lung NSC(5;0.000127)|Prostate(74;0.055)|Breast(144;0.0602)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;7.03e-37)														---	---	---	---
IPO11	51194	broad.mit.edu	37	5	61745778	61745778	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61745778T>C	uc003jtc.2	+	4	454	c.264T>C	c.(262-264)ACT>ACC	p.T88T	IPO11_uc011cqr.1_Silent_p.T128T|IPO11_uc003jtb.1_Silent_p.T88T	NM_016338	NP_057422	Q9UI26	IPO11_HUMAN	Ran binding protein 11 isoform 2	88	Importin N-terminal.					cytoplasm|nucleus	protein binding			lung(2)|skin(2)	4		Lung NSC(810;8.99e-06)|Prostate(74;0.0235)|Ovarian(174;0.0511)|Breast(144;0.077)		Lung(70;0.0613)														---	---	---	---
IPO11	51194	broad.mit.edu	37	5	61800724	61800724	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61800724C>T	uc003jtc.2	+	18	1854	c.1664C>T	c.(1663-1665)CCG>CTG	p.P555L	IPO11_uc011cqr.1_Missense_Mutation_p.P595L|IPO11_uc003jtd.1_RNA	NM_016338	NP_057422	Q9UI26	IPO11_HUMAN	Ran binding protein 11 isoform 2	555	HEAT 7.					cytoplasm|nucleus	protein binding			lung(2)|skin(2)	4		Lung NSC(810;8.99e-06)|Prostate(74;0.0235)|Ovarian(174;0.0511)|Breast(144;0.077)		Lung(70;0.0613)														---	---	---	---
MAST4	375449	broad.mit.edu	37	5	66440558	66440558	+	Missense_Mutation	SNP	A	C	C	rs114139516	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66440558A>C	uc003jut.1	+	21	2293	c.2225A>C	c.(2224-2226)GAC>GCC	p.D742A	MAST4_uc003juu.1_Missense_Mutation_p.D752A|MAST4_uc011cra.1_Missense_Mutation_p.D725A|MAST4_uc003juv.2_Missense_Mutation_p.D737A|MAST4_uc003juw.2_Missense_Mutation_p.D737A	NM_015183	NP_055998	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase	934						cytoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(6)|ovary(2)|kidney(2)|breast(2)|central_nervous_system(1)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)														---	---	---	---
MAST4	375449	broad.mit.edu	37	5	66461168	66461168	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66461168C>T	uc003jut.1	+	28	5662	c.5594C>T	c.(5593-5595)CCG>CTG	p.P1865L	MAST4_uc003juw.2_Missense_Mutation_p.P1793L|MAST4_uc003jux.2_5'Flank	NM_015183	NP_055998	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase	2057						cytoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity	p.R1865K(1)		lung(6)|ovary(2)|kidney(2)|breast(2)|central_nervous_system(1)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)														---	---	---	---
CCDC125	202243	broad.mit.edu	37	5	68616272	68616272	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68616272G>T	uc003jvv.1	-	1	139	c.96C>A	c.(94-96)CTC>CTA	p.L32L	CCDC125_uc003jvx.1_Silent_p.L32L|CCDC125_uc003jvy.1_Intron|CCDC125_uc003jvw.2_Intron|CCDC125_uc003jvz.1_Silent_p.L32L	NM_176816	NP_789786	Q86Z20	CC125_HUMAN	coiled-coil domain containing 125	32						cytoplasm					0		Lung NSC(167;7.26e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.2e-56)|Epithelial(20;2.31e-52)|all cancers(19;5.85e-48)|Lung(70;0.0183)														---	---	---	---
GTF2H2C	728340	broad.mit.edu	37	5	68863608	68863608	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:68863608C>T	uc003jwx.3	+						GTF2H2C_uc003jww.1_Intron|GTF2H2C_uc003jwz.3_Intron|GTF2H2C_uc011cre.1_Intron|GTF2H2C_uc003jwy.3_Intron	NM_001098728	NP_001092198			general transcription factor IIH, polypeptide						DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding				0																		---	---	---	---
ZNF366	167465	broad.mit.edu	37	5	71739577	71739577	+	3'UTR	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71739577G>A	uc003kce.1	-	5						NM_152625	NP_689838			zinc finger protein 366						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)|skin(1)	2		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)														---	---	---	---
ZNF366	167465	broad.mit.edu	37	5	71756346	71756346	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:71756346G>T	uc003kce.1	-	2	1164	c.978C>A	c.(976-978)CGC>CGA	p.R326R		NM_152625	NP_689838	Q8N895	ZN366_HUMAN	zinc finger protein 366	326	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)|skin(1)	2		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)														---	---	---	---
ENC1	8507	broad.mit.edu	37	5	73931560	73931560	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:73931560C>T	uc003kdc.3	-	2	1882	c.751G>A	c.(751-753)GCC>ACC	p.A251T	ENC1_uc011css.1_Missense_Mutation_p.A178T	NM_003633	NP_003624	O14682	ENC1_HUMAN	ectodermal-neural cortex (with BTB-like domain)	251					nervous system development	cytoplasm|cytoskeleton|nuclear matrix	actin binding			ovary(1)|pancreas(1)|skin(1)	3		all_lung(232;0.0154)|Lung NSC(167;0.0331)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;1.45e-59)														---	---	---	---
GFM2	84340	broad.mit.edu	37	5	74035830	74035830	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74035830G>A	uc003kdh.1	-	12	1367	c.1063C>T	c.(1063-1065)CGT>TGT	p.R355C	GFM2_uc003kdi.1_Missense_Mutation_p.R355C|GFM2_uc010izj.1_Missense_Mutation_p.R387C|GFM2_uc010izk.1_RNA|GFM2_uc003kdj.1_Missense_Mutation_p.R355C|GFM2_uc010izl.1_Missense_Mutation_p.R313C	NM_032380	NP_115756	Q969S9	RRF2M_HUMAN	mitochondrial elongation factor G2 isoform 1	355					mitochondrial translation|ribosome disassembly	mitochondrion	GTP binding|GTPase activity				0		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.86e-56)														---	---	---	---
FAM169A	26049	broad.mit.edu	37	5	74096864	74096864	+	Intron	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74096864A>C	uc003kdm.2	-						FAM169A_uc010izm.2_Intron|FAM169A_uc003kdl.2_Intron	NM_015566	NP_056381			hypothetical protein LOC26049												0																		---	---	---	---
GCNT4	51301	broad.mit.edu	37	5	74325251	74325251	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74325251C>A	uc003kdn.2	-	1	1474	c.612G>T	c.(610-612)CAG>CAT	p.Q204H		NM_016591	NP_057675	Q9P109	GCNT4_HUMAN	core 2 beta-1,6-N-acetylglucosaminyltransferase	204	Lumenal (Potential).				protein O-linked glycosylation	Golgi membrane|integral to membrane	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity|N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity			ovary(2)|skin(1)	3		all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;8.44e-57)														---	---	---	---
HMGCR	3156	broad.mit.edu	37	5	74640078	74640078	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74640078G>T	uc003kdp.2	+	4	442	c.286G>T	c.(286-288)GGC>TGC	p.G96C	HMGCR_uc011cst.1_Missense_Mutation_p.G116C|HMGCR_uc003kdq.2_Missense_Mutation_p.G96C|HMGCR_uc010izn.1_5'Flank	NM_000859	NP_000850	P04035	HMDH_HUMAN	3-hydroxy-3-methylglutaryl-Coenzyme A reductase	96	Helical; (Potential).				cholesterol biosynthetic process|coenzyme A metabolic process|germ cell migration|gonad development|isoprenoid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|peroxisomal membrane	hydroxymethylglutaryl-CoA reductase (NADPH) activity|NADP binding			ovary(1)	1		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;2.24e-54)	Atorvastatin(DB01076)|Bezafibrate(DB01393)|Cerivastatin(DB00439)|Fluvastatin(DB01095)|Lovastatin(DB00227)|NADH(DB00157)|Pravastatin(DB00175)|Rosuvastatin(DB01098)|Simvastatin(DB00641)													---	---	---	---
POLK	51426	broad.mit.edu	37	5	74892902	74892902	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:74892902A>G	uc003kdw.2	+	13	2480	c.2384A>G	c.(2383-2385)AAT>AGT	p.N795S	POLK_uc003kdx.2_RNA|POLK_uc003kdy.2_RNA|POLK_uc010izq.2_Missense_Mutation_p.N597S|POLK_uc003kec.2_Missense_Mutation_p.N705S|POLK_uc010izr.2_RNA|POLK_uc010izs.2_RNA|POLK_uc003ked.2_Intron|POLK_uc003kee.2_Intron|POLK_uc003kef.2_Missense_Mutation_p.N705S	NM_016218	NP_057302	Q9UBT6	POLK_HUMAN	DNA-directed DNA polymerase kappa	795	UBZ-type 2.				DNA replication|nucleotide-excision repair, DNA gap filling	nucleus	damaged DNA binding|DNA-directed DNA polymerase activity|metal ion binding			ovary(2)|kidney(2)	4		all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;2.9e-54)|all cancers(79;1.27e-42)									DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
IQGAP2	10788	broad.mit.edu	37	5	75884800	75884800	+	Splice_Site	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75884800T>C	uc003kek.2	+	6	748	c.526_splice	c.e6+2	p.E176_splice		NM_006633	NP_006624			IQ motif containing GTPase activating protein 2						small GTPase mediated signal transduction	actin cytoskeleton	actin binding|calmodulin binding|GTPase inhibitor activity|Ras GTPase activator activity			ovary(6)|central_nervous_system(1)	7		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)														---	---	---	---
IQGAP2	10788	broad.mit.edu	37	5	75991421	75991421	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:75991421G>A	uc003kek.2	+	32	4358	c.4136G>A	c.(4135-4137)CGG>CAG	p.R1379Q	IQGAP2_uc011csv.1_Missense_Mutation_p.R875Q|IQGAP2_uc003kel.2_Missense_Mutation_p.R875Q|IQGAP2_uc010izw.1_Missense_Mutation_p.R80Q	NM_006633	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	1379					small GTPase mediated signal transduction	actin cytoskeleton	actin binding|calmodulin binding|GTPase inhibitor activity|Ras GTPase activator activity			ovary(6)|central_nervous_system(1)	7		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)														---	---	---	---
PDE8B	8622	broad.mit.edu	37	5	76627247	76627247	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76627247C>T	uc003kfa.2	+	5	716	c.671C>T	c.(670-672)GCG>GTG	p.A224V	PDE8B_uc003kfb.2_Missense_Mutation_p.A204V|PDE8B_uc003kfc.2_Missense_Mutation_p.A224V|PDE8B_uc003kfd.2_Missense_Mutation_p.A224V|PDE8B_uc003kfe.2_Missense_Mutation_p.A224V	NM_003719	NP_003710	O95263	PDE8B_HUMAN	phosphodiesterase 8B isoform 1	224					cyclic nucleotide metabolic process|regulation of transcription, DNA-dependent	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|two-component response regulator activity				0		all_lung(232;0.00043)|Lung NSC(167;0.00114)|Ovarian(174;0.0107)|Prostate(461;0.0605)		OV - Ovarian serous cystadenocarcinoma(54;2.21e-49)|Epithelial(54;5.82e-43)|all cancers(79;4.06e-38)														---	---	---	---
PDE8B	8622	broad.mit.edu	37	5	76703292	76703292	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76703292G>A	uc003kfa.2	+						PDE8B_uc003kfb.2_Intron|PDE8B_uc003kfc.2_Intron|PDE8B_uc003kfd.2_Intron|PDE8B_uc003kfe.2_Intron	NM_003719	NP_003710			phosphodiesterase 8B isoform 1						cyclic nucleotide metabolic process|regulation of transcription, DNA-dependent	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|two-component response regulator activity				0		all_lung(232;0.00043)|Lung NSC(167;0.00114)|Ovarian(174;0.0107)|Prostate(461;0.0605)		OV - Ovarian serous cystadenocarcinoma(54;2.21e-49)|Epithelial(54;5.82e-43)|all cancers(79;4.06e-38)														---	---	---	---
HOMER1	9456	broad.mit.edu	37	5	78671921	78671921	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78671921G>T	uc003kfy.2	-	9	2079	c.976C>A	c.(976-978)CTG>ATG	p.L326M	HOMER1_uc010jab.2_3'UTR|HOMER1_uc010jac.2_Missense_Mutation_p.L196M|HOMER1_uc010jad.2_Missense_Mutation_p.L152M	NM_004272	NP_004263	Q86YM7	HOME1_HUMAN	homer 1	326	Potential.				activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic density|postsynaptic membrane					0		Lung NSC(167;0.00131)|all_lung(232;0.00151)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;1.87e-44)|Epithelial(54;7.07e-41)|all cancers(79;5.5e-36)														---	---	---	---
CMYA5	202333	broad.mit.edu	37	5	79029907	79029907	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79029907A>G	uc003kgc.2	+	2	5391	c.5319A>G	c.(5317-5319)CCA>CCG	p.P1773P		NM_153610	NP_705838	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	1773						perinuclear region of cytoplasm				ovary(6)|pancreas(2)|lung(1)	9		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)														---	---	---	---
CMYA5	202333	broad.mit.edu	37	5	79031458	79031458	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79031458A>G	uc003kgc.2	+	2	6942	c.6870A>G	c.(6868-6870)GGA>GGG	p.G2290G		NM_153610	NP_705838	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2290						perinuclear region of cytoplasm				ovary(6)|pancreas(2)|lung(1)	9		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)														---	---	---	---
ZFYVE16	9765	broad.mit.edu	37	5	79732852	79732852	+	Silent	SNP	G	A	A	rs151167740		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79732852G>A	uc003kgr.3	+	4	650	c.348G>A	c.(346-348)CCG>CCA	p.P116P	ZFYVE16_uc010jak.1_Silent_p.P116P|ZFYVE16_uc003kgp.2_Silent_p.P116P|ZFYVE16_uc003kgq.3_Silent_p.P116P|ZFYVE16_uc003kgs.3_Silent_p.P116P	NM_001105251	NP_001098721	Q7Z3T8	ZFY16_HUMAN	zinc finger, FYVE domain containing 16	116					BMP signaling pathway|endosome transport|protein targeting to lysosome|regulation of endocytosis|vesicle organization	early endosome membrane	1-phosphatidylinositol binding|metal ion binding|phosphatidylinositol-3,4,5-trisphosphate binding|protein binding|protein transporter activity				0		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;1.6e-46)|Epithelial(54;2.02e-41)|all cancers(79;5.05e-36)														---	---	---	---
FAM151B	167555	broad.mit.edu	37	5	79797664	79797664	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:79797664G>A	uc003kgv.1	+	2	222	c.79G>A	c.(79-81)GCA>ACA	p.A27T	FAM151B_uc010jal.1_RNA	NM_205548	NP_991111	Q6UXP7	F151B_HUMAN	hypothetical protein LOC167555	27											0		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;8.21e-47)|Epithelial(54;8.3e-42)|all cancers(79;1.97e-36)														---	---	---	---
MSH3	4437	broad.mit.edu	37	5	80074577	80074577	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80074577T>C	uc003kgz.2	+	17	2610	c.2357T>C	c.(2356-2358)GTA>GCA	p.V786A		NM_002439	NP_002430	P20585	MSH3_HUMAN	mutS homolog 3	786					maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments	MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding			lung(2)|ovary(1)|breast(1)	4		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)									MMR					---	---	---	---
RASGRF2	5924	broad.mit.edu	37	5	80363948	80363948	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80363948C>T	uc003kha.1	+	3	493	c.493C>T	c.(493-495)CGA>TGA	p.R165*	RASGRF2_uc011ctn.1_RNA|RASGRF2_uc003khb.1_5'Flank	NM_006909	NP_008840	O14827	RGRF2_HUMAN	Ras protein-specific guanine	165	Potential.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol|endoplasmic reticulum membrane|plasma membrane	protein binding|Rho guanyl-nucleotide exchange factor activity			breast(5)|ovary(3)|large_intestine(2)|central_nervous_system(1)|skin(1)	12		Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357)		OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29)														---	---	---	---
RASGRF2	5924	broad.mit.edu	37	5	80408631	80408631	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80408631A>G	uc003kha.1	+	14	2041	c.2041A>G	c.(2041-2043)AAA>GAA	p.K681E	RASGRF2_uc011ctn.1_RNA	NM_006909	NP_008840	O14827	RGRF2_HUMAN	Ras protein-specific guanine	681	N-terminal Ras-GEF.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol|endoplasmic reticulum membrane|plasma membrane	protein binding|Rho guanyl-nucleotide exchange factor activity			breast(5)|ovary(3)|large_intestine(2)|central_nervous_system(1)|skin(1)	12		Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357)		OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29)														---	---	---	---
CKMT2	1160	broad.mit.edu	37	5	80546983	80546983	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80546983G>A	uc003khc.3	+	3	274	c.32G>A	c.(31-33)GGC>GAC	p.G11D	RNU5E_uc011cto.1_Intron|CKMT2_uc010jaq.2_Missense_Mutation_p.G11D|CKMT2_uc003khd.3_Missense_Mutation_p.G11D|uc003khe.1_Intron|uc003khf.1_Intron|uc003khg.1_Intron	NM_001825	NP_001816	P17540	KCRS_HUMAN	sarcomeric mitochondrial creatine kinase	11					creatine metabolic process|muscle contraction	mitochondrial inner membrane	ATP binding|creatine kinase activity				0		Lung NSC(167;0.00475)|all_lung(232;0.00502)|Ovarian(174;0.0336)		OV - Ovarian serous cystadenocarcinoma(54;2.29e-44)|Epithelial(54;1.05e-38)|all cancers(79;4.15e-34)	Creatine(DB00148)													---	---	---	---
ZCCHC9	84240	broad.mit.edu	37	5	80604427	80604427	+	Silent	SNP	C	T	T	rs149561750	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:80604427C>T	uc003khj.2	+	3	565	c.432C>T	c.(430-432)CCC>CCT	p.P144P	RNU5E_uc011cto.1_Intron|ZCCHC9_uc003khk.3_Silent_p.P144P|ZCCHC9_uc003khi.2_Silent_p.P144P	NM_001131035	NP_001124507	Q8N567	ZCHC9_HUMAN	zinc finger, CCHC domain containing 9	144	CCHC-type 1.						nucleic acid binding|zinc ion binding			ovary(1)	1		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;8.18e-45)|Epithelial(54;2.72e-39)|all cancers(79;7.33e-34)														---	---	---	---
VCAN	1462	broad.mit.edu	37	5	82815997	82815997	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:82815997G>T	uc003kii.3	+	7	2228	c.1872G>T	c.(1870-1872)GAG>GAT	p.E624D	VCAN_uc003kij.3_Intron|VCAN_uc010jau.2_Missense_Mutation_p.E624D|VCAN_uc003kik.3_Intron	NM_004385	NP_004376	P13611	CSPG2_HUMAN	versican isoform 1 precursor	624	GAG-alpha (glucosaminoglycan attachment domain).				cell adhesion|cell recognition|glial cell migration	extracellular space|proteinaceous extracellular matrix	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(7)|skin(6)|lung(2)|central_nervous_system(1)	16		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)														---	---	---	---
CCNH	902	broad.mit.edu	37	5	86695210	86695210	+	Splice_Site	SNP	C	T	T	rs115449312	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:86695210C>T	uc003kjb.2	-	7	1104	c.872_splice	c.e7+1	p.T291_splice	CCNH_uc003kiy.1_Splice_Site|CCNH_uc003kiz.1_Splice_Site_p.T238_splice|CCNH_uc003kja.2_Splice_Site_p.T238_splice	NM_001239	NP_001230			cyclin H						G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mRNA capping|nucleotide-excision repair, DNA damage removal|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|protein phosphorylation|regulation of cyclin-dependent protein kinase activity|S phase of mitotic cell cycle|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	cyclin-dependent protein kinase activating kinase holoenzyme complex|holo TFIIH complex	protein kinase binding			ovary(2)|kidney(1)	3		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;9.01e-39)|Epithelial(54;5.08e-33)|all cancers(79;4.28e-28)									Direct_reversal_of_damage|NER					---	---	---	---
GPR98	84059	broad.mit.edu	37	5	89938472	89938472	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89938472G>T	uc003kju.2	+	12	2356	c.2260G>T	c.(2260-2262)GTG>TTG	p.V754L	GPR98_uc003kjt.2_5'UTR	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	754	Extracellular (Potential).				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)														---	---	---	---
GPR98	84059	broad.mit.edu	37	5	89977204	89977204	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:89977204T>A	uc003kju.2	+	27	5693	c.5597T>A	c.(5596-5598)TTT>TAT	p.F1866Y	GPR98_uc003kjt.2_5'UTR	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	1866	Extracellular (Potential).				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)														---	---	---	---
NR2F1	7025	broad.mit.edu	37	5	92924014	92924014	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:92924014G>A	uc003kkj.2	+	2	2542	c.855G>A	c.(853-855)TCG>TCA	p.S285S		NM_005654	NP_005645	P10589	COT1_HUMAN	nuclear receptor subfamily 2, group F, member 1	285					negative regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	ligand-regulated transcription factor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription coactivator activity|zinc ion binding			urinary_tract(1)|ovary(1)|lung(1)	3		all_cancers(142;1.62e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0126)|Lung NSC(167;0.0155)|Ovarian(174;0.0218)|Prostate(281;0.173)|Colorectal(57;0.19)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0416)|all cancers(79;9.57e-18)														---	---	---	---
ANKRD32	84250	broad.mit.edu	37	5	94022374	94022374	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94022374T>G	uc003kkr.3	+	16	2152	c.2072T>G	c.(2071-2073)CTA>CGA	p.L691R	ANKRD32_uc003kks.2_Missense_Mutation_p.L55R	NM_032290	NP_115666	Q9BQI6	ANR32_HUMAN	ankyrin repeat domain 32	691										ovary(2)	2		all_cancers(142;1.51e-09)|all_epithelial(76;4.68e-12)|all_lung(232;5.94e-05)|Ovarian(174;0.000953)|Lung NSC(167;0.00105)|Colorectal(57;0.122)|Lung SC(612;0.152)		all cancers(79;3.88e-18)														---	---	---	---
FAM81B	153643	broad.mit.edu	37	5	94785860	94785860	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94785860A>T	uc003kla.1	+	10	1279	c.1233A>T	c.(1231-1233)AAA>AAT	p.K411N	FAM81B_uc010jbe.1_3'UTR	NM_152548	NP_689761	Q96LP2	FA81B_HUMAN	hypothetical protein LOC153643	411	Potential.									ovary(1)|skin(1)	2		all_cancers(142;1.1e-06)|all_epithelial(76;1.48e-09)|all_lung(232;0.000696)|Lung NSC(167;0.000947)|Ovarian(225;0.00473)		all cancers(79;1.04e-16)														---	---	---	---
TTC37	9652	broad.mit.edu	37	5	94805571	94805571	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94805571G>A	uc003klb.2	-	41	4679	c.4409C>T	c.(4408-4410)GCT>GTT	p.A1470V		NM_014639	NP_055454	Q6PGP7	TTC37_HUMAN	tetratricopeptide repeat domain 37	1470							binding			ovary(3)|pancreas(1)	4																		---	---	---	---
TTC37	9652	broad.mit.edu	37	5	94859381	94859381	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:94859381A>C	uc003klb.2	-	17	1880	c.1610T>G	c.(1609-1611)CTA>CGA	p.L537R	TTC37_uc010jbf.1_Missense_Mutation_p.L489R	NM_014639	NP_055454	Q6PGP7	TTC37_HUMAN	tetratricopeptide repeat domain 37	537							binding			ovary(3)|pancreas(1)	4																		---	---	---	---
PCSK1	5122	broad.mit.edu	37	5	95728825	95728825	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:95728825T>G	uc003kls.1	-	14	2348	c.2142A>C	c.(2140-2142)AAA>AAC	p.K714N	PCSK1_uc010jbi.1_Missense_Mutation_p.K404N	NM_000439	NP_000430	P29120	NEC1_HUMAN	proprotein convertase subtilisin/kexin type 1	714					cell-cell signaling|cellular nitrogen compound metabolic process|energy reserve metabolic process|hormone biosynthetic process|peptide biosynthetic process|peptide hormone processing|regulation of insulin secretion	extracellular space|stored secretory granule|transport vesicle	serine-type endopeptidase activity			ovary(2)	2		all_cancers(142;2.67e-06)|all_epithelial(76;6.92e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0112)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;3.44e-16)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
ERAP1	51752	broad.mit.edu	37	5	96124224	96124224	+	Intron	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96124224G>T	uc003kmm.2	-						ERAP1_uc003kml.2_Intron|ERAP1_uc010jbm.1_Intron|ERAP1_uc003kmn.2_Intron	NM_001040458	NP_001035548			type 1 tumor necrosis factor receptor shedding						angiogenesis|antigen processing and presentation of endogenous peptide antigen via MHC class I|fat cell differentiation|membrane protein ectodomain proteolysis|regulation of blood pressure|regulation of innate immune response|response to bacterium	cytosol|endoplasmic reticulum lumen|endoplasmic reticulum membrane|extracellular region|integral to membrane	aminopeptidase activity|interleukin-1, Type II receptor binding|interleukin-6 receptor binding|metalloexopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)	2		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)														---	---	---	---
LNPEP	4012	broad.mit.edu	37	5	96315163	96315163	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96315163G>A	uc003kmv.1	+	2	855	c.341G>A	c.(340-342)TGT>TAT	p.C114Y	LNPEP_uc003kmw.1_Missense_Mutation_p.C100Y	NM_005575	NP_005566	Q9UIQ6	LCAP_HUMAN	leucyl/cystinyl aminopeptidase isoform 1	114	Helical; Signal-anchor for type II membrane protein; (Potential).				cell-cell signaling|female pregnancy|proteolysis	extracellular region|integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(3)|breast(1)	4		all_cancers(142;7e-07)|all_epithelial(76;9.52e-10)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0269)|Breast(839;0.244)		COAD - Colon adenocarcinoma(37;0.072)														---	---	---	---
RIOK2	55781	broad.mit.edu	37	5	96512842	96512842	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96512842A>G	uc003kmz.2	-	4	586	c.476T>C	c.(475-477)ATG>ACG	p.M159T	RIOK2_uc003kna.3_Missense_Mutation_p.M159T	NM_018343	NP_060813	Q9BVS4	RIOK2_HUMAN	RIO kinase 2 isoform 1	159							ATP binding|protein serine/threonine kinase activity			kidney(1)	1		all_cancers(142;0.000125)|all_epithelial(76;8.48e-07)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0676)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0657)														---	---	---	---
CHD1	1105	broad.mit.edu	37	5	98206439	98206439	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:98206439G>A	uc003knf.2	-	28	4078	c.3930C>T	c.(3928-3930)ATC>ATT	p.I1310I	CHD1_uc010jbn.2_Silent_p.I36I	NM_001270	NP_001261	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	1310					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|methylated histone residue binding			lung(2)|ovary(1)|breast(1)|pancreas(1)	5		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)													---	---	---	---
SLCO6A1	133482	broad.mit.edu	37	5	101834356	101834356	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:101834356G>A	uc003knn.2	-	1	365	c.193C>T	c.(193-195)CGA>TGA	p.R65*	SLCO6A1_uc003kno.2_Nonsense_Mutation_p.R65*|SLCO6A1_uc003knp.2_Nonsense_Mutation_p.R65*|SLCO6A1_uc003knq.2_Nonsense_Mutation_p.R65*	NM_173488	NP_775759	Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family,	65	Cytoplasmic (Potential).					integral to membrane|plasma membrane	transporter activity			ovary(3)|skin(3)|central_nervous_system(1)	7		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)														---	---	---	---
FER	2241	broad.mit.edu	37	5	108290606	108290606	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108290606G>T	uc003kop.1	+	12	1890	c.1506G>T	c.(1504-1506)AGG>AGT	p.R502S	FER_uc011cvf.1_Intron|FER_uc011cvg.1_Missense_Mutation_p.R327S	NM_005246	NP_005237	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase	502	SH2.				intracellular signal transduction|peptidyl-tyrosine phosphorylation	cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|stomach(1)|ovary(1)|kidney(1)	5		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)														---	---	---	---
FER	2241	broad.mit.edu	37	5	108516582	108516582	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:108516582C>T	uc003kop.1	+	18	2567	c.2183C>T	c.(2182-2184)GCA>GTA	p.A728V	FER_uc011cvg.1_Missense_Mutation_p.A553V	NM_005246	NP_005237	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase	728	Protein kinase.				intracellular signal transduction|peptidyl-tyrosine phosphorylation	cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity	p.A728S(1)		lung(2)|stomach(1)|ovary(1)|kidney(1)	5		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)														---	---	---	---
MAN2A1	4124	broad.mit.edu	37	5	109091115	109091115	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109091115G>T	uc003kou.1	+	5	1756	c.793G>T	c.(793-795)GAT>TAT	p.D265Y		NM_002372	NP_002363	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	265	Lumenal (Potential).				mannose metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-mannosidase activity|carbohydrate binding|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)														---	---	---	---
MAN2A1	4124	broad.mit.edu	37	5	109190854	109190854	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:109190854A>G	uc003kou.1	+	20	3953	c.2990A>G	c.(2989-2991)AAG>AGG	p.K997R		NM_002372	NP_002363	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	997	Lumenal (Potential).				mannose metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-mannosidase activity|carbohydrate binding|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)														---	---	---	---
EPB41L4A	64097	broad.mit.edu	37	5	111602007	111602007	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111602007A>G	uc003kpv.1	-	5	630	c.356T>C	c.(355-357)GTG>GCG	p.V119A	EPB41L4A_uc003kpw.1_Missense_Mutation_p.V119A	NM_022140	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte protein band 4.1-like 4	119	FERM.					cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)														---	---	---	---
YTHDC2	64848	broad.mit.edu	37	5	112889526	112889526	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112889526A>C	uc003kqn.2	+	15	2210	c.2027A>C	c.(2026-2028)AAC>ACC	p.N676T	YTHDC2_uc010jce.1_Missense_Mutation_p.N676T|YTHDC2_uc010jcf.1_Missense_Mutation_p.N376T	NM_022828	NP_073739	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	676	Helicase C-terminal.						ATP binding|ATP-dependent helicase activity|nucleic acid binding			skin(2)|central_nervous_system(1)	3		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)														---	---	---	---
AQPEP	206338	broad.mit.edu	37	5	115298714	115298714	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:115298714A>T	uc003kro.2	+	1	564	c.400A>T	c.(400-402)ACG>TCG	p.T134S	AQPEP_uc003krp.2_RNA|uc003krn.1_5'UTR	NM_173800	NP_776161	Q6Q4G3	AMPQ_HUMAN	laeverin	134	Lumenal (Potential).				proteolysis	integral to membrane	metallopeptidase activity|zinc ion binding				0																		---	---	---	---
DMXL1	1657	broad.mit.edu	37	5	118469547	118469547	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:118469547T>C	uc003ksd.2	+	12	2109	c.1928T>C	c.(1927-1929)TTA>TCA	p.L643S	DMXL1_uc010jcl.1_Missense_Mutation_p.L643S|DMXL1_uc003ksc.1_Missense_Mutation_p.L643S	NM_005509	NP_005500	Q9Y485	DMXL1_HUMAN	Dmx-like 1	643	WD 6.									ovary(2)	2		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)														---	---	---	---
PRR16	51334	broad.mit.edu	37	5	119800307	119800307	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:119800307C>T	uc003ksq.2	+	1	289	c.126C>T	c.(124-126)GGC>GGT	p.G42G	PRR16_uc003ksp.2_5'UTR	NM_016644	NP_057728	Q569H4	PRR16_HUMAN	proline rich 16	42	Potential.									pancreas(2)|ovary(1)	3		all_cancers(142;0.0464)|Prostate(80;0.00446)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.000126)|Epithelial(69;0.000331)|all cancers(49;0.00169)														---	---	---	---
ZNF474	133923	broad.mit.edu	37	5	121488398	121488398	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:121488398T>A	uc003ksv.2	+	2	1089	c.713T>A	c.(712-714)ATT>AAT	p.I238N		NM_207317	NP_997200	Q6S9Z5	ZN474_HUMAN	zinc finger protein 474	238						intracellular	zinc ion binding				0		all_cancers(142;0.229)|Prostate(80;0.0387)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000197)|Epithelial(69;0.00029)|all cancers(49;0.00415)														---	---	---	---
CEP120	153241	broad.mit.edu	37	5	122751787	122751787	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:122751787A>G	uc003ktk.2	-	4	320	c.238T>C	c.(238-240)TTT>CTT	p.F80L	CEP120_uc011cwq.1_5'UTR|CEP120_uc010jcz.1_Missense_Mutation_p.F54L	NM_153223	NP_694955	Q8N960	CE120_HUMAN	coiled-coil domain containing 100	80						centrosome				ovary(1)	1																		---	---	---	---
ZNF608	57507	broad.mit.edu	37	5	123979314	123979314	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:123979314T>C	uc003ktq.1	-	6	4309	c.4186A>G	c.(4186-4188)ACA>GCA	p.T1396A	ZNF608_uc003ktr.1_RNA|ZNF608_uc003ktp.1_Missense_Mutation_p.T91A	NM_020747	NP_065798	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	1396						intracellular	zinc ion binding			skin(3)|ovary(2)|lung(1)	6		all_cancers(142;0.186)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783)														---	---	---	---
ZNF608	57507	broad.mit.edu	37	5	124080449	124080449	+	Silent	SNP	G	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:124080449G>C	uc003ktq.1	-	1	357	c.234C>G	c.(232-234)GCC>GCG	p.A78A	ZNF608_uc003ktr.1_RNA|ZNF608_uc003kts.1_Silent_p.A78A|ZNF608_uc003ktt.1_Silent_p.A78A	NM_020747	NP_065798	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	78						intracellular	zinc ion binding			skin(3)|ovary(2)|lung(1)	6		all_cancers(142;0.186)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783)														---	---	---	---
GRAMD3	65983	broad.mit.edu	37	5	125820213	125820213	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125820213C>T	uc003ktu.2	+	10	1397	c.967C>T	c.(967-969)CAG>TAG	p.Q323*	GRAMD3_uc011cwt.1_Nonsense_Mutation_p.Q338*|GRAMD3_uc011cwv.1_Nonsense_Mutation_p.Q331*|GRAMD3_uc011cww.1_Nonsense_Mutation_p.Q219*|GRAMD3_uc011cwx.1_RNA|GRAMD3_uc011cwy.1_Nonsense_Mutation_p.Q214*|GRAMD3_uc011cwz.1_Nonsense_Mutation_p.Q307*|GRAMD3_uc011cwu.1_Nonsense_Mutation_p.Q307*	NM_023927	NP_076416	Q96HH9	GRAM3_HUMAN	GRAM domain containing 3 isoform 2	323										central_nervous_system(1)	1		Prostate(80;0.0928)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0401)|OV - Ovarian serous cystadenocarcinoma(64;0.0604)|all cancers(49;0.108)														---	---	---	---
ALDH7A1	501	broad.mit.edu	37	5	125919663	125919663	+	Silent	SNP	G	A	A	rs149228266	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:125919663G>A	uc003ktx.2	-	4	546	c.354C>T	c.(352-354)GGC>GGT	p.G118G	ALDH7A1_uc003kty.2_RNA|ALDH7A1_uc011cxa.1_Silent_p.G145G|ALDH7A1_uc003ktz.2_Silent_p.G145G	NM_001182	NP_001173	P49419	AL7A1_HUMAN	aldehyde dehydrogenase 7 family, member A1	118					cellular aldehyde metabolic process|lysine catabolic process|sensory perception of sound	cytosol|mitochondrial matrix|nucleus	aldehyde dehydrogenase (NAD) activity|betaine-aldehyde dehydrogenase activity|L-aminoadipate-semialdehyde dehydrogenase activity			kidney(2)|ovary(1)	3		all_cancers(142;0.24)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0417)|OV - Ovarian serous cystadenocarcinoma(64;0.068)|all cancers(49;0.109)	NADH(DB00157)|Pyridoxine(DB00165)													---	---	---	---
FBN2	2201	broad.mit.edu	37	5	127627337	127627337	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127627337T>C	uc003kuu.2	-	49	6615	c.6176A>G	c.(6175-6177)GAA>GGA	p.E2059G		NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor	2059	EGF-like 35; calcium-binding.				bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1)	15		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)														---	---	---	---
CHSY3	337876	broad.mit.edu	37	5	129520094	129520094	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:129520094G>A	uc003kvd.2	+	3	1259	c.1259G>A	c.(1258-1260)CGC>CAC	p.R420H		NM_175856	NP_787052	Q70JA7	CHSS3_HUMAN	chondroitin sulfate synthase 3	420	Lumenal (Potential).					Golgi cisterna membrane|integral to membrane	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity			ovary(2)|pancreas(1)	3		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.136)														---	---	---	---
FNIP1	96459	broad.mit.edu	37	5	130987643	130987643	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:130987643T>C	uc003kvs.1	-	16	3300	c.3158A>G	c.(3157-3159)GAC>GGC	p.D1053G	RAPGEF6_uc003kvp.1_Intron|FNIP1_uc003kvt.1_Missense_Mutation_p.D1025G	NM_133372	NP_588613	Q8TF40	FNIP1_HUMAN	folliculin interacting protein 1 isoform 1	1053					regulation of protein phosphorylation	cytoplasm	protein binding			pancreas(1)|skin(1)	2		all_cancers(142;0.00347)|Lung NSC(810;0.106)|all_lung(232;0.123)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0665)														---	---	---	---
ACSL6	23305	broad.mit.edu	37	5	131323746	131323746	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131323746C>T	uc010jdo.1	-	7	834	c.751G>A	c.(751-753)GTG>ATG	p.V251M	ACSL6_uc003kvv.1_RNA|ACSL6_uc003kvx.1_Missense_Mutation_p.V276M|ACSL6_uc003kvy.1_Missense_Mutation_p.V276M|ACSL6_uc003kwb.2_Missense_Mutation_p.V241M|ACSL6_uc003kvz.1_Missense_Mutation_p.V216M|ACSL6_uc003kwa.1_Missense_Mutation_p.V262M|ACSL6_uc010jdn.1_Missense_Mutation_p.V266M|ACSL6_uc010jdp.1_5'Flank	NM_015256	NP_056071	Q9UKU0	ACSL6_HUMAN	acyl-CoA synthetase long-chain family member 6	251	Cytoplasmic (Potential).				fatty acid metabolic process|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane|peroxisomal membrane|plasma membrane	ATP binding|long-chain fatty acid-CoA ligase activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3		all_cancers(142;0.107)|Breast(839;0.198)|Lung NSC(810;0.216)|all_lung(232;0.248)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
SHROOM1	134549	broad.mit.edu	37	5	132159202	132159202	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:132159202C>T	uc003kxx.2	-	9	2771	c.1966G>A	c.(1966-1968)GCC>ACC	p.A656T	SHROOM1_uc003kxy.1_Missense_Mutation_p.A656T	NM_133456	NP_597713	Q2M3G4	SHRM1_HUMAN	shroom family member 1	656	ASD2.				actin filament bundle assembly|cell morphogenesis	cytoplasm|microtubule	actin filament binding			pancreas(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
SAR1B	51128	broad.mit.edu	37	5	133948417	133948417	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:133948417T>G	uc003kzq.2	-	5	455	c.208A>C	c.(208-210)ACG>CCG	p.T70P	SAR1B_uc003kzr.2_Missense_Mutation_p.T70P	NM_001033503	NP_001028675	Q9Y6B6	SAR1B_HUMAN	SAR1a gene homolog 2	70					COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	cytosol|endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|Golgi cisterna membrane	GTP binding|GTPase activity|metal ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)															---	---	---	---
CAMLG	819	broad.mit.edu	37	5	134077064	134077064	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134077064G>A	uc003kzt.2	+	2	589	c.484G>A	c.(484-486)GCA>ACA	p.A162T	CAMLG_uc003kzu.2_Intron	NM_001745	NP_001736	P49069	CAMLG_HUMAN	calcium modulating ligand	162	Cytoplasmic (Potential).				defense response	endoplasmic reticulum|integral to membrane					0			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Cyclosporine(DB00091)													---	---	---	---
H2AFY	9555	broad.mit.edu	37	5	134724786	134724786	+	5'UTR	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:134724786C>T	uc003lam.1	-	2					H2AFY_uc003lao.1_5'UTR|H2AFY_uc003lan.1_5'UTR|H2AFY_uc003lap.1_RNA|H2AFY_uc003laq.1_RNA|H2AFY_uc003lar.1_RNA|H2AFY_uc011cxz.1_5'UTR|H2AFY_uc003las.1_5'UTR|H2AFY_uc003lat.1_5'UTR	NM_138610	NP_613258			H2A histone family, member Y isoform 3						chromatin modification|dosage compensation|nucleosome assembly	Barr body|nucleosome	DNA binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
TRPC7	57113	broad.mit.edu	37	5	135692669	135692669	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:135692669C>T	uc003lbn.1	-	1	407	c.404G>A	c.(403-405)CGC>CAC	p.R135H	TRPC7_uc010jef.1_Missense_Mutation_p.R127H|TRPC7_uc010jeg.1_RNA|TRPC7_uc010jeh.1_Missense_Mutation_p.R127H|TRPC7_uc010jei.1_Missense_Mutation_p.R127H|TRPC7_uc010jej.1_5'UTR	NM_020389	NP_065122	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel,	136	Cytoplasmic (Potential).				axon guidance|platelet activation	integral to membrane|plasma membrane	calcium channel activity|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
SPOCK1	6695	broad.mit.edu	37	5	136403476	136403476	+	Missense_Mutation	SNP	C	T	T	rs139465331	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:136403476C>T	uc003lbo.2	-	5	708	c.517G>A	c.(517-519)GCC>ACC	p.A173T	SPOCK1_uc003lbp.2_Missense_Mutation_p.A173T	NM_004598	NP_004589	Q08629	TICN1_HUMAN	sparc/osteonectin, cwcv and kazal-like domains	173	Kazal-like.				cell adhesion|cell proliferation|cellular component movement|nervous system development|signal transduction	proteinaceous extracellular matrix	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)															---	---	---	---
FAM13B	51306	broad.mit.edu	37	5	137354670	137354670	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137354670T>C	uc003lbz.2	-	3	665	c.131A>G	c.(130-132)CAC>CGC	p.H44R	FAM13B_uc003lcb.2_Intron|FAM13B_uc003lca.2_Missense_Mutation_p.H44R	NM_016603	NP_057687	Q9NYF5	FA13B_HUMAN	hypothetical protein LOC51306 isoform 1	44	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0																		---	---	---	---
WNT8A	7478	broad.mit.edu	37	5	137426383	137426383	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137426383G>T	uc003lcd.1	+	6	682	c.677G>T	c.(676-678)AGA>ATA	p.R226I	BRD8_uc003lcc.1_Intron|WNT8A_uc011cyj.1_Missense_Mutation_p.R244I|WNT8A_uc011cyk.1_Missense_Mutation_p.R244I	NM_058244	NP_490645	Q9H1J5	WNT8A_HUMAN	wingless-type MMTV integration site family,	226					brain segmentation|canonical Wnt receptor signaling pathway involved in neural crest cell differentiation|cell migration involved in gastrulation|dorsal/ventral pattern formation|ectoderm development|endoderm development|eye development|hindbrain development|mesodermal cell fate commitment|negative regulation of Wnt receptor signaling pathway|neural crest cell fate commitment|neural plate pattern specification|notochord development|palate development|polarity specification of anterior/posterior axis|polarity specification of proximal/distal axis|positive regulation of fibroblast growth factor receptor signaling pathway|regulation of transcription involved in anterior/posterior axis specification|response to retinoic acid|somitogenesis|spinal cord anterior/posterior patterning|tail morphogenesis|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	frizzled binding|signal transducer activity			ovary(1)|lung(1)|breast(1)|skin(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)															---	---	---	---
BRD8	10902	broad.mit.edu	37	5	137500599	137500599	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137500599G>T	uc003lcf.1	-	12	1590	c.1535C>A	c.(1534-1536)CCT>CAT	p.P512H	BRD8_uc003lcc.1_RNA|BRD8_uc011cyl.1_Missense_Mutation_p.P291H|BRD8_uc003lcg.2_Missense_Mutation_p.P585H|BRD8_uc003lci.2_Missense_Mutation_p.P515H|BRD8_uc003lch.2_Missense_Mutation_p.P406H|BRD8_uc011cym.1_Missense_Mutation_p.P496H|BRD8_uc010jer.1_Missense_Mutation_p.P481H|BRD8_uc011cyn.1_Missense_Mutation_p.P471H	NM_139199	NP_631938	Q9H0E9	BRD8_HUMAN	bromodomain containing 8 isoform 2	512					cell surface receptor linked signaling pathway|histone H2A acetylation|histone H4 acetylation|regulation of growth|regulation of transcription from RNA polymerase II promoter	mitochondrion|NuA4 histone acetyltransferase complex	sequence-specific DNA binding transcription factor activity|thyroid hormone receptor activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)															---	---	---	---
CDC25C	995	broad.mit.edu	37	5	137627784	137627784	+	Missense_Mutation	SNP	G	A	A	rs114224600	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137627784G>A	uc003lcp.1	-	8	908	c.637C>T	c.(637-639)CGC>TGC	p.R213C	CDC25C_uc003lcq.1_Missense_Mutation_p.R140C|CDC25C_uc003lcr.1_Missense_Mutation_p.R213C|CDC25C_uc011cyp.1_Missense_Mutation_p.R230C|CDC25C_uc003lcs.1_Missense_Mutation_p.R291C	NM_001790	NP_001781	P30307	MPIP3_HUMAN	cell division cycle 25C isoform a	213					cell cycle checkpoint|cell division|cell proliferation|DNA replication|G2/M transition of mitotic cell cycle|interspecies interaction between organisms|mitosis|regulation of cyclin-dependent protein kinase activity|regulation of mitosis|traversing start control point of mitotic cell cycle	cytosol|nucleoplasm	protein tyrosine phosphatase activity|WW domain binding			lung(3)	3			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)															---	---	---	---
KDM3B	51780	broad.mit.edu	37	5	137708521	137708521	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137708521G>A	uc003lcy.1	+	2	551	c.351G>A	c.(349-351)TGG>TGA	p.W117*	KDM3B_uc010jew.1_5'UTR	NM_016604	NP_057688	Q7LBC6	KDM3B_HUMAN	jumonji domain containing 1B	117					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			ovary(3)|upper_aerodigestive_tract(2)|lung(2)|kidney(2)|central_nervous_system(1)|skin(1)	11																		---	---	---	---
KDM3B	51780	broad.mit.edu	37	5	137721970	137721970	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137721970T>C	uc003lcy.1	+	7	1240	c.1040T>C	c.(1039-1041)GTC>GCC	p.V347A	KDM3B_uc010jew.1_Intron|KDM3B_uc011cys.1_5'Flank	NM_016604	NP_057688	Q7LBC6	KDM3B_HUMAN	jumonji domain containing 1B	347					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			ovary(3)|upper_aerodigestive_tract(2)|lung(2)|kidney(2)|central_nervous_system(1)|skin(1)	11																		---	---	---	---
KDM3B	51780	broad.mit.edu	37	5	137726923	137726923	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137726923A>G	uc003lcy.1	+	8	1802	c.1602A>G	c.(1600-1602)TTA>TTG	p.L534L	KDM3B_uc010jew.1_Silent_p.L190L|KDM3B_uc011cys.1_Intron	NM_016604	NP_057688	Q7LBC6	KDM3B_HUMAN	jumonji domain containing 1B	534					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			ovary(3)|upper_aerodigestive_tract(2)|lung(2)|kidney(2)|central_nervous_system(1)|skin(1)	11																		---	---	---	---
SIL1	64374	broad.mit.edu	37	5	138286904	138286904	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:138286904C>T	uc003ldm.2	-	8	1002	c.985G>A	c.(985-987)GCC>ACC	p.A329T	SIL1_uc003ldn.2_Missense_Mutation_p.A328T|SIL1_uc003ldo.2_Missense_Mutation_p.A329T|SIL1_uc003ldp.2_Missense_Mutation_p.A329T	NM_022464	NP_071909	Q9H173	SIL1_HUMAN	SIL1 protein precursor	329					intracellular protein transport|protein folding|transmembrane transport	endoplasmic reticulum lumen	unfolded protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)											Marinesco-Sj_gren_syndrome				---	---	---	---
SLC35A4	113829	broad.mit.edu	37	5	139947022	139947022	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:139947022G>A	uc003lgg.1	+	3	996	c.268G>A	c.(268-270)GCA>ACA	p.A90T	APBB3_uc003lgd.1_5'Flank|APBB3_uc003lge.1_5'Flank|APBB3_uc003lgf.1_5'Flank|APBB3_uc010jfp.1_5'Flank|APBB3_uc011czi.1_5'Flank|APBB3_uc010jfr.1_5'Flank|SLC35A4_uc003lgh.1_Missense_Mutation_p.A90T	NM_080670	NP_542401	Q96G79	S35A4_HUMAN	solute carrier family 35, member A4	90	Helical; (Potential).|Leu-rich.					Golgi membrane|integral to membrane	sugar:hydrogen symporter activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
WDR55	54853	broad.mit.edu	37	5	140048513	140048513	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140048513C>T	uc003lgr.3	+	5	712	c.598C>T	c.(598-600)CGT>TGT	p.R200C	WDR55_uc011czl.1_Missense_Mutation_p.R39C	NM_017706	NP_060176	Q9H6Y2	WDR55_HUMAN	WD repeat domain 55	200	WD 4.				rRNA processing	cytoplasm|nucleolus				ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
HARS2	23438	broad.mit.edu	37	5	140076607	140076607	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140076607C>G	uc003lgx.2	+	9	1122	c.906C>G	c.(904-906)GAC>GAG	p.D302E	HARS2_uc011czr.1_Missense_Mutation_p.D277E|HARS2_uc011czs.1_Missense_Mutation_p.D158E|HARS2_uc011czt.1_Missense_Mutation_p.D130E|HARS2_uc011czu.1_Missense_Mutation_p.D128E	NM_012208	NP_036340	P49590	SYHM_HUMAN	histidyl-tRNA synthetase 2 precursor	302					histidyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|histidine-tRNA ligase activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA1	56147	broad.mit.edu	37	5	140167021	140167021	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140167021C>T	uc003lhb.2	+	1	1146	c.1146C>T	c.(1144-1146)AAC>AAT	p.N382N	PCDHA1_uc003lha.2_Silent_p.N382N|PCDHA1_uc003lgz.2_Silent_p.N382N	NM_018900	NP_061723	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1 isoform 1 precursor	382	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA1	56147	broad.mit.edu	37	5	140167504	140167504	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140167504G>A	uc003lhb.2	+	1	1629	c.1629G>A	c.(1627-1629)CCG>CCA	p.P543P	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lgz.2_Silent_p.P543P	NM_018900	NP_061723	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1 isoform 1 precursor	543	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA2	56146	broad.mit.edu	37	5	140176586	140176586	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140176586G>A	uc003lhd.2	+	1	2143	c.2037G>A	c.(2035-2037)TCG>TCA	p.S679S	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhc.1_Silent_p.S679S|PCDHA2_uc011czy.1_Silent_p.S679S	NM_018905	NP_061728	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2 isoform 1 precursor	679	Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA4	56144	broad.mit.edu	37	5	140187859	140187859	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140187859G>A	uc003lhi.2	+	1	1188	c.1087G>A	c.(1087-1089)GCT>ACT	p.A363T	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhh.1_Missense_Mutation_p.A363T|PCDHA4_uc011daa.1_Missense_Mutation_p.A363T	NM_018907	NP_061730	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4 isoform 1 precursor	363	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(4)|skin(2)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA4	56144	broad.mit.edu	37	5	140188395	140188395	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140188395C>A	uc003lhi.2	+	1	1724	c.1623C>A	c.(1621-1623)GGC>GGA	p.G541G	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhh.1_Silent_p.G541G|PCDHA4_uc011daa.1_Silent_p.G541G	NM_018907	NP_061730	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4 isoform 1 precursor	541	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(4)|skin(2)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA4	56144	broad.mit.edu	37	5	140188625	140188625	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140188625C>T	uc003lhi.2	+	1	1954	c.1853C>T	c.(1852-1854)GCG>GTG	p.A618V	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhh.1_Missense_Mutation_p.A618V|PCDHA4_uc011daa.1_Missense_Mutation_p.A618V	NM_018907	NP_061730	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4 isoform 1 precursor	618	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(4)|skin(2)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA6	56142	broad.mit.edu	37	5	140207801	140207801	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140207801G>A	uc003lho.2	+	1	152	c.125G>A	c.(124-126)GGC>GAC	p.G42D	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Missense_Mutation_p.G42D|PCDHA6_uc011dab.1_Missense_Mutation_p.G42D	NM_018909	NP_061732	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6 isoform 1 precursor	42	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			haematopoietic_and_lymphoid_tissue(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA6	56142	broad.mit.edu	37	5	140208763	140208763	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140208763G>A	uc003lho.2	+	1	1114	c.1087G>A	c.(1087-1089)GCT>ACT	p.A363T	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Missense_Mutation_p.A363T|PCDHA6_uc011dab.1_Missense_Mutation_p.A363T	NM_018909	NP_061732	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6 isoform 1 precursor	363	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			haematopoietic_and_lymphoid_tissue(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA7	56141	broad.mit.edu	37	5	140215250	140215250	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140215250C>T	uc003lhq.2	+	1	1282	c.1282C>T	c.(1282-1284)CGG>TGG	p.R428W	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc011dac.1_Missense_Mutation_p.R428W	NM_018910	NP_061733	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7 isoform 1 precursor	428	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(2)|skin(2)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA7	56141	broad.mit.edu	37	5	140215693	140215693	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140215693C>T	uc003lhq.2	+	1	1725	c.1725C>T	c.(1723-1725)GGC>GGT	p.G575G	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc011dac.1_Silent_p.G575G	NM_018910	NP_061733	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7 isoform 1 precursor	575	Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(2)|skin(2)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA8	56140	broad.mit.edu	37	5	140221108	140221108	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140221108T>C	uc003lhs.2	+	1	202	c.202T>C	c.(202-204)TCC>CCC	p.S68P	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhr.1_Missense_Mutation_p.S68P	NM_018911	NP_061734	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8 isoform 1 precursor	68	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			upper_aerodigestive_tract(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA9	9752	broad.mit.edu	37	5	140229942	140229942	+	Missense_Mutation	SNP	C	T	T	rs146638035		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140229942C>T	uc003lhu.2	+	1	2586	c.1862C>T	c.(1861-1863)CCG>CTG	p.P621L	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lht.1_Missense_Mutation_p.P621L	NM_031857	NP_114063	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9 isoform 1 precursor	621	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding			large_intestine(2)|ovary(2)|skin(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA11	56138	broad.mit.edu	37	5	140248859	140248859	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140248859G>A	uc003lia.2	+	1	1029	c.171G>A	c.(169-171)GCG>GCA	p.A57A	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc011dae.1_Silent_p.A57A	NM_018902	NP_061725	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11 isoform 1 precursor	57	Extracellular (Potential).|Cadherin 1.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA11	56138	broad.mit.edu	37	5	140250709	140250709	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140250709C>T	uc003lia.2	+	1	2879	c.2021C>T	c.(2020-2022)GCG>GTG	p.A674V	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc011dae.1_Missense_Mutation_p.A674V	NM_018902	NP_061725	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11 isoform 1 precursor	674	Extracellular (Potential).|Cadherin 6.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHA13	56136	broad.mit.edu	37	5	140263023	140263023	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140263023G>A	uc003lif.2	+	1	1170	c.1170G>A	c.(1168-1170)ACG>ACA	p.T390T	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc003lia.2_Intron|PCDHA12_uc003lic.2_Intron|PCDHA13_uc003lie.1_Silent_p.T390T|PCDHA13_uc003lid.2_Silent_p.T390T	NM_018904	NP_061727	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13 isoform 1 precursor	390	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|skin(2)|central_nervous_system(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHB1	29930	broad.mit.edu	37	5	140431753	140431753	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140431753T>G	uc003lik.1	+	1	775	c.698T>G	c.(697-699)CTG>CGG	p.L233R		NM_013340	NP_037472	Q9Y5F3	PCDB1_HUMAN	protocadherin beta 1 precursor	233	Cadherin 2.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB1	29930	broad.mit.edu	37	5	140433012	140433012	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140433012C>A	uc003lik.1	+	1	2034	c.1957C>A	c.(1957-1959)CTT>ATT	p.L653I		NM_013340	NP_037472	Q9Y5F3	PCDB1_HUMAN	protocadherin beta 1 precursor	653	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB2	56133	broad.mit.edu	37	5	140475766	140475766	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140475766G>A	uc003lil.2	+	1	1530	c.1392G>A	c.(1390-1392)GAG>GAA	p.E464E	PCDHB2_uc003lim.1_Silent_p.E125E	NM_018936	NP_061759	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2 precursor	464	Extracellular (Potential).|Cadherin 5.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			ovary(3)|upper_aerodigestive_tract(2)|pancreas(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB3	56132	broad.mit.edu	37	5	140480875	140480875	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140480875G>A	uc003lio.2	+	1	642	c.642G>A	c.(640-642)GCG>GCA	p.A214A	uc003lin.2_Intron	NM_018937	NP_061760	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3 precursor	214	Extracellular (Potential).|Cadherin 2.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			ovary(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB4	56131	broad.mit.edu	37	5	140501880	140501880	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140501880G>A	uc003lip.1	+	1	300	c.300G>A	c.(298-300)CCG>CCA	p.P100P		NM_018938	NP_061761	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4 precursor	100	Cadherin 1.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	cytoplasm|integral to plasma membrane|intermediate filament cytoskeleton	calcium ion binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB4	56131	broad.mit.edu	37	5	140503473	140503473	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140503473G>A	uc003lip.1	+	1	1893	c.1893G>A	c.(1891-1893)GAG>GAA	p.E631E		NM_018938	NP_061761	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4 precursor	631	Cadherin 6.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	cytoplasm|integral to plasma membrane|intermediate filament cytoskeleton	calcium ion binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB5	26167	broad.mit.edu	37	5	140516326	140516326	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140516326C>T	uc003liq.2	+	1	1527	c.1310C>T	c.(1309-1311)ACG>ATG	p.T437M		NM_015669	NP_056484	Q9Y5E4	PCDB5_HUMAN	protocadherin beta 5 precursor	437	Cadherin 4.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding|protein binding			skin(3)|ovary(2)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB6	56130	broad.mit.edu	37	5	140531209	140531209	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140531209C>T	uc003lir.2	+	1	1371	c.1371C>T	c.(1369-1371)TTC>TTT	p.F457F	PCDHB6_uc011dah.1_Silent_p.F321F	NM_018939	NP_061762	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6 precursor	457	Cadherin 5.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB8	56128	broad.mit.edu	37	5	140559017	140559017	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140559017G>A	uc011dai.1	+	1	1588	c.1402G>A	c.(1402-1404)GCC>ACC	p.A468T	PCDHB16_uc003liv.2_5'Flank|PCDHB16_uc010jfw.1_5'Flank	NM_019120	NP_061993	Q9UN66	PCDB8_HUMAN	protocadherin beta 8 precursor	468	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			skin(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB8	56128	broad.mit.edu	37	5	140559262	140559262	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140559262C>T	uc011dai.1	+	1	1833	c.1647C>T	c.(1645-1647)CGC>CGT	p.R549R	PCDHB16_uc003liv.2_5'Flank|PCDHB16_uc010jfw.1_5'Flank	NM_019120	NP_061993	Q9UN66	PCDB8_HUMAN	protocadherin beta 8 precursor	549	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			skin(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB11	56125	broad.mit.edu	37	5	140580848	140580848	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140580848G>A	uc003liy.2	+	1	1501	c.1501G>A	c.(1501-1503)GCC>ACC	p.A501T	PCDHB11_uc011daj.1_Missense_Mutation_p.A136T	NM_018931	NP_061754	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11 precursor	501	Extracellular (Potential).|Cadherin 5.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			skin(3)|ovary(2)|upper_aerodigestive_tract(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB12	56124	broad.mit.edu	37	5	140589268	140589268	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140589268C>T	uc003liz.2	+	1	978	c.789C>T	c.(787-789)ACC>ACT	p.T263T	PCDHB12_uc011dak.1_Intron	NM_018932	NP_061755	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12 precursor	263	Extracellular (Potential).|Cadherin 3.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			skin(2)|ovary(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB13	56123	broad.mit.edu	37	5	140594136	140594136	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140594136T>C	uc003lja.1	+	1	628	c.441T>C	c.(439-441)AGT>AGC	p.S147S		NM_018933	NP_061756	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13 precursor	147	Cadherin 2.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			skin(2)|ovary(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB15	56121	broad.mit.edu	37	5	140625818	140625818	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140625818C>T	uc003lje.2	+	1	672	c.672C>T	c.(670-672)GGC>GGT	p.G224G		NM_018935	NP_061758	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15 precursor	224	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(2)|breast(2)|skin(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB15	56121	broad.mit.edu	37	5	140626336	140626336	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140626336T>C	uc003lje.2	+	1	1190	c.1190T>C	c.(1189-1191)GTT>GCT	p.V397A		NM_018935	NP_061758	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15 precursor	397	Extracellular (Potential).|Cadherin 4.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(2)|breast(2)|skin(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB15	56121	broad.mit.edu	37	5	140626471	140626471	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140626471C>T	uc003lje.2	+	1	1325	c.1325C>T	c.(1324-1326)TCG>TTG	p.S442L		NM_018935	NP_061758	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15 precursor	442	Extracellular (Potential).|Cadherin 4.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(2)|breast(2)|skin(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB15	56121	broad.mit.edu	37	5	140626487	140626487	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140626487C>T	uc003lje.2	+	1	1341	c.1341C>T	c.(1339-1341)AAC>AAT	p.N447N		NM_018935	NP_061758	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15 precursor	447	Extracellular (Potential).|Cadherin 4.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(2)|breast(2)|skin(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB15	56121	broad.mit.edu	37	5	140626494	140626494	+	Missense_Mutation	SNP	G	A	A	rs144325162		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140626494G>A	uc003lje.2	+	1	1348	c.1348G>A	c.(1348-1350)GCC>ACC	p.A450T		NM_018935	NP_061758	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15 precursor	450	Extracellular (Potential).|Cadherin 4.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(2)|breast(2)|skin(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHB15	56121	broad.mit.edu	37	5	140626719	140626719	+	Nonsense_Mutation	SNP	C	T	T	rs146266396		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140626719C>T	uc003lje.2	+	1	1573	c.1573C>T	c.(1573-1575)CAG>TAG	p.Q525*		NM_018935	NP_061758	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15 precursor	525	Extracellular (Potential).|Cadherin 5.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(2)|breast(2)|skin(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)															---	---	---	---
PCDHGA1	56114	broad.mit.edu	37	5	140710573	140710573	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140710573A>G	uc003lji.1	+	1	322	c.322A>G	c.(322-324)ATC>GTC	p.I108V	PCDHGA1_uc011dan.1_Missense_Mutation_p.I108V	NM_018912	NP_061735	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1 isoform 1	108	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|breast(1)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHGA2	56113	broad.mit.edu	37	5	140719882	140719882	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140719882C>T	uc003ljk.1	+	1	1529	c.1344C>T	c.(1342-1344)AAC>AAT	p.N448N	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc011dao.1_Silent_p.N448N	NM_018915	NP_061738	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2 isoform 1	448	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			skin(2)|ovary(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHGB2	56103	broad.mit.edu	37	5	140741993	140741993	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140741993A>G	uc003ljs.1	+	1	2291	c.2291A>G	c.(2290-2292)GAG>GGG	p.E764G	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGA5_uc003lju.1_5'Flank|PCDHGB2_uc011dar.1_Missense_Mutation_p.E764G|PCDHGA5_uc011das.1_5'Flank	NM_018923	NP_061746	Q9Y5G2	PCDGE_HUMAN	protocadherin gamma subfamily B, 2 isoform 1	764	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHGA5	56110	broad.mit.edu	37	5	140744633	140744633	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140744633G>T	uc003lju.1	+	1	736	c.736G>T	c.(736-738)GAG>TAG	p.E246*	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc011das.1_Nonsense_Mutation_p.E246*	NM_018918	NP_061741	Q9Y5G8	PCDG5_HUMAN	protocadherin gamma subfamily A, 5 isoform 1	246	Cadherin 3.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHGB7	56099	broad.mit.edu	37	5	140797977	140797977	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140797977A>C	uc003lkn.1	+	1	696	c.551A>C	c.(550-552)GAC>GCC	p.D184A	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkm.2_Missense_Mutation_p.D184A|PCDHGA11_uc003lko.1_5'Flank|PCDHGA11_uc003lkp.1_5'Flank|PCDHGA11_uc003lkq.1_5'Flank	NM_018927	NP_061750	Q9Y5F8	PCDGJ_HUMAN	protocadherin gamma subfamily B, 7 isoform 1	184	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHGA12	26025	broad.mit.edu	37	5	140811927	140811927	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140811927C>T	uc003lkt.1	+	1	1770	c.1601C>T	c.(1600-1602)GCG>GTG	p.A534V	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lkp.1_Intron|PCDHGA11_uc003lkq.1_Intron|PCDHGA12_uc011dba.1_Missense_Mutation_p.A534V	NM_003735	NP_003726	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12 isoform 1	534	Extracellular (Potential).|Cadherin 5.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|pancreas(1)|skin(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHGC3	5098	broad.mit.edu	37	5	140856630	140856630	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140856630A>G	uc003lkv.1	+	1	1062	c.947A>G	c.(946-948)AAA>AGA	p.K316R	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lkp.1_Intron|PCDHGA11_uc003lkq.1_Intron|PCDHGA12_uc003lkt.1_Intron|PCDHGC3_uc003lku.1_Missense_Mutation_p.K316R|PCDHGC3_uc003lkw.1_Intron	NM_002588	NP_002579	Q9UN70	PCDGK_HUMAN	protocadherin gamma subfamily C, 3 isoform 1	316	Cadherin 3.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHGC3	5098	broad.mit.edu	37	5	140857013	140857013	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140857013C>T	uc003lkv.1	+	1	1445	c.1330C>T	c.(1330-1332)CGT>TGT	p.R444C	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lkp.1_Intron|PCDHGA11_uc003lkq.1_Intron|PCDHGA12_uc003lkt.1_Intron|PCDHGC3_uc003lku.1_Missense_Mutation_p.R444C|PCDHGC3_uc003lkw.1_Intron	NM_002588	NP_002579	Q9UN70	PCDGK_HUMAN	protocadherin gamma subfamily C, 3 isoform 1	444	Cadherin 4.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
PCDHGC5	56097	broad.mit.edu	37	5	140870692	140870692	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140870692C>T	uc003lla.1	+	1	1885	c.1885C>T	c.(1885-1887)CGC>TGC	p.R629C	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lkp.1_Intron|PCDHGA11_uc003lkq.1_Intron|PCDHGA12_uc003lkt.1_Intron|PCDHGC3_uc003lkv.1_Intron|PCDHGC3_uc003lkw.1_Intron|PCDHGC4_uc003lky.1_Intron|PCDHGC5_uc011dbc.1_Missense_Mutation_p.R629C	NM_018929	NP_061752	Q9Y5F6	PCDGM_HUMAN	protocadherin gamma subfamily C, 5 isoform 1	629	Extracellular (Potential).|Cadherin 6.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
DIAPH1	1729	broad.mit.edu	37	5	140908384	140908384	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140908384C>T	uc003llb.3	-	23	3044	c.2903G>A	c.(2902-2904)CGT>CAT	p.R968H	DIAPH1_uc011dbd.1_5'Flank|DIAPH1_uc003llc.3_Missense_Mutation_p.R959H|DIAPH1_uc010jgc.1_Missense_Mutation_p.R404H	NM_005219	NP_005210	O60610	DIAP1_HUMAN	diaphanous 1 isoform 1	968	FH2.				regulation of microtubule-based process|sensory perception of sound	cytoplasm|cytoskeleton|ruffle membrane	actin binding|receptor binding|Rho GTPase binding			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
HDAC3	8841	broad.mit.edu	37	5	141008173	141008173	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141008173C>T	uc003llf.2	-	8	710	c.644G>A	c.(643-645)CGC>CAC	p.R215H	HDAC3_uc003lle.1_Missense_Mutation_p.R158H	NM_003883	NP_003874	O15379	HDAC3_HUMAN	histone deacetylase 3	215	Histone deacetylase.				anti-apoptosis|cellular lipid metabolic process|negative regulation of cell cycle|negative regulation of JNK cascade|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|spindle assembly|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|spindle microtubule|transcriptional repressor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|transcription corepressor activity|transcription factor binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Vorinostat(DB02546)													---	---	---	---
ARAP3	64411	broad.mit.edu	37	5	141035336	141035336	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141035336C>T	uc003llm.2	-						ARAP3_uc003lll.2_Intron|ARAP3_uc011dbe.1_Intron|ARAP3_uc003lln.2_Intron	NM_022481	NP_071926			ArfGAP with RhoGAP domain, ankyrin repeat and PH						cytoskeleton organization|negative regulation of cell migration|negative regulation of Rho protein signal transduction|regulation of ARF GTPase activity|regulation of cell shape|small GTPase mediated signal transduction|vesicle-mediated transport	cytoskeleton|cytosol|lamellipodium|plasma membrane|ruffle	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|Rho GTPase activator activity|zinc ion binding			breast(5)|ovary(1)|large_intestine(1)	7																		---	---	---	---
PCDH12	51294	broad.mit.edu	37	5	141336498	141336498	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141336498G>A	uc003llx.2	-	1	2130	c.919C>T	c.(919-921)CGT>TGT	p.R307C		NM_016580	NP_057664	Q9NPG4	PCD12_HUMAN	protocadherin 12 precursor	307	Extracellular (Potential).|Cadherin 3.				neuron recognition	integral to plasma membrane	calcium ion binding			ovary(3)	3		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
ARHGAP26	23092	broad.mit.edu	37	5	142264927	142264927	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142264927A>C	uc011dbj.1	+	5	484	c.449A>C	c.(448-450)AAT>ACT	p.N150T	ARHGAP26_uc003lmt.2_Missense_Mutation_p.N150T|ARHGAP26_uc003lmw.2_Missense_Mutation_p.N150T	NM_015071	NP_055886	Q9UNA1	RHG26_HUMAN	GTPase regulator associated with the focal	150					actin cytoskeleton organization|filopodium assembly|nervous system development|small GTPase mediated signal transduction	cytoskeleton|cytosol|focal adhesion	cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding			ovary(1)	1		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
NR3C1	2908	broad.mit.edu	37	5	142693590	142693590	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:142693590A>G	uc003lmz.2	-	3	1820	c.1328T>C	c.(1327-1329)GTT>GCT	p.V443A	NR3C1_uc003lmy.2_Missense_Mutation_p.V443A|NR3C1_uc003lna.2_Missense_Mutation_p.V443A|NR3C1_uc003lnb.2_Missense_Mutation_p.V443A|NR3C1_uc011dbk.1_Missense_Mutation_p.V46A|NR3C1_uc003lnc.2_Missense_Mutation_p.V443A|NR3C1_uc003lnd.2_Missense_Mutation_p.V443A|NR3C1_uc003lne.2_Missense_Mutation_p.V443A|NR3C1_uc003lnf.2_Missense_Mutation_p.V443A	NM_000176	NP_000167	P04150	GCR_HUMAN	glucocorticoid receptor isoform alpha	443	Nuclear receptor.				chromatin modification|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to protein stimulus|transcription from RNA polymerase II promoter	mitochondrial matrix|nucleoplasm	glucocorticoid receptor activity|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|zinc ion binding			ovary(2)	2		Acute lymphoblastic leukemia(2;3.2e-05)|all_hematologic(2;0.000361)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)		Amcinonide(DB00288)|Betamethasone(DB00443)|Budesonide(DB01222)|Dexamethasone(DB01234)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluticasone Propionate(DB00588)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Loteprednol Etabonate(DB00873)|Methylprednisolone(DB00959)|Mifepristone(DB00834)|Mometasone(DB00764)|Prednisone(DB00635)													---	---	---	---
TCERG1	10915	broad.mit.edu	37	5	145851099	145851099	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145851099G>A	uc003lob.2	+	9	1601	c.1561G>A	c.(1561-1563)GCA>ACA	p.A521T	TCERG1_uc003loc.2_Missense_Mutation_p.A500T|TCERG1_uc011dbt.1_Missense_Mutation_p.A500T	NM_006706	NP_006697	O14776	TCRG1_HUMAN	transcription elongation regulator 1 isoform 1	521					regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	protein binding|transcription coactivator activity			ovary(1)|skin(1)	2		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
GPR151	134391	broad.mit.edu	37	5	145894812	145894812	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:145894812C>A	uc003lod.1	-	1	865	c.865G>T	c.(865-867)GCC>TCC	p.A289S		NM_194251	NP_919227	Q8TDV0	GP151_HUMAN	G protein-coupled receptor 151	289	Helical; Name=7; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
JAKMIP2	9832	broad.mit.edu	37	5	147027964	147027964	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147027964A>C	uc003loq.1	-	5	1293	c.911T>G	c.(910-912)TTG>TGG	p.L304W	JAKMIP2_uc011dbx.1_Missense_Mutation_p.L262W|JAKMIP2_uc003lor.1_Missense_Mutation_p.L304W|uc003lop.1_Intron|JAKMIP2_uc010jgo.1_Missense_Mutation_p.L304W	NM_014790	NP_055605	Q96AA8	JKIP2_HUMAN	janus kinase and microtubule interacting protein	304	Potential.					Golgi apparatus				large_intestine(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
SPINK13	153218	broad.mit.edu	37	5	147653928	147653928	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147653928A>G	uc003lpc.2	+	3	151	c.89A>G	c.(88-90)GAC>GGC	p.D30G	uc003lpb.1_Intron|SPINK13_uc010jgt.2_RNA	NM_001040129	NP_001035218	Q1W4C9	ISK13_HUMAN	serine PI Kazal type 5-like 3 precursor	30						extracellular region	serine-type endopeptidase inhibitor activity				0																		---	---	---	---
SPINK9	643394	broad.mit.edu	37	5	147719249	147719249	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147719249A>G	uc003lpe.1	+	4	290	c.235A>G	c.(235-237)AAA>GAA	p.K79E	uc003lpb.1_Intron	NM_001040433	NP_001035523	Q5DT21	ISK9_HUMAN	serine peptidase inhibitor, Kazal type 9	79	Kazal-like.					extracellular region	protein binding|serine-type endopeptidase inhibitor activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
HTR4	3360	broad.mit.edu	37	5	147862857	147862857	+	Intron	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147862857C>A	uc003lpn.2	-						HTR4_uc010jgu.1_Intron|HTR4_uc003lpi.1_Intron|HTR4_uc003lpj.1_Intron|HTR4_uc003lpk.2_Intron|HTR4_uc011dby.1_Intron|HTR4_uc003lpl.2_Intron|HTR4_uc003lpm.2_Intron|HTR4_uc010jgv.2_Intron	NM_000870	NP_000861			serotonin 5-HT4 receptor isoform b						G-protein signaling, coupled to cyclic nucleotide second messenger|positive regulation of cell proliferation	endosome|integral to plasma membrane|membrane fraction	serotonin receptor activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Cisapride(DB00604)|Rizatriptan(DB00953)|Tegaserod(DB01079)|Zolmitriptan(DB00315)													---	---	---	---
ABLIM3	22885	broad.mit.edu	37	5	148620297	148620297	+	Silent	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148620297T>A	uc003lpy.2	+	14	1514	c.1263T>A	c.(1261-1263)ACT>ACA	p.T421T	ABLIM3_uc003lpz.1_Silent_p.T421T|ABLIM3_uc003lqa.1_Intron|ABLIM3_uc003lqb.2_Intron|ABLIM3_uc003lqc.1_Intron|ABLIM3_uc003lqd.1_Intron|ABLIM3_uc003lqf.2_Intron|ABLIM3_uc003lqe.1_Intron	NM_014945	NP_055760	O94929	ABLM3_HUMAN	actin binding LIM protein family, member 3	421					axon guidance|cytoskeleton organization	cytoplasm	actin binding|zinc ion binding			ovary(2)|skin(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
AFAP1L1	134265	broad.mit.edu	37	5	148699161	148699161	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:148699161A>G	uc003lqh.2	+	13	1627	c.1496A>G	c.(1495-1497)GAC>GGC	p.D499G	AFAP1L1_uc010jgy.2_Missense_Mutation_p.D499G|AFAP1L1_uc003lqi.1_Missense_Mutation_p.D114G	NM_152406	NP_689619	Q8TED9	AF1L1_HUMAN	actin filament associated protein 1-like 1	499	PH 2.						protein binding			breast(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
SLC26A2	1836	broad.mit.edu	37	5	149357902	149357902	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149357902T>C	uc003lrh.2	+	2	955	c.687T>C	c.(685-687)GCT>GCC	p.A229A		NM_000112	NP_000103	P50443	S26A2_HUMAN	solute carrier family 26 member 2	229	Helical; (Potential).					integral to plasma membrane|membrane fraction	secondary active sulfate transmembrane transporter activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)															---	---	---	---
SLC6A7	6534	broad.mit.edu	37	5	149580727	149580727	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149580727G>C	uc003lrr.2	+	6	1170	c.799G>C	c.(799-801)GCC>CCC	p.A267P		NM_014228	NP_055043	Q99884	SC6A7_HUMAN	solute carrier family 6, member 7	267						integral to plasma membrane|membrane fraction	neurotransmitter:sodium symporter activity|proline:sodium symporter activity				0		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Proline(DB00172)													---	---	---	---
ARSI	340075	broad.mit.edu	37	5	149677398	149677398	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149677398T>C	uc003lrv.2	-	2	1678	c.1089A>G	c.(1087-1089)TCA>TCG	p.S363S		NM_001012301	NP_001012301	Q5FYB1	ARSI_HUMAN	arylsulfatase family, member I precursor	363						endoplasmic reticulum|extracellular region	arylsulfatase activity|metal ion binding			ovary(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
NDST1	3340	broad.mit.edu	37	5	149918811	149918811	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:149918811G>A	uc003lsk.3	+	7	1961	c.1459G>A	c.(1459-1461)GGC>AGC	p.G487S	NDST1_uc011dcj.1_Missense_Mutation_p.G487S|NDST1_uc003lsl.2_Missense_Mutation_p.G487S	NM_001543	NP_001534	P52848	NDST1_HUMAN	N-deacetylase/N-sulfotransferase (heparan	487	Heparan sulfate N-deacetylase 1.|Lumenal (Potential).				heparan sulfate proteoglycan biosynthetic process|inflammatory response	Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			breast(1)|skin(1)	2		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
SYNPO	11346	broad.mit.edu	37	5	150029289	150029289	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150029289C>T	uc003lsn.2	+	3	2558	c.2184C>T	c.(2182-2184)TAC>TAT	p.Y728Y	SYNPO_uc003lso.3_Silent_p.Y484Y|SYNPO_uc003lsp.2_Silent_p.Y484Y	NM_001109974	NP_001103444	Q8N3V7	SYNPO_HUMAN	synaptopodin isoform B	728					positive regulation of actin filament bundle assembly|regulation of stress fiber assembly	actin cytoskeleton|cytoplasm|dendritic spine|perikaryon|postsynaptic density|postsynaptic membrane|tight junction	actin binding|protein binding			large_intestine(1)	1		Medulloblastoma(196;0.134)|all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
TNIP1	10318	broad.mit.edu	37	5	150436386	150436386	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150436386C>T	uc003ltf.2	-	6	1157	c.568G>A	c.(568-570)GAG>AAG	p.E190K	TNIP1_uc010jhl.2_RNA|TNIP1_uc010jhm.2_Missense_Mutation_p.E190K|TNIP1_uc010jhn.2_Missense_Mutation_p.E190K|TNIP1_uc011dco.1_Missense_Mutation_p.E190K|TNIP1_uc003lth.2_RNA|TNIP1_uc003lti.2_Missense_Mutation_p.E190K|TNIP1_uc003ltg.2_Missense_Mutation_p.E137K|TNIP1_uc003ltj.2_Missense_Mutation_p.E190K|TNIP1_uc010jho.1_RNA|TNIP1_uc010jhq.1_Missense_Mutation_p.E137K|TNIP1_uc010jhp.1_Missense_Mutation_p.E137K|TNIP1_uc010jhr.1_Missense_Mutation_p.E190K|TNIP1_uc003ltk.2_Missense_Mutation_p.E190K	NM_006058	NP_006049	Q15025	TNIP1_HUMAN	TNFAIP3 interacting protein 1	190	Interacts with Nef.				defense response|glycoprotein biosynthetic process|negative regulation of viral genome replication|translation	cytoplasm|nucleus	protein binding			ovary(1)|central_nervous_system(1)	2		Medulloblastoma(196;0.0911)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
GM2A	2760	broad.mit.edu	37	5	150646437	150646437	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150646437G>A	uc003ltr.3	+	3	554	c.389G>A	c.(388-390)CGT>CAT	p.R130H	GM2A_uc011dcs.1_RNA|GM2A_uc011dcr.1_Missense_Mutation_p.R130H|GM2A_uc003ltt.1_Missense_Mutation_p.R62H|GM2A_uc003ltu.1_5'Flank	NM_000405	NP_000396	P17900	SAP3_HUMAN	GM2 ganglioside activator precursor	130						lysosome|nucleolus	sphingolipid activator protein activity				0		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
SLC36A1	206358	broad.mit.edu	37	5	150844159	150844159	+	Missense_Mutation	SNP	C	T	T	rs142033033		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150844159C>T	uc003luc.2	+	4	536	c.319C>T	c.(319-321)CGC>TGC	p.R107C	GM2A_uc011dcs.1_Intron|SLC36A1_uc003lub.1_Missense_Mutation_p.R107C|SLC36A1_uc010jhw.1_Missense_Mutation_p.R107C	NM_078483	NP_510968	Q7Z2H8	S36A1_HUMAN	solute carrier family 36 member 1	107	Cytoplasmic (Potential).				cellular nitrogen compound metabolic process|ion transport	endoplasmic reticulum|integral to membrane|lysosomal membrane|plasma membrane	amino acid transmembrane transporter activity|symporter activity			skin(1)	1		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)|all_neural(839;0.138)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Glycine(DB00145)|L-Alanine(DB00160)													---	---	---	---
FAT2	2196	broad.mit.edu	37	5	150885391	150885391	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150885391C>T	uc003lue.3	-	23	12798	c.12785G>A	c.(12784-12786)CGC>CAC	p.R4262H	GM2A_uc011dcs.1_Intron|FAT2_uc003lud.3_Missense_Mutation_p.R869H	NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	4262	Cytoplasmic (Potential).				epithelial cell migration|homophilic cell adhesion	cell-cell adherens junction|integral to membrane|nucleus	calcium ion binding			ovary(4)|upper_aerodigestive_tract(1)|skin(1)	6		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
FAT2	2196	broad.mit.edu	37	5	150922553	150922553	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150922553A>C	uc003lue.3	-	9	8148	c.8135T>G	c.(8134-8136)ATT>AGT	p.I2712S	GM2A_uc011dcs.1_Intron	NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	2712	Cadherin 24.|Extracellular (Potential).				epithelial cell migration|homophilic cell adhesion	cell-cell adherens junction|integral to membrane|nucleus	calcium ion binding			ovary(4)|upper_aerodigestive_tract(1)|skin(1)	6		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
FAT2	2196	broad.mit.edu	37	5	150923300	150923300	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150923300G>A	uc003lue.3	-	9	7401	c.7388C>T	c.(7387-7389)GCA>GTA	p.A2463V	GM2A_uc011dcs.1_Intron	NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	2463	Extracellular (Potential).|Cadherin 21.				epithelial cell migration|homophilic cell adhesion	cell-cell adherens junction|integral to membrane|nucleus	calcium ion binding			ovary(4)|upper_aerodigestive_tract(1)|skin(1)	6		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
FAT2	2196	broad.mit.edu	37	5	150948467	150948467	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:150948467G>A	uc003lue.3	-	1	39	c.26C>T	c.(25-27)GCC>GTC	p.A9V	GM2A_uc011dcs.1_Intron|FAT2_uc010jhx.1_Missense_Mutation_p.A9V	NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	9					epithelial cell migration|homophilic cell adhesion	cell-cell adherens junction|integral to membrane|nucleus	calcium ion binding			ovary(4)|upper_aerodigestive_tract(1)|skin(1)	6		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)															---	---	---	---
GRIA1	2890	broad.mit.edu	37	5	153078456	153078456	+	Silent	SNP	C	T	T	rs142814149		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153078456C>T	uc003lva.3	+	10	1640	c.1275C>T	c.(1273-1275)AAC>AAT	p.N425N	GRIA1_uc003luy.3_Silent_p.N425N|GRIA1_uc003luz.3_Silent_p.N330N|GRIA1_uc011dcv.1_RNA|GRIA1_uc011dcw.1_Silent_p.N345N|GRIA1_uc011dcx.1_Silent_p.N356N|GRIA1_uc011dcy.1_Silent_p.N435N|GRIA1_uc011dcz.1_Silent_p.N435N|GRIA1_uc010jia.1_Silent_p.N405N	NM_001114183	NP_001107655	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1 isoform	425	Extracellular (Potential).				synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|dendritic spine|endocytic vesicle membrane|endoplasmic reticulum membrane|neuronal cell body|postsynaptic density|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity|PDZ domain binding	p.N425N(1)		ovary(4)|skin(2)	6		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|L-Glutamic Acid(DB00142)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)													---	---	---	---
GRIA1	2890	broad.mit.edu	37	5	153149891	153149891	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:153149891G>A	uc003lva.3	+	13	2551	c.2186G>A	c.(2185-2187)CGG>CAG	p.R729Q	GRIA1_uc003luy.3_Missense_Mutation_p.R729Q|GRIA1_uc003luz.3_Missense_Mutation_p.R634Q|GRIA1_uc011dcv.1_RNA|GRIA1_uc011dcw.1_Missense_Mutation_p.R649Q|GRIA1_uc011dcx.1_Missense_Mutation_p.R660Q|GRIA1_uc011dcy.1_Missense_Mutation_p.R739Q|GRIA1_uc011dcz.1_Missense_Mutation_p.R739Q	NM_001114183	NP_001107655	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1 isoform	729	Extracellular (Potential).				synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|dendritic spine|endocytic vesicle membrane|endoplasmic reticulum membrane|neuronal cell body|postsynaptic density|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity|PDZ domain binding			ovary(4)|skin(2)	6		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|L-Glutamic Acid(DB00142)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)													---	---	---	---
LARP1	23367	broad.mit.edu	37	5	154135696	154135696	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154135696T>C	uc003lvp.2	+	1	808	c.379T>C	c.(379-381)TGG>CGG	p.W127R	LARP1_uc003lvo.2_Intron|LARP1_uc010jie.1_5'Flank	NM_033551	NP_291029	Q6PKG0	LARP1_HUMAN	la related protein isoform 2	127							protein binding|RNA binding			ovary(2)|pancreas(1)|skin(1)	4	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)															---	---	---	---
HAVCR2	84868	broad.mit.edu	37	5	156535950	156535950	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156535950C>T	uc003lwk.1	-	1	189	c.45G>A	c.(43-45)CTG>CTA	p.L15L	HAVCR2_uc003lwl.2_Silent_p.L15L	NM_032782	NP_116171	Q8TDQ0	HAVR2_HUMAN	T cell immunoglobulin mucin 3 precursor	15						integral to membrane					0	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
CYFIP2	26999	broad.mit.edu	37	5	156751079	156751079	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156751079A>G	uc003lwq.2	+	18	1960	c.1822A>G	c.(1822-1824)AGT>GGT	p.S608G	CYFIP2_uc011ddn.1_Missense_Mutation_p.S582G|CYFIP2_uc011ddo.1_Missense_Mutation_p.S412G|CYFIP2_uc003lwr.2_Missense_Mutation_p.S608G|CYFIP2_uc003lws.2_Missense_Mutation_p.S608G|CYFIP2_uc003lwt.2_Missense_Mutation_p.S511G|CYFIP2_uc011ddp.1_Missense_Mutation_p.S342G	NM_001037333	NP_001032410	Q96F07	CYFP2_HUMAN	cytoplasmic FMR1 interacting protein 2	633					apoptosis|cell-cell adhesion	cell junction|perinuclear region of cytoplasm|synapse|synaptosome	protein binding				0	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
CYFIP2	26999	broad.mit.edu	37	5	156753210	156753210	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156753210G>T	uc003lwq.2	+	20	2152	c.2014G>T	c.(2014-2016)GAC>TAC	p.D672Y	CYFIP2_uc011ddn.1_Missense_Mutation_p.D646Y|CYFIP2_uc011ddo.1_Missense_Mutation_p.D476Y|CYFIP2_uc003lwr.2_Missense_Mutation_p.D672Y|CYFIP2_uc003lws.2_Missense_Mutation_p.D672Y|CYFIP2_uc003lwt.2_Missense_Mutation_p.D575Y|CYFIP2_uc011ddp.1_Missense_Mutation_p.D406Y	NM_001037333	NP_001032410	Q96F07	CYFP2_HUMAN	cytoplasmic FMR1 interacting protein 2	697					apoptosis|cell-cell adhesion	cell junction|perinuclear region of cytoplasm|synapse|synaptosome	protein binding				0	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
SOX30	11063	broad.mit.edu	37	5	157073789	157073789	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157073789G>A	uc003lxb.1	-	3	1585	c.1243C>T	c.(1243-1245)CGA>TGA	p.R415*	SOX30_uc003lxc.1_Nonsense_Mutation_p.R415*|SOX30_uc011dds.1_Nonsense_Mutation_p.R110*	NM_178424	NP_848511	O94993	SOX30_HUMAN	SRY (sex determining region Y)-box 30 isoform a	415					regulation of transcription from RNA polymerase II promoter|regulation of transcription, DNA-dependent|response to corticosteroid stimulus|transcription, DNA-dependent	nucleus|nucleus	sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity			ovary(1)|central_nervous_system(1)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
SOX30	11063	broad.mit.edu	37	5	157075845	157075845	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157075845C>T	uc003lxb.1	-	2	1369	c.1027G>A	c.(1027-1029)GCA>ACA	p.A343T	SOX30_uc003lxc.1_Missense_Mutation_p.A343T|SOX30_uc011dds.1_Missense_Mutation_p.A38T	NM_178424	NP_848511	O94993	SOX30_HUMAN	SRY (sex determining region Y)-box 30 isoform a	343	HMG box.				regulation of transcription from RNA polymerase II promoter|regulation of transcription, DNA-dependent|response to corticosteroid stimulus|transcription, DNA-dependent	nucleus|nucleus	sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity			ovary(1)|central_nervous_system(1)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
LSM11	134353	broad.mit.edu	37	5	157181040	157181040	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157181040G>A	uc003lxe.1	+	3	621	c.617G>A	c.(616-618)CGA>CAA	p.R206Q	LSM11_uc003lxf.1_5'Flank	NM_173491	NP_775762	P83369	LSM11_HUMAN	LSM11, U7 small nuclear RNA associated	206					histone mRNA 3'-end processing|S phase of mitotic cell cycle|termination of RNA polymerase II transcription	histone pre-mRNA 3'end processing complex|nucleoplasm|U7 snRNP	protein binding|U7 snRNA binding				0	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)															---	---	---	---
RNF145	153830	broad.mit.edu	37	5	158601042	158601042	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:158601042G>C	uc003lxp.2	-	6	1059	c.746C>G	c.(745-747)ACT>AGT	p.T249S	RNF145_uc011ddy.1_Missense_Mutation_p.T263S|RNF145_uc003lxo.1_Missense_Mutation_p.T277S|RNF145_uc011ddz.1_Missense_Mutation_p.T266S|RNF145_uc010jiq.1_Missense_Mutation_p.T279S|RNF145_uc011dea.1_Missense_Mutation_p.T265S	NM_144726	NP_653327	Q96MT1	RN145_HUMAN	ring finger protein 145	249						integral to membrane	zinc ion binding			ovary(3)|lung(1)|skin(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
TTC1	7265	broad.mit.edu	37	5	159478178	159478178	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159478178G>T	uc003lxu.2	+	7	783	c.733G>T	c.(733-735)GAA>TAA	p.E245*		NM_003314	NP_003305	Q99614	TTC1_HUMAN	tetratricopeptide repeat domain 1	245					protein folding		unfolded protein binding			skin(1)	1	Renal(175;0.00196)	all_hematologic(541;0.00014)|Breast(839;0.0101)|all_neural(177;0.0281)|Medulloblastoma(196;0.0425)|Lung NSC(249;0.119)|all_lung(500;0.163)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	Epithelial(171;8.37e-05)|all cancers(165;0.000694)|OV - Ovarian serous cystadenocarcinoma(192;0.0402)														---	---	---	---
C5orf54	63920	broad.mit.edu	37	5	159821178	159821178	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159821178G>A	uc003lye.1	-	2	1784	c.1320C>T	c.(1318-1320)GGC>GGT	p.G440G	C5orf54_uc003lyf.1_Silent_p.G440G	NM_022090	NP_071373	Q8IZ13	CE054_HUMAN	transposon-derived Buster3 transposase-like	440										pancreas(1)	1																		---	---	---	---
GABRG2	2566	broad.mit.edu	37	5	161530936	161530936	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:161530936A>G	uc003lyz.3	+	6	1031	c.673A>G	c.(673-675)AGT>GGT	p.S225G	GABRG2_uc010jjc.2_Missense_Mutation_p.S265G|GABRG2_uc003lyy.3_Missense_Mutation_p.S225G|GABRG2_uc011dej.1_Missense_Mutation_p.S130G	NM_000816	NP_000807	P18507	GBRG2_HUMAN	gamma-aminobutyric acid A receptor, gamma 2	225	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity|protein binding			ovary(4)|skin(1)	5	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)														---	---	---	---
NUDCD2	134492	broad.mit.edu	37	5	162887044	162887044	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:162887044A>C	uc003lze.2	-	1	100	c.13T>G	c.(13-15)TTT>GTT	p.F5V	HMMR_uc003lzh.2_5'Flank|HMMR_uc003lzf.2_5'Flank|HMMR_uc003lzg.2_5'Flank|HMMR_uc011dem.1_5'Flank	NM_145266	NP_660309	Q8WVJ2	NUDC2_HUMAN	NudC domain containing 2	5						intracellular					0	Renal(175;0.000281)	Medulloblastoma(196;0.0207)|all_neural(177;0.0966)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0981)|OV - Ovarian serous cystadenocarcinoma(192;0.183)|Epithelial(171;0.247)														---	---	---	---
ODZ2	57451	broad.mit.edu	37	5	167674764	167674764	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167674764G>T	uc010jjd.2	+	27	6793	c.6793G>T	c.(6793-6795)GGG>TGG	p.G2265W	ODZ2_uc003lzr.3_Missense_Mutation_p.G2035W|ODZ2_uc003lzt.3_Missense_Mutation_p.G1638W|ODZ2_uc010jje.2_Missense_Mutation_p.G1529W	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)														---	---	---	---
WWC1	23286	broad.mit.edu	37	5	167887733	167887733	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:167887733G>A	uc003lzu.2	+	20	2995	c.2902G>A	c.(2902-2904)GTC>ATC	p.V968I	WWC1_uc003lzv.2_Missense_Mutation_p.V968I|WWC1_uc011den.1_Missense_Mutation_p.V968I|WWC1_uc003lzw.2_Missense_Mutation_p.V767I|WWC1_uc010jjf.1_Missense_Mutation_p.V240I	NM_015238	NP_056053	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1 isoform 3	968	Interaction with PRKCZ.|Interaction with histone H3.				cell migration|positive regulation of MAPKKK cascade|regulation of hippo signaling cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|perinuclear region of cytoplasm|ruffle membrane	protein binding|transcription coactivator activity			ovary(2)|skin(2)|breast(1)	5	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)														---	---	---	---
SLIT3	6586	broad.mit.edu	37	5	168149293	168149293	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168149293G>A	uc003mab.2	-	23	2871	c.2451C>T	c.(2449-2451)CAC>CAT	p.H817H	SLIT3_uc010jjg.2_Silent_p.H817H	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 precursor	817	LRR 19.				apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
SLIT3	6586	broad.mit.edu	37	5	168180906	168180906	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:168180906C>T	uc003mab.2	-	17	2212	c.1792G>A	c.(1792-1794)GGG>AGG	p.G598R	SLIT3_uc010jjg.2_Missense_Mutation_p.G598R	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 precursor	598	LRR 14.				apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
DOCK2	1794	broad.mit.edu	37	5	169446041	169446041	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169446041C>T	uc003maf.2	+	33	3390	c.3310C>T	c.(3310-3312)CGG>TGG	p.R1104W	DOCK2_uc011der.1_RNA|DOCK2_uc010jjm.2_Missense_Mutation_p.R596W	NM_004946	NP_004937	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1104	Interaction with CRKL.				actin cytoskeleton organization|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|endomembrane system|membrane	electron carrier activity|GTP binding|GTPase binding|heme binding|Rac guanyl-nucleotide exchange factor activity|T cell receptor binding			ovary(5)|pancreas(2)	7	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
GABRP	2568	broad.mit.edu	37	5	170222351	170222351	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170222351A>C	uc003mau.2	+	5	578	c.380A>C	c.(379-381)AAG>ACG	p.K127T	GABRP_uc011dev.1_Missense_Mutation_p.K127T	NM_014211	NP_055026	O00591	GBRP_HUMAN	gamma-aminobutyric acid (GABA) A receptor, pi	127	Extracellular (Potential).					cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			breast(1)	1	Renal(175;0.000159)|Lung NSC(126;0.0122)|all_lung(126;0.0193)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)															---	---	---	---
GABRP	2568	broad.mit.edu	37	5	170224460	170224460	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170224460T>C	uc003mau.2	+						GABRP_uc011dev.1_Intron	NM_014211	NP_055026			gamma-aminobutyric acid (GABA) A receptor, pi							cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			breast(1)	1	Renal(175;0.000159)|Lung NSC(126;0.0122)|all_lung(126;0.0193)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)															---	---	---	---
RPL26L1	51121	broad.mit.edu	37	5	172395513	172395513	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:172395513T>C	uc003mcc.2	+	3	262	c.220T>C	c.(220-222)TAC>CAC	p.Y74H		NM_016093	NP_057177	Q9UNX3	RL26L_HUMAN	ribosomal protein L26-like 1	74					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosol|large ribosomal subunit	structural constituent of ribosome				0	Renal(175;0.000159)|Lung NSC(126;0.00344)|all_lung(126;0.00594)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)															---	---	---	---
DRD1	1812	broad.mit.edu	37	5	174869940	174869940	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:174869940G>A	uc003mcz.2	-	2	1108	c.163C>T	c.(163-165)CGG>TGG	p.R55W		NM_000794	NP_000785	P21728	DRD1_HUMAN	dopamine receptor D1	55	Cytoplasmic (Potential).				activation of adenylate cyclase activity by dopamine receptor signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|adult walking behavior|cerebral cortex GABAergic interneuron migration|elevation of cytosolic calcium ion concentration involved in G-protein signaling coupled to IP3 second messenger|mating behavior|positive regulation of cAMP biosynthetic process|positive regulation of cell migration|positive regulation of potassium ion transport|positive regulation of release of sequestered calcium ion into cytosol|positive regulation of synaptic transmission, glutamatergic|prepulse inhibition|response to drug|synapse assembly|visual learning	endoplasmic reticulum membrane|membrane fraction	protein binding			ovary(2)|skin(1)	3	all_cancers(89;0.00895)|Renal(175;0.000159)|Lung NSC(126;0.00625)|all_lung(126;0.0104)	Medulloblastoma(196;0.0208)|all_neural(177;0.0277)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)		Acetophenazine(DB01063)|Amantadine(DB00915)|Apomorphine(DB00714)|Carphenazine(DB01038)|Chlorprothixene(DB01239)|Clozapine(DB00363)|Cocaine(DB00907)|Dopamine(DB00988)|Fenoldopam(DB00800)|Flupenthixol(DB00875)|Fluphenazine(DB00623)|Haloperidol(DB00502)|Levodopa(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methylergonovine(DB00353)|Minaprine(DB00805)|Olanzapine(DB00334)|Pegademase bovine(DB00061)|Pergolide(DB01186)|Perphenazine(DB00850)|Prochlorperazine(DB00433)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Thiethylperazine(DB00372)|Thioridazine(DB00679)|Triflupromazine(DB00508)|Zuclopenthixol(DB01624)													---	---	---	---
GPRIN1	114787	broad.mit.edu	37	5	176024054	176024054	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176024054C>T	uc003meo.1	-	2	2957	c.2782G>A	c.(2782-2784)GCC>ACC	p.A928T		NM_052899	NP_443131	Q7Z2K8	GRIN1_HUMAN	G protein-regulated inducer of neurite outgrowth	928	Interaction with GNAO1 (By similarity).					growth cone|plasma membrane				ovary(2)	2	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
GPRIN1	114787	broad.mit.edu	37	5	176026409	176026409	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176026409C>G	uc003meo.1	-	2	602	c.427G>C	c.(427-429)GAT>CAT	p.D143H		NM_052899	NP_443131	Q7Z2K8	GRIN1_HUMAN	G protein-regulated inducer of neurite outgrowth	143						growth cone|plasma membrane				ovary(2)	2	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
GPRIN1	114787	broad.mit.edu	37	5	176026452	176026452	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176026452C>T	uc003meo.1	-	2	559	c.384G>A	c.(382-384)AAG>AAA	p.K128K		NM_052899	NP_443131	Q7Z2K8	GRIN1_HUMAN	G protein-regulated inducer of neurite outgrowth	128						growth cone|plasma membrane				ovary(2)	2	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
UIMC1	51720	broad.mit.edu	37	5	176395824	176395824	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176395824T>C	uc011dfp.1	-	6	1099	c.932A>G	c.(931-933)CAG>CGG	p.Q311R	UIMC1_uc003mfc.1_Missense_Mutation_p.Q188R|UIMC1_uc003mfd.1_Intron|UIMC1_uc003mfg.1_Intron|UIMC1_uc003mff.1_Intron	NM_016290	NP_057374	Q96RL1	UIMC1_HUMAN	ubiquitin interaction motif containing 1	311	AIR.				double-strand break repair|G2/M transition DNA damage checkpoint|histone H2A K63-linked deubiquitination|negative regulation of transcription, DNA-dependent|positive regulation of DNA repair|response to ionizing radiation|transcription, DNA-dependent	BRCA1-A complex	histone binding|K63-linked polyubiquitin binding			ovary(3)|skin(1)	4	all_cancers(89;7.96e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	Medulloblastoma(196;0.0145)|all_neural(177;0.0325)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
NSD1	64324	broad.mit.edu	37	5	176666747	176666747	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176666747T>C	uc003mfr.3	+						NSD1_uc003mft.3_Intron|NSD1_uc003mfs.1_Intron|NSD1_uc011dfx.1_Intron	NM_022455	NP_071900			nuclear receptor binding SET domain protein 1						negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding			ovary(2)|kidney(1)	3	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)				T	NUP98	AML		Sotos Syndrome		Beckwith-Wiedemann_syndrome|Sotos_syndrome|Weaver_syndrome	HNSCC(47;0.14)			---	---	---	---
NSD1	64324	broad.mit.edu	37	5	176671246	176671246	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176671246A>G	uc003mfr.3	+	9	4491	c.4353A>G	c.(4351-4353)ACA>ACG	p.T1451T	NSD1_uc003mft.3_Silent_p.T1182T|NSD1_uc003mfs.1_Silent_p.T1348T|NSD1_uc011dfx.1_Silent_p.T1099T	NM_022455	NP_071900	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	1451					negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding			ovary(2)|kidney(1)	3	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)				T	NUP98	AML		Sotos Syndrome		Beckwith-Wiedemann_syndrome|Sotos_syndrome|Weaver_syndrome	HNSCC(47;0.14)			---	---	---	---
NSD1	64324	broad.mit.edu	37	5	176718977	176718977	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:176718977A>G	uc003mfr.3	+	22	6419	c.6281A>G	c.(6280-6282)GAA>GGA	p.E2094G	NSD1_uc003mft.3_Missense_Mutation_p.E1825G|NSD1_uc011dfx.1_Missense_Mutation_p.E1742G	NM_022455	NP_071900	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	2094					negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding			ovary(2)|kidney(1)	3	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)				T	NUP98	AML		Sotos Syndrome		Beckwith-Wiedemann_syndrome|Sotos_syndrome|Weaver_syndrome	HNSCC(47;0.14)			---	---	---	---
N4BP3	23138	broad.mit.edu	37	5	177547629	177547629	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177547629G>A	uc003mik.1	+	3	1028	c.781G>A	c.(781-783)GTG>ATG	p.V261M	N4BP3_uc003mil.1_5'Flank	NM_015111	NP_055926	O15049	N4BP3_HUMAN	Nedd4 binding protein 3	261						cytoplasmic vesicle membrane					0	all_cancers(89;0.00294)|Renal(175;0.000269)|Lung NSC(126;0.00858)|all_lung(126;0.0139)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
COL23A1	91522	broad.mit.edu	37	5	177683360	177683360	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177683360C>T	uc003mje.2	-	15	1234	c.876G>A	c.(874-876)GGG>GGA	p.G292G	COL23A1_uc010jkt.2_Missense_Mutation_p.G140D	NM_173465	NP_775736	Q86Y22	CONA1_HUMAN	collagen, type XXIII, alpha 1	292	Extracellular (Potential).|Collagen-like 2.|Gly-rich.					collagen|integral to membrane|plasma membrane	protein binding			central_nervous_system(1)|skin(1)	2	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)														---	---	---	---
ZNF454	285676	broad.mit.edu	37	5	178391897	178391897	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178391897C>T	uc003mjo.1	+	5	763	c.492C>T	c.(490-492)CAC>CAT	p.H164H	ZNF454_uc010jkz.1_Silent_p.H164H	NM_182594	NP_872400	Q8N9F8	ZN454_HUMAN	zinc finger protein 454	164					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|lung(1)	3	all_cancers(89;0.000904)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.225)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.234)														---	---	---	---
ADAMTS2	9509	broad.mit.edu	37	5	178556994	178556994	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178556994T>A	uc003mjw.2	-	16	2396	c.2396A>T	c.(2395-2397)GAC>GTC	p.D799V		NM_014244	NP_055059	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1	799	Spacer.				collagen catabolic process	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)														---	---	---	---
RUFY1	80230	broad.mit.edu	37	5	179025833	179025833	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179025833C>T	uc003mka.1	+						RUFY1_uc003mkb.1_Intron|RUFY1_uc003mkc.1_Intron|RUFY1_uc003mkd.1_Intron	NM_025158	NP_079434			RUN and FYVE domain-containing 1 isoform a						endocytosis|protein transport	early endosome membrane	lipid binding|zinc ion binding			ovary(4)|breast(1)	5	all_cancers(89;0.00018)|all_epithelial(37;8.37e-05)|Renal(175;0.000159)|Lung NSC(126;0.00108)|all_lung(126;0.00195)	all_cancers(40;0.0322)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)												HNSCC(44;0.11)			---	---	---	---
CANX	821	broad.mit.edu	37	5	179150666	179150666	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179150666C>T	uc003mkk.2	+	12	1581	c.1404C>T	c.(1402-1404)GGC>GGT	p.G468G	CANX_uc011dgp.1_Silent_p.G503G|CANX_uc003mkl.2_Silent_p.G468G|CANX_uc011dgq.1_Silent_p.G360G	NM_001746	NP_001737	P27824	CALX_HUMAN	calnexin precursor	468	Lumenal (Potential).				post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|protein secretion	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane|melanosome	calcium ion binding|sugar binding|unfolded protein binding				0	all_cancers(89;0.000129)|all_epithelial(37;5.59e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0413)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
TBC1D9B	23061	broad.mit.edu	37	5	179290939	179290939	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179290939C>A	uc003mlh.2	-	22	3299	c.3262G>T	c.(3262-3264)GCA>TCA	p.A1088S	TBC1D9B_uc003mli.2_Missense_Mutation_p.A1071S|TBC1D9B_uc003mlj.2_Missense_Mutation_p.A1070S|TBC1D9B_uc003mlf.2_Missense_Mutation_p.A162S|TBC1D9B_uc003mlg.2_Missense_Mutation_p.A247S|TBC1D9B_uc011dgv.1_Missense_Mutation_p.A247S	NM_198868	NP_942568	Q66K14	TBC9B_HUMAN	TBC1 domain family, member 9B (with GRAM domain)	1088						integral to membrane|intracellular	calcium ion binding|Rab GTPase activator activity			breast(1)|skin(1)	2	all_cancers(89;0.000197)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0236)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
TBC1D9B	23061	broad.mit.edu	37	5	179305415	179305415	+	Missense_Mutation	SNP	C	T	T	rs140686469		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179305415C>T	uc003mlh.2	-	10	1713	c.1676G>A	c.(1675-1677)CGC>CAC	p.R559H	TBC1D9B_uc003mli.2_Missense_Mutation_p.R559H|TBC1D9B_uc003mlj.2_Missense_Mutation_p.R559H	NM_198868	NP_942568	Q66K14	TBC9B_HUMAN	TBC1 domain family, member 9B (with GRAM domain)	559	Rab-GAP TBC.					integral to membrane|intracellular	calcium ion binding|Rab GTPase activator activity			breast(1)|skin(1)	2	all_cancers(89;0.000197)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0236)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)															---	---	---	---
CNOT6	57472	broad.mit.edu	37	5	179996176	179996176	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179996176A>G	uc003mlx.2	+	10	1443	c.1094A>G	c.(1093-1095)GAC>GGC	p.D365G	CNOT6_uc010jld.2_Missense_Mutation_p.D365G|CNOT6_uc010jle.2_Missense_Mutation_p.D360G	NM_015455	NP_056270	Q9ULM6	CNOT6_HUMAN	CCR4-NOT transcription complex, subunit 6	365					nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	exonuclease activity|metal ion binding|protein binding|RNA binding				0	all_cancers(89;3.3e-05)|all_epithelial(37;7.38e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00543)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.023)														---	---	---	---
BTNL3	10917	broad.mit.edu	37	5	180432613	180432613	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180432613G>T	uc003mmr.2	+	8	1270	c.1142G>T	c.(1141-1143)AGA>ATA	p.R381I	BTNL3_uc010jlp.2_Missense_Mutation_p.R166I	NM_197975	NP_932079	Q6UXE8	BTNL3_HUMAN	butyrophilin-like 3 precursor	381	B30.2/SPRY.|Cytoplasmic (Potential).				lipid metabolic process	integral to membrane					0	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.00336)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)|all_lung(500;0.248)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000272)															---	---	---	---
TRIM7	81786	broad.mit.edu	37	5	180622431	180622431	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180622431G>A	uc003mmz.1	-	7	1338	c.1271C>T	c.(1270-1272)ACG>ATG	p.T424M	TRIM7_uc003mmv.1_Missense_Mutation_p.T242M|TRIM7_uc003mmw.1_Missense_Mutation_p.T216M|TRIM7_uc003mmx.1_Missense_Mutation_p.T216M|TRIM7_uc003mmy.1_Missense_Mutation_p.T216M	NM_203293	NP_976038	Q9C029	TRIM7_HUMAN	tripartite motif-containing 7 isoform 1	424	B30.2/SPRY.					cytoplasm|nucleus	zinc ion binding			ovary(2)|skin(1)	3	all_cancers(89;6.03e-06)|all_epithelial(37;7.1e-07)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0684)	all_cancers(40;0.000172)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;2e-06)|Epithelial(171;1.35e-05)|OV - Ovarian serous cystadenocarcinoma(192;0.000128)|Kidney(146;0.0674)|GBM - Glioblastoma multiforme(465;0.0802)														---	---	---	---
TRIM7	81786	broad.mit.edu	37	5	180630503	180630503	+	Intron	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:180630503C>A	uc003mmz.1	-						TRIM7_uc003mmv.1_5'Flank|TRIM7_uc003mmw.1_Translation_Start_Site|TRIM7_uc003mmx.1_Intron|TRIM7_uc003mmy.1_Intron|TRIM7_uc003mna.2_Missense_Mutation_p.E220D	NM_203293	NP_976038			tripartite motif-containing 7 isoform 1							cytoplasm|nucleus	zinc ion binding			ovary(2)|skin(1)	3	all_cancers(89;6.03e-06)|all_epithelial(37;7.1e-07)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0684)	all_cancers(40;0.000172)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;2e-06)|Epithelial(171;1.35e-05)|OV - Ovarian serous cystadenocarcinoma(192;0.000128)|Kidney(146;0.0674)|GBM - Glioblastoma multiforme(465;0.0802)														---	---	---	---
GMDS	2762	broad.mit.edu	37	6	1726663	1726663	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:1726663C>T	uc003mtq.2	-	9	1164	c.974G>A	c.(973-975)CGG>CAG	p.R325Q		NM_001500	NP_001491	O60547	GMDS_HUMAN	GDP-mannose 4,6-dehydratase	325					'de novo' GDP-L-fucose biosynthetic process|GDP-mannose metabolic process|leukocyte cell-cell adhesion		coenzyme binding|GDP-mannose 4,6-dehydratase activity			central_nervous_system(1)	1	Ovarian(93;0.0733)	all_cancers(2;7.64e-19)|all_epithelial(2;3.05e-16)|Colorectal(2;0.00414)|all_hematologic(90;0.00997)|all_lung(73;0.0141)|Lung NSC(90;0.0802)		Epithelial(2;7.61e-06)|all cancers(2;0.000111)|STAD - Stomach adenocarcinoma(2;0.000231)|Colorectal(2;0.00445)|COAD - Colon adenocarcinoma(2;0.0125)|OV - Ovarian serous cystadenocarcinoma(45;0.0563)														---	---	---	---
WRNIP1	56897	broad.mit.edu	37	6	2785445	2785445	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:2785445G>A	uc003mtz.2	+	7	2118	c.1927G>A	c.(1927-1929)GAG>AAG	p.E643K	WRNIP1_uc003mua.2_Missense_Mutation_p.E618K	NM_020135	NP_064520	Q96S55	WRIP1_HUMAN	Werner helicase interacting protein isoform 1	643					DNA replication|DNA synthesis involved in DNA repair|regulation of DNA-dependent DNA replication initiation	mitochondrion|nucleus|perinuclear region of cytoplasm	ATP binding|ATPase activity|DNA binding|metal ion binding|protein binding			ovary(1)|pancreas(1)	2	Ovarian(93;0.0412)	all_hematologic(90;0.0895)																---	---	---	---
NQO2	4835	broad.mit.edu	37	6	3017170	3017170	+	Missense_Mutation	SNP	C	T	T	rs143152254		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:3017170C>T	uc003mus.2	+	6	808	c.470C>T	c.(469-471)ACG>ATG	p.T157M	NQO2_uc003mut.2_Missense_Mutation_p.T157M	NM_000904	NP_000895	P16083	NQO2_HUMAN	NAD(P)H dehydrogenase, quinone 2	157						cytoplasm|nucleus	coenzyme binding|dihydronicotinamide riboside quinone reductase activity|electron carrier activity|metal ion binding|NADPH dehydrogenase (quinone) activity			ovary(1)	1	Ovarian(93;0.0412)	all_hematologic(90;0.0895)			Menadione(DB00170)|NADH(DB00157)													---	---	---	---
RPP40	10799	broad.mit.edu	37	6	5000832	5000832	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:5000832A>G	uc003mwl.2	-	3	337	c.302T>C	c.(301-303)ATT>ACT	p.I101T	RPP40_uc003mwm.2_Intron	NM_006638	NP_006629	O75818	RPP40_HUMAN	ribonuclease P 40kDa subunit	101					tRNA processing	nucleolar ribonuclease P complex	protein binding|ribonuclease P activity				0	Ovarian(93;0.11)	all_hematologic(90;0.0895)																---	---	---	---
F13A1	2162	broad.mit.edu	37	6	6145980	6145980	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6145980G>A	uc003mwv.2	-	15	2194	c.2071C>T	c.(2071-2073)CAG>TAG	p.Q691*	F13A1_uc011dib.1_Intron	NM_000129	NP_000120	P00488	F13A_HUMAN	coagulation factor XIII A1 subunit precursor	691					peptide cross-linking|platelet activation|platelet degranulation	extracellular region|platelet alpha granule lumen	acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|pancreas(1)|skin(1)	6	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)													---	---	---	---
F13A1	2162	broad.mit.edu	37	6	6196073	6196073	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:6196073C>T	uc003mwv.2	-	10	1385	c.1262G>A	c.(1261-1263)GGC>GAC	p.G421D	F13A1_uc011dib.1_Missense_Mutation_p.G358D	NM_000129	NP_000120	P00488	F13A_HUMAN	coagulation factor XIII A1 subunit precursor	421					peptide cross-linking|platelet activation|platelet degranulation	extracellular region|platelet alpha granule lumen	acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|pancreas(1)|skin(1)	6	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)													---	---	---	---
DSP	1832	broad.mit.edu	37	6	7580628	7580628	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7580628A>T	uc003mxp.1	+	23	4484	c.4205A>T	c.(4204-4206)AAC>ATC	p.N1402I	DSP_uc003mxq.1_Intron	NM_004415	NP_004406	P15924	DESP_HUMAN	desmoplakin isoform I	1402	Central fibrous rod domain.|Potential.				cellular component disassembly involved in apoptosis|keratinocyte differentiation|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural constituent of cytoskeleton			central_nervous_system(6)|ovary(2)|skin(1)	9	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)														---	---	---	---
SNRNP48	154007	broad.mit.edu	37	6	7609066	7609066	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7609066A>G	uc003mxr.2	+	9	1039	c.980A>G	c.(979-981)GAA>GGA	p.E327G	SNRNP48_uc003mxs.2_RNA	NM_152551	NP_689764	Q6IEG0	SNR48_HUMAN	U11/U12 snRNP 48K	327	Arg-rich.				mRNA processing	cytoplasm|U12-type spliceosomal complex	metal ion binding				0																		---	---	---	---
GCNT2	2651	broad.mit.edu	37	6	10529437	10529437	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10529437C>T	uc010joo.2	+	3	844	c.293C>T	c.(292-294)GCT>GTT	p.A98V	GCNT2_uc010jol.2_Intron|GCNT2_uc010jom.2_Intron|GCNT2_uc010jop.2_Intron|GCNT2_uc003mza.2_Intron|GCNT2_uc003mzc.3_Missense_Mutation_p.A97V|GCNT2_uc010jon.2_Missense_Mutation_p.A97V	NM_145649	NP_663624	Q8N0V5	GNT2A_HUMAN	glucosaminyl (N-acetyl) transferase 2,	98	Lumenal (Potential).					Golgi membrane|integral to membrane	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity			ovary(2)	2	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)														---	---	---	---
MAK	4117	broad.mit.edu	37	6	10770351	10770351	+	Silent	SNP	C	A	A	rs143121053	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10770351C>A	uc003mzl.2	-	12	1939	c.1710G>T	c.(1708-1710)ACG>ACT	p.T570T	SYCP2L_uc011dim.1_Intron|TMEM14B_uc010jos.1_RNA|MAK_uc010jot.2_RNA|MAK_uc010jou.2_RNA|MAK_uc003mzm.2_Silent_p.T570T	NM_005906	NP_005897	P20794	MAK_HUMAN	male germ cell-associated kinase	570					cell differentiation|multicellular organismal development|spermatogenesis		ATP binding|cyclin-dependent protein kinase activity			breast(2)|skin(1)	3	Breast(50;0.107)|Ovarian(93;0.107)	all_hematologic(90;0.117)																---	---	---	---
MAK	4117	broad.mit.edu	37	6	10796265	10796265	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10796265G>A	uc003mzl.2	-	8	1338	c.1109C>T	c.(1108-1110)ACG>ATG	p.T370M	SYCP2L_uc011dim.1_Intron|TMEM14B_uc010jos.1_Intron|MAK_uc010jot.2_RNA|MAK_uc010jou.2_RNA|MAK_uc003mzm.2_Missense_Mutation_p.T370M|MAK_uc010jov.1_RNA	NM_005906	NP_005897	P20794	MAK_HUMAN	male germ cell-associated kinase	370					cell differentiation|multicellular organismal development|spermatogenesis		ATP binding|cyclin-dependent protein kinase activity			breast(2)|skin(1)	3	Breast(50;0.107)|Ovarian(93;0.107)	all_hematologic(90;0.117)																---	---	---	---
NEDD9	4739	broad.mit.edu	37	6	11191424	11191424	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:11191424C>T	uc003mzv.2	-	5	845	c.678G>A	c.(676-678)CCG>CCA	p.P226P	NEDD9_uc010joz.2_Silent_p.P226P|NEDD9_uc003mzw.3_Silent_p.P80P	NM_006403	NP_006394	Q14511	CASL_HUMAN	neural precursor cell expressed, developmentally	226	Interacts strongly with spindle- regulatory protein D1M1.				actin filament bundle assembly|cell adhesion|cell division|integrin-mediated signaling pathway|mitosis|regulation of growth	cell cortex|focal adhesion|Golgi apparatus|lamellipodium|nucleus	protein binding				0	Breast(50;0.0768)|Ovarian(93;0.152)	all_hematologic(90;0.135)	Epithelial(50;0.0647)|all cancers(50;0.179)															---	---	---	---
HIVEP1	3096	broad.mit.edu	37	6	12121629	12121629	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12121629C>T	uc003nac.2	+	4	1780	c.1601C>T	c.(1600-1602)ACT>ATT	p.T534I	HIVEP1_uc011diq.1_RNA	NM_002114	NP_002105	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer	534					transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)																---	---	---	---
HIVEP1	3096	broad.mit.edu	37	6	12122234	12122234	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12122234C>T	uc003nac.2	+	4	2385	c.2206C>T	c.(2206-2208)CGC>TGC	p.R736C	HIVEP1_uc011diq.1_RNA	NM_002114	NP_002105	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer	736					transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)																---	---	---	---
HIVEP1	3096	broad.mit.edu	37	6	12130059	12130059	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:12130059G>A	uc003nac.2	+	5	6322	c.6143G>A	c.(6142-6144)AGT>AAT	p.S2048N	HIVEP1_uc011diq.1_Intron	NM_002114	NP_002105	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer	2048					transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)																---	---	---	---
PHACTR1	221692	broad.mit.edu	37	6	13053754	13053754	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:13053754G>A	uc010jpc.2	+	5	740	c.408G>A	c.(406-408)ACG>ACA	p.T136T	PHACTR1_uc011dir.1_Silent_p.T136T|PHACTR1_uc003nag.1_Silent_p.T136T|PHACTR1_uc003nah.1_Silent_p.T136T	NM_030948	NP_112210	Q9C0D0	PHAR1_HUMAN	phosphatase and actin regulator 1	136						cell junction|cytoplasm|synapse	actin binding|protein phosphatase inhibitor activity				0	Breast(50;0.0427)|Ovarian(93;0.12)	all_hematologic(90;0.122)|Lung SC(78;0.195)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239)															---	---	---	---
JARID2	3720	broad.mit.edu	37	6	15496616	15496616	+	Missense_Mutation	SNP	G	A	A	rs146276296	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15496616G>A	uc003nbj.2	+	7	1404	c.1160G>A	c.(1159-1161)CGC>CAC	p.R387H	JARID2_uc011diu.1_Missense_Mutation_p.R251H|JARID2_uc011div.1_Missense_Mutation_p.R215H|JARID2_uc011diw.1_Missense_Mutation_p.R349H	NM_004973	NP_004964	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2 protein	387					central nervous system development|chromatin modification|negative regulation of histone methylation|positive regulation of histone H3-K9 methylation|stem cell differentiation|transcription, DNA-dependent		chromatin binding			ovary(2)|lung(1)|pancreas(1)	4	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)																---	---	---	---
JARID2	3720	broad.mit.edu	37	6	15501190	15501190	+	Silent	SNP	C	T	T	rs139580359		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:15501190C>T	uc003nbj.2	+	8	2242	c.1998C>T	c.(1996-1998)GGC>GGT	p.G666G	JARID2_uc011div.1_Silent_p.G494G|JARID2_uc011diw.1_Silent_p.G628G	NM_004973	NP_004964	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2 protein	666	ARID.				central nervous system development|chromatin modification|negative regulation of histone methylation|positive regulation of histone H3-K9 methylation|stem cell differentiation|transcription, DNA-dependent		chromatin binding			ovary(2)|lung(1)|pancreas(1)	4	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)																---	---	---	---
RBM24	221662	broad.mit.edu	37	6	17292274	17292274	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17292274C>T	uc003nbz.3	+	4	639	c.635C>T	c.(634-636)GCC>GTC	p.A212V	RBM24_uc003nby.3_3'UTR|RBM24_uc011dix.1_Missense_Mutation_p.A154V|RBM24_uc003nca.2_Missense_Mutation_p.A167V|RBM24_uc011diy.1_Missense_Mutation_p.P126S|RBM24_uc011diz.1_Missense_Mutation_p.P111S	NM_001143942	NP_001137414	Q9BX46	RBM24_HUMAN	RNA binding motif protein 24 isoform 1	212	Ala-rich.				cell differentiation|regulation of mRNA stability|regulation of myotube differentiation	cytoplasm|nucleus	mRNA 3'-UTR binding|nucleotide binding			ovary(1)|skin(1)	2	Breast(50;0.0615)|Ovarian(93;0.0733)	all_hematologic(90;0.062)	all cancers(50;0.131)|Epithelial(50;0.15)															---	---	---	---
KIF13A	63971	broad.mit.edu	37	6	17834197	17834197	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17834197C>T	uc003ncg.3	-	12	1366	c.1261G>A	c.(1261-1263)GCA>ACA	p.A421T	KIF13A_uc003ncf.2_Missense_Mutation_p.A421T|KIF13A_uc003nch.3_Missense_Mutation_p.A421T|KIF13A_uc003nci.3_Missense_Mutation_p.A421T|KIF13A_uc003ncj.2_Missense_Mutation_p.A97T	NM_022113	NP_071396	Q9H1H9	KI13A_HUMAN	kinesin family member 13A isoform a	421	Potential.				cargo loading into vesicle|cell cycle|cytokinesis|endosome to lysosome transport|Golgi to plasma membrane protein transport|melanosome organization|plus-end-directed vesicle transport along microtubule	centrosome|endosome membrane|microtubule|midbody|trans-Golgi network membrane	ATP binding|microtubule motor activity|protein binding			large_intestine(2)|ovary(2)	4	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)															---	---	---	---
HDGFL1	154150	broad.mit.edu	37	6	22569943	22569943	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:22569943G>A	uc003nds.2	+	1	266	c.139G>A	c.(139-141)GAG>AAG	p.E47K		NM_138574	NP_612641	Q5TGJ6	HDGL1_HUMAN	hepatoma derived growth factor-like 1	47	PWWP.										0	Ovarian(93;0.163)																	---	---	---	---
DCDC2	51473	broad.mit.edu	37	6	24178828	24178828	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24178828A>G	uc003ndx.2	-	9	1358	c.1056T>C	c.(1054-1056)GAT>GAC	p.D352D	DCDC2_uc003ndy.2_Silent_p.D352D|DCDC2_uc003ndw.2_Silent_p.D103D	NM_016356	NP_057440	Q9UHG0	DCDC2_HUMAN	doublecortin domain containing 2	352					cellular defense response|intracellular signal transduction|neuron migration					ovary(1)	1		Ovarian(999;0.101)																---	---	---	---
ALDH5A1	7915	broad.mit.edu	37	6	24503660	24503660	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24503660C>T	uc003neg.2	+	3	636	c.608C>T	c.(607-609)CCG>CTG	p.P203L	ALDH5A1_uc003nef.2_Missense_Mutation_p.P203L	NM_001080	NP_001071	P51649	SSDH_HUMAN	aldehyde dehydrogenase 5A1 isoform 2 precursor	203					acetate metabolic process|central nervous system development|galactosylceramide metabolic process|gamma-aminobutyric acid catabolic process|glucose metabolic process|glutamate metabolic process|glutamine metabolic process|glutathione metabolic process|glycerophospholipid metabolic process|neurotransmitter catabolic process|neurotransmitter secretion|protein homotetramerization|respiratory electron transport chain|short-chain fatty acid metabolic process|succinate metabolic process	mitochondrial matrix|soluble fraction	succinate-semialdehyde dehydrogenase activity				0					Chlormerodrin(DB00534)|NADH(DB00157)|Succinic acid(DB00139)													---	---	---	---
LRRC16A	55604	broad.mit.edu	37	6	25452380	25452380	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25452380G>A	uc011djw.1	+						LRRC16A_uc010jpx.2_Intron|LRRC16A_uc010jpy.2_Intron|LRRC16A_uc003nez.1_Intron	NM_017640	NP_060110			leucine rich repeat containing 16A						actin filament organization|blood coagulation|cell migration|lamellipodium assembly|ruffle organization|urate metabolic process	cytosol|lamellipodium|nucleus				ovary(1)|breast(1)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
HIST1H2BA	255626	broad.mit.edu	37	6	25727239	25727239	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:25727239C>T	uc003nfd.2	+	1	103	c.103C>T	c.(103-105)CGT>TGT	p.R35C	HIST1H2AA_uc003nfc.2_5'Flank	NM_170610	NP_733759	Q96A08	H2B1A_HUMAN	histone cluster 1, H2ba	35					nucleosome assembly	nucleosome|nucleus	DNA binding			kidney(1)	1																		---	---	---	---
HIST1H4B	8366	broad.mit.edu	37	6	26027216	26027216	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26027216A>G	uc003nfr.2	-	1	265	c.265T>C	c.(265-267)TAC>CAC	p.Y89H		NM_003544	NP_003535	P62805	H4_HUMAN	histone cluster 1, H4b	89					CenH3-containing nucleosome assembly at centromere|negative regulation of megakaryocyte differentiation|phosphatidylinositol-mediated signaling|telomere maintenance	nucleoplasm|nucleosome	DNA binding|protein binding			ovary(2)	2																OREG0017238	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
HIST1H3B	8358	broad.mit.edu	37	6	26032152	26032152	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26032152G>A	uc003nfs.1	-	1	137	c.137C>T	c.(136-138)ACT>ATT	p.T46I		NM_003537	NP_003528	P68431	H31_HUMAN	histone cluster 1, H3b	46					blood coagulation|nucleosome assembly|regulation of gene silencing|S phase	nucleoplasm|nucleosome	DNA binding|protein binding			ovary(2)	2																		---	---	---	---
HFE	3077	broad.mit.edu	37	6	26092945	26092945	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26092945A>G	uc003nfx.1	+	4	809	c.649A>G	c.(649-651)ACC>GCC	p.T217A	HFE_uc003nfy.1_Missense_Mutation_p.T194A|HFE_uc010jqe.1_Intron|HFE_uc003nfz.1_Missense_Mutation_p.T129A|HFE_uc003ngd.1_Intron|HFE_uc003nga.1_Intron|HFE_uc003ngb.1_Intron|HFE_uc003ngc.1_Missense_Mutation_p.T125A|HFE_uc003nge.1_Missense_Mutation_p.T37A|HFE_uc003ngf.1_Intron	NM_000410	NP_000401	Q30201	HFE_HUMAN	hemochromatosis protein isoform 1 precursor	217	Alpha-3.|Ig-like C1-type.|Extracellular (Potential).				antigen processing and presentation of peptide antigen via MHC class I|cellular iron ion homeostasis|immune response|iron ion transport|protein complex assembly|receptor-mediated endocytosis	apical part of cell|basal part of cell|cytoplasmic vesicle|early endosome|integral to plasma membrane|MHC class I protein complex|perinuclear region of cytoplasm|recycling endosome	protein binding				0														Hemochromatosis				---	---	---	---
BTN2A3	54718	broad.mit.edu	37	6	26426513	26426513	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26426513C>T	uc011dkl.1	+	3	498	c.468C>T	c.(466-468)GAC>GAT	p.D156D	BTN2A3_uc011dkm.1_RNA					RecName: Full=Butyrophilin subfamily 2 member A3; Flags: Precursor;												0																		---	---	---	---
BTN2A3	54718	broad.mit.edu	37	6	26431522	26431522	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26431522T>C	uc011dkl.1	+	6	1470	c.1440T>C	c.(1438-1440)CCT>CCC	p.P480P	BTN2A3_uc011dkm.1_RNA					RecName: Full=Butyrophilin subfamily 2 member A3; Flags: Precursor;												0																		---	---	---	---
BTN1A1	696	broad.mit.edu	37	6	26508868	26508868	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26508868C>T	uc003nif.3	+	7	1067	c.1047C>T	c.(1045-1047)GGC>GGT	p.G349G		NM_001732	NP_001723	Q13410	BT1A1_HUMAN	butyrophilin, subfamily 1, member A1 precursor	349	B30.2/SPRY.|Cytoplasmic (Potential).					extracellular region|integral to plasma membrane	receptor activity			ovary(1)|skin(1)	2																		---	---	---	---
ZNF391	346157	broad.mit.edu	37	6	27368871	27368871	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27368871G>A	uc003njf.1	+	3	1240	c.722G>A	c.(721-723)CGA>CAA	p.R241Q		NM_001076781	NP_001070249	Q9UJN7	ZN391_HUMAN	zinc finger protein 391	241	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(2)|skin(1)	3																		---	---	---	---
HIST1H1B	3009	broad.mit.edu	37	6	27835274	27835274	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:27835274G>T	uc003njx.2	-	1	86	c.34C>A	c.(34-36)CCA>ACA	p.P12T		NM_005322	NP_005313	P16401	H15_HUMAN	histone cluster 1, H1b	12					nucleosome assembly	nucleosome|nucleus	DNA binding			large_intestine(2)|lung(1)	3																		---	---	---	---
ZSCAN16	80345	broad.mit.edu	37	6	28093563	28093563	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28093563G>A	uc003nkm.2	+	2	442	c.342G>A	c.(340-342)ACG>ACA	p.T114T	uc010jqw.1_Intron|uc003nkk.1_RNA|uc003nkl.1_Intron|ZSCAN16_uc011dky.1_Silent_p.T114T	NM_025231	NP_079507	Q9H4T2	ZSC16_HUMAN	zinc finger and SCAN domain containing 16	114	SCAN box.				viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			large_intestine(1)	1																		---	---	---	---
PGBD1	84547	broad.mit.edu	37	6	28251814	28251814	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28251814C>T	uc003nky.2	+	2	594	c.224C>T	c.(223-225)CCG>CTG	p.P75L	PGBD1_uc003nkz.2_Missense_Mutation_p.P75L	NM_032507	NP_115896	Q96JS3	PGBD1_HUMAN	piggyBac transposable element derived 1	75	SCAN box.				viral reproduction	membrane|nucleus	scavenger receptor activity|sequence-specific DNA binding transcription factor activity			ovary(4)	4																		---	---	---	---
ZNF323	64288	broad.mit.edu	37	6	28294247	28294247	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:28294247G>A	uc003nla.2	-	4	1317	c.917C>T	c.(916-918)GCC>GTC	p.A306V	ZNF323_uc003nld.2_Missense_Mutation_p.A306V|ZNF323_uc010jra.2_Missense_Mutation_p.A306V|ZNF323_uc003nlb.2_Missense_Mutation_p.A147V|ZNF323_uc010jrb.2_Missense_Mutation_p.A147V|ZNF323_uc003nlc.2_Missense_Mutation_p.A306V	NM_001135216	NP_001128688	Q96LW9	ZN323_HUMAN	zinc finger protein 323	306	C2H2-type 3.				viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
OR10C1	442194	broad.mit.edu	37	6	29408552	29408552	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29408552G>A	uc011dlp.1	+	1	760	c.760G>A	c.(760-762)GCA>ACA	p.A254T	OR11A1_uc010jrh.1_Intron	NM_013941	NP_039229	Q96KK4	O10C1_HUMAN	olfactory receptor, family 10, subfamily C,	254	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0																		---	---	---	---
GABBR1	2550	broad.mit.edu	37	6	29588987	29588987	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29588987T>G	uc003nmt.3	-	11	1550	c.1214A>C	c.(1213-1215)GAC>GCC	p.D405A	GABBR1_uc003nmp.3_Missense_Mutation_p.D288A|GABBR1_uc003nms.3_Missense_Mutation_p.D288A|GABBR1_uc003nmu.3_Missense_Mutation_p.D343A|GABBR1_uc011dlr.1_Missense_Mutation_p.D228A|GABBR1_uc011dls.1_Missense_Mutation_p.D405A	NM_001470	NP_001461	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor 1	405	Extracellular (Potential).				gamma-aminobutyric acid signaling pathway|negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|extracellular region|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(5)|liver(1)|skin(1)	7					Baclofen(DB00181)|Progabide(DB00837)													---	---	---	---
ZFP57	346171	broad.mit.edu	37	6	29640422	29640422	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29640422A>T	uc011dlw.1	-	4	1617	c.1466T>A	c.(1465-1467)GTC>GAC	p.V489D	ZFP57_uc003nnl.3_Missense_Mutation_p.V469D	NM_001109809	NP_001103279	Q9NU63	ZFP57_HUMAN	zinc finger protein 57 homolog	405					DNA methylation involved in embryo development|regulation of gene expression by genetic imprinting|transcription, DNA-dependent		DNA binding|zinc ion binding			ovary(3)|skin(2)	5																		---	---	---	---
HLA-E	3133	broad.mit.edu	37	6	30457316	30457316	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30457316A>T	uc003nqg.2	+	1	46	c.8A>T	c.(7-9)GAT>GTT	p.D3V	HLA-E_uc011dmg.1_RNA|HLA-E_uc011dmh.1_Missense_Mutation_p.M1L	NM_005516	NP_005507	P13747	HLAE_HUMAN	major histocompatibility complex, class I, E	3					antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex	MHC class I receptor activity			central_nervous_system(4)|ovary(1)	5																		---	---	---	---
GNL1	2794	broad.mit.edu	37	6	30514906	30514906	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30514906G>A	uc003nqh.2	-	10	2452	c.1424C>T	c.(1423-1425)GCC>GTC	p.A475V	GNL1_uc011dmi.1_Missense_Mutation_p.A272V|GNL1_uc011dmj.1_Missense_Mutation_p.A473V|GNL1_uc011dmk.1_Missense_Mutation_p.A130V	NM_005275	NP_005266	P36915	GNL1_HUMAN	guanine nucleotide binding protein-like 1	475					response to DNA damage stimulus|signal transduction|T cell mediated immunity	extracellular space|intracellular	GTP binding|structural molecule activity			ovary(3)	3																		---	---	---	---
DHX16	8449	broad.mit.edu	37	6	30632712	30632712	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30632712C>T	uc003nqz.2	-	7	1395	c.1183G>A	c.(1183-1185)GTC>ATC	p.V395I	DHX16_uc003nqy.2_5'Flank|DHX16_uc011dmo.1_Missense_Mutation_p.V335I	NM_003587	NP_003578	O60231	DHX16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 16	395					mRNA processing|RNA splicing	nucleus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|RNA helicase activity			ovary(2)|kidney(2)	4																		---	---	---	---
MDC1	9656	broad.mit.edu	37	6	30670626	30670626	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30670626G>A	uc003nrg.3	-	13	6334	c.5894C>T	c.(5893-5895)CCG>CTG	p.P1965L	MDC1_uc003nrf.3_Missense_Mutation_p.P596L	NM_014641	NP_055456	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	1965	BRCT 1.|Required for nuclear localization (NLS2).				cell cycle|double-strand break repair via homologous recombination|intra-S DNA damage checkpoint	focal adhesion|nucleoplasm	FHA domain binding|protein C-terminus binding			breast(2)|ovary(1)|kidney(1)	4													Other_conserved_DNA_damage_response_genes					---	---	---	---
MDC1	9656	broad.mit.edu	37	6	30672641	30672641	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30672641G>A	uc003nrg.3	-	10	4759	c.4319C>T	c.(4318-4320)TCC>TTC	p.S1440F	MDC1_uc003nrf.3_Intron|MDC1_uc011dmp.1_Missense_Mutation_p.S1047F	NM_014641	NP_055456	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	1440	Pro-rich.|Interaction with the PRKDC complex.				cell cycle|double-strand break repair via homologous recombination|intra-S DNA damage checkpoint	focal adhesion|nucleoplasm	FHA domain binding|protein C-terminus binding			breast(2)|ovary(1)|kidney(1)	4													Other_conserved_DNA_damage_response_genes					---	---	---	---
TUBB	203068	broad.mit.edu	37	6	30691379	30691379	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:30691379C>T	uc003nrl.2	+	4	667	c.540C>T	c.(538-540)GTC>GTT	p.V180V	TUBB_uc003nrk.1_Silent_p.V180V|TUBB_uc011dmq.1_Silent_p.V108V	NM_178014	NP_821133	P07437	TBB5_HUMAN	tubulin, beta	180					cellular component movement|G2/M transition of mitotic cell cycle|microtubule-based movement|natural killer cell mediated cytotoxicity|protein polymerization	cytosol|microtubule	GTP binding|GTPase activity|MHC class I protein binding			ovary(1)	1					Colchicine(DB01394)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)													---	---	---	---
PSORS1C1	170679	broad.mit.edu	37	6	31106510	31106510	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31106510G>A	uc003nsl.1	+	5	395	c.121G>A	c.(121-123)GTT>ATT	p.V41I	PSORS1C1_uc010jsj.1_Intron|PSORS1C1_uc003nsn.1_Intron|PSORS1C2_uc003nso.3_Intron	NM_014068	NP_054787	Q9UIG5	PS1C1_HUMAN	SEEK1 protein	41										ovary(1)	1																		---	---	---	---
HLA-B	3106	broad.mit.edu	37	6	31322882	31322882	+	Splice_Site	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31322882A>G	uc003nth.2	-	5	1066	c.1012_splice	c.e5+1	p.G338_splice	HLA-C_uc003ntb.2_Intron|HLA-C_uc003ntc.1_5'Flank|HLA-B_uc010jsm.1_Intron|HLA-B_uc011dnk.1_Splice_Site|HLA-B_uc003ntf.2_Intron|HLA-B_uc003ntg.1_Splice_Site_p.G217_splice|HLA-B_uc003nti.1_Intron	NM_005514	NP_005505			major histocompatibility complex, class I, B						antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to plasma membrane|MHC class I protein complex	MHC class I receptor activity				0														Melanoma_Familial_Clustering_of|Lichen_Sclerosis_et_Atrophicus_Familial_Clustering_of				---	---	---	---
HLA-B	3106	broad.mit.edu	37	6	31323001	31323001	+	Splice_Site	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31323001C>A	uc003nth.2	-	5	950	c.896_splice	c.e5-1	p.E299_splice	HLA-C_uc003ntb.2_Intron|HLA-C_uc003ntc.1_5'Flank|HLA-B_uc010jsm.1_Intron|HLA-B_uc011dnk.1_Splice_Site|HLA-B_uc003ntf.2_Intron|HLA-B_uc003ntg.1_Splice_Site_p.E178_splice|HLA-B_uc003nti.1_Intron	NM_005514	NP_005505			major histocompatibility complex, class I, B						antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to plasma membrane|MHC class I protein complex	MHC class I receptor activity				0														Melanoma_Familial_Clustering_of|Lichen_Sclerosis_et_Atrophicus_Familial_Clustering_of				---	---	---	---
HLA-B	3106	broad.mit.edu	37	6	31323135	31323135	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31323135A>G	uc003nth.2	-	4	908	c.854T>C	c.(853-855)GTA>GCA	p.V285A	HLA-C_uc003ntb.2_RNA|HLA-C_uc003ntc.1_5'Flank|HLA-B_uc010jsm.1_RNA|HLA-B_uc011dnk.1_RNA|HLA-B_uc003ntf.2_Intron|HLA-B_uc003ntg.1_Missense_Mutation_p.V164A|HLA-B_uc003nti.1_RNA|HLA-B_uc010jsn.1_RNA	NM_005514	NP_005505	P01889	1B07_HUMAN	major histocompatibility complex, class I, B	285	Alpha-3.|Ig-like C1-type.|Extracellular (Potential).				antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to plasma membrane|MHC class I protein complex	MHC class I receptor activity				0														Melanoma_Familial_Clustering_of|Lichen_Sclerosis_et_Atrophicus_Familial_Clustering_of				---	---	---	---
TNF	7124	broad.mit.edu	37	6	31544350	31544350	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31544350G>A	uc003nui.2	+	2	395	c.226G>A	c.(226-228)GCA>ACA	p.A76T	TNF_uc003nuj.2_5'UTR	NM_000594	NP_000585	P01375	TNFA_HUMAN	tumor necrosis factor alpha	76	Extracellular (Potential).	Cleavage; by ADAM17.			activation of caspase activity|activation of MAPK activity|activation of MAPKKK activity|anti-apoptosis|cellular response to nicotine|chronic inflammatory response to antigenic stimulus|embryonic digestive tract development|induction of apoptosis via death domain receptors|induction of necroptosis by extracellular signals|leukocyte tethering or rolling|necrotic cell death|negative regulation of branching involved in lung morphogenesis|negative regulation of cytokine secretion involved in immune response|negative regulation of fat cell differentiation|negative regulation of interleukin-6 production|negative regulation of lipid catabolic process|negative regulation of lipid storage|negative regulation of viral genome replication|positive regulation of calcidiol 1-monooxygenase activity|positive regulation of chemokine biosynthetic process|positive regulation of chemokine production|positive regulation of cytokine secretion|positive regulation of ERK1 and ERK2 cascade|positive regulation of fever generation|positive regulation of heterotypic cell-cell adhesion|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of membrane protein ectodomain proteolysis|positive regulation of NF-kappaB import into nucleus|positive regulation of NF-kappaB transcription factor activity|positive regulation of NFAT protein import into nucleus|positive regulation of nitric oxide biosynthetic process|positive regulation of osteoclast differentiation|positive regulation of peptidyl-serine phosphorylation|positive regulation of podosome assembly|positive regulation of protein complex disassembly|positive regulation of smooth muscle cell proliferation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of vitamin D biosynthetic process|protein import into nucleus, translocation|receptor biosynthetic process|regulation of insulin secretion|response to glucocorticoid stimulus|response to salt stress|response to virus|sequestering of triglyceride|transformed cell apoptosis|tumor necrosis factor-mediated signaling pathway	external side of plasma membrane|extracellular space|integral to plasma membrane|membrane raft|phagocytic cup|recycling endosome	cytokine activity|identical protein binding|protease binding|transcription regulatory region DNA binding|tumor necrosis factor receptor binding			ovary(1)|pancreas(1)|skin(1)	3		Ovarian(999;0.00556)			Adalimumab(DB00051)|Adenosine(DB00640)|Amrinone(DB01427)|Atorvastatin(DB01076)|Chloroquine(DB00608)|Clenbuterol(DB01407)|Etanercept(DB00005)|Glucosamine(DB01296)|Infliximab(DB00065)|Naltrexone(DB00704)|Pranlukast(DB01411)|Procaterol(DB01366)|Saquinavir(DB01232)|Simvastatin(DB00641)|Thalidomide(DB01041)									Naso-/Oropharyngeal/Laryngeal_Cancer_Familial_Clustering_of				---	---	---	---
BAT2	7916	broad.mit.edu	37	6	31600118	31600118	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31600118G>A	uc003nvb.3	+	16	3917	c.3668G>A	c.(3667-3669)CGC>CAC	p.R1223H	BAT2_uc011dnv.1_Intron|BAT2_uc003nvc.3_Missense_Mutation_p.R1223H	NM_080686	NP_542417	P48634	PRC2A_HUMAN	HLA-B associated transcript-2	1223	4 X 57 AA type A repeats.					cytoplasm|nucleus	protein binding				0																		---	---	---	---
BAT5	7920	broad.mit.edu	37	6	31669049	31669049	+	Splice_Site	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31669049A>G	uc003nvy.1	-	3	286	c.256_splice	c.e3+1	p.G86_splice	BAT5_uc003nvx.1_Splice_Site|BAT5_uc011dny.1_Intron|BAT5_uc003nvz.1_Intron|BAT5_uc011dnz.1_Splice_Site|BAT5_uc010jtc.1_Intron|BAT5_uc011doa.1_Intron	NM_021160	NP_066983			HLA-B associated transcript 5							integral to membrane	hydrolase activity|protein binding				0																		---	---	---	---
LY6G6F	259215	broad.mit.edu	37	6	31675244	31675244	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31675244A>G	uc003nwa.1	+	2	62	c.62A>G	c.(61-63)CAG>CGG	p.Q21R	BAT5_uc011dnz.1_Intron|LY6G6F_uc003nwb.1_Missense_Mutation_p.Q21R	NM_001003693	NP_001003693	Q5SQ64	LY66F_HUMAN	G6f protein precursor	21	Extracellular (Potential).|Ig-like V-type.					integral to membrane|plasma membrane				breast(1)|central_nervous_system(1)	2																		---	---	---	---
LY6G6F	259215	broad.mit.edu	37	6	31675489	31675489	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31675489C>T	uc003nwa.1	+	2	307	c.307C>T	c.(307-309)CGG>TGG	p.R103W	BAT5_uc011dnz.1_Intron|LY6G6F_uc003nwb.1_Missense_Mutation_p.R103W	NM_001003693	NP_001003693	Q5SQ64	LY66F_HUMAN	G6f protein precursor	103	Extracellular (Potential).|Ig-like V-type.					integral to membrane|plasma membrane				breast(1)|central_nervous_system(1)	2																		---	---	---	---
HSPA1L	3305	broad.mit.edu	37	6	31778410	31778410	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31778410C>T	uc003nxh.2	-	2	1523	c.1340G>A	c.(1339-1341)GGC>GAC	p.G447D	HSPA1L_uc010jte.2_Missense_Mutation_p.G447D	NM_005527	NP_005518	P34931	HS71L_HUMAN	heat shock 70kDa protein 1-like	447					response to unfolded protein		ATP binding			ovary(3)|pleura(1)|kidney(1)|skin(1)	6																		---	---	---	---
EHMT2	10919	broad.mit.edu	37	6	31855734	31855734	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31855734G>A	uc003nxz.1	-	14	1760	c.1750C>T	c.(1750-1752)CGG>TGG	p.R584W	EHMT2_uc003nxx.1_5'Flank|EHMT2_uc003nxy.1_Missense_Mutation_p.R375W|EHMT2_uc011don.1_Missense_Mutation_p.R607W|EHMT2_uc003nya.1_Missense_Mutation_p.R550W	NM_006709	NP_006700	Q96KQ7	EHMT2_HUMAN	euchromatic histone-lysine N-methyltransferase 2	584					DNA methylation|peptidyl-lysine dimethylation	chromosome|nucleus	histone methyltransferase activity (H3-K27 specific)|histone methyltransferase activity (H3-K9 specific)|p53 binding|zinc ion binding			ovary(1)	1																		---	---	---	---
CFB	629	broad.mit.edu	37	6	31912591	31912591	+	5'Flank	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31912591C>A	uc003nyj.3	+						C2_uc003nyc.2_Missense_Mutation_p.L451I|C2_uc011doo.1_Missense_Mutation_p.L418I|C2_uc011dop.1_Missense_Mutation_p.L450I|C2_uc003nyf.2_Missense_Mutation_p.L664I|C2_uc010jtk.2_Missense_Mutation_p.L532I|C2_uc011doq.1_Missense_Mutation_p.L635I|C2_uc003nyg.2_Missense_Mutation_p.L441I|CFB_uc011dor.1_Missense_Mutation_p.L511I|C2_uc003nyh.1_Missense_Mutation_p.L315I|CFB_uc011dos.1_5'Flank|CFB_uc003nyi.2_5'Flank	NM_001710	NP_001701			complement factor B preproprotein						complement activation, alternative pathway|proteolysis	extracellular region|plasma membrane	complement binding|serine-type endopeptidase activity			skin(1)	1																		---	---	---	---
TNXB	7148	broad.mit.edu	37	6	32015725	32015725	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32015725G>A	uc003nzl.2	-	30	10306	c.10104C>T	c.(10102-10104)TCC>TCT	p.S3368S	TNXB_uc003nzg.1_5'Flank|TNXB_uc003nzh.1_5'Flank	NM_019105	NP_061978	P22105	TENX_HUMAN	tenascin XB isoform 1 precursor	3415	Fibronectin type-III 26.				actin cytoskeleton organization|cell adhesion|collagen metabolic process|elastic fiber assembly|signal transduction	extracellular space|intracellular|proteinaceous extracellular matrix	heparin binding|integrin binding				0																		---	---	---	---
TNXB	7148	broad.mit.edu	37	6	32030171	32030171	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32030171C>T	uc003nzl.2	-	20	7133	c.6931G>A	c.(6931-6933)GTG>ATG	p.V2311M		NM_019105	NP_061978	P22105	TENX_HUMAN	tenascin XB isoform 1 precursor	2373	Fibronectin type-III 16.				actin cytoskeleton organization|cell adhesion|collagen metabolic process|elastic fiber assembly|signal transduction	extracellular space|intracellular|proteinaceous extracellular matrix	heparin binding|integrin binding				0																		---	---	---	---
TNXB	7148	broad.mit.edu	37	6	32037453	32037453	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32037453C>T	uc003nzl.2	-	15	5666	c.5464G>A	c.(5464-5466)GTG>ATG	p.V1822M		NM_019105	NP_061978	P22105	TENX_HUMAN	tenascin XB isoform 1 precursor	1904	Fibronectin type-III 11.				actin cytoskeleton organization|cell adhesion|collagen metabolic process|elastic fiber assembly|signal transduction	extracellular space|intracellular|proteinaceous extracellular matrix	heparin binding|integrin binding				0																		---	---	---	---
TNXB	7148	broad.mit.edu	37	6	32065211	32065211	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32065211C>T	uc003nzl.2	-	3	621	c.419G>A	c.(418-420)CGG>CAG	p.R140Q		NM_019105	NP_061978	P22105	TENX_HUMAN	tenascin XB isoform 1 precursor	140					actin cytoskeleton organization|cell adhesion|collagen metabolic process|elastic fiber assembly|signal transduction	extracellular space|intracellular|proteinaceous extracellular matrix	heparin binding|integrin binding				0																		---	---	---	---
C6orf10	10665	broad.mit.edu	37	6	32261558	32261558	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32261558C>T	uc011dpy.1	-	12	1065	c.892G>A	c.(892-894)GCT>ACT	p.A298T	C6orf10_uc011dpx.1_Missense_Mutation_p.A80T	NM_006781	NP_006772	Q5SRN2	CF010_HUMAN	chromosome 6 open reading frame 10	298						integral to membrane				skin(1)	1																		---	---	---	---
TAP2	6891	broad.mit.edu	37	6	32800108	32800108	+	Splice_Site	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32800108A>G	uc003occ.2	-	6	1303	c.1272_splice	c.e6+1	p.Q424_splice	TAP2_uc011dqf.1_Splice_Site_p.Q424_splice|TAP2_uc003ocb.1_Splice_Site_p.Q424_splice|TAP2_uc003ocd.2_Splice_Site_p.Q424_splice	NM_018833	NP_061313			transporter 2, ATP-binding cassette, sub-family						antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent|cytosol to ER transport|intracellular transport of viral proteins in host cell|peptide antigen transport|positive regulation of antigen processing and presentation of peptide antigen via MHC class I|positive regulation of T cell mediated cytotoxicity	nucleus|plasma membrane|TAP complex	ATP binding|MHC class I protein binding|oligopeptide-transporting ATPase activity|peptide antigen binding|peptide antigen-transporting ATPase activity|TAP1 binding|TAP2 binding|tapasin binding				0																		---	---	---	---
TAP2	6891	broad.mit.edu	37	6	32803556	32803556	+	Intron	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32803556G>T	uc003occ.2	-						TAP2_uc011dqf.1_Intron|TAP2_uc003ocb.1_Intron|TAP2_uc003ocd.2_Intron	NM_018833	NP_061313			transporter 2, ATP-binding cassette, sub-family						antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent|cytosol to ER transport|intracellular transport of viral proteins in host cell|peptide antigen transport|positive regulation of antigen processing and presentation of peptide antigen via MHC class I|positive regulation of T cell mediated cytotoxicity	nucleus|plasma membrane|TAP complex	ATP binding|MHC class I protein binding|oligopeptide-transporting ATPase activity|peptide antigen binding|peptide antigen-transporting ATPase activity|TAP1 binding|TAP2 binding|tapasin binding				0																		---	---	---	---
HLA-DMB	3109	broad.mit.edu	37	6	32905099	32905099	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32905099G>A	uc003ocl.1	-	3	705	c.472C>T	c.(472-474)CCT>TCT	p.P158S	HLA-DMB_uc003ocj.1_3'UTR|HLA-DMB_uc003ock.1_5'Flank|HLA-DMB_uc010jud.1_Missense_Mutation_p.P27S|HLA-DMB_uc010jue.1_Missense_Mutation_p.P27S|HLA-DMB_uc010juf.1_Missense_Mutation_p.P27S|HLA-DMB_uc011dql.1_Missense_Mutation_p.P158S	NM_002118	NP_002109	P28068	DMB_HUMAN	major histocompatibility complex, class II, DM	158	Lumenal (Potential).|Ig-like C1-type.|Beta-2.				antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway	integral to membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex					0																		---	---	---	---
HLA-DMA	3108	broad.mit.edu	37	6	32917430	32917430	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32917430C>T	uc003ocm.2	-	3	696	c.610G>A	c.(610-612)GTG>ATG	p.V204M	HLA-DMA_uc011dqm.1_3'UTR	NM_006120	NP_006111	Q31604	Q31604_HUMAN	major histocompatibility complex, class II, DM	204						integral to membrane|MHC class II protein complex					0																		---	---	---	---
HLA-DOA	3111	broad.mit.edu	37	6	32977254	32977254	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32977254C>T	uc003ocr.2	-	1	136	c.60G>A	c.(58-60)CCG>CCA	p.P20P	HLA-DOA_uc010juj.2_5'UTR|HLA-DOA_uc010jui.2_Silent_p.P20P	NM_002119	NP_002110	P06340	DOA_HUMAN	major histocompatibility complex, class II, DO	20					antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway	endosome membrane|integral to membrane|lysosomal membrane|MHC class II protein complex	MHC class II receptor activity				0																		---	---	---	---
COL11A2	1302	broad.mit.edu	37	6	33148791	33148791	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33148791T>C	uc003ocx.1	-						COL11A2_uc003ocy.1_Intron|COL11A2_uc003ocz.1_Intron	NM_080680	NP_542411			collagen, type XI, alpha 2 isoform 1						cartilage development|cell adhesion|collagen fibril organization|sensory perception of sound|soft palate development	collagen type XI	extracellular matrix structural constituent conferring tensile strength|protein binding, bridging			ovary(3)|skin(2)	5																		---	---	---	---
SLC39A7	7922	broad.mit.edu	37	6	33169661	33169661	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33169661C>A	uc003odf.2	+	3	668	c.551C>A	c.(550-552)GCT>GAT	p.A184D	RXRB_uc003odb.2_5'Flank|RXRB_uc003odc.2_5'Flank|RXRB_uc003odd.2_5'Flank|RXRB_uc011dqr.1_5'Flank|RXRB_uc011dqs.1_5'Flank|RXRB_uc011dqt.1_5'Flank|RXRB_uc011dqu.1_5'Flank|SLC39A7_uc003odg.2_Missense_Mutation_p.A184D|SLC39A7_uc011dqv.1_Missense_Mutation_p.A59D|SLC39A7_uc003odh.2_5'Flank|HSD17B8_uc003odi.1_5'Flank	NM_001077516	NP_001070984	Q92504	S39A7_HUMAN	solute carrier family 39, member 7	184	Helical; (Potential).					endoplasmic reticulum membrane|integral to membrane|membrane fraction	protein binding|zinc ion transmembrane transporter activity			large_intestine(1)	1																		---	---	---	---
VPS52	6293	broad.mit.edu	37	6	33235964	33235964	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33235964A>G	uc003odm.1	-	8	931	c.721T>C	c.(721-723)TTT>CTT	p.F241L	VPS52_uc003odn.1_Missense_Mutation_p.F116L|VPS52_uc003odo.1_Missense_Mutation_p.F166L|VPS52_uc011dqy.1_Missense_Mutation_p.F116L|VPS52_uc011dqz.1_Missense_Mutation_p.F116L	NM_022553	NP_072047	Q8N1B4	VPS52_HUMAN	vacuolar protein sorting 52	241					protein transport	endosome membrane|Golgi apparatus				ovary(4)|skin(1)	5																		---	---	---	---
RGL2	5863	broad.mit.edu	37	6	33259987	33259987	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33259987G>A	uc003odv.2	-	18	2359	c.2226C>T	c.(2224-2226)GGC>GGT	p.G742G	WDR46_uc003ods.2_5'Flank|WDR46_uc011dra.1_5'Flank|RGL2_uc003odu.2_Silent_p.G302G|RGL2_uc010jur.2_Silent_p.G302G|RGL2_uc003odw.2_Silent_p.G660G	NM_004761	NP_004752	O15211	RGL2_HUMAN	ral guanine nucleotide dissociation	742					Ras protein signal transduction|regulation of small GTPase mediated signal transduction	intracellular	Ras guanyl-nucleotide exchange factor activity			skin(3)|lung(1)|breast(1)|pancreas(1)	6																		---	---	---	---
TAPBP	6892	broad.mit.edu	37	6	33272235	33272235	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33272235G>A	uc003odx.1	-	5	1220	c.1049C>T	c.(1048-1050)TCG>TTG	p.S350L	TAPBP_uc010jus.1_Missense_Mutation_p.S368L|TAPBP_uc003ody.2_3'UTR|TAPBP_uc003odz.2_Missense_Mutation_p.S350L|TAPBP_uc010jut.1_Missense_Mutation_p.S263L|TAPBP_uc011drc.1_Missense_Mutation_p.S350L	NM_003190	NP_003181	O15533	TPSN_HUMAN	tapasin isoform 1 precursor	350	Ig-like C1-type.|Lumenal (Potential).				antigen processing and presentation of endogenous peptide antigen via MHC class I|immune response|peptide antigen stabilization|protein complex assembly|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane|MHC class I peptide loading complex|microsome	MHC class I protein binding|peptide antigen binding|peptide antigen-transporting ATPase activity|TAP1 binding|TAP2 binding|unfolded protein binding			ovary(1)	1																		---	---	---	---
KIFC1	3833	broad.mit.edu	37	6	33366122	33366122	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33366122C>T	uc003oef.3	+	3	658	c.208C>T	c.(208-210)CCA>TCA	p.P70S	KIFC1_uc011drf.1_Missense_Mutation_p.P70S|uc011drg.1_5'Flank	NM_002263	NP_002254	Q9BW19	KIFC1_HUMAN	kinesin family member C1	70					blood coagulation|cell division|microtubule-based movement|mitotic sister chromatid segregation	early endosome|microtubule|microtubule associated complex|microtubule organizing center|nucleus|spindle	ATP binding|microtubule motor activity				0																		---	---	---	---
PHF1	5252	broad.mit.edu	37	6	33383725	33383725	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33383725C>G	uc003oeh.2	+	15	1790	c.1554C>G	c.(1552-1554)TGC>TGG	p.C518W	PHF1_uc011drh.1_RNA|PHF1_uc003oei.2_3'UTR|PHF1_uc010jux.2_Missense_Mutation_p.C318W	NM_024165	NP_077084	O43189	PHF1_HUMAN	PHD finger protein 1 isoform b	518					chromatin modification	nucleus	nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Ovarian(999;0.0443)																---	---	---	---
ITPR3	3710	broad.mit.edu	37	6	33659672	33659672	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33659672C>T	uc011drk.1	+	54	7644	c.7425C>T	c.(7423-7425)GGC>GGT	p.G2475G	ITPR3_uc003oey.2_Silent_p.G562G	NM_002224	NP_002215	Q14573	ITPR3_HUMAN	inositol 1,4,5-triphosphate receptor, type 3	2475	Extracellular (Potential).				activation of phospholipase C activity|calcium ion transport into cytosol|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|protein heterooligomerization|protein homooligomerization|regulation of insulin secretion|response to calcium ion	apical part of cell|brush border|endoplasmic reticulum membrane|integral to plasma membrane|myelin sheath|neuronal cell body|nuclear outer membrane|platelet dense tubular network membrane	inositol 1,3,4,5 tetrakisphosphate binding|inositol 1,4,5 trisphosphate binding|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|inositol hexakisphosphate binding|intracellular ligand-gated calcium channel activity|protein binding			ovary(6)|lung(5)|central_nervous_system(5)|breast(2)|kidney(1)	19																		---	---	---	---
ITPR3	3710	broad.mit.edu	37	6	33659678	33659678	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33659678C>T	uc011drk.1	+	54	7650	c.7431C>T	c.(7429-7431)GGC>GGT	p.G2477G	ITPR3_uc003oey.2_Silent_p.G564G	NM_002224	NP_002215	Q14573	ITPR3_HUMAN	inositol 1,4,5-triphosphate receptor, type 3	2477	Extracellular (Potential).				activation of phospholipase C activity|calcium ion transport into cytosol|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|protein heterooligomerization|protein homooligomerization|regulation of insulin secretion|response to calcium ion	apical part of cell|brush border|endoplasmic reticulum membrane|integral to plasma membrane|myelin sheath|neuronal cell body|nuclear outer membrane|platelet dense tubular network membrane	inositol 1,3,4,5 tetrakisphosphate binding|inositol 1,4,5 trisphosphate binding|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|inositol hexakisphosphate binding|intracellular ligand-gated calcium channel activity|protein binding			ovary(6)|lung(5)|central_nervous_system(5)|breast(2)|kidney(1)	19																		---	---	---	---
GRM4	2914	broad.mit.edu	37	6	33996020	33996020	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33996020G>A	uc003oir.3	-	9	2736	c.2566C>T	c.(2566-2568)CGC>TGC	p.R856C	GRM4_uc011dsn.1_Missense_Mutation_p.R809C|GRM4_uc010jvh.2_Missense_Mutation_p.R856C|GRM4_uc010jvi.2_Missense_Mutation_p.R548C|GRM4_uc003oio.2_Missense_Mutation_p.R548C|GRM4_uc003oip.2_RNA|GRM4_uc011dsl.1_Missense_Mutation_p.R716C|GRM4_uc003oiq.2_Missense_Mutation_p.R723C|GRM4_uc011dsm.1_Missense_Mutation_p.R687C	NM_000841	NP_000832	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4 precursor	856	Cytoplasmic (Potential).				activation of MAPK activity|inhibition of adenylate cyclase activity by metabotropic glutamate receptor signaling pathway|neuroprotection|neurotransmitter secretion|positive regulation of MAPKKK cascade	cytoplasmic vesicle|integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(3)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	6					L-Glutamic Acid(DB00142)													---	---	---	---
GRM4	2914	broad.mit.edu	37	6	34101032	34101032	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34101032G>A	uc003oir.3	-	1	412	c.242C>T	c.(241-243)GCC>GTC	p.A81V	GRM4_uc011dsn.1_Missense_Mutation_p.A81V|GRM4_uc010jvh.2_Missense_Mutation_p.A81V|GRM4_uc010jvi.2_5'UTR|GRM4_uc010jvk.1_5'UTR	NM_000841	NP_000832	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4 precursor	81	Extracellular (Potential).				activation of MAPK activity|inhibition of adenylate cyclase activity by metabotropic glutamate receptor signaling pathway|neuroprotection|neurotransmitter secretion|positive regulation of MAPKKK cascade	cytoplasmic vesicle|integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(3)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	6					L-Glutamic Acid(DB00142)													---	---	---	---
C6orf1	221491	broad.mit.edu	37	6	34214912	34214912	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34214912C>T	uc003ojf.2	-	4	626	c.34G>A	c.(34-36)GCC>ACC	p.A12T	uc003oje.1_5'Flank|C6orf1_uc003ojg.2_Missense_Mutation_p.A12T|C6orf1_uc003ojh.2_Missense_Mutation_p.A12T|C6orf1_uc003oji.2_RNA	NM_178508	NP_848603	Q86T20	CF001_HUMAN	hypothetical protein LOC221491 precursor	12						extracellular region					0		Ovarian(999;0.0228)		BRCA - Breast invasive adenocarcinoma(397;1.11e-10)														---	---	---	---
C6orf106	64771	broad.mit.edu	37	6	34614586	34614586	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34614586G>A	uc003ojr.2	-						C6orf106_uc003ojs.2_Intron	NM_024294	NP_077270			chromosome 6 open reading frame 106 isoform a											skin(2)|ovary(1)	3																		---	---	---	---
ANKS1A	23294	broad.mit.edu	37	6	34985349	34985349	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34985349C>T	uc003ojx.3	+	11	1665	c.1523C>T	c.(1522-1524)CCG>CTG	p.P508L	ANKS1A_uc011dss.1_Intron|ANKS1A_uc011dst.1_Missense_Mutation_p.P48L|ANKS1A_uc010jvp.1_Intron	NM_015245	NP_056060	Q92625	ANS1A_HUMAN	ankyrin repeat and sterile alpha motif domain	508						cytoplasm	protein binding			ovary(3)|upper_aerodigestive_tract(1)	4																		---	---	---	---
ZNF76	7629	broad.mit.edu	37	6	35254101	35254101	+	Missense_Mutation	SNP	G	T	T	rs140950744		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35254101G>T	uc003oki.1	+	4	362	c.157G>T	c.(157-159)GCT>TCT	p.A53S	ZNF76_uc011dsy.1_Missense_Mutation_p.A53S|ZNF76_uc011dsz.1_Missense_Mutation_p.A53S|ZNF76_uc003okj.1_Missense_Mutation_p.A53S|ZNF76_uc011dsx.1_Missense_Mutation_p.A53S	NM_003427	NP_003418	P36508	ZNF76_HUMAN	zinc finger protein 76 (expressed in testis)	53	3 X 12 AA approximate repeats.				regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ZNF76	7629	broad.mit.edu	37	6	35260373	35260373	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35260373G>A	uc003oki.1	+	10	1179	c.974G>A	c.(973-975)CGC>CAC	p.R325H	ZNF76_uc011dsz.1_Missense_Mutation_p.R325H|ZNF76_uc003okj.1_Missense_Mutation_p.R325H	NM_003427	NP_003418	P36508	ZNF76_HUMAN	zinc finger protein 76 (expressed in testis)	325	C2H2-type 6.				regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
SLC26A8	116369	broad.mit.edu	37	6	35936664	35936664	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:35936664G>A	uc003olm.2	-	11	1466	c.1355C>T	c.(1354-1356)ACA>ATA	p.T452I	SLC26A8_uc010jwa.2_RNA|SLC26A8_uc003olk.2_Missense_Mutation_p.T34I|SLC26A8_uc003oln.2_Missense_Mutation_p.T452I|SLC26A8_uc003oll.2_Missense_Mutation_p.T347I	NM_052961	NP_443193	Q96RN1	S26A8_HUMAN	solute carrier family 26, member 8 isoform a	452	Cytoplasmic (Potential).				cell differentiation|meiosis|multicellular organismal development|spermatogenesis	integral to membrane|plasma membrane	anion:anion antiporter activity|chloride channel activity|oxalate transmembrane transporter activity|protein binding|sulfate transmembrane transporter activity			ovary(2)	2																		---	---	---	---
BRPF3	27154	broad.mit.edu	37	6	36182002	36182002	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36182002G>A	uc003olv.3	+	8	3052	c.2828G>A	c.(2827-2829)AGC>AAC	p.S943N	BRPF3_uc010jwb.2_Intron|BRPF3_uc011dtj.1_Intron|BRPF3_uc010jwc.2_RNA|BRPF3_uc011dtk.1_Intron	NM_015695	NP_056510	Q9ULD4	BRPF3_HUMAN	bromodomain and PHD finger containing, 3	943					histone H3 acetylation|platelet activation|platelet degranulation	cytosol|extracellular region|MOZ/MORF histone acetyltransferase complex	protein binding|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
PNPLA1	285848	broad.mit.edu	37	6	36270153	36270153	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36270153A>G	uc010jwf.2	+	6	1291	c.1291A>G	c.(1291-1293)ACT>GCT	p.T431A	PNPLA1_uc003olw.1_Missense_Mutation_p.T336A|PNPLA1_uc010jwe.1_Missense_Mutation_p.T345A	NM_001145717	NP_001139189	Q8N8W4	PLPL1_HUMAN	patatin-like phospholipase domain containing 1	431	Pro-rich.				lipid catabolic process		hydrolase activity			large_intestine(1)|pancreas(1)|breast(1)|skin(1)	4																OREG0017382	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
KCTD20	222658	broad.mit.edu	37	6	36449398	36449398	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36449398G>A	uc003ome.2	+	6	1109	c.718G>A	c.(718-720)GAA>AAA	p.E240K	KCTD20_uc011dtm.1_Missense_Mutation_p.E95K|KCTD20_uc011dtn.1_5'UTR|KCTD20_uc010jwk.2_Missense_Mutation_p.E74K|KCTD20_uc011dto.1_5'UTR	NM_173562	NP_775833	Q7Z5Y7	KCD20_HUMAN	potassium channel tetramerisation domain	240						voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(2)	2																		---	---	---	---
KCTD20	222658	broad.mit.edu	37	6	36454716	36454716	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36454716A>G	uc003ome.2	+	8	1415	c.1024A>G	c.(1024-1026)ATC>GTC	p.I342V	KCTD20_uc011dtm.1_Missense_Mutation_p.I197V|KCTD20_uc011dtn.1_Missense_Mutation_p.I96V|KCTD20_uc010jwk.2_Missense_Mutation_p.I176V|KCTD20_uc011dto.1_Missense_Mutation_p.I96V	NM_173562	NP_775833	Q7Z5Y7	KCD20_HUMAN	potassium channel tetramerisation domain	342						voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(2)	2																		---	---	---	---
PPIL1	51645	broad.mit.edu	37	6	36823711	36823711	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36823711T>A	uc003omu.2	-	4	631	c.379A>T	c.(379-381)ACC>TCC	p.T127S		NM_016059	NP_057143	Q9Y3C6	PPIL1_HUMAN	peptidylprolyl isomerase-like 1	127	PPIase cyclophilin-type.				protein folding	catalytic step 2 spliceosome	peptidyl-prolyl cis-trans isomerase activity			ovary(1)	1																		---	---	---	---
FGD2	221472	broad.mit.edu	37	6	36993703	36993703	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36993703G>A	uc010jwp.1	+	14	1765	c.1594G>A	c.(1594-1596)GGC>AGC	p.G532S	FGD2_uc003ong.2_Missense_Mutation_p.G254S|FGD2_uc011dtv.1_Missense_Mutation_p.G160S|FGD2_uc003onj.1_Missense_Mutation_p.G109S	NM_173558	NP_775829	Q7Z6J4	FGD2_HUMAN	FYVE, RhoGEF and PH domain containing 2	532					actin cytoskeleton organization|apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Cdc42 GTPase activity|regulation of cell shape|small GTPase mediated signal transduction	cytoskeleton|cytosol|early endosome membrane|Golgi apparatus|lamellipodium|nucleus|ruffle membrane	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			upper_aerodigestive_tract(1)|lung(1)|pancreas(1)	3																		---	---	---	---
FGD2	221472	broad.mit.edu	37	6	36995845	36995845	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36995845C>T	uc010jwp.1	+	16	2045	c.1874C>T	c.(1873-1875)ACG>ATG	p.T625M	FGD2_uc003ong.2_Missense_Mutation_p.T347M|FGD2_uc011dtv.1_Missense_Mutation_p.T253M|FGD2_uc003onj.1_3'UTR	NM_173558	NP_775829	Q7Z6J4	FGD2_HUMAN	FYVE, RhoGEF and PH domain containing 2	625	PH 2.				actin cytoskeleton organization|apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Cdc42 GTPase activity|regulation of cell shape|small GTPase mediated signal transduction	cytoskeleton|cytosol|early endosome membrane|Golgi apparatus|lamellipodium|nucleus|ruffle membrane	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			upper_aerodigestive_tract(1)|lung(1)|pancreas(1)	3																		---	---	---	---
PIM1	5292	broad.mit.edu	37	6	37139005	37139005	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37139005T>G	uc003onk.2	+	4	775	c.345T>G	c.(343-345)AGT>AGG	p.S115R	PIM1_uc011dtw.1_5'Flank	NM_002648	NP_002639	P11309	PIM1_HUMAN	non-specific serine/threonine protein kinase	206	Protein kinase.				cell cycle|cell proliferation|multicellular organismal development|negative regulation of apoptosis|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|protein autophosphorylation	cytoplasm|nucleus|plasma membrane	ATP binding|manganese ion binding|protein binding|protein binding|protein serine/threonine kinase activity|transcription factor binding			large_intestine(1)|central_nervous_system(1)	2			OV - Ovarian serous cystadenocarcinoma(102;0.241)		Adenosine monophosphate(DB00131)			T	BCL6	NHL								---	---	---	---
RNF8	9025	broad.mit.edu	37	6	37328361	37328361	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37328361T>C	uc003onq.3	+						RNF8_uc003onr.3_Intron|RNF8_uc011dtx.1_Intron	NM_003958	NP_003949			ring finger protein 8 isoform 1						cell division|double-strand break repair|histone H2A ubiquitination|histone H2B ubiquitination|mitosis|positive regulation of DNA repair|response to ionizing radiation	midbody|nucleus|ubiquitin ligase complex	chromatin binding|histone binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1																		---	---	---	---
MDGA1	266727	broad.mit.edu	37	6	37605179	37605179	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:37605179G>A	uc003onu.1	-	17	4012	c.2833C>T	c.(2833-2835)CCC>TCC	p.P945S	MDGA1_uc003onv.1_3'UTR	NM_153487	NP_705691	Q8NFP4	MDGA1_HUMAN	MAM domain containing	945					brain development|neuron migration|spinal cord association neuron differentiation	anchored to plasma membrane				central_nervous_system(2)	2																		---	---	---	---
ZFAND3	60685	broad.mit.edu	37	6	38120157	38120157	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38120157T>G	uc003onx.2	+	6	1091	c.676T>G	c.(676-678)TGC>GGC	p.C226G		NM_021943	NP_068762	Q9H8U3	ZFAN3_HUMAN	zinc finger, AN1-type domain 3	226							DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
DNAH8	1769	broad.mit.edu	37	6	38747763	38747763	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:38747763C>A	uc003ooe.1	+	13	2010	c.1410C>A	c.(1408-1410)CCC>CCA	p.P470P		NM_001371	NP_001362			dynein, axonemal, heavy polypeptide 8											skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	21																		---	---	---	---
KIF6	221458	broad.mit.edu	37	6	39328271	39328271	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:39328271T>G	uc003oot.2	-	18	2077	c.1982A>C	c.(1981-1983)AAG>ACG	p.K661T	KIF6_uc003oos.2_Missense_Mutation_p.K112T|KIF6_uc010jwz.1_Missense_Mutation_p.K36T|KIF6_uc010jxa.1_Missense_Mutation_p.K452T|KIF6_uc011dua.1_Missense_Mutation_p.K644T|KIF6_uc010jxb.1_Missense_Mutation_p.K605T	NM_145027	NP_659464	Q6ZMV9	KIF6_HUMAN	kinesin family member 6	661	Potential.				microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity|protein binding			breast(2)|central_nervous_system(1)	3																		---	---	---	---
LRFN2	57497	broad.mit.edu	37	6	40360386	40360386	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:40360386G>A	uc003oph.1	-	3	2131	c.1666C>T	c.(1666-1668)CGC>TGC	p.R556C		NM_020737	NP_065788	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III	556	Cytoplasmic (Potential).					cell junction|integral to membrane|postsynaptic membrane				ovary(2)|skin(1)	3	Ovarian(28;0.0418)|Colorectal(47;0.196)																	---	---	---	---
TREML4	285852	broad.mit.edu	37	6	41196169	41196169	+	Missense_Mutation	SNP	G	A	A	rs112680060	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41196169G>A	uc003oqc.2	+	1	108	c.4G>A	c.(4-6)GCC>ACC	p.A2T	TREML4_uc003oqd.2_5'Flank	NM_198153	NP_937796	Q6UXN2	TRML4_HUMAN	triggering receptor expressed on myeloid	2						extracellular region				breast(1)	1	Ovarian(28;0.0327)|Colorectal(47;0.196)																	---	---	---	---
FOXP4	116113	broad.mit.edu	37	6	41555160	41555160	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41555160C>T	uc003oql.2	+	7	1240	c.782C>T	c.(781-783)TCG>TTG	p.S261L	FOXP4_uc003oqm.2_Missense_Mutation_p.S259L|FOXP4_uc003oqn.2_Missense_Mutation_p.S260L	NM_001012426	NP_001012426	Q8IVH2	FOXP4_HUMAN	forkhead box P4 isoform 1	261					embryonic foregut morphogenesis|heart development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding			breast(1)	1	Ovarian(28;0.0327)|Colorectal(47;0.196)															OREG0004065	type=REGULATORY REGION|Gene=FOXP4|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	---	---	---	---
PRICKLE4	29964	broad.mit.edu	37	6	41752795	41752795	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41752795A>G	uc011duf.1	+	5	611	c.363A>G	c.(361-363)GGA>GGG	p.G121G	PRICKLE4_uc003ord.2_RNA|TOMM6_uc003org.2_5'Flank|TOMM6_uc011dug.1_5'Flank	NM_013397	NP_037529	Q2TBC4	PRIC4_HUMAN	over-expressed breast tumor protein	81	PET.					nucleus	zinc ion binding				0	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;8.38e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)															---	---	---	---
BYSL	705	broad.mit.edu	37	6	41900101	41900101	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:41900101C>T	uc003orl.2	+	7	1307	c.971C>T	c.(970-972)GCG>GTG	p.A324V		NM_004053	NP_004044	Q13895	BYST_HUMAN	bystin	324					cell adhesion|female pregnancy|ribosome biogenesis	cytoplasm|nucleolus					0	Colorectal(47;0.121)		STAD - Stomach adenocarcinoma(11;0.000204)|Epithelial(12;0.000473)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)															---	---	---	---
UBR2	23304	broad.mit.edu	37	6	42574393	42574393	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42574393A>G	uc011dur.1	+						UBR2_uc003osf.2_Intron	NM_015255	NP_056070			ubiquitin protein ligase E3 component n-recognin						cellular response to leucine|chromatin silencing|histone H2A ubiquitination|negative regulation of TOR signaling cascade	nucleus|plasma membrane	leucine binding|zinc ion binding			ovary(3)|pancreas(1)	4	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)															---	---	---	---
UBR2	23304	broad.mit.edu	37	6	42633967	42633967	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42633967C>T	uc011dur.1	+	34	3865	c.3865C>T	c.(3865-3867)CCT>TCT	p.P1289S	UBR2_uc011dus.1_Missense_Mutation_p.P934S|UBR2_uc003osh.2_RNA	NM_015255	NP_056070	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin	1289					cellular response to leucine|chromatin silencing|histone H2A ubiquitination|negative regulation of TOR signaling cascade	nucleus|plasma membrane	leucine binding|zinc ion binding			ovary(3)|pancreas(1)	4	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)															---	---	---	---
KIAA0240	23506	broad.mit.edu	37	6	42797809	42797809	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42797809C>T	uc003osn.1	+	6	1889	c.1738C>T	c.(1738-1740)CCA>TCA	p.P580S	KIAA0240_uc003osm.1_Missense_Mutation_p.P580S|KIAA0240_uc011duw.1_Missense_Mutation_p.P580S|KIAA0240_uc003oso.1_Missense_Mutation_p.P580S|KIAA0240_uc003osp.1_Missense_Mutation_p.P580S	NM_015349	NP_056164	Q6AI39	K0240_HUMAN	hypothetical protein LOC23506	580										ovary(1)	1	Colorectal(47;0.196)		Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|all cancers(41;0.00524)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.104)															---	---	---	---
GNMT	27232	broad.mit.edu	37	6	42930561	42930561	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42930561C>A	uc003otd.2	+	3	402	c.396C>A	c.(394-396)GGC>GGA	p.G132G	uc003ote.1_5'Flank	NM_018960	NP_061833	Q14749	GNMT_HUMAN	glycine N-methyltransferase	132					protein homotetramerization|protein modification process|S-adenosylmethionine metabolic process		folic acid binding|glycine binding|glycine N-methyltransferase activity				0	Colorectal(47;0.196)		all cancers(41;0.00196)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0461)		Glycine(DB00145)|S-Adenosylmethionine(DB00118)													---	---	---	---
PEX6	5190	broad.mit.edu	37	6	42932634	42932634	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42932634G>A	uc003otf.2	-	16	2793	c.2700C>T	c.(2698-2700)AAC>AAT	p.N900N	uc003ote.1_5'Flank|PEX6_uc010jya.2_RNA	NM_000287	NP_000278	Q13608	PEX6_HUMAN	peroxisomal biogenesis factor 6	900					protein import into peroxisome matrix, translocation|protein stabilization	cytosol|peroxisomal membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding|protein complex binding			ovary(1)	1			all cancers(41;0.00235)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0562)															---	---	---	---
PEX6	5190	broad.mit.edu	37	6	42936686	42936686	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42936686G>A	uc003otf.2	-	6	1498	c.1405C>T	c.(1405-1407)CGG>TGG	p.R469W	PEX6_uc010jya.2_RNA	NM_000287	NP_000278	Q13608	PEX6_HUMAN	peroxisomal biogenesis factor 6	469					protein import into peroxisome matrix, translocation|protein stabilization	cytosol|peroxisomal membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding|protein complex binding			ovary(1)	1			all cancers(41;0.00235)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0562)															---	---	---	---
KLC4	89953	broad.mit.edu	37	6	43042382	43042382	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43042382G>T	uc003otv.1	+	16	1909	c.1832G>T	c.(1831-1833)AGC>ATC	p.S611I	PTK7_uc003oub.1_5'Flank|PTK7_uc003ouc.1_5'Flank|PTK7_uc003oud.1_5'Flank|PTK7_uc003oue.1_5'Flank|PTK7_uc003ouf.1_5'Flank|PTK7_uc003oug.1_5'Flank|PTK7_uc011dve.1_5'Flank|KLC4_uc003otr.1_RNA|KLC4_uc011dvd.1_Missense_Mutation_p.S534I|KLC4_uc003otw.1_Missense_Mutation_p.S629I|KLC4_uc003otx.1_Missense_Mutation_p.S611I|KLC4_uc003oty.1_Missense_Mutation_p.S611I|KLC4_uc003otz.1_Missense_Mutation_p.S611I|PTK7_uc003oua.2_5'Flank	NM_201521	NP_958929	Q9NSK0	KLC4_HUMAN	kinesin-like 8 isoform a	611						cytoplasm|kinesin complex|microtubule	microtubule motor activity|protein binding			skin(3)|ovary(1)	4			all cancers(41;0.00169)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0376)|KIRC - Kidney renal clear cell carcinoma(2;0.0453)															---	---	---	---
C6orf108	10591	broad.mit.edu	37	6	43193692	43193692	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43193692C>T	uc003ouo.2	-						C6orf108_uc003oup.2_3'UTR	NM_006443	NP_006434			putative c-Myc-responsive isoform 1						cell proliferation|deoxyribonucleoside monophosphate catabolic process|positive regulation of cell growth	cytoplasm|nucleus	deoxyribonucleoside 5'-monophosphate N-glycosidase activity|nucleoside deoxyribosyltransferase activity				0			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0123)|OV - Ovarian serous cystadenocarcinoma(102;0.0531)															---	---	---	---
TJAP1	93643	broad.mit.edu	37	6	43473181	43473181	+	Missense_Mutation	SNP	G	A	A	rs41281812		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43473181G>A	uc003ovd.2	+	11	1638	c.1262G>A	c.(1261-1263)CGT>CAT	p.R421H	TJAP1_uc003ovf.2_Missense_Mutation_p.R411H|TJAP1_uc003ove.2_Missense_Mutation_p.R411H|TJAP1_uc003ovc.2_Missense_Mutation_p.R411H|TJAP1_uc010jyp.2_Missense_Mutation_p.R380H|TJAP1_uc011dvh.1_Missense_Mutation_p.R411H|TJAP1_uc003ovg.2_Missense_Mutation_p.R287H|TJAP1_uc011dvi.1_Missense_Mutation_p.R421H|TJAP1_uc011dvj.1_Missense_Mutation_p.R221H|TJAP1_uc003ovi.2_Missense_Mutation_p.R287H	NM_001146016	NP_001139488	Q5JTD0	TJAP1_HUMAN	tight junction associated protein 1 isoform a	421						Golgi apparatus|tight junction	protein binding				0	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0122)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)															---	---	---	---
YIPF3	25844	broad.mit.edu	37	6	43483340	43483340	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43483340G>A	uc003ovl.1	-	3	545	c.388C>T	c.(388-390)CGA>TGA	p.R130*	YIPF3_uc011dvk.1_Nonsense_Mutation_p.R95*|YIPF3_uc010jyr.1_Nonsense_Mutation_p.R136*|YIPF3_uc010jys.1_5'UTR|YIPF3_uc003ovm.1_Intron|YIPF3_uc010jyt.1_Intron|POLR1C_uc003ovn.2_5'Flank|POLR1C_uc003ovo.1_5'Flank	NM_015388	NP_056203	Q9GZM5	YIPF3_HUMAN	natural killer cell-specific antigen KLIP1	130					cell differentiation	integral to membrane|plasma membrane|transport vesicle					0	all_cancers(18;3.79e-05)|Lung NSC(15;0.00217)|all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00736)|OV - Ovarian serous cystadenocarcinoma(102;0.0711)															---	---	---	---
GTPBP2	54676	broad.mit.edu	37	6	43589775	43589775	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43589775G>A	uc003ovs.2	-	11	1634	c.1597C>T	c.(1597-1599)CGT>TGT	p.R533C	GTPBP2_uc010jyv.2_Missense_Mutation_p.R445C|GTPBP2_uc003ovt.1_Missense_Mutation_p.R533C	NM_019096	NP_061969	Q9BX10	GTPB2_HUMAN	GTP binding protein 2	533							GTP binding|GTPase activity			liver(1)|skin(1)	2	all_cancers(18;9.36e-06)|Lung NSC(15;0.00161)|all_lung(25;0.004)		all cancers(41;0.000501)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0826)|OV - Ovarian serous cystadenocarcinoma(102;0.167)															---	---	---	---
AARS2	57505	broad.mit.edu	37	6	44271107	44271107	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44271107G>A	uc010jza.1	-	15	2064	c.2061C>T	c.(2059-2061)GCC>GCT	p.A687A	SPATS1_uc003oxg.2_Intron|TMEM151B_uc003oxf.2_Intron	NM_020745	NP_065796	Q5JTZ9	SYAM_HUMAN	alanyl-tRNA synthetase 2, mitochondrial	687					alanyl-tRNA aminoacylation	mitochondrion	alanine-tRNA ligase activity|ATP binding|metal ion binding|tRNA binding			ovary(1)	1	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)		L-Alanine(DB00160)													---	---	---	---
CDC5L	988	broad.mit.edu	37	6	44393858	44393858	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44393858C>T	uc003oxl.2	+	12	1847	c.1588C>T	c.(1588-1590)CGT>TGT	p.R530C		NM_001253	NP_001244	Q99459	CDC5L_HUMAN	CDC5-like	530	Interaction with PPP1R8.|Interaction with DAPK3 (By similarity).				cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	catalytic step 2 spliceosome|cytoplasm|nuclear speck|nucleolus	DNA binding|RNA binding			lung(3)|ovary(1)|kidney(1)|skin(1)	6	all_lung(25;0.00433)|Ovarian(13;0.0273)|all_hematologic(164;0.208)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)															---	---	---	---
CDC5L	988	broad.mit.edu	37	6	44413480	44413480	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44413480G>A	uc003oxl.2	+	15	2439	c.2180G>A	c.(2179-2181)CGT>CAT	p.R727H		NM_001253	NP_001244	Q99459	CDC5L_HUMAN	CDC5-like	727	Interaction with PLRG1.				cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	catalytic step 2 spliceosome|cytoplasm|nuclear speck|nucleolus	DNA binding|RNA binding			lung(3)|ovary(1)|kidney(1)|skin(1)	6	all_lung(25;0.00433)|Ovarian(13;0.0273)|all_hematologic(164;0.208)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)															---	---	---	---
SUPT3H	8464	broad.mit.edu	37	6	44921066	44921066	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:44921066T>C	uc003oxo.2	-	11	1133	c.815A>G	c.(814-816)CAG>CGG	p.Q272R	SUPT3H_uc003oxn.1_Missense_Mutation_p.Q261R|SUPT3H_uc011dvv.1_Missense_Mutation_p.Q109R|SUPT3H_uc003oxp.2_Missense_Mutation_p.Q261R|SUPT3H_uc011dvw.1_Missense_Mutation_p.Q175R	NM_181356	NP_852001	O75486	SUPT3_HUMAN	suppressor of Ty 3 homolog isoform 2	343					histone deubiquitination|histone H3 acetylation|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	STAGA complex|transcription factor TFTC complex	DNA binding|transcription coactivator activity			ovary(2)|breast(1)	3																		---	---	---	---
ENPP4	22875	broad.mit.edu	37	6	46107514	46107514	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46107514T>G	uc003oxy.2	+	2	453	c.194T>G	c.(193-195)GTT>GGT	p.V65G		NM_014936	NP_055751	Q9Y6X5	ENPP4_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase	65	Extracellular (Potential).					integral to membrane	hydrolase activity			ovary(3)|skin(1)	4																		---	---	---	---
RCAN2	10231	broad.mit.edu	37	6	46190981	46190981	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46190981A>C	uc003oyb.1	-	4	806	c.491T>G	c.(490-492)GTG>GGG	p.V164G	RCAN2_uc003oyc.1_Missense_Mutation_p.V210G|RCAN2_uc003oyd.1_Missense_Mutation_p.V210G	NM_005822	NP_005813	Q14206	RCAN2_HUMAN	Down syndrome critical region gene 1-like 1	164					calcium-mediated signaling|central nervous system development		nucleotide binding|protein phosphatase 2B binding				0																		---	---	---	---
RCAN2	10231	broad.mit.edu	37	6	46293197	46293197	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46293197T>C	uc003oyb.1	-	1	335	c.20A>G	c.(19-21)GAC>GGC	p.D7G	RCAN2_uc003oyc.1_Intron|RCAN2_uc003oyd.1_Intron	NM_005822	NP_005813	Q14206	RCAN2_HUMAN	Down syndrome critical region gene 1-like 1	7					calcium-mediated signaling|central nervous system development		nucleotide binding|protein phosphatase 2B binding				0																		---	---	---	---
CYP39A1	51302	broad.mit.edu	37	6	46593242	46593242	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46593242C>T	uc003oyf.1	-	7	1048	c.844G>A	c.(844-846)GCA>ACA	p.A282T	CYP39A1_uc011dwa.1_Missense_Mutation_p.A262T|CYP39A1_uc010jzd.1_Missense_Mutation_p.A110T	NM_016593	NP_057677	Q9NYL5	CP39A_HUMAN	cytochrome P450, family 39, subfamily A,	282					bile acid biosynthetic process|bile acid catabolic process|digestion|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	24-hydroxycholesterol 7alpha-hydroxylase activity|electron carrier activity|heme binding|oxysterol 7-alpha-hydroxylase activity			ovary(1)	1																		---	---	---	---
PLA2G7	7941	broad.mit.edu	37	6	46677139	46677139	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46677139T>C	uc010jzf.2	-	9	1063	c.794A>G	c.(793-795)GAA>GGA	p.E265G	PLA2G7_uc010jzg.1_Missense_Mutation_p.E265G	NM_005084	NP_005075	Q13093	PAFA_HUMAN	phospholipase A2, group VII	265					inflammatory response|lipid catabolic process	extracellular space	1-alkyl-2-acetylglycerophosphocholine esterase activity|phospholipid binding				0			Lung(136;0.192)															---	---	---	---
GPR110	266977	broad.mit.edu	37	6	46979741	46979741	+	Splice_Site	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:46979741A>G	uc003oyt.2	-	10	1315	c.1116_splice	c.e10+1	p.E372_splice	GPR110_uc011dwl.1_Splice_Site_p.E60_splice	NM_153840	NP_722582			G-protein coupled receptor 110 isoform 1						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(2)|pancreas(1)	3																		---	---	---	---
MUT	4594	broad.mit.edu	37	6	49412422	49412422	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49412422C>T	uc003ozg.3	-	9	1861	c.1606G>A	c.(1606-1608)GCA>ACA	p.A536T		NM_000255	NP_000246	P22033	MUTA_HUMAN	methylmalonyl Coenzyme A mutase precursor	536					fatty acid beta-oxidation	mitochondrial matrix	cobalamin binding|metal ion binding|methylmalonyl-CoA mutase activity				0	Lung NSC(77;0.0376)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)													---	---	---	---
CRISP2	7180	broad.mit.edu	37	6	49667558	49667558	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49667558T>C	uc003ozq.2	-	6	486	c.230A>G	c.(229-231)AAG>AGG	p.K77R	CRISP2_uc003ozl.2_Missense_Mutation_p.K77R|CRISP2_uc003ozn.2_Missense_Mutation_p.K77R|CRISP2_uc003ozr.2_Missense_Mutation_p.K77R|CRISP2_uc003ozo.2_Missense_Mutation_p.K77R|CRISP2_uc003ozm.2_Missense_Mutation_p.K77R|CRISP2_uc003ozp.2_Missense_Mutation_p.K77R	NM_001142408	NP_001135880	P16562	CRIS2_HUMAN	cysteine-rich secretory protein 2 precursor	77						extracellular space				skin(1)	1	Lung NSC(77;0.0161)		KIRC - Kidney renal clear cell carcinoma(2;0.106)|Kidney(12;0.156)															---	---	---	---
PKHD1	5314	broad.mit.edu	37	6	51909781	51909781	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:51909781C>A	uc003pah.1	-	25	2974	c.2698G>T	c.(2698-2700)GCC>TCC	p.A900S	PKHD1_uc003pai.2_Missense_Mutation_p.A900S	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	900	Extracellular (Potential).				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)																	---	---	---	---
GCM1	8521	broad.mit.edu	37	6	52992995	52992995	+	3'UTR	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52992995A>C	uc003pbp.2	-	6						NM_003643	NP_003634			glial cells missing homolog a							transcription factor complex	DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			central_nervous_system(1)	1	Lung NSC(77;0.0755)																	---	---	---	---
C6orf142	90523	broad.mit.edu	37	6	53989542	53989542	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:53989542T>C	uc003pcg.3	+	3	604	c.491T>C	c.(490-492)CTA>CCA	p.L164P	C6orf142_uc003pcf.2_Missense_Mutation_p.L164P|C6orf142_uc003pch.3_Missense_Mutation_p.L102P|C6orf142_uc011dwz.1_Missense_Mutation_p.L123P|C6orf142_uc011dxa.1_Missense_Mutation_p.L175P	NM_138569	NP_612636	Q5VWP3	MLIP_HUMAN	hypothetical protein LOC90523	164						nuclear envelope|PML body	protein binding				0	Lung NSC(77;0.0317)																	---	---	---	---
FAM83B	222584	broad.mit.edu	37	6	54804539	54804539	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:54804539T>C	uc003pck.2	+	5	886	c.770T>C	c.(769-771)ATG>ACG	p.M257T		NM_001010872	NP_001010872	Q5T0W9	FA83B_HUMAN	hypothetical protein LOC222584	257										ovary(6)	6	Lung NSC(77;0.0178)|Renal(3;0.122)																	---	---	---	---
DST	667	broad.mit.edu	37	6	56352033	56352033	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56352033G>A	uc003pdf.2	-	81	14587	c.14559C>T	c.(14557-14559)TAC>TAT	p.Y4853Y	DST_uc003pcz.3_Silent_p.Y4675Y|DST_uc011dxj.1_Silent_p.Y4704Y|DST_uc011dxk.1_Silent_p.Y4715Y|DST_uc003pcy.3_Silent_p.Y4349Y|DST_uc003pda.3_Silent_p.Y45Y	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2	6761	Spectrin 18.				cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding	actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity			ovary(7)|central_nervous_system(6)|upper_aerodigestive_tract(1)	14	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)															---	---	---	---
BEND6	221336	broad.mit.edu	37	6	56857232	56857232	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:56857232A>G	uc010kab.2	+	3	763	c.177A>G	c.(175-177)GAA>GAG	p.E59E	BEND6_uc003pdg.2_RNA	NM_152731	NP_689944	Q5SZJ8	BEND6_HUMAN	BEN domain containing 6	59											0																		---	---	---	---
ZNF451	26036	broad.mit.edu	37	6	57011926	57011926	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57011926A>T	uc003pdm.1	+	10	1267	c.1043A>T	c.(1042-1044)GAG>GTG	p.E348V	ZNF451_uc003pdl.2_Missense_Mutation_p.E348V|ZNF451_uc003pdn.1_Missense_Mutation_p.E348V|uc003pdq.1_Intron|ZNF451_uc003pdk.1_Missense_Mutation_p.E348V	NM_001031623	NP_001026794	Q9Y4E5	ZN451_HUMAN	zinc finger protein 451 isoform 1	348					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(1)|pancreas(1)	2	Lung NSC(77;0.145)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)															---	---	---	---
PRIM2	5558	broad.mit.edu	37	6	57183306	57183306	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:57183306C>A	uc003pdx.2	+	2	150	c.63C>A	c.(61-63)TCC>TCA	p.S21S	PRIM2_uc003pdv.1_Silent_p.S21S|PRIM2_uc003pdw.2_Silent_p.S21S	NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2	21					DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)														---	---	---	---
KHDRBS2	202559	broad.mit.edu	37	6	62604582	62604582	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:62604582G>A	uc003peg.2	-	6	1015	c.768C>T	c.(766-768)TAC>TAT	p.Y256Y		NM_152688	NP_689901	Q5VWX1	KHDR2_HUMAN	KH domain-containing, RNA-binding, signal	256	Pro-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	SH3 domain binding			skin(7)|ovary(3)|liver(1)	11				BRCA - Breast invasive adenocarcinoma(397;0.149)														---	---	---	---
PHF3	23469	broad.mit.edu	37	6	64394338	64394338	+	Nonsense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:64394338A>T	uc003pep.1	+	3	741	c.715A>T	c.(715-717)AAG>TAG	p.K239*	PHF3_uc010kaf.1_Nonsense_Mutation_p.K239*|PHF3_uc003pem.2_Nonsense_Mutation_p.K192*|PHF3_uc010kag.1_Nonsense_Mutation_p.K151*|PHF3_uc010kah.1_Nonsense_Mutation_p.K53*|PHF3_uc003pen.2_Nonsense_Mutation_p.K151*|PHF3_uc011dxs.1_Intron|PHF3_uc003peo.2_Nonsense_Mutation_p.K239*	NM_015153	NP_055968	Q92576	PHF3_HUMAN	PHD finger protein 3	239					multicellular organismal development|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(3)|lung(1)|skin(1)	5	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)															---	---	---	---
BAI3	577	broad.mit.edu	37	6	70048876	70048876	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70048876C>A	uc003pev.3	+	25	3705	c.3257C>A	c.(3256-3258)GCT>GAT	p.A1086D	BAI3_uc010kak.2_Missense_Mutation_p.A1086D|BAI3_uc011dxx.1_Missense_Mutation_p.A292D|BAI3_uc003pex.1_Missense_Mutation_p.A216D	NM_001704	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	1086	Cytoplasmic (Potential).				negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1)	50		all_lung(197;0.212)																---	---	---	---
LMBRD1	55788	broad.mit.edu	37	6	70386108	70386108	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70386108T>G	uc003pfa.2	-	16	1680	c.1565A>C	c.(1564-1566)GAA>GCA	p.E522A	LMBRD1_uc003pey.2_Missense_Mutation_p.E318A|LMBRD1_uc003pez.2_Missense_Mutation_p.E449A|LMBRD1_uc010kal.2_Missense_Mutation_p.E449A|LMBRD1_uc003pfb.2_RNA	NM_018368	NP_060838	Q9NUN5	LMBD1_HUMAN	liver regeneration p-53 related protein	522	Cytoplasmic (Potential).				interspecies interaction between organisms|transport	integral to membrane|lysosomal membrane	cobalamin binding			ovary(1)	1																		---	---	---	---
LMBRD1	55788	broad.mit.edu	37	6	70506779	70506779	+	5'UTR	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:70506779C>T	uc003pfa.2	-	1					LMBRD1_uc010kal.2_5'Flank|LMBRD1_uc003pfb.2_RNA	NM_018368	NP_060838			liver regeneration p-53 related protein						interspecies interaction between organisms|transport	integral to membrane|lysosomal membrane	cobalamin binding			ovary(1)	1																OREG0017522	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
RIMS1	22999	broad.mit.edu	37	6	72806727	72806727	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:72806727C>T	uc003pga.2	+	3	398	c.321C>T	c.(319-321)GGC>GGT	p.G107G		NM_014989	NP_055804	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	107	RabBD.				calcium ion-dependent exocytosis|cellular membrane fusion|glutamate secretion|intracellular protein transport|protein complex assembly|regulated secretory pathway|response to stimulus|synaptic vesicle exocytosis|visual perception	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(7)|pancreas(2)|breast(1)	10		all_epithelial(107;0.179)|all_hematologic(105;0.212)																---	---	---	---
KCNQ5	56479	broad.mit.edu	37	6	73821104	73821104	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:73821104A>C	uc003pgk.2	+	7	1450	c.1103A>C	c.(1102-1104)AAC>ACC	p.N368T	KCNQ5_uc003pgj.3_Missense_Mutation_p.N368T|KCNQ5_uc011dyh.1_Missense_Mutation_p.N368T|KCNQ5_uc011dyi.1_Missense_Mutation_p.N368T|KCNQ5_uc010kat.2_Missense_Mutation_p.N368T|KCNQ5_uc011dyj.1_Missense_Mutation_p.N368T|KCNQ5_uc011dyk.1_Missense_Mutation_p.N127T	NM_019842	NP_062816	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like	368					protein complex assembly|synaptic transmission	voltage-gated potassium channel complex	inward rectifier potassium channel activity			ovary(4)|large_intestine(2)|skin(1)	7		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)														---	---	---	---
C6orf221	154288	broad.mit.edu	37	6	74072992	74072992	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74072992C>T	uc003pgt.3	+	2	397	c.344C>T	c.(343-345)GCG>GTG	p.A115V		NM_001017361	NP_001017361	Q587J8	ECAT1_HUMAN	hypothetical protein LOC154288	115										skin(2)	2																		---	---	---	---
DDX43	55510	broad.mit.edu	37	6	74124329	74124329	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74124329C>T	uc003pgw.2	+	14	2009	c.1665C>T	c.(1663-1665)GAC>GAT	p.D555D		NM_018665	NP_061135	Q9NXZ2	DDX43_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 43	555	Helicase C-terminal.					intracellular	ATP binding|ATP-dependent RNA helicase activity|RNA binding			ovary(2)|upper_aerodigestive_tract(1)|skin(1)	4																		---	---	---	---
COL12A1	1303	broad.mit.edu	37	6	75797411	75797411	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75797411A>G	uc003phs.2	-	65	9229	c.9063T>C	c.(9061-9063)GGT>GGC	p.G3021G	COL12A1_uc003pht.2_Silent_p.G1857G	NM_004370	NP_004361	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1 long isoform	3021	Triple-helical region (COL1) with 2 imperfections.				cell adhesion|collagen fibril organization|skeletal system development	collagen type XII|extracellular space	extracellular matrix structural constituent conferring tensile strength			ovary(6)|large_intestine(1)|breast(1)|skin(1)	9																		---	---	---	---
COL12A1	1303	broad.mit.edu	37	6	75798834	75798834	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:75798834G>A	uc003phs.2	-	64	9164	c.8998C>T	c.(8998-9000)CCT>TCT	p.P3000S	COL12A1_uc003pht.2_Missense_Mutation_p.P1836S	NM_004370	NP_004361	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1 long isoform	3000	Triple-helical region (COL1) with 2 imperfections.				cell adhesion|collagen fibril organization|skeletal system development	collagen type XII|extracellular space	extracellular matrix structural constituent conferring tensile strength			ovary(6)|large_intestine(1)|breast(1)|skin(1)	9																		---	---	---	---
MYO6	4646	broad.mit.edu	37	6	76576340	76576340	+	Splice_Site	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:76576340T>C	uc003pih.1	+	17	2049	c.1770_splice	c.e17+2	p.T590_splice	MYO6_uc003pig.1_Splice_Site_p.T590_splice|MYO6_uc003pii.1_Splice_Site_p.T590_splice	NM_004999	NP_004990			myosin VI						actin filament-based movement|DNA damage response, signal transduction by p53 class mediator|endocytosis|intracellular protein transport|positive regulation of transcription from RNA polymerase II promoter|regulation of secretion|sensory perception of sound|synaptic transmission	cell cortex|clathrin coated vesicle membrane|coated pit|cytosol|DNA-directed RNA polymerase II, holoenzyme|filamentous actin|Golgi apparatus|nuclear membrane|perinuclear region of cytoplasm|ruffle membrane|unconventional myosin complex	actin filament binding|ADP binding|ATP binding|calmodulin binding|minus-end directed microfilament motor activity|protein binding			kidney(1)|pancreas(1)	2		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)														---	---	---	---
PHIP	55023	broad.mit.edu	37	6	79707268	79707268	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79707268T>C	uc003pir.2	-	19	2290	c.2064A>G	c.(2062-2064)GGA>GGG	p.G688G	PHIP_uc011dyp.1_Silent_p.G688G	NM_017934	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	688					insulin receptor signaling pathway|negative regulation of apoptosis|positive regulation of cell proliferation|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of mitosis	nucleus	insulin receptor binding			large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)	6		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)														---	---	---	---
PHIP	55023	broad.mit.edu	37	6	79770476	79770476	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79770476T>C	uc003pir.2	-	5	475	c.249A>G	c.(247-249)GGA>GGG	p.G83G	PHIP_uc011dyp.1_Silent_p.G83G	NM_017934	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	83					insulin receptor signaling pathway|negative regulation of apoptosis|positive regulation of cell proliferation|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of mitosis	nucleus	insulin receptor binding			large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)	6		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)														---	---	---	---
HMGN3	9324	broad.mit.edu	37	6	79918292	79918292	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:79918292G>A	uc003pit.2	-	3	246	c.68C>T	c.(67-69)CCC>CTC	p.P23L	HMGN3_uc003pis.2_Missense_Mutation_p.P23L|HMGN3_uc003piu.1_Missense_Mutation_p.P23L	NM_004242	NP_004233	Q15651	HMGN3_HUMAN	high mobility group nucleosomal binding domain 3	23					chromatin modification	chromatin|cytoplasm|nucleus	DNA binding|thyroid hormone receptor binding				0		all_cancers(76;0.000116)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.0393)		BRCA - Breast invasive adenocarcinoma(397;0.125)														---	---	---	---
TTK	7272	broad.mit.edu	37	6	80720615	80720615	+	Missense_Mutation	SNP	G	A	A	rs151265706		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:80720615G>A	uc003pjc.2	+	5	628	c.554G>A	c.(553-555)CGG>CAG	p.R185Q	TTK_uc003pjb.3_Missense_Mutation_p.R185Q	NM_003318	NP_003309	P33981	TTK_HUMAN	TTK protein kinase	185					mitotic cell cycle spindle assembly checkpoint|mitotic spindle organization|positive regulation of cell proliferation|positive regulation of pathway-restricted SMAD protein phosphorylation	spindle	ATP binding|identical protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(4)|stomach(2)|lung(2)|large_intestine(2)|pancreas(1)	11		all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2)		BRCA - Breast invasive adenocarcinoma(397;0.0321)														---	---	---	---
DOPEY1	23033	broad.mit.edu	37	6	83872624	83872624	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83872624C>T	uc003pjs.1	+	38	7338	c.7078C>T	c.(7078-7080)CGG>TGG	p.R2360W	DOPEY1_uc011dyy.1_Missense_Mutation_p.R2351W|DOPEY1_uc010kbl.1_Missense_Mutation_p.R2351W|DOPEY1_uc003pjt.2_RNA	NM_015018	NP_055833	Q5JWR5	DOP1_HUMAN	dopey family member 1	2360					protein transport					ovary(2)|breast(1)|central_nervous_system(1)	4		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)														---	---	---	---
SNAP91	9892	broad.mit.edu	37	6	84302170	84302170	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84302170G>A	uc011dze.1	-						SNAP91_uc011dzd.1_Intron|SNAP91_uc003pkb.2_Intron|SNAP91_uc003pkc.2_Intron|SNAP91_uc003pkd.2_Intron|SNAP91_uc003pka.2_Intron	NM_014841	NP_055656			synaptosomal-associated protein, 91kDa homolog						clathrin coat assembly	clathrin coat|coated pit|plasma membrane	1-phosphatidylinositol binding|clathrin binding			ovary(1)	1		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)														---	---	---	---
MRAP2	112609	broad.mit.edu	37	6	84772656	84772656	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84772656A>T	uc003pkg.3	+	3	362	c.172A>T	c.(172-174)ATT>TTT	p.I58F	MRAP2_uc010kbo.2_Intron	NM_138409	NP_612418	Q96G30	MRAP2_HUMAN	melanocortin 2 receptor accessory protein 2	58					positive regulation of cAMP biosynthetic process|protein localization at cell surface	endoplasmic reticulum|plasma membrane	corticotropin hormone receptor binding|type 1 melanocortin receptor binding|type 3 melanocortin receptor binding|type 4 melanocortin receptor binding|type 5 melanocortin receptor binding			skin(2)	2																		---	---	---	---
KIAA1009	22832	broad.mit.edu	37	6	84930828	84930828	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:84930828T>A	uc010kbp.2	-	3	216	c.119A>T	c.(118-120)AAG>ATG	p.K40M	KIAA1009_uc003pkj.3_Translation_Start_Site|KIAA1009_uc003pkk.2_Missense_Mutation_p.K40M	NM_014895	NP_055710	Q5TB80	QN1_HUMAN	KIAA1009 protein	40					cell division|mitosis	centrosome|nucleus|plasma membrane|spindle	protein binding			ovary(1)	1		all_cancers(76;1.5e-06)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00258)		BRCA - Breast invasive adenocarcinoma(397;0.089)														---	---	---	---
SYNCRIP	10492	broad.mit.edu	37	6	86324746	86324746	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:86324746C>A	uc003pla.2	-	11	2141	c.1600G>T	c.(1600-1602)GGC>TGC	p.G534C	SYNCRIP_uc003pku.2_Missense_Mutation_p.G534C|SYNCRIP_uc003pkw.2_Missense_Mutation_p.G499C|SYNCRIP_uc003pky.2_Missense_Mutation_p.G436C|SYNCRIP_uc003pkv.2_Missense_Mutation_p.G534C|SYNCRIP_uc003pkx.2_Missense_Mutation_p.G382C|SYNCRIP_uc003pkz.2_Missense_Mutation_p.G499C	NM_006372	NP_006363	O60506	HNRPQ_HUMAN	synaptotagmin binding, cytoplasmic RNA	534	Interaction with SMN.|Interaction with APOBEC1.|8 X 3 AA repeats of R-G-G.				CRD-mediated mRNA stabilization|interspecies interaction between organisms	catalytic step 2 spliceosome|CRD-mediated mRNA stability complex|endoplasmic reticulum|histone pre-mRNA 3'end processing complex|microsome|nucleoplasm	nucleotide binding|protein binding			ovary(2)	2		all_cancers(76;0.000137)|Acute lymphoblastic leukemia(125;3.66e-08)|Prostate(29;8.2e-07)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0297)		BRCA - Breast invasive adenocarcinoma(108;0.0389)														---	---	---	---
HTR1E	3354	broad.mit.edu	37	6	87725443	87725443	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87725443G>A	uc003pli.2	+	2	1094	c.391G>A	c.(391-393)GCC>ACC	p.A131T		NM_000865	NP_000856	P28566	5HT1E_HUMAN	5-hydroxytryptamine (serotonin) receptor 1E	131	Cytoplasmic (By similarity).				G-protein signaling, coupled to cyclic nucleotide second messenger|synaptic transmission	integral to plasma membrane	protein binding|serotonin binding|serotonin receptor activity			ovary(2)|skin(1)	3		all_cancers(76;7.11e-06)|Acute lymphoblastic leukemia(125;1.2e-09)|Prostate(29;3.51e-09)|all_hematologic(105;7.43e-06)|all_epithelial(107;0.00819)		BRCA - Breast invasive adenocarcinoma(108;0.055)	Eletriptan(DB00216)													---	---	---	---
ZNF292	23036	broad.mit.edu	37	6	87964887	87964887	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87964887G>A	uc003plm.3	+	8	1581	c.1540G>A	c.(1540-1542)GAA>AAA	p.E514K		NM_015021	NP_055836	O60281	ZN292_HUMAN	zinc finger protein 292	514					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)	4		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)														---	---	---	---
ZNF292	23036	broad.mit.edu	37	6	87966198	87966198	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87966198T>G	uc003plm.3	+	8	2892	c.2851T>G	c.(2851-2853)TTT>GTT	p.F951V		NM_015021	NP_055836	O60281	ZN292_HUMAN	zinc finger protein 292	951					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)	4		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)														---	---	---	---
ZNF292	23036	broad.mit.edu	37	6	87967825	87967825	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:87967825C>A	uc003plm.3	+	8	4519	c.4478C>A	c.(4477-4479)GCT>GAT	p.A1493D		NM_015021	NP_055836	O60281	ZN292_HUMAN	zinc finger protein 292	1493					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)	4		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)														---	---	---	---
GABRR2	2570	broad.mit.edu	37	6	89974310	89974310	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:89974310T>G	uc003pnb.2	-	8	990	c.982A>C	c.(982-984)ACC>CCC	p.T328P	GABRR2_uc011dzx.1_Missense_Mutation_p.T204P	NM_002043	NP_002034	P28476	GBRR2_HUMAN	gamma-aminobutyric acid (GABA) receptor, rho 2	328	Helical; (Potential).				synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity				0		all_cancers(76;1.67e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.77e-07)|all_epithelial(107;2.51e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0158)														---	---	---	---
RRAGD	58528	broad.mit.edu	37	6	90082282	90082282	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90082282T>C	uc003pnd.3	-	6	1208	c.925A>G	c.(925-927)ACC>GCC	p.T309A	RRAGD_uc010kcc.2_Missense_Mutation_p.T158A	NM_021244	NP_067067	Q9NQL2	RRAGD_HUMAN	Ras-related GTP binding D	309					cellular protein localization|cellular response to amino acid stimulus|positive regulation of TOR signaling cascade	lysosome|nucleus	GTP binding|protein heterodimerization activity			ovary(2)|central_nervous_system(1)	3		all_cancers(76;7.01e-07)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00139)		BRCA - Breast invasive adenocarcinoma(108;0.0144)												OREG0017567	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
MDN1	23195	broad.mit.edu	37	6	90368526	90368526	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90368526C>G	uc003pnn.1	-	89	14940	c.14824G>C	c.(14824-14826)GAG>CAG	p.E4942Q		NM_014611	NP_055426	Q9NU22	MDN1_HUMAN	MDN1, midasin homolog	4942					protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)														---	---	---	---
MDN1	23195	broad.mit.edu	37	6	90432795	90432795	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90432795C>A	uc003pnn.1	-	40	5962	c.5846G>T	c.(5845-5847)CGG>CTG	p.R1949L		NM_014611	NP_055426	Q9NU22	MDN1_HUMAN	MDN1, midasin homolog	1949					protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)														---	---	---	---
CASP8AP2	9994	broad.mit.edu	37	6	90572058	90572058	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90572058T>C	uc003pnr.2	+	7	826	c.630T>C	c.(628-630)AGT>AGC	p.S210S	CASP8AP2_uc003pns.2_Intron|CASP8AP2_uc003pnt.2_Silent_p.S210S|CASP8AP2_uc011dzz.1_Silent_p.S210S	NM_001137667	NP_001131139	Q9UKL3	C8AP2_HUMAN	caspase 8 associated protein 2	210					cell cycle|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	cytoplasm|nucleus	caspase activator activity|death receptor binding|transcription corepressor activity			ovary(2)	2		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)														---	---	---	---
CASP8AP2	9994	broad.mit.edu	37	6	90572127	90572127	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90572127G>A	uc003pnr.2	+	7	895	c.699G>A	c.(697-699)CAG>CAA	p.Q233Q	CASP8AP2_uc003pns.2_Intron|CASP8AP2_uc003pnt.2_Silent_p.Q233Q|CASP8AP2_uc011dzz.1_Silent_p.Q233Q	NM_001137667	NP_001131139	Q9UKL3	C8AP2_HUMAN	caspase 8 associated protein 2	233					cell cycle|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	cytoplasm|nucleus	caspase activator activity|death receptor binding|transcription corepressor activity			ovary(2)	2		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)														---	---	---	---
CASP8AP2	9994	broad.mit.edu	37	6	90573346	90573346	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:90573346G>T	uc003pnr.2	+	7	2114	c.1918G>T	c.(1918-1920)GCA>TCA	p.A640S	CASP8AP2_uc003pns.2_Intron|CASP8AP2_uc003pnt.2_Missense_Mutation_p.A640S|CASP8AP2_uc011dzz.1_Missense_Mutation_p.A640S	NM_001137667	NP_001131139	Q9UKL3	C8AP2_HUMAN	caspase 8 associated protein 2	640					cell cycle|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	cytoplasm|nucleus	caspase activator activity|death receptor binding|transcription corepressor activity			ovary(2)	2		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)														---	---	---	---
FHL5	9457	broad.mit.edu	37	6	97051489	97051489	+	5'UTR	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97051489A>C	uc003pos.1	+	3					FHL5_uc003pot.1_5'UTR	NM_020482	NP_065228			activator of cAMP-responsive element modulator							nucleus	zinc ion binding			ovary(2)	2		all_cancers(76;1.57e-07)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00266)|Colorectal(196;0.0341)|Lung NSC(302;0.204)		BRCA - Breast invasive adenocarcinoma(108;0.0948)														---	---	---	---
C6orf167	253714	broad.mit.edu	37	6	97634387	97634387	+	Missense_Mutation	SNP	G	A	A	rs148291789		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97634387G>A	uc003ppb.2	-	15	2485	c.2219C>T	c.(2218-2220)GCG>GTG	p.A740V	C6orf167_uc011eaf.1_Missense_Mutation_p.A700V	NM_198468	NP_940870	Q6ZRQ5	MMS22_HUMAN	hypothetical protein LOC253714	740					double-strand break repair via homologous recombination|replication fork processing	nuclear replication fork	protein binding				0		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.148)|Colorectal(196;0.198)		BRCA - Breast invasive adenocarcinoma(108;0.0457)														---	---	---	---
C6orf167	253714	broad.mit.edu	37	6	97679332	97679332	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:97679332C>T	uc003ppb.2	-	13	1765	c.1499G>A	c.(1498-1500)GGC>GAC	p.G500D	C6orf167_uc011eaf.1_Missense_Mutation_p.G460D|C6orf167_uc010kcn.1_Missense_Mutation_p.G274D	NM_198468	NP_940870	Q6ZRQ5	MMS22_HUMAN	hypothetical protein LOC253714	500					double-strand break repair via homologous recombination|replication fork processing	nuclear replication fork	protein binding				0		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.148)|Colorectal(196;0.198)		BRCA - Breast invasive adenocarcinoma(108;0.0457)														---	---	---	---
SFRS18	25957	broad.mit.edu	37	6	99848915	99848915	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:99848915C>T	uc003ppo.3	-	12	2147	c.1919G>A	c.(1918-1920)CGT>CAT	p.R640H	SFRS18_uc003ppl.2_Missense_Mutation_p.R186H|SFRS18_uc003ppp.3_Missense_Mutation_p.R640H|SFRS18_uc011eag.1_Missense_Mutation_p.R640H	NM_032870	NP_116259	Q8TF01	PNISR_HUMAN	splicing factor, arginine/serine-rich 130	640						nuclear speck					0		all_cancers(76;1.24e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.00716)|Colorectal(196;0.0691)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.0631)														---	---	---	---
SIM1	6492	broad.mit.edu	37	6	100838386	100838386	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100838386G>A	uc003pqj.3	-	11	2359	c.2152C>T	c.(2152-2154)CTG>TTG	p.L718L	SIM1_uc010kcu.2_Silent_p.L718L	NM_005068	NP_005059	P81133	SIM1_HUMAN	single-minded homolog 1	718	Single-minded C-terminal.				cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(4)	4		all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0774)														---	---	---	---
SIM1	6492	broad.mit.edu	37	6	100896492	100896492	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100896492G>A	uc003pqj.3	-	6	813	c.606C>T	c.(604-606)GAC>GAT	p.D202D	SIM1_uc010kcu.2_Silent_p.D202D	NM_005068	NP_005059	P81133	SIM1_HUMAN	single-minded homolog 1	202					cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(4)	4		all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0774)														---	---	---	---
ASCC3	10973	broad.mit.edu	37	6	101073156	101073156	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:101073156C>T	uc003pqk.2	-	30	5026	c.4697G>A	c.(4696-4698)CGT>CAT	p.R1566H		NM_006828	NP_006819	Q8N3C0	HELC1_HUMAN	activating signal cointegrator 1 complex subunit	1566	Helicase C-terminal 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(5)|skin(1)	6		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)														---	---	---	---
AIM1	202	broad.mit.edu	37	6	107000083	107000083	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107000083C>T	uc003prh.2	+	13	4727	c.4240C>T	c.(4240-4242)CGA>TGA	p.R1414*	AIM1_uc003pri.2_Nonsense_Mutation_p.R218*	NM_001624	NP_001615	Q9Y4K1	AIM1_HUMAN	absent in melanoma 1	1414							sugar binding			breast(4)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)	9	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)														---	---	---	---
BEND3	57673	broad.mit.edu	37	6	107390847	107390847	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107390847G>A	uc003prs.2	-	5	2198	c.1548C>T	c.(1546-1548)AGC>AGT	p.S516S		NM_001080450	NP_001073919	Q5T5X7	BEND3_HUMAN	BEN domain containing 3	516										ovary(3)	3																		---	---	---	---
SOBP	55084	broad.mit.edu	37	6	107954790	107954790	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107954790C>A	uc003prx.2	+	6	1246	c.742C>A	c.(742-744)CAG>AAG	p.Q248K		NM_018013	NP_060483	A7XYQ1	SOBP_HUMAN	sine oculis binding protein homolog	248	FCS-type 2.						metal ion binding			ovary(1)	1		all_cancers(87;5.26e-06)|Acute lymphoblastic leukemia(125;2.87e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.00193)|Colorectal(196;0.156)		BRCA - Breast invasive adenocarcinoma(108;0.026)|all cancers(137;0.087)|Epithelial(106;0.104)|OV - Ovarian serous cystadenocarcinoma(136;0.154)														---	---	---	---
NR2E1	7101	broad.mit.edu	37	6	108489292	108489292	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108489292C>T	uc003psg.2	+							NM_003269	NP_003260			nuclear receptor subfamily 2, group E, member 1						regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	sequence-specific DNA binding|steroid hormone receptor activity|zinc ion binding			central_nervous_system(1)|skin(1)	2		all_cancers(87;8.13e-05)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00866)|Colorectal(196;0.0637)		BRCA - Breast invasive adenocarcinoma(108;0.013)|Epithelial(106;0.0521)|all cancers(137;0.068)|OV - Ovarian serous cystadenocarcinoma(136;0.0689)														---	---	---	---
LACE1	246269	broad.mit.edu	37	6	108645204	108645204	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:108645204C>T	uc003psj.2	+	2	501	c.315C>T	c.(313-315)CAC>CAT	p.H105H		NM_145315	NP_660358	Q8WV93	LACE1_HUMAN	lactation elevated 1	105							ATP binding			central_nervous_system(1)	1		all_cancers(87;1.5e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;6.79e-05)|Colorectal(196;0.0294)|all_lung(197;0.0486)|Lung SC(18;0.152)		BRCA - Breast invasive adenocarcinoma(108;0.00179)|Epithelial(106;0.0024)|all cancers(137;0.00379)|OV - Ovarian serous cystadenocarcinoma(136;0.0118)														---	---	---	---
SMPD2	6610	broad.mit.edu	37	6	109763976	109763976	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109763976C>T	uc003pti.2	+	7	907	c.513C>T	c.(511-513)GAC>GAT	p.D171D	PPIL6_uc003ptg.3_5'Flank|PPIL6_uc010kdo.2_5'Flank|PPIL6_uc010kdp.2_5'Flank|PPIL6_uc003pth.1_5'Flank	NM_003080	NP_003071	O60906	NSMA_HUMAN	sphingomyelin phosphodiesterase 2, neutral	171					induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|sphingomyelin metabolic process	integral to plasma membrane	metal ion binding|sphingomyelin phosphodiesterase activity				0		all_cancers(87;1.1e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000144)|all_lung(197;0.0221)|Colorectal(196;0.0488)|Lung SC(18;0.0548)		Epithelial(106;0.0137)|all cancers(137;0.0188)|OV - Ovarian serous cystadenocarcinoma(136;0.0228)|BRCA - Breast invasive adenocarcinoma(108;0.0566)														---	---	---	---
MICAL1	64780	broad.mit.edu	37	6	109768437	109768437	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109768437G>A	uc003ptj.2	-						MICAL1_uc003ptk.2_Intron|MICAL1_uc010kdr.2_Intron|MICAL1_uc011eaq.1_Intron	NM_022765	NP_073602			microtubule associated monoxygenase, calponin						cytoskeleton organization|signal transduction	cytoplasm|intermediate filament	SH3 domain binding|zinc ion binding			breast(2)|ovary(1)	3		all_cancers(87;0.000189)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00686)|Lung SC(18;0.0743)|Colorectal(196;0.101)|all_lung(197;0.149)		Epithelial(106;0.0142)|all cancers(137;0.0197)|OV - Ovarian serous cystadenocarcinoma(136;0.0233)|BRCA - Breast invasive adenocarcinoma(108;0.0574)														---	---	---	---
ZBTB24	9841	broad.mit.edu	37	6	109802514	109802514	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109802514T>A	uc003ptl.1	-	2	884	c.716A>T	c.(715-717)TAT>TTT	p.Y239F	ZBTB24_uc011ear.1_RNA|ZBTB24_uc010kds.1_Missense_Mutation_p.Y239F|ZBTB24_uc010kdt.1_RNA|ZBTB24_uc003ptm.2_Missense_Mutation_p.Y239F	NM_014797	NP_055612	O43167	ZBT24_HUMAN	zinc finger and BTB domain containing 24 isoform	239					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_cancers(87;0.000189)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00686)|Lung SC(18;0.0743)|Colorectal(196;0.101)|all_lung(197;0.149)		Epithelial(106;0.0154)|all cancers(137;0.0216)|OV - Ovarian serous cystadenocarcinoma(136;0.0242)|BRCA - Breast invasive adenocarcinoma(108;0.059)														---	---	---	---
AKD1	221264	broad.mit.edu	37	6	109954241	109954241	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:109954241C>T	uc003ptn.2	-	12	1216	c.1139G>A	c.(1138-1140)CGT>CAT	p.R380H	AKD1_uc003ptr.3_Missense_Mutation_p.R380H	NM_001145128	NP_001138600	Q5TCS8	AKD1_HUMAN	adenylate kinase domain containing 1 isoform 1	380					nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|nucleoside-triphosphatase activity			ovary(1)	1																		---	---	---	---
SLC16A10	117247	broad.mit.edu	37	6	111527860	111527860	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111527860C>T	uc003pus.2	+	4	1183	c.1008C>T	c.(1006-1008)GGC>GGT	p.G336G	SLC16A10_uc003put.2_Silent_p.G22G	NM_018593	NP_061063	Q8TF71	MOT10_HUMAN	solute carrier family 16, member 10	336	Helical; (Potential).				aromatic amino acid transport|cellular nitrogen compound metabolic process|ion transport	basolateral plasma membrane|integral to membrane	amino acid transmembrane transporter activity				0		all_cancers(87;0.00172)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0313)|Colorectal(196;0.0466)		OV - Ovarian serous cystadenocarcinoma(136;0.0703)|Epithelial(106;0.12)|all cancers(137;0.132)														---	---	---	---
REV3L	5980	broad.mit.edu	37	6	111697479	111697479	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111697479C>T	uc003puy.3	-	13	2402	c.2079G>A	c.(2077-2079)ATG>ATA	p.M693I	REV3L_uc003pux.3_Missense_Mutation_p.M615I|REV3L_uc003puz.3_Missense_Mutation_p.M615I	NM_002912	NP_002903	O60673	DPOLZ_HUMAN	DNA polymerase zeta	693					DNA-dependent DNA replication|translesion synthesis	nucleus|zeta DNA polymerase complex	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|nucleotide binding			large_intestine(2)|ovary(2)|skin(2)	6		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)									DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
TRAF3IP2	10758	broad.mit.edu	37	6	111880740	111880740	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111880740G>T	uc011ebc.1	-	10	2181	c.1566C>A	c.(1564-1566)ACC>ACA	p.T522T	TRAF3IP2_uc011ebb.1_Silent_p.T66T|TRAF3IP2_uc003pvd.2_Silent_p.T114T|TRAF3IP2_uc003pvg.2_Silent_p.T521T|TRAF3IP2_uc003pvf.2_Silent_p.T522T	NM_147686	NP_679211	O43734	CIKS_HUMAN	TRAF3 interacting protein 2 isoform 2	531	SEFIR.				intracellular signal transduction|positive regulation of I-kappaB kinase/NF-kappaB cascade	intracellular				ovary(2)|central_nervous_system(1)	3		all_cancers(87;7.87e-06)|Acute lymphoblastic leukemia(125;3.61e-09)|all_hematologic(75;2.63e-07)|all_epithelial(87;0.0024)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.033)|all cancers(137;0.0412)|Epithelial(106;0.0732)														---	---	---	---
WISP3	8838	broad.mit.edu	37	6	112386006	112386006	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112386006G>A	uc003pvm.2	+	4	505	c.395G>A	c.(394-396)GGC>GAC	p.G132D	WISP3_uc003pvn.2_RNA|WISP3_uc003pvo.2_Missense_Mutation_p.G150D	NM_003880	NP_003871	O95389	WISP3_HUMAN	WNT1 inducible signaling pathway protein 3	132					cell-cell signaling|regulation of cell growth|signal transduction	extracellular region|soluble fraction	growth factor activity|insulin-like growth factor binding				0		all_cancers(87;0.000196)|Acute lymphoblastic leukemia(125;1.18e-05)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0283)|OV - Ovarian serous cystadenocarcinoma(136;0.0613)|Epithelial(106;0.0827)|GBM - Glioblastoma multiforme(226;0.0972)|BRCA - Breast invasive adenocarcinoma(108;0.246)														---	---	---	---
LAMA4	3910	broad.mit.edu	37	6	112469412	112469412	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112469412T>C	uc003pvu.2	-	18	2609	c.2300A>G	c.(2299-2301)CAA>CGA	p.Q767R	LAMA4_uc003pvv.2_Missense_Mutation_p.Q760R|LAMA4_uc003pvt.2_Missense_Mutation_p.Q760R	NM_001105206	NP_001098676	Q16363	LAMA4_HUMAN	laminin, alpha 4 isoform 1 precursor	767	Domain II and I.				cell adhesion|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	extracellular matrix structural constituent|receptor binding			ovary(4)|breast(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	9		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)														---	---	---	---
HDAC2	3066	broad.mit.edu	37	6	114270214	114270214	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:114270214G>A	uc003pwd.1	-	8	1052	c.1052C>T	c.(1051-1053)GCT>GTT	p.A351V	HDAC2_uc003pwc.1_Missense_Mutation_p.A227V|HDAC2_uc003pwe.1_Missense_Mutation_p.A227V	NM_001527	NP_001518	Q92769	HDAC2_HUMAN	histone deacetylase 2	257	Histone deacetylase.				blood coagulation|dendrite development|embryonic digit morphogenesis|epidermal cell differentiation|eyelid development in camera-type eye|fungiform papilla formation|hair follicle placode formation|maintenance of chromatin silencing|negative regulation of apoptosis|negative regulation of cell cycle|negative regulation of neuron projection development|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|odontogenesis of dentine-containing tooth|positive regulation of cell proliferation|positive regulation of proteolysis|positive regulation of receptor biosynthetic process|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|ESC/E(Z) complex|NuRD complex|Sin3 complex	chromatin binding|enzyme binding|histone deacetylase activity (H3-K16 specific)|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|sequence-specific DNA binding|transcription factor binding			skin(2)|ovary(1)|central_nervous_system(1)	4		all_cancers(87;0.000629)|all_epithelial(87;0.00274)|Colorectal(196;0.0317)|all_lung(197;0.24)		all cancers(137;0.00318)|OV - Ovarian serous cystadenocarcinoma(136;0.00569)|Epithelial(106;0.0112)|GBM - Glioblastoma multiforme(226;0.0832)	Vorinostat(DB02546)													---	---	---	---
COL10A1	1300	broad.mit.edu	37	6	116442721	116442721	+	Silent	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:116442721T>A	uc003pwm.2	-	3	654	c.558A>T	c.(556-558)GGA>GGT	p.G186G	NT5DC1_uc003pwj.2_Intron|NT5DC1_uc003pwk.2_Intron|NT5DC1_uc003pwl.2_Intron	NM_000493	NP_000484	Q03692	COAA1_HUMAN	type X collagen alpha 1 precursor	186	Triple-helical region.				skeletal system development	collagen	metal ion binding			central_nervous_system(1)	1		all_cancers(87;0.0176)|all_epithelial(87;0.0263)|Colorectal(196;0.234)		all cancers(137;0.0157)|OV - Ovarian serous cystadenocarcinoma(136;0.0325)|GBM - Glioblastoma multiforme(226;0.0446)|Epithelial(106;0.0711)														---	---	---	---
ROS1	6098	broad.mit.edu	37	6	117710559	117710559	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117710559G>A	uc003pxp.1	-	12	1912	c.1713C>T	c.(1711-1713)CAC>CAT	p.H571H	ROS1_uc011ebi.1_Intron|GOPC_uc003pxq.1_Intron	NM_002944	NP_002935	P08922	ROS_HUMAN	proto-oncogene c-ros-1 protein precursor	571	Fibronectin type-III 3.|Extracellular (Potential).				transmembrane receptor protein tyrosine kinase signaling pathway	membrane fraction|sodium:potassium-exchanging ATPase complex	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(8)|ovary(6)|central_nervous_system(3)|skin(3)|stomach(2)|breast(2)|large_intestine(1)	25		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)				T	GOPC|ROS1	glioblastoma|NSCLC								---	---	---	---
ROS1	6098	broad.mit.edu	37	6	117710820	117710820	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117710820G>A	uc003pxp.1	-	12	1651	c.1452C>T	c.(1450-1452)GGC>GGT	p.G484G	ROS1_uc011ebi.1_RNA|GOPC_uc003pxq.1_Intron	NM_002944	NP_002935	P08922	ROS_HUMAN	proto-oncogene c-ros-1 protein precursor	484	Extracellular (Potential).				transmembrane receptor protein tyrosine kinase signaling pathway	membrane fraction|sodium:potassium-exchanging ATPase complex	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(8)|ovary(6)|central_nervous_system(3)|skin(3)|stomach(2)|breast(2)|large_intestine(1)	25		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)				T	GOPC|ROS1	glioblastoma|NSCLC								---	---	---	---
C6orf174	387104	broad.mit.edu	37	6	127796567	127796567	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:127796567G>A	uc003qbd.2	-	6	3469	c.2604C>T	c.(2602-2604)CAC>CAT	p.H868H	C6orf174_uc003qbc.2_Translation_Start_Site	NM_001012279	NP_001012279	Q5TF21	CF174_HUMAN	hypothetical protein LOC387104 precursor	868						integral to membrane				breast(3)|ovary(2)|skin(1)	6				GBM - Glioblastoma multiforme(226;0.026)|all cancers(137;0.161)														---	---	---	---
LAMA2	3908	broad.mit.edu	37	6	129785561	129785561	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:129785561G>A	uc003qbn.2	+	49	7224	c.7119G>A	c.(7117-7119)TCG>TCA	p.S2373S	LAMA2_uc003qbo.2_Silent_p.S2373S	NM_000426	NP_000417	P24043	LAMA2_HUMAN	laminin alpha 2 subunit isoform a precursor	2373	Laminin G-like 2.				cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)														---	---	---	---
TMEM200A	114801	broad.mit.edu	37	6	130761721	130761721	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130761721C>T	uc003qca.2	+	3	1025	c.154C>T	c.(154-156)CGT>TGT	p.R52C	TMEM200A_uc010kfh.2_Missense_Mutation_p.R52C|TMEM200A_uc010kfi.2_Missense_Mutation_p.R52C|TMEM200A_uc003qcb.2_Missense_Mutation_p.R52C	NM_052913	NP_443145	Q86VY9	T200A_HUMAN	transmembrane protein 200A	52	Cytoplasmic (Potential).					integral to membrane				ovary(1)	1				GBM - Glioblastoma multiforme(226;0.0139)|OV - Ovarian serous cystadenocarcinoma(155;0.12)														---	---	---	---
TMEM200A	114801	broad.mit.edu	37	6	130761894	130761894	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130761894C>T	uc003qca.2	+	3	1198	c.327C>T	c.(325-327)GGC>GGT	p.G109G	TMEM200A_uc010kfh.2_Silent_p.G109G|TMEM200A_uc010kfi.2_Silent_p.G109G|TMEM200A_uc003qcb.2_Silent_p.G109G	NM_052913	NP_443145	Q86VY9	T200A_HUMAN	transmembrane protein 200A	109	Extracellular (Potential).					integral to membrane				ovary(1)	1				GBM - Glioblastoma multiforme(226;0.0139)|OV - Ovarian serous cystadenocarcinoma(155;0.12)														---	---	---	---
MED23	9439	broad.mit.edu	37	6	131912516	131912516	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:131912516G>A	uc003qcs.1	-	26	3797	c.3623C>T	c.(3622-3624)ACG>ATG	p.T1208M	MED23_uc003qcq.2_Missense_Mutation_p.T1214M|MED23_uc003qcr.1_Missense_Mutation_p.T63M	NM_004830	NP_004821	Q9ULK4	MED23_HUMAN	mediator complex subunit 23 isoform a	1208					regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	transcription factor complex	protein binding|transcription coactivator activity			ovary(1)|kidney(1)|central_nervous_system(1)	3	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0115)|OV - Ovarian serous cystadenocarcinoma(155;0.0608)														---	---	---	---
MOXD1	26002	broad.mit.edu	37	6	132636911	132636911	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:132636911T>C	uc003qdf.2	-	10	1470	c.1371A>G	c.(1369-1371)GGA>GGG	p.G457G	MOXD1_uc003qde.2_Silent_p.G389G	NM_015529	NP_056344	Q6UVY6	MOXD1_HUMAN	monooxygenase, DBH-like 1 isoform 2	457	Lumenal (Potential).				catecholamine metabolic process	endoplasmic reticulum membrane|integral to membrane	copper ion binding|dopamine beta-monooxygenase activity			ovary(1)	1	Breast(56;0.0495)			OV - Ovarian serous cystadenocarcinoma(155;0.0132)|GBM - Glioblastoma multiforme(226;0.0191)														---	---	---	---
MYB	4602	broad.mit.edu	37	6	135507123	135507123	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135507123C>T	uc003qfc.2	+	2	305	c.106C>T	c.(106-108)CGT>TGT	p.R36C	MYB_uc003qfh.2_Missense_Mutation_p.R36C|MYB_uc003qfi.2_Missense_Mutation_p.R36C|MYB_uc010kgi.2_Missense_Mutation_p.R36C|MYB_uc003qfq.2_Missense_Mutation_p.R36C|MYB_uc010kgj.2_Missense_Mutation_p.R36C|MYB_uc003qfo.2_Missense_Mutation_p.R36C|MYB_uc003qfu.2_Missense_Mutation_p.R36C|MYB_uc003qfl.2_RNA|MYB_uc003qfv.2_RNA|MYB_uc003qfz.2_RNA|MYB_uc003qfx.2_RNA|MYB_uc003qga.2_RNA|MYB_uc003qgb.2_RNA|MYB_uc010kgk.2_RNA|MYB_uc003qfd.2_RNA|MYB_uc003qfe.2_RNA|MYB_uc003qfg.2_RNA|MYB_uc003qff.2_RNA|MYB_uc003qfj.2_RNA|MYB_uc003qfm.2_RNA|MYB_uc003qfp.2_RNA|MYB_uc003qfn.2_RNA|MYB_uc003qfk.2_RNA|MYB_uc003qfr.2_RNA|MYB_uc003qfs.2_5'UTR|MYB_uc003qft.2_RNA|MYB_uc003qfw.2_5'UTR|MYB_uc003qfy.2_RNA|MYB_uc003qgc.2_RNA|MYB_uc003qfb.1_Missense_Mutation_p.R36C|MYB_uc003qgd.1_5'Flank	NM_005375	NP_005366	P10242	MYB_HUMAN	v-myb myeloblastosis viral oncogene homolog	36	HTH myb-type 1.				blood coagulation|chromatin remodeling|negative regulation of transcription from RNA polymerase II promoter|positive regulation of histone H3-K4 methylation|positive regulation of histone H3-K9 methylation|positive regulation of T-helper cell differentiation|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear matrix	DNA binding|protein binding			lung(1)	1	all_epithelial(2;0.109)|Breast(56;0.158)|Colorectal(23;0.221)	Lung NSC(302;3.08e-05)|Ovarian(999;0.208)		OV - Ovarian serous cystadenocarcinoma(155;0.0079)|GBM - Glioblastoma multiforme(68;0.0117)				T	NFIB	adenoid cystic carcinoma								---	---	---	---
MYB	4602	broad.mit.edu	37	6	135520064	135520064	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135520064A>G	uc003qfc.2	+	10	1421	c.1222A>G	c.(1222-1224)AAC>GAC	p.N408D	MYB_uc003qfh.2_Missense_Mutation_p.N529D|MYB_uc003qfi.2_Missense_Mutation_p.N513D|MYB_uc010kgi.2_Missense_Mutation_p.N408D|MYB_uc003qfq.2_Missense_Mutation_p.N526D|MYB_uc010kgj.2_Missense_Mutation_p.N373D|MYB_uc003qfo.2_Missense_Mutation_p.N323D|MYB_uc003qfu.2_Missense_Mutation_p.N405D|MYB_uc003qfl.2_RNA|MYB_uc003qfv.2_RNA|MYB_uc003qfz.2_RNA|MYB_uc003qfx.2_RNA|MYB_uc003qga.2_RNA|MYB_uc003qgb.2_RNA|MYB_uc010kgk.2_RNA|MYB_uc003qfd.2_RNA|MYB_uc003qfe.2_RNA|MYB_uc003qfg.2_RNA|MYB_uc003qff.2_RNA|MYB_uc003qfj.2_RNA|MYB_uc003qfm.2_RNA|MYB_uc003qfp.2_RNA|MYB_uc003qfn.2_RNA|MYB_uc003qfk.2_RNA|MYB_uc003qfr.2_RNA|MYB_uc003qfs.2_Missense_Mutation_p.N34D|MYB_uc003qft.2_RNA|MYB_uc003qfw.2_Missense_Mutation_p.N220D|MYB_uc003qfy.2_RNA|MYB_uc003qgc.2_RNA|MYB_uc003qfb.1_Missense_Mutation_p.N408D	NM_005375	NP_005366	P10242	MYB_HUMAN	v-myb myeloblastosis viral oncogene homolog	408	Negative regulatory domain (By similarity).				blood coagulation|chromatin remodeling|negative regulation of transcription from RNA polymerase II promoter|positive regulation of histone H3-K4 methylation|positive regulation of histone H3-K9 methylation|positive regulation of T-helper cell differentiation|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear matrix	DNA binding|protein binding			lung(1)	1	all_epithelial(2;0.109)|Breast(56;0.158)|Colorectal(23;0.221)	Lung NSC(302;3.08e-05)|Ovarian(999;0.208)		OV - Ovarian serous cystadenocarcinoma(155;0.0079)|GBM - Glioblastoma multiforme(68;0.0117)				T	NFIB	adenoid cystic carcinoma								---	---	---	---
AHI1	54806	broad.mit.edu	37	6	135768283	135768283	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:135768283G>A	uc003qgi.2	-	13	2026	c.1642C>T	c.(1642-1644)CGC>TGC	p.R548C	AHI1_uc003qgg.2_5'UTR|AHI1_uc003qgh.2_Missense_Mutation_p.R548C|AHI1_uc003qgj.2_Missense_Mutation_p.R548C|AHI1_uc003qgk.3_RNA|AHI1_uc003qgl.3_Missense_Mutation_p.R548C	NM_001134831	NP_001128303	Q8N157	AHI1_HUMAN	Abelson helper integration site 1 isoform a	548						adherens junction|cilium|microtubule basal body				ovary(1)|kidney(1)|central_nervous_system(1)	3	Breast(56;0.239)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00904)|OV - Ovarian serous cystadenocarcinoma(155;0.00991)														---	---	---	---
PEX7	5191	broad.mit.edu	37	6	137146413	137146413	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:137146413A>G	uc003qhd.2	+						PEX7_uc010kgx.2_Intron	NM_000288	NP_000279			peroxisomal biogenesis factor 7						ether lipid biosynthetic process|protein import into peroxisome matrix	peroxisome	peroxisome matrix targeting signal-2 binding				0	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000257)|OV - Ovarian serous cystadenocarcinoma(155;0.00492)														---	---	---	---
ECT2L	345930	broad.mit.edu	37	6	139165650	139165650	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:139165650C>T	uc003qif.1	+	5	800	c.697C>T	c.(697-699)CGA>TGA	p.R233*	ECT2L_uc011edq.1_Nonsense_Mutation_p.R164*	NM_001077706	NP_001071174	Q008S8	ECT2L_HUMAN	epithelial cell transforming sequence 2	233					regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity				0																		---	---	---	---
NMBR	4829	broad.mit.edu	37	6	142399811	142399811	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:142399811A>C	uc003qiu.2	-	2	793	c.652T>G	c.(652-654)TTG>GTG	p.L218V		NM_002511	NP_002502	P28336	NMBR_HUMAN	neuromedin B receptor	218	Helical; Name=5; (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger	cytoplasm|integral to plasma membrane	bombesin receptor activity			central_nervous_system(3)|breast(1)	4	Breast(32;0.155)			OV - Ovarian serous cystadenocarcinoma(155;9.93e-06)|GBM - Glioblastoma multiforme(68;0.0013)														---	---	---	---
ADAT2	134637	broad.mit.edu	37	6	143753713	143753713	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:143753713G>A	uc003qjj.2	-	4	434	c.388C>T	c.(388-390)CGA>TGA	p.R130*		NM_182503	NP_872309	Q7Z6V5	ADAT2_HUMAN	deaminase domain containing 1	130					tRNA processing		hydrolase activity|zinc ion binding				0				OV - Ovarian serous cystadenocarcinoma(155;5.61e-06)|GBM - Glioblastoma multiforme(68;0.0115)														---	---	---	---
PHACTR2	9749	broad.mit.edu	37	6	144095271	144095271	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:144095271T>C	uc003qjq.3	+	8	1605	c.1475T>C	c.(1474-1476)CTA>CCA	p.L492P	PHACTR2_uc010khh.2_Missense_Mutation_p.L412P|PHACTR2_uc010khi.2_Missense_Mutation_p.L503P|PHACTR2_uc003qjr.3_Missense_Mutation_p.L423P	NM_014721	NP_055536	O75167	PHAR2_HUMAN	phosphatase and actin regulator 2 isoform 3	492	RPEL 2.						actin binding|protein phosphatase inhibitor activity			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(155;1.58e-05)|GBM - Glioblastoma multiforme(68;0.0386)														---	---	---	---
UTRN	7402	broad.mit.edu	37	6	145051513	145051513	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:145051513G>T	uc003qkt.2	+	53	7922	c.7830G>T	c.(7828-7830)AAG>AAT	p.K2610N		NM_007124	NP_009055	P46939	UTRO_HUMAN	utrophin	2610	Spectrin 18.				muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion	cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane	actin binding|calcium ion binding|zinc ion binding			ovary(4)|pancreas(1)	5		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)														---	---	---	---
SHPRH	257218	broad.mit.edu	37	6	146244827	146244827	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146244827A>T	uc003qlf.2	-	18	3896	c.3497T>A	c.(3496-3498)ATA>AAA	p.I1166K	SHPRH_uc003qld.2_Missense_Mutation_p.I1175K|SHPRH_uc003qle.2_Missense_Mutation_p.I1175K|SHPRH_uc003qlg.1_Missense_Mutation_p.I722K|SHPRH_uc003qlh.2_Missense_Mutation_p.I91K|SHPRH_uc003qli.1_Missense_Mutation_p.I91K	NM_001042683	NP_001036148	Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase isoform a	1166					DNA repair|nucleosome assembly	nucleosome|nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)|kidney(1)|central_nervous_system(1)	3		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)														---	---	---	---
SHPRH	257218	broad.mit.edu	37	6	146276182	146276182	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146276182A>G	uc003qlf.2	-	2	676	c.277T>C	c.(277-279)TCC>CCC	p.S93P	SHPRH_uc003qld.2_Missense_Mutation_p.S93P|SHPRH_uc003qle.2_Missense_Mutation_p.S93P|SHPRH_uc003qlg.1_5'UTR|SHPRH_uc003qlj.1_Intron|SHPRH_uc003qlk.1_Missense_Mutation_p.S93P	NM_001042683	NP_001036148	Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase isoform a	93					DNA repair|nucleosome assembly	nucleosome|nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)|kidney(1)|central_nervous_system(1)	3		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)														---	---	---	---
STXBP5	134957	broad.mit.edu	37	6	147705839	147705839	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:147705839T>C	uc003qlz.2	+						STXBP5_uc010khz.1_Intron|STXBP5_uc003qlx.2_Intron|STXBP5_uc003qly.2_Intron|uc003qmb.2_5'Flank	NM_001127715	NP_001121187			syntaxin binding protein 5 (tomosyn) isoform b						exocytosis|positive regulation of exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|nicotinic acetylcholine-gated receptor-channel complex|synaptic vesicle	syntaxin-1 binding				0		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.77e-09)|GBM - Glioblastoma multiforme(68;0.0694)														---	---	---	---
TAB2	23118	broad.mit.edu	37	6	149699251	149699251	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149699251G>T	uc003qmj.2	+	3	378	c.200G>T	c.(199-201)GGA>GTA	p.G67V	TAB2_uc011eec.1_Missense_Mutation_p.G35V|TAB2_uc010kia.1_Missense_Mutation_p.G67V|TAB2_uc010kib.1_Missense_Mutation_p.G67V|TAB2_uc003qmk.3_RNA	NM_015093	NP_055908	Q9NYJ8	TAB2_HUMAN	mitogen-activated protein kinase kinase kinase 7	67					activation of MAPK activity|heart development|I-kappaB kinase/NF-kappaB cascade|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane|plasma membrane	K63-linked polyubiquitin binding|zinc ion binding				0																		---	---	---	---
RAET1E	135250	broad.mit.edu	37	6	150210711	150210711	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:150210711C>T	uc003qnl.1	-	3	455	c.395G>A	c.(394-396)CGG>CAG	p.R132Q	uc003qni.1_Intron|RAET1E_uc003qnj.2_Missense_Mutation_p.R132Q|RAET1E_uc003qnk.1_Missense_Mutation_p.R96Q|RAET1E_uc010kih.1_RNA	NM_139165	NP_631904	Q8TD07	N2DL4_HUMAN	retinoic acid early transcript 1E precursor	132	Extracellular (Potential).|MHC class I alpha-2 like.				antigen processing and presentation|immune response|regulation of immune response	integral to membrane|MHC class I protein complex	protein binding				0		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.58e-12)														---	---	---	---
ZBTB2	57621	broad.mit.edu	37	6	151687616	151687616	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151687616T>C	uc003qoh.2	-	3	720	c.585A>G	c.(583-585)TCA>TCG	p.S195S		NM_020861	NP_065912	Q8N680	ZBTB2_HUMAN	zinc finger and BTB domain containing 2	195					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1			BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.63e-11)														---	---	---	---
C6orf97	80129	broad.mit.edu	37	6	151917673	151917673	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:151917673C>T	uc003qol.2	+	9	1760	c.1671C>T	c.(1669-1671)ACC>ACT	p.T557T		NM_025059	NP_079335	Q8IYT3	CF097_HUMAN	hypothetical protein LOC80129	557	Potential.										0		Ovarian(120;0.126)	BRCA - Breast invasive adenocarcinoma(37;0.111)	OV - Ovarian serous cystadenocarcinoma(155;1.48e-10)														---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152454579	152454579	+	Silent	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152454579A>C	uc010kiw.2	-	143	26435	c.25833T>G	c.(25831-25833)TCT>TCG	p.S8611S	SYNE1_uc010kiv.2_Silent_p.S3135S|SYNE1_uc003qos.3_Silent_p.S3135S|SYNE1_uc003qot.3_Silent_p.S8563S|SYNE1_uc003qou.3_Silent_p.S8611S|SYNE1_uc003qop.3_Silent_p.S796S|SYNE1_uc011eez.1_Silent_p.S813S|SYNE1_uc003qoq.3_Silent_p.S813S|SYNE1_uc003qor.3_Silent_p.S1534S	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	8611	Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)											HNSCC(10;0.0054)			---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152477105	152477105	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152477105G>A	uc010kiw.2	-	132	24520	c.23918C>T	c.(23917-23919)ACG>ATG	p.T7973M	SYNE1_uc010kiv.2_Missense_Mutation_p.T2497M|SYNE1_uc003qos.3_Missense_Mutation_p.T2497M|SYNE1_uc003qot.3_Missense_Mutation_p.T7902M|SYNE1_uc003qou.3_Missense_Mutation_p.T7973M|SYNE1_uc003qop.3_Missense_Mutation_p.T135M|SYNE1_uc011eez.1_Missense_Mutation_p.T175M|SYNE1_uc003qoq.3_Missense_Mutation_p.T175M|SYNE1_uc003qor.3_Missense_Mutation_p.T873M	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	7973	Spectrin 28.|Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)											HNSCC(10;0.0054)			---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152650875	152650875	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152650875C>T	uc010kiw.2	-	78	15547	c.14945G>A	c.(14944-14946)CGC>CAC	p.R4982H	SYNE1_uc003qot.3_Missense_Mutation_p.R4911H|SYNE1_uc003qou.3_Missense_Mutation_p.R4982H|SYNE1_uc010kiz.2_Missense_Mutation_p.R737H	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	4982	Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)											HNSCC(10;0.0054)			---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152671751	152671751	+	Splice_Site	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152671751A>G	uc010kiw.2	-	71	12335	c.11733_splice	c.e71+1	p.K3911_splice	SYNE1_uc003qot.3_Splice_Site_p.K3896_splice|SYNE1_uc003qou.3_Splice_Site_p.K3911_splice|SYNE1_uc010kja.1_Splice_Site_p.K616_splice	NM_182961	NP_892006			spectrin repeat containing, nuclear envelope 1						cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)											HNSCC(10;0.0054)			---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152737703	152737703	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152737703C>A	uc010kiw.2	-	41	6471	c.5869G>T	c.(5869-5871)GGA>TGA	p.G1957*	SYNE1_uc003qot.3_Nonsense_Mutation_p.G1964*|SYNE1_uc003qou.3_Nonsense_Mutation_p.G1957*|SYNE1_uc010kjb.1_Nonsense_Mutation_p.G1940*	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1957	Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)											HNSCC(10;0.0054)			---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152749430	152749430	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152749430G>A	uc010kiw.2	-	37	5488	c.4886C>T	c.(4885-4887)GCT>GTT	p.A1629V	SYNE1_uc003qot.3_Missense_Mutation_p.A1636V|SYNE1_uc003qou.3_Missense_Mutation_p.A1629V|SYNE1_uc010kjb.1_Missense_Mutation_p.A1612V|SYNE1_uc003qow.2_Missense_Mutation_p.A924V	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1629	Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)											HNSCC(10;0.0054)			---	---	---	---
SYNE1	23345	broad.mit.edu	37	6	152792721	152792721	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:152792721G>A	uc010kiw.2	-						SYNE1_uc003qot.3_Intron|SYNE1_uc003qou.3_Intron|SYNE1_uc010kjb.1_Intron|SYNE1_uc003qpa.1_Intron|SYNE1_uc003qox.1_Intron|SYNE1_uc003qoz.2_Intron|SYNE1_uc003qoy.2_Intron	NM_182961	NP_892006			spectrin repeat containing, nuclear envelope 1						cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)											HNSCC(10;0.0054)			---	---	---	---
IPCEF1	26034	broad.mit.edu	37	6	154489164	154489164	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154489164C>T	uc003qpx.2	-	11	1148	c.992G>A	c.(991-993)CGA>CAA	p.R331Q	OPRM1_uc003qpt.1_Intron|IPCEF1_uc003qpv.2_Missense_Mutation_p.R202Q|IPCEF1_uc003qpw.2_Missense_Mutation_p.R332Q|IPCEF1_uc010kjh.2_Missense_Mutation_p.R332Q	NM_015553	NP_056368	Q8WWN9	ICEF1_HUMAN	phosphoinositide-binding protein PIP3-E isoform	331					response to oxidative stress	cytoplasm|plasma membrane	oxygen transporter activity|peroxidase activity				0																		---	---	---	---
IPCEF1	26034	broad.mit.edu	37	6	154533925	154533925	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:154533925G>A	uc003qpx.2	-	9	669	c.513C>T	c.(511-513)CAC>CAT	p.H171H	OPRM1_uc003qpt.1_Intron|IPCEF1_uc003qpv.2_Silent_p.H42H|IPCEF1_uc003qpw.2_Silent_p.H172H|IPCEF1_uc010kjh.2_Silent_p.H172H	NM_015553	NP_056368	Q8WWN9	ICEF1_HUMAN	phosphoinositide-binding protein PIP3-E isoform	171					response to oxidative stress	cytoplasm|plasma membrane	oxygen transporter activity|peroxidase activity				0																		---	---	---	---
TIAM2	26230	broad.mit.edu	37	6	155451095	155451095	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155451095G>T	uc003qqb.2	+	6	2011	c.738G>T	c.(736-738)GAG>GAT	p.E246D	TIAM2_uc003qqe.2_Missense_Mutation_p.E246D	NM_012454	NP_036586	Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	246					apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			ovary(3)|breast(1)	4		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)														---	---	---	---
TIAM2	26230	broad.mit.edu	37	6	155571016	155571016	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:155571016C>T	uc003qqb.2	+	23	5137	c.3864C>T	c.(3862-3864)AGC>AGT	p.S1288S	TIAM2_uc003qqe.2_Silent_p.S1288S|TIAM2_uc010kjj.2_Silent_p.S821S|TIAM2_uc003qqf.2_Silent_p.S664S|TIAM2_uc011efl.1_Silent_p.S624S|TIAM2_uc003qqg.2_Silent_p.S600S|TIAM2_uc003qqh.2_Silent_p.S213S	NM_012454	NP_036586	Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	1288	DH.				apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			ovary(3)|breast(1)	4		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)														---	---	---	---
ARID1B	57492	broad.mit.edu	37	6	157150504	157150504	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157150504C>T	uc003qqn.2	+	2	1664	c.1512C>T	c.(1510-1512)ATC>ATT	p.I504I	ARID1B_uc003qqo.2_Silent_p.I504I|ARID1B_uc003qqp.2_Silent_p.I504I	NM_017519	NP_059989	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	562					chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent	SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			ovary(1)|breast(1)	2		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)														---	---	---	---
SYNJ2	8871	broad.mit.edu	37	6	158454575	158454575	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158454575C>T	uc003qqx.1	+	4	649	c.574C>T	c.(574-576)CGC>TGC	p.R192C	SYNJ2_uc011efm.1_RNA|SYNJ2_uc003qqw.1_Missense_Mutation_p.R192C|SYNJ2_uc003qqy.1_5'UTR|SYNJ2_uc011efn.1_Missense_Mutation_p.R141C|SYNJ2_uc010kjo.1_Missense_Mutation_p.R141C	NM_003898	NP_003889	O15056	SYNJ2_HUMAN	synaptojanin 2	192	SAC.						nucleotide binding|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|RNA binding			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05)														---	---	---	---
SYNJ2	8871	broad.mit.edu	37	6	158487608	158487608	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158487608C>T	uc003qqx.1	+	12	1733	c.1658C>T	c.(1657-1659)GCG>GTG	p.A553V	SYNJ2_uc011efm.1_RNA|SYNJ2_uc003qqw.1_Missense_Mutation_p.A553V|SYNJ2_uc003qqy.1_Missense_Mutation_p.A266V|SYNJ2_uc011efn.1_Missense_Mutation_p.A481V|SYNJ2_uc010kjo.1_Missense_Mutation_p.A502V|SYNJ2_uc003qqz.1_Missense_Mutation_p.A170V	NM_003898	NP_003889	O15056	SYNJ2_HUMAN	synaptojanin 2	553	Catalytic (By similarity).						nucleotide binding|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|RNA binding			skin(1)	1				OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05)														---	---	---	---
TULP4	56995	broad.mit.edu	37	6	158882766	158882766	+	Intron	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:158882766G>T	uc003qrf.2	+						TULP4_uc011efo.1_Intron|TULP4_uc003qrg.2_Intron	NM_020245	NP_064630			tubby like protein 4 isoform 1						intracellular signal transduction|response to nutrient	cytoplasm	protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)														---	---	---	---
SOD2	6648	broad.mit.edu	37	6	160109219	160109219	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160109219A>G	uc003qsg.2	-	3	436	c.282T>C	c.(280-282)GGT>GGC	p.G94G	SOD2_uc003qsh.2_Intron|SOD2_uc003qsi.1_Silent_p.G94G|SOD2_uc011efu.1_Silent_p.G94G|SOD2_uc011efv.1_Intron	NM_001024465	NP_001019636	P04179	SODM_HUMAN	manganese superoxide dismutase isoform A	94					age-dependent response to reactive oxygen species|negative regulation of neuron apoptosis|oxygen homeostasis|protein homotetramerization|regulation of transcription from RNA polymerase II promoter|release of cytochrome c from mitochondria|removal of superoxide radicals|vasodilation by acetylcholine involved in regulation of systemic arterial blood pressure		manganese ion binding|superoxide dismutase activity				0		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.103)		OV - Ovarian serous cystadenocarcinoma(65;1.4e-18)|BRCA - Breast invasive adenocarcinoma(81;5.77e-06)														---	---	---	---
IGF2R	3482	broad.mit.edu	37	6	160489293	160489293	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160489293C>T	uc003qta.2	+	30	4276	c.4128C>T	c.(4126-4128)GGC>GGT	p.G1376G		NM_000876	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor precursor	1376	9.|Lumenal (Potential).				receptor-mediated endocytosis	cell surface|endocytic vesicle|endosome|integral to plasma membrane|lysosomal membrane|trans-Golgi network transport vesicle	glycoprotein binding|insulin-like growth factor receptor activity|phosphoprotein binding|transporter activity			ovary(3)	3		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)														---	---	---	---
IGF2R	3482	broad.mit.edu	37	6	160500711	160500711	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160500711G>T	uc003qta.2	+	38	5726	c.5578G>T	c.(5578-5580)GGC>TGC	p.G1860C		NM_000876	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor precursor	1860	13.|Lumenal (Potential).				receptor-mediated endocytosis	cell surface|endocytic vesicle|endosome|integral to plasma membrane|lysosomal membrane|trans-Golgi network transport vesicle	glycoprotein binding|insulin-like growth factor receptor activity|phosphoprotein binding|transporter activity			ovary(3)	3		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)														---	---	---	---
SLC22A2	6582	broad.mit.edu	37	6	160666577	160666577	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:160666577G>A	uc003qtf.2	-	6	1128	c.958C>T	c.(958-960)CGC>TGC	p.R320C	SLC22A2_uc003qte.1_Missense_Mutation_p.R320C	NM_003058	NP_003049	O15244	S22A2_HUMAN	solute carrier family 22 member 2	320	Cytoplasmic (Potential).				body fluid secretion|neurotransmitter biosynthetic process|neurotransmitter secretion	integral to plasma membrane|membrane fraction	neurotransmitter transporter activity|organic cation transmembrane transporter activity			breast(1)|skin(1)	2		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.28e-17)|BRCA - Breast invasive adenocarcinoma(81;6.29e-06)														---	---	---	---
MAP3K4	4216	broad.mit.edu	37	6	161523751	161523751	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161523751G>A	uc003qtn.2	+	19	3938	c.3796G>A	c.(3796-3798)GAT>AAT	p.D1266N	MAP3K4_uc010kkc.1_Missense_Mutation_p.D1262N|MAP3K4_uc003qto.2_Missense_Mutation_p.D1216N|MAP3K4_uc011efz.1_RNA|MAP3K4_uc011ega.1_Missense_Mutation_p.D719N|MAP3K4_uc003qtp.2_Missense_Mutation_p.D202N|MAP3K4_uc003qtq.2_5'UTR	NM_005922	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	1266					activation of MAPKK activity|JNK cascade|positive regulation of JUN kinase activity	perinuclear region of cytoplasm	ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein binding			ovary(3)|lung(3)|skin(2)|stomach(1)	9		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)														---	---	---	---
T	6862	broad.mit.edu	37	6	166580295	166580295	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:166580295C>T	uc003quu.1	-	3	749	c.256G>A	c.(256-258)GCC>ACC	p.A86T	T_uc003qut.1_Missense_Mutation_p.A86T|T_uc003quv.1_Missense_Mutation_p.A86T	NM_003181	NP_003172	O15178	BRAC_HUMAN	transcription factor T	86	T-box.				anterior/posterior axis specification, embryo|mesoderm development|primitive streak formation	nucleus	sequence-specific DNA binding transcription factor activity			ovary(1)|pancreas(1)	2		Prostate(117;4.48e-07)|Ovarian(120;1.78e-06)|Breast(66;2.54e-06)|Lung SC(201;0.0225)|Esophageal squamous(34;0.0559)		OV - Ovarian serous cystadenocarcinoma(33;1.09e-113)|GBM - Glioblastoma multiforme(31;1.51e-108)|BRCA - Breast invasive adenocarcinoma(81;8.45e-09)|LUAD - Lung adenocarcinoma(999;0.0407)										Chordoma_Familial_Clustering_of				---	---	---	---
CCR6	1235	broad.mit.edu	37	6	167550223	167550223	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:167550223C>A	uc003qvl.2	+	13	2981	c.505C>A	c.(505-507)CTT>ATT	p.L169I	CCR6_uc010kkm.2_Missense_Mutation_p.L169I|CCR6_uc003qvn.3_Missense_Mutation_p.L169I|CCR6_uc003qvm.3_Missense_Mutation_p.L169I	NM_031409	NP_113597	P51684	CCR6_HUMAN	chemokine (C-C motif) receptor 6	169	Helical; Name=4; (Potential).				cellular defense response|dendritic cell chemotaxis|elevation of cytosolic calcium ion concentration|humoral immune response	integral to plasma membrane	C-C chemokine receptor activity			ovary(1)	1		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;8.21e-20)|BRCA - Breast invasive adenocarcinoma(81;4.55e-06)|GBM - Glioblastoma multiforme(31;0.00507)														---	---	---	---
MLLT4	4301	broad.mit.edu	37	6	168315893	168315893	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168315893G>A	uc003qwd.2	+	18	2463	c.2321G>A	c.(2320-2322)CGC>CAC	p.R774H	MLLT4_uc003qwb.1_Missense_Mutation_p.R759H|MLLT4_uc003qwc.1_Missense_Mutation_p.R775H|MLLT4_uc003qwg.1_Missense_Mutation_p.R84H	NM_001040001	NP_001035090	P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	775	Dilute.				adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction	adherens junction|cell-cell junction|cytosol|nucleus	protein C-terminus binding			ovary(2)|lung(1)|kidney(1)|central_nervous_system(1)	5		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)				T	MLL	AL								---	---	---	---
MLLT4	4301	broad.mit.edu	37	6	168352118	168352118	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168352118G>T	uc003qwd.2	+	29	4202	c.4060G>T	c.(4060-4062)GCC>TCC	p.A1354S	MLLT4_uc003qwb.1_Missense_Mutation_p.A1339S|MLLT4_uc003qwc.1_Missense_Mutation_p.A1355S|MLLT4_uc003qwg.1_Missense_Mutation_p.A664S	NM_001040001	NP_001035090	P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	1355	Pro-rich.				adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction	adherens junction|cell-cell junction|cytosol|nucleus	protein C-terminus binding			ovary(2)|lung(1)|kidney(1)|central_nervous_system(1)	5		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)				T	MLL	AL								---	---	---	---
FRMD1	79981	broad.mit.edu	37	6	168461499	168461499	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168461499C>T	uc003qwo.3	-	9	1349	c.1284G>A	c.(1282-1284)GAG>GAA	p.E428E	FRMD1_uc003qwm.3_Silent_p.E222E|FRMD1_uc011egs.1_Silent_p.E199E|FRMD1_uc011egt.1_Silent_p.E363E|FRMD1_uc003qwn.3_Silent_p.E360E	NM_024919	NP_079195	Q8N878	FRMD1_HUMAN	FERM domain containing 1 isoform 1	428						cytoskeleton	binding			ovary(1)	1		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)														---	---	---	---
FRMD1	79981	broad.mit.edu	37	6	168463623	168463623	+	Missense_Mutation	SNP	C	T	T	rs115999698	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168463623C>T	uc003qwo.3	-	7	886	c.821G>A	c.(820-822)CGT>CAT	p.R274H	FRMD1_uc003qwm.3_Missense_Mutation_p.R45H|FRMD1_uc011egs.1_Missense_Mutation_p.R45H|FRMD1_uc011egt.1_Missense_Mutation_p.R186H|FRMD1_uc003qwn.3_Missense_Mutation_p.R206H	NM_024919	NP_079195	Q8N878	FRMD1_HUMAN	FERM domain containing 1 isoform 1	274	FERM.					cytoskeleton	binding			ovary(1)	1		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)														---	---	---	---
FRMD1	79981	broad.mit.edu	37	6	168464304	168464304	+	Missense_Mutation	SNP	C	T	T	rs61751866	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:168464304C>T	uc003qwo.3	-	6	846	c.781G>A	c.(781-783)GTG>ATG	p.V261M	FRMD1_uc003qwm.3_Missense_Mutation_p.V32M|FRMD1_uc011egs.1_Missense_Mutation_p.V32M|FRMD1_uc011egt.1_Missense_Mutation_p.V173M|FRMD1_uc003qwn.3_Missense_Mutation_p.V193M	NM_024919	NP_079195	Q8N878	FRMD1_HUMAN	FERM domain containing 1 isoform 1	261	FERM.					cytoskeleton	binding			ovary(1)	1		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)														---	---	---	---
THBS2	7058	broad.mit.edu	37	6	169622360	169622360	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:169622360T>C	uc003qwt.2	-	20	3453	c.3205A>G	c.(3205-3207)AAC>GAC	p.N1069D		NM_003247	NP_003238	P35442	TSP2_HUMAN	thrombospondin 2 precursor	1069	TSP C-terminal.				cell adhesion	extracellular region	calcium ion binding|heparin binding|protein binding|structural molecule activity			ovary(5)	5		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)														---	---	---	---
PHF10	55274	broad.mit.edu	37	6	170105269	170105269	+	Silent	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170105269A>C	uc011egy.1	-	11	1450	c.1371T>G	c.(1369-1371)GGT>GGG	p.G457G	C6orf120_uc003qxb.2_3'UTR|PHF10_uc011egz.1_Silent_p.G455G	NM_018288	NP_060758	Q8WUB8	PHF10_HUMAN	PHD finger protein 10 isoform a	457	PHD-type 2; degenerate.				nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	npBAF complex	zinc ion binding			urinary_tract(1)	1		Breast(66;5.08e-05)|Ovarian(120;0.208)		OV - Ovarian serous cystadenocarcinoma(33;1.4e-21)|BRCA - Breast invasive adenocarcinoma(81;1.4e-07)|GBM - Glioblastoma multiforme(31;0.00176)														---	---	---	---
C6orf70	55780	broad.mit.edu	37	6	170176708	170176708	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170176708C>T	uc003qxg.1	+	16	1711	c.1678C>T	c.(1678-1680)CAG>TAG	p.Q560*	C6orf70_uc011ehb.1_Nonsense_Mutation_p.Q434*|C6orf70_uc003qxh.1_Intron|C6orf70_uc010kky.1_Intron|C6orf70_uc003qxi.1_Nonsense_Mutation_p.Q208*	NM_018341	NP_060811	Q5T6L9	CF070_HUMAN	hypothetical protein LOC55780	560						integral to membrane				ovary(1)	1		Breast(66;5.08e-05)|Ovarian(120;0.208)		OV - Ovarian serous cystadenocarcinoma(33;1.2e-22)|BRCA - Breast invasive adenocarcinoma(81;1.49e-07)|GBM - Glioblastoma multiforme(31;0.00191)														---	---	---	---
C6orf70	55780	broad.mit.edu	37	6	170176774	170176774	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170176774G>A	uc003qxg.1	+						C6orf70_uc011ehb.1_Intron|C6orf70_uc003qxh.1_Intron|C6orf70_uc010kky.1_Intron|C6orf70_uc003qxi.1_Intron	NM_018341	NP_060811			hypothetical protein LOC55780							integral to membrane				ovary(1)	1		Breast(66;5.08e-05)|Ovarian(120;0.208)		OV - Ovarian serous cystadenocarcinoma(33;1.2e-22)|BRCA - Breast invasive adenocarcinoma(81;1.49e-07)|GBM - Glioblastoma multiforme(31;0.00191)														---	---	---	---
FAM120B	84498	broad.mit.edu	37	6	170628024	170628024	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170628024T>C	uc003qxp.2	+	2	1654	c.1546T>C	c.(1546-1548)TCC>CCC	p.S516P	FAM120B_uc003qxo.1_Missense_Mutation_p.S516P|FAM120B_uc011ehd.1_Intron	NM_032448	NP_115824	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	516					cell differentiation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			ovary(1)	1		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)														---	---	---	---
TBP	6908	broad.mit.edu	37	6	170871279	170871279	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170871279C>T	uc003qxt.2	+	3	687	c.455C>T	c.(454-456)GCC>GTC	p.A152V	TBP_uc003qxu.2_Missense_Mutation_p.A152V|TBP_uc011ehf.1_Missense_Mutation_p.A132V|TBP_uc011ehg.1_Missense_Mutation_p.A152V	NM_003194	NP_003185	P20226	TBP_HUMAN	TATA box binding protein	152					cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction	transcription factor TFIIA complex|transcription factor TFIID complex	repressing transcription factor binding|transcription regulatory region DNA binding			ovary(1)	1		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)														---	---	---	---
PDCD2	5134	broad.mit.edu	37	6	170887994	170887994	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170887994T>G	uc003qxw.2	-	5	906	c.827A>C	c.(826-828)AAG>ACG	p.K276T	PDCD2_uc003qxv.2_Missense_Mutation_p.K243T|PDCD2_uc003qxx.1_Missense_Mutation_p.K276T	NM_002598	NP_002589	Q16342	PDCD2_HUMAN	programmed cell death 2 isoform 1	276					apoptosis	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding				0		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;6.91e-23)|BRCA - Breast invasive adenocarcinoma(81;4.82e-06)|GBM - Glioblastoma multiforme(31;0.142)														---	---	---	---
HEATR2	54919	broad.mit.edu	37	7	794268	794268	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:794268A>G	uc010krz.1	+	5	1087	c.1067A>G	c.(1066-1068)AAC>AGC	p.N356S	HEATR2_uc003siz.2_Missense_Mutation_p.N224S	NM_017802	NP_060272	Q86Y56	HEAT2_HUMAN	HEAT repeat containing 2	356	HEAT 5.						protein binding			skin(1)	1		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0182)|Epithelial(4;5.48e-17)|OV - Ovarian serous cystadenocarcinoma(56;1.95e-16)|all cancers(6;2.98e-14)														---	---	---	---
HEATR2	54919	broad.mit.edu	37	7	813814	813814	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:813814C>T	uc010krz.1	+	10	2081	c.2061C>T	c.(2059-2061)AGC>AGT	p.S687S	HEATR2_uc003siz.2_Silent_p.S555S|HEATR2_uc003sjb.2_Silent_p.S67S|HEATR2_uc003sjc.2_Silent_p.S112S	NM_017802	NP_060272	Q86Y56	HEAT2_HUMAN	HEAT repeat containing 2	687							protein binding			skin(1)	1		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0182)|Epithelial(4;5.48e-17)|OV - Ovarian serous cystadenocarcinoma(56;1.95e-16)|all cancers(6;2.98e-14)														---	---	---	---
MAD1L1	8379	broad.mit.edu	37	7	1997342	1997342	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:1997342C>A	uc003slh.1	-	16	1784	c.1518G>T	c.(1516-1518)GAG>GAT	p.E506D	MAD1L1_uc003sle.1_Missense_Mutation_p.E235D|MAD1L1_uc003slf.1_Missense_Mutation_p.E506D|MAD1L1_uc003slg.1_Missense_Mutation_p.E506D|MAD1L1_uc010ksh.1_Missense_Mutation_p.E506D|MAD1L1_uc003sli.1_Missense_Mutation_p.E414D|MAD1L1_uc010ksi.1_Missense_Mutation_p.E459D|MAD1L1_uc010ksj.2_Missense_Mutation_p.E506D	NM_001013836	NP_001013858	Q9Y6D9	MD1L1_HUMAN	MAD1-like 1 protein	506	Necessary for interaction with NEK2.|Potential.				cell division|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase|mitotic prometaphase|mitotic telophase	actin cytoskeleton|centrosome|condensed chromosome kinetochore|cytosol|mitochondrion|nucleus|spindle	protein binding			lung(1)|central_nervous_system(1)	2		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)														---	---	---	---
EIF3B	8662	broad.mit.edu	37	7	2414172	2414172	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2414172A>G	uc003slx.2	+	13	1903	c.1820A>G	c.(1819-1821)GAC>GGC	p.D607G	EIF3B_uc003sly.2_Missense_Mutation_p.D607G|EIF3B_uc003sma.2_Missense_Mutation_p.D335G|EIF3B_uc003smb.2_5'Flank	NM_003751	NP_003742	P55884	EIF3B_HUMAN	eukaryotic translation initiation factor 3,	607					regulation of translational initiation	cytosol|eukaryotic translation initiation factor 3 complex	nucleotide binding|protein complex scaffold|translation initiation factor activity				0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0833)|OV - Ovarian serous cystadenocarcinoma(56;7.76e-14)														---	---	---	---
CHST12	55501	broad.mit.edu	37	7	2472855	2472855	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2472855C>T	uc003smc.2	+	2	716	c.581C>T	c.(580-582)GCG>GTG	p.A194V	CHST12_uc003smd.2_Missense_Mutation_p.A194V	NM_018641	NP_061111	Q9NRB3	CHSTC_HUMAN	carbohydrate sulfotransferase 12	194	Lumenal (Potential).				dermatan sulfate biosynthetic process	integral to Golgi membrane	3'-phosphoadenosine 5'-phosphosulfate binding|chondroitin 4-sulfotransferase activity|protein binding			kidney(1)	1		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0847)|OV - Ovarian serous cystadenocarcinoma(56;2.25e-13)														---	---	---	---
CHST12	55501	broad.mit.edu	37	7	2473223	2473223	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2473223C>T	uc003smc.2	+	2	1084	c.949C>T	c.(949-951)CCC>TCC	p.P317S	CHST12_uc003smd.2_Missense_Mutation_p.P317S	NM_018641	NP_061111	Q9NRB3	CHSTC_HUMAN	carbohydrate sulfotransferase 12	317	Lumenal (Potential).				dermatan sulfate biosynthetic process	integral to Golgi membrane	3'-phosphoadenosine 5'-phosphosulfate binding|chondroitin 4-sulfotransferase activity|protein binding			kidney(1)	1		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0847)|OV - Ovarian serous cystadenocarcinoma(56;2.25e-13)														---	---	---	---
CARD11	84433	broad.mit.edu	37	7	2953027	2953027	+	Silent	SNP	G	A	A	rs61757651	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2953027G>A	uc003smv.2	-	22	3317	c.2913C>T	c.(2911-2913)TGC>TGT	p.C971C		NM_032415	NP_115791	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	971					positive regulation of cytokine production|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis|T cell costimulation|T cell receptor signaling pathway	cytosol|membrane raft|plasma membrane	CARD domain binding|guanylate kinase activity			haematopoietic_and_lymphoid_tissue(43)|ovary(2)|kidney(2)|skin(2)|central_nervous_system(1)	50		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)				Mis		DLBCL								---	---	---	---
CARD11	84433	broad.mit.edu	37	7	2962357	2962357	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2962357G>A	uc003smv.2	-	17	2584	c.2180C>T	c.(2179-2181)CCG>CTG	p.P727L		NM_032415	NP_115791	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	727	PDZ.				positive regulation of cytokine production|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis|T cell costimulation|T cell receptor signaling pathway	cytosol|membrane raft|plasma membrane	CARD domain binding|guanylate kinase activity			haematopoietic_and_lymphoid_tissue(43)|ovary(2)|kidney(2)|skin(2)|central_nervous_system(1)	50		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)				Mis		DLBCL								---	---	---	---
CARD11	84433	broad.mit.edu	37	7	2962936	2962936	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2962936G>A	uc003smv.2	-	16	2376	c.1972C>T	c.(1972-1974)CAC>TAC	p.H658Y		NM_032415	NP_115791	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	658					positive regulation of cytokine production|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis|T cell costimulation|T cell receptor signaling pathway	cytosol|membrane raft|plasma membrane	CARD domain binding|guanylate kinase activity			haematopoietic_and_lymphoid_tissue(43)|ovary(2)|kidney(2)|skin(2)|central_nervous_system(1)	50		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)				Mis		DLBCL								---	---	---	---
SDK1	221935	broad.mit.edu	37	7	3681600	3681600	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:3681600T>G	uc003smx.2	+	4	715	c.576T>G	c.(574-576)AGT>AGG	p.S192R		NM_152744	NP_689957	Q7Z5N4	SDK1_HUMAN	sidekick 1 precursor	192	Ig-like C2-type 2.				cell adhesion	integral to membrane				large_intestine(3)|ovary(2)|skin(1)	6		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)														---	---	---	---
PAPOLB	56903	broad.mit.edu	37	7	4901260	4901260	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4901260C>T	uc003snk.2	-	1	366	c.182G>A	c.(181-183)CGC>CAC	p.R61H	RADIL_uc003sng.1_Intron|RADIL_uc011jwd.1_Intron|RADIL_uc003snj.1_Intron	NM_020144	NP_064529	Q9NRJ5	PAPOB_HUMAN	poly(A) polymerase beta (testis specific)	60					mRNA processing|RNA polyadenylation|transcription, DNA-dependent	nucleus	ATP binding|metal ion binding|polynucleotide adenylyltransferase activity|RNA binding			ovary(1)	1		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.089)|OV - Ovarian serous cystadenocarcinoma(56;2.06e-14)														---	---	---	---
WIPI2	26100	broad.mit.edu	37	7	5269378	5269378	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5269378C>T	uc003snv.2	+						WIPI2_uc003snw.2_Intron|WIPI2_uc003snx.2_Intron|WIPI2_uc003sny.2_Intron|WIPI2_uc010ksv.2_Intron|WIPI2_uc003soa.2_Intron|WIPI2_uc003sob.2_Intron	NM_015610	NP_056425			WD repeat domain, phosphoinositide interacting 2						autophagic vacuole assembly	cytosol|PAS complex|pre-autophagosomal structure membrane	phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding			ovary(2)	2		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0925)|OV - Ovarian serous cystadenocarcinoma(56;2.59e-14)														---	---	---	---
SLC29A4	222962	broad.mit.edu	37	7	5340081	5340081	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5340081G>A	uc003sod.2	+	10	1399	c.1238G>A	c.(1237-1239)CGG>CAG	p.R413Q	SLC29A4_uc003soc.2_Missense_Mutation_p.R413Q|SLC29A4_uc003soe.2_Missense_Mutation_p.R399Q|SLC29A4_uc010ksw.2_Intron	NM_153247	NP_694979	Q7RTT9	S29A4_HUMAN	solute carrier family 29 (nucleoside	413	Cytoplasmic (Potential).				nucleobase, nucleoside and nucleotide metabolic process	apical plasma membrane|integral to membrane	nucleoside transmembrane transporter activity			liver(1)	1		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0903)|OV - Ovarian serous cystadenocarcinoma(56;2.65e-15)														---	---	---	---
EIF2AK1	27102	broad.mit.edu	37	7	6080723	6080723	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6080723A>G	uc003spp.2	-	9	1065	c.919T>C	c.(919-921)TAC>CAC	p.Y307H	EIF2AK1_uc003spq.2_Missense_Mutation_p.Y306H|EIF2AK1_uc011jwm.1_Missense_Mutation_p.Y183H|EIF2AK1_uc003spr.1_Missense_Mutation_p.Y99H	NM_014413	NP_055228	Q9BQI3	E2AK1_HUMAN	eukaryotic translation initiation factor 2-alpha	307	Protein kinase.				negative regulation of hemoglobin biosynthetic process|negative regulation of translational initiation by iron|protein autophosphorylation|response to external stimulus|response to stress	cytoplasm	ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|heme binding|protein homodimerization activity			upper_aerodigestive_tract(1)|stomach(1)|lung(1)|central_nervous_system(1)	4		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.106)|OV - Ovarian serous cystadenocarcinoma(56;5.22e-14)														---	---	---	---
CYTH3	9265	broad.mit.edu	37	7	6227301	6227301	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6227301A>G	uc003spt.2	-	3	273	c.169T>C	c.(169-171)TCC>CCC	p.S57P		NM_004227	NP_004218	O43739	CYH3_HUMAN	cytohesin 3	57	Potential.				regulation of ARF protein signal transduction|regulation of cell adhesion|vesicle-mediated transport	cytoplasm|membrane fraction|plasma membrane	1-phosphatidylinositol binding|ARF guanyl-nucleotide exchange factor activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity				0																		---	---	---	---
C7orf70	84792	broad.mit.edu	37	7	6370549	6370549	+	Silent	SNP	G	A	A	rs140253432		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6370549G>A	uc003spu.2	-	2	705	c.237C>T	c.(235-237)GGC>GGT	p.G79G		NM_001037163	NP_001032240	Q7Z4H9	SIPAR_HUMAN	hypothetical protein LOC84792	79						nucleus					0																		---	---	---	---
C1GALT1	56913	broad.mit.edu	37	7	7277898	7277898	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7277898A>G	uc010ktn.2	+	3	456	c.233A>G	c.(232-234)GAC>GGC	p.D78G	C1GALT1_uc003sra.2_Missense_Mutation_p.D78G|C1GALT1_uc010kto.1_Missense_Mutation_p.D78G	NM_020156	NP_064541	Q9NS00	C1GLT_HUMAN	core 1 synthase,	78	Lumenal (Potential).				angiogenesis|cell differentiation|kidney development	integral to membrane	glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase activity|metal ion binding				0				UCEC - Uterine corpus endometrioid carcinoma (126;0.177)														---	---	---	---
COL28A1	340267	broad.mit.edu	37	7	7472288	7472288	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7472288T>C	uc003src.1	-	24	2021	c.1904A>G	c.(1903-1905)AAA>AGA	p.K635R	COL28A1_uc011jxe.1_Missense_Mutation_p.K318R|COL28A1_uc003srd.2_Missense_Mutation_p.K190R|COL28A1_uc003sre.1_Missense_Mutation_p.K56R	NM_001037763	NP_001032852	Q2UY09	COSA1_HUMAN	collagen, type XXVIII precursor	635					cell adhesion	basement membrane|collagen	serine-type endopeptidase inhibitor activity			skin(3)	3		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)														---	---	---	---
MIOS	54468	broad.mit.edu	37	7	7645668	7645668	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:7645668G>T	uc003srf.2	+	12	2805	c.2497G>T	c.(2497-2499)GGT>TGT	p.G833C	MIOS_uc003srg.2_Missense_Mutation_p.G368C|MIOS_uc010ktq.2_Missense_Mutation_p.G228C	NM_019005	NP_061878	Q9NXC5	MIO_HUMAN	missing oocyte, meiosis regulator, homolog	833											0																		---	---	---	---
ICA1	3382	broad.mit.edu	37	7	8167518	8167518	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:8167518G>A	uc003srm.2	-	13	1382	c.1315C>T	c.(1315-1317)CAG>TAG	p.Q439*	ICA1_uc010ktr.2_Nonsense_Mutation_p.Q468*|ICA1_uc003srl.2_Nonsense_Mutation_p.Q427*|ICA1_uc003srn.3_Nonsense_Mutation_p.Q365*|ICA1_uc003srp.3_Nonsense_Mutation_p.Q438*|ICA1_uc010kts.2_RNA|ICA1_uc003srq.2_Nonsense_Mutation_p.Q439*|ICA1_uc003srr.2_Nonsense_Mutation_p.Q438*|ICA1_uc003sro.3_Nonsense_Mutation_p.Q439*	NM_022307	NP_071682	Q05084	ICA69_HUMAN	islet cell autoantigen 1	439					neurotransmitter transport	cell junction|cytosol|Golgi membrane|nucleus|secretory granule membrane|synaptic vesicle membrane|transport vesicle membrane				central_nervous_system(1)	1		Ovarian(82;0.0612)		UCEC - Uterine corpus endometrioid carcinoma (126;0.246)														---	---	---	---
PHF14	9678	broad.mit.edu	37	7	11022530	11022530	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11022530G>A	uc003sry.1	+	3	1079	c.644G>A	c.(643-645)CGA>CAA	p.R215Q	PHF14_uc011jxi.1_Intron|PHF14_uc003srz.2_Missense_Mutation_p.R215Q|PHF14_uc011jxj.1_Intron	NM_014660	NP_055475	O94880	PHF14_HUMAN	PHD finger protein 14 isoform 2	215							zinc ion binding			kidney(2)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.205)														---	---	---	---
THSD7A	221981	broad.mit.edu	37	7	11418819	11418819	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11418819A>G	uc003ssf.3	-	25	4931	c.4679T>C	c.(4678-4680)GTA>GCA	p.V1560A	uc003ssb.2_Intron|THSD7A_uc003ssd.3_Missense_Mutation_p.V64A	NM_015204	NP_056019	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	1560	Extracellular (Potential).					integral to membrane				ovary(3)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)											HNSCC(18;0.044)			---	---	---	---
THSD7A	221981	broad.mit.edu	37	7	11630129	11630129	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11630129C>T	uc003ssf.3	-	4	1663	c.1411G>A	c.(1411-1413)GAA>AAA	p.E471K		NM_015204	NP_056019	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	471	Extracellular (Potential).|TSP type-1 4.					integral to membrane				ovary(3)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)											HNSCC(18;0.044)			---	---	---	---
THSD7A	221981	broad.mit.edu	37	7	11676253	11676253	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:11676253A>G	uc003ssf.3	-	2	778	c.526T>C	c.(526-528)TAC>CAC	p.Y176H		NM_015204	NP_056019	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	176	Extracellular (Potential).					integral to membrane				ovary(3)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)											HNSCC(18;0.044)			---	---	---	---
SCIN	85477	broad.mit.edu	37	7	12683884	12683884	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:12683884A>G	uc003ssn.3	+	12	1913	c.1703A>G	c.(1702-1704)TAT>TGT	p.Y568C	SCIN_uc010ktt.2_Intron|SCIN_uc003sso.3_Missense_Mutation_p.Y321C	NM_001112706	NP_001106177	Q9Y6U3	ADSV_HUMAN	scinderin isoform 1	568	Ca(2+)-dependent actin binding.				actin filament capping|actin filament severing|actin nucleation|calcium ion-dependent exocytosis|negative regulation of cell proliferation|positive regulation of apoptosis|positive regulation of megakaryocyte differentiation|positive regulation of secretion|regulation of chondrocyte differentiation	cell cortex|cytoskeleton	1-phosphatidylinositol binding|actin filament binding|calcium ion binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylserine binding			ovary(2)	2				UCEC - Uterine corpus endometrioid carcinoma (126;0.195)														---	---	---	---
TMEM195	392636	broad.mit.edu	37	7	15470678	15470678	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:15470678G>T	uc003stb.1	-	4	635	c.465C>A	c.(463-465)AAC>AAA	p.N155K		NM_001004320	NP_001004320	Q6ZNB7	ALKMO_HUMAN	transmembrane protein 195	155					ether lipid metabolic process|fatty acid biosynthetic process|membrane lipid metabolic process	endoplasmic reticulum membrane|integral to membrane	glyceryl-ether monooxygenase activity|iron ion binding				0																		---	---	---	---
SOSTDC1	25928	broad.mit.edu	37	7	16502336	16502336	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16502336C>T	uc003stg.2	-	2	639	c.458G>A	c.(457-459)CGC>CAC	p.R153H	SOSTDC1_uc003sth.2_Missense_Mutation_p.R177H	NM_015464	NP_056279	Q6X4U4	SOSD1_HUMAN	sclerostin domain containing 1 precursor	153	CTCK.				Wnt receptor signaling pathway					ovary(2)|central_nervous_system(1)	3	Lung NSC(10;0.185)			UCEC - Uterine corpus endometrioid carcinoma (126;0.177)														---	---	---	---
TSPAN13	27075	broad.mit.edu	37	7	16823030	16823030	+	Intron	SNP	T	C	C	rs3840574		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:16823030T>C	uc003stq.2	+							NM_014399	NP_055214			tetraspan NET-6							integral to plasma membrane|membrane fraction				ovary(1)	1	Lung NSC(10;0.0494)|all_lung(11;0.109)			UCEC - Uterine corpus endometrioid carcinoma (126;0.188)														---	---	---	---
ABCB5	340273	broad.mit.edu	37	7	20691056	20691056	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20691056A>G	uc003suw.3	+	4	557	c.11A>G	c.(10-12)GAG>GGG	p.E4G	ABCB5_uc010kuh.2_Missense_Mutation_p.E449G|ABCB5_uc003suv.3_Missense_Mutation_p.E4G|ABCB5_uc011jyi.1_Missense_Mutation_p.E4G	NM_178559	NP_848654	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B, member 5	4	ABC transporter 1.|Extracellular (Potential).				regulation of membrane potential	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus	ATP binding|ATPase activity, coupled to transmembrane movement of substances|efflux transmembrane transporter activity			skin(2)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|pancreas(1)	6																		---	---	---	---
ABCB5	340273	broad.mit.edu	37	7	20691120	20691120	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20691120G>A	uc003suw.3	+	4	621	c.75G>A	c.(73-75)GAG>GAA	p.E25E	ABCB5_uc010kuh.2_Silent_p.E470E|ABCB5_uc003suv.3_Silent_p.E25E|ABCB5_uc011jyi.1_Silent_p.E25E	NM_178559	NP_848654	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B, member 5	25	ABC transporter 1.|Extracellular (Potential).				regulation of membrane potential	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus	ATP binding|ATPase activity, coupled to transmembrane movement of substances|efflux transmembrane transporter activity			skin(2)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|pancreas(1)	6																		---	---	---	---
SP8	221833	broad.mit.edu	37	7	20824257	20824257	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20824257C>T	uc003suy.2	-	3	1366	c.1125G>A	c.(1123-1125)GCG>GCA	p.A375A	SP8_uc003suz.2_Silent_p.A393A	NM_198956	NP_945194	Q8IXZ3	SP8_HUMAN	Sp8 transcription factor isoform 2	375	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1																		---	---	---	---
DNAH11	8701	broad.mit.edu	37	7	21609683	21609683	+	Intron	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21609683C>A	uc003svc.2	+							NM_003777	NP_003768			dynein, axonemal, heavy chain 11						microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15														Kartagener_syndrome				---	---	---	---
DNAH11	8701	broad.mit.edu	37	7	21646361	21646361	+	Intron	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21646361A>T	uc003svc.2	+							NM_003777	NP_003768			dynein, axonemal, heavy chain 11						microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15														Kartagener_syndrome				---	---	---	---
DNAH11	8701	broad.mit.edu	37	7	21818653	21818653	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21818653C>T	uc003svc.2	+	58	9466	c.9435C>T	c.(9433-9435)ATC>ATT	p.I3145I		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	3145	Stalk (By similarity).				microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15														Kartagener_syndrome				---	---	---	---
DNAH11	8701	broad.mit.edu	37	7	21901535	21901535	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21901535G>A	uc003svc.2	+	70	11319	c.11288G>A	c.(11287-11289)CGC>CAC	p.R3763H		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	3763					microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15														Kartagener_syndrome				---	---	---	---
DNAH11	8701	broad.mit.edu	37	7	21906254	21906254	+	Missense_Mutation	SNP	G	A	A	rs72658812		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:21906254G>A	uc003svc.2	+	72	11715	c.11684G>A	c.(11683-11685)CGC>CAC	p.R3895H		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	3895					microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15														Kartagener_syndrome				---	---	---	---
RAPGEF5	9771	broad.mit.edu	37	7	22347997	22347997	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22347997A>G	uc003svg.2	-	5	495	c.182T>C	c.(181-183)CTT>CCT	p.L61P		NM_012294	NP_036426	Q92565	RPGF5_HUMAN	Rap guanine nucleotide exchange factor (GEF) 5	Error:Variant_position_missing_in_Q92565_after_alignment					nervous system development|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	nucleus	GTP-dependent protein binding|Rap guanyl-nucleotide exchange factor activity			ovary(1)	1																		---	---	---	---
IL6	3569	broad.mit.edu	37	7	22769174	22769174	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:22769174T>G	uc011jyn.1	+	5	825	c.366T>G	c.(364-366)TTT>TTG	p.F122L	uc010kun.1_5'Flank|IL6_uc011jyo.1_Missense_Mutation_p.F122L|IL6_uc011jyp.1_Missense_Mutation_p.F46L|IL6_uc003svj.3_Missense_Mutation_p.F122L|IL6_uc011jyq.1_Missense_Mutation_p.F176L	NM_000600	NP_000591	P05231	IL6_HUMAN	interleukin 6 precursor	122					acute-phase response|cellular response to hydrogen peroxide|defense response to Gram-negative bacterium|defense response to Gram-positive bacterium|defense response to virus|endocrine pancreas development|glucagon secretion|hepatic immune response|interleukin-6-mediated signaling pathway|negative regulation of apoptosis|negative regulation of cell proliferation|negative regulation of chemokine biosynthetic process|negative regulation of collagen biosynthetic process|negative regulation of fat cell differentiation|negative regulation of lipid storage|neuron projection development|neutrophil apoptosis|platelet activation|positive regulation of acute inflammatory response|positive regulation of anti-apoptosis|positive regulation of B cell activation|positive regulation of chemokine production|positive regulation of immunoglobulin secretion|positive regulation of interleukin-6 production|positive regulation of osteoblast differentiation|positive regulation of peptidyl-serine phosphorylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of smooth muscle cell proliferation|positive regulation of T cell proliferation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of translation|positive regulation of tyrosine phosphorylation of Stat3 protein|regulation of vascular endothelial growth factor production|response to glucocorticoid stimulus|response to peptidoglycan	extracellular space|interleukin-6 receptor complex	cytokine activity|growth factor activity|interleukin-6 receptor binding				0					Arsenic trioxide(DB01169)|Bicalutamide(DB01128)|Ginseng(DB01404)|Simvastatin(DB00641)													---	---	---	---
OSBPL3	26031	broad.mit.edu	37	7	24874335	24874335	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:24874335G>A	uc003sxf.2	-	15	1921	c.1516C>T	c.(1516-1518)CGG>TGG	p.R506W	OSBPL3_uc003sxd.2_RNA|OSBPL3_uc003sxe.2_RNA|OSBPL3_uc003sxg.2_Missense_Mutation_p.R470W|OSBPL3_uc003sxh.2_Missense_Mutation_p.R475W|OSBPL3_uc003sxi.2_Missense_Mutation_p.R439W|OSBPL3_uc003sxj.1_Missense_Mutation_p.R235W|OSBPL3_uc003sxk.1_Missense_Mutation_p.R204W	NM_015550	NP_056365	Q9H4L5	OSBL3_HUMAN	oxysterol-binding protein-like protein 3 isoform	506					lipid transport		lipid binding|protein binding			skin(1)	1																		---	---	---	---
CYCS	54205	broad.mit.edu	37	7	25163363	25163363	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:25163363C>A	uc003sxl.2	-	3	420	c.275G>T	c.(274-276)AGG>ATG	p.R92M		NM_018947	NP_061820	P99999	CYC_HUMAN	cytochrome c	92					activation of caspase activity by cytochrome c|DNA fragmentation involved in apoptotic nuclear change|induction of apoptosis by intracellular signals|respiratory electron transport chain|transport	cytosol|mitochondrial inner membrane|mitochondrial intermembrane space|mitochondrial matrix|nucleus|protein phosphatase type 2A complex|respiratory chain	electron transporter, transferring electrons from CoQH2-cytochrome c reductase complex and cytochrome c oxidase complex activity|heme binding|protein binding			ovary(1)|lung(1)	2					Melatonin(DB01065)|Minocycline(DB01017)													---	---	---	---
NFE2L3	9603	broad.mit.edu	37	7	26224662	26224662	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:26224662T>C	uc003sxq.2	+	4	1616	c.1344T>C	c.(1342-1344)GGT>GGC	p.G448G		NM_004289	NP_004280	Q9Y4A8	NF2L3_HUMAN	nuclear factor erythroid 2-like 3	448					transcription from RNA polymerase II promoter	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			skin(3)|ovary(1)	4																		---	---	---	---
HOXA1	3198	broad.mit.edu	37	7	27135228	27135228	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27135228G>A	uc003sye.2	-	1	398	c.304C>T	c.(304-306)CAG>TAG	p.Q102*	HOXA1_uc003syd.2_Nonsense_Mutation_p.Q102*|uc003syg.2_5'Flank	NM_005522	NP_005513	P49639	HXA1_HUMAN	homeobox A1 isoform a	102						nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)	3																		---	---	---	---
HOXA2	3199	broad.mit.edu	37	7	27140710	27140710	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27140710G>T	uc003syh.2	-	2	1041	c.766C>A	c.(766-768)CTC>ATC	p.L256I		NM_006735	NP_006726	O43364	HXA2_HUMAN	homeobox A2	256						nucleus	sequence-specific DNA binding transcription factor activity			ovary(1)|skin(1)	2																		---	---	---	---
HOXA2	3199	broad.mit.edu	37	7	27140713	27140713	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27140713C>T	uc003syh.2	-	2	1038	c.763G>A	c.(763-765)GCC>ACC	p.A255T		NM_006735	NP_006726	O43364	HXA2_HUMAN	homeobox A2	255						nucleus	sequence-specific DNA binding transcription factor activity			ovary(1)|skin(1)	2																		---	---	---	---
HOXA4	3201	broad.mit.edu	37	7	27168979	27168979	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27168979C>T	uc003sym.3	-	2	875	c.828G>A	c.(826-828)CTG>CTA	p.L276L	HOXA3_uc003syk.2_5'Flank	NM_002141	NP_002132	Q00056	HXA4_HUMAN	homeobox A4	276				KL -> NC (in Ref. 7; AAA53290).		nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)	1																		---	---	---	---
HOXA7	3204	broad.mit.edu	37	7	27194706	27194706	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27194706C>T	uc003sys.2	-	2	647	c.515G>A	c.(514-516)CGC>CAC	p.R172H	HOXA6_uc003syq.1_5'Flank|uc003syr.1_3'UTR	NM_006896	NP_008827	P31268	HXA7_HUMAN	homeobox A7	172	Homeobox.				angiogenesis|negative regulation of cell-matrix adhesion|negative regulation of keratinocyte differentiation|negative regulation of leukocyte migration|negative regulation of monocyte differentiation|negative regulation of transcription from RNA polymerase II promoter		sequence-specific DNA binding|transcription factor binding				0																		---	---	---	---
HOXA6	3203	broad.mit.edu	37	7	27194847	27194847	+	5'Flank	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27194847A>G	uc003syq.1	-						uc003syr.1_3'UTR|HOXA7_uc003sys.2_Intron					Homo sapiens clone Affy08242H09, mRNA sequence.							nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
TAX1BP1	8887	broad.mit.edu	37	7	27868300	27868300	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:27868300A>G	uc003szl.2	+	17	2380	c.2222A>G	c.(2221-2223)TAT>TGT	p.Y741C	TAX1BP1_uc011jzo.1_Missense_Mutation_p.Y699C|TAX1BP1_uc003szk.2_Missense_Mutation_p.Y699C|TAX1BP1_uc011jzp.1_Missense_Mutation_p.Y542C	NM_006024	NP_006015	Q86VP1	TAXB1_HUMAN	Tax1 (human T-cell leukemia virus type I)	741					anti-apoptosis|apoptosis|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production	cytosol	identical protein binding|kinase binding|zinc ion binding			breast(1)	1			GBM - Glioblastoma multiforme(3;0.0823)															---	---	---	---
CREB5	9586	broad.mit.edu	37	7	28848909	28848909	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:28848909C>T	uc003szq.2	+	9	1522	c.1132C>T	c.(1132-1134)CGG>TGG	p.R378W	CREB5_uc003szo.2_Missense_Mutation_p.R345W|CREB5_uc003szr.2_Missense_Mutation_p.R371W|CREB5_uc003szs.2_Missense_Mutation_p.R239W	NM_182898	NP_878901	Q02930	CREB5_HUMAN	cAMP responsive element binding protein 5	378	Basic motif.				positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter		protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)	2																		---	---	---	---
NOD1	10392	broad.mit.edu	37	7	30491124	30491124	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:30491124G>A	uc003tav.2	-	6	2432	c.1909C>T	c.(1909-1911)CGC>TGC	p.R637C		NM_006092	NP_006083	Q9Y239	NOD1_HUMAN	nucleotide-binding oligomerization domain	637	LRR 1.				activation of MAPK activity|detection of bacterium|induction of apoptosis|inflammatory response|innate immune response|interleukin-8 biosynthetic process|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of dendritic cell antigen processing and presentation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|protein oligomerization|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	basolateral plasma membrane|cytosol	ATP binding|CARD domain binding|caspase activator activity|peptidoglycan binding|protein homodimerization activity			ovary(1)|skin(1)	2																		---	---	---	---
CCDC129	223075	broad.mit.edu	37	7	31683098	31683098	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31683098C>A	uc003tcj.1	+	11	3107	c.2114C>A	c.(2113-2115)TCC>TAC	p.S705Y	CCDC129_uc011kad.1_Missense_Mutation_p.S715Y|CCDC129_uc003tci.1_Missense_Mutation_p.S556Y|CCDC129_uc011kae.1_Missense_Mutation_p.S731Y|CCDC129_uc003tck.1_Missense_Mutation_p.S613Y	NM_194300	NP_919276	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	705											0																		---	---	---	---
AVL9	23080	broad.mit.edu	37	7	32615690	32615690	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:32615690C>T	uc003tcv.1	+						AVL9_uc011kai.1_Intron|AVL9_uc010kwj.1_Intron	NM_015060	NP_055875			AVL9 homolog (S. cerevisiase)							integral to membrane					0																		---	---	---	---
BBS9	27241	broad.mit.edu	37	7	33312693	33312693	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33312693T>C	uc003tdn.1	+	8	1285	c.772T>C	c.(772-774)TCC>CCC	p.S258P	BBS9_uc003tdo.1_Missense_Mutation_p.S258P|BBS9_uc003tdp.1_Missense_Mutation_p.S258P|BBS9_uc003tdq.1_Missense_Mutation_p.S258P|BBS9_uc010kwn.1_RNA|BBS9_uc011kan.1_Missense_Mutation_p.S258P|BBS9_uc011kao.1_Missense_Mutation_p.S136P	NM_198428	NP_940820	Q3SYG4	PTHB1_HUMAN	parathyroid hormone-responsive B1 isoform 2	258					fat cell differentiation|response to stimulus|visual perception	BBSome|cilium membrane|microtubule organizing center|nucleus	protein binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			GBM - Glioblastoma multiforme(11;0.0894)											Bardet-Biedl_syndrome				---	---	---	---
BBS9	27241	broad.mit.edu	37	7	33376211	33376211	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33376211T>C	uc003tdn.1	+	10	1688	c.1175T>C	c.(1174-1176)ATC>ACC	p.I392T	BBS9_uc003tdo.1_Missense_Mutation_p.I392T|BBS9_uc003tdp.1_Missense_Mutation_p.I392T|BBS9_uc003tdq.1_Missense_Mutation_p.I392T|BBS9_uc010kwn.1_RNA|BBS9_uc011kao.1_Missense_Mutation_p.I270T	NM_198428	NP_940820	Q3SYG4	PTHB1_HUMAN	parathyroid hormone-responsive B1 isoform 2	392					fat cell differentiation|response to stimulus|visual perception	BBSome|cilium membrane|microtubule organizing center|nucleus	protein binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			GBM - Glioblastoma multiforme(11;0.0894)											Bardet-Biedl_syndrome				---	---	---	---
HERPUD2	64224	broad.mit.edu	37	7	35674889	35674889	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35674889A>G	uc003tet.2	-	6	1602	c.797T>C	c.(796-798)GTA>GCA	p.V266A	HERPUD2_uc003tes.3_Missense_Mutation_p.V266A	NM_022373	NP_071768	Q9BSE4	HERP2_HUMAN	HERPUD family member 2	266					response to unfolded protein	integral to membrane				ovary(3)	3																		---	---	---	---
ANLN	54443	broad.mit.edu	37	7	36492123	36492123	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36492123C>A	uc003tff.2	+	24	3493	c.3289C>A	c.(3289-3291)CTC>ATC	p.L1097I	ANLN_uc011kaz.1_Missense_Mutation_p.L1009I|ANLN_uc003tfg.2_Missense_Mutation_p.L1060I|ANLN_uc010kxe.2_Missense_Mutation_p.L1059I	NM_018685	NP_061155	Q9NQW6	ANLN_HUMAN	anillin, actin binding protein	1097	PH.|Localization to the cleavage furrow.				cytokinesis|mitosis|regulation of exit from mitosis|septin ring assembly	actomyosin contractile ring|nucleus	actin binding			ovary(2)|skin(1)	3																		---	---	---	---
AOAH	313	broad.mit.edu	37	7	36656073	36656073	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36656073C>A	uc003tfh.3	-	11	1160	c.759G>T	c.(757-759)CAG>CAT	p.Q253H	AOAH_uc010kxf.2_Missense_Mutation_p.Q253H|AOAH_uc011kba.1_Missense_Mutation_p.Q221H	NM_001637	NP_001628	P28039	AOAH_HUMAN	acyloxyacyl hydrolase precursor	253					inflammatory response|lipid metabolic process	extracellular region	acyloxyacyl hydrolase activity|lipoprotein lipase activity			skin(1)	1																		---	---	---	---
AMPH	273	broad.mit.edu	37	7	38516521	38516521	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38516521G>A	uc003tgu.2	-	6	514	c.445C>T	c.(445-447)CGC>TGC	p.R149C	AMPH_uc003tgv.2_Missense_Mutation_p.R149C	NM_001635	NP_001626	P49418	AMPH_HUMAN	amphiphysin isoform 1	149	BAR.|Potential.				endocytosis|synaptic transmission	actin cytoskeleton|cell junction|synaptic vesicle membrane				ovary(3)|liver(1)|skin(1)	5																		---	---	---	---
VPS41	27072	broad.mit.edu	37	7	38768321	38768321	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:38768321C>T	uc003tgy.2	-	26	2356	c.2330G>A	c.(2329-2331)CGA>CAA	p.R777Q	VPS41_uc003tgz.2_Missense_Mutation_p.R752Q|VPS41_uc010kxn.2_Missense_Mutation_p.R688Q|VPS41_uc003tgx.2_RNA	NM_014396	NP_055211	P49754	VPS41_HUMAN	vacuolar protein sorting 41 isoform 1	777					Golgi vesicle transport|intracellular protein transport|vesicle-mediated transport	cytosol|Golgi-associated vesicle|HOPS complex|membrane fraction	zinc ion binding			skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	4																		---	---	---	---
C7orf36	57002	broad.mit.edu	37	7	39606066	39606066	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:39606066G>T	uc003thc.3	+	1	58	c.49G>T	c.(49-51)GGG>TGG	p.G17W		NM_020192	NP_064577	Q9NRH1	CG036_HUMAN	hypothetical protein LOC57002	17											0																		---	---	---	---
C7orf11	136647	broad.mit.edu	37	7	40172822	40172822	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:40172822G>A	uc003thl.3	-	2	468	c.376C>T	c.(376-378)CGT>TGT	p.R126C	C7orf10_uc003thm.1_5'Flank|C7orf10_uc003thn.1_5'Flank|C7orf10_uc003tho.1_5'Flank	NM_138701	NP_619646	Q8TAP9	TTDN1_HUMAN	chromosome 7 open reading frame 11	126					cell division|mitosis	microtubule organizing center|nucleus				breast(1)	1													Direct_reversal_of_damage|Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents					---	---	---	---
INHBA	3624	broad.mit.edu	37	7	41729665	41729665	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:41729665C>T	uc003thq.2	-	2	1099	c.864G>A	c.(862-864)TCG>TCA	p.S288S	INHBA_uc003thr.2_Silent_p.S288S	NM_002192	NP_002183	P08476	INHBA_HUMAN	inhibin beta A precursor	288					cell cycle arrest|cell surface receptor linked signaling pathway|defense response|erythrocyte differentiation|eyelid development in camera-type eye|G1/S transition of mitotic cell cycle|growth|hair follicle development|hemoglobin biosynthetic process|hemopoietic progenitor cell differentiation|induction of apoptosis|male gonad development|negative regulation of B cell differentiation|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of follicle-stimulating hormone secretion|negative regulation of interferon-gamma biosynthetic process|negative regulation of macrophage differentiation|negative regulation of phosphorylation|nervous system development|odontogenesis|ovarian follicle development|palate development|positive regulation of erythrocyte differentiation|positive regulation of follicle-stimulating hormone secretion|positive regulation of ovulation|positive regulation of transcription from RNA polymerase II promoter|progesterone secretion|regulation of activin receptor signaling pathway	activin A complex|inhibin A complex	cytokine activity|follistatin binding|growth factor activity|hormone activity|identical protein binding|signal transducer activity			lung(5)|ovary(1)	6															TSP Lung(11;0.080)			---	---	---	---
C7orf25	79020	broad.mit.edu	37	7	42950162	42950162	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:42950162C>T	uc003thw.2	-	2	802	c.338G>A	c.(337-339)GGT>GAT	p.G113D	C7orf25_uc010kxq.2_Missense_Mutation_p.G113D|C7orf25_uc003thx.3_Missense_Mutation_p.G171D|C7orf25_uc010kxr.2_Missense_Mutation_p.G171D	NM_024054	NP_076959	Q9BPX7	CG025_HUMAN	hypothetical protein LOC79020 b	113										skin(1)	1																		---	---	---	---
HECW1	23072	broad.mit.edu	37	7	43484700	43484700	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43484700C>T	uc003tid.1	+	11	2534	c.1929C>T	c.(1927-1929)GGC>GGT	p.G643G	HECW1_uc011kbi.1_Silent_p.G643G	NM_015052	NP_055867	Q76N89	HECW1_HUMAN	NEDD4-like ubiquitin-protein ligase 1	643					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1)	23																		---	---	---	---
HECW1	23072	broad.mit.edu	37	7	43506116	43506116	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43506116G>T	uc003tid.1	+	15	3467	c.2862G>T	c.(2860-2862)GCG>GCT	p.A954A	HECW1_uc011kbi.1_Silent_p.A920A	NM_015052	NP_055867	Q76N89	HECW1_HUMAN	NEDD4-like ubiquitin-protein ligase 1	954					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1)	23																		---	---	---	---
HECW1	23072	broad.mit.edu	37	7	43590168	43590168	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43590168C>T	uc003tid.1	+	27	4978	c.4373C>T	c.(4372-4374)GCG>GTG	p.A1458V	HECW1_uc011kbi.1_Missense_Mutation_p.A1424V	NM_015052	NP_055867	Q76N89	HECW1_HUMAN	NEDD4-like ubiquitin-protein ligase 1	1458	HECT.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(8)|lung(6)|breast(4)|skin(4)|pancreas(1)	23																		---	---	---	---
URGCP	55665	broad.mit.edu	37	7	43917496	43917496	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:43917496C>T	uc003tiw.2	-	6	1623	c.1566G>A	c.(1564-1566)GAG>GAA	p.E522E	URGCP_uc003tiu.2_Silent_p.E479E|URGCP_uc003tiv.2_Silent_p.E447E|URGCP_uc003tix.2_Silent_p.E513E|URGCP_uc003tiy.2_Silent_p.E479E|URGCP_uc003tiz.2_Silent_p.E479E|URGCP_uc011kbj.1_Silent_p.E479E	NM_001077663	NP_001071131	Q8TCY9	URGCP_HUMAN	up-regulated gene 4 isoform 3	522					cell cycle	centrosome|nucleus	GTP binding			ovary(2)|liver(1)|skin(1)	4																		---	---	---	---
NUDCD3	23386	broad.mit.edu	37	7	44507788	44507788	+	Intron	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44507788A>C	uc003tkz.2	-						NUDCD3_uc010kye.2_Intron	NM_015332	NP_056147			NudC domain containing 3												0																		---	---	---	---
NPC1L1	29881	broad.mit.edu	37	7	44579939	44579939	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44579939G>T	uc003tlb.2	-	2	113	c.57C>A	c.(55-57)GCC>GCA	p.A19A	NPC1L1_uc003tlc.2_Silent_p.A19A|NPC1L1_uc011kbw.1_Silent_p.A19A|NPC1L1_uc003tld.2_Silent_p.A19A	NM_013389	NP_037521	Q9UHC9	NPCL1_HUMAN	Niemann-Pick C1-like protein 1 isoform 1	19					cholesterol biosynthetic process|intestinal cholesterol absorption|lipoprotein metabolic process	apical plasma membrane|cytoplasmic vesicle membrane|integral to membrane	hedgehog receptor activity|protein binding			ovary(3)|central_nervous_system(1)|skin(1)	5					Ezetimibe(DB00973)													---	---	---	---
OGDH	4967	broad.mit.edu	37	7	44721424	44721424	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44721424G>A	uc003tln.2	+	10	1421	c.1312G>A	c.(1312-1314)GTG>ATG	p.V438M	OGDH_uc011kbx.1_Missense_Mutation_p.V434M|OGDH_uc011kby.1_Missense_Mutation_p.V288M|OGDH_uc003tlp.2_Missense_Mutation_p.V449M|OGDH_uc011kbz.1_Missense_Mutation_p.V233M|OGDH_uc003tlo.1_Missense_Mutation_p.V271M	NM_002541	NP_002532	Q02218	ODO1_HUMAN	oxoglutarate dehydrogenase isoform 1 precursor	438					glycolysis|lysine catabolic process|tricarboxylic acid cycle	mitochondrial matrix|mitochondrial membrane	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding			upper_aerodigestive_tract(1)|ovary(1)	2					NADH(DB00157)													---	---	---	---
MYO1G	64005	broad.mit.edu	37	7	45009759	45009759	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45009759G>A	uc003tmh.2	-						MYO1G_uc003tmf.2_5'Flank|MYO1G_uc003tmg.2_Intron|MYO1G_uc010kym.2_Intron|MYO1G_uc003tmi.1_Intron|MYO1G_uc003tmj.2_Intron	NM_033054	NP_149043			myosin IG							myosin complex|plasma membrane	actin binding|ATP binding|calmodulin binding|motor activity			breast(2)|ovary(1)|pancreas(1)	4																		---	---	---	---
CCM2	83605	broad.mit.edu	37	7	45077939	45077939	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45077939C>T	uc003tmo.2	+	2	264	c.118C>T	c.(118-120)CGC>TGC	p.R40C	CCM2_uc003tmn.2_RNA|CCM2_uc003tmp.2_Intron|CCM2_uc003tmq.2_RNA|CCM2_uc003tmr.2_Missense_Mutation_p.R40C|CCM2_uc011kcb.1_Intron|CCM2_uc011kcc.1_Missense_Mutation_p.R61C|CCM2_uc003tms.2_Missense_Mutation_p.R61C	NM_031443	NP_113631	Q9BSQ5	CCM2_HUMAN	cerebral cavernous malformation 2 isoform 2	40					endothelial tube morphogenesis|integrin-mediated signaling pathway|stress-activated MAPK cascade|vasculogenesis	cytoplasm	protein binding				0														Familial_Cerebral_Cavernous_Angioma				---	---	---	---
TBRG4	9238	broad.mit.edu	37	7	45141592	45141592	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45141592C>T	uc003tmv.2	-	8	1525	c.1399G>A	c.(1399-1401)GAG>AAG	p.E467K	TBRG4_uc003tmu.2_Missense_Mutation_p.E292K|TBRG4_uc003tmw.2_Missense_Mutation_p.E357K|TBRG4_uc003tmx.2_Missense_Mutation_p.E357K|TBRG4_uc011kcd.1_Missense_Mutation_p.E478K	NM_004749	NP_004740	Q969Z0	TBRG4_HUMAN	cell cycle progression 2 protein isoform 1	467					apoptosis|cell cycle arrest|cellular respiration|G1 phase of mitotic cell cycle|positive regulation of cell proliferation	mitochondrion	ATP binding|protein binding|protein kinase activity				0																		---	---	---	---
ADCY1	107	broad.mit.edu	37	7	45662354	45662354	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45662354G>A	uc003tne.3	+						ADCY1_uc003tnd.2_Intron	NM_021116	NP_066939			adenylate cyclase 1						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|calmodulin binding|metal ion binding			ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	6					Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)													---	---	---	---
TNS3	64759	broad.mit.edu	37	7	47336758	47336758	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47336758G>T	uc003tnv.2	-	24	3965	c.3598C>A	c.(3598-3600)CAT>AAT	p.H1200N	TNS3_uc003tnw.2_Missense_Mutation_p.H1200N	NM_022748	NP_073585	Q68CZ2	TENS3_HUMAN	tensin 3	1200	SH2.					focal adhesion	protein binding			ovary(4)	4																		---	---	---	---
PKD1L1	168507	broad.mit.edu	37	7	47920349	47920349	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47920349G>A	uc003tny.1	-	21	3497	c.3497C>T	c.(3496-3498)ACG>ATG	p.T1166M		NM_138295	NP_612152	Q8TDX9	PK1L1_HUMAN	polycystin-1L1	1166	Extracellular (Potential).|REJ.				cell-cell adhesion	integral to membrane				ovary(8)|upper_aerodigestive_tract(2)|breast(1)	11																		---	---	---	---
PKD1L1	168507	broad.mit.edu	37	7	47925326	47925326	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47925326C>A	uc003tny.1	-	18	3163	c.3163G>T	c.(3163-3165)GAG>TAG	p.E1055*		NM_138295	NP_612152	Q8TDX9	PK1L1_HUMAN	polycystin-1L1	1055	Extracellular (Potential).|REJ.				cell-cell adhesion	integral to membrane				ovary(8)|upper_aerodigestive_tract(2)|breast(1)	11																		---	---	---	---
PKD1L1	168507	broad.mit.edu	37	7	47944065	47944065	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:47944065A>G	uc003tny.1	-	12	1841	c.1841T>C	c.(1840-1842)ATC>ACC	p.I614T		NM_138295	NP_612152	Q8TDX9	PK1L1_HUMAN	polycystin-1L1	614	Extracellular (Potential).|PKD 2.				cell-cell adhesion	integral to membrane				ovary(8)|upper_aerodigestive_tract(2)|breast(1)	11																		---	---	---	---
VWC2	375567	broad.mit.edu	37	7	49842403	49842403	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:49842403G>A	uc003tot.1	+	3	1349	c.793G>A	c.(793-795)GAG>AAG	p.E265K		NM_198570	NP_940972	Q2TAL6	VWC2_HUMAN	von Willebrand factor C domain containing 2	265	VWFC 2.				negative regulation of BMP signaling pathway|positive regulation of neuron differentiation	basement membrane|extracellular space					0																		---	---	---	---
COBL	23242	broad.mit.edu	37	7	51095999	51095999	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:51095999G>A	uc003tpr.3	-	10	2979	c.2794C>T	c.(2794-2796)CCC>TCC	p.P932S	COBL_uc003tps.2_Missense_Mutation_p.P989S|COBL_uc011kcl.1_Missense_Mutation_p.P932S|COBL_uc003tpp.3_Missense_Mutation_p.P718S|COBL_uc003tpq.3_Missense_Mutation_p.P873S|COBL_uc003tpo.3_Missense_Mutation_p.P474S	NM_015198	NP_056013	O75128	COBL_HUMAN	cordon-bleu homolog	932										skin(3)|ovary(2)	5	Glioma(55;0.08)																	---	---	---	---
EGFR	1956	broad.mit.edu	37	7	55214367	55214367	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55214367C>T	uc003tqk.2	+	4	739	c.493C>T	c.(493-495)CGG>TGG	p.R165W	EGFR_uc003tqh.2_Missense_Mutation_p.R165W|EGFR_uc003tqi.2_Missense_Mutation_p.R165W|EGFR_uc003tqj.2_Missense_Mutation_p.R165W|EGFR_uc010kzg.1_Intron|EGFR_uc011kco.1_Missense_Mutation_p.R112W	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	165	Approximate.|Extracellular (Potential).				activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity	p.V30_R297>G(5)		lung(9213)|central_nervous_system(103)|stomach(41)|upper_aerodigestive_tract(39)|prostate(32)|ovary(31)|thyroid(24)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|kidney(8)|urinary_tract(6)|skin(5)|adrenal_gland(5)|soft_tissue(4)|bone(3)|NS(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)	9571	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)		8	A|O|Mis		glioma|NSCLC	NSCLC			Lung_Cancer_Familial_Clustering_of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			---	---	---	---
CCT6A	908	broad.mit.edu	37	7	56123378	56123378	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:56123378T>G	uc003trl.1	+	4	562	c.398T>G	c.(397-399)TTT>TGT	p.F133C	PSPH_uc003trj.2_Intron|CCT6A_uc003trm.1_Missense_Mutation_p.F88C|CCT6A_uc011kcu.1_Missense_Mutation_p.F102C	NM_001762	NP_001753	P40227	TCPZ_HUMAN	chaperonin containing TCP1, subunit 6A isoform	133					'de novo' posttranslational protein folding	cytosol	ATP binding|unfolded protein binding			upper_aerodigestive_tract(1)	1	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)															---	---	---	---
ZNF680	340252	broad.mit.edu	37	7	63982877	63982877	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:63982877A>G	uc003tta.2	-	4	428	c.255T>C	c.(253-255)GTT>GTC	p.V85V	ZNF680_uc010kzr.2_Silent_p.V12V	NM_178558	NP_848653	Q8NEM1	ZN680_HUMAN	zinc finger protein 680 isoform 1	85					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Lung NSC(55;0.118)|all_lung(88;0.243)																---	---	---	---
ZNF273	10793	broad.mit.edu	37	7	64377952	64377952	+	Intron	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64377952T>G	uc003tto.2	+						ZNF273_uc003ttl.2_Intron|ZNF273_uc003ttm.1_Intron|ZNF273_uc003ttn.2_Intron|ZNF273_uc003ttp.1_Intron	NM_021148	NP_066971			zinc finger protein 273						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Lung NSC(55;0.0295)|all_lung(88;0.0691)																---	---	---	---
ZNF273	10793	broad.mit.edu	37	7	64388627	64388627	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:64388627A>G	uc003tto.2	+	4	997	c.921A>G	c.(919-921)AAA>AAG	p.K307K	ZNF273_uc003ttl.2_Silent_p.K242K|ZNF273_uc003ttn.2_Silent_p.K242K	NM_021148	NP_066971	Q14593	ZN273_HUMAN	zinc finger protein 273	307	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Lung NSC(55;0.0295)|all_lung(88;0.0691)																---	---	---	---
ASL	435	broad.mit.edu	37	7	65557610	65557610	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65557610G>A	uc003tuo.2	+	16	1321	c.1210G>A	c.(1210-1212)GCC>ACC	p.A404T	ASL_uc003tup.2_Missense_Mutation_p.A404T|ASL_uc003tur.2_Missense_Mutation_p.A378T|ASL_uc003tuq.2_Missense_Mutation_p.A384T	NM_000048	NP_000039	P04424	ARLY_HUMAN	argininosuccinate lyase isoform 1	404					arginine biosynthetic process via ornithine|arginine catabolic process|urea cycle	cytosol	argininosuccinate lyase activity			breast(2)	2					L-Arginine(DB00125)													---	---	---	---
TYW1	55253	broad.mit.edu	37	7	66483127	66483127	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66483127C>T	uc003tvn.2	+	6	1007	c.858C>T	c.(856-858)ACC>ACT	p.T286T	TYW1_uc010lai.2_RNA	NM_018264	NP_060734	Q9NV66	TYW1_HUMAN	radical S-adenosyl methionine and flavodoxin	286					tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity			skin(1)	1		Lung NSC(55;0.0846)|all_lung(88;0.183)																---	---	---	---
TYW1	55253	broad.mit.edu	37	7	66582544	66582544	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:66582544G>A	uc003tvn.2	+	13	1786	c.1637G>A	c.(1636-1638)CGC>CAC	p.R546H	TYW1_uc010lai.2_RNA|TYW1_uc011kef.1_Missense_Mutation_p.R160H	NM_018264	NP_060734	Q9NV66	TYW1_HUMAN	radical S-adenosyl methionine and flavodoxin	546					tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity			skin(1)	1		Lung NSC(55;0.0846)|all_lung(88;0.183)																---	---	---	---
AUTS2	26053	broad.mit.edu	37	7	70254888	70254888	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:70254888G>T	uc003tvw.3	+	19	3429	c.2686G>T	c.(2686-2688)GAC>TAC	p.D896Y	AUTS2_uc003tvx.3_Missense_Mutation_p.D872Y|AUTS2_uc011keg.1_Missense_Mutation_p.D348Y	NM_015570	NP_056385	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2 isoform 1	896										ovary(2)|central_nervous_system(1)	3		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)														---	---	---	---
POM121	9883	broad.mit.edu	37	7	72397386	72397386	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72397386G>A	uc003twk.2	+	3	907	c.907G>A	c.(907-909)GCC>ACC	p.A303T	POM121_uc003twj.2_Missense_Mutation_p.A38T|POM121_uc010lam.1_Missense_Mutation_p.A38T	NM_172020	NP_742017	Q96HA1	P121A_HUMAN	nuclear pore membrane protein 121	303	Pore side (Potential).				carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	endoplasmic reticulum membrane|nuclear membrane|nuclear pore					0		Lung NSC(55;0.163)																---	---	---	---
POM121	9883	broad.mit.edu	37	7	72409140	72409140	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72409140A>C	uc003twk.2	+	6	1287	c.1287A>C	c.(1285-1287)AGA>AGC	p.R429S	POM121_uc003twj.2_Missense_Mutation_p.R164S|POM121_uc010lam.1_Missense_Mutation_p.R164S	NM_172020	NP_742017	Q96HA1	P121A_HUMAN	nuclear pore membrane protein 121	429	Ser-rich.|Pore side (Potential).				carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	endoplasmic reticulum membrane|nuclear membrane|nuclear pore					0		Lung NSC(55;0.163)																---	---	---	---
NSUN5	55695	broad.mit.edu	37	7	72717625	72717625	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72717625C>T	uc003txw.2	-	9	1294	c.1258G>A	c.(1258-1260)GCT>ACT	p.A420T	FKBP6_uc003twz.2_Intron|NSUN5_uc003txv.2_Missense_Mutation_p.A420T|NSUN5_uc003txx.2_Missense_Mutation_p.A382T|NSUN5_uc011kev.1_Missense_Mutation_p.A420T	NM_018044	NP_060514	Q96P11	NSUN5_HUMAN	NOL1/NOP2/Sun domain family, member 5 isoform 2	420							methyltransferase activity				0		Lung NSC(55;0.163)																---	---	---	---
STX1A	6804	broad.mit.edu	37	7	73118722	73118722	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73118722G>A	uc003tyx.2	-	5	342	c.315C>T	c.(313-315)GGC>GGT	p.G105G	WBSCR22_uc003tyw.1_3'UTR|STX1A_uc003tyy.2_Silent_p.G105G|STX1A_uc010lbj.1_Silent_p.G105G	NM_004603	NP_004594	Q16623	STX1A_HUMAN	syntaxin 1A isoform 1	105	Potential.|Cytoplasmic (Potential).				energy reserve metabolic process|glutamate secretion|intracellular protein transport|regulation of insulin secretion	cell junction|extracellular region|integral to membrane|neuron projection|synaptic vesicle membrane|synaptosome	SNAP receptor activity				0		Lung NSC(55;0.0908)|all_lung(88;0.198)																---	---	---	---
ELN	2006	broad.mit.edu	37	7	73455551	73455551	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73455551G>A	uc003tzw.2	+	5	293	c.202G>A	c.(202-204)GGA>AGA	p.G68R	RFC2_uc011kfa.1_Intron|ELN_uc003tzm.1_RNA|ELN_uc011kfe.1_Missense_Mutation_p.G68R|ELN_uc003tzn.2_Missense_Mutation_p.G68R|ELN_uc003tzz.2_Intron|ELN_uc003tzo.2_Missense_Mutation_p.G68R|ELN_uc003tzp.2_Missense_Mutation_p.G58R|ELN_uc003tzq.2_Missense_Mutation_p.G68R|ELN_uc003tzr.2_RNA|ELN_uc003tzs.2_Missense_Mutation_p.G68R|ELN_uc003tzt.2_Missense_Mutation_p.G68R|ELN_uc003tzu.2_Missense_Mutation_p.G68R|ELN_uc003tzv.2_Missense_Mutation_p.G58R|ELN_uc003tzx.2_Missense_Mutation_p.G58R|ELN_uc011kff.1_Missense_Mutation_p.G68R|ELN_uc003tzy.2_Missense_Mutation_p.G58R	NM_000501	NP_001075224	P15502	ELN_HUMAN	elastin isoform a precursor	68					blood circulation|cell proliferation|organ morphogenesis|respiratory gaseous exchange	proteinaceous extracellular matrix	extracellular matrix constituent conferring elasticity|protein binding			ovary(3)|pancreas(2)	5		Lung NSC(55;0.159)			Rofecoxib(DB00533)			T	PAX5	B-ALL		Supravalvular Aortic Stenosis|Cutis laxa |Williams-Beuren Syndrome						---	---	---	---
ELN	2006	broad.mit.edu	37	7	73456952	73456952	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73456952G>A	uc003tzw.2	+	6	332	c.241G>A	c.(241-243)GCC>ACC	p.A81T	RFC2_uc011kfa.1_Intron|ELN_uc003tzm.1_RNA|ELN_uc011kfe.1_Intron|ELN_uc003tzn.2_Missense_Mutation_p.A81T|ELN_uc003tzz.2_Missense_Mutation_p.A69T|ELN_uc003tzo.2_Missense_Mutation_p.A81T|ELN_uc003tzp.2_Missense_Mutation_p.A71T|ELN_uc003tzq.2_Intron|ELN_uc003tzr.2_RNA|ELN_uc003tzs.2_Missense_Mutation_p.A81T|ELN_uc003tzt.2_Missense_Mutation_p.A81T|ELN_uc003tzu.2_Missense_Mutation_p.A81T|ELN_uc003tzv.2_Missense_Mutation_p.A71T|ELN_uc003tzx.2_Missense_Mutation_p.A71T|ELN_uc011kff.1_Missense_Mutation_p.A81T|ELN_uc003tzy.2_Missense_Mutation_p.A71T	NM_000501	NP_001075224	P15502	ELN_HUMAN	elastin isoform a precursor	81					blood circulation|cell proliferation|organ morphogenesis|respiratory gaseous exchange	proteinaceous extracellular matrix	extracellular matrix constituent conferring elasticity|protein binding			ovary(3)|pancreas(2)	5		Lung NSC(55;0.159)			Rofecoxib(DB00533)			T	PAX5	B-ALL		Supravalvular Aortic Stenosis|Cutis laxa |Williams-Beuren Syndrome						---	---	---	---
ELN	2006	broad.mit.edu	37	7	73456960	73456960	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73456960C>T	uc003tzw.2	+	6	340	c.249C>T	c.(247-249)CCC>CCT	p.P83P	RFC2_uc011kfa.1_Intron|ELN_uc003tzm.1_RNA|ELN_uc011kfe.1_Intron|ELN_uc003tzn.2_Silent_p.P83P|ELN_uc003tzz.2_Silent_p.P71P|ELN_uc003tzo.2_Silent_p.P83P|ELN_uc003tzp.2_Silent_p.P73P|ELN_uc003tzq.2_Intron|ELN_uc003tzr.2_RNA|ELN_uc003tzs.2_Silent_p.P83P|ELN_uc003tzt.2_Silent_p.P83P|ELN_uc003tzu.2_Silent_p.P83P|ELN_uc003tzv.2_Silent_p.P73P|ELN_uc003tzx.2_Silent_p.P73P|ELN_uc011kff.1_Silent_p.P83P|ELN_uc003tzy.2_Silent_p.P73P	NM_000501	NP_001075224	P15502	ELN_HUMAN	elastin isoform a precursor	83					blood circulation|cell proliferation|organ morphogenesis|respiratory gaseous exchange	proteinaceous extracellular matrix	extracellular matrix constituent conferring elasticity|protein binding			ovary(3)|pancreas(2)	5		Lung NSC(55;0.159)			Rofecoxib(DB00533)			T	PAX5	B-ALL		Supravalvular Aortic Stenosis|Cutis laxa |Williams-Beuren Syndrome						---	---	---	---
ELN	2006	broad.mit.edu	37	7	73458210	73458210	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73458210T>C	uc003tzw.2	+	9	520	c.429T>C	c.(427-429)GGT>GGC	p.G143G	RFC2_uc011kfa.1_Intron|ELN_uc003tzm.1_Intron|ELN_uc011kfe.1_Silent_p.G112G|ELN_uc003tzn.2_Silent_p.G143G|ELN_uc003tzz.2_Silent_p.G131G|ELN_uc003tzo.2_Silent_p.G143G|ELN_uc003tzp.2_Silent_p.G133G|ELN_uc003tzq.2_Intron|ELN_uc003tzr.2_RNA|ELN_uc003tzs.2_Silent_p.G143G|ELN_uc003tzt.2_Silent_p.G148G|ELN_uc003tzu.2_Silent_p.G148G|ELN_uc003tzv.2_Silent_p.G133G|ELN_uc003tzx.2_Silent_p.G133G|ELN_uc011kff.1_Silent_p.G143G|ELN_uc003tzy.2_Silent_p.G138G	NM_000501	NP_001075224	P15502	ELN_HUMAN	elastin isoform a precursor	143					blood circulation|cell proliferation|organ morphogenesis|respiratory gaseous exchange	proteinaceous extracellular matrix	extracellular matrix constituent conferring elasticity|protein binding			ovary(3)|pancreas(2)	5		Lung NSC(55;0.159)			Rofecoxib(DB00533)			T	PAX5	B-ALL		Supravalvular Aortic Stenosis|Cutis laxa |Williams-Beuren Syndrome						---	---	---	---
GTF2IRD1	9569	broad.mit.edu	37	7	73953040	73953040	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:73953040C>T	uc003uaq.2	+	13	1871	c.1478C>T	c.(1477-1479)CCG>CTG	p.P493L	GTF2IRD1_uc010lbq.2_Missense_Mutation_p.P525L|GTF2IRD1_uc003uap.2_Missense_Mutation_p.P493L|GTF2IRD1_uc003uar.1_Missense_Mutation_p.P493L	NM_016328	NP_057412	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1 isoform 1	493						nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(4)	4																		---	---	---	---
GTF2IRD1	9569	broad.mit.edu	37	7	74005258	74005258	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:74005258C>T	uc003uaq.2	+	24	2941	c.2548C>T	c.(2548-2550)CGG>TGG	p.R850W	GTF2IRD1_uc010lbq.2_Missense_Mutation_p.R867W|GTF2IRD1_uc003uap.2_Missense_Mutation_p.R835W|GTF2IRD1_uc003uar.1_Missense_Mutation_p.R835W	NM_016328	NP_057412	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1 isoform 1	850	GTF2I-like 5.					nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(4)	4																		---	---	---	---
TRIM74	378108	broad.mit.edu	37	7	75028231	75028231	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75028231T>C	uc003udc.1	+	2	214	c.14T>C	c.(13-15)GTG>GCG	p.V5A	TRIM74_uc010ldc.2_Missense_Mutation_p.V5A|TRIM74_uc010ldd.2_Missense_Mutation_p.V5A	NM_198924	NP_944606	Q86UV6	TRI74_HUMAN	tripartite motif-containing 73	5						intracellular	zinc ion binding				0																		---	---	---	---
HIP1	3092	broad.mit.edu	37	7	75185453	75185453	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75185453G>A	uc003uds.1	-	18	1745	c.1704C>T	c.(1702-1704)GCC>GCT	p.A568A	HIP1_uc011kfz.1_Silent_p.A445A	NM_005338	NP_005329	O00291	HIP1_HUMAN	huntingtin interacting protein 1	568	Potential.				activation of caspase activity|cell differentiation|clathrin coat assembly|endocytosis|induction of apoptosis|positive regulation of receptor-mediated endocytosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	clathrin coated vesicle membrane|cytoskeleton|Golgi apparatus|membrane fraction|nucleus	actin binding|clathrin binding|phosphatidylinositol binding|structural constituent of cytoskeleton			lung(3)|pancreas(2)|ovary(1)|breast(1)|central_nervous_system(1)	8								T	PDGFRB	CMML								---	---	---	---
POR	5447	broad.mit.edu	37	7	75615516	75615516	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75615516C>T	uc003udy.2	+	15	1937	c.1855C>T	c.(1855-1857)CTG>TTG	p.L619L	POR_uc011kgc.1_Silent_p.L427L|POR_uc011kgd.1_Silent_p.L518L|POR_uc011kge.1_Silent_p.L357L|POR_uc003uea.2_Silent_p.L106L	NM_000941	NP_000932	P16435	NCPR_HUMAN	cytochrome P450 reductase	616			LKQDREHLW -> R (in AHV).		cellular organofluorine metabolic process|positive regulation of monooxygenase activity	endoplasmic reticulum membrane	iron ion binding|NADPH-hemoprotein reductase activity			central_nervous_system(1)	1					Benzphetamine(DB00865)|Daunorubicin(DB00694)|Lipoic Acid(DB00166)|Menadione(DB00170)|Methoxyflurane(DB01028)|Mitomycin(DB00305)|Nilutamide(DB00665)													---	---	---	---
MDH2	4191	broad.mit.edu	37	7	75684232	75684232	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:75684232A>G	uc003ueo.2	+	2	237	c.151A>G	c.(151-153)AGC>GGC	p.S51G	MDH2_uc003uep.2_Intron|MDH2_uc011kgh.1_Missense_Mutation_p.S51G	NM_005918	NP_005909	P40926	MDHM_HUMAN	mitochondrial malate dehydrogenase precursor	51					gluconeogenesis|malate metabolic process|tricarboxylic acid cycle	mitochondrial matrix|nucleus|plasma membrane	binding|L-malate dehydrogenase activity			ovary(1)|central_nervous_system(1)|skin(1)	3					NADH(DB00157)													---	---	---	---
SRCRB4D	136853	broad.mit.edu	37	7	76019543	76019543	+	Missense_Mutation	SNP	C	T	T	rs150122962		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76019543C>T	uc003ufb.2	-	11	1909	c.1561G>A	c.(1561-1563)GCA>ACA	p.A521T	SRCRB4D_uc003ufa.2_Silent_p.S22S	NM_080744	NP_542782	Q8WTU2	SRB4D_HUMAN	scavenger receptor cysteine rich domain	521	SRCR 4.					extracellular region|membrane	scavenger receptor activity			pancreas(1)	1																		---	---	---	---
ZP3	7784	broad.mit.edu	37	7	76062966	76062966	+	Splice_Site	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76062966T>C	uc003ufd.3	+	4	723	c.713_splice	c.e4+2	p.G238_splice	ZP3_uc003ufc.3_Splice_Site_p.G187_splice|ZP3_uc003ufe.2_Splice_Site_p.G146_splice	NM_001110354	NP_001103824			zona pellucida glycoprotein 3 isoform 1						binding of sperm to zona pellucida|blastocyst formation|egg coat formation|humoral immune response mediated by circulating immunoglobulin|intracellular protein transport|negative regulation of binding of sperm to zona pellucida|negative regulation of transcription, DNA-dependent|oocyte development|phosphatidylinositol-mediated signaling|positive regulation of acrosomal vesicle exocytosis|positive regulation of acrosome reaction|positive regulation of antral ovarian follicle growth|positive regulation of calcium ion import|positive regulation of calcium ion transport via store-operated calcium channel activity|positive regulation of humoral immune response|positive regulation of interferon-gamma production|positive regulation of interleukin-4 production|positive regulation of leukocyte migration|positive regulation of ovarian follicle development|positive regulation of phosphatidylinositol biosynthetic process|positive regulation of protein kinase activity|positive regulation of protein kinase B signaling cascade|positive regulation of T cell proliferation|positive regulation of transcription, DNA-dependent|positive regulation of type IV hypersensitivity|protein kinase C signaling cascade	endoplasmic reticulum|extracellular space|Golgi apparatus|integral to membrane|multivesicular body|outer acrosomal membrane|perinuclear region of cytoplasm|plasma membrane|proteinaceous extracellular matrix	acrosin binding|manganese ion transmembrane transporter activity|receptor activity|sugar binding				0																		---	---	---	---
CCDC146	57639	broad.mit.edu	37	7	76911894	76911894	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:76911894G>C	uc003uga.2	+	15	2067	c.1940G>C	c.(1939-1941)CGG>CCG	p.R647P	CCDC146_uc010ldp.2_Missense_Mutation_p.R361P|CCDC146_uc003ugc.2_5'UTR	NM_020879	NP_065930	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	647										ovary(1)|central_nervous_system(1)	2		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)																---	---	---	---
PHTF2	57157	broad.mit.edu	37	7	77569528	77569528	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:77569528T>G	uc003ugs.3	+	13	1775	c.1649T>G	c.(1648-1650)CTT>CGT	p.L550R	PHTF2_uc003ugp.2_Missense_Mutation_p.L512R|PHTF2_uc003ugq.3_Missense_Mutation_p.L512R|PHTF2_uc010ldv.2_Missense_Mutation_p.L512R|PHTF2_uc003ugt.3_Missense_Mutation_p.L516R|PHTF2_uc003ugu.3_Missense_Mutation_p.L512R|PHTF2_uc010ldw.1_Missense_Mutation_p.L332R	NM_001127357	NP_001120829	Q8N3S3	PHTF2_HUMAN	putative homeodomain transcription factor 2	550					regulation of transcription, DNA-dependent|transcription, DNA-dependent	endoplasmic reticulum|nucleus	DNA binding			ovary(1)	1																		---	---	---	---
PCLO	27445	broad.mit.edu	37	7	82581688	82581688	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82581688C>A	uc003uhx.2	-	5	8870	c.8581G>T	c.(8581-8583)GCA>TCA	p.A2861S	PCLO_uc003uhv.2_Missense_Mutation_p.A2861S|PCLO_uc010lec.2_5'Flank	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	2792					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7																		---	---	---	---
PCLO	27445	broad.mit.edu	37	7	82595213	82595213	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82595213A>G	uc003uhx.2	-	4	4180	c.3891T>C	c.(3889-3891)GGT>GGC	p.G1297G	PCLO_uc003uhv.2_Silent_p.G1297G	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	1236					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7																		---	---	---	---
PCLO	27445	broad.mit.edu	37	7	82764715	82764715	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82764715T>C	uc003uhx.2	-	3	2440	c.2151A>G	c.(2149-2151)TCA>TCG	p.S717S	PCLO_uc003uhv.2_Silent_p.S717S	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	663	Pro-rich.				cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7																		---	---	---	---
ABCB4	5244	broad.mit.edu	37	7	87047903	87047903	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87047903T>C	uc003uiv.1	-	20	2504	c.2428A>G	c.(2428-2430)ACT>GCT	p.T810A	ABCB4_uc003uiw.1_Missense_Mutation_p.T810A|ABCB4_uc003uix.1_Missense_Mutation_p.T810A	NM_018849	NP_061337	P21439	MDR3_HUMAN	ATP-binding cassette, subfamily B, member 4	810	ABC transmembrane type-1 2.|Cytoplasmic (By similarity).				cellular lipid metabolic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|xenobiotic-transporting ATPase activity			ovary(4)|skin(1)|pancreas(1)	6	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)																	---	---	---	---
ABCB1	5243	broad.mit.edu	37	7	87174181	87174181	+	Silent	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87174181T>A	uc003uiz.1	-	17	2440	c.2022A>T	c.(2020-2022)GGA>GGT	p.G674G	ABCB1_uc011khc.1_Silent_p.G610G	NM_000927	NP_000918	P08183	MDR1_HUMAN	ATP-binding cassette, subfamily B, member 1	674	Cytoplasmic (Potential).				G2/M transition of mitotic cell cycle|stem cell proliferation	apical plasma membrane|cell surface|Golgi membrane|integral to membrane|intercellular canaliculus|membrane fraction	ATP binding|protein binding|xenobiotic-transporting ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	Esophageal squamous(14;0.00164)				Adenosine triphosphate(DB00171)|Alfentanil(DB00802)|Arsenic trioxide(DB01169)|Atazanavir(DB01072)|Carvedilol(DB01136)|Colchicine(DB01394)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dipyridamole(DB00975)|Estramustine(DB01196)|Flupenthixol(DB00875)|Imatinib(DB00619)|Itraconazole(DB01167)|Nicardipine(DB00622)|Propafenone(DB01182)|Quinacrine(DB01103)|Quinidine(DB00908)|Ranolazine(DB00243)|Rifampin(DB01045)|Roxithromycin(DB00778)|Saquinavir(DB01232)|Tamoxifen(DB00675)|Vinblastine(DB00570)													---	---	---	---
DBF4	10926	broad.mit.edu	37	7	87507518	87507518	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:87507518A>G	uc003ujf.1	+	2	701	c.197A>G	c.(196-198)AAG>AGG	p.K66R	SLC25A40_uc003uje.2_5'Flank|DBF4_uc003ujh.1_5'UTR|DBF4_uc003ujg.1_Intron|DBF4_uc011khf.1_5'UTR	NM_006716	NP_006707	Q9UBU7	DBF4A_HUMAN	activator of S phase kinase	66	BRCT 1.				cell cycle checkpoint|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle	nucleoplasm	enzyme activator activity|nucleic acid binding|protein binding|zinc ion binding			lung(2)	2	Esophageal squamous(14;0.00202)	Breast(660;0.0334)																---	---	---	---
MGC26647	219557	broad.mit.edu	37	7	88424060	88424060	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:88424060G>A	uc003ujv.2	-	2	379	c.197C>T	c.(196-198)GCT>GTT	p.A66V	ZNF804B_uc011khi.1_Intron	NM_152706	NP_689919	Q8TBZ9	CG062_HUMAN	hypothetical protein LOC219557	66											0	Esophageal squamous(14;0.00802)|all_hematologic(106;0.109)|Lung NSC(181;0.168)|all_lung(186;0.169)		STAD - Stomach adenocarcinoma(171;0.229)															---	---	---	---
C7orf63	79846	broad.mit.edu	37	7	89891366	89891366	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:89891366T>C	uc010lep.2	+	4	603	c.352T>C	c.(352-354)TGT>CGT	p.C118R	C7orf63_uc003ukf.2_RNA|C7orf63_uc003ukg.2_5'UTR|C7orf63_uc011khj.1_Missense_Mutation_p.C118R|C7orf63_uc010leo.2_Splice_Site_p.L117_splice	NM_001039706	NP_001034795	A5D8W1	CG063_HUMAN	hypothetical protein LOC79846 isoform 1	118							binding			ovary(1)	1																		---	---	---	---
CDK14	5218	broad.mit.edu	37	7	90747439	90747439	+	Missense_Mutation	SNP	C	T	T	rs145303395		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90747439C>T	uc003uky.2	+	14	1576	c.1354C>T	c.(1354-1356)CGG>TGG	p.R452W	CDK14_uc003ukz.1_Missense_Mutation_p.R434W|CDK14_uc010les.1_Missense_Mutation_p.R406W|CDK14_uc011khl.1_Missense_Mutation_p.R323W	NM_012395	NP_036527	O94921	CDK14_HUMAN	PFTAIRE protein kinase 1	452					cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4																		---	---	---	---
FZD1	8321	broad.mit.edu	37	7	90895662	90895662	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90895662C>T	uc003ula.2	+	1	1880	c.1467C>T	c.(1465-1467)GGC>GGT	p.G489G		NM_003505	NP_003496	Q9UP38	FZD1_HUMAN	frizzled 1 precursor	489	Extracellular (Potential).				autocrine signaling|axonogenesis|brain development|canonical Wnt receptor signaling pathway involved in mesenchymal stem cell differentiation|canonical Wnt receptor signaling pathway involved in osteoblast differentiation|embryo development|epithelial cell differentiation|G-protein signaling, coupled to cGMP nucleotide second messenger|gonad development|lung alveolus development|negative regulation of BMP signaling pathway|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|response to drug|vasculature development|Wnt receptor signaling pathway, calcium modulating pathway	apical part of cell|cell surface|cytoplasm|integral to membrane|neuron projection membrane	G-protein coupled receptor activity|PDZ domain binding|receptor binding|Wnt receptor activity|Wnt-protein binding				0	all_cancers(62;3.1e-10)|all_epithelial(64;1.66e-08)|Breast(17;0.000635)|Lung NSC(181;0.153)|all_lung(186;0.154)|all_hematologic(106;0.215)		STAD - Stomach adenocarcinoma(171;0.0134)															---	---	---	---
FZD1	8321	broad.mit.edu	37	7	90895824	90895824	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90895824G>A	uc003ula.2	+	1	2042	c.1629G>A	c.(1627-1629)CTG>CTA	p.L543L		NM_003505	NP_003496	Q9UP38	FZD1_HUMAN	frizzled 1 precursor	543	Helical; Name=6; (Potential).				autocrine signaling|axonogenesis|brain development|canonical Wnt receptor signaling pathway involved in mesenchymal stem cell differentiation|canonical Wnt receptor signaling pathway involved in osteoblast differentiation|embryo development|epithelial cell differentiation|G-protein signaling, coupled to cGMP nucleotide second messenger|gonad development|lung alveolus development|negative regulation of BMP signaling pathway|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|response to drug|vasculature development|Wnt receptor signaling pathway, calcium modulating pathway	apical part of cell|cell surface|cytoplasm|integral to membrane|neuron projection membrane	G-protein coupled receptor activity|PDZ domain binding|receptor binding|Wnt receptor activity|Wnt-protein binding				0	all_cancers(62;3.1e-10)|all_epithelial(64;1.66e-08)|Breast(17;0.000635)|Lung NSC(181;0.153)|all_lung(186;0.154)|all_hematologic(106;0.215)		STAD - Stomach adenocarcinoma(171;0.0134)															---	---	---	---
AKAP9	10142	broad.mit.edu	37	7	91713967	91713967	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91713967C>A	uc003ulg.2	+	34	8885	c.8660C>A	c.(8659-8661)CCT>CAT	p.P2887H	AKAP9_uc003ulf.2_Missense_Mutation_p.P2879H|AKAP9_uc003uli.2_Missense_Mutation_p.P2510H|AKAP9_uc003ulj.2_Missense_Mutation_p.P657H|AKAP9_uc003ulk.2_Missense_Mutation_p.P162H	NM_005751	NP_005742	Q99996	AKAP9_HUMAN	A-kinase anchor protein 9 isoform 2	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1)	26	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)					T	BRAF	papillary thyroid								---	---	---	---
AKAP9	10142	broad.mit.edu	37	7	91715695	91715695	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91715695T>C	uc003ulg.2	+	37	9403	c.9178T>C	c.(9178-9180)TTA>CTA	p.L3060L	AKAP9_uc003ulf.2_Silent_p.L3052L|AKAP9_uc003uli.2_Silent_p.L2683L|AKAP9_uc003ulj.2_Silent_p.L830L|AKAP9_uc003ulk.2_Silent_p.L335L	NM_005751	NP_005742	Q99996	AKAP9_HUMAN	A-kinase anchor protein 9 isoform 2	3064					G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1)	26	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)					T	BRAF	papillary thyroid								---	---	---	---
CYP51A1	1595	broad.mit.edu	37	7	91743029	91743029	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91743029T>C	uc003ulm.3	-	10	1642	c.1480A>G	c.(1480-1482)ATT>GTT	p.I494V	CYP51A1_uc011khn.1_Missense_Mutation_p.I389V|CYP51A1_uc003uln.3_Missense_Mutation_p.I431V	NM_000786	NP_000777	Q16850	CP51A_HUMAN	cytochrome P450, family 51, subfamily A,	488					cholesterol biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	electron carrier activity|heme binding|sterol 14-demethylase activity				0	all_cancers(62;2.16e-09)|all_epithelial(64;3.86e-08)|Breast(17;0.00206)|all_lung(186;0.169)|all_hematologic(106;0.215)|Lung NSC(181;0.227)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)		Fluconazole(DB00196)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Miconazole(DB01110)|Terconazole(DB00251)													---	---	---	---
ANKIB1	54467	broad.mit.edu	37	7	91972370	91972370	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91972370A>G	uc003ulw.2	+	6	1196	c.820A>G	c.(820-822)ATG>GTG	p.M274V		NM_019004	NP_061877	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1	274							protein binding|zinc ion binding			lung(1)	1	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)															---	---	---	---
SAMD9L	219285	broad.mit.edu	37	7	92763538	92763538	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92763538T>G	uc003umh.1	-	5	2963	c.1747A>C	c.(1747-1749)AAC>CAC	p.N583H	SAMD9L_uc003umj.1_Missense_Mutation_p.N583H|SAMD9L_uc003umi.1_Missense_Mutation_p.N583H|SAMD9L_uc010lfb.1_Missense_Mutation_p.N583H|SAMD9L_uc003umk.1_Missense_Mutation_p.N583H|SAMD9L_uc010lfc.1_Missense_Mutation_p.N583H|SAMD9L_uc010lfd.1_Missense_Mutation_p.N583H|SAMD9L_uc011khx.1_Intron	NM_152703	NP_689916	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	583										ovary(4)	4	all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989)		STAD - Stomach adenocarcinoma(171;0.000302)															---	---	---	---
HEPACAM2	253012	broad.mit.edu	37	7	92844772	92844772	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92844772G>A	uc003umm.2	-	3	680	c.657C>T	c.(655-657)TGC>TGT	p.C219C	HEPACAM2_uc003uml.2_Silent_p.C207C|HEPACAM2_uc010lff.2_Silent_p.C207C|HEPACAM2_uc011khy.1_Silent_p.C242C	NM_001039372	NP_001034461	A8MVW5	HECA2_HUMAN	HEPACAM family member 2 isoform 1	219	Ig-like C2-type 1.|Extracellular (Potential).					integral to membrane				ovary(3)|breast(1)|kidney(1)	5																		---	---	---	---
PPP1R9A	55607	broad.mit.edu	37	7	94916443	94916443	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:94916443G>A	uc003unp.2	+	14	3181	c.2899G>A	c.(2899-2901)GAG>AAG	p.E967K	PPP1R9A_uc010lfj.2_Intron|PPP1R9A_uc011kif.1_Intron|PPP1R9A_uc003unq.2_Intron|PPP1R9A_uc011kig.1_Intron|PPP1R9A_uc003unr.2_Intron	NM_017650	NP_060120	Q9ULJ8	NEB1_HUMAN	protein phosphatase 1, regulatory (inhibitor)	967	Interacts with TGN38 (By similarity).					cell junction|synapse|synaptosome	actin binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4	all_cancers(62;9.12e-11)|all_epithelial(64;4.34e-09)		STAD - Stomach adenocarcinoma(171;0.0031)												HNSCC(28;0.073)			---	---	---	---
SLC25A13	10165	broad.mit.edu	37	7	95761168	95761168	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95761168T>C	uc003uof.3	-	15	1669	c.1478A>G	c.(1477-1479)GAC>GGC	p.D493G	SLC25A13_uc003uog.3_Missense_Mutation_p.D494G|SLC25A13_uc011kik.1_Missense_Mutation_p.D385G	NM_014251	NP_055066	Q9UJS0	CMC2_HUMAN	solute carrier family 25, member 13 isoform 2	493	Helical; Name=4; (Potential).|Solcar 2.				ATP biosynthetic process|gluconeogenesis|malate-aspartate shuttle|response to calcium ion	integral to plasma membrane|mitochondrial inner membrane	calcium ion binding|L-aspartate transmembrane transporter activity|L-glutamate transmembrane transporter activity			central_nervous_system(3)|skin(1)	4	all_cancers(62;7.75e-08)|all_epithelial(64;1.16e-07)		STAD - Stomach adenocarcinoma(171;0.194)		L-Aspartic Acid(DB00128)													---	---	---	---
SLC25A13	10165	broad.mit.edu	37	7	95818969	95818969	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:95818969C>T	uc003uof.3	-	8	963	c.772G>A	c.(772-774)GCT>ACT	p.A258T	SLC25A13_uc003uog.3_Missense_Mutation_p.A258T|SLC25A13_uc011kik.1_Missense_Mutation_p.A150T	NM_014251	NP_055066	Q9UJS0	CMC2_HUMAN	solute carrier family 25, member 13 isoform 2	258					ATP biosynthetic process|gluconeogenesis|malate-aspartate shuttle|response to calcium ion	integral to plasma membrane|mitochondrial inner membrane	calcium ion binding|L-aspartate transmembrane transporter activity|L-glutamate transmembrane transporter activity			central_nervous_system(3)|skin(1)	4	all_cancers(62;7.75e-08)|all_epithelial(64;1.16e-07)		STAD - Stomach adenocarcinoma(171;0.194)		L-Aspartic Acid(DB00128)													---	---	---	---
DLX5	1749	broad.mit.edu	37	7	96650178	96650178	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96650178G>A	uc003uon.2	-	3	948	c.740C>T	c.(739-741)TCC>TTC	p.S247F		NM_005221	NP_005212	P56178	DLX5_HUMAN	distal-less homeobox 5	247					cell proliferation|endochondral ossification|osteoblast differentiation|positive regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			ovary(1)	1	all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858)																	---	---	---	---
DLX5	1749	broad.mit.edu	37	7	96651488	96651488	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:96651488C>T	uc003uon.2	-						DLX5_uc011kim.1_Silent_p.T183T	NM_005221	NP_005212			distal-less homeobox 5						cell proliferation|endochondral ossification|osteoblast differentiation|positive regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			ovary(1)	1	all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858)																	---	---	---	---
LMTK2	22853	broad.mit.edu	37	7	97823088	97823088	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97823088C>T	uc003upd.1	+	11	3604	c.3311C>T	c.(3310-3312)GCG>GTG	p.A1104V		NM_014916	NP_055731	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2 precursor	1104					early endosome to late endosome transport|endocytic recycling|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|protein autophosphorylation|receptor recycling|transferrin transport	early endosome|Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|recycling endosome	ATP binding|myosin VI binding|protein phosphatase inhibitor activity|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(9)|stomach(3)|pancreas(2)|large_intestine(1)|breast(1)	16	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)																	---	---	---	---
TRRAP	8295	broad.mit.edu	37	7	98497065	98497065	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98497065A>G	uc003upp.2	+	9	863	c.654A>G	c.(652-654)GGA>GGG	p.G218G	TRRAP_uc011kis.1_Silent_p.G218G|TRRAP_uc003upr.2_5'Flank	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated	218					histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
TRRAP	8295	broad.mit.edu	37	7	98508207	98508207	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98508207A>G	uc003upp.2	+	16	1998	c.1789A>G	c.(1789-1791)ATG>GTG	p.M597V	TRRAP_uc011kis.1_Missense_Mutation_p.M597V|TRRAP_uc003upr.2_Missense_Mutation_p.M289V	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated	597					histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
TRRAP	8295	broad.mit.edu	37	7	98508242	98508242	+	Intron	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98508242C>A	uc003upp.2	+						TRRAP_uc011kis.1_Intron|TRRAP_uc003upr.2_Intron	NM_003496	NP_003487			transformation/transcription domain-associated						histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
TRRAP	8295	broad.mit.edu	37	7	98547895	98547895	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98547895A>G	uc003upp.2	+						TRRAP_uc011kis.1_Intron|TRRAP_uc003upr.2_Intron	NM_003496	NP_003487			transformation/transcription domain-associated						histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
TRRAP	8295	broad.mit.edu	37	7	98579440	98579440	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98579440C>T	uc003upp.2	+	58	8871	c.8662C>T	c.(8662-8664)CGC>TGC	p.R2888C	TRRAP_uc011kis.1_Missense_Mutation_p.R2870C|TRRAP_uc003upr.2_Missense_Mutation_p.R2587C	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated	2888	FAT.				histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
TRRAP	8295	broad.mit.edu	37	7	98609113	98609113	+	Silent	SNP	G	A	A	rs55637395		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98609113G>A	uc003upp.2	+	71	11459	c.11250G>A	c.(11248-11250)GCG>GCA	p.A3750A	TRRAP_uc011kis.1_Silent_p.A3721A|TRRAP_uc003upr.2_Silent_p.A3456A|TRRAP_uc003ups.2_5'Flank	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated	3750	PI3K/PI4K.				histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
ARPC1B	10095	broad.mit.edu	37	7	98985781	98985781	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98985781C>T	uc003upz.2	+	4	378	c.289C>T	c.(289-291)CGG>TGG	p.R97W	ARPC1A_uc011kit.1_RNA|ARPC1B_uc003uqa.2_Missense_Mutation_p.R97W|ARPC1B_uc003uqb.2_Missense_Mutation_p.R97W|ARPC1B_uc003uqc.2_Missense_Mutation_p.R97W|ARPC1B_uc003uqd.2_5'Flank	NM_005720	NP_005711	O15143	ARC1B_HUMAN	actin related protein 2/3 complex subunit 1B	97	WD 3.				cellular component movement|regulation of actin filament polymerization	Arp2/3 protein complex|cytoplasm	actin binding|structural constituent of cytoskeleton				0	all_cancers(62;3.49e-09)|all_epithelial(64;2.57e-10)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
ZNF789	285989	broad.mit.edu	37	7	99084682	99084682	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99084682A>C	uc003uqq.1	+	5	1068	c.849A>C	c.(847-849)AAA>AAC	p.K283N	ZNF789_uc010lfw.1_Missense_Mutation_p.K188N|ZNF789_uc003uqr.1_Missense_Mutation_p.K225N	NM_213603	NP_998768	Q5FWF6	ZN789_HUMAN	zinc finger protein 789 isoform 1	283					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)																	---	---	---	---
ZNF394	84124	broad.mit.edu	37	7	99092061	99092061	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99092061A>G	uc003uqs.2	-	3	938	c.777T>C	c.(775-777)CCT>CCC	p.P259P	ZNF394_uc003uqt.2_Silent_p.P52P	NM_032164	NP_115540	Q53GI3	ZN394_HUMAN	zinc finger protein 394	259					viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)																	---	---	---	---
ZNF498	221785	broad.mit.edu	37	7	99219179	99219179	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99219179C>T	uc003url.1	+	5	898	c.571C>T	c.(571-573)CGG>TGG	p.R191W	ZNF498_uc003urm.1_Missense_Mutation_p.R27W|ZNF498_uc010lge.1_Missense_Mutation_p.R27W|ZNF498_uc003urn.2_RNA|ZNF498_uc010lgf.1_Missense_Mutation_p.R191W|ZNF498_uc003uro.1_Translation_Start_Site	NM_145115	NP_660090	Q6NSZ9	ZN498_HUMAN	zinc finger and SCAN domain containing 25	191					viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2	all_epithelial(64;1.95e-08)|Lung NSC(181;0.0066)|all_lung(186;0.011)|Esophageal squamous(72;0.0166)																	---	---	---	---
ZNF498	221785	broad.mit.edu	37	7	99226842	99226842	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99226842A>C	uc003url.1	+	8	1161	c.834A>C	c.(832-834)AAA>AAC	p.K278N	ZNF498_uc003urm.1_Missense_Mutation_p.K114N|ZNF498_uc010lge.1_Missense_Mutation_p.K114N|ZNF498_uc003urn.2_Intron|ZNF498_uc010lgf.1_Missense_Mutation_p.K206N|ZNF498_uc003uro.1_Missense_Mutation_p.K62N	NM_145115	NP_660090	Q6NSZ9	ZN498_HUMAN	zinc finger and SCAN domain containing 25	278					viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2	all_epithelial(64;1.95e-08)|Lung NSC(181;0.0066)|all_lung(186;0.011)|Esophageal squamous(72;0.0166)																	---	---	---	---
TRIM4	89122	broad.mit.edu	37	7	99490036	99490036	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99490036G>A	uc003usd.2	-	7	1383	c.1253C>T	c.(1252-1254)GCG>GTG	p.A418V	TRIM4_uc003use.2_Missense_Mutation_p.A392V|TRIM4_uc011kjc.1_Missense_Mutation_p.A248V	NM_033017	NP_148977	Q9C037	TRIM4_HUMAN	tripartite motif protein TRIM4 isoform alpha	418	B30.2/SPRY.				protein trimerization	cytoplasm|plasma membrane	zinc ion binding			ovary(1)|kidney(1)	2	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)	Ovarian(593;0.238)																---	---	---	---
MCM7	4176	broad.mit.edu	37	7	99695817	99695817	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99695817C>T	uc003usw.1	-	7	1327	c.817G>A	c.(817-819)GTC>ATC	p.V273I	MCM7_uc003usv.1_Missense_Mutation_p.V97I|MCM7_uc003usx.1_Missense_Mutation_p.V97I	NM_005916	NP_005907	P33993	MCM7_HUMAN	minichromosome maintenance complex component 7	273					cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|regulation of phosphorylation|response to DNA damage stimulus|S phase of mitotic cell cycle	chromatin|MCM complex	ATP binding|protein binding				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)				Atorvastatin(DB01076)													---	---	---	---
AP4M1	9179	broad.mit.edu	37	7	99703095	99703095	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99703095G>A	uc003utb.3	+	11	1070	c.862G>A	c.(862-864)GAT>AAT	p.D288N	AP4M1_uc011kjg.1_Missense_Mutation_p.D242N|AP4M1_uc010lgl.1_Intron|AP4M1_uc003utc.3_Missense_Mutation_p.D295N|AP4M1_uc010lgm.2_Missense_Mutation_p.D160N|AP4M1_uc003utd.2_Missense_Mutation_p.D288N|AP4M1_uc011kjh.1_Missense_Mutation_p.D240N|AP4M1_uc003ute.3_Missense_Mutation_p.D63N|AP4M1_uc003utf.3_Missense_Mutation_p.D160N	NM_004722	NP_004713	O00189	AP4M1_HUMAN	adaptor-related protein complex 4, mu 1 subunit	288	MHD.				intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|coated pit|Golgi trans cisterna	transporter activity				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
TAF6	6878	broad.mit.edu	37	7	99707683	99707683	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99707683A>C	uc003uti.2	-	12	1253	c.1172T>G	c.(1171-1173)CTG>CGG	p.L391R	AP4M1_uc003utd.2_Intron|TAF6_uc003utg.2_Missense_Mutation_p.L313R|TAF6_uc003uth.2_Missense_Mutation_p.L448R|TAF6_uc003utk.2_Missense_Mutation_p.L391R|TAF6_uc011kji.1_Missense_Mutation_p.L428R|TAF6_uc003utj.2_Missense_Mutation_p.L381R|TAF6_uc003utl.2_Missense_Mutation_p.L391R|TAF6_uc003utm.2_Missense_Mutation_p.L391R	NM_139315	NP_647476	P49848	TAF6_HUMAN	TBP-associated factor 6 isoform alpha	391					negative regulation of cell cycle|negative regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|MLL1 complex|transcription factor TFIID complex|transcription factor TFIID complex|transcription factor TFTC complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
GAL3ST4	79690	broad.mit.edu	37	7	99758356	99758356	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99758356G>A	uc003utt.2	-	3	1673	c.656C>T	c.(655-657)CCC>CTC	p.P219L	C7orf43_uc011kjj.1_5'Flank|C7orf43_uc003utr.2_5'Flank|C7orf43_uc003uts.2_5'Flank|GAL3ST4_uc003utu.2_Missense_Mutation_p.P219L|GAL3ST4_uc010lgq.2_Missense_Mutation_p.P157L	NM_024637	NP_078913	Q96RP7	G3ST4_HUMAN	galactose-3-O-sulfotransferase 4	219	Lumenal (Potential).				cell-cell signaling|oligosaccharide metabolic process|proteoglycan biosynthetic process|sulfur compound metabolic process	Golgi cisterna membrane|integral to membrane|membrane fraction	3'-phosphoadenosine 5'-phosphosulfate binding|galactosylceramide sulfotransferase activity|proteoglycan sulfotransferase activity			ovary(3)	3	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
STAG3	10734	broad.mit.edu	37	7	99783816	99783816	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99783816T>C	uc003utx.1	+						STAG3_uc010lgs.1_Intron|STAG3_uc011kjk.1_Intron	NM_012447	NP_036579			stromal antigen 3						chromosome segregation|synaptonemal complex assembly	chromosome, centromeric region|meiotic cohesin complex|synaptonemal complex	binding			ovary(4)|skin(2)|lung(1)|kidney(1)	8	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)																	---	---	---	---
FBXO24	26261	broad.mit.edu	37	7	100190641	100190641	+	Splice_Site	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100190641G>A	uc003uvm.1	+	5	1086	c.793_splice	c.e5+1	p.E265_splice	FBXO24_uc003uvl.1_Splice_Site_p.E251_splice|FBXO24_uc003uvn.1_Intron|uc011kjy.1_RNA|FBXO24_uc011kjz.1_Splice_Site_p.E303_splice|FBXO24_uc011kka.1_Splice_Site_p.E253_splice	NM_033506	NP_277041			F-box only protein 24 isoform 1							ubiquitin ligase complex	ubiquitin-protein ligase activity			ovary(3)|skin(1)	4	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)																	---	---	---	---
FBXO24	26261	broad.mit.edu	37	7	100197681	100197681	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100197681C>A	uc003uvm.1	+	9	1527	c.1234C>A	c.(1234-1236)CTG>ATG	p.L412M	FBXO24_uc003uvn.1_Intron|uc011kjy.1_RNA|FBXO24_uc011kjz.1_Missense_Mutation_p.L450M|FBXO24_uc011kka.1_Missense_Mutation_p.L400M|PCOLCE_uc011kkb.1_5'Flank|PCOLCE_uc003uvo.2_5'Flank|PCOLCE_uc010lhb.1_5'Flank	NM_033506	NP_277041	O75426	FBX24_HUMAN	F-box only protein 24 isoform 1	412	RCC1.					ubiquitin ligase complex	ubiquitin-protein ligase activity			ovary(3)|skin(1)	4	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)																	---	---	---	---
GNB2	2783	broad.mit.edu	37	7	100274163	100274163	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100274163C>A	uc003uwb.2	+	3	336	c.63C>A	c.(61-63)GCC>GCA	p.A21A	GNB2_uc003uwc.2_5'UTR|GNB2_uc010lhd.2_Intron|GNB2_uc010lhe.2_Intron|GNB2_uc003uwd.2_Intron|GNB2_uc010lhf.2_Intron|GNB2_uc003uwe.2_Silent_p.A21A|GNB2_uc003uwf.2_5'Flank	NM_005273	NP_005264	P62879	GBB2_HUMAN	guanine nucleotide-binding protein, beta-2	21					cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|synaptic transmission	perinuclear region of cytoplasm|plasma membrane	GTPase activity|GTPase binding|signal transducer activity			ovary(2)	2	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)	Ovarian(593;0.238)																---	---	---	---
EPHB4	2050	broad.mit.edu	37	7	100421491	100421491	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100421491G>A	uc003uwn.1	-	3	677	c.186C>T	c.(184-186)GAC>GAT	p.D62D	EPHB4_uc003uwm.1_Translation_Start_Site|EPHB4_uc010lhj.1_Silent_p.D62D|EPHB4_uc011kkf.1_Silent_p.D62D|EPHB4_uc011kkg.1_Silent_p.D62D|EPHB4_uc011kkh.1_Silent_p.D62D	NM_004444	NP_004435	P54760	EPHB4_HUMAN	EPH receptor B4 precursor	62	Extracellular (Potential).			D -> E (in Ref. 1; AAA20598).	cell proliferation|organ morphogenesis|regulation of angiogenesis	cell surface|integral to plasma membrane	ATP binding|ephrin receptor activity			lung(4)|stomach(3)|skin(3)|central_nervous_system(2)|ovary(2)|breast(1)	15	Lung NSC(181;0.041)|all_lung(186;0.0581)																	---	---	---	---
MUC17	140453	broad.mit.edu	37	7	100678915	100678915	+	Silent	SNP	G	A	A	rs138415845		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100678915G>A	uc003uxp.1	+	3	4271	c.4218G>A	c.(4216-4218)ACG>ACA	p.T1406T	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	1406	Extracellular (Potential).|59 X approximate tandem repeats.|21.|Ser-rich.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|skin(8)|breast(3)|lung(2)	27	Lung NSC(181;0.136)|all_lung(186;0.182)																	---	---	---	---
VGF	7425	broad.mit.edu	37	7	100806363	100806363	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100806363C>T	uc003uxx.3	-	2	1980	c.1762G>A	c.(1762-1764)GAG>AAG	p.E588K		NM_003378	NP_003369	O15240	VGF_HUMAN	VGF nerve growth factor inducible precursor	588					response to cAMP	extracellular space|transport vesicle	growth factor activity				0	Lung NSC(181;0.168)|all_lung(186;0.215)																	---	---	---	---
MOGAT3	346606	broad.mit.edu	37	7	100842080	100842080	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100842080C>T	uc003uyc.2	-	4	487	c.320G>A	c.(319-321)CGG>CAG	p.R107Q	MOGAT3_uc010lhr.2_Missense_Mutation_p.R107Q	NM_178176	NP_835470	Q86VF5	MOGT3_HUMAN	monoacylglycerol O-acyltransferase 3	107					glycerol metabolic process|lipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	2-acylglycerol O-acyltransferase activity|diacylglycerol O-acyltransferase activity			ovary(2)	2	Lung NSC(181;0.168)|all_lung(186;0.215)																	---	---	---	---
MYL10	93408	broad.mit.edu	37	7	101256835	101256835	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101256835C>T	uc003uyr.2	-	8	779	c.601G>A	c.(601-603)GCA>ACA	p.A201T		NM_138403	NP_612412	Q9BUA6	MYL10_HUMAN	myosin, light chain 10, regulatory	201	EF-hand 3.					mitochondrion	calcium ion binding			ovary(1)|breast(1)	2																		---	---	---	---
CUX1	1523	broad.mit.edu	37	7	101921282	101921282	+	Silent	SNP	C	T	T	rs146927122	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101921282C>T	uc003uyt.2	+	18	1645	c.1626C>T	c.(1624-1626)GCC>GCT	p.A542A	CUX1_uc011kkn.1_Silent_p.A503A|CUX1_uc003uyw.2_Silent_p.A496A|CUX1_uc003uyv.2_Silent_p.A526A|CUX1_uc003uyu.2_Silent_p.A540A|CUX1_uc003uyz.2_RNA	NM_001913	NP_001904	P39880	CUX1_HUMAN	cut-like homeobox 1 isoform b	349	Potential.				negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1)	8																		---	---	---	---
LRWD1	222229	broad.mit.edu	37	7	102109488	102109488	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102109488G>A	uc003uzn.2	+	9	1345	c.1207G>A	c.(1207-1209)GCC>ACC	p.A403T	LRWD1_uc003uzo.2_Missense_Mutation_p.A251T	NM_152892	NP_690852	Q9UFC0	LRWD1_HUMAN	leucine-rich repeats and WD repeat domain	403	WD 1.				chromatin modification|DNA-dependent DNA replication initiation|establishment of protein localization to chromatin|G1 phase of mitotic cell cycle	centromeric heterochromatin|nuclear origin of replication recognition complex|telomeric heterochromatin	chromatin binding|methyl-CpG binding|methylated histone residue binding			skin(1)	1																		---	---	---	---
PSMC2	5701	broad.mit.edu	37	7	103004631	103004631	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103004631C>T	uc003vbs.2	+	8	703	c.633C>T	c.(631-633)GGC>GGT	p.G211G	SLC26A5_uc003vbt.1_Intron|SLC26A5_uc003vbu.1_Intron|SLC26A5_uc003vbv.1_Intron|PSMC2_uc011klo.1_Silent_p.G74G	NM_002803	NP_002794	P35998	PRS7_HUMAN	proteasome 26S ATPase subunit 2	211					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	mitochondrion|nucleus|proteasome complex	ATP binding|ATPase activity|protein binding				0																		---	---	---	---
RELN	5649	broad.mit.edu	37	7	103206759	103206759	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103206759C>T	uc003vca.2	-	33	5008	c.4848G>A	c.(4846-4848)TTG>TTA	p.L1616L	RELN_uc010liz.2_Silent_p.L1616L	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	1616					axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|upper_aerodigestive_tract(5)|large_intestine(2)|central_nervous_system(2)|skin(1)|pancreas(1)	19				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)														---	---	---	---
RELN	5649	broad.mit.edu	37	7	103214740	103214740	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103214740T>C	uc003vca.2	-	30	4470	c.4310A>G	c.(4309-4311)CAA>CGA	p.Q1437R	RELN_uc010liz.2_Missense_Mutation_p.Q1437R	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	1437	EGF-like 3.				axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|upper_aerodigestive_tract(5)|large_intestine(2)|central_nervous_system(2)|skin(1)|pancreas(1)	19				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)														---	---	---	---
MLL5	55904	broad.mit.edu	37	7	104748048	104748048	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104748048G>A	uc003vcm.2	+	22	3678	c.3144G>A	c.(3142-3144)GAG>GAA	p.E1048E	MLL5_uc010ljc.2_Silent_p.E1048E|MLL5_uc010lje.1_RNA|MLL5_uc010ljf.1_RNA|MLL5_uc010ljg.2_5'UTR|MLL5_uc010ljh.1_5'Flank	NM_182931	NP_891847	Q8IZD2	MLL5_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 5	1048					cell cycle arrest|cellular response to retinoic acid|DNA methylation|erythrocyte differentiation|neutrophil activation|neutrophil mediated immunity|positive regulation of granulocyte differentiation|positive regulation of transcription, DNA-dependent|retinoic acid receptor signaling pathway|transcription, DNA-dependent	MLL5-L complex|nuclear speck	enzyme binding|histone methyltransferase activity (H3-K4 specific)|transcription coactivator activity|zinc ion binding			ovary(2)|pancreas(1)	3																		---	---	---	---
RINT1	60561	broad.mit.edu	37	7	105190924	105190924	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105190924G>A	uc003vda.1	+	9	1555	c.1324G>A	c.(1324-1326)GAG>AAG	p.E442K	RINT1_uc010ljj.1_Missense_Mutation_p.E17K	NM_021930	NP_068749	Q6NUQ1	RINT1_HUMAN	RAD50 interactor 1	442	RINT1/TIP20.				cell cycle|G2/M transition DNA damage checkpoint|protein transport|vesicle-mediated transport	endoplasmic reticulum membrane	protein binding			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
DUS4L	11062	broad.mit.edu	37	7	107217047	107217047	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107217047A>G	uc003veh.2	+						DUS4L_uc003veg.2_Intron|DUS4L_uc011klw.1_Intron|DUS4L_uc011klx.1_Intron|DUS4L_uc010ljl.2_Intron	NM_181581	NP_853559			dihydrouridine synthase 4-like						tRNA processing		flavin adenine dinucleotide binding|tRNA dihydrouridine synthase activity				0																		---	---	---	---
SLC26A4	5172	broad.mit.edu	37	7	107323940	107323940	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107323940A>G	uc003vep.2	+	8	1183	c.959A>G	c.(958-960)GAA>GGA	p.E320G		NM_000441	NP_000432	O43511	S26A4_HUMAN	pendrin	320	Extracellular (Potential).				regulation of pH|regulation of protein localization|sensory perception of sound	apical plasma membrane|integral to membrane	chloride transmembrane transporter activity|inorganic anion exchanger activity|iodide transmembrane transporter activity|secondary active sulfate transmembrane transporter activity			ovary(3)|central_nervous_system(2)|skin(2)	7														Pendred_syndrome				---	---	---	---
SLC26A4	5172	broad.mit.edu	37	7	107330628	107330628	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107330628C>T	uc003vep.2	+	10	1433	c.1209C>T	c.(1207-1209)GCC>GCT	p.A403A	SLC26A4_uc011kmb.1_5'Flank|SLC26A4_uc011kmc.1_5'Flank	NM_000441	NP_000432	O43511	S26A4_HUMAN	pendrin	403	Helical; (Potential).				regulation of pH|regulation of protein localization|sensory perception of sound	apical plasma membrane|integral to membrane	chloride transmembrane transporter activity|inorganic anion exchanger activity|iodide transmembrane transporter activity|secondary active sulfate transmembrane transporter activity			ovary(3)|central_nervous_system(2)|skin(2)	7														Pendred_syndrome				---	---	---	---
SLC26A4	5172	broad.mit.edu	37	7	107338528	107338528	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107338528T>A	uc003vep.2	+	14	1810	c.1586T>A	c.(1585-1587)ATC>AAC	p.I529N	SLC26A4_uc011kmb.1_Missense_Mutation_p.I116N|SLC26A4_uc011kmc.1_Missense_Mutation_p.I90N|SLC26A4_uc011kmd.1_Missense_Mutation_p.I98N	NM_000441	NP_000432	O43511	S26A4_HUMAN	pendrin	529	Cytoplasmic (Potential).				regulation of pH|regulation of protein localization|sensory perception of sound	apical plasma membrane|integral to membrane	chloride transmembrane transporter activity|inorganic anion exchanger activity|iodide transmembrane transporter activity|secondary active sulfate transmembrane transporter activity			ovary(3)|central_nervous_system(2)|skin(2)	7														Pendred_syndrome				---	---	---	---
SLC26A4	5172	broad.mit.edu	37	7	107341545	107341545	+	Splice_Site	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107341545G>T	uc003vep.2	+	16	1932	c.1708_splice	c.e16-1	p.V570_splice	SLC26A4_uc011kmb.1_Splice_Site_p.V157_splice|SLC26A4_uc011kmc.1_Splice_Site_p.V131_splice|SLC26A4_uc011kmd.1_Splice_Site_p.V139_splice	NM_000441	NP_000432			pendrin						regulation of pH|regulation of protein localization|sensory perception of sound	apical plasma membrane|integral to membrane	chloride transmembrane transporter activity|inorganic anion exchanger activity|iodide transmembrane transporter activity|secondary active sulfate transmembrane transporter activity			ovary(3)|central_nervous_system(2)|skin(2)	7														Pendred_syndrome				---	---	---	---
CBLL1	79872	broad.mit.edu	37	7	107399540	107399540	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107399540C>T	uc003veq.2	+	6	1723	c.1393C>T	c.(1393-1395)CGA>TGA	p.R465*	CBLL1_uc011kme.1_Nonsense_Mutation_p.R344*|CBLL1_uc011kmf.1_Nonsense_Mutation_p.R464*	NM_024814	NP_079090	Q75N03	HAKAI_HUMAN	Cas-Br-M (murine) ecotropic retroviral	465	Pro-rich.				cell-cell adhesion|negative regulation of cell adhesion|positive regulation of cell migration|positive regulation of endocytosis		protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)|skin(2)|lung(1)	5																		---	---	---	---
LAMB1	3912	broad.mit.edu	37	7	107605057	107605057	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107605057A>G	uc003vew.2	-	14	1973	c.1638T>C	c.(1636-1638)GGT>GGC	p.G546G	LAMB1_uc003vev.2_Silent_p.G570G|LAMB1_uc003vex.2_Silent_p.G546G|LAMB1_uc010ljn.1_Silent_p.G632G	NM_002291	NP_002282	P07942	LAMB1_HUMAN	laminin, beta 1 precursor	546					axon guidance|odontogenesis|positive regulation of cell migration|positive regulation of epithelial cell proliferation|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-2 complex|laminin-8 complex|perinuclear region of cytoplasm	extracellular matrix structural constituent			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	8					Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
PNPLA8	50640	broad.mit.edu	37	7	108155378	108155378	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:108155378T>C	uc003vff.1	-	4	965	c.558A>G	c.(556-558)AAA>AAG	p.K186K	PNPLA8_uc003vfg.1_RNA|PNPLA8_uc003vfh.1_Silent_p.K186K|PNPLA8_uc003vfi.1_Silent_p.K86K|PNPLA8_uc003vfj.1_Silent_p.K186K|PNPLA8_uc003vfk.1_Silent_p.K86K	NM_015723	NP_056538	Q9NP80	PLPL8_HUMAN	patatin-like phospholipase domain containing 8	186					fatty acid metabolic process|lipid catabolic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|membrane fraction|perinuclear region of cytoplasm|peroxisomal membrane	ATP binding|calcium-independent phospholipase A2 activity|lysophospholipase activity			breast(2)	2																		---	---	---	---
LRRN3	54674	broad.mit.edu	37	7	110763654	110763654	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110763654C>T	uc003vft.3	+	4	1872	c.826C>T	c.(826-828)CGA>TGA	p.R276*	IMMP2L_uc003vfq.1_Intron|IMMP2L_uc010ljr.1_Intron|IMMP2L_uc003vfr.2_Intron|LRRN3_uc003vfu.3_Nonsense_Mutation_p.R276*|LRRN3_uc003vfs.3_Nonsense_Mutation_p.R276*	NM_001099660	NP_001093130	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3 precursor	276	Extracellular (Potential).|LRR 9.					integral to membrane				skin(3)|ovary(2)|pancreas(2)|central_nervous_system(1)	8				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)														---	---	---	---
LRRN3	54674	broad.mit.edu	37	7	110763877	110763877	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110763877A>G	uc003vft.3	+	4	2095	c.1049A>G	c.(1048-1050)TAC>TGC	p.Y350C	IMMP2L_uc003vfq.1_Intron|IMMP2L_uc010ljr.1_Intron|IMMP2L_uc003vfr.2_Intron|LRRN3_uc003vfu.3_Missense_Mutation_p.Y350C|LRRN3_uc003vfs.3_Missense_Mutation_p.Y350C	NM_001099660	NP_001093130	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3 precursor	350	Extracellular (Potential).|LRR 12.					integral to membrane				skin(3)|ovary(2)|pancreas(2)|central_nervous_system(1)	8				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)														---	---	---	---
LRRN3	54674	broad.mit.edu	37	7	110764734	110764734	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:110764734C>A	uc003vft.3	+	4	2952	c.1906C>A	c.(1906-1908)CTT>ATT	p.L636I	IMMP2L_uc003vfq.1_Intron|IMMP2L_uc010ljr.1_Intron|IMMP2L_uc003vfr.2_Intron|LRRN3_uc003vfu.3_Missense_Mutation_p.L636I|LRRN3_uc003vfs.3_Missense_Mutation_p.L636I	NM_001099660	NP_001093130	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3 precursor	636	Helical; (Potential).					integral to membrane				skin(3)|ovary(2)|pancreas(2)|central_nervous_system(1)	8				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)														---	---	---	---
DOCK4	9732	broad.mit.edu	37	7	111368719	111368719	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:111368719A>T	uc003vfx.2	-	52	5781	c.5512T>A	c.(5512-5514)TCC>ACC	p.S1838T	DOCK4_uc011kml.1_Missense_Mutation_p.S719T|DOCK4_uc011kmm.1_Missense_Mutation_p.S707T|DOCK4_uc003vfw.2_Missense_Mutation_p.S1250T|DOCK4_uc003vfy.2_Missense_Mutation_p.S1883T|DOCK4_uc003vfv.2_Missense_Mutation_p.S151T	NM_014705	NP_055520	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	1838	Ser-rich.				cell chemotaxis	cytosol|endomembrane system|membrane|stereocilium	GTP binding|guanyl-nucleotide exchange factor activity|PDZ domain binding|Rac GTPase activator activity|Rac GTPase binding|receptor tyrosine kinase binding|SH3 domain binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)	4		Acute lymphoblastic leukemia(1;0.0441)																---	---	---	---
PPP1R3A	5506	broad.mit.edu	37	7	113558312	113558312	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:113558312A>C	uc010ljy.1	-	1	771	c.740T>G	c.(739-741)GTT>GGT	p.V247G		NM_002711	NP_002702	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory (inhibitor)	247					glycogen metabolic process	integral to membrane				lung(9)|ovary(9)|pancreas(7)|skin(6)|breast(2)|prostate(1)	34																		---	---	---	---
TES	26136	broad.mit.edu	37	7	115890347	115890347	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:115890347T>G	uc003vho.2	+	4	680	c.499T>G	c.(499-501)TTG>GTG	p.L167V	TES_uc011kmy.1_Intron|TES_uc003vhp.2_Missense_Mutation_p.L158V|uc003vhq.1_5'Flank	NM_015641	NP_056456	Q9UGI8	TES_HUMAN	testin isoform 1	167	PET.				negative regulation of cell proliferation	cytoplasm|focal adhesion|nucleus|protein complex	zinc ion binding				0	Lung NSC(10;0.0137)|all_lung(10;0.0148)	Breast(660;0.0602)	STAD - Stomach adenocarcinoma(10;0.00878)															---	---	---	---
CTTNBP2	83992	broad.mit.edu	37	7	117432218	117432218	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:117432218G>A	uc003vjf.2	-	4	1124	c.1032C>T	c.(1030-1032)AGC>AGT	p.S344S		NM_033427	NP_219499	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	344										ovary(4)|central_nervous_system(1)	5	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)														---	---	---	---
KCND2	3751	broad.mit.edu	37	7	120387848	120387848	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120387848G>C	uc003vjj.1	+	6	2794	c.1829G>C	c.(1828-1830)GGA>GCA	p.G610A		NM_012281	NP_036413	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related	610	Cytoplasmic (Potential).				regulation of action potential|synaptic transmission	cell surface|dendritic spine	metal ion binding			ovary(2)|central_nervous_system(2)|skin(1)	5	all_neural(327;0.117)																	---	---	---	---
C7orf58	79974	broad.mit.edu	37	7	120737760	120737760	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:120737760A>G	uc003vjq.3	+	6	1071	c.624A>G	c.(622-624)CAA>CAG	p.Q208Q	C7orf58_uc003vjr.1_Silent_p.Q208Q|C7orf58_uc003vjs.3_Silent_p.Q208Q|C7orf58_uc003vjt.3_5'UTR|C7orf58_uc010lkk.1_5'UTR	NM_024913	NP_079189	A4D0V7	CG058_HUMAN	hypothetical protein LOC79974 isoform 1	208						endoplasmic reticulum				ovary(4)|large_intestine(2)|skin(2)|pancreas(1)	9	all_neural(327;0.117)																	---	---	---	---
FEZF1	389549	broad.mit.edu	37	7	121942175	121942175	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:121942175C>T	uc003vkd.2	-	4	1378	c.1304G>A	c.(1303-1305)GGC>GAC	p.G435D	FEZF1_uc003vkc.2_Missense_Mutation_p.G385D|uc010lko.1_5'Flank	NM_001024613	NP_001019784	A0PJY2	FEZF1_HUMAN	FEZ family zinc finger 1 isoform 1	435	Pro-rich.				cell differentiation|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|breast(1)	3																		---	---	---	---
CADPS2	93664	broad.mit.edu	37	7	122261623	122261623	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122261623C>T	uc010lkp.2	-	5	1179	c.1016G>A	c.(1015-1017)CGT>CAT	p.R339H	CADPS2_uc003vkg.3_Missense_Mutation_p.R39H|CADPS2_uc010lkq.2_Missense_Mutation_p.R339H	NM_017954	NP_060424	Q86UW7	CAPS2_HUMAN	Ca2+-dependent activator protein for secretion 2	339					exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|synapse	lipid binding|metal ion binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
IQUB	154865	broad.mit.edu	37	7	123097521	123097521	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123097521T>C	uc003vkn.2	-	12	2684	c.2107A>G	c.(2107-2109)AAA>GAA	p.K703E	IQUB_uc011kny.1_Missense_Mutation_p.K36E|IQUB_uc003vko.2_Missense_Mutation_p.K703E|IQUB_uc010lkt.2_RNA	NM_178827	NP_849149	Q8NA54	IQUB_HUMAN	IQ motif and ubiquitin domain containing	703										ovary(3)|large_intestine(1)	4																		---	---	---	---
LMOD2	442721	broad.mit.edu	37	7	123302621	123302621	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123302621G>A	uc003vky.2	+	2	1138	c.981G>A	c.(979-981)ACG>ACA	p.T327T		NM_207163	NP_997046	Q6P5Q4	LMOD2_HUMAN	leiomodin 2 (cardiac)	327						cytoskeleton	actin binding|tropomyosin binding				0																		---	---	---	---
HYAL4	23553	broad.mit.edu	37	7	123508893	123508893	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:123508893T>C	uc003vlc.2	+	3	1204	c.566T>C	c.(565-567)GTG>GCG	p.V189A	HYAL4_uc011knz.1_Missense_Mutation_p.V189A	NM_012269	NP_036401	Q2M3T9	HYAL4_HUMAN	hyaluronoglucosaminidase 4	189	Extracellular (Potential).				fusion of sperm to egg plasma membrane|glycosaminoglycan catabolic process	integral to membrane	hyalurononglucosaminidase activity			skin(1)	1																		---	---	---	---
GPR37	2861	broad.mit.edu	37	7	124404612	124404612	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:124404612G>A	uc003vli.2	-	1	1070	c.419C>T	c.(418-420)ACG>ATG	p.T140M		NM_005302	NP_005293	O15354	GPR37_HUMAN	G protein-coupled receptor 37 precursor	140	Extracellular (Potential).					endoplasmic reticulum membrane|integral to plasma membrane	G-protein coupled receptor activity			ovary(1)|lung(1)|central_nervous_system(1)	3																		---	---	---	---
GRM8	2918	broad.mit.edu	37	7	126542709	126542709	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126542709C>T	uc003vlr.2	-	5	1354	c.1043G>A	c.(1042-1044)CGA>CAA	p.R348Q	GRM8_uc003vls.2_RNA|GRM8_uc011kof.1_RNA|GRM8_uc003vlt.2_Missense_Mutation_p.R348Q|GRM8_uc010lkz.1_RNA|GRM8_uc003vlu.1_Missense_Mutation_p.R69Q	NM_000845	NP_000836	O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8 isoform a	348	Extracellular (Potential).				negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception	integral to plasma membrane				lung(15)|ovary(5)|pancreas(1)|breast(1)|skin(1)	23		Prostate(267;0.186)			L-Glutamic Acid(DB00142)										HNSCC(24;0.065)			---	---	---	---
FSCN3	29999	broad.mit.edu	37	7	127235471	127235471	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127235471C>T	uc003vmd.1	+	2	474	c.255C>T	c.(253-255)GGC>GGT	p.G85G	FSCN3_uc003vmc.1_Silent_p.G40G|FSCN3_uc011kog.1_RNA|FSCN3_uc011koh.1_5'UTR|FSCN3_uc010llc.1_Silent_p.G85G	NM_020369	NP_065102	Q9NQT6	FSCN3_HUMAN	fascin 3	85						actin cytoskeleton|cytoplasm	actin filament binding|protein binding, bridging			ovary(1)	1																		---	---	---	---
LRRC4	64101	broad.mit.edu	37	7	127669172	127669172	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:127669172C>T	uc003vmk.2	-	2	1659	c.1522G>A	c.(1522-1524)GCG>ACG	p.A508T	SND1_uc003vmi.2_Intron|SND1_uc010lle.2_Intron	NM_022143	NP_071426	Q9HBW1	LRRC4_HUMAN	leucine rich repeat containing 4 precursor	508	Thr-rich.|Extracellular (Potential).					cell junction|integral to membrane|postsynaptic membrane				large_intestine(1)|breast(1)|central_nervous_system(1)|pancreas(1)	4				Lung(243;0.124)														---	---	---	---
FLNC	2318	broad.mit.edu	37	7	128485150	128485150	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128485150A>G	uc003vnz.3	+	21	3840	c.3631A>G	c.(3631-3633)ACC>GCC	p.T1211A	FLNC_uc003voa.3_Missense_Mutation_p.T1211A	NM_001458	NP_001449	Q14315	FLNC_HUMAN	gamma filamin isoform a	1211	Filamin 10.				cell junction assembly	cytoskeleton|cytosol|plasma membrane|sarcomere	actin binding			breast(5)|large_intestine(3)|ovary(2)|central_nervous_system(1)|skin(1)	12																		---	---	---	---
FLNC	2318	broad.mit.edu	37	7	128488751	128488751	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128488751T>A	uc003vnz.3	+	27	4926	c.4717T>A	c.(4717-4719)TTG>ATG	p.L1573M	FLNC_uc003voa.3_Missense_Mutation_p.L1573M	NM_001458	NP_001449	Q14315	FLNC_HUMAN	gamma filamin isoform a	1573	Filamin 14.				cell junction assembly	cytoskeleton|cytosol|plasma membrane|sarcomere	actin binding			breast(5)|large_intestine(3)|ovary(2)|central_nervous_system(1)|skin(1)	12																		---	---	---	---
FLNC	2318	broad.mit.edu	37	7	128489556	128489556	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128489556C>T	uc003vnz.3	+	30	5332	c.5123C>T	c.(5122-5124)GCG>GTG	p.A1708V	FLNC_uc003voa.3_Missense_Mutation_p.A1708V	NM_001458	NP_001449	Q14315	FLNC_HUMAN	gamma filamin isoform a	1708	Filamin 15.				cell junction assembly	cytoskeleton|cytosol|plasma membrane|sarcomere	actin binding			breast(5)|large_intestine(3)|ovary(2)|central_nervous_system(1)|skin(1)	12																		---	---	---	---
FLNC	2318	broad.mit.edu	37	7	128493066	128493066	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128493066C>T	uc003vnz.3	+	37	6398	c.6189C>T	c.(6187-6189)ATC>ATT	p.I2063I	FLNC_uc003voa.3_Silent_p.I2030I	NM_001458	NP_001449	Q14315	FLNC_HUMAN	gamma filamin isoform a	2063	Filamin 19.				cell junction assembly	cytoskeleton|cytosol|plasma membrane|sarcomere	actin binding			breast(5)|large_intestine(3)|ovary(2)|central_nervous_system(1)|skin(1)	12																		---	---	---	---
NRF1	4899	broad.mit.edu	37	7	129357091	129357091	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129357091T>C	uc003voz.2	+	9	1215	c.1098T>C	c.(1096-1098)GGT>GGC	p.G366G	NRF1_uc003vpa.2_Silent_p.G366G|NRF1_uc011kpa.1_Silent_p.G205G|NRF1_uc003vpb.2_Silent_p.G366G	NM_005011	NP_005002	Q16656	NRF1_HUMAN	nuclear respiratory factor 1	366	Required for transcriptional activation.				generation of precursor metabolites and energy|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1																		---	---	---	---
ZC3HC1	51530	broad.mit.edu	37	7	129666030	129666030	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129666030G>A	uc003vpi.2	-	6	771	c.744C>T	c.(742-744)GCC>GCT	p.A248A	ZC3HC1_uc003vph.2_Silent_p.A135A|ZC3HC1_uc010lma.2_Silent_p.A135A	NM_016478	NP_057562	Q86WB0	NIPA_HUMAN	zinc finger, C3HC type 1	248					cell division|mitosis	nucleus	protein kinase binding|zinc ion binding				0	Melanoma(18;0.0435)																	---	---	---	---
TMEM209	84928	broad.mit.edu	37	7	129841826	129841826	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129841826C>T	uc003vpn.2	-	5	560	c.437G>A	c.(436-438)CGT>CAT	p.R146H	TMEM209_uc010lmc.1_Missense_Mutation_p.R146H|TMEM209_uc003vpo.2_Missense_Mutation_p.R146H	NM_032842	NP_116231	Q96SK2	TM209_HUMAN	transmembrane protein 209	146	Ser-rich.					integral to membrane				ovary(2)|large_intestine(1)	3	Melanoma(18;0.0435)																	---	---	---	---
TMEM209	84928	broad.mit.edu	37	7	129843679	129843679	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:129843679T>C	uc003vpn.2	-	3	271	c.148A>G	c.(148-150)AAA>GAA	p.K50E	TMEM209_uc010lmc.1_Missense_Mutation_p.K50E|TMEM209_uc003vpo.2_Missense_Mutation_p.K50E	NM_032842	NP_116231	Q96SK2	TM209_HUMAN	transmembrane protein 209	50						integral to membrane				ovary(2)|large_intestine(1)	3	Melanoma(18;0.0435)																	---	---	---	---
PLXNA4	91584	broad.mit.edu	37	7	131887584	131887584	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:131887584T>C	uc003vra.3	-	12	2636	c.2407A>G	c.(2407-2409)AAG>GAG	p.K803E		NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1	803	PSI 3.|Extracellular (Potential).					integral to membrane|intracellular|plasma membrane				ovary(1)	1																		---	---	---	---
SLC35B4	84912	broad.mit.edu	37	7	133984902	133984902	+	Splice_Site	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:133984902A>G	uc003vrn.2	-	7	921	c.597_splice	c.e7+1	p.N199_splice	SLC35B4_uc010lmk.2_Splice_Site_p.N63_splice|SLC35B4_uc010lml.1_Splice_Site_p.N131_splice|SLC35B4_uc003vro.3_Splice_Site_p.N199_splice	NM_032826	NP_116215			solute carrier family 35, member B4							Golgi membrane|integral to membrane	UDP-N-acetylglucosamine transmembrane transporter activity|UDP-xylose transmembrane transporter activity			skin(1)	1																		---	---	---	---
AKR1B10	57016	broad.mit.edu	37	7	134221460	134221460	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:134221460G>T	uc003vrr.2	+	5	808	c.488G>T	c.(487-489)AGC>ATC	p.S163I		NM_020299	NP_064695	O60218	AK1BA_HUMAN	aldo-keto reductase family 1, member B10	163					cellular aldehyde metabolic process|digestion|steroid metabolic process	cytoplasm	aldo-keto reductase (NADP) activity|protein binding			skin(5)	5																		---	---	---	---
CNOT4	4850	broad.mit.edu	37	7	135106961	135106961	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135106961C>T	uc003vsv.1	-	3	623	c.316G>A	c.(316-318)GTA>ATA	p.V106I	CNOT4_uc003vss.2_Missense_Mutation_p.V106I|CNOT4_uc011kpz.1_Missense_Mutation_p.V106I|CNOT4_uc003vst.2_Missense_Mutation_p.V106I|CNOT4_uc003vsu.1_Missense_Mutation_p.V106I|CNOT4_uc011kpy.1_Missense_Mutation_p.V106I	NM_001008225	NP_001008226	O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	106					nuclear-transcribed mRNA poly(A) tail shortening|protein autoubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	nucleotide binding|protein binding|RNA binding|ubiquitin-protein ligase activity|zinc ion binding				0																		---	---	---	---
NUP205	23165	broad.mit.edu	37	7	135258539	135258539	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135258539T>C	uc003vsw.2	+	3	340	c.309T>C	c.(307-309)ATT>ATC	p.I103I	NUP205_uc011kqa.1_RNA	NM_015135	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	103					carbohydrate metabolic process|glucose transport|mRNA transport|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
NUP205	23165	broad.mit.edu	37	7	135333280	135333280	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135333280C>T	uc003vsw.2	+	43	6046	c.6015C>T	c.(6013-6015)GGC>GGT	p.G2005G	NUP205_uc003vsx.2_RNA	NM_015135	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	2005					carbohydrate metabolic process|glucose transport|mRNA transport|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
FAM180A	389558	broad.mit.edu	37	7	135418799	135418799	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135418799G>A	uc003vtd.2	-	3	712	c.446C>T	c.(445-447)GCG>GTG	p.A149V	FAM180A_uc010lmt.2_RNA|FAM180A_uc010lmu.2_Missense_Mutation_p.A149V	NM_205855	NP_995327	Q6UWF9	F180A_HUMAN	hypothetical protein LOC389558 precursor	149						extracellular region				ovary(2)	2																		---	---	---	---
DGKI	9162	broad.mit.edu	37	7	137128811	137128811	+	Intron	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137128811G>T	uc003vtt.2	-						DGKI_uc003vtu.2_Intron	NM_004717	NP_004708			diacylglycerol kinase, iota						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	nucleus|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(1)|kidney(1)|skin(1)	3																		---	---	---	---
AKR1D1	6718	broad.mit.edu	37	7	137776547	137776547	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:137776547C>T	uc003vtz.2	+	3	364	c.295C>T	c.(295-297)CGC>TGC	p.R99C	AKR1D1_uc011kqb.1_Missense_Mutation_p.R99C|AKR1D1_uc011kqc.1_RNA|AKR1D1_uc011kqd.1_Intron|AKR1D1_uc011kqe.1_Missense_Mutation_p.R99C|AKR1D1_uc011kqf.1_Missense_Mutation_p.R99C|AKR1D1_uc010lmy.1_RNA	NM_005989	NP_005980	P51857	AK1D1_HUMAN	aldo-keto reductase family 1, member D1	99					androgen metabolic process|bile acid biosynthetic process|bile acid catabolic process|C21-steroid hormone metabolic process|cholesterol catabolic process|digestion	cytosol	aldo-keto reductase (NADP) activity|delta4-3-oxosteroid 5beta-reductase activity|steroid binding			skin(1)	1																		---	---	---	---
KIAA1549	57670	broad.mit.edu	37	7	138603797	138603797	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:138603797G>T	uc011kql.1	-	2	624	c.575C>A	c.(574-576)CCT>CAT	p.P192H	KIAA1549_uc003vuk.3_Missense_Mutation_p.P142H|KIAA1549_uc011kqj.1_Missense_Mutation_p.P192H	NM_020910	NP_065961	Q9HCM3	K1549_HUMAN	hypothetical protein LOC57670 isoform 1	192						integral to membrane			KIAA1549/BRAF(229)	central_nervous_system(229)|pancreas(1)	230								O	BRAF	pilocytic astrocytoma								---	---	---	---
HIPK2	28996	broad.mit.edu	37	7	139416092	139416092	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139416092C>A	uc003vvf.3	-	2	916	c.742G>T	c.(742-744)GCC>TCC	p.A248S	HIPK2_uc003vvd.3_Missense_Mutation_p.A248S	NM_022740	NP_073577	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2 isoform	248	Protein kinase.|Interaction with DAXX.				apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|negative regulation of BMP signaling pathway|positive regulation of JNK cascade|positive regulation of transforming growth factor beta receptor signaling pathway|SMAD protein signal transduction|transcription, DNA-dependent|virus-host interaction	centrosome|nuclear membrane|PML body	ATP binding|protein serine/threonine kinase activity|SMAD binding|transcription corepressor activity|virion binding			ovary(3)|central_nervous_system(3)|skin(1)	7	Melanoma(164;0.205)																	---	---	---	---
TBXAS1	6916	broad.mit.edu	37	7	139657454	139657454	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139657454T>C	uc011kqv.1	+	9	1015	c.851T>C	c.(850-852)GTC>GCC	p.V284A	TBXAS1_uc003vvh.2_Missense_Mutation_p.V238A|TBXAS1_uc010lne.2_Missense_Mutation_p.V170A|TBXAS1_uc011kqu.1_Missense_Mutation_p.V189A|TBXAS1_uc003vvi.2_Missense_Mutation_p.V238A|TBXAS1_uc003vvj.2_Missense_Mutation_p.V238A|TBXAS1_uc011kqw.1_Missense_Mutation_p.V218A	NM_001130966	NP_001124438	P24557	THAS_HUMAN	thromboxane A synthase 1, platelet isoform	237	Helical; (Potential).				hormone biosynthetic process|prostaglandin biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane	electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|thromboxane-A synthase activity			ovary(2)|breast(1)	3	Melanoma(164;0.0142)																	---	---	---	---
JHDM1D	80853	broad.mit.edu	37	7	139791643	139791643	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139791643C>A	uc003vvm.2	-	19	2696	c.2692G>T	c.(2692-2694)GCA>TCA	p.A898S	JHDM1D_uc010lng.2_RNA	NM_030647	NP_085150	Q6ZMT4	KDM7_HUMAN	jumonji C domain containing histone demethylase	898					midbrain development|transcription, DNA-dependent	nucleolus	histone demethylase activity (H3-K27 specific)|histone demethylase activity (H3-K36 specific)|histone demethylase activity (H3-K9 specific)|histone demethylase activity (H4-K20 specific)|iron ion binding|methylated histone residue binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1	Melanoma(164;0.0142)																	---	---	---	---
RAB19	401409	broad.mit.edu	37	7	140125841	140125841	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140125841G>A	uc010lni.2	+	4	743	c.545G>A	c.(544-546)CGC>CAC	p.R182H	RAB19_uc011krc.1_Missense_Mutation_p.R182H	NM_001008749	NP_001008749	A4D1S5	RAB19_HUMAN	RAB19, member RAS oncogene family	182					protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding				0	Melanoma(164;0.0142)																	---	---	---	---
DENND2A	27147	broad.mit.edu	37	7	140221776	140221776	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140221776C>T	uc010lnj.2	-	16	2935	c.2790G>A	c.(2788-2790)CGG>CGA	p.R930R	DENND2A_uc011kre.1_RNA|DENND2A_uc010lnk.2_Silent_p.R930R|DENND2A_uc003vvw.2_Silent_p.R930R	NM_015689	NP_056504	Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	930	dDENN.									ovary(3)|breast(1)	4	Melanoma(164;0.00956)																	---	---	---	---
TAS2R3	50831	broad.mit.edu	37	7	141464043	141464043	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141464043T>C	uc003vwp.1	+	1	147	c.85T>C	c.(85-87)TTG>CTG	p.L29L		NM_016943	NP_058639	Q9NYW6	TA2R3_HUMAN	taste receptor T2R3	29	Cytoplasmic (Potential).				sensory perception of taste		taste receptor activity			central_nervous_system(1)	1	Melanoma(164;0.0171)																	---	---	---	---
Unknown	0	broad.mit.edu	37	7	142001029	142001029	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142001029C>T	uc011kro.1	+	2	166	c.121C>T	c.(121-123)CAC>TAC	p.H41Y						SubName: Full=V_segment translation product; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	142021276	142021276	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142021276C>T	uc011kro.1	+						uc011krp.1_Intron|uc011krr.1_Missense_Mutation_p.R86C|uc011krq.1_Missense_Mutation_p.R86C					SubName: Full=V_segment translation product; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	142045761	142045761	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142045761C>T	uc011kro.1	+						uc011krp.1_Intron|uc011krr.1_Intron|uc003vxp.3_Silent_p.L97L|uc011krt.1_Silent_p.L79L					SubName: Full=V_segment translation product; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	142180764	142180764	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142180764A>G	uc011kro.1	+						uc011krp.1_Intron|uc011krr.1_Intron|uc011krx.1_Intron|uc011ksa.1_RNA|uc011krz.1_Missense_Mutation_p.L32P					SubName: Full=V_segment translation product; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	7	142364232	142364232	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142364232C>T	uc011krp.1	+						uc011krr.1_Intron|uc003vzp.2_Intron|uc011ksh.1_Intron|uc011ksi.1_Intron|uc003vzw.1_Intron|uc010loj.1_5'Flank|uc011ksg.1_Intron|uc003vzx.3_5'UTR					Homo sapiens mRNA for T cell receptor beta variable 3, partial cds, clone: un 191.																														---	---	---	---
EPHB6	2051	broad.mit.edu	37	7	142567724	142567724	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142567724G>A	uc011kst.1	+						EPHB6_uc011ksu.1_Intron|EPHB6_uc003wbs.2_Intron|EPHB6_uc003wbt.2_Intron|EPHB6_uc003wbu.2_Intron|EPHB6_uc003wbv.2_Intron	NM_004445	NP_004436			ephrin receptor EphB6 precursor							extracellular region|integral to plasma membrane	ATP binding|ephrin receptor activity			lung(8)|large_intestine(4)|central_nervous_system(3)|stomach(1)|skin(1)|ovary(1)|pancreas(1)	19	Melanoma(164;0.059)																	---	---	---	---
TRPV6	55503	broad.mit.edu	37	7	142569696	142569696	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142569696C>T	uc003wbx.1	-	15	2158	c.1942G>A	c.(1942-1944)GCA>ACA	p.A648T	TRPV6_uc003wbw.1_Missense_Mutation_p.A434T|TRPV6_uc010lou.1_Missense_Mutation_p.A519T	NM_018646	NP_061116	Q9H1D0	TRPV6_HUMAN	transient receptor potential cation channel,	648	Cytoplasmic (Potential).				regulation of calcium ion-dependent exocytosis	integral to plasma membrane	calcium channel activity|calmodulin binding			ovary(2)	2	Melanoma(164;0.059)																	---	---	---	---
PIP	5304	broad.mit.edu	37	7	142829214	142829214	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142829214G>A	uc003wcf.1	+	1	41	c.5G>A	c.(4-6)CGC>CAC	p.R2H		NM_002652	NP_002643	P12273	PIP_HUMAN	prolactin-induced protein precursor	2						extracellular region	actin binding			ovary(1)	1	Melanoma(164;0.059)	Ovarian(593;2.82e-05)|Breast(660;0.012)		BRCA - Breast invasive adenocarcinoma(188;0.0026)|LUSC - Lung squamous cell carcinoma(290;0.0733)|Lung(243;0.08)														---	---	---	---
TAS2R40	259286	broad.mit.edu	37	7	142919586	142919586	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:142919586A>G	uc011ksx.1	+	1	415	c.415A>G	c.(415-417)ATA>GTA	p.I139V		NM_176882	NP_795363	P59535	T2R40_HUMAN	taste receptor, type 2, member 40	139	Cytoplasmic (Potential).				sensory perception of taste	integral to membrane	G-protein coupled receptor activity			ovary(1)	1	Melanoma(164;0.059)																	---	---	---	---
CASP2	835	broad.mit.edu	37	7	143000888	143000888	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143000888C>T	uc003wco.2	+	9	1126	c.979C>T	c.(979-981)CGT>TGT	p.R327C	CASP2_uc003wcp.2_3'UTR|CASP2_uc011kta.1_Missense_Mutation_p.R211C|CASP2_uc003wcq.2_RNA|CASP2_uc011ktb.1_Missense_Mutation_p.R77C	NM_032982	NP_116764	P42575	CASP2_HUMAN	caspase 2 isoform 1 preproprotein	327					apoptosis|cellular response to mechanical stimulus|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|protein maturation by peptide bond cleavage	cytosol	cysteine-type endopeptidase activity|enzyme binding|protein binding|protein domain specific binding			lung(2)|ovary(1)	3	Melanoma(164;0.059)																	---	---	---	---
CLCN1	1180	broad.mit.edu	37	7	143013445	143013445	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143013445G>A	uc003wcr.1	+	1	227	c.140G>A	c.(139-141)CGG>CAG	p.R47Q	CLCN1_uc011ktc.1_5'UTR	NM_000083	NP_000074	P35523	CLCN1_HUMAN	chloride channel 1, skeletal muscle	47	Cytoplasmic (By similarity).				muscle contraction	chloride channel complex|integral to plasma membrane	voltage-gated chloride channel activity			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5	Melanoma(164;0.205)																	---	---	---	---
FAM131B	9715	broad.mit.edu	37	7	143055940	143055940	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143055940T>G	uc003wct.2	-	4	2068	c.362A>C	c.(361-363)AAG>ACG	p.K121T	FAM131B_uc010loz.2_Missense_Mutation_p.K89T|FAM131B_uc003wcu.3_Missense_Mutation_p.K121T|FAM131B_uc010lpa.2_Missense_Mutation_p.K149T|ZYX_uc011ktd.1_5'Flank	NM_014690	NP_055505	Q86XD5	F131B_HUMAN	hypothetical protein LOC9715 isoform b	121											0	Melanoma(164;0.205)																	---	---	---	---
TAS2R60	338398	broad.mit.edu	37	7	143140911	143140911	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143140911T>C	uc011ktg.1	+	1	366	c.366T>C	c.(364-366)ATT>ATC	p.I122I	uc003wda.2_Intron	NM_177437	NP_803186	P59551	T2R60_HUMAN	taste receptor, type 2, member 60	122	Cytoplasmic (Potential).				sensory perception of bitter taste	integral to membrane	G-protein coupled receptor activity			skin(6)	6	Melanoma(164;0.172)																	---	---	---	---
OR2A5	393046	broad.mit.edu	37	7	143747976	143747976	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143747976T>C	uc011ktw.1	+	1	482	c.482T>C	c.(481-483)GTT>GCT	p.V161A		NM_012365	NP_036497	Q96R48	OR2A5_HUMAN	olfactory receptor, family 2, subfamily A,	161	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)	3	Melanoma(164;0.0783)																	---	---	---	---
OR2A2	442361	broad.mit.edu	37	7	143807435	143807435	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:143807435G>A	uc011ktz.1	+	1	760	c.760G>A	c.(760-762)GCC>ACC	p.A254T		NM_001005480	NP_001005480	Q6IF42	OR2A2_HUMAN	olfactory receptor, family 2, subfamily A,	254	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2	Melanoma(164;0.0783)																	---	---	---	---
ARHGEF5	7984	broad.mit.edu	37	7	144075965	144075965	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:144075965C>T	uc003wel.2	+						ARHGEF5_uc003wem.2_Intron	NM_005435	NP_005426			rho guanine nucleotide exchange factor 5						intracellular signal transduction|regulation of Rho protein signal transduction	intracellular	GTP binding|protein binding|Rho guanyl-nucleotide exchange factor activity			skin(2)	2	Melanoma(164;0.14)																	---	---	---	---
CUL1	8454	broad.mit.edu	37	7	148427227	148427227	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148427227C>T	uc010lpg.2	+	2	539	c.13C>T	c.(13-15)CGG>TGG	p.R5W	CUL1_uc003wey.2_Missense_Mutation_p.R5W|CUL1_uc003wez.2_5'UTR	NM_003592	NP_003583	Q13616	CUL1_HUMAN	cullin 1	5					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell cycle arrest|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein ubiquitination|S phase of mitotic cell cycle|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	cytosol|nucleoplasm|SCF ubiquitin ligase complex	ubiquitin protein ligase binding			lung(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)															---	---	---	---
PDIA4	9601	broad.mit.edu	37	7	148712091	148712091	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148712091C>T	uc003wff.2	-	4	801	c.519G>A	c.(517-519)ACG>ACA	p.T173T		NM_004911	NP_004902	P13667	PDIA4_HUMAN	protein disulfide isomerase A4 precursor	173	Thioredoxin 2.				cell redox homeostasis|glycerol ether metabolic process|protein secretion	endoplasmic reticulum lumen|melanosome	electron carrier activity|protein binding|protein disulfide isomerase activity|protein disulfide oxidoreductase activity			lung(5)|ovary(1)	6	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00385)															---	---	---	---
ZNF282	8427	broad.mit.edu	37	7	148895819	148895819	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148895819C>T	uc003wfm.2	+	2	665	c.560C>T	c.(559-561)CCG>CTG	p.P187L	ZNF282_uc011kun.1_Missense_Mutation_p.P187L|ZNF282_uc003wfn.2_Missense_Mutation_p.P127L|ZNF282_uc003wfo.2_Missense_Mutation_p.P127L	NM_003575	NP_003566	Q9UDV7	ZN282_HUMAN	zinc finger protein 282	187					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00171)	Lung(243;0.145)														---	---	---	---
Unknown	0	broad.mit.edu	37	7	148963517	148963517	+	RNA	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148963517C>T	uc003wfr.3	+	2		c.279C>T								Homo sapiens cDNA FLJ36716 fis, clone UTERU2010651.																														---	---	---	---
ZNF777	27153	broad.mit.edu	37	7	149152997	149152997	+	Silent	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149152997A>T	uc003wfv.2	-	2	280	c.117T>A	c.(115-117)CCT>CCA	p.P39P		NM_015694	NP_056509	Q9ULD5	ZN777_HUMAN	zinc finger protein 777	39					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)															---	---	---	---
SSPO	23145	broad.mit.edu	37	7	149500859	149500859	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149500859C>T	uc010lpk.2	+	56	8177	c.8177C>T	c.(8176-8178)CCC>CTC	p.P2726L		NM_198455	NP_940857	A2VEC9	SSPO_HUMAN	SCO-spondin precursor	2726	TSP type-1 6.				cell adhesion	extracellular space	peptidase inhibitor activity				0	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)															---	---	---	---
SSPO	23145	broad.mit.edu	37	7	149510800	149510800	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:149510800C>T	uc010lpk.2	+	72	10085	c.10085C>T	c.(10084-10086)CCG>CTG	p.P3362L		NM_198455	NP_940857	A2VEC9	SSPO_HUMAN	SCO-spondin precursor	3362	TIL 5.				cell adhesion	extracellular space	peptidase inhibitor activity				0	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)															---	---	---	---
ZNF775	285971	broad.mit.edu	37	7	150094966	150094966	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150094966G>A	uc003whf.1	+	3	1522	c.1397G>A	c.(1396-1398)CGC>CAC	p.R466H	LOC728743_uc003whg.2_5'Flank	NM_173680	NP_775951	Q96BV0	ZN775_HUMAN	zinc finger protein 775	466	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Ovarian(565;0.183)|Melanoma(164;0.226)		OV - Ovarian serous cystadenocarcinoma(82;0.0173)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)														---	---	---	---
GIMAP8	155038	broad.mit.edu	37	7	150174635	150174635	+	Missense_Mutation	SNP	C	T	T	rs139453539		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150174635C>T	uc003whj.2	+	5	2095	c.1765C>T	c.(1765-1767)CGC>TGC	p.R589C		NM_175571	NP_783161	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	589						endoplasmic reticulum|Golgi apparatus|mitochondrion	GTP binding	p.R589H(1)		skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)														---	---	---	---
GIMAP4	55303	broad.mit.edu	37	7	150269721	150269721	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150269721C>T	uc003whl.2	+	3	645	c.563C>T	c.(562-564)GCG>GTG	p.A188V	GIMAP4_uc011kuu.1_Missense_Mutation_p.A49V|GIMAP4_uc011kuv.1_Missense_Mutation_p.A202V	NM_018326	NP_060796	Q9NUV9	GIMA4_HUMAN	GTPase, IMAP family member 4	188	Potential.						GTP binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(82;0.0179)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)														---	---	---	---
GIMAP6	474344	broad.mit.edu	37	7	150325361	150325361	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150325361C>T	uc003whn.2	-	3	749	c.325G>A	c.(325-327)GCA>ACA	p.A109T	GIMAP6_uc003whm.2_Missense_Mutation_p.A29T	NM_024711	NP_078987	Q6P9H5	GIMA6_HUMAN	GTPase, IMAP family member 6	109							GTP binding			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)														---	---	---	---
GIMAP1	170575	broad.mit.edu	37	7	150417174	150417174	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150417174C>T	uc003whq.2	+	3	169	c.82C>T	c.(82-84)CGG>TGG	p.R28W	GIMAP1_uc003whp.2_Missense_Mutation_p.R36W	NM_130759	NP_570115	Q8WWP7	GIMA1_HUMAN	GTPase, IMAP family member 1	28	Cytoplasmic (Potential).					endoplasmic reticulum membrane|integral to membrane	GTP binding			ovary(1)|breast(1)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)														---	---	---	---
ATG9B	285973	broad.mit.edu	37	7	150715802	150715802	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150715802C>T	uc011kvc.1	-	6	1699	c.1623G>A	c.(1621-1623)GCG>GCA	p.A541A	ATG9B_uc003wig.3_Intron	NM_173681	NP_775952	Q674R7	ATG9B_HUMAN	ATG9 autophagy related 9 homolog B	541	Helical; (Potential).				autophagic vacuole assembly	autophagic vacuole membrane|cytoplasmic vesicle|integral to membrane				ovary(1)	1	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)														---	---	---	---
ATG9B	285973	broad.mit.edu	37	7	150716460	150716460	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150716460T>C	uc011kvc.1	-	6	1041	c.965A>G	c.(964-966)GAG>GGG	p.E322G	ATG9B_uc003wig.3_Intron	NM_173681	NP_775952	Q674R7	ATG9B_HUMAN	ATG9 autophagy related 9 homolog B	322	Cytoplasmic (By similarity).				autophagic vacuole assembly	autophagic vacuole membrane|cytoplasmic vesicle|integral to membrane				ovary(1)	1	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)														---	---	---	---
FASTK	10922	broad.mit.edu	37	7	150774460	150774460	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150774460G>A	uc003wix.1	-	7	1326	c.1228C>T	c.(1228-1230)CGC>TGC	p.R410C	uc011kvf.1_5'Flank|FASTK_uc003wiw.1_Missense_Mutation_p.R171C|FASTK_uc003wiy.1_Missense_Mutation_p.R269C|FASTK_uc003wiz.1_Missense_Mutation_p.R383C|FASTK_uc003wja.1_3'UTR	NM_006712	NP_006703	Q14296	FASTK_HUMAN	Fas-activated serine/threonine kinase isoform 1	410					apoptosis|induction of apoptosis by extracellular signals|regulation of RNA splicing		ATP binding|Fas-activated serine/threonine kinase activity|protein binding			lung(2)|stomach(2)	4			OV - Ovarian serous cystadenocarcinoma(82;0.00989)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)|LUSC - Lung squamous cell carcinoma(290;0.0718)|Lung(243;0.138)														---	---	---	---
AGAP3	116988	broad.mit.edu	37	7	150814195	150814195	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150814195A>T	uc003wjg.1	+	3	407	c.404A>T	c.(403-405)AAC>ATC	p.N135I	AGAP3_uc003wje.1_5'UTR|AGAP3_uc003wjf.1_Missense_Mutation_p.N135I|AGAP3_uc010lpy.1_Missense_Mutation_p.N135I|AGAP3_uc003wjh.1_Missense_Mutation_p.N315I	NM_031946	NP_114152	Q96P47	AGAP3_HUMAN	centaurin, gamma 3 isoform a	99	Small GTPase-like.|GTP (Potential).				regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytoplasm|membrane	ARF GTPase activator activity|GTP binding|GTPase activity|zinc ion binding			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
GBX1	2636	broad.mit.edu	37	7	150846022	150846022	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150846022G>A	uc011kvg.1	-	2	978	c.746C>T	c.(745-747)CCG>CTG	p.P249L		NM_001098834	NP_001092304	Q14549	GBX1_HUMAN	gastrulation brain homeo box 1	249						nuclear chromosome	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0			OV - Ovarian serous cystadenocarcinoma(82;0.00989)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)														---	---	---	---
CHPF2	54480	broad.mit.edu	37	7	150932515	150932515	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150932515C>T	uc003wjr.1	+	2	2158	c.645C>T	c.(643-645)GGC>GGT	p.G215G	CHPF2_uc003wjq.1_Silent_p.G207G|MIR671_hsa-mir-671|MI0003760_5'Flank	NM_019015	NP_061888	Q9P2E5	CHPF2_HUMAN	chondroitin polymerizing factor 2	215	Lumenal (Potential).					Golgi cisterna membrane|integral to membrane	N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity			ovary(1)	1																		---	---	---	---
WDR86	349136	broad.mit.edu	37	7	151093171	151093171	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151093171G>A	uc003wkb.2	-	3	866	c.417C>T	c.(415-417)TGC>TGT	p.C139C	WDR86_uc003wka.2_Silent_p.C97C|WDR86_uc011kvk.1_Silent_p.C139C|WDR86_uc003wkc.2_Silent_p.C11C	NM_198285	NP_938026	Q86TI4	WDR86_HUMAN	WD repeat domain 86	139	WD 4.										0			OV - Ovarian serous cystadenocarcinoma(82;0.00419)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)														---	---	---	---
RHEB	6009	broad.mit.edu	37	7	151174510	151174510	+	Intron	SNP	A	G	G	rs78256132		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151174510A>G	uc003wkh.1	-							NM_005614	NP_005605			Ras homolog enriched in brain precursor						cell cycle arrest|insulin receptor signaling pathway|positive regulation of TOR signaling cascade|small GTPase mediated signal transduction	cytosol|plasma membrane	GTP binding|GTPase activity|metal ion binding|protein binding			large_intestine(1)|lung(1)	2			OV - Ovarian serous cystadenocarcinoma(82;0.00306)	UCEC - Uterine corpus endometrioid carcinoma (81;0.174)														---	---	---	---
GALNTL5	168391	broad.mit.edu	37	7	151700048	151700048	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151700048G>A	uc003wkp.2	+	6	1131	c.908G>A	c.(907-909)CGG>CAG	p.R303Q	GALNTL5_uc003wkq.2_Missense_Mutation_p.R54Q|GALNTL5_uc003wkr.2_RNA|GALNTL5_uc003wks.2_RNA|GALNTL5_uc010lqf.2_Missense_Mutation_p.R192Q	NM_145292	NP_660335	Q7Z4T8	GLTL5_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide	303	Catalytic subdomain B.|Lumenal (Potential).					Golgi membrane|integral to membrane	transferase activity, transferring glycosyl groups			ovary(2)	2	all_neural(206;0.187)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00427)	UCEC - Uterine corpus endometrioid carcinoma (81;0.18)|BRCA - Breast invasive adenocarcinoma(188;0.166)														---	---	---	---
MLL3	58508	broad.mit.edu	37	7	151864311	151864311	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151864311G>A	uc003wla.2	-	42	9889	c.9670C>T	c.(9670-9672)CGT>TGT	p.R3224C	MLL3_uc003wkz.2_Missense_Mutation_p.R2285C|MLL3_uc003wky.2_Missense_Mutation_p.R733C	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	3224	Gln-rich.|Potential.				intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)				N		medulloblastoma								---	---	---	---
MLL3	58508	broad.mit.edu	37	7	151878694	151878694	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151878694T>A	uc003wla.2	-	36	6470	c.6251A>T	c.(6250-6252)AAT>ATT	p.N2084I	MLL3_uc003wkz.2_Missense_Mutation_p.N1145I	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	2084	Pro-rich.				intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)				N		medulloblastoma								---	---	---	---
MLL3	58508	broad.mit.edu	37	7	151927008	151927008	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151927008C>T	uc003wla.2	-	18	3195	c.2976G>A	c.(2974-2976)AAG>AAA	p.K992K	MLL3_uc003wkz.2_Silent_p.K53K	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	992	PHD-type 4.				intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)				N		medulloblastoma								---	---	---	---
MLL3	58508	broad.mit.edu	37	7	151945048	151945048	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151945048C>T	uc003wla.2	-	14	2690	c.2471G>A	c.(2470-2472)GGC>GAC	p.G824D		NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	824					intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)				N		medulloblastoma								---	---	---	---
PAXIP1	22976	broad.mit.edu	37	7	154738271	154738271	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154738271G>T	uc003wlp.2	-	19	3127	c.3084C>A	c.(3082-3084)TCC>TCA	p.S1028S	LOC100132707_uc011kvr.1_Intron|LOC100132707_uc003wlo.2_Intron|PAXIP1_uc003wlq.1_Silent_p.S994S|PAXIP1_uc011kvs.1_Silent_p.S992S	NM_007349	NP_031375	Q6ZW49	PAXI1_HUMAN	PAX interacting protein 1	1028	Interaction with TP53BP1.|BRCT 6.				DNA damage response, signal transduction by p53 class mediator|DNA recombination|DNA repair|histone H3-K4 methylation|positive regulation of histone acetylation|positive regulation of histone H3-K36 methylation|positive regulation of histone H3-K4 methylation|positive regulation of isotype switching|positive regulation of protein ubiquitination|positive regulation of transcription initiation from RNA polymerase II promoter|response to ionizing radiation|transcription, DNA-dependent	histone methyltransferase complex|nuclear matrix				lung(2)|ovary(1)|breast(1)|pancreas(1)	5	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0296)	UCEC - Uterine corpus endometrioid carcinoma (81;0.178)														---	---	---	---
PAXIP1	22976	broad.mit.edu	37	7	154767599	154767599	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:154767599G>A	uc003wlp.2	-	6	924	c.881C>T	c.(880-882)GCC>GTC	p.A294V	PAXIP1_uc003wlq.1_Missense_Mutation_p.A260V|PAXIP1_uc011kvs.1_Missense_Mutation_p.A258V|PAXIP1_uc003wlr.1_Missense_Mutation_p.A203V	NM_007349	NP_031375	Q6ZW49	PAXI1_HUMAN	PAX interacting protein 1	294					DNA damage response, signal transduction by p53 class mediator|DNA recombination|DNA repair|histone H3-K4 methylation|positive regulation of histone acetylation|positive regulation of histone H3-K36 methylation|positive regulation of histone H3-K4 methylation|positive regulation of isotype switching|positive regulation of protein ubiquitination|positive regulation of transcription initiation from RNA polymerase II promoter|response to ionizing radiation|transcription, DNA-dependent	histone methyltransferase complex|nuclear matrix				lung(2)|ovary(1)|breast(1)|pancreas(1)	5	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0296)	UCEC - Uterine corpus endometrioid carcinoma (81;0.178)														---	---	---	---
PTPRN2	5799	broad.mit.edu	37	7	158109539	158109539	+	Silent	SNP	G	A	A	rs143408207	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158109539G>A	uc003wno.2	-	3	370	c.249C>T	c.(247-249)CGC>CGT	p.R83R	PTPRN2_uc003wnp.2_Silent_p.R66R|PTPRN2_uc003wnq.2_Silent_p.R83R|PTPRN2_uc003wnr.2_Intron|PTPRN2_uc011kwa.1_Silent_p.R106R	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N	83	Extracellular (Potential).					integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)|skin(1)	7	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)														---	---	---	---
VIPR2	7434	broad.mit.edu	37	7	158851230	158851230	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:158851230C>A	uc003woh.2	-	5	583	c.397G>T	c.(397-399)GGC>TGC	p.G133C	VIPR2_uc010lqx.2_RNA|VIPR2_uc010lqy.2_RNA	NM_003382	NP_003373	P41587	VIPR2_HUMAN	vasoactive intestinal peptide receptor 2	133	Helical; Name=1; (Potential).				cell-cell signaling	integral to plasma membrane				lung(1)|central_nervous_system(1)	2	Ovarian(565;0.152)	all_cancers(7;1.13e-11)|all_epithelial(9;0.000545)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)|STAD - Stomach adenocarcinoma(7;0.18)														---	---	---	---
ERICH1	157697	broad.mit.edu	37	8	642531	642531	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:642531T>C	uc003wph.2	-	3	316	c.251A>G	c.(250-252)GAG>GGG	p.E84G	ERICH1_uc011kwh.1_Missense_Mutation_p.E84G|ERICH1_uc003wpe.1_Intron	NM_207332	NP_997215	Q86X53	ERIC1_HUMAN	glutamate-rich 1	84										large_intestine(2)	2		Colorectal(14;0.158)|Ovarian(12;0.17)|Myeloproliferative disorder(644;0.185)|Hepatocellular(245;0.236)		Epithelial(5;3.29e-14)|BRCA - Breast invasive adenocarcinoma(11;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(5;3.65e-06)|READ - Rectum adenocarcinoma(1;0.0325)														---	---	---	---
MYOM2	9172	broad.mit.edu	37	8	2005740	2005740	+	Splice_Site	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:2005740G>T	uc003wpx.3	+	5	541	c.403_splice	c.e5-1	p.M135_splice	MYOM2_uc011kwi.1_Intron	NM_003970	NP_003961			myomesin 2						muscle contraction	myosin filament	structural constituent of muscle			ovary(4)|central_nervous_system(1)|skin(1)	6		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)														---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	3253804	3253804	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:3253804C>T	uc011kwk.1	-	17	2898	c.2508G>A	c.(2506-2508)CAG>CAA	p.Q836Q	CSMD1_uc011kwj.1_Silent_p.Q228Q|CSMD1_uc003wqe.2_5'UTR	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	836	Extracellular (Potential).|CUB 5.					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)														---	---	---	---
SGK223	157285	broad.mit.edu	37	8	8233763	8233763	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8233763C>T	uc003wsh.3	-	2	2156	c.2156G>A	c.(2155-2157)CGG>CAG	p.R719Q		NM_001080826	NP_001074295	Q86YV5	SG223_HUMAN	pragmin	719							ATP binding|non-membrane spanning protein tyrosine kinase activity				0																		---	---	---	---
PPP1R3B	79660	broad.mit.edu	37	8	8998948	8998948	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:8998948C>A	uc003wsn.3	-	2	379	c.214G>T	c.(214-216)GCC>TCC	p.A72S	PPP1R3B_uc003wso.3_Missense_Mutation_p.A71S	NM_024607	NP_078883	Q86XI6	PPR3B_HUMAN	protein phosphatase 1, regulatory (inhibitor)	72					glycogen metabolic process					ovary(1)|skin(1)	2				COAD - Colon adenocarcinoma(149;0.0717)|READ - Rectum adenocarcinoma(644;0.241)														---	---	---	---
RP1L1	94137	broad.mit.edu	37	8	10466282	10466282	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10466282T>G	uc003wtc.2	-	4	5555	c.5326A>C	c.(5326-5328)ACC>CCC	p.T1776P		NM_178857	NP_849188	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1776					intracellular signal transduction					ovary(4)|breast(3)|central_nervous_system(1)	8				COAD - Colon adenocarcinoma(149;0.0811)														---	---	---	---
RP1L1	94137	broad.mit.edu	37	8	10468543	10468543	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:10468543G>T	uc003wtc.2	-	4	3294	c.3065C>A	c.(3064-3066)CCA>CAA	p.P1022Q		NM_178857	NP_849188	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1022					intracellular signal transduction					ovary(4)|breast(3)|central_nervous_system(1)	8				COAD - Colon adenocarcinoma(149;0.0811)														---	---	---	---
LONRF1	91694	broad.mit.edu	37	8	12583257	12583257	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12583257G>A	uc003wwd.1	-	11	2205	c.2142C>T	c.(2140-2142)CCC>CCT	p.P714P	LONRF1_uc011kxv.1_Silent_p.P303P|LONRF1_uc010lsp.1_Silent_p.P314P	NM_152271	NP_689484	Q17RB8	LONF1_HUMAN	LON peptidase N-terminal domain and ring finger	714	Lon.				proteolysis		ATP-dependent peptidase activity|zinc ion binding			ovary(1)	1				READ - Rectum adenocarcinoma(644;0.236)														---	---	---	---
C8orf79	57604	broad.mit.edu	37	8	12878673	12878673	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:12878673G>T	uc010lsq.2	+	5	977	c.485G>T	c.(484-486)AGG>ATG	p.R162M	C8orf79_uc011kxw.1_Intron|C8orf79_uc003wwj.3_Missense_Mutation_p.R75M|C8orf79_uc010lsr.2_Missense_Mutation_p.R36M	NM_020844	NP_065895	Q9P272	K1456_HUMAN	hypothetical protein LOC57604 isoform 1	162							methyltransferase activity				0																		---	---	---	---
DLC1	10395	broad.mit.edu	37	8	13072127	13072127	+	Intron	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:13072127A>C	uc003wwm.2	-						DLC1_uc003wwl.1_Intron|DLC1_uc003wwn.2_3'UTR	NM_182643	NP_872584			deleted in liver cancer 1 isoform 1						actin cytoskeleton organization|activation of caspase activity|focal adhesion assembly|forebrain development|heart morphogenesis|hindbrain morphogenesis|induction of apoptosis|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of stress fiber assembly|neural tube closure|positive regulation of protein dephosphorylation|regulation of cell shape|small GTPase mediated signal transduction	caveola|cytosol|focal adhesion|nucleus	Rho GTPase activator activity|SH2 domain binding			ovary(3)|pancreas(2)|lung(1)|kidney(1)	7																		---	---	---	---
SLC7A2	6542	broad.mit.edu	37	8	17409481	17409481	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:17409481C>T	uc011kyc.1	+	6	1210	c.1041C>T	c.(1039-1041)TGC>TGT	p.C347C	SLC7A2_uc011kyd.1_Silent_p.C387C|SLC7A2_uc011kye.1_Silent_p.C387C|SLC7A2_uc011kyf.1_Silent_p.C347C	NM_001008539	NP_001008539	P52569	CTR2_HUMAN	solute carrier family 7, member 2 isoform 2	347	Helical; (Potential).				cellular amino acid metabolic process|ion transport	cytoplasm|integral to plasma membrane|membrane fraction	basic amino acid transmembrane transporter activity			ovary(2)|skin(1)	3				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	L-Lysine(DB00123)|L-Ornithine(DB00129)													---	---	---	---
CSGALNACT1	55790	broad.mit.edu	37	8	19263541	19263541	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:19263541T>C	uc011kyn.1	-	10	2413	c.1349A>G	c.(1348-1350)GAT>GGT	p.D450G	CSGALNACT1_uc011kyo.1_Missense_Mutation_p.D450G|CSGALNACT1_uc003wzg.2_RNA|CSGALNACT1_uc011kyp.1_Missense_Mutation_p.D449G	NM_001130518	NP_001123990	Q8TDX6	CGAT1_HUMAN	chondroitin sulfate	450	Lumenal (Potential).				anatomical structure morphogenesis|cell proliferation|cell recognition|chondroitin sulfate biosynthetic process|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|dermatan sulfate proteoglycan biosynthetic process|extracellular matrix organization|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|heparin biosynthetic process|nervous system development|UDP-glucuronate metabolic process|UDP-N-acetylgalactosamine metabolic process	Golgi cisterna membrane|integral to Golgi membrane|soluble fraction	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|glucuronosyltransferase activity|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|peptidoglycan glycosyltransferase activity			central_nervous_system(2)|ovary(1)	3				Colorectal(111;0.182)														---	---	---	---
GFRA2	2675	broad.mit.edu	37	8	21608229	21608229	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21608229C>T	uc003wzu.1	-	4	1340	c.665G>A	c.(664-666)TGC>TAC	p.C222Y	GFRA2_uc003wzv.1_Missense_Mutation_p.C117Y|GFRA2_uc003wzw.1_Missense_Mutation_p.C89Y|DOK2_uc003wzx.1_Intron	NM_001495	NP_001486	O00451	GFRA2_HUMAN	GDNF family receptor alpha 2 isoform a	222						anchored to membrane|extrinsic to membrane|plasma membrane	glial cell-derived neurotrophic factor receptor activity				0				Colorectal(74;0.0189)|COAD - Colon adenocarcinoma(73;0.0727)														---	---	---	---
HR	55806	broad.mit.edu	37	8	21984654	21984654	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:21984654G>T	uc003xas.2	-	3	1966	c.1301C>A	c.(1300-1302)CCT>CAT	p.P434H	HR_uc003xat.2_Missense_Mutation_p.P434H	NM_005144	NP_005135	O43593	HAIR_HUMAN	hairless protein isoform a	434							DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity			large_intestine(1)|ovary(1)	2		Breast(100;0.000162)|Acute lymphoblastic leukemia(644;0.0775)|Prostate(55;0.116)		KIRC - Kidney renal clear cell carcinoma(542;1.19e-05)|BRCA - Breast invasive adenocarcinoma(99;3.56e-05)|Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)														---	---	---	---
PHYHIP	9796	broad.mit.edu	37	8	22084439	22084439	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22084439G>A	uc003xbk.3	-	4	959	c.265C>T	c.(265-267)CAG>TAG	p.Q89*	PHYHIP_uc003xbj.3_Nonsense_Mutation_p.Q89*	NM_001099335	NP_001092805	Q92561	PHYIP_HUMAN	phytanoyl-CoA 2-hydroxylase interacting protein	89	Fibronectin type-III.										0				Colorectal(74;0.0152)|COAD - Colon adenocarcinoma(73;0.0629)														---	---	---	---
SORBS3	10174	broad.mit.edu	37	8	22429841	22429841	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22429841C>T	uc003xbv.2	+						SORBS3_uc003xbw.3_Intron	NM_005775	NP_005766			sorbin and SH3 domain containing 3 isoform 1						muscle contraction|positive regulation of stress fiber assembly	cytoskeleton|cytosol|nucleus	protein binding|structural constituent of cytoskeleton|vinculin binding				0		Prostate(55;0.0421)|Breast(100;0.102)		BRCA - Breast invasive adenocarcinoma(99;0.00566)|Colorectal(74;0.0146)|COAD - Colon adenocarcinoma(73;0.061)														---	---	---	---
KIAA1967	57805	broad.mit.edu	37	8	22471779	22471779	+	Silent	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22471779T>G	uc003xch.2	+	9	1016	c.879T>G	c.(877-879)GCT>GCG	p.A293A	KIAA1967_uc003xci.2_Silent_p.A293A|KIAA1967_uc003xcj.1_5'UTR	NM_199205	NP_954675	Q8N163	K1967_HUMAN	p30 DBC protein	293					apoptosis|positive regulation of apoptosis	mitochondrial matrix|nucleus	enzyme binding|enzyme inhibitor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Prostate(55;0.0421)|Breast(100;0.102)|all_epithelial(46;0.142)		BRCA - Breast invasive adenocarcinoma(99;0.00593)|Colorectal(74;0.0157)|COAD - Colon adenocarcinoma(73;0.064)														---	---	---	---
KIAA1967	57805	broad.mit.edu	37	8	22472985	22472985	+	Missense_Mutation	SNP	G	A	A	rs149267963		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22472985G>A	uc003xch.2	+	12	1390	c.1253G>A	c.(1252-1254)CGG>CAG	p.R418Q	KIAA1967_uc003xci.2_Missense_Mutation_p.R418Q|KIAA1967_uc003xcj.1_Missense_Mutation_p.R87Q	NM_199205	NP_954675	Q8N163	K1967_HUMAN	p30 DBC protein	418					apoptosis|positive regulation of apoptosis	mitochondrial matrix|nucleus	enzyme binding|enzyme inhibitor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Prostate(55;0.0421)|Breast(100;0.102)|all_epithelial(46;0.142)		BRCA - Breast invasive adenocarcinoma(99;0.00593)|Colorectal(74;0.0157)|COAD - Colon adenocarcinoma(73;0.064)														---	---	---	---
TNFRSF10C	8794	broad.mit.edu	37	8	22972271	22972271	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:22972271G>A	uc003xcy.2	+	3	469	c.268G>A	c.(268-270)GTT>ATT	p.V90I	TNFRSF10C_uc011kzr.1_RNA	NM_003841	NP_003832	O14798	TR10C_HUMAN	tumor necrosis factor receptor superfamily,	90	TNFR-Cys 2.				apoptosis	anchored to membrane|integral to plasma membrane	TRAIL binding|transmembrane receptor activity				0		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0147)|COAD - Colon adenocarcinoma(73;0.0612)														---	---	---	---
NEFM	4741	broad.mit.edu	37	8	24772079	24772079	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24772079G>A	uc003xed.3	+	1	806	c.773G>A	c.(772-774)CGC>CAC	p.R258H	NEFM_uc011lac.1_Missense_Mutation_p.R258H|NEFM_uc010lue.2_5'Flank|uc010luc.1_5'UTR	NM_005382	NP_005373	P07197	NFM_HUMAN	neurofilament, medium polypeptide 150kDa isoform	258	Linker 12.|Rod.					neurofilament	protein binding|structural constituent of cytoskeleton			breast(1)	1		Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)														---	---	---	---
NEFL	4747	broad.mit.edu	37	8	24813874	24813874	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:24813874G>A	uc003xee.2	-	1	258	c.156C>T	c.(154-156)TCC>TCT	p.S52S		NM_006158	NP_006149	P07196	NFL_HUMAN	neurofilament, light polypeptide 68kDa	52	Head.				anterograde axon cargo transport|axon transport of mitochondrion|neurofilament bundle assembly|retrograde axon cargo transport|synaptic transmission	cytosol|neurofilament	identical protein binding|protein C-terminus binding|structural constituent of cytoskeleton			ovary(1)|central_nervous_system(1)	2		Ovarian(32;0.00965)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)														---	---	---	---
PPP2R2A	5520	broad.mit.edu	37	8	25293741	25293741	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25293741T>C	uc003xek.2	+						KCTD9_uc003xeo.2_Intron|KCTD9_uc011lad.1_5'Flank	NM_002717	NP_002708			alpha isoform of regulatory subunit B55, protein						protein dephosphorylation|signal transduction	protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity|protein serine/threonine phosphatase activity			ovary(1)|kidney(1)	2		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155)														---	---	---	---
EBF2	64641	broad.mit.edu	37	8	25718725	25718725	+	Silent	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:25718725T>A	uc003xes.1	-	13	1199	c.1182A>T	c.(1180-1182)CGA>CGT	p.R394R	PPP2R2A_uc003xek.2_Intron|EBF2_uc010lug.1_RNA	NM_022659	NP_073150	Q9HAK2	COE2_HUMAN	early B-cell factor 2	394					multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|metal ion binding			ovary(3)|skin(1)	4		all_cancers(63;0.0989)|Ovarian(32;2.74e-05)|all_epithelial(46;0.0608)|Prostate(55;0.0845)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0277)|Epithelial(17;3.29e-10)|Colorectal(74;0.00383)|COAD - Colon adenocarcinoma(73;0.00738)														---	---	---	---
PTK2B	2185	broad.mit.edu	37	8	27309003	27309003	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27309003C>T	uc003xfn.1	+	32	3333	c.2525C>T	c.(2524-2526)ACG>ATG	p.T842M	PTK2B_uc003xfo.1_Missense_Mutation_p.T842M|PTK2B_uc003xfp.1_Missense_Mutation_p.T842M|PTK2B_uc003xfq.1_Missense_Mutation_p.T800M|PTK2B_uc003xfs.1_Missense_Mutation_p.T39M	NM_173174	NP_775266	Q14289	FAK2_HUMAN	PTK2B protein tyrosine kinase 2 beta isoform a	842	Interaction with TGFB1I1 (By similarity).|Pro-rich.				apoptosis|bone resorption|positive regulation of cell proliferation|signal complex assembly	cytosol	ATP binding|non-membrane spanning protein tyrosine kinase activity|signal transducer activity			lung(3)|ovary(1)|skin(1)	5		Ovarian(32;2.72e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|Epithelial(17;6.61e-10)|BRCA - Breast invasive adenocarcinoma(99;0.226)|Colorectal(74;0.229)														---	---	---	---
EPHX2	2053	broad.mit.edu	37	8	27364405	27364405	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27364405A>T	uc003xfu.2	+	5	635	c.554A>T	c.(553-555)GAC>GTC	p.D185V	EPHX2_uc010lut.1_Missense_Mutation_p.D185V|EPHX2_uc010luu.2_Missense_Mutation_p.D185V|EPHX2_uc010luv.2_Missense_Mutation_p.D119V|EPHX2_uc003xfv.2_Missense_Mutation_p.D132V|EPHX2_uc010luw.2_Missense_Mutation_p.D119V|EPHX2_uc011lam.1_Missense_Mutation_p.D41V	NM_001979	NP_001970	P34913	HYES_HUMAN	epoxide hydrolase 2, cytoplasmic	185	Phosphatase.	Magnesium.			aromatic compound catabolic process|cellular calcium ion homeostasis|drug metabolic process|inflammatory response|positive regulation of vasodilation|reactive oxygen species metabolic process|regulation of blood pressure|response to toxin|xenobiotic metabolic process	cytosol|focal adhesion|Golgi apparatus|nucleolus|peroxisome|soluble fraction	epoxide hydrolase activity|metal ion binding|protein homodimerization activity			ovary(1)	1		Ovarian(32;2.61e-05)|all_epithelial(46;0.207)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0226)|Epithelial(17;1.12e-09)|Colorectal(74;0.157)	Tamoxifen(DB00675)													---	---	---	---
EPHX2	2053	broad.mit.edu	37	8	27369349	27369349	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27369349A>G	uc003xfu.2	+						EPHX2_uc010lut.1_Intron|EPHX2_uc010luu.2_Intron|EPHX2_uc010luv.2_Intron|EPHX2_uc003xfv.2_Intron|EPHX2_uc010luw.2_Intron|EPHX2_uc011lam.1_Intron	NM_001979	NP_001970			epoxide hydrolase 2, cytoplasmic						aromatic compound catabolic process|cellular calcium ion homeostasis|drug metabolic process|inflammatory response|positive regulation of vasodilation|reactive oxygen species metabolic process|regulation of blood pressure|response to toxin|xenobiotic metabolic process	cytosol|focal adhesion|Golgi apparatus|nucleolus|peroxisome|soluble fraction	epoxide hydrolase activity|metal ion binding|protein homodimerization activity			ovary(1)	1		Ovarian(32;2.61e-05)|all_epithelial(46;0.207)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0226)|Epithelial(17;1.12e-09)|Colorectal(74;0.157)	Tamoxifen(DB00675)													---	---	---	---
EXTL3	2137	broad.mit.edu	37	8	28574283	28574283	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:28574283G>A	uc003xgz.1	+	3	1300	c.707G>A	c.(706-708)TGC>TAC	p.C236Y		NM_001440	NP_001431	O43909	EXTL3_HUMAN	exostoses-like 3	236	Lumenal (Potential).					integral to membrane|intrinsic to endoplasmic reticulum membrane	glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|metal ion binding|protein binding			skin(2)	2		Ovarian(32;0.069)		KIRC - Kidney renal clear cell carcinoma(542;0.107)|Kidney(114;0.129)|Colorectal(74;0.228)														---	---	---	---
KIF13B	23303	broad.mit.edu	37	8	29039466	29039466	+	Silent	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:29039466T>A	uc003xhh.3	-	7	614	c.555A>T	c.(553-555)GGA>GGT	p.G185G	KIF13B_uc003xhj.2_Silent_p.G82G|KIF13B_uc010lvf.1_Silent_p.G121G	NM_015254	NP_056069	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	185	Kinesin-motor.				microtubule-based movement|protein targeting|signal transduction|T cell activation	cytoplasm|microtubule	ATP binding|microtubule motor activity|protein kinase binding				0		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)														---	---	---	---
TEX15	56154	broad.mit.edu	37	8	30695530	30695530	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30695530G>A	uc003xil.2	-	3	7121	c.7121C>T	c.(7120-7122)TCA>TTA	p.S2374L		NM_031271	NP_112561	Q9BXT5	TEX15_HUMAN	testis expressed 15	2374										ovary(3)|upper_aerodigestive_tract(2)|skin(2)	7				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)														---	---	---	---
TEX15	56154	broad.mit.edu	37	8	30701002	30701002	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:30701002T>G	uc003xil.2	-	1	5532	c.5532A>C	c.(5530-5532)AAA>AAC	p.K1844N		NM_031271	NP_112561	Q9BXT5	TEX15_HUMAN	testis expressed 15	1844										ovary(3)|upper_aerodigestive_tract(2)|skin(2)	7				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)														---	---	---	---
WRN	7486	broad.mit.edu	37	8	31004623	31004623	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:31004623G>A	uc003xio.3	+	29	4226	c.3438G>A	c.(3436-3438)TCG>TCA	p.S1146S	WRN_uc010lvk.2_Silent_p.S613S	NM_000553	NP_000544	Q14191	WRN_HUMAN	Werner syndrome protein	1146					base-excision repair|cellular response to starvation|DNA recombination|DNA synthesis involved in DNA repair|multicellular organismal aging|nucleolus to nucleoplasm transport|positive regulation of hydrolase activity|regulation of apoptosis|replication fork processing|response to oxidative stress|response to UV-C|telomere maintenance	centrosome|nucleolus|nucleoplasm	3'-5' exonuclease activity|ATP binding|ATP-dependent 3'-5' DNA helicase activity|bubble DNA binding|four-way junction helicase activity|G-quadruplex DNA binding|magnesium ion binding|manganese ion binding|protein complex binding|protein homodimerization activity|Y-form DNA binding			ovary(2)|kidney(2)|large_intestine(1)|lung(1)|skin(1)	7		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)				Mis|N|F|S			osteosarcoma|meningioma|others		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Werner_syndrome				---	---	---	---
NRG1	3084	broad.mit.edu	37	8	32453420	32453420	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:32453420A>C	uc003xiv.2	+	2	692	c.175A>C	c.(175-177)ACC>CCC	p.T59P	NRG1_uc003xip.2_Missense_Mutation_p.T274P|NRG1_uc003xir.2_Missense_Mutation_p.T59P|NRG1_uc010lvl.2_Missense_Mutation_p.T59P|NRG1_uc010lvm.2_Missense_Mutation_p.T59P|NRG1_uc010lvn.2_Missense_Mutation_p.T59P|NRG1_uc003xis.2_Missense_Mutation_p.T59P|NRG1_uc011lbf.1_Missense_Mutation_p.T59P|NRG1_uc010lvo.2_Missense_Mutation_p.T59P|NRG1_uc003xiu.2_Missense_Mutation_p.T59P|NRG1_uc003xiw.2_Missense_Mutation_p.T59P|NRG1_uc003xit.2_Missense_Mutation_p.T59P|NRG1_uc010lvr.2_5'UTR|NRG1_uc010lvs.2_5'UTR|NRG1_uc010lvp.2_Missense_Mutation_p.T25P|NRG1_uc010lvq.2_Missense_Mutation_p.T25P	NM_013964	NP_039258	Q02297	NRG1_HUMAN	neuregulin 1 isoform HRG-alpha	59	Extracellular (Potential).|Ig-like C2-type.				activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)														---	---	---	---
UNC5D	137970	broad.mit.edu	37	8	35406926	35406926	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:35406926A>G	uc003xjr.1	+	2	548	c.220A>G	c.(220-222)AGG>GGG	p.R74G	UNC5D_uc003xjs.1_Missense_Mutation_p.R69G	NM_080872	NP_543148	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D precursor	74	Extracellular (Potential).|Ig-like.				apoptosis|axon guidance	integral to membrane	receptor activity			upper_aerodigestive_tract(2)|ovary(2)|pancreas(1)|skin(1)	6				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)														---	---	---	---
KCNU1	157855	broad.mit.edu	37	8	36644945	36644945	+	Splice_Site	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:36644945T>C	uc010lvw.2	+	2	402	c.315_splice	c.e2+2	p.L105_splice	KCNU1_uc003xjw.2_Splice_Site	NM_001031836	NP_001027006			potassium channel, subfamily U, member 1							voltage-gated potassium channel complex	binding|large conductance calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)														---	---	---	---
PPAPDC1B	84513	broad.mit.edu	37	8	38123735	38123735	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38123735A>G	uc003xlf.3	-	6	579	c.558T>C	c.(556-558)TGT>TGC	p.C186C	PPAPDC1B_uc003xle.3_Silent_p.C145C|PPAPDC1B_uc003xlg.3_Silent_p.C186C	NM_001102559	NP_001096029	Q8NEB5	PPC1B_HUMAN	phosphatidic acid phosphatase type 2 domain	186	Helical; (Potential).				phospholipid dephosphorylation	cytoplasm|integral to membrane|plasma membrane	phosphatidate phosphatase activity				0	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.121)	BRCA - Breast invasive adenocarcinoma(5;3.04e-26)|COAD - Colon adenocarcinoma(9;0.188)															---	---	---	---
PLEKHA2	59339	broad.mit.edu	37	8	38810173	38810173	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38810173G>A	uc003xmi.3	+	8	887	c.653G>A	c.(652-654)CGC>CAC	p.R218H	PLEKHA2_uc011lce.1_Missense_Mutation_p.R168H	NM_021623	NP_067636	Q9HB19	PKHA2_HUMAN	pleckstrin homology domain containing, family A	218	PH 2.				positive regulation of cell-matrix adhesion	cytoplasm|nucleus|plasma membrane|protein complex	fibronectin binding|laminin binding				0		all_lung(54;0.0413)|Lung NSC(58;0.115)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;4.68e-08)|COAD - Colon adenocarcinoma(9;0.235)															---	---	---	---
ADAM32	203102	broad.mit.edu	37	8	39009067	39009067	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39009067A>C	uc003xmt.3	+	6	770	c.525A>C	c.(523-525)AAA>AAC	p.K175N	ADAM32_uc011lch.1_Missense_Mutation_p.K182N|ADAM32_uc003xmu.3_Missense_Mutation_p.K175N	NM_145004	NP_659441	Q8TC27	ADA32_HUMAN	a disintegrin and metalloprotease domain 32	175	Extracellular (Potential).				proteolysis	integral to membrane	metalloendopeptidase activity|zinc ion binding			ovary(1)|lung(1)|kidney(1)	3		all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503)	LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146)															---	---	---	---
ADAM18	8749	broad.mit.edu	37	8	39442826	39442826	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:39442826T>C	uc003xni.2	+	2	87	c.87T>C	c.(85-87)GTT>GTC	p.V29V	ADAM18_uc003xnh.2_Silent_p.V29V|ADAM18_uc010lww.2_RNA|ADAM18_uc010lwx.2_Silent_p.V29V	NM_014237	NP_055052	Q9Y3Q7	ADA18_HUMAN	a disintegrin and metalloprotease domain 18	29					cell differentiation|multicellular organismal development|proteolysis|spermatogenesis	integral to membrane|membrane fraction	metalloendopeptidase activity|zinc ion binding			central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)|kidney(1)|skin(1)	6		all_cancers(7;1.32e-05)|all_epithelial(6;3.08e-10)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00769)|Breast(189;0.0112)	LUSC - Lung squamous cell carcinoma(45;0.000199)															---	---	---	---
ANK1	286	broad.mit.edu	37	8	41547771	41547771	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41547771T>G	uc003xok.2	-	33	4162	c.4078A>C	c.(4078-4080)AAC>CAC	p.N1360H	NKX6-3_uc010lxa.1_Intron|ANK1_uc003xoh.2_Missense_Mutation_p.N676H|ANK1_uc003xoi.2_Missense_Mutation_p.N1360H|ANK1_uc003xoj.2_Missense_Mutation_p.N1360H|ANK1_uc003xol.2_Missense_Mutation_p.N1360H|ANK1_uc003xom.2_Missense_Mutation_p.N1401H	NM_020476	NP_065209	P16157	ANK1_HUMAN	ankyrin 1 isoform 1	1360					axon guidance|cytoskeleton organization|exocytosis|maintenance of epithelial cell apical/basal polarity|signal transduction	basolateral plasma membrane|cytosol|sarcomere|sarcoplasmic reticulum|spectrin-associated cytoskeleton	cytoskeletal adaptor activity|enzyme binding|protein binding|spectrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(3)|lung(2)|breast(1)	9	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)															---	---	---	---
ANK1	286	broad.mit.edu	37	8	41552256	41552256	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41552256G>A	uc003xok.2	-	28	3265	c.3181C>T	c.(3181-3183)CTG>TTG	p.L1061L	NKX6-3_uc010lxa.1_Intron|ANK1_uc003xoh.2_Silent_p.L377L|ANK1_uc003xoi.2_Silent_p.L1061L|ANK1_uc003xoj.2_Silent_p.L1061L|ANK1_uc003xol.2_Silent_p.L1061L|ANK1_uc003xom.2_Silent_p.L1102L	NM_020476	NP_065209	P16157	ANK1_HUMAN	ankyrin 1 isoform 1	1061					axon guidance|cytoskeleton organization|exocytosis|maintenance of epithelial cell apical/basal polarity|signal transduction	basolateral plasma membrane|cytosol|sarcomere|sarcoplasmic reticulum|spectrin-associated cytoskeleton	cytoskeletal adaptor activity|enzyme binding|protein binding|spectrin binding|structural constituent of cytoskeleton	p.L1061V(1)		ovary(3)|central_nervous_system(3)|lung(2)|breast(1)	9	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)															---	---	---	---
MYST3	7994	broad.mit.edu	37	8	41791556	41791556	+	Silent	SNP	G	A	A	rs150230451		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41791556G>A	uc010lxb.2	-	18	4726	c.4182C>T	c.(4180-4182)GAC>GAT	p.D1394D	MYST3_uc010lxc.2_Silent_p.D1394D|MYST3_uc003xon.3_Silent_p.D1394D	NM_001099412	NP_001092882	Q92794	MYST3_HUMAN	MYST histone acetyltransferase (monocytic	1394					histone H3 acetylation|myeloid cell differentiation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription coactivator activity|transcription factor binding|zinc ion binding			ovary(4)|pancreas(1)|central_nervous_system(1)|skin(1)	7	all_epithelial(6;1.12e-27)|all_lung(13;3.94e-12)|Lung NSC(13;6.54e-11)|Ovarian(28;0.00744)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211)	all_lung(54;0.000294)|Lung NSC(58;0.00105)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983)	Epithelial(1;2.82e-19)|all cancers(1;1.15e-16)|BRCA - Breast invasive adenocarcinoma(8;9.17e-11)|OV - Ovarian serous cystadenocarcinoma(14;9.4e-05)|Colorectal(10;0.000728)|Lung(22;0.00153)|LUSC - Lung squamous cell carcinoma(45;0.00741)|COAD - Colon adenocarcinoma(11;0.0171)															---	---	---	---
MYST3	7994	broad.mit.edu	37	8	41905935	41905935	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:41905935A>C	uc010lxb.2	-	3	1105	c.561T>G	c.(559-561)TGT>TGG	p.C187W	MYST3_uc010lxc.2_Missense_Mutation_p.C187W|MYST3_uc003xon.3_Missense_Mutation_p.C187W|MYST3_uc010lxd.2_Missense_Mutation_p.C187W	NM_001099412	NP_001092882	Q92794	MYST3_HUMAN	MYST histone acetyltransferase (monocytic	187					histone H3 acetylation|myeloid cell differentiation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription coactivator activity|transcription factor binding|zinc ion binding			ovary(4)|pancreas(1)|central_nervous_system(1)|skin(1)	7	all_epithelial(6;1.12e-27)|all_lung(13;3.94e-12)|Lung NSC(13;6.54e-11)|Ovarian(28;0.00744)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211)	all_lung(54;0.000294)|Lung NSC(58;0.00105)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983)	Epithelial(1;2.82e-19)|all cancers(1;1.15e-16)|BRCA - Breast invasive adenocarcinoma(8;9.17e-11)|OV - Ovarian serous cystadenocarcinoma(14;9.4e-05)|Colorectal(10;0.000728)|Lung(22;0.00153)|LUSC - Lung squamous cell carcinoma(45;0.00741)|COAD - Colon adenocarcinoma(11;0.0171)															---	---	---	---
AP3M2	10947	broad.mit.edu	37	8	42024726	42024726	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42024726G>A	uc003xop.2	+	8	1139	c.848G>A	c.(847-849)CGG>CAG	p.R283Q	AP3M2_uc003xoo.2_Missense_Mutation_p.R283Q|AP3M2_uc010lxe.2_Intron	NM_001134296	NP_001127768	P53677	AP3M2_HUMAN	adaptor-related protein complex 3, mu 2 subunit	283	MHD.				intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|Golgi apparatus					0	all_cancers(6;8.14e-25)|all_epithelial(6;2.41e-27)|all_lung(13;5.09e-13)|Lung NSC(13;8.38e-12)|Ovarian(28;0.00438)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983)	BRCA - Breast invasive adenocarcinoma(8;5.23e-10)|Colorectal(10;0.00165)|OV - Ovarian serous cystadenocarcinoma(14;0.00346)|Lung(22;0.00467)|COAD - Colon adenocarcinoma(11;0.0171)|LUSC - Lung squamous cell carcinoma(45;0.024)															---	---	---	---
CHRNA6	8973	broad.mit.edu	37	8	42620307	42620307	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42620307T>G	uc003xpj.2	-	2	166	c.120A>C	c.(118-120)AAA>AAC	p.K40N	CHRNA6_uc011lcw.1_Missense_Mutation_p.K40N	NM_004198	NP_004189	Q15825	ACHA6_HUMAN	cholinergic receptor, nicotinic, alpha 6	40	Extracellular.					cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity				0	all_lung(13;3.33e-12)|Lung NSC(13;9.17e-11)|Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00439)|Lung NSC(58;0.0124)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	Lung(22;0.0252)|LUSC - Lung squamous cell carcinoma(45;0.0869)															---	---	---	---
RNF170	81790	broad.mit.edu	37	8	42711434	42711434	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42711434T>C	uc003xpo.2	-	7	1122	c.645A>G	c.(643-645)TCA>TCG	p.S215S	RNF170_uc011lcx.1_Intron|RNF170_uc010lxp.2_Silent_p.S131S|RNF170_uc003xpm.2_Silent_p.S215S|RNF170_uc003xpp.2_Silent_p.S119S|RNF170_uc003xpn.2_Silent_p.S119S	NM_001160223	NP_001153695	Q96K19	RN170_HUMAN	ring finger protein 170 isoform a	215	Helical; (Potential).					integral to membrane	zinc ion binding				0	all_lung(13;1.25e-11)|Lung NSC(13;3.55e-10)|Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00645)|Lung NSC(58;0.0176)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)															---	---	---	---
HOOK3	84376	broad.mit.edu	37	8	42821659	42821659	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42821659T>C	uc003xpr.2	+	10	1065	c.823T>C	c.(823-825)TTA>CTA	p.L275L	HOOK3_uc010lxq.1_Silent_p.L275L	NM_032410	NP_115786	Q86VS8	HOOK3_HUMAN	golgi-associated microtubule-binding protein	275	Potential.				cytoplasmic microtubule organization|early endosome to late endosome transport|endosome organization|endosome to lysosome transport|Golgi localization|interkinetic nuclear migration|lysosome organization|microtubule anchoring|negative regulation of neurogenesis|protein localization to centrosome|protein transport	cis-Golgi network|FHF complex|microtubule|pericentriolar material	identical protein binding|microtubule binding			ovary(1)|breast(1)	2	Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.000105)|Lung NSC(58;0.000419)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)					T	RET	papillary thyroid								---	---	---	---
SGK196	84197	broad.mit.edu	37	8	42958754	42958754	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:42958754T>C	uc003xpw.2	+	4	322	c.63T>C	c.(61-63)GTT>GTC	p.V21V		NM_032237	NP_115613	Q9H5K3	SG196_HUMAN	protein kinase-like protein SgK196	21	Helical; (Potential).					integral to membrane	ATP binding|protein kinase activity				0																		---	---	---	---
POTEA	340441	broad.mit.edu	37	8	43147779	43147779	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43147779A>C	uc003xpz.1	+	1	195	c.152A>C	c.(151-153)GAC>GCC	p.D51A	POTEA_uc003xqa.1_Missense_Mutation_p.D51A	NM_001005365	NP_001005365	Q6S8J7	POTEA_HUMAN	POTE ankyrin domain family, member A isoform 2	51										ovary(1)	1																		---	---	---	---
KIAA0146	23514	broad.mit.edu	37	8	48508483	48508483	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48508483C>T	uc003xqd.2	+	9	1217	c.1208C>T	c.(1207-1209)CCG>CTG	p.P403L	KIAA0146_uc011lcz.1_RNA|KIAA0146_uc011lda.1_Missense_Mutation_p.P92L|KIAA0146_uc011ldb.1_Missense_Mutation_p.P403L|KIAA0146_uc010lxs.2_Intron|KIAA0146_uc011ldc.1_Missense_Mutation_p.P333L|KIAA0146_uc011ldd.1_Missense_Mutation_p.P343L|KIAA0146_uc003xqe.2_5'UTR|KIAA0146_uc003xqf.2_RNA|KIAA0146_uc011lde.1_Missense_Mutation_p.P92L|KIAA0146_uc010lxt.2_Missense_Mutation_p.P92L	NM_001080394	NP_001073863	Q14159	K0146_HUMAN	hypothetical protein LOC23514	403											0		Lung NSC(58;0.175)																---	---	---	---
PXDNL	137902	broad.mit.edu	37	8	52287195	52287195	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52287195C>T	uc003xqu.3	-	18	3755	c.3654G>A	c.(3652-3654)CTG>CTA	p.L1218L	PXDNL_uc003xqt.3_RNA	NM_144651	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog-like precursor	1218					hydrogen peroxide catabolic process	extracellular space	heme binding|peroxidase activity			ovary(1)|pancreas(1)	2		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)																---	---	---	---
PXDNL	137902	broad.mit.edu	37	8	52320785	52320785	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52320785C>T	uc003xqu.3	-	17	3500	c.3399G>A	c.(3397-3399)GCG>GCA	p.A1133A	PXDNL_uc003xqt.3_RNA	NM_144651	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog-like precursor	1133					hydrogen peroxide catabolic process	extracellular space	heme binding|peroxidase activity			ovary(1)|pancreas(1)	2		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)																---	---	---	---
PXDNL	137902	broad.mit.edu	37	8	52321999	52321999	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52321999C>T	uc003xqu.3	-	17	2286	c.2185G>A	c.(2185-2187)GCC>ACC	p.A729T	PXDNL_uc003xqt.3_RNA	NM_144651	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog-like precursor	729					hydrogen peroxide catabolic process	extracellular space	heme binding|peroxidase activity			ovary(1)|pancreas(1)	2		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)																---	---	---	---
PCMTD1	115294	broad.mit.edu	37	8	52744104	52744104	+	Silent	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:52744104T>A	uc003xqx.3	-	5	947	c.606A>T	c.(604-606)GGA>GGT	p.G202G	PCMTD1_uc011ldm.1_Silent_p.G72G|PCMTD1_uc003xqw.3_Silent_p.G202G|PCMTD1_uc011ldn.1_Silent_p.G14G|PCMTD1_uc010lya.2_Silent_p.G126G	NM_052937	NP_443169	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate)	202						cytoplasm	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity				0		Lung NSC(129;0.0795)|all_lung(136;0.144)																---	---	---	---
ST18	9705	broad.mit.edu	37	8	53084552	53084552	+	Missense_Mutation	SNP	G	A	A	rs145432477		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53084552G>A	uc003xqz.2	-	5	1025	c.869C>T	c.(868-870)ACG>ATG	p.T290M	ST18_uc011ldq.1_Translation_Start_Site|ST18_uc011ldr.1_Missense_Mutation_p.T255M|ST18_uc011lds.1_Missense_Mutation_p.T195M|ST18_uc003xra.2_Missense_Mutation_p.T290M|ST18_uc003xrb.2_Missense_Mutation_p.T290M	NM_014682	NP_055497	O60284	ST18_HUMAN	suppression of tumorigenicity 18	290						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|skin(1)	5		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)																---	---	---	---
RGS20	8601	broad.mit.edu	37	8	54866751	54866751	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:54866751G>T	uc003xrp.2	+	5	951	c.859G>T	c.(859-861)GAA>TAA	p.E287*	RGS20_uc003xrq.2_Nonsense_Mutation_p.E172*|RGS20_uc010lye.2_Nonsense_Mutation_p.E79*|RGS20_uc010lyf.2_Nonsense_Mutation_p.E51*|RGS20_uc003xrs.2_Nonsense_Mutation_p.E140*|RGS20_uc003xrt.2_Nonsense_Mutation_p.E21*	NM_170587	NP_733466	O76081	RGS20_HUMAN	regulator of G-protein signaling 20 isoform a	287	RGS.				negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|nucleus|plasma membrane	GTPase activator activity|protein binding|signal transducer activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(7;1.37e-06)|Epithelial(17;0.000126)|all cancers(17;0.0009)															---	---	---	---
MRPL15	29088	broad.mit.edu	37	8	55049106	55049106	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:55049106A>C	uc003xsa.2	+	2	207	c.144A>C	c.(142-144)AAA>AAC	p.K48N		NM_014175	NP_054894	Q9P015	RM15_HUMAN	mitochondrial ribosomal protein L15 precursor	48	Arg-rich.				translation	large ribosomal subunit|mitochondrion	structural constituent of ribosome				0		Lung NSC(129;0.109)|all_epithelial(80;0.134)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;4.3e-07)|Epithelial(17;5.79e-05)|all cancers(17;0.000458)															---	---	---	---
XKR4	114786	broad.mit.edu	37	8	56015464	56015464	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56015464G>A	uc003xsf.2	+	1	448	c.416G>A	c.(415-417)CGC>CAC	p.R139H		NM_052898	NP_443130	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related	139						integral to membrane				pancreas(2)	2			Epithelial(17;0.000117)|all cancers(17;0.000836)															---	---	---	---
XKR4	114786	broad.mit.edu	37	8	56436176	56436176	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56436176T>A	uc003xsf.2	+	3	1375	c.1343T>A	c.(1342-1344)GTC>GAC	p.V448D		NM_052898	NP_443130	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related	448	Helical; (Potential).					integral to membrane				pancreas(2)	2			Epithelial(17;0.000117)|all cancers(17;0.000836)															---	---	---	---
TGS1	96764	broad.mit.edu	37	8	56699578	56699578	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56699578G>T	uc003xsj.3	+	4	1508	c.1121G>T	c.(1120-1122)AGC>ATC	p.S374I	TGS1_uc010lyh.2_Missense_Mutation_p.S278I	NM_024831	NP_079107	Q96RS0	TGS1_HUMAN	trimethylguanosine synthase homolog	374					cellular lipid metabolic process|ncRNA metabolic process|regulation of transcription, DNA-dependent|RNA capping|spliceosomal snRNP assembly|transcription, DNA-dependent	Cajal body|cytosol	RNA trimethylguanosine synthase activity			ovary(1)|lung(1)|breast(1)	3		all_lung(136;0.119)|all_epithelial(80;0.125)|Lung NSC(129;0.147)	Epithelial(17;0.00027)|all cancers(17;0.00251)															---	---	---	---
TGS1	96764	broad.mit.edu	37	8	56715066	56715066	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56715066C>T	uc003xsj.3	+	9	2287	c.1900C>T	c.(1900-1902)CTG>TTG	p.L634L	TGS1_uc010lyh.2_Silent_p.L538L	NM_024831	NP_079107	Q96RS0	TGS1_HUMAN	trimethylguanosine synthase homolog	634	Sufficient for catalytic activity.				cellular lipid metabolic process|ncRNA metabolic process|regulation of transcription, DNA-dependent|RNA capping|spliceosomal snRNP assembly|transcription, DNA-dependent	Cajal body|cytosol	RNA trimethylguanosine synthase activity			ovary(1)|lung(1)|breast(1)	3		all_lung(136;0.119)|all_epithelial(80;0.125)|Lung NSC(129;0.147)	Epithelial(17;0.00027)|all cancers(17;0.00251)															---	---	---	---
LYN	4067	broad.mit.edu	37	8	56912074	56912074	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56912074C>T	uc003xsk.3	+	12	1584	c.1302C>T	c.(1300-1302)TAC>TAT	p.Y434Y	LYN_uc003xsl.3_Silent_p.Y413Y	NM_002350	NP_002341	P07948	LYN_HUMAN	Yamaguchi sarcoma viral (v-yes-1) oncogene	434	Protein kinase.				erythrocyte differentiation|interspecies interaction between organisms|leukocyte migration|platelet activation|positive regulation of cellular component movement|positive regulation of stress-activated protein kinase signaling cascade|positive regulation of tyrosine phosphorylation of STAT protein|response to DNA damage stimulus|T cell costimulation	cytosol|Golgi apparatus|membrane raft|nucleus|perinuclear region of cytoplasm	ATP binding|ion channel binding|non-membrane spanning protein tyrosine kinase activity|receptor signaling protein tyrosine kinase activity			ovary(1)|breast(1)|central_nervous_system(1)	3		all_lung(136;0.0555)|Lung NSC(129;0.0726)|all_epithelial(80;0.0772)	Epithelial(17;0.000834)|all cancers(17;0.00598)															---	---	---	---
LYN	4067	broad.mit.edu	37	8	56922615	56922615	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:56922615C>T	uc003xsk.3	+	13	1767	c.1485C>T	c.(1483-1485)AGC>AGT	p.S495S	LYN_uc003xsl.3_Silent_p.S474S	NM_002350	NP_002341	P07948	LYN_HUMAN	Yamaguchi sarcoma viral (v-yes-1) oncogene	495	Protein kinase.				erythrocyte differentiation|interspecies interaction between organisms|leukocyte migration|platelet activation|positive regulation of cellular component movement|positive regulation of stress-activated protein kinase signaling cascade|positive regulation of tyrosine phosphorylation of STAT protein|response to DNA damage stimulus|T cell costimulation	cytosol|Golgi apparatus|membrane raft|nucleus|perinuclear region of cytoplasm	ATP binding|ion channel binding|non-membrane spanning protein tyrosine kinase activity|receptor signaling protein tyrosine kinase activity			ovary(1)|breast(1)|central_nervous_system(1)	3		all_lung(136;0.0555)|Lung NSC(129;0.0726)|all_epithelial(80;0.0772)	Epithelial(17;0.000834)|all cancers(17;0.00598)															---	---	---	---
FAM110B	90362	broad.mit.edu	37	8	59059198	59059198	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59059198C>T	uc003xtj.1	+	5	1289	c.409C>T	c.(409-411)CAC>TAC	p.H137Y		NM_147189	NP_671722	Q8TC76	F110B_HUMAN	hypothetical protein LOC90362	137						microtubule organizing center|mitochondrion|nucleus				large_intestine(1)	1		all_epithelial(80;0.025)|all_lung(136;0.0274)|Lung NSC(129;0.0355)																---	---	---	---
NSMAF	8439	broad.mit.edu	37	8	59555601	59555601	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59555601A>G	uc003xtt.2	-	2	305	c.91T>C	c.(91-93)TAC>CAC	p.Y31H	NSMAF_uc011lee.1_Missense_Mutation_p.Y62H|NSMAF_uc003xtu.2_Missense_Mutation_p.Y31H	NM_003580	NP_003571	Q92636	FAN_HUMAN	neutral sphingomyelinase (N-SMase) activation	31					ceramide metabolic process	cytoplasm|soluble fraction	protein binding|receptor signaling protein activity			ovary(1)	1		all_lung(136;0.174)|Lung NSC(129;0.2)																---	---	---	---
CHD7	55636	broad.mit.edu	37	8	61742873	61742873	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61742873T>C	uc003xue.2	+							NM_017780	NP_060250			chromodomain helicase DNA binding protein 7						central nervous system development|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	nucleus	ATP binding|chromatin binding|DNA binding|helicase activity			ovary(4)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|pancreas(1)	9		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)															---	---	---	---
CHD7	55636	broad.mit.edu	37	8	61757621	61757621	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:61757621C>T	uc003xue.2	+	22	5526	c.5049C>T	c.(5047-5049)TCC>TCT	p.S1683S		NM_017780	NP_060250	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	1683					central nervous system development|chromatin modification|cognition|cranial nerve development|face development|heart morphogenesis|in utero embryonic development|inner ear morphogenesis|nose development|palate development|regulation of growth hormone secretion|regulation of transcription, DNA-dependent|retina development in camera-type eye|skeletal system development|T cell differentiation|transcription, DNA-dependent	nucleus	ATP binding|chromatin binding|DNA binding|helicase activity			ovary(4)|large_intestine(1)|central_nervous_system(1)|lung(1)|breast(1)|pancreas(1)	9		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)															---	---	---	---
CYP7B1	9420	broad.mit.edu	37	8	65528656	65528656	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:65528656T>C	uc003xvj.2	-	3	646	c.442A>G	c.(442-444)AAA>GAA	p.K148E		NM_004820	NP_004811	O75881	CP7B1_HUMAN	cytochrome P450, family 7, subfamily B,	148					bile acid biosynthetic process|cell death|cholesterol metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	25-hydroxycholesterol 7alpha-hydroxylase activity|electron carrier activity|heme binding|oxysterol 7-alpha-hydroxylase activity			ovary(3)	3		all_cancers(86;0.217)|Lung NSC(129;0.0521)|all_lung(136;0.0906)|all_epithelial(80;0.215)																---	---	---	---
MTFR1	9650	broad.mit.edu	37	8	66617040	66617040	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:66617040G>A	uc003xvm.2	+	5	605	c.393G>A	c.(391-393)AAG>AAA	p.K131K	MTFR1_uc011lep.1_Silent_p.K131K|MTFR1_uc003xvn.2_Silent_p.K98K|MTFR1_uc003xvo.1_Silent_p.K121K	NM_014637	NP_055452	Q15390	MTFR1_HUMAN	mitochondrial fission regulator 1 isoform 1	131						mitochondrion|plasma membrane				pancreas(1)	1			Epithelial(68;0.0526)|BRCA - Breast invasive adenocarcinoma(89;0.156)|all cancers(69;0.171)|OV - Ovarian serous cystadenocarcinoma(28;0.194)															---	---	---	---
ADHFE1	137872	broad.mit.edu	37	8	67357486	67357486	+	Silent	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67357486A>C	uc003xwb.3	+	6	421	c.387A>C	c.(385-387)GGA>GGC	p.G129G	ADHFE1_uc003xwd.3_RNA|ADHFE1_uc003xwc.3_Silent_p.G81G|ADHFE1_uc003xwe.3_RNA|ADHFE1_uc003xwf.3_Intron|ADHFE1_uc011les.1_Silent_p.G59G|ADHFE1_uc011leq.1_Intron|ADHFE1_uc011ler.1_Intron	NM_144650	NP_653251	Q8IWW8	HOT_HUMAN	alcohol dehydrogenase, iron containing, 1	129					2-oxoglutarate metabolic process|molecular hydrogen transport	mitochondrial matrix	hydroxyacid-oxoacid transhydrogenase activity|metal ion binding			ovary(1)|lung(1)|breast(1)|skin(1)	4		Lung NSC(129;0.197)	Epithelial(68;0.0321)|all cancers(69;0.0751)|BRCA - Breast invasive adenocarcinoma(89;0.0855)|OV - Ovarian serous cystadenocarcinoma(28;0.226)															---	---	---	---
ARFGEF1	10565	broad.mit.edu	37	8	68113821	68113821	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68113821C>A	uc003xxo.1	-	37	5538	c.5148G>T	c.(5146-5148)AAG>AAT	p.K1716N	ARFGEF1_uc003xxl.1_Missense_Mutation_p.K1170N|ARFGEF1_uc003xxm.1_Missense_Mutation_p.K119N|ARFGEF1_uc003xxn.1_Missense_Mutation_p.K661N|ARFGEF1_uc003xxp.1_5'UTR	NM_006421	NP_006412	Q9Y6D6	BIG1_HUMAN	brefeldin A-inhibited guanine	1716					exocytosis|regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity|myosin binding			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|kidney(1)	8	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)															---	---	---	---
ARFGEF1	10565	broad.mit.edu	37	8	68138292	68138292	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68138292C>T	uc003xxo.1	-	28	4433	c.4043G>A	c.(4042-4044)CGC>CAC	p.R1348H	ARFGEF1_uc003xxl.1_Missense_Mutation_p.R802H|ARFGEF1_uc003xxn.1_Missense_Mutation_p.R331H	NM_006421	NP_006412	Q9Y6D6	BIG1_HUMAN	brefeldin A-inhibited guanine	1348					exocytosis|regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity|myosin binding			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|kidney(1)	8	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)															---	---	---	---
ARFGEF1	10565	broad.mit.edu	37	8	68179349	68179349	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68179349C>A	uc003xxo.1	-	12	2179	c.1789G>T	c.(1789-1791)GAA>TAA	p.E597*	ARFGEF1_uc003xxl.1_Nonsense_Mutation_p.E51*	NM_006421	NP_006412	Q9Y6D6	BIG1_HUMAN	brefeldin A-inhibited guanine	597					exocytosis|regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity|myosin binding			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|kidney(1)	8	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)															---	---	---	---
PREX2	80243	broad.mit.edu	37	8	68982065	68982065	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68982065C>T	uc003xxv.1	+						PREX2_uc003xxu.1_Intron|PREX2_uc011lez.1_Intron	NM_024870	NP_079146			DEP domain containing 2 isoform a						G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity			skin(6)|large_intestine(4)|pancreas(3)|lung(2)|ovary(1)|kidney(1)	17																		---	---	---	---
C8orf34	116328	broad.mit.edu	37	8	69434138	69434138	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69434138G>T	uc010lyz.2	+	6	661	c.612G>T	c.(610-612)CAG>CAT	p.Q204H	C8orf34_uc010lyy.1_Missense_Mutation_p.Q204H|C8orf34_uc003xyb.2_Missense_Mutation_p.Q179H	NM_052958	NP_443190	Q49A92	CH034_HUMAN	hypothetical protein LOC116328	204					signal transduction		cAMP-dependent protein kinase regulator activity			large_intestine(1)	1			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)															---	---	---	---
KCNB2	9312	broad.mit.edu	37	8	73849840	73849840	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:73849840G>T	uc003xzb.2	+	3	2838	c.2250G>T	c.(2248-2250)CAG>CAT	p.Q750H		NM_004770	NP_004761	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related	750	Cytoplasmic (Potential).				regulation of smooth muscle contraction	voltage-gated potassium channel complex	delayed rectifier potassium channel activity|protein binding			skin(3)|large_intestine(1)|pancreas(1)|ovary(1)|central_nervous_system(1)	7	Breast(64;0.137)		Epithelial(68;0.105)															---	---	---	---
STAU2	27067	broad.mit.edu	37	8	74464497	74464497	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74464497C>T	uc003xzm.2	-	13	1516	c.1280G>A	c.(1279-1281)CGC>CAC	p.R427H	STAU2_uc011lfg.1_Missense_Mutation_p.R255H|STAU2_uc003xzn.2_Missense_Mutation_p.R395H|STAU2_uc011lfh.1_Missense_Mutation_p.R323H|STAU2_uc003xzo.2_Missense_Mutation_p.R427H|STAU2_uc003xzp.2_Missense_Mutation_p.R395H|STAU2_uc011lfi.1_Missense_Mutation_p.R389H|STAU2_uc003xzq.2_Missense_Mutation_p.R207H|STAU2_uc010lzk.2_Missense_Mutation_p.R395H|STAU2_uc010lzl.1_Missense_Mutation_p.R255H	NM_014393	NP_055208	Q9NUL3	STAU2_HUMAN	staufen homolog 2 isoform e	427	Required for dendritic transport (By similarity).				transport	endoplasmic reticulum|microtubule|nucleolus	double-stranded RNA binding				0	Breast(64;0.0138)		Epithelial(68;0.026)|BRCA - Breast invasive adenocarcinoma(89;0.0483)|all cancers(69;0.0972)															---	---	---	---
LY96	23643	broad.mit.edu	37	8	74903786	74903786	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74903786T>C	uc003yad.2	+	1	200	c.109T>C	c.(109-111)TGT>CGT	p.C37R		NM_015364	NP_056179	Q9Y6Y9	LY96_HUMAN	MD-2 protein precursor	37					cellular defense response|detection of lipopolysaccharide|I-kappaB kinase/NF-kappaB cascade|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	extracellular space|lipopolysaccharide receptor complex|plasma membrane	coreceptor activity|lipopolysaccharide receptor activity|protein binding				0	Breast(64;0.0311)		Epithelial(68;0.0208)|BRCA - Breast invasive adenocarcinoma(89;0.0499)|all cancers(69;0.0619)															---	---	---	---
JPH1	56704	broad.mit.edu	37	8	75227597	75227597	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:75227597C>T	uc003yae.2	-	2	678	c.638G>A	c.(637-639)CGG>CAG	p.R213Q	JPH1_uc003yaf.2_Missense_Mutation_p.R213Q|JPH1_uc003yag.1_Missense_Mutation_p.R77Q	NM_020647	NP_065698	Q9HDC5	JPH1_HUMAN	junctophilin 1	213	Cytoplasmic (Potential).				calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional membrane complex|junctional sarcoplasmic reticulum membrane|plasma membrane				ovary(1)	1	Breast(64;0.00576)		BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.0728)|all cancers(69;0.176)															---	---	---	---
ZFHX4	79776	broad.mit.edu	37	8	77768319	77768319	+	Silent	SNP	G	T	T	rs113880836		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77768319G>T	uc003yav.2	+	10	9414	c.9027G>T	c.(9025-9027)ACG>ACT	p.T3009T	ZFHX4_uc003yau.1_Silent_p.T3054T|ZFHX4_uc003yaw.1_Silent_p.T3009T	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	3009						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)												HNSCC(33;0.089)			---	---	---	---
PEX2	5828	broad.mit.edu	37	8	77896392	77896392	+	Missense_Mutation	SNP	G	A	A	rs148428490		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:77896392G>A	uc003yax.2	-	4	481	c.23C>T	c.(22-24)GCG>GTG	p.A8V	PEX2_uc003yay.2_Missense_Mutation_p.A8V|PEX2_uc003yaz.2_Missense_Mutation_p.A8V	NM_000318	NP_000309	P28328	PEX2_HUMAN	peroxin 2	8					peroxisome organization	integral to peroxisomal membrane	protein binding|zinc ion binding			ovary(1)	1																		---	---	---	---
ZBTB10	65986	broad.mit.edu	37	8	81430771	81430771	+	Silent	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:81430771A>T	uc003ybx.3	+	4	2692	c.2094A>T	c.(2092-2094)GGA>GGT	p.G698G	ZBTB10_uc003ybv.3_Silent_p.G406G|ZBTB10_uc003ybw.3_Silent_p.G674G|ZBTB10_uc010lzt.2_Silent_p.G696G	NM_001105539	NP_001099009	Q96DT7	ZBT10_HUMAN	zinc finger and BTB domain containing 10 isoform	698					transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			lung(1)	1	all_cancers(3;1.68e-09)|all_epithelial(4;5.13e-11)|Lung NSC(7;1.75e-07)|all_lung(9;7.38e-07)|Breast(3;2.96e-06)		BRCA - Breast invasive adenocarcinoma(6;0.000434)|Epithelial(68;0.00486)|all cancers(69;0.0296)															---	---	---	---
ZFAND1	79752	broad.mit.edu	37	8	82629476	82629476	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:82629476T>C	uc003ycj.1	-						ZFAND1_uc010lzx.1_Intron|ZFAND1_uc003yck.1_Intron	NM_024699	NP_078975			zinc finger, AN1-type domain 1								zinc ion binding			ovary(1)	1																		---	---	---	---
CA3	761	broad.mit.edu	37	8	86351967	86351967	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86351967C>T	uc003ydj.2	+	2	144	c.61C>T	c.(61-63)CCA>TCA	p.P21S	CA13_uc003ydf.1_RNA|CA3_uc011lfv.1_RNA	NM_005181	NP_005172	P07451	CAH3_HUMAN	carbonic anhydrase III	21					one-carbon metabolic process	cytoplasm	carbonate dehydratase activity|zinc ion binding				0																		---	---	---	---
PSKH2	85481	broad.mit.edu	37	8	87060821	87060821	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87060821C>A	uc011lfy.1	-	3	1028	c.1028G>T	c.(1027-1029)AGG>ATG	p.R343M		NM_033126	NP_149117	Q96QS6	KPSH2_HUMAN	protein serine kinase H2	343							ATP binding|protein serine/threonine kinase activity			stomach(2)|lung(2)|ovary(1)	5			STAD - Stomach adenocarcinoma(118;0.129)															---	---	---	---
WWP1	11059	broad.mit.edu	37	8	87464904	87464904	+	Nonsense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87464904T>G	uc003ydt.2	+	21	2670	c.2390T>G	c.(2389-2391)TTA>TGA	p.L797*		NM_007013	NP_008944	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase	797	HECT.				central nervous system development|entry of virus into host cell|negative regulation of transcription, DNA-dependent|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|signal transduction	cytoplasm|nucleus|plasma membrane|ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			lung(1)|liver(1)	2																		---	---	---	---
CPNE3	8895	broad.mit.edu	37	8	87557059	87557059	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87557059G>T	uc003ydv.2	+	9	887	c.725G>T	c.(724-726)AGC>ATC	p.S242I	CPNE3_uc003ydw.1_5'Flank	NM_003909	NP_003900	O75131	CPNE3_HUMAN	copine III	242					lipid metabolic process|vesicle-mediated transport	cytosol	calcium-dependent phospholipid binding|protein serine/threonine kinase activity|transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
CPNE3	8895	broad.mit.edu	37	8	87560566	87560566	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87560566G>T	uc003ydv.2	+	12	1079	c.917G>T	c.(916-918)AGG>ATG	p.R306M	CPNE3_uc003ydw.1_Missense_Mutation_p.R22M	NM_003909	NP_003900	O75131	CPNE3_HUMAN	copine III	306	VWFA.				lipid metabolic process|vesicle-mediated transport	cytosol	calcium-dependent phospholipid binding|protein serine/threonine kinase activity|transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
CPNE3	8895	broad.mit.edu	37	8	87567171	87567171	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87567171G>A	uc003ydv.2	+	15	1375	c.1213G>A	c.(1213-1215)GCC>ACC	p.A405T	CPNE3_uc003ydw.1_Missense_Mutation_p.A121T	NM_003909	NP_003900	O75131	CPNE3_HUMAN	copine III	405	VWFA.				lipid metabolic process|vesicle-mediated transport	cytosol	calcium-dependent phospholipid binding|protein serine/threonine kinase activity|transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
MMP16	4325	broad.mit.edu	37	8	89180147	89180147	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:89180147G>T	uc003yeb.3	-	4	742	c.460C>A	c.(460-462)CGT>AGT	p.R154S	MMP16_uc003yec.2_Missense_Mutation_p.R154S	NM_005941	NP_005932	P51512	MMP16_HUMAN	matrix metalloproteinase 16 isoform 1	154	Extracellular (Potential).				collagen catabolic process|proteolysis	cell surface|integral to plasma membrane|proteinaceous extracellular matrix	calcium ion binding|enzyme activator activity|metalloendopeptidase activity|zinc ion binding			upper_aerodigestive_tract(2)|ovary(2)|central_nervous_system(1)|urinary_tract(1)|skin(1)|kidney(1)	8																		---	---	---	---
RIPK2	8767	broad.mit.edu	37	8	90777595	90777595	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90777595G>T	uc003yee.2	+	3	668	c.354G>T	c.(352-354)TGG>TGT	p.W118C	RIPK2_uc003yef.2_5'UTR	NM_003821	NP_003812	O43353	RIPK2_HUMAN	receptor-interacting serine-threonine kinase 2	118	Protein kinase.				activation of MAPK activity|anti-apoptosis|apoptosis|inflammatory response|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of protein ubiquitination|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	ATP binding|CARD domain binding|LIM domain binding|protein homodimerization activity|protein serine/threonine kinase activity|signal transducer activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(11;0.0474)															---	---	---	---
NBN	4683	broad.mit.edu	37	8	90967512	90967512	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90967512T>C	uc003yej.1	-	10	1506	c.1396A>G	c.(1396-1398)AGG>GGG	p.R466G	NBN_uc003yei.1_Missense_Mutation_p.R384G|NBN_uc011lgb.1_Missense_Mutation_p.R466G	NM_002485	NP_002476	O60934	NBN_HUMAN	nibrin	466	Nuclear localization signal.			KR->AA: Blocks the association with KPNA2, and reduces nuclear foci formation in response to ionizing radiation.	cell cycle arrest|DNA damage response, signal transduction by p53 class mediator|DNA duplex unwinding|double-strand break repair via homologous recombination|meiosis|mitotic cell cycle G1/S transition checkpoint|mitotic cell cycle G2/M transition DNA damage checkpoint|positive regulation of kinase activity|positive regulation of protein autophosphorylation|regulation of DNA-dependent DNA replication initiation|telomere maintenance	Mre11 complex|nuclear chromosome, telomeric region|nuclear inclusion body|nucleolus|nucleoplasm	protein N-terminus binding|transcription factor binding			central_nervous_system(3)|kidney(3)|lung(1)	7			BRCA - Breast invasive adenocarcinoma(11;0.0344)										Direct_reversal_of_damage|Homologous_recombination	Nijmegen_Breakage_syndrome				---	---	---	---
TMEM64	169200	broad.mit.edu	37	8	91643842	91643842	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:91643842G>A	uc003yen.2	-	2	889	c.889C>T	c.(889-891)CGG>TGG	p.R297W	TMEM64_uc003yeo.2_Missense_Mutation_p.R36W|TMEM64_uc011lgf.1_Intron	NM_001008495	NP_001008495	Q6YI46	TMM64_HUMAN	transmembrane protein 64 isoform 1	297						integral to membrane					0			BRCA - Breast invasive adenocarcinoma(11;0.0598)															---	---	---	---
RBM12B	389677	broad.mit.edu	37	8	94747677	94747677	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94747677T>C	uc003yfz.2	-	3	1155	c.962A>G	c.(961-963)GAA>GGA	p.E321G		NM_203390	NP_976324	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B	321	RRM 2.						nucleotide binding|RNA binding				0	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)															---	---	---	---
CDH17	1015	broad.mit.edu	37	8	95140548	95140548	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95140548A>G	uc003ygh.2	-	18	2544	c.2419T>C	c.(2419-2421)TTT>CTT	p.F807L	CDH17_uc011lgo.1_Missense_Mutation_p.F555L|CDH17_uc011lgp.1_Missense_Mutation_p.F807L	NM_004063	NP_004054	Q12864	CAD17_HUMAN	cadherin 17 precursor	807	Helical; (Potential).					integral to membrane	calcium ion binding			ovary(5)|skin(1)	6	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)															---	---	---	---
KIAA1429	25962	broad.mit.edu	37	8	95523749	95523749	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95523749C>T	uc003ygo.1	-	13	3067	c.3054G>A	c.(3052-3054)ACG>ACA	p.T1018T	KIAA1429_uc003ygp.2_Silent_p.T1018T|KIAA1429_uc010maz.1_RNA	NM_015496	NP_056311	Q69YN4	VIR_HUMAN	hypothetical protein LOC25962 isoform 1	1018					mRNA processing|RNA splicing	nucleus				ovary(1)|skin(1)	2	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)															---	---	---	---
KIAA1429	25962	broad.mit.edu	37	8	95524232	95524232	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95524232G>A	uc003ygo.1	-	12	2850	c.2837C>T	c.(2836-2838)CCT>CTT	p.P946L	KIAA1429_uc003ygp.2_Missense_Mutation_p.P946L|KIAA1429_uc010maz.1_RNA	NM_015496	NP_056311	Q69YN4	VIR_HUMAN	hypothetical protein LOC25962 isoform 1	946	Poly-Pro.				mRNA processing|RNA splicing	nucleus				ovary(1)|skin(1)	2	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)															---	---	---	---
INTS8	55656	broad.mit.edu	37	8	95837241	95837241	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:95837241T>G	uc003yhb.2	+	2	377	c.251T>G	c.(250-252)CTT>CGT	p.L84R	INTS8_uc003yha.1_Missense_Mutation_p.L84R|INTS8_uc011lgq.1_RNA|INTS8_uc011lgr.1_RNA	NM_017864	NP_060334	Q75QN2	INT8_HUMAN	integrator complex subunit 8	84					snRNA processing	integrator complex	protein binding				0	Breast(36;1.05e-06)																	---	---	---	---
C8orf38	137682	broad.mit.edu	37	8	96053830	96053830	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96053830G>A	uc003yhj.2	+	4	469	c.453G>A	c.(451-453)TGG>TGA	p.W151*	C8orf38_uc003yhe.1_RNA|C8orf38_uc003yhf.2_Nonsense_Mutation_p.W59*|C8orf38_uc011lgs.1_RNA|C8orf38_uc003yhi.2_Nonsense_Mutation_p.W99*|C8orf38_uc003yhk.2_RNA|C8orf38_uc003yhl.2_Nonsense_Mutation_p.W59*	NM_152416	NP_689629	Q330K2	CH038_HUMAN	hypothetical protein LOC137682 precursor	151					biosynthetic process	mitochondrion	transferase activity				0	Breast(36;3.32e-06)																	---	---	---	---
PLEKHF2	79666	broad.mit.edu	37	8	96166569	96166569	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:96166569A>G	uc003yhn.1	+	2	544	c.297A>G	c.(295-297)GGA>GGG	p.G99G		NM_024613	NP_078889	Q9H8W4	PKHF2_HUMAN	phafin 2	99	PH.					transport vesicle	metal ion binding|protein binding			ovary(2)	2	Breast(36;3.18e-05)																	---	---	---	---
MTERFD1	51001	broad.mit.edu	37	8	97251806	97251806	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97251806T>G	uc003yhs.1	-	8	1245	c.1167A>C	c.(1165-1167)AAA>AAC	p.K389N	MTERFD1_uc003yhr.1_Missense_Mutation_p.K268N|MTERFD1_uc010mbd.1_3'UTR	NM_015942	NP_057026	Q96E29	MTER1_HUMAN	MTERF domain containing 1 precursor	389					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrion	transcription regulatory region DNA binding			ovary(1)	1	Breast(36;5.16e-05)																	---	---	---	---
PGCP	10404	broad.mit.edu	37	8	97797319	97797319	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:97797319A>G	uc003yhw.2	+	2	360	c.194A>G	c.(193-195)GAG>GGG	p.E65G	PGCP_uc010mbe.2_Missense_Mutation_p.E65G	NM_016134	NP_057218	Q9Y646	PGCP_HUMAN	plasma glutamate carboxypeptidase precursor	65					peptide metabolic process|proteolysis	cytoplasm|extracellular space	metal ion binding|metallocarboxypeptidase activity			upper_aerodigestive_tract(1)	1	Breast(36;1.86e-05)																	---	---	---	---
STK3	6788	broad.mit.edu	37	8	99560286	99560286	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:99560286A>G	uc003yip.2	-	9	1193	c.1052T>C	c.(1051-1053)ATT>ACT	p.I351T	STK3_uc003yio.2_Missense_Mutation_p.I379T|STK3_uc010mbm.1_Missense_Mutation_p.I240T	NM_006281	NP_006272	Q13188	STK3_HUMAN	serine/threonine kinase 3	351					apoptosis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of apoptosis	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein dimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity			lung(3)|ovary(1)	4	Breast(36;2.4e-06)	Breast(495;0.106)	OV - Ovarian serous cystadenocarcinoma(57;0.0382)	KIRC - Kidney renal clear cell carcinoma(542;9.44e-06)														---	---	---	---
VPS13B	157680	broad.mit.edu	37	8	100883848	100883848	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:100883848G>A	uc003yiv.2	+	61	11854	c.11743G>A	c.(11743-11745)GAC>AAC	p.D3915N	VPS13B_uc003yiw.2_Missense_Mutation_p.D3890N	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5	3915					protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)															---	---	---	---
UBR5	51366	broad.mit.edu	37	8	103283377	103283377	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103283377C>T	uc003ykr.1	-	49	7103	c.7070G>A	c.(7069-7071)CGG>CAG	p.R2357Q	UBR5_uc003yks.1_Missense_Mutation_p.R2357Q	NM_015902	NP_056986	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin	2357	Arg/Asp-rich (mixed charge).				cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			lung(16)|ovary(4)|large_intestine(3)|breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	28	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)															---	---	---	---
UBR5	51366	broad.mit.edu	37	8	103323604	103323604	+	Missense_Mutation	SNP	C	A	A	rs145670915		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103323604C>A	uc003ykr.1	-	20	2572	c.2539G>T	c.(2539-2541)GGT>TGT	p.G847C	UBR5_uc003yks.1_Missense_Mutation_p.G847C	NM_015902	NP_056986	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin	847					cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			lung(16)|ovary(4)|large_intestine(3)|breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	28	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)															---	---	---	---
KLF10	7071	broad.mit.edu	37	8	103663553	103663553	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103663553G>A	uc011lhk.1	-	3	1161	c.1007C>T	c.(1006-1008)CCG>CTG	p.P336L	KLF10_uc011lhj.1_Missense_Mutation_p.P325L	NM_005655	NP_005646	Q13118	KLF10_HUMAN	Kruppel-like factor 10 isoform a	336					cell proliferation|cell-cell signaling|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|skeletal system development|transforming growth factor beta receptor signaling pathway	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_epithelial(15;5.63e-07)|Lung NSC(17;8.18e-05)|all_lung(17;0.000169)		OV - Ovarian serous cystadenocarcinoma(57;0.000112)|STAD - Stomach adenocarcinoma(118;0.0826)															---	---	---	---
RIMS2	9699	broad.mit.edu	37	8	105263871	105263871	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105263871T>C	uc003yls.2	+	28	4168	c.3927T>C	c.(3925-3927)TCT>TCC	p.S1309S	RIMS2_uc003ylp.2_Silent_p.S1291S|RIMS2_uc003ylq.2_Silent_p.S1105S|RIMS2_uc003ylr.2_Silent_p.S1130S	NM_014677	NP_055492	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	1353	C2 2.				intracellular protein transport	cell junction|presynaptic membrane	metal ion binding|Rab GTPase binding			ovary(6)|lung(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	15			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)												HNSCC(12;0.0054)			---	---	---	---
ABRA	137735	broad.mit.edu	37	8	107782160	107782160	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:107782160C>T	uc003ymm.3	-	1	313	c.259G>A	c.(259-261)GAA>AAA	p.E87K		NM_139166	NP_631905	Q8N0Z2	ABRA_HUMAN	actin-binding Rho activating protein	87					positive regulation of Rho protein signal transduction|positive regulation of sequence-specific DNA binding transcription factor activity|transcription, DNA-dependent|transmembrane transport	actin cytoskeleton|plasma membrane|sarcomere	actin binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(57;3.83e-09)															---	---	---	---
ANGPT1	284	broad.mit.edu	37	8	108315575	108315575	+	Silent	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108315575T>G	uc003ymn.2	-	5	1297	c.829A>C	c.(829-831)AGA>CGA	p.R277R	ANGPT1_uc011lhv.1_Silent_p.R77R|ANGPT1_uc003ymo.2_Silent_p.R276R|ANGPT1_uc003ymp.3_Silent_p.R76R	NM_001146	NP_001137	Q15389	ANGP1_HUMAN	angiopoietin 1 precursor	277	Fibrinogen C-terminal.				activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|blood coagulation|cell differentiation|heparin biosynthetic process|leukocyte migration|negative regulation of cell adhesion|negative regulation of endothelial cell apoptosis|negative regulation of vascular permeability|positive chemotaxis|positive regulation of blood vessel endothelial cell migration|positive regulation of ERK1 and ERK2 cascade|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of protein ubiquitination|positive regulation of receptor internalization|protein localization at cell surface|regulation of satellite cell proliferation|sprouting angiogenesis|Tie receptor signaling pathway	extracellular space|membrane raft|microvillus|plasma membrane	receptor tyrosine kinase binding			ovary(3)|skin(3)|upper_aerodigestive_tract(1)	7	Breast(1;5.06e-08)		OV - Ovarian serous cystadenocarcinoma(57;5.53e-09)															---	---	---	---
ANGPT1	284	broad.mit.edu	37	8	108359167	108359167	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:108359167T>C	uc003ymn.2	-						ANGPT1_uc003ymo.2_Intron	NM_001146	NP_001137			angiopoietin 1 precursor						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|blood coagulation|cell differentiation|heparin biosynthetic process|leukocyte migration|negative regulation of cell adhesion|negative regulation of endothelial cell apoptosis|negative regulation of vascular permeability|positive chemotaxis|positive regulation of blood vessel endothelial cell migration|positive regulation of ERK1 and ERK2 cascade|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of protein ubiquitination|positive regulation of receptor internalization|protein localization at cell surface|regulation of satellite cell proliferation|sprouting angiogenesis|Tie receptor signaling pathway	extracellular space|membrane raft|microvillus|plasma membrane	receptor tyrosine kinase binding			ovary(3)|skin(3)|upper_aerodigestive_tract(1)	7	Breast(1;5.06e-08)		OV - Ovarian serous cystadenocarcinoma(57;5.53e-09)															---	---	---	---
TRHR	7201	broad.mit.edu	37	8	110100514	110100514	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110100514T>C	uc003ymz.3	+	1	789	c.773T>C	c.(772-774)GTA>GCA	p.V258A		NM_003301	NP_003292	P34981	TRFR_HUMAN	thyrotropin-releasing hormone receptor	258	Cytoplasmic (Potential).					integral to plasma membrane	thyrotropin-releasing hormone receptor activity			skin(2)|lung(1)	3			OV - Ovarian serous cystadenocarcinoma(57;2.3e-11)															---	---	---	---
PKHD1L1	93035	broad.mit.edu	37	8	110439335	110439335	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110439335G>A	uc003yne.2	+	25	3054	c.2950G>A	c.(2950-2952)GCG>ACG	p.A984T		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor	984	Extracellular (Potential).				immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)												HNSCC(38;0.096)			---	---	---	---
SYBU	55638	broad.mit.edu	37	8	110587413	110587413	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110587413G>A	uc003ynj.3	-	7	1877	c.1714C>T	c.(1714-1716)CGC>TGC	p.R572C	SYBU_uc003yni.3_Missense_Mutation_p.R569C|SYBU_uc003ynk.3_Missense_Mutation_p.R453C|SYBU_uc010mco.2_Missense_Mutation_p.R571C|SYBU_uc003ynl.3_Missense_Mutation_p.R571C|SYBU_uc010mcp.2_Missense_Mutation_p.R572C|SYBU_uc010mcq.2_Missense_Mutation_p.R572C|SYBU_uc003yno.3_Missense_Mutation_p.R453C|SYBU_uc010mcr.2_Missense_Mutation_p.R572C|SYBU_uc003ynm.3_Missense_Mutation_p.R571C|SYBU_uc003ynn.3_Missense_Mutation_p.R571C|SYBU_uc010mcs.2_Missense_Mutation_p.R453C|SYBU_uc010mct.2_Missense_Mutation_p.R572C|SYBU_uc010mcu.2_Missense_Mutation_p.R571C|SYBU_uc003ynp.3_Missense_Mutation_p.R504C|SYBU_uc010mcv.2_Missense_Mutation_p.R572C|SYBU_uc003ynh.3_Missense_Mutation_p.R366C|SYBU_uc011lhw.1_Missense_Mutation_p.R442C	NM_001099754	NP_001093224	Q9NX95	SYBU_HUMAN	Golgi-localized syntaphilin-related protein	572						cytoplasmic membrane-bounded vesicle|cytoskeleton|Golgi membrane|integral to membrane				ovary(1)	1																		---	---	---	---
SYBU	55638	broad.mit.edu	37	8	110590244	110590244	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110590244C>T	uc003ynj.3	-	6	900	c.737G>A	c.(736-738)CGT>CAT	p.R246H	SYBU_uc003yni.3_Missense_Mutation_p.R243H|SYBU_uc003ynk.3_Missense_Mutation_p.R127H|SYBU_uc010mco.2_Missense_Mutation_p.R245H|SYBU_uc003ynl.3_Missense_Mutation_p.R245H|SYBU_uc010mcp.2_Missense_Mutation_p.R246H|SYBU_uc010mcq.2_Missense_Mutation_p.R246H|SYBU_uc003yno.3_Missense_Mutation_p.R127H|SYBU_uc010mcr.2_Missense_Mutation_p.R246H|SYBU_uc003ynm.3_Missense_Mutation_p.R245H|SYBU_uc003ynn.3_Missense_Mutation_p.R245H|SYBU_uc010mcs.2_Missense_Mutation_p.R127H|SYBU_uc010mct.2_Missense_Mutation_p.R246H|SYBU_uc010mcu.2_Missense_Mutation_p.R245H|SYBU_uc003ynp.3_Missense_Mutation_p.R178H|SYBU_uc010mcv.2_Missense_Mutation_p.R246H|SYBU_uc003ynh.3_Missense_Mutation_p.R40H|SYBU_uc011lhw.1_Missense_Mutation_p.R116H	NM_001099754	NP_001093224	Q9NX95	SYBU_HUMAN	Golgi-localized syntaphilin-related protein	246	Sufficient for interaction with KIF5B.					cytoplasmic membrane-bounded vesicle|cytoskeleton|Golgi membrane|integral to membrane				ovary(1)	1																		---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113585846	113585846	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113585846G>A	uc003ynu.2	-	24	4085	c.3926C>T	c.(3925-3927)GCT>GTT	p.A1309V	CSMD3_uc003yns.2_Missense_Mutation_p.A581V|CSMD3_uc003ynt.2_Missense_Mutation_p.A1269V|CSMD3_uc011lhx.1_Missense_Mutation_p.A1205V	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	1309	Extracellular (Potential).|CUB 7.					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113668485	113668485	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113668485T>C	uc003ynu.2	-	18	3061	c.2902A>G	c.(2902-2904)ACC>GCC	p.T968A	CSMD3_uc003yns.2_Missense_Mutation_p.T240A|CSMD3_uc003ynt.2_Missense_Mutation_p.T928A|CSMD3_uc011lhx.1_Missense_Mutation_p.T864A	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	968	Extracellular (Potential).|CUB 5.					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
CSMD3	114788	broad.mit.edu	37	8	113812404	113812404	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:113812404C>A	uc003ynu.2	-	13	2118	c.1959G>T	c.(1957-1959)AAG>AAT	p.K653N	CSMD3_uc003ynt.2_Missense_Mutation_p.K613N|CSMD3_uc011lhx.1_Missense_Mutation_p.K549N	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	653	Extracellular (Potential).|CUB 3.					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63															HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			---	---	---	---
EXT1	2131	broad.mit.edu	37	8	119122851	119122851	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:119122851G>T	uc003yok.1	-	1	1208	c.435C>A	c.(433-435)ACC>ACA	p.T145T		NM_000127	NP_000118	Q16394	EXT1_HUMAN	exostosin 1	145	Lumenal (Potential).				glycosaminoglycan biosynthetic process|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|ossification|signal transduction|skeletal system development	Golgi membrane|integral to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|heparan sulfate N-acetylglucosaminyltransferase activity|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity			ovary(2)|lung(2)	4	all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.012)					Mis|N|F|S			exostoses|osteosarcoma			Hereditary_Multiple_Exostoses|Langer-Giedion_syndrome				---	---	---	---
HAS2	3037	broad.mit.edu	37	8	122626567	122626567	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:122626567C>A	uc003yph.2	-	4	1979	c.1441G>T	c.(1441-1443)GTA>TTA	p.V481L		NM_005328	NP_005319	Q92819	HAS2_HUMAN	hyaluronan synthase 2	481	Helical; Name=6; (Potential).					integral to plasma membrane	hyaluronan synthase activity		HAS2/PLAG1(10)	soft_tissue(10)|ovary(5)	15	Lung NSC(37;3.12e-08)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)|all_neural(195;0.142)		STAD - Stomach adenocarcinoma(47;0.00503)															---	---	---	---
ZHX2	22882	broad.mit.edu	37	8	123964375	123964375	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:123964375G>A	uc003ypk.1	+	3	1192	c.625G>A	c.(625-627)GAG>AAG	p.E209K		NM_014943	NP_055758	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	209	Required for homodimerization.					cytoplasm|nucleus|plasma membrane	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)															---	---	---	---
C8orf76	84933	broad.mit.edu	37	8	124243877	124243877	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124243877G>A	uc003yqc.1	-	4	509	c.478C>T	c.(478-480)CAT>TAT	p.H160Y	C8orf76_uc003yqd.2_Missense_Mutation_p.H128Y	NM_032847	NP_116236	Q96K31	CH076_HUMAN	hypothetical protein LOC84933	160							binding			ovary(2)	2	Lung NSC(37;1.25e-09)|Ovarian(258;0.0154)		STAD - Stomach adenocarcinoma(47;0.00527)															---	---	---	---
ZHX1	11244	broad.mit.edu	37	8	124266609	124266609	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124266609C>T	uc003yqe.2	-	3	2008	c.1578G>A	c.(1576-1578)CAG>CAA	p.Q526Q	C8orf76_uc003yqd.2_Intron|ZHX1_uc003yqf.2_Silent_p.Q526Q|ZHX1_uc003yqg.2_Intron|ZHX1_uc010mdi.2_Silent_p.Q526Q	NM_007222	NP_009153	Q9UKY1	ZHX1_HUMAN	zinc fingers and homeoboxes 1	526	Homeobox 2.|Required for interaction with NFYA.				negative regulation of transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	Lung NSC(37;1.25e-09)|Ovarian(258;0.0154)		STAD - Stomach adenocarcinoma(47;0.00527)															---	---	---	---
ATAD2	29028	broad.mit.edu	37	8	124371905	124371905	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:124371905C>T	uc003yqh.3	-	10	1286	c.1178G>A	c.(1177-1179)CGG>CAG	p.R393Q	ATAD2_uc011lii.1_Missense_Mutation_p.R184Q|ATAD2_uc003yqi.3_RNA|ATAD2_uc003yqj.2_Missense_Mutation_p.R393Q	NM_014109	NP_054828	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	393					regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrion|nucleus	ATP binding|ATPase activity			ovary(2)	2	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)															---	---	---	---
GSDMC	56169	broad.mit.edu	37	8	130777941	130777941	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130777941G>A	uc003ysr.2	-	4	1385	c.503C>T	c.(502-504)ACT>ATT	p.T168I		NM_031415	NP_113603	Q9BYG8	GSDMC_HUMAN	melanoma-derived leucine zipper, extra-nuclear	168						mitochondrion				ovary(2)|skin(1)	3																		---	---	---	---
FAM49B	51571	broad.mit.edu	37	8	130863164	130863164	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:130863164T>C	uc003yss.2	-						FAM49B_uc003yst.2_Intron|FAM49B_uc003ysu.2_Intron|FAM49B_uc003ysv.2_Intron|FAM49B_uc003ysw.2_Intron|FAM49B_uc003ysx.2_Intron|FAM49B_uc003ysy.1_Intron	NM_016623	NP_057707			hypothetical protein LOC51571												0	Ovarian(5;0.000567)|Esophageal squamous(12;0.00693)|Acute lymphoblastic leukemia(118;0.155)		LUAD - Lung adenocarcinoma(14;0.0989)															---	---	---	---
ADCY8	114	broad.mit.edu	37	8	132002758	132002758	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132002758T>C	uc003ytd.3	-	2	1247	c.991A>G	c.(991-993)ATG>GTG	p.M331V	ADCY8_uc010mds.2_Missense_Mutation_p.M331V	NM_001115	NP_001106	P40145	ADCY8_HUMAN	adenylate cyclase 8	331	Helical; (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|membrane fraction|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|metal ion binding			skin(4)|large_intestine(1)|central_nervous_system(1)	6	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)												HNSCC(32;0.087)			---	---	---	---
EFR3A	23167	broad.mit.edu	37	8	132998485	132998485	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:132998485G>A	uc003yte.2	+	17	2115	c.1914G>A	c.(1912-1914)GAG>GAA	p.E638E		NM_015137	NP_055952	Q14156	EFR3A_HUMAN	EFR3 homolog A	638						plasma membrane	binding			ovary(3)|breast(1)|central_nervous_system(1)	5	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)|LUAD - Lung adenocarcinoma(14;0.102)															---	---	---	---
PHF20L1	51105	broad.mit.edu	37	8	133806768	133806768	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133806768C>T	uc003ytt.2	+	3	521	c.196C>T	c.(196-198)CGA>TGA	p.R66*	PHF20L1_uc003ytr.2_Nonsense_Mutation_p.R66*|PHF20L1_uc010mdv.2_Nonsense_Mutation_p.R66*|PHF20L1_uc003yts.2_Nonsense_Mutation_p.R66*|PHF20L1_uc011lja.1_Nonsense_Mutation_p.R66*|PHF20L1_uc003ytu.1_RNA|PHF20L1_uc003ytq.2_Nonsense_Mutation_p.R66*	NM_016018	NP_057102	A8MW92	P20L1_HUMAN	PHD finger protein 20-like 1 isoform 1	66	Tudor 1.						nucleic acid binding|zinc ion binding			ovary(2)	2	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)															---	---	---	---
PHF20L1	51105	broad.mit.edu	37	8	133844614	133844614	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133844614G>A	uc003ytt.2	+	15	2204	c.1879G>A	c.(1879-1881)GCA>ACA	p.A627T	PHF20L1_uc011lja.1_Missense_Mutation_p.A601T	NM_016018	NP_057102	A8MW92	P20L1_HUMAN	PHD finger protein 20-like 1 isoform 1	627							nucleic acid binding|zinc ion binding			ovary(2)	2	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)															---	---	---	---
PHF20L1	51105	broad.mit.edu	37	8	133848922	133848922	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133848922C>T	uc003ytt.2	+	16	2372	c.2047C>T	c.(2047-2049)CGA>TGA	p.R683*	PHF20L1_uc011lja.1_Nonsense_Mutation_p.R657*	NM_016018	NP_057102	A8MW92	P20L1_HUMAN	PHD finger protein 20-like 1 isoform 1	683	PHD-type.						nucleic acid binding|zinc ion binding			ovary(2)	2	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)															---	---	---	---
TG	7038	broad.mit.edu	37	8	133879259	133879259	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133879259T>C	uc003ytw.2	+	1	55	c.14T>C	c.(13-15)CTG>CCG	p.L5P		NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor	5					hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)														---	---	---	---
TG	7038	broad.mit.edu	37	8	133885382	133885382	+	Missense_Mutation	SNP	C	T	T	rs142432006		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133885382C>T	uc003ytw.2	+	5	595	c.554C>T	c.(553-555)GCG>GTG	p.A185V		NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor	185	Thyroglobulin type-1 3.				hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)														---	---	---	---
TG	7038	broad.mit.edu	37	8	133984942	133984942	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:133984942A>G	uc003ytw.2	+	34	6196	c.6155A>G	c.(6154-6156)GAC>GGC	p.D2052G	TG_uc010mdw.2_Missense_Mutation_p.D811G|TG_uc011ljb.1_Missense_Mutation_p.D421G|TG_uc011ljc.1_Missense_Mutation_p.D206G	NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor	2052	Type IIIB.				hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)														---	---	---	---
ZFAT	57623	broad.mit.edu	37	8	135621016	135621016	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:135621016G>A	uc003yup.2	-	5	916	c.741C>T	c.(739-741)TAC>TAT	p.Y247Y	ZFAT_uc003yun.2_Silent_p.Y235Y|ZFAT_uc003yuo.2_Silent_p.Y235Y|ZFAT_uc010meh.2_Silent_p.Y235Y|ZFAT_uc010mei.2_RNA|ZFAT_uc003yuq.2_Silent_p.Y235Y|ZFAT_uc010mej.2_Silent_p.Y185Y|ZFAT_uc003yur.2_Silent_p.Y235Y	NM_020863	NP_065914	Q9P243	ZFAT_HUMAN	zinc finger protein 406 isoform ZFAT-1	247					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)															---	---	---	---
FAM135B	51059	broad.mit.edu	37	8	139163847	139163847	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139163847G>A	uc003yuy.2	-	13	3042	c.2871C>T	c.(2869-2871)AGC>AGT	p.S957S	FAM135B_uc003yux.2_Silent_p.S858S|FAM135B_uc003yuz.2_RNA|FAM135B_uc003yva.2_Silent_p.S519S|FAM135B_uc003yvb.2_Silent_p.S519S	NM_015912	NP_056996	Q49AJ0	F135B_HUMAN	hypothetical protein LOC51059	957										ovary(7)|skin(2)	9	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)												HNSCC(54;0.14)			---	---	---	---
FAM135B	51059	broad.mit.edu	37	8	139164785	139164785	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:139164785T>G	uc003yuy.2	-	13	2104	c.1933A>C	c.(1933-1935)AGT>CGT	p.S645R	FAM135B_uc003yux.2_Missense_Mutation_p.S546R|FAM135B_uc003yuz.2_RNA|FAM135B_uc003yva.2_Missense_Mutation_p.S207R|FAM135B_uc003yvb.2_Missense_Mutation_p.S207R	NM_015912	NP_056996	Q49AJ0	F135B_HUMAN	hypothetical protein LOC51059	645										ovary(7)|skin(2)	9	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)												HNSCC(54;0.14)			---	---	---	---
TRAPPC9	83696	broad.mit.edu	37	8	140744403	140744403	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:140744403G>A	uc003yvj.2	-	22	3232	c.3098C>T	c.(3097-3099)GCG>GTG	p.A1033V	TRAPPC9_uc003yvh.2_Missense_Mutation_p.A1131V	NM_001160372	NP_001153844	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9 isoform	1033					cell differentiation	endoplasmic reticulum|Golgi apparatus				skin(2)	2																		---	---	---	---
MIR151	442893	broad.mit.edu	37	8	141742675	141742675	+	RNA	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141742675A>G	hsa-mir-151|MI0000809	-			c.78A>G			PTK2_uc003yvo.2_Intron|PTK2_uc011ljq.1_Intron|PTK2_uc003yvp.2_Intron|PTK2_uc003yvq.2_Intron|PTK2_uc003yvr.2_Intron|PTK2_uc003yvs.2_Intron|PTK2_uc003yvt.2_Intron|PTK2_uc003yvu.2_Intron|PTK2_uc003yvv.2_Intron|PTK2_uc011ljr.1_Intron																	0																		---	---	---	---
PTK2	5747	broad.mit.edu	37	8	141813630	141813630	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141813630A>G	uc003yvu.2	-						PTK2_uc011ljq.1_5'Flank|PTK2_uc003yvp.2_5'Flank|PTK2_uc003yvq.2_Intron|PTK2_uc003yvr.2_Intron|PTK2_uc003yvs.2_Intron|PTK2_uc003yvt.2_Intron|PTK2_uc003yvv.2_Intron|PTK2_uc011ljr.1_Intron	NM_153831	NP_722560			PTK2 protein tyrosine kinase 2 isoform a						axon guidance|blood coagulation|cellular component disassembly involved in apoptosis|ephrin receptor signaling pathway|growth hormone receptor signaling pathway|integrin-mediated signaling pathway|peptidyl-tyrosine phosphorylation|protein autophosphorylation|regulation of cell adhesion mediated by integrin|signal complex assembly	cytoskeleton|cytosol|focal adhesion	ATP binding|JUN kinase binding|non-membrane spanning protein tyrosine kinase activity|SH2 domain binding|signal transducer activity			ovary(2)|lung(2)|central_nervous_system(1)|skin(1)	6	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)															---	---	---	---
FLJ43860	389690	broad.mit.edu	37	8	142481257	142481257	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142481257A>G	uc003ywi.2	-	16	1985	c.1904T>C	c.(1903-1905)GTG>GCG	p.V635A	FLJ43860_uc011ljs.1_RNA|FLJ43860_uc010meu.1_RNA	NM_207414	NP_997297	Q6ZUA9	Q6ZUA9_HUMAN	hypothetical protein LOC389690	635							binding				0	all_cancers(97;7.79e-15)|all_epithelial(106;4.52e-13)|Lung NSC(106;2.07e-05)|all_lung(105;2.89e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)															---	---	---	---
TSNARE1	203062	broad.mit.edu	37	8	143412262	143412262	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143412262A>G	uc003ywk.2	-	6	1011	c.893T>C	c.(892-894)CTG>CCG	p.L298P	TSNARE1_uc011lju.1_Missense_Mutation_p.L298P|TSNARE1_uc003ywj.2_Missense_Mutation_p.L298P|TSNARE1_uc003ywl.3_Missense_Mutation_p.L79P	NM_145003	NP_659440	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1	298					vesicle-mediated transport	integral to membrane					0	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)																	---	---	---	---
BAI1	575	broad.mit.edu	37	8	143623645	143623645	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143623645G>A	uc003ywm.2	+	27	4233	c.4050G>A	c.(4048-4050)ACG>ACA	p.T1350T		NM_001702	NP_001693	O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1	1350	Cytoplasmic (Potential).				axonogenesis|cell adhesion|negative regulation of angiogenesis|negative regulation of cell proliferation|neuropeptide signaling pathway|peripheral nervous system development	cell-cell junction|integral to plasma membrane	G-protein coupled receptor activity|protein binding			lung(3)|ovary(2)|breast(1)|central_nervous_system(1)|pancreas(1)	8	all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)																	---	---	---	---
ARC	23237	broad.mit.edu	37	8	143694621	143694621	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143694621G>A	uc003ywn.1	-	1	1213	c.1012C>T	c.(1012-1014)CGC>TGC	p.R338C		NM_015193	NP_056008	Q7LC44	ARC_HUMAN	activity-regulated cytoskeleton-associated	338					endocytosis	acrosomal vesicle|cell junction|dendritic spine|endosome|postsynaptic density|postsynaptic membrane		p.R338C(1)		breast(1)	1	all_cancers(97;3.55e-12)|all_epithelial(106;1.03e-08)|Lung NSC(106;0.000353)|all_lung(105;0.00092)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;0.0279)																---	---	---	---
JRK	8629	broad.mit.edu	37	8	143747395	143747395	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:143747395A>G	uc003ywo.2	-	2	597	c.83T>C	c.(82-84)ATC>ACC	p.I28T	JRK_uc003ywp.2_Missense_Mutation_p.I28T|JRK_uc010mew.1_Missense_Mutation_p.I28T	NM_001077527	NP_001070995			jerky isoform b												0	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;2.31e-05)																---	---	---	---
GPIHBP1	338328	broad.mit.edu	37	8	144297333	144297333	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144297333C>T	uc003yxu.1	+	4	570	c.495C>T	c.(493-495)GGC>GGT	p.G165G		NM_178172	NP_835466	Q8IV16	HDBP1_HUMAN	glycosylphosphatidylinositol anchored high	165	Helical; (Potential).				cholesterol homeostasis|intracellular protein transport|positive regulation of chylomicron remnant clearance|positive regulation of lipoprotein lipase activity|protein import|protein localization at cell surface|protein stabilization|response to heparin|triglyceride homeostasis	anchored to external side of plasma membrane|apical plasma membrane|basolateral plasma membrane|high-density lipoprotein particle|integral to membrane|intracellular	apolipoprotein binding|chylomicron binding|lipase binding|lipid binding|protein transmembrane transporter activity				0	all_cancers(97;6.49e-11)|all_epithelial(106;2.77e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)																	---	---	---	---
RHPN1	114822	broad.mit.edu	37	8	144463817	144463817	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144463817G>T	uc003yyb.2	+	13	1697	c.1564G>T	c.(1564-1566)GGC>TGC	p.G522C		NM_052924	NP_443156	Q8TCX5	RHPN1_HUMAN	rhophilin 1	547	PDZ.				signal transduction	intracellular				large_intestine(1)	1	all_cancers(97;7.39e-11)|all_epithelial(106;5.44e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.156)															---	---	---	---
C8orf73	642475	broad.mit.edu	37	8	144652164	144652164	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144652164G>T	uc010mff.2	-	7	1159	c.1115C>A	c.(1114-1116)GCG>GAG	p.A372E	C8orf73_uc010mfg.1_Silent_p.R384R	NM_001100878	NP_001094348	A6NGR9	CH073_HUMAN	hypothetical protein LOC642475	372	Leu-rich.						binding			ovary(1)	1	all_cancers(97;6.49e-11)|all_epithelial(106;4.73e-09)|Lung NSC(106;0.000202)|all_lung(105;0.000548)|Ovarian(258;0.014)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.146)															---	---	---	---
FAM83H	286077	broad.mit.edu	37	8	144811218	144811218	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144811218C>T	uc003yzk.2	-	4	725	c.656G>A	c.(655-657)CGC>CAC	p.R219H	FAM83H_uc010mfk.1_5'Flank	NM_198488	NP_940890	Q6ZRV2	FA83H_HUMAN	FAM83H	219					biomineral tissue development					lung(1)|central_nervous_system(1)|pancreas(1)	3	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)															---	---	---	---
SCRIB	23513	broad.mit.edu	37	8	144892938	144892938	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144892938G>A	uc003yzp.1	-	12	1329	c.1322C>T	c.(1321-1323)CCG>CTG	p.P441L	SCRIB_uc003yzo.1_Missense_Mutation_p.P441L	NM_015356	NP_056171	Q14160	SCRIB_HUMAN	scribble isoform b	441	Sufficient for targeting to adherens junction and to inhibit cell proliferation.				activation of Rac GTPase activity|apoptosis involved in morphogenesis|cell migration|cell proliferation|cell-cell adhesion|establishment of apical/basal cell polarity|interspecies interaction between organisms|mammary gland duct morphogenesis|negative regulation of mitotic cell cycle|positive chemotaxis|positive regulation of apoptosis|positive regulation of receptor recycling|protein localization to adherens junction	cell-cell adherens junction|Scrib-APC-beta-catenin complex	protein binding			urinary_tract(1)|ovary(1)|kidney(1)|central_nervous_system(1)|pancreas(1)	5	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)															---	---	---	---
SCRIB	23513	broad.mit.edu	37	8	144893367	144893367	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144893367G>A	uc003yzp.1	-	10	1062	c.1055C>T	c.(1054-1056)CCA>CTA	p.P352L	SCRIB_uc003yzo.1_Missense_Mutation_p.P352L	NM_015356	NP_056171	Q14160	SCRIB_HUMAN	scribble isoform b	352	LRR 14.|Sufficient for targeting to adherens junction and to inhibit cell proliferation.				activation of Rac GTPase activity|apoptosis involved in morphogenesis|cell migration|cell proliferation|cell-cell adhesion|establishment of apical/basal cell polarity|interspecies interaction between organisms|mammary gland duct morphogenesis|negative regulation of mitotic cell cycle|positive chemotaxis|positive regulation of apoptosis|positive regulation of receptor recycling|protein localization to adherens junction	cell-cell adherens junction|Scrib-APC-beta-catenin complex	protein binding			urinary_tract(1)|ovary(1)|kidney(1)|central_nervous_system(1)|pancreas(1)	5	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)															---	---	---	---
EPPK1	83481	broad.mit.edu	37	8	144940278	144940278	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144940278C>T	uc003zaa.1	-	2	15167	c.15154G>A	c.(15154-15156)GAC>AAC	p.D5052N		NM_031308	NP_112598	P58107	EPIPL_HUMAN	epiplakin 1	5052	Plectin 65.					cytoplasm|cytoskeleton	protein binding|structural molecule activity			pancreas(1)|skin(1)	2	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)															---	---	---	---
EPPK1	83481	broad.mit.edu	37	8	144940665	144940665	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144940665C>T	uc003zaa.1	-	2	14780	c.14767G>A	c.(14767-14769)GTG>ATG	p.V4923M		NM_031308	NP_112598	P58107	EPIPL_HUMAN	epiplakin 1	4923	Plectin 61.					cytoplasm|cytoskeleton	protein binding|structural molecule activity			pancreas(1)|skin(1)	2	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)															---	---	---	---
PLEC	5339	broad.mit.edu	37	8	144990990	144990990	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144990990G>A	uc003zaf.1	-	32	13580	c.13410C>T	c.(13408-13410)ACC>ACT	p.T4470T	PLEC_uc003zab.1_Silent_p.T4333T|PLEC_uc003zac.1_Silent_p.T4337T|PLEC_uc003zad.2_Silent_p.T4333T|PLEC_uc003zae.1_Silent_p.T4301T|PLEC_uc003zag.1_Silent_p.T4311T|PLEC_uc003zah.2_Silent_p.T4319T|PLEC_uc003zaj.2_Silent_p.T4360T	NM_201380	NP_958782	Q15149	PLEC_HUMAN	plectin isoform 1	4470	Globular 2.|Plectin 30.				cellular component disassembly involved in apoptosis|hemidesmosome assembly	cytosol|focal adhesion|hemidesmosome|intermediate filament cytoskeleton|sarcolemma	actin binding|structural constituent of muscle|structural constituent of muscle			large_intestine(2)|ovary(2)|pancreas(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	9																		---	---	---	---
PLEC	5339	broad.mit.edu	37	8	144993581	144993581	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:144993581C>T	uc003zaf.1	-	32	10989	c.10819G>A	c.(10819-10821)GCC>ACC	p.A3607T	PLEC_uc003zab.1_Missense_Mutation_p.A3470T|PLEC_uc003zac.1_Missense_Mutation_p.A3474T|PLEC_uc003zad.2_Missense_Mutation_p.A3470T|PLEC_uc003zae.1_Missense_Mutation_p.A3438T|PLEC_uc003zag.1_Missense_Mutation_p.A3448T|PLEC_uc003zah.2_Missense_Mutation_p.A3456T|PLEC_uc003zaj.2_Missense_Mutation_p.A3497T	NM_201380	NP_958782	Q15149	PLEC_HUMAN	plectin isoform 1	3607	Globular 2.|Plectin 15.				cellular component disassembly involved in apoptosis|hemidesmosome assembly	cytosol|focal adhesion|hemidesmosome|intermediate filament cytoskeleton|sarcolemma	actin binding|structural constituent of muscle|structural constituent of muscle			large_intestine(2)|ovary(2)|pancreas(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	9																		---	---	---	---
MAF1	84232	broad.mit.edu	37	8	145160580	145160580	+	5'UTR	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145160580C>T	uc003zbc.1	+	2					SHARPIN_uc003zba.2_5'Flank|SHARPIN_uc003zbb.2_5'Flank|KIAA1875_uc003zbd.3_5'Flank	NM_032272	NP_115648			MAF1 protein						negative regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent	cytoplasm|nucleus					0	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.1e-42)|Epithelial(56;1.23e-40)|all cancers(56;4.84e-36)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)															---	---	---	---
HEATR7A	727957	broad.mit.edu	37	8	145234438	145234438	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145234438C>T	uc003zbk.3	+	5	486	c.249C>T	c.(247-249)GAC>GAT	p.D83D	HEATR7A_uc003zbg.2_Silent_p.D83D|HEATR7A_uc003zbh.3_Silent_p.D83D|HEATR7A_uc003zbi.3_Silent_p.D83D|HEATR7A_uc011lla.1_Silent_p.D83D|HEATR7A_uc010mft.2_Silent_p.D83D	NM_032450	NP_115826	Q8NDA8	HTR7A_HUMAN	HEAT repeat containing 7A isoform 1	83							binding				0																		---	---	---	---
GPR172A	79581	broad.mit.edu	37	8	145584072	145584072	+	Missense_Mutation	SNP	G	A	A	rs143091206		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145584072G>A	uc003zcc.1	+	3	1077	c.920G>A	c.(919-921)CGT>CAT	p.R307H	FBXL6_uc003zbz.2_5'Flank|FBXL6_uc003zca.2_5'Flank|FBXL6_uc003zcb.2_5'Flank|FBXL6_uc010mfx.2_5'Flank|GPR172A_uc003zcd.1_Missense_Mutation_p.R307H|GPR172A_uc003zce.1_Missense_Mutation_p.R307H|GPR172A_uc010mfy.1_Missense_Mutation_p.R307H|GPR172A_uc003zcf.1_Missense_Mutation_p.R307H|GPR172A_uc011llc.1_Missense_Mutation_p.R219H	NM_024531	NP_078807	Q9HAB3	RFT3_HUMAN	G protein-coupled receptor 172A precursor	307						integral to plasma membrane	receptor activity|riboflavin transporter activity				0	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;4.43e-40)|Epithelial(56;1.48e-39)|all cancers(56;1.49e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0441)|Colorectal(110;0.055)															---	---	---	---
SLC39A4	55630	broad.mit.edu	37	8	145638020	145638020	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145638020G>A	uc003zcq.2	-	12	1946	c.1846C>T	c.(1846-1848)CGG>TGG	p.R616W	SLC39A4_uc003zcm.1_3'UTR|SLC39A4_uc003zcn.2_Missense_Mutation_p.R118W|SLC39A4_uc003zco.2_Missense_Mutation_p.R340W|SLC39A4_uc003zcp.2_Missense_Mutation_p.R591W	NM_130849	NP_570901	Q6P5W5	S39A4_HUMAN	solute carrier family 39 (zinc transporter),	616	Cytoplasmic (Potential).					cytoplasmic membrane-bounded vesicle|integral to membrane|recycling endosome membrane	zinc ion transmembrane transporter activity				0	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;1.12e-40)|all cancers(56;8.17e-36)|BRCA - Breast invasive adenocarcinoma(115;0.0407)|Colorectal(110;0.055)															---	---	---	---
CYHR1	50626	broad.mit.edu	37	8	145689713	145689713	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145689713T>C	uc003zcv.2	-						CYHR1_uc003zcw.2_Missense_Mutation_p.T126A|CYHR1_uc003zcx.2_Missense_Mutation_p.T126A|CYHR1_uc003zcy.2_Missense_Mutation_p.T126A|KIFC2_uc003zcz.2_5'Flank	NM_138496	NP_612505			cysteine/histidine-rich 1 isoform 1							perinuclear region of cytoplasm	zinc ion binding				0	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)													OREG0019056	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
PPP1R16A	84988	broad.mit.edu	37	8	145724416	145724416	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145724416C>A	uc003zdd.2	+	4	1361	c.448C>A	c.(448-450)CTG>ATG	p.L150M	uc003zde.1_5'Flank|PPP1R16A_uc003zdf.2_Missense_Mutation_p.L150M	NM_032902	NP_116291	Q96I34	PP16A_HUMAN	protein phosphatase 1, regulatory (inhibitor)	150	ANK 3.					plasma membrane	protein binding				0	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)															---	---	---	---
LRRC14	9684	broad.mit.edu	37	8	145745956	145745956	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145745956C>A	uc003zdk.1	+	3	810	c.664C>A	c.(664-666)CTG>ATG	p.L222M	RECQL4_uc003zdj.2_5'Flank|LRRC14_uc003zdl.1_Missense_Mutation_p.L222M|LRRC14_uc003zdo.2_5'Flank	NM_014665	NP_055480	Q15048	LRC14_HUMAN	leucine rich repeat containing 14	222											0	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)															---	---	---	---
ARHGAP39	80728	broad.mit.edu	37	8	145755898	145755898	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145755898G>A	uc003zdt.1	-	12	3715	c.3160C>T	c.(3160-3162)CGC>TGC	p.R1054C	LRRC24_uc003zdn.2_5'Flank|MGC70857_uc003zdp.1_5'Flank|MGC70857_uc003zdq.1_5'Flank|MGC70857_uc003zdr.1_5'Flank|ARHGAP39_uc011llk.1_Missense_Mutation_p.R1054C|ARHGAP39_uc003zds.1_Missense_Mutation_p.R1085C	NM_025251	NP_079527	Q9C0H5	RHG39_HUMAN	KIAA1688 protein	1054	Rho-GAP.				axon guidance|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytoskeleton|cytosol|nucleus	GTPase activator activity				0																		---	---	---	---
ZNF34	80778	broad.mit.edu	37	8	145999543	145999543	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145999543G>A	uc003zdy.3	-	6	893	c.791C>T	c.(790-792)GCC>GTC	p.A264V	ZNF34_uc010mgb.2_Missense_Mutation_p.A161V|ZNF34_uc003zdx.3_Missense_Mutation_p.A243V	NM_030580	NP_085057	Q8IZ26	ZNF34_HUMAN	zinc finger protein 34	264	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(97;3.54e-11)|all_epithelial(106;2.65e-10)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;0.221)	OV - Ovarian serous cystadenocarcinoma(54;2.75e-39)|Epithelial(56;5.18e-38)|all cancers(56;4.41e-33)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.11)	GBM - Glioblastoma multiforme(99;0.0179)														---	---	---	---
FOXD4	2298	broad.mit.edu	37	9	118009	118009	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:118009G>A	uc003zfz.2	-	1	409	c.111C>T	c.(109-111)GAC>GAT	p.D37D		NM_207305	NP_997188	Q12950	FOXD4_HUMAN	forkhead box D4	37					axon extension involved in axon guidance|cartilage development|dichotomous subdivision of terminal units involved in ureteric bud branching|embryo development|enteric nervous system development|iridophore differentiation|lateral line nerve glial cell development|melanocyte differentiation|neural crest cell migration|pattern specification process|peripheral nervous system development|positive regulation of BMP signaling pathway|positive regulation of kidney development|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|sympathetic nervous system development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			skin(1)	1	all_lung(41;0.218)	all_cancers(5;0.0395)|Acute lymphoblastic leukemia(5;1.91e-07)|all_hematologic(5;1.95e-06)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)														---	---	---	---
CBWD1	55871	broad.mit.edu	37	9	156502	156502	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:156502C>T	uc003zga.3	-	7	660	c.554G>A	c.(553-555)GGC>GAC	p.G185D	CBWD1_uc010mgs.2_RNA|CBWD1_uc003zgb.3_Missense_Mutation_p.G149D|CBWD1_uc003zgc.3_Missense_Mutation_p.G185D|CBWD1_uc011llr.1_Missense_Mutation_p.G149D	NM_018491	NP_060961	Q9BRT8	CBWD1_HUMAN	COBW domain containing 1 isoform 1	185							ATP binding|protein binding			ovary(1)	1	all_lung(41;0.218)	all_cancers(5;3.04e-16)|all_epithelial(5;4.68e-12)|all_lung(10;1.94e-10)|Lung NSC(10;3.61e-10)|Acute lymphoblastic leukemia(5;0.00439)|Breast(48;0.0148)|all_hematologic(5;0.024)|Prostate(43;0.122)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)														---	---	---	---
C9orf66	157983	broad.mit.edu	37	9	214547	214547	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:214547T>G	uc003zge.3	-	1	1347	c.850A>C	c.(850-852)AAA>CAA	p.K284Q	DOCK8_uc011lls.1_5'Flank|DOCK8_uc003zgf.2_5'Flank	NM_152569	NP_689782	Q5T8R8	CI066_HUMAN	hypothetical protein LOC157983	284										central_nervous_system(1)	1	all_lung(41;0.218)	all_cancers(5;2.09e-12)|all_epithelial(5;6.16e-09)|all_lung(10;1.15e-08)|Lung NSC(10;1.91e-08)|Acute lymphoblastic leukemia(5;0.00457)|all_hematologic(5;0.0332)|Breast(48;0.0646)|Prostate(43;0.137)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)														---	---	---	---
DOCK8	81704	broad.mit.edu	37	9	325746	325746	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:325746G>A	uc003zgf.2	+						DOCK8_uc011lls.1_Intron|DOCK8_uc010mgu.2_Intron|DOCK8_uc010mgv.2_Intron|DOCK8_uc003zgg.2_Intron|DOCK8_uc003zgh.2_Intron	NM_203447	NP_982272			dedicator of cytokinesis 8						blood coagulation	cytosol	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)	6		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)														---	---	---	---
DOCK8	81704	broad.mit.edu	37	9	386336	386336	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:386336C>T	uc003zgf.2	+	23	2896	c.2784C>T	c.(2782-2784)GCC>GCT	p.A928A	DOCK8_uc010mgu.2_Silent_p.A230A|DOCK8_uc010mgv.2_Intron|DOCK8_uc010mgw.1_Silent_p.A230A|DOCK8_uc003zgk.2_Silent_p.A386A	NM_203447	NP_982272	Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	928					blood coagulation	cytosol	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)	6		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)												OREG0019067	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
KANK1	23189	broad.mit.edu	37	9	732483	732483	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:732483G>T	uc003zgl.1	+	10	3760	c.3111G>T	c.(3109-3111)GAG>GAT	p.E1037D	KANK1_uc003zgm.2_3'UTR|KANK1_uc003zgn.1_Missense_Mutation_p.E1037D|KANK1_uc003zgs.1_Missense_Mutation_p.E879D|KANK1_uc010mgx.1_Translation_Start_Site|KANK1_uc010mgy.1_Translation_Start_Site|KANK1_uc003zgt.1_5'Flank	NM_015158	NP_055973	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1 isoform a	1037					negative regulation of actin filament polymerization	cytoplasm				ovary(2)|central_nervous_system(1)|pancreas(1)	4		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)														---	---	---	---
SMARCA2	6595	broad.mit.edu	37	9	2056699	2056699	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2056699C>T	uc003zhc.2	+	7	1300	c.1201C>T	c.(1201-1203)CGC>TGC	p.R401C	SMARCA2_uc003zhd.2_Missense_Mutation_p.R401C|SMARCA2_uc010mha.2_Missense_Mutation_p.R392C	NM_003070	NP_003061	P51531	SMCA2_HUMAN	SWI/SNF-related matrix-associated	401					chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development	intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex	ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding			ovary(2)|central_nervous_system(1)	3		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)														---	---	---	---
SMARCA2	6595	broad.mit.edu	37	9	2086914	2086914	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2086914A>G	uc003zhc.2	+	18	2711	c.2612A>G	c.(2611-2613)TAT>TGT	p.Y871C	SMARCA2_uc003zhd.2_Missense_Mutation_p.Y871C|SMARCA2_uc010mha.2_Intron	NM_003070	NP_003061	P51531	SMCA2_HUMAN	SWI/SNF-related matrix-associated	871	Helicase ATP-binding.				chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development	intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex	ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding			ovary(2)|central_nervous_system(1)	3		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)														---	---	---	---
SMARCA2	6595	broad.mit.edu	37	9	2086920	2086920	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2086920C>T	uc003zhc.2	+	18	2717	c.2618C>T	c.(2617-2619)GCC>GTC	p.A873V	SMARCA2_uc003zhd.2_Missense_Mutation_p.A873V|SMARCA2_uc010mha.2_Intron	NM_003070	NP_003061	P51531	SMCA2_HUMAN	SWI/SNF-related matrix-associated	873	Helicase ATP-binding.				chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development	intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex	ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding			ovary(2)|central_nervous_system(1)	3		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)														---	---	---	---
SMARCA2	6595	broad.mit.edu	37	9	2186119	2186119	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2186119A>G	uc003zhc.2	+	32	4584	c.4485A>G	c.(4483-4485)TTA>TTG	p.L1495L	SMARCA2_uc003zhd.2_Silent_p.L1477L|SMARCA2_uc010mha.2_Silent_p.L1410L|SMARCA2_uc011llw.1_Silent_p.L181L|SMARCA2_uc003zhf.2_Silent_p.L159L|SMARCA2_uc011llx.1_Silent_p.L141L|SMARCA2_uc003zhe.2_Silent_p.L183L|SMARCA2_uc003zhg.2_Silent_p.L141L|SMARCA2_uc010mhb.2_Silent_p.L165L	NM_003070	NP_003061	P51531	SMCA2_HUMAN	SWI/SNF-related matrix-associated	1495					chromatin remodeling|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|nervous system development	intermediate filament cytoskeleton|nBAF complex|npBAF complex|nuclear chromatin|nucleoplasm|SWI/SNF complex|WINAC complex	ATP binding|DNA-dependent ATPase activity|helicase activity|protein binding|RNA polymerase II transcription coactivator activity|transcription regulatory region DNA binding			ovary(2)|central_nervous_system(1)	3		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)														---	---	---	---
VLDLR	7436	broad.mit.edu	37	9	2643838	2643838	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:2643838C>T	uc003zhk.1	+	7	1342	c.945C>T	c.(943-945)GTC>GTT	p.V315V	VLDLR_uc003zhl.1_Silent_p.V315V|VLDLR_uc003zhm.1_RNA|VLDLR_uc003zhn.1_Silent_p.V274V	NM_003383	NP_003374	P98155	VLDLR_HUMAN	very low density lipoprotein receptor isoform a	315	Extracellular (Potential).				cholesterol metabolic process|endocytosis|lipid transport|memory|very-low-density lipoprotein particle clearance	coated pit|integral to membrane|membrane fraction|plasma membrane|very-low-density lipoprotein particle	apolipoprotein binding|calcium ion binding|low-density lipoprotein receptor activity|very-low-density lipoprotein particle receptor activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3				GBM - Glioblastoma multiforme(50;0.0668)|Lung(218;0.123)														---	---	---	---
PTPRD	5789	broad.mit.edu	37	9	8341267	8341267	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8341267C>T	uc003zkk.2	-	40	5660	c.4949G>A	c.(4948-4950)CGT>CAT	p.R1650H	PTPRD_uc003zkp.2_Missense_Mutation_p.R1244H|PTPRD_uc003zkq.2_Missense_Mutation_p.R1243H|PTPRD_uc003zkr.2_Missense_Mutation_p.R1234H|PTPRD_uc003zks.2_Missense_Mutation_p.R1243H|PTPRD_uc003zkl.2_Missense_Mutation_p.R1641H|PTPRD_uc003zkm.2_Missense_Mutation_p.R1637H|PTPRD_uc003zkn.2_Missense_Mutation_p.R1239H|PTPRD_uc003zko.2_Missense_Mutation_p.R1240H	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1650	Cytoplasmic (Potential).|Tyrosine-protein phosphatase 2.				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)											TSP Lung(15;0.13)			---	---	---	---
PTPRD	5789	broad.mit.edu	37	9	8507344	8507344	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:8507344G>A	uc003zkk.2	-	21	2345	c.1634C>T	c.(1633-1635)GCC>GTC	p.A545V	PTPRD_uc003zkp.2_Missense_Mutation_p.A545V|PTPRD_uc003zkq.2_Missense_Mutation_p.A545V|PTPRD_uc003zkr.2_Missense_Mutation_p.A539V|PTPRD_uc003zks.2_Missense_Mutation_p.A535V|PTPRD_uc003zkl.2_Missense_Mutation_p.A545V|PTPRD_uc003zkm.2_Missense_Mutation_p.A532V|PTPRD_uc003zkn.2_Missense_Mutation_p.A545V|PTPRD_uc003zko.2_Missense_Mutation_p.A542V	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	545	Fibronectin type-III 3.|Extracellular (Potential).				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)											TSP Lung(15;0.13)			---	---	---	---
CER1	9350	broad.mit.edu	37	9	14720314	14720314	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14720314A>T	uc003zlj.2	-	2	623	c.578T>A	c.(577-579)GTT>GAT	p.V193D		NM_005454	NP_005445	O95813	CER1_HUMAN	cerberus 1 precursor	193	CTCK.				BMP signaling pathway	extracellular space	cytokine activity				0				GBM - Glioblastoma multiforme(50;3.16e-06)														---	---	---	---
FREM1	158326	broad.mit.edu	37	9	14769746	14769746	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14769746G>A	uc003zlm.2	-	27	5770	c.5180C>T	c.(5179-5181)ACA>ATA	p.T1727I	FREM1_uc010mic.2_Intron|FREM1_uc003zlk.2_RNA|FREM1_uc003zll.2_Missense_Mutation_p.T263I	NM_144966	NP_659403	Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1 precursor	1727	CSPG 12.				cell communication|multicellular organismal development	basement membrane|integral to membrane	metal ion binding|sugar binding			ovary(2)|breast(2)|pancreas(1)	5				GBM - Glioblastoma multiforme(50;3.53e-06)														---	---	---	---
FREM1	158326	broad.mit.edu	37	9	14797519	14797519	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14797519A>T	uc003zlm.2	-	21	4406	c.3816T>A	c.(3814-3816)AAT>AAA	p.N1272K	FREM1_uc010mic.2_RNA	NM_144966	NP_659403	Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1 precursor	1272	CSPG 9.				cell communication|multicellular organismal development	basement membrane|integral to membrane	metal ion binding|sugar binding			ovary(2)|breast(2)|pancreas(1)	5				GBM - Glioblastoma multiforme(50;3.53e-06)														---	---	---	---
FREM1	158326	broad.mit.edu	37	9	14842388	14842388	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14842388T>A	uc003zlm.2	-	9	2254	c.1664A>T	c.(1663-1665)GAC>GTC	p.D555V	FREM1_uc010mic.2_RNA	NM_144966	NP_659403	Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1 precursor	555	CSPG 3.				cell communication|multicellular organismal development	basement membrane|integral to membrane	metal ion binding|sugar binding			ovary(2)|breast(2)|pancreas(1)	5				GBM - Glioblastoma multiforme(50;3.53e-06)														---	---	---	---
FREM1	158326	broad.mit.edu	37	9	14868974	14868974	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:14868974A>C	uc003zlm.2	-	2	592	c.2T>G	c.(1-3)ATG>AGG	p.M1R	FREM1_uc010mic.2_RNA	NM_144966	NP_659403	Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1 precursor	1					cell communication|multicellular organismal development	basement membrane|integral to membrane	metal ion binding|sugar binding			ovary(2)|breast(2)|pancreas(1)	5				GBM - Glioblastoma multiforme(50;3.53e-06)														---	---	---	---
CNTLN	54875	broad.mit.edu	37	9	17394830	17394830	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17394830A>C	uc003zmz.2	+	15	2404	c.2378A>C	c.(2377-2379)AAC>ACC	p.N793T	CNTLN_uc003zmy.2_Missense_Mutation_p.N793T|CNTLN_uc010mio.2_Missense_Mutation_p.N472T	NM_017738	NP_060208	Q9NXG0	CNTLN_HUMAN	centlein isoform 1	793	Potential.					centriole|membrane	two-component sensor activity			pancreas(1)	1				GBM - Glioblastoma multiforme(50;6.14e-10)														---	---	---	---
SH3GL2	6456	broad.mit.edu	37	9	17795530	17795530	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:17795530T>C	uc003zna.2	+						SH3GL2_uc011lmy.1_Intron	NM_003026	NP_003017			SH3-domain GRB2-like 2						axon guidance|central nervous system development|endocytosis|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|post-Golgi vesicle-mediated transport	cytosol|Golgi membrane|plasma membrane	identical protein binding|lipid binding			skin(1)	1				GBM - Glioblastoma multiforme(50;2.71e-10)|Lung(42;0.203)														---	---	---	---
ADAMTSL1	92949	broad.mit.edu	37	9	18721662	18721662	+	Silent	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18721662A>C	uc003zne.3	+	15	2132	c.2005A>C	c.(2005-2007)AGG>CGG	p.R669R		NM_001040272	NP_001035362	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1 isoform 4 precursor	669	TSP type-1 6.					proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)	5				GBM - Glioblastoma multiforme(50;1.29e-17)														---	---	---	---
ADAMTSL1	92949	broad.mit.edu	37	9	18777598	18777598	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18777598A>G	uc003zne.3	+	19	3498	c.3371A>G	c.(3370-3372)GAG>GGG	p.E1124G		NM_001040272	NP_001035362	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1 isoform 4 precursor	1124						proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)	5				GBM - Glioblastoma multiforme(50;1.29e-17)														---	---	---	---
ADAMTSL1	92949	broad.mit.edu	37	9	18887843	18887843	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:18887843G>T	uc003zne.3	+	24	4391	c.4264G>T	c.(4264-4266)GGT>TGT	p.G1422C	ADAMTSL1_uc003znf.3_Missense_Mutation_p.G123C	NM_001040272	NP_001035362	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1 isoform 4 precursor	1422	Ig-like C2-type 4.					proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)	5				GBM - Glioblastoma multiforme(50;1.29e-17)														---	---	---	---
ACER2	340485	broad.mit.edu	37	9	19424835	19424835	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:19424835G>T	uc003zny.1	+	3	519	c.361G>T	c.(361-363)GAC>TAC	p.D121Y	ACER2_uc003znx.1_RNA|ACER2_uc003znz.1_Missense_Mutation_p.D72Y	NM_001010887	NP_001010887	Q5QJU3	ACER2_HUMAN	alkaline ceramidase 2	121	Cytoplasmic (Potential).				ceramide metabolic process|negative regulation of cell adhesion mediated by integrin|negative regulation of cell-matrix adhesion|negative regulation of protein glycosylation in Golgi|positive regulation of cell proliferation|response to retinoic acid|sphingosine biosynthetic process	integral to Golgi membrane	ceramidase activity			haematopoietic_and_lymphoid_tissue(1)|skin(1)	2																		---	---	---	---
IFNA10	3446	broad.mit.edu	37	9	21206573	21206573	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21206573A>G	uc003zoq.1	-	1	570	c.524T>C	c.(523-525)CTC>CCC	p.L175P	IFNA14_uc003zoo.1_Intron	NM_002171	NP_002162	P01566	IFN10_HUMAN	interferon, alpha 10 precursor	175					blood coagulation|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	extracellular space	cytokine activity|cytokine receptor binding				0				Lung(24;1.26e-23)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.17)														---	---	---	---
IFNA6	3443	broad.mit.edu	37	9	21350835	21350835	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:21350835A>G	uc011lni.1	-	1	52	c.52T>C	c.(52-54)TCA>CCA	p.S18P		NM_021002	NP_066282	P05013	IFNA6_HUMAN	interferon, alpha 6 precursor	18					blood coagulation|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	extracellular space	cytokine activity|cytokine receptor binding				0				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.116)														---	---	---	---
IFT74	80173	broad.mit.edu	37	9	26962050	26962050	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26962050C>T	uc010mja.2	+	2	212	c.85C>T	c.(85-87)CGA>TGA	p.R29*	IFT74_uc010mjb.2_Nonsense_Mutation_p.R29*|IFT74_uc003zqf.3_Nonsense_Mutation_p.R29*|IFT74_uc003zqg.3_Nonsense_Mutation_p.R29*	NM_001099223	NP_001092693	Q96LB3	IFT74_HUMAN	coiled-coil domain containing 2 isoform a	29						cytoplasmic membrane-bounded vesicle|intraflagellar transport particle B|microtubule-based flagellum				skin(1)	1		all_neural(11;2.36e-10)		Lung(218;1.4e-05)|LUSC - Lung squamous cell carcinoma(38;0.000114)														---	---	---	---
IFT74	80173	broad.mit.edu	37	9	26984545	26984545	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26984545A>G	uc010mja.2	+	6	580	c.453A>G	c.(451-453)GCA>GCG	p.A151A	IFT74_uc010mjb.2_Silent_p.A151A|IFT74_uc003zqf.3_Silent_p.A151A|IFT74_uc003zqg.3_Silent_p.A151A	NM_001099223	NP_001092693	Q96LB3	IFT74_HUMAN	coiled-coil domain containing 2 isoform a	151	Potential.					cytoplasmic membrane-bounded vesicle|intraflagellar transport particle B|microtubule-based flagellum				skin(1)	1		all_neural(11;2.36e-10)		Lung(218;1.4e-05)|LUSC - Lung squamous cell carcinoma(38;0.000114)														---	---	---	---
TOPORS	10210	broad.mit.edu	37	9	32541518	32541518	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:32541518C>T	uc003zrb.2	-	3	3172	c.3005G>A	c.(3004-3006)AGC>AAC	p.S1002N	TOPORS_uc003zrc.2_Missense_Mutation_p.S935N	NM_005802	NP_005793	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich	1002					DNA damage response, signal transduction resulting in induction of apoptosis|maintenance of protein location in nucleus|proteasomal ubiquitin-dependent protein catabolic process|protein sumoylation|transcription, DNA-dependent	nuclear speck|PML body	antigen binding|DNA binding|DNA topoisomerase I binding|SUMO ligase activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)														---	---	---	---
UBE2R2	54926	broad.mit.edu	37	9	33917237	33917237	+	3'UTR	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33917237G>A	uc003ztm.2	+	5						NM_017811	NP_060281			ubiquitin-conjugating enzyme UBC3B						protein K48-linked ubiquitination|protein monoubiquitination		ATP binding|ubiquitin-protein ligase activity				0			LUSC - Lung squamous cell carcinoma(29;0.0176)	GBM - Glioblastoma multiforme(74;0.188)														---	---	---	---
UBAP2	55833	broad.mit.edu	37	9	33923409	33923409	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33923409G>A	uc003ztq.1	-	25	2977	c.2864C>T	c.(2863-2865)GCC>GTC	p.A955V	UBAP2_uc011loc.1_Missense_Mutation_p.A864V|UBAP2_uc011lod.1_Missense_Mutation_p.A688V|UBAP2_uc011loe.1_Missense_Mutation_p.A710V|UBAP2_uc011lof.1_Missense_Mutation_p.A880V|UBAP2_uc003ztn.1_Missense_Mutation_p.A194V|UBAP2_uc003zto.1_Missense_Mutation_p.A194V|UBAP2_uc003ztp.1_Missense_Mutation_p.A194V	NM_018449	NP_060919	Q5T6F2	UBAP2_HUMAN	ubiquitin associated protein 2	955										ovary(3)	3			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)														---	---	---	---
KIF24	347240	broad.mit.edu	37	9	34256135	34256135	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34256135C>G	uc003zua.3	-	11	3590	c.3470G>C	c.(3469-3471)AGA>ACA	p.R1157T	KIF24_uc010mkb.2_Intron	NM_194313	NP_919289	Q5T7B8	KIF24_HUMAN	kinesin family member 24	1157					microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			central_nervous_system(1)	1			LUSC - Lung squamous cell carcinoma(29;0.0107)															---	---	---	---
DNAI1	27019	broad.mit.edu	37	9	34489382	34489382	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34489382G>T	uc003zum.2	+	5	516	c.323G>T	c.(322-324)GGG>GTG	p.G108V		NM_012144	NP_036276	Q9UI46	DNAI1_HUMAN	dynein, axonemal, intermediate chain 1	108					cell projection organization	cilium axoneme|cytoplasm|dynein complex|microtubule	motor activity				0	all_epithelial(49;0.244)		LUSC - Lung squamous cell carcinoma(29;0.0107)|STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.0222)										Kartagener_syndrome				---	---	---	---
ARID3C	138715	broad.mit.edu	37	9	34622490	34622490	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34622490G>T	uc011lon.1	-	5	902	c.902C>A	c.(901-903)CCT>CAT	p.P301H	DCTN3_uc003zuw.1_5'Flank|DCTN3_uc003zux.1_5'Flank	NM_001017363	NP_001017363	A6NKF2	ARI3C_HUMAN	AT rich interactive domain 3C (BRIGHT- like)	301	Pro-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.175)														---	---	---	---
VCP	7415	broad.mit.edu	37	9	35068236	35068236	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35068236G>A	uc003zvy.2	-						VCP_uc003zvz.2_Intron|VCP_uc010mkh.1_Intron|VCP_uc010mki.1_Intron	NM_007126	NP_009057			valosin-containing protein						activation of caspase activity|double-strand break repair|endoplasmic reticulum unfolded protein response|ER-associated protein catabolic process|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination|retrograde protein transport, ER to cytosol	cytosol|endoplasmic reticulum|microsome|nucleus|proteasome complex	ATP binding|ATPase activity|lipid binding|polyubiquitin binding|protein domain specific binding|protein phosphatase binding			upper_aerodigestive_tract(1)	1			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)															---	---	---	---
FANCG	2189	broad.mit.edu	37	9	35075014	35075014	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35075014C>T	uc003zwb.1	-	12	2038	c.1546G>A	c.(1546-1548)GCC>ACC	p.A516T	VCP_uc003zvy.2_5'Flank|VCP_uc003zvz.2_5'Flank|VCP_uc010mkh.1_5'Flank|FANCG_uc003zwa.1_Missense_Mutation_p.A258T|FANCG_uc010mkj.1_Missense_Mutation_p.A258T	NM_004629	NP_004620	O15287	FANCG_HUMAN	Fanconi anemia, complementation group G	516	TPR 4.				cell cycle checkpoint|DNA repair|mitochondrion organization	mitochondrion|nucleoplasm	damaged DNA binding|protein binding			ovary(2)|large_intestine(1)|lung(1)	4			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)					Mis|N|F|S			AML|leukemia		Direct_reversal_of_damage|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
FANCG	2189	broad.mit.edu	37	9	35078217	35078217	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35078217C>T	uc003zwb.1	-	4	923	c.431G>A	c.(430-432)GGC>GAC	p.G144D	FANCG_uc003zwa.1_5'Flank|FANCG_uc010mkj.1_Intron|FANCG_uc011lot.1_Missense_Mutation_p.G144D	NM_004629	NP_004620	O15287	FANCG_HUMAN	Fanconi anemia, complementation group G	144					cell cycle checkpoint|DNA repair|mitochondrion organization	mitochondrion|nucleoplasm	damaged DNA binding|protein binding			ovary(2)|large_intestine(1)|lung(1)	4			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)					Mis|N|F|S			AML|leukemia		Direct_reversal_of_damage|Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
UNC13B	10497	broad.mit.edu	37	9	35378347	35378347	+	Silent	SNP	C	T	T	rs144394180		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35378347C>T	uc003zwq.2	+	16	2164	c.1872C>T	c.(1870-1872)TAC>TAT	p.Y624Y	UNC13B_uc003zwr.2_Silent_p.Y624Y	NM_006377	NP_006368	O14795	UN13B_HUMAN	UNC13 (C. elegans)-like	624	C2 2.				excretion|induction of apoptosis|intracellular signal transduction	cell junction|Golgi apparatus|synapse	metal ion binding|receptor activity			ovary(3)|large_intestine(1)|skin(1)	5	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)															---	---	---	---
RUSC2	9853	broad.mit.edu	37	9	35548113	35548113	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35548113C>T	uc003zww.2	+	2	1850	c.1595C>T	c.(1594-1596)GCC>GTC	p.A532V	RUSC2_uc010mkq.2_RNA|RUSC2_uc003zwx.3_Missense_Mutation_p.A532V	NM_014806	NP_055621	Q8N2Y8	RUSC2_HUMAN	RUN and SH3 domain containing 2	532						cytosol				ovary(1)	1			Lung(28;0.000837)|LUSC - Lung squamous cell carcinoma(32;0.00109)|STAD - Stomach adenocarcinoma(86;0.194)															---	---	---	---
TESK1	7016	broad.mit.edu	37	9	35608200	35608200	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35608200A>G	uc003zxa.2	+	8	1175	c.839A>G	c.(838-840)GAT>GGT	p.D280G	TESK1_uc003zwz.1_RNA|TESK1_uc010mks.2_Missense_Mutation_p.D120G	NM_006285	NP_006276	Q15569	TESK1_HUMAN	testis-specific protein kinase 1	280	Protein kinase.				cell junction assembly|spermatogenesis	cytosol	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			stomach(2)|breast(2)|lung(1)|ovary(1)|skin(1)	7			Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)															---	---	---	---
C9orf100	84904	broad.mit.edu	37	9	35664395	35664395	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35664395A>G	uc003zxm.1	-	3	440	c.328T>C	c.(328-330)TCA>CCA	p.S110P	C9orf100_uc003zxl.2_RNA|C9orf100_uc011loz.1_Missense_Mutation_p.S110P	NM_032818	NP_116207	Q8N4T4	CI100_HUMAN	hypothetical protein LOC84904	110	DH.				regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity				0	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)															---	---	---	---
TLN1	7094	broad.mit.edu	37	9	35725276	35725276	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35725276T>C	uc003zxt.2	-	3	527	c.173A>G	c.(172-174)AAG>AGG	p.K58R	TLN1_uc003zxu.3_Missense_Mutation_p.K58R	NM_006289	NP_006280	Q9Y490	TLN1_HUMAN	talin 1	58					axon guidance|cell adhesion|cell-cell junction assembly|cellular component movement|cytoskeletal anchoring at plasma membrane|muscle contraction|platelet activation|platelet degranulation	actin cytoskeleton|centrosome|cytosol|extracellular region|focal adhesion|intracellular membrane-bounded organelle|ruffle membrane	actin binding|insulin receptor binding|LIM domain binding|structural constituent of cytoskeleton|vinculin binding			lung(7)|breast(3)|ovary(2)|central_nervous_system(1)	13	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)															---	---	---	---
CREB3	10488	broad.mit.edu	37	9	35736450	35736450	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35736450C>A	uc003zxv.2	+	9	1296	c.843C>A	c.(841-843)GCC>GCA	p.A281A	CREB3_uc010mla.2_Silent_p.A200A	NM_006368	NP_006359	O43889	CREB3_HUMAN	cAMP responsive element binding protein 3	305	Lumenal (Potential).				chemotaxis|induction of positive chemotaxis|interspecies interaction between organisms|negative regulation of cell cycle|positive regulation of calcium ion transport|positive regulation of cell migration|positive regulation of transcription, DNA-dependent|reactivation of latent virus|regulation of cell proliferation	cytosol|endoplasmic reticulum|endoplasmic reticulum membrane|Golgi apparatus|integral to membrane|integral to membrane|nucleus|nucleus	cAMP response element binding protein binding|CCR1 chemokine receptor binding|DNA binding|protein dimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity				0	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)	GBM - Glioblastoma multiforme(74;0.0285)												OREG0019176	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
GBA2	57704	broad.mit.edu	37	9	35740342	35740342	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35740342G>A	uc003zxw.2	-	7	1671	c.1147C>T	c.(1147-1149)CAG>TAG	p.Q383*	GBA2_uc003zxx.1_5'Flank|GBA2_uc011lpb.1_Nonsense_Mutation_p.Q383*|GBA2_uc011lpc.1_Nonsense_Mutation_p.Q383*|GBA2_uc011lpd.1_Nonsense_Mutation_p.Q389*|GBA2_uc003zxy.1_Nonsense_Mutation_p.Q96*	NM_020944	NP_065995	Q9HCG7	GBA2_HUMAN	bile acid beta-glucosidase	383	Extracellular (Potential).				bile acid metabolic process|glucosylceramide catabolic process|O-glycoside catabolic process	integral to membrane|microsome|plasma membrane|smooth endoplasmic reticulum	beta-glucosidase activity|glucosylceramidase activity			ovary(3)|skin(1)	4	all_epithelial(49;0.167)		Lung(28;0.00416)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)															---	---	---	---
RGP1	9827	broad.mit.edu	37	9	35750839	35750839	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35750839T>C	uc011lpf.1	+	5	481	c.340T>C	c.(340-342)TCC>CCC	p.S114P	GBA2_uc011lpb.1_5'Flank|GBA2_uc003zxw.2_5'Flank|GBA2_uc011lpc.1_5'Flank|GBA2_uc011lpd.1_5'Flank|RGP1_uc011lpe.1_Missense_Mutation_p.S154P	NM_001080496	NP_001073965	Q92546	RGP1_HUMAN	RGP1 retrograde golgi transport homolog	114										ovary(1)	1	all_epithelial(49;0.167)		Lung(28;0.00416)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)															---	---	---	---
NPR2	4882	broad.mit.edu	37	9	35802240	35802240	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35802240G>A	uc003zyd.2	+	10	1670	c.1670G>A	c.(1669-1671)CGC>CAC	p.R557H	NPR2_uc010mlb.2_Missense_Mutation_p.R557H	NM_003995	NP_003986	P20594	ANPRB_HUMAN	natriuretic peptide receptor B precursor	557	Protein kinase.|Cytoplasmic (Potential).				intracellular signal transduction|ossification|receptor guanylyl cyclase signaling pathway|regulation of blood pressure	integral to membrane|plasma membrane	GTP binding|guanylate cyclase activity|natriuretic peptide receptor activity|protein kinase activity|transmembrane receptor activity			ovary(2)|stomach(1)	3	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)		Erythrityl Tetranitrate(DB01613)|Nesiritide(DB04899)													---	---	---	---
NPR2	4882	broad.mit.edu	37	9	35809192	35809192	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35809192T>C	uc003zyd.2	+	21	3026	c.3026T>C	c.(3025-3027)CTA>CCA	p.L1009P	NPR2_uc010mlb.2_Missense_Mutation_p.L985P|SPAG8_uc003zye.2_Intron	NM_003995	NP_003986	P20594	ANPRB_HUMAN	natriuretic peptide receptor B precursor	1009	Cytoplasmic (Potential).				intracellular signal transduction|ossification|receptor guanylyl cyclase signaling pathway|regulation of blood pressure	integral to membrane|plasma membrane	GTP binding|guanylate cyclase activity|natriuretic peptide receptor activity|protein kinase activity|transmembrane receptor activity			ovary(2)|stomach(1)	3	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)		Erythrityl Tetranitrate(DB01613)|Nesiritide(DB04899)													---	---	---	---
TMEM8B	51754	broad.mit.edu	37	9	35846850	35846850	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35846850C>T	uc003zym.2	+	11	1692	c.677C>T	c.(676-678)GCG>GTG	p.A226V	TMEM8B_uc003zyk.2_Missense_Mutation_p.A226V|TMEM8B_uc003zyl.2_Missense_Mutation_p.A393V|TMEM8B_uc003zyn.2_Silent_p.C121C|TMEM8B_uc003zyo.2_Missense_Mutation_p.A226V	NM_001042589	NP_001036054	A6NDV4	TMM8B_HUMAN	transmembrane protein 8B isoform a	226	Extracellular (Potential).				cell-matrix adhesion|regulation of growth|regulation of mitotic cell cycle	cell surface|endoplasmic reticulum|integral to membrane|mitochondrion|nucleus|plasma membrane	protein binding			ovary(1)	1																		---	---	---	---
OR13J1	392309	broad.mit.edu	37	9	35869498	35869498	+	Missense_Mutation	SNP	C	T	T	rs146834712	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35869498C>T	uc011lph.1	-	1	901	c.901G>A	c.(901-903)GCC>ACC	p.A301T		NM_001004487	NP_001004487	Q8NGT2	O13J1_HUMAN	olfactory receptor, family 13, subfamily J,	301	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1	all_epithelial(49;0.169)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00494)|STAD - Stomach adenocarcinoma(86;0.194)															---	---	---	---
ZCCHC7	84186	broad.mit.edu	37	9	37126594	37126594	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37126594T>C	uc003zzq.2	+	2	438	c.265T>C	c.(265-267)TCA>CCA	p.S89P	ZCCHC7_uc011lqh.1_Intron|ZCCHC7_uc011lqi.1_Missense_Mutation_p.S88P|ZCCHC7_uc010mlt.2_Missense_Mutation_p.S88P|ZCCHC7_uc003zzs.1_Missense_Mutation_p.S88P	NM_032226	NP_115602	Q8N3Z6	ZCHC7_HUMAN	zinc finger, CCHC domain containing 7	89							nucleic acid binding|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3				GBM - Glioblastoma multiforme(29;0.0137)														---	---	---	---
POLR1E	64425	broad.mit.edu	37	9	37487905	37487905	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37487905A>T	uc003zzz.1	+	2	700	c.412A>T	c.(412-414)ACT>TCT	p.T138S	POLR1E_uc011lqj.1_Missense_Mutation_p.T76S|POLR1E_uc003zzy.1_Missense_Mutation_p.T76S|POLR1E_uc011lqk.1_5'UTR	NM_022490	NP_071935	Q9GZS1	RPA49_HUMAN	RNA polymerase I associated factor 53	138					rRNA transcription	cell junction|cytoplasm|nucleolus	DNA binding|DNA-directed RNA polymerase activity|protein binding				0				GBM - Glioblastoma multiforme(29;0.00851)|Lung(182;0.229)														---	---	---	---
FRMPD1	22844	broad.mit.edu	37	9	37731012	37731012	+	Missense_Mutation	SNP	G	A	A	rs148192224	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37731012G>A	uc004aag.1	+	9	814	c.770G>A	c.(769-771)CGC>CAC	p.R257H	FRMPD1_uc004aah.1_Missense_Mutation_p.R257H|FRMPD1_uc011lqm.1_Missense_Mutation_p.R79H|FRMPD1_uc011lqn.1_Missense_Mutation_p.R126H	NM_014907	NP_055722	Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	257	FERM.					cytoskeleton|cytosol|plasma membrane				ovary(4)|central_nervous_system(2)|skin(2)|breast(1)	9				GBM - Glioblastoma multiforme(29;0.00655)														---	---	---	---
FRMPD1	22844	broad.mit.edu	37	9	37731074	37731074	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37731074G>A	uc004aag.1	+	9	876	c.832G>A	c.(832-834)GTG>ATG	p.V278M	FRMPD1_uc004aah.1_Missense_Mutation_p.V278M|FRMPD1_uc011lqm.1_Missense_Mutation_p.V100M|FRMPD1_uc011lqn.1_Missense_Mutation_p.V147M	NM_014907	NP_055722	Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	278	FERM.					cytoskeleton|cytosol|plasma membrane				ovary(4)|central_nervous_system(2)|skin(2)|breast(1)	9				GBM - Glioblastoma multiforme(29;0.00655)														---	---	---	---
FRMPD1	22844	broad.mit.edu	37	9	37746123	37746123	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:37746123C>A	uc004aag.1	+	16	4138	c.4094C>A	c.(4093-4095)CCC>CAC	p.P1365H	FRMPD1_uc004aah.1_Missense_Mutation_p.P1365H	NM_014907	NP_055722	Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	1365						cytoskeleton|cytosol|plasma membrane				ovary(4)|central_nervous_system(2)|skin(2)|breast(1)	9				GBM - Glioblastoma multiforme(29;0.00655)														---	---	---	---
ZNF658	26149	broad.mit.edu	37	9	40774872	40774872	+	Missense_Mutation	SNP	T	G	G	rs143353803		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:40774872T>G	uc004abs.2	-	5	555	c.403A>C	c.(403-405)ATA>CTA	p.I135L	ZNF658_uc010mmm.1_Missense_Mutation_p.I135L|ZNF658_uc010mmn.1_Missense_Mutation_p.I135L	NM_033160	NP_149350	Q5TYW1	ZN658_HUMAN	zinc finger protein 658	135					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)														---	---	---	---
ZNF658	26149	broad.mit.edu	37	9	40774889	40774889	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:40774889G>T	uc004abs.2	-	5	538	c.386C>A	c.(385-387)CCA>CAA	p.P129Q	ZNF658_uc010mmm.1_Missense_Mutation_p.P129Q|ZNF658_uc010mmn.1_Missense_Mutation_p.P129Q	NM_033160	NP_149350	Q5TYW1	ZN658_HUMAN	zinc finger protein 658	129					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)														---	---	---	---
PGM5	5239	broad.mit.edu	37	9	70993105	70993105	+	Intron	SNP	G	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:70993105G>C	uc004agr.2	+							NM_021965	NP_068800			phosphoglucomutase 5						cell adhesion|cellular calcium ion homeostasis|glucose metabolic process	costamere|dystrophin-associated glycoprotein complex|focal adhesion|intercalated disc|internal side of plasma membrane|sarcolemma|spot adherens junction|stress fiber|Z disc	intramolecular transferase activity, phosphotransferases|magnesium ion binding|structural molecule activity			ovary(1)|pancreas(1)	2																		---	---	---	---
PGM5	5239	broad.mit.edu	37	9	70993106	70993106	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:70993106A>G	uc004agr.2	+							NM_021965	NP_068800			phosphoglucomutase 5						cell adhesion|cellular calcium ion homeostasis|glucose metabolic process	costamere|dystrophin-associated glycoprotein complex|focal adhesion|intercalated disc|internal side of plasma membrane|sarcolemma|spot adherens junction|stress fiber|Z disc	intramolecular transferase activity, phosphotransferases|magnesium ion binding|structural molecule activity			ovary(1)|pancreas(1)	2																		---	---	---	---
TJP2	9414	broad.mit.edu	37	9	71864371	71864371	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:71864371G>A	uc004ahe.2	+	20	3161	c.2961G>A	c.(2959-2961)CCG>CCA	p.P987P	TJP2_uc011lrs.1_Intron|TJP2_uc004ahf.2_Intron|TJP2_uc011lru.1_Intron|TJP2_uc011lrv.1_Silent_p.P1009P|TJP2_uc010mom.1_Intron	NM_004817	NP_004808	Q9UDY2	ZO2_HUMAN	tight junction protein 2 (zona occludens 2)	987					cellular component disassembly involved in apoptosis	adherens junction|cytoplasm|nucleus|tight junction	guanylate kinase activity|protein binding				0																		---	---	---	---
APBA1	320	broad.mit.edu	37	9	72047534	72047534	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72047534C>T	uc004ahh.2	-	12	2636	c.2360G>A	c.(2359-2361)CGG>CAG	p.R787Q		NM_001163	NP_001154	Q02410	APBA1_HUMAN	amyloid beta A4 precursor protein-binding,	787	PDZ 2.				axon cargo transport|cell adhesion|intracellular protein transport|nervous system development|protein complex assembly|synaptic transmission	synaptic vesicle				lung(1)	1																		---	---	---	---
MAMDC2	256691	broad.mit.edu	37	9	72741146	72741146	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:72741146A>G	uc004ahm.2	+	6	1332	c.715A>G	c.(715-717)ACC>GCC	p.T239A	MAMDC2_uc004ahn.2_RNA	NM_153267	NP_694999	Q7Z304	MAMC2_HUMAN	MAM domain containing 2 precursor	239	MAM 2.					endoplasmic reticulum|membrane				central_nervous_system(1)|pancreas(1)	2																		---	---	---	---
TRPM3	80036	broad.mit.edu	37	9	73240179	73240179	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:73240179G>A	uc004aid.2	-	13	1945	c.1701C>T	c.(1699-1701)GGC>GGT	p.G567G	TRPM3_uc004ahu.2_Silent_p.G397G|TRPM3_uc004ahv.2_Silent_p.G379G|TRPM3_uc004ahw.2_Silent_p.G439G|TRPM3_uc004ahx.2_Silent_p.G426G|TRPM3_uc004ahy.2_Silent_p.G439G|TRPM3_uc004ahz.2_Silent_p.G426G|TRPM3_uc004aia.2_Silent_p.G414G|TRPM3_uc004aib.2_Silent_p.G414G|TRPM3_uc004aic.2_Silent_p.G567G	NM_001007471	NP_001007472	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel,	592	Cytoplasmic (Potential).					integral to membrane	calcium channel activity			ovary(3)|pancreas(2)|central_nervous_system(2)|skin(2)	9																		---	---	---	---
RORB	6096	broad.mit.edu	37	9	77300423	77300423	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77300423C>T	uc004aji.2	+	10	1351	c.1302C>T	c.(1300-1302)CAC>CAT	p.H434H	RORB_uc004ajh.2_Silent_p.H423H	NM_006914	NP_008845	Q92753	RORB_HUMAN	RAR-related orphan receptor B	434	Ligand-binding (Potential).				eye photoreceptor cell development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|visual perception	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(2)|lung(1)|skin(1)	4																		---	---	---	---
PCSK5	5125	broad.mit.edu	37	9	78772047	78772047	+	Missense_Mutation	SNP	G	A	A	rs112718462		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78772047G>A	uc004ajz.2	+	11	1937	c.1399G>A	c.(1399-1401)GTG>ATG	p.V467M	PCSK5_uc004ajy.2_Missense_Mutation_p.V467M|PCSK5_uc004aka.2_RNA	NM_006200	NP_006191	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	467	Homo B/P.				anterior/posterior pattern formation|cell-cell signaling|cytokine biosynthetic process|embryo implantation|embryonic digestive tract development|embryonic skeletal system development|heart development|kidney development|limb morphogenesis|nerve growth factor processing|nerve growth factor receptor signaling pathway|peptide biosynthetic process|renin secretion into blood stream|respiratory tube development|signal peptide processing|viral assembly, maturation, egress, and release	extracellular space|Golgi lumen|stored secretory granule	peptide binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3																		---	---	---	---
PCSK5	5125	broad.mit.edu	37	9	78794550	78794550	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78794550G>A	uc004ajz.2	+	15	2477	c.1939G>A	c.(1939-1941)GGG>AGG	p.G647R	PCSK5_uc004aka.2_RNA|PCSK5_uc004akb.2_5'Flank	NM_006200	NP_006191	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	647	CRM (Cys-rich motif).				anterior/posterior pattern formation|cell-cell signaling|cytokine biosynthetic process|embryo implantation|embryonic digestive tract development|embryonic skeletal system development|heart development|kidney development|limb morphogenesis|nerve growth factor processing|nerve growth factor receptor signaling pathway|peptide biosynthetic process|renin secretion into blood stream|respiratory tube development|signal peptide processing|viral assembly, maturation, egress, and release	extracellular space|Golgi lumen|stored secretory granule	peptide binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3																		---	---	---	---
GCNT1	2650	broad.mit.edu	37	9	79118429	79118429	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79118429C>T	uc010mpf.2	+	3	1473	c.1132C>T	c.(1132-1134)CGC>TGC	p.R378C	GCNT1_uc010mpg.2_Missense_Mutation_p.R378C|GCNT1_uc010mph.2_Missense_Mutation_p.R378C|GCNT1_uc004akf.3_Missense_Mutation_p.R378C|GCNT1_uc010mpi.2_Missense_Mutation_p.R378C|GCNT1_uc004akh.3_Missense_Mutation_p.R378C	NM_001490	NP_001481	Q02742	GCNT1_HUMAN	beta-1,3-galactosyl-O-glycosyl-glycoprotein	378	Lumenal (Potential).|Catalytic (By similarity).				protein O-linked glycosylation	Golgi membrane|integral to membrane	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity				0																		---	---	---	---
PRUNE2	158471	broad.mit.edu	37	9	79323159	79323159	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79323159A>G	uc010mpk.2	-	8	4155	c.4031T>C	c.(4030-4032)GTG>GCG	p.V1344A		NM_015225	NP_056040	Q8WUY3	PRUN2_HUMAN	prune homolog 2	1344					apoptosis|G1 phase|induction of apoptosis	cytoplasm	metal ion binding|pyrophosphatase activity				0																		---	---	---	---
VPS13A	23230	broad.mit.edu	37	9	79984230	79984230	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79984230T>C	uc004akr.2	+	63	8829	c.8569T>C	c.(8569-8571)TAT>CAT	p.Y2857H	VPS13A_uc004akp.3_Missense_Mutation_p.Y2857H|VPS13A_uc004akq.3_Missense_Mutation_p.Y2857H|VPS13A_uc004aks.2_Missense_Mutation_p.Y2818H	NM_033305	NP_150648	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13A isoform A	2857					Golgi to endosome transport|protein transport	intracellular	protein binding			pancreas(3)|skin(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)	10																		---	---	---	---
VPS13A	23230	broad.mit.edu	37	9	79985958	79985958	+	Silent	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:79985958A>C	uc004akr.2	+	67	9230	c.8970A>C	c.(8968-8970)GGA>GGC	p.G2990G	VPS13A_uc004akp.3_Silent_p.G2990G|VPS13A_uc004akq.3_Silent_p.G2990G|VPS13A_uc004aks.2_Silent_p.G2951G	NM_033305	NP_150648	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13A isoform A	2990					Golgi to endosome transport|protein transport	intracellular	protein binding			pancreas(3)|skin(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)	10																		---	---	---	---
TLE4	7091	broad.mit.edu	37	9	82227567	82227567	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:82227567G>A	uc004ald.2	+						TLE4_uc004alc.2_Intron|TLE4_uc010mpr.2_Intron|TLE4_uc004ale.2_Intron|TLE4_uc011lsq.1_Intron|TLE4_uc010mps.2_Intron|TLE4_uc004alf.2_Intron	NM_007005	NP_008936			transducin-like enhancer protein 4											lung(2)|ovary(1)|breast(1)|skin(1)	5																		---	---	---	---
C9orf79	286234	broad.mit.edu	37	9	90501034	90501034	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90501034C>T	uc004app.3	+	4	1667	c.1632C>T	c.(1630-1632)GGC>GGT	p.G544G	C9orf79_uc004apo.1_Silent_p.G356G	NM_178828	NP_849150	Q6ZUB1	CI079_HUMAN	chromosome 9 open reading frame 79	544						integral to membrane				ovary(3)	3																		---	---	---	---
C9orf79	286234	broad.mit.edu	37	9	90502884	90502884	+	Missense_Mutation	SNP	T	C	C	rs41286019		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90502884T>C	uc004app.3	+	4	3517	c.3482T>C	c.(3481-3483)ATG>ACG	p.M1161T		NM_178828	NP_849150	Q6ZUB1	CI079_HUMAN	chromosome 9 open reading frame 79	1161						integral to membrane				ovary(3)	3																		---	---	---	---
CDK20	23552	broad.mit.edu	37	9	90584172	90584172	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:90584172C>A	uc004apr.2	-	7	1086	c.780G>T	c.(778-780)CAG>CAT	p.Q260H	CDK20_uc004aps.2_Missense_Mutation_p.Q239H|CDK20_uc004apt.2_Missense_Mutation_p.Q252H|CDK20_uc004apu.2_Missense_Mutation_p.R198M	NM_001039803	NP_001034892	Q8IZL9	CDK20_HUMAN	cell cycle related kinase isoform 3	260	Protein kinase.				cell division|multicellular organismal development	cilium|mitochondrion|nucleus	ATP binding|cyclin-dependent protein kinase activity			skin(1)	1																		---	---	---	---
NXNL2	158046	broad.mit.edu	37	9	91150613	91150613	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:91150613C>T	uc011ltj.1	+	1	598	c.264C>T	c.(262-264)GGC>GGT	p.G88G	NXNL2_uc004aqa.2_Silent_p.G88G	NM_001161625	NP_001155097	Q5VZ03	NXNL2_HUMAN	nucleoredoxin-like 2 isoform 1	88	Thioredoxin.										0																		---	---	---	---
BICD2	23299	broad.mit.edu	37	9	95483003	95483003	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95483003C>T	uc004aso.1	-	4	698	c.641G>A	c.(640-642)CGT>CAT	p.R214H	BICD2_uc004asp.1_Missense_Mutation_p.R214H	NM_015250	NP_056065	Q8TD16	BICD2_HUMAN	bicaudal D homolog 2 isoform 2	214	Potential.				microtubule anchoring at microtubule organizing center|minus-end-directed organelle transport along microtubule	cytoplasmic vesicle|cytoskeleton|Golgi apparatus|plasma membrane	Rab GTPase binding			skin(1)	1																		---	---	---	---
WNK2	65268	broad.mit.edu	37	9	95997147	95997147	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95997147A>G	uc004ati.1	+	4	1133	c.1133A>G	c.(1132-1134)GAC>GGC	p.D378G	WNK2_uc011lud.1_Missense_Mutation_p.D378G|WNK2_uc004atj.2_Missense_Mutation_p.D378G|WNK2_uc004atk.2_Missense_Mutation_p.D15G|WNK2_uc010mrc.1_Missense_Mutation_p.D378G|WNK2_uc010mrd.1_Missense_Mutation_p.D15G	NM_006648	NP_006639	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	378	Protein kinase.				intracellular protein kinase cascade		ATP binding|protein binding|protein serine/threonine kinase activity			lung(4)|stomach(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)|breast(1)	12																		---	---	---	---
PHF2	5253	broad.mit.edu	37	9	96408078	96408078	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96408078G>A	uc004aub.2	+						PHF2_uc011lug.1_Intron	NM_005392	NP_005383			PHD finger protein 2						liver development|negative regulation of chromatin silencing at rDNA|transcription, DNA-dependent	nucleolus	histone demethylase activity (H3-K9 specific)|iron ion binding|methylated histone residue binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)														---	---	---	---
PTPDC1	138639	broad.mit.edu	37	9	96850543	96850543	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:96850543G>A	uc004auf.1	+	5	792	c.452G>A	c.(451-453)GGC>GAC	p.G151D	PTPDC1_uc004aug.1_Missense_Mutation_p.G151D|PTPDC1_uc004auh.1_Missense_Mutation_p.G203D|PTPDC1_uc010mrj.1_Missense_Mutation_p.G205D|PTPDC1_uc010mri.1_Missense_Mutation_p.G203D	NM_177995	NP_818931	A2A3K4	PTPC1_HUMAN	protein tyrosine phosphatase domain containing 1	151							protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(1)	1																		---	---	---	---
ZNF169	169841	broad.mit.edu	37	9	97062813	97062813	+	Silent	SNP	C	A	A	rs146740357		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97062813C>A	uc004aum.1	+	5	1078	c.973C>A	c.(973-975)CGA>AGA	p.R325R		NM_194320	NP_919301	Q14929	ZN169_HUMAN	zinc finger protein 169	325	C2H2-type 4.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2		Acute lymphoblastic leukemia(62;0.136)																---	---	---	---
C9orf3	84909	broad.mit.edu	37	9	97844901	97844901	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97844901C>T	uc004ava.2	+	15	2499	c.2364C>T	c.(2362-2364)GAC>GAT	p.D788D	C9orf3_uc004auy.2_Silent_p.D689D|C9orf3_uc004avc.2_Intron|C9orf3_uc011luj.1_Silent_p.D150D|C9orf3_uc011luk.1_Silent_p.D129D|C9orf3_uc004avd.2_Silent_p.D150D|MIR23B_hsa-mir-23b|MI0000439_5'Flank|uc004avg.3_5'Flank|MIR27B_hsa-mir-27b|MI0000440_5'Flank	NM_032823	NP_116212	Q8N6M6	AMPO_HUMAN	aminopeptidase O	788					leukotriene biosynthetic process|proteolysis	cytoplasm	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(323;0.000275)														---	---	---	---
PTCH1	5727	broad.mit.edu	37	9	98209651	98209651	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98209651C>T	uc004avk.3	-	23	4075	c.3887G>A	c.(3886-3888)GGA>GAA	p.G1296E	PTCH1_uc010mrn.2_Missense_Mutation_p.G88E|PTCH1_uc010mro.2_Missense_Mutation_p.G1145E|PTCH1_uc010mrp.2_Missense_Mutation_p.G1145E|PTCH1_uc010mrq.2_Missense_Mutation_p.G1145E|PTCH1_uc004avl.3_Missense_Mutation_p.G1145E|PTCH1_uc010mrr.2_Missense_Mutation_p.G1230E|PTCH1_uc004avm.3_Missense_Mutation_p.G1295E	NM_000264	NP_000255	Q13635	PTC1_HUMAN	patched isoform L	1296	Cytoplasmic (Potential).				embryonic limb morphogenesis|negative regulation of multicellular organism growth|protein processing|regulation of smoothened signaling pathway|smoothened signaling pathway	integral to plasma membrane	hedgehog receptor activity			skin(242)|central_nervous_system(72)|bone(33)|upper_aerodigestive_tract(11)|lung(6)|large_intestine(4)|breast(4)|oesophagus(3)|ovary(3)|vulva(1)	379		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)												Basal_Cell_Nevus_syndrome				---	---	---	---
PTCH1	5727	broad.mit.edu	37	9	98215818	98215818	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98215818C>T	uc004avk.3	-	20	3579	c.3391G>A	c.(3391-3393)GTG>ATG	p.V1131M	PTCH1_uc010mro.2_Missense_Mutation_p.V980M|PTCH1_uc010mrp.2_Missense_Mutation_p.V980M|PTCH1_uc010mrq.2_Missense_Mutation_p.V980M|PTCH1_uc004avl.3_Missense_Mutation_p.V980M|PTCH1_uc010mrr.2_Missense_Mutation_p.V1065M|PTCH1_uc004avm.3_Missense_Mutation_p.V1130M	NM_000264	NP_000255	Q13635	PTC1_HUMAN	patched isoform L	1131	Helical; (Potential).				embryonic limb morphogenesis|negative regulation of multicellular organism growth|protein processing|regulation of smoothened signaling pathway|smoothened signaling pathway	integral to plasma membrane	hedgehog receptor activity			skin(242)|central_nervous_system(72)|bone(33)|upper_aerodigestive_tract(11)|lung(6)|large_intestine(4)|breast(4)|oesophagus(3)|ovary(3)|vulva(1)	379		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)												Basal_Cell_Nevus_syndrome				---	---	---	---
PTCH1	5727	broad.mit.edu	37	9	98231166	98231166	+	Missense_Mutation	SNP	C	T	T	rs140497736		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98231166C>T	uc004avk.3	-	14	2305	c.2117G>A	c.(2116-2118)AGC>AAC	p.S706N	PTCH1_uc010mro.2_Missense_Mutation_p.S555N|PTCH1_uc010mrp.2_Missense_Mutation_p.S555N|PTCH1_uc010mrq.2_Missense_Mutation_p.S555N|PTCH1_uc004avl.3_Missense_Mutation_p.S555N|PTCH1_uc010mrr.2_Missense_Mutation_p.S640N|PTCH1_uc004avm.3_Missense_Mutation_p.S705N|PTCH1_uc010mrs.1_Missense_Mutation_p.S374N	NM_000264	NP_000255	Q13635	PTC1_HUMAN	patched isoform L	706	Cytoplasmic (Potential).				embryonic limb morphogenesis|negative regulation of multicellular organism growth|protein processing|regulation of smoothened signaling pathway|smoothened signaling pathway	integral to plasma membrane	hedgehog receptor activity			skin(242)|central_nervous_system(72)|bone(33)|upper_aerodigestive_tract(11)|lung(6)|large_intestine(4)|breast(4)|oesophagus(3)|ovary(3)|vulva(1)	379		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)												Basal_Cell_Nevus_syndrome				---	---	---	---
PTCH1	5727	broad.mit.edu	37	9	98231380	98231380	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:98231380C>T	uc004avk.3	-	14	2091	c.1903G>A	c.(1903-1905)GAC>AAC	p.D635N	PTCH1_uc010mro.2_Missense_Mutation_p.D484N|PTCH1_uc010mrp.2_Missense_Mutation_p.D484N|PTCH1_uc010mrq.2_Missense_Mutation_p.D484N|PTCH1_uc004avl.3_Missense_Mutation_p.D484N|PTCH1_uc010mrr.2_Missense_Mutation_p.D569N|PTCH1_uc004avm.3_Missense_Mutation_p.D634N|PTCH1_uc010mrs.1_Missense_Mutation_p.D303N	NM_000264	NP_000255	Q13635	PTC1_HUMAN	patched isoform L	635	Cytoplasmic (Potential).				embryonic limb morphogenesis|negative regulation of multicellular organism growth|protein processing|regulation of smoothened signaling pathway|smoothened signaling pathway	integral to plasma membrane	hedgehog receptor activity			skin(242)|central_nervous_system(72)|bone(33)|upper_aerodigestive_tract(11)|lung(6)|large_intestine(4)|breast(4)|oesophagus(3)|ovary(3)|vulva(1)	379		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)												Basal_Cell_Nevus_syndrome				---	---	---	---
KIAA1529	57653	broad.mit.edu	37	9	100071719	100071719	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100071719G>A	uc011lut.1	+	15	1415	c.642G>A	c.(640-642)GCG>GCA	p.A214A	KIAA1529_uc004axe.1_Silent_p.A214A|KIAA1529_uc004axg.1_Silent_p.A75A|KIAA1529_uc011lus.1_Silent_p.A75A|KIAA1529_uc010msm.1_RNA|KIAA1529_uc004axf.2_Silent_p.A75A|KIAA1529_uc011luv.1_Silent_p.A75A	NM_020893	NP_065944			hypothetical protein LOC57653											ovary(4)|large_intestine(2)|skin(1)	7		Acute lymphoblastic leukemia(62;0.154)																---	---	---	---
TMOD1	7111	broad.mit.edu	37	9	100308588	100308588	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100308588G>A	uc004axk.1	+	3	455	c.242G>A	c.(241-243)CGA>CAA	p.R81Q	TMOD1_uc004axl.1_Missense_Mutation_p.R81Q	NM_003275	NP_003266	P28289	TMOD1_HUMAN	tropomodulin 1	81	Tropomyosin-binding (Potential).				muscle filament sliding	cytosol	actin binding				0		Acute lymphoblastic leukemia(62;0.154)		STAD - Stomach adenocarcinoma(157;0.105)														---	---	---	---
HEMGN	55363	broad.mit.edu	37	9	100692595	100692595	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100692595G>T	uc004axy.2	-	3	1190	c.1082C>A	c.(1081-1083)CCT>CAT	p.P361H	HEMGN_uc004axz.2_Missense_Mutation_p.P361H	NM_197978	NP_932095	Q9BXL5	HEMGN_HUMAN	hemogen	361					cell differentiation|multicellular organismal development					ovary(1)	1		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
NANS	54187	broad.mit.edu	37	9	100819127	100819127	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:100819127G>C	uc004ayb.2	+	2	679	c.37G>C	c.(37-39)GTG>CTG	p.V13L	NANS_uc004ayc.2_Missense_Mutation_p.V13L	NM_018946	NP_061819	Q9NR45	SIAS_HUMAN	N-acetylneuraminic acid phosphate synthase	13					lipopolysaccharide biosynthetic process	cytoplasm	N-acetylneuraminate synthase activity|N-acylneuraminate cytidylyltransferase activity|N-acylneuraminate-9-phosphate synthase activity			skin(1)	1		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
ANKS6	203286	broad.mit.edu	37	9	101552626	101552626	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101552626G>A	uc004ayu.2	-	2	643	c.622C>T	c.(622-624)CGT>TGT	p.R208C	ANKS6_uc004ayy.1_RNA	NM_173551	NP_775822	Q68DC2	ANKS6_HUMAN	ankyrin repeat and sterile alpha motif domain	208	ANK 5.									ovary(2)	2		Acute lymphoblastic leukemia(62;0.0527)																---	---	---	---
GALNT12	79695	broad.mit.edu	37	9	101608364	101608364	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101608364G>A	uc004ayz.2	+	9	1564	c.1564G>A	c.(1564-1566)GAA>AAA	p.E522K		NM_024642	NP_078918	Q8IXK2	GLT12_HUMAN	N-acetylgalactosaminyltransferase 12	522	Ricin B-type lectin.|Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			upper_aerodigestive_tract(1)|ovary(1)	2		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
TGFBR1	7046	broad.mit.edu	37	9	101904807	101904807	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101904807C>T	uc004azc.2	+						TGFBR1_uc004azd.2_Intron|TGFBR1_uc011lvc.1_Intron	NM_004612	NP_004603			transforming growth factor, beta receptor I						activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway		ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding			lung(2)|ovary(1)	3		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
ALG2	85365	broad.mit.edu	37	9	101980565	101980565	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:101980565C>A	uc004azf.2	-	2	972	c.902G>T	c.(901-903)AGG>ATG	p.R301M	ALG2_uc004azg.2_Missense_Mutation_p.R208M	NM_033087	NP_149078	Q9H553	ALG2_HUMAN	alpha-1,3-mannosyltransferase ALG2	301					dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein glycosylation in endoplasmic reticulum|protein N-linked glycosylation via asparagine|response to calcium ion	endoplasmic reticulum membrane|integral to membrane|membrane fraction|nucleus|perinuclear region of cytoplasm	alpha-1,3-mannosyltransferase activity|calcium-dependent protein binding|glycolipid 3-alpha-mannosyltransferase activity|protein anchor|protein heterodimerization activity|protein N-terminus binding			ovary(2)	2		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
NR4A3	8013	broad.mit.edu	37	9	102590525	102590525	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:102590525C>T	uc004baf.1	+	3	930	c.201C>T	c.(199-201)AGC>AGT	p.S67S	NR4A3_uc004bae.2_Silent_p.S67S|NR4A3_uc004bag.1_Silent_p.S67S|NR4A3_uc004bai.2_Silent_p.S78S	NM_006981	NP_008912	Q92570	NR4A3_HUMAN	nuclear receptor subfamily 4, group A, member 3	67					regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor		steroid hormone receptor activity|thyroid hormone receptor activity|zinc ion binding		EWSR1/NR4A3(140)|TAF15/NR4A3(33)	bone(173)	173		Acute lymphoblastic leukemia(62;0.0559)|all_hematologic(171;0.189)						T	EWSR1	extraskeletal myxoid chondrosarcoma								---	---	---	---
INVS	27130	broad.mit.edu	37	9	103046680	103046680	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103046680G>T	uc004bap.1	+	13	2075	c.1863G>T	c.(1861-1863)CAG>CAT	p.Q621H	INVS_uc011lve.1_Missense_Mutation_p.Q525H|INVS_uc004bao.1_Missense_Mutation_p.Q621H|INVS_uc004baq.1_Missense_Mutation_p.Q525H|INVS_uc004bar.1_Missense_Mutation_p.Q525H|INVS_uc010mtb.1_Missense_Mutation_p.Q295H	NM_014425	NP_055240	Q9Y283	INVS_HUMAN	inversin isoform a	621					negative regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasm|membrane|microtubule|nucleus|spindle	calmodulin binding			ovary(2)	2		Acute lymphoblastic leukemia(62;0.056)																---	---	---	---
TEX10	54881	broad.mit.edu	37	9	103109223	103109223	+	Missense_Mutation	SNP	G	A	A	rs138309909		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:103109223G>A	uc004bas.2	-	3	861	c.646C>T	c.(646-648)CGG>TGG	p.R216W	TEX10_uc011lvf.1_Intron|TEX10_uc011lvg.1_Missense_Mutation_p.R219W|TEX10_uc011lvh.1_Missense_Mutation_p.R151W|TEX10_uc004bat.2_Missense_Mutation_p.R216W	NM_017746	NP_060216	Q9NXF1	TEX10_HUMAN	testis expressed 10 isoform 1	216						integral to membrane|MLL1 complex|nuclear membrane|nucleolus	binding			ovary(1)|skin(1)	2		Acute lymphoblastic leukemia(62;0.0527)		OV - Ovarian serous cystadenocarcinoma(323;0.157)														---	---	---	---
BAAT	570	broad.mit.edu	37	9	104124908	104124908	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104124908G>T	uc010mtd.2	-	4	1168	c.1059C>A	c.(1057-1059)ACC>ACA	p.T353T	BAAT_uc004bbd.3_Silent_p.T353T	NM_001127610	NP_001121082	Q14032	BAAT_HUMAN	bile acid Coenzyme A: amino acid	353					acyl-CoA metabolic process|bile acid and bile salt transport|bile acid biosynthetic process|digestion|fatty acid metabolic process|glycine metabolic process	cytosol|peroxisomal matrix	carboxylesterase activity|glycine N-choloyltransferase activity|N-acyltransferase activity|palmitoyl-CoA hydrolase activity			ovary(1)|lung(1)|skin(1)	3		Acute lymphoblastic leukemia(62;0.0559)			Glycine(DB00145)													---	---	---	---
ALDOB	229	broad.mit.edu	37	9	104187203	104187203	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104187203C>A	uc004bbk.2	-	8	1003	c.921G>T	c.(919-921)CAG>CAT	p.Q307H		NM_000035	NP_000026	P05062	ALDOB_HUMAN	aldolase B, fructose-bisphosphate	307					fructose 1,6-bisphosphate metabolic process|fructose catabolic process|gluconeogenesis|glycolysis|NADH oxidation|positive regulation of ATPase activity|vacuolar proton-transporting V-type ATPase complex assembly	centriolar satellite|cytosol	ATPase binding|cytoskeletal protein binding|fructose binding|fructose-bisphosphate aldolase activity|identical protein binding			skin(1)	1		Acute lymphoblastic leukemia(62;0.0559)																---	---	---	---
SMC2	10592	broad.mit.edu	37	9	106896800	106896800	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:106896800G>T	uc004bbv.2	+	23	3501	c.3213G>T	c.(3211-3213)AAG>AAT	p.K1071N	SMC2_uc004bbw.2_Missense_Mutation_p.K1071N|SMC2_uc011lvl.1_Missense_Mutation_p.K1071N|SMC2_uc004bbx.2_Missense_Mutation_p.K1071N|SMC2_uc004bby.2_RNA	NM_001042551	NP_001036016	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2	1071					cell division|mitotic chromosome condensation|symbiosis, encompassing mutualism through parasitism	condensin complex|cytoplasm|nuclear chromosome	ATP binding|protein heterodimerization activity			ovary(4)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|breast(1)	9																		---	---	---	---
OR13C3	138803	broad.mit.edu	37	9	107298237	107298237	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107298237G>T	uc004bcb.1	-	1	858	c.858C>A	c.(856-858)TTC>TTA	p.F286L		NM_001001961	NP_001001961	Q8NGS6	O13C3_HUMAN	olfactory receptor, family 13, subfamily C,	286	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)	1																		---	---	---	---
ABCA1	19	broad.mit.edu	37	9	107589265	107589265	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:107589265C>T	uc004bcl.2	-	16	2614	c.2301G>A	c.(2299-2301)TGG>TGA	p.W767*		NM_005502	NP_005493	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A member 1	767					Cdc42 protein signal transduction|cellular lipid metabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|endosome transport|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|interleukin-1 beta secretion|intracellular cholesterol transport|lysosome organization|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|platelet dense granule organization|positive regulation of cAMP biosynthetic process|reverse cholesterol transport	integral to plasma membrane|membrane fraction|membrane raft|phagocytic vesicle	anion transmembrane transporter activity|apolipoprotein A-I receptor activity|ATP binding|ATPase activity|cholesterol transporter activity|phospholipid transporter activity|small GTPase binding|syntaxin-13 binding			large_intestine(4)|lung(4)|ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	17				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)													---	---	---	---
ZNF462	58499	broad.mit.edu	37	9	109687547	109687547	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109687547C>T	uc004bcz.2	+	3	1643	c.1354C>T	c.(1354-1356)CGT>TGT	p.R452C	ZNF462_uc010mto.2_Missense_Mutation_p.R300C|ZNF462_uc004bda.2_Missense_Mutation_p.R300C	NM_021224	NP_067047	Q96JM2	ZN462_HUMAN	zinc finger protein 462	452	C2H2-type 4.				transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	p.R452C(1)		ovary(5)	5																		---	---	---	---
ZNF462	58499	broad.mit.edu	37	9	109690544	109690544	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:109690544T>C	uc004bcz.2	+	3	4640	c.4351T>C	c.(4351-4353)TCC>CCC	p.S1451P	ZNF462_uc010mto.2_Missense_Mutation_p.S1299P|ZNF462_uc004bda.2_Missense_Mutation_p.S1299P	NM_021224	NP_067047	Q96JM2	ZN462_HUMAN	zinc finger protein 462	1451					transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(5)	5																		---	---	---	---
RAD23B	5887	broad.mit.edu	37	9	110081071	110081071	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110081071A>G	uc004bde.2	+	6	959	c.592A>G	c.(592-594)ATG>GTG	p.M198V	RAD23B_uc011lwa.1_Missense_Mutation_p.M198V|RAD23B_uc011lwb.1_Missense_Mutation_p.M177V	NM_002874	NP_002865	P54727	RD23B_HUMAN	UV excision repair protein RAD23 homolog B	198	UBA 1.				nucleotide-excision repair, DNA damage recognition|nucleotide-excision repair, DNA damage removal|proteasomal ubiquitin-dependent protein catabolic process|regulation of proteasomal ubiquitin-dependent protein catabolic process	cytoplasm|nucleoplasm|proteasome complex|XPC complex	damaged DNA binding|polyubiquitin binding|single-stranded DNA binding			ovary(1)	1													Direct_reversal_of_damage|NER					---	---	---	---
KLF4	9314	broad.mit.edu	37	9	110249364	110249364	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:110249364G>T	uc004bdh.2	-	3	1905	c.1284C>A	c.(1282-1284)TGC>TGA	p.C428*	KLF4_uc004bdf.1_Nonsense_Mutation_p.C353*|KLF4_uc004bdg.2_Nonsense_Mutation_p.C403*	NM_004235	NP_004226	O43474	KLF4_HUMAN	Kruppel-like factor 4 (gut)	437	C2H2-type 1.				fat cell differentiation|mesodermal cell fate determination|negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|stem cell maintenance|transcription from RNA polymerase II promoter	nucleus	RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor recruiting transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			central_nervous_system(2)|lung(1)	3																		---	---	---	---
IKBKAP	8518	broad.mit.edu	37	9	111674606	111674606	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:111674606G>A	uc004bdm.3	-	11	1647	c.1127C>T	c.(1126-1128)ACG>ATG	p.T376M	IKBKAP_uc004bdl.2_Missense_Mutation_p.T27M|IKBKAP_uc011lwc.1_Missense_Mutation_p.T262M|IKBKAP_uc010mtq.2_Missense_Mutation_p.T27M	NM_003640	NP_003631	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene	376					immune response|protein complex assembly|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|DNA-directed RNA polymerase II, holoenzyme|nucleolus|transcription elongation factor complex	phosphorylase kinase regulator activity|protein binding|signal transducer activity			ovary(2)|skin(2)|upper_aerodigestive_tract(1)|breast(1)|kidney(1)	7																		---	---	---	---
PALM2-AKAP2	445815	broad.mit.edu	37	9	112898894	112898894	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112898894C>T	uc004bei.2	+	9	1958	c.1766C>T	c.(1765-1767)GCA>GTA	p.A589V	PALM2-AKAP2_uc004bek.3_Missense_Mutation_p.A357V|PALM2-AKAP2_uc004bej.3_Missense_Mutation_p.A357V|PALM2-AKAP2_uc004bel.1_Missense_Mutation_p.A167V|AKAP2_uc011lwi.1_Missense_Mutation_p.A215V|AKAP2_uc004bem.2_Missense_Mutation_p.A215V|PALM2-AKAP2_uc010mtw.1_Missense_Mutation_p.A175V|AKAP2_uc011lwj.1_Missense_Mutation_p.A126V|PALM2-AKAP2_uc004ben.2_Missense_Mutation_p.A126V	NM_001136562	NP_001130034	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2 isoform 2	126							enzyme binding			ovary(3)|central_nervous_system(2)|skin(1)	6																		---	---	---	---
PALM2-AKAP2	445815	broad.mit.edu	37	9	112898916	112898916	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:112898916C>T	uc004bei.2	+	9	1980	c.1788C>T	c.(1786-1788)GGC>GGT	p.G596G	PALM2-AKAP2_uc004bek.3_Silent_p.G364G|PALM2-AKAP2_uc004bej.3_Silent_p.G364G|PALM2-AKAP2_uc004bel.1_Silent_p.G174G|AKAP2_uc011lwi.1_Silent_p.G222G|AKAP2_uc004bem.2_Silent_p.G222G|PALM2-AKAP2_uc010mtw.1_Silent_p.G182G|AKAP2_uc011lwj.1_Silent_p.G133G|PALM2-AKAP2_uc004ben.2_Silent_p.G133G	NM_001136562	NP_001130034	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2 isoform 2	133							enzyme binding			ovary(3)|central_nervous_system(2)|skin(1)	6																		---	---	---	---
DNAJC25	548645	broad.mit.edu	37	9	114412057	114412057	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114412057A>G	uc004bfl.2	+	3	870	c.814A>G	c.(814-816)ATC>GTC	p.I272V	DNAJC25-GNG10_uc004bfn.2_Intron|DNAJC25_uc004bfm.2_Missense_Mutation_p.I150V	NM_001015882	NP_001015882	Q9H1X3	DJC25_HUMAN	DnaJ (Hsp40) homolog, subfamily C , member 25	272					protein folding	integral to membrane	heat shock protein binding|unfolded protein binding				0																		---	---	---	---
ROD1	9991	broad.mit.edu	37	9	115015056	115015056	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115015056A>C	uc004bfw.2	-	7	800	c.613T>G	c.(613-615)TTT>GTT	p.F205V	ROD1_uc004bfv.2_Missense_Mutation_p.F211V|ROD1_uc004bfx.2_Missense_Mutation_p.F208V|ROD1_uc011lwu.1_Missense_Mutation_p.F177V|ROD1_uc004bfy.2_Missense_Mutation_p.F110V|ROD1_uc004bfz.2_Missense_Mutation_p.F177V	NM_005156	NP_005147	O95758	ROD1_HUMAN	ROD1 regulator of differentiation 1 isoform 1	205	RRM 2.				anatomical structure morphogenesis|mRNA processing	nucleus	nucleotide binding|RNA binding			skin(1)	1																		---	---	---	---
ZFP37	7539	broad.mit.edu	37	9	115805810	115805810	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115805810G>A	uc004bgm.1	-	4	1116	c.1088C>T	c.(1087-1089)GCA>GTA	p.A363V	ZFP37_uc011lwz.1_Missense_Mutation_p.A378V|ZFP37_uc011lxa.1_Missense_Mutation_p.A364V	NM_003408	NP_003399	Q9Y6Q3	ZFP37_HUMAN	zinc finger protein 37 homolog	363	C2H2-type 3; atypical.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
FKBP15	23307	broad.mit.edu	37	9	115930746	115930746	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:115930746G>A	uc004bgs.2	-	27	3694	c.3576C>T	c.(3574-3576)GAC>GAT	p.D1192D	FKBP15_uc004bgr.2_Silent_p.D629D|FKBP15_uc011lxc.1_Silent_p.D773D	NM_015258	NP_056073	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	1192					endocytosis|protein folding	axon|early endosome	actin binding			ovary(3)	3																		---	---	---	---
RNF183	138065	broad.mit.edu	37	9	116060423	116060423	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116060423G>A	uc004bgz.2	-	2	160	c.42C>T	c.(40-42)CCC>CCT	p.P14P	RNF183_uc004bha.2_Silent_p.P14P	NM_145051	NP_659488	Q96D59	RN183_HUMAN	ring finger protein 183	14	RING-type.					integral to membrane	zinc ion binding				0																		---	---	---	---
BSPRY	54836	broad.mit.edu	37	9	116123005	116123005	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116123005C>A	uc004bhg.3	+	3	567	c.519C>A	c.(517-519)GAC>GAA	p.D173E	BSPRY_uc010muw.2_Missense_Mutation_p.D173E	NM_017688	NP_060158	Q5W0U4	BSPRY_HUMAN	B-box and SPRY domain containing	173					calcium ion transport	cytoplasm|membrane	zinc ion binding			breast(1)	1																		---	---	---	---
BSPRY	54836	broad.mit.edu	37	9	116132116	116132116	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:116132116C>T	uc004bhg.3	+	6	951	c.903C>T	c.(901-903)GGC>GGT	p.G301G	BSPRY_uc010muw.2_3'UTR	NM_017688	NP_060158	Q5W0U4	BSPRY_HUMAN	B-box and SPRY domain containing	301	B30.2/SPRY.				calcium ion transport	cytoplasm|membrane	zinc ion binding			breast(1)	1																		---	---	---	---
TNC	3371	broad.mit.edu	37	9	117808757	117808757	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117808757T>C	uc004bjj.3	-	17	5419	c.5057A>G	c.(5056-5058)TAC>TGC	p.Y1686C	TNC_uc010mvf.2_Intron	NM_002160	NP_002151	P24821	TENA_HUMAN	tenascin C precursor	1686	Fibronectin type-III 12.				cell adhesion|response to wounding|signal transduction	extracellular space	receptor binding|syndecan binding			central_nervous_system(4)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	7																		---	---	---	---
TNC	3371	broad.mit.edu	37	9	117846649	117846649	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:117846649G>A	uc004bjj.3	-	4	2332	c.1970C>T	c.(1969-1971)ACG>ATG	p.T657M	TNC_uc010mvf.2_Missense_Mutation_p.T657M	NM_002160	NP_002151	P24821	TENA_HUMAN	tenascin C precursor	657	Fibronectin type-III 1.				cell adhesion|response to wounding|signal transduction	extracellular space	receptor binding|syndecan binding			central_nervous_system(4)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	7																		---	---	---	---
PAPPA	5069	broad.mit.edu	37	9	119109372	119109372	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119109372T>G	uc004bjn.2	+	15	4229	c.3848T>G	c.(3847-3849)GTC>GGC	p.V1283G	PAPPA_uc011lxq.1_Missense_Mutation_p.V658G	NM_002581	NP_002572	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A	1283	Sushi 2.				cell differentiation|female pregnancy	cytoplasm|extracellular region|membrane	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(4)|pancreas(1)	9																		---	---	---	---
TRIM32	22954	broad.mit.edu	37	9	119461878	119461878	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:119461878G>A	uc004bjx.2	+	2	2015	c.1857G>A	c.(1855-1857)CCG>CCA	p.P619P	ASTN2_uc004bjr.1_Intron|ASTN2_uc004bjs.1_Intron|ASTN2_uc004bjt.1_Intron|TRIM32_uc004bjw.2_Silent_p.P619P	NM_001099679	NP_001093149	Q13049	TRI32_HUMAN	tripartite motif-containing 32	619	NHL 5.				fat cell differentiation|innate immune response|negative regulation of apoptosis|negative regulation of fibroblast proliferation|positive regulation of cell cycle|positive regulation of cell growth|positive regulation of cell migration|positive regulation of neurogenesis|positive regulation of neuron differentiation|positive regulation of NF-kappaB transcription factor activity|positive regulation of protein catabolic process|positive regulation of proteolysis|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to tumor necrosis factor|response to UV	nucleus	myosin binding|protein self-association|RNA binding|Tat protein binding|transcription coactivator activity|translation initiation factor binding|ubiquitin binding|ubiquitin-protein ligase activity|zinc ion binding			central_nervous_system(2)|kidney(1)	3														Bardet-Biedl_syndrome				---	---	---	---
DBC1	1620	broad.mit.edu	37	9	122004449	122004449	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:122004449C>A	uc004bkc.2	-	4	911	c.455G>T	c.(454-456)AGG>ATG	p.R152M	DBC1_uc004bkd.2_Missense_Mutation_p.R152M	NM_014618	NP_055433	O60477	DBC1_HUMAN	deleted in bladder cancer 1 precursor	152	MACPF.				cell cycle arrest|cell death	cytoplasm	protein binding			skin(3)|ovary(2)|central_nervous_system(2)|large_intestine(1)	8																		---	---	---	---
CDK5RAP2	55755	broad.mit.edu	37	9	123292304	123292304	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:123292304G>A	uc004bkf.2	-	8	958	c.777C>T	c.(775-777)CTC>CTT	p.L259L	CDK5RAP2_uc004bkg.2_Silent_p.L259L|CDK5RAP2_uc011lxw.1_5'UTR|CDK5RAP2_uc011lxx.1_RNA|CDK5RAP2_uc011lxy.1_RNA|CDK5RAP2_uc011lxz.1_5'UTR|CDK5RAP2_uc011lya.1_5'UTR|CDK5RAP2_uc004bkh.1_Silent_p.L259L|CDK5RAP2_uc004bki.2_Silent_p.L58L	NM_018249	NP_060719	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	259					brain development|centrosome organization|chromosome segregation|G2/M transition of mitotic cell cycle|microtubule bundle formation|negative regulation of centriole replication|positive regulation of transcription, DNA-dependent|regulation of neuron differentiation|regulation of spindle checkpoint	cytosol|Golgi apparatus|microtubule|pericentriolar material|perinuclear region of cytoplasm|spindle pole	calmodulin binding|microtubule binding|neuronal Cdc2-like kinase binding|transcription regulatory region DNA binding			ovary(2)|lung(1)|skin(1)	4																		---	---	---	---
STOM	2040	broad.mit.edu	37	9	124110353	124110353	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124110353A>G	uc004blh.2	-	6	680	c.600T>C	c.(598-600)CCT>CCC	p.P200P	STOM_uc011lyk.1_Silent_p.P149P|STOM_uc004bli.2_Intron	NM_004099	NP_004090	P27105	STOM_HUMAN	stomatin isoform a	200	Cytoplasmic (Potential).				protein homooligomerization	cytoskeleton|integral to plasma membrane|melanosome|membrane raft	protein binding				0				OV - Ovarian serous cystadenocarcinoma(323;0.00107)|GBM - Glioblastoma multiforme(294;0.0137)														---	---	---	---
STOM	2040	broad.mit.edu	37	9	124116904	124116904	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124116904A>G	uc004blh.2	-	3	293	c.213T>C	c.(211-213)ATT>ATC	p.I71I	STOM_uc011lyk.1_Silent_p.I20I|STOM_uc004bli.2_Intron	NM_004099	NP_004090	P27105	STOM_HUMAN	stomatin isoform a	71	Cytoplasmic (Potential).				protein homooligomerization	cytoskeleton|integral to plasma membrane|melanosome|membrane raft	protein binding				0				OV - Ovarian serous cystadenocarcinoma(323;0.00107)|GBM - Glioblastoma multiforme(294;0.0137)														---	---	---	---
DAB2IP	153090	broad.mit.edu	37	9	124528908	124528908	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124528908G>A	uc004bln.2	+	9	1581	c.1512G>A	c.(1510-1512)TCG>TCA	p.S504S	DAB2IP_uc004blo.2_Silent_p.S408S|DAB2IP_uc004blp.2_5'Flank	NM_032552	NP_115941	Q5VWQ8	DAB2P_HUMAN	disabled homolog 2 interacting protein isoform	532	Ras-GAP.				activation of JUN kinase activity|apoptosis in response to endoplasmic reticulum stress|cellular response to epidermal growth factor stimulus|cellular response to tumor necrosis factor|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|negative regulation of epithelial to mesenchymal transition|negative regulation of fibroblast proliferation|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of MAP kinase activity|negative regulation of NF-kappaB transcription factor activity|negative regulation of Ras GTPase activity|negative regulation of transcription from RNA polymerase II promoter|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|intrinsic to internal side of plasma membrane	14-3-3 protein binding|death receptor binding|mitogen-activated protein kinase kinase kinase binding|protein homodimerization activity|protein phosphatase 2A binding|Ras GTPase activator activity|signaling adaptor activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
DAB2IP	153090	broad.mit.edu	37	9	124536602	124536602	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124536602G>A	uc004bln.2	+	13	3016	c.2947G>A	c.(2947-2949)GCG>ACG	p.A983T	DAB2IP_uc004blo.2_Missense_Mutation_p.A887T|DAB2IP_uc004blp.2_Missense_Mutation_p.A416T	NM_032552	NP_115941	Q5VWQ8	DAB2P_HUMAN	disabled homolog 2 interacting protein isoform	1011					activation of JUN kinase activity|apoptosis in response to endoplasmic reticulum stress|cellular response to epidermal growth factor stimulus|cellular response to tumor necrosis factor|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|negative regulation of epithelial to mesenchymal transition|negative regulation of fibroblast proliferation|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of MAP kinase activity|negative regulation of NF-kappaB transcription factor activity|negative regulation of Ras GTPase activity|negative regulation of transcription from RNA polymerase II promoter|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|intrinsic to internal side of plasma membrane	14-3-3 protein binding|death receptor binding|mitogen-activated protein kinase kinase kinase binding|protein homodimerization activity|protein phosphatase 2A binding|Ras GTPase activator activity|signaling adaptor activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
TTLL11	158135	broad.mit.edu	37	9	124751869	124751869	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124751869C>T	uc004blt.1	-	4	1332	c.1144G>A	c.(1144-1146)GAC>AAC	p.D382N	TTLL11_uc011lyl.1_Missense_Mutation_p.D382N|TTLL11_uc004blr.2_RNA|TTLL11_uc011lym.1_Missense_Mutation_p.D59N|TTLL11_uc004blu.1_3'UTR	NM_194252	NP_919228	Q8NHH1	TTL11_HUMAN	tubulin tyrosine ligase-like family, member 11	382	TTL.				protein modification process	cilium|microtubule basal body	tubulin-tyrosine ligase activity				0																		---	---	---	---
MORN5	254956	broad.mit.edu	37	9	124922303	124922303	+	Intron	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:124922303G>T	uc004blw.2	+						NDUFA8_uc004blv.2_5'Flank|MORN5_uc011lyn.1_Intron|MORN5_uc011lyo.1_Intron	NM_198469	NP_940871			MORN repeat containing 5												0																		---	---	---	---
OR1J2	26740	broad.mit.edu	37	9	125273177	125273177	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125273177G>T	uc004bmj.1	+	4	952	c.97G>T	c.(97-99)GGC>TGC	p.G33C	OR1J2_uc011lyv.1_Missense_Mutation_p.G33C	NM_054107	NP_473448	Q8NGS2	OR1J2_HUMAN	olfactory receptor, family 1, subfamily J,	33	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(3)|pancreas(1)|breast(1)	5																		---	---	---	---
OR1J2	26740	broad.mit.edu	37	9	125273878	125273878	+	Missense_Mutation	SNP	T	G	G	rs79136414		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125273878T>G	uc004bmj.1	+	4	1653	c.798T>G	c.(796-798)AGT>AGG	p.S266R	OR1J2_uc011lyv.1_Missense_Mutation_p.S266R	NM_054107	NP_473448	Q8NGS2	OR1J2_HUMAN	olfactory receptor, family 1, subfamily J,	266	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(3)|pancreas(1)|breast(1)	5																		---	---	---	---
OR1L8	138881	broad.mit.edu	37	9	125329855	125329855	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125329855A>G	uc004bmp.1	-	1	902	c.902T>C	c.(901-903)CTG>CCG	p.L301P		NM_001004454	NP_001004454	Q8NGR8	OR1L8_HUMAN	olfactory receptor, family 1, subfamily L,	301	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
ZBTB6	10773	broad.mit.edu	37	9	125673923	125673923	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125673923A>G	uc004bnh.2	-	2	518	c.429T>C	c.(427-429)TGT>TGC	p.C143C		NM_006626	NP_006617	Q15916	ZBTB6_HUMAN	zinc finger and BTB domain containing 6	143					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
STRBP	55342	broad.mit.edu	37	9	125920678	125920678	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:125920678C>T	uc004bns.2	-	10	1296	c.866G>A	c.(865-867)CGA>CAA	p.R289Q	STRBP_uc004bnt.2_Missense_Mutation_p.R107Q|STRBP_uc004bnu.2_Missense_Mutation_p.R275Q|STRBP_uc004bnv.2_Missense_Mutation_p.R289Q	NM_018387	NP_060857	Q96SI9	STRBP_HUMAN	spermatid perinuclear RNA binding protein	289	DZF.				multicellular organismal development	cytoplasm|nucleus	DNA binding			breast(1)|skin(1)	2																		---	---	---	---
CRB2	286204	broad.mit.edu	37	9	126125283	126125283	+	Silent	SNP	C	T	T	rs148051468		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126125283C>T	uc004bnx.1	+	2	326	c.234C>T	c.(232-234)CAC>CAT	p.H78H	CRB2_uc004bnw.1_Silent_p.H78H	NM_173689	NP_775960	Q5IJ48	CRUM2_HUMAN	crumbs homolog 2 precursor	78	Extracellular (Potential).|EGF-like 1.					extracellular region|integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1																		---	---	---	---
PSMB7	5695	broad.mit.edu	37	9	127177648	127177648	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127177648G>A	uc004boj.2	-	1	74	c.57C>T	c.(55-57)TGC>TGT	p.C19C	PSMB7_uc010mwm.2_Silent_p.C19C	NM_002799	NP_002790	Q99436	PSB7_HUMAN	proteasome beta 7 subunit proprotein	19					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome core complex	threonine-type endopeptidase activity				0																OREG0019476	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
GOLGA1	2800	broad.mit.edu	37	9	127683473	127683473	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127683473C>T	uc004bpc.2	-	10	1120	c.778G>A	c.(778-780)GCC>ACC	p.A260T	GOLGA1_uc010mws.2_RNA|GOLGA1_uc010mwt.1_Missense_Mutation_p.A235T	NM_002077	NP_002068	Q92805	GOGA1_HUMAN	golgin 97	260	Potential.					Golgi cisterna membrane				ovary(1)	1																		---	---	---	---
GAPVD1	26130	broad.mit.edu	37	9	128117043	128117043	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128117043C>T	uc010mwx.2	+	24	4060	c.3734C>T	c.(3733-3735)GCC>GTC	p.A1245V	GAPVD1_uc004bpp.2_Missense_Mutation_p.A1254V|GAPVD1_uc004bpq.2_Missense_Mutation_p.A1227V|GAPVD1_uc004bpr.2_Missense_Mutation_p.A1206V|GAPVD1_uc004bps.2_Missense_Mutation_p.A1200V|GAPVD1_uc004bpt.2_Missense_Mutation_p.A260V	NM_015635	NP_056450	Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1	1245					endocytosis|regulation of protein transport|regulation of small GTPase mediated signal transduction|signal transduction	cytosol|endosome|membrane	GTPase activating protein binding|GTPase activator activity|guanyl-nucleotide exchange factor activity			ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
PBX3	5090	broad.mit.edu	37	9	128697875	128697875	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128697875A>G	uc004bqb.2	+	5	948	c.832A>G	c.(832-834)ACA>GCA	p.T278A	PBX3_uc004bqc.2_Missense_Mutation_p.T97A|PBX3_uc004bqd.2_Missense_Mutation_p.T97A|PBX3_uc011lzw.1_Missense_Mutation_p.T203A|PBX3_uc011lzx.1_Missense_Mutation_p.T189A|PBX3_uc004bqe.2_Missense_Mutation_p.T165A	NM_006195	NP_006186	P40426	PBX3_HUMAN	pre-B-cell leukemia homeobox 3 isoform 1	278	Homeobox; TALE-type.				anterior compartment pattern formation|posterior compartment specification		sequence-specific DNA binding transcription factor activity			upper_aerodigestive_tract(1)	1																		---	---	---	---
ST6GALNAC4	27090	broad.mit.edu	37	9	130674805	130674805	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130674805C>T	uc004bss.2	-	4	629	c.353G>A	c.(352-354)CGC>CAC	p.R118H	ST6GALNAC4_uc004bst.2_Missense_Mutation_p.R34H	NM_175039	NP_778204	Q9H4F1	SIA7D_HUMAN	sialyltransferase 7D isoform a	118	Lumenal (Potential).				glycolipid metabolic process|protein glycosylation	integral to Golgi membrane|nucleus|soluble fraction	(alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl-galactosaminide 6-alpha-sialyltransferase activity				0																		---	---	---	---
C9orf119	375757	broad.mit.edu	37	9	131038591	131038591	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131038591A>G	uc004bup.2	+	1	167	c.167A>G	c.(166-168)CAC>CGC	p.H56R	GOLGA2_uc011maw.1_5'Flank|GOLGA2_uc010mxw.2_5'Flank|GOLGA2_uc004bul.1_5'Flank|C9orf119_uc010mxx.1_Missense_Mutation_p.H56R	NM_001040011	NP_001035100	Q1ZZU3	SWI5_HUMAN	hypothetical protein LOC375757	56					double-strand break repair via homologous recombination	Swi5-Sfr1 complex	protein binding				0																		---	---	---	---
ODF2	4957	broad.mit.edu	37	9	131219708	131219708	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131219708C>T	uc011mbd.1	+	2	335	c.24C>T	c.(22-24)GGC>GGT	p.G8G	ODF2_uc011maz.1_Intron|ODF2_uc011mba.1_Intron|ODF2_uc010myb.2_Intron|ODF2_uc011mbb.1_Intron|ODF2_uc011mbc.1_Intron|ODF2_uc004bva.2_Intron|ODF2_uc004bvb.2_5'UTR|ODF2_uc011mbe.1_Intron|ODF2_uc004bvc.2_Intron|ODF2_uc010myc.2_Intron|ODF2_uc011mbf.1_Intron|ODF2_uc004bvd.3_Silent_p.G8G|ODF2_uc004bve.2_Silent_p.G8G	NM_002540	NP_002531	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2 isoform 1	8					cell differentiation|G2/M transition of mitotic cell cycle|multicellular organismal development|spermatogenesis	centriole|cilium|cytosol|microtubule|spindle pole	protein binding|structural molecule activity			ovary(1)	1																		---	---	---	---
ODF2	4957	broad.mit.edu	37	9	131247655	131247655	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131247655C>T	uc011mbd.1	+	13	1613	c.1302C>T	c.(1300-1302)GTC>GTT	p.V434V	ODF2_uc011maz.1_Silent_p.V434V|ODF2_uc011mbb.1_Silent_p.V368V|ODF2_uc011mbc.1_Silent_p.V353V|ODF2_uc004bva.2_Silent_p.V387V|ODF2_uc004bvb.2_Silent_p.V410V|ODF2_uc011mbe.1_Silent_p.V429V|ODF2_uc004bvc.2_Silent_p.V410V|ODF2_uc010myc.2_Silent_p.V377V|ODF2_uc011mbf.1_Silent_p.V415V|ODF2_uc004bvd.3_Silent_p.V434V|ODF2_uc004bve.2_Silent_p.V415V|uc004bvg.2_5'Flank	NM_002540	NP_002531	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2 isoform 1	434					cell differentiation|G2/M transition of mitotic cell cycle|multicellular organismal development|spermatogenesis	centriole|cilium|cytosol|microtubule|spindle pole	protein binding|structural molecule activity			ovary(1)	1																		---	---	---	---
SPTAN1	6709	broad.mit.edu	37	9	131386717	131386717	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131386717G>A	uc004bvl.3	+	45	6041	c.5928G>A	c.(5926-5928)TCG>TCA	p.S1976S	SPTAN1_uc004bvm.3_Silent_p.S1981S|SPTAN1_uc004bvn.3_Silent_p.S1956S|SPTAN1_uc010mye.1_5'Flank|SPTAN1_uc010myf.1_5'Flank	NM_003127	NP_003118	Q13813	SPTA2_HUMAN	spectrin, alpha, non-erythrocytic 1	1976	Spectrin 21.				actin filament capping|axon guidance|cellular component disassembly involved in apoptosis	cytosol|intracellular membrane-bounded organelle|membrane fraction|microtubule cytoskeleton|spectrin	actin binding|calcium ion binding|calmodulin binding|structural constituent of cytoskeleton			breast(5)|ovary(4)|pancreas(1)	10																		---	---	---	---
ZER1	10444	broad.mit.edu	37	9	131515105	131515105	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131515105C>T	uc004bwa.1	-	5	1203	c.770G>A	c.(769-771)CGC>CAC	p.R257H		NM_006336	NP_006327	Q7Z7L7	ZER1_HUMAN	zyg-11 homolog B (C. elegans)-like	257	LRR 2.				ATP hydrolysis coupled proton transport|regulation of ubiquitin-protein ligase activity	Cul2-RING ubiquitin ligase complex|vacuolar proton-transporting V-type ATPase, V1 domain	protein binding|proton-transporting ATPase activity, rotational mechanism|ubiquitin-protein ligase activity			ovary(1)	1																		---	---	---	---
TBC1D13	54662	broad.mit.edu	37	9	131559453	131559453	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131559453A>G	uc010myj.2	+	7	626	c.503A>G	c.(502-504)AAA>AGA	p.K168R	TBC1D13_uc010myk.2_Missense_Mutation_p.K168R|TBC1D13_uc010myl.2_5'UTR	NM_018201	NP_060671	Q9NVG8	TBC13_HUMAN	TBC1 domain family, member 13	168	Rab-GAP TBC.					intracellular	Rab GTPase activator activity				0																		---	---	---	---
LRRC8A	56262	broad.mit.edu	37	9	131671141	131671141	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131671141C>T	uc004bwl.3	+	3	1952	c.1698C>T	c.(1696-1698)GGC>GGT	p.G566G	LRRC8A_uc010myp.2_Silent_p.G566G|LRRC8A_uc010myq.2_Silent_p.G566G	NM_019594	NP_062540	Q8IWT6	LRC8A_HUMAN	leucine rich repeat containing 8 family, member	566	LRR 8.				pre-B cell differentiation	integral to membrane					0																		---	---	---	---
PHYHD1	254295	broad.mit.edu	37	9	131698734	131698734	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131698734C>T	uc004bwo.2	+	7	1257	c.324C>T	c.(322-324)CAC>CAT	p.H108H	PHYHD1_uc004bwn.2_Silent_p.H108H|PHYHD1_uc004bwm.2_RNA|PHYHD1_uc004bwp.2_Silent_p.H108H	NM_001100876	NP_001094346	Q5SRE7	PHYD1_HUMAN	phytanoyl-CoA dioxygenase domain containing 1	108							metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0																		---	---	---	---
METTL11A	28989	broad.mit.edu	37	9	132397699	132397699	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132397699C>A	uc004byd.1	+	4	822	c.628C>A	c.(628-630)CTC>ATC	p.L210I	METTL11A_uc010myw.1_RNA|METTL11A_uc011mbs.1_3'UTR|ASB6_uc004bye.1_3'UTR|ASB6_uc004byf.1_3'UTR|ASB6_uc004byg.1_3'UTR|ASB6_uc011mbt.1_3'UTR|ASB6_uc010myx.1_3'UTR	NM_014064	NP_054783	Q9BV86	NTM1A_HUMAN	methyltransferase like 11A	210					chromosome segregation|N-terminal peptidyl-proline dimethylation|N-terminal peptidyl-serine dimethylation|N-terminal peptidyl-serine trimethylation|spindle organization	nucleus	protein binding|protein methyltransferase activity				0																		---	---	---	---
USP20	10868	broad.mit.edu	37	9	132623323	132623323	+	Intron	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132623323C>A	uc004bys.2	+						USP20_uc004byr.2_Intron|USP20_uc004byt.1_Intron	NM_001110303	NP_001103773			ubiquitin specific protease 20						endocytosis|protein K48-linked deubiquitination|protein K63-linked deubiquitination|regulation of G-protein coupled receptor protein signaling pathway|ubiquitin-dependent protein catabolic process	perinuclear region of cytoplasm	cysteine-type endopeptidase activity|G-protein-coupled receptor binding|ubiquitin thiolesterase activity|zinc ion binding			lung(1)|breast(1)	2		Ovarian(14;0.00556)																---	---	---	---
ASS1	445	broad.mit.edu	37	9	133355830	133355830	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133355830T>A	uc004bzm.2	+	12	1188	c.832T>A	c.(832-834)TCC>ACC	p.S278T	ASS1_uc004bzn.2_Missense_Mutation_p.S278T|ASS1_uc010mza.2_Missense_Mutation_p.S354T|ASS1_uc004bzo.2_Missense_Mutation_p.S259T|ASS1_uc010mzb.2_Missense_Mutation_p.S316T|ASS1_uc004bzp.2_Missense_Mutation_p.S278T|ASS1_uc010mzc.2_Missense_Mutation_p.S278T	NM_000050	NP_000041	P00966	ASSY_HUMAN	argininosuccinate synthetase 1	278					arginine biosynthetic process|urea cycle	cytosol	argininosuccinate synthase activity|ATP binding|protein binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(145;0.000514)	Adenosine triphosphate(DB00171)|L-Arginine(DB00125)|L-Aspartic Acid(DB00128)|L-Citrulline(DB00155)													---	---	---	---
FUBP3	8939	broad.mit.edu	37	9	133470944	133470944	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133470944C>T	uc004bzr.1	+	2	267	c.159C>T	c.(157-159)TAC>TAT	p.Y53Y	FUBP3_uc010mzd.1_Translation_Start_Site|FUBP3_uc004bzs.1_Intron	NM_003934	NP_003925	Q96I24	FUBP3_HUMAN	far upstream element (FUSE) binding protein 3	53					positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|RNA binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(145;0.000279)														---	---	---	---
LAMC3	10319	broad.mit.edu	37	9	133954577	133954577	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133954577G>T	uc004caa.1	+	23	3917	c.3819G>T	c.(3817-3819)AAG>AAT	p.K1273N	LAMC3_uc010mze.1_Translation_Start_Site	NM_006059	NP_006050	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3 precursor	1273	Domain II and I.				cell adhesion	basement membrane|membrane	structural molecule activity			ovary(2)|pancreas(1)	3	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)														---	---	---	---
NUP214	8021	broad.mit.edu	37	9	134105106	134105106	+	Intron	SNP	C	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134105106C>G	uc004cag.2	+						NUP214_uc004cah.2_Intron|NUP214_uc004cai.2_Intron|NUP214_uc010mzg.2_RNA|NUP214_uc011mcg.1_Intron	NM_005085	NP_005076			nucleoporin 214kDa						carbohydrate metabolic process|glucose transport|mRNA metabolic process|protein export from nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore|nucleoplasm	protein binding			breast(7)|lung(3)|skin(3)|ovary(2)|central_nervous_system(1)	16	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)				T	DEK|SET|ABL1	AML|T-ALL								---	---	---	---
UCK1	83549	broad.mit.edu	37	9	134404979	134404979	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134404979G>A	uc004cay.2	-						UCK1_uc010mzk.2_Intron|UCK1_uc004cba.2_Intron|UCK1_uc004caz.2_Intron	NM_031432	NP_113620			uridine-cytidine kinase 1 isoform a						pyrimidine base metabolic process|pyrimidine nucleoside salvage	cytosol	ATP binding|phosphotransferase activity, alcohol group as acceptor|uridine kinase activity				0				OV - Ovarian serous cystadenocarcinoma(145;2.34e-05)|Epithelial(140;0.000219)														---	---	---	---
SETX	23064	broad.mit.edu	37	9	135156916	135156916	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135156916G>A	uc004cbk.2	-	20	6775	c.6592C>T	c.(6592-6594)CGC>TGC	p.R2198C	SETX_uc004cbj.2_Missense_Mutation_p.R1817C|SETX_uc010mzt.2_Missense_Mutation_p.R1817C	NM_015046	NP_055861	Q7Z333	SETX_HUMAN	senataxin	2198					cell death|double-strand break repair|RNA processing	cytoplasm|nucleolus|nucleoplasm	ATP binding|DNA helicase activity			ovary(2)|skin(1)	3		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)														---	---	---	---
SETX	23064	broad.mit.edu	37	9	135158790	135158790	+	Missense_Mutation	SNP	C	T	T	rs121434378		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135158790C>T	uc004cbk.2	-	19	6590	c.6407G>A	c.(6406-6408)CGC>CAC	p.R2136H	SETX_uc004cbj.2_Missense_Mutation_p.R1755H|SETX_uc010mzt.2_Missense_Mutation_p.R1755H	NM_015046	NP_055861	Q7Z333	SETX_HUMAN	senataxin	2136	Potential.		R -> H (in ALS4).		cell death|double-strand break repair|RNA processing	cytoplasm|nucleolus|nucleoplasm	ATP binding|DNA helicase activity			ovary(2)|skin(1)	3		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)														---	---	---	---
SETX	23064	broad.mit.edu	37	9	135202262	135202262	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135202262C>A	uc004cbk.2	-	10	4906	c.4723G>T	c.(4723-4725)GAT>TAT	p.D1575Y	SETX_uc004cbj.2_Missense_Mutation_p.D1194Y|SETX_uc010mzt.2_Missense_Mutation_p.D1194Y	NM_015046	NP_055861	Q7Z333	SETX_HUMAN	senataxin	1575					cell death|double-strand break repair|RNA processing	cytoplasm|nucleolus|nucleoplasm	ATP binding|DNA helicase activity			ovary(2)|skin(1)	3		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)														---	---	---	---
SETX	23064	broad.mit.edu	37	9	135203619	135203619	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135203619A>G	uc004cbk.2	-	10	3549	c.3366T>C	c.(3364-3366)GGT>GGC	p.G1122G	SETX_uc004cbj.2_Silent_p.G741G|SETX_uc010mzt.2_Silent_p.G741G	NM_015046	NP_055861	Q7Z333	SETX_HUMAN	senataxin	1122					cell death|double-strand break repair|RNA processing	cytoplasm|nucleolus|nucleoplasm	ATP binding|DNA helicase activity			ovary(2)|skin(1)	3		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)														---	---	---	---
TTF1	7270	broad.mit.edu	37	9	135275530	135275530	+	Missense_Mutation	SNP	C	T	T	rs145243204		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:135275530C>T	uc004cbl.2	-	3	1535	c.1483G>A	c.(1483-1485)GTG>ATG	p.V495M	TTF1_uc011mcp.1_RNA|TTF1_uc004cbm.2_Translation_Start_Site	NM_007344	NP_031370	Q15361	TTF1_HUMAN	transcription termination factor, RNA polymerase	495					negative regulation of DNA replication|regulation of transcription, DNA-dependent|termination of RNA polymerase I transcription	nucleolus|nucleoplasm	DNA binding			ovary(2)|upper_aerodigestive_tract(1)|pancreas(1)	4		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;4.25e-06)|Epithelial(140;9.09e-05)														---	---	---	---
SURF2	6835	broad.mit.edu	37	9	136227985	136227985	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136227985G>T	uc004cdi.2	+	6	789	c.741G>T	c.(739-741)AAG>AAT	p.K247N		NM_017503	NP_059973	Q15527	SURF2_HUMAN	surfeit 2	247							protein binding				0				OV - Ovarian serous cystadenocarcinoma(145;4.87e-07)|Epithelial(140;4.02e-06)|all cancers(34;3.71e-05)														---	---	---	---
DBH	1621	broad.mit.edu	37	9	136513028	136513028	+	Missense_Mutation	SNP	C	T	T	rs75215331	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:136513028C>T	uc004cel.2	+	6	1094	c.1085C>T	c.(1084-1086)GCG>GTG	p.A362V		NM_000787	NP_000778	P09172	DOPO_HUMAN	dopamine beta hydroxylase precursor	362	Intragranular (Potential).				hormone biosynthetic process	chromaffin granule lumen|chromaffin granule membrane|extracellular region|integral to membrane|membrane fraction|soluble fraction|transport vesicle membrane	dopamine beta-monooxygenase activity|L-ascorbic acid binding			ovary(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(145;2.33e-07)|Epithelial(140;1.5e-06)|all cancers(34;1.66e-05)	Dopamine(DB00988)|Vitamin C(DB00126)													---	---	---	---
WDR5	11091	broad.mit.edu	37	9	137023061	137023061	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137023061C>A	uc004cey.2	+	14	1122	c.951C>A	c.(949-951)GCC>GCA	p.A317A	WDR5_uc004cez.2_Silent_p.A317A	NM_017588	NP_060058	P61964	WDR5_HUMAN	WD repeat domain 5	317	WD 7.				histone H3 acetylation|histone H3-K4 methylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	Ada2/Gcn5/Ada3 transcription activator complex|MLL1 complex|Set1C/COMPASS complex	protein binding				0		Myeloproliferative disorder(178;0.0255)|Medulloblastoma(224;0.123)		Epithelial(140;6.61e-13)|all cancers(34;5.66e-12)|OV - Ovarian serous cystadenocarcinoma(145;3.93e-08)|GBM - Glioblastoma multiforme(294;0.00326)|READ - Rectum adenocarcinoma(205;0.154)														---	---	---	---
RXRA	6256	broad.mit.edu	37	9	137293679	137293679	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137293679T>C	uc004cfb.2	+	2	392	c.230T>C	c.(229-231)ATG>ACG	p.M77T	RXRA_uc004cfa.1_Silent_p.H127H	NM_002957	NP_002948	P19793	RXRA_HUMAN	retinoid X receptor, alpha	77	Modulating (By similarity).				cellular lipid metabolic process|cholesterol metabolic process|interspecies interaction between organisms|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to retinoic acid|vitamin metabolic process	nuclear chromatin|nucleoplasm	enzyme binding|ligand-regulated transcription factor activity|protein heterodimerization activity|retinoic acid-responsive element binding|retinoid-X receptor activity|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|transcription coactivator activity|vitamin D receptor binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2				OV - Ovarian serous cystadenocarcinoma(145;4.66e-08)|Epithelial(140;6.72e-08)|all cancers(34;2.22e-07)	Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)													---	---	---	---
RXRA	6256	broad.mit.edu	37	9	137321021	137321021	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137321021G>A	uc004cfb.2	+	7	1140	c.978G>A	c.(976-978)CTG>CTA	p.L326L	RXRA_uc004cfc.1_Silent_p.L229L	NM_002957	NP_002948	P19793	RXRA_HUMAN	retinoid X receptor, alpha	326	Ligand-binding.				cellular lipid metabolic process|cholesterol metabolic process|interspecies interaction between organisms|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to retinoic acid|vitamin metabolic process	nuclear chromatin|nucleoplasm	enzyme binding|ligand-regulated transcription factor activity|protein heterodimerization activity|retinoic acid-responsive element binding|retinoid-X receptor activity|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|transcription coactivator activity|vitamin D receptor binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2				OV - Ovarian serous cystadenocarcinoma(145;4.66e-08)|Epithelial(140;6.72e-08)|all cancers(34;2.22e-07)	Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)													---	---	---	---
COL5A1	1289	broad.mit.edu	37	9	137711996	137711996	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137711996C>T	uc004cfe.2	+	58	4863	c.4481C>T	c.(4480-4482)CCG>CTG	p.P1494L	uc004cff.2_RNA	NM_000093	NP_000084	P20908	CO5A1_HUMAN	alpha 1 type V collagen preproprotein	1494	Triple-helical region.				axon guidance|cell adhesion|collagen biosynthetic process|collagen fibril organization|eye morphogenesis|fibril organization|integrin biosynthetic process|skin development|wound healing, spreading of epidermal cells	collagen type V	heparin binding|integrin binding|platelet-derived growth factor binding|proteoglycan binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|kidney(1)	11		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)														---	---	---	---
OLFM1	10439	broad.mit.edu	37	9	138011519	138011519	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138011519A>G	uc010nar.2	+	6	1269	c.953A>G	c.(952-954)CAC>CGC	p.H318R	OLFM1_uc004cfl.3_Missense_Mutation_p.H300R|OLFM1_uc004cfn.3_Missense_Mutation_p.H69R	NM_014279	NP_055094	Q99784	NOE1_HUMAN	olfactomedin related ER localized protein	318	Olfactomedin-like.				nervous system development	endoplasmic reticulum lumen	protein binding			ovary(1)|skin(1)	2		Myeloproliferative disorder(178;0.0333)		Epithelial(140;5.49e-08)|OV - Ovarian serous cystadenocarcinoma(145;9.68e-08)|all cancers(34;1.88e-07)														---	---	---	---
KCNT1	57582	broad.mit.edu	37	9	138660717	138660717	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138660717G>A	uc011mdq.1	+	15	1518	c.1444G>A	c.(1444-1446)GCC>ACC	p.A482T	KCNT1_uc011mdr.1_Missense_Mutation_p.A309T|KCNT1_uc010nbf.2_Missense_Mutation_p.A437T|KCNT1_uc004cgo.1_Missense_Mutation_p.A231T	NM_020822	NP_065873	Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1	482						membrane	binding|calcium-activated potassium channel activity			large_intestine(2)|ovary(1)|pancreas(1)	4		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)														---	---	---	---
NOTCH1	4851	broad.mit.edu	37	9	139390969	139390969	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139390969G>T	uc004chz.2	-	34	7222	c.7222C>A	c.(7222-7224)CTG>ATG	p.L2408M		NM_017617	NP_060087	P46531	NOTC1_HUMAN	notch1 preproprotein	2408	Cytoplasmic (Potential).				aortic valve morphogenesis|immune response|negative regulation of BMP signaling pathway|negative regulation of cell-substrate adhesion|negative regulation of myoblast differentiation|negative regulation of osteoblast differentiation|negative regulation of transcription, DNA-dependent|Notch receptor processing	cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity	p.S2408N(2)		haematopoietic_and_lymphoid_tissue(791)|upper_aerodigestive_tract(29)|lung(13)|central_nervous_system(10)|breast(9)|large_intestine(1)|skin(1)|oesophagus(1)|pancreas(1)	856	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)				T|Mis|O	TRB@	T-ALL					HNSCC(8;0.001)			---	---	---	---
NOTCH1	4851	broad.mit.edu	37	9	139407528	139407528	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139407528G>A	uc004chz.2	-	15	2412	c.2412C>T	c.(2410-2412)GGC>GGT	p.G804G	NOTCH1_uc004cia.1_Silent_p.G34G	NM_017617	NP_060087	P46531	NOTC1_HUMAN	notch1 preproprotein	804	Extracellular (Potential).|EGF-like 21; calcium-binding (Potential).				aortic valve morphogenesis|immune response|negative regulation of BMP signaling pathway|negative regulation of cell-substrate adhesion|negative regulation of myoblast differentiation|negative regulation of osteoblast differentiation|negative regulation of transcription, DNA-dependent|Notch receptor processing	cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity			haematopoietic_and_lymphoid_tissue(791)|upper_aerodigestive_tract(29)|lung(13)|central_nervous_system(10)|breast(9)|large_intestine(1)|skin(1)|oesophagus(1)|pancreas(1)	856	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)				T|Mis|O	TRB@	T-ALL					HNSCC(8;0.001)			---	---	---	---
PHPT1	29085	broad.mit.edu	37	9	139743896	139743896	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139743896A>G	uc004cjp.2	+	2	636	c.14A>G	c.(13-15)GAC>GGC	p.D5G	PHPT1_uc011mei.1_Missense_Mutation_p.D5G|PHPT1_uc004cjq.3_Missense_Mutation_p.D5G|MAMDC4_uc004cjs.2_5'Flank|MAMDC4_uc011mej.1_5'Flank	NM_014172	NP_054891	Q9NRX4	PHP14_HUMAN	phosphohistidine phosphatase 1 isoform 3	5						cytosol	phosphohistidine phosphatase activity|phosphoprotein phosphatase activity				0	all_cancers(76;0.0763)|all_epithelial(76;0.198)	Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171)														---	---	---	---
ABCA2	20	broad.mit.edu	37	9	139905933	139905933	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139905933T>C	uc011mem.1	-	36	5870	c.5722A>G	c.(5722-5724)ATT>GTT	p.I1908V	ABCA2_uc011mel.1_Missense_Mutation_p.I1909V|ABCA2_uc004ckl.1_Missense_Mutation_p.I1839V|ABCA2_uc004ckm.1_Missense_Mutation_p.I1939V	NM_001606	NP_001597	Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A, member 2	1908	Helical; (Potential).				cholesterol homeostasis|lipid metabolic process|regulation of intracellular cholesterol transport|regulation of transcription from RNA polymerase II promoter|response to drug|response to steroid hormone stimulus	ATP-binding cassette (ABC) transporter complex|cytoplasmic membrane-bounded vesicle|endosome|integral to membrane|microtubule organizing center	ATP binding|ATPase activity, coupled to transmembrane movement of substances				0	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)														---	---	---	---
ABCA2	20	broad.mit.edu	37	9	139910614	139910614	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139910614G>A	uc011mem.1	-	21	3262	c.3114C>T	c.(3112-3114)ACC>ACT	p.T1038T	ABCA2_uc011mel.1_Silent_p.T1039T|ABCA2_uc004ckl.1_Silent_p.T969T|ABCA2_uc004ckm.1_Silent_p.T1069T|ABCA2_uc004ckn.1_RNA	NM_001606	NP_001597	Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A, member 2	1038	ABC transporter 1.				cholesterol homeostasis|lipid metabolic process|regulation of intracellular cholesterol transport|regulation of transcription from RNA polymerase II promoter|response to drug|response to steroid hormone stimulus	ATP-binding cassette (ABC) transporter complex|cytoplasmic membrane-bounded vesicle|endosome|integral to membrane|microtubule organizing center	ATP binding|ATPase activity, coupled to transmembrane movement of substances				0	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)														---	---	---	---
GRIN1	2902	broad.mit.edu	37	9	140040200	140040200	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140040200G>A	uc004clk.2	+	3	746	c.416G>A	c.(415-417)CGC>CAC	p.R139H	GRIN1_uc004cli.1_5'UTR|GRIN1_uc004clj.1_Missense_Mutation_p.R136H|GRIN1_uc004cll.2_Missense_Mutation_p.R139H|GRIN1_uc004clm.2_Missense_Mutation_p.R139H|GRIN1_uc004cln.2_Missense_Mutation_p.R136H|GRIN1_uc004clo.2_Missense_Mutation_p.R136H	NM_007327	NP_015566	Q05586	NMDZ1_HUMAN	NMDA receptor 1 isoform NR1-3 precursor	139	Extracellular (Potential).				ionotropic glutamate receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|regulation of excitatory postsynaptic membrane potential|response to ethanol|visual learning	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic density|postsynaptic membrane|synaptic vesicle|synaptosome	calcium ion binding|calmodulin binding|extracellular-glutamate-gated ion channel activity|glutamate binding|glycine binding			skin(1)	1	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;6.87e-05)|Epithelial(140;0.00095)	L-Glutamic Acid(DB00142)|Orphenadrine(DB01173)													---	---	---	---
GRIN1	2902	broad.mit.edu	37	9	140043540	140043540	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140043540G>A	uc004clk.2	+	4	980	c.650G>A	c.(649-651)CGG>CAG	p.R217Q	GRIN1_uc004cli.1_5'UTR|GRIN1_uc004clj.1_Missense_Mutation_p.R214Q|GRIN1_uc004cll.2_Missense_Mutation_p.R217Q|GRIN1_uc004clm.2_Missense_Mutation_p.R217Q|GRIN1_uc004cln.2_Missense_Mutation_p.R235Q|GRIN1_uc004clo.2_Missense_Mutation_p.R235Q	NM_007327	NP_015566	Q05586	NMDZ1_HUMAN	NMDA receptor 1 isoform NR1-3 precursor	217	Extracellular (Potential).				ionotropic glutamate receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|regulation of excitatory postsynaptic membrane potential|response to ethanol|visual learning	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic density|postsynaptic membrane|synaptic vesicle|synaptosome	calcium ion binding|calmodulin binding|extracellular-glutamate-gated ion channel activity|glutamate binding|glycine binding			skin(1)	1	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;6.87e-05)|Epithelial(140;0.00095)	L-Glutamic Acid(DB00142)|Orphenadrine(DB01173)													---	---	---	---
TPRN	286262	broad.mit.edu	37	9	140093731	140093731	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140093731G>T	uc004clt.2	-	1	1250	c.1250C>A	c.(1249-1251)CCT>CAT	p.P417H	TPRN_uc004clu.2_Missense_Mutation_p.P417H	NM_173691	NP_775962	Q4KMQ1	TPRN_HUMAN	hypothetical protein LOC286262 isoform 2	478					sensory perception of sound	stereocilium					0																		---	---	---	---
PNPLA7	375775	broad.mit.edu	37	9	140361907	140361907	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140361907G>A	uc004cnf.2	-	25	3163	c.2826C>T	c.(2824-2826)GGC>GGT	p.G942G	C9orf167_uc011mew.1_Intron|PNPLA7_uc004cnd.1_Silent_p.G208G|PNPLA7_uc004cne.1_Silent_p.G208G|PNPLA7_uc011mfa.1_Silent_p.G350G|PNPLA7_uc010ncj.1_Silent_p.G967G	NM_152286	NP_689499	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	942	Patatin.				lipid metabolic process	endoplasmic reticulum|integral to membrane|lysosomal membrane|microsome|mitochondrial membrane|nuclear membrane	hydrolase activity			skin(1)	1	all_cancers(76;0.126)			OV - Ovarian serous cystadenocarcinoma(145;0.000268)|Epithelial(140;0.000839)														---	---	---	---
EHMT1	79813	broad.mit.edu	37	9	140622893	140622893	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140622893A>G	uc011mfc.1	+	4	772	c.735A>G	c.(733-735)GGA>GGG	p.G245G	EHMT1_uc004coa.2_Silent_p.G245G|EHMT1_uc004cob.1_Silent_p.G214G	NM_024757	NP_079033	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	245					DNA methylation|embryo development|peptidyl-lysine dimethylation|peptidyl-lysine monomethylation	chromosome|nucleus	histone methyltransferase activity (H3-K27 specific)|histone methyltransferase activity (H3-K9 specific)|p53 binding|zinc ion binding			breast(2)|pancreas(1)	3	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)														---	---	---	---
DIP2C	22982	broad.mit.edu	37	10	408477	408477	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:408477G>A	uc001ifp.2	-	22	2837	c.2747C>T	c.(2746-2748)CCC>CTC	p.P916L	DIP2C_uc009xhi.1_Missense_Mutation_p.P302L|DIP2C_uc010pzz.1_Missense_Mutation_p.P237L	NM_014974	NP_055789	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C	916						nucleus	catalytic activity|transcription factor binding			breast(4)|ovary(2)|large_intestine(1)	7		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)														---	---	---	---
DIP2C	22982	broad.mit.edu	37	10	436262	436262	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:436262G>A	uc001ifp.2	-	12	1526	c.1436C>T	c.(1435-1437)CCG>CTG	p.P479L	DIP2C_uc009xhj.1_Missense_Mutation_p.P175L	NM_014974	NP_055789	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C	479						nucleus	catalytic activity|transcription factor binding			breast(4)|ovary(2)|large_intestine(1)	7		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)														---	---	---	---
DIP2C	22982	broad.mit.edu	37	10	465108	465108	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:465108C>T	uc001ifp.2	-	6	726	c.636G>A	c.(634-636)ACG>ACA	p.T212T		NM_014974	NP_055789	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C	212						nucleus	catalytic activity|transcription factor binding			breast(4)|ovary(2)|large_intestine(1)	7		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)														---	---	---	---
GTPBP4	23560	broad.mit.edu	37	10	1046962	1046962	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1046962C>T	uc001ift.2	+						GTPBP4_uc010qac.1_Intron|GTPBP4_uc001ifu.2_Intron|GTPBP4_uc010qad.1_Intron|GTPBP4_uc010qae.1_Intron	NM_012341	NP_036473			G protein-binding protein CRFG						negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of collagen binding|negative regulation of DNA replication|negative regulation of protein ubiquitination|protein stabilization|regulation of cyclin-dependent protein kinase activity|ribosome biogenesis	nucleolus|perinuclear region of cytoplasm	GTP binding|GTPase activity|protein binding			ovary(1)|skin(1)	2		all_epithelial(10;0.107)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.0814)	Epithelial(11;0.0513)|all cancers(11;0.135)|OV - Ovarian serous cystadenocarcinoma(14;0.173)														---	---	---	---
GTPBP4	23560	broad.mit.edu	37	10	1058522	1058522	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1058522C>T	uc001ift.2	+	14	1533	c.1462C>T	c.(1462-1464)CGA>TGA	p.R488*	GTPBP4_uc001ifu.2_RNA|GTPBP4_uc010qad.1_Nonsense_Mutation_p.R372*|GTPBP4_uc010qae.1_Nonsense_Mutation_p.R441*	NM_012341	NP_036473	Q9BZE4	NOG1_HUMAN	G protein-binding protein CRFG	488					negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of collagen binding|negative regulation of DNA replication|negative regulation of protein ubiquitination|protein stabilization|regulation of cyclin-dependent protein kinase activity|ribosome biogenesis	nucleolus|perinuclear region of cytoplasm	GTP binding|GTPase activity|protein binding			ovary(1)|skin(1)	2		all_epithelial(10;0.107)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.0814)	Epithelial(11;0.0513)|all cancers(11;0.135)|OV - Ovarian serous cystadenocarcinoma(14;0.173)														---	---	---	---
GTPBP4	23560	broad.mit.edu	37	10	1061799	1061799	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:1061799G>A	uc001ift.2	+	16	1786	c.1715G>A	c.(1714-1716)CGA>CAA	p.R572Q	GTPBP4_uc001ifu.2_RNA|GTPBP4_uc010qad.1_Missense_Mutation_p.R456Q|GTPBP4_uc010qae.1_Missense_Mutation_p.R525Q	NM_012341	NP_036473	Q9BZE4	NOG1_HUMAN	G protein-binding protein CRFG	572					negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of collagen binding|negative regulation of DNA replication|negative regulation of protein ubiquitination|protein stabilization|regulation of cyclin-dependent protein kinase activity|ribosome biogenesis	nucleolus|perinuclear region of cytoplasm	GTP binding|GTPase activity|protein binding			ovary(1)|skin(1)	2		all_epithelial(10;0.107)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.0814)	Epithelial(11;0.0513)|all cancers(11;0.135)|OV - Ovarian serous cystadenocarcinoma(14;0.173)														---	---	---	---
FBXO18	84893	broad.mit.edu	37	10	5957531	5957531	+	Missense_Mutation	SNP	G	A	A	rs149880430		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5957531G>A	uc001iis.2	+	9	1657	c.1562G>A	c.(1561-1563)CGG>CAG	p.R521Q	FBXO18_uc001iir.2_Missense_Mutation_p.R447Q|FBXO18_uc009xig.2_Missense_Mutation_p.R447Q|FBXO18_uc001iit.2_Missense_Mutation_p.R572Q	NM_178150	NP_835363	Q8NFZ0	FBX18_HUMAN	F-box only protein, helicase, 18 isoform 2	521					DNA repair	nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding			ovary(2)|skin(1)	3																		---	---	---	---
SFMBT2	57713	broad.mit.edu	37	10	7214078	7214078	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7214078C>T	uc009xio.1	-	19	2285	c.2194G>A	c.(2194-2196)GCC>ACC	p.A732T	SFMBT2_uc001ijn.1_Missense_Mutation_p.A732T|SFMBT2_uc010qay.1_Missense_Mutation_p.A567T	NM_001029880	NP_001025051	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	732					regulation of transcription, DNA-dependent	nucleus				ovary(4)|upper_aerodigestive_tract(2)|large_intestine(1)|central_nervous_system(1)	8																		---	---	---	---
SFMBT2	57713	broad.mit.edu	37	10	7285588	7285588	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7285588G>A	uc009xio.1	-	9	1143	c.1052C>T	c.(1051-1053)GCA>GTA	p.A351V	SFMBT2_uc001ijn.1_Missense_Mutation_p.A351V|SFMBT2_uc010qay.1_Missense_Mutation_p.A351V	NM_001029880	NP_001025051	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	351	MBT 3.				regulation of transcription, DNA-dependent	nucleus				ovary(4)|upper_aerodigestive_tract(2)|large_intestine(1)|central_nervous_system(1)	8																		---	---	---	---
SFMBT2	57713	broad.mit.edu	37	10	7409619	7409619	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7409619G>A	uc009xio.1	-	4	519	c.428C>T	c.(427-429)CCG>CTG	p.P143L	SFMBT2_uc001ijn.1_Missense_Mutation_p.P143L|SFMBT2_uc010qay.1_Missense_Mutation_p.P143L|SFMBT2_uc001ijo.1_Missense_Mutation_p.P143L	NM_001029880	NP_001025051	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	143	MBT 1.				regulation of transcription, DNA-dependent	nucleus				ovary(4)|upper_aerodigestive_tract(2)|large_intestine(1)|central_nervous_system(1)	8																		---	---	---	---
SFMBT2	57713	broad.mit.edu	37	10	7409703	7409703	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7409703C>T	uc009xio.1	-	4	435	c.344G>A	c.(343-345)CGC>CAC	p.R115H	SFMBT2_uc001ijn.1_Missense_Mutation_p.R115H|SFMBT2_uc010qay.1_Missense_Mutation_p.R115H|SFMBT2_uc001ijo.1_Missense_Mutation_p.R115H	NM_001029880	NP_001025051	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	115	MBT 1.				regulation of transcription, DNA-dependent	nucleus				ovary(4)|upper_aerodigestive_tract(2)|large_intestine(1)|central_nervous_system(1)	8																		---	---	---	---
ITIH2	3698	broad.mit.edu	37	10	7780699	7780699	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7780699G>A	uc001ijs.2	+	16	2235	c.2073G>A	c.(2071-2073)ACG>ACA	p.T691T		NM_002216	NP_002207	P19823	ITIH2_HUMAN	inter-alpha globulin inhibitor H2 polypeptide	691					hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
KIN	22944	broad.mit.edu	37	10	7801864	7801864	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:7801864C>T	uc001ijt.2	-	12	1156	c.1108G>A	c.(1108-1110)GTC>ATC	p.V370I	KIN_uc010qaz.1_RNA|KIN_uc009xip.2_Intron|KIN_uc010qba.1_Missense_Mutation_p.V264I	NM_012311	NP_036443	O60870	KIN17_HUMAN	HsKin17 protein	370	C-terminal subdomain B.				DNA recombination|DNA repair|DNA replication|interspecies interaction between organisms|mRNA processing	cytoplasm|nuclear matrix	double-stranded DNA binding|RNA binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
TAF3	83860	broad.mit.edu	37	10	8006344	8006344	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:8006344T>A	uc010qbd.1	+	3	871	c.871T>A	c.(871-873)TCA>ACA	p.S291T		NM_031923	NP_114129	Q5VWG9	TAF3_HUMAN	RNA polymerase II transcription factor TAFII140	291					maintenance of protein location in nucleus|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	transcription factor TFIID complex	protein binding|zinc ion binding			ovary(1)	1																		---	---	---	---
CELF2	10659	broad.mit.edu	37	10	11330494	11330494	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11330494C>T	uc001iki.3	+	9	1026	c.934C>T	c.(934-936)CTG>TTG	p.L312L	CELF2_uc010qbi.1_Silent_p.L84L|CELF2_uc010qbj.1_Silent_p.L312L|CELF2_uc001ikk.2_Silent_p.L319L|CELF2_uc001ikl.3_Silent_p.L319L|CELF2_uc010qbk.1_RNA|CELF2_uc010qbl.1_Silent_p.L288L|CELF2_uc010qbm.1_Silent_p.L84L|CELF2_uc001iko.3_Silent_p.L288L|CELF2_uc001ikp.3_Silent_p.L288L|CELF2_uc010qbn.1_Silent_p.L296L|CELF2_uc010qbo.1_Silent_p.L201L|CELF2_uc010qbp.1_Silent_p.L84L	NM_001025077	NP_001020248	O95319	CELF2_HUMAN	CUG triplet repeat, RNA binding protein 2	312	Ala-rich.				mRNA processing|regulation of heart contraction	cytoplasm|nucleus	nucleotide binding|protein binding|RNA binding				0																		---	---	---	---
C10orf47	254427	broad.mit.edu	37	10	11894104	11894104	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:11894104G>A	uc001ikx.2	+	2	182	c.28G>A	c.(28-30)GCA>ACA	p.A10T	uc001iky.1_Intron	NM_153256	NP_694988	Q86WR7	CJ047_HUMAN	hypothetical protein LOC254427	10	Ser-rich.									central_nervous_system(1)	1																		---	---	---	---
DHTKD1	55526	broad.mit.edu	37	10	12142239	12142239	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12142239C>A	uc001ild.3	+	9	1833	c.1734C>A	c.(1732-1734)GCC>GCA	p.A578A		NM_018706	NP_061176	Q96HY7	DHTK1_HUMAN	dehydrogenase E1 and transketolase domain	578					glycolysis	mitochondrion	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding			ovary(1)|central_nervous_system(1)	2		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)															---	---	---	---
SEC61A2	55176	broad.mit.edu	37	10	12175298	12175298	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12175298G>A	uc001ile.2	+	2	213	c.66G>A	c.(64-66)CCG>CCA	p.P22P	SEC61A2_uc010qbq.1_Silent_p.P22P|SEC61A2_uc001ilf.3_RNA|SEC61A2_uc001ilh.3_RNA|SEC61A2_uc001ilg.3_Silent_p.P22P	NM_018144	NP_060614	Q9H9S3	S61A2_HUMAN	Sec61 alpha form 2 isoform a	22	Cytoplasmic (Potential).					endoplasmic reticulum membrane|integral to membrane	P-P-bond-hydrolysis-driven protein transmembrane transporter activity			ovary(1)	1		Renal(717;0.228)																---	---	---	---
NUDT5	11164	broad.mit.edu	37	10	12228242	12228242	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12228242T>C	uc001ilj.2	-	2	465	c.49A>G	c.(49-51)ATC>GTC	p.I17V	NUDT5_uc001ilk.2_Missense_Mutation_p.I17V	NM_014142	NP_054861	Q9UKK9	NUDT5_HUMAN	nudix-type motif 5	17					D-ribose catabolic process|ribonucleoside diphosphate catabolic process	intracellular	ADP-ribose diphosphatase activity|magnesium ion binding			ovary(1)|pancreas(1)	2		Renal(717;0.228)																---	---	---	---
CDC123	8872	broad.mit.edu	37	10	12279192	12279192	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12279192A>C	uc001ill.2	+	9	899	c.615A>C	c.(613-615)CAA>CAC	p.Q205H	CDC123_uc001ilm.2_Missense_Mutation_p.Q217H	NM_006023	NP_006014	O75794	CD123_HUMAN	cell division cycle 123	205					cell cycle arrest|cell division|positive regulation of cell proliferation|regulation of mitotic cell cycle	cytoplasm				central_nervous_system(1)	1																		---	---	---	---
CAMK1D	57118	broad.mit.edu	37	10	12595304	12595304	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12595304C>A	uc001ilo.2	+	2	408	c.173C>A	c.(172-174)GCG>GAG	p.A58E	CAMK1D_uc001iln.2_Missense_Mutation_p.A58E	NM_153498	NP_705718	Q8IU85	KCC1D_HUMAN	calcium/calmodulin-dependent protein kinase ID	58	Protein kinase.					calcium- and calmodulin-dependent protein kinase complex|cytoplasm|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)|stomach(1)	2				GBM - Glioblastoma multiforme(1;3.16e-05)														---	---	---	---
OPTN	10133	broad.mit.edu	37	10	13169809	13169809	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13169809C>T	uc001ilu.1	+	13	1745	c.1307C>T	c.(1306-1308)GCT>GTT	p.A436V	OPTN_uc001ilv.1_Missense_Mutation_p.A436V|OPTN_uc001ilw.1_Missense_Mutation_p.A436V|OPTN_uc001ilx.1_Missense_Mutation_p.A436V|OPTN_uc001ily.1_Missense_Mutation_p.A430V|OPTN_uc010qbr.1_Missense_Mutation_p.A379V|OPTN_uc001ilz.1_Missense_Mutation_p.A430V	NM_001008213	NP_001008214	Q96CV9	OPTN_HUMAN	optineurin	436	Potential.|Interaction with MYO6.|Interaction with HD.			A -> V (in Ref. 8; AAC26850).	cell death|Golgi ribbon formation|Golgi to plasma membrane protein transport|protein targeting to Golgi|signal transduction	perinuclear region of cytoplasm|trans-Golgi network	protein C-terminus binding			ovary(2)	2																		---	---	---	---
MCM10	55388	broad.mit.edu	37	10	13217658	13217658	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13217658A>G	uc001ima.2	+	6	845	c.744A>G	c.(742-744)GAA>GAG	p.E248E	MCM10_uc001imb.2_Silent_p.E247E|MCM10_uc001imc.2_Silent_p.E247E	NM_182751	NP_877428	Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	248					cell cycle checkpoint|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle	nucleoplasm	metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
SEPHS1	22929	broad.mit.edu	37	10	13380718	13380718	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13380718T>G	uc001imk.2	-	3	643	c.284A>C	c.(283-285)GAC>GCC	p.D95A	SEPHS1_uc001imh.2_5'Flank|SEPHS1_uc010qbs.1_Missense_Mutation_p.D47A|SEPHS1_uc001imi.2_Missense_Mutation_p.D95A|SEPHS1_uc001imj.2_Missense_Mutation_p.D95A|SEPHS1_uc010qbt.1_Missense_Mutation_p.D28A|SEPHS1_uc009xje.2_Missense_Mutation_p.D95A	NM_012247	NP_036379	P49903	SPS1_HUMAN	selenophosphate synthetase 1	95					protein modification process		ATP binding|GTP binding|selenide, water dikinase activity			skin(1)	1																		---	---	---	---
BEND7	222389	broad.mit.edu	37	10	13523136	13523136	+	Intron	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:13523136A>T	uc001imm.2	-						BEND7_uc001imn.2_5'Flank|BEND7_uc001imo.3_Intron	NM_152751	NP_689964			BEN domain containing 7 isoform 1								protein binding			ovary(1)|breast(1)	2																		---	---	---	---
HSPA14	51182	broad.mit.edu	37	10	14881909	14881909	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14881909C>A	uc001inf.2	+	2	204	c.63C>A	c.(61-63)GGC>GGA	p.G21G	CDNF_uc001inb.1_5'Flank|CDNF_uc010qbv.1_5'Flank|CDNF_uc001inc.1_5'Flank|HSPA14_uc001ind.2_5'UTR|HSPA14_uc001ine.2_Silent_p.G21G|HSPA14_uc010qbw.1_Silent_p.G21G	NM_016299	NP_057383	Q0VDF9	HSP7E_HUMAN	heat shock 70kDa protein 14 isoform 1	21					'de novo' cotranslational protein folding	cytosol	ATP binding|protein binding			ovary(2)|breast(2)|lung(1)	5																		---	---	---	---
DCLRE1C	64421	broad.mit.edu	37	10	14978549	14978549	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:14978549G>A	uc001inn.2	-	5	435	c.350C>T	c.(349-351)CCG>CTG	p.P117L	DCLRE1C_uc010qbx.1_Missense_Mutation_p.P117L|DCLRE1C_uc001inl.2_5'UTR|DCLRE1C_uc009xji.2_Intron|DCLRE1C_uc001inm.2_5'UTR|DCLRE1C_uc001ino.2_Intron|DCLRE1C_uc009xjh.2_RNA|DCLRE1C_uc001inp.2_5'UTR|DCLRE1C_uc001inq.2_5'UTR|DCLRE1C_uc001inr.2_Intron|DCLRE1C_uc009xjj.1_5'Flank	NM_001033855	NP_001029027	Q96SD1	DCR1C_HUMAN	artemis protein isoform a	117					DNA recombination	nucleus	5'-3' exonuclease activity|single-stranded DNA specific endodeoxyribonuclease activity			ovary(1)	1													Involved_in_tolerance_or_repair_of_DNA_crosslinks|NHEJ					---	---	---	---
FAM171A1	221061	broad.mit.edu	37	10	15255728	15255728	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15255728T>C	uc001iob.2	-	8	1866	c.1859A>G	c.(1858-1860)AAT>AGT	p.N620S		NM_001010924	NP_001010924	Q5VUB5	F1711_HUMAN	hypothetical protein LOC221061 precursor	620	Cytoplasmic (Potential).					integral to membrane				ovary(2)|breast(1)|skin(1)	4																		---	---	---	---
FAM171A1	221061	broad.mit.edu	37	10	15290656	15290656	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15290656G>A	uc001iob.2	-	5	743	c.736C>T	c.(736-738)CGG>TGG	p.R246W		NM_001010924	NP_001010924	Q5VUB5	F1711_HUMAN	hypothetical protein LOC221061 precursor	246	Extracellular (Potential).					integral to membrane				ovary(2)|breast(1)|skin(1)	4																		---	---	---	---
FAM171A1	221061	broad.mit.edu	37	10	15290737	15290737	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15290737G>A	uc001iob.2	-	5	662	c.655C>T	c.(655-657)CTG>TTG	p.L219L		NM_001010924	NP_001010924	Q5VUB5	F1711_HUMAN	hypothetical protein LOC221061 precursor	219	Extracellular (Potential).					integral to membrane				ovary(2)|breast(1)|skin(1)	4																		---	---	---	---
ITGA8	8516	broad.mit.edu	37	10	15686103	15686103	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15686103G>A	uc001ioc.1	-	13	1325	c.1325C>T	c.(1324-1326)GCC>GTC	p.A442V	ITGA8_uc010qcb.1_Missense_Mutation_p.A427V	NM_003638	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8 precursor	442	Extracellular (Potential).|FG-GAP 7.				cell differentiation|cell-cell adhesion|cell-matrix adhesion|integrin-mediated signaling pathway|nervous system development	integrin complex	receptor activity			ovary(3)|lung(3)	6																		---	---	---	---
ITGA8	8516	broad.mit.edu	37	10	15701041	15701041	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:15701041T>C	uc001ioc.1	-	10	905	c.905A>G	c.(904-906)AAC>AGC	p.N302S	ITGA8_uc010qcb.1_Missense_Mutation_p.N287S	NM_003638	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8 precursor	302	Extracellular (Potential).|FG-GAP 4.				cell differentiation|cell-cell adhesion|cell-matrix adhesion|integrin-mediated signaling pathway|nervous system development	integrin complex	receptor activity			ovary(3)|lung(3)	6																		---	---	---	---
RSU1	6251	broad.mit.edu	37	10	16794989	16794989	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:16794989A>G	uc001iok.2	-	5	713	c.411T>C	c.(409-411)CGT>CGC	p.R137R	RSU1_uc001iol.2_Silent_p.R137R|RSU1_uc001iom.2_Silent_p.R84R|RSU1_uc001ion.2_Silent_p.R137R	NM_152724	NP_689937	Q15404	RSU1_HUMAN	ras suppressor protein 1 isoform 2	137	LRR 5.				cell junction assembly|signal transduction	cytosol	protein binding			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(1;7.54e-08)														---	---	---	---
PLXDC2	84898	broad.mit.edu	37	10	20290827	20290827	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:20290827G>A	uc001iqg.1	+	2	873	c.236G>A	c.(235-237)CGA>CAA	p.R79Q	PLXDC2_uc001iqh.1_Missense_Mutation_p.R79Q	NM_032812	NP_116201	Q6UX71	PXDC2_HUMAN	plexin domain containing 2 precursor	79	Extracellular (Potential).					integral to membrane				ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
NEBL	10529	broad.mit.edu	37	10	21169712	21169712	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21169712C>T	uc001iqi.2	-						NEBL_uc001iqj.2_Intron|NEBL_uc001iqk.2_Intron	NM_006393	NP_006384			nebulette sarcomeric isoform						regulation of actin filament length		actin binding|structural constituent of muscle			ovary(2)	2																		---	---	---	---
C10orf140	387640	broad.mit.edu	37	10	21804505	21804505	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21804505A>G	uc009xkd.2	-	4	4500	c.2247T>C	c.(2245-2247)AAT>AAC	p.N749N	uc001iqp.1_Intron	NM_207371	NP_997254	Q1XH10	DLN1_HUMAN	hypothetical protein LOC387640	668						nucleus	nucleotide binding			ovary(1)	1																		---	---	---	---
DNAJC1	64215	broad.mit.edu	37	10	22048426	22048426	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22048426C>T	uc001irc.2	-	11	1556	c.1269G>A	c.(1267-1269)GAG>GAA	p.E423E	DNAJC1_uc001ird.2_Silent_p.E309E	NM_022365	NP_071760	Q96KC8	DNJC1_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 1	423	Cytoplasmic (By similarity).				negative regulation of proteolysis|regulation of protein secretion|regulation of transcription, DNA-dependent	endoplasmic reticulum membrane|integral to membrane|microsome|nuclear membrane	ATPase activator activity|DNA binding|heat shock protein binding|unfolded protein binding			lung(1)	1		Breast(68;0.00869)|Prostate(175;0.0181)|Lung SC(717;0.0262)																---	---	---	---
COMMD3	23412	broad.mit.edu	37	10	22607783	22607783	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:22607783A>C	uc001irf.2	+	6	508	c.460A>C	c.(460-462)AGT>CGT	p.S154R	COMMD3_uc001ire.2_3'UTR|COMMD3_uc001irg.2_RNA|BMI1_uc009xkg.2_Intron|BMI1_uc001irh.2_5'Flank	NM_012071	NP_036203	Q9UBI1	COMD3_HUMAN	COMM domain containing 3	154	COMM.						protein binding				0																		---	---	---	---
GPR158	57512	broad.mit.edu	37	10	25464549	25464549	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:25464549G>A	uc001isj.2	+	1	260	c.200G>A	c.(199-201)GGC>GAC	p.G67D	LOC100128811_uc010qde.1_Intron	NM_020752	NP_065803	Q5T848	GP158_HUMAN	G protein-coupled receptor 158 precursor	67	Extracellular (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(4)|large_intestine(2)|pancreas(1)|skin(1)	8																		---	---	---	---
GAD2	2572	broad.mit.edu	37	10	26575305	26575305	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:26575305C>T	uc001isp.2	+	13	1771	c.1268C>T	c.(1267-1269)GCC>GTC	p.A423V	GAD2_uc001isq.2_Missense_Mutation_p.A423V	NM_001134366	NP_001127838	Q05329	DCE2_HUMAN	glutamate decarboxylase 2	423					glutamate decarboxylation to succinate|neurotransmitter biosynthetic process|neurotransmitter secretion	cell junction|clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|cytosol|Golgi membrane|presynaptic membrane	glutamate decarboxylase activity|protein binding|pyridoxal phosphate binding			central_nervous_system(1)|skin(1)	2					L-Glutamic Acid(DB00142)													---	---	---	---
MASTL	84930	broad.mit.edu	37	10	27447500	27447500	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27447500T>A	uc001itm.2	+	2	848	c.209T>A	c.(208-210)ATC>AAC	p.I70N	MASTL_uc001itl.2_Missense_Mutation_p.I70N|MASTL_uc009xkw.1_Missense_Mutation_p.I70N|MASTL_uc009xkx.1_RNA	NM_032844	NP_116233	Q96GX5	GWL_HUMAN	microtubule associated serine/threonine	70	Protein kinase.				cell division|G2/M transition of mitotic cell cycle|mitosis|negative regulation of protein phosphatase type 2A activity|regulation of cell cycle|response to DNA damage stimulus	centrosome|cleavage furrow|nucleus	ATP binding|protein phosphatase 2A binding|protein serine/threonine kinase activity			stomach(1)|ovary(1)|lung(1)	3																		---	---	---	---
MASTL	84930	broad.mit.edu	37	10	27458863	27458863	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27458863T>C	uc001itm.2	+						MASTL_uc001itl.2_Intron|MASTL_uc009xkw.1_Intron|MASTL_uc009xkx.1_Intron	NM_032844	NP_116233			microtubule associated serine/threonine						cell division|G2/M transition of mitotic cell cycle|mitosis|negative regulation of protein phosphatase type 2A activity|regulation of cell cycle|response to DNA damage stimulus	centrosome|cleavage furrow|nucleus	ATP binding|protein phosphatase 2A binding|protein serine/threonine kinase activity			stomach(1)|ovary(1)|lung(1)	3																		---	---	---	---
PTCHD3	374308	broad.mit.edu	37	10	27687250	27687250	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:27687250T>C	uc001itu.2	-	4	2395	c.2277A>G	c.(2275-2277)TCA>TCG	p.S759S		NM_001034842	NP_001030014	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	759					spermatid development	integral to membrane	hedgehog receptor activity			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
ARMC4	55130	broad.mit.edu	37	10	28276327	28276327	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28276327C>A	uc009xky.2	-	3	468	c.370G>T	c.(370-372)GCA>TCA	p.A124S	ARMC4_uc001itz.2_Missense_Mutation_p.A124S	NM_018076	NP_060546	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	124							binding			ovary(4)|skin(2)	6																		---	---	---	---
WAC	51322	broad.mit.edu	37	10	28899659	28899659	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:28899659G>A	uc001iuf.2	+	9	1282	c.1197G>A	c.(1195-1197)CTG>CTA	p.L399L	WAC_uc001iud.2_Silent_p.L354L|WAC_uc001iue.2_Silent_p.L89L|WAC_uc001iug.2_Silent_p.L296L|WAC_uc001iuh.2_Silent_p.L351L	NM_016628	NP_057712	Q9BTA9	WAC_HUMAN	WW domain-containing adapter with a coiled-coil	399					cell cycle checkpoint|histone H2B conserved C-terminal lysine ubiquitination|histone monoubiquitination|positive regulation of transcription, DNA-dependent|response to DNA damage stimulus|transcription, DNA-dependent	nuclear speck	chromatin binding|RNA polymerase II core binding			large_intestine(1)|ovary(1)	2																		---	---	---	---
SVIL	6840	broad.mit.edu	37	10	29770644	29770644	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29770644G>A	uc001iut.1	-	28	5722	c.4969C>T	c.(4969-4971)CGG>TGG	p.R1657W	LOC387647_uc001iup.2_Intron|LOC387647_uc001iuq.1_Intron|SVIL_uc010qdw.1_Missense_Mutation_p.R571W|SVIL_uc001iuu.1_Missense_Mutation_p.R1231W|SVIL_uc009xlc.2_Missense_Mutation_p.R449W	NM_021738	NP_068506	O95425	SVIL_HUMAN	supervillin isoform 2	1657	Gelsolin-like 2.|Interaction with NEB.				cytoskeleton organization|skeletal muscle tissue development	cell junction|costamere|invadopodium|nucleus|podosome	actin filament binding			ovary(5)|upper_aerodigestive_tract(1)	6		Breast(68;0.103)																---	---	---	---
SVIL	6840	broad.mit.edu	37	10	29840003	29840003	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:29840003G>A	uc001iut.1	-	6	1103	c.350C>T	c.(349-351)GCA>GTA	p.A117V	SVIL_uc001iuu.1_Missense_Mutation_p.A117V|SVIL_uc009xld.1_Missense_Mutation_p.A117V	NM_021738	NP_068506	O95425	SVIL_HUMAN	supervillin isoform 2	117	Interaction with MYLK (By similarity).				cytoskeleton organization|skeletal muscle tissue development	cell junction|costamere|invadopodium|nucleus|podosome	actin filament binding	p.A117S(1)		ovary(5)|upper_aerodigestive_tract(1)	6		Breast(68;0.103)																---	---	---	---
KIAA1462	57608	broad.mit.edu	37	10	30317978	30317978	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30317978A>C	uc001iux.2	-	2	1158	c.1099T>G	c.(1099-1101)TGT>GGT	p.C367G	KIAA1462_uc001iuy.2_Intron|KIAA1462_uc001iuz.2_Missense_Mutation_p.C229G|KIAA1462_uc009xle.1_Missense_Mutation_p.C367G	NM_020848	NP_065899	Q9P266	K1462_HUMAN	hypothetical protein LOC57608	367	Pro-rich.									ovary(4)	4																		---	---	---	---
KIAA1462	57608	broad.mit.edu	37	10	30318505	30318505	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30318505T>C	uc001iux.2	-	2	631	c.572A>G	c.(571-573)CAG>CGG	p.Q191R	KIAA1462_uc001iuy.2_Intron|KIAA1462_uc001iuz.2_Missense_Mutation_p.Q53R|KIAA1462_uc009xle.1_Missense_Mutation_p.Q191R	NM_020848	NP_065899	Q9P266	K1462_HUMAN	hypothetical protein LOC57608	191										ovary(4)	4																		---	---	---	---
ZEB1	6935	broad.mit.edu	37	10	31812932	31812932	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:31812932G>A	uc001ivs.3	+	8	2736	c.2673G>A	c.(2671-2673)CCG>CCA	p.P891P	ZEB1_uc001ivr.3_Silent_p.P673P|ZEB1_uc010qee.1_Silent_p.P673P|ZEB1_uc010qef.1_Silent_p.P673P|ZEB1_uc009xlk.1_Silent_p.P673P|ZEB1_uc001ivt.3_Silent_p.P673P|ZEB1_uc001ivu.3_Silent_p.P892P|ZEB1_uc001ivv.3_Silent_p.P871P|ZEB1_uc010qeh.1_Silent_p.P824P|ZEB1_uc009xlp.2_Silent_p.P875P	NM_030751	NP_110378	P37275	ZEB1_HUMAN	zinc finger E-box binding homeobox 1 isoform b	891					cell proliferation|immune response|negative regulation of transcription from RNA polymerase II promoter|positive regulation of neuron differentiation	cytoplasm	E-box binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(3)|central_nervous_system(2)	5		Prostate(175;0.0156)																---	---	---	---
FZD8	8325	broad.mit.edu	37	10	35929001	35929001	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:35929001A>C	uc001iyz.1	-	1	1362	c.1357T>G	c.(1357-1359)TCC>GCC	p.S453A		NM_031866	NP_114072	Q9H461	FZD8_HUMAN	frizzled 8 precursor	453	Helical; Name=4; (Potential).				axonogenesis|brain development|canonical Wnt receptor signaling pathway|embryo development|gonad development|T cell differentiation in thymus|vasculature development	cell projection|Golgi apparatus|integral to membrane|plasma membrane	G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding				0																		---	---	---	---
BMS1	9790	broad.mit.edu	37	10	43318571	43318571	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:43318571G>A	uc001jaj.2	+	20	3496	c.3138G>A	c.(3136-3138)ATG>ATA	p.M1046I		NM_014753	NP_055568	Q14692	BMS1_HUMAN	BMS1-like, ribosome assembly protein	1046					ribosome assembly	nucleolus	ATP binding|GTP binding|GTPase activity			ovary(2)|upper_aerodigestive_tract(1)	3																		---	---	---	---
RASSF4	83937	broad.mit.edu	37	10	45467291	45467291	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45467291C>T	uc001jbo.2	+	3	267	c.133C>T	c.(133-135)CGT>TGT	p.R45C	RASSF4_uc001jbp.2_Missense_Mutation_p.R76C|RASSF4_uc009xmn.2_Intron|RASSF4_uc001jbq.2_5'UTR	NM_032023	NP_114412	Q9H2L5	RASF4_HUMAN	Ras association domain family 4	45					cell cycle|signal transduction		protein binding			large_intestine(1)	1																		---	---	---	---
ALOX5	240	broad.mit.edu	37	10	45919491	45919491	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45919491T>C	uc001jce.2	+	5	656	c.557T>C	c.(556-558)ATG>ACG	p.M186T	ALOX5_uc009xmt.2_Missense_Mutation_p.M186T|ALOX5_uc010qfg.1_Missense_Mutation_p.M186T	NM_000698	NP_000689	P09917	LOX5_HUMAN	arachidonate 5-lipoxygenase	186	Lipoxygenase.				hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process	cytosol|nuclear envelope lumen|nuclear matrix|nuclear membrane	arachidonate 5-lipoxygenase activity|iron ion binding|lipoxygenase activity|protein binding			ovary(1)|pancreas(1)	2		Lung SC(717;0.0257)			Diethylcarbamazine(DB00711)|Hydrocortisone(DB00741)|Leflunomide(DB01097)|Masoprocol(DB00179)|Meclofenamic acid(DB00939)|Minocycline(DB01017)|Montelukast(DB00471)|Quinacrine(DB01103)|Vitamin E(DB00163)|Zileuton(DB00744)													---	---	---	---
MARCH8	220972	broad.mit.edu	37	10	45953792	45953792	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45953792C>A	uc001jci.1	-	7	1010	c.771G>T	c.(769-771)GAG>GAT	p.E257D	MARCH8_uc001jch.2_Missense_Mutation_p.E539D|MARCH8_uc001jcj.1_Missense_Mutation_p.E257D|MARCH8_uc001jck.1_Missense_Mutation_p.E257D|uc001jcf.2_5'Flank|MARCH8_uc001jcg.1_Missense_Mutation_p.E126D	NM_001002266	NP_001002266	Q5T0T0	MARH8_HUMAN	cellular modulator of immune recognition isoform	257						cytoplasmic vesicle membrane|early endosome membrane|integral to membrane|lysosomal membrane	ubiquitin-protein ligase activity|zinc ion binding				0																		---	---	---	---
ANUBL1	93550	broad.mit.edu	37	10	46111992	46111992	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46111992A>G	uc001jcp.3	-	10	2318	c.2076T>C	c.(2074-2076)CAT>CAC	p.H692H	ANUBL1_uc001jcl.3_Silent_p.H212H|ANUBL1_uc001jcm.3_Silent_p.H692H|ANUBL1_uc009xmu.2_Silent_p.H618H|ANUBL1_uc001jcn.3_Silent_p.H618H|ANUBL1_uc001jco.3_3'UTR	NM_001128324	NP_001121796	Q86XD8	ANUB1_HUMAN	AN1, ubiquitin-like, homolog	692	AN1-type.						zinc ion binding				0																		---	---	---	---
GPRIN2	9721	broad.mit.edu	37	10	46999908	46999908	+	Missense_Mutation	SNP	C	T	T	rs143570360	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:46999908C>T	uc001jec.2	+	3	1163	c.1028C>T	c.(1027-1029)GCG>GTG	p.A343V	GPRIN2_uc010qfq.1_Missense_Mutation_p.A106V	NM_014696	NP_055511	O60269	GRIN2_HUMAN	G protein-regulated inducer of neurite outgrowth	343											0																		---	---	---	---
GDF2	2658	broad.mit.edu	37	10	48414422	48414422	+	Missense_Mutation	SNP	T	G	G	rs139866781		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:48414422T>G	uc001jfa.1	-	2	609	c.446A>C	c.(445-447)GAG>GCG	p.E149A		NM_016204	NP_057288	Q9UK05	GDF2_HUMAN	growth differentiation factor 2 precursor	149					activin receptor signaling pathway|BMP signaling pathway|cartilage development|cellular iron ion homeostasis|growth|negative regulation of angiogenesis|negative regulation of blood vessel endothelial cell migration|negative regulation of cell growth|negative regulation of DNA replication|negative regulation of endothelial cell proliferation|ossification|pathway-restricted SMAD protein phosphorylation|patterning of blood vessels|positive regulation of angiogenesis|positive regulation of endothelial cell proliferation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of transcription, DNA-dependent	extracellular space	cytokine activity|growth factor activity			ovary(2)|skin(1)	3																		---	---	---	---
MAPK8	5599	broad.mit.edu	37	10	49628343	49628343	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49628343G>A	uc009xnz.2	+	6	820	c.596G>A	c.(595-597)GGC>GAC	p.G199D	MAPK8_uc001jgl.2_Missense_Mutation_p.G199D|MAPK8_uc001jgm.2_Missense_Mutation_p.G199D|MAPK8_uc001jgo.2_Missense_Mutation_p.G199D|MAPK8_uc009xoa.2_Missense_Mutation_p.G199D|MAPK8_uc001jgn.2_Missense_Mutation_p.G199D|MAPK8_uc010qgk.1_Missense_Mutation_p.G199D|MAPK8_uc001jgp.2_Missense_Mutation_p.G199D|MAPK8_uc001jgq.2_Missense_Mutation_p.G199D	NM_139047	NP_620635	P45983	MK08_HUMAN	mitogen-activated protein kinase 8 isoform JNK1	199	Protein kinase.				activation of pro-apoptotic gene products|cellular response to mechanical stimulus|induction of apoptosis by intracellular signals|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of apoptosis|negative regulation of protein binding|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of deacetylase activity|regulation of protein localization|regulation of sequence-specific DNA binding transcription factor activity|response to UV|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|histone deacetylase binding|histone deacetylase regulator activity|JUN kinase activity|protein binding			central_nervous_system(3)|lung(2)|stomach(1)|ovary(1)|kidney(1)	8		Ovarian(717;0.0221)|Lung SC(717;0.113)|all_neural(218;0.116)		Epithelial(53;3.46e-65)|Lung(62;0.125)														---	---	---	---
MAPK8	5599	broad.mit.edu	37	10	49634019	49634019	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:49634019C>T	uc009xnz.2	+	8	1001	c.777C>T	c.(775-777)TAC>TAT	p.Y259Y	MAPK8_uc001jgl.2_Silent_p.Y259Y|MAPK8_uc001jgm.2_Silent_p.Y259Y|MAPK8_uc001jgo.2_Silent_p.Y259Y|MAPK8_uc009xoa.2_Intron|MAPK8_uc001jgn.2_Silent_p.Y259Y|MAPK8_uc010qgk.1_Silent_p.Y259Y|MAPK8_uc001jgp.2_Silent_p.Y259Y|MAPK8_uc001jgq.2_Silent_p.Y259Y	NM_139047	NP_620635	P45983	MK08_HUMAN	mitogen-activated protein kinase 8 isoform JNK1	259	Protein kinase.				activation of pro-apoptotic gene products|cellular response to mechanical stimulus|induction of apoptosis by intracellular signals|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of apoptosis|negative regulation of protein binding|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of deacetylase activity|regulation of protein localization|regulation of sequence-specific DNA binding transcription factor activity|response to UV|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|histone deacetylase binding|histone deacetylase regulator activity|JUN kinase activity|protein binding			central_nervous_system(3)|lung(2)|stomach(1)|ovary(1)|kidney(1)	8		Ovarian(717;0.0221)|Lung SC(717;0.113)|all_neural(218;0.116)		Epithelial(53;3.46e-65)|Lung(62;0.125)														---	---	---	---
C10orf71	118461	broad.mit.edu	37	10	50531730	50531730	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50531730A>G	uc010qgp.1	+	3	1479	c.1140A>G	c.(1138-1140)CCA>CCG	p.P380P		NM_199459	NP_955629	Q711Q0	CJ071_HUMAN	hypothetical protein LOC118461 isoform 2	380											0																		---	---	---	---
ERCC6	2074	broad.mit.edu	37	10	50682117	50682117	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50682117G>A	uc001jhs.3	-	13	2708	c.2554C>T	c.(2554-2556)CAC>TAC	p.H852Y	ERCC6_uc009xod.2_Missense_Mutation_p.H12Y|ERCC6_uc010qgr.1_Missense_Mutation_p.H222Y|ERCC6_uc001jhr.3_Missense_Mutation_p.H220Y	NM_000124	NP_000115	Q03468	ERCC6_HUMAN	excision repair cross-complementing rodent	852	Helicase C-terminal.				base-excision repair|positive regulation of transcription elongation, DNA-dependent|transcription from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair	nucleolus|soluble fraction|transcription elongation factor complex	ATP binding|chromatin binding|DNA binding|DNA-dependent ATPase activity|helicase activity|protein C-terminus binding|protein complex binding|protein N-terminus binding			lung(5)|breast(5)|ovary(3)|large_intestine(2)|skin(1)	16													Direct_reversal_of_damage|NER					---	---	---	---
ERCC6	2074	broad.mit.edu	37	10	50691414	50691414	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50691414G>A	uc001jhs.3	-	9	2124	c.1970C>T	c.(1969-1971)GCT>GTT	p.A657V	ERCC6_uc010qgr.1_Missense_Mutation_p.A27V|ERCC6_uc001jhr.3_Missense_Mutation_p.A57V	NM_000124	NP_000115	Q03468	ERCC6_HUMAN	excision repair cross-complementing rodent	657	Helicase ATP-binding.				base-excision repair|positive regulation of transcription elongation, DNA-dependent|transcription from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair	nucleolus|soluble fraction|transcription elongation factor complex	ATP binding|chromatin binding|DNA binding|DNA-dependent ATPase activity|helicase activity|protein C-terminus binding|protein complex binding|protein N-terminus binding			lung(5)|breast(5)|ovary(3)|large_intestine(2)|skin(1)	16													Direct_reversal_of_damage|NER					---	---	---	---
ERCC6	2074	broad.mit.edu	37	10	50732279	50732279	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50732279A>G	uc001jhs.3	-	5	1351	c.1197T>C	c.(1195-1197)GGT>GGC	p.G399G	PGBD3_uc001jht.2_5'UTR|PGBD3_uc009xoe.2_Silent_p.G399G|PGBD3_uc001jhu.2_Silent_p.G399G	NM_000124	NP_000115	Q03468	ERCC6_HUMAN	excision repair cross-complementing rodent	399					base-excision repair|positive regulation of transcription elongation, DNA-dependent|transcription from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair	nucleolus|soluble fraction|transcription elongation factor complex	ATP binding|chromatin binding|DNA binding|DNA-dependent ATPase activity|helicase activity|protein C-terminus binding|protein complex binding|protein N-terminus binding			lung(5)|breast(5)|ovary(3)|large_intestine(2)|skin(1)	16													Direct_reversal_of_damage|NER					---	---	---	---
BICC1	80114	broad.mit.edu	37	10	60560760	60560760	+	Silent	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:60560760A>C	uc001jki.1	+	14	1969	c.1969A>C	c.(1969-1971)AGG>CGG	p.R657R	BICC1_uc001jkj.1_Silent_p.R298R	NM_001080512	NP_001073981	Q9H694	BICC1_HUMAN	bicaudal C homolog 1	657					multicellular organismal development		RNA binding			ovary(2)|lung(1)|skin(1)	4																		---	---	---	---
CCDC6	8030	broad.mit.edu	37	10	61554264	61554264	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61554264G>A	uc001jks.3	-	8	1833	c.1197C>T	c.(1195-1197)CAC>CAT	p.H399H		NM_005436	NP_005427	Q16204	CCDC6_HUMAN	coiled-coil domain containing 6	399						cytoplasm|cytoskeleton	SH3 domain binding|structural constituent of cytoskeleton			ovary(3)|breast(1)	4				Kidney(211;0.0597)														---	---	---	---
ANK3	288	broad.mit.edu	37	10	61815549	61815549	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61815549C>T	uc001jky.2	-	42	13124	c.12932G>A	c.(12931-12933)AGC>AAC	p.S4311N	ANK3_uc001jkw.2_Missense_Mutation_p.S935N|ANK3_uc009xpa.2_Missense_Mutation_p.S935N|ANK3_uc001jkx.2_Missense_Mutation_p.S979N|ANK3_uc010qih.1_Missense_Mutation_p.S1802N|ANK3_uc001jkz.3_Missense_Mutation_p.S1795N|ANK3_uc001jkv.2_Missense_Mutation_p.S334N	NM_020987	NP_066267	Q12955	ANK3_HUMAN	ankyrin 3 isoform 1	4311					establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			skin(9)|ovary(6)|pancreas(2)|central_nervous_system(2)	19																		---	---	---	---
ANK3	288	broad.mit.edu	37	10	61836046	61836046	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61836046C>T	uc001jky.2	-	37	4785	c.4593G>A	c.(4591-4593)ACG>ACA	p.T1531T	ANK3_uc001jkw.2_Intron|ANK3_uc009xpa.2_Intron|ANK3_uc001jkx.2_Intron|ANK3_uc010qih.1_Intron|ANK3_uc001jkz.3_Intron|ANK3_uc001jkv.2_Intron|ANK3_uc009xpb.1_Intron	NM_020987	NP_066267	Q12955	ANK3_HUMAN	ankyrin 3 isoform 1	1531	Ser-rich.				establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			skin(9)|ovary(6)|pancreas(2)|central_nervous_system(2)	19																		---	---	---	---
RHOBTB1	9886	broad.mit.edu	37	10	62632016	62632016	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:62632016A>C	uc001jli.2	-	11	2286	c.1848T>G	c.(1846-1848)TGT>TGG	p.C616W	RHOBTB1_uc001jlh.2_Missense_Mutation_p.C616W|RHOBTB1_uc001jlj.2_Missense_Mutation_p.C616W|RHOBTB1_uc001jlk.2_Missense_Mutation_p.C616W|RHOBTB1_uc009xpe.1_Missense_Mutation_p.C554W|RHOBTB1_uc009xpd.2_Intron|RHOBTB1_uc001jll.2_Missense_Mutation_p.C366W	NM_014836	NP_055651	O94844	RHBT1_HUMAN	Rho-related BTB domain containing 1	616					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|plasma membrane	GTP binding			upper_aerodigestive_tract(1)	1	Prostate(12;0.0112)																	---	---	---	---
ARID5B	84159	broad.mit.edu	37	10	63816964	63816964	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:63816964C>A	uc001jlt.1	+	6	961	c.935C>A	c.(934-936)GCC>GAC	p.A312D	ARID5B_uc001jlu.1_Missense_Mutation_p.A69D	NM_032199	NP_115575	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)	312					liver development|negative regulation of transcription, DNA-dependent|positive regulation of sequence-specific DNA binding transcription factor activity|transcription, DNA-dependent		protein binding|transcription regulatory region DNA binding			ovary(2)|upper_aerodigestive_tract(1)|kidney(1)	4	Prostate(12;0.016)|all_hematologic(501;0.215)																	---	---	---	---
RTKN2	219790	broad.mit.edu	37	10	64000901	64000901	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64000901G>A	uc001jlw.2	-	4	467	c.370C>T	c.(370-372)CGA>TGA	p.R124*	RTKN2_uc001jlx.2_Nonsense_Mutation_p.R124*	NM_145307	NP_660350	Q8IZC4	RTKN2_HUMAN	rhotekin 2	124					signal transduction	intracellular					0	Prostate(12;0.0297)|all_hematologic(501;0.215)																	---	---	---	---
JMJD1C	221037	broad.mit.edu	37	10	64967761	64967761	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64967761C>T	uc001jmn.2	-	10	3968	c.3668G>A	c.(3667-3669)AGC>AAC	p.S1223N	JMJD1C_uc001jml.2_Missense_Mutation_p.S1004N|JMJD1C_uc001jmm.2_Missense_Mutation_p.S935N|JMJD1C_uc010qiq.1_Missense_Mutation_p.S1041N|JMJD1C_uc009xpi.2_Missense_Mutation_p.S1041N|JMJD1C_uc009xpj.1_RNA|JMJD1C_uc009xpk.1_Missense_Mutation_p.S260N	NM_032776	NP_116165	Q15652	JHD2C_HUMAN	jumonji domain containing 1C isoform a	1223					blood coagulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	histone demethylase activity (H3-K9 specific)|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|thyroid hormone receptor binding			ovary(4)|breast(1)|central_nervous_system(1)	6	Prostate(12;0.0119)|all_hematologic(501;0.191)																	---	---	---	---
JMJD1C	221037	broad.mit.edu	37	10	64974683	64974683	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:64974683T>G	uc001jmn.2	-	8	1544	c.1244A>C	c.(1243-1245)AAA>ACA	p.K415T	JMJD1C_uc001jml.2_Missense_Mutation_p.K196T|JMJD1C_uc001jmm.2_Missense_Mutation_p.K127T|JMJD1C_uc010qiq.1_Missense_Mutation_p.K233T|JMJD1C_uc009xpi.2_Missense_Mutation_p.K233T|JMJD1C_uc009xpj.1_RNA|JMJD1C_uc001jmp.1_Missense_Mutation_p.K127T	NM_032776	NP_116165	Q15652	JHD2C_HUMAN	jumonji domain containing 1C isoform a	415					blood coagulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	histone demethylase activity (H3-K9 specific)|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|thyroid hormone receptor binding			ovary(4)|breast(1)|central_nervous_system(1)	6	Prostate(12;0.0119)|all_hematologic(501;0.191)																	---	---	---	---
CTNNA3	29119	broad.mit.edu	37	10	67680383	67680383	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:67680383G>A	uc009xpn.1	-						CTNNA3_uc001jmw.2_Intron	NM_001127384	NP_001120856			catenin, alpha 3						cell-cell adhesion	actin cytoskeleton|cytoplasm|fascia adherens	cadherin binding|structural molecule activity			skin(3)|ovary(2)|pancreas(1)|lung(1)|central_nervous_system(1)	8																		---	---	---	---
DNA2	1763	broad.mit.edu	37	10	70192160	70192160	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70192160G>A	uc001jof.2	-	11	2012	c.2012C>T	c.(2011-2013)ACG>ATG	p.T671M	DNA2_uc001jog.1_Missense_Mutation_p.T585M|DNA2_uc001joh.1_RNA	NM_001080449	NP_001073918	P51530	DNA2L_HUMAN	DNA replication helicase 2 homolog	585					base-excision repair|DNA replication, removal of RNA primer|mitochondrial DNA repair|mitochondrial DNA replication|positive regulation of DNA replication|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	mitochondrial nucleoid|nucleoplasm	5'-flap endonuclease activity|ATP binding|ATP-dependent DNA helicase activity|DNA binding|site-specific endodeoxyribonuclease activity, specific for altered base				0																		---	---	---	---
TET1	80312	broad.mit.edu	37	10	70451546	70451546	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70451546C>T	uc001jok.3	+	12	6891	c.6386C>T	c.(6385-6387)GCG>GTG	p.A2129V		NM_030625	NP_085128	Q8NFU7	TET1_HUMAN	CXXC finger 6	2129					DNA demethylation|inner cell mass cell differentiation|negative regulation of methylation-dependent chromatin silencing|stem cell maintenance		iron ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|structure-specific DNA binding|zinc ion binding			ovary(5)|lung(2)|prostate(1)|breast(1)	9																		---	---	---	---
CCAR1	55749	broad.mit.edu	37	10	70509286	70509286	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70509286A>T	uc001joo.2	+	10	1081	c.962A>T	c.(961-963)GAG>GTG	p.E321V	CCAR1_uc001jol.1_RNA|CCAR1_uc001jom.1_Missense_Mutation_p.E126V|CCAR1_uc009xpx.1_Missense_Mutation_p.E295V|CCAR1_uc001jon.1_Missense_Mutation_p.E267V|CCAR1_uc010qiz.1_Missense_Mutation_p.E306V|CCAR1_uc010qja.1_Missense_Mutation_p.E306V|CCAR1_uc010qjb.1_RNA	NM_018237	NP_060707	Q8IX12	CCAR1_HUMAN	cell-cycle and apoptosis regulatory protein 1	321	Arg-rich.				apoptosis|cell cycle|nuclear mRNA splicing, via spliceosome|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm|perinuclear region of cytoplasm	calcium ion binding|nucleic acid binding|protein binding			ovary(6)|large_intestine(1)	7																		---	---	---	---
CCAR1	55749	broad.mit.edu	37	10	70530993	70530993	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:70530993A>G	uc001joo.2	+	18	2448	c.2329A>G	c.(2329-2331)ATG>GTG	p.M777V	CCAR1_uc001jol.1_RNA|CCAR1_uc001jom.1_Missense_Mutation_p.M582V|CCAR1_uc009xpx.1_Missense_Mutation_p.M751V|CCAR1_uc001jon.1_Missense_Mutation_p.M723V|CCAR1_uc010qiz.1_Missense_Mutation_p.M762V|CCAR1_uc010qja.1_Missense_Mutation_p.M762V|CCAR1_uc010qjb.1_RNA	NM_018237	NP_060707	Q8IX12	CCAR1_HUMAN	cell-cycle and apoptosis regulatory protein 1	777	Glu-rich.				apoptosis|cell cycle|nuclear mRNA splicing, via spliceosome|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm|perinuclear region of cytoplasm	calcium ion binding|nucleic acid binding|protein binding			ovary(6)|large_intestine(1)	7																		---	---	---	---
HKDC1	80201	broad.mit.edu	37	10	71008426	71008426	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71008426C>T	uc001jpf.3	+	10	1645	c.1512C>T	c.(1510-1512)CAC>CAT	p.H504H	HKDC1_uc010qje.1_Silent_p.H367H	NM_025130	NP_079406	Q2TB90	HKDC1_HUMAN	hexokinase domain containing 1	504					glycolysis	mitochondrion|nucleus	ATP binding|hexokinase activity			ovary(4)|skin(1)	5																		---	---	---	---
HKDC1	80201	broad.mit.edu	37	10	71010336	71010336	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71010336G>T	uc001jpf.3	+	12	1897	c.1764G>T	c.(1762-1764)ATG>ATT	p.M588I	HKDC1_uc010qje.1_Missense_Mutation_p.M451I	NM_025130	NP_079406	Q2TB90	HKDC1_HUMAN	hexokinase domain containing 1	588					glycolysis	mitochondrion|nucleus	ATP binding|hexokinase activity			ovary(4)|skin(1)	5																		---	---	---	---
AIFM2	84883	broad.mit.edu	37	10	71883711	71883711	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:71883711C>T	uc010qjg.1	-	1	143	c.130G>A	c.(130-132)GAC>AAC	p.D44N	AIFM2_uc001jqp.1_Missense_Mutation_p.D44N	NM_032797	NP_116186	Q9BRQ8	AIFM2_HUMAN	apoptosis-inducing factor (AIF)-like	44					apoptotic mitochondrial changes|chromosome condensation|induction of apoptosis	cytosol|integral to membrane|mitochondrial outer membrane	DNA binding|electron-transferring-flavoprotein dehydrogenase activity|flavin adenine dinucleotide binding			central_nervous_system(1)	1																		---	---	---	---
NPFFR1	64106	broad.mit.edu	37	10	72025825	72025825	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72025825G>A	uc010qjk.1	-							NM_022146	NP_071429			neuropeptide FF receptor 1							integral to membrane|plasma membrane	neuropeptide receptor activity				0																		---	---	---	---
KIAA1274	27143	broad.mit.edu	37	10	72326399	72326399	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72326399C>T	uc001jrd.3	+	20	2762	c.2481C>T	c.(2479-2481)AGC>AGT	p.S827S	KIAA1274_uc001jre.3_Silent_p.S118S	NM_014431	NP_055246	Q9ULE6	PALD_HUMAN	KIAA1274	827										ovary(2)|central_nervous_system(1)	3																		---	---	---	---
ADAMTS14	140766	broad.mit.edu	37	10	72509640	72509640	+	Missense_Mutation	SNP	C	T	T	rs144054532		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:72509640C>T	uc001jrh.2	+	16	2326	c.2326C>T	c.(2326-2328)CGG>TGG	p.R776W	ADAMTS14_uc001jrg.2_Missense_Mutation_p.R779W	NM_080722	NP_542453	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1	776	Spacer.				collagen catabolic process|proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|upper_aerodigestive_tract(1)	6																		---	---	---	---
SLC29A3	55315	broad.mit.edu	37	10	73111529	73111529	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73111529C>T	uc001jrr.3	+	4	651	c.594C>T	c.(592-594)TCC>TCT	p.S198S	SLC29A3_uc001jrs.3_Silent_p.S198S|SLC29A3_uc010qjq.1_Silent_p.S52S|SLC29A3_uc001jrt.3_Intron|SLC29A3_uc001jru.3_Silent_p.S10S	NM_018344	NP_060814	Q9BZD2	S29A3_HUMAN	solute carrier family 29 (nucleoside	198	Cytoplasmic (Potential).				nucleobase, nucleoside and nucleotide metabolic process	integral to membrane|late endosome membrane|lysosomal membrane	nucleoside transmembrane transporter activity				0																		---	---	---	---
CDH23	64072	broad.mit.edu	37	10	73550913	73550913	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73550913T>G	uc001jrx.3	+	45	6451	c.6074T>G	c.(6073-6075)GTC>GGC	p.V2025G		NM_022124	NP_071407	Q9H251	CAD23_HUMAN	cadherin-like 23 isoform 1 precursor	2025	Cadherin 19.|Extracellular (Potential).				calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11																		---	---	---	---
PLA2G12B	84647	broad.mit.edu	37	10	74714377	74714377	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74714377T>G	uc001jtf.1	-	1	134	c.67A>C	c.(67-69)ACG>CCG	p.T23P	PLA2G12B_uc009xqt.1_5'UTR|PLA2G12B_uc010qjz.1_Missense_Mutation_p.T23P	NM_032562	NP_115951	Q9BX93	PG12B_HUMAN	phospholipase A2, group XIIB precursor	23					lipid catabolic process	extracellular region	calcium ion binding|phospholipase A2 activity			ovary(1)	1	Prostate(51;0.0198)																	---	---	---	---
P4HA1	5033	broad.mit.edu	37	10	74790132	74790132	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:74790132A>G	uc010qka.1	-						P4HA1_uc001jtg.2_Intron|P4HA1_uc001jth.2_Intron|P4HA1_uc010qkb.1_Intron|P4HA1_uc001jti.2_Intron	NM_001142595	NP_001136067			prolyl 4-hydroxylase, alpha I subunit isoform 2							endoplasmic reticulum lumen|mitochondrion	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-proline 4-dioxygenase activity			ovary(1)	1	Prostate(51;0.0198)				Hydralazine(DB01275)|L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)													---	---	---	---
ANXA7	310	broad.mit.edu	37	10	75142956	75142956	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75142956G>A	uc001jtz.2	-	10	1034	c.961C>T	c.(961-963)CGT>TGT	p.R321C	ANXA7_uc001jua.2_Missense_Mutation_p.R299C|ANXA7_uc001jub.2_Missense_Mutation_p.R259C|ANXA7_uc010qki.1_Missense_Mutation_p.R209C|ANXA7_uc009xre.2_Missense_Mutation_p.R228C|ANXA7_uc009xrf.1_Missense_Mutation_p.R241C	NM_004034	NP_004025	P20073	ANXA7_HUMAN	annexin VII isoform 2	321	Annexin 2.						calcium ion binding|calcium-dependent phospholipid binding|calcium-dependent protein binding			ovary(2)|central_nervous_system(1)	3	Prostate(51;0.0119)																	---	---	---	---
ZMYND17	118490	broad.mit.edu	37	10	75187917	75187917	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75187917A>G	uc001jud.2	-	2	192	c.126T>C	c.(124-126)ATT>ATC	p.I42I	ZMYND17_uc001juc.2_Silent_p.I42I|ZMYND17_uc009xrh.2_Silent_p.I65I|ZMYND17_uc009xrg.2_5'UTR	NM_001024593	NP_001019764	Q4VC12	ZMY17_HUMAN	zinc finger, MYND domain containing 17	42							zinc ion binding			ovary(1)	1	Prostate(51;0.0119)																	---	---	---	---
KIAA0913	23053	broad.mit.edu	37	10	75549963	75549963	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75549963G>T	uc009xrl.2	+	7	886	c.854G>T	c.(853-855)AGT>ATT	p.S285I	KIAA0913_uc001jve.2_Missense_Mutation_p.S285I|KIAA0913_uc001jvf.2_Missense_Mutation_p.S285I|KIAA0913_uc001jvh.2_5'Flank|KIAA0913_uc001jvi.2_5'Flank|KIAA0913_uc010qkr.1_5'Flank|KIAA0913_uc001jvj.2_5'Flank	NM_015037	NP_055852	A7E2V4	K0913_HUMAN	hypothetical protein LOC23053	285							zinc ion binding			breast(1)	1	Prostate(51;0.0112)																	---	---	---	---
KIAA0913	23053	broad.mit.edu	37	10	75556610	75556610	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75556610C>A	uc009xrl.2	+	16	3129	c.3097C>A	c.(3097-3099)CCA>ACA	p.P1033T	KIAA0913_uc001jve.2_Missense_Mutation_p.P1038T|KIAA0913_uc001jvf.2_Missense_Mutation_p.P1033T|KIAA0913_uc001jvh.2_RNA|KIAA0913_uc001jvi.2_Missense_Mutation_p.P468T|KIAA0913_uc010qkr.1_Missense_Mutation_p.P456T|KIAA0913_uc001jvj.2_Missense_Mutation_p.P456T|KIAA0913_uc009xrn.1_5'Flank	NM_015037	NP_055852	A7E2V4	K0913_HUMAN	hypothetical protein LOC23053	1033							zinc ion binding			breast(1)	1	Prostate(51;0.0112)																	---	---	---	---
KIAA0913	23053	broad.mit.edu	37	10	75558958	75558958	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75558958C>T	uc009xrl.2	+	21	4392	c.4360C>T	c.(4360-4362)CGG>TGG	p.R1454W	KIAA0913_uc001jve.2_Missense_Mutation_p.R1459W|KIAA0913_uc001jvf.2_Intron|KIAA0913_uc001jvh.2_RNA|KIAA0913_uc001jvi.2_Missense_Mutation_p.R889W|KIAA0913_uc010qkr.1_Missense_Mutation_p.R877W|KIAA0913_uc001jvj.2_Missense_Mutation_p.R877W|KIAA0913_uc009xrn.1_5'Flank	NM_015037	NP_055852	A7E2V4	K0913_HUMAN	hypothetical protein LOC23053	1454							zinc ion binding			breast(1)	1	Prostate(51;0.0112)																	---	---	---	---
MYST4	23522	broad.mit.edu	37	10	76780947	76780947	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:76780947C>A	uc001jwn.1	+	15	3418	c.2925C>A	c.(2923-2925)TCC>TCA	p.S975S	MYST4_uc001jwm.1_Silent_p.S683S|MYST4_uc001jwo.1_Silent_p.S683S|MYST4_uc001jwp.1_Silent_p.S792S	NM_012330	NP_036462	Q8WYB5	MYST4_HUMAN	MYST histone acetyltransferase (monocytic	975	Catalytic.|Interaction with BRPF1.				histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription factor binding|zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|breast(2)|skin(1)|prostate(1)	16	all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964)							T	CREBBP	AML								---	---	---	---
KCNMA1	3778	broad.mit.edu	37	10	78869966	78869966	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:78869966G>A	uc001jxn.2	-	8	1273	c.1096C>T	c.(1096-1098)CGC>TGC	p.R366C	KCNMA1_uc001jxj.2_Missense_Mutation_p.R366C|KCNMA1_uc001jxk.1_Silent_p.G11G|KCNMA1_uc009xrt.1_Missense_Mutation_p.R186C|KCNMA1_uc001jxl.1_Missense_Mutation_p.R20C|KCNMA1_uc001jxo.2_Missense_Mutation_p.R366C|KCNMA1_uc001jxm.2_Missense_Mutation_p.R366C|KCNMA1_uc001jxq.2_Missense_Mutation_p.R366C	NM_001161352	NP_001154824	Q12791	KCMA1_HUMAN	large conductance calcium-activated potassium	366	Extracellular (Potential).				cellular potassium ion homeostasis|negative regulation of cell volume|platelet activation|positive regulation of apoptosis|regulation of membrane potential|response to calcium ion|response to carbon monoxide|response to hypoxia|response to osmotic stress|smooth muscle contraction involved in micturition	apical plasma membrane|caveola|integral to membrane|voltage-gated potassium channel complex	actin binding|calcium-activated potassium channel activity|large conductance calcium-activated potassium channel activity|metal ion binding|voltage-gated potassium channel activity			pancreas(2)|ovary(1)	3	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Chlorzoxazone(DB00356)|Cromoglicate(DB01003)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Enflurane(DB00228)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)													---	---	---	---
DLG5	9231	broad.mit.edu	37	10	79570985	79570985	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79570985G>T	uc001jzk.2	-	23	4400	c.4330C>A	c.(4330-4332)CTG>ATG	p.L1444M	DLG5_uc001jzi.2_Missense_Mutation_p.L199M|DLG5_uc001jzj.2_Missense_Mutation_p.L859M|DLG5_uc009xru.1_RNA	NM_004747	NP_004738	Q8TDM6	DLG5_HUMAN	discs large homolog 5	1444					cell-cell adhesion|intracellular signal transduction|negative regulation of cell proliferation|regulation of apoptosis	cell junction|cytoplasm	beta-catenin binding|cytoskeletal protein binding|receptor signaling complex scaffold activity			ovary(5)|breast(3)	8	all_cancers(46;0.0316)|all_epithelial(25;0.00147)|Breast(12;0.0015)|Prostate(51;0.0146)		Epithelial(14;0.00105)|OV - Ovarian serous cystadenocarcinoma(4;0.00151)|all cancers(16;0.00446)															---	---	---	---
DLG5	9231	broad.mit.edu	37	10	79584227	79584227	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79584227C>T	uc001jzk.2	-	14	2367	c.2297G>A	c.(2296-2298)GGC>GAC	p.G766D	DLG5_uc001jzj.2_Missense_Mutation_p.G521D|DLG5_uc009xru.1_RNA|DLG5_uc001jzl.3_Missense_Mutation_p.G370D	NM_004747	NP_004738	Q8TDM6	DLG5_HUMAN	discs large homolog 5	766	PDZ 2.				cell-cell adhesion|intracellular signal transduction|negative regulation of cell proliferation|regulation of apoptosis	cell junction|cytoplasm	beta-catenin binding|cytoskeletal protein binding|receptor signaling complex scaffold activity			ovary(5)|breast(3)	8	all_cancers(46;0.0316)|all_epithelial(25;0.00147)|Breast(12;0.0015)|Prostate(51;0.0146)		Epithelial(14;0.00105)|OV - Ovarian serous cystadenocarcinoma(4;0.00151)|all cancers(16;0.00446)															---	---	---	---
POLR3A	11128	broad.mit.edu	37	10	79745651	79745651	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79745651G>A	uc001jzn.2	-							NM_007055	NP_008986			polymerase (RNA) III (DNA directed) polypeptide						innate immune response|positive regulation of interferon-beta production|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	DNA-directed RNA polymerase III complex	DNA binding|DNA-directed RNA polymerase activity|ribonucleoside binding|zinc ion binding				0	all_cancers(46;0.0356)|all_epithelial(25;0.00102)|Breast(12;0.00124)|Prostate(51;0.0095)		Epithelial(14;0.00161)|OV - Ovarian serous cystadenocarcinoma(4;0.00323)|all cancers(16;0.00646)															---	---	---	---
ZMIZ1	57178	broad.mit.edu	37	10	81053235	81053235	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81053235C>T	uc001kaf.2	+	12	1627	c.1055C>T	c.(1054-1056)GCG>GTG	p.A352V	ZMIZ1_uc001kag.2_Missense_Mutation_p.A228V|ZMIZ1_uc001kah.1_Missense_Mutation_p.A234V	NM_020338	NP_065071	Q9ULJ6	ZMIZ1_HUMAN	retinoic acid induced 17	352	Pro-rich.				transcription, DNA-dependent	cytoplasm|nuclear speck	zinc ion binding			ovary(2)|breast(1)|skin(1)	4	all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985)		Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229)															---	---	---	---
ZMIZ1	57178	broad.mit.edu	37	10	81053296	81053296	+	Silent	SNP	G	A	A	rs138100226		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81053296G>A	uc001kaf.2	+	12	1688	c.1116G>A	c.(1114-1116)CCG>CCA	p.P372P	ZMIZ1_uc001kag.2_Silent_p.P248P|ZMIZ1_uc001kah.1_Silent_p.P254P	NM_020338	NP_065071	Q9ULJ6	ZMIZ1_HUMAN	retinoic acid induced 17	372	Pro-rich.				transcription, DNA-dependent	cytoplasm|nuclear speck	zinc ion binding			ovary(2)|breast(1)|skin(1)	4	all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985)		Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229)															---	---	---	---
ZMIZ1	57178	broad.mit.edu	37	10	81067245	81067245	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81067245C>T	uc001kaf.2	+	23	3324	c.2752C>T	c.(2752-2754)CCC>TCC	p.P918S	ZMIZ1_uc001kag.2_Missense_Mutation_p.P794S|ZMIZ1_uc010qlq.1_Missense_Mutation_p.P71S	NM_020338	NP_065071	Q9ULJ6	ZMIZ1_HUMAN	retinoic acid induced 17	918	Pro-rich.				transcription, DNA-dependent	cytoplasm|nuclear speck	zinc ion binding			ovary(2)|breast(1)|skin(1)	4	all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985)		Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229)															---	---	---	---
MAT1A	4143	broad.mit.edu	37	10	82043687	82043687	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82043687C>T	uc001kbw.2	-	3	532	c.277G>A	c.(277-279)GAT>AAT	p.D93N		NM_000429	NP_000420	Q00266	METK1_HUMAN	methionine adenosyltransferase I, alpha	93					methylation|S-adenosylmethionine biosynthetic process|xenobiotic metabolic process	cytosol	ATP binding|metal ion binding|methionine adenosyltransferase activity				0			Colorectal(32;0.229)		L-Methionine(DB00134)|S-Adenosylmethionine(DB00118)													---	---	---	---
SH2D4B	387694	broad.mit.edu	37	10	82369292	82369292	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:82369292G>A	uc001kck.1	+	6	1400	c.970G>A	c.(970-972)GCC>ACC	p.A324T	SH2D4B_uc001kcl.1_Missense_Mutation_p.A276T|SH2D4B_uc001kcm.1_Missense_Mutation_p.A71T	NM_207372	NP_997255	Q5SQS7	SH24B_HUMAN	SH2 domain containing 4B isoform 1	323											0			Colorectal(32;0.229)															---	---	---	---
CDHR1	92211	broad.mit.edu	37	10	85968551	85968551	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:85968551A>G	uc001kcv.2	+	12	1234	c.1234A>G	c.(1234-1236)ACA>GCA	p.T412A	CDHR1_uc001kcw.2_Missense_Mutation_p.T412A|CDHR1_uc009xst.2_Missense_Mutation_p.T171A	NM_033100	NP_149091	Q96JP9	CDHR1_HUMAN	protocadherin 21 precursor	412	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion		calcium ion binding|receptor activity			ovary(1)	1																		---	---	---	---
FAM190B	54462	broad.mit.edu	37	10	86185640	86185640	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86185640A>G	uc001kdh.1	+	5	2053	c.1859A>G	c.(1858-1860)GAC>GGC	p.D620G	FAM190B_uc010qmd.1_Missense_Mutation_p.D620G|FAM190B_uc001kdi.1_5'UTR|FAM190B_uc010qme.1_Missense_Mutation_p.D47G	NM_018999	NP_061872	Q9H7U1	F190B_HUMAN	granule cell antiserum positive 14	620										ovary(3)|skin(1)	4																		---	---	---	---
GRID1	2894	broad.mit.edu	37	10	87379759	87379759	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87379759T>C	uc001kdl.1	-	14	2326	c.2225A>G	c.(2224-2226)GAT>GGT	p.D742G	GRID1_uc009xsu.1_Intron|GRID1_uc010qmf.1_Missense_Mutation_p.D313G	NM_017551	NP_060021	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	742	Extracellular (Potential).					cell junction|integral to membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(5)|upper_aerodigestive_tract(2)|large_intestine(2)|central_nervous_system(1)	10					L-Glutamic Acid(DB00142)										Multiple Myeloma(13;0.14)			---	---	---	---
GRID1	2894	broad.mit.edu	37	10	87407021	87407021	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87407021T>C	uc001kdl.1	-	13	2232	c.2131A>G	c.(2131-2133)ACC>GCC	p.T711A	GRID1_uc009xsu.1_RNA|GRID1_uc010qmf.1_Missense_Mutation_p.T282A|uc001kdm.1_RNA	NM_017551	NP_060021	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	711	Extracellular (Potential).					cell junction|integral to membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(5)|upper_aerodigestive_tract(2)|large_intestine(2)|central_nervous_system(1)	10					L-Glutamic Acid(DB00142)										Multiple Myeloma(13;0.14)			---	---	---	---
WAPAL	23063	broad.mit.edu	37	10	88230756	88230756	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88230756T>C	uc001kdo.2	-	8	2577	c.2135A>G	c.(2134-2136)CAC>CGC	p.H712R	WAPAL_uc009xsv.2_Missense_Mutation_p.H26R|WAPAL_uc001kdn.2_Missense_Mutation_p.H749R|WAPAL_uc009xsw.2_Missense_Mutation_p.H706R	NM_015045	NP_055860	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog	712	WAPL.				cell division|interspecies interaction between organisms|mitosis|negative regulation of chromatin binding|negative regulation of DNA replication|negative regulation of sister chromatid cohesion|protein localization to chromatin|regulation of cohesin localization to chromatin	chromatin|cohesin complex|cytoplasm	protein binding			ovary(1)	1																		---	---	---	---
LDB3	11155	broad.mit.edu	37	10	88476273	88476273	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88476273C>T	uc001kdv.2	+	9	1444	c.1421C>T	c.(1420-1422)TCG>TTG	p.S474L	LDB3_uc010qml.1_Missense_Mutation_p.S411L|LDB3_uc010qmm.1_Missense_Mutation_p.S479L|LDB3_uc001kdu.2_Missense_Mutation_p.S364L|LDB3_uc009xsz.2_Missense_Mutation_p.S103L|LDB3_uc009xta.1_5'Flank	NM_007078	NP_009009	O75112	LDB3_HUMAN	LIM domain binding 3 isoform 1	474						cytoskeleton|perinuclear region of cytoplasm|pseudopodium	zinc ion binding			ovary(1)	1																		---	---	---	---
LDB3	11155	broad.mit.edu	37	10	88492713	88492713	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88492713G>A	uc001kdv.2	+	13	2187	c.2164G>A	c.(2164-2166)GCA>ACA	p.A722T	LDB3_uc010qmm.1_Missense_Mutation_p.A727T|LDB3_uc001kdu.2_Missense_Mutation_p.A612T|LDB3_uc009xsz.2_Missense_Mutation_p.A351T	NM_007078	NP_009009	O75112	LDB3_HUMAN	LIM domain binding 3 isoform 1	722	LIM zinc-binding 3.					cytoskeleton|perinuclear region of cytoplasm|pseudopodium	zinc ion binding			ovary(1)	1																		---	---	---	---
MMRN2	79812	broad.mit.edu	37	10	88703470	88703470	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88703470C>T	uc001kea.2	-	6	1198	c.1071G>A	c.(1069-1071)ACG>ACA	p.T357T	MMRN2_uc010qmn.1_Intron|MMRN2_uc009xtb.2_Silent_p.T314T	NM_024756	NP_079032	Q9H8L6	MMRN2_HUMAN	multimerin 2 precursor	357	Potential.					extracellular space				large_intestine(1)	1																		---	---	---	---
FAM35A	54537	broad.mit.edu	37	10	88911510	88911510	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88911510C>T	uc001kei.3	+	3	513	c.399C>T	c.(397-399)ACC>ACT	p.T133T		NM_019054	NP_061927	Q86V20	FA35A_HUMAN	hypothetical protein LOC54537	133										ovary(2)|skin(2)	4																		---	---	---	---
LIPJ	142910	broad.mit.edu	37	10	90356646	90356646	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90356646A>G	uc001kff.2	+	8	990	c.676A>G	c.(676-678)AAT>GAT	p.N226D		NM_001010939	NP_001010939	Q5W064	LIPJ_HUMAN	lipase, family member J	226					lipid catabolic process		hydrolase activity			ovary(1)	1		all_cancers(4;2.79e-10)|Prostate(4;1.68e-15)|all_epithelial(4;1.43e-09)|Colorectal(252;0.0381)|Breast(4;0.141)|Melanoma(5;0.2)|all_hematologic(4;0.222)		Colorectal(12;1.02e-05)|COAD - Colon adenocarcinoma(12;1.54e-05)														---	---	---	---
LIPA	3988	broad.mit.edu	37	10	90988117	90988117	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:90988117C>T	uc001kga.3	-	4	436	c.268G>A	c.(268-270)GCA>ACA	p.A90T	LIPA_uc001kgb.3_Missense_Mutation_p.A34T|LIPA_uc001kgc.3_Missense_Mutation_p.A85T|LIPA_uc009xtq.2_Missense_Mutation_p.A90T	NM_000235	NP_000226	P38571	LICH_HUMAN	lipase A precursor	90					lipid catabolic process	lysosome	lipase activity|sterol esterase activity				0		Colorectal(252;0.0162)		GBM - Glioblastoma multiforme(2;0.00406)														---	---	---	---
KIF20B	9585	broad.mit.edu	37	10	91474923	91474923	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:91474923C>T	uc001kgs.1	+	8	996	c.924C>T	c.(922-924)GGC>GGT	p.G308G	KIF20B_uc001kgr.1_Silent_p.G308G	NM_016195	NP_057279	Q96Q89	KI20B_HUMAN	M-phase phosphoprotein 1	308	Kinesin-motor.				cell cycle arrest|cell division|microtubule-based movement|mitosis|regulation of mitosis	centrosome|microtubule|nucleolus|nucleoplasm|spindle	ATP binding|ATPase activity|microtubule motor activity|WW domain binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
ANKRD1	27063	broad.mit.edu	37	10	92679034	92679034	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:92679034G>A	uc001khe.1	-							NM_014391	NP_055206			cardiac ankyrin repeat protein						cellular lipid metabolic process|defense response|signal transduction		DNA binding				0		Colorectal(252;0.0475)																---	---	---	---
TNKS2	80351	broad.mit.edu	37	10	93621820	93621820	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93621820G>A	uc001khp.2	+	26	3643	c.3346G>A	c.(3346-3348)GCA>ACA	p.A1116T		NM_025235	NP_079511	Q9H2K2	TNKS2_HUMAN	tankyrase, TRF1-interacting ankyrin-related	1116	PARP catalytic.				positive regulation of canonical Wnt receptor signaling pathway|protein auto-ADP-ribosylation|protein localization to chromosome, telomeric region|protein polyubiquitination|Wnt receptor signaling pathway	Golgi membrane|microsome|nuclear envelope|pericentriolar material|perinuclear region of cytoplasm	NAD+ ADP-ribosyltransferase activity|protein binding			kidney(3)|skin(3)|ovary(1)|lung(1)	8		Colorectal(252;0.162)																---	---	---	---
TNKS2	80351	broad.mit.edu	37	10	93621884	93621884	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93621884C>A	uc001khp.2	+	26	3707	c.3410C>A	c.(3409-3411)GCT>GAT	p.A1137D		NM_025235	NP_079511	Q9H2K2	TNKS2_HUMAN	tankyrase, TRF1-interacting ankyrin-related	1137	PARP catalytic.				positive regulation of canonical Wnt receptor signaling pathway|protein auto-ADP-ribosylation|protein localization to chromosome, telomeric region|protein polyubiquitination|Wnt receptor signaling pathway	Golgi membrane|microsome|nuclear envelope|pericentriolar material|perinuclear region of cytoplasm	NAD+ ADP-ribosyltransferase activity|protein binding			kidney(3)|skin(3)|ovary(1)|lung(1)	8		Colorectal(252;0.162)																---	---	---	---
CYP26C1	340665	broad.mit.edu	37	10	94824266	94824266	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94824266C>T	uc010qns.1	+	4	834	c.834C>T	c.(832-834)GGC>GGT	p.G278G	CYP26C1_uc009xud.2_Intron	NM_183374	NP_899230	Q6V0L0	CP26C_HUMAN	cytochrome P450, family 26, subfamily C,	278					anterior/posterior pattern formation|central nervous system development|negative regulation of retinoic acid receptor signaling pathway|neural crest cell development|organelle fusion|retinoic acid catabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	electron carrier activity|heme binding|retinoic acid 4-hydroxylase activity|retinoic acid binding			central_nervous_system(1)	1		Colorectal(252;0.122)																---	---	---	---
CYP26C1	340665	broad.mit.edu	37	10	94828098	94828098	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94828098T>G	uc010qns.1	+	6	1213	c.1213T>G	c.(1213-1215)TGG>GGG	p.W405G	CYP26C1_uc009xud.2_RNA	NM_183374	NP_899230	Q6V0L0	CP26C_HUMAN	cytochrome P450, family 26, subfamily C,	405					anterior/posterior pattern formation|central nervous system development|negative regulation of retinoic acid receptor signaling pathway|neural crest cell development|organelle fusion|retinoic acid catabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	electron carrier activity|heme binding|retinoic acid 4-hydroxylase activity|retinoic acid binding			central_nervous_system(1)	1		Colorectal(252;0.122)																---	---	---	---
MYOF	26509	broad.mit.edu	37	10	95123759	95123759	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95123759C>T	uc001kin.2	-	27	2950	c.2827G>A	c.(2827-2829)GGG>AGG	p.G943R	MYOF_uc001kio.2_Missense_Mutation_p.G930R|MYOF_uc009xue.2_RNA	NM_013451	NP_038479	Q9NZM1	MYOF_HUMAN	myoferlin isoform a	943	Cytoplasmic (Potential).				blood circulation|muscle contraction|plasma membrane repair	caveola|cytoplasmic vesicle membrane|integral to membrane|nuclear membrane	phospholipid binding|protein binding			ovary(3)|breast(1)	4																		---	---	---	---
MYOF	26509	broad.mit.edu	37	10	95126212	95126212	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95126212T>C	uc001kin.2	-	26	2813	c.2690A>G	c.(2689-2691)GAA>GGA	p.E897G	MYOF_uc001kio.2_Missense_Mutation_p.E884G|MYOF_uc009xue.2_RNA	NM_013451	NP_038479	Q9NZM1	MYOF_HUMAN	myoferlin isoform a	897	Cytoplasmic (Potential).				blood circulation|muscle contraction|plasma membrane repair	caveola|cytoplasmic vesicle membrane|integral to membrane|nuclear membrane	phospholipid binding|protein binding			ovary(3)|breast(1)	4																		---	---	---	---
MYOF	26509	broad.mit.edu	37	10	95162048	95162048	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95162048C>A	uc001kin.2	-	11	1054	c.931G>T	c.(931-933)GGT>TGT	p.G311C	MYOF_uc001kio.2_Missense_Mutation_p.G311C|MYOF_uc001kip.3_Missense_Mutation_p.G311C|MYOF_uc009xuf.2_Missense_Mutation_p.G293C	NM_013451	NP_038479	Q9NZM1	MYOF_HUMAN	myoferlin isoform a	311	Cytoplasmic (Potential).				blood circulation|muscle contraction|plasma membrane repair	caveola|cytoplasmic vesicle membrane|integral to membrane|nuclear membrane	phospholipid binding|protein binding			ovary(3)|breast(1)	4																		---	---	---	---
RBP4	5950	broad.mit.edu	37	10	95353689	95353689	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95353689G>A	uc001kit.2	-	5	543	c.459C>T	c.(457-459)TTC>TTT	p.F153F		NM_006744	NP_006735	P02753	RET4_HUMAN	retinol-binding protein 4, plasma precursor	153					cardiac muscle tissue development|embryonic organ morphogenesis|embryonic retina morphogenesis in camera-type eye|embryonic skeletal system development|female genitalia morphogenesis|gluconeogenesis|glucose homeostasis|heart trabecula formation|lung development|maintenance of gastrointestinal epithelium|negative regulation of cardiac muscle cell proliferation|positive regulation of immunoglobulin secretion|positive regulation of insulin secretion|response to retinoic acid|retinol metabolic process|urinary bladder development|uterus development|vagina development	extracellular space	protein binding|retinal binding|retinol binding				0		Colorectal(252;0.122)			Vitamin A(DB00162)													---	---	---	---
RBP4	5950	broad.mit.edu	37	10	95360240	95360240	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95360240C>T	uc001kit.2	-	4	349	c.265G>A	c.(265-267)GCA>ACA	p.A89T		NM_006744	NP_006735	P02753	RET4_HUMAN	retinol-binding protein 4, plasma precursor	89					cardiac muscle tissue development|embryonic organ morphogenesis|embryonic retina morphogenesis in camera-type eye|embryonic skeletal system development|female genitalia morphogenesis|gluconeogenesis|glucose homeostasis|heart trabecula formation|lung development|maintenance of gastrointestinal epithelium|negative regulation of cardiac muscle cell proliferation|positive regulation of immunoglobulin secretion|positive regulation of insulin secretion|response to retinoic acid|retinol metabolic process|urinary bladder development|uterus development|vagina development	extracellular space	protein binding|retinal binding|retinol binding				0		Colorectal(252;0.122)			Vitamin A(DB00162)													---	---	---	---
PLCE1	51196	broad.mit.edu	37	10	96012097	96012097	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:96012097A>G	uc001kjk.2	+	9	3755	c.3121A>G	c.(3121-3123)ACT>GCT	p.T1041A	PLCE1_uc010qnx.1_Missense_Mutation_p.T1041A|PLCE1_uc001kjm.2_Missense_Mutation_p.T733A	NM_016341	NP_057425	Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1 isoform 1	1041					activation of MAPK activity|activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|calcium-mediated signaling|cell proliferation|cytoskeleton organization|diacylglycerol biosynthetic process|elevation of cytosolic calcium ion concentration|epidermal growth factor receptor signaling pathway|glomerulus development|heart development|lipid catabolic process|Ras protein signal transduction|regulation of cell growth|regulation of G-protein coupled receptor protein signaling pathway|regulation of Ras protein signal transduction|regulation of smooth muscle contraction	cytosol|Golgi membrane|membrane fraction|plasma membrane	calcium ion binding|guanyl-nucleotide exchange factor activity|phosphatidylinositol phospholipase C activity|Ras GTPase binding|receptor signaling protein activity			ovary(2)|skin(1)	3		Colorectal(252;0.0458)																---	---	---	---
PDLIM1	9124	broad.mit.edu	37	10	97028571	97028571	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97028571A>G	uc001kkh.2	-	3	406	c.297T>C	c.(295-297)CGT>CGC	p.R99R	PDLIM1_uc001kki.2_Silent_p.R99R|PDLIM1_uc009xuv.2_Silent_p.R99R|PDLIM1_uc001kkj.1_Silent_p.R99R	NM_020992	NP_066272	O00151	PDLI1_HUMAN	PDZ and LIM domain 1	99					response to oxidative stress	cytoplasm|cytoskeleton	zinc ion binding				0		Colorectal(252;0.083)		Epithelial(162;1.64e-06)|all cancers(201;3.71e-05)														---	---	---	---
ALDH18A1	5832	broad.mit.edu	37	10	97366600	97366600	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97366600G>A	uc001kkz.2	-	18	2549	c.2307C>T	c.(2305-2307)CAC>CAT	p.H769H	ALDH18A1_uc001kky.2_Silent_p.H767H|ALDH18A1_uc010qog.1_Silent_p.H658H|ALDH18A1_uc010qoh.1_Silent_p.H557H	NM_002860	NP_002851	P54886	P5CS_HUMAN	pyrroline-5-carboxylate synthetase isoform 1	769	Gamma-glutamyl phosphate reductase.				proline biosynthetic process	mitochondrial inner membrane	ATP binding|glutamate 5-kinase activity|glutamate-5-semialdehyde dehydrogenase activity			pancreas(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.0402)		Epithelial(162;9.1e-07)|all cancers(201;2.55e-05)	L-Glutamic Acid(DB00142)													---	---	---	---
TCTN3	26123	broad.mit.edu	37	10	97442458	97442458	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:97442458C>T	uc001klb.3	-	12	1646	c.1402G>A	c.(1402-1404)GCC>ACC	p.A468T	TCTN3_uc001kla.3_Missense_Mutation_p.A312T|TCTN3_uc010qoi.1_Missense_Mutation_p.A320T	NM_015631	NP_056446	Q6NUS6	TECT3_HUMAN	tectonic 3 isoform a precursor	468	Extracellular (Potential).				apoptosis	integral to membrane					0		Colorectal(252;0.0815)		Epithelial(162;1.69e-07)|all cancers(201;5.63e-06)														---	---	---	---
TM9SF3	56889	broad.mit.edu	37	10	98336527	98336527	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98336527A>G	uc001kmm.3	-	2	379	c.162T>C	c.(160-162)CGT>CGC	p.R54R	TM9SF3_uc010qot.1_Silent_p.R54R	NM_020123	NP_064508	Q9HD45	TM9S3_HUMAN	transmembrane 9 superfamily member 3 precursor	54						integral to membrane	binding				0		Colorectal(252;0.158)		Epithelial(162;1.84e-09)|all cancers(201;2.84e-08)														---	---	---	---
C10orf12	26148	broad.mit.edu	37	10	98708806	98708806	+	5'UTR	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98708806C>T	uc009xvg.1	+	6					LCOR_uc001kmr.2_5'UTR|LCOR_uc001kms.1_5'UTR|LCOR_uc001kmt.1_5'UTR|LCOR_uc001kmu.1_5'UTR	NM_015652	NP_056467			hypothetical protein LOC26148											skin(2)	2		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)														---	---	---	---
SLIT1	6585	broad.mit.edu	37	10	98762758	98762758	+	Intron	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98762758G>T	uc001kmw.2	-							NM_003061	NP_003052			slit homolog 1 precursor						axon extension involved in axon guidance|forebrain morphogenesis|motor axon guidance|negative chemotaxis|negative regulation of synaptogenesis	cytoplasm|extracellular space	calcium ion binding|Roundabout binding			ovary(4)	4		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)														---	---	---	---
ARHGAP19	84986	broad.mit.edu	37	10	99024660	99024660	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99024660T>G	uc001knb.2	-	3	355	c.326A>C	c.(325-327)AAA>ACA	p.K109T	ARHGAP19_uc001kmy.2_RNA|ARHGAP19_uc001kna.2_Missense_Mutation_p.K100T|ARHGAP19_uc009xvi.2_RNA|ARHGAP19_uc009xvj.2_Missense_Mutation_p.K109T|ARHGAP19_uc009xvk.2_Intron	NM_032900	NP_116289	Q14CB8	RHG19_HUMAN	Rho GTPase activating protein 19	109	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|nucleus	GTPase activator activity				0		Colorectal(252;0.0854)		Epithelial(162;7.65e-09)|all cancers(201;4.49e-07)														---	---	---	---
CRTAC1	55118	broad.mit.edu	37	10	99655136	99655136	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99655136C>T	uc001kou.1	-	11	1708	c.1352G>A	c.(1351-1353)CGC>CAC	p.R451H	CRTAC1_uc001kov.2_Missense_Mutation_p.R440H|CRTAC1_uc001kot.1_Missense_Mutation_p.R241H	NM_018058	NP_060528	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1 precursor	451						proteinaceous extracellular matrix	calcium ion binding			ovary(4)|pancreas(1)	5		Colorectal(252;0.24)		Epithelial(162;2.18e-10)|all cancers(201;3.27e-09)														---	---	---	---
LOXL4	84171	broad.mit.edu	37	10	100013496	100013496	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100013496T>C	uc001kpa.1	-	11	1800	c.1649A>G	c.(1648-1650)GAC>GGC	p.D550G		NM_032211	NP_115587	Q96JB6	LOXL4_HUMAN	lysyl oxidase-like 4 precursor	550	Lysyl-oxidase like.					extracellular space|membrane	copper ion binding|protein binding|scavenger receptor activity			ovary(3)|breast(1)|skin(1)	5		Colorectal(252;0.234)		Epithelial(162;2.14e-11)|all cancers(201;2.49e-09)														---	---	---	---
PYROXD2	84795	broad.mit.edu	37	10	100159994	100159994	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100159994A>T	uc001kpc.2	-	5	422	c.336T>A	c.(334-336)CAT>CAA	p.H112Q	PYROXD2_uc001kpb.2_RNA|PYROXD2_uc001kpd.2_RNA|PYROXD2_uc010qpe.1_Missense_Mutation_p.H112Q	NM_032709	NP_116098	Q8N2H3	PYRD2_HUMAN	pyridine nucleotide-disulphide oxidoreductase	112							oxidoreductase activity			central_nervous_system(1)	1																		---	---	---	---
HPS1	3257	broad.mit.edu	37	10	100183652	100183652	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:100183652C>T	uc010qpf.1	-						HPS1_uc001kpi.1_Intron|HPS1_uc001kpj.1_Intron|HPS1_uc001kpk.1_Intron|HPS1_uc010qpg.1_Intron|HPS1_uc009xwb.2_Intron	NM_000195	NP_000186			Hermansky-Pudlak syndrome 1 protein isoform a						lysosome organization|response to stimulus|visual perception	cytoplasmic membrane-bounded vesicle|integral to plasma membrane|lysosome|membrane fraction|soluble fraction	protein dimerization activity			skin(1)	1		Colorectal(252;0.234)		Epithelial(162;3.87e-12)|all cancers(201;5.63e-10)										Hermansky-Pudlak_syndrome				---	---	---	---
ABCC2	1244	broad.mit.edu	37	10	101591866	101591866	+	Missense_Mutation	SNP	G	A	A	rs145672804	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101591866G>A	uc001kqf.2	+	23	3375	c.3236G>A	c.(3235-3237)CGG>CAG	p.R1079Q		NM_000392	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP),	1079	ABC transmembrane type-1 2.|Cytoplasmic (By similarity).					apical plasma membrane|integral to plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|organic anion transmembrane transporter activity			ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Norgestimate(DB00957)|Pravastatin(DB00175)|Saquinavir(DB01232)|Sulfinpyrazone(DB01138)													---	---	---	---
ABCC2	1244	broad.mit.edu	37	10	101611318	101611318	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:101611318A>G	uc001kqf.2	+	32	4707	c.4568A>G	c.(4567-4569)CAA>CGA	p.Q1523R		NM_000392	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP),	1523	Cytoplasmic (By similarity).|ABC transporter 2.					apical plasma membrane|integral to plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|organic anion transmembrane transporter activity			ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Norgestimate(DB00957)|Pravastatin(DB00175)|Saquinavir(DB01232)|Sulfinpyrazone(DB01138)													---	---	---	---
PKD2L1	9033	broad.mit.edu	37	10	102049881	102049881	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102049881A>G	uc001kqx.1	-	14	2524	c.2141T>C	c.(2140-2142)GTT>GCT	p.V714A	PKD2L1_uc009xwm.1_Missense_Mutation_p.V667A	NM_016112	NP_057196	Q9P0L9	PK2L1_HUMAN	polycystic kidney disease 2-like 1	714	Cytoplasmic (Potential).				signal transduction	integral to membrane	calcium activated cation channel activity|calcium ion binding|cytoskeletal protein binding			ovary(4)	4		Colorectal(252;0.117)		Epithelial(162;6.15e-10)|all cancers(201;5.14e-08)														---	---	---	---
SCD	6319	broad.mit.edu	37	10	102107936	102107936	+	Missense_Mutation	SNP	C	A	A	rs150416868	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102107936C>A	uc001kqy.2	+	2	633	c.143C>A	c.(142-144)CCT>CAT	p.P48H		NM_005063	NP_005054	O00767	ACOD_HUMAN	stearoyl-CoA desaturase 1	48	Cytoplasmic (Potential).				fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	iron ion binding|stearoyl-CoA 9-desaturase activity				0		Colorectal(252;0.0323)		Epithelial(162;1.97e-10)|all cancers(201;1.73e-08)														---	---	---	---
SCD	6319	broad.mit.edu	37	10	102108064	102108064	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102108064A>G	uc001kqy.2	+	2	761	c.271A>G	c.(271-273)ACT>GCT	p.T91A		NM_005063	NP_005054	O00767	ACOD_HUMAN	stearoyl-CoA desaturase 1	91	Helical; (Potential).				fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	iron ion binding|stearoyl-CoA 9-desaturase activity				0		Colorectal(252;0.0323)		Epithelial(162;1.97e-10)|all cancers(201;1.73e-08)														---	---	---	---
SEMA4G	57715	broad.mit.edu	37	10	102740097	102740097	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102740097C>T	uc010qpt.1	+	11	1790	c.1347C>T	c.(1345-1347)GGC>GGT	p.G449G	SEMA4G_uc001krv.2_RNA|SEMA4G_uc001krw.1_Silent_p.G449G|SEMA4G_uc001krx.2_Silent_p.G449G|MRPL43_uc001kry.1_Intron|MRPL43_uc010qpu.1_Intron	NM_017893	NP_060363	Q9NTN9	SEM4G_HUMAN	semaphorin 4G	449	Extracellular (Potential).|Sema.				cell differentiation|nervous system development	integral to membrane	receptor activity			breast(1)	1		Colorectal(252;0.234)		Epithelial(162;3.71e-09)|all cancers(201;2.1e-07)														---	---	---	---
PDZD7	79955	broad.mit.edu	37	10	102782103	102782103	+	Silent	SNP	G	A	A	rs137967850	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102782103G>A	uc001kso.1	-	5	797	c.582C>T	c.(580-582)TGC>TGT	p.C194C	PDZD7_uc001ksn.2_Silent_p.C194C	NM_024895	NP_079171	Q9H5P4	PDZD7_HUMAN	PDZ domain containing 7	194						cilium|nucleus	protein binding			ovary(1)|breast(1)|central_nervous_system(1)	3				Epithelial(162;6.98e-09)|all cancers(201;3.55e-07)														---	---	---	---
FBXW4	6468	broad.mit.edu	37	10	103436129	103436129	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103436129G>A	uc001kto.2	-	2	671	c.325C>T	c.(325-327)CGA>TGA	p.R109*		NM_022039	NP_071322	P57775	FBXW4_HUMAN	F-box and WD repeat domain containing 4	109					ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway	ubiquitin ligase complex				skin(1)	1		Colorectal(252;0.123)		Epithelial(162;4.35e-08)|all cancers(201;1.92e-06)														---	---	---	---
KCNIP2	30819	broad.mit.edu	37	10	103587107	103587107	+	3'UTR	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103587107G>T	uc001kub.2	-	10					KCNIP2_uc010qqg.1_3'UTR|KCNIP2_uc001ktx.2_RNA|KCNIP2_uc001kty.2_3'UTR|KCNIP2_uc001ktz.2_3'UTR|KCNIP2_uc009xwu.2_3'UTR|KCNIP2_uc009xwv.2_3'UTR|KCNIP2_uc001kuc.2_3'UTR|KCNIP2_uc001kue.2_3'UTR|KCNIP2_uc001kud.2_3'UTR|KCNIP2_uc001kuf.2_3'UTR|KCNIP2_uc001kua.2_3'UTR|KCNIP2_uc009xww.2_RNA	NM_173191	NP_775283			Kv channel interacting protein 2 isoform 2						clustering of voltage-gated potassium channels|detection of calcium ion|muscle contraction|regulation of heart contraction|signal transduction|synaptic transmission	cytoplasm|voltage-gated potassium channel complex	A-type (transient outward) potassium channel activity|calcium ion binding|ER retention sequence binding|identical protein binding|protein N-terminus binding				0		Colorectal(252;0.122)		Epithelial(162;4.93e-09)|all cancers(201;2.63e-07)														---	---	---	---
LDB1	8861	broad.mit.edu	37	10	103868030	103868030	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103868030G>A	uc009xwz.2	-	11	1399	c.1056C>T	c.(1054-1056)GAC>GAT	p.D352D	LDB1_uc001kuk.3_Silent_p.D316D	NM_001113407	NP_001106878	Q86U70	LDB1_HUMAN	LIM domain binding 1 isoform 1	352	LIM-binding domain (LID) (By similarity).				histone H3-K4 acetylation|negative regulation of erythrocyte differentiation|negative regulation of transcription, DNA-dependent|positive regulation of hemoglobin biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription elongation, DNA-dependent|transcription, DNA-dependent|transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery	nuclear chromatin|protein complex	LIM domain binding|protein homodimerization activity|transcription corepressor activity			large_intestine(1)	1		Colorectal(252;0.122)		Epithelial(162;1.11e-07)|all cancers(201;1.82e-06)														---	---	---	---
CALHM2	51063	broad.mit.edu	37	10	105209369	105209369	+	Silent	SNP	C	T	T	rs142422269	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105209369C>T	uc001kwz.2	-	2	716	c.330G>A	c.(328-330)GCG>GCA	p.A110A	CALHM2_uc001kxa.2_Silent_p.A110A|CALHM2_uc001kxc.2_Silent_p.A110A|CALHM2_uc001kxb.2_Silent_p.A110A|CALHM2_uc001kxd.1_Silent_p.A110A	NM_015916	NP_057000	Q9HA72	CAHM2_HUMAN	calcium homeostasis modulator 2	110	Helical; (Potential).					integral to membrane				skin(1)	1																		---	---	---	---
CALHM1	255022	broad.mit.edu	37	10	105217983	105217983	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105217983C>T	uc001kxe.2	-	1	666	c.526G>A	c.(526-528)GCC>ACC	p.A176T		NM_001001412	NP_001001412	Q8IU99	CAHM1_HUMAN	calcium homeostasis modulator 1	176						endoplasmic reticulum membrane|integral to membrane|plasma membrane	calcium channel activity|identical protein binding			ovary(1)	1																		---	---	---	---
SH3PXD2A	9644	broad.mit.edu	37	10	105495505	105495505	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105495505G>A	uc001kxj.1	-	4	431	c.291C>T	c.(289-291)ATC>ATT	p.I97I	SH3PXD2A_uc010qqu.1_Silent_p.I27I	NM_014631	NP_055446	Q5TCZ1	SPD2A_HUMAN	SH3 multiple domains 1	97	PX.				cell communication|superoxide metabolic process	cell junction|cell projection|cytoplasm|podosome	phosphatidylinositol binding|protein binding				0		Colorectal(252;0.0815)|Breast(234;0.131)		Epithelial(162;4.09e-10)|all cancers(201;2.73e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0119)														---	---	---	---
SLK	9748	broad.mit.edu	37	10	105765330	105765330	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105765330A>C	uc001kxo.1	+	10	2395	c.2361A>C	c.(2359-2361)AGA>AGC	p.R787S	SLK_uc001kxp.1_Missense_Mutation_p.R787S	NM_014720	NP_055535	Q9H2G2	SLK_HUMAN	serine/threonine kinase 2	787					apoptosis|nucleotide-excision repair	cytoplasm|plasma membrane	ATP binding|DNA binding|nuclease activity|protein serine/threonine kinase activity			ovary(2)|stomach(2)|skin(2)|lung(1)|kidney(1)	8		Colorectal(252;0.178)		Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)														---	---	---	---
COL17A1	1308	broad.mit.edu	37	10	105803343	105803343	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105803343A>G	uc001kxr.2	-							NM_000494	NP_000485			alpha 1 type XVII collagen						cell-matrix adhesion|epidermis development|hemidesmosome assembly	basement membrane|cell-cell junction|collagen|hemidesmosome|integral to plasma membrane	protein binding			ovary(4)|pancreas(1)	5		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)														---	---	---	---
COL17A1	1308	broad.mit.edu	37	10	105840407	105840407	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105840407G>A	uc001kxr.2	-	2	194	c.25C>T	c.(25-27)CGA>TGA	p.R9*	COL17A1_uc010qqv.1_Nonsense_Mutation_p.R9*|COL17A1_uc009xxp.1_Nonsense_Mutation_p.R9*	NM_000494	NP_000485	Q9UMD9	COHA1_HUMAN	alpha 1 type XVII collagen	9	Cytoplasmic (Potential).|Nonhelical region (NC16).				cell-matrix adhesion|epidermis development|hemidesmosome assembly	basement membrane|cell-cell junction|collagen|hemidesmosome|integral to plasma membrane	protein binding			ovary(4)|pancreas(1)	5		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)														---	---	---	---
C10orf79	80217	broad.mit.edu	37	10	105926421	105926421	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:105926421T>C	uc001kxw.2	-	23	2980	c.2864A>G	c.(2863-2865)CAT>CGT	p.H955R	C10orf79_uc009xxq.2_Missense_Mutation_p.H263R	NM_025145	NP_079421	Q8NDM7	WDR96_HUMAN	hypothetical protein LOC80217	955	Potential.										0		Colorectal(252;0.178)		Epithelial(162;4.83e-10)|all cancers(201;2.26e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0194)														---	---	---	---
ITPRIP	85450	broad.mit.edu	37	10	106074864	106074864	+	Missense_Mutation	SNP	C	T	T	rs144093219		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106074864C>T	uc001kye.2	-	2	1019	c.946G>A	c.(946-948)GCC>ACC	p.A316T	ITPRIP_uc001kyf.2_Missense_Mutation_p.A316T|ITPRIP_uc001kyg.2_Missense_Mutation_p.A316T	NM_033397	NP_203755	Q8IWB1	IPRI_HUMAN	inositol 1,4,5-triphosphate receptor interacting	316						plasma membrane					0																		---	---	---	---
SORCS3	22986	broad.mit.edu	37	10	106865245	106865245	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:106865245T>C	uc001kyi.1	+	7	1411	c.1184T>C	c.(1183-1185)GTT>GCT	p.V395A		NM_014978	NP_055793	Q9UPU3	SORC3_HUMAN	VPS10 domain receptor protein SORCS 3 precursor	395	Lumenal (Potential).					integral to membrane	neuropeptide receptor activity			ovary(6)|skin(3)|central_nervous_system(1)	10		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)														---	---	---	---
SORCS1	114815	broad.mit.edu	37	10	108431071	108431071	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108431071G>A	uc001kym.2	-	16	2121	c.2113C>T	c.(2113-2115)CGG>TGG	p.R705W	SORCS1_uc001kyl.2_Missense_Mutation_p.R705W|SORCS1_uc009xxs.2_Missense_Mutation_p.R705W|SORCS1_uc001kyn.1_Missense_Mutation_p.R705W|SORCS1_uc001kyo.2_Missense_Mutation_p.R705W	NM_052918	NP_443150	Q8WY21	SORC1_HUMAN	SORCS receptor 1 isoform a	705	Lumenal (Potential).					integral to membrane	neuropeptide receptor activity|protein binding			breast(1)|central_nervous_system(1)	2		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)														---	---	---	---
SHOC2	8036	broad.mit.edu	37	10	112771429	112771429	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:112771429C>A	uc001kzl.3	+	9	1951	c.1602C>A	c.(1600-1602)CCC>CCA	p.P534P	SHOC2_uc009xxx.2_Silent_p.P534P|SHOC2_uc010qrg.1_Silent_p.P173P|SHOC2_uc001kzn.2_Silent_p.P488P	NM_007373	NP_031399	Q9UQ13	SHOC2_HUMAN	soc-2 suppressor of clear homolog	534	LRR 19.				fibroblast growth factor receptor signaling pathway|positive regulation of Ras protein signal transduction|Ras protein signal transduction	nucleus|protein phosphatase type 1 complex	protein phosphatase binding|protein phosphatase regulator activity			ovary(1)|skin(1)	2				Epithelial(162;0.000796)|all cancers(201;0.011)|BRCA - Breast invasive adenocarcinoma(275;0.126)														---	---	---	---
TECTB	6975	broad.mit.edu	37	10	114053579	114053579	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114053579A>C	uc001kzr.1	+	5	567	c.567A>C	c.(565-567)GAA>GAC	p.E189D		NM_058222	NP_478129	Q96PL2	TECTB_HUMAN	tectorin beta precursor	189	ZP.					anchored to membrane|plasma membrane|proteinaceous extracellular matrix					0		Colorectal(252;0.198)		Epithelial(162;0.0143)|all cancers(201;0.0242)														---	---	---	---
ZDHHC6	64429	broad.mit.edu	37	10	114192134	114192134	+	Missense_Mutation	SNP	C	T	T	rs140777505		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:114192134C>T	uc001kzv.2	-	9	1515	c.1091G>A	c.(1090-1092)CGA>CAA	p.R364Q	ZDHHC6_uc001kzw.2_Missense_Mutation_p.R360Q	NM_022494	NP_071939	Q9H6R6	ZDHC6_HUMAN	zinc finger, DHHC-type containing 6	364						integral to membrane	acyltransferase activity|zinc ion binding				0		Colorectal(252;0.198)		Epithelial(162;0.0291)|all cancers(201;0.117)														---	---	---	---
HABP2	3026	broad.mit.edu	37	10	115345563	115345563	+	Missense_Mutation	SNP	C	T	T	rs141433300		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115345563C>T	uc001lai.3	+	12	1487	c.1384C>T	c.(1384-1386)CGC>TGC	p.R462C		NM_004132	NP_004123	Q14520	HABP2_HUMAN	hyaluronan binding protein 2 preproprotein	462	Peptidase S1.				cell adhesion|proteolysis	extracellular space	glycosaminoglycan binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3		Colorectal(252;0.0233)|Breast(234;0.0672)		Epithelial(162;0.00319)|all cancers(201;0.0112)														---	---	---	---
NRAP	4892	broad.mit.edu	37	10	115377298	115377298	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115377298C>T	uc001laj.2	-	26	3053	c.2889G>A	c.(2887-2889)CAG>CAA	p.Q963Q	NRAP_uc009xyb.2_Intron|NRAP_uc001lak.2_Silent_p.Q928Q|NRAP_uc001lal.3_Silent_p.Q963Q	NM_198060	NP_932326	Q86VF7	NRAP_HUMAN	nebulin-related anchoring protein isoform S	963	Nebulin 24.					fascia adherens|muscle tendon junction	actin binding|muscle alpha-actinin binding|zinc ion binding			ovary(6)|central_nervous_system(3)|upper_aerodigestive_tract(1)	10		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)														---	---	---	---
NRAP	4892	broad.mit.edu	37	10	115411638	115411638	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115411638C>T	uc001laj.2	-	7	763	c.599G>A	c.(598-600)CGC>CAC	p.R200H	NRAP_uc001lak.2_Missense_Mutation_p.R200H|NRAP_uc001lal.3_Missense_Mutation_p.R200H	NM_198060	NP_932326	Q86VF7	NRAP_HUMAN	nebulin-related anchoring protein isoform S	200	Nebulin 3.					fascia adherens|muscle tendon junction	actin binding|muscle alpha-actinin binding|zinc ion binding			ovary(6)|central_nervous_system(3)|upper_aerodigestive_tract(1)	10		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)														---	---	---	---
DCLRE1A	9937	broad.mit.edu	37	10	115609809	115609809	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115609809A>G	uc001law.2	-	2	1973	c.1055T>C	c.(1054-1056)CTG>CCG	p.L352P		NM_014881	NP_055696	Q6PJP8	DCR1A_HUMAN	DNA cross-link repair 1A	352					cell division|mitosis	nucleus	hydrolase activity			skin(2)	2				Epithelial(162;0.0157)|all cancers(201;0.0171)									Direct_reversal_of_damage|Other_identified_genes_with_known_or_suspected_DNA_repair_function					---	---	---	---
VWA2	340706	broad.mit.edu	37	10	116014763	116014763	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116014763T>G	uc001lbl.1	+	4	538	c.217T>G	c.(217-219)TTT>GTT	p.F73V	VWA2_uc001lbk.1_Missense_Mutation_p.F73V|VWA2_uc009xyf.1_Intron	NM_198496	NP_940898	Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	73	VWFA 1.					extracellular region				ovary(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5				Epithelial(162;0.036)|all cancers(201;0.0793)														---	---	---	---
AFAP1L2	84632	broad.mit.edu	37	10	116062116	116062116	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:116062116G>A	uc001lbn.2	-	12	1713	c.1412C>T	c.(1411-1413)GCG>GTG	p.A471V	AFAP1L2_uc001lbo.2_Missense_Mutation_p.A471V|AFAP1L2_uc010qse.1_Missense_Mutation_p.A524V|AFAP1L2_uc001lbp.2_Missense_Mutation_p.A499V|AFAP1L2_uc001lbr.1_Missense_Mutation_p.A471V|AFAP1L2_uc001lbm.2_5'Flank|AFAP1L2_uc010qsd.1_Missense_Mutation_p.A37V|AFAP1L2_uc001lbq.1_5'Flank	NM_001001936	NP_001001936	Q8N4X5	AF1L2_HUMAN	KIAA1914 protein isoform 1	471					inflammatory response|positive regulation of epidermal growth factor receptor signaling pathway|positive regulation of interleukin-8 production|positive regulation of transcription, DNA-dependent|regulation of interleukin-6 production|regulation of mitotic cell cycle	cytoplasm	protein tyrosine kinase activator activity|SH2 domain binding|SH3 domain binding			ovary(1)|breast(1)	2		Colorectal(252;0.175)|Breast(234;0.231)		Epithelial(162;0.0219)|all cancers(201;0.0561)														---	---	---	---
ATRNL1	26033	broad.mit.edu	37	10	117027871	117027871	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:117027871C>A	uc001lcg.2	+	13	2436	c.2050C>A	c.(2050-2052)CAA>AAA	p.Q684K		NM_207303	NP_997186	Q5VV63	ATRN1_HUMAN	attractin-like 1 precursor	684	PSI 2.|Extracellular (Potential).					integral to membrane	sugar binding			ovary(5)|lung(1)|central_nervous_system(1)	7		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)														---	---	---	---
PNLIP	5406	broad.mit.edu	37	10	118319943	118319943	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118319943T>C	uc001lcm.2	+	11	1119	c.1076T>C	c.(1075-1077)GTA>GCA	p.V359A		NM_000936	NP_000927	P16233	LIPP_HUMAN	pancreatic lipase precursor	359	PLAT.				lipid catabolic process|retinoid metabolic process|steroid metabolic process	extracellular region	retinyl-palmitate esterase activity|triglyceride lipase activity			ovary(1)|central_nervous_system(1)|skin(1)	3				all cancers(201;0.0131)	Bentiromide(DB00522)|Orlistat(DB01083)													---	---	---	---
EIF3A	8661	broad.mit.edu	37	10	120825065	120825065	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120825065A>C	uc001ldu.2	-	7	1114	c.968T>G	c.(967-969)CTT>CGT	p.L323R	EIF3A_uc010qsu.1_Missense_Mutation_p.L289R	NM_003750	NP_003741	Q14152	EIF3A_HUMAN	eukaryotic translation initiation factor 3,	323					formation of translation initiation complex	cytosol|eukaryotic translation initiation factor 3 complex	protein binding|structural molecule activity|translation initiation factor activity				0		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0236)														---	---	---	---
FAM45A	404636	broad.mit.edu	37	10	120867592	120867592	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120867592C>A	uc001ldw.2	+	2	212	c.168C>A	c.(166-168)CTC>CTA	p.L56L	FAM45A_uc010qsv.1_Silent_p.L48L|FAM45A_uc010qsw.1_5'UTR|FAM45A_uc010qsx.1_RNA|FAM45A_uc010qsy.1_Missense_Mutation_p.S6Y	NM_207009	NP_996892	Q8TCE6	FA45A_HUMAN	hypothetical protein LOC404636	56										ovary(1)	1		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0293)														---	---	---	---
INPP5F	22876	broad.mit.edu	37	10	121569627	121569627	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:121569627A>G	uc001leo.2	+	14	1751	c.1585A>G	c.(1585-1587)ACA>GCA	p.T529A		NM_014937	NP_055752	Q9Y2H2	SAC2_HUMAN	inositol polyphosphate-5-phosphatase F	529							phosphoric ester hydrolase activity			ovary(2)	2		Lung NSC(174;0.109)|all_lung(145;0.142)		all cancers(201;0.00205)|BRCA - Breast invasive adenocarcinoma(275;0.158)														---	---	---	---
ATE1	11101	broad.mit.edu	37	10	123503332	123503332	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123503332A>C	uc001lfp.2	-	12	1502	c.1420T>G	c.(1420-1422)TTT>GTT	p.F474V	ATE1_uc001lfq.2_Missense_Mutation_p.F474V|ATE1_uc010qtr.1_Missense_Mutation_p.F359V|ATE1_uc010qts.1_Missense_Mutation_p.F378V|ATE1_uc010qtt.1_Missense_Mutation_p.F467V|ATE1_uc001lfr.2_Missense_Mutation_p.F175V|ATE1_uc009xzu.2_RNA	NM_007041	NP_008972	O95260	ATE1_HUMAN	arginyltransferase 1 isoform 2	474					protein arginylation	cytoplasm|nucleus	acyltransferase activity|arginyltransferase activity				0		all_neural(114;0.061)|Lung NSC(174;0.095)|all_lung(145;0.124)|Breast(234;0.212)																---	---	---	---
NSMCE4A	54780	broad.mit.edu	37	10	123719083	123719083	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123719083T>C	uc001lfs.2	-	9	1046	c.1016A>G	c.(1015-1017)GAG>GGG	p.E339G	NSMCE4A_uc009xzv.2_Missense_Mutation_p.E339G|NSMCE4A_uc001lft.2_Missense_Mutation_p.E180G	NM_017615	NP_060085	Q9NXX6	NSE4A_HUMAN	non-SMC element 4 homolog A	339											0		all_neural(114;0.138)|Glioma(114;0.222)																---	---	---	---
TACC2	10579	broad.mit.edu	37	10	123846133	123846133	+	Missense_Mutation	SNP	G	A	A	rs149524584	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123846133G>A	uc001lfv.2	+	4	4478	c.4118G>A	c.(4117-4119)AGC>AAC	p.S1373N	TACC2_uc001lfw.2_Intron|TACC2_uc009xzx.2_Missense_Mutation_p.S1373N|TACC2_uc010qtv.1_Missense_Mutation_p.S1373N	NM_206862	NP_996744	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing	1373						microtubule organizing center|nucleus	nuclear hormone receptor binding			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)																---	---	---	---
TACC2	10579	broad.mit.edu	37	10	123892154	123892154	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123892154C>T	uc001lfv.2	+	6	5964	c.5604C>T	c.(5602-5604)CCC>CCT	p.P1868P	TACC2_uc001lfw.2_Silent_p.P59P|TACC2_uc009xzx.2_Silent_p.P1868P|TACC2_uc010qtv.1_Silent_p.P1917P|TACC2_uc001lfx.2_5'UTR|TACC2_uc001lfy.2_5'UTR	NM_206862	NP_996744	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing	1868						microtubule organizing center|nucleus	nuclear hormone receptor binding			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)																---	---	---	---
PLEKHA1	59338	broad.mit.edu	37	10	124166109	124166109	+	Silent	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124166109A>C	uc001lge.1	+	5	385	c.262A>C	c.(262-264)AGG>CGG	p.R88R	PLEKHA1_uc001lgf.1_Silent_p.R88R|PLEKHA1_uc001lgg.1_Silent_p.R88R|PLEKHA1_uc001lgh.2_Silent_p.R88R	NM_001001974	NP_001001974	Q9HB21	PKHA1_HUMAN	pleckstrin homology domain containing, family A	88	PH 1.				B cell receptor signaling pathway|cellular response to hydrogen peroxide|establishment of protein localization|negative regulation of protein kinase B signaling cascade|phosphatidylinositol 3-kinase cascade|ruffle organization	cytoplasm|nucleus|ruffle membrane	PDZ domain binding|phosphatidylinositol-3,4-bisphosphate binding			kidney(1)	1		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)																---	---	---	---
DMBT1	1755	broad.mit.edu	37	10	124331871	124331871	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124331871G>A	uc001lgk.1	+	5	335	c.229G>A	c.(229-231)GCA>ACA	p.A77T	DMBT1_uc001lgl.1_Missense_Mutation_p.A77T|DMBT1_uc001lgm.1_Missense_Mutation_p.A77T|DMBT1_uc009xzz.1_Missense_Mutation_p.A77T|DMBT1_uc010qtx.1_Missense_Mutation_p.A77T|DMBT1_uc009yaa.1_5'UTR	NM_007329	NP_015568	Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1 isoform b	77					epithelial cell differentiation|induction of bacterial agglutination|innate immune response|interspecies interaction between organisms|protein transport|response to virus	extrinsic to membrane|phagocytic vesicle membrane|zymogen granule membrane	calcium-dependent protein binding|Gram-negative bacterial cell surface binding|Gram-positive bacterial cell surface binding|pattern recognition receptor activity|scavenger receptor activity|zymogen binding			central_nervous_system(7)	7		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)																---	---	---	---
DMBT1	1755	broad.mit.edu	37	10	124377558	124377558	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124377558A>G	uc001lgk.1	+	38	4636	c.4530A>G	c.(4528-4530)AGA>AGG	p.R1510R	DMBT1_uc001lgl.1_Silent_p.R1500R|DMBT1_uc001lgm.1_Silent_p.R882R|DMBT1_uc009xzz.1_Silent_p.R1510R|DMBT1_uc010qtx.1_Silent_p.R361R|DMBT1_uc009yab.1_Silent_p.R213R	NM_007329	NP_015568	Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1 isoform b	1510	SRCR 12.				epithelial cell differentiation|induction of bacterial agglutination|innate immune response|interspecies interaction between organisms|protein transport|response to virus	extrinsic to membrane|phagocytic vesicle membrane|zymogen granule membrane	calcium-dependent protein binding|Gram-negative bacterial cell surface binding|Gram-positive bacterial cell surface binding|pattern recognition receptor activity|scavenger receptor activity|zymogen binding			central_nervous_system(7)	7		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)																---	---	---	---
DMBT1	1755	broad.mit.edu	37	10	124377666	124377666	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124377666C>T	uc001lgk.1	+	38	4744	c.4638C>T	c.(4636-4638)GTC>GTT	p.V1546V	DMBT1_uc001lgl.1_Silent_p.V1536V|DMBT1_uc001lgm.1_Silent_p.V918V|DMBT1_uc009xzz.1_Silent_p.V1546V|DMBT1_uc010qtx.1_Silent_p.V397V|DMBT1_uc009yab.1_Silent_p.V249V|DMBT1_uc009yac.1_5'Flank	NM_007329	NP_015568	Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1 isoform b	1546	SRCR 12.				epithelial cell differentiation|induction of bacterial agglutination|innate immune response|interspecies interaction between organisms|protein transport|response to virus	extrinsic to membrane|phagocytic vesicle membrane|zymogen granule membrane	calcium-dependent protein binding|Gram-negative bacterial cell surface binding|Gram-positive bacterial cell surface binding|pattern recognition receptor activity|scavenger receptor activity|zymogen binding			central_nervous_system(7)	7		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)																---	---	---	---
DMBT1	1755	broad.mit.edu	37	10	124377695	124377695	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124377695T>C	uc001lgk.1	+	38	4773	c.4667T>C	c.(4666-4668)ATG>ACG	p.M1556T	DMBT1_uc001lgl.1_Missense_Mutation_p.M1546T|DMBT1_uc001lgm.1_Missense_Mutation_p.M928T|DMBT1_uc009xzz.1_Missense_Mutation_p.M1556T|DMBT1_uc010qtx.1_Missense_Mutation_p.M407T|DMBT1_uc009yab.1_Missense_Mutation_p.M259T|DMBT1_uc009yac.1_5'Flank	NM_007329	NP_015568	Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1 isoform b	1556	SRCR 12.				epithelial cell differentiation|induction of bacterial agglutination|innate immune response|interspecies interaction between organisms|protein transport|response to virus	extrinsic to membrane|phagocytic vesicle membrane|zymogen granule membrane	calcium-dependent protein binding|Gram-negative bacterial cell surface binding|Gram-positive bacterial cell surface binding|pattern recognition receptor activity|scavenger receptor activity|zymogen binding			central_nervous_system(7)	7		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)																---	---	---	---
DMBT1	1755	broad.mit.edu	37	10	124390530	124390530	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:124390530C>T	uc001lgk.1	+	46	5798	c.5692C>T	c.(5692-5694)CGT>TGT	p.R1898C	DMBT1_uc001lgl.1_Missense_Mutation_p.R1888C|DMBT1_uc001lgm.1_Missense_Mutation_p.R1270C|DMBT1_uc009xzz.1_Missense_Mutation_p.R1898C|DMBT1_uc010qtx.1_Missense_Mutation_p.R618C|DMBT1_uc009yab.1_Missense_Mutation_p.R601C|DMBT1_uc009yac.1_Missense_Mutation_p.R192C	NM_007329	NP_015568	Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1 isoform b	1898	SRCR 14.				epithelial cell differentiation|induction of bacterial agglutination|innate immune response|interspecies interaction between organisms|protein transport|response to virus	extrinsic to membrane|phagocytic vesicle membrane|zymogen granule membrane	calcium-dependent protein binding|Gram-negative bacterial cell surface binding|Gram-positive bacterial cell surface binding|pattern recognition receptor activity|scavenger receptor activity|zymogen binding			central_nervous_system(7)	7		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)																---	---	---	---
GPR26	2849	broad.mit.edu	37	10	125447465	125447465	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:125447465C>T	uc001lhh.2	+	3	856	c.803C>T	c.(802-804)ACG>ATG	p.T268M		NM_153442	NP_703143	Q8NDV2	GPR26_HUMAN	G protein-coupled receptor 26	268	Extracellular (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			skin(1)	1		Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)																---	---	---	---
ZRANB1	54764	broad.mit.edu	37	10	126672031	126672031	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126672031T>C	uc001lic.2	+	8	2053	c.1682T>C	c.(1681-1683)GTT>GCT	p.V561A	ZRANB1_uc010qug.1_Missense_Mutation_p.V587A	NM_017580	NP_060050	Q9UGI0	ZRAN1_HUMAN	zinc finger, RAN-binding domain containing 1	561	OTU.|TRAF-binding.				positive regulation of Wnt receptor signaling pathway|protein K63-linked deubiquitination|Wnt receptor signaling pathway	aggresome|centrosome|intermediate filament cytoskeleton|nucleolus	cysteine-type peptidase activity|protein binding|ubiquitin thiolesterase activity|zinc ion binding			ovary(1)|kidney(1)	2		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.172)		Colorectal(40;0.113)|COAD - Colon adenocarcinoma(40;0.119)														---	---	---	---
CTBP2	1488	broad.mit.edu	37	10	126683237	126683237	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:126683237G>A	uc009yak.2	-	7	868	c.581C>T	c.(580-582)GCG>GTG	p.A194V	CTBP2_uc009yal.2_Missense_Mutation_p.A194V|CTBP2_uc001lif.3_Missense_Mutation_p.A194V|CTBP2_uc001lih.3_Missense_Mutation_p.A194V|CTBP2_uc001lid.3_Missense_Mutation_p.A262V|CTBP2_uc001lie.3_Missense_Mutation_p.A734V	NM_001329	NP_001320	P56545	CTBP2_HUMAN	C-terminal binding protein 2 isoform 1	194					negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent|viral genome replication|white fat cell differentiation	cell junction|synapse|transcriptional repressor complex	NAD binding|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor|protein binding				0		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173)		Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147)														---	---	---	---
ADAM12	8038	broad.mit.edu	37	10	127787013	127787013	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:127787013G>A	uc001ljk.2	-	10	1390	c.977C>T	c.(976-978)ACG>ATG	p.T326M	ADAM12_uc010qul.1_Missense_Mutation_p.T277M|ADAM12_uc001ljm.2_Missense_Mutation_p.T326M|ADAM12_uc001ljn.2_Missense_Mutation_p.T323M|ADAM12_uc001ljl.3_Missense_Mutation_p.T323M	NM_003474	NP_003465	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12 isoform 1	326	Extracellular (Potential).|Peptidase M12B.				cell adhesion|epidermal growth factor receptor signaling pathway|myoblast fusion|proteolysis	extracellular region|integral to membrane|plasma membrane	metalloendopeptidase activity|protein binding|SH3 domain binding|zinc ion binding			breast(4)|ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	9		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)														---	---	---	---
DOCK1	1793	broad.mit.edu	37	10	128823027	128823027	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:128823027C>T	uc001ljt.2	+	15	1532	c.1468C>T	c.(1468-1470)CGC>TGC	p.R490C	DOCK1_uc010qun.1_Missense_Mutation_p.R511C	NM_001380	NP_001371	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	490	DHR-1.				apoptosis|axon guidance|blood coagulation|integrin-mediated signaling pathway|phagocytosis, engulfment|small GTPase mediated signal transduction	cytosol|membrane	GTP binding|GTPase activator activity|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding			central_nervous_system(4)|ovary(2)|lung(1)|breast(1)|kidney(1)	9		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)														---	---	---	---
MKI67	4288	broad.mit.edu	37	10	129901422	129901422	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:129901422G>A	uc001lke.2	-	13	8877	c.8682C>T	c.(8680-8682)GAC>GAT	p.D2894D	MKI67_uc001lkf.2_Silent_p.D2534D|MKI67_uc009yav.1_Silent_p.D2469D|MKI67_uc009yaw.1_Silent_p.D2044D	NM_002417	NP_002408	P46013	KI67_HUMAN	antigen identified by monoclonal antibody Ki-67	2894	16 X 122 AA approximate repeats.|16.				cell proliferation	nucleolus	ATP binding|protein C-terminus binding			ovary(4)|central_nervous_system(2)|skin(1)	7		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)																---	---	---	---
MGMT	4255	broad.mit.edu	37	10	131557572	131557572	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131557572G>A	uc001lkh.2	+	4	500	c.474G>A	c.(472-474)GCG>GCA	p.A158A		NM_002412	NP_002403	P16455	MGMT_HUMAN	O-6-methylguanine-DNA methyltransferase	127										ovary(1)|breast(1)	2		all_cancers(35;9.44e-09)|all_epithelial(44;6.98e-08)|Lung NSC(174;0.0157)|all_lung(145;0.0201)|all_neural(114;0.0732)|Colorectal(57;0.0792)|Breast(234;0.167)		OV - Ovarian serous cystadenocarcinoma(35;0.00291)									Direct_reversal_of_damage					---	---	---	---
EBF3	253738	broad.mit.edu	37	10	131671823	131671823	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:131671823A>G	uc001lki.1	-	8	733	c.674T>C	c.(673-675)GTG>GCG	p.V225A		NM_001005463	NP_001005463	Q9H4W6	COE3_HUMAN	early B-cell factor 3	225					multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|metal ion binding|protein binding			central_nervous_system(1)|pancreas(1)	2		all_cancers(35;1.8e-08)|all_epithelial(44;8.26e-08)|Lung NSC(174;0.0091)|all_lung(145;0.0123)|Breast(234;0.039)|all_neural(114;0.0722)|Colorectal(57;0.0764)		OV - Ovarian serous cystadenocarcinoma(35;0.00513)														---	---	---	---
PPP2R2D	55844	broad.mit.edu	37	10	133747968	133747968	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133747968T>C	uc001lks.2	+	1	251	c.8T>C	c.(7-9)ATC>ACC	p.I3T	PPP2R2D_uc001lkr.2_5'UTR|PPP2R2D_uc001lkt.2_5'UTR	NM_018461	NP_060931	Q66LE6	2ABD_HUMAN	protein phosphatase 2, regulatory subunit B,	36	WD 1.				cell division|exit from mitosis|mitosis|signal transduction	cytoplasm|protein phosphatase type 2A complex	protein phosphatase type 2A regulator activity			skin(1)	1		all_cancers(35;2.16e-12)|all_epithelial(44;2.77e-09)|Lung NSC(174;0.00237)|all_lung(145;0.00354)|Colorectal(31;0.0124)|Breast(234;0.023)|all_neural(114;0.0299)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;7.86e-05)|Epithelial(32;8.82e-05)|all cancers(32;0.000106)|BRCA - Breast invasive adenocarcinoma(275;0.21)														---	---	---	---
PPP2R2D	55844	broad.mit.edu	37	10	133761284	133761284	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133761284C>T	uc001lks.2	+	6	1215	c.972C>T	c.(970-972)AAC>AAT	p.N324N	PPP2R2D_uc001lkr.2_Silent_p.N130N|PPP2R2D_uc001lkt.2_Silent_p.N130N|PPP2R2D_uc009yay.2_Silent_p.N192N	NM_018461	NP_060931	Q66LE6	2ABD_HUMAN	protein phosphatase 2, regulatory subunit B,	357	WD 6.				cell division|exit from mitosis|mitosis|signal transduction	cytoplasm|protein phosphatase type 2A complex	protein phosphatase type 2A regulator activity			skin(1)	1		all_cancers(35;2.16e-12)|all_epithelial(44;2.77e-09)|Lung NSC(174;0.00237)|all_lung(145;0.00354)|Colorectal(31;0.0124)|Breast(234;0.023)|all_neural(114;0.0299)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;7.86e-05)|Epithelial(32;8.82e-05)|all cancers(32;0.000106)|BRCA - Breast invasive adenocarcinoma(275;0.21)														---	---	---	---
JAKMIP3	282973	broad.mit.edu	37	10	133930794	133930794	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133930794C>T	uc001lkx.3	+	2	349	c.349C>T	c.(349-351)CAG>TAG	p.Q117*		NM_001105521	NP_001098991			Janus kinase and microtubule interacting protein											breast(1)	1		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)														---	---	---	---
STK32C	282974	broad.mit.edu	37	10	134038001	134038001	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134038001G>A	uc001lle.1	-	8	1043	c.903C>T	c.(901-903)AAC>AAT	p.N301N	STK32C_uc001lld.1_Silent_p.N184N|STK32C_uc010quu.1_Silent_p.N314N|STK32C_uc009ybc.1_Silent_p.N184N|STK32C_uc001llb.2_Silent_p.N72N|STK32C_uc001llc.1_RNA	NM_173575	NP_775846	Q86UX6	ST32C_HUMAN	serine/threonine kinase 32C	301	Protein kinase.						ATP binding|metal ion binding|protein serine/threonine kinase activity			large_intestine(2)|lung(2)|breast(1)	5		all_cancers(35;2.72e-11)|all_epithelial(44;2.33e-08)|Lung NSC(174;0.000855)|all_lung(145;0.00146)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.112)|Melanoma(40;0.124)|Glioma(114;0.203)		Epithelial(32;3.99e-05)|all cancers(32;5.58e-05)|OV - Ovarian serous cystadenocarcinoma(35;9.96e-05)|BRCA - Breast invasive adenocarcinoma(275;0.222)														---	---	---	---
PWWP2B	170394	broad.mit.edu	37	10	134218130	134218130	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134218130G>A	uc001lll.3	+	2	155	c.126G>A	c.(124-126)AAG>AAA	p.K42K	PWWP2B_uc009ybe.2_Silent_p.K42K	NM_138499	NP_612508	Q6NUJ5	PWP2B_HUMAN	PWWP domain containing 2 isoform 1	42											0		all_cancers(35;6.69e-12)|all_epithelial(44;1.55e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.109)|Melanoma(40;0.123)|Glioma(114;0.203)|all_hematologic(284;0.224)		OV - Ovarian serous cystadenocarcinoma(35;7.49e-05)|Epithelial(32;0.00016)|all cancers(32;0.000186)														---	---	---	---
NKX6-2	84504	broad.mit.edu	37	10	134598541	134598541	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134598541T>C	uc001llr.2	-	3	798	c.713A>G	c.(712-714)TAC>TGC	p.Y238C		NM_177400	NP_796374	Q9C056	NKX62_HUMAN	NK6 transcription factor related, locus 2	238						nucleus	sequence-specific DNA binding transcription factor activity				0		all_cancers(35;2.79e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0584)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;4.06e-05)|Epithelial(32;5.53e-05)|all cancers(32;5.99e-05)														---	---	---	---
ADAM8	101	broad.mit.edu	37	10	135086461	135086461	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135086461C>A	uc010qva.1	-	6	570	c.519G>T	c.(517-519)GAG>GAT	p.E173D	ADAM8_uc010quz.1_Missense_Mutation_p.E212D|ADAM8_uc009ybi.2_Missense_Mutation_p.E212D|ADAM8_uc010qvb.1_Missense_Mutation_p.E187D|ADAM8_uc009ybj.1_RNA			P78325	ADAM8_HUMAN	SubName: Full=cDNA FLJ50704, highly similar to ADAM 8 (EC 3.4.24.-) (A disintegrinand metalloproteinase domain 8);	173					integrin-mediated signaling pathway|proteolysis		metalloendopeptidase activity			large_intestine(2)|central_nervous_system(1)	3		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		all cancers(32;7.72e-06)|OV - Ovarian serous cystadenocarcinoma(35;8.23e-06)|Epithelial(32;1.02e-05)														---	---	---	---
TUBGCP2	10844	broad.mit.edu	37	10	135111445	135111445	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135111445G>A	uc001lmg.1	-						TUBGCP2_uc010qvc.1_Intron|TUBGCP2_uc009ybk.1_Intron|TUBGCP2_uc010qvd.1_Intron|TUBGCP2_uc001lmh.1_Intron	NM_006659	NP_006650			tubulin, gamma complex associated protein 2						G2/M transition of mitotic cell cycle|microtubule nucleation|protein complex assembly	centrosome|cytoplasmic microtubule|cytosol|spindle pole	protein binding				0		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.87e-06)|all cancers(32;8.98e-06)|Epithelial(32;1.15e-05)														---	---	---	---
TUBGCP2	10844	broad.mit.edu	37	10	135111452	135111452	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135111452G>A	uc001lmg.1	-						TUBGCP2_uc010qvc.1_Intron|TUBGCP2_uc009ybk.1_Intron|TUBGCP2_uc010qvd.1_Intron|TUBGCP2_uc001lmh.1_Intron	NM_006659	NP_006650			tubulin, gamma complex associated protein 2						G2/M transition of mitotic cell cycle|microtubule nucleation|protein complex assembly	centrosome|cytoplasmic microtubule|cytosol|spindle pole	protein binding				0		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.87e-06)|all cancers(32;8.98e-06)|Epithelial(32;1.15e-05)														---	---	---	---
CYP2E1	1571	broad.mit.edu	37	10	135342073	135342073	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135342073C>T	uc001lnj.1	+	2	299	c.266C>T	c.(265-267)GCG>GTG	p.A89V	CYP2E1_uc001lnk.1_Intron|CYP2E1_uc009ybl.1_Intron|CYP2E1_uc009ybm.1_Intron	NM_000773	NP_000764	P05181	CP2E1_HUMAN	cytochrome P450, family 2, subfamily E,	89					drug metabolic process|heterocycle metabolic process|monoterpenoid metabolic process|steroid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	electron carrier activity|enzyme binding|heme binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen|oxygen binding			central_nervous_system(3)	3		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)	Acetaminophen(DB00316)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Clofibrate(DB00636)|Dacarbazine(DB00851)|Dapsone(DB00250)|Enflurane(DB00228)|Eszopiclone(DB00402)|Ethanol(DB00898)|Ethosuximide(DB00593)|Fomepizole(DB01213)|Glutathione(DB00143)|Halothane(DB01159)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Isoniazid(DB00951)|Menadione(DB00170)|Mephenytoin(DB00532)|Methoxyflurane(DB01028)|Midazolam(DB00683)|Mitoxantrone(DB01204)|Nicotine(DB00184)|Nifedipine(DB01115)|Nitrofurantoin(DB00698)|Orphenadrine(DB01173)|Phenelzine(DB00780)|Quinidine(DB00908)|S-Adenosylmethionine(DB00118)|Sevoflurane(DB01236)|Theophylline(DB00277)|Tolbutamide(DB01124)									Naso-/Oropharyngeal/Laryngeal_Cancer_Familial_Clustering_of				---	---	---	---
CYP2E1	1571	broad.mit.edu	37	10	135346185	135346185	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135346185T>C	uc001lnj.1	+						CYP2E1_uc001lnk.1_Intron|CYP2E1_uc009ybl.1_Intron|CYP2E1_uc009ybm.1_Intron|CYP2E1_uc001lnl.1_Intron	NM_000773	NP_000764			cytochrome P450, family 2, subfamily E,						drug metabolic process|heterocycle metabolic process|monoterpenoid metabolic process|steroid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	electron carrier activity|enzyme binding|heme binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen|oxygen binding			central_nervous_system(3)	3		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)	Acetaminophen(DB00316)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Clofibrate(DB00636)|Dacarbazine(DB00851)|Dapsone(DB00250)|Enflurane(DB00228)|Eszopiclone(DB00402)|Ethanol(DB00898)|Ethosuximide(DB00593)|Fomepizole(DB01213)|Glutathione(DB00143)|Halothane(DB01159)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Isoniazid(DB00951)|Menadione(DB00170)|Mephenytoin(DB00532)|Methoxyflurane(DB01028)|Midazolam(DB00683)|Mitoxantrone(DB01204)|Nicotine(DB00184)|Nifedipine(DB01115)|Nitrofurantoin(DB00698)|Orphenadrine(DB01173)|Phenelzine(DB00780)|Quinidine(DB00908)|S-Adenosylmethionine(DB00118)|Sevoflurane(DB01236)|Theophylline(DB00277)|Tolbutamide(DB01124)									Naso-/Oropharyngeal/Laryngeal_Cancer_Familial_Clustering_of				---	---	---	---
SIRT3	23410	broad.mit.edu	37	11	236066	236066	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:236066G>A	uc001lok.3	-	1	297	c.263C>T	c.(262-264)CCC>CTC	p.P88L	SIRT3_uc001loj.3_Intron|SIRT3_uc010qvm.1_Missense_Mutation_p.P88L|SIRT3_uc010qvn.1_Intron|SIRT3_uc010qvo.1_Missense_Mutation_p.P88L|SIRT3_uc010qvp.1_Missense_Mutation_p.P88L|SIRT3_uc010qvq.1_Intron|SIRT3_uc009ybt.1_Intron|PSMD13_uc010qvr.1_5'Flank|PSMD13_uc001lol.2_5'Flank|PSMD13_uc001loo.2_5'Flank|PSMD13_uc001lon.2_5'Flank|PSMD13_uc001lom.2_5'Flank	NM_012239	NP_036371	Q9NTG7	SIRT3_HUMAN	sirtuin 3 isoform a	88					chromatin silencing|protein ADP-ribosylation|protein deacetylation	mitochondrial matrix	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides|NAD+ ADP-ribosyltransferase activity|NAD+ binding|protein binding|zinc ion binding			urinary_tract(1)	1		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;3.66e-27)|Epithelial(43;2.02e-26)|OV - Ovarian serous cystadenocarcinoma(40;2.9e-21)|BRCA - Breast invasive adenocarcinoma(625;3.88e-05)|Lung(200;0.111)|LUSC - Lung squamous cell carcinoma(625;0.129)														---	---	---	---
B4GALNT4	338707	broad.mit.edu	37	11	372659	372659	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:372659C>T	uc001lpb.2	+							NM_178537	NP_848632			beta							Golgi cisterna membrane|integral to membrane	N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity			pancreas(1)	1		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)														---	---	---	---
SIGIRR	59307	broad.mit.edu	37	11	407849	407849	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:407849T>C	uc001lpd.2	-	5	779	c.449A>G	c.(448-450)TAC>TGC	p.Y150C	SIGIRR_uc001lpf.2_Missense_Mutation_p.Y150C|SIGIRR_uc001lpe.1_Missense_Mutation_p.Y150C|SIGIRR_uc001lpg.2_Missense_Mutation_p.Y150C	NM_001135054	NP_001128526	Q6IA17	SIGIR_HUMAN	single Ig IL-1R-related molecule	150	Cytoplasmic (Potential).				acute-phase response|innate immune response|negative regulation of chemokine biosynthetic process|negative regulation of cytokine-mediated signaling pathway|negative regulation of lipopolysaccharide-mediated signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity	integral to membrane	protein binding|transmembrane receptor activity				0		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)														---	---	---	---
PHRF1	57661	broad.mit.edu	37	11	607698	607698	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:607698T>C	uc001lqe.2	+	14	2373	c.2242T>C	c.(2242-2244)TCC>CCC	p.S748P	PHRF1_uc010qwc.1_Missense_Mutation_p.S747P|PHRF1_uc010qwd.1_Missense_Mutation_p.S746P|PHRF1_uc010qwe.1_Missense_Mutation_p.S744P|PHRF1_uc009ybz.1_Missense_Mutation_p.S538P|PHRF1_uc009yca.1_RNA	NM_020901	NP_065952	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	748							RNA polymerase binding|zinc ion binding				0																		---	---	---	---
LRDD	55367	broad.mit.edu	37	11	800227	800227	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:800227G>A	uc001lro.1	-	14	2320	c.2178C>T	c.(2176-2178)GGC>GGT	p.G726G	SLC25A22_uc009yci.2_5'Flank|SLC25A22_uc001lrj.2_5'Flank|LRDD_uc009yck.1_RNA|LRDD_uc001lrk.1_Silent_p.G709G|LRDD_uc001lrl.1_Silent_p.G569G|LRDD_uc001lrm.1_Silent_p.G413G|LRDD_uc001lrn.1_Silent_p.G569G|LRDD_uc001lrp.1_Silent_p.G371G	NM_145886	NP_665893	Q9HB75	PIDD_HUMAN	leucine rich repeat and death domain containing	726					apoptosis|signal transduction	cytoplasm|nucleus	death receptor binding				0		all_cancers(49;1.13e-08)|all_epithelial(84;2.95e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.159)|all_lung(207;0.198)		all cancers(45;1.45e-25)|Epithelial(43;1.17e-24)|OV - Ovarian serous cystadenocarcinoma(40;6.76e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)														---	---	---	---
EFCAB4A	283229	broad.mit.edu	37	11	828709	828709	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:828709T>C	uc001lrv.2	+	1	480	c.102T>C	c.(100-102)GCT>GCC	p.A34A	EFCAB4A_uc010qwt.1_Silent_p.A34A|EFCAB4A_uc009ycm.1_Silent_p.A34A|EFCAB4A_uc001lrw.2_5'Flank			Q8N4Y2	EFC4A_HUMAN	RecName: Full=EF-hand calcium-binding domain-containing protein 4A;	34	EF-hand 1.				store-operated calcium entry		calcium ion binding				0		all_cancers(49;2.31e-08)|all_epithelial(84;3.72e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.179)|all_lung(207;0.227)		all cancers(45;1.45e-25)|Epithelial(43;1.17e-24)|OV - Ovarian serous cystadenocarcinoma(40;6.76e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)														---	---	---	---
CHID1	66005	broad.mit.edu	37	11	884168	884168	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:884168T>C	uc001lsl.2	-	9	864	c.703A>G	c.(703-705)ACC>GCC	p.T235A	CHID1_uc010qwu.1_Missense_Mutation_p.T265A|CHID1_uc010qwv.1_Missense_Mutation_p.T296A|CHID1_uc001lsn.2_Missense_Mutation_p.T260A|CHID1_uc001lsm.2_Missense_Mutation_p.T235A|CHID1_uc001lso.2_Missense_Mutation_p.T235A|CHID1_uc001lsp.2_Missense_Mutation_p.T204A|CHID1_uc010qww.1_Missense_Mutation_p.T235A|uc001lsq.1_5'Flank|uc001lsr.1_5'Flank	NM_023947	NP_076436	Q9BWS9	CHID1_HUMAN	chitinase domain containing 1 isoform a	235					chitin catabolic process|innate immune response	extracellular region|lysosome	cation binding|chitinase activity				0		all_cancers(49;9.46e-06)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;5.48e-25)|Epithelial(43;3.75e-24)|BRCA - Breast invasive adenocarcinoma(625;4.65e-05)|Lung(200;0.0624)|LUSC - Lung squamous cell carcinoma(625;0.0735)														---	---	---	---
AP2A2	161	broad.mit.edu	37	11	988599	988599	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:988599C>T	uc001lss.2	+	10	1360	c.1179C>T	c.(1177-1179)TAC>TAT	p.Y393Y	AP2A2_uc001lst.1_Silent_p.Y394Y|AP2A2_uc009yco.1_RNA	NM_012305	NP_036437	O94973	AP2A2_HUMAN	adaptor-related protein complex 2, alpha 2	393					axon guidance|endocytosis|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of defense response to virus by virus|synaptic transmission|viral reproduction	AP-2 adaptor complex|cytosol	lipid binding|protein transporter activity				0		all_cancers(49;9.46e-06)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.75e-24)|BRCA - Breast invasive adenocarcinoma(625;5.73e-05)|Lung(200;0.0696)|LUSC - Lung squamous cell carcinoma(625;0.082)														---	---	---	---
MUC6	4588	broad.mit.edu	37	11	1017102	1017102	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1017102C>T	uc001lsw.2	-	31	5750	c.5699G>A	c.(5698-5700)AGT>AAT	p.S1900N		NM_005961	NP_005952	Q6W4X9	MUC6_HUMAN	mucin 6, gastric	1900	Thr-rich.|2.|Approximate repeats.				maintenance of gastrointestinal epithelium	extracellular region	extracellular matrix structural constituent			ovary(1)	1		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)														---	---	---	---
MUC2	4583	broad.mit.edu	37	11	1092171	1092171	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1092171C>T	uc001lsx.1	+	30	4017	c.3990C>T	c.(3988-3990)TGC>TGT	p.C1330C		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	1330						inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)													---	---	---	---
MUC5B	727897	broad.mit.edu	37	11	1247968	1247968	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1247968G>A	uc009ycr.1	+	20	2417	c.2291G>A	c.(2290-2292)CGC>CAC	p.R764H	MUC5B_uc009yct.1_Missense_Mutation_p.R108H|MUC5B_uc001ltb.2_Missense_Mutation_p.R108H|MUC5B_uc001lta.2_5'Flank	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;	108	VWFD 1.				cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)														---	---	---	---
MUC5B	727897	broad.mit.edu	37	11	1262377	1262377	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1262377C>T	uc009ycr.1	+	47	6472	c.6346C>T	c.(6346-6348)CGG>TGG	p.R2116W	MUC5B_uc001ltb.2_Missense_Mutation_p.R1426W	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;	1423	7 X Cys-rich subdomain repeats.|Cys-rich subdomain 1.				cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)														---	---	---	---
MUC5B	727897	broad.mit.edu	37	11	1263218	1263218	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1263218C>T	uc009ycr.1	+	47	7313	c.7187C>T	c.(7186-7188)ACG>ATG	p.T2396M	MUC5B_uc001ltb.2_Missense_Mutation_p.T1706M	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;	1703	7 X Cys-rich subdomain repeats.|Thr-rich.				cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)														---	---	---	---
MUC5B	727897	broad.mit.edu	37	11	1269156	1269156	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1269156G>A	uc009ycr.1	+	50	12756	c.12630G>A	c.(12628-12630)ACG>ACA	p.T4210T	MUC5B_uc001ltb.2_Silent_p.T3685T	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;	3682	7 X Cys-rich subdomain repeats.|11 X approximate tandem repeats, Ser/Thr- rich.|Thr-rich.			Missing (in Ref. 6; AAB61398).	cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)														---	---	---	---
MUC5B	727897	broad.mit.edu	37	11	1270890	1270890	+	Silent	SNP	T	C	C	rs61760238		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1270890T>C	uc009ycr.1	+	51	14325	c.14199T>C	c.(14197-14199)ACT>ACC	p.T4733T	MUC5B_uc001ltb.2_Silent_p.T4263T	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;	4260	23 X approximate tandem repeats, Ser/Thr- rich.|Thr-rich.				cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)														---	---	---	---
MUC5B	727897	broad.mit.edu	37	11	1271360	1271360	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1271360C>T	uc009ycr.1	+	51	14795	c.14669C>T	c.(14668-14670)ACC>ATC	p.T4890I	MUC5B_uc001ltb.2_Missense_Mutation_p.T4420I	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;	4417	23 X approximate tandem repeats, Ser/Thr- rich.|Thr-rich.				cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)														---	---	---	---
MUC5B	727897	broad.mit.edu	37	11	1278795	1278795	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1278795C>T	uc009ycr.1	+	63	17442	c.17316C>T	c.(17314-17316)TGC>TGT	p.C5772C	MUC5B_uc001ltb.2_Silent_p.C5438C	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;	5435	VWFC 2.				cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)														---	---	---	---
CTSD	1509	broad.mit.edu	37	11	1780737	1780737	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1780737G>A	uc001luc.1	-						CTSD_uc009yda.1_Intron	NM_001909	NP_001900			cathepsin D preproprotein						cell death|proteolysis	extracellular space|lysosome|melanosome	aspartic-type endopeptidase activity				0		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00136)|Lung(200;0.0684)|LUSC - Lung squamous cell carcinoma(625;0.0822)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
TNNI2	7136	broad.mit.edu	37	11	1862140	1862140	+	Splice_Site	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1862140T>C	uc010qxe.1	+	4	298	c.276_splice	c.e4+2	p.E92_splice	TNNI2_uc010qxc.1_Splice_Site_p.E90_splice|TNNI2_uc010qxd.1_Splice_Site_p.E90_splice	NM_001145841	NP_001139313			fast-twitch skeletal muscle troponin I isoform						muscle filament sliding|positive regulation of transcription, DNA-dependent|skeletal muscle contraction	cytosol|nucleus|troponin complex	actin binding|troponin T binding				0		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00136)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)														---	---	---	---
LSP1	4046	broad.mit.edu	37	11	1901407	1901407	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1901407C>T	uc001lui.2	+	2	319	c.144C>T	c.(142-144)GAC>GAT	p.D48D	LSP1_uc001luj.2_Silent_p.D176D|LSP1_uc001luk.2_Translation_Start_Site|LSP1_uc001lul.2_Translation_Start_Site|LSP1_uc001lum.2_Translation_Start_Site	NM_002339	NP_002330	P33241	LSP1_HUMAN	lymphocyte-specific protein 1 isoform 1	48					cellular component movement|cellular defense response	actin cytoskeleton|Golgi apparatus|plasma membrane	actin binding|signal transducer activity			large_intestine(1)	1		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|Lung(200;0.0729)|LUSC - Lung squamous cell carcinoma(625;0.0856)														---	---	---	---
CARS	833	broad.mit.edu	37	11	3040482	3040482	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3040482G>A	uc001lxh.2	-	11	1107	c.1033C>T	c.(1033-1035)CAT>TAT	p.H345Y	CARS_uc001lxe.2_Missense_Mutation_p.H335Y|CARS_uc001lxf.2_Missense_Mutation_p.H428Y|CARS_uc001lxg.2_Missense_Mutation_p.H345Y|CARS_uc010qxo.1_Missense_Mutation_p.H428Y|CARS_uc010qxp.1_Missense_Mutation_p.H358Y	NM_001751	NP_001742	P49589	SYCC_HUMAN	cysteinyl-tRNA synthetase isoform b	345					cysteinyl-tRNA aminoacylation	cytoplasm|cytosol	ATP binding|cysteine-tRNA ligase activity|metal ion binding|protein homodimerization activity|protein homodimerization activity|tRNA binding|tRNA binding		CARS/ALK(5)	soft_tissue(5)|ovary(2)	7		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00317)|LUSC - Lung squamous cell carcinoma(625;0.218)	L-Cysteine(DB00151)			T	ALK	ALCL								---	---	---	---
CARS	833	broad.mit.edu	37	11	3059436	3059436	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3059436C>T	uc001lxh.2	-						CARS_uc001lxe.2_Intron|CARS_uc001lxf.2_Intron|CARS_uc001lxg.2_Intron|CARS_uc010qxo.1_Intron|CARS_uc010qxp.1_Intron|uc001lxi.1_Intron	NM_001751	NP_001742			cysteinyl-tRNA synthetase isoform b						cysteinyl-tRNA aminoacylation	cytoplasm|cytosol	ATP binding|cysteine-tRNA ligase activity|metal ion binding|protein homodimerization activity|protein homodimerization activity|tRNA binding|tRNA binding		CARS/ALK(5)	soft_tissue(5)|ovary(2)	7		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00317)|LUSC - Lung squamous cell carcinoma(625;0.218)	L-Cysteine(DB00151)			T	ALK	ALCL						OREG0020690	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
OSBPL5	114879	broad.mit.edu	37	11	3114854	3114854	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3114854T>C	uc001lxk.2	-	17	2007	c.1849A>G	c.(1849-1851)AGT>GGT	p.S617G	OSBPL5_uc010qxq.1_Missense_Mutation_p.S528G|OSBPL5_uc009ydw.2_Missense_Mutation_p.S549G|OSBPL5_uc001lxl.2_Missense_Mutation_p.S549G|OSBPL5_uc009ydx.2_Missense_Mutation_p.S641G|OSBPL5_uc001lxj.2_Missense_Mutation_p.S71G	NM_020896	NP_065947	Q9H0X9	OSBL5_HUMAN	oxysterol-binding protein-like protein 5 isoform	617					cholesterol metabolic process|cholesterol transport|Golgi to plasma membrane transport	cytosol	oxysterol binding|protein binding			large_intestine(2)|central_nervous_system(1)	3		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)														---	---	---	---
MRGPRE	116534	broad.mit.edu	37	11	3249890	3249890	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3249890C>A	uc001lxq.3	-	2	447	c.137G>T	c.(136-138)TGG>TTG	p.W46L		NM_001039165	NP_001034254	Q86SM8	MRGRE_HUMAN	MAS-related GPR, member E	46	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			large_intestine(1)|ovary(1)	2		Medulloblastoma(188;0.00106)|all_epithelial(84;0.00111)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00529)|LUSC - Lung squamous cell carcinoma(625;0.19)														---	---	---	---
STIM1	6786	broad.mit.edu	37	11	4104524	4104524	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4104524C>T	uc001lyv.2	+	10	1838	c.1270C>T	c.(1270-1272)CGG>TGG	p.R424W	STIM1_uc009yef.2_Missense_Mutation_p.R424W|STIM1_uc009yeg.2_Missense_Mutation_p.R251W	NM_003156	NP_003147	Q13586	STIM1_HUMAN	stromal interaction molecule 1 precursor	424	Cytoplasmic (Potential).				activation of store-operated calcium channel activity|calcium ion transport|detection of calcium ion|platelet activation	integral to endoplasmic reticulum membrane|integral to plasma membrane|microtubule	calcium ion binding|microtubule plus-end binding			pancreas(1)	1		Breast(177;0.00159)|Medulloblastoma(188;0.00258)|all_neural(188;0.0233)		BRCA - Breast invasive adenocarcinoma(625;0.114)|LUSC - Lung squamous cell carcinoma(625;0.141)														---	---	---	---
STIM1	6786	broad.mit.edu	37	11	4104648	4104648	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4104648G>A	uc001lyv.2	+	10	1962	c.1394G>A	c.(1393-1395)CGC>CAC	p.R465H	STIM1_uc009yef.2_Missense_Mutation_p.R465H|STIM1_uc009yeg.2_Missense_Mutation_p.R292H	NM_003156	NP_003147	Q13586	STIM1_HUMAN	stromal interaction molecule 1 precursor	465	Cytoplasmic (Potential).				activation of store-operated calcium channel activity|calcium ion transport|detection of calcium ion|platelet activation	integral to endoplasmic reticulum membrane|integral to plasma membrane|microtubule	calcium ion binding|microtubule plus-end binding			pancreas(1)	1		Breast(177;0.00159)|Medulloblastoma(188;0.00258)|all_neural(188;0.0233)		BRCA - Breast invasive adenocarcinoma(625;0.114)|LUSC - Lung squamous cell carcinoma(625;0.141)														---	---	---	---
STIM1	6786	broad.mit.edu	37	11	4112558	4112558	+	Missense_Mutation	SNP	C	T	T	rs142239530	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4112558C>T	uc001lyv.2	+	12	2156	c.1588C>T	c.(1588-1590)CGC>TGC	p.R530C	STIM1_uc009yef.2_3'UTR|STIM1_uc009yeg.2_Missense_Mutation_p.R357C	NM_003156	NP_003147	Q13586	STIM1_HUMAN	stromal interaction molecule 1 precursor	530	Cytoplasmic (Potential).				activation of store-operated calcium channel activity|calcium ion transport|detection of calcium ion|platelet activation	integral to endoplasmic reticulum membrane|integral to plasma membrane|microtubule	calcium ion binding|microtubule plus-end binding			pancreas(1)	1		Breast(177;0.00159)|Medulloblastoma(188;0.00258)|all_neural(188;0.0233)		BRCA - Breast invasive adenocarcinoma(625;0.114)|LUSC - Lung squamous cell carcinoma(625;0.141)														---	---	---	---
RRM1	6240	broad.mit.edu	37	11	4148010	4148010	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4148010G>A	uc001lyw.3	+	13	1736	c.1417G>A	c.(1417-1419)GTT>ATT	p.V473I	RRM1_uc009yej.2_RNA|RRM1_uc009yei.2_Missense_Mutation_p.V433I|RRM1_uc010qyc.1_Missense_Mutation_p.V376I|RRM1_uc010qyd.1_Missense_Mutation_p.V135I	NM_001033	NP_001024	P23921	RIR1_HUMAN	ribonucleoside-diphosphate reductase M1 chain	473					deoxyribonucleotide biosynthetic process|DNA replication|nucleobase, nucleoside and nucleotide interconversion	cytosol|nucleoplasm|ribonucleoside-diphosphate reductase complex	ATP binding|ribonucleoside-diphosphate reductase activity			skin(1)	1		Medulloblastoma(188;0.0025)|Breast(177;0.00502)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0848)|LUSC - Lung squamous cell carcinoma(625;0.205)	Clofarabine(DB00631)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Hydroxyurea(DB01005)													---	---	---	---
OR52B4	143496	broad.mit.edu	37	11	4389159	4389159	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4389159C>T	uc010qye.1	-	1	367	c.367G>A	c.(367-369)GAC>AAC	p.D123N		NM_001005161	NP_001005161	Q8NGK2	O52B4_HUMAN	olfactory receptor, family 52, subfamily B,	123	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0075)|Breast(177;0.0249)|all_neural(188;0.0577)		Epithelial(150;1.57e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0826)|LUSC - Lung squamous cell carcinoma(625;0.19)														---	---	---	---
OR52M1	119772	broad.mit.edu	37	11	4566584	4566584	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4566584G>A	uc010qyf.1	+	1	164	c.164G>A	c.(163-165)CGC>CAC	p.R55H		NM_001004137	NP_001004137	Q8NGK5	O52M1_HUMAN	olfactory receptor, family 52, subfamily M,	55	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)														---	---	---	---
OR52I2	143502	broad.mit.edu	37	11	4608096	4608096	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4608096T>C	uc010qyh.1	+	1	54	c.54T>C	c.(52-54)ATT>ATC	p.I18I		NM_001005170	NP_001005170	Q8NH67	O52I2_HUMAN	olfactory receptor, family 52, subfamily I,	18	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)	1		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)														---	---	---	---
OR52I1	390037	broad.mit.edu	37	11	4615722	4615722	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4615722G>A	uc010qyi.1	+	1	454	c.454G>A	c.(454-456)GTC>ATC	p.V152I		NM_001005169	NP_001005169	Q8NGK6	O52I1_HUMAN	olfactory receptor, family 52, subfamily I,	152	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)	2		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;7.98e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)														---	---	---	---
OR51D1	390038	broad.mit.edu	37	11	4661217	4661217	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4661217G>A	uc010qyk.1	+	1	197	c.197G>A	c.(196-198)AGG>AAG	p.R66K		NM_001004751	NP_001004751	Q8NGF3	O51D1_HUMAN	olfactory receptor, family 51, subfamily D,	66	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;2.74e-13)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|GBM - Glioblastoma multiforme(2;0.0841)|LUSC - Lung squamous cell carcinoma(625;0.19)														---	---	---	---
OR51E2	81285	broad.mit.edu	37	11	4703145	4703145	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4703145C>T	uc001lzk.2	-	2	1041	c.797G>A	c.(796-798)AGC>AAC	p.S266N		NM_030774	NP_110401	Q9H255	O51E2_HUMAN	olfactory receptor, family 51, subfamily E,	266	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			lung(3)|ovary(2)	5		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;3e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00476)|LUSC - Lung squamous cell carcinoma(625;0.2)														---	---	---	---
OR51E2	81285	broad.mit.edu	37	11	4703554	4703554	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4703554G>A	uc001lzk.2	-	2	632	c.388C>T	c.(388-390)CGC>TGC	p.R130C		NM_030774	NP_110401	Q9H255	O51E2_HUMAN	olfactory receptor, family 51, subfamily E,	130	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			lung(3)|ovary(2)	5		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;3e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00476)|LUSC - Lung squamous cell carcinoma(625;0.2)														---	---	---	---
OR51F2	119694	broad.mit.edu	37	11	4843063	4843063	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:4843063C>A	uc010qyn.1	+	1	448	c.448C>A	c.(448-450)CTT>ATT	p.L150I		NM_001004753	NP_001004753	Q8NH61	O51F2_HUMAN	olfactory receptor, family 51, subfamily F,	150	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)	2		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.0778)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)														---	---	---	---
OR51L1	119682	broad.mit.edu	37	11	5020211	5020211	+	5'Flank	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5020211C>A	uc010qyu.1	+							NM_001004755	NP_001004755			olfactory receptor, family 51, subfamily L,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1		Medulloblastoma(188;0.0061)|all_neural(188;0.0479)|Breast(177;0.086)		Epithelial(150;1.75e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)														---	---	---	---
OR51L1	119682	broad.mit.edu	37	11	5020894	5020894	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5020894C>A	uc010qyu.1	+	1	682	c.682C>A	c.(682-684)CTG>ATG	p.L228M		NM_001004755	NP_001004755	Q8NGJ5	O51L1_HUMAN	olfactory receptor, family 51, subfamily L,	228	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1		Medulloblastoma(188;0.0061)|all_neural(188;0.0479)|Breast(177;0.086)		Epithelial(150;1.75e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)														---	---	---	---
OR51B2	79345	broad.mit.edu	37	11	5344658	5344658	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5344658G>A	uc001mao.1	-	1	925	c.870C>T	c.(868-870)TAC>TAT	p.Y290Y	HBG2_uc001mak.1_Intron|HBE1_uc001mam.1_Intron	NM_033180	NP_149420	Q9Y5P1	O51B2_HUMAN	olfactory receptor, family 51, subfamily B,	290	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(1)	3		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
OR51Q1	390061	broad.mit.edu	37	11	5443810	5443810	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5443810C>T	uc010qzd.1	+	1	380	c.380C>T	c.(379-381)GCC>GTC	p.A127V	HBG2_uc001mak.1_Intron|HBE1_uc001mam.1_Intron|OR51B5_uc001maq.1_Intron	NM_001004757	NP_001004757	Q8NH59	O51Q1_HUMAN	olfactory receptor, family 51, subfamily Q,	127	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.18e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
TRIM5	85363	broad.mit.edu	37	11	5686300	5686300	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5686300T>C	uc001mbm.1	-	8	1478	c.1221A>G	c.(1219-1221)GGA>GGG	p.G407G	TRIM78P_uc009yer.2_Intron|TRIM5_uc001mbl.1_RNA|TRIM5_uc001mbn.2_Intron|TRIM5_uc001mbo.2_Intron	NM_033034	NP_149023	Q9C035	TRIM5_HUMAN	tripartite motif protein TRIM5 isoform alpha	407	B30.2/SPRY.				interspecies interaction between organisms|protein trimerization|response to virus	cytoplasm|cytoplasmic mRNA processing body	ligase activity|protein binding|protein homodimerization activity|zinc ion binding			ovary(1)	1		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)|Lung NSC(207;0.138)|all_lung(207;0.221)		Epithelial(150;7.21e-09)|BRCA - Breast invasive adenocarcinoma(625;0.139)														---	---	---	---
TRIM22	10346	broad.mit.edu	37	11	5730720	5730720	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5730720C>A	uc001mbr.2	+	8	1616	c.1339C>A	c.(1339-1341)CTA>ATA	p.L447I	TRIM5_uc001mbq.1_Intron|TRIM22_uc009yet.1_Intron|TRIM22_uc009yes.2_Missense_Mutation_p.L443I|TRIM22_uc010qzm.1_Missense_Mutation_p.L275I|TRIM22_uc009yeu.2_Missense_Mutation_p.L258I|OR56B1_uc001mbs.1_Intron|OR56B1_uc009yev.1_Intron	NM_006074	NP_006065	Q8IYM9	TRI22_HUMAN	tripartite motif-containing 22	447	B30.2/SPRY.				immune response|interspecies interaction between organisms|protein trimerization|response to virus	Cajal body|Golgi apparatus|nuclear speck	ligase activity|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding				0		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;7.54e-09)|BRCA - Breast invasive adenocarcinoma(625;0.14)														---	---	---	---
FAM160A2	84067	broad.mit.edu	37	11	6239391	6239391	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6239391A>G	uc001mcl.3	-						FAM160A2_uc001mck.3_Intron|FAM160A2_uc001mcm.2_Intron	NM_001098794	NP_001092264			hypothetical protein LOC84067 isoform 2						early endosome to late endosome transport|endosome organization|endosome to lysosome transport|lysosome organization|protein transport	FHF complex	protein binding			skin(2)	2																		---	---	---	---
FAM160A2	84067	broad.mit.edu	37	11	6239872	6239872	+	Missense_Mutation	SNP	C	T	T	rs147077635	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6239872C>T	uc001mcl.3	-	8	1752	c.1393G>A	c.(1393-1395)GCC>ACC	p.A465T	FAM160A2_uc001mck.3_Missense_Mutation_p.A465T|FAM160A2_uc001mcm.2_Missense_Mutation_p.A465T	NM_001098794	NP_001092264	Q8N612	F16A2_HUMAN	hypothetical protein LOC84067 isoform 2	465					early endosome to late endosome transport|endosome organization|endosome to lysosome transport|lysosome organization|protein transport	FHF complex	protein binding			skin(2)	2																		---	---	---	---
CCKBR	887	broad.mit.edu	37	11	6292299	6292299	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6292299C>T	uc001mcp.2	+	5	1063	c.870C>T	c.(868-870)AGC>AGT	p.S290S	CCKBR_uc001mcq.2_Silent_p.S218S|CCKBR_uc001mcr.2_Silent_p.S290S|CCKBR_uc001mcs.2_Silent_p.S359S|CCKBR_uc001mct.1_RNA	NM_176875	NP_795344	P32239	GASR_HUMAN	cholecystokinin B receptor	290	Cytoplasmic (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|cell proliferation|digestion|elevation of cytosolic calcium ion concentration|feeding behavior|positive regulation of cell proliferation|sensory perception		1-phosphatidylinositol-3-kinase regulator activity|gastrin receptor activity|phosphatidylinositol phospholipase C activity|type B gastrin/cholecystokinin receptor binding			lung(5)|ovary(2)|breast(1)	8		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.139)	Pentagastrin(DB00183)													---	---	---	---
SMPD1	6609	broad.mit.edu	37	11	6415458	6415458	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6415458A>G	uc001mcw.2	+	6	1691	c.1517A>G	c.(1516-1518)TAC>TGC	p.Y506C	SMPD1_uc001mcv.1_RNA|SMPD1_uc009yex.2_RNA|SMPD1_uc001mcx.2_Missense_Mutation_p.Y462C|SMPD1_uc009yew.2_Missense_Mutation_p.Y505C	NM_000543	NP_000534	P17405	ASM_HUMAN	sphingomyelin phosphodiesterase 1, acid	504					cell death|ceramide biosynthetic process|negative regulation of MAP kinase activity|nervous system development|positive regulation of protein dephosphorylation|signal transduction|sphingomyelin catabolic process|termination of signal transduction	lysosome	hydrolase activity, acting on glycosyl bonds|sphingomyelin phosphodiesterase activity				0		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;4.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)	Desipramine(DB01151)													---	---	---	---
HPX	3263	broad.mit.edu	37	11	6452437	6452437	+	3'UTR	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6452437C>T	uc001mdg.2	-	10					HPX_uc001mdf.2_3'UTR|HPX_uc009yfc.2_RNA	NM_000613	NP_000604			hemopexin precursor						cellular iron ion homeostasis|interspecies interaction between organisms	extracellular space	heme transporter activity|metal ion binding|protein binding				0		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;5.46e-08)|BRCA - Breast invasive adenocarcinoma(625;0.19)														---	---	---	---
HPX	3263	broad.mit.edu	37	11	6458305	6458305	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6458305T>G	uc001mdg.2	-	7	867	c.806A>C	c.(805-807)GAC>GCC	p.D269A	HPX_uc001mdf.2_Missense_Mutation_p.D15A|HPX_uc009yfc.2_RNA	NM_000613	NP_000604	P02790	HEMO_HUMAN	hemopexin precursor	269	Hemopexin-like 4.				cellular iron ion homeostasis|interspecies interaction between organisms	extracellular space	heme transporter activity|metal ion binding|protein binding				0		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;5.46e-08)|BRCA - Breast invasive adenocarcinoma(625;0.19)														---	---	---	---
DCHS1	8642	broad.mit.edu	37	11	6652604	6652604	+	Missense_Mutation	SNP	G	A	A	rs142768745		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6652604G>A	uc001mem.1	-	8	4120	c.3710C>T	c.(3709-3711)ACG>ATG	p.T1237M		NM_003737	NP_003728	Q96JQ0	PCD16_HUMAN	dachsous 1 precursor	1237	Cadherin 12.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|large_intestine(1)|pancreas(1)	5		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
DCHS1	8642	broad.mit.edu	37	11	6654194	6654194	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6654194C>T	uc001mem.1	-	6	2959	c.2549G>A	c.(2548-2550)CGC>CAC	p.R850H		NM_003737	NP_003728	Q96JQ0	PCD16_HUMAN	dachsous 1 precursor	850	Cadherin 8.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|large_intestine(1)|pancreas(1)	5		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
OR10A4	283297	broad.mit.edu	37	11	6898519	6898519	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6898519T>G	uc010rat.1	+	1	641	c.641T>G	c.(640-642)CTG>CGG	p.L214R		NM_207186	NP_997069	Q9H209	O10A4_HUMAN	olfactory receptor, family 10, subfamily A,	214	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)														---	---	---	---
ZNF215	7762	broad.mit.edu	37	11	6977081	6977081	+	Silent	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6977081T>G	uc001mey.2	+	7	1461	c.873T>G	c.(871-873)CCT>CCG	p.P291P	ZNF215_uc010raw.1_3'UTR|ZNF215_uc010rax.1_Silent_p.P53P|ZNF215_uc001mez.1_Intron	NM_013250	NP_037382	Q9UL58	ZN215_HUMAN	zinc finger protein 215	291					viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0				Epithelial(150;6.33e-08)|BRCA - Breast invasive adenocarcinoma(625;0.134)														---	---	---	---
ZNF214	7761	broad.mit.edu	37	11	7022447	7022447	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7022447A>G	uc001mfa.2	-	3	770	c.467T>C	c.(466-468)ATG>ACG	p.M156T	ZNF214_uc010ray.1_Missense_Mutation_p.M156T|ZNF214_uc009yfh.1_Missense_Mutation_p.M156T	NM_013249	NP_037381	Q9UL59	ZN214_HUMAN	zinc finger protein 214	156					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1				Epithelial(150;3.87e-08)|BRCA - Breast invasive adenocarcinoma(625;0.081)														---	---	---	---
RBMXL2	27288	broad.mit.edu	37	11	7111226	7111226	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7111226C>G	uc001mfc.2	+	1	1062	c.875C>G	c.(874-876)GCC>GGC	p.A292G		NM_014469	NP_055284	O75526	HNRGT_HUMAN	testes-specific heterogenous nuclear	292	Arg/Gly/Pro-rich.					nucleus|ribonucleoprotein complex	nucleotide binding|RNA binding				0				Epithelial(150;5.14e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)														---	---	---	---
OVCH2	341277	broad.mit.edu	37	11	7718081	7718081	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:7718081A>G	uc010rbf.1	-	10	1072	c.1072T>C	c.(1072-1074)TCC>CCC	p.S358P		NM_198185	NP_937828			ovochymase 2 precursor												0				Epithelial(150;7.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.197)														---	---	---	---
TMEM9B	56674	broad.mit.edu	37	11	8969963	8969963	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8969963G>A	uc001mhe.1	-	5	630	c.501C>T	c.(499-501)AAC>AAT	p.N167N	TMEM9B_uc001mhf.1_Silent_p.N93N|TMEM9B_uc010rbt.1_Silent_p.N93N	NM_020644	NP_065695	Q9NQ34	TMM9B_HUMAN	TMEM9 domain family, member B precursor	167					positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to membrane	signal transducer activity				0				Epithelial(150;4.39e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0237)														---	---	---	---
DENND5A	23258	broad.mit.edu	37	11	9225550	9225550	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9225550G>A	uc001mhl.2	-	4	861	c.606C>T	c.(604-606)TAC>TAT	p.Y202Y	DENND5A_uc010rbw.1_Silent_p.Y202Y|DENND5A_uc010rbx.1_RNA	NM_015213	NP_056028	Q6IQ26	DEN5A_HUMAN	RAB6 interacting protein 1	202	DENN.									liver(1)	1																		---	---	---	---
IPO7	10527	broad.mit.edu	37	11	9463624	9463624	+	Intron	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9463624A>T	uc001mho.2	+							NM_006391	NP_006382			importin 7						interspecies interaction between organisms|signal transduction	Golgi apparatus|nuclear pore|soluble fraction	protein transporter activity|Ran GTPase binding|small GTPase regulator activity			lung(1)|breast(1)	2				all cancers(16;8.29e-09)|Epithelial(150;4.76e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0217)														---	---	---	---
ZNF143	7702	broad.mit.edu	37	11	9496097	9496097	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9496097C>T	uc001mhr.2	+	5	408	c.290C>T	c.(289-291)ACA>ATA	p.T97I	ZNF143_uc009yfu.2_Intron|ZNF143_uc010rby.1_Missense_Mutation_p.T66I	NM_003442	NP_003433	P52747	ZN143_HUMAN	zinc finger protein 143	97					regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase III promoter|transcription from RNA polymerase II promoter|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding|zinc ion binding				0				all cancers(16;4.12e-09)|Epithelial(150;2.29e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0212)														---	---	---	---
MRVI1	10335	broad.mit.edu	37	11	10673740	10673740	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10673740G>A	uc010rcc.1	-						MRVI1_uc001miw.2_Silent_p.G10G|MRVI1_uc010rcb.1_Silent_p.G10G|MRVI1_uc009ygb.1_Intron|MRVI1_uc001mix.2_Intron|MRVI1_uc001miz.2_Intron|MRVI1_uc009ygc.1_Intron|MRVI1_uc010rcd.1_Intron|MRVI1_uc009ygd.1_Intron	NM_001100167	NP_001093637			JAW1-related protein isoform c						platelet activation	endoplasmic reticulum membrane|integral to membrane|perinuclear region of cytoplasm|platelet dense tubular network membrane|sarcoplasmic reticulum				ovary(2)|central_nervous_system(1)	3				all cancers(16;2.68e-07)|Epithelial(150;3.04e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0723)														---	---	---	---
CTR9	9646	broad.mit.edu	37	11	10794725	10794725	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10794725C>T	uc001mja.2	+	21	2781	c.2632C>T	c.(2632-2634)CGG>TGG	p.R878W		NM_014633	NP_055448	Q6PD62	CTR9_HUMAN	SH2 domain binding protein 1	878	Lys-rich.				histone H2B ubiquitination|histone monoubiquitination	Cdc73/Paf1 complex|nuclear speck				ovary(2)	2				all cancers(16;1.64e-07)|Epithelial(150;2.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)														---	---	---	---
ARNTL	406	broad.mit.edu	37	11	13397151	13397151	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13397151A>G	uc001mkr.2	+						ARNTL_uc001mko.2_Intron|ARNTL_uc001mkp.2_Intron|ARNTL_uc001mkq.2_Intron|ARNTL_uc001mks.2_Intron|ARNTL_uc001mkt.2_Intron|ARNTL_uc001mku.2_Intron|ARNTL_uc009ygm.1_Intron|ARNTL_uc001mkw.2_Intron|ARNTL_uc001mkx.2_Intron|ARNTL_uc001mky.2_5'Flank	NM_001178	NP_001169			aryl hydrocarbon receptor nuclear						circadian rhythm|positive regulation of transcription from RNA polymerase II promoter	transcription factor complex	aryl hydrocarbon receptor binding|DNA binding|Hsp90 protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity				0				Epithelial(150;0.0243)														---	---	---	---
ARNTL	406	broad.mit.edu	37	11	13402809	13402809	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13402809T>C	uc001mkr.2	+						ARNTL_uc001mko.2_Intron|ARNTL_uc001mkp.2_Intron|ARNTL_uc001mkq.2_Intron|ARNTL_uc001mks.2_Intron|ARNTL_uc001mkt.2_Intron|ARNTL_uc001mku.2_Intron|ARNTL_uc001mkw.2_Intron|ARNTL_uc001mkx.2_Intron|ARNTL_uc001mky.2_Intron	NM_001178	NP_001169			aryl hydrocarbon receptor nuclear						circadian rhythm|positive regulation of transcription from RNA polymerase II promoter	transcription factor complex	aryl hydrocarbon receptor binding|DNA binding|Hsp90 protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity				0				Epithelial(150;0.0243)														---	---	---	---
ARNTL	406	broad.mit.edu	37	11	13408253	13408253	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:13408253G>A	uc001mkr.2	+	20	2239	c.1831G>A	c.(1831-1833)GCT>ACT	p.A611T	ARNTL_uc001mko.2_Missense_Mutation_p.A567T|ARNTL_uc001mkp.2_Missense_Mutation_p.A610T|ARNTL_uc001mkq.2_Missense_Mutation_p.A610T|ARNTL_uc001mks.2_Missense_Mutation_p.A568T|ARNTL_uc001mkt.2_Missense_Mutation_p.A611T|ARNTL_uc001mku.2_RNA|ARNTL_uc001mkw.2_Missense_Mutation_p.A568T|ARNTL_uc001mkx.2_Missense_Mutation_p.A609T|ARNTL_uc001mky.2_Missense_Mutation_p.A149T	NM_001178	NP_001169	O00327	BMAL1_HUMAN	aryl hydrocarbon receptor nuclear	611				A->S,T: Increased desensitization to CRY1, in the presence of CLOCK. Approximately 2-fold increase in CLOCK- ARNTL transcriptional activity in the absence of CRY1; when associated with E- 407.	circadian rhythm|positive regulation of transcription from RNA polymerase II promoter	transcription factor complex	aryl hydrocarbon receptor binding|DNA binding|Hsp90 protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity				0				Epithelial(150;0.0243)														---	---	---	---
INSC	387755	broad.mit.edu	37	11	15222446	15222446	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:15222446C>T	uc001mly.2	+	7	957	c.911C>T	c.(910-912)ACG>ATG	p.T304M	INSC_uc001mlz.2_Missense_Mutation_p.T257M|INSC_uc001mma.2_Missense_Mutation_p.T257M|INSC_uc010rcs.1_Missense_Mutation_p.T292M|INSC_uc001mmb.2_Missense_Mutation_p.T257M|INSC_uc001mmc.2_Intron	NM_001031853	NP_001027024	Q1MX18	INSC_HUMAN	inscuteable isoform a	304					cell differentiation|nervous system development	cytoplasm	binding			upper_aerodigestive_tract(2)|ovary(2)|central_nervous_system(1)	5																		---	---	---	---
USH1C	10083	broad.mit.edu	37	11	17527468	17527468	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17527468C>T	uc001mnf.2	-						USH1C_uc001mne.2_Missense_Mutation_p.R681Q|USH1C_uc009yhb.2_Intron|USH1C_uc001mng.2_Intron|USH1C_uc001mnd.2_Intron	NM_005709	NP_005700			harmonin isoform a						equilibrioception|G2/M transition of mitotic cell cycle|photoreceptor cell maintenance|sensory perception of sound	apical part of cell|cytoplasm|stereocilium	protein binding			ovary(1)	1																		---	---	---	---
USH1C	10083	broad.mit.edu	37	11	17531025	17531025	+	Intron	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:17531025T>G	uc001mnf.2	-						USH1C_uc001mne.2_Missense_Mutation_p.S631R|USH1C_uc009yhb.2_Intron|USH1C_uc001mng.2_Intron|USH1C_uc001mnd.2_Intron	NM_005709	NP_005700			harmonin isoform a						equilibrioception|G2/M transition of mitotic cell cycle|photoreceptor cell maintenance|sensory perception of sound	apical part of cell|cytoplasm|stereocilium	protein binding			ovary(1)	1																		---	---	---	---
PTPN5	84867	broad.mit.edu	37	11	18751122	18751122	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:18751122C>T	uc001mpd.2	-						PTPN5_uc001mpb.2_Intron|PTPN5_uc001mpc.2_Intron|PTPN5_uc001mpe.2_Intron|PTPN5_uc010rdj.1_Intron|PTPN5_uc001mpf.2_Intron|PTPN5_uc010rdk.1_Intron	NM_006906	NP_008837			protein-tyrosine-phosphatase non-receptor 5							integral to membrane	phosphotyrosine binding|protein tyrosine phosphatase activity			ovary(2)	2																		---	---	---	---
MRGPRX2	117194	broad.mit.edu	37	11	19077528	19077528	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19077528C>T	uc001mph.2	-	2	510	c.422G>A	c.(421-423)CGC>CAC	p.R141H		NM_054030	NP_473371	Q96LB1	MRGX2_HUMAN	MAS-related GPR, member X2	141	Cytoplasmic (Potential).				sensory perception of pain|sleep	plasma membrane	G-protein coupled receptor activity|neuropeptide binding			ovary(1)	1																		---	---	---	---
E2F8	79733	broad.mit.edu	37	11	19255954	19255954	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19255954A>G	uc001mpm.2	-	6	1403	c.881T>C	c.(880-882)TTA>TCA	p.L294S	E2F8_uc009yhv.2_RNA|E2F8_uc001mpn.3_Missense_Mutation_p.L294S	NM_024680	NP_078956	A0AVK6	E2F8_HUMAN	E2F family member 8	294	Potential.				cell cycle	transcription factor complex	DNA binding|sequence-specific DNA binding transcription factor activity			skin(1)	1																		---	---	---	---
NAV2	89797	broad.mit.edu	37	11	19914063	19914063	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:19914063G>A	uc010rdm.1	+	7	1284	c.923G>A	c.(922-924)CGC>CAC	p.R308H	NAV2_uc001mpp.2_Missense_Mutation_p.R221H|NAV2_uc001mpr.3_Missense_Mutation_p.R285H	NM_145117	NP_660093	Q8IVL1	NAV2_HUMAN	neuron navigator 2 isoform 2	308						nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6																		---	---	---	---
NAV2	89797	broad.mit.edu	37	11	20066629	20066629	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20066629C>A	uc010rdm.1	+	15	3745	c.3384C>A	c.(3382-3384)CCC>CCA	p.P1128P	NAV2_uc001mpp.2_Silent_p.P1041P|NAV2_uc001mpr.3_Silent_p.P1105P|NAV2_uc001mpt.2_Silent_p.P191P|NAV2_uc009yhx.2_Silent_p.P191P|NAV2_uc009yhy.1_Silent_p.P104P	NM_145117	NP_660093	Q8IVL1	NAV2_HUMAN	neuron navigator 2 isoform 2	1128						nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6																		---	---	---	---
NAV2	89797	broad.mit.edu	37	11	20070749	20070749	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20070749C>T	uc010rdm.1	+						NAV2_uc001mpp.2_Intron|NAV2_uc001mpr.3_Intron|NAV2_uc001mpt.2_Intron|NAV2_uc009yhx.2_Intron|NAV2_uc009yhy.1_Intron|NAV2_uc009yhz.2_Intron	NM_145117	NP_660093			neuron navigator 2 isoform 2							nucleus	ATP binding|helicase activity			skin(4)|ovary(1)|pancreas(1)	6																		---	---	---	---
ANO5	203859	broad.mit.edu	37	11	22272398	22272398	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:22272398T>C	uc001mqi.2	+						ANO5_uc001mqj.2_Intron	NM_213599	NP_998764			anoctamin 5 isoform a							chloride channel complex|endoplasmic reticulum membrane	chloride channel activity			central_nervous_system(3)|ovary(1)	4																		---	---	---	---
ANO3	63982	broad.mit.edu	37	11	26656598	26656598	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:26656598A>G	uc001mqt.3	+	20	2169	c.2024A>G	c.(2023-2025)GAC>GGC	p.D675G	ANO3_uc010rdr.1_Missense_Mutation_p.D659G|ANO3_uc010rds.1_Missense_Mutation_p.D514G|ANO3_uc010rdt.1_Missense_Mutation_p.D529G	NM_031418	NP_113606	Q9BYT9	ANO3_HUMAN	transmembrane protein 16C	675	Extracellular (Potential).					chloride channel complex	chloride channel activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
LGR4	55366	broad.mit.edu	37	11	27389756	27389756	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:27389756T>G	uc001mrj.3	-	18	2999	c.2514A>C	c.(2512-2514)GAA>GAC	p.E838D	LGR4_uc001mrk.3_Missense_Mutation_p.E814D	NM_018490	NP_060960	Q9BXB1	LGR4_HUMAN	leucine-rich repeat-containing G protein-coupled	838	Cytoplasmic (Potential).					integral to membrane|plasma membrane	protein-hormone receptor activity			ovary(1)	1																		---	---	---	---
IMMP1L	196294	broad.mit.edu	37	11	31477941	31477941	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31477941G>A	uc001msy.1	-						IMMP1L_uc001msz.1_Intron|IMMP1L_uc009yjo.2_Intron|IMMP1L_uc009yjp.2_Intron	NM_144981	NP_659418			IMP1 inner mitochondrial membrane						proteolysis	mitochondrial inner membrane	serine-type peptidase activity				0	Lung SC(675;0.225)																	---	---	---	---
RCN1	5954	broad.mit.edu	37	11	32118795	32118795	+	Silent	SNP	C	T	T	rs141697360		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32118795C>T	uc010reb.1	+	2	626	c.360C>T	c.(358-360)GTC>GTT	p.V120V	RCN1_uc010rea.1_Silent_p.V69V|RCN1_uc001mtk.2_5'UTR	NM_002901	NP_002892	Q15293	RCN1_HUMAN	reticulocalbin 1 precursor	120	EF-hand 2.					endoplasmic reticulum lumen	calcium ion binding			large_intestine(1)	1	Lung SC(675;0.225)																	---	---	---	---
CCDC73	493860	broad.mit.edu	37	11	32632744	32632744	+	Silent	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32632744T>A	uc001mtv.2	-	17	3008	c.2964A>T	c.(2962-2964)GGA>GGT	p.G988G		NM_001008391	NP_001008392	Q6ZRK6	CCD73_HUMAN	sarcoma antigen NY-SAR-79	988										ovary(1)|central_nervous_system(1)	2	Breast(20;0.112)																	---	---	---	---
CD59	966	broad.mit.edu	37	11	33731827	33731827	+	Missense_Mutation	SNP	G	A	A	rs146075291	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33731827G>A	uc001mus.3	-	3	514	c.232C>T	c.(232-234)CGC>TGC	p.R78C	CD59_uc009yjx.2_Missense_Mutation_p.R78C|CD59_uc009yjy.2_Missense_Mutation_p.R78C|CD59_uc009yjz.2_Missense_Mutation_p.R78C|CD59_uc001mut.3_Missense_Mutation_p.R78C|CD59_uc009yka.2_Missense_Mutation_p.R78C|CD59_uc001muu.3_Missense_Mutation_p.R78C|CD59_uc001muv.3_Missense_Mutation_p.R78C|CD59_uc001mux.3_Silent_p.P118P	NM_001127223	NP_001120695	P13987	CD59_HUMAN	CD59 antigen preproprotein	78	UPAR/Ly6.			R->E: Loss of function. Lysis.	blood coagulation|cell surface receptor linked signaling pathway	anchored to external side of plasma membrane|extracellular region|membrane fraction					0																		---	---	---	---
NAT10	55226	broad.mit.edu	37	11	34161946	34161946	+	Splice_Site	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34161946G>A	uc001mvk.2	+	24	2664	c.2420_splice	c.e24-1	p.A807_splice	NAT10_uc010ren.1_Splice_Site_p.A735_splice	NM_024662	NP_078938			N-acetyltransferase 10 isoform a							nucleolus	ATP binding|N-acetyltransferase activity|protein binding			ovary(1)|skin(1)	2		Acute lymphoblastic leukemia(5;0.0119)|all_hematologic(20;0.0231)																---	---	---	---
ABTB2	25841	broad.mit.edu	37	11	34184189	34184189	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:34184189G>A	uc001mvl.1	-	10	1824	c.1594C>T	c.(1594-1596)CAG>TAG	p.Q532*		NM_145804	NP_665803	Q8N961	ABTB2_HUMAN	ankyrin repeat and BTB (POZ) domain containing	532							DNA binding			central_nervous_system(1)|skin(1)	2		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(20;0.0691)																---	---	---	---
PAMR1	25891	broad.mit.edu	37	11	35456235	35456235	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:35456235G>A	uc001mwg.2	-	10	1494	c.1451C>T	c.(1450-1452)GCG>GTG	p.A484V	PAMR1_uc001mwf.2_Missense_Mutation_p.A501V|PAMR1_uc010rew.1_Missense_Mutation_p.A373V|PAMR1_uc010rex.1_Missense_Mutation_p.A444V	NM_001001991	NP_001001991	Q6UXH9	PAMR1_HUMAN	regeneration associated muscle protease isoform	484	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			ovary(2)	2																		---	---	---	---
COMMD9	29099	broad.mit.edu	37	11	36293304	36293304	+	RNA	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36293304C>T	uc009yki.1	-	2		c.268G>A								Homo sapiens cDNA FLJ45212 fis, clone BRCAN2018667.											ovary(1)	1	all_lung(20;0.211)	all_hematologic(20;0.107)																---	---	---	---
RAG1	5896	broad.mit.edu	37	11	36596629	36596629	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:36596629G>A	uc001mwu.3	+	2	1899	c.1775G>A	c.(1774-1776)GGC>GAC	p.G592D	RAG1_uc001mwt.2_RNA	NM_000448	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	592					histone monoubiquitination|immune response|pre-B cell allelic exclusion|protein autoubiquitination|T cell differentiation in thymus|V(D)J recombination	nucleus	endonuclease activity|histone binding|protein homodimerization activity|sequence-specific DNA binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|pancreas(1)|lung(1)|kidney(1)|skin(1)	5	all_lung(20;0.226)	all_hematologic(20;0.107)												Familial_Hemophagocytic_Lymphohistiocytosis				---	---	---	---
API5	8539	broad.mit.edu	37	11	43345027	43345027	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43345027A>G	uc010rfh.1	+	6	764	c.591A>G	c.(589-591)ATA>ATG	p.I197M	API5_uc010rfg.1_Missense_Mutation_p.I186M|API5_uc001mxf.2_Missense_Mutation_p.I197M|API5_uc010rfi.1_Missense_Mutation_p.I143M|API5_uc001mxg.2_Missense_Mutation_p.I71M	NM_001142930	NP_001136402	Q9BZZ5	API5_HUMAN	apoptosis inhibitor 5 isoform a	197					anti-apoptosis|apoptosis	cytoplasm|spliceosomal complex	fibroblast growth factor binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3																		---	---	---	---
ACCSL	390110	broad.mit.edu	37	11	44081473	44081473	+	3'UTR	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44081473C>T	uc001mxw.1	+	14					ACCSL_uc009ykr.2_3'UTR	NM_001031854	NP_001027025			1-aminocyclopropane-1-carboxylate synthase								1-aminocyclopropane-1-carboxylate synthase activity|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups			ovary(5)	5																		---	---	---	---
ACCS	84680	broad.mit.edu	37	11	44105303	44105303	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44105303T>C	uc009yks.1	+	15	1611	c.1467T>C	c.(1465-1467)CGT>CGC	p.R489R	EXT2_uc010rfo.1_Intron|ACCS_uc001mxx.2_Silent_p.R489R	NM_001127219	NP_001120691	Q96QU6	1A1L1_HUMAN	1-aminocyclopropane-1-carboxylate synthase	489							1-aminocyclopropane-1-carboxylate synthase activity|protein homodimerization activity|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups			breast(2)|ovary(1)|lung(1)	4																		---	---	---	---
EXT2	2132	broad.mit.edu	37	11	44129412	44129412	+	Silent	SNP	C	T	T	rs138982530	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44129412C>T	uc001mxz.2	+	2	484	c.150C>T	c.(148-150)ATC>ATT	p.I50I	EXT2_uc010rfo.1_Silent_p.I78I|EXT2_uc001mxy.2_Silent_p.I63I|EXT2_uc009ykt.2_Silent_p.I50I|EXT2_uc001mya.2_Silent_p.I83I	NM_207122	NP_997005	Q93063	EXT2_HUMAN	exostosin 2 isoform 2	50	Lumenal (Potential).				glycosaminoglycan biosynthetic process|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|ossification|signal transduction	Golgi membrane|integral to membrane|intrinsic to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|heparan sulfate N-acetylglucosaminyltransferase activity|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity|protein heterodimerization activity			lung(2)|breast(2)|skin(1)	5								Mis|N|F|S			exostoses|osteosarcoma			Hereditary_Multiple_Exostoses				---	---	---	---
EXT2	2132	broad.mit.edu	37	11	44148431	44148431	+	Missense_Mutation	SNP	A	C	C	rs141977888	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44148431A>C	uc001mxz.2	+	6	1339	c.1005A>C	c.(1003-1005)TTA>TTC	p.L335F	EXT2_uc010rfo.1_Missense_Mutation_p.L363F|EXT2_uc001mxy.2_Missense_Mutation_p.L348F|EXT2_uc009ykt.2_Missense_Mutation_p.L335F|EXT2_uc001mya.2_Missense_Mutation_p.L368F	NM_207122	NP_997005	Q93063	EXT2_HUMAN	exostosin 2 isoform 2	335	Lumenal (Potential).				glycosaminoglycan biosynthetic process|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|ossification|signal transduction	Golgi membrane|integral to membrane|intrinsic to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|heparan sulfate N-acetylglucosaminyltransferase activity|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity|protein heterodimerization activity			lung(2)|breast(2)|skin(1)	5								Mis|N|F|S			exostoses|osteosarcoma			Hereditary_Multiple_Exostoses				---	---	---	---
EXT2	2132	broad.mit.edu	37	11	44219390	44219390	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44219390C>T	uc001mxz.2	+	9	1651	c.1317C>T	c.(1315-1317)AGC>AGT	p.S439S	EXT2_uc010rfo.1_Silent_p.S467S|EXT2_uc001mxy.2_Silent_p.S452S|EXT2_uc009ykt.2_Silent_p.S449S|EXT2_uc001mya.2_Silent_p.S472S	NM_207122	NP_997005	Q93063	EXT2_HUMAN	exostosin 2 isoform 2	439	Lumenal (Potential).				glycosaminoglycan biosynthetic process|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|ossification|signal transduction	Golgi membrane|integral to membrane|intrinsic to endoplasmic reticulum membrane	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|heparan sulfate N-acetylglucosaminyltransferase activity|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity|protein heterodimerization activity			lung(2)|breast(2)|skin(1)	5								Mis|N|F|S			exostoses|osteosarcoma			Hereditary_Multiple_Exostoses				---	---	---	---
PRDM11	56981	broad.mit.edu	37	11	45246360	45246360	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45246360G>T	uc001myo.2	+	8	1686	c.1437G>T	c.(1435-1437)CAG>CAT	p.Q479H		NM_020229	NP_064614	Q9NQV5	PRD11_HUMAN	PR domain containing 11	479										upper_aerodigestive_tract(1)	1																		---	---	---	---
CHST1	8534	broad.mit.edu	37	11	45671522	45671522	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45671522C>T	uc001mys.1	-	4	1623	c.952G>A	c.(952-954)GGG>AGG	p.G318R		NM_003654	NP_003645	O43916	CHST1_HUMAN	carbohydrate (keratan sulfate Gal-6)	318	Lumenal (Potential).				galactose metabolic process|inflammatory response|keratan sulfate metabolic process	Golgi membrane|integral to membrane	keratan sulfotransferase activity			skin(4)|pancreas(1)	5				GBM - Glioblastoma multiforme(35;3e-06)|BRCA - Breast invasive adenocarcinoma(625;0.0781)														---	---	---	---
CHST1	8534	broad.mit.edu	37	11	45671646	45671646	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45671646G>A	uc001mys.1	-	4	1499	c.828C>T	c.(826-828)TGC>TGT	p.C276C		NM_003654	NP_003645	O43916	CHST1_HUMAN	carbohydrate (keratan sulfate Gal-6)	276	Lumenal (Potential).				galactose metabolic process|inflammatory response|keratan sulfate metabolic process	Golgi membrane|integral to membrane	keratan sulfotransferase activity			skin(4)|pancreas(1)	5				GBM - Glioblastoma multiforme(35;3e-06)|BRCA - Breast invasive adenocarcinoma(625;0.0781)														---	---	---	---
CHST1	8534	broad.mit.edu	37	11	45672403	45672403	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45672403C>T	uc001mys.1	-	4	742	c.71G>A	c.(70-72)CGC>CAC	p.R24H		NM_003654	NP_003645	O43916	CHST1_HUMAN	carbohydrate (keratan sulfate Gal-6)	24	Lumenal (Potential).				galactose metabolic process|inflammatory response|keratan sulfate metabolic process	Golgi membrane|integral to membrane	keratan sulfotransferase activity			skin(4)|pancreas(1)	5				GBM - Glioblastoma multiforme(35;3e-06)|BRCA - Breast invasive adenocarcinoma(625;0.0781)														---	---	---	---
CRY2	1408	broad.mit.edu	37	11	45880363	45880363	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:45880363G>A	uc010rgn.1	+	3	491	c.469G>A	c.(469-471)GCC>ACC	p.A157T	CRY2_uc009ykw.2_Missense_Mutation_p.A75T	NM_021117	NP_066940	Q49AN0	CRY2_HUMAN	cryptochrome 2 (photolyase-like) isoform 1	136	DNA photolyase.				DNA repair|protein-chromophore linkage|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	blue light photoreceptor activity|damaged DNA binding|DNA photolyase activity|nucleotide binding|protein binding|single-stranded DNA binding			central_nervous_system(1)	1																		---	---	---	---
KIAA0652	9776	broad.mit.edu	37	11	46690383	46690383	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46690383C>A	uc009yld.2	+	16	1954	c.1270C>A	c.(1270-1272)CAG>AAG	p.Q424K	KIAA0652_uc001nda.2_Missense_Mutation_p.Q457K|KIAA0652_uc001ndb.2_Missense_Mutation_p.Q424K|KIAA0652_uc001ncz.2_Missense_Mutation_p.Q387K|KIAA0652_uc001ndc.2_Missense_Mutation_p.Q387K|KIAA0652_uc010rgv.1_Missense_Mutation_p.Q308K	NM_001142673	NP_001136145	O75143	ATG13_HUMAN	autophagy-related protein 13 isoform 1	424					autophagic vacuole assembly	cytosol|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	protein binding				0				GBM - Glioblastoma multiforme(35;0.226)														---	---	---	---
F2	2147	broad.mit.edu	37	11	46747618	46747618	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46747618C>T	uc001ndf.3	+	7	812	c.769C>T	c.(769-771)CTG>TTG	p.L257L	F2_uc001ndg.3_RNA	NM_000506	NP_000497	P00734	THRB_HUMAN	coagulation factor II preproprotein	257	Kringle 2.				activation of caspase activity|acute-phase response|blood coagulation, intrinsic pathway|cell surface receptor linked signaling pathway|cytosolic calcium ion homeostasis|fibrinolysis|leukocyte migration|negative regulation of astrocyte differentiation|negative regulation of fibrinolysis|negative regulation of platelet activation|negative regulation of proteolysis|peptidyl-glutamic acid carboxylation|platelet activation|positive regulation of collagen biosynthetic process|positive regulation of protein phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of release of sequestered calcium ion into cytosol|post-translational protein modification|proteolysis|STAT protein import into nucleus|tyrosine phosphorylation of STAT protein	cytosol|endoplasmic reticulum lumen|extracellular space|Golgi lumen|plasma membrane|soluble fraction	calcium ion binding|growth factor activity|serine-type endopeptidase activity|thrombospondin receptor activity			ovary(3)	3		all_lung(304;0.000414)|Lung NSC(402;0.0011)		BRCA - Breast invasive adenocarcinoma(625;0.146)	Antihemophilic Factor(DB00025)|Argatroban(DB00278)|Bivalirudin(DB00006)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)|Enoxaparin(DB01225)|Heparin(DB01109)|Lepirudin(DB00001)|Menadione(DB00170)|Proflavine(DB01123)|Simvastatin(DB00641)|Suramin(DB04786)|Warfarin(DB00682)|Ximelagatran(DB04898)													---	---	---	---
CKAP5	9793	broad.mit.edu	37	11	46776497	46776497	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46776497T>C	uc001ndi.1	-	36	4920	c.4810A>G	c.(4810-4812)AAA>GAA	p.K1604E	CKAP5_uc009ylg.1_Missense_Mutation_p.K1490E|CKAP5_uc001ndj.1_Intron|CKAP5_uc001ndh.1_Missense_Mutation_p.K533E	NM_001008938	NP_001008938	Q14008	CKAP5_HUMAN	colonic and hepatic tumor over-expressed protein	1604					cell division|centrosome organization|establishment or maintenance of microtubule cytoskeleton polarity|G2/M transition of mitotic cell cycle|mitotic prometaphase|RNA transport|spindle organization	centrosome|cytosol	protein binding|protein binding			ovary(1)|skin(1)	2																		---	---	---	---
PACSIN3	29763	broad.mit.edu	37	11	47200558	47200558	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47200558C>A	uc001ndw.2	-	9	1262	c.924G>T	c.(922-924)AGG>AGT	p.R308S	ARFGAP2_uc001ndt.2_5'Flank|ARFGAP2_uc010rhb.1_5'Flank|ARFGAP2_uc001ndu.2_5'Flank|ARFGAP2_uc010rhc.1_5'Flank|ARFGAP2_uc010rhd.1_5'Flank|ARFGAP2_uc001ndv.1_5'Flank|PACSIN3_uc001ndx.2_Missense_Mutation_p.R308S|PACSIN3_uc001ndy.2_Missense_Mutation_p.R308S|PACSIN3_uc001ndz.2_RNA|PACSIN3_uc001nea.2_RNA	NM_016223	NP_057307	Q9UKS6	PACN3_HUMAN	protein kinase C and casein kinase substrate in	308					endocytosis|negative regulation of endocytosis|positive regulation of membrane protein ectodomain proteolysis	cytoplasm|plasma membrane	cytoskeletal protein binding				0																		---	---	---	---
MADD	8567	broad.mit.edu	37	11	47311442	47311442	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47311442G>A	uc001ner.1	+	18	3032	c.2841G>A	c.(2839-2841)GAG>GAA	p.E947E	MADD_uc001neq.2_Silent_p.E927E|MADD_uc001nev.1_Silent_p.E884E|MADD_uc001nes.1_Silent_p.E904E|MADD_uc001net.1_Silent_p.E947E|MADD_uc009yln.1_Silent_p.E884E|MADD_uc001neu.1_Silent_p.E884E|MADD_uc001nex.2_Silent_p.E947E|MADD_uc001nez.2_Silent_p.E884E|MADD_uc001new.2_Silent_p.E927E|MADD_uc009ylo.2_5'Flank	NM_003682	NP_003673	Q8WXG6	MADD_HUMAN	MAP-kinase activating death domain-containing	947					activation of MAPK activity|apoptosis|cell surface receptor linked signaling pathway|regulation of apoptosis|regulation of cell cycle	cytoplasm|integral to membrane|plasma membrane	death receptor binding|protein kinase activator activity|Rab guanyl-nucleotide exchange factor activity			ovary(5)|skin(4)|central_nervous_system(2)	11				Lung(87;0.182)														---	---	---	---
MADD	8567	broad.mit.edu	37	11	47350233	47350233	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47350233G>T	uc001ner.1	+	35	5008	c.4817G>T	c.(4816-4818)AGC>ATC	p.S1606I	MADD_uc001neq.2_Missense_Mutation_p.S1547I|MADD_uc001nev.1_3'UTR|MADD_uc001nes.1_Missense_Mutation_p.S1524I|MADD_uc001net.1_Missense_Mutation_p.S1567I|MADD_uc009yln.1_Missense_Mutation_p.S1500I|MADD_uc001neu.1_Missense_Mutation_p.S1504I|MADD_uc001nex.2_3'UTR|MADD_uc001nez.2_Missense_Mutation_p.S1503I|MADD_uc001new.2_Missense_Mutation_p.S1546I	NM_003682	NP_003673	Q8WXG6	MADD_HUMAN	MAP-kinase activating death domain-containing	1606					activation of MAPK activity|apoptosis|cell surface receptor linked signaling pathway|regulation of apoptosis|regulation of cell cycle	cytoplasm|integral to membrane|plasma membrane	death receptor binding|protein kinase activator activity|Rab guanyl-nucleotide exchange factor activity			ovary(5)|skin(4)|central_nervous_system(2)	11				Lung(87;0.182)														---	---	---	---
PSMC3	5702	broad.mit.edu	37	11	47440693	47440693	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47440693G>T	uc001nfh.2	-	11	1377	c.1183C>A	c.(1183-1185)CAG>AAG	p.Q395K	PSMC3_uc009ylr.1_Missense_Mutation_p.Q353K	NM_002804	NP_002795	P17980	PRS6A_HUMAN	proteasome 26S ATPase subunit 3	395					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome complex	ATP binding|nucleoside-triphosphatase activity|protein binding|transcription coactivator activity|transcription corepressor activity			ovary(4)	4				Lung(87;0.0932)|BRCA - Breast invasive adenocarcinoma(625;0.13)														---	---	---	---
CELF1	10658	broad.mit.edu	37	11	47504330	47504330	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47504330G>A	uc001nfl.2	-	6	614	c.604C>T	c.(604-606)CAG>TAG	p.Q202*	CELF1_uc001nfm.2_Nonsense_Mutation_p.Q202*|CELF1_uc001nfn.2_Nonsense_Mutation_p.Q202*|CELF1_uc001nfo.1_Nonsense_Mutation_p.Q228*|CELF1_uc010rhm.1_Nonsense_Mutation_p.Q201*|CELF1_uc001nfp.2_Nonsense_Mutation_p.Q229*|CELF1_uc001nfq.1_Nonsense_Mutation_p.Q202*|CELF1_uc001nfr.1_Nonsense_Mutation_p.Q202*	NM_001025596	NP_001020767	Q92879	CELF1_HUMAN	CUG triplet repeat, RNA-binding protein 1	202					embryo development|mRNA splice site selection|regulation of RNA splicing|RNA interference	cytoplasm|nucleus|ribonucleoprotein complex	BRE binding|mRNA binding|nucleotide binding|translation repressor activity, nucleic acid binding			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
PTPRJ	5795	broad.mit.edu	37	11	48158545	48158545	+	Intron	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48158545T>A	uc001ngp.3	+						PTPRJ_uc010rhr.1_Intron	NM_002843	NP_002834			protein tyrosine phosphatase, receptor type, J						contact inhibition|negative regulation of cell growth|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of MAP kinase activity|negative regulation of platelet-derived growth factor receptor signaling pathway|negative regulation of protein kinase B signaling cascade|negative regulation of T cell receptor signaling pathway|negative regulation of vascular permeability|platelet-derived growth factor receptor signaling pathway|positive chemotaxis|positive regulation of focal adhesion assembly|positive regulation of protein kinase B signaling cascade|positive regulation of survival gene product expression	cell surface|cell-cell junction|immunological synapse|integral to plasma membrane|ruffle membrane	beta-catenin binding|delta-catenin binding|gamma-catenin binding|mitogen-activated protein kinase binding|platelet-derived growth factor receptor binding|protein tyrosine phosphatase activity			breast(3)|kidney(3)|ovary(1)|skin(1)	8																		---	---	---	---
TRIM48	79097	broad.mit.edu	37	11	55035844	55035844	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55035844T>C	uc010rid.1	+	4	660	c.574T>C	c.(574-576)TAC>CAC	p.Y192H		NM_024114	NP_077019	Q8IWZ4	TRI48_HUMAN	tripartite motif-containing 48	176						intracellular	zinc ion binding				0																		---	---	---	---
TRIM48	79097	broad.mit.edu	37	11	55035854	55035854	+	Intron	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55035854T>A	uc010rid.1	+							NM_024114	NP_077019			tripartite motif-containing 48							intracellular	zinc ion binding				0																		---	---	---	---
TRIM48	79097	broad.mit.edu	37	11	55035855	55035855	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55035855A>G	uc010rid.1	+							NM_024114	NP_077019			tripartite motif-containing 48							intracellular	zinc ion binding				0																		---	---	---	---
OR5I1	10798	broad.mit.edu	37	11	55703398	55703398	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55703398A>C	uc010ris.1	-	1	479	c.479T>G	c.(478-480)GTT>GGT	p.V160G		NM_006637	NP_006628	Q13606	OR5I1_HUMAN	olfactory receptor, family 5, subfamily I,	160	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1																		---	---	---	---
OR5J2	282775	broad.mit.edu	37	11	55944713	55944713	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55944713C>A	uc010rjb.1	+	1	620	c.620C>A	c.(619-621)GCC>GAC	p.A207D		NM_001005492	NP_001005492	Q8NH18	OR5J2_HUMAN	olfactory receptor, family 5, subfamily J,	207	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|large_intestine(1)|breast(1)|pancreas(1)	4	Esophageal squamous(21;0.00693)																	---	---	---	---
OR8J1	219477	broad.mit.edu	37	11	56127954	56127954	+	Missense_Mutation	SNP	G	A	A	rs138373932		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56127954G>A	uc010rjh.1	+	1	232	c.232G>A	c.(232-234)GCC>ACC	p.A78T		NM_001005205	NP_001005205	Q8NGP2	OR8J1_HUMAN	olfactory receptor, family 8, subfamily J,	78	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	Esophageal squamous(21;0.00448)																	---	---	---	---
OR5M11	219487	broad.mit.edu	37	11	56310343	56310343	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56310343A>G	uc010rjl.1	-	1	391	c.391T>C	c.(391-393)TAC>CAC	p.Y131H		NM_001005245	NP_001005245	Q96RB7	OR5MB_HUMAN	olfactory receptor, family 5, subfamily M,	131	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0																		---	---	---	---
OR5M1	390168	broad.mit.edu	37	11	56380763	56380763	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56380763G>A	uc001nja.1	-	1	216	c.216C>T	c.(214-216)TGC>TGT	p.C72C		NM_001004740	NP_001004740	Q8NGP8	OR5M1_HUMAN	olfactory receptor, family 5, subfamily M,	72	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1																		---	---	---	---
OR5AP2	338675	broad.mit.edu	37	11	56408970	56408970	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:56408970A>C	uc001njb.1	-	1	946	c.946T>G	c.(946-948)TTG>GTG	p.L316V		NM_001002925	NP_001002925	Q8NGF4	O5AP2_HUMAN	olfactory receptor, family 5, subfamily AP,	316	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
TNKS1BP1	85456	broad.mit.edu	37	11	57076294	57076294	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57076294A>G	uc001njr.2	-	5	4203	c.3891T>C	c.(3889-3891)AGT>AGC	p.S1297S	TNKS1BP1_uc001njs.2_Silent_p.S1297S|TNKS1BP1_uc009ymd.1_Silent_p.S748S	NM_033396	NP_203754	Q9C0C2	TB182_HUMAN	tankyrase 1-binding protein 1	1297	Gly-rich.|Acidic.				nuclear-transcribed mRNA poly(A) tail shortening|telomere maintenance via telomerase	cytoskeleton|cytosol|nuclear telomeric heterochromatin	ankyrin binding|enzyme binding			skin(1)	1		all_epithelial(135;0.21)																---	---	---	---
PRG2	5553	broad.mit.edu	37	11	57156156	57156156	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57156156C>T	uc001njz.2	-	3	419	c.392G>A	c.(391-393)GGC>GAC	p.G131D	PRG2_uc001njw.1_RNA|PRG2_uc001njx.1_RNA|PRG2_uc001njy.1_RNA|PRG2_uc001nka.2_Missense_Mutation_p.G131D|PRG2_uc001nkb.2_Missense_Mutation_p.G131D|PRG2_uc001nkd.2_Missense_Mutation_p.G120D|PRG2_uc001nkc.2_Missense_Mutation_p.G131D|PRG2_uc001nke.2_Missense_Mutation_p.G411D	NM_002728	NP_002719	P13727	PRG2_HUMAN	proteoglycan 2 preproprotein	131	C-type lectin.				defense response to bacterium|immune response	extracellular region|transport vesicle	heparin binding|sugar binding			central_nervous_system(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Sargramostim(DB00020)													---	---	---	---
SERPING1	710	broad.mit.edu	37	11	57367421	57367421	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57367421G>T	uc001nkp.1	+	3	312	c.121G>T	c.(121-123)GGC>TGC	p.G41C	SERPING1_uc001nkq.1_Missense_Mutation_p.G41C|SERPING1_uc010rju.1_Translation_Start_Site|SERPING1_uc010rjv.1_Missense_Mutation_p.G46C|SERPING1_uc001nkr.1_Missense_Mutation_p.G41C|SERPING1_uc009ymi.1_Missense_Mutation_p.G41C|SERPING1_uc009ymj.1_Missense_Mutation_p.G41C|SERPING1_uc001nks.1_Intron	NM_000062	NP_000053	P05155	IC1_HUMAN	serpin peptidase inhibitor, clade G, member 1	41					blood circulation|blood coagulation, intrinsic pathway|complement activation, classical pathway|innate immune response|negative regulation of complement activation, lectin pathway|platelet activation|platelet degranulation	extracellular space|platelet alpha granule lumen	protein binding|serine-type endopeptidase inhibitor activity			central_nervous_system(1)	1														Hereditary_Angioedema				---	---	---	---
SERPING1	710	broad.mit.edu	37	11	57374021	57374021	+	Splice_Site	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57374021G>A	uc001nkp.1	+	6	1220	c.1029_splice	c.e6+1	p.K343_splice	SERPING1_uc001nkq.1_Splice_Site_p.K343_splice|SERPING1_uc010rju.1_Splice_Site_p.K291_splice|SERPING1_uc010rjv.1_Splice_Site_p.K348_splice|SERPING1_uc001nkr.1_Splice_Site_p.K343_splice|SERPING1_uc009ymi.1_Splice_Site_p.K352_splice|SERPING1_uc009ymj.1_Splice_Site_p.K343_splice|SERPING1_uc001nks.1_Splice_Site_p.K34_splice	NM_000062	NP_000053			serpin peptidase inhibitor, clade G, member 1						blood circulation|blood coagulation, intrinsic pathway|complement activation, classical pathway|innate immune response|negative regulation of complement activation, lectin pathway|platelet activation|platelet degranulation	extracellular space|platelet alpha granule lumen	protein binding|serine-type endopeptidase inhibitor activity			central_nervous_system(1)	1														Hereditary_Angioedema				---	---	---	---
CLP1	10978	broad.mit.edu	37	11	57428560	57428560	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57428560C>T	uc001nkw.2	+	3	1069	c.930C>T	c.(928-930)GGC>GGT	p.G310G	CLP1_uc010rjw.1_Silent_p.G246G|CLP1_uc009yml.2_Silent_p.G310G	NM_006831	NP_006822	Q92989	CLP1_HUMAN	ATP/GTP-binding protein isoform 1	310					mRNA 3'-end processing|nuclear mRNA splicing, via spliceosome|siRNA loading onto RISC involved in RNA interference|targeting of mRNA for destruction involved in RNA interference|termination of RNA polymerase II transcription|tRNA splicing, via endonucleolytic cleavage and ligation	nucleoplasm|tRNA-intron endonuclease complex	ATP binding|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity|ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity			ovary(1)	1																		---	---	---	---
TMX2	51075	broad.mit.edu	37	11	57506705	57506705	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57506705A>G	uc001nlc.1	+	7	766	c.717A>G	c.(715-717)GGA>GGG	p.G239G	CTNND1_uc001nlf.1_Intron|TMX2_uc001nld.1_Silent_p.G145G|TMX2_uc001nle.1_Silent_p.G201G|C11orf31_uc010rjx.1_5'Flank	NM_015959	NP_057043	Q9Y320	TMX2_HUMAN	thioredoxin domain containing 14 isoform 1	239	Cytoplasmic (Potential).|Thioredoxin.				cell redox homeostasis	integral to membrane					0																		---	---	---	---
OR5B3	441608	broad.mit.edu	37	11	58169970	58169970	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58169970T>G	uc010rkf.1	-	1	913	c.913A>C	c.(913-915)AAG>CAG	p.K305Q		NM_001005469	NP_001005469	Q8NH48	OR5B3_HUMAN	olfactory receptor, family 5, subfamily B,	305	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	Esophageal squamous(5;0.0027)	Breast(21;0.0778)																---	---	---	---
GLYATL1	92292	broad.mit.edu	37	11	58723328	58723328	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58723328G>A	uc001nnf.2	+	8	1113	c.737G>A	c.(736-738)CGA>CAA	p.R246Q	uc001nng.1_Intron|GLYATL1_uc001nnh.1_Missense_Mutation_p.R277Q|GLYATL1_uc001nni.1_Missense_Mutation_p.R246Q|GLYATL1_uc001nnj.1_Missense_Mutation_p.R246Q			Q969I3	GLYL1_HUMAN	SubName: Full=Glycine acyltransferase family-C; SubName: Full=Glycine-N-acyltransferase-like 1, isoform CRA_a;	246						mitochondrion	glycine N-acyltransferase activity			ovary(1)	1					Glycine(DB00145)													---	---	---	---
FAM111A	63901	broad.mit.edu	37	11	58919767	58919767	+	Missense_Mutation	SNP	G	A	A	rs142722244	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58919767G>A	uc010rkp.1	+	5	853	c.626G>A	c.(625-627)CGC>CAC	p.R209H	FAM111A_uc010rkq.1_Missense_Mutation_p.R209H|FAM111A_uc010rkr.1_Missense_Mutation_p.R209H|FAM111A_uc001nno.2_Missense_Mutation_p.R209H|FAM111A_uc001nnp.2_Missense_Mutation_p.R209H|FAM111A_uc001nnq.2_Missense_Mutation_p.R209H	NM_001142521	NP_001135993	Q96PZ2	F111A_HUMAN	hypothetical protein LOC63901	209					proteolysis		serine-type endopeptidase activity			ovary(3)	3		all_epithelial(135;0.139)																---	---	---	---
FAM111A	63901	broad.mit.edu	37	11	58920195	58920195	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58920195C>T	uc010rkp.1	+	5	1281	c.1054C>T	c.(1054-1056)CGT>TGT	p.R352C	FAM111A_uc010rkq.1_Missense_Mutation_p.R352C|FAM111A_uc010rkr.1_Missense_Mutation_p.R352C|FAM111A_uc001nno.2_Missense_Mutation_p.R352C|FAM111A_uc001nnp.2_Missense_Mutation_p.R352C|FAM111A_uc001nnq.2_Missense_Mutation_p.R352C	NM_001142521	NP_001135993	Q96PZ2	F111A_HUMAN	hypothetical protein LOC63901	352					proteolysis		serine-type endopeptidase activity			ovary(3)	3		all_epithelial(135;0.139)																---	---	---	---
DTX4	23220	broad.mit.edu	37	11	58949271	58949271	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:58949271G>A	uc001nns.2	+	2	528	c.271G>A	c.(271-273)GTG>ATG	p.V91M	DTX4_uc001nnr.2_Translation_Start_Site	NM_015177	NP_055992	Q9Y2E6	DTX4_HUMAN	deltex 4 homolog	91	WWE 2.				Notch signaling pathway	cytoplasm	zinc ion binding			lung(2)|central_nervous_system(1)	3		all_epithelial(135;0.125)																---	---	---	---
OR5A1	219982	broad.mit.edu	37	11	59211390	59211390	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59211390T>C	uc001nnx.1	+	1	749	c.749T>C	c.(748-750)GTG>GCG	p.V250A		NM_001004728	NP_001004728	Q8NGJ0	OR5A1_HUMAN	olfactory receptor, family 5, subfamily A,	250	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
STX3	6809	broad.mit.edu	37	11	59523100	59523100	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59523100C>T	uc001nog.2	+	1	212	c.22C>T	c.(22-24)CTG>TTG	p.L8L	STX3_uc010rkx.1_Silent_p.L8L|STX3_uc010rky.1_5'UTR	NM_004177	NP_004168	Q13277	STX3_HUMAN	syntaxin 3	8	Cytoplasmic (Potential).			Missing (in Ref. 2).	cellular response to oxidative stress|intracellular protein transport|neuron projection development|neurotransmitter transport	apical plasma membrane|azurophil granule|cell-cell junction|growth cone|integral to membrane|plasma membrane enriched fraction|SNARE complex|specific granule	arachidonic acid binding|SNAP receptor activity			ovary(2)	2																		---	---	---	---
GIF	2694	broad.mit.edu	37	11	59610049	59610049	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59610049G>A	uc001noi.2	-	4	426	c.378C>T	c.(376-378)AAC>AAT	p.N126N	GIF_uc010rkz.1_3'UTR	NM_005142	NP_005133	P27352	IF_HUMAN	gastric intrinsic factor (vitamin B synthesis)	126					cobalamin metabolic process|cobalamin transport|cobalt ion transport	apical plasma membrane|endosome|extracellular space|microvillus	cobalamin binding			ovary(1)|liver(1)	2																		---	---	---	---
MS4A3	932	broad.mit.edu	37	11	59834421	59834421	+	Intron	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59834421T>A	uc001nom.2	+						MS4A3_uc001non.2_Intron|MS4A3_uc001noo.2_Intron	NM_006138	NP_006129			membrane-spanning 4-domains, subfamily A, member							endomembrane system|integral to membrane|perinuclear region of cytoplasm	protein binding|receptor activity			ovary(2)|skin(1)	3		all_epithelial(135;0.245)																---	---	---	---
ZP1	22917	broad.mit.edu	37	11	60641020	60641020	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60641020G>A	uc001nqd.2	+	8	1433	c.1413G>A	c.(1411-1413)TGG>TGA	p.W471*	ZP1_uc001nqe.2_Nonsense_Mutation_p.W178*	NM_207341	NP_997224	P60852	ZP1_HUMAN	zona pellucida glycoprotein 1 precursor	471	Extracellular (Potential).|ZP.				single fertilization	integral to membrane|plasma membrane|proteinaceous extracellular matrix					0																		---	---	---	---
TMEM109	79073	broad.mit.edu	37	11	60688364	60688364	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60688364T>C	uc001nqg.2	+	3	622	c.244T>C	c.(244-246)TCC>CCC	p.S82P	TMEM109_uc001nqh.2_Missense_Mutation_p.S82P	NM_024092	NP_076997	Q9BVC6	TM109_HUMAN	transmembrane protein 109 precursor	82						integral to membrane|nuclear outer membrane|sarcoplasmic reticulum membrane					0																		---	---	---	---
TMEM132A	54972	broad.mit.edu	37	11	60704341	60704341	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60704341C>T	uc001nqj.2	+	11	3227	c.3034C>T	c.(3034-3036)CTT>TTT	p.L1012F	TMEM132A_uc001nqi.2_Missense_Mutation_p.L1013F|TMEM132A_uc001nqm.2_Missense_Mutation_p.L222F	NM_178031	NP_821174	Q24JP5	T132A_HUMAN	transmembrane protein 132A isoform b	1012	Cytoplasmic (Potential).|Confers cellular localization similar to full-length form (By similarity).					endoplasmic reticulum membrane|Golgi membrane|integral to membrane				skin(1)	1																		---	---	---	---
TMEM132A	54972	broad.mit.edu	37	11	60704345	60704345	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60704345G>A	uc001nqj.2	+	11	3231	c.3038G>A	c.(3037-3039)CGC>CAC	p.R1013H	TMEM132A_uc001nqi.2_Missense_Mutation_p.R1014H|TMEM132A_uc001nqm.2_Missense_Mutation_p.R223H	NM_178031	NP_821174	Q24JP5	T132A_HUMAN	transmembrane protein 132A isoform b	1013	Cytoplasmic (Potential).|Confers cellular localization similar to full-length form (By similarity).					endoplasmic reticulum membrane|Golgi membrane|integral to membrane				skin(1)	1																		---	---	---	---
DAGLA	747	broad.mit.edu	37	11	61502413	61502413	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61502413G>A	uc001nsa.2	+	10	1178	c.1067G>A	c.(1066-1068)CGC>CAC	p.R356H		NM_006133	NP_006124	Q9Y4D2	DGLA_HUMAN	neural stem cell-derived dendrite regulator	356	Cytoplasmic (Potential).				cell death|lipid catabolic process|platelet activation	integral to membrane|plasma membrane	acylglycerol lipase activity|metal ion binding|triglyceride lipase activity			ovary(2)|central_nervous_system(1)	3				READ - Rectum adenocarcinoma(4;0.219)														---	---	---	---
FEN1	2237	broad.mit.edu	37	11	61563039	61563039	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61563039A>G	uc001nsg.2	+	2	578	c.206A>G	c.(205-207)TAC>TGC	p.Y69C	C11orf10_uc001nsf.2_5'Flank	NM_004111	NP_004102	P39748	FEN1_HUMAN	flap structure-specific endonuclease 1	69	N-domain.				base-excision repair|DNA replication, removal of RNA primer|double-strand break repair|phosphatidylinositol-mediated signaling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|UV protection	mitochondrion|nucleolus|nucleoplasm	5'-3' exonuclease activity|5'-flap endonuclease activity|damaged DNA binding|double-stranded DNA binding|double-stranded DNA specific exodeoxyribonuclease activity|metal ion binding|protein binding|ribonuclease H activity			ovary(1)	1													Direct_reversal_of_damage|Editing_and_processing_nucleases					---	---	---	---
SCGB1D2	10647	broad.mit.edu	37	11	62009813	62009813	+	Missense_Mutation	SNP	C	A	A	rs139406960		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62009813C>A	uc001ntb.2	+	1	90	c.34C>A	c.(34-36)CTG>ATG	p.L12M		NM_006551	NP_006542	O95969	SG1D2_HUMAN	lipophilin B precursor	12						extracellular space	binding				0																		---	---	---	---
AHNAK	79026	broad.mit.edu	37	11	62287678	62287678	+	Silent	SNP	G	A	A	rs114273507	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62287678G>A	uc001ntl.2	-	5	14511	c.14211C>T	c.(14209-14211)GGC>GGT	p.G4737G	AHNAK_uc001ntk.1_Intron	NM_001620	NP_001611	Q09666	AHNK_HUMAN	AHNAK nucleoprotein isoform 1	4737					nervous system development	nucleus	protein binding			ovary(10)|pancreas(4)|skin(4)|upper_aerodigestive_tract(1)	19		Melanoma(852;0.155)																---	---	---	---
AHNAK	79026	broad.mit.edu	37	11	62293612	62293612	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62293612G>A	uc001ntl.2	-	5	8577	c.8277C>T	c.(8275-8277)GGC>GGT	p.G2759G	AHNAK_uc001ntk.1_Intron	NM_001620	NP_001611	Q09666	AHNK_HUMAN	AHNAK nucleoprotein isoform 1	2759					nervous system development	nucleus	protein binding			ovary(10)|pancreas(4)|skin(4)|upper_aerodigestive_tract(1)	19		Melanoma(852;0.155)																---	---	---	---
AHNAK	79026	broad.mit.edu	37	11	62296386	62296386	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62296386C>T	uc001ntl.2	-	5	5803	c.5503G>A	c.(5503-5505)GAT>AAT	p.D1835N	AHNAK_uc001ntk.1_Intron	NM_001620	NP_001611	Q09666	AHNK_HUMAN	AHNAK nucleoprotein isoform 1	1835					nervous system development	nucleus	protein binding			ovary(10)|pancreas(4)|skin(4)|upper_aerodigestive_tract(1)	19		Melanoma(852;0.155)																---	---	---	---
EEF1G	1937	broad.mit.edu	37	11	62340167	62340167	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62340167G>A	uc001ntm.1	-	2	206	c.60C>T	c.(58-60)ATC>ATT	p.I20I	EEF1G_uc010rlw.1_Silent_p.I70I|EEF1G_uc001ntn.1_5'UTR	NM_001404	NP_001395	P26641	EF1G_HUMAN	eukaryotic translation elongation factor 1	20	GST N-terminal.				response to virus	cytosol|eukaryotic translation elongation factor 1 complex	protein binding|translation elongation factor activity				0																		---	---	---	---
TUT1	64852	broad.mit.edu	37	11	62343519	62343519	+	Missense_Mutation	SNP	G	A	A	rs138696433		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62343519G>A	uc001nto.2	-	9	1824	c.1786C>T	c.(1786-1788)CGG>TGG	p.R596W	EEF1G_uc001ntm.1_5'Flank|EEF1G_uc010rlw.1_5'Flank|TUT1_uc001ntp.1_Missense_Mutation_p.R92W	NM_022830	NP_073741	Q9H6E5	STPAP_HUMAN	terminal uridylyl transferase 1, U6	558					mRNA cleavage|mRNA polyadenylation|snRNA processing	nuclear speck|nucleolus	ATP binding|enzyme binding|mRNA 3'-UTR binding|polynucleotide adenylyltransferase activity|RNA uridylyltransferase activity|zinc ion binding			central_nervous_system(1)|skin(1)	2																		---	---	---	---
B3GAT3	26229	broad.mit.edu	37	11	62384683	62384683	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62384683A>G	uc001ntw.2	-	3	423	c.394T>C	c.(394-396)TTC>CTC	p.F132L	B3GAT3_uc009ynz.2_Missense_Mutation_p.F125L|B3GAT3_uc001ntx.2_RNA|B3GAT3_uc010rlz.1_Missense_Mutation_p.F132L	NM_012200	NP_036332	O94766	B3GA3_HUMAN	beta-1,3-glucuronyltransferase 3	132	Lumenal (Potential).				glycosaminoglycan biosynthetic process	Golgi membrane|integral to membrane	galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity|manganese ion binding				0																		---	---	---	---
C11orf48	79081	broad.mit.edu	37	11	62435121	62435121	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62435121T>A	uc001nue.2	-	4	847	c.412A>T	c.(412-414)ATT>TTT	p.I138F	C11orf48_uc001nuf.2_Missense_Mutation_p.I138F|METTL12_uc001nuh.2_3'UTR|C11orf48_uc010rmd.1_Missense_Mutation_p.I138F	NM_024099	NP_077004	Q9BQE6	CK048_HUMAN	hypothetical protein LOC79081	164											0																		---	---	---	---
HNRNPUL2	221092	broad.mit.edu	37	11	62484561	62484561	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62484561C>A	uc001nuw.2	-	11	2074	c.1881G>T	c.(1879-1881)GAG>GAT	p.E627D	HNRNPUL2_uc001nuu.1_RNA	NM_001079559	NP_001073027	Q1KMD3	HNRL2_HUMAN	heterogeneous nuclear ribonucleoprotein U-like	627					cell killing	nucleus	ATP binding|nucleic acid binding				0																		---	---	---	---
HNRNPUL2	221092	broad.mit.edu	37	11	62491095	62491095	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62491095G>A	uc001nuw.2	-	4	1048	c.855C>T	c.(853-855)TAC>TAT	p.Y285Y	HNRNPUL2_uc001nuu.1_RNA	NM_001079559	NP_001073027	Q1KMD3	HNRL2_HUMAN	heterogeneous nuclear ribonucleoprotein U-like	285	B30.2/SPRY.				cell killing	nucleus	ATP binding|nucleic acid binding				0																		---	---	---	---
POLR2G	5436	broad.mit.edu	37	11	62529143	62529143	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62529143C>T	uc001nva.2	+						POLR2G_uc001nvb.2_Intron	NM_002696	NP_002687			DNA directed RNA polymerase II polypeptide G						mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA-directed RNA polymerase activity|protein binding|RNA binding				0																		---	---	---	---
CHRM1	1128	broad.mit.edu	37	11	62678155	62678155	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62678155G>A	uc001nwi.2	-	2	819	c.418C>T	c.(418-420)CGC>TGC	p.R140C		NM_000738	NP_000729	P11229	ACM1_HUMAN	cholinergic receptor, muscarinic 1	140	Cytoplasmic (Potential).				activation of phospholipase C activity by muscarinic acetylcholine receptor signaling pathway|activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell proliferation|nervous system development|positive regulation of cell proliferation|protein modification process	cell junction|integral to plasma membrane|membrane fraction|postsynaptic membrane	muscarinic acetylcholine receptor activity|phosphatidylinositol phospholipase C activity|protein binding				0					Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Benztropine(DB00245)|Bethanechol(DB01019)|Biperiden(DB00810)|Buclizine(DB00354)|Carbachol(DB00411)|Carbinoxamine(DB00748)|Cevimeline(DB00185)|Clidinium(DB00771)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Cyclopentolate(DB00979)|Cycrimine(DB00942)|Desipramine(DB01151)|Dicyclomine(DB00804)|Diphenidol(DB01231)|Doxylamine(DB00366)|Ethopropazine(DB00392)|Flavoxate(DB01148)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Ipratropium(DB00332)|Methantheline(DB00940)|Methotrimeprazine(DB01403)|Methylscopolamine(DB00462)|Metixene(DB00340)|Metoclopramide(DB01233)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Oxyphenonium(DB00219)|Pilocarpine(DB01085)|Pirenzepine(DB00670)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propantheline(DB00782)|Propiomazine(DB00777)|Quinacrine(DB01103)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Thiethylperazine(DB00372)|Tolterodine(DB01036)|Tridihexethyl(DB00505)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trospium(DB00209)													---	---	---	---
HRASLS5	117245	broad.mit.edu	37	11	63256453	63256453	+	Intron	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63256453A>C	uc001nwy.2	-						HRASLS5_uc001nwz.2_Intron|HRASLS5_uc010rmq.1_Intron|HRASLS5_uc009yos.2_Intron	NM_054108	NP_473449			HRAS-like suppressor family, member 5 isoform 1											ovary(1)	1																		---	---	---	---
HRASLS5	117245	broad.mit.edu	37	11	63257797	63257797	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63257797C>T	uc001nwy.2	-	2	361	c.187G>A	c.(187-189)GTG>ATG	p.V63M	HRASLS5_uc001nwz.2_Missense_Mutation_p.V53M|HRASLS5_uc010rmq.1_Missense_Mutation_p.V63M|HRASLS5_uc009yos.2_RNA	NM_054108	NP_473449	Q96KN8	HRSL5_HUMAN	HRAS-like suppressor family, member 5 isoform 1	63										ovary(1)	1																		---	---	---	---
MARK2	2011	broad.mit.edu	37	11	63676611	63676611	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63676611C>T	uc001nxw.2	+	19	2848	c.2269C>T	c.(2269-2271)CGG>TGG	p.R757W	MARK2_uc001nxx.2_Missense_Mutation_p.R688W|MARK2_uc001nxy.2_Missense_Mutation_p.R678W|MARK2_uc001nxv.3_Missense_Mutation_p.R693W|MARK2_uc001nxz.3_Missense_Mutation_p.R714W|MARK2_uc009yoy.2_Missense_Mutation_p.R668W	NM_001039469	NP_001034558	Q7KZI7	MARK2_HUMAN	MAP/microtubule affinity-regulating kinase 2	757	KA1.				cell differentiation|establishment or maintenance of epithelial cell apical/basal polarity|intracellular protein kinase cascade|multicellular organismal development|response to oxidative stress	plasma membrane	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			stomach(1)|ovary(1)|lung(1)	3																		---	---	---	---
FLRT1	23769	broad.mit.edu	37	11	63884235	63884235	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63884235G>A	uc001nyi.1	+	2	837	c.496G>A	c.(496-498)GTC>ATC	p.V166I	MACROD1_uc001nyh.2_Intron	NM_013280	NP_037412	Q9NZU1	FLRT1_HUMAN	fibronectin leucine rich transmembrane protein	138	LRR 4.|Extracellular (Potential).				cell adhesion	integral to plasma membrane|proteinaceous extracellular matrix	protein binding, bridging|receptor signaling protein activity				0																		---	---	---	---
FERMT3	83706	broad.mit.edu	37	11	63978790	63978790	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63978790G>A	uc001nyl.2	+	5	707	c.558G>A	c.(556-558)TCG>TCA	p.S186S	FERMT3_uc001nym.2_Silent_p.S186S	NM_178443	NP_848537	Q86UX7	URP2_HUMAN	fermitin family homolog 3 long form	186					integrin activation|leukocyte cell-cell adhesion|platelet aggregation|regulation of cell-cell adhesion mediated by integrin	cell junction|cell projection|podosome	integrin binding			ovary(1)	1																		---	---	---	---
FERMT3	83706	broad.mit.edu	37	11	63987261	63987261	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63987261G>A	uc001nyl.2	+	9	1228	c.1079G>A	c.(1078-1080)CGC>CAC	p.R360H	FERMT3_uc001nym.2_Missense_Mutation_p.R360Q	NM_178443	NP_848537	Q86UX7	URP2_HUMAN	fermitin family homolog 3 long form	360	PH.|FERM.				integrin activation|leukocyte cell-cell adhesion|platelet aggregation|regulation of cell-cell adhesion mediated by integrin	cell junction|cell projection|podosome	integrin binding			ovary(1)	1																		---	---	---	---
PRDX5	25824	broad.mit.edu	37	11	64088529	64088529	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64088529A>G	uc001nzu.2	+	5	647	c.528A>G	c.(526-528)CGA>CGG	p.R176R	PRDX5_uc001nzv.2_Silent_p.R132R|PRDX5_uc001nzw.2_Silent_p.R87R|PRDX5_uc001nzx.2_RNA	NM_012094	NP_036226	P30044	PRDX5_HUMAN	peroxiredoxin 5 isoform a precursor	176	Thioredoxin.				cell redox homeostasis|cellular response to reactive oxygen species|inflammatory response|negative regulation of apoptosis	cytosolic part|mitochondrion|peroxisome	caspase inhibitor activity|peroxidase activity|peroxiredoxin activity			breast(1)	1					Auranofin(DB00995)													---	---	---	---
SLC22A11	55867	broad.mit.edu	37	11	64335111	64335111	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64335111C>A	uc001oai.2	+	7	1473	c.1099C>A	c.(1099-1101)CTG>ATG	p.L367M	SLC22A11_uc001oaj.2_Missense_Mutation_p.L367M|SLC22A11_uc009ypq.2_Intron	NM_018484	NP_060954	Q9NSA0	S22AB_HUMAN	solute carrier family 22 member 11	367	Helical; (Potential).				urate metabolic process	apical plasma membrane|external side of plasma membrane|integral to plasma membrane	inorganic anion exchanger activity|protein binding|sodium-independent organic anion transmembrane transporter activity			ovary(1)|central_nervous_system(1)	2					Probenecid(DB01032)													---	---	---	---
SLC22A12	116085	broad.mit.edu	37	11	64360990	64360990	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64360990C>T	uc001oam.1	+	3	1367	c.620C>T	c.(619-621)GCC>GTC	p.A207V	SLC22A12_uc009ypr.1_Missense_Mutation_p.A207V|SLC22A12_uc001oal.1_Intron|SLC22A12_uc009yps.1_Intron|SLC22A12_uc001oan.1_Intron|SLC22A12_uc009ypt.2_Missense_Mutation_p.A25V	NM_144585	NP_653186	Q96S37	S22AC_HUMAN	urate anion exchanger 1 isoform a	207	Helical; (Potential).				cellular homeostasis|response to drug|urate metabolic process	apical plasma membrane|brush border membrane|integral to membrane	PDZ domain binding|urate transmembrane transporter activity			ovary(1)	1																		---	---	---	---
MAP4K2	5871	broad.mit.edu	37	11	64568378	64568378	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64568378G>T	uc001obh.2	-	9	748	c.656C>A	c.(655-657)CCC>CAC	p.P219H	MAP4K2_uc001obi.2_Missense_Mutation_p.P219H	NM_004579	NP_004570	Q12851	M4K2_HUMAN	mitogen-activated protein kinase kinase kinase	219	Protein kinase.				activation of JUN kinase activity|immune response|positive regulation of JNK cascade|vesicle targeting	basolateral plasma membrane|Golgi membrane|soluble fraction	ATP binding|mitogen-activated protein kinase kinase kinase binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(1)|pancreas(1)	2																		---	---	---	---
ATG2A	23130	broad.mit.edu	37	11	64677610	64677610	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64677610C>T	uc001obx.2	-	13	1880	c.1765G>A	c.(1765-1767)GCC>ACC	p.A589T		NM_015104	NP_055919	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	589							protein binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
ATG2A	23130	broad.mit.edu	37	11	64681357	64681357	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64681357C>T	uc001obx.2	-	4	641	c.526G>A	c.(526-528)GTG>ATG	p.V176M	ATG2A_uc010rnt.1_Missense_Mutation_p.V176M	NM_015104	NP_055919	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	176							protein binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
C11orf85	283129	broad.mit.edu	37	11	64717913	64717913	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64717913T>C	uc001ocb.1	-						C11orf85_uc001occ.1_Intron|C11orf85_uc001ocd.1_Intron	NM_001037225	NP_001032302			hypothetical protein LOC283129												0																		---	---	---	---
ZFPL1	7542	broad.mit.edu	37	11	64852645	64852645	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64852645G>A	uc001ocq.1	+	3	326	c.161G>A	c.(160-162)CGC>CAC	p.R54H	CDCA5_uc001ocp.2_5'Flank|ZFPL1_uc009yqa.2_Missense_Mutation_p.R54H|ZFPL1_uc010rnx.1_Missense_Mutation_p.R54H	NM_006782	NP_006773	O95159	ZFPL1_HUMAN	zinc finger protein-like 1	54	RING-type; degenerate.|Cytoplasmic (Potential).				regulation of transcription, DNA-dependent|vesicle-mediated transport	Golgi apparatus|integral to membrane|nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
ZFPL1	7542	broad.mit.edu	37	11	64854270	64854270	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64854270T>C	uc001ocq.1	+						CDCA5_uc001ocp.2_5'Flank	NM_006782	NP_006773			zinc finger protein-like 1						regulation of transcription, DNA-dependent|vesicle-mediated transport	Golgi apparatus|integral to membrane|nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
C11orf2	738	broad.mit.edu	37	11	64875106	64875106	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64875106C>T	uc001ocr.1	+	3	452	c.412C>T	c.(412-414)CGG>TGG	p.R138W	C11orf2_uc001ocs.1_Missense_Mutation_p.R14W	NM_013265	NP_037397	Q9UID3	FFR_HUMAN	chromosome 11 open reading frame 2	138	Potential.				lipid transport|protein transport	Golgi apparatus|integral to membrane					0																		---	---	---	---
FAU	2197	broad.mit.edu	37	11	64888201	64888201	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64888201G>A	uc001ocx.2	-	5	461	c.354C>T	c.(352-354)AAC>AAT	p.N118N	FAU_uc001ocy.1_3'UTR|MRPL49_uc001ocz.1_5'Flank|MRPL49_uc001oda.1_5'Flank	NM_001997	NP_001988	P35544	UBIM_HUMAN	ubiquitin-like protein fubi and ribosomal	Error:Variant_position_missing_in_P35544_after_alignment											0																		---	---	---	---
MRPL49	740	broad.mit.edu	37	11	64892055	64892055	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64892055G>A	uc001oda.1	+	2	251	c.160G>A	c.(160-162)GCT>ACT	p.A54T	FAU_uc001ocx.2_5'Flank|FAU_uc001ocy.1_5'Flank|MRPL49_uc001ocz.1_RNA	NM_004927	NP_004918	Q13405	RM49_HUMAN	mitochondrial ribosomal protein L49	54					translation	mitochondrial ribosome	protein binding|structural constituent of ribosome				0																		---	---	---	---
CAPN1	823	broad.mit.edu	37	11	64972319	64972319	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64972319C>T	uc009yqd.1	+	11	1442	c.1331C>T	c.(1330-1332)GCG>GTG	p.A444V	CAPN1_uc001odf.1_Missense_Mutation_p.A444V|CAPN1_uc001odg.1_Missense_Mutation_p.A444V|CAPN1_uc010roa.1_Missense_Mutation_p.A185V	NM_005186	NP_005177	P07384	CAN1_HUMAN	calpain 1, large subunit	444	Domain III.				positive regulation of cell proliferation|proteolysis	cytoplasm|plasma membrane	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity|protein binding			ovary(1)	1		Lung NSC(402;0.094)|Melanoma(852;0.16)		Lung(977;0.00168)|LUSC - Lung squamous cell carcinoma(976;0.00813)												OREG0021073	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SLC22A20	440044	broad.mit.edu	37	11	64981844	64981844	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64981844C>T	uc010roc.1	+	2	426	c.423C>T	c.(421-423)TCC>TCT	p.S141S	SLC22A20_uc010rob.1_Silent_p.S141S	NM_001004326	NP_001004326	A6NK97	S22AK_HUMAN	solute carrier family 22, member 20	141	Helical; (Potential).				ion transport	integral to membrane	transmembrane transporter activity			central_nervous_system(1)	1																		---	---	---	---
TIGD3	220359	broad.mit.edu	37	11	65124296	65124296	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65124296C>T	uc001odo.3	+	2	1180	c.1017C>T	c.(1015-1017)GAC>GAT	p.D339D		NM_145719	NP_663771	Q6B0B8	TIGD3_HUMAN	tigger transposable element derived 3	339	DDE.				regulation of transcription, DNA-dependent	chromosome, centromeric region|nucleus	DNA binding				0																		---	---	---	---
SLC25A45	283130	broad.mit.edu	37	11	65147628	65147628	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65147628A>G	uc001odp.1	-	2	478	c.56T>C	c.(55-57)CTG>CCG	p.L19P	SLC25A45_uc009yqi.1_Missense_Mutation_p.L19P|SLC25A45_uc001odq.1_Missense_Mutation_p.L19P|SLC25A45_uc001odr.1_Missense_Mutation_p.L19P|SLC25A45_uc001ods.1_5'UTR|SLC25A45_uc001odt.1_5'UTR	NM_001077241	NP_001070709	Q8N413	S2545_HUMAN	solute carrier family 25, member 45 isoform b	19	Solcar 1.|Helical; Name=1; (Potential).				transmembrane transport	integral to membrane|mitochondrial inner membrane	binding				0																		---	---	---	---
MALAT1	378938	broad.mit.edu	37	11	65270988	65270988	+	RNA	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65270988A>G	uc010roh.1	+	1		c.5756A>G			uc001ody.2_RNA|MALAT1_uc001odz.2_RNA	NR_002819				Homo sapiens clone alpha1 mRNA sequence.												0																		---	---	---	---
PCNXL3	399909	broad.mit.edu	37	11	65401745	65401745	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65401745T>A	uc001oey.2	+	28	4619	c.4619T>A	c.(4618-4620)CTC>CAC	p.L1540H	PCNXL3_uc001oez.2_Missense_Mutation_p.L427H	NM_032223	NP_115599	Q9H6A9	PCX3_HUMAN	pecanex-like 3	1540						integral to membrane					0																		---	---	---	---
RELA	5970	broad.mit.edu	37	11	65421979	65421979	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65421979C>T	uc001ofg.2	-	11	1666	c.1526G>A	c.(1525-1527)AGG>AAG	p.R509K	RELA_uc001ofh.2_Missense_Mutation_p.R506K|RELA_uc010ron.1_Missense_Mutation_p.R520K|RELA_uc009yqr.2_Missense_Mutation_p.R456K|RELA_uc001ofe.2_3'UTR|RELA_uc001off.2_Missense_Mutation_p.R406K	NM_021975	NP_068810	Q04206	TF65_HUMAN	v-rel reticuloendotheliosis viral oncogene	509					anti-apoptosis|cellular defense response|cytokine-mediated signaling pathway|defense response to virus|inflammatory response|innate immune response|interspecies interaction between organisms|membrane protein intracellular domain proteolysis|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription, DNA-dependent|nerve growth factor receptor signaling pathway|nucleotide-binding oligomerization domain containing 2 signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of inflammatory response|response to interleukin-1|response to UV-B|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|transcription factor complex	activating transcription factor binding|chromatin binding|identical protein binding|NF-kappaB binding|phosphate binding|protein kinase binding|protein N-terminus binding|repressing transcription factor binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|ubiquitin protein ligase binding			lung(3)|ovary(1)	4																		---	---	---	---
SNX32	254122	broad.mit.edu	37	11	65617489	65617489	+	Silent	SNP	C	T	T	rs146369776		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65617489C>T	uc001ofr.2	+	3	367	c.240C>T	c.(238-240)TAC>TAT	p.Y80Y	SNX32_uc009yqt.2_3'UTR|SNX32_uc010rop.1_Silent_p.Y80Y	NM_152760	NP_689973	Q86XE0	SNX32_HUMAN	sorting nexin 6B	80	PX.				cell communication|protein transport		phosphatidylinositol binding				0				READ - Rectum adenocarcinoma(159;0.171)														---	---	---	---
SART1	9092	broad.mit.edu	37	11	65746471	65746471	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65746471T>C	uc001ogl.2	+							NM_005146	NP_005137			squamous cell carcinoma antigen recognized by T						cell cycle arrest|induction of apoptosis by intracellular signals|positive regulation of cytotoxic T cell differentiation|spliceosomal snRNP assembly	Cajal body|catalytic step 2 spliceosome|cytosol				ovary(1)	1																		---	---	---	---
SF3B2	10992	broad.mit.edu	37	11	65831133	65831133	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65831133C>T	uc001ogy.1	+	19	2303	c.2263C>T	c.(2263-2265)CCT>TCT	p.P755S		NM_006842	NP_006833	Q13435	SF3B2_HUMAN	splicing factor 3B subunit 2	755					interspecies interaction between organisms	catalytic step 2 spliceosome|nucleoplasm|U12-type spliceosomal complex	nucleic acid binding|protein binding			ovary(2)|breast(1)	3																		---	---	---	---
KLC2	64837	broad.mit.edu	37	11	66032643	66032643	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66032643A>T	uc010rov.1	+	11	1514	c.1271A>T	c.(1270-1272)AAG>ATG	p.K424M	KLC2_uc010row.1_Missense_Mutation_p.K424M|KLC2_uc009yra.2_Intron|KLC2_uc001ohb.2_Missense_Mutation_p.K424M|KLC2_uc010rox.1_Missense_Mutation_p.K347M|KLC2_uc001ohc.2_Missense_Mutation_p.K424M|KLC2_uc001ohd.2_Missense_Mutation_p.K347M|KLC2_uc001ohe.1_Missense_Mutation_p.K285M	NM_001134775	NP_001128247	Q9H0B6	KLC2_HUMAN	kinesin light chain 2 isoform 1	424					blood coagulation	cytosol|kinesin complex|microtubule	microtubule motor activity|protein binding				0																OREG0021098	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
YIF1A	10897	broad.mit.edu	37	11	66052968	66052968	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66052968C>T	uc001ohk.3	-	6	707	c.525G>A	c.(523-525)GCG>GCA	p.A175A	YIF1A_uc001ohj.2_Silent_p.A32A	NM_020470	NP_065203	O95070	YIF1A_HUMAN	Yip1 interacting factor homolog	175	Helical; (Potential).				protein transport|vesicle-mediated transport	centrosome|endoplasmic reticulum membrane|ER-Golgi intermediate compartment|Golgi membrane|integral to membrane					0																		---	---	---	---
NPAS4	266743	broad.mit.edu	37	11	66190698	66190698	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66190698G>A	uc001ohx.1	+	5	979	c.803G>A	c.(802-804)CGC>CAC	p.R268H	NPAS4_uc010rpc.1_Intron	NM_178864	NP_849195	Q8IUM7	NPAS4_HUMAN	neuronal PAS domain protein 4	268	PAS 2.				transcription, DNA-dependent		DNA binding|signal transducer activity				0																		---	---	---	---
NPAS4	266743	broad.mit.edu	37	11	66191979	66191979	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66191979G>T	uc001ohx.1	+	7	1794	c.1618G>T	c.(1618-1620)GCA>TCA	p.A540S	NPAS4_uc010rpc.1_Missense_Mutation_p.A330S	NM_178864	NP_849195	Q8IUM7	NPAS4_HUMAN	neuronal PAS domain protein 4	540					transcription, DNA-dependent		DNA binding|signal transducer activity				0																		---	---	---	---
DPP3	10072	broad.mit.edu	37	11	66261008	66261008	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66261008G>A	uc001oig.1	+						DPP3_uc001oif.1_Intron|DPP3_uc010rpe.1_Intron	NM_005700	NP_005691			dipeptidyl peptidase III						proteolysis	cytoplasm	aminopeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metallopeptidase activity			ovary(1)|skin(1)	2																		---	---	---	---
BBS1	582	broad.mit.edu	37	11	66278531	66278531	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66278531C>T	uc001oij.1	+	2	107	c.95C>T	c.(94-96)GCC>GTC	p.A32V	BBS1_uc001oii.1_Missense_Mutation_p.A69V|BBS1_uc010rpf.1_RNA|BBS1_uc010rpg.1_Missense_Mutation_p.A32V|BBS1_uc001oik.1_5'UTR|BBS1_uc001oil.1_Missense_Mutation_p.A32V	NM_024649	NP_078925	Q8NFJ9	BBS1_HUMAN	Bardet-Biedl syndrome 1	32					nonmotile primary cilium assembly|photoreceptor cell maintenance|response to stimulus|retina homeostasis	BBSome|cilium membrane|cytoplasm	protein binding			ovary(1)	1														Bardet-Biedl_syndrome				---	---	---	---
ACTN3	89	broad.mit.edu	37	11	66326809	66326809	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66326809C>T	uc001oio.1	+	12	1397	c.1379C>T	c.(1378-1380)GCG>GTG	p.A460V	ACTN3_uc010rpi.1_RNA	NM_001104	NP_001095	Q08043	ACTN3_HUMAN	actinin, alpha 3	460	Spectrin 2.				focal adhesion assembly|muscle filament sliding|regulation of apoptosis	actin filament|cytosol|focal adhesion|pseudopodium	actin binding|calcium ion binding|integrin binding|protein homodimerization activity|structural constituent of muscle				0																		---	---	---	---
SPTBN2	6712	broad.mit.edu	37	11	66456277	66456277	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66456277C>A	uc001ojd.2	-	30	6150	c.6078G>T	c.(6076-6078)GAG>GAT	p.E2026D	SPTBN2_uc001ojc.1_5'Flank	NM_006946	NP_008877	O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	2026	Spectrin 17.				actin filament capping|axon guidance|cell death|vesicle-mediated transport	cytosol|spectrin	actin binding|structural constituent of cytoskeleton			large_intestine(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
SPTBN2	6712	broad.mit.edu	37	11	66475201	66475201	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66475201C>T	uc001ojd.2	-	12	1511	c.1439G>A	c.(1438-1440)CGG>CAG	p.R480Q		NM_006946	NP_008877	O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	480	Spectrin 2.				actin filament capping|axon guidance|cell death|vesicle-mediated transport	cytosol|spectrin	actin binding|structural constituent of cytoskeleton	p.R480W(1)		large_intestine(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
SYT12	91683	broad.mit.edu	37	11	66813300	66813300	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66813300G>A	uc009yrl.2	+	7	1274	c.1044G>A	c.(1042-1044)CCG>CCA	p.P348P	SYT12_uc001oju.2_Silent_p.P348P	NM_177963	NP_808878	Q8IV01	SYT12_HUMAN	synaptotagmin XII	348	C2 2.|Cytoplasmic (Potential).					cell junction|integral to membrane|synaptic vesicle membrane				ovary(1)	1																		---	---	---	---
PITPNM1	9600	broad.mit.edu	37	11	67269771	67269771	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67269771C>T	uc001olx.2	-	3	596	c.407G>A	c.(406-408)CGC>CAC	p.R136H	PITPNM1_uc001oly.2_Missense_Mutation_p.R136H|PITPNM1_uc001olz.2_Missense_Mutation_p.R136H	NM_004910	NP_004901	O00562	PITM1_HUMAN	phosphatidylinositol transfer protein,	136					brain development|lipid metabolic process|phototransduction|protein transport	cleavage furrow|endoplasmic reticulum membrane|Golgi cisterna membrane|lipid particle|membrane fraction|midbody	metal ion binding|phosphatidylinositol transporter activity			lung(2)|central_nervous_system(1)	3																		---	---	---	---
TBX10	347853	broad.mit.edu	37	11	67399148	67399148	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67399148C>T	uc001omp.2	-	8	1174	c.1086G>A	c.(1084-1086)CTG>CTA	p.L362L	NUDT8_uc001omn.2_5'Flank|NUDT8_uc001omo.1_5'Flank	NM_005995	NP_005986	O75333	TBX10_HUMAN	T-box 10	362					anatomical structure morphogenesis|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
LRP5	4041	broad.mit.edu	37	11	68177484	68177484	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68177484C>A	uc001ont.2	+	10	2269	c.2194C>A	c.(2194-2196)CTC>ATC	p.L732I	LRP5_uc009ysg.2_Missense_Mutation_p.L142I	NM_002335	NP_002326	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein	732	LDL-receptor class B 12.|Beta-propeller 3.|Extracellular (Potential).				adipose tissue development|bone marrow development|bone morphogenesis|canonical Wnt receptor signaling pathway|cholesterol homeostasis|endocytosis|glucose catabolic process|negative regulation of osteoblast differentiation|negative regulation of protein serine/threonine kinase activity|positive regulation of fat cell differentiation|positive regulation of mesenchymal cell proliferation|positive regulation of mitosis|positive regulation of transcription from RNA polymerase II promoter|regulation of blood pressure|regulation of canonical Wnt receptor signaling pathway|retina morphogenesis in camera-type eye|retinal blood vessel morphogenesis|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	endoplasmic reticulum|integral to membrane|plasma membrane|receptor complex	protein binding|receptor activity			lung(2)|skin(2)|ovary(1)|pancreas(1)|breast(1)	7																		---	---	---	---
SAPS3	55291	broad.mit.edu	37	11	68343476	68343476	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68343476T>G	uc001onw.2	+	14	1777	c.1510T>G	c.(1510-1512)TTA>GTA	p.L504V	SAPS3_uc001onv.2_Missense_Mutation_p.L504V|SAPS3_uc001ony.3_Missense_Mutation_p.L504V|SAPS3_uc001onx.2_Missense_Mutation_p.L504V|SAPS3_uc009ysh.2_Missense_Mutation_p.L453V|SAPS3_uc001onu.2_Missense_Mutation_p.L453V|SAPS3_uc010rqc.1_Missense_Mutation_p.L272V|SAPS3_uc010rqd.1_Missense_Mutation_p.L216V|SAPS3_uc001onz.2_5'UTR	NM_001164161	NP_001157633	Q5H9R7	PP6R3_HUMAN	SAPS domain family, member 3 isoform 6	504					regulation of phosphoprotein phosphatase activity	cytoplasm|nucleus	protein phosphatase binding				0			LUAD - Lung adenocarcinoma(13;0.102)															---	---	---	---
SAPS3	55291	broad.mit.edu	37	11	68377453	68377453	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68377453C>T	uc001onw.2	+	23	2799	c.2532C>T	c.(2530-2532)TGC>TGT	p.C844C	SAPS3_uc001onv.2_Silent_p.C850C|SAPS3_uc001ony.3_Silent_p.C815C|SAPS3_uc001onx.2_Silent_p.C838C|SAPS3_uc009ysh.2_Silent_p.C764C|SAPS3_uc001onu.2_Silent_p.C764C|SAPS3_uc010rqc.1_Silent_p.C612C|SAPS3_uc010rqd.1_Silent_p.C527C|SAPS3_uc001onz.2_Silent_p.C172C|SAPS3_uc001ooa.2_Silent_p.C300C	NM_001164161	NP_001157633	Q5H9R7	PP6R3_HUMAN	SAPS domain family, member 3 isoform 6	844					regulation of phosphoprotein phosphatase activity	cytoplasm|nucleus	protein phosphatase binding				0			LUAD - Lung adenocarcinoma(13;0.102)															---	---	---	---
IGHMBP2	3508	broad.mit.edu	37	11	68682369	68682369	+	Missense_Mutation	SNP	C	T	T	rs139497493	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68682369C>T	uc001ook.1	+	6	892	c.790C>T	c.(790-792)CGC>TGC	p.R264C	IGHMBP2_uc001ooj.1_RNA	NM_002180	NP_002171	P38935	SMBP2_HUMAN	immunoglobulin mu binding protein 2	264	Leu-rich.				cell death|DNA recombination|DNA repair|DNA replication|protein homooligomerization|transcription, DNA-dependent|translation	axon|growth cone|nucleus|ribonucleoprotein complex	ATP binding|ATP-dependent 5'-3' DNA helicase activity|ATP-dependent 5'-3' RNA helicase activity|ribosome binding|single-stranded DNA binding|transcription factor binding|tRNA binding|zinc ion binding				0			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)															---	---	---	---
SHANK2	22941	broad.mit.edu	37	11	70331640	70331640	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70331640C>T	uc001oqc.2	-	21	4836	c.4758G>A	c.(4756-4758)CCG>CCA	p.P1586P	SHANK2_uc010rqn.1_Silent_p.P998P|SHANK2_uc001opz.2_Silent_p.P991P|uc009ysn.1_Intron|SHANK2_uc001opy.2_Intron	NM_012309	NP_036441	Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2	1207					intracellular signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	GKAP/Homer scaffold activity|ionotropic glutamate receptor binding|SH3 domain binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)															---	---	---	---
SHANK2	22941	broad.mit.edu	37	11	70331658	70331658	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70331658G>A	uc001oqc.2	-	21	4818	c.4740C>T	c.(4738-4740)CCC>CCT	p.P1580P	SHANK2_uc010rqn.1_Silent_p.P992P|SHANK2_uc001opz.2_Silent_p.P985P|uc009ysn.1_Intron|SHANK2_uc001opy.2_Intron	NM_012309	NP_036441	Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2	1201					intracellular signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	GKAP/Homer scaffold activity|ionotropic glutamate receptor binding|SH3 domain binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)															---	---	---	---
SHANK2	22941	broad.mit.edu	37	11	70333161	70333161	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70333161G>A	uc001oqc.2	-	21	3315	c.3237C>T	c.(3235-3237)GCC>GCT	p.A1079A	SHANK2_uc010rqn.1_Silent_p.A491A|SHANK2_uc001opz.2_Silent_p.A484A|uc009ysn.1_Intron|SHANK2_uc001opy.2_Intron	NM_012309	NP_036441	Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2	700					intracellular signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	GKAP/Homer scaffold activity|ionotropic glutamate receptor binding|SH3 domain binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)															---	---	---	---
SHANK2	22941	broad.mit.edu	37	11	70507706	70507706	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70507706G>A	uc001oqc.2	-	13	2009	c.1931C>T	c.(1930-1932)GCC>GTC	p.A644V	SHANK2_uc010rqn.1_Missense_Mutation_p.A56V|SHANK2_uc001opz.2_Missense_Mutation_p.A56V|uc009ysn.1_Intron|SHANK2_uc010rqp.1_Missense_Mutation_p.A56V	NM_012309	NP_036441	Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2	265	PDZ.				intracellular signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	GKAP/Homer scaffold activity|ionotropic glutamate receptor binding|SH3 domain binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)															---	---	---	---
NADSYN1	55191	broad.mit.edu	37	11	71174472	71174472	+	Intron	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71174472C>A	uc001oqn.2	+						NADSYN1_uc001oqm.2_Intron|NADSYN1_uc001oqo.2_Intron	NM_018161	NP_060631			NAD synthetase 1						NAD biosynthetic process|water-soluble vitamin metabolic process	cytosol	ATP binding|hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds|NAD+ synthase (glutamine-hydrolyzing) activity|protein binding			ovary(2)	2					L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)													---	---	---	---
NADSYN1	55191	broad.mit.edu	37	11	71175152	71175152	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71175152G>A	uc001oqn.2	+	5	497	c.371G>A	c.(370-372)CGC>CAC	p.R124H	NADSYN1_uc001oqm.2_RNA|NADSYN1_uc001oqo.2_5'UTR	NM_018161	NP_060631	Q6IA69	NADE_HUMAN	NAD synthetase 1	124	CN hydrolase.				NAD biosynthetic process|water-soluble vitamin metabolic process	cytosol	ATP binding|hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds|NAD+ synthase (glutamine-hydrolyzing) activity|protein binding			ovary(2)	2					L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)													---	---	---	---
NADSYN1	55191	broad.mit.edu	37	11	71184685	71184685	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71184685C>T	uc001oqn.2	+	8	745	c.619C>T	c.(619-621)CGC>TGC	p.R207C	NADSYN1_uc001oqm.2_RNA|NADSYN1_uc001oqo.2_5'UTR	NM_018161	NP_060631	Q6IA69	NADE_HUMAN	NAD synthetase 1	207	CN hydrolase.			R -> H (in Ref. 3; CAG33567).	NAD biosynthetic process|water-soluble vitamin metabolic process	cytosol	ATP binding|hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds|NAD+ synthase (glutamine-hydrolyzing) activity|protein binding			ovary(2)	2					L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)													---	---	---	---
NUMA1	4926	broad.mit.edu	37	11	71724131	71724131	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71724131C>G	uc001orl.1	-	15	4590	c.4418G>C	c.(4417-4419)CGG>CCG	p.R1473P	NUMA1_uc009ysw.1_Missense_Mutation_p.R1036P|NUMA1_uc001ork.1_Intron|NUMA1_uc001orm.1_Missense_Mutation_p.R1473P|NUMA1_uc001orn.2_Missense_Mutation_p.R1036P|NUMA1_uc009ysx.1_Missense_Mutation_p.R1473P|NUMA1_uc001oro.1_Missense_Mutation_p.R1473P	NM_006185	NP_006176	Q14980	NUMA1_HUMAN	nuclear mitotic apparatus protein 1	1473	Potential.				G2/M transition of mitotic cell cycle|mitotic anaphase|nucleus organization	chromosome|cytosol|nucleoplasm|spindle microtubule|spindle pole	protein binding|structural molecule activity			ovary(3)|lung(2)|skin(2)|central_nervous_system(1)	8								T	RARA	APL								---	---	---	---
NUMA1	4926	broad.mit.edu	37	11	71727513	71727513	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71727513A>G	uc001orl.1	-	14	1355	c.1183T>C	c.(1183-1185)TCC>CCC	p.S395P	NUMA1_uc009ysw.1_5'Flank|NUMA1_uc001ork.1_Missense_Mutation_p.S395P|NUMA1_uc001orm.1_Missense_Mutation_p.S395P|NUMA1_uc001orn.2_5'Flank|NUMA1_uc009ysx.1_Missense_Mutation_p.S395P|NUMA1_uc001oro.1_Missense_Mutation_p.S395P	NM_006185	NP_006176	Q14980	NUMA1_HUMAN	nuclear mitotic apparatus protein 1	395	Potential.				G2/M transition of mitotic cell cycle|mitotic anaphase|nucleus organization	chromosome|cytosol|nucleoplasm|spindle microtubule|spindle pole	protein binding|structural molecule activity			ovary(3)|lung(2)|skin(2)|central_nervous_system(1)	8								T	RARA	APL								---	---	---	---
LRTOMT	220074	broad.mit.edu	37	11	71804586	71804586	+	Missense_Mutation	SNP	C	T	T	rs146300359		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:71804586C>T	uc001orr.2	+	4	505	c.127C>T	c.(127-129)CGT>TGT	p.R43C	LRTOMT_uc009ysz.2_RNA|LRTOMT_uc010rqt.1_Missense_Mutation_p.R43C|LRTOMT_uc010rqu.1_Missense_Mutation_p.R25C|LRTOMT_uc009yta.2_Intron|LRTOMT_uc010rqv.1_5'UTR|LRTOMT_uc010rqw.1_5'UTR|LRTOMT_uc001ors.3_5'UTR|LRTOMT_uc010rqs.1_Missense_Mutation_p.R43C	NM_145309	NP_660352	Q96E66	LRC51_HUMAN	leucine rich transmembrane and	43						cytoplasm					0																		---	---	---	---
ARHGEF17	9828	broad.mit.edu	37	11	73067400	73067400	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73067400C>T	uc001otu.2	+							NM_014786	NP_055601			Rho guanine nucleotide exchange factor (GEF) 17						actin cytoskeleton organization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity				0																		---	---	---	---
ARHGEF17	9828	broad.mit.edu	37	11	73074799	73074799	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73074799G>A	uc001otu.2	+	16	5275	c.5254G>A	c.(5254-5256)GTG>ATG	p.V1752M		NM_014786	NP_055601	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	1752					actin cytoskeleton organization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity				0																		---	---	---	---
C2CD3	26005	broad.mit.edu	37	11	73814214	73814214	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73814214C>T	uc001ouu.2	-	14	2769	c.2542G>A	c.(2542-2544)GCA>ACA	p.A848T		NM_015531	NP_056346	Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	848						centrosome				ovary(4)|pancreas(2)|skin(1)	7	Breast(11;4.16e-06)																	---	---	---	---
P4HA3	283208	broad.mit.edu	37	11	73988195	73988195	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73988195A>G	uc001ouz.2	-						P4HA3_uc001ouy.3_Intron|P4HA3_uc010rrj.1_Intron	NM_182904	NP_878907			prolyl 4-hydroxylase, alpha III subunit							endoplasmic reticulum lumen	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-proline 4-dioxygenase activity			skin(1)	1	Breast(11;2.31e-05)																	---	---	---	---
SERPINH1	871	broad.mit.edu	37	11	75277622	75277622	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75277622G>A	uc001owr.2	+	2	457	c.228G>A	c.(226-228)TCG>TCA	p.S76S	SERPINH1_uc009yuf.2_Silent_p.S76S|SERPINH1_uc009yug.2_Silent_p.S76S|SERPINH1_uc001ows.2_Silent_p.S76S|SERPINH1_uc001owt.2_5'Flank	NM_001235	NP_001226	P50454	SERPH_HUMAN	serine (or cysteine) proteinase inhibitor, clade	76					regulation of proteolysis|response to unfolded protein	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	collagen binding|serine-type endopeptidase inhibitor activity			ovary(2)	2	Ovarian(111;0.11)																	---	---	---	---
MOGAT2	80168	broad.mit.edu	37	11	75428978	75428978	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:75428978G>A	uc010rru.1	+	1	45	c.45G>A	c.(43-45)CTG>CTA	p.L15L	MOGAT2_uc001oww.1_Silent_p.L15L|MOGAT2_uc010rrv.1_5'Flank	NM_025098	NP_079374	Q3SYC2	MOGT2_HUMAN	monoacylglycerol O-acyltransferase 2	15					glycerol metabolic process	endoplasmic reticulum membrane|integral to membrane	2-acylglycerol O-acyltransferase activity			ovary(2)	2	Ovarian(111;0.103)																	---	---	---	---
PRKRIR	5612	broad.mit.edu	37	11	76063421	76063421	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76063421T>C	uc001oxh.1	-	5	773	c.773A>G	c.(772-774)CAC>CGC	p.H258R	PRKRIR_uc010rrz.1_Missense_Mutation_p.H83R	NM_004705	NP_004696	O43422	P52K_HUMAN	protein-kinase, interferon-inducible double	258					negative regulation of cell proliferation|response to stress|signal transduction		DNA binding|metal ion binding|protein dimerization activity			ovary(2)|pancreas(1)	3																		---	---	---	---
LRRC32	2615	broad.mit.edu	37	11	76372336	76372336	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76372336G>A	uc001oxq.3	-	3	544	c.301C>T	c.(301-303)CAC>TAC	p.H101Y	LRRC32_uc001oxr.3_Missense_Mutation_p.H101Y|LRRC32_uc010rsf.1_Missense_Mutation_p.H101Y	NM_005512	NP_005503	Q14392	LRC32_HUMAN	leucine rich repeat containing 32 precursor	101	LRR 3.|Extracellular (Potential).					integral to plasma membrane					0																		---	---	---	---
INTS4	92105	broad.mit.edu	37	11	77649761	77649761	+	Silent	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77649761A>T	uc001oys.2	-	10	1129	c.1101T>A	c.(1099-1101)GCT>GCA	p.A367A	INTS4_uc001oyt.2_RNA|INTS4_uc001oyu.1_Silent_p.A367A	NM_033547	NP_291025	Q96HW7	INT4_HUMAN	integrator complex subunit 4	367					snRNA processing	integrator complex	protein binding			ovary(2)	2	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)															---	---	---	---
ODZ4	26011	broad.mit.edu	37	11	78383286	78383286	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:78383286C>T	uc001ozl.3	-	31	6048	c.5585G>A	c.(5584-5586)CGG>CAG	p.R1862Q	ODZ4_uc001ozk.3_Missense_Mutation_p.R87Q|ODZ4_uc009yvb.1_Missense_Mutation_p.R446Q	NM_001098816	NP_001092286	Q6N022	TEN4_HUMAN	odz, odd Oz/ten-m homolog 4	1862	Extracellular (Potential).				signal transduction	integral to membrane				ovary(2)|pancreas(2)	4																		---	---	---	---
C11orf82	220042	broad.mit.edu	37	11	82644478	82644478	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82644478A>C	uc001ozt.2	+	6	2342	c.2098A>C	c.(2098-2100)ATT>CTT	p.I700L	C11orf82_uc010rsr.1_Missense_Mutation_p.I399L|C11orf82_uc010rss.1_Missense_Mutation_p.I399L|C11orf82_uc009yvd.2_Intron	NM_145018	NP_659455	Q8IXT1	NOXIN_HUMAN	nitric oxide-inducible gene protein	700					apoptosis|cell cycle arrest	cytoplasm|nucleus				ovary(2)	2																		---	---	---	---
PCF11	51585	broad.mit.edu	37	11	82877600	82877600	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82877600A>G	uc001ozx.3	+	5	2006	c.1661A>G	c.(1660-1662)GAT>GGT	p.D554G	PCF11_uc010rsu.1_Missense_Mutation_p.D554G	NM_015885	NP_056969	O94913	PCF11_HUMAN	pre-mRNA cleavage complex II protein Pcf11	554					mRNA 3'-end processing|mRNA cleavage|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage factor complex				ovary(1)	1																		---	---	---	---
PCF11	51585	broad.mit.edu	37	11	82882871	82882871	+	Silent	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:82882871T>G	uc001ozx.3	+	9	4017	c.3672T>G	c.(3670-3672)GGT>GGG	p.G1224G		NM_015885	NP_056969	O94913	PCF11_HUMAN	pre-mRNA cleavage complex II protein Pcf11	1224					mRNA 3'-end processing|mRNA cleavage|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage factor complex				ovary(1)	1																		---	---	---	---
DLG2	1740	broad.mit.edu	37	11	83673939	83673939	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83673939G>A	uc001paj.2	-	9	1317	c.1014C>T	c.(1012-1014)GAC>GAT	p.D338D	DLG2_uc001pai.2_Silent_p.D287D|DLG2_uc010rsy.1_Silent_p.D305D|DLG2_uc010rsz.1_Silent_p.D338D|DLG2_uc010rta.1_Silent_p.D338D|DLG2_uc001pak.2_Silent_p.D443D|DLG2_uc010rtb.1_Silent_p.D305D|DLG2_uc001pal.1_Silent_p.D338D|DLG2_uc001pam.1_Silent_p.D377D	NM_001364	NP_001355	Q15700	DLG2_HUMAN	chapsyn-110 isoform 2	338						cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)																---	---	---	---
SYTL2	54843	broad.mit.edu	37	11	85429849	85429849	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85429849C>T	uc010rth.1	-	9	1875	c.1599G>A	c.(1597-1599)GTG>GTA	p.V533V	SYTL2_uc010rtg.1_Silent_p.V534V|SYTL2_uc010rti.1_Silent_p.V533V|SYTL2_uc010rtj.1_Silent_p.V485V|SYTL2_uc010rte.1_5'UTR|SYTL2_uc001pax.2_5'UTR|SYTL2_uc001paz.2_5'UTR|SYTL2_uc001pba.2_5'UTR|SYTL2_uc001pay.2_5'UTR|SYTL2_uc001paw.2_5'UTR|SYTL2_uc009yvj.2_RNA|SYTL2_uc001pbd.2_Silent_p.V855V|SYTL2_uc001pbb.2_Silent_p.V855V|SYTL2_uc001pbc.2_Silent_p.V855V|SYTL2_uc010rtf.1_Silent_p.V391V	NM_001162951	NP_001156423	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2 isoform g	533					intracellular protein transport|vesicle docking involved in exocytosis	exocytic vesicle|extrinsic to plasma membrane|melanosome|membrane fraction	neurexin binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylserine binding|Rab GTPase binding			ovary(2)|large_intestine(1)	3		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)														---	---	---	---
PICALM	8301	broad.mit.edu	37	11	85692221	85692221	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:85692221T>C	uc001pbm.2	-	17	2016	c.1730A>G	c.(1729-1731)AAC>AGC	p.N577S	PICALM_uc001pbl.2_Missense_Mutation_p.N527S|PICALM_uc001pbn.2_Missense_Mutation_p.N570S|PICALM_uc010rtl.1_Missense_Mutation_p.N476S|PICALM_uc001pbk.2_RNA|PICALM_uc010rtk.1_Missense_Mutation_p.N154S|PICALM_uc001pbo.1_Missense_Mutation_p.N209S	NM_007166	NP_009097	Q13492	PICAL_HUMAN	phosphatidylinositol-binding clathrin assembly	577					clathrin coat assembly|endosome transport|negative regulation of receptor-mediated endocytosis|positive regulation of transcription, DNA-dependent|receptor internalization|regulation of protein localization	clathrin coat|clathrin-coated vesicle|coated pit|Golgi apparatus|nucleus|postsynaptic membrane|presynaptic membrane	1-phosphatidylinositol binding|clathrin heavy chain binding			urinary_tract(1)|ovary(1)	2		Acute lymphoblastic leukemia(157;7.42e-07)|all_hematologic(158;0.00092)						T	MLLT10|MLL	TALL|AML|								---	---	---	---
ME3	10873	broad.mit.edu	37	11	86270824	86270824	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:86270824G>A	uc001pbz.2	-	2	479	c.225C>T	c.(223-225)ATC>ATT	p.I75I	ME3_uc001pca.2_Silent_p.I75I|ME3_uc009yvk.2_Silent_p.I75I|ME3_uc010rtr.1_RNA	NM_001014811	NP_001014811	Q16798	MAON_HUMAN	mitochondrial malic enzyme 3 precursor	75					aerobic respiration|malate metabolic process|oxygen metabolic process|pyruvate metabolic process	mitochondrial matrix	malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) activity|metal ion binding|NAD binding			ovary(1)	1		Acute lymphoblastic leukemia(157;4.34e-06)|all_hematologic(158;0.00252)			NADH(DB00157)													---	---	---	---
CTSC	1075	broad.mit.edu	37	11	88029401	88029401	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:88029401A>G	uc001pck.3	-	6	890	c.789T>C	c.(787-789)TCT>TCC	p.S263S	CTSC_uc001pcl.3_Silent_p.S115S	NM_001814	NP_001805	P53634	CATC_HUMAN	cathepsin C isoform a preproprotein	263					immune response	lysosome	cysteine-type endopeptidase activity				0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)																---	---	---	---
GRM5	2915	broad.mit.edu	37	11	88300345	88300345	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:88300345C>T	uc001pcq.2	-	7	2706	c.2506G>A	c.(2506-2508)GCC>ACC	p.A836T	GRM5_uc009yvm.2_Missense_Mutation_p.A836T	NM_001143831	NP_001137303	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5 isoform a	836	Cytoplasmic (Potential).				activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway|synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			central_nervous_system(4)|ovary(2)|lung(2)|breast(1)	9		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)													---	---	---	---
FAT3	120114	broad.mit.edu	37	11	92534123	92534123	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92534123C>T	uc001pdj.3	+	9	7961	c.7944C>T	c.(7942-7944)GCC>GCT	p.A2648A		NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	2648	Cadherin 24.|Extracellular (Potential).				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)													TCGA Ovarian(4;0.039)			---	---	---	---
FAT3	120114	broad.mit.edu	37	11	92577151	92577151	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92577151C>T	uc001pdj.3	+	18	10635	c.10618C>T	c.(10618-10620)CGA>TGA	p.R3540*	FAT3_uc001pdi.3_5'UTR	NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	3540	Cadherin 32.|Extracellular (Potential).				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)													TCGA Ovarian(4;0.039)			---	---	---	---
HEPHL1	341208	broad.mit.edu	37	11	93796832	93796832	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93796832G>A	uc001pep.2	+	3	731	c.574G>A	c.(574-576)GCC>ACC	p.A192T		NM_001098672	NP_001092142	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1 precursor	192	Plastocyanin-like 1.|Extracellular (Potential).				copper ion transport	integral to membrane	copper ion binding|oxidoreductase activity			ovary(3)	3		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)																---	---	---	---
HEPHL1	341208	broad.mit.edu	37	11	93844939	93844939	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93844939T>C	uc001pep.2	+	20	3516	c.3359T>C	c.(3358-3360)TTC>TCC	p.F1120S	uc001pen.1_Intron	NM_001098672	NP_001092142	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1 precursor	1120	Helical; (Potential).				copper ion transport	integral to membrane	copper ion binding|oxidoreductase activity			ovary(3)	3		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)																---	---	---	---
FOLR4	390243	broad.mit.edu	37	11	94040719	94040719	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:94040719G>A	uc010rud.1	+	4	593	c.593G>A	c.(592-594)CGG>CAG	p.R198Q		NM_001080486	NP_001073955	A6ND01	FOLR4_HUMAN	folate receptor 4 (delta) homolog	205						extracellular region	folic acid binding|receptor activity			ovary(1)	1																		---	---	---	---
BIRC3	330	broad.mit.edu	37	11	102206765	102206765	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102206765C>A	uc001pgx.2	+	8	1615	c.1393C>A	c.(1393-1395)CTG>ATG	p.L465M		NM_182962	NP_892007	Q13489	BIRC3_HUMAN	baculoviral IAP repeat-containing protein 3	465	CARD.				anti-apoptosis|apoptosis|cell surface receptor linked signaling pathway	cytoplasm|nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|skin(1)	4	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0146)				T	MALT1	MALT								---	---	---	---
MMP12	4321	broad.mit.edu	37	11	102736657	102736657	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102736657T>C	uc001phk.2	-	9	1100	c.1055A>G	c.(1054-1056)TAC>TGC	p.Y352C		NM_002426	NP_002417	P39900	MMP12_HUMAN	matrix metalloproteinase 12 preproprotein	352	Hemopexin-like 2.				positive regulation of epithelial cell proliferation involved in wound healing|proteolysis|wound healing, spreading of epidermal cells	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding				0		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.014)	Acetohydroxamic Acid(DB00551)													---	---	---	---
DYNC2H1	79659	broad.mit.edu	37	11	102988484	102988484	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102988484C>T	uc001pho.2	+	6	1035	c.891C>T	c.(889-891)GTC>GTT	p.V297V	DYNC2H1_uc001phn.1_Silent_p.V297V|DYNC2H1_uc009yxe.1_Silent_p.V297V	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	297	Stem (By similarity).				cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)														---	---	---	---
DYNC2H1	79659	broad.mit.edu	37	11	103270505	103270505	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:103270505C>A	uc001pho.2	+	84	12415	c.12271C>A	c.(12271-12273)CAC>AAC	p.H4091N	DYNC2H1_uc001phn.1_Missense_Mutation_p.H4098N|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	4091					cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)														---	---	---	---
CASP1	834	broad.mit.edu	37	11	104901116	104901116	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104901116T>G	uc010rve.1	-	5	585	c.568A>C	c.(568-570)ACA>CCA	p.T190P	CASP1_uc001pig.2_Missense_Mutation_p.T97P|CASP1_uc001pik.2_Missense_Mutation_p.T153P|CASP1_uc010rvf.1_Missense_Mutation_p.T97P|CASP1_uc010rvg.1_Missense_Mutation_p.T169P|CASP1_uc010rvh.1_Missense_Mutation_p.T97P|CASP1_uc010rvi.1_Intron|CASP1_uc001pim.3_Missense_Mutation_p.T190P|CASP1_uc009yxi.2_Missense_Mutation_p.T169P|CASP1_uc010rvj.1_Missense_Mutation_p.T190P|CASP1_uc009yxj.2_Missense_Mutation_p.T35P|CASP1_uc010rvk.1_Missense_Mutation_p.T151P	NM_033292	NP_150634	P29466	CASP1_HUMAN	caspase 1 isoform alpha precursor	190					cellular response to mechanical stimulus|cellular response to organic substance|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteolysis|signal transduction	cytosol	caspase activator activity|cysteine-type endopeptidase activity|protein binding			ovary(2)	2		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000525)|Epithelial(105;0.0128)|all cancers(92;0.0482)	Minocycline(DB01017)|Penicillamine(DB00859)													---	---	---	---
CARD17	440068	broad.mit.edu	37	11	104971503	104971503	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:104971503T>G	uc001pir.1	-	2	28	c.11A>C	c.(10-12)AAG>ACG	p.K4T	CASP1_uc010rve.1_Intron|CASP1_uc010rvf.1_Intron|CASP1_uc010rvg.1_Intron|CASP1_uc010rvh.1_Intron|CASP1_uc010rvi.1_Intron	NM_001007232	NP_001007233	Q5XLA6	CAR17_HUMAN	caspase recruitment domain family, member 17	4	CARD.				proteolysis|regulation of apoptosis	cytoplasm	cysteine-type endopeptidase activity|cysteine-type endopeptidase inhibitor activity			ovary(1)	1																		---	---	---	---
GRIA4	2893	broad.mit.edu	37	11	105732740	105732740	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105732740T>C	uc001pix.2	+						GRIA4_uc001piu.1_Intron|GRIA4_uc001piw.2_Intron|GRIA4_uc001piv.2_Intron|GRIA4_uc009yxk.1_Intron	NM_000829	NP_000820			glutamate receptor, ionotrophic, AMPA 4 isoform						glutamate signaling pathway|synaptic transmission	cell junction|endocytic vesicle membrane|integral to membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)	L-Glutamic Acid(DB00142)													---	---	---	---
GRIA4	2893	broad.mit.edu	37	11	105804547	105804547	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:105804547C>T	uc001pix.2	+	14	2592	c.2146C>T	c.(2146-2148)CGC>TGC	p.R716C	GRIA4_uc001piw.2_Missense_Mutation_p.R716C|GRIA4_uc010rvm.1_RNA|GRIA4_uc009yxl.1_RNA	NM_000829	NP_000820	P48058	GRIA4_HUMAN	glutamate receptor, ionotrophic, AMPA 4 isoform	716	Extracellular (Potential).				glutamate signaling pathway|synaptic transmission	cell junction|endocytic vesicle membrane|integral to membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)	L-Glutamic Acid(DB00142)													---	---	---	---
GUCY1A2	2977	broad.mit.edu	37	11	106681093	106681093	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:106681093G>T	uc001pjg.1	-	5	1708	c.1318C>A	c.(1318-1320)CTC>ATC	p.L440I	GUCY1A2_uc010rvo.1_Missense_Mutation_p.L461I|GUCY1A2_uc009yxn.1_Missense_Mutation_p.L440I	NM_000855	NP_000846	P33402	GCYA2_HUMAN	guanylate cyclase 1, soluble, alpha 2	440					intracellular signal transduction|platelet activation	cytoplasm	GTP binding|guanylate cyclase activity|heme binding			large_intestine(3)|lung(2)|pancreas(2)|ovary(1)	8		all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068)		BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476)														---	---	---	---
CWF19L2	143884	broad.mit.edu	37	11	107289002	107289002	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:107289002C>T	uc010rvp.1	-	9	1475	c.1445G>A	c.(1444-1446)CGT>CAT	p.R482H	CWF19L2_uc001pjh.3_RNA|CWF19L2_uc009yxo.2_RNA	NM_152434	NP_689647	Q2TBE0	C19L2_HUMAN	CWF19-like 2, cell cycle control	482							catalytic activity				0		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)														---	---	---	---
ACAT1	38	broad.mit.edu	37	11	108009620	108009620	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108009620C>T	uc001pjy.2	+						ACAT1_uc001pjx.2_Intron	NM_000019	NP_000010			acetyl-Coenzyme A acetyltransferase 1 precursor						acetoacetic acid biosynthetic process|branched chain family amino acid catabolic process|ketone body biosynthetic process|ketone body catabolic process	mitochondrial matrix	acetyl-CoA C-acetyltransferase activity|metal ion binding			ovary(3)	3		all_cancers(61;6.41e-10)|all_epithelial(67;2.83e-06)|Melanoma(852;1.46e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;2.96e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.00108)|OV - Ovarian serous cystadenocarcinoma(223;0.192)	Sulfasalazine(DB00795)													---	---	---	---
NPAT	4863	broad.mit.edu	37	11	108032154	108032154	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108032154A>G	uc001pjz.3	-	17	3761	c.3659T>C	c.(3658-3660)GTA>GCA	p.V1220A	NPAT_uc010rvv.1_Missense_Mutation_p.V276A	NM_002519	NP_002510	Q14207	NPAT_HUMAN	nuclear protein,  ataxia-telangiectasia locus	1220					positive regulation of transcription, DNA-dependent|regulation of transcription involved in G1/S phase of mitotic cell cycle	Cajal body	protein C-terminus binding|protein N-terminus binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity			ovary(2)	2		all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116)														---	---	---	---
ATM	472	broad.mit.edu	37	11	108203493	108203493	+	Missense_Mutation	SNP	G	A	A	rs140263969		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:108203493G>A	uc001pkb.1	+	53	8178	c.7793G>A	c.(7792-7794)CGA>CAA	p.R2598Q	ATM_uc009yxr.1_Missense_Mutation_p.R2598Q|C11orf65_uc010rvx.1_Intron|C11orf65_uc009yxu.1_Intron|ATM_uc001pke.1_Missense_Mutation_p.R1250Q|ATM_uc001pkg.1_Missense_Mutation_p.R955Q	NM_000051	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated isoform 1	2598					cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding			haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	240		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)				D|Mis|N|F|S		T-PLL	leukemia|lymphoma|medulloblastoma|glioma		Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents	Ataxia_Telangiectasia	TSP Lung(14;0.12)			---	---	---	---
ZC3H12C	85463	broad.mit.edu	37	11	110035639	110035639	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110035639G>A	uc009yxw.2	+	6	1880	c.1829G>A	c.(1828-1830)CGT>CAT	p.R610H	ZC3H12C_uc010rwc.1_Missense_Mutation_p.R611H|ZC3H12C_uc010rwd.1_Missense_Mutation_p.R611H|ZC3H12C_uc001pkr.3_Missense_Mutation_p.R579H	NM_033390	NP_203748	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	610							endonuclease activity|nucleic acid binding|zinc ion binding				0		all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.72e-06)|BRCA - Breast invasive adenocarcinoma(274;1.17e-05)|all cancers(92;9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0279)														---	---	---	---
ZC3H12C	85463	broad.mit.edu	37	11	110036166	110036166	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:110036166G>A	uc009yxw.2	+	6	2407	c.2356G>A	c.(2356-2358)GCC>ACC	p.A786T	ZC3H12C_uc010rwc.1_Missense_Mutation_p.A787T|ZC3H12C_uc010rwd.1_Missense_Mutation_p.A787T|ZC3H12C_uc001pkr.3_Missense_Mutation_p.A755T	NM_033390	NP_203748	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	786							endonuclease activity|nucleic acid binding|zinc ion binding				0		all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.72e-06)|BRCA - Breast invasive adenocarcinoma(274;1.17e-05)|all cancers(92;9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0279)														---	---	---	---
C11orf52	91894	broad.mit.edu	37	11	111796808	111796808	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:111796808G>A	uc001pmh.2	+	5	740	c.257G>A	c.(256-258)CGT>CAT	p.R86H	C11orf52_uc001pmi.2_Missense_Mutation_p.R86H	NM_080659	NP_542390	Q96A22	CK052_HUMAN	hypothetical protein LOC91894	86										ovary(1)	1		all_cancers(61;8.8e-15)|all_epithelial(67;6.27e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;3.63e-07)|BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|all cancers(92;6.7e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0512)														---	---	---	---
BCO2	83875	broad.mit.edu	37	11	112071486	112071486	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112071486G>A	uc001pnf.2	+	7	1133	c.1016G>A	c.(1015-1017)CGC>CAC	p.R339H	BCO2_uc001pne.1_Missense_Mutation_p.R166H|BCO2_uc001png.2_Missense_Mutation_p.R266H|BCO2_uc001pnh.2_Missense_Mutation_p.R305H|BCO2_uc010rwt.1_Missense_Mutation_p.R234H|BCO2_uc009yyn.2_Missense_Mutation_p.R305H|BCO2_uc001pni.2_Missense_Mutation_p.R305H	NM_031938	NP_114144	Q9BYV7	BCDO2_HUMAN	beta-carotene dioxygenase 2 isoform a	339					carotene metabolic process|retinal metabolic process|retinoic acid metabolic process		metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0																		---	---	---	---
BCO2	83875	broad.mit.edu	37	11	112085569	112085569	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112085569T>C	uc001pnf.2	+	10	1534	c.1417T>C	c.(1417-1419)TTC>CTC	p.F473L	BCO2_uc001pne.1_Missense_Mutation_p.F300L|BCO2_uc001png.2_Missense_Mutation_p.F400L|BCO2_uc001pnh.2_Missense_Mutation_p.F439L|BCO2_uc010rwt.1_Missense_Mutation_p.F368L|BCO2_uc009yyn.2_Missense_Mutation_p.F439L|BCO2_uc001pni.2_Missense_Mutation_p.F439L	NM_031938	NP_114144	Q9BYV7	BCDO2_HUMAN	beta-carotene dioxygenase 2 isoform a	473					carotene metabolic process|retinal metabolic process|retinoic acid metabolic process		metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0																		---	---	---	---
TMPRSS5	80975	broad.mit.edu	37	11	113563829	113563829	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113563829C>T	uc001poc.3	-	9	1050	c.928G>A	c.(928-930)GCC>ACC	p.A310T	TMPRSS5_uc009yys.2_Missense_Mutation_p.A301T|TMPRSS5_uc009yyt.2_Missense_Mutation_p.A266T|TMPRSS5_uc001pod.3_Missense_Mutation_p.A51T|TMPRSS5_uc010rww.1_Missense_Mutation_p.A231T|TMPRSS5_uc009yyu.2_Missense_Mutation_p.A51T|TMPRSS5_uc010rwx.1_Missense_Mutation_p.A197T	NM_030770	NP_110397	Q9H3S3	TMPS5_HUMAN	transmembrane protease, serine 5	310	Peptidase S1.|Extracellular (Potential).				proteolysis	integral to membrane|plasma membrane	scavenger receptor activity|serine-type endopeptidase activity			ovary(1)	1		all_cancers(61;2.71e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.75e-06)|Epithelial(105;6.34e-05)|all cancers(92;0.000502)														---	---	---	---
USP28	57646	broad.mit.edu	37	11	113679041	113679041	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113679041A>G	uc001poh.2	-	18	2316	c.2283T>C	c.(2281-2283)GGT>GGC	p.G761G	USP28_uc001pog.2_Silent_p.G469G|USP28_uc010rwy.1_Silent_p.G636G|USP28_uc001poi.2_Silent_p.G116G	NM_020886	NP_065937	Q96RU2	UBP28_HUMAN	ubiquitin specific protease 28	761					cell proliferation|DNA damage checkpoint|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA repair|protein deubiquitination|response to ionizing radiation|ubiquitin-dependent protein catabolic process	nucleolus|nucleoplasm	protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			lung(2)|breast(2)|ovary(1)|large_intestine(1)|kidney(1)	7		all_cancers(61;3.74e-18)|all_epithelial(67;3.75e-11)|Melanoma(852;1.46e-05)|all_hematologic(158;4.65e-05)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|Prostate(24;0.0153)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|Epithelial(105;0.000122)|all cancers(92;0.00104)														---	---	---	---
ZBTB16	7704	broad.mit.edu	37	11	114112937	114112937	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114112937C>T	uc001pop.2	+	5	1766	c.1502C>T	c.(1501-1503)GCG>GTG	p.A501V	ZBTB16_uc001poq.2_Missense_Mutation_p.A501V	NM_006006	NP_005997	Q05516	ZBT16_HUMAN	promyelocytic leukemia zinc finger protein	501	C2H2-type 4.				apoptosis|central nervous system development|mesonephros development|myeloid cell differentiation|negative regulation of myeloid cell differentiation|negative regulation of transcription, DNA-dependent	nuclear speck|PML body|transcriptional repressor complex	protein homodimerization activity|zinc ion binding			central_nervous_system(1)|skin(1)	2		all_cancers(61;3.79e-18)|all_epithelial(67;2.32e-10)|all_hematologic(158;2.96e-05)|Melanoma(852;0.000362)|Acute lymphoblastic leukemia(157;0.00108)|Breast(348;0.0104)|all_neural(223;0.0294)|Prostate(24;0.0318)|Medulloblastoma(222;0.0438)		BRCA - Breast invasive adenocarcinoma(274;6.75e-06)|Epithelial(105;0.000181)|all cancers(92;0.0018)														---	---	---	---
NNMT	4837	broad.mit.edu	37	11	114168715	114168715	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114168715C>A	uc001por.1	+	4	461	c.197C>A	c.(196-198)CCC>CAC	p.P66H	NNMT_uc001pos.1_Missense_Mutation_p.P66H	NM_006169	NP_006160	P40261	NNMT_HUMAN	nicotinamide N-methyltransferase	66					xenobiotic metabolic process	cytosol	nicotinamide N-methyltransferase activity|pyridine N-methyltransferase activity			ovary(1)	1		all_cancers(61;4.83e-16)|all_epithelial(67;7.28e-09)|all_hematologic(158;0.000135)|Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0906)		BRCA - Breast invasive adenocarcinoma(274;2.79e-06)|Epithelial(105;1.32e-05)|all cancers(92;0.000144)|OV - Ovarian serous cystadenocarcinoma(223;0.128)	Niacin(DB00627)													---	---	---	---
FAM55D	54827	broad.mit.edu	37	11	114453112	114453112	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:114453112C>T	uc001ppc.2	-	3	909	c.728G>A	c.(727-729)TGT>TAT	p.C243Y	FAM55D_uc001ppd.2_Intron	NM_001077639	NP_001071107	Q6UWF7	FA55D_HUMAN	hypothetical protein LOC54827 isoform 1	243						extracellular region				ovary(2)|skin(2)	4		all_cancers(61;8.53e-16)|all_epithelial(67;1.71e-08)|all_hematologic(158;3.05e-05)|Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0194)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.0906)		BRCA - Breast invasive adenocarcinoma(274;2.82e-06)|Epithelial(105;0.000129)|all cancers(92;0.000938)														---	---	---	---
PCSK7	9159	broad.mit.edu	37	11	117097990	117097990	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117097990G>A	uc001pqr.2	-	5	853	c.652C>T	c.(652-654)CCC>TCC	p.P218S		NM_004716	NP_004707	Q16549	PCSK7_HUMAN	proprotein convertase subtilisin/kexin type 7	218	Catalytic.|Extracellular (Potential).				peptide hormone processing	integral to Golgi membrane	serine-type endopeptidase activity				0	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|Epithelial(105;6.71e-05)|all cancers(92;0.000537)				T	IGH@	MLCLS								---	---	---	---
DSCAML1	57453	broad.mit.edu	37	11	117392019	117392019	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117392019G>A	uc001prh.1	-	6	1221	c.1219C>T	c.(1219-1221)CGC>TGC	p.R407C	DSCAML1_uc001pri.1_Missense_Mutation_p.R211C	NM_020693	NP_065744	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	347	Extracellular (Potential).|Ig-like C2-type 4.				axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)|skin(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)														---	---	---	---
DSCAML1	57453	broad.mit.edu	37	11	117403175	117403175	+	Missense_Mutation	SNP	C	T	T	rs142110596		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117403175C>T	uc001prh.1	-	4	756	c.754G>A	c.(754-756)GCC>ACC	p.A252T	DSCAML1_uc001pri.1_Missense_Mutation_p.A56T	NM_020693	NP_065744	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	192	Extracellular (Potential).|Ig-like C2-type 2.				axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)|skin(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)														---	---	---	---
DSCAML1	57453	broad.mit.edu	37	11	117651364	117651364	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117651364C>T	uc001prh.1	-	2	390	c.388G>A	c.(388-390)GTG>ATG	p.V130M	DSCAML1_uc001pri.1_Translation_Start_Site	NM_020693	NP_065744	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	70	Extracellular (Potential).|Ig-like C2-type 1.				axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)|skin(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)														---	---	---	---
TMPRSS4	56649	broad.mit.edu	37	11	117969715	117969715	+	Missense_Mutation	SNP	G	A	A	rs144849681		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117969715G>A	uc010rxo.1	+	3	350	c.59G>A	c.(58-60)CGC>CAC	p.R20H	TMPRSS4_uc010rxp.1_Missense_Mutation_p.R20H|TMPRSS4_uc010rxq.1_5'UTR|TMPRSS4_uc010rxr.1_5'UTR|TMPRSS4_uc010rxs.1_Intron|TMPRSS4_uc009yzu.2_RNA|TMPRSS4_uc010rxt.1_5'UTR	NM_019894	NP_063947	Q9NRS4	TMPS4_HUMAN	transmembrane protease, serine 4 isoform 1	20	Cytoplasmic (Potential).				proteolysis	integral to membrane	scavenger receptor activity|serine-type endopeptidase activity			large_intestine(1)|central_nervous_system(1)	2	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0431)|all_hematologic(192;0.164)|Breast(348;0.183)|all_neural(223;0.238)		BRCA - Breast invasive adenocarcinoma(274;4.16e-05)|Epithelial(105;0.00204)														---	---	---	---
AMICA1	120425	broad.mit.edu	37	11	118081366	118081366	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118081366C>T	uc001psk.2	-	4	434	c.260G>A	c.(259-261)CGC>CAC	p.R87H	AMICA1_uc001psh.2_Missense_Mutation_p.R48H|AMICA1_uc009yzw.1_RNA|AMICA1_uc001psi.2_Missense_Mutation_p.R77H|AMICA1_uc001psj.2_Missense_Mutation_p.R87H|AMICA1_uc010rxw.1_Missense_Mutation_p.R48H|AMICA1_uc010rxx.1_Missense_Mutation_p.R87H|AMICA1_uc001psl.1_Missense_Mutation_p.R43H	NM_001098526	NP_001091996	Q86YT9	JAML1_HUMAN	adhesion molecule, interacts with CXADR antigen	87	Ig-like V-type 1.|Extracellular (Potential).				blood coagulation|cell adhesion|leukocyte migration|regulation of immune response	cell junction|integral to membrane				ovary(1)	1	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)														---	---	---	---
MPZL2	10205	broad.mit.edu	37	11	118133244	118133244	+	Silent	SNP	G	A	A	rs149678028	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118133244G>A	uc001psn.2	-	3	486	c.345C>T	c.(343-345)TTC>TTT	p.F115F	MPZL2_uc001pso.2_Silent_p.F115F|MPZL2_uc001psp.1_Silent_p.F115F	NM_005797	NP_005788	O60487	MPZL2_HUMAN	myelin protein zero-like 2 precursor	115	Extracellular (Potential).|Ig-like V-type.				anatomical structure morphogenesis|homophilic cell adhesion	cytoskeleton|integral to membrane				skin(1)	1	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.04e-05)														---	---	---	---
CD3E	916	broad.mit.edu	37	11	118184458	118184458	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118184458T>C	uc001psq.3	+	7	645	c.389T>C	c.(388-390)GTG>GCG	p.V130A		NM_000733	NP_000724	P07766	CD3E_HUMAN	CD3E antigen, epsilon polypeptide precursor	130	Helical; (Potential).				G-protein coupled receptor protein signaling pathway|signal complex assembly|T cell costimulation|T cell receptor signaling pathway|transmembrane receptor protein tyrosine kinase signaling pathway	external side of plasma membrane|integral to plasma membrane	protein heterodimerization activity|protein kinase binding|receptor signaling complex scaffold activity|receptor signaling protein activity|SH3 domain binding|T cell receptor binding|transmembrane receptor activity			ovary(2)	2	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.09e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0251)	Muromonab(DB00075)													---	---	---	---
UBE4A	9354	broad.mit.edu	37	11	118245656	118245656	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118245656T>G	uc001psw.2	+	9	1291	c.1162T>G	c.(1162-1164)TTA>GTA	p.L388V	UBE4A_uc001psv.2_Missense_Mutation_p.L395V	NM_004788	NP_004779	Q14139	UBE4A_HUMAN	ubiquitination factor E4A	388					ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding			ovary(2)|upper_aerodigestive_tract(1)|breast(1)|kidney(1)	5	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)														---	---	---	---
MLL	4297	broad.mit.edu	37	11	118342593	118342593	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118342593A>G	uc001pta.2	+	3	742	c.719A>G	c.(718-720)GAC>GGC	p.D240G	MLL_uc001ptb.2_Missense_Mutation_p.D240G|MLL_uc001psz.1_Missense_Mutation_p.D273G|MLL_uc001ptd.1_Intron	NM_005933	NP_005924	Q03164	MLL1_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	240					apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter	MLL1 complex	AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding			lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1)	25	all_hematologic(175;0.046)	all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244)		OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144)				T|O	MLL|MLLT1|MLLT2|MLLT3|MLLT4|MLLT7|MLLT10|MLLT6|ELL|EPS15|AF1Q|CREBBP|SH3GL1|FNBP1|PNUTL1|MSF|GPHN|GMPS|SSH3BP1|ARHGEF12|GAS7|FOXO3A|LAF4|LCX|SEPT6|LPP|CBFA2T1|GRAF|EP300|PICALM|HEAB	AML|ALL								---	---	---	---
MLL	4297	broad.mit.edu	37	11	118373723	118373723	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118373723C>A	uc001pta.2	+	27	7130	c.7107C>A	c.(7105-7107)CAC>CAA	p.H2369Q	MLL_uc001ptb.2_Missense_Mutation_p.H2372Q	NM_005933	NP_005924	Q03164	MLL1_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	2369					apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter	MLL1 complex	AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding			lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1)	25	all_hematologic(175;0.046)	all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244)		OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144)				T|O	MLL|MLLT1|MLLT2|MLLT3|MLLT4|MLLT7|MLLT10|MLLT6|ELL|EPS15|AF1Q|CREBBP|SH3GL1|FNBP1|PNUTL1|MSF|GPHN|GMPS|SSH3BP1|ARHGEF12|GAS7|FOXO3A|LAF4|LCX|SEPT6|LPP|CBFA2T1|GRAF|EP300|PICALM|HEAB	AML|ALL								---	---	---	---
PHLDB1	23187	broad.mit.edu	37	11	118499314	118499314	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118499314A>G	uc001ptr.1	+	7	2128	c.1775A>G	c.(1774-1776)TAC>TGC	p.Y592C	PHLDB1_uc001pts.2_Missense_Mutation_p.Y592C|PHLDB1_uc001ptt.2_Missense_Mutation_p.Y592C|PHLDB1_uc001ptu.1_Intron|PHLDB1_uc001ptv.1_Missense_Mutation_p.Y392C|PHLDB1_uc001ptw.1_5'Flank	NM_015157	NP_055972	Q86UU1	PHLB1_HUMAN	pleckstrin homology-like domain, family B,	592											0	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.0735)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)														---	---	---	---
TREH	11181	broad.mit.edu	37	11	118533639	118533639	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118533639C>T	uc001pty.1	-	4	419	c.374G>A	c.(373-375)CGT>CAT	p.R125H	TREH_uc009zaj.1_Missense_Mutation_p.R125H|TREH_uc001ptz.1_Missense_Mutation_p.V5M|TREH_uc009zak.2_Missense_Mutation_p.R125H	NM_007180	NP_009111	O43280	TREA_HUMAN	trehalase precursor	125					polysaccharide digestion|trehalose catabolic process	anchored to plasma membrane	alpha,alpha-trehalase activity			pancreas(1)	1	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.0564)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;3.16e-05)														---	---	---	---
CXCR5	643	broad.mit.edu	37	11	118764536	118764536	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118764536G>A	uc001pue.3	+	2	393	c.283G>A	c.(283-285)GTG>ATG	p.V95M	CXCR5_uc001puf.2_Missense_Mutation_p.V50M	NM_001716	NP_001707	P32302	CXCR5_HUMAN	Burkitt lymphoma receptor 1 isoform 1	95	Helical; Name=2; (Potential).				B cell activation|cellular component movement	integral to plasma membrane	C-X-C chemokine receptor activity			breast(1)	1	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.62e-05)														---	---	---	---
BCL9L	283149	broad.mit.edu	37	11	118772485	118772485	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118772485G>A	uc001pug.2	-	6	2932	c.1967C>T	c.(1966-1968)ACC>ATC	p.T656I	BCL9L_uc009zal.2_Missense_Mutation_p.T651I	NM_182557	NP_872363	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	656					negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		transcription coactivator activity			ovary(1)|pancreas(1)	2	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)														---	---	---	---
HYOU1	10525	broad.mit.edu	37	11	118916532	118916532	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118916532C>A	uc001puu.2	-	25	3092	c.2899G>T	c.(2899-2901)GGA>TGA	p.G967*	HYOU1_uc001put.2_Nonsense_Mutation_p.G933*|HYOU1_uc010ryu.1_Nonsense_Mutation_p.G925*|HYOU1_uc010ryv.1_Nonsense_Mutation_p.G856*|HYOU1_uc001pux.3_Nonsense_Mutation_p.G967*	NM_006389	NP_006380	Q9Y4L1	HYOU1_HUMAN	hypoxia up-regulated 1 precursor	967						endoplasmic reticulum lumen	ATP binding|protein binding				0	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.78e-05)														---	---	---	---
VPS11	55823	broad.mit.edu	37	11	118944066	118944066	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118944066G>A	uc010ryx.1	+	7	1085	c.1043G>A	c.(1042-1044)CGG>CAG	p.R348Q	VPS11_uc010ryy.1_Missense_Mutation_p.R194Q	NM_021729	NP_068375	Q9H270	VPS11_HUMAN	vacuolar protein sorting 11	348					protein transport	endocytic vesicle|HOPS complex|late endosome membrane|lysosomal membrane	nucleotide binding|protein binding|zinc ion binding			ovary(2)|central_nervous_system(1)	3	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.88e-05)														---	---	---	---
VPS11	55823	broad.mit.edu	37	11	118948925	118948925	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118948925C>T	uc010ryx.1	+	12	1846	c.1804C>T	c.(1804-1806)CGA>TGA	p.R602*	VPS11_uc010ryy.1_Nonsense_Mutation_p.R448*	NM_021729	NP_068375	Q9H270	VPS11_HUMAN	vacuolar protein sorting 11	602					protein transport	endocytic vesicle|HOPS complex|late endosome membrane|lysosomal membrane	nucleotide binding|protein binding|zinc ion binding			ovary(2)|central_nervous_system(1)	3	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.88e-05)														---	---	---	---
HINFP	25988	broad.mit.edu	37	11	119004908	119004908	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119004908G>A	uc001pvp.2	+	11	1443	c.1254G>A	c.(1252-1254)TCG>TCA	p.S418S	HINFP_uc001pvq.2_Silent_p.S418S|HINFP_uc001pvr.2_Silent_p.S171S	NM_015517	NP_056332	Q9BQA5	HINFP_HUMAN	MBD2 (methyl-CpG-binding protein)-interacting	418	Interaction with NPAT.				DNA damage checkpoint|DNA repair|establishment of protein localization|in utero embryonic development|myoblast differentiation|negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of transcription involved in G1/S phase of mitotic cell cycle	Cajal body	enzyme binding|histone binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription regulatory region DNA binding|zinc ion binding			pancreas(2)|ovary(1)|skin(1)	4																OREG0021397	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
NLRX1	79671	broad.mit.edu	37	11	119043675	119043675	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119043675T>G	uc001pvu.2	+	4	421	c.206T>G	c.(205-207)CTG>CGG	p.L69R	NLRX1_uc010rzc.1_5'UTR|NLRX1_uc001pvv.2_Missense_Mutation_p.L69R|NLRX1_uc001pvw.2_Missense_Mutation_p.L69R|NLRX1_uc001pvx.2_Missense_Mutation_p.L69R	NM_024618	NP_078894	Q86UT6	NLRX1_HUMAN	NLR family member X1 isoform 1	69					innate immune response|interspecies interaction between organisms|negative regulation of type I interferon production	mitochondrial outer membrane	ATP binding			ovary(1)|skin(1)	2	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)														---	---	---	---
CBL	867	broad.mit.edu	37	11	119155742	119155742	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:119155742C>T	uc001pwe.2	+	10	1633	c.1495C>T	c.(1495-1497)CGA>TGA	p.R499*		NM_005188	NP_005179	P22681	CBL_HUMAN	Cas-Br-M (murine) ecotropic retroviral	499	Pro-rich.				epidermal growth factor receptor signaling pathway|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of receptor-mediated endocytosis	cytosol|nucleus	calcium ion binding|sequence-specific DNA binding transcription factor activity|SH3 domain binding|signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding	p.R499L(1)		haematopoietic_and_lymphoid_tissue(135)|lung(10)|central_nervous_system(2)|ovary(1)|breast(1)	149		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)										CBL_gene-associated_Juvenile_Myelomonocytic_Leukemia_and_Developmental_Anomalies|Noonan_syndrome		OREG0021401	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
TMEM136	219902	broad.mit.edu	37	11	120201123	120201123	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120201123C>T	uc001pxh.1	+	3	700	c.637C>T	c.(637-639)CGC>TGC	p.R213C	TMEM136_uc001pxg.2_Missense_Mutation_p.R116C|TMEM136_uc010rzm.1_Missense_Mutation_p.R94C|TMEM136_uc001pxj.2_Missense_Mutation_p.R235C|TMEM136_uc009zas.1_Missense_Mutation_p.R99C|TMEM136_uc001pxi.1_Missense_Mutation_p.R99C	NM_174926	NP_777586	Q6ZRR5	TM136_HUMAN	transmembrane protein 136	213						integral to membrane				ovary(1)	1		Breast(109;0.00663)|Medulloblastoma(222;0.0523)|Hepatocellular(160;0.206)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;5.07e-06)														---	---	---	---
ARHGEF12	23365	broad.mit.edu	37	11	120317150	120317150	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120317150C>T	uc001pxl.1	+	17	1391	c.1384C>T	c.(1384-1386)CGC>TGC	p.R462C	ARHGEF12_uc009zat.2_Missense_Mutation_p.R443C|ARHGEF12_uc010rzn.1_Missense_Mutation_p.R359C|ARHGEF12_uc009zau.1_Missense_Mutation_p.R359C	NM_015313	NP_056128	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12	462	RGSL.				apoptosis|axon guidance|G-protein coupled receptor protein signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane	G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(2)|breast(2)|skin(2)|ovary(1)	7		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)				T	MLL	AML								---	---	---	---
GRIK4	2900	broad.mit.edu	37	11	120827622	120827622	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120827622G>A	uc001pxn.2	+	16	2121	c.1834G>A	c.(1834-1836)GCC>ACC	p.A612T	GRIK4_uc009zav.1_Missense_Mutation_p.A612T|GRIK4_uc009zaw.1_Missense_Mutation_p.A612T|GRIK4_uc009zax.1_Missense_Mutation_p.A612T	NM_014619	NP_055434	Q16099	GRIK4_HUMAN	glutamate receptor KA1 precursor	612	Cytoplasmic (Potential).				glutamate signaling pathway|synaptic transmission	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|central_nervous_system(1)	3		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)	L-Glutamic Acid(DB00142)													---	---	---	---
GRIK4	2900	broad.mit.edu	37	11	120837915	120837915	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120837915C>T	uc001pxn.2	+	19	2565	c.2278C>T	c.(2278-2280)CGG>TGG	p.R760W	GRIK4_uc009zaw.1_Missense_Mutation_p.R760W|GRIK4_uc009zax.1_Missense_Mutation_p.R760W	NM_014619	NP_055434	Q16099	GRIK4_HUMAN	glutamate receptor KA1 precursor	760	Extracellular (Potential).				glutamate signaling pathway|synaptic transmission	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|central_nervous_system(1)	3		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)	L-Glutamic Acid(DB00142)													---	---	---	---
TBCEL	219899	broad.mit.edu	37	11	120957754	120957754	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120957754C>A	uc009zay.2	+	8	1302	c.1224C>A	c.(1222-1224)TCC>TCA	p.S408S	TBCEL_uc001pxo.2_Silent_p.S408S|TBCEL_uc001pxp.2_Silent_p.S264S|TBCEL_uc001pxq.2_RNA	NM_001130047	NP_001123519	Q5QJ74	TBCEL_HUMAN	tubulin folding cofactor E-like	408	Ubiquitin-like.					cytoplasm|cytoskeleton				skin(1)	1		Breast(109;0.00526)|Medulloblastoma(222;0.0523)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;5.89e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.121)														---	---	---	---
TECTA	7007	broad.mit.edu	37	11	120984351	120984351	+	Silent	SNP	C	T	T	rs148478527		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:120984351C>T	uc010rzo.1	+	5	714	c.714C>T	c.(712-714)AAC>AAT	p.N238N		NM_005422	NP_005413	O75443	TECTA_HUMAN	tectorin alpha precursor	238	NIDO.				cell-matrix adhesion|sensory perception of sound	anchored to membrane|plasma membrane|proteinaceous extracellular matrix				breast(6)|ovary(2)|skin(2)	10	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)														---	---	---	---
TECTA	7007	broad.mit.edu	37	11	121033075	121033075	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121033075T>A	uc010rzo.1	+	15	5268	c.5268T>A	c.(5266-5268)AAT>AAA	p.N1756K		NM_005422	NP_005413	O75443	TECTA_HUMAN	tectorin alpha precursor	1756					cell-matrix adhesion|sensory perception of sound	anchored to membrane|plasma membrane|proteinaceous extracellular matrix				breast(6)|ovary(2)|skin(2)	10	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)														---	---	---	---
HSPA8	3312	broad.mit.edu	37	11	122930645	122930645	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:122930645A>G	uc001pyo.2	-	5	734	c.656T>C	c.(655-657)GTC>GCC	p.V219A	HSPA8_uc009zbc.2_5'UTR|HSPA8_uc001pyp.2_Missense_Mutation_p.V219A|HSPA8_uc010rzu.1_Missense_Mutation_p.V142A|HSPA8_uc009zbd.1_Missense_Mutation_p.V219A|HSPA8_uc010rzv.1_3'UTR	NM_006597	NP_006588	P11142	HSP7C_HUMAN	heat shock 70kDa protein 8 isoform 1	219	Interaction with BAG1.				cellular membrane organization|interspecies interaction between organisms|mRNA metabolic process|negative regulation of transcription, DNA-dependent|neurotransmitter secretion|post-Golgi vesicle-mediated transport|protein folding|response to unfolded protein|transcription, DNA-dependent	cell surface|clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|cytosol|melanosome|plasma membrane|ribonucleoprotein complex	ATP binding|ATPase activity, coupled|protein binding			central_nervous_system(7)|lung(1)	8		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)														---	---	---	---
GRAMD1B	57476	broad.mit.edu	37	11	123480901	123480901	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123480901C>T	uc001pyx.2	+						GRAMD1B_uc001pyw.2_Intron|GRAMD1B_uc010rzw.1_Intron|GRAMD1B_uc010rzx.1_Intron|GRAMD1B_uc001pyy.2_Intron	NM_020716	NP_065767			GRAM domain containing 1B							integral to membrane				ovary(1)	1		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394)														---	---	---	---
ZNF202	7753	broad.mit.edu	37	11	123600516	123600516	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:123600516G>A	uc001pzd.1	-	5	820	c.420C>T	c.(418-420)CAC>CAT	p.H140H	ZNF202_uc001pzc.1_Translation_Start_Site|ZNF202_uc001pze.1_Silent_p.H140H|ZNF202_uc001pzf.1_Silent_p.H140H	NM_003455	NP_003446	O95125	ZN202_HUMAN	zinc finger protein 202	140					lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.03)														---	---	---	---
OR8G2	26492	broad.mit.edu	37	11	124095563	124095563	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124095563T>G	uc010saf.1	+	1	166	c.166T>G	c.(166-168)TTG>GTG	p.L56V		NM_001007249	NP_001007250	Q15614	OR8G2_HUMAN	olfactory receptor, family 8, subfamily G,	56						integral to membrane	olfactory receptor activity				0		Breast(109;0.0157)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.91e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0528)														---	---	---	---
OR8G2	26492	broad.mit.edu	37	11	124095920	124095920	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124095920T>G	uc010saf.1	+	1	523	c.523T>G	c.(523-525)TTT>GTT	p.F175V		NM_001007249	NP_001007250	Q15614	OR8G2_HUMAN	olfactory receptor, family 8, subfamily G,	175						integral to membrane	olfactory receptor activity				0		Breast(109;0.0157)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.91e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0528)														---	---	---	---
Unknown	0	broad.mit.edu	37	11	124120967	124120967	+	IGR	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124120967T>C								OR8G2 (24657 upstream) : OR8D1 (58770 downstream)																																			---	---	---	---
TBRG1	84897	broad.mit.edu	37	11	124500355	124500355	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124500355A>C	uc001qak.3	+	6	1048	c.810A>C	c.(808-810)GAA>GAC	p.E270D	TBRG1_uc001qaj.3_Missense_Mutation_p.E119D|TBRG1_uc001qal.3_Missense_Mutation_p.E46D|TBRG1_uc001qam.3_RNA|TBRG1_uc009zbf.2_RNA|TBRG1_uc009zbg.2_Missense_Mutation_p.E119D|TBRG1_uc009zbh.2_Missense_Mutation_p.E46D	NM_032811	NP_116200	Q3YBR2	TBRG1_HUMAN	transforming growth factor beta regulator 1	270	FYR C-terminal.				cell cycle arrest|DNA replication|negative regulation of cell proliferation|nucleolus to nucleoplasm transport|protein stabilization	nucleus	DNA binding|protein binding				0	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0218)														---	---	---	---
C11orf61	79684	broad.mit.edu	37	11	124637402	124637402	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124637402G>A	uc001qba.1	-	4	1373	c.1350C>T	c.(1348-1350)GGC>GGT	p.G450G	C11orf61_uc001qaz.1_Silent_p.G398G|C11orf61_uc010sap.1_Silent_p.G170G|C11orf61_uc001qay.1_Silent_p.G220G	NM_024631	NP_078907	Q6P1R3	CK061_HUMAN	hypothetical protein LOC79684	450											0	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.63e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0079)														---	---	---	---
C11orf61	79684	broad.mit.edu	37	11	124637864	124637864	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124637864T>C	uc001qba.1	-	4	911	c.888A>G	c.(886-888)GAA>GAG	p.E296E	C11orf61_uc001qaz.1_Silent_p.E244E|C11orf61_uc010sap.1_Silent_p.E16E|C11orf61_uc001qay.1_Silent_p.E66E	NM_024631	NP_078907	Q6P1R3	CK061_HUMAN	hypothetical protein LOC79684	296											0	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.63e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0079)														---	---	---	---
ROBO3	64221	broad.mit.edu	37	11	124740111	124740111	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124740111G>A	uc001qbc.2	+	5	1009	c.817G>A	c.(817-819)GCC>ACC	p.A273T		NM_022370	NP_071765	Q96MS0	ROBO3_HUMAN	roundabout, axon guidance receptor, homolog 3	273	Ig-like C2-type 3.|Extracellular (Potential).				axon midline choice point recognition	integral to membrane	receptor activity			breast(1)|central_nervous_system(1)	2	all_hematologic(175;0.215)	Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|Breast(109;0.0481)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0296)														---	---	---	---
ROBO3	64221	broad.mit.edu	37	11	124744124	124744124	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124744124G>A	uc001qbc.2	+	12	2135	c.1943G>A	c.(1942-1944)CGT>CAT	p.R648H	ROBO3_uc010saq.1_5'Flank|ROBO3_uc001qbd.2_5'Flank|ROBO3_uc010sar.1_5'Flank|ROBO3_uc001qbe.2_5'Flank	NM_022370	NP_071765	Q96MS0	ROBO3_HUMAN	roundabout, axon guidance receptor, homolog 3	648	Extracellular (Potential).				axon midline choice point recognition	integral to membrane	receptor activity			breast(1)|central_nervous_system(1)	2	all_hematologic(175;0.215)	Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|Breast(109;0.0481)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0296)														---	---	---	---
ROBO4	54538	broad.mit.edu	37	11	124755000	124755000	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124755000G>A	uc001qbg.2	-	17	3078	c.2938C>T	c.(2938-2940)CCC>TCC	p.P980S	ROBO4_uc010sas.1_Missense_Mutation_p.P835S	NM_019055	NP_061928	Q8WZ75	ROBO4_HUMAN	roundabout homolog 4, magic roundabout	980					angiogenesis|cell differentiation	integral to membrane	receptor activity			ovary(1)|skin(1)	2	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)														---	---	---	---
SLC37A2	219855	broad.mit.edu	37	11	124947210	124947210	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124947210G>A	uc001qbn.2	+	3	477	c.226G>A	c.(226-228)GCC>ACC	p.A76T	SLC37A2_uc010sau.1_Missense_Mutation_p.A76T	NM_001145290	NP_001138762	Q8TED4	SPX2_HUMAN	solute carrier family 37 (glycerol-3-phosphate	76					carbohydrate transport|transmembrane transport	integral to membrane				ovary(2)	2	all_hematologic(175;0.215)	Breast(109;0.012)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.152)|all_lung(97;0.159)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0384)														---	---	---	---
PKNOX2	63876	broad.mit.edu	37	11	125280160	125280160	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125280160A>G	uc001qbu.2	+	8	971	c.657A>G	c.(655-657)CCA>CCG	p.P219P	PKNOX2_uc010saz.1_Silent_p.P190P|PKNOX2_uc010sba.1_Silent_p.P190P|PKNOX2_uc010sbb.1_Silent_p.P155P|PKNOX2_uc001qbv.2_5'Flank	NM_022062	NP_071345	Q96KN3	PKNX2_HUMAN	PBX/knotted 1 homeobox 2	219						nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3		Breast(109;0.00234)|all_lung(97;0.0191)|Lung NSC(97;0.0196)|Medulloblastoma(222;0.0447)|all_neural(223;0.116)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.117)														---	---	---	---
PKNOX2	63876	broad.mit.edu	37	11	125300013	125300013	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125300013G>A	uc001qbu.2	+	12	1482	c.1168G>A	c.(1168-1170)GGT>AGT	p.G390S	PKNOX2_uc010saz.1_Missense_Mutation_p.G361S|PKNOX2_uc010sba.1_Missense_Mutation_p.G361S|PKNOX2_uc010sbb.1_Missense_Mutation_p.G326S|PKNOX2_uc001qbv.2_Missense_Mutation_p.G155S	NM_022062	NP_071345	Q96KN3	PKNX2_HUMAN	PBX/knotted 1 homeobox 2	390						nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3		Breast(109;0.00234)|all_lung(97;0.0191)|Lung NSC(97;0.0196)|Medulloblastoma(222;0.0447)|all_neural(223;0.116)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.117)														---	---	---	---
HYLS1	219844	broad.mit.edu	37	11	125770018	125770018	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:125770018A>G	uc009zbv.2	+	4	1289	c.755A>G	c.(754-756)CAA>CGA	p.Q252R	HYLS1_uc001qcx.3_Missense_Mutation_p.Q252R|PUS3_uc001qcy.2_Intron	NM_145014	NP_659451	Q96M11	HYLS1_HUMAN	hydrolethalus syndrome 1	252						centrosome|nucleus				upper_aerodigestive_tract(1)	1	all_hematologic(175;0.177)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.131)|all_lung(97;0.139)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0446)														---	---	---	---
FOXRED1	55572	broad.mit.edu	37	11	126143316	126143316	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126143316C>T	uc001qdi.2	+	4	550	c.503C>T	c.(502-504)GCT>GTT	p.A168V	FOXRED1_uc010sbn.1_5'UTR|FOXRED1_uc010sbo.1_RNA|FOXRED1_uc010sbp.1_5'UTR|FOXRED1_uc010sbq.1_Silent_p.C36C|FOXRED1_uc001qdj.2_5'UTR|FOXRED1_uc010sbr.1_Missense_Mutation_p.A154V|FOXRED1_uc001qdk.2_5'UTR	NM_017547	NP_060017	Q96CU9	FXRD1_HUMAN	FAD-dependent oxidoreductase domain containing	168						integral to membrane|mitochondrion	oxidoreductase activity|protein binding				0	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0739)|all_lung(97;0.0798)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0729)														---	---	---	---
FOXRED1	55572	broad.mit.edu	37	11	126145710	126145710	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:126145710G>A	uc001qdi.2	+	7	802	c.755G>A	c.(754-756)CGC>CAC	p.R252H	FOXRED1_uc010sbn.1_Missense_Mutation_p.R82H|FOXRED1_uc010sbo.1_RNA|FOXRED1_uc010sbp.1_Missense_Mutation_p.R65H|FOXRED1_uc010sbq.1_Missense_Mutation_p.R119H|FOXRED1_uc001qdj.2_Missense_Mutation_p.R41H|FOXRED1_uc010sbr.1_Missense_Mutation_p.R238H|FOXRED1_uc001qdk.2_Missense_Mutation_p.R41H	NM_017547	NP_060017	Q96CU9	FXRD1_HUMAN	FAD-dependent oxidoreductase domain containing	252						integral to membrane|mitochondrion	oxidoreductase activity|protein binding				0	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0739)|all_lung(97;0.0798)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0729)														---	---	---	---
TMEM45B	120224	broad.mit.edu	37	11	129727348	129727348	+	Silent	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129727348T>G	uc001qfe.1	+	5	772	c.711T>G	c.(709-711)GTT>GTG	p.V237V	TMEM45B_uc001qff.1_Silent_p.V237V	NM_138788	NP_620143	Q96B21	TM45B_HUMAN	transmembrane protein 45B	237						integral to membrane					0	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.012)|Lung(977;0.179)|LUSC - Lung squamous cell carcinoma(976;0.189)														---	---	---	---
NFRKB	4798	broad.mit.edu	37	11	129743745	129743745	+	Silent	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129743745A>C	uc001qfi.2	-	22	2646	c.2445T>G	c.(2443-2445)GCT>GCG	p.A815A	NFRKB_uc001qfg.2_Silent_p.A840A|NFRKB_uc001qfh.2_Silent_p.A838A|NFRKB_uc010sbw.1_Silent_p.A825A|NFRKB_uc009zcr.2_Silent_p.A101A	NM_001143835	NP_001137307	Q6P4R8	NFRKB_HUMAN	nuclear factor related to kappaB binding protein	815					DNA recombination|DNA repair|inflammatory response|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	Ino80 complex	DNA binding|protease binding			ovary(3)	3	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0167)|Lung(977;0.171)|LUSC - Lung squamous cell carcinoma(976;0.184)														---	---	---	---
PRDM10	56980	broad.mit.edu	37	11	129784767	129784767	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129784767C>T	uc001qfm.2	-	18	2917	c.2685G>A	c.(2683-2685)ACG>ACA	p.T895T	PRDM10_uc001qfj.2_Silent_p.T809T|PRDM10_uc001qfk.2_Silent_p.T805T|PRDM10_uc001qfl.2_Silent_p.T809T|PRDM10_uc010sbx.1_Silent_p.T805T|PRDM10_uc001qfn.2_Silent_p.T891T|PRDM10_uc009zcs.1_Silent_p.T78T	NM_020228	NP_064613	Q9NQV6	PRD10_HUMAN	PR domain containing 10 isoform 1	895	Thr-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1	all_hematologic(175;0.0537)	Breast(109;0.000496)|Lung NSC(97;0.000693)|all_lung(97;0.00151)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0174)|Lung(977;0.176)|LUSC - Lung squamous cell carcinoma(976;0.185)														---	---	---	---
PRDM10	56980	broad.mit.edu	37	11	129784836	129784836	+	Silent	SNP	C	T	T	rs144412505		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129784836C>T	uc001qfm.2	-	18	2848	c.2616G>A	c.(2614-2616)ACG>ACA	p.T872T	PRDM10_uc001qfj.2_Silent_p.T786T|PRDM10_uc001qfk.2_Silent_p.T782T|PRDM10_uc001qfl.2_Silent_p.T786T|PRDM10_uc010sbx.1_Silent_p.T782T|PRDM10_uc001qfn.2_Silent_p.T868T|PRDM10_uc009zcs.1_Silent_p.T55T	NM_020228	NP_064613	Q9NQV6	PRD10_HUMAN	PR domain containing 10 isoform 1	872	Thr-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1	all_hematologic(175;0.0537)	Breast(109;0.000496)|Lung NSC(97;0.000693)|all_lung(97;0.00151)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0174)|Lung(977;0.176)|LUSC - Lung squamous cell carcinoma(976;0.185)														---	---	---	---
PRDM10	56980	broad.mit.edu	37	11	129784892	129784892	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:129784892G>A	uc001qfm.2	-	18	2792	c.2560C>T	c.(2560-2562)CGA>TGA	p.R854*	PRDM10_uc001qfj.2_Nonsense_Mutation_p.R768*|PRDM10_uc001qfk.2_Nonsense_Mutation_p.R764*|PRDM10_uc001qfl.2_Nonsense_Mutation_p.R768*|PRDM10_uc010sbx.1_Nonsense_Mutation_p.R764*|PRDM10_uc001qfn.2_Nonsense_Mutation_p.R850*|PRDM10_uc009zcs.1_Nonsense_Mutation_p.R37*	NM_020228	NP_064613	Q9NQV6	PRD10_HUMAN	PR domain containing 10 isoform 1	854	C2H2-type 10.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1	all_hematologic(175;0.0537)	Breast(109;0.000496)|Lung NSC(97;0.000693)|all_lung(97;0.00151)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0174)|Lung(977;0.176)|LUSC - Lung squamous cell carcinoma(976;0.185)														---	---	---	---
ZBTB44	29068	broad.mit.edu	37	11	130106899	130106899	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130106899G>A	uc001qga.2	-	5	1751	c.1357C>T	c.(1357-1359)CGC>TGC	p.R453C	ZBTB44_uc001qgb.3_Intron|ZBTB44_uc001qfx.2_Intron|ZBTB44_uc001qfz.2_Intron	NM_014155	NP_054874	Q8NCP5	ZBT44_HUMAN	zinc finger and BTB domain containing 44	453					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0192)|Lung(977;0.235)														---	---	---	---
ZBTB44	29068	broad.mit.edu	37	11	130131566	130131566	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:130131566T>C	uc001qga.2	-	2	597	c.203A>G	c.(202-204)AAC>AGC	p.N68S	ZBTB44_uc001qgb.3_Missense_Mutation_p.N68S|ZBTB44_uc001qfx.2_RNA|ZBTB44_uc001qgc.1_Missense_Mutation_p.N68S|ZBTB44_uc001qfz.2_Missense_Mutation_p.N68S	NM_014155	NP_054874	Q8NCP5	ZBT44_HUMAN	zinc finger and BTB domain containing 44	68	BTB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0192)|Lung(977;0.235)														---	---	---	---
IGSF9B	22997	broad.mit.edu	37	11	133794795	133794795	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:133794795G>A	uc001qgx.3	-	15	2270	c.2039C>T	c.(2038-2040)ACG>ATG	p.T680M	IGSF9B_uc001qgy.1_Missense_Mutation_p.T522M	NM_014987	NP_055802	Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	680	Fibronectin type-III 2.|Extracellular (Potential).					integral to membrane|plasma membrane					0	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)														---	---	---	---
JAM3	83700	broad.mit.edu	37	11	134014198	134014198	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134014198C>T	uc001qhb.1	+	4	478	c.454C>T	c.(454-456)CGG>TGG	p.R152W	JAM3_uc009zcz.1_Intron	NM_032801	NP_116190	Q9BX67	JAM3_HUMAN	junctional adhesion molecule 3 precursor	107	Extracellular (Potential).|Ig-like V-type.				angiogenesis|blood coagulation|regulation of neutrophil chemotaxis	cell-cell contact zone|desmosome|extracellular space|integral to membrane	integrin binding			ovary(1)	1	all_hematologic(175;0.127)	all_cancers(12;1.06e-21)|all_epithelial(12;3.37e-16)|all_lung(97;7.03e-06)|Lung NSC(97;1.67e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0506)|Esophageal squamous(93;0.0566)		Epithelial(10;1.55e-09)|BRCA - Breast invasive adenocarcinoma(10;1.35e-08)|all cancers(11;2.81e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00402)|Lung(977;0.245)														---	---	---	---
NCAPD3	23310	broad.mit.edu	37	11	134079056	134079056	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134079056A>G	uc001qhd.1	-	6	1383	c.777T>C	c.(775-777)TGT>TGC	p.C259C	NCAPD3_uc010scm.1_RNA|NCAPD3_uc009zda.1_RNA	NM_015261	NP_056076	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3	259					cell division|mitotic chromosome condensation	nuclear centromeric heterochromatin|nuclear condensin complex	methylated histone residue binding			ovary(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	5	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)														---	---	---	---
GLB1L3	112937	broad.mit.edu	37	11	134147815	134147815	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134147815C>T	uc009zdf.2	+						GLB1L3_uc010scs.1_Intron|GLB1L3_uc010sct.1_Intron	NM_001080407	NP_001073876			galactosidase, beta 1 like 3						carbohydrate metabolic process		cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			pancreas(1)	1	all_hematologic(175;0.127)	all_cancers(12;5.52e-23)|all_epithelial(12;2.15e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|all_neural(223;0.0182)|Medulloblastoma(222;0.0208)|Esophageal squamous(93;0.0559)		Epithelial(10;1.3e-11)|all cancers(11;2.07e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000873)|Lung(977;0.222)														---	---	---	---
GLB1L3	112937	broad.mit.edu	37	11	134163047	134163047	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134163047G>A	uc009zdf.2	+	9	1180	c.820G>A	c.(820-822)GCC>ACC	p.A274T	GLB1L3_uc010scs.1_Missense_Mutation_p.A274T|GLB1L3_uc010sct.1_Missense_Mutation_p.A126T|GLB1L3_uc010scu.1_5'UTR	NM_001080407	NP_001073876	Q8NCI6	GLBL3_HUMAN	galactosidase, beta 1 like 3	274					carbohydrate metabolic process		cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			pancreas(1)	1	all_hematologic(175;0.127)	all_cancers(12;5.52e-23)|all_epithelial(12;2.15e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|all_neural(223;0.0182)|Medulloblastoma(222;0.0208)|Esophageal squamous(93;0.0559)		Epithelial(10;1.3e-11)|all cancers(11;2.07e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000873)|Lung(977;0.222)														---	---	---	---
IQSEC3	440073	broad.mit.edu	37	12	284168	284168	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:284168G>A	uc001qhw.1	+	11	2615	c.2609G>A	c.(2608-2610)CGC>CAC	p.R870H		NM_015232	NP_056047	Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3	1173					regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity			central_nervous_system(2)|large_intestine(1)|skin(1)	4	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)														---	---	---	---
SLC6A12	6539	broad.mit.edu	37	12	313795	313795	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:313795G>A	uc001qhz.2	-	5	827	c.284C>T	c.(283-285)GCG>GTG	p.A95V	SLC6A12_uc001qia.2_Missense_Mutation_p.A95V|SLC6A12_uc001qib.2_Missense_Mutation_p.A95V|SLC6A12_uc009zdh.1_Missense_Mutation_p.A95V|SLC6A12_uc009zdi.1_RNA	NM_003044	NP_003035	P48065	S6A12_HUMAN	solute carrier family 6 (neurotransmitter	95					cellular nitrogen compound metabolic process|neurotransmitter secretion	integral to plasma membrane	gamma-aminobutyric acid:sodium symporter activity|neurotransmitter:sodium symporter activity			ovary(1)	1	all_cancers(10;0.0172)|all_epithelial(11;0.0283)|all_lung(10;0.0392)|Lung NSC(10;0.0567)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00227)															---	---	---	---
SLC6A12	6539	broad.mit.edu	37	12	318927	318927	+	Intron	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:318927A>C	uc001qhz.2	-						SLC6A12_uc001qia.2_Intron|SLC6A12_uc001qib.2_Intron|SLC6A12_uc009zdh.1_Intron|SLC6A12_uc009zdi.1_Intron	NM_003044	NP_003035			solute carrier family 6 (neurotransmitter						cellular nitrogen compound metabolic process|neurotransmitter secretion	integral to plasma membrane	gamma-aminobutyric acid:sodium symporter activity|neurotransmitter:sodium symporter activity			ovary(1)	1	all_cancers(10;0.0172)|all_epithelial(11;0.0283)|all_lung(10;0.0392)|Lung NSC(10;0.0567)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00227)															---	---	---	---
KDM5A	5927	broad.mit.edu	37	12	427308	427308	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:427308C>T	uc001qif.1	-	19	3224	c.2861G>A	c.(2860-2862)CGA>CAA	p.R954Q	KDM5A_uc001qie.1_Missense_Mutation_p.R954Q|KDM5A_uc010sdn.1_Missense_Mutation_p.R913Q	NM_001042603	NP_001036068	P29375	KDM5A_HUMAN	retinoblastoma binding protein 2 isoform 1	954					chromatin modification|multicellular organismal development|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|ovary(1)	3								T 	NUP98	AML								---	---	---	---
KDM5A	5927	broad.mit.edu	37	12	437991	437991	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:437991G>A	uc001qif.1	-						KDM5A_uc001qie.1_Intron|KDM5A_uc010sdn.1_Intron|KDM5A_uc010sdo.1_Intron	NM_001042603	NP_001036068			retinoblastoma binding protein 2 isoform 1						chromatin modification|multicellular organismal development|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(2)|ovary(1)	3								T 	NUP98	AML								---	---	---	---
CCDC77	84318	broad.mit.edu	37	12	550073	550073	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:550073C>T	uc001qig.2	+	12	1411	c.1231C>T	c.(1231-1233)CGT>TGT	p.R411C	CCDC77_uc009zdk.2_Missense_Mutation_p.R379C|CCDC77_uc010sdp.1_Missense_Mutation_p.R379C|CCDC77_uc010sdq.1_Missense_Mutation_p.R379C	NM_032358	NP_115734	Q9BR77	CCD77_HUMAN	coiled-coil domain containing 77 isoform a	411	Potential.					centrosome				ovary(1)	1	all_cancers(10;0.0149)|all_epithelial(11;0.035)|all_lung(10;0.111)|Ovarian(42;0.142)|Lung NSC(10;0.156)		OV - Ovarian serous cystadenocarcinoma(31;0.00123)|BRCA - Breast invasive adenocarcinoma(9;0.033)															---	---	---	---
WNK1	65125	broad.mit.edu	37	12	936230	936230	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:936230A>G	uc001qio.3	+	3	1462	c.955A>G	c.(955-957)ATG>GTG	p.M319V	WNK1_uc001qin.2_Missense_Mutation_p.M319V|WNK1_uc001qip.3_Missense_Mutation_p.M319V	NM_018979	NP_061852	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	319	Protein kinase.				intracellular protein kinase cascade|ion transport|neuron development	cytoplasm	ATP binding|protein binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			stomach(6)|breast(6)|ovary(5)|lung(4)|large_intestine(1)|central_nervous_system(1)	23	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)															---	---	---	---
CACNA2D4	93589	broad.mit.edu	37	12	1953648	1953648	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1953648C>T	uc001qjp.2	-	25	2621	c.2390G>A	c.(2389-2391)CGC>CAC	p.R797H	CACNA2D4_uc009zds.1_RNA|CACNA2D4_uc009zdt.1_Missense_Mutation_p.R661H|CACNA2D4_uc009zdr.1_RNA	NM_172364	NP_758952	Q7Z3S7	CA2D4_HUMAN	voltage-gated calcium channel alpha(2)delta-4	797	Extracellular (Potential).					integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			ovary(1)	1	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)														---	---	---	---
CACNA2D4	93589	broad.mit.edu	37	12	1965202	1965202	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:1965202T>G	uc001qjp.2	-	22	2359	c.2128A>C	c.(2128-2130)ACC>CCC	p.T710P	CACNA2D4_uc009zds.1_RNA|CACNA2D4_uc009zdt.1_Missense_Mutation_p.T574P|CACNA2D4_uc009zdr.1_5'Flank	NM_172364	NP_758952	Q7Z3S7	CA2D4_HUMAN	voltage-gated calcium channel alpha(2)delta-4	710	Extracellular (Potential).			T -> A (in Ref. 2; CAD97679).		integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			ovary(1)	1	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)														---	---	---	---
CACNA1C	775	broad.mit.edu	37	12	2224653	2224653	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2224653C>T	uc009zdu.1	+	2	626	c.313C>T	c.(313-315)CTC>TTC	p.L105F	CACNA1C_uc009zdv.1_Missense_Mutation_p.L105F|CACNA1C_uc001qkb.2_Missense_Mutation_p.L105F|CACNA1C_uc001qkc.2_Missense_Mutation_p.L105F|CACNA1C_uc001qke.2_Missense_Mutation_p.L105F|CACNA1C_uc001qkf.2_Missense_Mutation_p.L105F|CACNA1C_uc001qjz.2_Missense_Mutation_p.L105F|CACNA1C_uc001qkd.2_Missense_Mutation_p.L105F|CACNA1C_uc001qkg.2_Missense_Mutation_p.L105F|CACNA1C_uc009zdw.1_Missense_Mutation_p.L105F|CACNA1C_uc001qkh.2_Missense_Mutation_p.L105F|CACNA1C_uc001qkl.2_Missense_Mutation_p.L105F|CACNA1C_uc001qkn.2_Missense_Mutation_p.L105F|CACNA1C_uc001qko.2_Missense_Mutation_p.L105F|CACNA1C_uc001qkp.2_Missense_Mutation_p.L105F|CACNA1C_uc001qkr.2_Missense_Mutation_p.L105F|CACNA1C_uc001qku.2_Missense_Mutation_p.L105F|CACNA1C_uc001qkq.2_Missense_Mutation_p.L105F|CACNA1C_uc001qks.2_Missense_Mutation_p.L105F|CACNA1C_uc001qkt.2_Missense_Mutation_p.L105F	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,	105	Cytoplasmic (Potential).				axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)													---	---	---	---
CACNA1C	775	broad.mit.edu	37	12	2558202	2558202	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2558202G>A	uc009zdu.1	+	4	851	c.538G>A	c.(538-540)GCC>ACC	p.A180T	CACNA1C_uc009zdv.1_Missense_Mutation_p.A180T|CACNA1C_uc001qkb.2_Missense_Mutation_p.A180T|CACNA1C_uc001qkc.2_Missense_Mutation_p.A180T|CACNA1C_uc001qke.2_Missense_Mutation_p.A180T|CACNA1C_uc001qkf.2_Missense_Mutation_p.A180T|CACNA1C_uc001qjz.2_Missense_Mutation_p.A180T|CACNA1C_uc001qkd.2_Missense_Mutation_p.A180T|CACNA1C_uc001qkg.2_Missense_Mutation_p.A180T|CACNA1C_uc009zdw.1_Missense_Mutation_p.A180T|CACNA1C_uc001qkh.2_Missense_Mutation_p.A180T|CACNA1C_uc001qkl.2_Missense_Mutation_p.A180T|CACNA1C_uc001qkn.2_Missense_Mutation_p.A180T|CACNA1C_uc001qko.2_Missense_Mutation_p.A180T|CACNA1C_uc001qkp.2_Missense_Mutation_p.A180T|CACNA1C_uc001qkr.2_Missense_Mutation_p.A180T|CACNA1C_uc001qku.2_Missense_Mutation_p.A180T|CACNA1C_uc001qkq.2_Missense_Mutation_p.A180T|CACNA1C_uc001qks.2_Missense_Mutation_p.A180T|CACNA1C_uc001qkt.2_Missense_Mutation_p.A180T|CACNA1C_uc001qka.1_5'UTR|CACNA1C_uc001qki.1_5'UTR|CACNA1C_uc001qkj.1_5'UTR|CACNA1C_uc001qkk.1_5'UTR|CACNA1C_uc001qkm.1_5'UTR	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,	180	I.|Helical; Name=S2 of repeat I; (Potential).				axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)													---	---	---	---
CACNA1C	775	broad.mit.edu	37	12	2602473	2602473	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2602473A>G	uc009zdu.1	+	7	1347	c.1034A>G	c.(1033-1035)AAC>AGC	p.N345S	CACNA1C_uc009zdv.1_Missense_Mutation_p.N342S|CACNA1C_uc001qkb.2_Missense_Mutation_p.N345S|CACNA1C_uc001qkc.2_Missense_Mutation_p.N345S|CACNA1C_uc001qke.2_Missense_Mutation_p.N345S|CACNA1C_uc001qkf.2_Missense_Mutation_p.N345S|CACNA1C_uc001qjz.2_Missense_Mutation_p.N345S|CACNA1C_uc001qkd.2_Missense_Mutation_p.N345S|CACNA1C_uc001qkg.2_Missense_Mutation_p.N345S|CACNA1C_uc009zdw.1_Missense_Mutation_p.N345S|CACNA1C_uc001qkh.2_Missense_Mutation_p.N345S|CACNA1C_uc001qkl.2_Missense_Mutation_p.N345S|CACNA1C_uc001qkn.2_Missense_Mutation_p.N345S|CACNA1C_uc001qko.2_Missense_Mutation_p.N345S|CACNA1C_uc001qkp.2_Missense_Mutation_p.N345S|CACNA1C_uc001qkr.2_Missense_Mutation_p.N345S|CACNA1C_uc001qku.2_Missense_Mutation_p.N345S|CACNA1C_uc001qkq.2_Missense_Mutation_p.N345S|CACNA1C_uc001qks.2_Missense_Mutation_p.N345S|CACNA1C_uc001qkt.2_Missense_Mutation_p.N345S|CACNA1C_uc001qka.1_5'UTR|CACNA1C_uc001qki.1_Missense_Mutation_p.N81S|CACNA1C_uc001qkj.1_Missense_Mutation_p.N81S|CACNA1C_uc001qkk.1_Missense_Mutation_p.N81S|CACNA1C_uc001qkm.1_Missense_Mutation_p.N81S	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,	345	I.|Extracellular (Potential).				axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)													---	---	---	---
FOXM1	2305	broad.mit.edu	37	12	2983624	2983624	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2983624C>T	uc001qlf.2	-	2	286	c.21G>A	c.(19-21)CGG>CGA	p.R7R	TULP3_uc010sef.1_5'Flank|FOXM1_uc001qle.2_Silent_p.R7R|FOXM1_uc001qlg.2_Silent_p.R7R|FOXM1_uc009zea.2_Silent_p.R7R|FOXM1_uc009zeb.2_Silent_p.R7R|C12orf32_uc001qlh.2_5'Flank|C12orf32_uc010see.1_5'Flank|C12orf32_uc001qli.2_5'Flank	NM_021953	NP_068772	Q08050	FOXM1_HUMAN	forkhead box M1 isoform 2	7					cell cycle|embryo development|liver development|negative regulation of cell aging|negative regulation of stress-activated MAPK cascade|negative regulation of transcription from RNA polymerase II promoter|pattern specification process|positive regulation of cell proliferation|positive regulation of transcription from RNA polymerase II promoter|regulation of cell cycle arrest|regulation of cell growth|regulation of cell proliferation|regulation of oxygen and reactive oxygen species metabolic process|regulation of Ras protein signal transduction|regulation of reactive oxygen species metabolic process|regulation of sequence-specific DNA binding transcription factor activity|tissue development|transcription from RNA polymerase II promoter|vasculogenesis	cytoplasm|transcription factor complex	DNA bending activity|DNA binding|DNA binding|double-stranded DNA binding|promoter binding|protein binding|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|transcription factor binding			central_nervous_system(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(31;0.000622)															---	---	---	---
FOXM1	2305	broad.mit.edu	37	12	2983628	2983628	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2983628C>T	uc001qlf.2	-	2	282	c.17G>A	c.(16-18)CGT>CAT	p.R6H	TULP3_uc010sef.1_5'Flank|FOXM1_uc001qle.2_Missense_Mutation_p.R6H|FOXM1_uc001qlg.2_Missense_Mutation_p.R6H|FOXM1_uc009zea.2_Missense_Mutation_p.R6H|FOXM1_uc009zeb.2_Missense_Mutation_p.R6H|C12orf32_uc001qlh.2_5'Flank|C12orf32_uc010see.1_5'Flank|C12orf32_uc001qli.2_5'Flank	NM_021953	NP_068772	Q08050	FOXM1_HUMAN	forkhead box M1 isoform 2	6					cell cycle|embryo development|liver development|negative regulation of cell aging|negative regulation of stress-activated MAPK cascade|negative regulation of transcription from RNA polymerase II promoter|pattern specification process|positive regulation of cell proliferation|positive regulation of transcription from RNA polymerase II promoter|regulation of cell cycle arrest|regulation of cell growth|regulation of cell proliferation|regulation of oxygen and reactive oxygen species metabolic process|regulation of Ras protein signal transduction|regulation of reactive oxygen species metabolic process|regulation of sequence-specific DNA binding transcription factor activity|tissue development|transcription from RNA polymerase II promoter|vasculogenesis	cytoplasm|transcription factor complex	DNA bending activity|DNA binding|DNA binding|double-stranded DNA binding|promoter binding|protein binding|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|transcription factor binding			central_nervous_system(1)|skin(1)	2			OV - Ovarian serous cystadenocarcinoma(31;0.000622)															---	---	---	---
TEAD4	7004	broad.mit.edu	37	12	3120178	3120178	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3120178G>A	uc010sej.1	+	4	509	c.232G>A	c.(232-234)GAG>AAG	p.E78K	TEAD4_uc010sek.1_Missense_Mutation_p.E78K|TEAD4_uc001qln.2_5'UTR	NM_003213	NP_003204	Q15561	TEAD4_HUMAN	TEA domain family member 4 isoform 1	79	TEA.				hippo signaling cascade|muscle organ development|skeletal system development		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0	Ovarian(42;0.211)		OV - Ovarian serous cystadenocarcinoma(31;0.000563)|COAD - Colon adenocarcinoma(12;0.0831)															---	---	---	---
PRMT8	56341	broad.mit.edu	37	12	3659123	3659123	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3659123C>T	uc001qmf.2	+	3	650	c.283C>T	c.(283-285)CGG>TGG	p.R95W	PRMT8_uc009zed.2_Missense_Mutation_p.R86W|PRMT8_uc009zee.1_RNA	NM_019854	NP_062828	Q9NR22	ANM8_HUMAN	HMT1 hnRNP methyltransferase-like 4	95		S-adenosyl-L-methionine (By similarity).			regulation of protein binding	cytoplasm|plasma membrane	histone-arginine N-methyltransferase activity|protein heterodimerization activity|protein homodimerization activity|protein-arginine omega-N asymmetric methyltransferase activity|protein-arginine omega-N monomethyltransferase activity			ovary(3)|central_nervous_system(1)|skin(1)	5			OV - Ovarian serous cystadenocarcinoma(31;0.0109)|COAD - Colon adenocarcinoma(12;0.0264)															---	---	---	---
EFCAB4B	84766	broad.mit.edu	37	12	3768788	3768788	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:3768788T>C	uc001qmj.2	-	8	1276	c.704A>G	c.(703-705)CAT>CGT	p.H235R	EFCAB4B_uc010sen.1_Missense_Mutation_p.H235R|EFCAB4B_uc010seo.1_Missense_Mutation_p.H235R|EFCAB4B_uc001qmi.1_RNA	NM_032680	NP_116069	Q9BSW2	EFC4B_HUMAN	EF-hand calcium binding domain 4B isoform c	235	Potential.				activation of store-operated calcium channel activity|store-operated calcium entry	cytoplasm	calcium ion binding|protein binding			ovary(1)|pancreas(1)	2			OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264)															---	---	---	---
FGF6	2251	broad.mit.edu	37	12	4543499	4543499	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4543499G>A	uc001qmr.1	-	3	553	c.509C>T	c.(508-510)GCC>GTC	p.A170V		NM_020996	NP_066276	P10767	FGF6_HUMAN	fibroblast growth factor 6 precursor	170					angiogenesis|cell proliferation|cell-cell signaling|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|positive regulation of cell division|positive regulation of cell proliferation	extracellular space	growth factor activity			lung(2)|ovary(1)	3			Colorectal(7;0.00165)|COAD - Colon adenocarcinoma(12;0.0229)															---	---	---	---
NDUFA9	4704	broad.mit.edu	37	12	4777687	4777687	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4777687A>G	uc001qnc.2	+	7	730	c.720A>G	c.(718-720)GTA>GTG	p.V240V	NDUFA9_uc009zei.1_3'UTR|NDUFA9_uc010ses.1_Silent_p.V21V	NM_005002	NP_004993	Q16795	NDUA9_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha	240					mitochondrial electron transport, NADH to ubiquinone|sodium ion transport	mitochondrial matrix|mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity|protein binding			ovary(1)	1					NADH(DB00157)													---	---	---	---
GALNT8	26290	broad.mit.edu	37	12	4854629	4854629	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:4854629C>T	uc001qne.1	+	5	987	c.895C>T	c.(895-897)CGC>TGC	p.R299C		NM_017417	NP_059113	Q9NY28	GALT8_HUMAN	polypeptide N-acetylgalactosaminyltransferase 8	299	Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
KCNA5	3741	broad.mit.edu	37	12	5154251	5154251	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5154251C>A	uc001qni.2	+	1	1167	c.938C>A	c.(937-939)GCA>GAA	p.A313E		NM_002234	NP_002225	P22460	KCNA5_HUMAN	potassium voltage-gated channel, shaker-related	313						Golgi apparatus|voltage-gated potassium channel complex	delayed rectifier potassium channel activity			ovary(2)|breast(2)	4																		---	---	---	---
ANO2	57101	broad.mit.edu	37	12	5724430	5724430	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:5724430C>T	uc001qnm.2	-	18	1922	c.1850G>A	c.(1849-1851)CGC>CAC	p.R617H		NM_020373	NP_065106	Q9NQ90	ANO2_HUMAN	anoctamin 2	622	Cytoplasmic (Potential).					chloride channel complex|plasma membrane	intracellular calcium activated chloride channel activity			ovary(4)|large_intestine(2)|central_nervous_system(1)	7																		---	---	---	---
VWF	7450	broad.mit.edu	37	12	6134769	6134769	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6134769C>T	uc001qnn.1	-	24	3449	c.3199G>A	c.(3199-3201)GTC>ATC	p.V1067I	VWF_uc010set.1_Intron	NM_000552	NP_000543	P04275	VWF_HUMAN	von Willebrand factor preproprotein	1067	VWFD 3.				blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)	12					Antihemophilic Factor(DB00025)													---	---	---	---
NCAPD2	9918	broad.mit.edu	37	12	6623699	6623699	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6623699T>C	uc001qoo.2	+	8	831	c.785T>C	c.(784-786)GTG>GCG	p.V262A	NCAPD2_uc009zen.1_Missense_Mutation_p.V134A|NCAPD2_uc010sfd.1_Missense_Mutation_p.V217A	NM_014865	NP_055680	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	262	Interactions with SMC2 and SMC4.				cell division|mitotic chromosome condensation	condensin core heterodimer|cytoplasm	histone binding			ovary(2)|lung(1)|breast(1)|kidney(1)	5																		---	---	---	---
CHD4	1108	broad.mit.edu	37	12	6682310	6682310	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6682310C>T	uc001qpo.2	-	38	5651	c.5487G>A	c.(5485-5487)GCG>GCA	p.A1829A	CHD4_uc001qpn.2_Silent_p.A1822A|CHD4_uc001qpp.2_Silent_p.A1854A	NM_001273	NP_001264	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	1829	Required for interaction with PCNT.				chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	microtubule organizing center|NuRD complex	ATP binding|ATP-dependent DNA helicase activity|DNA binding|zinc ion binding			central_nervous_system(2)	2																		---	---	---	---
CHD4	1108	broad.mit.edu	37	12	6696578	6696578	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6696578T>C	uc001qpo.2	-	25	4015	c.3851A>G	c.(3850-3852)CAG>CGG	p.Q1284R	CHD4_uc001qpn.2_Missense_Mutation_p.Q1277R|CHD4_uc001qpp.2_Missense_Mutation_p.Q1281R	NM_001273	NP_001264	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	1284					chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	microtubule organizing center|NuRD complex	ATP binding|ATP-dependent DNA helicase activity|DNA binding|zinc ion binding			central_nervous_system(2)	2																		---	---	---	---
CHD4	1108	broad.mit.edu	37	12	6701118	6701118	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6701118G>A	uc001qpo.2	-	20	3218	c.3054C>T	c.(3052-3054)TGC>TGT	p.C1018C	CHD4_uc001qpn.2_Silent_p.C1011C|CHD4_uc001qpp.2_Silent_p.C1015C	NM_001273	NP_001264	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	1018					chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	microtubule organizing center|NuRD complex	ATP binding|ATP-dependent DNA helicase activity|DNA binding|zinc ion binding			central_nervous_system(2)	2																		---	---	---	---
C12orf53	196500	broad.mit.edu	37	12	6806691	6806691	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6806691C>A	uc001qqf.1	-	3	361	c.285G>T	c.(283-285)GAG>GAT	p.E95D	C12orf53_uc001qqg.1_Missense_Mutation_p.E95D	NM_153685	NP_710152	Q8IYJ0	CL053_HUMAN	hypothetical protein LOC196500 precursor	95	Extracellular (Potential).					integral to membrane					0																		---	---	---	---
CD4	920	broad.mit.edu	37	12	6923409	6923409	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6923409A>G	uc001qqv.1	+	4	561	c.316A>G	c.(316-318)ACT>GCT	p.T106A	CD4_uc009zez.1_Missense_Mutation_p.T51A|CD4_uc009zfa.1_RNA|CD4_uc009zfb.1_RNA|CD4_uc010sfj.1_Translation_Start_Site|CD4_uc009zfc.1_Translation_Start_Site|CD4_uc010sfk.1_Translation_Start_Site|CD4_uc010sfl.1_Translation_Start_Site|CD4_uc010sfm.1_Translation_Start_Site	NM_000616	NP_000607	P01730	CD4_HUMAN	CD4 antigen precursor	106	Extracellular (Potential).|Ig-like V-type.				cell adhesion|entry into host cell|immune response|induction by virus of host cell-cell fusion|initiation of viral infection|maintenance of protein location in cell|positive regulation of interleukin-2 biosynthetic process|positive regulation of protein kinase activity|protein palmitoleylation|regulation of defense response to virus by virus|T cell costimulation|T cell receptor signaling pathway|T cell selection|transmembrane receptor protein tyrosine kinase signaling pathway	early endosome|endoplasmic reticulum membrane|integral to membrane|T cell receptor complex	coreceptor activity|extracellular matrix structural constituent|glycoprotein binding|MHC class II protein binding|protein homodimerization activity|protein kinase binding|transmembrane receptor activity|zinc ion binding				0		Myeloproliferative disorder(1001;0.0122)																---	---	---	---
GNB3	2784	broad.mit.edu	37	12	6954793	6954793	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6954793C>A	uc001qrd.2	+	10	1148	c.743C>A	c.(742-744)GCT>GAT	p.A248D	GNB3_uc001qrc.2_Missense_Mutation_p.A204D|GNB3_uc009zfe.2_Missense_Mutation_p.A247D|CDCA3_uc001qre.2_3'UTR|uc001qrf.1_RNA	NM_002075	NP_002066	P16520	GBB3_HUMAN	guanine nucleotide-binding protein, beta-3	248	WD 5.				cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|regulation of blood pressure|synaptic transmission	plasma membrane	GTPase activity|GTPase binding|signal transducer activity				0																		---	---	---	---
USP5	8078	broad.mit.edu	37	12	6968675	6968675	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6968675C>T	uc001qri.3	+	9	1159	c.1100C>T	c.(1099-1101)ACG>ATG	p.T367M	USP5_uc001qrh.3_Missense_Mutation_p.T367M	NM_001098536	NP_001092006	P45974	UBP5_HUMAN	ubiquitin specific peptidase 5 isoform 1	367					positive regulation of proteasomal ubiquitin-dependent protein catabolic process|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process	lysosome	cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|zinc ion binding			lung(2)|breast(1)|skin(1)	4																		---	---	---	---
C1R	715	broad.mit.edu	37	12	7188284	7188284	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7188284T>C	uc010sfy.1	-	10	1729	c.1670A>G	c.(1669-1671)GAC>GGC	p.D557G		NM_001733	NP_001724	P00736	C1R_HUMAN	complement component 1, r subcomponent	557	Peptidase S1.	Charge relay system.			complement activation, classical pathway|innate immune response|proteolysis	extracellular region	calcium ion binding|serine-type endopeptidase activity				0					Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)													---	---	---	---
C1R	715	broad.mit.edu	37	12	7188536	7188536	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7188536C>A	uc010sfy.1	-	10	1477	c.1418G>T	c.(1417-1419)GGC>GTC	p.G473V		NM_001733	NP_001724	P00736	C1R_HUMAN	complement component 1, r subcomponent	473	Peptidase S1.				complement activation, classical pathway|innate immune response|proteolysis	extracellular region	calcium ion binding|serine-type endopeptidase activity				0					Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)													---	---	---	---
C1R	715	broad.mit.edu	37	12	7241899	7241899	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7241899T>G	uc010sfy.1	-	5	817	c.758A>C	c.(757-759)GAC>GCC	p.D253A	C1R_uc010sfz.1_Missense_Mutation_p.D267A|C1R_uc010sga.1_Missense_Mutation_p.D219A	NM_001733	NP_001724	P00736	C1R_HUMAN	complement component 1, r subcomponent	253	CUB 2.				complement activation, classical pathway|innate immune response|proteolysis	extracellular region	calcium ion binding|serine-type endopeptidase activity				0					Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)													---	---	---	---
CLSTN3	9746	broad.mit.edu	37	12	7302277	7302277	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7302277C>A	uc001qsr.2	+	14	2511	c.2233C>A	c.(2233-2235)CTC>ATC	p.L745I	CLSTN3_uc001qss.2_Missense_Mutation_p.L757I	NM_014718	NP_055533	Q9BQT9	CSTN3_HUMAN	calsyntenin 3 precursor	745	Extracellular (Potential).				homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			large_intestine(1)	1																		---	---	---	---
CD163L1	283316	broad.mit.edu	37	12	7548933	7548933	+	Missense_Mutation	SNP	C	T	T	rs145169248		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7548933C>T	uc001qsy.2	-	8	1834	c.1808G>A	c.(1807-1809)CGG>CAG	p.R603Q	CD163L1_uc010sge.1_Missense_Mutation_p.R613Q	NM_174941	NP_777601	Q9NR16	C163B_HUMAN	scavenger receptor cysteine-rich type 1	603	SRCR 6.|Extracellular (Potential).					extracellular region|integral to membrane|plasma membrane	scavenger receptor activity			ovary(8)|skin(2)|central_nervous_system(1)	11																		---	---	---	---
CD163	9332	broad.mit.edu	37	12	7640377	7640377	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7640377A>C	uc001qsz.3	-	7	1855	c.1727T>G	c.(1726-1728)GTC>GGC	p.V576G	CD163_uc001qta.3_Missense_Mutation_p.V576G|CD163_uc009zfw.2_Missense_Mutation_p.V576G	NM_004244	NP_004235	Q86VB7	C163A_HUMAN	CD163 antigen isoform a	576	SRCR 5.|Extracellular (Potential).				acute-phase response	extracellular region|integral to plasma membrane	protein binding|scavenger receptor activity			ovary(6)|pancreas(1)|skin(1)	8																		---	---	---	---
A2ML1	144568	broad.mit.edu	37	12	9009922	9009922	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9009922G>A	uc001quz.3	+	24	3109	c.3011G>A	c.(3010-3012)GGT>GAT	p.G1004D	A2ML1_uc001qva.1_Missense_Mutation_p.G584D|A2ML1_uc010sgm.1_Missense_Mutation_p.G504D	NM_144670	NP_653271	A8K2U0	A2ML1_HUMAN	alpha-2-macroglobulin-like 1 precursor	848						extracellular space	endopeptidase inhibitor activity			ovary(2)|skin(1)	3																		---	---	---	---
A2M	2	broad.mit.edu	37	12	9251287	9251287	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9251287C>T	uc001qvk.1	-	15	1880	c.1767G>A	c.(1765-1767)GCG>GCA	p.A589A	A2M_uc009zgk.1_Silent_p.A439A	NM_000014	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin precursor	589					blood coagulation, intrinsic pathway|negative regulation of complement activation, lectin pathway|platelet activation|platelet degranulation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|extracellular space|platelet alpha granule lumen	enzyme binding|GTPase activator activity|interleukin-1 binding|interleukin-8 binding|serine-type endopeptidase inhibitor activity|tumor necrosis factor binding			central_nervous_system(4)|skin(1)	5					Bacitracin(DB00626)|Becaplermin(DB00102)													---	---	---	---
A2M	2	broad.mit.edu	37	12	9266118	9266118	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9266118G>A	uc001qvk.1	-	2	221	c.108C>T	c.(106-108)CCC>CCT	p.P36P	A2M_uc009zgk.1_5'UTR	NM_000014	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin precursor	36					blood coagulation, intrinsic pathway|negative regulation of complement activation, lectin pathway|platelet activation|platelet degranulation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|extracellular space|platelet alpha granule lumen	enzyme binding|GTPase activator activity|interleukin-1 binding|interleukin-8 binding|serine-type endopeptidase inhibitor activity|tumor necrosis factor binding			central_nervous_system(4)|skin(1)	5					Bacitracin(DB00626)|Becaplermin(DB00102)													---	---	---	---
CLEC1B	51266	broad.mit.edu	37	12	10147799	10147799	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10147799G>A	uc001qwu.2	-	5	685	c.485C>T	c.(484-486)TCT>TTT	p.S162F	CLEC1B_uc009zhd.2_Missense_Mutation_p.S129F	NM_016509	NP_057593	Q9P126	CLC1B_HUMAN	C-type lectin domain family 1, member B isoform	162	C-type lectin.|Extracellular (Potential).				cell surface receptor linked signaling pathway|defense response	integral to plasma membrane	protein binding|sugar binding|transmembrane receptor activity				0																		---	---	---	---
CSDA	8531	broad.mit.edu	37	12	10854719	10854719	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10854719C>T	uc001qyt.2	-	8	1136	c.893G>A	c.(892-894)CGC>CAC	p.R298H	CSDA_uc001qyu.2_Missense_Mutation_p.R229H	NM_003651	NP_003642	P16989	DBPA_HUMAN	cold shock domain protein A isoform a	298					negative regulation of transcription from RNA polymerase II promoter|response to cold	cytoplasm|nucleus	double-stranded DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(2)|lung(1)|large_intestine(1)	4	Glioma(1;0.155)																	---	---	---	---
TAS2R10	50839	broad.mit.edu	37	12	10978475	10978475	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10978475T>C	uc001qyy.1	-	1	394	c.394A>G	c.(394-396)ATG>GTG	p.M132V		NM_023921	NP_076410	Q9NYW0	T2R10_HUMAN	taste receptor, type 2, member 10	132	Helical; Name=4; (Potential).				sensory perception of taste	integral to membrane	taste receptor activity				0																		---	---	---	---
LRP6	4040	broad.mit.edu	37	12	12312810	12312810	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:12312810C>T	uc001rah.3	-	11	2510	c.2368G>A	c.(2368-2370)GTG>ATG	p.V790M	BCL2L14_uc001raf.1_Intron|LRP6_uc010shl.1_Missense_Mutation_p.V790M	NM_002336	NP_002327	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein	790	Extracellular (Potential).|LDL-receptor class B 13.|Beta-propeller 3.				cellular response to cholesterol|negative regulation of protein phosphorylation|negative regulation of protein serine/threonine kinase activity|negative regulation of smooth muscle cell apoptosis|neural crest formation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell cycle|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	cell surface|cytoplasmic vesicle|endoplasmic reticulum|integral to membrane|plasma membrane	coreceptor activity|frizzled binding|kinase inhibitor activity|low-density lipoprotein receptor activity|protein homodimerization activity|toxin transporter activity|Wnt-protein binding			lung(4)|skin(4)|ovary(2)|kidney(1)|central_nervous_system(1)	12		Prostate(47;0.0865)																---	---	---	---
GPRC5A	9052	broad.mit.edu	37	12	13065417	13065417	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13065417G>C	uc001rba.2	+	4	1668	c.1018G>C	c.(1018-1020)GCC>CCC	p.A340P	uc001rbb.3_5'Flank	NM_003979	NP_003970	Q8NFJ5	RAI3_HUMAN	G protein-coupled receptor, family C, group 5,	340	Cytoplasmic (Potential).					cytoplasmic vesicle membrane|Golgi apparatus|integral to plasma membrane	G-protein coupled receptor activity				0		Prostate(47;0.141)		BRCA - Breast invasive adenocarcinoma(232;0.0708)	Tretinoin(DB00755)													---	---	---	---
KIAA1467	57613	broad.mit.edu	37	12	13224228	13224228	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13224228G>A	uc001rbi.2	+	10	1445	c.1422G>A	c.(1420-1422)CCG>CCA	p.P474P	KIAA1467_uc009zhx.1_RNA	NM_020853	NP_065904	A2RU67	K1467_HUMAN	hypothetical protein LOC57613	474						integral to membrane				central_nervous_system(2)|skin(1)	3		Prostate(47;0.184)		BRCA - Breast invasive adenocarcinoma(232;0.157)														---	---	---	---
EMP1	2012	broad.mit.edu	37	12	13367595	13367595	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13367595C>T	uc001rbr.2	+	5	691	c.444C>T	c.(442-444)GGC>GGT	p.G148G	EMP1_uc009zhy.2_Silent_p.G81G|EMP1_uc010shr.1_Missense_Mutation_p.A136V	NM_001423	NP_001414	P54849	EMP1_HUMAN	epithelial membrane protein 1	148	Helical; (Potential).				cell growth|cell proliferation|epidermis development	integral to membrane|membrane fraction					0		Prostate(47;0.194)		BRCA - Breast invasive adenocarcinoma(232;0.153)														---	---	---	---
GRIN2B	2904	broad.mit.edu	37	12	13716656	13716656	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13716656G>T	uc001rbt.2	-	13	3695	c.3516C>A	c.(3514-3516)CCC>CCA	p.P1172P		NM_000834	NP_000825	Q13224	NMDE2_HUMAN	N-methyl-D-aspartate receptor subunit 2B	1172	Cytoplasmic (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			central_nervous_system(4)|ovary(3)|skin(3)|lung(2)	12					Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)													---	---	---	---
GRIN2B	2904	broad.mit.edu	37	12	13717425	13717425	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13717425C>T	uc001rbt.2	-	13	2926	c.2747G>A	c.(2746-2748)GGC>GAC	p.G916D		NM_000834	NP_000825	Q13224	NMDE2_HUMAN	N-methyl-D-aspartate receptor subunit 2B	916	Cytoplasmic (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			central_nervous_system(4)|ovary(3)|skin(3)|lung(2)	12					Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)													---	---	---	---
GRIN2B	2904	broad.mit.edu	37	12	13906551	13906551	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13906551G>A	uc001rbt.2	-	3	889	c.710C>T	c.(709-711)GCC>GTC	p.A237V		NM_000834	NP_000825	Q13224	NMDE2_HUMAN	N-methyl-D-aspartate receptor subunit 2B	237	Extracellular (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			central_nervous_system(4)|ovary(3)|skin(3)|lung(2)	12					Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)													---	---	---	---
HIST4H4	121504	broad.mit.edu	37	12	14924027	14924027	+	5'UTR	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:14924027C>T	uc001rcf.3	-	1					HIST4H4_uc001rce.2_RNA	NM_175054	NP_778224			histone cluster 4, H4						CenH3-containing nucleosome assembly at centromere|negative regulation of megakaryocyte differentiation|phosphatidylinositol-mediated signaling|telomere maintenance	nucleoplasm|nucleosome	DNA binding|protein binding			ovary(2)	2																		---	---	---	---
MGST1	4257	broad.mit.edu	37	12	16507209	16507209	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:16507209T>C	uc001rdf.2	+	2	88	c.23T>C	c.(22-24)ATG>ACG	p.M8T	MGST1_uc001rdg.2_Missense_Mutation_p.M8T|MGST1_uc009zih.1_Intron|MGST1_uc001rdh.2_Missense_Mutation_p.M8T|MGST1_uc001rdi.2_Missense_Mutation_p.M8T	NM_145792	NP_665735	P10620	MGST1_HUMAN	microsomal glutathione S-transferase 1	8	Lumenal (By similarity).				protein homotrimerization|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane	glutathione transferase activity				0		Hepatocellular(102;0.121)			Glutathione(DB00143)													---	---	---	---
PLCZ1	89869	broad.mit.edu	37	12	18838559	18838559	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:18838559G>A	uc010sid.1	-						PLCZ1_uc001rdv.3_Intron|PLCZ1_uc001rdw.3_Intron|PLCZ1_uc001rdu.1_Intron|PLCZ1_uc009zil.1_RNA	NM_033123	NP_149114			phospholipase C, zeta 1						intracellular signal transduction|lipid catabolic process|multicellular organismal development	nucleus|perinuclear region of cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|lung(1)|skin(1)	3	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.0241)																	---	---	---	---
PDE3A	5139	broad.mit.edu	37	12	20522817	20522817	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:20522817C>T	uc001reh.1	+	1	621	c.599C>T	c.(598-600)GCC>GTC	p.A200V		NM_000921	NP_000912	Q14432	PDE3A_HUMAN	phosphodiesterase 3A	200	Helical; (Potential).				lipid metabolic process|platelet activation|signal transduction	cytosol|integral to membrane	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity|metal ion binding			ovary(3)|upper_aerodigestive_tract(1)	4	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Cilostazol(DB01166)|Enoximone(DB04880)|Milrinone(DB00235)|Theophylline(DB00277)													---	---	---	---
SLCO1A2	6579	broad.mit.edu	37	12	21453355	21453355	+	Silent	SNP	A	C	C	rs45629461	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21453355A>C	uc001rer.2	-	7	1088	c.837T>G	c.(835-837)GCT>GCG	p.A279A	SLCO1A2_uc001res.2_Silent_p.A279A|SLCO1A2_uc010siq.1_Silent_p.A147A|SLCO1A2_uc010sio.1_Silent_p.A147A|SLCO1A2_uc010sip.1_Silent_p.A147A|SLCO1A2_uc001ret.2_Silent_p.A277A|SLCO1A2_uc001reu.2_Silent_p.A259A	NM_021094	NP_066580	P46721	SO1A2_HUMAN	organic anion transporting polypeptide A	279	Cytoplasmic (Potential).				bile acid metabolic process|sodium-independent organic anion transport	integral to membrane|plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(1)|pancreas(1)|ovary(1)|skin(1)	4																		---	---	---	---
SLCO1A2	6579	broad.mit.edu	37	12	21457447	21457447	+	Missense_Mutation	SNP	C	T	T	rs148616059	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21457447C>T	uc001rer.2	-	5	754	c.503G>A	c.(502-504)CGT>CAT	p.R168H	SLCO1A2_uc001res.2_Missense_Mutation_p.R168H|SLCO1A2_uc010siq.1_Missense_Mutation_p.R36H|SLCO1A2_uc010sio.1_Missense_Mutation_p.R36H|SLCO1A2_uc010sip.1_Missense_Mutation_p.R36H|SLCO1A2_uc001ret.2_Missense_Mutation_p.R166H|SLCO1A2_uc001reu.2_Missense_Mutation_p.R148H	NM_021094	NP_066580	P46721	SO1A2_HUMAN	organic anion transporting polypeptide A	168	Helical; Name=4; (Potential).				bile acid metabolic process|sodium-independent organic anion transport	integral to membrane|plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(1)|pancreas(1)|ovary(1)|skin(1)	4																		---	---	---	---
LDHB	3945	broad.mit.edu	37	12	21807503	21807503	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21807503C>T	uc001rfc.2	-	1	121	c.103G>A	c.(103-105)GCG>ACG	p.A35T	LDHB_uc001rfd.2_Missense_Mutation_p.A35T|LDHB_uc001rfe.2_Missense_Mutation_p.A35T	NM_002300	NP_002291	P07195	LDHB_HUMAN	L-lactate dehydrogenase B	35	NAD (By similarity).		A -> E (in LDHB deficiency).		glycolysis|pyruvate metabolic process	cytosol	L-lactate dehydrogenase activity			breast(2)|ovary(1)	3					NADH(DB00157)													---	---	---	---
ETNK1	55500	broad.mit.edu	37	12	22796687	22796687	+	Intron	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:22796687T>A	uc001rft.2	+						ETNK1_uc009ziz.2_Intron|ETNK1_uc001rfs.2_Intron	NM_018638	NP_061108			ethanolamine kinase 1 isoform A						phosphatidylethanolamine biosynthetic process	cytoplasm	ATP binding|ethanolamine kinase activity				0																		---	---	---	---
KRAS	3845	broad.mit.edu	37	12	25380283	25380283	+	Missense_Mutation	SNP	C	T	T	rs121913528		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:25380283C>T	uc001rgp.1	-	3	356	c.175G>A	c.(175-177)GCA>ACA	p.A59T	KRAS_uc001rgq.1_Missense_Mutation_p.A59T	NM_033360	NP_203524	P01116	RASK_HUMAN	c-K-ras2 protein isoform a precursor	59	GTP.		A -> T (in bladder cancer and GASC; somatic mutation).		activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	plasma membrane	GTP binding|GTPase activity|protein binding	p.A59T(8)|p.A59E(3)|p.A59G(2)		large_intestine(12391)|pancreas(3285)|lung(2847)|biliary_tract(521)|ovary(443)|endometrium(339)|haematopoietic_and_lymphoid_tissue(318)|stomach(203)|thyroid(149)|prostate(85)|soft_tissue(77)|small_intestine(62)|upper_aerodigestive_tract(59)|cervix(49)|urinary_tract(48)|skin(38)|liver(31)|breast(28)|testis(17)|oesophagus(15)|central_nervous_system(9)|peritoneum(6)|salivary_gland(6)|kidney(5)|gastrointestinal_tract_(site_indeterminate)(5)|thymus(5)|eye(4)|autonomic_ganglia(2)|bone(2)|genital_tract(1)|penis(1)|adrenal_gland(1)	21052	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			A59T(143B_BONE)	119	Mis		pancreatic|colorectal|lung|thyroid|AML|others				Cardiofaciocutaneous_syndrome|Noonan_syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)			---	---	---	---
ITPR2	3709	broad.mit.edu	37	12	26634080	26634080	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26634080A>G	uc001rhg.2	-	43	6524	c.6107T>C	c.(6106-6108)CTG>CCG	p.L2036P	ITPR2_uc009zjg.1_Missense_Mutation_p.L187P	NM_002223	NP_002214	Q14571	ITPR2_HUMAN	inositol 1,4,5-triphosphate receptor, type 2	2036	Cytoplasmic (Potential).				activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)																	---	---	---	---
ITPR2	3709	broad.mit.edu	37	12	26864179	26864179	+	Missense_Mutation	SNP	C	T	T	rs144621254	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:26864179C>T	uc001rhg.2	-	9	1295	c.878G>A	c.(877-879)CGT>CAT	p.R293H		NM_002223	NP_002214	Q14571	ITPR2_HUMAN	inositol 1,4,5-triphosphate receptor, type 2	293	Cytoplasmic (Potential).				activation of phospholipase C activity|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	integral to membrane|plasma membrane enriched fraction|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity			kidney(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	14	Colorectal(261;0.0847)																	---	---	---	---
C12orf11	55726	broad.mit.edu	37	12	27089686	27089686	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:27089686G>A	uc001rhk.3	-	2	588	c.51C>T	c.(49-51)TGC>TGT	p.C17C	C12orf11_uc010sjk.1_Intron|FGFR1OP2_uc001rhl.2_5'Flank|FGFR1OP2_uc001rhm.2_5'Flank|FGFR1OP2_uc001rhn.2_5'Flank	NM_018164	NP_060634	Q9NVM9	M89BB_HUMAN	hypothetical protein LOC55726	17					cell division|mitosis|regulation of mitotic cell cycle		protein binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3	Colorectal(261;0.0847)																	---	---	---	---
OVCH1	341350	broad.mit.edu	37	12	29614923	29614923	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:29614923C>T	uc001rix.1	-	19	2144	c.2144G>A	c.(2143-2145)CGC>CAC	p.R715H		NM_183378	NP_899234	Q7RTY7	OVCH1_HUMAN	ovochymase 1 precursor	715	Peptidase S1 2.				proteolysis	extracellular region	metal ion binding|serine-type endopeptidase activity			ovary(3)|central_nervous_system(3)|pancreas(3)|large_intestine(1)	10	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)																	---	---	---	---
IPO8	10526	broad.mit.edu	37	12	30837379	30837379	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:30837379A>G	uc001rjd.2	-	3	349	c.179T>C	c.(178-180)CTG>CCG	p.L60P		NM_006390	NP_006381	O15397	IPO8_HUMAN	importin 8	60	Importin N-terminal.				intracellular protein transport|signal transduction	cytoplasm|nucleus	protein transporter activity|Ran GTPase binding			skin(2)|central_nervous_system(1)	3	all_lung(12;6.66e-10)|Lung NSC(12;4.84e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)																	---	---	---	---
C12orf35	55196	broad.mit.edu	37	12	32134148	32134148	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32134148C>T	uc001rks.2	+	4	673	c.259C>T	c.(259-261)CAC>TAC	p.H87Y		NM_018169	NP_060639	Q9HCM1	CL035_HUMAN	hypothetical protein LOC55196	87										ovary(1)|skin(1)	2	all_cancers(9;3.36e-11)|all_epithelial(9;2.56e-11)|all_lung(12;5.67e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0336)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0114)															---	---	---	---
C12orf35	55196	broad.mit.edu	37	12	32134702	32134702	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32134702G>A	uc001rks.2	+	4	1227	c.813G>A	c.(811-813)ACG>ACA	p.T271T		NM_018169	NP_060639	Q9HCM1	CL035_HUMAN	hypothetical protein LOC55196	271										ovary(1)|skin(1)	2	all_cancers(9;3.36e-11)|all_epithelial(9;2.56e-11)|all_lung(12;5.67e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0336)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0114)															---	---	---	---
PKP2	5318	broad.mit.edu	37	12	33021923	33021923	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:33021923T>C	uc001rlj.3	-	4	1223	c.1108A>G	c.(1108-1110)ATT>GTT	p.I370V	PKP2_uc001rlk.3_Missense_Mutation_p.I370V|PKP2_uc010skj.1_Missense_Mutation_p.I370V	NM_004572	NP_004563	Q99959	PKP2_HUMAN	plakophilin 2 isoform 2b	370	ARM 1.				cell-cell adhesion	desmosome|integral to membrane|nucleus	binding			ovary(1)|pancreas(1)	2	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)																	---	---	---	---
KIF21A	55605	broad.mit.edu	37	12	39760964	39760964	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39760964C>T	uc001rly.2	-	5	749	c.603G>A	c.(601-603)ATG>ATA	p.M201I	KIF21A_uc001rlx.2_Missense_Mutation_p.M201I|KIF21A_uc001rlz.2_Missense_Mutation_p.M201I|KIF21A_uc010skl.1_Missense_Mutation_p.M201I|KIF21A_uc001rma.1_Missense_Mutation_p.M209I	NM_017641	NP_060111	Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	201	Kinesin-motor.				microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(4)|pancreas(1)|lung(1)|skin(1)	7		Lung NSC(34;0.179)|all_lung(34;0.213)																---	---	---	---
ABCD2	225	broad.mit.edu	37	12	39967605	39967605	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39967605A>G	uc001rmb.2	-	9	2342	c.1916T>C	c.(1915-1917)GTC>GCC	p.V639A		NM_005164	NP_005155	Q9UBJ2	ABCD2_HUMAN	ATP-binding cassette, sub-family D, member 2	639	ABC transporter.				fatty acid metabolic process|transport	ATP-binding cassette (ABC) transporter complex|integral to plasma membrane|peroxisomal membrane	ATP binding|ATPase activity|protein binding			ovary(2)|upper_aerodigestive_tract(1)|pancreas(1)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
SLC2A13	114134	broad.mit.edu	37	12	40441892	40441892	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40441892A>G	uc010skm.1	-	2	728	c.677T>C	c.(676-678)GTT>GCT	p.V226A	SLC2A13_uc001rmf.2_Missense_Mutation_p.V226A	NM_052885	NP_443117	Q96QE2	MYCT_HUMAN	solute carrier family 2 (facilitated glucose	226	Helical; Name=5; (Potential).					integral to membrane|plasma membrane	myo-inositol:hydrogen symporter activity			ovary(1)	1		Lung NSC(34;0.105)|all_lung(34;0.123)													HNSCC(50;0.14)			---	---	---	---
CNTN1	1272	broad.mit.edu	37	12	41419122	41419122	+	Silent	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41419122T>G	uc001rmm.1	+	21	2807	c.2694T>G	c.(2692-2694)GCT>GCG	p.A898A	CNTN1_uc001rmn.1_Silent_p.A887A	NM_001843	NP_001834	Q12860	CNTN1_HUMAN	contactin 1 isoform 1 precursor	898	Fibronectin type-III 3.				axon guidance|cell adhesion|Notch signaling pathway	anchored to membrane|membrane fraction|plasma membrane				lung(4)|ovary(3)|large_intestine(1)|skin(1)	9	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)																---	---	---	---
PRICKLE1	144165	broad.mit.edu	37	12	42860069	42860069	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:42860069G>A	uc010skv.1	-	6	989	c.702C>T	c.(700-702)GAC>GAT	p.D234D	PRICKLE1_uc001rnl.2_Silent_p.D234D|PRICKLE1_uc010skw.1_Silent_p.D234D|PRICKLE1_uc001rnm.2_Silent_p.D234D	NM_001144881	NP_001138353	Q96MT3	PRIC1_HUMAN	prickle homolog 1	234	LIM zinc-binding 2.				negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cardiac muscle cell myoblast differentiation|negative regulation of transcription, DNA-dependent|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein import into nucleus	cytosol|nuclear membrane	zinc ion binding			ovary(3)|skin(1)	4	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)														---	---	---	---
ADAMTS20	80070	broad.mit.edu	37	12	43925963	43925963	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:43925963G>T	uc010skx.1	-	3	489	c.489C>A	c.(487-489)TTC>TTA	p.F163L		NM_025003	NP_079279	P59510	ATS20_HUMAN	a disintegrin-like and metalloprotease with	163						proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)														---	---	---	---
TMEM117	84216	broad.mit.edu	37	12	44782188	44782188	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44782188T>C	uc001rod.2	+	8	1344	c.1278T>C	c.(1276-1278)AAT>AAC	p.N426N	TMEM117_uc001roe.2_Silent_p.N322N|TMEM117_uc009zkc.2_3'UTR	NM_032256	NP_115632	Q9H0C3	TM117_HUMAN	transmembrane protein 117	426						endoplasmic reticulum|integral to membrane					0	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.124)														---	---	---	---
NELL2	4753	broad.mit.edu	37	12	44917162	44917162	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:44917162G>A	uc001rog.2	-	17	2505	c.1910C>T	c.(1909-1911)ACA>ATA	p.T637I	NELL2_uc001rof.3_Missense_Mutation_p.T636I|NELL2_uc001roh.2_Missense_Mutation_p.T637I|NELL2_uc009zkd.2_Missense_Mutation_p.T589I|NELL2_uc010skz.1_Missense_Mutation_p.T687I|NELL2_uc010sla.1_Missense_Mutation_p.T660I|NELL2_uc001roi.1_Missense_Mutation_p.T637I	NM_001145108	NP_001138580	Q99435	NELL2_HUMAN	NEL-like protein 2 isoform b precursor	637	EGF-like 6; calcium-binding (Potential).				cell adhesion	extracellular region	calcium ion binding|protein binding|structural molecule activity			skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	4	Lung SC(27;0.192)	Lung NSC(34;0.144)		GBM - Glioblastoma multiforme(48;0.092)														---	---	---	---
NELL2	4753	broad.mit.edu	37	12	45170873	45170873	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45170873C>T	uc001rog.2	-	7	1309	c.714G>A	c.(712-714)GTG>GTA	p.V238V	NELL2_uc001rof.3_Silent_p.V237V|NELL2_uc001roh.2_Silent_p.V238V|NELL2_uc009zkd.2_Silent_p.V237V|NELL2_uc010skz.1_Silent_p.V288V|NELL2_uc010sla.1_Silent_p.V261V|NELL2_uc001roi.1_Silent_p.V238V|NELL2_uc010slb.1_Silent_p.V237V|NELL2_uc001roj.2_Silent_p.V238V	NM_001145108	NP_001138580	Q99435	NELL2_HUMAN	NEL-like protein 2 isoform b precursor	238	TSP N-terminal.				cell adhesion	extracellular region	calcium ion binding|protein binding|structural molecule activity			skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	4	Lung SC(27;0.192)	Lung NSC(34;0.144)		GBM - Glioblastoma multiforme(48;0.092)														---	---	---	---
ANO6	196527	broad.mit.edu	37	12	45610102	45610102	+	5'UTR	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:45610102G>T	uc001roo.2	+	1					ANO6_uc010sld.1_5'UTR|ANO6_uc010sle.1_5'UTR|ANO6_uc010slf.1_5'UTR|PLEKHA9_uc001rom.1_5'Flank|PLEKHA9_uc009zke.2_5'Flank	NM_001025356	NP_001020527			anoctamin 6 isoform a						activation of blood coagulation via clotting cascade|phosphatidylserine exposure on blood platelet	chloride channel complex|plasma membrane	chloride channel activity			ovary(1)|kidney(1)	2																		---	---	---	---
SLC38A4	55089	broad.mit.edu	37	12	47163147	47163147	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:47163147A>G	uc001rpi.2	-	15	1763	c.1364T>C	c.(1363-1365)CTG>CCG	p.L455P	SLC38A4_uc001rpj.2_Missense_Mutation_p.L455P	NM_018018	NP_060488	Q969I6	S38A4_HUMAN	solute carrier family 38, member 4	455	Helical; (Potential).				cellular nitrogen compound metabolic process|sodium ion transport	integral to membrane|plasma membrane	amino acid transmembrane transporter activity|symporter activity			ovary(2)|central_nervous_system(1)|skin(1)	4	Lung SC(27;0.192)|Renal(347;0.236)																	---	---	---	---
VDR	7421	broad.mit.edu	37	12	48251388	48251388	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48251388G>A	uc001rqm.2	-	6	643	c.361C>T	c.(361-363)CGG>TGG	p.R121W	VDR_uc001rql.2_Missense_Mutation_p.R171W|VDR_uc001rqn.2_Missense_Mutation_p.R121W|VDR_uc010slq.1_Missense_Mutation_p.R89W	NM_001017535	NP_001017535	P11473	VDR_HUMAN	vitamin D (1,25-dihydroxyvitamin D3) receptor	121	Hinge.				decidualization|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of vitamin D 24-hydroxylase activity|regulation of calcidiol 1-monooxygenase activity|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	retinoid X receptor binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|vitamin D3 receptor activity|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Acute lymphoblastic leukemia(13;0.109)|all_hematologic(14;0.214)		GBM - Glioblastoma multiforme(48;0.17)	Calcidiol(DB00146)|Calcipotriol(DB02300)|Calcitriol(DB00136)|Dihydrotachysterol(DB01070)|Ergocalciferol(DB00153)|Paricalcitol(DB00910)													---	---	---	---
TMEM106C	79022	broad.mit.edu	37	12	48359116	48359116	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48359116G>A	uc001rqp.2	+	3	354	c.239G>A	c.(238-240)CGC>CAC	p.R80H	TMEM106C_uc001rqo.2_Missense_Mutation_p.R80H|TMEM106C_uc001rqr.2_Missense_Mutation_p.R80H|TMEM106C_uc001rqq.2_Missense_Mutation_p.R80H	NM_024056	NP_076961	Q9BVX2	T106C_HUMAN	transmembrane protein 106C isoform a	80						endoplasmic reticulum membrane|integral to membrane					0		Acute lymphoblastic leukemia(13;0.11)		GBM - Glioblastoma multiforme(48;0.241)														---	---	---	---
OR10AD1	121275	broad.mit.edu	37	12	48596534	48596534	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48596534T>G	uc001rrl.1	-	1	542	c.542A>C	c.(541-543)GAG>GCG	p.E181A		NM_001004134	NP_001004134	Q8NGE0	O10AD_HUMAN	olfactory receptor, family 10, subfamily AD,	181	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1																		---	---	---	---
H1FNT	341567	broad.mit.edu	37	12	48723179	48723179	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:48723179C>T	uc001rrm.2	+	1	417	c.105C>T	c.(103-105)CAC>CAT	p.H35H		NM_181788	NP_861453	Q75WM6	H1FNT_HUMAN	H1 histone family, member N, testis-specific	35					chromosome condensation|multicellular organismal development|sperm chromatin condensation|spermatid nucleus elongation	nuclear chromatin	ATP binding|DNA binding			pancreas(1)	1																		---	---	---	---
CCNT1	904	broad.mit.edu	37	12	49089809	49089809	+	Missense_Mutation	SNP	C	T	T	rs35965578		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49089809C>T	uc001rse.1	-	7	1002	c.679G>A	c.(679-681)GCC>ACC	p.A227T	CCNT1_uc009zkz.1_Intron	NM_001240	NP_001231	O60563	CCNT1_HUMAN	cyclin T1	227					cell cycle|cell division|interspecies interaction between organisms|positive regulation of viral transcription|protein phosphorylation|regulation of cyclin-dependent protein kinase activity|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|viral reproduction	nucleoplasm	DNA binding|protein kinase binding			ovary(3)|lung(1)|breast(1)|skin(1)	6																		---	---	---	---
DDX23	9416	broad.mit.edu	37	12	49231854	49231854	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49231854G>T	uc001rsm.2	-	6	581	c.490C>A	c.(490-492)CTC>ATC	p.L164I		NM_004818	NP_004809	Q9BUQ8	DDX23_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23	164	Glu-rich.					catalytic step 2 spliceosome|nucleoplasm|U5 snRNP	ATP binding|ATP-dependent RNA helicase activity|nucleic acid binding|protein binding			kidney(3)|ovary(1)|lung(1)|skin(1)	6																		---	---	---	---
MLL2	8085	broad.mit.edu	37	12	49425831	49425831	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49425831C>T	uc001rta.3	-	39	12657	c.12657G>A	c.(12655-12657)CAG>CAA	p.Q4219Q		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	4219	Gln-rich.				chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2)	41								N|F|Mis		medulloblastoma|renal					HNSCC(34;0.089)			---	---	---	---
LMBR1L	55716	broad.mit.edu	37	12	49496713	49496713	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49496713G>A	uc001rth.3	-	8	995	c.653C>T	c.(652-654)GCC>GTC	p.A218V	LMBR1L_uc001rtg.3_Missense_Mutation_p.A213V|LMBR1L_uc001rti.3_Missense_Mutation_p.A218V|LMBR1L_uc001rtj.1_Missense_Mutation_p.A62V|LMBR1L_uc009zld.1_Missense_Mutation_p.A91V|LMBR1L_uc010smf.1_RNA	NM_018113	NP_060583	Q6UX01	LMBRL_HUMAN	lipocalin-interacting membrane receptor	218	Cytoplasmic (Potential).				endocytosis	integral to membrane|plasma membrane	receptor activity			pancreas(1)	1																		---	---	---	---
C1QL4	338761	broad.mit.edu	37	12	49726939	49726939	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49726939G>A	uc001rtz.1	-	2	1326	c.615C>T	c.(613-615)GAC>GAT	p.D205D		NM_001008223	NP_001008224	Q86Z23	C1QL4_HUMAN	complement component 1, q subcomponent-like 4	205	C1q.					collagen					0																		---	---	---	---
SPATS2	65244	broad.mit.edu	37	12	49918641	49918641	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49918641G>T	uc001rud.2	+	13	2277	c.1288G>T	c.(1288-1290)GCA>TCA	p.A430S	SPATS2_uc001rue.2_RNA|SPATS2_uc009zli.1_Missense_Mutation_p.A430S|SPATS2_uc001ruf.2_Missense_Mutation_p.A430S|SPATS2_uc001rug.2_Missense_Mutation_p.A430S	NM_023071	NP_075559	Q86XZ4	SPAS2_HUMAN	spermatogenesis associated, serine-rich 2	430						cytoplasm				breast(1)	1																		---	---	---	---
KCNH3	23416	broad.mit.edu	37	12	49943959	49943959	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49943959G>T	uc001ruh.1	+	10	2025	c.1765G>T	c.(1765-1767)GGC>TGC	p.G589C	KCNH3_uc010smj.1_Missense_Mutation_p.G529C	NM_012284	NP_036416	Q9ULD8	KCNH3_HUMAN	potassium voltage-gated channel, subfamily H	589	cNMP.|Cytoplasmic (Potential).				regulation of transcription, DNA-dependent	integral to membrane	two-component sensor activity|voltage-gated potassium channel activity				0																		---	---	---	---
FAM186B	84070	broad.mit.edu	37	12	49999160	49999160	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49999160G>A	uc001ruo.2	-						FAM186B_uc010smk.1_5'UTR	NM_032130	NP_115506			hypothetical protein LOC84070							protein complex				ovary(1)	1																		---	---	---	---
FMNL3	91010	broad.mit.edu	37	12	50050855	50050855	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50050855T>C	uc001ruv.1	-						FMNL3_uc001ruw.1_Intron|FMNL3_uc001ruu.1_Intron	NM_175736	NP_783863			formin-like 3 isoform 1						actin cytoskeleton organization		actin binding|Rho GTPase binding			breast(2)|pancreas(2)	4																		---	---	---	---
CELA1	1990	broad.mit.edu	37	12	51722372	51722372	+	Missense_Mutation	SNP	C	T	T	rs141584534		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:51722372C>T	uc001ryi.1	-	8	807	c.766G>A	c.(766-768)GCC>ACC	p.A256T		NM_001971	NP_001962	Q9UNI1	CELA1_HUMAN	chymotrypsin-like elastase family, member 1	256	Peptidase S1.				proteolysis	extracellular region	metal ion binding|serine-type endopeptidase activity			breast(1)	1																		---	---	---	---
ACVRL1	94	broad.mit.edu	37	12	52307527	52307527	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52307527A>G	uc001rzj.2	+	4	781	c.498A>G	c.(496-498)GCA>GCG	p.A166A	ACVRL1_uc001rzk.2_Silent_p.A166A|ACVRL1_uc010snm.1_Intron	NM_000020	NP_000011	P37023	ACVL1_HUMAN	activin A receptor type II-like 1 precursor	166	Cytoplasmic (Potential).				blood vessel endothelial cell proliferation involved in sprouting angiogenesis|blood vessel maturation|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of endothelial cell migration|negative regulation of focal adhesion assembly|positive regulation of BMP signaling pathway|positive regulation of transcription, DNA-dependent|regulation of blood pressure|regulation of blood vessel endothelial cell migration|regulation of DNA replication|regulation of endothelial cell proliferation|transforming growth factor beta receptor signaling pathway|wound healing, spreading of epidermal cells	cell surface|integral to plasma membrane	activin binding|activin receptor activity, type I|ATP binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity			lung(2)	2				BRCA - Breast invasive adenocarcinoma(357;0.0991)	Adenosine triphosphate(DB00171)									Hereditary_Hemorrhagic_Telangiectasia				---	---	---	---
ACVR1B	91	broad.mit.edu	37	12	52374839	52374839	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52374839C>T	uc001rzn.2	+	4	709	c.667C>T	c.(667-669)CGG>TGG	p.R223W	ACVR1B_uc001rzl.2_Missense_Mutation_p.R223W|ACVR1B_uc001rzm.2_Missense_Mutation_p.R223W|ACVR1B_uc010snn.1_Missense_Mutation_p.R223W	NM_004302	NP_004293	P36896	ACV1B_HUMAN	activin A receptor, type IB isoform a precursor	223	Protein kinase.|Cytoplasmic (Potential).			WR -> MA (in Ref. 3; AAA60555/AAA60556).	G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|peptidyl-threonine phosphorylation|positive regulation of activin receptor signaling pathway|positive regulation of erythrocyte differentiation|protein autophosphorylation|transmembrane receptor protein serine/threonine kinase signaling pathway	cell surface	activin receptor activity, type I|ATP binding|metal ion binding|SMAD binding|transforming growth factor beta receptor activity|ubiquitin protein ligase binding			pancreas(4)|breast(2)|ovary(1)|lung(1)|kidney(1)	9				BRCA - Breast invasive adenocarcinoma(357;0.104)	Adenosine triphosphate(DB00171)											OREG0021829	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
KRT83	3889	broad.mit.edu	37	12	52709769	52709769	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52709769C>T	uc001saf.2	-	7	1233	c.1170G>A	c.(1168-1170)CTG>CTA	p.L390L		NM_002282	NP_002273	P78385	KRT83_HUMAN	keratin 83	390	Rod.|Coil 2.				epidermis development	keratin filament	structural molecule activity			skin(1)	1	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)														---	---	---	---
KRT83	3889	broad.mit.edu	37	12	52710345	52710345	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52710345G>A	uc001saf.2	-	6	1011	c.948C>T	c.(946-948)CAC>CAT	p.H316H		NM_002282	NP_002273	P78385	KRT83_HUMAN	keratin 83	316	Rod.|Coil 2.				epidermis development	keratin filament	structural molecule activity			skin(1)	1	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)														---	---	---	---
KRT85	3891	broad.mit.edu	37	12	52757866	52757866	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52757866G>A	uc001sag.2	-	4	892	c.772C>T	c.(772-774)CGC>TGC	p.R258C		NM_002283	NP_002274	P78386	KRT85_HUMAN	keratin 85	258	Rod.|Coil 1B.				epidermis development	keratin filament	protein binding|structural molecule activity			ovary(1)	1	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)														---	---	---	---
KRT82	3888	broad.mit.edu	37	12	52794336	52794336	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52794336T>C	uc001sai.1	-	4	867	c.752A>G	c.(751-753)GAC>GGC	p.D251G		NM_033033	NP_149022	Q9NSB4	KRT82_HUMAN	keratin 82	251	Coil 1B.|Rod.					keratin filament	protein binding|structural constituent of epidermis			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(357;0.193)														---	---	---	---
KRT3	3850	broad.mit.edu	37	12	53189794	53189794	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53189794G>A	uc001say.2	-	1	99	c.33C>T	c.(31-33)GGC>GGT	p.G11G		NM_057088	NP_476429	P12035	K2C3_HUMAN	keratin 3	11	Gly-rich.|Head.				epithelial cell differentiation|intermediate filament cytoskeleton organization	keratin filament	structural molecule activity				0																		---	---	---	---
KRT8	3856	broad.mit.edu	37	12	53298457	53298457	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53298457G>T	uc001sbd.2	-	1	412	c.309C>A	c.(307-309)GCC>GCA	p.A103A	KRT8_uc009zmj.2_Silent_p.A103A|KRT8_uc009zmk.1_Silent_p.A131A|KRT8_uc009zml.1_Silent_p.A103A|KRT8_uc009zmm.1_Silent_p.A103A	NM_002273	NP_002264	P05787	K2C8_HUMAN	keratin 8	103	Coil 1A.|Rod.				cytoskeleton organization|interspecies interaction between organisms	cytoplasm|keratin filament|nuclear matrix|nucleoplasm	protein binding|structural molecule activity			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(357;0.108)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
KRT18	3875	broad.mit.edu	37	12	53343226	53343226	+	Missense_Mutation	SNP	G	A	A	rs11551641		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53343226G>A	uc001sbe.2	+	2	338	c.269G>A	c.(268-270)CGC>CAC	p.R90H	KRT18_uc009zmn.1_Missense_Mutation_p.R90H|KRT18_uc001sbf.1_5'UTR|KRT18_uc001sbg.2_Missense_Mutation_p.R90H|KRT18_uc009zmo.2_Missense_Mutation_p.R90H|KRT8_uc009zml.1_Intron|KRT8_uc009zmm.1_Intron	NM_199187	NP_954657	P05783	K1C18_HUMAN	keratin 18	90	Coil 1A.|Rod.|Interaction with TRADD.|Necessary for interaction with PNN.			R->C,H: In transgenic mice, induces marked disruption of liver and pancreas keratin filament network. Increases phosphorylation and glycosylation.	anatomical structure morphogenesis|cell cycle|Golgi to plasma membrane CFTR protein transport|interspecies interaction between organisms|negative regulation of apoptosis	centriolar satellite|keratin filament|perinuclear region of cytoplasm	protein binding|structural molecule activity			skin(1)	1																		---	---	---	---
SOAT2	8435	broad.mit.edu	37	12	53499765	53499765	+	Missense_Mutation	SNP	G	A	A	rs111828989		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53499765G>A	uc001sbv.2	+	5	498	c.410G>A	c.(409-411)AGC>AAC	p.S137N	SOAT2_uc009zms.2_RNA	NM_003578	NP_003569	O75908	SOAT2_HUMAN	acyl-CoA:cholesterol acyltransferase 2	137	Helical; (Potential).				cholesterol efflux|cholesterol esterification|cholesterol homeostasis|cholesterol metabolic process|macrophage derived foam cell differentiation|very-low-density lipoprotein particle assembly	brush border|endoplasmic reticulum membrane|integral to membrane|microsome	cholesterol binding|cholesterol O-acyltransferase activity|fatty-acyl-CoA binding			ovary(1)	1																		---	---	---	---
CSAD	51380	broad.mit.edu	37	12	53565750	53565750	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53565750C>T	uc001sby.2	-	6	493	c.367G>A	c.(367-369)GTG>ATG	p.V123M	CSAD_uc001sbw.2_Intron|CSAD_uc009zmt.2_Translation_Start_Site|CSAD_uc010snx.1_Missense_Mutation_p.V150M|CSAD_uc001sbz.2_Missense_Mutation_p.V123M|CSAD_uc009zmu.2_Intron|CSAD_uc001sca.3_RNA|CSAD_uc010sny.1_Missense_Mutation_p.V123M	NM_015989	NP_057073	Q9Y600	CSAD_HUMAN	cysteine sulfinic acid decarboxylase	123					carboxylic acid metabolic process		pyridoxal phosphate binding|sulfinoalanine decarboxylase activity			ovary(1)	1					L-Cysteine(DB00151)|Pyridoxal Phosphate(DB00114)									Hereditary_Prostate_Cancer				---	---	---	---
AMHR2	269	broad.mit.edu	37	12	53824034	53824034	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53824034T>C	uc001scx.1	+	10	1471	c.1393T>C	c.(1393-1395)TAC>CAC	p.Y465H	AMHR2_uc009zmy.1_Silent_p.P463P	NM_020547	NP_065434	Q16671	AMHR2_HUMAN	anti-Mullerian hormone receptor, type II isoform	465	Cytoplasmic (Potential).|Protein kinase.				Mullerian duct regression		ATP binding|hormone binding|metal ion binding			ovary(1)|skin(1)	2					Adenosine triphosphate(DB00171)									Persistant_Mullerian_Duct_Syndrome_(type_I_and_II)				---	---	---	---
HOXC6	3223	broad.mit.edu	37	12	54423507	54423507	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54423507G>T	uc001sev.2	+	2	581	c.469G>T	c.(469-471)GAG>TAG	p.E157*	HOXC6_uc001ses.2_Nonsense_Mutation_p.E75*|HOXC5_uc001set.2_Intron|HOXC4_uc001seu.2_Intron	NM_004503	NP_004494	P09630	HXC6_HUMAN	homeobox C6 isoform 1	157	Homeobox.				regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(2)|upper_aerodigestive_tract(1)	3																		---	---	---	---
PDE1B	5153	broad.mit.edu	37	12	54966477	54966477	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54966477C>T	uc001sgd.1	+	7	853	c.687C>T	c.(685-687)GCC>GCT	p.A229A	PDE1B_uc010soz.1_Silent_p.A92A|PDE1B_uc010spa.1_Silent_p.A188A|PDE1B_uc001sgf.2_Silent_p.A92A|PDE1B_uc001sge.2_Silent_p.A209A|PDE1B_uc009znq.2_Silent_p.A25A	NM_000924	NP_000915	Q01064	PDE1B_HUMAN	phosphodiesterase 1B isoform 1	229	Catalytic (By similarity).				activation of phospholipase C activity|apoptosis|nerve growth factor receptor signaling pathway|platelet activation	cytosol|nucleus	3',5'-cyclic-AMP phosphodiesterase activity|calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding			upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
DCD	117159	broad.mit.edu	37	12	55042060	55042060	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55042060T>G	uc001sgj.2	-	1	90	c.28A>C	c.(28-30)ACA>CCA	p.T10P	DCD_uc009znt.2_Missense_Mutation_p.T10P|DCD_uc009znu.2_RNA	NM_053283	NP_444513	P81605	DCD_HUMAN	dermcidin preproprotein	10					defense response to bacterium|defense response to fungus|killing of cells of other organism	extracellular region	protein binding			ovary(1)	1		Myeloproliferative disorder(1001;0.0255)																---	---	---	---
MUCL1	118430	broad.mit.edu	37	12	55250643	55250643	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55250643G>A	uc001sgk.2	+	3	258	c.190G>A	c.(190-192)GCT>ACT	p.A64T		NM_058173	NP_477521	Q96DR8	MUCL1_HUMAN	small breast epithelial mucin precursor	64	Thr-rich.|3.|3 X 8 AA tandem repeat of T-T-A-A-[APS]- T-T-A.					extracellular region|membrane					0																		---	---	---	---
OR6C6	283365	broad.mit.edu	37	12	55688653	55688653	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55688653C>T	uc010sph.1	-	1	364	c.364G>A	c.(364-366)GTT>ATT	p.V122I		NM_001005493	NP_001005493	A6NF89	OR6C6_HUMAN	olfactory receptor, family 6, subfamily C,	122	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(1)|skin(1)	2																		---	---	---	---
OR6C68	403284	broad.mit.edu	37	12	55886873	55886873	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:55886873A>G	uc010spo.1	+	1	727	c.727A>G	c.(727-729)ACC>GCC	p.T243A		NM_001005519	NP_001005519	A6NDL8	O6C68_HUMAN	olfactory receptor, family 6, subfamily C,	238	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1																		---	---	---	---
MMP19	4327	broad.mit.edu	37	12	56231032	56231032	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56231032G>A	uc001sib.2	-	9	1436	c.1315C>T	c.(1315-1317)CGA>TGA	p.R439*	MMP19_uc001sia.2_Nonsense_Mutation_p.R153*|MMP19_uc001sid.2_RNA|MMP19_uc010spw.1_3'UTR	NM_002429	NP_002420	Q99542	MMP19_HUMAN	matrix metalloproteinase 19 isoform rasi-1	439	Hemopexin-like 4.				angiogenesis|cell differentiation|collagen catabolic process|proteolysis	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(1)	1																		---	---	---	---
ERBB3	2065	broad.mit.edu	37	12	56486584	56486584	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56486584G>A	uc001sjh.2	+	10	1356	c.1163G>A	c.(1162-1164)CGG>CAG	p.R388Q	ERBB3_uc009zoj.2_Intron|ERBB3_uc010sqb.1_Intron|ERBB3_uc010sqc.1_Missense_Mutation_p.R329Q|ERBB3_uc009zok.2_5'Flank|ERBB3_uc001sjj.1_5'Flank	NM_001982	NP_001973	P21860	ERBB3_HUMAN	erbB-3 isoform 1 precursor	388	Extracellular (Potential).				cranial nerve development|heart development|negative regulation of cell adhesion|negative regulation of neuron apoptosis|negative regulation of secretion|negative regulation of signal transduction|neuron apoptosis|phosphatidylinositol 3-kinase cascade|positive regulation of phosphatidylinositol 3-kinase cascade|regulation of cell proliferation|Schwann cell differentiation|transmembrane receptor protein tyrosine kinase signaling pathway|wound healing	basolateral plasma membrane|extracellular space|integral to plasma membrane|receptor complex	ATP binding|growth factor binding|protein heterodimerization activity|protein homodimerization activity|protein tyrosine kinase activator activity|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(3)|central_nervous_system(2)|stomach(1)|ovary(1)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)															---	---	---	---
ESYT1	23344	broad.mit.edu	37	12	56526074	56526074	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56526074T>C	uc001sjq.2	+	8	992	c.942T>C	c.(940-942)CCT>CCC	p.P314P	ESYT1_uc001sjr.2_Silent_p.P314P	NM_015292	NP_056107	Q9BSJ8	ESYT1_HUMAN	extended synaptotagmin-like protein 1	314						integral to membrane				ovary(4)|skin(1)	5																		---	---	---	---
SMARCC2	6601	broad.mit.edu	37	12	56565122	56565122	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56565122C>T	uc001skb.2	-	21	2293	c.2187G>A	c.(2185-2187)GCG>GCA	p.A729A	SMARCC2_uc001skd.2_Silent_p.A760A|SMARCC2_uc001ska.2_Silent_p.A760A|SMARCC2_uc001skc.2_Silent_p.A759A|SMARCC2_uc010sqf.1_Silent_p.A649A	NM_003075	NP_003066	Q8TAQ2	SMRC2_HUMAN	SWI/SNF-related matrix-associated	729					chromatin remodeling|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			lung(2)|central_nervous_system(2)|ovary(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(18;0.123)															---	---	---	---
PAN2	9924	broad.mit.edu	37	12	56722277	56722277	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56722277C>T	uc001skx.2	-	3	804	c.431G>A	c.(430-432)GGC>GAC	p.G144D	PAN2_uc001skz.2_Missense_Mutation_p.G144D|PAN2_uc001sky.2_Missense_Mutation_p.G144D	NM_001127460	NP_001120932	Q504Q3	PAN2_HUMAN	PAN2 polyA specific ribonuclease subunit homolog	144					nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|ubiquitin-dependent protein catabolic process	cytosol|nucleus	nucleic acid binding|poly(A)-specific ribonuclease activity|ubiquitin thiolesterase activity			ovary(2)|skin(2)|large_intestine(1)|breast(1)	6																		---	---	---	---
GLS2	27165	broad.mit.edu	37	12	56866504	56866504	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56866504G>A	uc001slj.2	-	15	1760	c.1481C>T	c.(1480-1482)GCC>GTC	p.A494V	GLS2_uc009zos.2_RNA|GLS2_uc001slk.2_Missense_Mutation_p.A229V|GLS2_uc009zot.2_Missense_Mutation_p.A155V	NM_013267	NP_037399	Q9UI32	GLSL_HUMAN	glutaminase 2 precursor	494					cellular amino acid biosynthetic process|glutamate secretion|glutamine metabolic process|neurotransmitter secretion	mitochondrial matrix	glutaminase activity|protein binding			ovary(1)|central_nervous_system(1)	2					L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)													---	---	---	---
RBMS2	5939	broad.mit.edu	37	12	56963735	56963735	+	Silent	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56963735A>C	uc001sln.2	+	4	544	c.345A>C	c.(343-345)ACA>ACC	p.T115T	RBMS2_uc010sqp.1_5'UTR|RBMS2_uc010sqq.1_5'UTR|RBMS2_uc009zou.2_5'UTR	NM_002898	NP_002889	Q15434	RBMS2_HUMAN	RNA binding motif, single stranded interacting	115	RRM 1.				RNA processing	nucleus	nucleotide binding|RNA binding				0																		---	---	---	---
BAZ2A	11176	broad.mit.edu	37	12	56994770	56994770	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56994770C>A	uc001slq.1	-	22	4607	c.4413G>T	c.(4411-4413)AAG>AAT	p.K1471N	BAZ2A_uc001slp.1_Missense_Mutation_p.K1469N|BAZ2A_uc001slo.1_Missense_Mutation_p.K277N|BAZ2A_uc009zov.1_Missense_Mutation_p.K437N|BAZ2A_uc009zow.1_Missense_Mutation_p.K1439N	NM_013449	NP_038477	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	1471					chromatin silencing at rDNA|DNA methylation|transcription, DNA-dependent	chromatin silencing complex|nucleolus|rDNA heterochromatin	DNA binding|histone acetyl-lysine binding|ligand-dependent nuclear receptor binding|RNA binding|zinc ion binding				0																		---	---	---	---
BAZ2A	11176	broad.mit.edu	37	12	56995846	56995846	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:56995846C>A	uc001slq.1	-	20	3755	c.3561G>T	c.(3559-3561)CGG>CGT	p.R1187R	BAZ2A_uc001slp.1_Silent_p.R1185R|BAZ2A_uc001slo.1_Silent_p.R15R|BAZ2A_uc009zov.1_Silent_p.R157R|BAZ2A_uc009zow.1_Silent_p.R1155R	NM_013449	NP_038477	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	1187	A.T hook 3.				chromatin silencing at rDNA|DNA methylation|transcription, DNA-dependent	chromatin silencing complex|nucleolus|rDNA heterochromatin	DNA binding|histone acetyl-lysine binding|ligand-dependent nuclear receptor binding|RNA binding|zinc ion binding				0																		---	---	---	---
MYO1A	4640	broad.mit.edu	37	12	57430851	57430851	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57430851G>A	uc001smw.3	-	20	2323	c.2080C>T	c.(2080-2082)CGC>TGC	p.R694C	MYO1A_uc010sqz.1_Missense_Mutation_p.R532C|MYO1A_uc009zpd.2_Missense_Mutation_p.R694C	NM_005379	NP_005370	Q9UBC5	MYO1A_HUMAN	myosin IA	694					sensory perception of sound|vesicle localization	brush border|cortical actin cytoskeleton|filamentous actin|lateral plasma membrane|microvillus|myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			skin(4)|ovary(2)|urinary_tract(1)	7																		---	---	---	---
LRP1	4035	broad.mit.edu	37	12	57567708	57567708	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57567708G>A	uc001snd.2	+	22	3958	c.3492G>A	c.(3490-3492)AAG>AAA	p.K1164K		NM_002332	NP_002323	Q07954	LRP1_HUMAN	low density lipoprotein-related protein 1	1164	LDL-receptor class A 10.|Extracellular (Potential).				aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity	coated pit|integral to plasma membrane|nucleus	apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity			ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2)	22				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)													---	---	---	---
LRP1	4035	broad.mit.edu	37	12	57571337	57571337	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57571337G>A	uc001snd.2	+	26	4790	c.4324G>A	c.(4324-4326)GAC>AAC	p.D1442N		NM_002332	NP_002323	Q07954	LRP1_HUMAN	low density lipoprotein-related protein 1	1442	LDL-receptor class B 10.|Extracellular (Potential).				aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity	coated pit|integral to plasma membrane|nucleus	apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity			ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2)	22				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)													---	---	---	---
LRP1	4035	broad.mit.edu	37	12	57596209	57596209	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57596209C>T	uc001snd.2	+	68	11066	c.10600C>T	c.(10600-10602)CGC>TGC	p.R3534C		NM_002332	NP_002323	Q07954	LRP1_HUMAN	low density lipoprotein-related protein 1	3534	LDL-receptor class A 26.|Extracellular (Potential).				aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity	coated pit|integral to plasma membrane|nucleus	apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity			ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2)	22				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)													---	---	---	---
LRP1	4035	broad.mit.edu	37	12	57598258	57598258	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57598258T>C	uc001snd.2	+	71	11483	c.11017T>C	c.(11017-11019)TGC>CGC	p.C3673R		NM_002332	NP_002323	Q07954	LRP1_HUMAN	low density lipoprotein-related protein 1	3673	Extracellular (Potential).|LDL-receptor class A 29.				aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity	coated pit|integral to plasma membrane|nucleus	apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity			ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2)	22				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)													---	---	---	---
SHMT2	6472	broad.mit.edu	37	12	57623551	57623551	+	5'Flank	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57623551T>C	uc001snf.1	+						SHMT2_uc001sng.1_5'Flank|SHMT2_uc001snh.1_5'Flank|SHMT2_uc009zpk.1_5'Flank|SHMT2_uc001sni.1_5'Flank|SHMT2_uc010srg.1_5'Flank|SHMT2_uc001snj.1_5'Flank|SHMT2_uc010srh.1_5'Flank|SHMT2_uc001snk.1_5'Flank|SHMT2_uc010sri.1_5'Flank|SHMT2_uc001snl.2_5'Flank	NM_005412	NP_005403			serine hydroxymethyltransferase 2							microtubule cytoskeleton|mitochondrial nucleoid	glycine hydroxymethyltransferase activity|methyltransferase activity			ovary(1)|central_nervous_system(1)	2					Glycine(DB00145)|Pyridoxal Phosphate(DB00114)|Tetrahydrofolic acid(DB00116)													---	---	---	---
R3HDM2	22864	broad.mit.edu	37	12	57663668	57663668	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57663668T>C	uc009zpm.1	-	13	1447	c.1412A>G	c.(1411-1413)CAC>CGC	p.H471R	R3HDM2_uc010srn.1_RNA|R3HDM2_uc001snu.2_Missense_Mutation_p.H166R|R3HDM2_uc001snr.2_Missense_Mutation_p.H198R|R3HDM2_uc001sns.2_Missense_Mutation_p.H471R|R3HDM2_uc001snt.2_Missense_Mutation_p.H485R|R3HDM2_uc009zpn.1_Missense_Mutation_p.H94R	NM_014925	NP_055740	Q9Y2K5	R3HD2_HUMAN	R3H domain containing 2	471	Gln-rich.					nucleus	nucleic acid binding			ovary(2)	2																		---	---	---	---
GLI1	2735	broad.mit.edu	37	12	57857876	57857876	+	Splice_Site	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57857876T>G	uc001snx.2	+	3	271	c.193_splice	c.e3+2	p.G65_splice	GLI1_uc009zpp.2_Splice_Site|GLI1_uc009zpq.2_Intron|GLI1_uc009zpr.1_Intron	NM_005269	NP_005260			GLI family zinc finger 1 isoform 1						epidermal cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|osteoblast differentiation|positive regulation of DNA replication|positive regulation of smoothened signaling pathway|positive regulation of transcription from RNA polymerase II promoter	cytosol|nucleus	transcription regulatory region DNA binding|zinc ion binding			skin(4)|ovary(4)|breast(3)|central_nervous_system(1)|urinary_tract(1)|kidney(1)|pancreas(1)	15			GBM - Glioblastoma multiforme(3;3.99e-32)															---	---	---	---
MARS	4141	broad.mit.edu	37	12	57884049	57884049	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57884049C>T	uc001sog.2	+	6	573	c.550C>T	c.(550-552)CGA>TGA	p.R184*	ARHGAP9_uc001sod.2_5'Flank|ARHGAP9_uc001soe.1_5'Flank|MARS_uc001sof.1_RNA|MARS_uc010srp.1_Nonsense_Mutation_p.R57*|MARS_uc010srq.1_5'UTR	NM_004990	NP_004981	P56192	SYMC_HUMAN	methionyl-tRNA synthetase	184	GST C-terminal.				methionyl-tRNA aminoacylation	cytosol	ATP binding|methionine-tRNA ligase activity|protein binding|tRNA binding			ovary(3)|central_nervous_system(1)|pancreas(1)	5			GBM - Glioblastoma multiforme(3;4.27e-41)		L-Methionine(DB00134)													---	---	---	---
B4GALNT1	2583	broad.mit.edu	37	12	58022851	58022851	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58022851G>T	uc001spg.1	-	7	1223	c.791C>A	c.(790-792)CCT>CAT	p.P264H	B4GALNT1_uc010sru.1_Missense_Mutation_p.P209H|B4GALNT1_uc010srv.1_Intron	NM_001478	NP_001469	Q00973	B4GN1_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 1	264	Lumenal (Potential).				lipid glycosylation	integral to Golgi membrane|membrane fraction	(N-acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase activity				0	Melanoma(17;0.122)		BRCA - Breast invasive adenocarcinoma(9;0.109)															---	---	---	---
OS9	10956	broad.mit.edu	37	12	58112930	58112930	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58112930T>C	uc001spj.2	+	12	1624	c.1565T>C	c.(1564-1566)GTC>GCC	p.V522A	OS9_uc010srx.1_Missense_Mutation_p.V316A|OS9_uc001spk.2_Missense_Mutation_p.V507A|OS9_uc001spl.2_Missense_Mutation_p.V522A|OS9_uc001spm.2_Missense_Mutation_p.V507A|OS9_uc001spn.2_Missense_Mutation_p.V523A|OS9_uc010sry.1_Missense_Mutation_p.V490A|OS9_uc010srz.1_Missense_Mutation_p.V448A	NM_006812	NP_006803	Q13438	OS9_HUMAN	osteosarcoma amplified 9, endoplasmic reticulum	522					ER-associated protein catabolic process|protein retention in ER lumen|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to endoplasmic reticulum stress	endoplasmic reticulum lumen|Hrd1p ubiquitin ligase complex	glycoprotein binding|protein binding|sugar binding			ovary(1)	1	all_neural(12;0.00548)|Glioma(12;0.0126)|Melanoma(17;0.122)		BRCA - Breast invasive adenocarcinoma(9;0.109)															---	---	---	---
AGAP2	116986	broad.mit.edu	37	12	58121336	58121336	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58121336C>T	uc001spq.2	-	17	2887	c.2887G>A	c.(2887-2889)GCC>ACC	p.A963T	AGAP2_uc001spo.1_5'Flank|AGAP2_uc001spp.2_Missense_Mutation_p.A962T|AGAP2_uc001spr.2_Missense_Mutation_p.A607T|LOC100130776_uc001sps.3_Silent_p.G187G	NM_001122772	NP_001116244	Q99490	AGAP2_HUMAN	centaurin, gamma 1 isoform PIKE-L	963	C4-type.|Arf-GAP.				axon guidance|negative regulation of neuron apoptosis|negative regulation of protein catabolic process|protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	mitochondrion|nucleolus	ARF GTPase activator activity|GTP binding|zinc ion binding			central_nervous_system(3)|breast(2)	5																		---	---	---	---
AVIL	10677	broad.mit.edu	37	12	58193624	58193624	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58193624T>G	uc001sqj.1	-	18	2329	c.2300A>C	c.(2299-2301)AAC>ACC	p.N767T	AVIL_uc009zqe.1_Missense_Mutation_p.N760T	NM_006576	NP_006567	O75366	AVIL_HUMAN	advillin	767	Headpiece (By similarity).|HP.				actin filament capping|cilium morphogenesis|cytoskeleton organization|positive regulation of neuron projection development	actin cytoskeleton|axon|cytoplasm	actin binding			central_nervous_system(1)	1	Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)																	---	---	---	---
AVIL	10677	broad.mit.edu	37	12	58193685	58193685	+	Missense_Mutation	SNP	G	T	T	rs79289432	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:58193685G>T	uc001sqj.1	-	18	2268	c.2239C>A	c.(2239-2241)CTC>ATC	p.L747I	AVIL_uc009zqe.1_Missense_Mutation_p.L740I	NM_006576	NP_006567	O75366	AVIL_HUMAN	advillin	747	Headpiece (By similarity).				actin filament capping|cilium morphogenesis|cytoskeleton organization|positive regulation of neuron projection development	actin cytoskeleton|axon|cytoplasm	actin binding			central_nervous_system(1)	1	Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)																	---	---	---	---
DPY19L2	283417	broad.mit.edu	37	12	63989810	63989810	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:63989810A>G	uc001srp.1	-	15	1650	c.1469T>C	c.(1468-1470)CTG>CCG	p.L490P	DPY19L2_uc009zqk.1_RNA	NM_173812	NP_776173	Q6NUT2	D19L2_HUMAN	dpy-19-like 2	490	Helical; (Potential).				multicellular organismal development|spermatid development	integral to membrane				central_nervous_system(1)|skin(1)	2			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)														---	---	---	---
SRGAP1	57522	broad.mit.edu	37	12	64502736	64502736	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64502736C>T	uc010ssp.1	+	16	1894	c.1838C>T	c.(1837-1839)GCG>GTG	p.A613V	SRGAP1_uc001srv.2_Missense_Mutation_p.A550V	NM_020762	NP_065813	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	613	Rho-GAP.				axon guidance	cytosol		p.A613V(1)		ovary(2)|central_nervous_system(2)	4			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)														---	---	---	---
XPOT	11260	broad.mit.edu	37	12	64825450	64825450	+	Silent	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:64825450A>T	uc001ssb.2	+	18	2535	c.2109A>T	c.(2107-2109)GGA>GGT	p.G703G		NM_007235	NP_009166	O43592	XPOT_HUMAN	tRNA exportin	703	Necessary for tRNA-binding, cytoplasmic localization and nuclear export.				intracellular protein transport|tRNA export from nucleus	cytoplasm|nucleoplasm	protein transporter activity|tRNA binding			ovary(2)	2				GBM - Glioblastoma multiforme(28;0.0404)														---	---	---	---
RASSF3	283349	broad.mit.edu	37	12	65085254	65085254	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65085254C>T	uc001ssd.2	+	4	582	c.462C>T	c.(460-462)TAC>TAT	p.Y154Y	RASSF3_uc009zqn.2_RNA|RASSF3_uc001sse.2_Silent_p.Y84Y	NM_178169	NP_835463	Q86WH2	RASF3_HUMAN	Ras association (RalGDS/AF-6) domain family	154	Ras-associating.				signal transduction	cytoplasm|microtubule	identical protein binding				0			Lung(2;0.00133)|LUAD - Lung adenocarcinoma(6;0.0665)|LUSC - Lung squamous cell carcinoma(43;0.132)	GBM - Glioblastoma multiforme(28;0.0611)														---	---	---	---
LEMD3	23592	broad.mit.edu	37	12	65564793	65564793	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:65564793T>C	uc001ssl.1	+	1	1423	c.1417T>C	c.(1417-1419)TTG>CTG	p.L473L	LEMD3_uc009zqo.1_Silent_p.L473L	NM_014319	NP_055134	Q9Y2U8	MAN1_HUMAN	LEM domain containing 3	473					negative regulation of activin receptor signaling pathway|negative regulation of BMP signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway	integral to nuclear inner membrane|membrane fraction	DNA binding|nucleotide binding|protein binding			central_nervous_system(3)|ovary(1)	4			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0104)														---	---	---	---
HELB	92797	broad.mit.edu	37	12	66712578	66712578	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66712578T>C	uc001sti.2	+						HELB_uc010ssz.1_Intron|HELB_uc009zqt.1_Intron	NM_033647	NP_387467			helicase (DNA) B						DNA replication, synthesis of RNA primer		ATP binding|ATP-dependent 5'-3' DNA helicase activity|single-stranded DNA-dependent ATP-dependent DNA helicase activity			central_nervous_system(1)|pancreas(1)	2			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)														---	---	---	---
GRIP1	23426	broad.mit.edu	37	12	66935667	66935667	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:66935667G>A	uc001stk.2	-	3	441	c.200C>T	c.(199-201)ACG>ATG	p.T67M	GRIP1_uc010sta.1_Missense_Mutation_p.T11M|GRIP1_uc001stl.1_Missense_Mutation_p.T11M|GRIP1_uc001stm.2_Missense_Mutation_p.T67M	NM_021150	NP_066973	Q9Y3R0	GRIP1_HUMAN	glutamate receptor interacting protein 1	67	PDZ 1.				androgen receptor signaling pathway|intracellular signal transduction|positive regulation of transcription, DNA-dependent|synaptic transmission	cell junction|cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|postsynaptic membrane	androgen receptor binding|beta-catenin binding|protein C-terminus binding|receptor signaling complex scaffold activity|transcription coactivator activity			ovary(2)	2			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)														---	---	---	---
CAND1	55832	broad.mit.edu	37	12	67703861	67703861	+	Intron	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:67703861T>G	uc001stn.2	+						CAND1_uc001sto.2_Intron	NM_018448	NP_060918			TIP120 protein						cell differentiation|negative regulation of catalytic activity|protein ubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|ubiquitin ligase complex	protein binding			central_nervous_system(1)|skin(1)	2			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)														---	---	---	---
IFNG	3458	broad.mit.edu	37	12	68552050	68552050	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:68552050A>G	uc001stw.1	-							NM_000619	NP_000610			interferon, gamma precursor						cell cycle arrest|interferon-gamma-mediated signaling pathway|negative regulation of interleukin-17 production|negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of metanephric nephron tubule epithelial cell differentiation|negative regulation of smooth muscle cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of calcidiol 1-monooxygenase activity|positive regulation of fructose 1,6-bisphosphate 1-phosphatase activity|positive regulation of fructose 1,6-bisphosphate metabolic process|positive regulation of interleukin-12 production|positive regulation of interleukin-23 production|positive regulation of killing of cells of other organism|positive regulation of membrane protein ectodomain proteolysis|positive regulation of mesenchymal cell proliferation|positive regulation of nitric oxide biosynthetic process|positive regulation of osteoclast differentiation|positive regulation of peptidyl-serine phosphorylation of STAT protein|positive regulation of smooth muscle cell apoptosis|positive regulation of tumor necrosis factor (ligand) superfamily member 11 production|positive regulation of tyrosine phosphorylation of Stat1 protein|positive regulation of vitamin D biosynthetic process|protein import into nucleus, translocation|regulation of insulin secretion|regulation of interferon-gamma-mediated signaling pathway|response to virus	extracellular space	cytokine activity|interferon-gamma receptor binding				0			Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000829)	Glucosamine(DB01296)|Interferon gamma-1b(DB00033)|Simvastatin(DB00641)													---	---	---	---
NUP107	57122	broad.mit.edu	37	12	69127311	69127311	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69127311C>T	uc001suf.2	+	24	2296	c.2181C>T	c.(2179-2181)TGC>TGT	p.C727C	NUP107_uc001sug.2_Silent_p.C486C|NUP107_uc010stj.1_Silent_p.C698C	NM_020401	NP_065134	P57740	NU107_HUMAN	nucleoporin 107kDa	727					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			skin(1)	1	Breast(13;6.25e-06)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)															---	---	---	---
SLC35E3	55508	broad.mit.edu	37	12	69158620	69158620	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69158620A>G	uc001suh.2	+	5	1114	c.892A>G	c.(892-894)AAG>GAG	p.K298E		NM_018656	NP_061126	Q7Z769	S35E3_HUMAN	solute carrier family 35, member E2	298						integral to membrane					0	Breast(13;2.31e-06)|Renal(347;0.0684)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00372)															---	---	---	---
FRS2	10818	broad.mit.edu	37	12	69968607	69968607	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69968607C>T	uc001suy.2	+	10	1909	c.1399C>T	c.(1399-1401)CGC>TGC	p.R467C	FRS2_uc001suz.2_Missense_Mutation_p.R467C|FRS2_uc009zrj.2_Missense_Mutation_p.R467C|FRS2_uc009zrk.2_Missense_Mutation_p.R467C	NM_006654	NP_006645	Q8WU20	FRS2_HUMAN	fibroblast growth factor receptor substrate 2	467					activation of MAPKK activity|activation of phospholipase C activity|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|transmembrane receptor protein tyrosine phosphatase signaling pathway	endomembrane system|endosome|integral to plasma membrane|membrane fraction	fibroblast growth factor receptor binding|insulin receptor binding|phosphatase activator activity|transmembrane receptor protein tyrosine kinase adaptor activity			prostate(1)|kidney(1)	2	Breast(13;2.15e-06)|Esophageal squamous(21;0.187)		Epithelial(6;2.94e-18)|Lung(24;9.68e-05)|OV - Ovarian serous cystadenocarcinoma(12;0.000984)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|Kidney(9;0.143)|LUSC - Lung squamous cell carcinoma(43;0.24)															---	---	---	---
CCT2	10576	broad.mit.edu	37	12	69980554	69980554	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:69980554G>A	uc001svb.1	+	3	194	c.100G>A	c.(100-102)GCC>ACC	p.A34T	CCT2_uc009zrm.1_RNA|CCT2_uc009zrn.1_Missense_Mutation_p.A34T|CCT2_uc010stl.1_5'UTR	NM_006431	NP_006422	P78371	TCPB_HUMAN	chaperonin containing TCP1, subunit 2	34					'de novo' posttranslational protein folding	nucleus	ATP binding|unfolded protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3	all_cancers(2;7.7e-106)|Breast(13;2.15e-06)|Esophageal squamous(21;0.187)		Epithelial(6;2.72e-18)|GBM - Glioblastoma multiforme(2;2.58e-10)|Lung(24;0.000185)|OV - Ovarian serous cystadenocarcinoma(12;0.00126)|STAD - Stomach adenocarcinoma(21;0.00501)|Kidney(9;0.143)|LUSC - Lung squamous cell carcinoma(43;0.24)															---	---	---	---
BEST3	144453	broad.mit.edu	37	12	70087570	70087570	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70087570C>T	uc001svg.2	-	4	592	c.365G>A	c.(364-366)CGC>CAC	p.R122H	BEST3_uc001svd.1_Missense_Mutation_p.R122H|BEST3_uc001sve.1_RNA|BEST3_uc010stm.1_Missense_Mutation_p.R16H|BEST3_uc001svh.2_5'UTR|BEST3_uc001svi.1_RNA	NM_032735	NP_116124	Q8N1M1	BEST3_HUMAN	vitelliform macular dystrophy 2-like 3 isoform	122	Cytoplasmic (Potential).					chloride channel complex|plasma membrane	chloride channel activity				0	Breast(13;2.31e-06)|Esophageal squamous(21;0.187)		Lung(24;0.000278)|OV - Ovarian serous cystadenocarcinoma(12;0.0019)|STAD - Stomach adenocarcinoma(21;0.00694)															---	---	---	---
PTPRB	5787	broad.mit.edu	37	12	70980859	70980859	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:70980859G>A	uc001swb.3	-	7	1615	c.1585C>T	c.(1585-1587)CGA>TGA	p.R529*	PTPRB_uc010sto.1_Nonsense_Mutation_p.R529*|PTPRB_uc010stp.1_Nonsense_Mutation_p.R439*|PTPRB_uc001swc.3_Nonsense_Mutation_p.R747*|PTPRB_uc001swa.3_Nonsense_Mutation_p.R747*|PTPRB_uc001swd.3_Nonsense_Mutation_p.R746*|PTPRB_uc009zrr.1_Nonsense_Mutation_p.R626*	NM_002837	NP_002828	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	529	Fibronectin type-III 6.|Extracellular (Potential).				angiogenesis	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(2)|skin(1)	3	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)															---	---	---	---
LGR5	8549	broad.mit.edu	37	12	71977972	71977972	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:71977972G>A	uc001swl.2	+	18	2230	c.2182G>A	c.(2182-2184)GCT>ACT	p.A728T	LGR5_uc001swm.2_Missense_Mutation_p.A704T|LGR5_uc001swn.1_Intron	NM_003667	NP_003658	O75473	LGR5_HUMAN	leucine-rich repeat-containing G protein-coupled	728	Helical; Name=5; (Potential).					integral to plasma membrane	protein-hormone receptor activity			lung(4)|skin(3)|ovary(1)|pancreas(1)	9																		---	---	---	---
ZFC3H1	196441	broad.mit.edu	37	12	72026010	72026010	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72026010T>C	uc001swo.2	-	15	3461	c.3102A>G	c.(3100-3102)GAA>GAG	p.E1034E		NM_144982	NP_659419	O60293	ZC3H1_HUMAN	proline/serine-rich coiled-coil 2	1034					RNA processing	intracellular	metal ion binding			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
ZFC3H1	196441	broad.mit.edu	37	12	72026136	72026136	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72026136C>A	uc001swo.2	-	15	3335	c.2976G>T	c.(2974-2976)AAG>AAT	p.K992N		NM_144982	NP_659419	O60293	ZC3H1_HUMAN	proline/serine-rich coiled-coil 2	992					RNA processing	intracellular	metal ion binding			ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
CAPS2	84698	broad.mit.edu	37	12	75678817	75678817	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75678817C>T	uc001sxk.3	-	16	1693	c.1496G>A	c.(1495-1497)GGC>GAC	p.G499D	CAPS2_uc001sxm.3_Missense_Mutation_p.G267D|CAPS2_uc009zsa.2_Missense_Mutation_p.G89D|CAPS2_uc001sxi.3_Missense_Mutation_p.G235D|CAPS2_uc001sxj.3_Missense_Mutation_p.G410D|CAPS2_uc001sxl.3_Missense_Mutation_p.G480D	NM_032606	NP_115995	Q9BXY5	CAYP2_HUMAN	calcyphosine 2	499	EF-hand 2.|2 (Potential).						calcium ion binding			ovary(2)	2																		---	---	---	---
CAPS2	84698	broad.mit.edu	37	12	75698653	75698653	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:75698653A>G	uc001sxk.3	-	9	917	c.720T>C	c.(718-720)GCT>GCC	p.A240A	CAPS2_uc001sxm.3_Silent_p.A8A|CAPS2_uc009zsa.2_5'UTR|CAPS2_uc001sxi.3_Silent_p.A8A|CAPS2_uc001sxj.3_Silent_p.A183A|CAPS2_uc001sxl.3_Silent_p.A221A	NM_032606	NP_115995	Q9BXY5	CAYP2_HUMAN	calcyphosine 2	240							calcium ion binding			ovary(2)	2																		---	---	---	---
BBS10	79738	broad.mit.edu	37	12	76740465	76740465	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76740465T>C	uc001syd.1	-	2	1384	c.1300A>G	c.(1300-1302)ACA>GCA	p.T434A		NM_024685	NP_078961	Q8TAM1	BBS10_HUMAN	Bardet-Biedl syndrome 10	434					cellular protein metabolic process|nonmotile primary cilium assembly|photoreceptor cell maintenance|response to stimulus|retina homeostasis	cilium	ATP binding			ovary(1)|skin(1)	2														Bardet-Biedl_syndrome				---	---	---	---
OSBPL8	114882	broad.mit.edu	37	12	76772299	76772299	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:76772299T>C	uc001sye.1	-	16	2142	c.1662A>G	c.(1660-1662)GAA>GAG	p.E554E	OSBPL8_uc001syf.1_Silent_p.E512E|OSBPL8_uc001syg.1_Silent_p.E512E|OSBPL8_uc001syh.1_Silent_p.E529E	NM_020841	NP_065892	Q9BZF1	OSBL8_HUMAN	oxysterol-binding protein-like protein 8 isoform	554					lipid transport		lipid binding			ovary(1)	1																		---	---	---	---
NAV3	89795	broad.mit.edu	37	12	78552991	78552991	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78552991T>C	uc001syp.2	+	23	4967	c.4794T>C	c.(4792-4794)CTT>CTC	p.L1598L	NAV3_uc001syo.2_Silent_p.L1598L|NAV3_uc010sub.1_Silent_p.L1084L|NAV3_uc009zsf.2_Silent_p.L429L	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3	1598	Potential.					nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	17															HNSCC(70;0.22)			---	---	---	---
NAV3	89795	broad.mit.edu	37	12	78598707	78598707	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:78598707A>G	uc001syp.2	+						NAV3_uc001syo.2_Intron|NAV3_uc010sub.1_Intron|NAV3_uc009zsf.2_Intron	NM_014903	NP_055718			neuron navigator 3							nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	17															HNSCC(70;0.22)			---	---	---	---
MIR618	693203	broad.mit.edu	37	12	81329572	81329572	+	RNA	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:81329572T>C	hsa-mir-618|MI0003632	-			c.41T>C			LIN7A_uc001szj.1_Intron|LIN7A_uc001szk.1_Intron																	0																		---	---	---	---
C12orf26	84190	broad.mit.edu	37	12	82796808	82796808	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:82796808A>C	uc001szq.2	+	5	1199	c.1178A>C	c.(1177-1179)AAT>ACT	p.N393T		NM_032230	NP_115606	Q8N6Q8	CL026_HUMAN	hypothetical protein LOC84190	393											0																		---	---	---	---
TMTC2	160335	broad.mit.edu	37	12	83324268	83324268	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:83324268C>T	uc001szt.2	+	4	1974	c.1542C>T	c.(1540-1542)AGC>AGT	p.S514S	TMTC2_uc001szr.1_Silent_p.S514S|TMTC2_uc001szs.1_Silent_p.S514S|TMTC2_uc010suk.1_Silent_p.S269S	NM_152588	NP_689801	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat	514	TPR 2.					endoplasmic reticulum|integral to membrane	binding			ovary(2)	2																		---	---	---	---
LRRIQ1	84125	broad.mit.edu	37	12	85521781	85521781	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85521781A>T	uc001tac.2	+	18	4290	c.4179A>T	c.(4177-4179)AAA>AAT	p.K1393N		NM_001079910	NP_001073379	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	1393										ovary(4)|central_nervous_system(1)|skin(1)	6				GBM - Glioblastoma multiforme(134;0.212)														---	---	---	---
LRRIQ1	84125	broad.mit.edu	37	12	85638590	85638590	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:85638590C>T	uc001tac.2	+	27	5151	c.5040C>T	c.(5038-5040)GAC>GAT	p.D1680D		NM_001079910	NP_001073379	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	1680										ovary(4)|central_nervous_system(1)|skin(1)	6				GBM - Glioblastoma multiforme(134;0.212)														---	---	---	---
RASSF9	9182	broad.mit.edu	37	12	86198958	86198958	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:86198958C>T	uc001taf.1	-	2	1169	c.830G>A	c.(829-831)CGA>CAA	p.R277Q		NM_005447	NP_005438	O75901	RASF9_HUMAN	Ras association (RalGDS/AF-6) domain family	277	Potential.				endosome transport|protein targeting|signal transduction	cytosol|endosome|trans-Golgi network transport vesicle membrane	protein binding|transporter activity			ovary(1)	1																		---	---	---	---
CEP290	80184	broad.mit.edu	37	12	88472893	88472893	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:88472893A>G	uc001tar.2	-	39	5684	c.5340T>C	c.(5338-5340)GTT>GTC	p.V1780V	CEP290_uc001taq.2_Silent_p.V840V	NM_025114	NP_079390	O15078	CE290_HUMAN	centrosomal protein 290kDa	1780	Potential.				cilium assembly|eye photoreceptor cell development|G2/M transition of mitotic cell cycle|hindbrain development|otic vesicle formation|positive regulation of transcription, DNA-dependent|pronephros development|protein transport	cell surface|centrosome|cytosol|nucleus|photoreceptor connecting cilium	protein binding			ovary(5)|breast(1)|pancreas(1)	7																		---	---	---	---
ATP2B1	490	broad.mit.edu	37	12	89992959	89992959	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:89992959C>T	uc001tbh.2	-	19	3467	c.3286G>A	c.(3286-3288)GCT>ACT	p.A1096T	ATP2B1_uc001tbg.2_Missense_Mutation_p.A1096T|ATP2B1_uc009zsr.2_RNA|ATP2B1_uc001tbf.2_Missense_Mutation_p.A730T	NM_001682	NP_001673	P20020	AT2B1_HUMAN	plasma membrane calcium ATPase 1 isoform 1b	1096	Cytoplasmic (Potential).				ATP biosynthetic process|platelet activation	integral to plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
EEA1	8411	broad.mit.edu	37	12	93247708	93247708	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93247708A>C	uc001tck.2	-	6	654	c.389T>G	c.(388-390)GTG>GGG	p.V130G		NM_003566	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1, 162kD	130	Potential.				early endosome to late endosome transport|synaptic vesicle to endosome fusion|vesicle fusion	cytosol|early endosome membrane|extrinsic to plasma membrane|membrane fraction	1-phosphatidylinositol binding|calmodulin binding|GTP-dependent protein binding|protein homodimerization activity|zinc ion binding			ovary(2)|skin(1)	3																		---	---	---	---
NUDT4	11163	broad.mit.edu	37	12	93793138	93793138	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93793138C>T	uc001tcm.2	+	5	924	c.526C>T	c.(526-528)CCA>TCA	p.P176S	NUDT4_uc010sup.1_Missense_Mutation_p.P176S|NUDT4_uc001tcn.2_Missense_Mutation_p.P124S|NUDT4_uc010suq.1_Missense_Mutation_p.P125S|NUDT4_uc001tco.2_Missense_Mutation_p.P124S	NM_019094	NP_061967	Q9NZJ9	NUDT4_HUMAN	nudix-type motif 4 isoform alpha	176					calcium-mediated signaling|cyclic nucleotide metabolic process|cyclic-nucleotide-mediated signaling|intracellular transport|regulation of RNA export from nucleus	cytoplasm	diphosphoinositol-polyphosphate diphosphatase activity|metal ion binding				0																		---	---	---	---
UBE2N	7334	broad.mit.edu	37	12	93805012	93805012	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:93805012C>T	uc001tcp.2	-	2	460	c.94G>A	c.(94-96)GCC>ACC	p.A32T		NM_003348	NP_003339	P61088	UBE2N_HUMAN	ubiquitin-conjugating enzyme E2N	32					DNA double-strand break processing|double-strand break repair via homologous recombination|histone ubiquitination|innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of DNA repair|positive regulation of histone modification|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of ubiquitin-protein ligase activity|postreplication repair|protein K63-linked ubiquitination|proteolysis|regulation of histone ubiquitination|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleus|UBC13-MMS2 complex|UBC13-UEV1A complex|ubiquitin ligase complex	ATP binding|ubiquitin binding|ubiquitin-protein ligase activity				0													Direct_reversal_of_damage|Rad6_pathway					---	---	---	---
PLXNC1	10154	broad.mit.edu	37	12	94654425	94654425	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94654425T>C	uc001tdc.2	+	20	3508	c.3259T>C	c.(3259-3261)TTT>CTT	p.F1087L	PLXNC1_uc010sut.1_Missense_Mutation_p.F134L|PLXNC1_uc009zsv.2_5'Flank	NM_005761	NP_005752	O60486	PLXC1_HUMAN	plexin C1 precursor	1087	Cytoplasmic (Potential).				axon guidance|cell adhesion	integral to membrane|intracellular|plasma membrane	receptor activity|receptor binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
PLXNC1	10154	broad.mit.edu	37	12	94691082	94691082	+	Intron	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:94691082T>G	uc001tdc.2	+						PLXNC1_uc010sut.1_Intron|PLXNC1_uc009zsv.2_Intron	NM_005761	NP_005752			plexin C1 precursor						axon guidance|cell adhesion	integral to membrane|intracellular|plasma membrane	receptor activity|receptor binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
USP44	84101	broad.mit.edu	37	12	95927945	95927945	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:95927945C>T	uc001teg.2	-	2	232	c.88G>A	c.(88-90)GTG>ATG	p.V30M	USP44_uc001teh.2_Missense_Mutation_p.V30M|USP44_uc009zte.2_Missense_Mutation_p.V27M	NM_001042403	NP_001035862	Q9H0E7	UBP44_HUMAN	ubiquitin thiolesterase 44	30	UBP-type.				anaphase|cell division|mitosis|negative regulation of mitotic anaphase-promoting complex activity|protein deubiquitination|regulation of spindle checkpoint|ubiquitin-dependent protein catabolic process	nucleus	protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(1)|breast(1)|central_nervous_system(1)	3																OREG0022039	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
NTN4	59277	broad.mit.edu	37	12	96076500	96076500	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:96076500G>T	uc001tei.2	-	7	1942	c.1493C>A	c.(1492-1494)TCT>TAT	p.S498Y	NTN4_uc009ztf.2_Missense_Mutation_p.S498Y|NTN4_uc009ztg.2_Missense_Mutation_p.S461Y	NM_021229	NP_067052	Q9HB63	NET4_HUMAN	netrin 4 precursor	498					axon guidance	basement membrane|plasma membrane				upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
TMPO	7112	broad.mit.edu	37	12	98921799	98921799	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98921799A>G	uc001tfj.2	+						TMPO_uc001tfi.1_Intron|TMPO_uc001tfk.2_Intron|TMPO_uc001tfl.2_Intron|TMPO_uc001tfh.1_Intron	NM_001032283	NP_001027454			thymopoietin isoform beta							integral to membrane|nuclear inner membrane	DNA binding|lamin binding			ovary(2)	2																		---	---	---	---
ACTR6	64431	broad.mit.edu	37	12	100598729	100598729	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100598729A>G	uc001thb.1	+	2	136	c.80A>G	c.(79-81)AAT>AGT	p.N27S	ACTR6_uc010svh.1_Missense_Mutation_p.N27S|ACTR6_uc001thc.1_5'UTR|ACTR6_uc001thd.1_Missense_Mutation_p.N27S|ACTR6_uc009ztu.1_5'UTR|ACTR6_uc001the.1_5'UTR|ACTR6_uc001thf.1_5'UTR|uc001thg.1_Intron	NM_022496	NP_071941	Q9GZN1	ARP6_HUMAN	ARP6 actin-related protein 6 homolog	27						cytoplasm|cytoskeleton				ovary(1)	1																		---	---	---	---
SLC17A8	246213	broad.mit.edu	37	12	100790109	100790109	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100790109G>A	uc010svi.1	+	5	903	c.590G>A	c.(589-591)GGT>GAT	p.G197D	SLC17A8_uc009ztx.2_Missense_Mutation_p.G197D	NM_139319	NP_647480	Q8NDX2	VGLU3_HUMAN	solute carrier family 17 (sodium-dependent	197	Helical; (Potential).				neurotransmitter transport|sensory perception of sound|sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)	3																		---	---	---	---
UTP20	27340	broad.mit.edu	37	12	101728288	101728288	+	Intron	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101728288A>C	uc001tia.1	+							NM_014503	NP_055318			down-regulated in metastasis						endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|negative regulation of cell proliferation	90S preribosome|cytoplasm|nucleolus|nucleoplasm|preribosome, small subunit precursor|small-subunit processome	protein binding			ovary(2)|breast(2)	4																		---	---	---	---
UTP20	27340	broad.mit.edu	37	12	101750765	101750765	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101750765C>T	uc001tia.1	+	43	5752	c.5596C>T	c.(5596-5598)CGC>TGC	p.R1866C		NM_014503	NP_055318	O75691	UTP20_HUMAN	down-regulated in metastasis	1866	HEAT 2.				endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|negative regulation of cell proliferation	90S preribosome|cytoplasm|nucleolus|nucleoplasm|preribosome, small subunit precursor|small-subunit processome	protein binding			ovary(2)|breast(2)	4																		---	---	---	---
SPIC	121599	broad.mit.edu	37	12	101880256	101880256	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:101880256G>A	uc001tid.2	+	6	613	c.454G>A	c.(454-456)GAG>AAG	p.E152K	SPIC_uc009zua.2_Missense_Mutation_p.E27K|SPIC_uc010svp.1_Missense_Mutation_p.E151K	NM_152323	NP_689536	Q8N5J4	SPIC_HUMAN	Spi-C transcription factor (Spi-1/PU.1 related)	152	ETS.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(1)	1																		---	---	---	---
MYBPC1	4604	broad.mit.edu	37	12	102020662	102020662	+	Intron	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102020662T>A	uc001tii.2	+						MYBPC1_uc001tif.1_Missense_Mutation_p.V39D|MYBPC1_uc001tig.2_Missense_Mutation_p.V39D|MYBPC1_uc010svq.1_Missense_Mutation_p.V13D|MYBPC1_uc001tih.2_Missense_Mutation_p.V39D|MYBPC1_uc001tij.2_Intron|MYBPC1_uc010svr.1_Intron|MYBPC1_uc010svs.1_Intron|MYBPC1_uc010svt.1_Intron|MYBPC1_uc010svu.1_Intron|MYBPC1_uc001tik.2_Intron	NM_206820	NP_996556			myosin binding protein C, slow type isoform 3						cell adhesion|muscle filament sliding	cytosol|myofibril|myosin filament	actin binding|structural constituent of muscle|titin binding			ovary(2)|liver(1)|skin(1)	4																		---	---	---	---
MYBPC1	4604	broad.mit.edu	37	12	102045143	102045143	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102045143G>T	uc001tii.2	+	14	1525	c.1423G>T	c.(1423-1425)GAC>TAC	p.D475Y	MYBPC1_uc001tif.1_Missense_Mutation_p.D488Y|MYBPC1_uc001tig.2_Missense_Mutation_p.D500Y|MYBPC1_uc010svq.1_Missense_Mutation_p.D462Y|MYBPC1_uc001tih.2_Missense_Mutation_p.D500Y|MYBPC1_uc001tij.2_Missense_Mutation_p.D475Y|MYBPC1_uc010svr.1_Missense_Mutation_p.D475Y|MYBPC1_uc010svs.1_Missense_Mutation_p.D475Y|MYBPC1_uc010svt.1_Missense_Mutation_p.D463Y|MYBPC1_uc010svu.1_Missense_Mutation_p.D456Y|MYBPC1_uc001tik.2_Missense_Mutation_p.D449Y	NM_206820	NP_996556	Q00872	MYPC1_HUMAN	myosin binding protein C, slow type isoform 3	475	Ig-like C2-type 4.				cell adhesion|muscle filament sliding	cytosol|myofibril|myosin filament	actin binding|structural constituent of muscle|titin binding			ovary(2)|liver(1)|skin(1)	4																		---	---	---	---
NUP37	79023	broad.mit.edu	37	12	102512283	102512283	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102512283G>A	uc001tjc.2	-	1	79	c.14C>T	c.(13-15)GCC>GTC	p.A5V	NUP37_uc009zub.1_Missense_Mutation_p.A5V|C12orf48_uc001tjd.2_5'Flank|C12orf48_uc001tje.2_5'Flank|C12orf48_uc001tjg.2_5'Flank|C12orf48_uc010swa.1_5'Flank|C12orf48_uc001tjf.2_5'Flank|C12orf48_uc001tjh.2_5'Flank|C12orf48_uc010swb.1_5'Flank|C12orf48_uc001tji.2_5'Flank	NM_024057	NP_076962	Q8NFH4	NUP37_HUMAN	nucleoporin 37kDa	5					carbohydrate metabolic process|cell division|chromosome segregation|glucose transport|mitotic prometaphase|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	protein binding			ovary(1)	1																		---	---	---	---
PAH	5053	broad.mit.edu	37	12	103288555	103288555	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103288555C>T	uc001tjq.1	-	4	782	c.310G>A	c.(310-312)GCC>ACC	p.A104T	PAH_uc010swc.1_Missense_Mutation_p.A104T	NM_000277	NP_000268	P00439	PH4H_HUMAN	phenylalanine hydroxylase	104	ACT.		A -> D (in PKU; mild; haplotype 1).		catecholamine biosynthetic process|L-phenylalanine catabolic process|neurotransmitter biosynthetic process	cytosol	phenylalanine 4-monooxygenase activity			ovary(4)	4					Epinephrine(DB00668)|L-Phenylalanine(DB00120)|Levodopa(DB01235)|Norepinephrine(DB00368)|Tetrahydrobiopterin(DB00360)													---	---	---	---
C12orf42	374470	broad.mit.edu	37	12	103695884	103695884	+	3'UTR	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:103695884G>A	uc001tjt.2	-	6					C12orf42_uc001tjs.2_Intron|C12orf42_uc009zuf.1_3'UTR|C12orf42_uc001tju.2_3'UTR	NM_198521	NP_940923			hypothetical protein LOC374470											ovary(1)|central_nervous_system(1)	2																		---	---	---	---
STAB2	55576	broad.mit.edu	37	12	104033936	104033936	+	Silent	SNP	C	T	T	rs144975292		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104033936C>T	uc001tjw.2	+	9	1128	c.942C>T	c.(940-942)TTC>TTT	p.F314F		NM_017564	NP_060034	Q8WWQ8	STAB2_HUMAN	stabilin 2 precursor	314	Extracellular (Potential).				angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity	p.F314F(1)		ovary(9)|skin(5)	14																		---	---	---	---
STAB2	55576	broad.mit.edu	37	12	104109667	104109667	+	Splice_Site	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104109667G>A	uc001tjw.2	+	43	4797	c.4611_splice	c.e43+1	p.Q1537_splice	STAB2_uc009zug.2_Splice_Site	NM_017564	NP_060034			stabilin 2 precursor						angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			ovary(9)|skin(5)	14																		---	---	---	---
STAB2	55576	broad.mit.edu	37	12	104136313	104136313	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:104136313A>T	uc001tjw.2	+	56	6198	c.6012A>T	c.(6010-6012)AGA>AGT	p.R2004S	STAB2_uc009zug.2_RNA	NM_017564	NP_060034	Q8WWQ8	STAB2_HUMAN	stabilin 2 precursor	2004	Extracellular (Potential).|Laminin EGF-like 2.				angiogenesis|cell adhesion|defense response to bacterium|receptor-mediated endocytosis	cytoplasm|external side of plasma membrane|integral to plasma membrane	Gram-negative bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			ovary(9)|skin(5)	14																		---	---	---	---
C12orf45	121053	broad.mit.edu	37	12	105381991	105381991	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105381991G>A	uc001tlb.2	+	2	195	c.162G>A	c.(160-162)AAG>AAA	p.K54K		NM_152318	NP_689531	Q8N5I9	CL045_HUMAN	hypothetical protein LOC121053	54											0																		---	---	---	---
ALDH1L2	160428	broad.mit.edu	37	12	105462503	105462503	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:105462503C>A	uc001tlc.2	-	4	715	c.588G>T	c.(586-588)AAG>AAT	p.K196N	ALDH1L2_uc009zuo.2_5'Flank|ALDH1L2_uc009zup.2_RNA	NM_001034173	NP_001029345	Q3SY69	AL1L2_HUMAN	aldehyde dehydrogenase 1 family, member L2	196	GART.				10-formyltetrahydrofolate catabolic process|biosynthetic process	mitochondrion	acyl carrier activity|cofactor binding|formyltetrahydrofolate dehydrogenase activity|hydroxymethyl-, formyl- and related transferase activity|methyltransferase activity|phosphopantetheine binding			skin(1)	1																		---	---	---	---
POLR3B	55703	broad.mit.edu	37	12	106824127	106824127	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:106824127C>A	uc001tlp.2	+	14	1562	c.1340C>A	c.(1339-1341)TCC>TAC	p.S447Y	POLR3B_uc001tlq.2_Missense_Mutation_p.S389Y	NM_018082	NP_060552	Q9NW08	RPC2_HUMAN	DNA-directed RNA polymerase III B isoform 1	447					innate immune response|positive regulation of innate immune response|positive regulation of interferon-beta production|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|ribonucleoside binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
SART3	9733	broad.mit.edu	37	12	108939075	108939075	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:108939075C>T	uc001tmz.1	-	4	804	c.569G>A	c.(568-570)GGC>GAC	p.G190D	SART3_uc009zux.1_5'UTR|SART3_uc010swx.1_Missense_Mutation_p.G190D|SART3_uc010swy.1_Missense_Mutation_p.G58D|SART3_uc010swz.1_Missense_Mutation_p.G190D|SART3_uc001tna.1_RNA	NM_014706	NP_055521	Q15020	SART3_HUMAN	squamous cell carcinoma antigen recognized by T	190	HAT 2.				RNA processing	cytoplasm|nuclear speck	nucleotide binding|protein binding|RNA binding			pancreas(1)	1														Porokeratosis				---	---	---	---
ACACB	32	broad.mit.edu	37	12	109684039	109684039	+	Missense_Mutation	SNP	G	T	T	rs144673785	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109684039G>T	uc001tob.2	+	39	5476	c.5357G>T	c.(5356-5358)CGG>CTG	p.R1786L	ACACB_uc001toc.2_Missense_Mutation_p.R1786L|ACACB_uc010sxl.1_RNA|ACACB_uc001tod.2_RNA|ACACB_uc010sxm.1_Missense_Mutation_p.R452L	NM_001093	NP_001084	O00763	ACACB_HUMAN	acetyl-Coenzyme A carboxylase beta	1786					acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation	cytosol|endomembrane system|Golgi apparatus|membrane	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8					Biotin(DB00121)													---	---	---	---
ACACB	32	broad.mit.edu	37	12	109685400	109685400	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109685400T>C	uc001tob.2	+						ACACB_uc001toc.2_Intron|ACACB_uc010sxl.1_Intron|ACACB_uc001tod.2_Intron|ACACB_uc010sxm.1_Intron	NM_001093	NP_001084			acetyl-Coenzyme A carboxylase beta						acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation	cytosol|endomembrane system|Golgi apparatus|membrane	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8					Biotin(DB00121)													---	---	---	---
ACACB	32	broad.mit.edu	37	12	109690813	109690813	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109690813A>G	uc001tob.2	+						ACACB_uc001toc.2_Intron|ACACB_uc010sxl.1_Intron|ACACB_uc001tod.2_Intron|ACACB_uc010sxm.1_Intron	NM_001093	NP_001084			acetyl-Coenzyme A carboxylase beta						acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation	cytosol|endomembrane system|Golgi apparatus|membrane	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8					Biotin(DB00121)													---	---	---	---
ACACB	32	broad.mit.edu	37	12	109702951	109702951	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109702951T>C	uc001tob.2	+	51	7098	c.6979T>C	c.(6979-6981)TAT>CAT	p.Y2327H	ACACB_uc001toc.2_Missense_Mutation_p.Y2327H|ACACB_uc001tod.2_RNA|ACACB_uc010sxm.1_Missense_Mutation_p.Y993H	NM_001093	NP_001084	O00763	ACACB_HUMAN	acetyl-Coenzyme A carboxylase beta	2327					acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation	cytosol|endomembrane system|Golgi apparatus|membrane	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8					Biotin(DB00121)													---	---	---	---
FOXN4	121643	broad.mit.edu	37	12	109717639	109717639	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109717639C>A	uc001toe.3	-	10	1496	c.1391G>T	c.(1390-1392)GGC>GTC	p.G464V	FOXN4_uc009zvg.2_Missense_Mutation_p.G261V|FOXN4_uc001tof.3_Missense_Mutation_p.G284V	NM_213596	NP_998761	Q96NZ1	FOXN4_HUMAN	forkhead box N4	464					axon extension|embryo development|organ development|pattern specification process|regulation of heart contraction|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			ovary(1)|lung(1)	2																		---	---	---	---
MYO1H	283446	broad.mit.edu	37	12	109839007	109839007	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109839007G>A	uc010sxn.1	+	5	632	c.632G>A	c.(631-633)GGT>GAT	p.G211D		NM_001101421	NP_001094891	Q8N1T3	MYO1H_HUMAN	myosin 1H	Error:Variant_position_missing_in_B4DNW6_after_alignment						myosin complex	motor activity				0																		---	---	---	---
MYO1H	283446	broad.mit.edu	37	12	109858794	109858794	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109858794G>A	uc010sxn.1	+	15	1558	c.1558G>A	c.(1558-1560)GAA>AAA	p.E520K		NM_001101421	NP_001094891	Q8N1T3	MYO1H_HUMAN	myosin 1H	Error:Variant_position_missing_in_B4DNW6_after_alignment						myosin complex	motor activity				0																		---	---	---	---
MMAB	326625	broad.mit.edu	37	12	109994921	109994921	+	Missense_Mutation	SNP	G	A	A	rs142070439		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109994921G>A	uc001tou.2	-	9	738	c.665C>T	c.(664-666)ACG>ATG	p.T222M	MMAB_uc001tov.2_RNA|MMAB_uc001tow.2_RNA|MMAB_uc010sxq.1_Missense_Mutation_p.T131M|MMAB_uc001tox.2_Missense_Mutation_p.T170M	NM_052845	NP_443077	Q96EY8	MMAB_HUMAN	cob(I)alamin adenosyltransferase precursor	222					cobalamin biosynthetic process	mitochondrion	ATP binding|cob(I)yrinic acid a,c-diamide adenosyltransferase activity				0					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)													---	---	---	---
TRPV4	59341	broad.mit.edu	37	12	110240891	110240891	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110240891C>T	uc001tpj.1	-	3	712	c.617G>A	c.(616-618)CGC>CAC	p.R206H	TRPV4_uc001tpg.1_Missense_Mutation_p.R172H|TRPV4_uc001tph.1_Missense_Mutation_p.R206H|TRPV4_uc001tpi.1_Missense_Mutation_p.R206H|TRPV4_uc001tpk.1_Missense_Mutation_p.R206H|TRPV4_uc001tpl.1_Missense_Mutation_p.R206H	NM_021625	NP_067638	Q9HBA0	TRPV4_HUMAN	transient receptor potential cation channel,	206	Cytoplasmic (Potential).				actin cytoskeleton reorganization|actin filament organization|calcium ion import|cell death|cell volume homeostasis|cell-cell junction assembly|cellular hypotonic response|cortical microtubule organization|elevation of cytosolic calcium ion concentration|microtubule polymerization|negative regulation of neuron projection development|osmosensory signaling pathway|positive regulation of microtubule depolymerization|response to mechanical stimulus	cortical actin cytoskeleton|filopodium|focal adhesion|growth cone|integral to membrane|lamellipodium|ruffle membrane	actin filament binding|alpha-tubulin binding|beta-tubulin binding|calcium channel activity|calmodulin binding|microtubule binding|protein binding|protein kinase C binding|SH2 domain binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4																		---	---	---	---
TRPV4	59341	broad.mit.edu	37	12	110252435	110252435	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110252435C>T	uc001tpj.1	-	1	262	c.167G>A	c.(166-168)CGC>CAC	p.R56H	TRPV4_uc001tpg.1_Intron|TRPV4_uc001tph.1_Missense_Mutation_p.R56H|TRPV4_uc001tpi.1_Missense_Mutation_p.R56H|TRPV4_uc001tpk.1_Missense_Mutation_p.R56H|TRPV4_uc001tpl.1_Missense_Mutation_p.R56H	NM_021625	NP_067638	Q9HBA0	TRPV4_HUMAN	transient receptor potential cation channel,	56	Cytoplasmic (Potential).				actin cytoskeleton reorganization|actin filament organization|calcium ion import|cell death|cell volume homeostasis|cell-cell junction assembly|cellular hypotonic response|cortical microtubule organization|elevation of cytosolic calcium ion concentration|microtubule polymerization|negative regulation of neuron projection development|osmosensory signaling pathway|positive regulation of microtubule depolymerization|response to mechanical stimulus	cortical actin cytoskeleton|filopodium|focal adhesion|growth cone|integral to membrane|lamellipodium|ruffle membrane	actin filament binding|alpha-tubulin binding|beta-tubulin binding|calcium channel activity|calmodulin binding|microtubule binding|protein binding|protein kinase C binding|SH2 domain binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4																		---	---	---	---
ANKRD13A	88455	broad.mit.edu	37	12	110474111	110474111	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110474111A>G	uc001tpx.2	+	14	1814	c.1555A>G	c.(1555-1557)ACC>GCC	p.T519A	ANKRD13A_uc010sxw.1_Missense_Mutation_p.T518A|ANKRD13A_uc001tpy.2_Missense_Mutation_p.T119A|ANKRD13A_uc001tpz.2_Missense_Mutation_p.T157A|ANKRD13A_uc001tqa.2_Missense_Mutation_p.H103R	NM_033121	NP_149112	Q8IZ07	AN13A_HUMAN	ankyrin repeat domain 13	519	UIM 1.										0																		---	---	---	---
IFT81	28981	broad.mit.edu	37	12	110581320	110581320	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110581320C>A	uc001tqi.2	+	9	1045	c.915C>A	c.(913-915)GGC>GGA	p.G305G	IFT81_uc001tqh.2_Silent_p.G305G|IFT81_uc001tqj.2_RNA|IFT81_uc001tqg.2_Silent_p.G305G	NM_001143779	NP_001137251	Q8WYA0	IFT81_HUMAN	intraflagellar transport 81-like isoform 1	305					cell differentiation|multicellular organismal development|spermatogenesis	intraflagellar transport particle B|microtubule-based flagellum				ovary(1)	1																		---	---	---	---
ATP2A2	488	broad.mit.edu	37	12	110778609	110778609	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:110778609G>A	uc001tqk.3	+	14	2470	c.1907G>A	c.(1906-1908)CGC>CAC	p.R636H	ATP2A2_uc001tql.3_Missense_Mutation_p.R636H|ATP2A2_uc010sxy.1_Missense_Mutation_p.R609H	NM_170665	NP_733765	P16615	AT2A2_HUMAN	ATPase, Ca++ transporting, slow twitch 2 isoform	636	Cytoplasmic (By similarity).				ATP biosynthetic process|cell adhesion|epidermis development|platelet activation|sarcoplasmic reticulum calcium ion transport	integral to plasma membrane|microsome|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	ATP binding|calcium-transporting ATPase activity|protein C-terminus binding|S100 alpha binding			ovary(3)|skin(1)	4																		---	---	---	---
HVCN1	84329	broad.mit.edu	37	12	111093099	111093099	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111093099A>G	uc001trs.1	-	5	516	c.351T>C	c.(349-351)CTT>CTC	p.L117L	HVCN1_uc001trq.1_Silent_p.L117L|HVCN1_uc001trt.1_Silent_p.L117L|HVCN1_uc010syd.1_Silent_p.L97L	NM_032369	NP_115745	Q96D96	HVCN1_HUMAN	hydrogen voltage-gated channel 1	117	Helical; Name=Segment S1; (By similarity).				response to pH|response to zinc ion	integral to membrane	voltage-gated proton channel activity			skin(1)	1																		---	---	---	---
ACAD10	80724	broad.mit.edu	37	12	112167606	112167606	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112167606G>A	uc001tsq.2	+						ACAD10_uc001tsp.2_Intron|ACAD10_uc009zvx.2_Intron|ACAD10_uc001tss.1_Intron	NM_025247	NP_079523			acyl-Coenzyme A dehydrogenase family, member 10								acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding|hydrolase activity|transferase activity, transferring phosphorus-containing groups			ovary(2)	2																		---	---	---	---
C12orf51	283450	broad.mit.edu	37	12	112699234	112699234	+	Splice_Site	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112699234C>A	uc009zwc.2	-	11	1471	c.1453_splice	c.e11-1	p.E485_splice	C12orf51_uc010syk.1_Splice_Site_p.E308_splice|C12orf51_uc001tts.2_Splice_Site_p.E308_splice|C12orf51_uc001ttt.3_Splice_Site_p.E306_splice	NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)|lung(1)	2																		---	---	---	---
PTPN11	5781	broad.mit.edu	37	12	112924326	112924326	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:112924326G>A	uc001ttx.2	+	11	1652	c.1272G>A	c.(1270-1272)CCG>CCA	p.P424P	PTPN11_uc001ttw.1_Silent_p.P424P	NM_002834	NP_002825	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type	428	Tyrosine-protein phosphatase.				axon guidance|cell junction assembly|ephrin receptor signaling pathway|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|interferon-gamma-mediated signaling pathway|leukocyte migration|platelet activation|regulation of cell adhesion mediated by integrin|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|T cell costimulation|type I interferon-mediated signaling pathway	cytosol	non-membrane spanning protein tyrosine phosphatase activity|protein binding			haematopoietic_and_lymphoid_tissue(375)|lung(6)|autonomic_ganglia(2)|soft_tissue(2)|central_nervous_system(2)|large_intestine(1)|skin(1)|ovary(1)|NS(1)|kidney(1)	392								Mis		JMML|AML|MDS		Noonan Syndrome		Noonan_syndrome				---	---	---	---
DDX54	79039	broad.mit.edu	37	12	113614685	113614685	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113614685G>A	uc001tup.2	-	7	740	c.712C>T	c.(712-714)CTG>TTG	p.L238L	DDX54_uc001tuq.3_Silent_p.L238L	NM_024072	NP_076977	Q8TDD1	DDX54_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 54	238	Helicase ATP-binding.				estrogen receptor signaling pathway|regulation of transcription, DNA-dependent|RNA processing|transcription, DNA-dependent	nucleolus	ATP binding|ATP-dependent RNA helicase activity|estrogen receptor binding|RNA binding|transcription corepressor activity			skin(2)|central_nervous_system(1)	3																		---	---	---	---
IQCD	115811	broad.mit.edu	37	12	113633618	113633618	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113633618A>G	uc001tuu.2	-	3	978	c.806T>C	c.(805-807)GTG>GCG	p.V269A		NM_138451	NP_612460	Q96DY2	IQCD_HUMAN	IQ motif containing D	261										ovary(1)	1																		---	---	---	---
SDSL	113675	broad.mit.edu	37	12	113872039	113872039	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:113872039G>A	uc001tvi.2	+						SDSL_uc009zwh.2_Intron	NM_138432	NP_612441			serine dehydratase-like						cellular amino acid metabolic process		L-serine ammonia-lyase activity|L-threonine ammonia-lyase activity|pyridoxal phosphate binding				0					Pyridoxal Phosphate(DB00114)													---	---	---	---
TBX5	6910	broad.mit.edu	37	12	114793779	114793779	+	Missense_Mutation	SNP	G	A	A	rs143068551	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114793779G>A	uc001tvo.2	-	9	1610	c.1115C>T	c.(1114-1116)TCG>TTG	p.S372L	TBX5_uc001tvp.2_Missense_Mutation_p.S372L|TBX5_uc001tvq.2_Missense_Mutation_p.S322L	NM_181486	NP_852259	Q99593	TBX5_HUMAN	T-box 5 isoform 1	372					cardiac left ventricle formation|cell migration involved in coronary vasculogenesis|cell-cell signaling|embryonic arm morphogenesis|induction of apoptosis|negative regulation of cardiac muscle cell proliferation|negative regulation of cell migration|negative regulation of epithelial to mesenchymal transition|pericardium development|positive regulation of cardioblast differentiation|positive regulation of transcription from RNA polymerase II promoter|ventricular septum development	cytoplasm|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding	p.S372S(1)		ovary(6)|pancreas(1)|skin(1)	8	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0893)														---	---	---	---
TBX5	6910	broad.mit.edu	37	12	114841607	114841607	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:114841607C>T	uc001tvo.2	-	2	592	c.97G>A	c.(97-99)GGG>AGG	p.G33R	TBX5_uc001tvp.2_Missense_Mutation_p.G33R|TBX5_uc001tvq.2_Intron|TBX5_uc010syv.1_Missense_Mutation_p.G33R	NM_181486	NP_852259	Q99593	TBX5_HUMAN	T-box 5 isoform 1	33				GFGLAHTPLEPDAKDLPCDSKPESALGAPSKSPSSPQAAFT QQ -> ALAGAHLWSLTQKTCLRFEPRARSGPPASPPGRPR SRLHPA (in Ref. 1; CAA70592).	cardiac left ventricle formation|cell migration involved in coronary vasculogenesis|cell-cell signaling|embryonic arm morphogenesis|induction of apoptosis|negative regulation of cardiac muscle cell proliferation|negative regulation of cell migration|negative regulation of epithelial to mesenchymal transition|pericardium development|positive regulation of cardioblast differentiation|positive regulation of transcription from RNA polymerase II promoter|ventricular septum development	cytoplasm|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			ovary(6)|pancreas(1)|skin(1)	8	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0893)														---	---	---	---
TBX3	6926	broad.mit.edu	37	12	115112422	115112422	+	Missense_Mutation	SNP	C	T	T	rs149324108		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:115112422C>T	uc001tvt.1	-	7	2282	c.1318G>A	c.(1318-1320)GCC>ACC	p.A440T	TBX3_uc001tvu.1_Missense_Mutation_p.A420T	NM_016569	NP_057653	O15119	TBX3_HUMAN	T-box 3 protein isoform 2	440					anterior/posterior axis specification, embryo|anti-apoptosis|cell aging|embryonic arm morphogenesis|embryonic digit morphogenesis|female genitalia development|follicle-stimulating hormone secretion|luteinizing hormone secretion|male genitalia development|mesoderm morphogenesis|negative regulation of myoblast differentiation|negative regulation of transcription, DNA-dependent|positive regulation of cell cycle|positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter|skeletal system development	nucleus	sequence-specific DNA binding			ovary(2)|skin(1)	3	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)														---	---	---	---
MED13L	23389	broad.mit.edu	37	12	116413356	116413356	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116413356A>G	uc001tvw.2	-	24	5607	c.5552T>C	c.(5551-5553)TTA>TCA	p.L1851S		NM_015335	NP_056150	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	1851					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent					skin(4)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	8	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)														---	---	---	---
MED13L	23389	broad.mit.edu	37	12	116420250	116420250	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116420250C>T	uc001tvw.2	-	22	5169	c.5114G>A	c.(5113-5115)CGC>CAC	p.R1705H		NM_015335	NP_056150	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	1705					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent					skin(4)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	8	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)														---	---	---	---
MED13L	23389	broad.mit.edu	37	12	116422119	116422119	+	Missense_Mutation	SNP	C	T	T	rs140136426		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116422119C>T	uc001tvw.2	-	20	4452	c.4397G>A	c.(4396-4398)CGC>CAC	p.R1466H		NM_015335	NP_056150	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	1466					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent					skin(4)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	8	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)														---	---	---	---
MED13L	23389	broad.mit.edu	37	12	116434474	116434474	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116434474C>T	uc001tvw.2	-	16	2858	c.2803G>A	c.(2803-2805)GTG>ATG	p.V935M		NM_015335	NP_056150	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	935					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent					skin(4)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	8	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)														---	---	---	---
MED13L	23389	broad.mit.edu	37	12	116457631	116457631	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116457631C>T	uc001tvw.2	-	6	827	c.772G>A	c.(772-774)GAG>AAG	p.E258K		NM_015335	NP_056150	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	258					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent					skin(4)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	8	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)														---	---	---	---
NCRNA00173	100287569	broad.mit.edu	37	12	116972462	116972462	+	RNA	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:116972462A>G	uc001tvx.1	+	2		c.733A>G			NCRNA00173_uc001tvy.2_Intron	NR_027345				Homo sapiens cDNA FLJ42957 fis, clone BRSTN2010500.												0																		---	---	---	---
KSR2	283455	broad.mit.edu	37	12	118199014	118199014	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118199014C>T	uc001two.2	-	4	756	c.701G>A	c.(700-702)CGC>CAC	p.R234H		NM_173598	NP_775869	Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2	263	Pro-rich.				intracellular signal transduction	cytoplasm|membrane	ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(10)|central_nervous_system(2)|stomach(1)|large_intestine(1)|breast(1)	15	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
KSR2	283455	broad.mit.edu	37	12	118199122	118199122	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:118199122A>C	uc001two.2	-	4	648	c.593T>G	c.(592-594)CTT>CGT	p.L198R		NM_173598	NP_775869	Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2	227	Pro-rich.				intracellular signal transduction	cytoplasm|membrane	ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(10)|central_nervous_system(2)|stomach(1)|large_intestine(1)|breast(1)	15	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
SRRM4	84530	broad.mit.edu	37	12	119594290	119594290	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:119594290G>A	uc001txa.1	+							NM_194286	NP_919262			KIAA1853 protein						cell differentiation|mRNA processing|nervous system development|regulation of RNA splicing|RNA splicing	nucleus	mRNA binding			ovary(2)	2																		---	---	---	---
CIT	11113	broad.mit.edu	37	12	120204937	120204937	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120204937T>A	uc001txi.1	-	18	2185	c.2132A>T	c.(2131-2133)GAA>GTA	p.E711V	CIT_uc001txh.1_Missense_Mutation_p.E245V|CIT_uc001txj.1_Missense_Mutation_p.E753V	NM_007174	NP_009105	O14578	CTRO_HUMAN	citron	711	Potential.				intracellular signal transduction		ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity			ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1)	10	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)														---	---	---	---
GCN1L1	10985	broad.mit.edu	37	12	120567261	120567261	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120567261G>T	uc001txo.2	-	57	7722	c.7709C>A	c.(7708-7710)GCT>GAT	p.A2570D		NM_006836	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis	2570	HEAT 23.				regulation of translation	ribosome	protein binding|translation factor activity, nucleic acid binding			ovary(4)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
GCN1L1	10985	broad.mit.edu	37	12	120575696	120575696	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120575696G>A	uc001txo.2	-							NM_006836	NP_006827			GCN1 general control of amino-acid synthesis						regulation of translation	ribosome	protein binding|translation factor activity, nucleic acid binding			ovary(4)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
PXN	5829	broad.mit.edu	37	12	120652775	120652775	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120652775C>T	uc001txt.2	-	9	1262	c.1131G>A	c.(1129-1131)TGG>TGA	p.W377*	PXN_uc001txu.2_Nonsense_Mutation_p.W189*|PXN_uc001txv.2_Nonsense_Mutation_p.W258*|PXN_uc001txx.2_Nonsense_Mutation_p.W210*|PXN_uc001txy.2_Nonsense_Mutation_p.W343*|PXN_uc001txz.2_RNA	NM_001080855	NP_001074324	P49023	PAXI_HUMAN	paxillin isoform 1	377	LIM zinc-binding 1.				cell junction assembly|cell-matrix adhesion|cellular response to reactive oxygen species|epidermal growth factor receptor signaling pathway|growth hormone receptor signaling pathway|muscle contraction|signal complex assembly	cytoplasm|focal adhesion|lamellipodium|microtubule associated complex	beta-catenin binding|vinculin binding|zinc ion binding			ovary(1)|breast(1)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
COQ5	84274	broad.mit.edu	37	12	120966813	120966813	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120966813G>T	uc001tyn.2	-	1	152	c.132C>A	c.(130-132)TCC>TCA	p.S44S	COQ5_uc001tyo.2_5'UTR|COQ5_uc010szj.1_Silent_p.S44S	NM_032314	NP_115690	Q5HYK3	COQ5_HUMAN	coenzyme Q5 homolog, methyltransferase	44					ubiquinone biosynthetic process	mitochondrion	methyltransferase activity			ovary(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
RNF10	9921	broad.mit.edu	37	12	120984235	120984235	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120984235G>A	uc001typ.3	+	2	668	c.185G>A	c.(184-186)CGT>CAT	p.R62H	RNF10_uc010szk.1_RNA|RNF10_uc001tyq.3_5'UTR	NM_014868	NP_055683	Q8N5U6	RNF10_HUMAN	ring finger protein 10	62	Ser-rich.				negative regulation of Schwann cell proliferation|positive regulation of myelination|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	protein binding|transcription regulatory region DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
HNF1A	6927	broad.mit.edu	37	12	121435467	121435467	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121435467C>T	uc001tzg.2	+	7	1523	c.1500C>T	c.(1498-1500)CAC>CAT	p.H500H	HNF1A_uc001tzf.2_Silent_p.H500H|HNF1A_uc010szn.1_Silent_p.H500H	NM_000545	NP_000536	P20823	HNF1A_HUMAN	hepatic nuclear factor-1-alpha	500					glucose homeostasis|glucose import|insulin secretion|positive regulation of transcription initiation from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|renal glucose absorption	cytoplasm|nucleus|protein complex	DNA binding|protein dimerization activity|protein heterodimerization activity|protein homodimerization activity|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			liver(92)|large_intestine(15)|endometrium(6)|breast(2)|lung(1)	116	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)													Hepatic_Adenoma_Familial_Clustering_of				---	---	---	---
OASL	8638	broad.mit.edu	37	12	121458471	121458471	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121458471C>T	uc001tzj.1	-	6	1444	c.1438G>A	c.(1438-1440)GGC>AGC	p.G480S	OASL_uc001tzk.1_3'UTR	NM_003733	NP_003724	Q15646	OASL_HUMAN	2'-5'-oligoadenylate synthetase-like isoform a	480	Ubiquitin-like 2.				interferon-gamma-mediated signaling pathway|type I interferon-mediated signaling pathway	cytoplasm|nucleolus	ATP binding|DNA binding|double-stranded RNA binding|thyroid hormone receptor binding|transferase activity			skin(1)	1	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)																	---	---	---	---
ANAPC5	51433	broad.mit.edu	37	12	121783710	121783710	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121783710A>G	uc001uag.2	-	4	644	c.522T>C	c.(520-522)GAT>GAC	p.D174D	ANAPC5_uc001uah.2_Silent_p.D75D	NM_016237	NP_057321	Q9UJX4	APC5_HUMAN	anaphase-promoting complex subunit 5 isoform a	174					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|G2/M transition of mitotic cell cycle|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm	protein phosphatase binding|ubiquitin-protein ligase activity			skin(3)|breast(2)|kidney(1)	6	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)																	---	---	---	---
KDM2B	84678	broad.mit.edu	37	12	121880788	121880788	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121880788A>G	uc001uat.2	-						KDM2B_uc001uaq.2_Intron|KDM2B_uc010szy.1_Intron|KDM2B_uc001uar.2_Intron|KDM2B_uc001uas.2_Intron|KDM2B_uc001uau.2_Intron|KDM2B_uc001uao.2_Intron|KDM2B_uc010szx.1_Intron|KDM2B_uc001uap.2_Intron	NM_032590	NP_115979			F-box and leucine-rich repeat protein 10 isoform						embryonic camera-type eye morphogenesis|fourth ventricle development|histone H2A monoubiquitination|initiation of neural tube closure|lateral ventricle development|midbrain development|midbrain-hindbrain boundary morphogenesis|negative regulation of neural precursor cell proliferation|negative regulation of neuron apoptosis|negative regulation of transcription from RNA polymerase II promoter|spermatogenesis|third ventricle development|transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-K36 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|rRNA binding|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
KDM2B	84678	broad.mit.edu	37	12	121947648	121947648	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121947648G>T	uc001uat.2	-	11	1473	c.1369C>A	c.(1369-1371)CTC>ATC	p.L457I	KDM2B_uc001uar.2_Missense_Mutation_p.L48I|KDM2B_uc001uas.2_Missense_Mutation_p.L426I|KDM2B_uc001uau.2_Missense_Mutation_p.L340I|KDM2B_uc001uav.3_Missense_Mutation_p.L367I	NM_032590	NP_115979	Q8NHM5	KDM2B_HUMAN	F-box and leucine-rich repeat protein 10 isoform	457					embryonic camera-type eye morphogenesis|fourth ventricle development|histone H2A monoubiquitination|initiation of neural tube closure|lateral ventricle development|midbrain development|midbrain-hindbrain boundary morphogenesis|negative regulation of neural precursor cell proliferation|negative regulation of neuron apoptosis|negative regulation of transcription from RNA polymerase II promoter|spermatogenesis|third ventricle development|transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-K36 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|rRNA binding|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
KDM2B	84678	broad.mit.edu	37	12	121987409	121987409	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121987409A>C	uc001uat.2	-	5	636	c.532T>G	c.(532-534)TTC>GTC	p.F178V	KDM2B_uc001uas.2_Missense_Mutation_p.F147V|KDM2B_uc001uau.2_Missense_Mutation_p.F61V|KDM2B_uc001uav.3_Missense_Mutation_p.F178V	NM_032590	NP_115979	Q8NHM5	KDM2B_HUMAN	F-box and leucine-rich repeat protein 10 isoform	178	JmjC.				embryonic camera-type eye morphogenesis|fourth ventricle development|histone H2A monoubiquitination|initiation of neural tube closure|lateral ventricle development|midbrain development|midbrain-hindbrain boundary morphogenesis|negative regulation of neural precursor cell proliferation|negative regulation of neuron apoptosis|negative regulation of transcription from RNA polymerase II promoter|spermatogenesis|third ventricle development|transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-K36 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|rRNA binding|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
VPS33A	65082	broad.mit.edu	37	12	122724466	122724466	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122724466T>G	uc001ucd.2	-	9	1236	c.1123A>C	c.(1123-1125)ACC>CCC	p.T375P	VPS33A_uc001ucc.2_RNA	NM_022916	NP_075067	Q96AX1	VP33A_HUMAN	vacuolar protein sorting 33A	375					lysosome localization|melanosome localization|platelet formation|protein transport|regulation of developmental pigmentation|vesicle docking involved in exocytosis	early endosome|late endosome membrane|lysosomal membrane|perinuclear region of cytoplasm	protein binding			skin(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000336)|Epithelial(86;0.000606)|BRCA - Breast invasive adenocarcinoma(302;0.23)														---	---	---	---
VPS33A	65082	broad.mit.edu	37	12	122729202	122729202	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122729202G>A	uc001ucd.2	-	7	996	c.883C>T	c.(883-885)CTC>TTC	p.L295F	VPS33A_uc001ucc.2_RNA	NM_022916	NP_075067	Q96AX1	VP33A_HUMAN	vacuolar protein sorting 33A	295					lysosome localization|melanosome localization|platelet formation|protein transport|regulation of developmental pigmentation|vesicle docking involved in exocytosis	early endosome|late endosome membrane|lysosomal membrane|perinuclear region of cytoplasm	protein binding			skin(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000336)|Epithelial(86;0.000606)|BRCA - Breast invasive adenocarcinoma(302;0.23)														---	---	---	---
ZCCHC8	55596	broad.mit.edu	37	12	122962779	122962779	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122962779T>C	uc001ucn.2	-	12	1332	c.1201A>G	c.(1201-1203)AAT>GAT	p.N401D	ZCCHC8_uc001ucl.2_Missense_Mutation_p.N12D|ZCCHC8_uc001ucm.2_Missense_Mutation_p.N163D|ZCCHC8_uc009zxp.2_Missense_Mutation_p.N163D|ZCCHC8_uc009zxq.2_Missense_Mutation_p.N163D	NM_017612	NP_060082	Q6NZY4	ZCHC8_HUMAN	zinc finger, CCHC domain containing 8	401						catalytic step 2 spliceosome	nucleic acid binding|protein binding|zinc ion binding				0	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.25e-05)|Epithelial(86;0.000113)|BRCA - Breast invasive adenocarcinoma(302;0.202)														---	---	---	---
HIP1R	9026	broad.mit.edu	37	12	123344342	123344342	+	Silent	SNP	C	T	T	rs149876989		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123344342C>T	uc001udj.1	+	24	2489	c.2430C>T	c.(2428-2430)CAC>CAT	p.H810H	HIP1R_uc001udk.1_Silent_p.H75H	NM_003959	NP_003950	O75146	HIP1R_HUMAN	huntingtin interacting protein-1-related	810	I/LWEQ.				receptor-mediated endocytosis	clathrin coated vesicle membrane|coated pit|perinuclear region of cytoplasm	actin binding|phosphatidylinositol binding			ovary(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;4.6e-05)|Epithelial(86;0.000119)|BRCA - Breast invasive adenocarcinoma(302;0.2)														---	---	---	---
HIP1R	9026	broad.mit.edu	37	12	123345695	123345695	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123345695G>T	uc001udj.1	+	30	2967	c.2908G>T	c.(2908-2910)GGC>TGC	p.G970C	HIP1R_uc001udk.1_Missense_Mutation_p.G235C	NM_003959	NP_003950	O75146	HIP1R_HUMAN	huntingtin interacting protein-1-related	970	I/LWEQ.				receptor-mediated endocytosis	clathrin coated vesicle membrane|coated pit|perinuclear region of cytoplasm	actin binding|phosphatidylinositol binding			ovary(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;4.6e-05)|Epithelial(86;0.000119)|BRCA - Breast invasive adenocarcinoma(302;0.2)														---	---	---	---
DDX55	57696	broad.mit.edu	37	12	124092219	124092219	+	Intron	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124092219C>A	uc001ufi.2	+						DDX55_uc001ufh.2_5'UTR|DDX55_uc001ufj.1_Intron|DDX55_uc001ufk.2_5'UTR	NM_020936	NP_065987			DEAD (Asp-Glu-Ala-Asp) box polypeptide 55								ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000142)|Epithelial(86;0.000637)|all cancers(50;0.00772)														---	---	---	---
DNAH10	196385	broad.mit.edu	37	12	124330580	124330580	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124330580C>T	uc001uft.3	+	31	5364	c.5339C>T	c.(5338-5340)CCG>CTG	p.P1780L		NM_207437	NP_997320	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	1780	Stem (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(3)|skin(2)|central_nervous_system(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)														---	---	---	---
DNAH10	196385	broad.mit.edu	37	12	124337904	124337904	+	Intron	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124337904G>T	uc001uft.3	+							NM_207437	NP_997320			dynein, axonemal, heavy chain 10						microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(3)|skin(2)|central_nervous_system(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)														---	---	---	---
CCDC92	80212	broad.mit.edu	37	12	124421726	124421726	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124421726G>A	uc001ufw.1	-	5	1022	c.875C>T	c.(874-876)GCA>GTA	p.A292V	CCDC92_uc001ufv.1_Missense_Mutation_p.A275V|CCDC92_uc001ufx.1_Missense_Mutation_p.A292V|CCDC92_uc001ufy.1_Missense_Mutation_p.A275V	NM_025140	NP_079416	Q53HC0	CCD92_HUMAN	coiled-coil domain containing 92	292											0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			Epithelial(86;0.0002)|OV - Ovarian serous cystadenocarcinoma(86;0.000222)|all cancers(50;0.00129)|BRCA - Breast invasive adenocarcinoma(302;0.242)														---	---	---	---
NCOR2	9612	broad.mit.edu	37	12	124824637	124824637	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124824637G>T	uc010tay.1	-	39	5788	c.5632C>A	c.(5632-5634)CTC>ATC	p.L1878I	NCOR2_uc010taz.1_Missense_Mutation_p.L1862I|NCOR2_uc010tax.1_5'UTR	NM_006312	NP_006303	Q9Y618	NCOR2_HUMAN	nuclear receptor co-repressor 2 isoform 1	1879					cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity			skin(3)|ovary(1)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)														---	---	---	---
NCOR2	9612	broad.mit.edu	37	12	124862889	124862889	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124862889C>T	uc010tba.1	-	18	2178	c.2061G>A	c.(2059-2061)CCG>CCA	p.P687P	NCOR2_uc010tay.1_Silent_p.P687P|NCOR2_uc010taz.1_Silent_p.P687P|NCOR2_uc010tbb.1_Silent_p.P687P|NCOR2_uc010tbc.1_Silent_p.P686P|NCOR2_uc001ugj.1_Silent_p.P687P	NM_001077261	NP_001070729	Q9Y618	NCOR2_HUMAN	nuclear receptor co-repressor 2 isoform 2	687					cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity			skin(3)|ovary(1)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)														---	---	---	---
NCOR2	9612	broad.mit.edu	37	12	124885119	124885119	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:124885119G>A	uc010tba.1	-	15	1858	c.1741C>T	c.(1741-1743)CGC>TGC	p.R581C	NCOR2_uc010tay.1_Missense_Mutation_p.R581C|NCOR2_uc010taz.1_Missense_Mutation_p.R581C|NCOR2_uc010tbb.1_Missense_Mutation_p.R581C|NCOR2_uc010tbc.1_Missense_Mutation_p.R580C|NCOR2_uc001ugj.1_Missense_Mutation_p.R581C	NM_001077261	NP_001070729	Q9Y618	NCOR2_HUMAN	nuclear receptor co-repressor 2 isoform 2	581					cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity			skin(3)|ovary(1)	4	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)														---	---	---	---
DHX37	57647	broad.mit.edu	37	12	125453203	125453203	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125453203C>T	uc001ugy.2	-							NM_032656	NP_116045			DEAH (Asp-Glu-Ala-His) box polypeptide 37								ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			skin(1)	1	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;8.05e-05)|Epithelial(86;0.000486)|all cancers(50;0.00653)														---	---	---	---
TMEM132D	121256	broad.mit.edu	37	12	129822247	129822247	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:129822247A>C	uc009zyl.1	-	4	1559	c.1231T>G	c.(1231-1233)TCT>GCT	p.S411A		NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor	411	Extracellular (Potential).					integral to membrane				ovary(10)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)														---	---	---	---
TMEM132D	121256	broad.mit.edu	37	12	130185007	130185007	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130185007C>T	uc009zyl.1	-	2	644	c.316G>A	c.(316-318)GTG>ATG	p.V106M		NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor	106	Extracellular (Potential).					integral to membrane				ovary(10)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)														---	---	---	---
PIWIL1	9271	broad.mit.edu	37	12	130839145	130839145	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130839145C>T	uc001uik.2	+	10	1198	c.1108C>T	c.(1108-1110)CGG>TGG	p.R370W	PIWIL1_uc001uij.1_Missense_Mutation_p.R370W	NM_004764	NP_004755	Q96J94	PIWL1_HUMAN	piwi-like 1	370	PAZ.				gene silencing by RNA|meiosis|multicellular organismal development|regulation of translation|spermatid development	chromatoid body|P granule	mRNA binding|piRNA binding|protein binding			ovary(2)	2	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.02e-06)|Epithelial(86;3.85e-05)|all cancers(50;4.65e-05)														---	---	---	---
RIMBP2	23504	broad.mit.edu	37	12	130897156	130897156	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130897156G>A	uc001uil.2	-							NM_015347	NP_056162			RIM-binding protein 2							cell junction|synapse				upper_aerodigestive_tract(3)|ovary(3)|large_intestine(2)|central_nervous_system(2)|pancreas(1)	11	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)														---	---	---	---
RIMBP2	23504	broad.mit.edu	37	12	130898735	130898735	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130898735T>G	uc001uil.2	-	14	2751	c.2587A>C	c.(2587-2589)ACC>CCC	p.T863P		NM_015347	NP_056162	O15034	RIMB2_HUMAN	RIM-binding protein 2	863	SH3 2.					cell junction|synapse				upper_aerodigestive_tract(3)|ovary(3)|large_intestine(2)|central_nervous_system(2)|pancreas(1)	11	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)														---	---	---	---
RAN	5901	broad.mit.edu	37	12	131360267	131360267	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131360267C>T	uc001uir.2	+	6	611	c.546C>T	c.(544-546)CTC>CTT	p.L182L	RAN_uc010tbk.1_Silent_p.L94L|RAN_uc010tbl.1_Silent_p.L94L|RAN_uc001uis.2_Silent_p.L202L	NM_006325	NP_006316	P62826	RAN_HUMAN	ras-related nuclear protein	182					androgen receptor signaling pathway|cell division|DNA metabolic process|mitosis|mitotic spindle organization|positive regulation of transcription, DNA-dependent|protein export from nucleus|RNA export from nucleus|viral genome transport in host cell|viral infectious cycle	cytosol|melanosome|nuclear pore|nucleoplasm	androgen receptor binding|chromatin binding|GTP binding|GTPase activity|transcription coactivator activity				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	Lung NSC(355;7.46e-07)|all_epithelial(31;7.36e-06)		OV - Ovarian serous cystadenocarcinoma(86;9.18e-49)|Epithelial(86;1.42e-45)|all cancers(50;6.28e-40)														---	---	---	---
GPR133	283383	broad.mit.edu	37	12	131471802	131471802	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131471802A>C	uc001uit.3	+	6	1212	c.653A>C	c.(652-654)AAG>ACG	p.K218T	GPR133_uc010tbm.1_Missense_Mutation_p.K250T	NM_198827	NP_942122	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133 precursor	218	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(5)|ovary(3)|skin(2)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)														---	---	---	---
GPR133	283383	broad.mit.edu	37	12	131498894	131498894	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:131498894C>T	uc001uit.3	+						GPR133_uc010tbm.1_Intron	NM_198827	NP_942122			G protein-coupled receptor 133 precursor						neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(5)|ovary(3)|skin(2)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)														---	---	---	---
PUS1	80324	broad.mit.edu	37	12	132425995	132425995	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132425995C>T	uc001ujf.2	+	5	1182	c.703C>T	c.(703-705)CTC>TTC	p.L235F	PUS1_uc001ujg.2_Missense_Mutation_p.L207F|PUS1_uc001ujh.2_Missense_Mutation_p.L207F|PUS1_uc001uji.2_Missense_Mutation_p.L182F	NM_025215	NP_079491	Q9Y606	TRUA_HUMAN	pseudouridine synthase 1 isoform 1	235						mitochondrion	pseudouridine synthase activity|pseudouridylate synthase activity|RNA binding			breast(1)|central_nervous_system(1)	2	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.05e-08)|Epithelial(86;2.51e-07)|all cancers(50;2.94e-07)														---	---	---	---
EP400	57634	broad.mit.edu	37	12	132476714	132476714	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132476714T>C	uc001ujn.2	+						EP400_uc001ujl.2_Intron|EP400_uc001ujm.2_Intron|EP400_uc001ujk.2_Intron	NM_015409	NP_056224			E1A binding protein p400						histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent	NuA4 histone acetyltransferase complex|nuclear speck	ATP binding|DNA binding|helicase activity			central_nervous_system(4)|ovary(3)|breast(3)|skin(2)	12	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)														---	---	---	---
EP400	57634	broad.mit.edu	37	12	132514620	132514620	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132514620T>C	uc001ujn.2	+	28	5706	c.5671T>C	c.(5671-5673)TTG>CTG	p.L1891L	EP400_uc001ujl.2_Silent_p.L1890L|EP400_uc001ujm.2_Silent_p.L1810L|SNORA49_uc001ujo.2_5'Flank	NM_015409	NP_056224	Q96L91	EP400_HUMAN	E1A binding protein p400	1927	Helicase C-terminal.				histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent	NuA4 histone acetyltransferase complex|nuclear speck	ATP binding|DNA binding|helicase activity			central_nervous_system(4)|ovary(3)|breast(3)|skin(2)	12	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)														---	---	---	---
EP400	57634	broad.mit.edu	37	12	132516703	132516703	+	Intron	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132516703C>A	uc001ujn.2	+						EP400_uc001ujl.2_Intron|EP400_uc001ujm.2_Intron	NM_015409	NP_056224			E1A binding protein p400						histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent	NuA4 histone acetyltransferase complex|nuclear speck	ATP binding|DNA binding|helicase activity			central_nervous_system(4)|ovary(3)|breast(3)|skin(2)	12	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)														---	---	---	---
DDX51	317781	broad.mit.edu	37	12	132624452	132624452	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132624452C>T	uc001ujy.3	-	13	1832	c.1793G>A	c.(1792-1794)CGC>CAC	p.R598H		NM_175066	NP_778236	Q8N8A6	DDX51_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 51	598	Helicase C-terminal.				rRNA processing	nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			lung(1)|pancreas(1)	2	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.59e-08)|Epithelial(86;3.62e-07)|all cancers(50;2.13e-05)														---	---	---	---
DDX51	317781	broad.mit.edu	37	12	132626504	132626504	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:132626504G>A	uc001ujy.3	-						NOC4L_uc001ujz.1_5'Flank	NM_175066	NP_778236			DEAD (Asp-Glu-Ala-Asp) box polypeptide 51						rRNA processing	nucleolus	ATP binding|ATP-dependent helicase activity|RNA binding			lung(1)|pancreas(1)	2	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.59e-08)|Epithelial(86;3.62e-07)|all cancers(50;2.13e-05)														---	---	---	---
P2RX2	22953	broad.mit.edu	37	12	133195530	133195530	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133195530T>G	uc001ukj.1	+	1	128	c.128T>G	c.(127-129)GTC>GGC	p.V43G	P2RX2_uc001uki.1_Missense_Mutation_p.V43G|P2RX2_uc001ukk.1_Missense_Mutation_p.V43G|P2RX2_uc001ukl.1_Missense_Mutation_p.V43G|P2RX2_uc001ukm.1_Intron|P2RX2_uc001ukn.1_Intron|P2RX2_uc009zyt.1_Missense_Mutation_p.V43G|P2RX2_uc001uko.1_Missense_Mutation_p.V43G	NM_170682	NP_733782	Q9UBL9	P2RX2_HUMAN	purinergic receptor P2X2 isoform A	43	Helical; Name=1; (Potential).				positive regulation of calcium ion transport into cytosol|positive regulation of calcium-mediated signaling|protein homooligomerization	integral to membrane	ATP binding|extracellular ATP-gated cation channel activity|identical protein binding|purinergic nucleotide receptor activity				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0767)		OV - Ovarian serous cystadenocarcinoma(86;2.32e-08)|Epithelial(86;8.62e-08)|all cancers(50;4.5e-06)														---	---	---	---
POLE	5426	broad.mit.edu	37	12	133218948	133218948	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133218948T>C	uc001uks.1	-	38	5032	c.4988A>G	c.(4987-4989)GAC>GGC	p.D1663G	POLE_uc001ukq.1_5'Flank|POLE_uc001ukr.1_Missense_Mutation_p.D467G|POLE_uc010tbq.1_RNA	NM_006231	NP_006222	Q07864	DPOE1_HUMAN	DNA-directed DNA polymerase epsilon	1663					base-excision repair, gap-filling|DNA synthesis involved in DNA repair|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	chromatin binding|DNA binding|DNA-directed DNA polymerase activity|nucleotide binding|protein binding|zinc ion binding			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)									DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
GOLGA3	2802	broad.mit.edu	37	12	133351808	133351808	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133351808C>T	uc001ukz.1	-	22	4621	c.4062G>A	c.(4060-4062)TCG>TCA	p.S1354S	GOLGA3_uc001ula.1_Silent_p.S1354S	NM_005895	NP_005886	Q08378	GOGA3_HUMAN	Golgi autoantigen, golgin subfamily a, 3	1354	Potential.|Gln-rich.				intra-Golgi vesicle-mediated transport	Golgi cisterna membrane|Golgi transport complex	protein binding|transporter activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)														---	---	---	---
GOLGA3	2802	broad.mit.edu	37	12	133365849	133365849	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133365849C>T	uc001ukz.1	-	13	3134	c.2575G>A	c.(2575-2577)GCC>ACC	p.A859T	GOLGA3_uc001ula.1_Missense_Mutation_p.A859T|GOLGA3_uc001ulb.2_Missense_Mutation_p.A859T	NM_005895	NP_005886	Q08378	GOGA3_HUMAN	Golgi autoantigen, golgin subfamily a, 3	859	Potential.				intra-Golgi vesicle-mediated transport	Golgi cisterna membrane|Golgi transport complex	protein binding|transporter activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)														---	---	---	---
ZNF10	7556	broad.mit.edu	37	12	133733492	133733492	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133733492C>T	uc009zzb.2	+	5	2107	c.1660C>T	c.(1660-1662)CTT>TTT	p.L554F	ZNF268_uc010tbv.1_Intron|ZNF10_uc001ulq.2_Missense_Mutation_p.L554F	NM_015394	NP_056209	P21506	ZNF10_HUMAN	zinc finger protein 10	554					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			breast(1)|central_nervous_system(1)|skin(1)	3	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;1.28e-06)|all_epithelial(31;0.0051)|Lung NSC(355;0.00948)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)														---	---	---	---
ZNF268	10795	broad.mit.edu	37	12	133768187	133768187	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133768187A>G	uc010tcf.1	+	4	677	c.347A>G	c.(346-348)AAC>AGC	p.N116S	ZNF268_uc010tbv.1_5'UTR|ZNF268_uc010tbw.1_Intron|ZNF268_uc010tbx.1_Intron|ZNF268_uc010tby.1_Intron|ZNF268_uc010tbz.1_5'UTR|ZNF268_uc010tca.1_5'UTR|ZNF268_uc010tcb.1_Intron|ZNF268_uc010tcc.1_Intron|ZNF268_uc010tcd.1_5'UTR|ZNF268_uc010tce.1_Intron|ZNF268_uc010tcg.1_5'UTR|ZNF268_uc010tch.1_Missense_Mutation_p.N116S	NM_003415	NP_003406	Q14587	ZN268_HUMAN	zinc finger protein 268 isoform a	116	KRAB.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.000215)|all_epithelial(31;0.096)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)														---	---	---	---
MPHOSPH8	54737	broad.mit.edu	37	13	20220606	20220606	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20220606A>G	uc001umh.2	+	3	402	c.393A>G	c.(391-393)ATA>ATG	p.I131M	MPHOSPH8_uc001umf.1_Missense_Mutation_p.I131M|MPHOSPH8_uc001umg.2_Missense_Mutation_p.I131M|MPHOSPH8_uc001umi.2_Translation_Start_Site	NM_017520	NP_059990	Q99549	MPP8_HUMAN	M-phase phosphoprotein 8	131					cell cycle	cytoplasm|nucleus					0		all_cancers(29;2.83e-16)|all_lung(29;1.16e-17)|all_epithelial(30;8.13e-16)|Lung NSC(5;6.91e-15)|Lung SC(185;0.0367)		all cancers(112;8.43e-05)|Epithelial(112;0.000426)|OV - Ovarian serous cystadenocarcinoma(117;0.00596)|Lung(94;0.015)|LUSC - Lung squamous cell carcinoma(192;0.0795)														---	---	---	---
PSPC1	55269	broad.mit.edu	37	13	20346397	20346397	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:20346397G>A	uc001uml.2	-	2	845	c.659C>T	c.(658-660)GCA>GTA	p.A220V	PSPC1_uc001umj.1_RNA|PSPC1_uc001umk.1_RNA	NM_001042414	NP_001035879	Q8WXF1	PSPC1_HUMAN	paraspeckle protein 1	220	RRM 2.|Sufficient for paraspeckles localization.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nuclear matrix|nucleolus	nucleotide binding|protein binding|RNA binding			breast(1)	1		all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483)														---	---	---	---
CRYL1	51084	broad.mit.edu	37	13	21063527	21063527	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21063527C>A	uc001une.2	-	3	337	c.258G>T	c.(256-258)GAG>GAT	p.E86D	CRYL1_uc001unf.2_Missense_Mutation_p.E64D|CRYL1_uc001ung.2_Missense_Mutation_p.E64D	NM_015974	NP_057058	Q9Y2S2	CRYL1_HUMAN	lambda-crystallin	86					fatty acid metabolic process	cytosol	3-hydroxyacyl-CoA dehydrogenase activity|L-gulonate 3-dehydrogenase activity|NAD+ binding|protein homodimerization activity				0		all_cancers(29;2.27e-23)|all_epithelial(30;1.69e-19)|all_lung(29;8.29e-18)|Lung SC(185;0.0262)|Ovarian(182;0.0827)|Hepatocellular(188;0.244)		all cancers(112;6.6e-05)|Epithelial(112;0.00178)|OV - Ovarian serous cystadenocarcinoma(117;0.0169)|Lung(94;0.0215)|GBM - Glioblastoma multiforme(144;0.0402)|LUSC - Lung squamous cell carcinoma(192;0.061)												OREG0022283	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
XPO4	64328	broad.mit.edu	37	13	21382694	21382694	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21382694A>G	uc001unq.3	-	12	1556	c.1520T>C	c.(1519-1521)CTC>CCC	p.L507P		NM_022459	NP_071904	Q9C0E2	XPO4_HUMAN	exportin 4	507					protein transport	cytoplasm|nucleus	protein binding			large_intestine(1)|ovary(1)|kidney(1)	3		all_cancers(29;5.05e-24)|all_epithelial(30;5.56e-20)|all_lung(29;2.38e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000521)|Epithelial(112;0.000892)|OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Lung(94;0.0189)|LUSC - Lung squamous cell carcinoma(192;0.0548)														---	---	---	---
XPO4	64328	broad.mit.edu	37	13	21417166	21417166	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:21417166A>C	uc001unq.3	-	6	631	c.595T>G	c.(595-597)TTC>GTC	p.F199V	XPO4_uc010tcr.1_Missense_Mutation_p.F125V	NM_022459	NP_071904	Q9C0E2	XPO4_HUMAN	exportin 4	199					protein transport	cytoplasm|nucleus	protein binding			large_intestine(1)|ovary(1)|kidney(1)	3		all_cancers(29;5.05e-24)|all_epithelial(30;5.56e-20)|all_lung(29;2.38e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000521)|Epithelial(112;0.000892)|OV - Ovarian serous cystadenocarcinoma(117;0.0148)|Lung(94;0.0189)|LUSC - Lung squamous cell carcinoma(192;0.0548)														---	---	---	---
SACS	26278	broad.mit.edu	37	13	23905481	23905481	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23905481C>T	uc001uon.2	-	10	13123	c.12534G>A	c.(12532-12534)CCG>CCA	p.P4178P	SACS_uc001uoo.2_Silent_p.P4031P|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Intron	NM_014363	NP_055178	Q9NZJ4	SACS_HUMAN	sacsin	4178					cell death|negative regulation of inclusion body assembly|protein folding	axon|cell body fiber|dendrite|mitochondrion|nucleus	ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)														---	---	---	---
SACS	26278	broad.mit.edu	37	13	23909907	23909907	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23909907C>T	uc001uon.2	-	10	8697	c.8108G>A	c.(8107-8109)CGT>CAT	p.R2703H	SACS_uc001uoo.2_Missense_Mutation_p.R2556H|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Intron	NM_014363	NP_055178	Q9NZJ4	SACS_HUMAN	sacsin	2703			R -> C (in SACS).		cell death|negative regulation of inclusion body assembly|protein folding	axon|cell body fiber|dendrite|mitochondrion|nucleus	ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)														---	---	---	---
SACS	26278	broad.mit.edu	37	13	23915465	23915465	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23915465A>G	uc001uon.2	-	10	3139	c.2550T>C	c.(2548-2550)TTT>TTC	p.F850F	SACS_uc001uoo.2_Silent_p.F703F|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Intron	NM_014363	NP_055178	Q9NZJ4	SACS_HUMAN	sacsin	850					cell death|negative regulation of inclusion body assembly|protein folding	axon|cell body fiber|dendrite|mitochondrion|nucleus	ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)														---	---	---	---
SACS	26278	broad.mit.edu	37	13	23932516	23932516	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23932516C>T	uc001uon.2	-	7	1151	c.562G>A	c.(562-564)GGA>AGA	p.G188R	SACS_uc001uoo.2_Missense_Mutation_p.G41R|SACS_uc001uop.1_5'Flank|SACS_uc001uoq.1_Missense_Mutation_p.G41R	NM_014363	NP_055178	Q9NZJ4	SACS_HUMAN	sacsin	188					cell death|negative regulation of inclusion body assembly|protein folding	axon|cell body fiber|dendrite|mitochondrion|nucleus	ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)														---	---	---	---
SPATA13	221178	broad.mit.edu	37	13	24869018	24869018	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24869018G>A	uc001upg.1	+						SPATA13_uc001upd.1_Intron|C1QTNF9_uc001upe.2_Intron|SPATA13_uc010tcy.1_Intron|SPATA13_uc010tcz.1_Intron|SPATA13_uc010tda.1_Intron|SPATA13_uc001uph.2_Intron|SPATA13_uc010tdb.1_Intron|SPATA13_uc009zzz.1_Intron|SPATA13_uc001upi.1_5'Flank	NM_153023	NP_694568			spermatogenesis associated 13						cell migration|filopodium assembly|lamellipodium assembly|regulation of cell migration|regulation of Rho protein signal transduction	cytoplasm|filopodium|lamellipodium|ruffle membrane	protein binding|Rac guanyl-nucleotide exchange factor activity			skin(2)|ovary(1)	3		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)														---	---	---	---
C1QTNF9	338872	broad.mit.edu	37	13	24895771	24895771	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:24895771C>T	uc001upj.2	+	4	928	c.867C>T	c.(865-867)GGC>GGT	p.G289G	C1QTNF9_uc001upe.2_RNA	NM_178540	NP_848635	P0C862	C1T9A_HUMAN	C1q and tumor necrosis factor related protein 9	289	C1q.					collagen	hormone activity				0		all_cancers(29;3.55e-20)|all_epithelial(30;4.25e-17)|all_lung(29;1.04e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.00565)|Epithelial(112;0.027)|OV - Ovarian serous cystadenocarcinoma(117;0.115)|Lung(94;0.159)														---	---	---	---
PARP4	143	broad.mit.edu	37	13	25052390	25052390	+	Silent	SNP	C	T	T	rs149131599		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25052390C>T	uc001upl.2	-	13	1579	c.1473G>A	c.(1471-1473)CCG>CCA	p.P491P	PARP4_uc010tdc.1_Silent_p.P491P	NM_006437	NP_006428	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	491	PARP catalytic.				cell death|DNA repair|inflammatory response|protein ADP-ribosylation|response to drug|transport	cytoplasm|nucleus|ribonucleoprotein complex|spindle microtubule	DNA binding|enzyme binding|NAD+ ADP-ribosyltransferase activity			ovary(3)|skin(1)	4		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)														---	---	---	---
CENPJ	55835	broad.mit.edu	37	13	25458472	25458472	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25458472C>A	uc001upt.3	-	14	3860	c.3607G>T	c.(3607-3609)GAC>TAC	p.D1203Y	CENPJ_uc010tdf.1_RNA|CENPJ_uc010aae.2_RNA|CENPJ_uc010aaf.2_RNA	NM_018451	NP_060921	Q9HC77	CENPJ_HUMAN	centromere protein J	1203					cell division|centriole replication|G2/M transition of mitotic cell cycle|microtubule nucleation|microtubule polymerization	centriole|cytosol|gamma-tubulin small complex|microtubule	protein domain specific binding|tubulin binding			ovary(2)	2		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.00793)|Epithelial(112;0.0411)|OV - Ovarian serous cystadenocarcinoma(117;0.139)														---	---	---	---
CENPJ	55835	broad.mit.edu	37	13	25480005	25480005	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25480005C>T	uc001upt.3	-	7	2424	c.2171G>A	c.(2170-2172)GGC>GAC	p.G724D	CENPJ_uc010tdf.1_RNA|CENPJ_uc010aae.2_RNA|CENPJ_uc010aaf.2_RNA|CENPJ_uc001upu.2_5'Flank	NM_018451	NP_060921	Q9HC77	CENPJ_HUMAN	centromere protein J	724					cell division|centriole replication|G2/M transition of mitotic cell cycle|microtubule nucleation|microtubule polymerization	centriole|cytosol|gamma-tubulin small complex|microtubule	protein domain specific binding|tubulin binding			ovary(2)	2		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.00793)|Epithelial(112;0.0411)|OV - Ovarian serous cystadenocarcinoma(117;0.139)														---	---	---	---
MTMR6	9107	broad.mit.edu	37	13	25831917	25831917	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25831917C>T	uc001uqf.3	-	8	1245	c.926G>A	c.(925-927)CGC>CAC	p.R309H	MTMR6_uc001uqe.1_Missense_Mutation_p.R309H	NM_004685	NP_004676	Q9Y217	MTMR6_HUMAN	myotubularin related protein 6	309	Myotubularin phosphatase.					cytoplasm|nuclear envelope	calcium-activated potassium channel activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity			ovary(2)|skin(2)	4		Lung SC(185;0.0225)|Breast(139;0.0351)		all cancers(112;0.00927)|Epithelial(112;0.0474)|OV - Ovarian serous cystadenocarcinoma(117;0.164)														---	---	---	---
CDK8	1024	broad.mit.edu	37	13	26923321	26923321	+	Splice_Site	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:26923321T>C	uc001uqr.1	+	3	341	c.315_splice	c.e3+2	p.W105_splice	CDK8_uc001uqs.1_Splice_Site_p.W105_splice|CDK8_uc001uqt.1_Splice_Site	NM_001260	NP_001251			cyclin-dependent kinase 8						regulation of transcription, DNA-dependent|transcription, DNA-dependent	mediator complex	ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity			lung(2)|large_intestine(1)|ovary(1)|skin(1)	5	Colorectal(5;0.000442)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0384)|Epithelial(112;0.142)|OV - Ovarian serous cystadenocarcinoma(117;0.188)														---	---	---	---
WASF3	10810	broad.mit.edu	37	13	27250749	27250749	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27250749C>T	uc001uqv.2	+	7	829	c.604C>T	c.(604-606)CGC>TGC	p.R202C	WASF3_uc001uqw.2_Intron	NM_006646	NP_006637	Q9UPY6	WASF3_HUMAN	WAS protein family, member 3	202	Potential.				actin filament polymerization	cytoplasm|cytoskeleton	actin binding			pancreas(1)	1	Colorectal(5;0.000247)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0114)|Epithelial(112;0.046)|OV - Ovarian serous cystadenocarcinoma(117;0.0547)|Lung(94;0.105)|LUSC - Lung squamous cell carcinoma(192;0.155)														---	---	---	---
GPR12	2835	broad.mit.edu	37	13	27333332	27333332	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:27333332C>T	uc010aal.2	-	2	855	c.633G>A	c.(631-633)GCG>GCA	p.A211A	GPR12_uc010tdl.1_Silent_p.A52A	NM_005288	NP_005279	P47775	GPR12_HUMAN	G protein-coupled receptor 12	211	Helical; Name=5; (Potential).					integral to plasma membrane					0	Colorectal(5;5.77e-05)	Breast(139;0.198)		Epithelial(112;9.37e-07)|OV - Ovarian serous cystadenocarcinoma(117;1.16e-06)|all cancers(112;8.31e-06)|GBM - Glioblastoma multiforme(144;0.00121)|Lung(94;0.111)|LUSC - Lung squamous cell carcinoma(192;0.184)														---	---	---	---
LNX2	222484	broad.mit.edu	37	13	28155540	28155540	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:28155540T>C	uc001url.3	-	2	610	c.301A>G	c.(301-303)ATT>GTT	p.I101V	LNX2_uc001urm.1_Missense_Mutation_p.I101V	NM_153371	NP_699202	Q8N448	LNX2_HUMAN	ligand of numb-protein X 2	101							zinc ion binding			ovary(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)|central_nervous_system(1)	6		Lung SC(185;0.0156)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.113)|all cancers(112;0.127)|Epithelial(112;0.248)														---	---	---	---
KATNAL1	84056	broad.mit.edu	37	13	30782696	30782696	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30782696A>G	uc001uss.2	-	11	1555	c.1454T>C	c.(1453-1455)GTT>GCT	p.V485A	KATNAL1_uc001ust.2_Missense_Mutation_p.V485A	NM_001014380	NP_001014402	Q9BW62	KATL1_HUMAN	katanin p60 subunit A-like 1	485						cytoplasm|microtubule	ATP binding|microtubule-severing ATPase activity				0		Lung SC(185;0.0257)		all cancers(112;0.114)|OV - Ovarian serous cystadenocarcinoma(117;0.213)														---	---	---	---
KATNAL1	84056	broad.mit.edu	37	13	30782846	30782846	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30782846C>T	uc001uss.2	-	11	1405	c.1304G>A	c.(1303-1305)CGT>CAT	p.R435H	KATNAL1_uc001ust.2_Missense_Mutation_p.R435H	NM_001014380	NP_001014402	Q9BW62	KATL1_HUMAN	katanin p60 subunit A-like 1	435						cytoplasm|microtubule	ATP binding|microtubule-severing ATPase activity				0		Lung SC(185;0.0257)		all cancers(112;0.114)|OV - Ovarian serous cystadenocarcinoma(117;0.213)														---	---	---	---
KATNAL1	84056	broad.mit.edu	37	13	30815125	30815125	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30815125G>A	uc001uss.2	-	5	692	c.591C>T	c.(589-591)GAC>GAT	p.D197D	KATNAL1_uc001ust.2_Silent_p.D197D	NM_001014380	NP_001014402	Q9BW62	KATL1_HUMAN	katanin p60 subunit A-like 1	197						cytoplasm|microtubule	ATP binding|microtubule-severing ATPase activity				0		Lung SC(185;0.0257)		all cancers(112;0.114)|OV - Ovarian serous cystadenocarcinoma(117;0.213)														---	---	---	---
KATNAL1	84056	broad.mit.edu	37	13	30857820	30857820	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:30857820A>C	uc001uss.2	-	2	196	c.95T>G	c.(94-96)GTG>GGG	p.V32G	KATNAL1_uc001ust.2_Missense_Mutation_p.V32G	NM_001014380	NP_001014402	Q9BW62	KATL1_HUMAN	katanin p60 subunit A-like 1	32						cytoplasm|microtubule	ATP binding|microtubule-severing ATPase activity				0		Lung SC(185;0.0257)		all cancers(112;0.114)|OV - Ovarian serous cystadenocarcinoma(117;0.213)														---	---	---	---
USPL1	10208	broad.mit.edu	37	13	31231823	31231823	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31231823G>T	uc001utc.2	+	9	2041	c.1609G>T	c.(1609-1611)GGT>TGT	p.G537C	USPL1_uc001utd.2_Missense_Mutation_p.G208C|USPL1_uc001ute.1_Missense_Mutation_p.G208C	NM_005800	NP_005791	Q5W0Q7	USPL1_HUMAN	ubiquitin specific peptidase like 1	537					ubiquitin-dependent protein catabolic process		ubiquitin thiolesterase activity			pancreas(2)|skin(1)	3		Lung SC(185;0.0257)|Breast(139;0.203)		all cancers(112;0.0306)|Epithelial(112;0.131)|OV - Ovarian serous cystadenocarcinoma(117;0.134)														---	---	---	---
C13orf33	84935	broad.mit.edu	37	13	31495915	31495915	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:31495915A>G	uc001uth.3	+	4	1060	c.719A>G	c.(718-720)GAA>GGA	p.E240G	uc001utg.1_Intron	NM_032849	NP_116238	Q5VYS4	CM033_HUMAN	hypothetical protein LOC84935	240											0		Lung SC(185;0.0281)		all cancers(112;0.00914)|Epithelial(112;0.0474)|OV - Ovarian serous cystadenocarcinoma(117;0.0559)|GBM - Glioblastoma multiforme(144;0.244)														---	---	---	---
RXFP2	122042	broad.mit.edu	37	13	32363332	32363332	+	Splice_Site	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32363332T>C	uc001utt.2	+	14	1216	c.1145_splice	c.e14+2	p.I382_splice	RXFP2_uc010aba.2_Splice_Site_p.I341_splice	NM_130806	NP_570718			relaxin/insulin-like family peptide receptor 2							integral to membrane|plasma membrane					0		Lung SC(185;0.0262)		all cancers(112;0.000559)|Epithelial(112;0.0017)|OV - Ovarian serous cystadenocarcinoma(117;0.0145)|BRCA - Breast invasive adenocarcinoma(63;0.0535)														---	---	---	---
FRY	10129	broad.mit.edu	37	13	32711016	32711016	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32711016C>T	uc001utx.2	+	11	1582	c.1086C>T	c.(1084-1086)TAC>TAT	p.Y362Y	FRY_uc010tdw.1_RNA	NM_023037	NP_075463	Q5TBA9	FRY_HUMAN	furry homolog	362					regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)														---	---	---	---
FRY	10129	broad.mit.edu	37	13	32758793	32758793	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32758793T>C	uc001utx.2	+	25	3607	c.3111T>C	c.(3109-3111)TTT>TTC	p.F1037F	FRY_uc010tdw.1_RNA	NM_023037	NP_075463	Q5TBA9	FRY_HUMAN	furry homolog	1037					regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)														---	---	---	---
FRY	10129	broad.mit.edu	37	13	32839585	32839585	+	Splice_Site	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32839585A>C	uc001utx.2	+	54	8276	c.7780_splice	c.e54-2	p.A2594_splice	FRY_uc010tdw.1_Splice_Site|FRY_uc001uty.2_Splice_Site_p.A149_splice|FRY_uc001utz.2_Splice_Site_p.A119_splice|FRY_uc010tdx.1_Splice_Site	NM_023037	NP_075463			furry homolog						regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane				ovary(5)|large_intestine(1)|skin(1)	7		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)														---	---	---	---
BRCA2	675	broad.mit.edu	37	13	32914136	32914136	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32914136T>C	uc001uub.1	+	11	5871	c.5644T>C	c.(5644-5646)TCA>CCA	p.S1882P		NM_000059	NP_000050	P51587	BRCA2_HUMAN	breast cancer 2, early onset	1882					cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle	BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule	gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding	p.S1882*(1)		ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1)	64		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)				D|Mis|N|F|S		breast|ovarian|pancreatic	breast|ovarian|pancreatic|leukemia  (FANCB|FANCD1)		Direct_reversal_of_damage|Homologous_recombination	Fanconi_Anemia_type_D1_bi-allelic_BRCA2_mutations|Fanconi_Anemia|Pancreatic_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_BRCA2_type|Hereditary_Prostate_Cancer|Li-Fraumeni_syndrome	TCGA Ovarian(8;0.087)			---	---	---	---
BRCA2	675	broad.mit.edu	37	13	32954273	32954273	+	Missense_Mutation	SNP	A	G	G	rs80359190		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:32954273A>G	uc001uub.1	+	24	9474	c.9247A>G	c.(9247-9249)AAA>GAA	p.K3083E		NM_000059	NP_000050	P51587	BRCA2_HUMAN	breast cancer 2, early onset	3083					cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle	BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule	gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding			ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1)	64		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)				D|Mis|N|F|S		breast|ovarian|pancreatic	breast|ovarian|pancreatic|leukemia  (FANCB|FANCD1)		Direct_reversal_of_damage|Homologous_recombination	Fanconi_Anemia_type_D1_bi-allelic_BRCA2_mutations|Fanconi_Anemia|Pancreatic_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_BRCA2_type|Hereditary_Prostate_Cancer|Li-Fraumeni_syndrome	TCGA Ovarian(8;0.087)			---	---	---	---
STARD13	90627	broad.mit.edu	37	13	33687026	33687026	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33687026A>G	uc001uuw.2	-	9	2450	c.2324T>C	c.(2323-2325)ATC>ACC	p.I775T	STARD13_uc001uuu.2_Missense_Mutation_p.I767T|STARD13_uc001uuv.2_Missense_Mutation_p.I657T|STARD13_uc001uux.2_Missense_Mutation_p.I740T|STARD13_uc010tec.1_RNA	NM_178006	NP_821074	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain	775	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|lipid particle|mitochondrial membrane	GTPase activator activity|protein binding			ovary(2)|pancreas(1)|skin(1)	4	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)														---	---	---	---
DCLK1	9201	broad.mit.edu	37	13	36521484	36521484	+	Intron	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:36521484T>G	uc001uvf.2	-							NM_004734	NP_004725			doublecortin-like kinase 1						cell differentiation|central nervous system development|endosome transport|intracellular signal transduction|response to virus	integral to plasma membrane	ATP binding|protein serine/threonine kinase activity|receptor signaling protein activity			stomach(6)|ovary(2)|skin(1)	9		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)														---	---	---	---
SMAD9	4093	broad.mit.edu	37	13	37427737	37427737	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37427737C>T	uc001uvw.2	-	6	1422	c.1079G>A	c.(1078-1080)CGG>CAG	p.R360Q	SMAD9_uc001uvx.2_Missense_Mutation_p.R323Q|SMAD9_uc010tep.1_Missense_Mutation_p.R153Q	NM_001127217	NP_001120689	O15198	SMAD9_HUMAN	SMAD family member 9 isoform a	360	MH2.				BMP signaling pathway|transforming growth factor beta receptor signaling pathway	cytosol|transcription factor complex	sequence-specific DNA binding transcription factor activity|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity				0		Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)		all cancers(112;3.38e-07)|Epithelial(112;1.93e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00804)|BRCA - Breast invasive adenocarcinoma(63;0.0129)|GBM - Glioblastoma multiforme(144;0.026)														---	---	---	---
CSNK1A1L	122011	broad.mit.edu	37	13	37678867	37678867	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37678867C>A	uc001uwm.1	-	1	935	c.527G>T	c.(526-528)AGA>ATA	p.R176I		NM_145203	NP_660204	Q8N752	KC1AL_HUMAN	casein kinase 1, alpha 1-like	176	Protein kinase.				Wnt receptor signaling pathway	cytoplasm	ATP binding|protein serine/threonine kinase activity			large_intestine(1)	1		Lung NSC(96;7.97e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.109)		all cancers(112;3.58e-07)|Epithelial(112;1.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00695)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0407)														---	---	---	---
FREM2	341640	broad.mit.edu	37	13	39422735	39422735	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39422735C>T	uc001uwv.2	+	8	6616	c.6307C>T	c.(6307-6309)CGC>TGC	p.R2103C	FREM2_uc001uww.2_Missense_Mutation_p.R189C	NM_207361	NP_997244	Q5SZK8	FREM2_HUMAN	FRAS1-related extracellular matrix protein 2	2103	Extracellular (Potential).|Calx-beta 3.				cell communication|homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(7)|pancreas(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	11		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)														---	---	---	---
C13orf23	80209	broad.mit.edu	37	13	39587553	39587553	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:39587553T>C	uc001uwy.2	-	11	2709	c.1836A>G	c.(1834-1836)ACA>ACG	p.T612T	C13orf23_uc001uwz.2_Silent_p.T590T	NM_025138	NP_079414	Q86XN7	CM023_HUMAN	hypothetical protein LOC80209 isoform 1	612	Ser-rich.									ovary(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)	5		Lung NSC(96;6.01e-07)|Breast(139;0.00394)|Prostate(109;0.00676)|Lung SC(185;0.0548)|Hepatocellular(188;0.114)		all cancers(112;3.7e-08)|Epithelial(112;4.28e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00114)|BRCA - Breast invasive adenocarcinoma(63;0.00366)|GBM - Glioblastoma multiforme(144;0.0146)														---	---	---	---
FOXO1	2308	broad.mit.edu	37	13	41134097	41134097	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41134097C>T	uc001uxl.3	-	2	1916	c.1531G>A	c.(1531-1533)GCA>ACA	p.A511T	FOXO1_uc010acc.1_Missense_Mutation_p.A326T	NM_002015	NP_002006	Q12778	FOXO1_HUMAN	forkhead box O1	511					anti-apoptosis|blood vessel development|embryo development|endocrine pancreas development|insulin receptor signaling pathway|negative regulation of stress-activated MAPK cascade|nerve growth factor receptor signaling pathway|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|response to DNA damage stimulus|tissue development	cytosol|transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding		PAX3/FOXO1(749)|PAX7/FOXO1(197)	soft_tissue(946)|lung(1)|central_nervous_system(1)	948		Lung NSC(96;1.18e-05)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;7.32e-09)|Epithelial(112;2.87e-06)|OV - Ovarian serous cystadenocarcinoma(117;6.98e-05)|GBM - Glioblastoma multiforme(144;0.00394)|BRCA - Breast invasive adenocarcinoma(63;0.0815)														---	---	---	---
MTRF1	9617	broad.mit.edu	37	13	41800649	41800649	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41800649G>T	uc001uxx.2	-	10	1514	c.1044C>A	c.(1042-1044)GCC>GCA	p.A348A	MTRF1_uc001uxy.2_Silent_p.A348A|MTRF1_uc001uxz.2_Silent_p.A184A|MTRF1_uc010tff.1_Silent_p.A361A|uc001uxv.1_Intron	NM_004294	NP_004285	O75570	RF1M_HUMAN	mitochondrial translational release factor 1	348					regulation of translational termination	mitochondrion	translation release factor activity, codon specific				0		Lung NSC(96;4.52e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)|Ovarian(182;0.125)		OV - Ovarian serous cystadenocarcinoma(117;4.24e-10)|all cancers(112;2.05e-09)|Epithelial(112;2.48e-09)|GBM - Glioblastoma multiforme(144;0.00115)|BRCA - Breast invasive adenocarcinoma(63;0.0721)|KIRC - Kidney renal clear cell carcinoma(186;0.248)														---	---	---	---
DGKH	160851	broad.mit.edu	37	13	42729508	42729508	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42729508G>A	uc001uyl.1	+	4	487	c.466G>A	c.(466-468)GTA>ATA	p.V156I	DGKH_uc010tfh.1_Missense_Mutation_p.V156I|DGKH_uc001uym.1_Missense_Mutation_p.V156I|DGKH_uc010tfi.1_5'UTR|DGKH_uc010tfj.1_Missense_Mutation_p.V11I|DGKH_uc001uyn.1_RNA|DGKH_uc001uyo.1_Missense_Mutation_p.V11I|DGKH_uc001uyp.2_RNA	NM_178009	NP_821077	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta isoform 2	156	PH.				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation|protein oligomerization	endosome|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(2)	2		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)														---	---	---	---
DGKH	160851	broad.mit.edu	37	13	42773983	42773983	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42773983C>A	uc001uyl.1	+	20	2452	c.2431C>A	c.(2431-2433)CTT>ATT	p.L811I	DGKH_uc010tfh.1_Missense_Mutation_p.L811I|DGKH_uc001uym.1_Missense_Mutation_p.L811I|DGKH_uc010tfi.1_Missense_Mutation_p.L566I|DGKH_uc010tfj.1_Missense_Mutation_p.L666I|DGKH_uc001uyn.1_RNA|DGKH_uc001uyo.1_Missense_Mutation_p.L666I|DGKH_uc001uyp.2_RNA	NM_178009	NP_821077	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta isoform 2	811					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation|protein oligomerization	endosome|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			ovary(2)	2		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)														---	---	---	---
AKAP11	11215	broad.mit.edu	37	13	42872860	42872860	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:42872860A>G	uc001uys.1	+	7	718	c.543A>G	c.(541-543)TCA>TCG	p.S181S		NM_016248	NP_057332	Q9UKA4	AKA11_HUMAN	A-kinase anchor protein 11	181					intracellular protein kinase cascade	microtubule organizing center	protein kinase A binding|protein phosphatase 1 binding			ovary(1)|central_nervous_system(1)	2		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)														---	---	---	---
KIAA1704	55425	broad.mit.edu	37	13	45578557	45578557	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:45578557G>A	uc001uzq.2	+	2	309	c.206G>A	c.(205-207)AGT>AAT	p.S69N	KIAA1704_uc010tfo.1_RNA|KIAA1704_uc001uzr.1_Missense_Mutation_p.S69N|KIAA1704_uc001uzs.2_Translation_Start_Site|KIAA1704_uc001uzt.2_5'Flank	NM_018559	NP_061029	Q8IXQ4	K1704_HUMAN	hypothetical protein LOC55425	69										pancreas(1)|skin(1)	2		Lung NSC(96;0.00143)|Prostate(109;0.0137)|Breast(139;0.0192)|Lung SC(185;0.0367)|Hepatocellular(98;0.133)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000313)|BRCA - Breast invasive adenocarcinoma(63;0.126)														---	---	---	---
SPERT	220082	broad.mit.edu	37	13	46287384	46287384	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46287384C>T	uc001van.1	+	3	304	c.224C>T	c.(223-225)GCC>GTC	p.A75V	SPERT_uc001vao.2_Missense_Mutation_p.A39V	NM_152719	NP_689932	Q8NA61	SPERT_HUMAN	spermatid associated	75						cytoplasmic membrane-bounded vesicle				central_nervous_system(1)|pancreas(1)	2		Breast(56;0.000819)|Lung NSC(96;0.00227)|Prostate(109;0.00703)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;7.26e-05)														---	---	---	---
CPB2	1361	broad.mit.edu	37	13	46652954	46652954	+	Missense_Mutation	SNP	T	C	C	rs61730120		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46652954T>C	uc001vaw.2	-	5	534	c.467A>G	c.(466-468)TAC>TGC	p.Y156C	uc001vau.1_Intron|uc001vav.1_Intron|CPB2_uc001vax.2_Missense_Mutation_p.Y156C	NM_001872	NP_001863	Q96IY4	CBPB2_HUMAN	plasma carboxypeptidase B2 isoform a	156					blood coagulation|fibrinolysis|proteolysis	extracellular space	metallocarboxypeptidase activity|zinc ion binding			ovary(1)|skin(1)	2		Lung NSC(96;4.21e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|all_neural(104;0.235)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.44e-05)														---	---	---	---
HTR2A	3356	broad.mit.edu	37	13	47469795	47469795	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:47469795C>T	uc001vbq.2	-	1	381	c.247G>A	c.(247-249)GTA>ATA	p.V83I	HTR2A_uc001vbr.2_Intron|HTR2A_uc010acr.2_Missense_Mutation_p.V83I	NM_000621	NP_000612	P28223	5HT2A_HUMAN	5-hydroxytryptamine receptor 2A isoform 1	83	Helical; Name=1; (By similarity).				ERK1 and ERK2 cascade|phosphatidylinositol 3-kinase cascade|phosphatidylinositol biosynthetic process|release of sequestered calcium ion into cytosol|response to drug|synaptic transmission	integral to plasma membrane	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding|drug binding|phosphatidylinositol phospholipase C activity|serotonin binding|serotonin receptor activity			ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	6		all_lung(13;7.2e-10)|Lung NSC(96;3.77e-07)|Breast(56;2.06e-05)|Prostate(109;0.00116)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|Myeloproliferative disorder(33;0.0333)		GBM - Glioblastoma multiforme(144;4.67e-05)|COAD - Colon adenocarcinoma(199;0.224)	Aripiprazole(DB01238)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cisapride(DB00604)|Clomipramine(DB01242)|Clozapine(DB00363)|Cyclobenzaprine(DB00924)|Cyproheptadine(DB00434)|Dihydroergotamine(DB00320)|Donepezil(DB00843)|Epinastine(DB00751)|Ergotamine(DB00696)|Fluvoxamine(DB00176)|Mesoridazine(DB00933)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Olanzapine(DB00334)|Paliperidone(DB01267)|Paroxetine(DB00715)|Prochlorperazine(DB00433)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Sertindole(DB06144)|Thiethylperazine(DB00372)|Thioridazine(DB00679)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Venlafaxine(DB00285)|Ziprasidone(DB00246)													---	---	---	---
RB1	5925	broad.mit.edu	37	13	48953730	48953730	+	Nonsense_Mutation	SNP	C	T	T	rs3092891		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48953730C>T	uc001vcb.2	+	14	1499	c.1333C>T	c.(1333-1335)CGA>TGA	p.R445*		NM_000321	NP_000312	P06400	RB_HUMAN	retinoblastoma 1	445	Domain A.|Pocket; binds T and E1A.				androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation	chromatin|PML body|Rb-E2F complex|SWI/SNF complex	androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding	p.?(7)|p.R445*(2)		lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1)	358		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)		6	D|Mis|N|F|S		retinoblastoma|sarcoma|breast|small cell lung	retinoblastoma|sarcoma|breast|small cell lung			Hereditary_Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			---	---	---	---
FNDC3A	22862	broad.mit.edu	37	13	49719939	49719939	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:49719939T>C	uc001vcm.2	+	8	1150	c.845T>C	c.(844-846)GTA>GCA	p.V282A	FNDC3A_uc001vcl.1_Missense_Mutation_p.V282A|FNDC3A_uc001vcn.2_Missense_Mutation_p.V282A|FNDC3A_uc001vco.2_RNA|FNDC3A_uc001vcp.1_Missense_Mutation_p.V226A|FNDC3A_uc001vcq.2_Missense_Mutation_p.V226A	NM_001079673	NP_001073141	Q9Y2H6	FND3A_HUMAN	fibronectin type III domain containing 3A	282	Fibronectin type-III 1.					Golgi membrane|integral to membrane				lung(2)	2		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)														---	---	---	---
INTS6	26512	broad.mit.edu	37	13	52026657	52026657	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52026657G>T	uc001vfk.2	-	1	619	c.5C>A	c.(4-6)CCC>CAC	p.P2H	INTS6_uc001vfj.2_Intron|INTS6_uc001vfl.2_5'UTR|INTS6_uc001vfm.2_Missense_Mutation_p.P2H|uc001vfn.2_5'Flank	NM_012141	NP_036273	Q9UL03	INT6_HUMAN	integrator complex subunit 6 isoform a	2					snRNA processing	actin cytoskeleton|integrator complex	protein binding|transmembrane receptor activity			ovary(1)|lung(1)	2		Breast(56;0.000286)|Lung NSC(96;0.00145)|Prostate(109;0.00403)|Hepatocellular(98;0.065)|Myeloproliferative disorder(33;0.163)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;7.7e-08)														---	---	---	---
WDFY2	115825	broad.mit.edu	37	13	52325529	52325529	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52325529A>G	uc001vfp.2	+	8	1149	c.809A>G	c.(808-810)AAC>AGC	p.N270S	WDFY2_uc010ads.1_Missense_Mutation_p.N270S|WDFY2_uc010adt.1_RNA	NM_052950	NP_443182	Q96P53	WDFY2_HUMAN	WD repeat and FYVE domain containing 2	270	WD 6.						metal ion binding				0		Breast(56;0.000208)|Lung NSC(96;0.000517)|Prostate(109;0.0041)|Hepatocellular(98;0.0652)|Myeloproliferative disorder(33;0.164)|all_neural(104;0.191)		GBM - Glioblastoma multiforme(99;9e-08)														---	---	---	---
ATP7B	540	broad.mit.edu	37	13	52508941	52508941	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52508941T>C	uc001vfw.2	-	21	4506	c.4349A>G	c.(4348-4350)GAC>GGC	p.D1450G	ATP7B_uc010adv.2_Missense_Mutation_p.D1020G|ATP7B_uc001vfx.2_Missense_Mutation_p.D1243G|ATP7B_uc001vfy.2_Missense_Mutation_p.D1339G|ATP7B_uc010tgt.1_Missense_Mutation_p.D1385G|ATP7B_uc010tgu.1_Missense_Mutation_p.D1402G|ATP7B_uc010tgv.1_Missense_Mutation_p.D1372G|ATP7B_uc001vfv.2_Missense_Mutation_p.D722G|ATP7B_uc010tgs.1_Missense_Mutation_p.D661G	NM_000053	NP_000044	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	1450	Cytoplasmic (Potential).				ATP biosynthetic process|cellular copper ion homeostasis|copper ion import|response to copper ion|sequestering of calcium ion	Golgi membrane|integral to plasma membrane|late endosome|mitochondrion	ATP binding|copper ion binding|copper-exporting ATPase activity|protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)										Wilson_disease				---	---	---	---
ATP7B	540	broad.mit.edu	37	13	52524527	52524527	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52524527T>C	uc001vfw.2	-	10	2613	c.2456A>G	c.(2455-2457)CAA>CGA	p.Q819R	ATP7B_uc010adv.2_Intron|ATP7B_uc001vfx.2_Missense_Mutation_p.Q657R|ATP7B_uc001vfy.2_Missense_Mutation_p.Q708R|ATP7B_uc010tgt.1_Missense_Mutation_p.Q819R|ATP7B_uc010tgu.1_Missense_Mutation_p.Q771R|ATP7B_uc010tgv.1_Missense_Mutation_p.Q741R|ATP7B_uc001vfv.2_Missense_Mutation_p.Q91R|ATP7B_uc010tgs.1_Missense_Mutation_p.Q91R	NM_000053	NP_000044	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	819	Cytoplasmic (Potential).				ATP biosynthetic process|cellular copper ion homeostasis|copper ion import|response to copper ion|sequestering of calcium ion	Golgi membrane|integral to plasma membrane|late endosome|mitochondrion	ATP binding|copper ion binding|copper-exporting ATPase activity|protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)										Wilson_disease				---	---	---	---
PCDH8	5100	broad.mit.edu	37	13	53418912	53418912	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53418912C>T	uc001vhi.2	-	3	3199	c.2996G>A	c.(2995-2997)CGC>CAC	p.R999H	PCDH8_uc001vhj.2_Missense_Mutation_p.R902H	NM_002590	NP_002581	O95206	PCDH8_HUMAN	protocadherin 8 isoform 1 precursor	999	Cytoplasmic (Potential).				cell-cell signaling|homophilic cell adhesion	cell junction|dendrite|integral to plasma membrane|postsynaptic membrane|presynaptic membrane	calcium ion binding			breast(1)	1		Lung NSC(96;0.0019)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.19e-08)														---	---	---	---
PCDH8	5100	broad.mit.edu	37	13	53420707	53420707	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53420707G>A	uc001vhi.2	-	1	2068	c.1865C>T	c.(1864-1866)GCG>GTG	p.A622V	PCDH8_uc001vhj.2_Missense_Mutation_p.A622V	NM_002590	NP_002581	O95206	PCDH8_HUMAN	protocadherin 8 isoform 1 precursor	622	Extracellular (Potential).|Cadherin 6.				cell-cell signaling|homophilic cell adhesion	cell junction|dendrite|integral to plasma membrane|postsynaptic membrane|presynaptic membrane	calcium ion binding			breast(1)	1		Lung NSC(96;0.0019)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.19e-08)														---	---	---	---
OLFM4	10562	broad.mit.edu	37	13	53602977	53602977	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:53602977G>A	uc001vhl.2	+	1	6	c.6G>A	c.(4-6)AGG>AGA	p.R2R	OLFM4_uc001vhk.1_Silent_p.R2R	NM_006418	NP_006409	Q6UX06	OLFM4_HUMAN	olfactomedin 4 precursor	2					cell adhesion	extracellular space				skin(1)	1		Breast(56;0.000776)|Lung NSC(96;0.000814)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.13e-08)														---	---	---	---
PCDH17	27253	broad.mit.edu	37	13	58207723	58207723	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:58207723C>T	uc001vhq.1	+	1	1935	c.1043C>T	c.(1042-1044)GCG>GTG	p.A348V	PCDH17_uc010aec.1_Missense_Mutation_p.A348V	NM_001040429	NP_001035519	O14917	PCD17_HUMAN	protocadherin 17 precursor	348	Extracellular (Potential).|Cadherin 3.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding			ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	7		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)														---	---	---	---
DIAPH3	81624	broad.mit.edu	37	13	60348935	60348935	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60348935C>A	uc001vht.2	-	26	3405	c.3186G>T	c.(3184-3186)ATG>ATT	p.M1062I	DIAPH3_uc001vhu.2_Missense_Mutation_p.M799I	NM_001042517	NP_001035982	Q9NSV4	DIAP3_HUMAN	diaphanous homolog 3 isoform a	1062	DAD.				actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)	2		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)														---	---	---	---
DIAPH3	81624	broad.mit.edu	37	13	60407234	60407234	+	Intron	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:60407234A>C	uc001vht.2	-						DIAPH3_uc001vhu.2_Intron	NM_001042517	NP_001035982			diaphanous homolog 3 isoform a						actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)	2		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)														---	---	---	---
PCDH20	64881	broad.mit.edu	37	13	61986677	61986677	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:61986677T>C	uc001vid.3	-	2	1919	c.1555A>G	c.(1555-1557)AGG>GGG	p.R519G	PCDH20_uc010thj.1_Missense_Mutation_p.R519G	NM_022843	NP_073754	Q8N6Y1	PCD20_HUMAN	protocadherin 20	492	Cadherin 3.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|breast(1)|central_nervous_system(1)	6		Breast(118;0.195)|Prostate(109;0.229)		GBM - Glioblastoma multiforme(99;0.000118)														---	---	---	---
PCDH9	5101	broad.mit.edu	37	13	67205464	67205464	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67205464G>A	uc001vik.2	-	4	3910	c.3218C>T	c.(3217-3219)CCG>CTG	p.P1073L	PCDH9_uc010aei.2_RNA|PCDH9_uc001vil.2_Missense_Mutation_p.P1039L|PCDH9_uc010thl.1_Intron	NM_203487	NP_982354	Q9HC56	PCDH9_HUMAN	protocadherin 9 isoform 1 precursor	1073	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)|skin(1)	6		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)														---	---	---	---
C13orf34	79866	broad.mit.edu	37	13	73309097	73309097	+	Splice_Site	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73309097G>T	uc001viv.1	+	4	380	c.261_splice	c.e4-1	p.R87_splice	C13orf34_uc010thq.1_Intron|C13orf34_uc010aen.1_Splice_Site_p.R162_splice|C13orf34_uc010thr.1_Splice_Site_p.Q17_splice|C13orf34_uc001viw.1_Intron	NM_024808	NP_079084			aurora borealis						cell division|mitosis|regulation of mitosis|regulation of mitotic spindle organization|regulation of protein localization		protein kinase binding				0		Breast(118;0.0735)		GBM - Glioblastoma multiforme(99;0.000227)														---	---	---	---
DIS3	22894	broad.mit.edu	37	13	73346042	73346042	+	Intron	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73346042A>C	uc001vix.3	-						DIS3_uc001viy.3_Intron|DIS3_uc001viz.2_Intron	NM_014953	NP_055768			DIS3 mitotic control isoform a						CUT catabolic process|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|rRNA catabolic process|rRNA processing	cytosol|exosome (RNase complex)|nucleolus|nucleoplasm	3'-5'-exoribonuclease activity|endonuclease activity|guanyl-nucleotide exchange factor activity|protein binding|RNA binding			central_nervous_system(1)	1		Breast(118;0.0074)|Acute lymphoblastic leukemia(28;0.0195)		GBM - Glioblastoma multiforme(99;0.000181)											Multiple Myeloma(4;0.011)			---	---	---	---
DIS3	22894	broad.mit.edu	37	13	73346378	73346378	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:73346378A>G	uc001vix.3	-	10	1796	c.1422T>C	c.(1420-1422)TGT>TGC	p.C474C	DIS3_uc001viy.3_Silent_p.C444C|DIS3_uc001viz.2_RNA	NM_014953	NP_055768	Q9Y2L1	RRP44_HUMAN	DIS3 mitotic control isoform a	474					CUT catabolic process|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|rRNA catabolic process|rRNA processing	cytosol|exosome (RNase complex)|nucleolus|nucleoplasm	3'-5'-exoribonuclease activity|endonuclease activity|guanyl-nucleotide exchange factor activity|protein binding|RNA binding			central_nervous_system(1)	1		Breast(118;0.0074)|Acute lymphoblastic leukemia(28;0.0195)		GBM - Glioblastoma multiforme(99;0.000181)											Multiple Myeloma(4;0.011)			---	---	---	---
TBC1D4	9882	broad.mit.edu	37	13	76055893	76055893	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76055893G>T	uc001vjl.1	-	1	358	c.11C>A	c.(10-12)CCC>CAC	p.P4H	TBC1D4_uc010aer.2_Missense_Mutation_p.P4H|TBC1D4_uc010aes.2_Missense_Mutation_p.P4H	NM_014832	NP_055647	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	4						cytoplasm	Rab GTPase activator activity			ovary(4)|central_nervous_system(1)|skin(1)	6		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)														---	---	---	---
LMO7	4008	broad.mit.edu	37	13	76397906	76397906	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:76397906C>A	uc001vjv.2	+	12	2907	c.2147C>A	c.(2146-2148)GCT>GAT	p.A716D	LMO7_uc010thv.1_Missense_Mutation_p.A667D|LMO7_uc001vjt.1_Missense_Mutation_p.A615D|LMO7_uc010thw.1_Missense_Mutation_p.A566D|LMO7_uc001vjw.1_Missense_Mutation_p.A622D	NM_015842	NP_056667	Q8WWI1	LMO7_HUMAN	LIM domain only 7 isoform 2	1001						cytoplasm|nucleus|ubiquitin ligase complex	ubiquitin-protein ligase activity|zinc ion binding			large_intestine(2)|ovary(1)|prostate(1)|skin(1)	5		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)														---	---	---	---
MYCBP2	23077	broad.mit.edu	37	13	77671835	77671835	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77671835A>T	uc001vkf.2	-	57	9431	c.9340T>A	c.(9340-9342)TCT>ACT	p.S3114T	MYCBP2_uc010aev.2_Missense_Mutation_p.S2518T|MYCBP2_uc001vkg.1_Missense_Mutation_p.S637T|MYCBP2_uc010aew.2_Missense_Mutation_p.S500T	NM_015057	NP_055872	O75592	MYCB2_HUMAN	MYC binding protein 2	3114					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ligase activity|protein binding|zinc ion binding			ovary(4)|breast(4)|skin(3)|lung(2)|pancreas(1)	14		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)														---	---	---	---
MYCBP2	23077	broad.mit.edu	37	13	77672984	77672984	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77672984A>T	uc001vkf.2	-	57	8282	c.8191T>A	c.(8191-8193)TCC>ACC	p.S2731T	MYCBP2_uc010aev.2_Missense_Mutation_p.S2135T|MYCBP2_uc001vkg.1_Missense_Mutation_p.S254T|MYCBP2_uc010aew.2_Missense_Mutation_p.S117T	NM_015057	NP_055872	O75592	MYCB2_HUMAN	MYC binding protein 2	2731	Ser-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ligase activity|protein binding|zinc ion binding			ovary(4)|breast(4)|skin(3)|lung(2)|pancreas(1)	14		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)														---	---	---	---
MYCBP2	23077	broad.mit.edu	37	13	77700630	77700630	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77700630G>A	uc001vkf.2	-	54	7684	c.7593C>T	c.(7591-7593)TGC>TGT	p.C2531C	MYCBP2_uc010aev.2_Silent_p.C1935C|MYCBP2_uc001vkg.1_5'UTR	NM_015057	NP_055872	O75592	MYCB2_HUMAN	MYC binding protein 2	2531					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ligase activity|protein binding|zinc ion binding			ovary(4)|breast(4)|skin(3)|lung(2)|pancreas(1)	14		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)														---	---	---	---
MYCBP2	23077	broad.mit.edu	37	13	77748440	77748440	+	Intron	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:77748440A>C	uc001vkf.2	-						MYCBP2_uc010aev.2_Intron	NM_015057	NP_055872			MYC binding protein 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ligase activity|protein binding|zinc ion binding			ovary(4)|breast(4)|skin(3)|lung(2)|pancreas(1)	14		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)														---	---	---	---
SCEL	8796	broad.mit.edu	37	13	78130014	78130014	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78130014T>C	uc001vki.2	+	2	174	c.4T>C	c.(4-6)TCC>CCC	p.S2P	SCEL_uc001vkj.2_Missense_Mutation_p.S2P|SCEL_uc010thx.1_Missense_Mutation_p.S2P	NM_144777	NP_659001	O95171	SCEL_HUMAN	sciellin isoform 1	2					embryo development|keratinocyte differentiation	cornified envelope|cytoplasm|membrane	protein binding|zinc ion binding			ovary(4)|breast(1)	5		Acute lymphoblastic leukemia(28;0.0282)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0233)														---	---	---	---
SCEL	8796	broad.mit.edu	37	13	78146277	78146277	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:78146277G>A	uc001vki.2	+	9	668	c.498G>A	c.(496-498)CCG>CCA	p.P166P	SCEL_uc001vkj.2_Silent_p.P166P|SCEL_uc010thx.1_Intron	NM_144777	NP_659001	O95171	SCEL_HUMAN	sciellin isoform 1	166					embryo development|keratinocyte differentiation	cornified envelope|cytoplasm|membrane	protein binding|zinc ion binding			ovary(4)|breast(1)	5		Acute lymphoblastic leukemia(28;0.0282)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0233)														---	---	---	---
SLITRK1	114798	broad.mit.edu	37	13	84454751	84454751	+	Missense_Mutation	SNP	G	T	T	rs146746846		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:84454751G>T	uc001vlk.2	-	1	1778	c.892C>A	c.(892-894)CAT>AAT	p.H298N		NM_052910	NP_443142	Q96PX8	SLIK1_HUMAN	slit and trk like 1 protein precursor	298	Extracellular (Potential).					integral to membrane				ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5	Medulloblastoma(90;0.18)	Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.07)														---	---	---	---
SLITRK5	26050	broad.mit.edu	37	13	88330488	88330488	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:88330488C>T	uc001vln.2	+	2	3064	c.2845C>T	c.(2845-2847)CTG>TTG	p.L949L	SLITRK5_uc010tic.1_Silent_p.L708L	NM_015567	NP_056382	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5 precursor	949	Cytoplasmic (Potential).					integral to membrane				ovary(2)|pancreas(2)|central_nervous_system(1)	5	all_neural(89;0.101)|Medulloblastoma(90;0.163)																	---	---	---	---
TGDS	23483	broad.mit.edu	37	13	95243203	95243203	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:95243203T>C	uc001vlw.2	-						TGDS_uc001vlx.2_Intron	NM_014305	NP_055120			TDP-glucose 4,6-dehydratase						cellular metabolic process		coenzyme binding|dTDP-glucose 4,6-dehydratase activity|protein binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)																	---	---	---	---
DZIP1	22873	broad.mit.edu	37	13	96293904	96293904	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96293904G>A	uc001vmk.2	-	5	1094	c.242C>T	c.(241-243)GCG>GTG	p.A81V	DZIP1_uc001vml.2_Missense_Mutation_p.A81V|DZIP1_uc001vmn.2_Missense_Mutation_p.A70V	NM_198968	NP_945319	Q86YF9	DZIP1_HUMAN	DAZ interacting protein 1 isoform 2	81					germ cell development|multicellular organismal development|spermatogenesis	cytoplasm|nucleus	nucleic acid binding|protein binding|zinc ion binding			ovary(2)	2	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.141)															---	---	---	---
UGGT2	55757	broad.mit.edu	37	13	96489332	96489332	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:96489332A>G	uc001vmt.2	-						UGGT2_uc001vms.2_Intron	NM_020121	NP_064506			UDP-glucose ceramide glucosyltransferase-like 2						post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
MBNL2	10150	broad.mit.edu	37	13	98009896	98009896	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:98009896G>A	uc010aft.2	+						MBNL2_uc001vmz.2_Intron|MBNL2_uc001vna.2_Intron|MBNL2_uc001vnb.2_Intron|MBNL2_uc010tij.1_Intron|MBNL2_uc001vnc.2_Missense_Mutation_p.C55Y	NM_144778	NP_659002			muscleblind-like 2 isoform 1						mRNA processing|regulation of RNA splicing|RNA splicing	cytoplasm|nucleus	RNA binding|zinc ion binding				0	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.218)															---	---	---	---
NALCN	259232	broad.mit.edu	37	13	101720313	101720313	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101720313C>T	uc001vox.1	-	39	4592	c.4403G>A	c.(4402-4404)CGC>CAC	p.R1468H		NM_052867	NP_443099	Q8IZF0	NALCN_HUMAN	voltage gated channel like 1	1468	Cytoplasmic (Potential).					integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|skin(2)|pancreas(1)|central_nervous_system(1)	16	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)																	---	---	---	---
NALCN	259232	broad.mit.edu	37	13	101833669	101833669	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101833669T>C	uc001vox.1	-						NALCN_uc001voy.2_Intron|NALCN_uc001voz.2_Missense_Mutation_p.D595G|NALCN_uc001vpa.2_Missense_Mutation_p.D595G	NM_052867	NP_443099			voltage gated channel like 1							integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|skin(2)|pancreas(1)|central_nervous_system(1)	16	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)																	---	---	---	---
ERCC5	2073	broad.mit.edu	37	13	103506667	103506667	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103506667T>C	uc001vpw.2	+	4	853	c.410T>C	c.(409-411)GTT>GCT	p.V137A	ERCC5_uc001vpu.1_Missense_Mutation_p.V591A|ERCC5_uc010tjb.1_Missense_Mutation_p.V137A|ERCC5_uc010tjc.1_RNA|ERCC5_uc010tjd.1_5'UTR	NM_000123	NP_000114	P28715	ERCC5_HUMAN	XPG-complementing protein	137					negative regulation of apoptosis|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|response to UV-C|transcription-coupled nucleotide-excision repair|UV protection	nucleoplasm	bubble DNA binding|double-stranded DNA binding|endodeoxyribonuclease activity|metal ion binding|protein homodimerization activity|protein N-terminus binding|single-stranded DNA binding			ovary(4)|lung(1)|central_nervous_system(1)|skin(1)	7	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)							Mis|N|F			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				---	---	---	---
ERCC5	2073	broad.mit.edu	37	13	103508454	103508454	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103508454G>A	uc001vpw.2	+	5	963	c.520G>A	c.(520-522)GCA>ACA	p.A174T	ERCC5_uc001vpu.1_Missense_Mutation_p.A628T|ERCC5_uc010tjb.1_Missense_Mutation_p.A174T|ERCC5_uc010tjc.1_RNA|ERCC5_uc010tjd.1_Missense_Mutation_p.A6T	NM_000123	NP_000114	P28715	ERCC5_HUMAN	XPG-complementing protein	174					negative regulation of apoptosis|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|response to UV-C|transcription-coupled nucleotide-excision repair|UV protection	nucleoplasm	bubble DNA binding|double-stranded DNA binding|endodeoxyribonuclease activity|metal ion binding|protein homodimerization activity|protein N-terminus binding|single-stranded DNA binding			ovary(4)|lung(1)|central_nervous_system(1)|skin(1)	7	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)							Mis|N|F			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				---	---	---	---
ERCC5	2073	broad.mit.edu	37	13	103514647	103514647	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103514647T>C	uc001vpw.2	+	8	1591	c.1148T>C	c.(1147-1149)ATA>ACA	p.I383T	ERCC5_uc001vpu.1_Missense_Mutation_p.I837T|ERCC5_uc010tjb.1_Missense_Mutation_p.I383T|ERCC5_uc010tjc.1_RNA|ERCC5_uc010tjd.1_Missense_Mutation_p.I215T	NM_000123	NP_000114	P28715	ERCC5_HUMAN	XPG-complementing protein	383					negative regulation of apoptosis|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|response to UV-C|transcription-coupled nucleotide-excision repair|UV protection	nucleoplasm	bubble DNA binding|double-stranded DNA binding|endodeoxyribonuclease activity|metal ion binding|protein homodimerization activity|protein N-terminus binding|single-stranded DNA binding			ovary(4)|lung(1)|central_nervous_system(1)|skin(1)	7	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)							Mis|N|F			skin basal cell|skin squamous cell|melanoma		Direct_reversal_of_damage|NER	Xeroderma_Pigmentosum				---	---	---	---
COL4A2	1284	broad.mit.edu	37	13	111111149	111111149	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111111149C>T	uc001vqx.2	+	22	1753	c.1464C>T	c.(1462-1464)GGC>GGT	p.G488G		NM_001846	NP_001837	P08572	CO4A2_HUMAN	alpha 2 type IV collagen preproprotein	488	Triple-helical region.				angiogenesis|axon guidance|extracellular matrix organization|negative regulation of angiogenesis	collagen type IV	extracellular matrix structural constituent|protein binding			skin(3)|central_nervous_system(2)|ovary(1)	6	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)															---	---	---	---
ING1	3621	broad.mit.edu	37	13	111371852	111371852	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:111371852C>T	uc001vri.2	+	2	1274	c.842C>T	c.(841-843)GCG>GTG	p.A281V	ING1_uc001vrf.2_Missense_Mutation_p.A94V|ING1_uc001vrg.2_Missense_Mutation_p.A69V|ING1_uc001vrh.2_Missense_Mutation_p.A138V	NM_005537	NP_005528	Q9UK53	ING1_HUMAN	inhibitor of growth family, member 1 isoform D	281					cell cycle|negative regulation of cell growth|negative regulation of cell proliferation	nucleus	zinc ion binding			ovary(1)	1	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.188)															---	---	---	---
MCF2L	23263	broad.mit.edu	37	13	113699198	113699198	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:113699198G>A	uc001vsu.2	+						MCF2L_uc001vsq.2_Intron|MCF2L_uc010tjr.1_Intron|MCF2L_uc001vsr.2_Intron|MCF2L_uc001vss.3_Intron|MCF2L_uc010tjs.1_Intron|MCF2L_uc001vst.1_Missense_Mutation_p.V54M	NM_001112732	NP_001106203			MCF.2 cell line derived transforming						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|plasma membrane	Rho guanyl-nucleotide exchange factor activity			ovary(1)|kidney(1)	2	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)																---	---	---	---
DCUN1D2	55208	broad.mit.edu	37	13	114128485	114128485	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114128485A>G	uc001vtr.1	-	4	513	c.474T>C	c.(472-474)TAT>TAC	p.Y158Y	DCUN1D2_uc001vts.1_RNA|DCUN1D2_uc010agw.1_Silent_p.Y25Y	NM_001014283	NP_001014305	Q6PH85	DCNL2_HUMAN	DCN1, defective in cullin neddylation 1, domain	158	DCUN1.										0	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0395)|all_epithelial(44;0.011)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.029)|GBM - Glioblastoma multiforme(44;0.234)															---	---	---	---
GAS6	2621	broad.mit.edu	37	13	114530036	114530036	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:114530036G>A	uc001vud.2	-	12	1563	c.1410C>T	c.(1408-1410)TGC>TGT	p.C470C	GAS6_uc001vug.2_Silent_p.C171C|GAS6_uc001vuf.2_Silent_p.C197C	NM_000820	NP_000811	Q14393	GAS6_HUMAN	growth arrest-specific 6 isoform 1 precursor	513	Laminin G-like 1.				cell proliferation|leukocyte migration|peptidyl-glutamic acid carboxylation|platelet activation|platelet degranulation|positive regulation of ERK1 and ERK2 cascade|positive regulation of fibroblast proliferation|post-translational protein modification|proteolysis|regulation of growth	endoplasmic reticulum lumen|extracellular space|Golgi lumen|platelet alpha granule lumen	calcium ion binding|receptor agonist activity			central_nervous_system(4)	4	Lung NSC(43;0.00976)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0176)|all_epithelial(44;0.0104)|all_lung(25;0.0249)|Lung NSC(25;0.0908)|Breast(118;0.188)																---	---	---	---
TEP1	7011	broad.mit.edu	37	14	20841910	20841910	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20841910G>A	uc001vxe.2	-	45	6571	c.6531C>T	c.(6529-6531)GGC>GGT	p.G2177G	TEP1_uc010ahj.1_5'Flank|TEP1_uc010ahk.2_Silent_p.G1520G|TEP1_uc010tlf.1_RNA|TEP1_uc010tlg.1_Silent_p.G2069G|TEP1_uc010tlh.1_Silent_p.G515G	NM_007110	NP_009041	Q99973	TEP1_HUMAN	telomerase-associated protein 1	2177	WD 13.				telomere maintenance via recombination	chromosome, telomeric region|cytoplasm|nuclear matrix|soluble fraction|telomerase holoenzyme complex	ATP binding|RNA binding			ovary(5)	5	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)														---	---	---	---
TEP1	7011	broad.mit.edu	37	14	20851907	20851907	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:20851907G>T	uc001vxe.2	-	25	3745	c.3705C>A	c.(3703-3705)ACC>ACA	p.T1235T	TEP1_uc010ahk.2_Silent_p.T585T|TEP1_uc010tlf.1_RNA|TEP1_uc010tlg.1_Silent_p.T1127T|TEP1_uc010tlh.1_5'Flank	NM_007110	NP_009041	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1235	NACHT.				telomere maintenance via recombination	chromosome, telomeric region|cytoplasm|nuclear matrix|soluble fraction|telomerase holoenzyme complex	ATP binding|RNA binding			ovary(5)	5	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)														---	---	---	---
OR6S1	341799	broad.mit.edu	37	14	21109222	21109222	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21109222A>T	uc001vxv.1	-	1	629	c.629T>A	c.(628-630)ATT>AAT	p.I210N		NM_001001968	NP_001001968	Q8NH40	OR6S1_HUMAN	olfactory receptor, family 6, subfamily S,	210	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2	all_cancers(95;0.00304)		Epithelial(56;1.23e-06)|all cancers(55;1.01e-05)	GBM - Glioblastoma multiforme(265;0.0135)														---	---	---	---
EDDM3A	10876	broad.mit.edu	37	14	21215801	21215801	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21215801T>G	uc001vyb.2	+	2	129	c.62T>G	c.(61-63)CTG>CGG	p.L21R	EDDM3A_uc001vyc.2_Missense_Mutation_p.L21R	NM_006683	NP_006674	Q14507	EP3A_HUMAN	human epididymis-specific 3 alpha precursor	21					sperm displacement	extracellular space					0																		---	---	---	---
RNASE2	6036	broad.mit.edu	37	14	21424197	21424197	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21424197T>C	uc010aif.2	+	2	336	c.267T>C	c.(265-267)TGT>TGC	p.C89C	RNASE2_uc001vyl.1_Silent_p.C89C	NM_002934	NP_002925	P10153	RNAS2_HUMAN	ribonuclease, RNase A family, 2 (liver,	89					chemotaxis|RNA catabolic process	extracellular region|lysosome	nucleic acid binding|pancreatic ribonuclease activity			ovary(1)	1	all_cancers(95;0.00381)		OV - Ovarian serous cystadenocarcinoma(11;6.3e-09)|Epithelial(56;1.42e-07)|all cancers(55;5.48e-07)	GBM - Glioblastoma multiforme(265;0.0187)														---	---	---	---
NDRG2	57447	broad.mit.edu	37	14	21491406	21491406	+	Silent	SNP	C	T	T	rs113588489		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21491406C>T	uc001vyy.2	-	3	219	c.69G>A	c.(67-69)GCG>GCA	p.A23A	NDRG2_uc010tll.1_Silent_p.A33A|NDRG2_uc001vyt.2_5'Flank|NDRG2_uc001vyu.2_Silent_p.A23A|NDRG2_uc001vyv.2_Silent_p.A23A|NDRG2_uc001vyw.2_Silent_p.A23A|NDRG2_uc001vzb.2_5'UTR|NDRG2_uc001vyx.2_Silent_p.A23A|NDRG2_uc001vza.2_Silent_p.A23A|NDRG2_uc001vyz.2_Silent_p.A23A|NDRG2_uc001vzc.2_Silent_p.A23A|NDRG2_uc001vze.2_Silent_p.A23A|NDRG2_uc001vzd.2_Silent_p.A23A|NDRG2_uc001vzg.2_Silent_p.A23A|NDRG2_uc001vzf.2_Silent_p.A23A|NDRG2_uc010aig.2_Silent_p.A23A	NM_201540	NP_963834	Q9UN36	NDRG2_HUMAN	N-myc downstream-regulated gene 2 isoform a	23					cell differentiation|nervous system development	centrosome|cytosol|Golgi apparatus|nucleus|perinuclear region of cytoplasm				ovary(1)|breast(1)	2	all_cancers(95;0.00185)		OV - Ovarian serous cystadenocarcinoma(11;6.85e-11)|Epithelial(56;9.49e-09)|all cancers(55;3.84e-08)	GBM - Glioblastoma multiforme(265;0.0191)														---	---	---	---
RNASE13	440163	broad.mit.edu	37	14	21502303	21502303	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21502303G>A	uc001vzj.2	-	2	283	c.145C>T	c.(145-147)CGG>TGG	p.R49W	NDRG2_uc010tll.1_Intron	NM_001012264	NP_001012264	Q5GAN3	RNS13_HUMAN	ribonuclease, RNase A family, 13 precursor	49						extracellular region	nucleic acid binding|pancreatic ribonuclease activity	p.R49Q(1)		upper_aerodigestive_tract(1)	1	all_cancers(95;0.000759)		OV - Ovarian serous cystadenocarcinoma(11;6.85e-11)|Epithelial(56;9.49e-09)|all cancers(55;3.84e-08)	GBM - Glioblastoma multiforme(265;0.019)														---	---	---	---
HNRNPC	3183	broad.mit.edu	37	14	21699218	21699218	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21699218A>G	uc001vzy.2	-	4	499	c.255T>C	c.(253-255)GCT>GCC	p.A85A	HNRNPC_uc001vzw.2_Silent_p.A85A|HNRNPC_uc001wad.2_Intron|HNRNPC_uc001vzx.2_Intron|HNRNPC_uc001vzz.2_Silent_p.A85A|HNRNPC_uc001waa.2_Silent_p.A85A|HNRNPC_uc010ail.2_Silent_p.A85A|HNRNPC_uc010tlq.1_RNA|HNRNPC_uc001wab.2_Silent_p.A85A|HNRNPC_uc001wac.2_Silent_p.A85A|HNRNPC_uc010tlr.1_5'Flank|HNRNPC_uc001waf.2_Silent_p.A85A|HNRNPC_uc001wae.2_Silent_p.A85A	NM_031314	NP_112604	P07910	HNRPC_HUMAN	heterogeneous nuclear ribonucleoprotein C	85	RRM.					catalytic step 2 spliceosome|nucleoplasm	identical protein binding|nucleotide binding|RNA binding				0	all_cancers(95;0.00176)		Epithelial(56;1.08e-06)|all cancers(55;8.95e-06)	GBM - Glioblastoma multiforme(265;0.00783)														---	---	---	---
CHD8	57680	broad.mit.edu	37	14	21897203	21897203	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21897203G>A	uc001was.1	-	3	392	c.298C>T	c.(298-300)CAG>TAG	p.Q100*	CHD8_uc001war.1_5'UTR	NM_020920	NP_065971	Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	379	Gln-rich.				ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent	MLL1 complex	ATP binding|beta-catenin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding			ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1)	10	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)														---	---	---	---
TOX4	9878	broad.mit.edu	37	14	21961062	21961062	+	Silent	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21961062T>A	uc001waz.2	+	7	1390	c.1287T>A	c.(1285-1287)GCT>GCA	p.A429A	TOX4_uc001way.2_Silent_p.A299A|TOX4_uc001wba.2_RNA|TOX4_uc010tlu.1_Silent_p.A406A|TOX4_uc010tlv.1_Silent_p.A299A	NM_014828	NP_055643	O94842	TOX4_HUMAN	epidermal Langerhans cell protein LCP1	429	Gln/Pro-rich.|Poly-Ala.					chromatin|nucleus|PTW/PP1 phosphatase complex	DNA binding|protein binding			ovary(1)	1	all_cancers(95;0.000465)		Epithelial(56;6.61e-06)|all cancers(55;5.15e-05)	GBM - Glioblastoma multiforme(265;0.0149)														---	---	---	---
SALL2	6297	broad.mit.edu	37	14	21993017	21993017	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21993017C>A	uc001wbe.2	-	2	1127	c.845G>T	c.(844-846)GGG>GTG	p.G282V	SALL2_uc010tly.1_Missense_Mutation_p.G280V|SALL2_uc010tlz.1_Missense_Mutation_p.G145V|SALL2_uc001wbf.3_Intron|SALL2_uc010tma.1_Missense_Mutation_p.G147V|SALL2_uc001wbg.1_Intron	NM_005407	NP_005398	Q9Y467	SALL2_HUMAN	sal-like 2	282							DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|large_intestine(1)	3	all_cancers(95;0.000662)			GBM - Glioblastoma multiforme(265;0.0151)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	22591489	22591489	+	Intron	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22591489G>T	uc001wbw.2	+						uc010aiv.1_Intron|uc010tmi.1_Intron|uc010tmj.1_Intron|uc010aja.1_Intron|uc010tmk.1_Intron|uc010tmo.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc010ajg.1_Intron|uc001wcx.3_Intron|uc001wdd.2_Missense_Mutation_p.R2M|uc010ajj.1_Missense_Mutation_p.R2M|uc001wde.1_5'Flank|uc010aji.1_Missense_Mutation_p.R2M					SubName: Full=Alpha-chain C region; Flags: Fragment;																														---	---	---	---
Unknown	0	broad.mit.edu	37	14	22600882	22600882	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22600882G>A	uc001wbw.2	+						uc010aiv.1_Intron|uc010tmi.1_Intron|uc010tmj.1_Intron|uc010aja.1_Intron|uc010tmk.1_Intron|uc010tmo.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc010ajg.1_Intron|uc001wcx.3_Intron|uc001wdd.2_Intron|uc010ajj.1_Intron|uc001wde.1_Intron|uc010tmq.1_RNA					SubName: Full=Alpha-chain C region; Flags: Fragment;																														---	---	---	---
RBM23	55147	broad.mit.edu	37	14	23371265	23371265	+	Silent	SNP	G	A	A	rs138407530		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23371265G>A	uc001whg.2	-	12	1369	c.1170C>T	c.(1168-1170)GCC>GCT	p.A390A	RBM23_uc001whh.2_Silent_p.A374A|RBM23_uc001whi.2_Silent_p.A356A|RBM23_uc010tne.1_Silent_p.A220A|RBM23_uc001whj.2_Silent_p.A140A	NM_001077351	NP_001070819	Q86U06	RBM23_HUMAN	RNA binding motif protein 23 isoform 1	390	Ala-rich.				mRNA processing	nucleus	nucleotide binding|RNA binding			skin(1)	1	all_cancers(95;4.69e-05)			GBM - Glioblastoma multiforme(265;0.0128)														---	---	---	---
HAUS4	54930	broad.mit.edu	37	14	23421902	23421902	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23421902A>G	uc001whp.2	-						HAUS4_uc001who.2_Intron|HAUS4_uc001whq.2_Intron|HAUS4_uc001whr.2_Intron|HAUS4_uc001whs.2_Intron|HAUS4_uc001wht.2_Intron|HAUS4_uc001whu.2_Intron|HAUS4_uc001whv.2_Intron|HAUS4_uc001whw.2_Intron|HAUS4_uc001whx.2_Intron	NM_017815	NP_060285			HAUS augmin-like complex, subunit 4						cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|spindle				ovary(1)	1																		---	---	---	---
C14orf93	60686	broad.mit.edu	37	14	23456533	23456533	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23456533T>C	uc001wib.1	-	7	1818	c.1508A>G	c.(1507-1509)GAG>GGG	p.E503G	C14orf93_uc001wic.1_Missense_Mutation_p.E323G|C14orf93_uc001wid.1_Missense_Mutation_p.E503G|C14orf93_uc001wig.2_Missense_Mutation_p.E503G|C14orf93_uc001wih.2_Missense_Mutation_p.E503G|C14orf93_uc001wie.2_Missense_Mutation_p.E503G|C14orf93_uc001wia.3_Missense_Mutation_p.E463G|C14orf93_uc001wif.2_Missense_Mutation_p.E323G	NM_021944	NP_068763	Q9H972	CN093_HUMAN	hypothetical protein LOC60686 precursor	503						extracellular region				ovary(1)	1	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.0127)												OREG0022593	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
C14orf93	60686	broad.mit.edu	37	14	23457139	23457139	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23457139C>A	uc001wib.1	-	6	1480	c.1170G>T	c.(1168-1170)GAG>GAT	p.E390D	C14orf93_uc001wic.1_Missense_Mutation_p.E210D|C14orf93_uc001wid.1_Missense_Mutation_p.E390D|C14orf93_uc001wig.2_Missense_Mutation_p.E390D|C14orf93_uc001wih.2_Missense_Mutation_p.E390D|C14orf93_uc001wie.2_Missense_Mutation_p.E390D|C14orf93_uc001wia.3_Missense_Mutation_p.E390D|C14orf93_uc001wif.2_Missense_Mutation_p.E210D	NM_021944	NP_068763	Q9H972	CN093_HUMAN	hypothetical protein LOC60686 precursor	390						extracellular region				ovary(1)	1	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.0127)														---	---	---	---
C14orf93	60686	broad.mit.edu	37	14	23457192	23457192	+	Missense_Mutation	SNP	G	A	A	rs145175744		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23457192G>A	uc001wib.1	-	6	1427	c.1117C>T	c.(1117-1119)CGT>TGT	p.R373C	C14orf93_uc001wic.1_Missense_Mutation_p.R193C|C14orf93_uc001wid.1_Missense_Mutation_p.R373C|C14orf93_uc001wig.2_Missense_Mutation_p.R373C|C14orf93_uc001wih.2_Missense_Mutation_p.R373C|C14orf93_uc001wie.2_Missense_Mutation_p.R373C|C14orf93_uc001wia.3_Missense_Mutation_p.R373C|C14orf93_uc001wif.2_Missense_Mutation_p.R193C	NM_021944	NP_068763	Q9H972	CN093_HUMAN	hypothetical protein LOC60686 precursor	373						extracellular region				ovary(1)	1	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.0127)														---	---	---	---
ACIN1	22985	broad.mit.edu	37	14	23531690	23531690	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23531690G>A	uc001wit.3	-	15	3428	c.3100C>T	c.(3100-3102)CGC>TGC	p.R1034C	ACIN1_uc001wio.3_RNA|ACIN1_uc001wip.3_Missense_Mutation_p.R276C|ACIN1_uc001wiq.3_Missense_Mutation_p.R276C|ACIN1_uc001wir.3_Missense_Mutation_p.R307C|ACIN1_uc001wis.3_Missense_Mutation_p.R715C|ACIN1_uc010akg.2_Missense_Mutation_p.R1021C	NM_014977	NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	1034					apoptotic chromosome condensation|erythrocyte differentiation|positive regulation of monocyte differentiation	cytosol	ATPase activity|enzyme binding|nucleic acid binding|nucleotide binding			ovary(2)|large_intestine(1)|skin(1)	4	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)														---	---	---	---
ACIN1	22985	broad.mit.edu	37	14	23549375	23549375	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23549375A>T	uc001wit.3	-	6	1671	c.1343T>A	c.(1342-1344)GTC>GAC	p.V448D	ACIN1_uc001wis.3_Missense_Mutation_p.V130D|ACIN1_uc010akg.2_Missense_Mutation_p.V448D|ACIN1_uc010tnj.1_Missense_Mutation_p.V408D	NM_014977	NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	448					apoptotic chromosome condensation|erythrocyte differentiation|positive regulation of monocyte differentiation	cytosol	ATPase activity|enzyme binding|nucleic acid binding|nucleotide binding			ovary(2)|large_intestine(1)|skin(1)	4	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)														---	---	---	---
EFS	10278	broad.mit.edu	37	14	23828142	23828142	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23828142C>T	uc001wjo.2	-	5	1802	c.1194G>A	c.(1192-1194)CCG>CCA	p.P398P	EFS_uc001wjp.2_Silent_p.P305P|EFS_uc010tnm.1_Silent_p.P229P	NM_005864	NP_005855	O43281	EFS_HUMAN	embryonal Fyn-associated substrate isoform 1	398					cell adhesion|intracellular signal transduction	cytoplasm	SH3 domain binding			large_intestine(1)	1	all_cancers(95;7.12e-06)			GBM - Glioblastoma multiforme(265;0.00649)														---	---	---	---
MYH7	4625	broad.mit.edu	37	14	23894056	23894056	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23894056C>A	uc001wjx.2	-	22	2707	c.2601G>T	c.(2599-2601)GAG>GAT	p.E867D		NM_000257	NP_000248	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	867	Potential.				adult heart development|muscle filament sliding|regulation of heart rate|ventricular cardiac muscle tissue morphogenesis	focal adhesion|muscle myosin complex|myosin filament|nucleus|sarcomere	actin binding|actin-dependent ATPase activity|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(3)|skin(1)	4	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)														---	---	---	---
NGDN	25983	broad.mit.edu	37	14	23945498	23945498	+	Missense_Mutation	SNP	C	T	T	rs142475495		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23945498C>T	uc001wjy.2	+	8	622	c.595C>T	c.(595-597)CGG>TGG	p.R199W	NGDN_uc001wjz.2_Missense_Mutation_p.R199W|NGDN_uc001wka.2_RNA	NM_001042635	NP_001036100	Q8NEJ9	NGDN_HUMAN	neuroguidin isoform 1	199	Potential.				regulation of translation	axon|cytoplasm|dendrite|filopodium|nucleus					0	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00654)														---	---	---	---
IRF9	10379	broad.mit.edu	37	14	24633873	24633873	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24633873G>A	uc001wmq.2	+	7	827	c.700G>A	c.(700-702)GCC>ACC	p.A234T	RNF31_uc001wmp.2_RNA|IRF9_uc010alj.2_Intron	NM_006084	NP_006075	Q00978	IRF9_HUMAN	interferon-stimulated transcription factor 3,	234					interferon-gamma-mediated signaling pathway|response to virus|transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	cytosol|nucleoplasm	DNA binding|identical protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1				GBM - Glioblastoma multiforme(265;0.00853)														---	---	---	---
IRF9	10379	broad.mit.edu	37	14	24635113	24635113	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24635113A>G	uc001wmq.2	+	8	1176	c.1049A>G	c.(1048-1050)AAT>AGT	p.N350S	RNF31_uc001wmp.2_RNA|IRF9_uc010alj.2_Missense_Mutation_p.N134S	NM_006084	NP_006075	Q00978	IRF9_HUMAN	interferon-stimulated transcription factor 3,	350					interferon-gamma-mediated signaling pathway|response to virus|transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	cytosol|nucleoplasm	DNA binding|identical protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1				GBM - Glioblastoma multiforme(265;0.00853)														---	---	---	---
TM9SF1	10548	broad.mit.edu	37	14	24661406	24661406	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24661406T>C	uc001wnb.1	-	4	1472	c.1124A>G	c.(1123-1125)AAC>AGC	p.N375S	IPO4_uc001wmx.1_5'Flank|IPO4_uc001wmy.1_5'Flank|IPO4_uc010tnz.1_5'Flank|IPO4_uc001wmw.1_5'Flank|IPO4_uc001wmz.1_5'Flank|TM9SF1_uc010toa.1_Missense_Mutation_p.N288S|TM9SF1_uc001wna.1_RNA|TM9SF1_uc010tob.1_Missense_Mutation_p.N610S|TM9SF1_uc001wnc.2_Missense_Mutation_p.N375S|TM9SF1_uc001wnd.2_Missense_Mutation_p.N231S	NM_006405	NP_006396	O15321	TM9S1_HUMAN	transmembrane 9 superfamily member 1 isoform a	375	Helical; (Potential).				autophagy	autophagic vacuole membrane|cytoplasmic vesicle|integral to membrane|lysosomal membrane				ovary(1)	1				GBM - Glioblastoma multiforme(265;0.0183)														---	---	---	---
C14orf21	161424	broad.mit.edu	37	14	24771222	24771222	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24771222T>C	uc001wol.1	+	4	923	c.860T>C	c.(859-861)GTT>GCT	p.V287A	C14orf21_uc001wom.1_5'Flank|DHRS1_uc001woj.1_5'Flank|DHRS1_uc001wok.2_5'Flank	NM_174913	NP_777573	Q86U38	CN021_HUMAN	hypothetical protein LOC161424	287							RNA binding			breast(2)|central_nervous_system(1)|skin(1)	4				GBM - Glioblastoma multiforme(265;0.0185)														---	---	---	---
LTB4R	1241	broad.mit.edu	37	14	24785186	24785186	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24785186C>T	uc001wos.2	+	2	650	c.329C>T	c.(328-330)GCC>GTC	p.A110V	LTB4R_uc010alp.2_Missense_Mutation_p.A110V|LTB4R_uc001wou.2_Missense_Mutation_p.A110V	NM_001143919	NP_001137391	Q15722	LT4R1_HUMAN	leukotriene B4 receptor	110	Helical; Name=3; (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|cellular component movement|immune response|inflammatory response|muscle contraction	integral to plasma membrane	nucleotide binding				0				GBM - Glioblastoma multiforme(265;0.018)														---	---	---	---
ADCY4	196883	broad.mit.edu	37	14	24798413	24798413	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24798413C>T	uc001wov.2	-	10	1384	c.1378G>A	c.(1378-1380)GCA>ACA	p.A460T	ADCY4_uc001wow.2_Missense_Mutation_p.A460T|ADCY4_uc010toh.1_Missense_Mutation_p.A146T|ADCY4_uc001wox.2_Missense_Mutation_p.A460T|ADCY4_uc001woy.2_Missense_Mutation_p.A460T	NM_139247	NP_640340	Q8NFM4	ADCY4_HUMAN	adenylate cyclase 4	460	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	cytoplasm|integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding|protein binding			ovary(1)|lung(1)|pancreas(1)	3				GBM - Glioblastoma multiforme(265;0.0192)														---	---	---	---
NFATC4	4776	broad.mit.edu	37	14	24843582	24843582	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24843582G>A	uc001wpc.2	+	6	2104	c.1783G>A	c.(1783-1785)GCC>ACC	p.A595T	NFATC4_uc010tok.1_Missense_Mutation_p.A658T|NFATC4_uc010tol.1_Missense_Mutation_p.A658T|NFATC4_uc010alr.2_Missense_Mutation_p.A658T|NFATC4_uc010als.2_3'UTR|NFATC4_uc010tom.1_Missense_Mutation_p.A608T|NFATC4_uc010ton.1_Missense_Mutation_p.A608T|NFATC4_uc010too.1_Missense_Mutation_p.A608T|NFATC4_uc010alt.2_Missense_Mutation_p.A627T|NFATC4_uc010top.1_Missense_Mutation_p.A627T|NFATC4_uc010toq.1_Missense_Mutation_p.A627T|NFATC4_uc010alu.2_3'UTR|NFATC4_uc010tor.1_Missense_Mutation_p.A595T|NFATC4_uc010tos.1_Missense_Mutation_p.A525T|NFATC4_uc010tot.1_Missense_Mutation_p.A583T|NFATC4_uc010tou.1_Missense_Mutation_p.A525T|NFATC4_uc010tov.1_Missense_Mutation_p.A583T|NFATC4_uc010tow.1_Missense_Mutation_p.A525T|NFATC4_uc010alv.2_Missense_Mutation_p.A583T|NFATC4_uc010tox.1_Missense_Mutation_p.A525T|NFATC4_uc001wpd.2_Missense_Mutation_p.A130T|NFATC4_uc010toy.1_Missense_Mutation_p.A130T|NFATC4_uc010toz.1_Missense_Mutation_p.A130T|NFATC4_uc010tpa.1_5'UTR|NFATC4_uc010tpb.1_5'UTR	NM_004554	NP_004545	Q14934	NFAC4_HUMAN	nuclear factor of activated T-cells,	595	IPT/TIG.				cell differentiation|inflammatory response|transcription from RNA polymerase II promoter	cytoplasm|intermediate filament cytoskeleton|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(1)|central_nervous_system(1)|skin(1)	3				GBM - Glioblastoma multiforme(265;0.018)														---	---	---	---
KHNYN	23351	broad.mit.edu	37	14	24906310	24906310	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24906310G>A	uc001wph.3	+	8	2058	c.1856G>A	c.(1855-1857)GGG>GAG	p.G619E	KHNYN_uc010tpc.1_Missense_Mutation_p.G660E|KHNYN_uc010alw.2_Missense_Mutation_p.G619E	NM_015299	NP_056114	O15037	KHNYN_HUMAN	hypothetical protein LOC23351	619										ovary(2)|liver(1)	3																OREG0022628	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CMA1	1215	broad.mit.edu	37	14	24975666	24975666	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24975666T>C	uc001wpp.1	-						CMA1_uc010alx.1_Intron	NM_001836	NP_001827			chymase 1, mast cell preproprotein						interleukin-1 beta biosynthetic process|proteolysis	extracellular region	serine-type endopeptidase activity				0				GBM - Glioblastoma multiforme(265;0.0271)														---	---	---	---
CTSG	1511	broad.mit.edu	37	14	25043662	25043662	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25043662G>A	uc001wpq.2	-	4	420	c.383C>T	c.(382-384)GCT>GTT	p.A128V		NM_001911	NP_001902	P08311	CATG_HUMAN	cathepsin G preproprotein	128	Peptidase S1.				immune response|proteolysis	cell surface|extracellular space|plasma membrane|stored secretory granule	heparin binding|serine-type endopeptidase activity			ovary(2)	2				GBM - Glioblastoma multiforme(265;0.0269)														---	---	---	---
STXBP6	29091	broad.mit.edu	37	14	25288337	25288337	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:25288337G>A	uc001wpu.2	-	5	1230	c.515C>T	c.(514-516)GCC>GTC	p.A172V	STXBP6_uc001wpv.2_Missense_Mutation_p.A172V|STXBP6_uc001wpw.2_Missense_Mutation_p.A172V|STXBP6_uc001wpx.1_RNA|STXBP6_uc001wpt.2_Missense_Mutation_p.A70V	NM_014178	NP_054897	Q8NFX7	STXB6_HUMAN	amisyn	172	v-SNARE coiled-coil homology.				vesicle-mediated transport	cytoplasm|integral to membrane					0				GBM - Glioblastoma multiforme(265;0.0296)														---	---	---	---
PRKD1	5587	broad.mit.edu	37	14	30046617	30046617	+	Missense_Mutation	SNP	C	T	T	rs149150061		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:30046617C>T	uc001wqh.2	-	18	2747	c.2566G>A	c.(2566-2568)GGG>AGG	p.G856R		NM_002742	NP_002733	Q15139	KPCD1_HUMAN	protein kinase D1	856					cell proliferation|intracellular signal transduction|sphingolipid metabolic process	cytosol|integral to plasma membrane	ATP binding|metal ion binding|protein binding|protein kinase C activity			lung(3)|large_intestine(2)|ovary(2)|skin(1)	8	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)														---	---	---	---
COCH	1690	broad.mit.edu	37	14	31354708	31354708	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31354708A>G	uc001wqr.2	+	10	922	c.842A>G	c.(841-843)GAC>GGC	p.D281G	COCH_uc001wqp.2_Missense_Mutation_p.D281G|COCH_uc001wqq.3_Missense_Mutation_p.D281G|uc001wqs.2_RNA|COCH_uc001wqt.1_Missense_Mutation_p.D132G	NM_004086	NP_004077	O43405	COCH_HUMAN	cochlin precursor	281	VWFA 1.				sensory perception of sound	proteinaceous extracellular matrix				pancreas(1)|central_nervous_system(1)|skin(1)	3	Hepatocellular(127;0.0877)|Breast(36;0.148)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)|BRCA - Breast invasive adenocarcinoma(188;0.0805)	GBM - Glioblastoma multiforme(265;0.00645)														---	---	---	---
HECTD1	25831	broad.mit.edu	37	14	31576773	31576773	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31576773G>A	uc001wrc.1	-	37	7107	c.6618C>T	c.(6616-6618)CAC>CAT	p.H2206H	HECTD1_uc001wra.1_Silent_p.H332H|HECTD1_uc001wrb.1_Silent_p.H332H	NM_015382	NP_056197	Q9ULT8	HECD1_HUMAN	HECT domain containing 1	2206	HECT.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	metal ion binding|protein binding|ubiquitin-protein ligase activity			ovary(3)|large_intestine(1)|lung(1)	5	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)														---	---	---	---
HECTD1	25831	broad.mit.edu	37	14	31641119	31641119	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:31641119C>A	uc001wrc.1	-	8	1769	c.1280G>T	c.(1279-1281)AGG>ATG	p.R427M		NM_015382	NP_056197	Q9ULT8	HECD1_HUMAN	HECT domain containing 1	427	ANK 2.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	metal ion binding|protein binding|ubiquitin-protein ligase activity			ovary(3)|large_intestine(1)|lung(1)	5	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)														---	---	---	---
BAZ1A	11177	broad.mit.edu	37	14	35234228	35234228	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35234228T>C	uc001wsk.2	-	22	4116	c.3548A>G	c.(3547-3549)AAG>AGG	p.K1183R	BAZ1A_uc001wsl.2_Missense_Mutation_p.K1151R	NM_013448	NP_038476	Q9NRL2	BAZ1A_HUMAN	bromodomain adjacent to zinc finger domain, 1A	1183	PHD-type.				chromatin remodeling|regulation of transcription, DNA-dependent|transcription, DNA-dependent	ACF complex	zinc ion binding			lung(2)|central_nervous_system(2)|ovary(1)|breast(1)|skin(1)	7	Breast(36;0.0388)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;7.23e-05)|Lung(238;0.00019)|Epithelial(34;0.0793)|all cancers(34;0.175)	GBM - Glioblastoma multiforme(112;0.0659)														---	---	---	---
BAZ1A	11177	broad.mit.edu	37	14	35234457	35234457	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35234457G>A	uc001wsk.2	-	22	3887	c.3319C>T	c.(3319-3321)CGT>TGT	p.R1107C	BAZ1A_uc001wsl.2_Missense_Mutation_p.R1075C	NM_013448	NP_038476	Q9NRL2	BAZ1A_HUMAN	bromodomain adjacent to zinc finger domain, 1A	1107					chromatin remodeling|regulation of transcription, DNA-dependent|transcription, DNA-dependent	ACF complex	zinc ion binding			lung(2)|central_nervous_system(2)|ovary(1)|breast(1)|skin(1)	7	Breast(36;0.0388)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;7.23e-05)|Lung(238;0.00019)|Epithelial(34;0.0793)|all cancers(34;0.175)	GBM - Glioblastoma multiforme(112;0.0659)														---	---	---	---
Unknown	0	broad.mit.edu	37	14	38310783	38310783	+	Intron	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:38310783G>T	uc001wug.2	+						uc001wuh.2_Missense_Mutation_p.S444I|uc001wui.2_RNA|uc001wuj.2_Missense_Mutation_p.S541I					Homo sapiens chromosome 14 open reading frame 25, mRNA (cDNA clone IMAGE:5268731), partial cds.																														---	---	---	---
LRFN5	145581	broad.mit.edu	37	14	42360855	42360855	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:42360855C>T	uc001wvm.2	+	4	2986	c.1788C>T	c.(1786-1788)CAC>CAT	p.H596H	LRFN5_uc010ana.2_Intron	NM_152447	NP_689660	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III	596	Cytoplasmic (Potential).					integral to membrane				ovary(5)|pancreas(2)|central_nervous_system(1)	8			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)											HNSCC(30;0.082)			---	---	---	---
FANCM	57697	broad.mit.edu	37	14	45665590	45665590	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:45665590C>T	uc001wwd.3	+	21	5655	c.5556C>T	c.(5554-5556)GGC>GGT	p.G1852G	FANCM_uc010anf.2_Silent_p.G1826G|FANCM_uc001wwe.3_Silent_p.G1388G|FANCM_uc010ang.2_Silent_p.G1101G	NM_020937	NP_065988	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1852	Interaction with FAAP24 and EME1.				DNA repair	Fanconi anaemia nuclear complex	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|nuclease activity|protein binding			ovary(3)|lung(2)|breast(2)	7													Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
MDGA2	161357	broad.mit.edu	37	14	47343266	47343266	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:47343266G>A	uc001wwj.3	-	13	2564	c.2368C>T	c.(2368-2370)CGT>TGT	p.R790C	MDGA2_uc001wwh.3_5'UTR|MDGA2_uc001wwi.3_Missense_Mutation_p.R561C|MDGA2_uc010ani.2_Missense_Mutation_p.R350C	NM_001113498	NP_001106970	Q7Z553	MDGA2_HUMAN	MAM domain containing 1 isoform 1	790	MAM.				spinal cord motor neuron differentiation	anchored to membrane|plasma membrane				ovary(4)|large_intestine(1)|pancreas(1)	6																		---	---	---	---
MDGA2	161357	broad.mit.edu	37	14	47566132	47566132	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:47566132C>T	uc001wwj.3	-	6	1109	c.913G>A	c.(913-915)GCT>ACT	p.A305T	MDGA2_uc001wwi.3_Missense_Mutation_p.A76T|MDGA2_uc010ani.2_5'UTR	NM_001113498	NP_001106970	Q7Z553	MDGA2_HUMAN	MAM domain containing 1 isoform 1	305	Ig-like 3.				spinal cord motor neuron differentiation	anchored to membrane|plasma membrane				ovary(4)|large_intestine(1)|pancreas(1)	6																		---	---	---	---
L2HGDH	79944	broad.mit.edu	37	14	50713777	50713777	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50713777T>C	uc001wxu.2	-	10	1470	c.1391A>G	c.(1390-1392)TAA>TGA	p.*464*	L2HGDH_uc010tqn.1_Intron|L2HGDH_uc010tqo.1_Silent_p.*464*	NM_024884	NP_079160	Q9H9P8	L2HDH_HUMAN	L-2-hydroxyglutarate dehydrogenase precursor	464					2-oxoglutarate metabolic process|cellular protein metabolic process	integral to mitochondrial inner membrane	2-hydroxyglutarate dehydrogenase activity			ovary(2)	2	all_epithelial(31;0.000599)|Breast(41;0.0102)																	---	---	---	---
MAP4K5	11183	broad.mit.edu	37	14	50929418	50929418	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:50929418C>T	uc001wya.2	-	13	1221	c.901G>A	c.(901-903)GCA>ACA	p.A301T	MAP4K5_uc001wyb.2_Missense_Mutation_p.A301T|MAP4K5_uc010anv.1_Missense_Mutation_p.A301T	NM_006575	NP_006566	Q9Y4K4	M4K5_HUMAN	mitogen-activated protein kinase kinase kinase	301					activation of JUN kinase activity	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			large_intestine(1)	1	all_epithelial(31;0.000415)|Breast(41;0.0102)																	---	---	---	---
NIN	51199	broad.mit.edu	37	14	51233036	51233036	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51233036G>A	uc001wym.2	-	14	1815	c.1624C>T	c.(1624-1626)CGG>TGG	p.R542W	NIN_uc001wyi.2_Missense_Mutation_p.R542W|NIN_uc001wyj.2_RNA|NIN_uc001wyk.2_Missense_Mutation_p.R542W|NIN_uc010tqp.1_Missense_Mutation_p.R548W|NIN_uc001wyo.2_Missense_Mutation_p.R542W	NM_182946	NP_891991	Q8N4C6	NIN_HUMAN	ninein isoform 5	542	Potential.				centrosome localization	centrosome|microtubule	calcium ion binding|GTP binding|protein binding			skin(3)|ovary(1)|kidney(1)|central_nervous_system(1)	6	all_epithelial(31;0.00244)|Breast(41;0.127)							T	PDGFRB	MPD								---	---	---	---
ABHD12B	145447	broad.mit.edu	37	14	51370844	51370844	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51370844T>C	uc001wys.2	+	12	1010	c.995T>C	c.(994-996)GTT>GCT	p.V332A	ABHD12B_uc001wyq.2_Missense_Mutation_p.V225A|ABHD12B_uc001wyr.2_Missense_Mutation_p.V255A|ABHD12B_uc010any.2_RNA	NM_181533	NP_853511	Q7Z5M8	AB12B_HUMAN	abhydrolase domain containing 12B isoform b	332							hydrolase activity			breast(1)	1	all_epithelial(31;0.00481)|Breast(41;0.148)																	---	---	---	---
PYGL	5836	broad.mit.edu	37	14	51401903	51401903	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51401903G>A	uc001wyu.2	-	3	473	c.346C>T	c.(346-348)CTT>TTT	p.L116F	PYGL_uc010tqq.1_Missense_Mutation_p.L82F|PYGL_uc001wyv.2_5'UTR|PYGL_uc001wyw.3_Missense_Mutation_p.L116F	NM_002863	NP_002854	P06737	PYGL_HUMAN	liver glycogen phosphorylase isoform 1	116					glucose homeostasis|glucose metabolic process|glycogen catabolic process	cytosol|soluble fraction	AMP binding|ATP binding|bile acid binding|drug binding|glucose binding|glycogen phosphorylase activity|protein homodimerization activity|purine base binding|pyridoxal phosphate binding			skin(1)	1	all_epithelial(31;0.00825)|Breast(41;0.148)				Adenosine monophosphate(DB00131)|Pyridoxal Phosphate(DB00114)|Riboflavin(DB00140)													---	---	---	---
FRMD6	122786	broad.mit.edu	37	14	52182158	52182158	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52182158G>A	uc001wzd.2	+	10	1250	c.965G>A	c.(964-966)CGC>CAC	p.R322H	FRMD6_uc001wzb.2_Missense_Mutation_p.R314H|FRMD6_uc001wzc.2_Missense_Mutation_p.R314H|FRMD6_uc001wze.2_Missense_Mutation_p.R245H|FRMD6_uc001wzf.2_Missense_Mutation_p.R15H|FRMD6_uc001wzg.2_5'Flank	NM_152330	NP_689543	Q96NE9	FRMD6_HUMAN	FERM domain containing 6	322	FERM.					cytoskeleton|mitochondrion|plasma membrane	binding			ovary(1)|breast(1)|central_nervous_system(1)	3	all_epithelial(31;0.0163)|Breast(41;0.089)																	---	---	---	---
PTGDR	5729	broad.mit.edu	37	14	52734937	52734937	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52734937G>A	uc001wzq.2	+	1	507	c.405G>A	c.(403-405)GGG>GGA	p.G135G		NM_000953	NP_000944	Q13258	PD2R_HUMAN	prostaglandin D2 receptor	135	Cytoplasmic (Potential).					integral to membrane|plasma membrane	prostaglandin D receptor activity|protein binding			ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4	Breast(41;0.0639)|all_epithelial(31;0.0887)				Nedocromil(DB00716)													---	---	---	---
PTGDR	5729	broad.mit.edu	37	14	52735335	52735335	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:52735335C>T	uc001wzq.2	+	1	905	c.803C>T	c.(802-804)GCG>GTG	p.A268V		NM_000953	NP_000944	Q13258	PD2R_HUMAN	prostaglandin D2 receptor	268	Helical; Name=6; (Potential).					integral to membrane|plasma membrane	prostaglandin D receptor activity|protein binding			ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4	Breast(41;0.0639)|all_epithelial(31;0.0887)				Nedocromil(DB00716)													---	---	---	---
KIAA0831	22863	broad.mit.edu	37	14	55848683	55848683	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:55848683G>A	uc001xbx.1	-	6	910	c.874C>T	c.(874-876)CCT>TCT	p.P292S	FBXO34_uc001xbv.2_Intron|KIAA0831_uc001xbw.1_Missense_Mutation_p.P179S	NM_014924	NP_055739	Q6ZNE5	BAKOR_HUMAN	Barkor	292					autophagic vacuole assembly|positive regulation of autophagy	autophagic vacuole|endoplasmic reticulum|pre-autophagosomal structure membrane	protein binding				0																		---	---	---	---
C14orf101	54916	broad.mit.edu	37	14	57103318	57103318	+	Splice_Site	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:57103318T>C	uc001xcm.2	+	15	1991	c.1869_splice	c.e15+2	p.D623_splice	C14orf101_uc001xcj.2_Splice_Site|C14orf101_uc001xcn.2_Splice_Site|C14orf101_uc010trf.1_Splice_Site_p.D156_splice|C14orf101_uc001xco.2_Splice_Site_p.D156_splice	NM_017799	NP_060269			hypothetical protein LOC54916							integral to membrane				breast(1)|central_nervous_system(1)	2				OV - Ovarian serous cystadenocarcinoma(311;0.226)														---	---	---	---
SIX1	6495	broad.mit.edu	37	14	61115817	61115817	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61115817C>A	uc001xfb.3	-	1	339	c.91G>T	c.(91-93)GGC>TGC	p.G31C		NM_005982	NP_005973	Q15475	SIX1_HUMAN	SIX homeobox 1	31					branching involved in ureteric bud morphogenesis|embryonic cranial skeleton morphogenesis|epithelial cell differentiation|inner ear morphogenesis|mesonephric tubule formation|metanephric mesenchyme development|myoblast migration|negative regulation of neuron apoptosis|organ induction|pattern specification process|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of ureteric bud formation|protein localization to nucleus|regulation of branch elongation involved in ureteric bud branching|regulation of neuron differentiation|skeletal muscle tissue development|thymus development|thyroid gland development	nucleolus|transcription factor complex	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding				0				OV - Ovarian serous cystadenocarcinoma(108;0.0201)														---	---	---	---
PRKCH	5583	broad.mit.edu	37	14	61997178	61997178	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:61997178G>A	uc001xfn.2	+	12	1931	c.1626G>A	c.(1624-1626)GTG>GTA	p.V542V	PRKCH_uc010tsa.1_Silent_p.V381V|PRKCH_uc010tsb.1_Silent_p.V110V	NM_006255	NP_006246	P24723	KPCL_HUMAN	protein kinase C, eta	542	Protein kinase.				intracellular signal transduction|platelet activation	cytosol|plasma membrane	ATP binding|enzyme binding|metal ion binding|protein kinase C activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|large_intestine(1)|skin(1)	6				OV - Ovarian serous cystadenocarcinoma(108;0.045)|BRCA - Breast invasive adenocarcinoma(234;0.0906)|KIRC - Kidney renal clear cell carcinoma(182;0.182)														---	---	---	---
SYT16	83851	broad.mit.edu	37	14	62547925	62547925	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:62547925T>A	uc001xfu.1	+	4	1564	c.1367T>A	c.(1366-1368)CTC>CAC	p.L456H	SYT16_uc010tsd.1_3'UTR|SYT16_uc010tse.1_Missense_Mutation_p.L14H	NM_031914	NP_114120	Q17RD7	SYT16_HUMAN	synaptotagmin XIV-like	456										central_nervous_system(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)														---	---	---	---
KCNH5	27133	broad.mit.edu	37	14	63473200	63473200	+	Intron	SNP	A	G	G	rs36103415		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63473200A>G	uc001xfx.2	-						KCNH5_uc001xfy.2_Intron|KCNH5_uc001xfz.1_Intron|KCNH5_uc001xga.2_Intron	NM_139318	NP_647479			potassium voltage-gated channel, subfamily H,						regulation of transcription, DNA-dependent	integral to membrane	calmodulin binding|two-component sensor activity|voltage-gated potassium channel activity			ovary(4)|skin(4)|central_nervous_system(1)	9				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)														---	---	---	---
SYNE2	23224	broad.mit.edu	37	14	64463826	64463826	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64463826C>T	uc001xgm.2	+	24	3332	c.3102C>T	c.(3100-3102)TCC>TCT	p.S1034S	SYNE2_uc001xgl.2_Silent_p.S1034S	NM_015180	NP_055995	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	1034	Potential.|Cytoplasmic (Potential).				centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)														---	---	---	---
ESR2	2100	broad.mit.edu	37	14	64727288	64727288	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64727288C>T	uc001xha.1	-	5	1299	c.831G>A	c.(829-831)CCG>CCA	p.P277P	ESR2_uc001xgu.2_Silent_p.P277P|ESR2_uc001xgv.2_Silent_p.P277P|ESR2_uc001xgw.2_RNA|ESR2_uc001xgx.2_Silent_p.P277P|ESR2_uc001xgy.1_Silent_p.P277P|ESR2_uc001xgz.1_Silent_p.P277P|ESR2_uc010aqb.1_RNA|ESR2_uc010aqc.1_Silent_p.P277P|ESR2_uc010aqd.1_RNA	NM_001437	NP_001428	Q92731	ESR2_HUMAN	estrogen receptor beta isoform 1	277	Steroid-binding.				cell-cell signaling|negative regulation of cell growth|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	mitochondrion|nucleoplasm	enzyme binding|estrogen receptor activity|receptor antagonist activity|sequence-specific DNA binding transcription factor activity|steroid binding|transcription coactivator activity|zinc ion binding			central_nervous_system(2)|ovary(1)	3				all cancers(60;0.00916)|OV - Ovarian serous cystadenocarcinoma(108;0.0111)|BRCA - Breast invasive adenocarcinoma(234;0.0437)	Bicalutamide(DB01128)|Estradiol(DB00783)|Estramustine(DB01196)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Trilostane(DB01108)													---	---	---	---
HSPA2	3306	broad.mit.edu	37	14	65009184	65009184	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65009184C>T	uc001xhj.2	+	2	1693	c.1617C>T	c.(1615-1617)GTC>GTT	p.V539V	HSPA2_uc001xhk.3_Silent_p.V539V	NM_021979	NP_068814	P54652	HSP72_HUMAN	heat shock 70kDa protein 2	539					response to unfolded protein|spermatid development	cell surface	ATP binding|unfolded protein binding			skin(1)	1				all cancers(60;0.00515)|OV - Ovarian serous cystadenocarcinoma(108;0.00584)|BRCA - Breast invasive adenocarcinoma(234;0.045)														---	---	---	---
SPTB	6710	broad.mit.edu	37	14	65241879	65241879	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65241879C>A	uc001xht.2	-	22	4860	c.4806G>T	c.(4804-4806)GAG>GAT	p.E1602D	SPTB_uc001xhr.2_Missense_Mutation_p.E1602D|SPTB_uc001xhs.2_Missense_Mutation_p.E1602D|SPTB_uc001xhu.2_Missense_Mutation_p.E1602D|SPTB_uc010aqi.2_Missense_Mutation_p.E263D	NM_000347	NP_000338	P11277	SPTB1_HUMAN	spectrin beta isoform b	1602	Spectrin 13.				actin filament capping|axon guidance	cell surface|cytosol|intrinsic to internal side of plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	actin filament binding|structural constituent of cytoskeleton			ovary(7)|skin(2)|lung(1)|central_nervous_system(1)	11		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)														---	---	---	---
SPTB	6710	broad.mit.edu	37	14	65261188	65261188	+	Nonsense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65261188T>A	uc001xht.2	-	12	1846	c.1792A>T	c.(1792-1794)AAA>TAA	p.K598*	SPTB_uc001xhr.2_Nonsense_Mutation_p.K598*|SPTB_uc001xhs.2_Nonsense_Mutation_p.K598*|SPTB_uc001xhu.2_Nonsense_Mutation_p.K598*	NM_000347	NP_000338	P11277	SPTB1_HUMAN	spectrin beta isoform b	598	Spectrin 3.				actin filament capping|axon guidance	cell surface|cytosol|intrinsic to internal side of plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	actin filament binding|structural constituent of cytoskeleton			ovary(7)|skin(2)|lung(1)|central_nervous_system(1)	11		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)														---	---	---	---
PLEKHH1	57475	broad.mit.edu	37	14	68039983	68039983	+	Intron	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68039983C>A	uc001xjl.1	+						PLEKHH1_uc010tsw.1_Intron|PLEKHH1_uc001xjm.1_Intron|PLEKHH1_uc001xjn.1_Intron	NM_020715	NP_065766			pleckstrin homology domain containing, family H							cytoskeleton	binding				0				all cancers(60;0.000771)|OV - Ovarian serous cystadenocarcinoma(108;0.00502)|BRCA - Breast invasive adenocarcinoma(234;0.011)														---	---	---	---
EXD2	55218	broad.mit.edu	37	14	69701732	69701732	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69701732G>A	uc001xkt.2	+	7	1317	c.658G>A	c.(658-660)GTG>ATG	p.V220M	EXD2_uc001xku.2_Missense_Mutation_p.V90M|EXD2_uc001xkv.2_Missense_Mutation_p.V345M|EXD2_uc001xkw.2_Missense_Mutation_p.V220M|EXD2_uc010aqt.2_Missense_Mutation_p.V345M|EXD2_uc010tte.1_Missense_Mutation_p.V345M|EXD2_uc001xky.2_Missense_Mutation_p.V220M	NM_018199	NP_060669	Q9NVH0	EXD2_HUMAN	exonuclease 3'-5' domain containing 2	220					nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	intracellular	3'-5' exonuclease activity|nucleic acid binding				0																		---	---	---	---
SLC39A9	55334	broad.mit.edu	37	14	69908958	69908958	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:69908958T>C	uc001xle.2	+	3	1058	c.378T>C	c.(376-378)GGT>GGC	p.G126G	SLC39A9_uc010aqx.2_Silent_p.G126G|SLC39A9_uc001xlf.3_Silent_p.G126G|SLC39A9_uc001xlg.3_RNA	NM_018375	NP_060845	Q9NUM3	S39A9_HUMAN	solute carrier family 39 (zinc transporter),	126	Helical; (Potential).				zinc ion transport	integral to membrane	metal ion transmembrane transporter activity				0				all cancers(60;0.00299)|BRCA - Breast invasive adenocarcinoma(234;0.0145)|OV - Ovarian serous cystadenocarcinoma(108;0.0373)														---	---	---	---
KIAA0247	9766	broad.mit.edu	37	14	70171391	70171391	+	Silent	SNP	G	A	A	rs148189458	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70171391G>A	uc001xlk.2	+	4	706	c.390G>A	c.(388-390)GCG>GCA	p.A130A	KIAA0247_uc010aqz.2_Silent_p.A105A	NM_014734	NP_055549	Q92537	K0247_HUMAN	hypothetical protein LOC9766 precursor	130	Helical; (Potential).					integral to membrane				ovary(3)	3				all cancers(60;0.00155)|BRCA - Breast invasive adenocarcinoma(234;0.0164)|OV - Ovarian serous cystadenocarcinoma(108;0.0196)														---	---	---	---
MED6	10001	broad.mit.edu	37	14	71059660	71059660	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71059660A>G	uc001xmf.2	-	5	433	c.403T>C	c.(403-405)TCA>CCA	p.S135P	MED6_uc010tth.1_Missense_Mutation_p.S142P|MED6_uc010tti.1_Missense_Mutation_p.S135P|MED6_uc001xmg.1_Missense_Mutation_p.S135P|MED6_uc010ttj.1_3'UTR	NM_005466	NP_005457	O75586	MED6_HUMAN	mediator of RNA polymerase II transcription,	135					positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex	transcription coactivator activity				0				all cancers(60;0.00315)|BRCA - Breast invasive adenocarcinoma(234;0.00685)|OV - Ovarian serous cystadenocarcinoma(108;0.0352)														---	---	---	---
PCNX	22990	broad.mit.edu	37	14	71455358	71455358	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71455358C>T	uc001xmo.2	+	7	2832	c.2386C>T	c.(2386-2388)CGG>TGG	p.R796W	PCNX_uc001xmn.3_Missense_Mutation_p.R796W|PCNX_uc010are.1_Intron	NM_014982	NP_055797	Q96RV3	PCX1_HUMAN	pecanex-like 1	796						integral to membrane				ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)														---	---	---	---
SIPA1L1	26037	broad.mit.edu	37	14	72054805	72054805	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72054805A>G	uc001xms.2	+	2	564	c.216A>G	c.(214-216)CCA>CCG	p.P72P	SIPA1L1_uc001xmt.2_Silent_p.P72P|SIPA1L1_uc001xmu.2_Silent_p.P72P|SIPA1L1_uc001xmv.2_Silent_p.P72P	NM_015556	NP_056371	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like	72					actin cytoskeleton reorganization|activation of Rap GTPase activity|regulation of dendritic spine morphogenesis	cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane|synaptosome	GTPase activator activity			ovary(3)|breast(1)	4				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)														---	---	---	---
SIPA1L1	26037	broad.mit.edu	37	14	72138296	72138296	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:72138296G>C	uc001xms.2	+	8	3064	c.2716G>C	c.(2716-2718)GGG>CGG	p.G906R	SIPA1L1_uc001xmt.2_Missense_Mutation_p.G906R|SIPA1L1_uc001xmu.2_Missense_Mutation_p.G906R|SIPA1L1_uc001xmv.2_Missense_Mutation_p.G906R|SIPA1L1_uc010ttm.1_Missense_Mutation_p.G381R	NM_015556	NP_056371	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like	906					actin cytoskeleton reorganization|activation of Rap GTPase activity|regulation of dendritic spine morphogenesis	cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane|synaptosome	GTPase activator activity			ovary(3)|breast(1)	4				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)														---	---	---	---
ZFYVE1	53349	broad.mit.edu	37	14	73440894	73440894	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73440894G>A	uc001xnm.2	-	11	2635	c.1995C>T	c.(1993-1995)ACC>ACT	p.T665T	ZFYVE1_uc001xnl.2_Silent_p.T250T|ZFYVE1_uc010arj.2_Silent_p.T651T	NM_021260	NP_067083	Q9HBF4	ZFYV1_HUMAN	zinc finger, FYVE domain containing 1 isoform 1	665						endoplasmic reticulum|Golgi stack|perinuclear region of cytoplasm	1-phosphatidylinositol binding|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|zinc ion binding			skin(1)	1		all_lung(585;1.33e-09)		OV - Ovarian serous cystadenocarcinoma(108;1.6e-46)|BRCA - Breast invasive adenocarcinoma(234;0.00349)														---	---	---	---
ZFYVE1	53349	broad.mit.edu	37	14	73464590	73464590	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73464590A>C	uc001xnm.2	-	3	1557	c.917T>G	c.(916-918)GTC>GGC	p.V306G	ZFYVE1_uc010arj.2_Missense_Mutation_p.V306G	NM_021260	NP_067083	Q9HBF4	ZFYV1_HUMAN	zinc finger, FYVE domain containing 1 isoform 1	306						endoplasmic reticulum|Golgi stack|perinuclear region of cytoplasm	1-phosphatidylinositol binding|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|zinc ion binding			skin(1)	1		all_lung(585;1.33e-09)		OV - Ovarian serous cystadenocarcinoma(108;1.6e-46)|BRCA - Breast invasive adenocarcinoma(234;0.00349)														---	---	---	---
PAPLN	89932	broad.mit.edu	37	14	73727421	73727421	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73727421G>A	uc010ttx.1	+	16	2153	c.1990G>A	c.(1990-1992)GGG>AGG	p.G664R	PAPLN_uc001xnw.3_Missense_Mutation_p.G637R|PAPLN_uc010arl.2_RNA|PAPLN_uc010ttw.1_RNA|PAPLN_uc010tty.1_Missense_Mutation_p.G664R|PAPLN_uc010arm.2_5'UTR|PAPLN_uc010arn.2_5'Flank	NM_173462	NP_775733	O95428	PPN_HUMAN	papilin	664						proteinaceous extracellular matrix	metalloendopeptidase activity|serine-type endopeptidase inhibitor activity|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)														---	---	---	---
HEATR4	399671	broad.mit.edu	37	14	73989117	73989117	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:73989117C>A	uc010tub.1	-	3	1062	c.740G>T	c.(739-741)CGG>CTG	p.R247L	HEATR4_uc010tua.1_Missense_Mutation_p.R200L	NM_203309	NP_976054			HEAT repeat containing 4											ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00386)|OV - Ovarian serous cystadenocarcinoma(108;0.0719)														---	---	---	---
PNMA1	9240	broad.mit.edu	37	14	74179339	74179339	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74179339T>A	uc001xor.1	-	1	1790	c.1004A>T	c.(1003-1005)GAG>GTG	p.E335V		NM_006029	NP_006020	Q8ND90	PNMA1_HUMAN	paraneoplastic antigen MA1	335	Poly-Glu.				apoptosis|central nervous system development|inflammatory response to antigenic stimulus|spermatogenesis	cytoplasm|focal adhesion|nucleolus	protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00331)|KIRC - Kidney renal clear cell carcinoma(182;0.0797)														---	---	---	---
PNMA1	9240	broad.mit.edu	37	14	74179645	74179645	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74179645A>C	uc001xor.1	-	1	1484	c.698T>G	c.(697-699)CTT>CGT	p.L233R		NM_006029	NP_006020	Q8ND90	PNMA1_HUMAN	paraneoplastic antigen MA1	233					apoptosis|central nervous system development|inflammatory response to antigenic stimulus|spermatogenesis	cytoplasm|focal adhesion|nucleolus	protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00331)|KIRC - Kidney renal clear cell carcinoma(182;0.0797)														---	---	---	---
COQ6	51004	broad.mit.edu	37	14	74428015	74428015	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74428015T>C	uc001xph.2	+	9	1111	c.1031T>C	c.(1030-1032)GTT>GCT	p.V344A	ENTPD5_uc001xpi.2_Intron|COQ6_uc001xpe.2_Missense_Mutation_p.V269A|COQ6_uc001xpf.2_Missense_Mutation_p.V269A|COQ6_uc010tuk.1_Missense_Mutation_p.V319A|COQ6_uc001xpg.2_Missense_Mutation_p.V344A	NM_182476	NP_872282	Q9Y2Z9	COQ6_HUMAN	coenzyme Q6 homolog isoform a	344					ubiquinone biosynthetic process	mitochondrion	flavin adenine dinucleotide binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen				0				BRCA - Breast invasive adenocarcinoma(234;0.00337)														---	---	---	---
C14orf115	55237	broad.mit.edu	37	14	74825556	74825556	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:74825556G>A	uc001xpw.3	+	2	2261	c.2070G>A	c.(2068-2070)AAG>AAA	p.K690K		NM_018228	NP_060698	Q9H8Y1	VRTN_HUMAN	hypothetical protein LOC55237	690					transposition, DNA-mediated		DNA binding|transposase activity				0				BRCA - Breast invasive adenocarcinoma(234;0.00147)														---	---	---	---
KIAA0317	9870	broad.mit.edu	37	14	75136761	75136761	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75136761C>A	uc001xqb.2	-	14	2182	c.1677G>T	c.(1675-1677)GTG>GTT	p.V559V	KIAA0317_uc010tut.1_Silent_p.V398V	NM_001039479	NP_001034568	O15033	K0317_HUMAN	hypothetical protein LOC9870	559	HECT.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	integral to membrane|intracellular	ubiquitin-protein ligase activity			ovary(2)|kidney(1)|central_nervous_system(1)|pancreas(1)	5				BRCA - Breast invasive adenocarcinoma(234;0.00404)														---	---	---	---
KIAA0317	9870	broad.mit.edu	37	14	75137524	75137524	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75137524C>T	uc001xqb.2	-	13	2054	c.1549G>A	c.(1549-1551)GCA>ACA	p.A517T	KIAA0317_uc010tut.1_Missense_Mutation_p.A356T|KIAA0317_uc001xqc.2_Missense_Mutation_p.A517T	NM_001039479	NP_001034568	O15033	K0317_HUMAN	hypothetical protein LOC9870	517	HECT.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	integral to membrane|intracellular	ubiquitin-protein ligase activity			ovary(2)|kidney(1)|central_nervous_system(1)|pancreas(1)	5				BRCA - Breast invasive adenocarcinoma(234;0.00404)														---	---	---	---
PROX2	283571	broad.mit.edu	37	14	75329487	75329487	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75329487C>A	uc001xqr.1	-	1	1051	c.1051G>T	c.(1051-1053)GGT>TGT	p.G351C	PROX2_uc001xqq.1_Intron	NM_001080408	NP_001073877	Q3B8N5	PROX2_HUMAN	prospero homeobox 2	351					multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding				0			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00652)														---	---	---	---
TTLL5	23093	broad.mit.edu	37	14	76245942	76245942	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76245942G>A	uc001xrx.2	+	24	2617	c.2412G>A	c.(2410-2412)TTG>TTA	p.L804L	TTLL5_uc010ask.1_Silent_p.L818L|TTLL5_uc001xrz.2_Silent_p.L379L|TTLL5_uc001xry.1_RNA	NM_015072	NP_055887	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5	804					protein modification process|transcription, DNA-dependent	centrosome|cilium|microtubule basal body|nucleus	tubulin-tyrosine ligase activity			ovary(2)|central_nervous_system(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.029)														---	---	---	---
TTLL5	23093	broad.mit.edu	37	14	76259334	76259334	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:76259334G>A	uc001xrx.2	+	27	3267	c.3062G>A	c.(3061-3063)AGC>AAC	p.S1021N	TTLL5_uc010ask.1_Missense_Mutation_p.S1036N|TTLL5_uc001xrz.2_Missense_Mutation_p.S596N|TTLL5_uc001xsa.2_Missense_Mutation_p.S95N	NM_015072	NP_055887	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5	1021					protein modification process|transcription, DNA-dependent	centrosome|cilium|microtubule basal body|nucleus	tubulin-tyrosine ligase activity			ovary(2)|central_nervous_system(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.029)														---	---	---	---
POMT2	29954	broad.mit.edu	37	14	77746189	77746189	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77746189G>A	uc001xti.2	-	18	2069	c.1868C>T	c.(1867-1869)GCA>GTA	p.A623V	POMT2_uc001xth.1_Missense_Mutation_p.A321V	NM_013382	NP_037514	Q9UKY4	POMT2_HUMAN	protein-O-mannosyltransferase 2	623					protein O-linked glycosylation	endoplasmic reticulum membrane|integral to membrane	dolichyl-phosphate-mannose-protein mannosyltransferase activity|metal ion binding			ovary(1)	1			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0292)														---	---	---	---
VIPAR	63894	broad.mit.edu	37	14	77896080	77896080	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77896080G>A	uc001xtt.1	-	18	1548	c.1210C>T	c.(1210-1212)CCC>TCC	p.P404S	VIPAR_uc001xtu.1_Missense_Mutation_p.P404S|VIPAR_uc010tvj.1_Missense_Mutation_p.P355S|VIPAR_uc001xtv.1_Missense_Mutation_p.P404S	NM_022067	NP_071350	Q9H9C1	VIPAR_HUMAN	hypothetical protein LOC63894	404					endosome to lysosome transport|intracellular protein transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	early endosome|late endosome|recycling endosome	protein binding			central_nervous_system(1)	1																		---	---	---	---
AHSA1	10598	broad.mit.edu	37	14	77929054	77929054	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:77929054A>G	uc001xtw.2	+	4	584	c.424A>G	c.(424-426)AAA>GAA	p.K142E	AHSA1_uc010tvk.1_Missense_Mutation_p.K142E	NM_012111	NP_036243	O95433	AHSA1_HUMAN	activator of heat shock 90kDa protein ATPase	142					protein folding|response to stress	cytosol|endoplasmic reticulum	ATPase activator activity|chaperone binding				0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)														---	---	---	---
SPTLC2	9517	broad.mit.edu	37	14	78036801	78036801	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:78036801C>A	uc001xub.2	-	5	870	c.682G>T	c.(682-684)GGA>TGA	p.G228*		NM_004863	NP_004854	O15270	SPTC2_HUMAN	serine palmitoyltransferase, long chain base	228						integral to membrane|serine C-palmitoyltransferase complex	pyridoxal phosphate binding|serine C-palmitoyltransferase activity|transferase activity, transferring nitrogenous groups			upper_aerodigestive_tract(1)|ovary(1)	2			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0346)	L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)													---	---	---	---
TSHR	7253	broad.mit.edu	37	14	81554320	81554320	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81554320T>G	uc001xvd.1	+	4	496	c.340T>G	c.(340-342)TTA>GTA	p.L114V	TSHR_uc001xvb.1_Missense_Mutation_p.L114V|TSHR_uc001xvc.2_Missense_Mutation_p.L114V|TSHR_uc010tvs.1_Missense_Mutation_p.L114V	NM_000369	NP_000360	P16473	TSHR_HUMAN	thyroid stimulating hormone receptor isoform 1	114	Extracellular (Potential).|LRR 1.				cell-cell signaling|positive regulation of cell proliferation	integral to plasma membrane	protein binding|thyroid-stimulating hormone receptor activity			thyroid(289)|ovary(5)|lung(3)|kidney(1)|skin(1)	299				BRCA - Breast invasive adenocarcinoma(234;0.0402)	Thyrotropin Alfa(DB00024)			Mis		toxic thyroid adenoma	thyroid  adenoma	Hereditary nonautoimmune hyperthyroidism; subclinical hypothyroidism 						---	---	---	---
FLRT2	23768	broad.mit.edu	37	14	86089367	86089367	+	Silent	SNP	G	A	A	rs147101710	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:86089367G>A	uc001xvr.2	+	2	2276	c.1509G>A	c.(1507-1509)GCG>GCA	p.A503A	FLRT2_uc010atd.2_Silent_p.A503A	NM_013231	NP_037363	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	503	Fibronectin type-III.|Extracellular (Potential).				cell adhesion	integral to plasma membrane|proteinaceous extracellular matrix	protein binding, bridging|receptor signaling protein activity			ovary(3)|haematopoietic_and_lymphoid_tissue(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.0319)														---	---	---	---
PTPN21	11099	broad.mit.edu	37	14	88946027	88946027	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:88946027C>T	uc001xwv.3	-	13	2079	c.1748G>A	c.(1747-1749)CGC>CAC	p.R583H	PTPN21_uc010twc.1_Missense_Mutation_p.R379H	NM_007039	NP_008970	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type	583						cytoplasm|cytoskeleton	binding|protein tyrosine phosphatase activity			ovary(3)|skin(1)	4																		---	---	---	---
PTPN21	11099	broad.mit.edu	37	14	89016642	89016642	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89016642G>A	uc001xwv.3	-	2	451	c.120C>T	c.(118-120)TCC>TCT	p.S40S	PTPN21_uc010twc.1_5'UTR|PTPN21_uc010atf.1_Silent_p.S40S	NM_007039	NP_008970	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type	40	FERM.					cytoplasm|cytoskeleton	binding|protein tyrosine phosphatase activity			ovary(3)|skin(1)	4																		---	---	---	---
EML5	161436	broad.mit.edu	37	14	89091315	89091315	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:89091315G>A	uc001xxg.2	-	36	5083	c.4897C>T	c.(4897-4899)CCG>TCG	p.P1633S	EML5_uc001xxf.2_Missense_Mutation_p.P420S|EML5_uc001xxh.1_Missense_Mutation_p.P764S	NM_183387	NP_899243	Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like	1625	WD 24.					cytoplasm|microtubule				ovary(3)	3																		---	---	---	---
C14orf102	55051	broad.mit.edu	37	14	90759096	90759096	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:90759096C>T	uc001xyi.1	-	9	1818	c.1787G>A	c.(1786-1788)CGC>CAC	p.R596H	C14orf102_uc010atp.1_Missense_Mutation_p.R101H|C14orf102_uc001xyj.1_Missense_Mutation_p.R365H	NM_017970	NP_060440	Q9H7Z3	CN102_HUMAN	hypothetical protein LOC55051 isoform 1	596							protein binding			ovary(2)|lung(1)	3		all_cancers(154;0.118)		COAD - Colon adenocarcinoma(157;0.218)														---	---	---	---
SMEK1	55671	broad.mit.edu	37	14	91942311	91942311	+	Splice_Site	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:91942311C>A	uc001xzn.2	-	7	1933	c.1111_splice	c.e7-1	p.G371_splice	SMEK1_uc001xzm.2_Splice_Site_p.G371_splice|SMEK1_uc001xzo.2_Splice_Site_p.G371_splice|SMEK1_uc010atz.2_Splice_Site_p.G132_splice|SMEK1_uc001xzp.1_Splice_Site|SMEK1_uc001xzq.1_Intron	NM_032560	NP_115949			SMEK homolog 1, suppressor of mek1							microtubule organizing center|nucleus	protein binding				0		all_cancers(154;0.0691)|all_epithelial(191;0.219)		COAD - Colon adenocarcinoma(157;0.221)														---	---	---	---
TRIP11	9321	broad.mit.edu	37	14	92482149	92482149	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92482149T>C	uc001xzy.2	-	6	1502	c.714A>G	c.(712-714)GTA>GTG	p.V238V	TRIP11_uc010auf.1_Silent_p.V3V	NM_004239	NP_004230	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	238	Potential.				transcription from RNA polymerase II promoter	cytoskeleton|Golgi apparatus|membrane|nucleus	protein binding|transcription coactivator activity			ovary(6)|skin(2)|kidney(2)|central_nervous_system(1)|lung(1)|breast(1)	13				COAD - Colon adenocarcinoma(157;0.223)				T	PDGFRB	AML								---	---	---	---
ATXN3	4287	broad.mit.edu	37	14	92563031	92563031	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:92563031C>T	uc001yac.3	-	2	245	c.176G>A	c.(175-177)CGC>CAC	p.R59H	ATXN3_uc010aug.2_Missense_Mutation_p.R59H|ATXN3_uc001yad.3_Intron|ATXN3_uc010auh.2_Missense_Mutation_p.R59H|ATXN3_uc001yae.3_5'UTR|ATXN3_uc010twl.1_Intron	NM_004993	NP_004984	P54252	ATX3_HUMAN	ataxin 3 reference isoform	59	Josephin.				cell death|nervous system development|nucleotide-excision repair|regulation of transcription, DNA-dependent|synaptic transmission|transcription, DNA-dependent	cytoplasm|nuclear matrix|nucleoplasm	cysteine-type peptidase activity|protein binding				0		all_cancers(154;0.0768)		COAD - Colon adenocarcinoma(157;0.224)														---	---	---	---
RIN3	79890	broad.mit.edu	37	14	93022173	93022173	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93022173A>G	uc001yap.2	+	2	274	c.122A>G	c.(121-123)AAA>AGA	p.K41R	RIN3_uc010auk.2_5'UTR	NM_024832	NP_079108	Q8TB24	RIN3_HUMAN	Ras and Rab interactor 3	41					endocytosis|signal transduction	cytoplasmic membrane-bounded vesicle|early endosome	GTPase activator activity|Ras GTPase binding			lung(2)|ovary(1)	3		all_cancers(154;0.0701)																---	---	---	---
ITPK1	3705	broad.mit.edu	37	14	93408203	93408203	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93408203G>A	uc001ybg.2	-	11	1237	c.948C>T	c.(946-948)ATC>ATT	p.I316I	ITPK1_uc001ybe.2_Intron|ITPK1_uc001ybf.2_Silent_p.I197I|ITPK1_uc001ybh.2_Silent_p.I316I	NM_014216	NP_055031	Q13572	ITPK1_HUMAN	inositol 1,3,4-triphosphate 5/6 kinase isoform	316	ATP-grasp.				blood coagulation|inositol trisphosphate metabolic process|signal transduction	cytosol	ATP binding|hydrolase activity|inositol tetrakisphosphate 1-kinase activity|inositol-1,3,4-trisphosphate 5/6-kinase activity|isomerase activity|ligase activity|magnesium ion binding				0		all_cancers(154;0.077)|all_epithelial(191;0.247)		Epithelial(152;0.124)|all cancers(159;0.169)														---	---	---	---
SERPINA1	5265	broad.mit.edu	37	14	94845821	94845821	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94845821C>T	uc001ycx.3	-	4	1306	c.1045G>A	c.(1045-1047)GCA>ACA	p.A349T	SERPINA1_uc001ycw.3_RNA|SERPINA1_uc010auw.2_Missense_Mutation_p.A349T|SERPINA1_uc010aux.2_Missense_Mutation_p.A349T|SERPINA1_uc001ycy.3_Missense_Mutation_p.A349T|SERPINA1_uc010auy.2_Missense_Mutation_p.A349T|SERPINA1_uc001ycz.3_Missense_Mutation_p.A349T|SERPINA1_uc010auz.2_Missense_Mutation_p.A349T|SERPINA1_uc010ava.2_Missense_Mutation_p.A349T|SERPINA1_uc001ydb.3_Missense_Mutation_p.A349T|SERPINA1_uc010avb.2_Missense_Mutation_p.A349T|SERPINA1_uc001ydc.3_Missense_Mutation_p.A349T|SERPINA1_uc001yda.1_Missense_Mutation_p.A349T	NM_000295	NP_000286	P01009	A1AT_HUMAN	serine proteinase inhibitor, clade A, member 1	349					acute-phase response|platelet activation|platelet degranulation|regulation of proteolysis	extracellular space|platelet alpha granule lumen|proteinaceous extracellular matrix	protease binding|serine-type endopeptidase inhibitor activity			skin(1)	1		all_cancers(154;0.0649)|all_epithelial(191;0.223)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)	Alpha-1-proteinase inhibitor(DB00058)									Alpha-1-Antitrypsin_Deficiency				---	---	---	---
SERPINA11	256394	broad.mit.edu	37	14	94915091	94915091	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:94915091C>A	uc001ydd.1	-	2	81	c.21G>T	c.(19-21)TGG>TGT	p.W7C		NM_001080451	NP_001073920	Q86U17	SPA11_HUMAN	serpin peptidase inhibitor, clade A (alpha-1	7					regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			kidney(1)	1				COAD - Colon adenocarcinoma(157;0.211)														---	---	---	---
DICER1	23405	broad.mit.edu	37	14	95570364	95570364	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95570364C>T	uc001ydw.2	-	22	3551	c.3369G>A	c.(3367-3369)AAG>AAA	p.K1123K	DICER1_uc010avh.1_Silent_p.K21K|DICER1_uc001ydv.2_Silent_p.K1113K|DICER1_uc001ydx.2_Silent_p.K1123K|DICER1_uc001ydy.1_5'UTR	NM_030621	NP_085124	Q9UPY3	DICER_HUMAN	dicer1	1123					negative regulation of Schwann cell proliferation|negative regulation of transcription from RNA polymerase II promoter|nerve development|neuron projection morphogenesis|peripheral nervous system myelin formation|positive regulation of myelination|positive regulation of Schwann cell differentiation|pre-miRNA processing|production of siRNA involved in RNA interference|targeting of mRNA for destruction involved in RNA interference	cytosol|RNA-induced silencing complex	ATP binding|ATP-dependent helicase activity|double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity			skin(2)|ovary(1)|pancreas(1)|lung(1)	5		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)				Mis F|N			pleuropulmonary blastoma			DICER_1_syndrome_|Familial_Multinodular_Goiter_				---	---	---	---
DICER1	23405	broad.mit.edu	37	14	95574679	95574679	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95574679C>T	uc001ydw.2	-	16	2600	c.2418G>A	c.(2416-2418)ACG>ACA	p.T806T	DICER1_uc010avh.1_5'Flank|DICER1_uc001ydv.2_Silent_p.T796T|DICER1_uc001ydx.2_Silent_p.T806T	NM_030621	NP_085124	Q9UPY3	DICER_HUMAN	dicer1	806					negative regulation of Schwann cell proliferation|negative regulation of transcription from RNA polymerase II promoter|nerve development|neuron projection morphogenesis|peripheral nervous system myelin formation|positive regulation of myelination|positive regulation of Schwann cell differentiation|pre-miRNA processing|production of siRNA involved in RNA interference|targeting of mRNA for destruction involved in RNA interference	cytosol|RNA-induced silencing complex	ATP binding|ATP-dependent helicase activity|double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity	p.T806M(1)		skin(2)|ovary(1)|pancreas(1)|lung(1)	5		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)				Mis F|N			pleuropulmonary blastoma			DICER_1_syndrome_|Familial_Multinodular_Goiter_				---	---	---	---
DICER1	23405	broad.mit.edu	37	14	95582098	95582098	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95582098T>C	uc001ydw.2	-	12	1995	c.1813A>G	c.(1813-1815)ATG>GTG	p.M605V	DICER1_uc001ydv.2_Missense_Mutation_p.M595V|DICER1_uc001ydx.2_Missense_Mutation_p.M605V	NM_030621	NP_085124	Q9UPY3	DICER_HUMAN	dicer1	605					negative regulation of Schwann cell proliferation|negative regulation of transcription from RNA polymerase II promoter|nerve development|neuron projection morphogenesis|peripheral nervous system myelin formation|positive regulation of myelination|positive regulation of Schwann cell differentiation|pre-miRNA processing|production of siRNA involved in RNA interference|targeting of mRNA for destruction involved in RNA interference	cytosol|RNA-induced silencing complex	ATP binding|ATP-dependent helicase activity|double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity			skin(2)|ovary(1)|pancreas(1)|lung(1)	5		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)				Mis F|N			pleuropulmonary blastoma			DICER_1_syndrome_|Familial_Multinodular_Goiter_				---	---	---	---
DICER1	23405	broad.mit.edu	37	14	95598918	95598918	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:95598918G>T	uc001ydw.2	-	4	423	c.241C>A	c.(241-243)CTG>ATG	p.L81M	DICER1_uc001ydv.2_Missense_Mutation_p.L71M|DICER1_uc001ydx.2_Missense_Mutation_p.L81M|DICER1_uc001ydz.1_RNA|DICER1_uc001yea.1_RNA|DICER1_uc001yeb.1_RNA	NM_030621	NP_085124	Q9UPY3	DICER_HUMAN	dicer1	81	Helicase ATP-binding.			VLLTKELSYQIRGDFS -> STTLLKSCLYLDLGETSA (in Ref. 1; BAA78691).	negative regulation of Schwann cell proliferation|negative regulation of transcription from RNA polymerase II promoter|nerve development|neuron projection morphogenesis|peripheral nervous system myelin formation|positive regulation of myelination|positive regulation of Schwann cell differentiation|pre-miRNA processing|production of siRNA involved in RNA interference|targeting of mRNA for destruction involved in RNA interference	cytosol|RNA-induced silencing complex	ATP binding|ATP-dependent helicase activity|double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity			skin(2)|ovary(1)|pancreas(1)|lung(1)	5		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)				Mis F|N			pleuropulmonary blastoma			DICER_1_syndrome_|Familial_Multinodular_Goiter_				---	---	---	---
ATG2B	55102	broad.mit.edu	37	14	96769422	96769422	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96769422C>T	uc001yfi.2	-	33	5378	c.5013G>A	c.(5011-5013)ATG>ATA	p.M1671I		NM_018036	NP_060506	Q96BY7	ATG2B_HUMAN	ATG2 autophagy related 2 homolog B	1671										ovary(1)|kidney(1)|skin(1)	3		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)														---	---	---	---
ATG2B	55102	broad.mit.edu	37	14	96770877	96770877	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96770877T>C	uc001yfi.2	-	32	5162	c.4797A>G	c.(4795-4797)GGA>GGG	p.G1599G		NM_018036	NP_060506	Q96BY7	ATG2B_HUMAN	ATG2 autophagy related 2 homolog B	1599										ovary(1)|kidney(1)|skin(1)	3		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)														---	---	---	---
ATG2B	55102	broad.mit.edu	37	14	96784187	96784187	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:96784187A>G	uc001yfi.2	-	19	3250	c.2885T>C	c.(2884-2886)TTT>TCT	p.F962S		NM_018036	NP_060506	Q96BY7	ATG2B_HUMAN	ATG2 autophagy related 2 homolog B	962										ovary(1)|kidney(1)|skin(1)	3		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)														---	---	---	---
VRK1	7443	broad.mit.edu	37	14	97322890	97322890	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:97322890A>G	uc001yft.2	+	10	962	c.856A>G	c.(856-858)ATG>GTG	p.M286V		NM_003384	NP_003375	Q99986	VRK1_HUMAN	vaccinia related kinase 1	286	Protein kinase.					cytoplasm|nucleolus	ATP binding|protein binding|protein serine/threonine kinase activity			large_intestine(1)|stomach(1)	2		Melanoma(154;0.155)		COAD - Colon adenocarcinoma(157;0.234)														---	---	---	---
BCL11B	64919	broad.mit.edu	37	14	99723941	99723941	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99723941C>T	uc001yga.2	-	2	561	c.294G>A	c.(292-294)CCG>CCA	p.P98P	BCL11B_uc001ygb.2_Silent_p.P98P	NM_138576	NP_612808	Q9C0K0	BC11B_HUMAN	B-cell CLL/lymphoma 11B isoform 1	98						nucleus	zinc ion binding			central_nervous_system(8)|large_intestine(1)|lung(1)	10		Melanoma(154;0.0866)|all_epithelial(191;0.241)		COAD - Colon adenocarcinoma(157;0.103)				T	TLX3	T-ALL								---	---	---	---
SETD3	84193	broad.mit.edu	37	14	99879338	99879338	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:99879338T>C	uc001ygc.2	-	8	969	c.799A>G	c.(799-801)ACC>GCC	p.T267A	SETD3_uc001ygd.2_Missense_Mutation_p.T267A|SETD3_uc001ygf.2_Missense_Mutation_p.T267A	NM_032233	NP_115609	Q86TU7	SETD3_HUMAN	SET domain containing 3 isoform a	267	SET.				peptidyl-lysine dimethylation|peptidyl-lysine monomethylation|peptidyl-lysine trimethylation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	histone methyltransferase activity (H3-K36 specific)|transcription coactivator activity				0		all_cancers(154;0.224)|all_epithelial(191;0.0644)|Melanoma(154;0.0866)																---	---	---	---
CYP46A1	10858	broad.mit.edu	37	14	100191741	100191741	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:100191741T>C	uc001ygo.2	+	13	1190	c.1190T>C	c.(1189-1191)GTC>GCC	p.V397A	CYP46A1_uc001ygp.2_Missense_Mutation_p.V234A	NM_006668	NP_006659	Q9Y6A2	CP46A_HUMAN	cytochrome P450, family 46	397					bile acid biosynthetic process|cholesterol catabolic process|nervous system development|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	cholesterol 24-hydroxylase activity|electron carrier activity|heme binding|steroid hydroxylase activity				0		Melanoma(154;0.0866)|all_epithelial(191;0.179)																---	---	---	---
SNORD114-9	767585	broad.mit.edu	37	14	101431131	101431131	+	5'Flank	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101431131G>A	uc001yiz.2	+						SNORD114-8_uc001yiy.1_RNA|SNORD114-10_uc001yja.2_5'Flank	NR_003201				Homo sapiens small nucleolar RNA, C/D box 114-9 (SNORD114-9), non-coding RNA.												0																		---	---	---	---
DIO3	1735	broad.mit.edu	37	14	102028169	102028169	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102028169G>A	uc010txq.1	+	1	482	c.258G>A	c.(256-258)GCG>GCA	p.A86A	DIO3OS_uc001ykd.1_5'Flank|uc001yke.2_5'Flank|uc001ykf.2_5'Flank|uc001ykg.2_5'Flank|uc001ykh.3_5'Flank|MIR1247_hsa-mir-1247|MI0006382_5'Flank	NM_001362	NP_001353	P55073	IOD3_HUMAN	deiodinase, iodothyronine, type III	86	Extracellular (Potential).				cellular nitrogen compound metabolic process|hormone biosynthetic process	endosome membrane|integral to membrane|plasma membrane	thyroxine 5'-deiodinase activity|thyroxine 5-deiodinase activity			ovary(1)|central_nervous_system(1)|skin(1)	3		all_neural(303;0.185)																---	---	---	---
DYNC1H1	1778	broad.mit.edu	37	14	102452396	102452396	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102452396G>A	uc001yks.2	+	8	1998	c.1834G>A	c.(1834-1836)GTG>ATG	p.V612M		NM_001376	NP_001367	Q14204	DYHC1_HUMAN	cytoplasmic dynein 1 heavy chain 1	612	Interaction with DYNC1I2 (By similarity).|Stem (By similarity).				cytoplasmic mRNA processing body assembly|G2/M transition of mitotic cell cycle|microtubule-based movement|mitotic spindle organization|stress granule assembly|transport	centrosome|cytoplasmic dynein complex|cytosol|Golgi apparatus|microtubule	ATP binding|ATPase activity, coupled|microtubule motor activity|protein binding			ovary(7)|central_nervous_system(2)|pancreas(1)	10																		---	---	---	---
DYNC1H1	1778	broad.mit.edu	37	14	102478265	102478265	+	Silent	SNP	G	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102478265G>C	uc001yks.2	+	33	6836	c.6672G>C	c.(6670-6672)GGG>GGC	p.G2224G		NM_001376	NP_001367	Q14204	DYHC1_HUMAN	cytoplasmic dynein 1 heavy chain 1	2224	AAA 2 (By similarity).|ATP (Potential).				cytoplasmic mRNA processing body assembly|G2/M transition of mitotic cell cycle|microtubule-based movement|mitotic spindle organization|stress granule assembly|transport	centrosome|cytoplasmic dynein complex|cytosol|Golgi apparatus|microtubule	ATP binding|ATPase activity, coupled|microtubule motor activity|protein binding			ovary(7)|central_nervous_system(2)|pancreas(1)	10																		---	---	---	---
RAGE	5891	broad.mit.edu	37	14	102718302	102718302	+	Missense_Mutation	SNP	A	T	T	rs145834415	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102718302A>T	uc001ylm.2	-	5	540	c.314T>A	c.(313-315)ATT>AAT	p.I105N	RAGE_uc010txv.1_Missense_Mutation_p.I75N|RAGE_uc001yln.2_5'UTR	NM_014226	NP_055041	Q9UQ07	MOK_HUMAN	MAPK/MAK/MRK overlapping kinase	105	Protein kinase.				signal transduction	Golgi apparatus	ATP binding|cyclin-dependent protein kinase activity|protein binding			ovary(2)|breast(1)|central_nervous_system(1)	4																		---	---	---	---
TECPR2	9895	broad.mit.edu	37	14	102900787	102900787	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102900787G>A	uc001ylw.1	+	9	1781	c.1633G>A	c.(1633-1635)GAA>AAA	p.E545K	TECPR2_uc010awl.2_Missense_Mutation_p.E545K|TECPR2_uc010txx.1_Intron	NM_014844	NP_055659	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2	545							protein binding			lung(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
TECPR2	9895	broad.mit.edu	37	14	102900889	102900889	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:102900889C>T	uc001ylw.1	+	9	1883	c.1735C>T	c.(1735-1737)CGG>TGG	p.R579W	TECPR2_uc010awl.2_Missense_Mutation_p.R579W|TECPR2_uc010txx.1_Intron	NM_014844	NP_055659	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2	579							protein binding			lung(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
TNFAIP2	7127	broad.mit.edu	37	14	103601607	103601607	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103601607T>C	uc001ymm.1	+	11	2006	c.1875T>C	c.(1873-1875)AGT>AGC	p.S625S	TNFAIP2_uc010awo.1_Silent_p.S285S|TNFAIP2_uc010txz.1_Silent_p.S294S|TNFAIP2_uc010tya.1_Silent_p.S108S	NM_006291	NP_006282	Q03169	TNAP2_HUMAN	tumor necrosis factor, alpha-induced protein 2	625					angiogenesis|cell differentiation	extracellular space				central_nervous_system(1)	1		Melanoma(154;0.155)	Epithelial(46;0.191)															---	---	---	---
KLC1	3831	broad.mit.edu	37	14	104129098	104129098	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104129098G>A	uc001yno.2	+	5	939	c.631G>A	c.(631-633)GCG>ACG	p.A211T	KLC1_uc010tyd.1_Missense_Mutation_p.A370T|KLC1_uc010tye.1_Missense_Mutation_p.A207T|KLC1_uc001ynm.1_Missense_Mutation_p.A211T|KLC1_uc001ynn.1_Missense_Mutation_p.A207T|KLC1_uc010tyf.1_Missense_Mutation_p.A211T	NM_182923	NP_891553	Q07866	KLC1_HUMAN	kinesin light chain 1 isoform 2	211					blood coagulation|microtubule-based movement|stress granule disassembly	cytosol|kinesin complex|microtubule	microtubule motor activity|protein binding				0		Melanoma(154;0.155)|all_epithelial(191;0.19)																---	---	---	---
TDRD9	122402	broad.mit.edu	37	14	104473026	104473026	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:104473026G>A	uc001yom.3	+	17	1953	c.1923G>A	c.(1921-1923)CGG>CGA	p.R641R	TDRD9_uc001yon.3_Silent_p.R379R	NM_153046	NP_694591	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	641					cell differentiation|DNA methylation involved in gamete generation|fertilization|gene silencing by RNA|male meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	nucleus|piP-body	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(2)|central_nervous_system(1)	3		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)																---	---	---	---
ADSSL1	122622	broad.mit.edu	37	14	105209428	105209428	+	Missense_Mutation	SNP	C	T	T	rs150880740		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105209428C>T	uc001ypd.2	+	10	1047	c.973C>T	c.(973-975)CGC>TGC	p.R325C	INF2_uc010tyi.1_Intron|ADSSL1_uc001ype.2_Missense_Mutation_p.R368C|ADSSL1_uc001ypf.2_RNA	NM_152328	NP_689541	Q8N142	PURA1_HUMAN	adenylosuccinate synthase like 1 isoform 2	325					AMP biosynthetic process|immune system process|purine base metabolic process	cytosol	adenylosuccinate synthase activity|GTP binding|magnesium ion binding|phosphate binding			ovary(1)|central_nervous_system(1)	2		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00153)|OV - Ovarian serous cystadenocarcinoma(23;0.0148)|Epithelial(46;0.0396)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.18)	L-Aspartic Acid(DB00128)													---	---	---	---
AKT1	207	broad.mit.edu	37	14	105238768	105238768	+	Silent	SNP	G	A	A	rs151254374		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105238768G>A	uc001ypk.2	-	12	1748	c.1194C>T	c.(1192-1194)GAC>GAT	p.D398D	INF2_uc010tyi.1_Intron|AKT1_uc001ypl.2_Silent_p.D398D|AKT1_uc010axa.2_Silent_p.D398D|AKT1_uc001ypm.2_Silent_p.D398D|AKT1_uc001ypn.2_Silent_p.D398D|AKT1_uc001ypj.2_5'Flank|AKT1_uc010tyk.1_Silent_p.D336D	NM_005163	NP_005154	P31749	AKT1_HUMAN	AKT1 kinase	398	Protein kinase.				activation of pro-apoptotic gene products|activation-induced cell death of T cells|endocrine pancreas development|G-protein coupled receptor protein signaling pathway|glucose metabolic process|glycogen biosynthetic process|induction of apoptosis by intracellular signals|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|mRNA metabolic process|negative regulation of fatty acid beta-oxidation|negative regulation of plasma membrane long-chain fatty acid transport|negative regulation of protein kinase activity|nerve growth factor receptor signaling pathway|nitric oxide biosynthetic process|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of blood vessel endothelial cell migration|positive regulation of cell growth|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of establishment of protein localization in plasma membrane|positive regulation of fat cell differentiation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of lipid biosynthetic process|positive regulation of nitric oxide biosynthetic process|positive regulation of nitric-oxide synthase activity|positive regulation of peptidyl-serine phosphorylation|positive regulation of sequence-specific DNA binding transcription factor activity|protein autophosphorylation|protein import into nucleus, translocation|regulation of neuron projection development|regulation of translation|response to fluid shear stress|response to heat|response to UV-A|T cell costimulation	cytosol|nucleoplasm|plasma membrane	enzyme binding|identical protein binding|nitric-oxide synthase regulator activity|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|protein serine/threonine kinase activity			breast(86)|urinary_tract(12)|thyroid(10)|lung(7)|endometrium(5)|large_intestine(4)|skin(4)|prostate(3)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|NS(1)	134		all_cancers(154;3.77e-06)|all_lung(585;3.24e-07)|all_epithelial(191;3.45e-05)|all_neural(303;0.0459)|Melanoma(154;0.155)	all cancers(16;0.000486)|OV - Ovarian serous cystadenocarcinoma(23;0.00647)|Epithelial(46;0.0153)|GBM - Glioblastoma multiforme(11;0.116)	all cancers(159;0.0107)|OV - Ovarian serous cystadenocarcinoma(161;0.0132)|Epithelial(152;0.243)	Adenosine triphosphate(DB00171)|Arsenic trioxide(DB01169)		1	Mis		breast|colorectal|ovarian|NSCLC								---	---	---	---
AHNAK2	113146	broad.mit.edu	37	14	105413846	105413846	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105413846A>G	uc010axc.1	-	7	8062	c.7942T>C	c.(7942-7944)TTC>CTC	p.F2648L	AHNAK2_uc001ypx.2_Missense_Mutation_p.F2548L	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2648						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)															---	---	---	---
AHNAK2	113146	broad.mit.edu	37	14	105414893	105414893	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105414893G>A	uc010axc.1	-	7	7015	c.6895C>T	c.(6895-6897)CGG>TGG	p.R2299W	AHNAK2_uc001ypx.2_Missense_Mutation_p.R2199W	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2299						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)															---	---	---	---
AHNAK2	113146	broad.mit.edu	37	14	105418864	105418864	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105418864A>T	uc010axc.1	-	7	3044	c.2924T>A	c.(2923-2925)CTG>CAG	p.L975Q	AHNAK2_uc001ypx.2_Missense_Mutation_p.L875Q	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	975						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)															---	---	---	---
C14orf79	122616	broad.mit.edu	37	14	105457853	105457853	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105457853G>A	uc001ypy.1	+	3	748	c.595G>A	c.(595-597)GCC>ACC	p.A199T	C14orf79_uc001ypz.1_RNA|C14orf79_uc010tym.1_RNA	NM_174891	NP_777551	Q96F83	CN079_HUMAN	hypothetical protein LOC122616	199											0		all_cancers(154;0.0798)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.00326)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0181)															---	---	---	---
CDCA4	55038	broad.mit.edu	37	14	105478046	105478046	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105478046G>A	uc001yqa.2	-	2	317	c.221C>T	c.(220-222)ACG>ATG	p.T74M	CDCA4_uc001yqb.2_Missense_Mutation_p.T74M	NM_145701	NP_663747	Q9BXL8	CDCA4_HUMAN	cell division cycle associated 4	74	SERTA.					nucleus				ovary(1)	1		all_cancers(154;0.0798)|Melanoma(154;0.155)|all_epithelial(191;0.183)	OV - Ovarian serous cystadenocarcinoma(23;0.00778)|all cancers(16;0.00936)|Epithelial(46;0.0227)	Epithelial(152;0.142)														---	---	---	---
BRF1	2972	broad.mit.edu	37	14	105688094	105688094	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105688094G>A	uc001yqp.2	-	11	1569	c.1206C>T	c.(1204-1206)GGC>GGT	p.G402G	BRF1_uc010tyo.1_Silent_p.G287G|BRF1_uc010typ.1_Silent_p.G287G|BRF1_uc001yqk.2_5'UTR|BRF1_uc001yql.2_Silent_p.G198G|BRF1_uc001yqo.2_Silent_p.G164G|BRF1_uc010axg.1_Silent_p.G375G|BRF1_uc001yqn.2_Intron|BRF1_uc010axh.1_Intron|BRF1_uc010axi.1_5'UTR	NM_001519	NP_001510	Q92994	TF3B_HUMAN	transcription initiation factor IIIB isoform 1	402					positive regulation of transcription, DNA-dependent|rRNA transcription|transcription initiation from RNA polymerase III promoter|tRNA transcription	transcription factor TFIIIB complex	translation initiation factor activity|zinc ion binding			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4		all_cancers(154;0.0231)|all_epithelial(191;0.0694)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00753)|all cancers(16;0.00925)|Epithelial(46;0.0221)	Epithelial(152;0.14)														---	---	---	---
BRF1	2972	broad.mit.edu	37	14	105695168	105695168	+	Silent	SNP	C	T	T	rs140779507	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105695168C>T	uc001yqp.2	-	7	1140	c.777G>A	c.(775-777)ACG>ACA	p.T259T	BRF1_uc010tyo.1_Silent_p.T144T|BRF1_uc010typ.1_Silent_p.T144T|BRF1_uc001yql.2_Silent_p.T55T|BRF1_uc001yqo.2_Silent_p.T21T|BRF1_uc010axg.1_Silent_p.T232T|BRF1_uc001yqn.2_RNA|BRF1_uc010axh.1_RNA|BRF1_uc010axj.1_RNA	NM_001519	NP_001510	Q92994	TF3B_HUMAN	transcription initiation factor IIIB isoform 1	259	2.				positive regulation of transcription, DNA-dependent|rRNA transcription|transcription initiation from RNA polymerase III promoter|tRNA transcription	transcription factor TFIIIB complex	translation initiation factor activity|zinc ion binding			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4		all_cancers(154;0.0231)|all_epithelial(191;0.0694)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00753)|all cancers(16;0.00925)|Epithelial(46;0.0221)	Epithelial(152;0.14)														---	---	---	---
BRF1	2972	broad.mit.edu	37	14	105739062	105739062	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105739062C>T	uc001yqp.2	-	3	798	c.435G>A	c.(433-435)ACG>ACA	p.T145T	BRF1_uc010tyo.1_Silent_p.T30T|BRF1_uc010typ.1_Silent_p.T30T|BRF1_uc010axg.1_Silent_p.T118T|BRF1_uc001yqr.2_Silent_p.T145T	NM_001519	NP_001510	Q92994	TF3B_HUMAN	transcription initiation factor IIIB isoform 1	145	1.				positive regulation of transcription, DNA-dependent|rRNA transcription|transcription initiation from RNA polymerase III promoter|tRNA transcription	transcription factor TFIIIB complex	translation initiation factor activity|zinc ion binding			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4		all_cancers(154;0.0231)|all_epithelial(191;0.0694)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00753)|all cancers(16;0.00925)|Epithelial(46;0.0221)	Epithelial(152;0.14)														---	---	---	---
BRF1	2972	broad.mit.edu	37	14	105739066	105739066	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105739066C>T	uc001yqp.2	-	3	794	c.431G>A	c.(430-432)GGC>GAC	p.G144D	BRF1_uc010tyo.1_Missense_Mutation_p.G29D|BRF1_uc010typ.1_Missense_Mutation_p.G29D|BRF1_uc010axg.1_Missense_Mutation_p.G117D|BRF1_uc001yqr.2_Missense_Mutation_p.G144D	NM_001519	NP_001510	Q92994	TF3B_HUMAN	transcription initiation factor IIIB isoform 1	144	1.				positive regulation of transcription, DNA-dependent|rRNA transcription|transcription initiation from RNA polymerase III promoter|tRNA transcription	transcription factor TFIIIB complex	translation initiation factor activity|zinc ion binding			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4		all_cancers(154;0.0231)|all_epithelial(191;0.0694)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00753)|all cancers(16;0.00925)|Epithelial(46;0.0221)	Epithelial(152;0.14)														---	---	---	---
PACS2	23241	broad.mit.edu	37	14	105843177	105843177	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105843177A>G	uc001yqt.2	+	9	1049	c.874A>G	c.(874-876)ACC>GCC	p.T292A	PACS2_uc001yqs.2_Missense_Mutation_p.T217A|PACS2_uc001yqv.2_Missense_Mutation_p.T292A|PACS2_uc001yqu.2_Missense_Mutation_p.T292A	NM_015197	NP_056012	Q86VP3	PACS2_HUMAN	phosphofurin acidic cluster sorting protein 2	292					apoptosis|interspecies interaction between organisms	endoplasmic reticulum lumen|mitochondrion				pancreas(1)	1		all_cancers(154;0.0351)|all_epithelial(191;0.153)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.0145)|Epithelial(46;0.036)	Epithelial(152;0.138)														---	---	---	---
MTA1	9112	broad.mit.edu	37	14	105916463	105916463	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105916463C>T	uc001yqx.2	+	5	497	c.310C>T	c.(310-312)CGG>TGG	p.R104W	MTA1_uc001yqy.2_RNA|MTA1_uc001yqz.1_Missense_Mutation_p.R18W|MTA1_uc001yra.1_Missense_Mutation_p.R18W	NM_004689	NP_004680	Q13330	MTA1_HUMAN	metastasis associated protein	104	BAH.				signal transduction	cytoplasm|nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(154;0.0293)|all_epithelial(191;0.128)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00897)|Epithelial(46;0.026)	Epithelial(152;0.19)														---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106091303	106091303	+	RNA	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106091303C>A	uc010tyt.1	-	3647		c.62205G>T			uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron					Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106111021	106111021	+	RNA	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106111021G>A	uc010tyt.1	-	3640		c.60740C>T			uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_RNA					Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106208430	106208430	+	RNA	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106208430T>G	uc010tyt.1	-	3627		c.58784A>C			uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron|uc001yse.2_Missense_Mutation_p.K23T|uc001ysf.2_Missense_Mutation_p.K23T					Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	106236064	106236064	+	RNA	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106236064C>A	uc010tyt.1	-	3616		c.57880G>T			uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron|uc001yse.2_Intron|uc001ysf.2_Intron|uc001ysh.1_RNA|uc001ysi.1_RNA					Parts of antibodies, mostly variable regions.												0																		---	---	---	---
ADAM6	8755	broad.mit.edu	37	14	107211375	107211375	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107211375C>T	uc010tyt.1	-											Parts of antibodies, mostly variable regions.												0																		---	---	---	---
CYFIP1	23191	broad.mit.edu	37	15	22955288	22955288	+	Intron	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22955288T>A	uc001yus.2	+						CYFIP1_uc001yut.2_Intron|CYFIP1_uc010aya.1_Intron|CYFIP1_uc001yuu.2_5'Flank	NM_014608	NP_055423			cytoplasmic FMR1 interacting protein 1 isoform						axon extension|lamellipodium assembly|regulation of cell shape|ruffle organization	cell junction|lamellipodium|mRNA cap binding complex|perinuclear region of cytoplasm|ruffle|synapse|synaptosome	actin filament binding|Rac GTPase binding			ovary(4)|pancreas(3)|liver(1)|skin(1)	9		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.22e-06)|Epithelial(43;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00101)														---	---	---	---
NIPA2	81614	broad.mit.edu	37	15	23021252	23021252	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23021252T>C	uc001yux.2	-	4	698	c.85A>G	c.(85-87)ATT>GTT	p.I29V	NIPA2_uc001yuy.2_Missense_Mutation_p.I29V|NIPA2_uc001yuz.2_Missense_Mutation_p.I29V|NIPA2_uc001yva.2_Missense_Mutation_p.I29V|NIPA2_uc001yvb.2_Missense_Mutation_p.I29V|NIPA2_uc010ayb.2_Missense_Mutation_p.I29V	NM_030922	NP_112184	Q8N8Q9	NIPA2_HUMAN	non imprinted in Prader-Willi/Angelman syndrome	29	Helical; (Potential).					early endosome|integral to membrane|plasma membrane				haematopoietic_and_lymphoid_tissue(1)	1		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;1.48e-06)|Epithelial(43;1.44e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000353)														---	---	---	---
MAGEL2	54551	broad.mit.edu	37	15	23889820	23889820	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23889820C>T	uc001ywj.3	-	1	1356	c.1261G>A	c.(1261-1263)GCA>ACA	p.A421T		NM_019066	NP_061939			MAGE-like protein 2												0		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;1.84e-06)|Epithelial(43;1.2e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)														---	---	---	---
C15orf2	23742	broad.mit.edu	37	15	24921158	24921158	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:24921158C>T	uc001ywo.2	+	1	618	c.144C>T	c.(142-144)CGC>CGT	p.R48R		NM_018958	NP_061831	Q9NZP6	CO002_HUMAN	hypothetical protein LOC23742	48					cell differentiation|multicellular organismal development|spermatogenesis					ovary(2)|large_intestine(2)|skin(2)|kidney(1)|central_nervous_system(1)	8		all_cancers(20;2.14e-21)|all_epithelial(15;4.77e-19)|Lung NSC(15;1.43e-14)|all_lung(15;9.57e-14)|Breast(32;0.00086)		all cancers(64;3.19e-24)|Epithelial(43;2.67e-17)|GBM - Glioblastoma multiforme(186;7.36e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000273)|Lung(196;0.229)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	25485014	25485014	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25485014T>C	uc001zae.2	+						SNORD115-38_uc001zag.1_RNA|SNORD115-39_uc001zah.1_5'Flank					Homo sapiens clone Rt-16 SNURF-SNRPN mRNA, downstream untranslated exons, alternatively spliced.																														---	---	---	---
ATP10A	57194	broad.mit.edu	37	15	25981255	25981255	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25981255C>T	uc010ayu.2	-	3	794	c.688G>A	c.(688-690)GTG>ATG	p.V230M		NM_024490	NP_077816	O60312	AT10A_HUMAN	ATPase, class V, type 10A	230	Cytoplasmic (Potential).				ATP biosynthetic process|regulation of cell shape	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			pancreas(2)|ovary(1)|breast(1)|liver(1)	5		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)														---	---	---	---
GABRB3	2562	broad.mit.edu	37	15	26806306	26806306	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26806306T>A	uc001zaz.2	-	8	995	c.853A>T	c.(853-855)ACA>TCA	p.T285S	GABRB3_uc010uae.1_Missense_Mutation_p.T200S|GABRB3_uc001zba.2_Missense_Mutation_p.T285S|GABRB3_uc001zbb.2_Missense_Mutation_p.T341S	NM_000814	NP_000805	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta	285	Helical; (Probable).				synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			upper_aerodigestive_tract(1)|ovary(1)|lung(1)|liver(1)|central_nervous_system(1)	5		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)													---	---	---	---
GABRB3	2562	broad.mit.edu	37	15	26812720	26812720	+	Intron	SNP	G	T	T	rs75812437		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:26812720G>T	uc001zaz.2	-						GABRB3_uc010uae.1_Intron|GABRB3_uc001zba.2_Intron|GABRB3_uc001zbb.2_Intron	NM_000814	NP_000805			gamma-aminobutyric acid (GABA) A receptor, beta						synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			upper_aerodigestive_tract(1)|ovary(1)|lung(1)|liver(1)|central_nervous_system(1)	5		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)													---	---	---	---
HERC2	8924	broad.mit.edu	37	15	28459890	28459890	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28459890G>A	uc001zbj.2	-	40	6375	c.6269C>T	c.(6268-6270)GCG>GTG	p.A2090V		NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2	2090					DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)														---	---	---	---
HERC2	8924	broad.mit.edu	37	15	28474855	28474855	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28474855C>T	uc001zbj.2	-	32	5054	c.4948G>A	c.(4948-4950)GAT>AAT	p.D1650N		NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2	1650					DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)														---	---	---	---
HERC2	8924	broad.mit.edu	37	15	28501109	28501109	+	Missense_Mutation	SNP	C	T	T	rs112608670		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28501109C>T	uc001zbj.2	-	19	2886	c.2780G>A	c.(2779-2781)CGT>CAT	p.R927H	HERC2_uc001zbl.1_Missense_Mutation_p.R622H	NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2	927					DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)														---	---	---	---
HERC2	8924	broad.mit.edu	37	15	28519546	28519546	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28519546C>A	uc001zbj.2	-	7	797	c.691G>T	c.(691-693)GCC>TCC	p.A231S	HERC2_uc001zbl.1_5'UTR	NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2	231					DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)														---	---	---	---
APBA2	321	broad.mit.edu	37	15	29409315	29409315	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:29409315G>T	uc001zck.2	+	14	2436	c.2229G>T	c.(2227-2229)CAG>CAT	p.Q743H	APBA2_uc010uat.1_Missense_Mutation_p.Q731H|APBA2_uc001zcl.2_Missense_Mutation_p.Q731H	NM_005503	NP_005494	Q99767	APBA2_HUMAN	amyloid beta A4 precursor protein-binding,	743					nervous system development|protein transport		protein binding				0		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)														---	---	---	---
MTMR15	22909	broad.mit.edu	37	15	31196980	31196980	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31196980A>G	uc001zff.2	+	2	405	c.114A>G	c.(112-114)CCA>CCG	p.P38P	MTMR15_uc001zfc.3_Silent_p.P38P|MTMR15_uc010azw.2_Silent_p.P38P|MTMR15_uc001zfd.3_Silent_p.P38P|MTMR15_uc001zfe.2_5'UTR	NM_014967	NP_055782	Q9Y2M0	FAN1_HUMAN	myotubularin related protein 15 isoform a	38					double-strand break repair via homologous recombination|nucleotide-excision repair, DNA incision	nucleus	5'-3' exonuclease activity|5'-flap endonuclease activity|DNA binding|magnesium ion binding|phosphodiesterase I activity|ubiquitin binding				0		all_lung(180;2.23e-09)		all cancers(64;4.72e-15)|Epithelial(43;5.4e-11)|GBM - Glioblastoma multiforme(186;0.000136)|BRCA - Breast invasive adenocarcinoma(123;0.00402)|Lung(196;0.168)									Direct_reversal_of_damage|Editing_and_processing_nucleases					---	---	---	---
OTUD7A	161725	broad.mit.edu	37	15	31776612	31776612	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31776612A>T	uc001zfq.2	-	11	1759	c.1666T>A	c.(1666-1668)TCG>ACG	p.S556T	OTUD7A_uc001zfr.2_Missense_Mutation_p.S563T	NM_130901	NP_570971	Q8TE49	OTU7A_HUMAN	OTU domain containing 7A	556						cytoplasm|nucleus	cysteine-type peptidase activity|DNA binding|zinc ion binding			pancreas(1)|skin(1)	2		all_lung(180;1.6e-09)		all cancers(64;2.44e-19)|Epithelial(43;6.82e-14)|GBM - Glioblastoma multiforme(186;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00189)|Lung(196;0.208)														---	---	---	---
FMN1	342184	broad.mit.edu	37	15	33091085	33091085	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33091085G>A	uc001zhf.3	-	15	3381	c.3381C>T	c.(3379-3381)TAC>TAT	p.Y1127Y		NM_001103184	NP_001096654	Q68DA7	FMN1_HUMAN	formin 1	1350	FH2.				actin cytoskeleton organization	actin cytoskeleton|adherens junction|cytoplasm|nucleus	actin binding			ovary(1)	1		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)														---	---	---	---
FMN1	342184	broad.mit.edu	37	15	33358922	33358922	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33358922G>T	uc001zhf.3	-	1	1164	c.1164C>A	c.(1162-1164)ACC>ACA	p.T388T	FMN1_uc001zhg.2_Silent_p.T388T	NM_001103184	NP_001096654	Q68DA7	FMN1_HUMAN	formin 1	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					actin cytoskeleton organization	actin cytoskeleton|adherens junction|cytoplasm|nucleus	actin binding			ovary(1)	1		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)														---	---	---	---
RYR3	6263	broad.mit.edu	37	15	33878301	33878301	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33878301A>G	uc001zhi.2	+	16	1842	c.1772A>G	c.(1771-1773)CAC>CGC	p.H591R	RYR3_uc010bar.2_Missense_Mutation_p.H591R	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	591	Cytoplasmic (By similarity).|B30.2/SPRY 1.				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)														---	---	---	---
RYR3	6263	broad.mit.edu	37	15	33926831	33926831	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33926831A>G	uc001zhi.2	+	25	3142	c.3072A>G	c.(3070-3072)TTA>TTG	p.L1024L	RYR3_uc010bar.2_Silent_p.L1024L	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	1024	2.|B30.2/SPRY 2.|Cytoplasmic (By similarity).|4 X approximate repeats.				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)														---	---	---	---
RYR3	6263	broad.mit.edu	37	15	33988480	33988480	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33988480G>T	uc001zhi.2	+	39	5992	c.5922G>T	c.(5920-5922)CAG>CAT	p.Q1974H	RYR3_uc010bar.2_Missense_Mutation_p.Q1974H	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	1974	4 X approximate repeats.|Cytoplasmic (By similarity).				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)														---	---	---	---
C15orf55	256646	broad.mit.edu	37	15	34646043	34646043	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34646043C>A	uc001zif.2	+	4	1116	c.961C>A	c.(961-963)CCC>ACC	p.P321T	C15orf55_uc010ucc.1_Missense_Mutation_p.P349T|C15orf55_uc010ucd.1_Missense_Mutation_p.P339T	NM_175741	NP_786883	Q86Y26	NUT_HUMAN	nuclear protein in testis	321						cytoplasm|nucleus			BRD4_ENST00000263377/C15orf55(24)|BRD3/C15orf55(3)	midline_organs(25)|ovary(2)|lung(2)|skin(1)	30		all_lung(180;2.78e-08)		all cancers(64;4.53e-18)|GBM - Glioblastoma multiforme(113;8.29e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0249)				T	BRD3|BRD4	lethal midline carcinoma								---	---	---	---
C15orf55	256646	broad.mit.edu	37	15	34648116	34648116	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34648116G>T	uc001zif.2	+	7	1978	c.1823G>T	c.(1822-1824)GGG>GTG	p.G608V	C15orf55_uc010ucc.1_Missense_Mutation_p.G636V|C15orf55_uc010ucd.1_Missense_Mutation_p.G626V	NM_175741	NP_786883	Q86Y26	NUT_HUMAN	nuclear protein in testis	608						cytoplasm|nucleus			BRD4_ENST00000263377/C15orf55(24)|BRD3/C15orf55(3)	midline_organs(25)|ovary(2)|lung(2)|skin(1)	30		all_lung(180;2.78e-08)		all cancers(64;4.53e-18)|GBM - Glioblastoma multiforme(113;8.29e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0249)				T	BRD3|BRD4	lethal midline carcinoma								---	---	---	---
ACTC1	70	broad.mit.edu	37	15	35084705	35084705	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:35084705G>A	uc001ziu.1	-	4	763	c.520C>T	c.(520-522)CCC>TCC	p.P174S	uc001zit.1_Intron	NM_005159	NP_005150	P68032	ACTC_HUMAN	cardiac muscle alpha actin 1 proprotein	174					apoptosis|cardiac muscle tissue morphogenesis|cardiac myofibril assembly|muscle filament sliding|skeletal muscle thin filament assembly	actomyosin, actin part|cytosol|I band	ATP binding|ATPase activity|myosin binding			upper_aerodigestive_tract(1)|ovary(1)	2		all_lung(180;2.3e-08)		all cancers(64;5.83e-19)|GBM - Glioblastoma multiforme(113;1.98e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0244)														---	---	---	---
THBS1	7057	broad.mit.edu	37	15	39876348	39876348	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:39876348G>A	uc001zkh.2	+	5	1042	c.863G>A	c.(862-864)CGC>CAC	p.R288H		NM_003246	NP_003237	P07996	TSP1_HUMAN	thrombospondin 1 precursor	288					activation of MAPK activity|anti-apoptosis|apoptosis|cell adhesion|cell cycle arrest|cell migration|cellular response to heat|chronic inflammatory response|engulfment of apoptotic cell|immune response|induction of apoptosis|negative regulation of angiogenesis|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|negative regulation of blood vessel endothelial cell migration|negative regulation of caspase activity|negative regulation of cGMP-mediated signaling|negative regulation of dendritic cell antigen processing and presentation|negative regulation of endothelial cell proliferation|negative regulation of fibrinolysis|negative regulation of fibroblast growth factor receptor signaling pathway|negative regulation of focal adhesion assembly|negative regulation of interleukin-12 production|negative regulation of nitric oxide mediated signal transduction|negative regulation of plasma membrane long-chain fatty acid transport|negative regulation of plasminogen activation|peptide cross-linking|platelet activation|platelet degranulation|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of fibroblast migration|positive regulation of macrophage activation|positive regulation of macrophage chemotaxis|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of reactive oxygen species metabolic process|positive regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transforming growth factor-beta1 production|positive regulation of translation|positive regulation of tumor necrosis factor biosynthetic process|response to calcium ion|response to drug|response to glucose stimulus|response to hypoxia|response to magnesium ion|response to progesterone stimulus|sprouting angiogenesis	external side of plasma membrane|extracellular matrix|fibrinogen complex|platelet alpha granule lumen	calcium ion binding|collagen V binding|eukaryotic cell surface binding|fibrinogen binding|fibroblast growth factor 2 binding|fibronectin binding|heparin binding|identical protein binding|integrin binding|laminin binding|low-density lipoprotein particle binding|phosphatidylserine binding|proteoglycan binding|structural molecule activity|transforming growth factor beta binding			ovary(3)|central_nervous_system(3)	6		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)	Becaplermin(DB00102)													---	---	---	---
EIF2AK4	440275	broad.mit.edu	37	15	40295463	40295463	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40295463C>T	uc001zkm.1	+	23	3355	c.3305C>T	c.(3304-3306)GCC>GTC	p.A1102V	EIF2AK4_uc010bbj.1_Missense_Mutation_p.A803V|EIF2AK4_uc001zkn.1_Missense_Mutation_p.A202V|EIF2AK4_uc001zko.1_Missense_Mutation_p.A40V	NM_001013703	NP_001013725	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha	1102	Histidyl-tRNA synthetase-like.				translation	cytosolic ribosome	aminoacyl-tRNA ligase activity|ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|protein homodimerization activity			lung(2)|stomach(1)|skin(1)	4		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)														---	---	---	---
PAK6	56924	broad.mit.edu	37	15	40557116	40557116	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40557116C>A	uc010bbl.2	+	4	570	c.130C>A	c.(130-132)CTG>ATG	p.L44M	PAK6_uc010bbm.2_Missense_Mutation_p.L44M|PAK6_uc001zky.3_Missense_Mutation_p.L44M|PAK6_uc010bbn.2_Missense_Mutation_p.L44M|PAK6_uc001zlb.2_Missense_Mutation_p.L44M	NM_001128628	NP_001122100	Q9NQU5	PAK6_HUMAN	p21-activated kinase 6	44	Linker.						ATP binding|protein binding|protein serine/threonine kinase activity			lung(5)|large_intestine(1)|ovary(1)|skin(1)	8		all_cancers(109;1.13e-18)|all_epithelial(112;1.62e-15)|Lung NSC(122;5.67e-11)|all_lung(180;1.41e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0823)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.51e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0544)														---	---	---	---
C15orf57	90416	broad.mit.edu	37	15	40846200	40846200	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40846200G>A	uc001zmc.1	-	4	618	c.528C>T	c.(526-528)GCC>GCT	p.A176A	uc001zlx.1_Intron|MRPL42P5_uc010bbq.1_5'Flank|C15orf57_uc001zly.2_Intron|C15orf57_uc001zma.1_Silent_p.A185A|C15orf57_uc001zmb.1_Silent_p.A176A	NM_001080792	NP_001074261	Q9BV29	CO057_HUMAN	coiled-coil domain containing 32 isoform a	176										ovary(1)	1																		---	---	---	---
VPS18	57617	broad.mit.edu	37	15	41191412	41191412	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41191412G>A	uc001zne.2	+	4	735	c.396G>A	c.(394-396)CGG>CGA	p.R132R		NM_020857	NP_065908	Q9P253	VPS18_HUMAN	vacuolar protein sorting 18	132					endosome organization|lysosome organization|protein transport	HOPS complex|late endosome membrane|lysosomal membrane	metal ion binding|protein binding			ovary(2)|large_intestine(1)	3		all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;1.07e-05)|COAD - Colon adenocarcinoma(120;0.15)|BRCA - Breast invasive adenocarcinoma(123;0.164)														---	---	---	---
INO80	54617	broad.mit.edu	37	15	41377751	41377751	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41377751C>T	uc001zni.2	-	7	902	c.689G>A	c.(688-690)CGA>CAA	p.R230Q	INO80_uc010ucu.1_RNA	NM_017553	NP_060023	Q9ULG1	INO80_HUMAN	INO80 complex homolog 1	230	Assembles INO80 complex module with putative regulatory components INO80E, INO80F, UCHL5, NFRKB, MCRS1 and IN80D.|Assembles INO80 complex module consisting of conserved components ACTR8, ACTL6A and YY1.				cell division|cellular response to ionizing radiation|cellular response to UV|chromatin remodeling|double-strand break repair via homologous recombination|mitotic sister chromatid segregation|positive regulation of cell growth|positive regulation of DNA replication involved in S phase|positive regulation of transcription from RNA polymerase II promoter|regulation of G1/S transition of mitotic cell cycle|spindle assembly|UV-damage excision repair	Ino80 complex|microtubule	actin binding|alpha-tubulin binding|ATP binding|ATPase activity|DNA binding|DNA helicase activity			ovary(2)|pancreas(1)|skin(1)	4																		---	---	---	---
LTK	4058	broad.mit.edu	37	15	41796833	41796833	+	Missense_Mutation	SNP	A	G	G	rs148593397		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41796833A>G	uc001zoa.3	-	18	2304	c.2126T>C	c.(2125-2127)TTT>TCT	p.F709S	LTK_uc001zob.3_Missense_Mutation_p.F648S|LTK_uc010ucx.1_Missense_Mutation_p.F579S|LTK_uc010bcg.2_Missense_Mutation_p.F407S	NM_002344	NP_002335	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase isoform 1	709	Protein kinase.|Cytoplasmic (Potential).				apoptosis|cell proliferation|phosphatidylinositol 3-kinase cascade|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane|soluble fraction	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(6)|central_nervous_system(1)	7		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)											TSP Lung(18;0.14)			---	---	---	---
RPAP1	26015	broad.mit.edu	37	15	41815048	41815048	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41815048C>A	uc001zod.2	-	19	2781	c.2657G>T	c.(2656-2658)GGC>GTC	p.G886V	RPAP1_uc001zoc.2_Intron	NM_015540	NP_056355	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	886	Leu-rich.					nucleus	DNA binding|DNA-directed RNA polymerase activity			large_intestine(1)	1		all_cancers(109;6.59e-20)|all_epithelial(112;7.67e-17)|Lung NSC(122;5.34e-11)|all_lung(180;4.17e-10)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		OV - Ovarian serous cystadenocarcinoma(18;2.84e-17)|GBM - Glioblastoma multiforme(113;1.68e-06)|Colorectal(105;0.0163)|BRCA - Breast invasive adenocarcinoma(123;0.117)														---	---	---	---
TYRO3	7301	broad.mit.edu	37	15	41865300	41865300	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:41865300G>A	uc001zof.1	+	16	2200	c.1976G>A	c.(1975-1977)CGG>CAG	p.R659Q		NM_006293	NP_006284	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase precursor	659	Protein kinase.|Cytoplasmic (Potential).					integral to plasma membrane	ATP binding|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			ovary(3)|lung(2)|central_nervous_system(1)	6		all_cancers(109;7.33e-15)|all_epithelial(112;2.8e-12)|Lung NSC(122;3.48e-08)|all_lung(180;1.71e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.31e-18)|GBM - Glioblastoma multiforme(113;9.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.117)														---	---	---	---
MGA	23269	broad.mit.edu	37	15	42032167	42032167	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42032167G>A	uc010uda.1	+	3	325	c.199G>A	c.(199-201)GCC>ACC	p.A67T	MGA_uc010ucy.1_Intron|MGA_uc010ucz.1_Intron	NM_001164273	NP_001157745	Q8IWI9	MGAP_HUMAN	MAX-interacting protein isoform 1	1459						MLL1 complex	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	12		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)														---	---	---	---
MGA	23269	broad.mit.edu	37	15	42042275	42042275	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42042275A>T	uc010ucy.1	+	17	6651	c.6470A>T	c.(6469-6471)GAG>GTG	p.E2157V	MGA_uc010ucz.1_Missense_Mutation_p.E1948V|MGA_uc010uda.1_Missense_Mutation_p.E773V|MGA_uc001zoi.2_Missense_Mutation_p.E371V	NM_001164273	NP_001157745	Q8IWI9	MGAP_HUMAN	MAX-interacting protein isoform 1	2118	Basic motif.					MLL1 complex	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	12		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)														---	---	---	---
MAPKBP1	23005	broad.mit.edu	37	15	42104734	42104734	+	Silent	SNP	C	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42104734C>G	uc001zok.3	+	7	805	c.519C>G	c.(517-519)TCC>TCG	p.S173S	MAPKBP1_uc001zoj.3_Silent_p.S173S|MAPKBP1_uc010bcj.2_5'UTR|MAPKBP1_uc010bci.2_Silent_p.S173S|MAPKBP1_uc010udb.1_Silent_p.S61S|MAPKBP1_uc010bck.2_5'UTR|MAPKBP1_uc010bcl.2_5'UTR	NM_001128608	NP_001122080	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein	173	WD 2.									central_nervous_system(5)|breast(2)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	10		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)														---	---	---	---
JMJD7-PLA2G4B	8681	broad.mit.edu	37	15	42127037	42127037	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42127037G>A	uc001zoo.3	+	2	204	c.164G>A	c.(163-165)CGC>CAC	p.R55H	JMJD7-PLA2G4B_uc010bcm.1_RNA|JMJD7-PLA2G4B_uc001zom.2_Intron|JMJD7-PLA2G4B_uc001zon.2_Missense_Mutation_p.R55H|JMJD7-PLA2G4B_uc010bcn.2_Missense_Mutation_p.R55H|JMJD7-PLA2G4B_uc001zop.1_5'UTR|JMJD7-PLA2G4B_uc001zoq.3_5'Flank	NM_005090	NP_005081	P0C869	PA24B_HUMAN	JMJD7-PLA2G4B protein	Error:Variant_position_missing_in_P0C869_after_alignment					arachidonic acid metabolic process|calcium-mediated signaling|glycerophospholipid catabolic process|inflammatory response|parturition	cytosol|early endosome membrane|extracellular region|mitochondrial membrane	calcium ion binding|calcium-dependent phospholipase A2 activity|calcium-dependent phospholipid binding|lysophospholipase activity			large_intestine(1)	1																		---	---	---	---
PLA2G4E	123745	broad.mit.edu	37	15	42292137	42292137	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42292137C>T	uc001zow.1	-	8	827	c.827G>A	c.(826-828)GGT>GAT	p.G276D	PLA2G4E_uc010udc.1_5'Flank|PLA2G4E_uc001zov.1_5'Flank	NM_001080490	NP_001073959	Q3MJ16	PA24E_HUMAN	phospholipase A2, group 4E	298					phospholipid catabolic process	cytosol|lysosomal membrane	metal ion binding|phospholipase A2 activity				0		all_cancers(109;8.09e-13)|all_epithelial(112;2.03e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.0273)		OV - Ovarian serous cystadenocarcinoma(18;7.61e-18)|GBM - Glioblastoma multiforme(94;3.07e-06)														---	---	---	---
PLA2G4D	283748	broad.mit.edu	37	15	42373193	42373193	+	Splice_Site	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42373193A>C	uc001zox.2	-	12	1189	c.1094_splice	c.e12+1	p.W365_splice		NM_178034	NP_828848			phospholipase A2, group IVD						phospholipid catabolic process	cytoplasmic vesicle membrane|cytosol	metal ion binding|phospholipase A2 activity			large_intestine(1)|skin(1)	2		all_cancers(109;6.37e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.019)|Ovarian(310;0.143)|Colorectal(260;0.245)		OV - Ovarian serous cystadenocarcinoma(18;4.9e-17)|GBM - Glioblastoma multiforme(94;1.02e-06)														---	---	---	---
CDAN1	146059	broad.mit.edu	37	15	43023991	43023991	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43023991G>A	uc001zql.2	-	11	1683	c.1566C>T	c.(1564-1566)ACC>ACT	p.T522T	CDAN1_uc001zqj.2_5'Flank|CDAN1_uc001zqk.2_5'UTR	NM_138477	NP_612486	Q8IWY9	CDAN1_HUMAN	codanin 1	522						integral to membrane	protein binding			ovary(2)	2		all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;2.49e-07)														---	---	---	---
UBR1	197131	broad.mit.edu	37	15	43360173	43360173	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43360173C>T	uc001zqq.2	-	6	787	c.721G>A	c.(721-723)GTC>ATC	p.V241I	UBR1_uc010udk.1_Missense_Mutation_p.V241I	NM_174916	NP_777576	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin	241					cellular response to leucine|negative regulation of TOR signaling cascade	cytosol	leucine binding|zinc ion binding			lung(1)	1		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)														---	---	---	---
TGM5	9333	broad.mit.edu	37	15	43545714	43545714	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43545714A>C	uc001zrd.1	-	5	682	c.674T>G	c.(673-675)GTG>GGG	p.V225G	TGM5_uc001zre.1_Missense_Mutation_p.V143G	NM_201631	NP_963925	O43548	TGM5_HUMAN	transglutaminase 5 isoform 1	225					epidermis development|peptide cross-linking	cytoplasm	acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			central_nervous_system(1)	1		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;4e-07)	L-Glutamine(DB00130)													---	---	---	---
TGM7	116179	broad.mit.edu	37	15	43584291	43584291	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43584291G>A	uc001zrf.1	-	4	449	c.444C>T	c.(442-444)GAC>GAT	p.D148D		NM_052955	NP_443187	Q96PF1	TGM7_HUMAN	transglutaminase 7	148					peptide cross-linking		acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(2)	2		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.14e-07)	L-Glutamine(DB00130)													---	---	---	---
CKMT1B	1159	broad.mit.edu	37	15	43891449	43891449	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43891449C>A	uc001zsc.2	+	10	1624	c.1232C>A	c.(1231-1233)CCT>CAT	p.P411H	CKMT1B_uc010uds.1_Missense_Mutation_p.P442H|CKMT1B_uc001zsd.3_Missense_Mutation_p.P411H|CKMT1B_uc010bdj.2_RNA	NM_020990	NP_066270	P12532	KCRU_HUMAN	creatine kinase, mitochondrial 1B precursor	411					creatine metabolic process	mitochondrial inner membrane	ATP binding|creatine kinase activity				0		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)	Creatine(DB00148)													---	---	---	---
SPG11	80208	broad.mit.edu	37	15	44865934	44865934	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44865934A>C	uc001ztx.2	-	32	6047	c.6016T>G	c.(6016-6018)TGT>GGT	p.C2006G	SPG11_uc010bdw.2_Intron|SPG11_uc010ueh.1_Intron|SPG11_uc010uei.1_Missense_Mutation_p.C2006G|SPG11_uc001zty.1_Missense_Mutation_p.C735G	NM_025137	NP_079413	Q96JI7	SPTCS_HUMAN	spatacsin isoform 1	2006	Extracellular (Potential).				cell death	cytosol|integral to membrane|nucleus	protein binding			ovary(4)|skin(1)	5		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)														---	---	---	---
SPG11	80208	broad.mit.edu	37	15	44876211	44876211	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:44876211G>T	uc001ztx.2	-	30	5698	c.5667C>A	c.(5665-5667)GGC>GGA	p.G1889G	SPG11_uc010bdw.2_Silent_p.G178G|SPG11_uc010ueh.1_Silent_p.G1889G|SPG11_uc010uei.1_Silent_p.G1889G|SPG11_uc001zty.1_Silent_p.G618G	NM_025137	NP_079413	Q96JI7	SPTCS_HUMAN	spatacsin isoform 1	1889	Extracellular (Potential).				cell death	cytosol|integral to membrane|nucleus	protein binding			ovary(4)|skin(1)	5		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)														---	---	---	---
DUOX2	50506	broad.mit.edu	37	15	45392018	45392018	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45392018G>A	uc010bea.2	-	25	3460	c.3257C>T	c.(3256-3258)ACG>ATG	p.T1086M	DUOX2_uc001zun.2_Missense_Mutation_p.T1086M	NM_014080	NP_054799	Q9NRD8	DUOX2_HUMAN	dual oxidase 2 precursor	1086	Interaction with TXNDC11 (By similarity).|Helical; (Potential).|Ferric oxidoreductase.				cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide catabolic process|response to cAMP|response to virus	apical plasma membrane|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|peroxidase activity			ovary(2)|skin(2)|pancreas(1)	5		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)														---	---	---	---
DUOXA2	405753	broad.mit.edu	37	15	45408757	45408757	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45408757G>A	uc001zuo.2	+	4	664	c.384G>A	c.(382-384)GAG>GAA	p.E128E	DUOX2_uc010bea.2_5'Flank|DUOX2_uc001zun.2_5'Flank|DUOXA2_uc010beb.2_RNA	NM_207581	NP_997464	Q1HG44	DOXA2_HUMAN	dual oxidase activator 2	128	Extracellular (Potential).				protein transport	endoplasmic reticulum membrane|integral to membrane					0		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;2.88e-18)|GBM - Glioblastoma multiforme(94;3.95e-07)|COAD - Colon adenocarcinoma(120;0.0652)|Colorectal(133;0.0659)														---	---	---	---
DUOXA1	90527	broad.mit.edu	37	15	45410209	45410209	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45410209C>T	uc001zup.2	-	10	1450	c.1050G>A	c.(1048-1050)GCG>GCA	p.A350A	DUOXA2_uc001zuo.2_3'UTR|DUOXA2_uc010beb.2_RNA|DUOXA1_uc010uem.1_Silent_p.A305A|DUOXA1_uc010bec.2_Silent_p.A350A	NM_144565	NP_653166	Q1HG43	DOXA1_HUMAN	Numb-interacting protein	Error:Variant_position_missing_in_Q1HG43_after_alignment					protein transport	endoplasmic reticulum membrane|integral to membrane				ovary(1)	1		all_cancers(109;6.02e-08)|all_epithelial(112;1.83e-06)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;3.82e-18)|GBM - Glioblastoma multiforme(94;4.39e-07)|COAD - Colon adenocarcinoma(120;0.0676)|Colorectal(133;0.0686)												OREG0023102	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
DUOX1	53905	broad.mit.edu	37	15	45428767	45428767	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45428767C>T	uc001zus.1	+	10	1312	c.966C>T	c.(964-966)TTC>TTT	p.F322F	DUOX1_uc001zut.1_Silent_p.F322F|DUOX1_uc010bee.1_5'UTR	NM_017434	NP_059130	Q9NRD9	DUOX1_HUMAN	dual oxidase 1 precursor	322	Peroxidase-like; mediates peroxidase activity.|Extracellular (Potential).				cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide biosynthetic process|hydrogen peroxide catabolic process|response to cAMP|superoxide anion generation	apical plasma membrane|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|NADP binding|peroxidase activity			ovary(5)|skin(2)|breast(1)	8		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)														---	---	---	---
TNFAIP8L3	388121	broad.mit.edu	37	15	51350267	51350267	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51350267C>A	uc001zyy.2	-	3	790	c.690G>T	c.(688-690)AAG>AAT	p.K230N		NM_207381	NP_997264	Q5GJ75	TP8L3_HUMAN	tumor necrosis factor, alpha-induced protein	230											0				all cancers(107;0.000389)|GBM - Glioblastoma multiforme(94;0.00338)														---	---	---	---
TMOD3	29766	broad.mit.edu	37	15	52194224	52194224	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52194224A>G	uc002abm.2	+	9	1234	c.1015A>G	c.(1015-1017)AAT>GAT	p.N339D	TMOD3_uc010bfc.1_RNA	NM_014547	NP_055362	Q9NYL9	TMOD3_HUMAN	tropomodulin 3 (ubiquitous)	339						cytoplasm|cytoskeleton	actin binding|tropomyosin binding			ovary(1)	1				all cancers(107;0.00194)														---	---	---	---
KIAA1370	56204	broad.mit.edu	37	15	52897384	52897384	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:52897384T>C	uc002acg.3	-	7	2559	c.2406A>G	c.(2404-2406)GGA>GGG	p.G802G	KIAA1370_uc002ach.3_RNA|KIAA1370_uc010bfg.1_Silent_p.G714G|KIAA1370_uc010ugf.1_Silent_p.G809G	NM_019600	NP_062546	Q32MH5	K1370_HUMAN	hypothetical protein LOC56204	802											0				all cancers(107;0.0803)														---	---	---	---
WDR72	256764	broad.mit.edu	37	15	53901763	53901763	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:53901763C>T	uc002acj.2	-	17	2941	c.2899G>A	c.(2899-2901)GCT>ACT	p.A967T		NM_182758	NP_877435	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	967										lung(1)|skin(1)	2				all cancers(107;0.0511)														---	---	---	---
CCPG1	9236	broad.mit.edu	37	15	55677861	55677861	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:55677861G>A	uc002acv.1	-	3	277	c.112C>T	c.(112-114)CCC>TCC	p.P38S	CCPG1_uc002acy.2_Missense_Mutation_p.P38S|DYX1C1_uc010ugh.1_RNA|CCPG1_uc002acw.1_5'UTR|CCPG1_uc002acx.2_Missense_Mutation_p.P38S|CCPG1_uc010bfk.1_Missense_Mutation_p.P38S|CCPG1_uc002acz.1_Missense_Mutation_p.P38S	NM_020739	NP_065790	Q9ULG6	CCPG1_HUMAN	cell cycle progression 1 isoform 2	38	Cytoplasmic (Potential).|Interaction with MCF2L and SRC (By similarity).				cell cycle	integral to membrane				ovary(1)	1				all cancers(107;0.0354)														---	---	---	---
RFX7	64864	broad.mit.edu	37	15	56388500	56388500	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:56388500T>C	uc010bfn.2	-	9	1426	c.1426A>G	c.(1426-1428)ACA>GCA	p.T476A	RFX7_uc010ugk.1_RNA|RFX7_uc002adn.1_Missense_Mutation_p.T290A	NM_022841	NP_073752	Q2KHR2	RFX7_HUMAN	regulatory factor X domain containing 2	379					regulation of transcription, DNA-dependent	nucleus	DNA binding				0																		---	---	---	---
TCF12	6938	broad.mit.edu	37	15	57555309	57555309	+	Splice_Site	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57555309G>T	uc002aec.2	+	17	1795	c.1511_splice	c.e17-1	p.G504_splice	TCF12_uc010ugm.1_Splice_Site_p.G556_splice|TCF12_uc010ugn.1_Splice_Site_p.G524_splice|TCF12_uc002aea.2_Splice_Site_p.G528_splice|TCF12_uc010bfs.2_Intron|TCF12_uc002aeb.2_Splice_Site_p.G528_splice|TCF12_uc002aed.2_Splice_Site_p.G504_splice|TCF12_uc002aee.2_Splice_Site_p.G334_splice|TCF12_uc010bft.2_Splice_Site_p.G358_splice|TCF12_uc010ugo.1_Splice_Site_p.G268_splice|TCF12_uc010ugp.1_Splice_Site_p.G162_splice|TCF12_uc010ugq.1_Splice_Site_p.G138_splice|TCF12_uc010ugr.1_Splice_Site_p.G117_splice	NM_207038	NP_996921			transcription factor 12 isoform b						immune response|muscle organ development|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity	p.?(1)		central_nervous_system(5)|ovary(2)|lung(1)	8		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)				T	TEC	extraskeletal myxoid chondrosarcoma								---	---	---	---
CGNL1	84952	broad.mit.edu	37	15	57815798	57815798	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:57815798C>T	uc002aeg.2	+	11	2903	c.2827C>T	c.(2827-2829)CGG>TGG	p.R943W	CGNL1_uc010bfw.2_Missense_Mutation_p.R943W	NM_032866	NP_116255	Q0VF96	CGNL1_HUMAN	cingulin-like 1	943	Potential.					myosin complex|tight junction	motor activity			skin(6)|ovary(4)|central_nervous_system(1)	11				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)														---	---	---	---
ALDH1A2	8854	broad.mit.edu	37	15	58306173	58306173	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58306173C>A	uc002aex.2	-	3	304	c.246G>T	c.(244-246)CAG>CAT	p.Q82H	ALDH1A2_uc002aey.2_Missense_Mutation_p.Q82H|ALDH1A2_uc010ugv.1_Missense_Mutation_p.Q61H|ALDH1A2_uc010ugw.1_Missense_Mutation_p.Q53H|ALDH1A2_uc002aew.2_Translation_Start_Site	NM_003888	NP_003879	O94788	AL1A2_HUMAN	aldehyde dehydrogenase 1A2 isoform 1	82					negative regulation of cell proliferation|neural tube development|response to cytokine stimulus	nucleus	3-chloroallyl aldehyde dehydrogenase activity|retinal binding|retinal dehydrogenase activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(80;0.152)|all cancers(107;0.18)	NADH(DB00157)|Tretinoin(DB00755)|Vitamin A(DB00162)													---	---	---	---
ALDH1A2	8854	broad.mit.edu	37	15	58357721	58357721	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58357721C>T	uc002aex.2	-						ALDH1A2_uc002aey.2_Intron|ALDH1A2_uc010ugv.1_Intron|ALDH1A2_uc010ugw.1_Intron	NM_003888	NP_003879			aldehyde dehydrogenase 1A2 isoform 1						negative regulation of cell proliferation|neural tube development|response to cytokine stimulus	nucleus	3-chloroallyl aldehyde dehydrogenase activity|retinal binding|retinal dehydrogenase activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(80;0.152)|all cancers(107;0.18)	NADH(DB00157)|Tretinoin(DB00755)|Vitamin A(DB00162)													---	---	---	---
ADAM10	102	broad.mit.edu	37	15	58933011	58933011	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58933011C>T	uc002afd.1	-	8	1421	c.977G>A	c.(976-978)GGC>GAC	p.G326D	ADAM10_uc010bgc.1_RNA|ADAM10_uc010ugz.1_Missense_Mutation_p.G25D|ADAM10_uc002afe.1_RNA	NM_001110	NP_001101	O14672	ADA10_HUMAN	ADAM metallopeptidase domain 10 precursor	326	Peptidase M12B.|Extracellular (Potential).				cell-cell signaling|constitutive protein ectodomain proteolysis|epidermal growth factor receptor signaling pathway|in utero embryonic development|integrin-mediated signaling pathway|monocyte activation|negative regulation of cell adhesion|Notch receptor processing|Notch signaling pathway|PMA-inducible membrane protein ectodomain proteolysis|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of T cell chemotaxis|protein phosphorylation|response to tumor necrosis factor	cell surface|endomembrane system|Golgi-associated vesicle|integral to membrane|nucleus|plasma membrane	integrin binding|metalloendopeptidase activity|protein homodimerization activity|protein kinase binding|SH3 domain binding|zinc ion binding			skin(2)	2				GBM - Glioblastoma multiforme(80;0.202)														---	---	---	---
ADAM10	102	broad.mit.edu	37	15	58936093	58936093	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:58936093G>A	uc002afd.1	-	7	1264	c.820C>T	c.(820-822)CGC>TGC	p.R274C	ADAM10_uc010bgc.1_RNA|ADAM10_uc010ugz.1_Intron|ADAM10_uc002afe.1_Intron	NM_001110	NP_001101	O14672	ADA10_HUMAN	ADAM metallopeptidase domain 10 precursor	274	Peptidase M12B.|Extracellular (Potential).				cell-cell signaling|constitutive protein ectodomain proteolysis|epidermal growth factor receptor signaling pathway|in utero embryonic development|integrin-mediated signaling pathway|monocyte activation|negative regulation of cell adhesion|Notch receptor processing|Notch signaling pathway|PMA-inducible membrane protein ectodomain proteolysis|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of T cell chemotaxis|protein phosphorylation|response to tumor necrosis factor	cell surface|endomembrane system|Golgi-associated vesicle|integral to membrane|nucleus|plasma membrane	integrin binding|metalloendopeptidase activity|protein homodimerization activity|protein kinase binding|SH3 domain binding|zinc ion binding			skin(2)	2				GBM - Glioblastoma multiforme(80;0.202)														---	---	---	---
FAM63B	54629	broad.mit.edu	37	15	59063927	59063927	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59063927C>T	uc002afj.2	+	1	535	c.333C>T	c.(331-333)TCC>TCT	p.S111S	FAM63B_uc002afi.2_Silent_p.S111S|FAM63B_uc002afk.2_RNA|FAM63B_uc002afl.2_RNA	NM_001040450	NP_001035540	Q8NBR6	FA63B_HUMAN	hypothetical protein LOC54629 isoform a	111										central_nervous_system(1)	1																		---	---	---	---
RNF111	54778	broad.mit.edu	37	15	59323305	59323305	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59323305G>A	uc002afv.2	+	2	563	c.284G>A	c.(283-285)CGC>CAC	p.R95H	RNF111_uc002afs.2_Missense_Mutation_p.R95H|RNF111_uc002aft.2_Missense_Mutation_p.R95H|RNF111_uc002afu.2_Missense_Mutation_p.R95H|RNF111_uc002afw.2_Missense_Mutation_p.R95H	NM_017610	NP_060080	Q6ZNA4	RN111_HUMAN	ring finger protein 111	95					multicellular organismal development|positive regulation of transcription, DNA-dependent	cytoplasm|nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)	2				all cancers(107;0.194)														---	---	---	---
MYO1E	4643	broad.mit.edu	37	15	59464190	59464190	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59464190G>A	uc002aga.2	-	22	2758	c.2386C>T	c.(2386-2388)CGA>TGA	p.R796*	MIR2116_hsa-mir-2116|MI0010635_5'Flank	NM_004998	NP_004989	Q12965	MYO1E_HUMAN	myosin IE	796					actin filament-based movement	myosin complex	actin binding|ATP binding|ATPase activity, coupled|calmodulin binding|microfilament motor activity			central_nervous_system(3)	3				all cancers(107;0.207)														---	---	---	---
GCNT3	9245	broad.mit.edu	37	15	59910504	59910504	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59910504G>A	uc002age.2	+	3	516	c.67G>A	c.(67-69)GCC>ACC	p.A23T	GCNT3_uc002agd.2_Missense_Mutation_p.A23T	NM_004751	NP_004742	O95395	GCNT3_HUMAN	glucosaminyl (N-acetyl) transferase 3, mucin	23	Helical; Signal-anchor for type II membrane protein; (Potential).				protein O-linked glycosylation	Golgi membrane|integral to membrane|membrane fraction	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity|N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
ANXA2	302	broad.mit.edu	37	15	60656708	60656708	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:60656708T>C	uc002agn.2	-	5	323	c.163A>G	c.(163-165)ACC>GCC	p.T55A	ANXA2_uc002agk.2_Missense_Mutation_p.T55A|ANXA2_uc002agl.2_Missense_Mutation_p.T55A|ANXA2_uc002agm.2_Missense_Mutation_p.T73A|ANXA2_uc010uhd.1_RNA|ANXA2_uc010bgj.2_Missense_Mutation_p.T55A	NM_001136015	NP_001129487	P07355	ANXA2_HUMAN	annexin A2 isoform 2	55	Annexin 1.				angiogenesis|positive regulation of vesicle fusion|skeletal system development	basement membrane|melanosome|midbody|soluble fraction	calcium ion binding|calcium-dependent phospholipid binding|cytoskeletal protein binding|phospholipase inhibitor activity			ovary(1)	1					Alteplase(DB00009)|Anistreplase(DB00029)|Tenecteplase(DB00031)													---	---	---	---
VPS13C	54832	broad.mit.edu	37	15	62174814	62174814	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62174814G>A	uc002agz.2	-	69	9679	c.9605C>T	c.(9604-9606)GCC>GTC	p.A3202V	VPS13C_uc002aha.2_Missense_Mutation_p.A3159V|VPS13C_uc002ahb.1_Missense_Mutation_p.A3202V|VPS13C_uc002ahc.1_Missense_Mutation_p.A3159V	NM_020821	NP_065872	Q709C8	VP13C_HUMAN	vacuolar protein sorting 13C protein isoform 2A	3202					protein localization					ovary(2)	2																		---	---	---	---
VPS13C	54832	broad.mit.edu	37	15	62214725	62214725	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62214725G>T	uc002agz.2	-	54	6920	c.6846C>A	c.(6844-6846)TCC>TCA	p.S2282S	VPS13C_uc002aha.2_Silent_p.S2239S|VPS13C_uc002ahb.1_Silent_p.S2282S|VPS13C_uc002ahc.1_Silent_p.S2239S	NM_020821	NP_065872	Q709C8	VP13C_HUMAN	vacuolar protein sorting 13C protein isoform 2A	2282					protein localization					ovary(2)	2																		---	---	---	---
VPS13C	54832	broad.mit.edu	37	15	62315719	62315719	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62315719T>A	uc002agz.2	-	8	589	c.515A>T	c.(514-516)GAT>GTT	p.D172V	VPS13C_uc002aha.2_Missense_Mutation_p.D129V|VPS13C_uc002ahb.1_Missense_Mutation_p.D172V|VPS13C_uc002ahc.1_Missense_Mutation_p.D129V	NM_020821	NP_065872	Q709C8	VP13C_HUMAN	vacuolar protein sorting 13C protein isoform 2A	172	Lys-rich.				protein localization					ovary(2)	2																		---	---	---	---
TLN2	83660	broad.mit.edu	37	15	62991001	62991001	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62991001G>A	uc002alb.3	+	13	1522	c.1522G>A	c.(1522-1524)GCC>ACC	p.A508T		NM_015059	NP_055874	Q9Y4G6	TLN2_HUMAN	talin 2	508					cell adhesion|cell-cell junction assembly|cytoskeletal anchoring at plasma membrane	actin cytoskeleton|cytoplasm|focal adhesion|ruffle|synapse	actin binding|insulin receptor binding|structural constituent of cytoskeleton			ovary(5)|upper_aerodigestive_tract(2)|lung(2)|breast(2)	11																		---	---	---	---
TLN2	83660	broad.mit.edu	37	15	62993337	62993337	+	Silent	SNP	C	T	T	rs139848057		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62993337C>T	uc002alb.3	+	14	1620	c.1620C>T	c.(1618-1620)GAC>GAT	p.D540D		NM_015059	NP_055874	Q9Y4G6	TLN2_HUMAN	talin 2	540					cell adhesion|cell-cell junction assembly|cytoskeletal anchoring at plasma membrane	actin cytoskeleton|cytoplasm|focal adhesion|ruffle|synapse	actin binding|insulin receptor binding|structural constituent of cytoskeleton			ovary(5)|upper_aerodigestive_tract(2)|lung(2)|breast(2)	11																		---	---	---	---
TLN2	83660	broad.mit.edu	37	15	62994217	62994217	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:62994217G>T	uc002alb.3	+	15	1723	c.1723G>T	c.(1723-1725)GCT>TCT	p.A575S		NM_015059	NP_055874	Q9Y4G6	TLN2_HUMAN	talin 2	575					cell adhesion|cell-cell junction assembly|cytoskeletal anchoring at plasma membrane	actin cytoskeleton|cytoplasm|focal adhesion|ruffle|synapse	actin binding|insulin receptor binding|structural constituent of cytoskeleton			ovary(5)|upper_aerodigestive_tract(2)|lung(2)|breast(2)	11																		---	---	---	---
TLN2	83660	broad.mit.edu	37	15	63054635	63054635	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63054635T>C	uc002alb.3	+	36	4944	c.4944T>C	c.(4942-4944)AGT>AGC	p.S1648S	TLN2_uc002alc.3_Silent_p.S41S|TLN2_uc002ald.2_Silent_p.S41S	NM_015059	NP_055874	Q9Y4G6	TLN2_HUMAN	talin 2	1648					cell adhesion|cell-cell junction assembly|cytoskeletal anchoring at plasma membrane	actin cytoskeleton|cytoplasm|focal adhesion|ruffle|synapse	actin binding|insulin receptor binding|structural constituent of cytoskeleton			ovary(5)|upper_aerodigestive_tract(2)|lung(2)|breast(2)	11																		---	---	---	---
HERC1	8925	broad.mit.edu	37	15	63928207	63928207	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63928207G>A	uc002amp.2	-	65	12515	c.12367C>T	c.(12367-12369)CGG>TGG	p.R4123W		NM_003922	NP_003913	Q15751	HERC1_HUMAN	hect domain and RCC1-like domain 1	4123	RCC1 10.				protein modification process|transport	cytosol|Golgi apparatus|membrane	acid-amino acid ligase activity|ARF guanyl-nucleotide exchange factor activity			ovary(6)|breast(6)|lung(5)|central_nervous_system(2)	19																		---	---	---	---
CSNK1G1	53944	broad.mit.edu	37	15	64592661	64592661	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64592661C>T	uc002anf.2	-	2	518	c.38G>A	c.(37-39)CGG>CAG	p.R13Q	CSNK1G1_uc002ane.2_RNA|CSNK1G1_uc002ang.1_Missense_Mutation_p.R13Q|CSNK1G1_uc002anh.1_Missense_Mutation_p.R13Q|CSNK1G1_uc002anj.2_5'UTR|CSNK1G1_uc010uip.1_RNA	NM_022048	NP_071331	Q9HCP0	KC1G1_HUMAN	casein kinase 1, gamma 1	13					Wnt receptor signaling pathway	cytoplasm	ATP binding|protein serine/threonine kinase activity				0																		---	---	---	---
ZNF609	23060	broad.mit.edu	37	15	64791739	64791739	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64791739G>A	uc002ann.2	+	1	121	c.121G>A	c.(121-123)GAT>AAT	p.D41N	ZNF609_uc010bgy.2_Missense_Mutation_p.D41N	NM_015042	NP_055857	O15014	ZN609_HUMAN	zinc finger protein 609	41						nucleus	zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3																		---	---	---	---
CILP	8483	broad.mit.edu	37	15	65502063	65502063	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65502063A>G	uc002aon.2	-	2	212	c.31T>C	c.(31-33)TTC>CTC	p.F11L		NM_003613	NP_003604	O75339	CILP1_HUMAN	cartilage intermediate layer protein	11					negative regulation of insulin-like growth factor receptor signaling pathway	extracellular matrix part|extracellular space|proteinaceous extracellular matrix				ovary(4)|pancreas(2)|skin(1)	7																		---	---	---	---
MAP2K5	5607	broad.mit.edu	37	15	67855642	67855642	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:67855642G>A	uc002aqu.2	+	3	859	c.206G>A	c.(205-207)CGA>CAA	p.R69Q	MAP2K5_uc002aqt.1_Missense_Mutation_p.R69Q|MAP2K5_uc002aqv.2_Missense_Mutation_p.R69Q|MAP2K5_uc010ujw.1_Missense_Mutation_p.R33Q	NM_145160	NP_660143	Q13163	MP2K5_HUMAN	mitogen-activated protein kinase kinase 5	69	OPR.				nerve growth factor receptor signaling pathway		ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(2)	2																		---	---	---	---
FEM1B	10116	broad.mit.edu	37	15	68583302	68583302	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68583302C>A	uc002arg.2	+	2	2221	c.1606C>A	c.(1606-1608)CTT>ATT	p.L536I	FEM1B_uc002arh.2_Missense_Mutation_p.L456I	NM_015322	NP_056137	Q9UK73	FEM1B_HUMAN	fem-1 homolog b	536	ANK 8.				apoptosis|induction of apoptosis|regulation of DNA damage checkpoint|regulation of ubiquitin-protein ligase activity	cytoplasm|nucleus	death receptor binding|ubiquitin-protein ligase activity				0																		---	---	---	---
THSD4	79875	broad.mit.edu	37	15	71633946	71633946	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:71633946T>C	uc002atb.1	+						THSD4_uc002atd.1_Intron	NM_024817	NP_079093			thrombospondin, type I, domain containing 4							proteinaceous extracellular matrix	metalloendopeptidase activity			ovary(2)	2																		---	---	---	---
THSD4	79875	broad.mit.edu	37	15	72021036	72021036	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72021036T>C	uc002atb.1	+	8	1585	c.1506T>C	c.(1504-1506)GGT>GGC	p.G502G	THSD4_uc002atd.1_Silent_p.G176G|THSD4_uc010ukg.1_Silent_p.G142G|THSD4_uc002ate.2_Silent_p.G142G	NM_024817	NP_079093	Q6ZMP0	THSD4_HUMAN	thrombospondin, type I, domain containing 4	502						proteinaceous extracellular matrix	metalloendopeptidase activity			ovary(2)	2																		---	---	---	---
MYO9A	4649	broad.mit.edu	37	15	72119245	72119245	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72119245C>A	uc002atl.3	-	42	7796	c.7323G>T	c.(7321-7323)ACG>ACT	p.T2441T	MYO9A_uc002atj.2_Silent_p.T372T|MYO9A_uc002atk.2_Silent_p.T1236T	NM_006901	NP_008832	B2RTY4	MYO9A_HUMAN	myosin IXA	2441	Tail.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction|visual perception	cytosol|integral to membrane|unconventional myosin complex	actin binding|ATP binding|GTPase activator activity|metal ion binding|motor activity			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
MYO9A	4649	broad.mit.edu	37	15	72122643	72122643	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72122643G>A	uc002atl.3	-	40	7320	c.6847C>T	c.(6847-6849)CGT>TGT	p.R2283C	MYO9A_uc002atj.2_Missense_Mutation_p.R214C|MYO9A_uc002atk.2_Missense_Mutation_p.R1078C	NM_006901	NP_008832	B2RTY4	MYO9A_HUMAN	myosin IXA	2283	Tail.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction|visual perception	cytosol|integral to membrane|unconventional myosin complex	actin binding|ATP binding|GTPase activator activity|metal ion binding|motor activity	p.R2283H(1)		ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
MYO9A	4649	broad.mit.edu	37	15	72338315	72338315	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72338315G>T	uc002atl.3	-	2	1063	c.590C>A	c.(589-591)CCC>CAC	p.P197H	MYO9A_uc010biq.2_Intron|MYO9A_uc002ato.2_Missense_Mutation_p.P197H|MYO9A_uc002atn.1_Missense_Mutation_p.P197H	NM_006901	NP_008832	B2RTY4	MYO9A_HUMAN	myosin IXA	197	Myosin head-like 1.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction|visual perception	cytosol|integral to membrane|unconventional myosin complex	actin binding|ATP binding|GTPase activator activity|metal ion binding|motor activity			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
GOLGA6B	55889	broad.mit.edu	37	15	72953666	72953666	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:72953666C>T	uc010uks.1	+	8	667	c.626C>T	c.(625-627)GCG>GTG	p.A209V		NM_018652	NP_061122	A6NDN3	GOG6B_HUMAN	golgi autoantigen, golgin subfamily a, 6B	209	Potential.										0																		---	---	---	---
HCN4	10021	broad.mit.edu	37	15	73624612	73624612	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:73624612G>T	uc002avp.2	-	3	2225	c.1231C>A	c.(1231-1233)CTG>ATG	p.L411M		NM_005477	NP_005468	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic	411	Cytoplasmic (Potential).				blood circulation|muscle contraction	integral to membrane	cAMP binding|protein binding|sodium channel activity|voltage-gated potassium channel activity			ovary(5)|liver(1)	6				COAD - Colon adenocarcinoma(1;0.142)														---	---	---	---
PML	5371	broad.mit.edu	37	15	74327566	74327566	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74327566G>A	uc002awv.2	+						PML_uc002awm.2_3'UTR|PML_uc002awl.2_3'UTR|PML_uc002awj.1_3'UTR|PML_uc002awk.2_Silent_p.S588S|PML_uc002awn.2_3'UTR|PML_uc002awo.2_Silent_p.S540S|PML_uc002awp.2_Intron|PML_uc002awq.2_Intron|PML_uc002awr.2_Intron|PML_uc002aws.2_Intron|PML_uc002awt.2_Intron|PML_uc002awu.2_Intron|PML_uc010ule.1_Intron|PML_uc002awx.2_3'UTR|PML_uc002awy.2_Silent_p.S17S	NM_033238	NP_150241			promyelocytic leukemia protein isoform 1						cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction resulting in induction of apoptosis|endoplasmic reticulum calcium ion homeostasis|induction of apoptosis|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|maintenance of protein location in nucleus|negative regulation of angiogenesis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of mitotic cell cycle|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|negative regulation of telomerase activity|negative regulation of telomere maintenance via telomerase|negative regulation of transcription, DNA-dependent|negative regulation of translation in response to oxidative stress|PML body organization|PML body organization|positive regulation of defense response to virus by host|positive regulation of histone deacetylation|protein complex assembly|protein stabilization|protein targeting|regulation of calcium ion transport into cytosol|regulation of protein phosphorylation|response to hypoxia|response to virus|transcription, DNA-dependent	cytoplasm|cytosol|early endosome membrane|extrinsic to endoplasmic reticulum membrane|insoluble fraction|nuclear matrix|nuclear membrane|nucleolus|nucleus|PML body	cobalt ion binding|DNA binding|protein binding|protein binding|protein heterodimerization activity|protein homodimerization activity|SUMO binding|transcription coactivator activity|ubiquitin protein ligase binding|zinc ion binding|zinc ion binding			central_nervous_system(2)|kidney(2)|breast(1)	5								T	RARA|PAX5	APL|ALL								---	---	---	---
PML	5371	broad.mit.edu	37	15	74336766	74336766	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74336766G>A	uc002awv.2	+	9	2206	c.2066G>A	c.(2065-2067)CGG>CAG	p.R689Q	PML_uc002awu.2_Missense_Mutation_p.R641Q|PML_uc010ule.1_Missense_Mutation_p.R250Q	NM_033238	NP_150241	P29590	PML_HUMAN	promyelocytic leukemia protein isoform 1	689					cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction resulting in induction of apoptosis|endoplasmic reticulum calcium ion homeostasis|induction of apoptosis|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|maintenance of protein location in nucleus|negative regulation of angiogenesis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of mitotic cell cycle|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|negative regulation of telomerase activity|negative regulation of telomere maintenance via telomerase|negative regulation of transcription, DNA-dependent|negative regulation of translation in response to oxidative stress|PML body organization|PML body organization|positive regulation of defense response to virus by host|positive regulation of histone deacetylation|protein complex assembly|protein stabilization|protein targeting|regulation of calcium ion transport into cytosol|regulation of protein phosphorylation|response to hypoxia|response to virus|transcription, DNA-dependent	cytoplasm|cytosol|early endosome membrane|extrinsic to endoplasmic reticulum membrane|insoluble fraction|nuclear matrix|nuclear membrane|nucleolus|nucleus|PML body	cobalt ion binding|DNA binding|protein binding|protein binding|protein heterodimerization activity|protein homodimerization activity|SUMO binding|transcription coactivator activity|ubiquitin protein ligase binding|zinc ion binding|zinc ion binding			central_nervous_system(2)|kidney(2)|breast(1)	5								T	RARA|PAX5	APL|ALL								---	---	---	---
ISLR2	57611	broad.mit.edu	37	15	74425199	74425199	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74425199C>T	uc002axd.2	+	4	873	c.104C>T	c.(103-105)GCG>GTG	p.A35V	ISLR2_uc002axe.2_Missense_Mutation_p.A35V|ISLR2_uc010bjg.2_Missense_Mutation_p.A35V|ISLR2_uc010bjf.2_Missense_Mutation_p.A35V	NM_001130136	NP_001123608	Q6UXK2	ISLR2_HUMAN	immunoglobulin superfamily containing	35	Extracellular (Potential).|LRRNT.				positive regulation of axon extension	cell surface|integral to membrane|plasma membrane					0																		---	---	---	---
EDC3	80153	broad.mit.edu	37	15	74924995	74924995	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74924995C>T	uc002ayn.2	-	10	1973	c.1485G>A	c.(1483-1485)TCG>TCA	p.S495S	EDC3_uc002ayo.2_Silent_p.S495S|EDC3_uc002aym.2_Silent_p.S495S	NM_001142443	NP_001135915	Q96F86	EDC3_HUMAN	enhancer of mRNA decapping 3	495					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay	cytoplasmic mRNA processing body|cytosol	protein binding|RNA binding			ovary(1)	1																OREG0023286	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CSK	1445	broad.mit.edu	37	15	75093352	75093352	+	Splice_Site	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75093352G>T	uc010bkb.1	+	10	906	c.723_splice	c.e10-1	p.T241_splice	CSK_uc002ays.2_Splice_Site_p.T241_splice|CSK_uc010bkc.1_Splice_Site_p.T50_splice	NM_001127190	NP_001120662			c-src tyrosine kinase						blood coagulation|epidermal growth factor receptor signaling pathway|T cell costimulation|T cell receptor signaling pathway	centrosome|cytosol|Golgi apparatus	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein C-terminus binding			lung(2)|central_nervous_system(1)	3																		---	---	---	---
CSPG4	1464	broad.mit.edu	37	15	75969007	75969007	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75969007C>A	uc002baw.2	-	10	5946	c.5853G>T	c.(5851-5853)GAG>GAT	p.E1951D		NM_001897	NP_001888	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4 precursor	1951	Extracellular (Potential).|CSPG 14.|Cysteine-containing.|Neurite growth inhibition (By similarity).				angiogenesis|cell differentiation|intracellular signal transduction|positive regulation of peptidyl-tyrosine phosphorylation|tissue remodeling	apical plasma membrane|cell surface|integral to plasma membrane|intracellular|lamellipodium membrane	protein kinase binding|signal transducer activity			ovary(2)|pancreas(1)	3																		---	---	---	---
CSPG4	1464	broad.mit.edu	37	15	75981635	75981635	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75981635T>C	uc002baw.2	-	3	1864	c.1771A>G	c.(1771-1773)ACC>GCC	p.T591A		NM_001897	NP_001888	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4 precursor	591	Extracellular (Potential).|CSPG 2.|Globular or compact configuration stabilized by disulfide bonds.|Interaction with COL6A2 (By similarity).|Neurite growth inhibition (By similarity).				angiogenesis|cell differentiation|intracellular signal transduction|positive regulation of peptidyl-tyrosine phosphorylation|tissue remodeling	apical plasma membrane|cell surface|integral to plasma membrane|intracellular|lamellipodium membrane	protein kinase binding|signal transducer activity			ovary(2)|pancreas(1)	3																		---	---	---	---
ODF3L1	161753	broad.mit.edu	37	15	76017485	76017485	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76017485C>T	uc002bax.1	+	2	377	c.155C>T	c.(154-156)ACG>ATG	p.T52M		NM_175881	NP_787077	Q8IXM7	OD3L1_HUMAN	outer dense fiber of sperm tails 3-like 1	52											0																		---	---	---	---
ODF3L1	161753	broad.mit.edu	37	15	76019665	76019665	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76019665G>A	uc002bax.1	+	4	831	c.609G>A	c.(607-609)ACG>ACA	p.T203T		NM_175881	NP_787077	Q8IXM7	OD3L1_HUMAN	outer dense fiber of sperm tails 3-like 1	203	DUF1309 1.										0																		---	---	---	---
PSTPIP1	9051	broad.mit.edu	37	15	77317659	77317659	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77317659C>T	uc002bcf.2	+	4	697	c.247C>T	c.(247-249)CAA>TAA	p.Q83*	PSTPIP1_uc010bkt.1_RNA|PSTPIP1_uc010umo.1_5'UTR|PSTPIP1_uc010bku.1_Nonsense_Mutation_p.Q74*|PSTPIP1_uc002bcg.2_Nonsense_Mutation_p.Q83*|PSTPIP1_uc010bkv.1_RNA|PSTPIP1_uc010bkw.1_Nonsense_Mutation_p.Q83*	NM_003978	NP_003969	O43586	PPIP1_HUMAN	proline-serine-threonine phosphatase interacting	83					cell adhesion|signal transduction	cleavage furrow|lamellipodium|perinuclear region of cytoplasm	catalytic activity			ovary(1)	1																		---	---	---	---
CIB2	10518	broad.mit.edu	37	15	78397675	78397675	+	Intron	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78397675C>A	uc002bdb.1	-						CIB2_uc002bdc.1_Intron|CIB2_uc010ums.1_3'UTR	NM_006383	NP_006374			DNA-dependent protein kinase catalytic								calcium ion binding				0																		---	---	---	---
ACSBG1	23205	broad.mit.edu	37	15	78471109	78471109	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78471109C>T	uc002bdh.2	-	11	1605	c.1549G>A	c.(1549-1551)GAG>AAG	p.E517K	ACSBG1_uc010umw.1_Missense_Mutation_p.E513K|ACSBG1_uc010umx.1_Missense_Mutation_p.E275K	NM_015162	NP_055977	Q96GR2	ACBG1_HUMAN	lipidosin	517					long-chain fatty acid metabolic process|myelination|very long-chain fatty acid metabolic process	cytoplasmic membrane-bounded vesicle|endoplasmic reticulum|microsome	ATP binding|long-chain fatty acid-CoA ligase activity|very long-chain fatty acid-CoA ligase activity			ovary(1)	1																		---	---	---	---
ACSBG1	23205	broad.mit.edu	37	15	78471155	78471155	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78471155G>A	uc002bdh.2	-	11	1559	c.1503C>T	c.(1501-1503)CCC>CCT	p.P501P	ACSBG1_uc010umw.1_Silent_p.P497P|ACSBG1_uc010umx.1_Silent_p.P259P	NM_015162	NP_055977	Q96GR2	ACBG1_HUMAN	lipidosin	501					long-chain fatty acid metabolic process|myelination|very long-chain fatty acid metabolic process	cytoplasmic membrane-bounded vesicle|endoplasmic reticulum|microsome	ATP binding|long-chain fatty acid-CoA ligase activity|very long-chain fatty acid-CoA ligase activity			ovary(1)	1																		---	---	---	---
ACSBG1	23205	broad.mit.edu	37	15	78471967	78471967	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78471967A>C	uc002bdh.2	-	10	1465	c.1409T>G	c.(1408-1410)TTG>TGG	p.L470W	ACSBG1_uc010umw.1_Missense_Mutation_p.L466W|ACSBG1_uc010umx.1_Missense_Mutation_p.L228W	NM_015162	NP_055977	Q96GR2	ACBG1_HUMAN	lipidosin	470					long-chain fatty acid metabolic process|myelination|very long-chain fatty acid metabolic process	cytoplasmic membrane-bounded vesicle|endoplasmic reticulum|microsome	ATP binding|long-chain fatty acid-CoA ligase activity|very long-chain fatty acid-CoA ligase activity			ovary(1)	1																		---	---	---	---
CHRNB4	1143	broad.mit.edu	37	15	78922013	78922013	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78922013C>T	uc002bed.1	-	5	746	c.634G>A	c.(634-636)GTG>ATG	p.V212M	CHRNB4_uc002bee.1_Intron|CHRNB4_uc010blh.1_Missense_Mutation_p.V30M	NM_000750	NP_000741	P30926	ACHB4_HUMAN	cholinergic receptor, nicotinic, beta 4	212	Extracellular (Potential).				regulation of neurotransmitter secretion|synaptic transmission involved in micturition|synaptic transmission, cholinergic	cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity				0																		---	---	---	---
MORF4L1	10933	broad.mit.edu	37	15	79183848	79183848	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79183848C>T	uc002bel.2	+	8	677	c.489C>T	c.(487-489)GGC>GGT	p.G163G	MORF4L1_uc010bli.1_3'UTR|MORF4L1_uc010blj.1_Silent_p.G97G|MORF4L1_uc002bem.2_Silent_p.G124G|MORF4L1_uc010une.1_Silent_p.G36G	NM_206839	NP_996670	Q9UBU8	MO4L1_HUMAN	MORF-related gene 15 isoform 2	163	Sufficient for interaction with SIN3A.				double-strand break repair via homologous recombination|histone deacetylation|histone H2A acetylation|histone H4 acetylation|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|Sin3 complex	protein N-terminus binding				0																		---	---	---	---
CTSH	1512	broad.mit.edu	37	15	79229674	79229674	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79229674T>C	uc002ben.2	-	4	276	c.179A>G	c.(178-180)AAC>AGC	p.N60S	CTSH_uc010unf.1_RNA|CTSH_uc010bll.1_Intron|CTSH_uc010ung.1_Missense_Mutation_p.N72S	NM_148979	NP_683880	P09668	CATH_HUMAN	cathepsin H isoform b precursor	72					protein destabilization|proteolysis	lysosome	cysteine-type endopeptidase activity			central_nervous_system(2)|large_intestine(1)	3																		---	---	---	---
RASGRF1	5923	broad.mit.edu	37	15	79277516	79277516	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79277516G>A	uc002beq.2	-	24	3670	c.3295C>T	c.(3295-3297)CGC>TGC	p.R1099C	RASGRF1_uc002bep.2_Missense_Mutation_p.R1083C|RASGRF1_uc010blm.1_Missense_Mutation_p.R1008C|RASGRF1_uc002ber.3_Missense_Mutation_p.R1083C|RASGRF1_uc002beo.2_Missense_Mutation_p.R315C	NM_002891	NP_002882	Q13972	RGRF1_HUMAN	Ras protein-specific guanine	1101	Ras-GEF.				activation of Rac GTPase activity|apoptosis|induction of apoptosis by extracellular signals|long-term memory|nerve growth factor receptor signaling pathway|neuron projection development|regulation of Rac protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol|growth cone|plasma membrane|synaptosome	Rho guanyl-nucleotide exchange factor activity			skin(4)|ovary(1)|central_nervous_system(1)	6																		---	---	---	---
RASGRF1	5923	broad.mit.edu	37	15	79323803	79323803	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79323803G>T	uc002beq.2	-	8	1576	c.1201C>A	c.(1201-1203)CAT>AAT	p.H401N	RASGRF1_uc002bep.2_Missense_Mutation_p.H401N|RASGRF1_uc010blm.1_Missense_Mutation_p.H323N|RASGRF1_uc002ber.3_Missense_Mutation_p.H401N	NM_002891	NP_002882	Q13972	RGRF1_HUMAN	Ras protein-specific guanine	401	DH.				activation of Rac GTPase activity|apoptosis|induction of apoptosis by extracellular signals|long-term memory|nerve growth factor receptor signaling pathway|neuron projection development|regulation of Rac protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol|growth cone|plasma membrane|synaptosome	Rho guanyl-nucleotide exchange factor activity			skin(4)|ovary(1)|central_nervous_system(1)	6																		---	---	---	---
RASGRF1	5923	broad.mit.edu	37	15	79339218	79339218	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79339218C>A	uc002beq.2	-	5	1123	c.748G>T	c.(748-750)GAG>TAG	p.E250*	RASGRF1_uc002bep.2_Nonsense_Mutation_p.E250*|RASGRF1_uc010blm.1_Nonsense_Mutation_p.E172*|RASGRF1_uc002ber.3_Nonsense_Mutation_p.E250*	NM_002891	NP_002882	Q13972	RGRF1_HUMAN	Ras protein-specific guanine	250	DH.				activation of Rac GTPase activity|apoptosis|induction of apoptosis by extracellular signals|long-term memory|nerve growth factor receptor signaling pathway|neuron projection development|regulation of Rac protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol|growth cone|plasma membrane|synaptosome	Rho guanyl-nucleotide exchange factor activity			skin(4)|ovary(1)|central_nervous_system(1)	6																		---	---	---	---
FAH	2184	broad.mit.edu	37	15	80472514	80472514	+	Missense_Mutation	SNP	G	A	A	rs80338900		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:80472514G>A	uc002bfj.2	+	13	1091	c.1009G>A	c.(1009-1011)GGC>AGC	p.G337S	FAH_uc002bfk.1_Missense_Mutation_p.G337S|FAH_uc002bfm.1_Missense_Mutation_p.G337S|FAH_uc002bfn.1_Missense_Mutation_p.G267S|FAH_uc010bln.1_RNA|FAH_uc010blo.1_Intron	NM_000137	NP_000128	P16930	FAAA_HUMAN	fumarylacetoacetase	337			G -> S (in TYRO1).		L-phenylalanine catabolic process|tyrosine catabolic process	cytosol	fumarylacetoacetase activity|metal ion binding				0														Tyrosinemia_type_1				---	---	---	---
KIAA1199	57214	broad.mit.edu	37	15	81229140	81229140	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81229140G>A	uc002bfw.1	+	23	3395	c.3135G>A	c.(3133-3135)CCG>CCA	p.P1045P	KIAA1199_uc010unn.1_Silent_p.P1045P	NM_018689	NP_061159	Q8WUJ3	K1199_HUMAN	KIAA1199 precursor	1045										upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3																		---	---	---	---
KIAA1199	57214	broad.mit.edu	37	15	81241146	81241146	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81241146G>A	uc002bfw.1	+	29	4227	c.3967G>A	c.(3967-3969)GCA>ACA	p.A1323T	KIAA1199_uc010unn.1_Missense_Mutation_p.A1323T|MESDC2_uc002bfx.2_RNA|MESDC2_uc010uno.1_RNA	NM_018689	NP_061159	Q8WUJ3	K1199_HUMAN	KIAA1199 precursor	1323										upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3																		---	---	---	---
TMC3	342125	broad.mit.edu	37	15	81637208	81637208	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:81637208T>C	uc002bgo.1	-	13	1417	c.1417A>G	c.(1417-1419)ACC>GCC	p.T473A	TMC3_uc010blr.1_RNA|TMC3_uc002bgp.2_Missense_Mutation_p.T473A	NM_001080532	NP_001074001	Q7Z5M5	TMC3_HUMAN	transmembrane channel-like 3	473	Cytoplasmic (Potential).					integral to membrane				ovary(1)|liver(1)	2																		---	---	---	---
AP3B2	8120	broad.mit.edu	37	15	83333221	83333221	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:83333221G>A	uc010uoh.1	-	18	2279	c.2102C>T	c.(2101-2103)TCG>TTG	p.S701L	AP3B2_uc010uoi.1_Missense_Mutation_p.S720L|AP3B2_uc010uoj.1_Missense_Mutation_p.S669L|AP3B2_uc010bmp.2_5'Flank|AP3B2_uc010uog.1_Missense_Mutation_p.S337L|AP3B2_uc002biy.1_5'Flank	NM_004644	NP_004635	Q13367	AP3B2_HUMAN	adaptor-related protein complex 3, beta 2	701	Glu/Ser-rich.				endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport	clathrin coated vesicle membrane|COPI-coated vesicle|membrane coat	binding|protein transporter activity			ovary(3)|breast(1)|pancreas(1)	5			BRCA - Breast invasive adenocarcinoma(143;0.229)															---	---	---	---
ADAMTSL3	57188	broad.mit.edu	37	15	84683410	84683410	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84683410A>G	uc002bjz.3	+	24	4314	c.4090A>G	c.(4090-4092)ACC>GCC	p.T1364A	ADAMTSL3_uc010bmt.1_Missense_Mutation_p.T1364A|ADAMTSL3_uc010bmu.1_Missense_Mutation_p.T1364A	NM_207517	NP_997400	P82987	ATL3_HUMAN	ADAMTS-like 3 precursor	1364	Ig-like C2-type 3.					proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(6)|central_nervous_system(5)|lung(5)|large_intestine(4)|breast(3)|skin(2)|kidney(1)|pancreas(1)	27			BRCA - Breast invasive adenocarcinoma(143;0.211)															---	---	---	---
ADAMTSL3	57188	broad.mit.edu	37	15	84700101	84700101	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84700101C>T	uc002bjz.3	+	28	4895	c.4671C>T	c.(4669-4671)TGC>TGT	p.C1557C	ADAMTSL3_uc010bmu.1_Silent_p.C1557C	NM_207517	NP_997400	P82987	ATL3_HUMAN	ADAMTS-like 3 precursor	1557						proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(6)|central_nervous_system(5)|lung(5)|large_intestine(4)|breast(3)|skin(2)|kidney(1)|pancreas(1)	27			BRCA - Breast invasive adenocarcinoma(143;0.211)															---	---	---	---
ALPK3	57538	broad.mit.edu	37	15	85401085	85401085	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85401085G>A	uc002ble.2	+	6	3889	c.3722G>A	c.(3721-3723)CGC>CAC	p.R1241H		NM_020778	NP_065829	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1241					heart development	nucleus	ATP binding|protein serine/threonine kinase activity			stomach(3)|ovary(3)|lung(2)|skin(2)|central_nervous_system(1)|breast(1)	12			BRCA - Breast invasive adenocarcinoma(143;0.0587)															---	---	---	---
AKAP13	11214	broad.mit.edu	37	15	86124908	86124908	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86124908C>T	uc002blv.1	+	7	3779	c.3609C>T	c.(3607-3609)GCC>GCT	p.A1203A	AKAP13_uc002blt.1_Silent_p.A1203A|AKAP13_uc002blu.1_Silent_p.A1203A|AKAP13_uc010bne.1_5'Flank	NM_007200	NP_009131	Q12802	AKP13_HUMAN	A-kinase anchor protein 13 isoform 2	1203					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane|membrane fraction|nucleus	cAMP-dependent protein kinase activity|metal ion binding|protein binding|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			central_nervous_system(3)|kidney(2)|urinary_tract(1)|liver(1)|skin(1)|ovary(1)	9																		---	---	---	---
AKAP13	11214	broad.mit.edu	37	15	86207830	86207830	+	Silent	SNP	C	T	T	rs146553883		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86207830C>T	uc002blv.1	+	13	5006	c.4836C>T	c.(4834-4836)GTC>GTT	p.V1612V	AKAP13_uc002blt.1_Silent_p.V1594V|AKAP13_uc002blu.1_Silent_p.V1616V|AKAP13_uc010bnf.1_Silent_p.V234V|AKAP13_uc002blw.1_Silent_p.V79V|AKAP13_uc010bne.1_Silent_p.V265V	NM_007200	NP_009131	Q12802	AKP13_HUMAN	A-kinase anchor protein 13 isoform 2	1612					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane|membrane fraction|nucleus	cAMP-dependent protein kinase activity|metal ion binding|protein binding|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			central_nervous_system(3)|kidney(2)|urinary_tract(1)|liver(1)|skin(1)|ovary(1)	9																		---	---	---	---
AKAP13	11214	broad.mit.edu	37	15	86266404	86266404	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86266404C>T	uc002blv.1	+	26	6768	c.6598C>T	c.(6598-6600)CGT>TGT	p.R2200C	AKAP13_uc002blu.1_Missense_Mutation_p.R2204C|AKAP13_uc010bnf.1_Missense_Mutation_p.R821C|AKAP13_uc002blw.1_Missense_Mutation_p.R665C|AKAP13_uc002blx.1_Missense_Mutation_p.R445C	NM_007200	NP_009131	Q12802	AKP13_HUMAN	A-kinase anchor protein 13 isoform 2	2200	Interaction with ESR1.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane|membrane fraction|nucleus	cAMP-dependent protein kinase activity|metal ion binding|protein binding|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			central_nervous_system(3)|kidney(2)|urinary_tract(1)|liver(1)|skin(1)|ovary(1)	9																		---	---	---	---
KLHL25	64410	broad.mit.edu	37	15	86312887	86312887	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86312887G>A	uc002bly.2	-	2	358	c.155C>T	c.(154-156)GCG>GTG	p.A52V		NM_022480	NP_071925	Q9H0H3	ENC2_HUMAN	BTB/POZ KELCH domain protein	52	BTB.					cytoplasm				ovary(2)	2																		---	---	---	---
AGBL1	123624	broad.mit.edu	37	15	86814916	86814916	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86814916G>A	uc002blz.1	+	14	1996	c.1916G>A	c.(1915-1917)GGC>GAC	p.G639D	AGBL1_uc002bma.1_Missense_Mutation_p.G370D|AGBL1_uc002bmb.1_Missense_Mutation_p.G333D	NM_152336	NP_689549	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	639					C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis	cytosol	metallocarboxypeptidase activity|tubulin binding|zinc ion binding				0																		---	---	---	---
ACAN	176	broad.mit.edu	37	15	89401397	89401397	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89401397G>A	uc010upo.1	+	12	5955	c.5581G>A	c.(5581-5583)GGA>AGA	p.G1861R	ACAN_uc010upp.1_Missense_Mutation_p.G1861R|ACAN_uc002bna.2_RNA	NM_013227	NP_037359	E7EX88	E7EX88_HUMAN	aggrecan isoform 2 precursor	1861					cell adhesion		hyaluronic acid binding|sugar binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)															---	---	---	---
HAPLN3	145864	broad.mit.edu	37	15	89421274	89421274	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:89421274G>T	uc002bnc.2	-	5	1138	c.1010C>A	c.(1009-1011)CCT>CAT	p.P337H	HAPLN3_uc002bne.2_RNA|HAPLN3_uc002bnd.2_Missense_Mutation_p.P399H	NM_178232	NP_839946	Q96S86	HPLN3_HUMAN	hyaluronan and proteoglycan link protein 3	337	Link 2.				cell adhesion	proteinaceous extracellular matrix	hyaluronic acid binding				0	Lung NSC(78;0.0392)|all_lung(78;0.077)																	---	---	---	---
RHCG	51458	broad.mit.edu	37	15	90023598	90023598	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90023598G>A	uc002bnz.2	-	4	588	c.564C>T	c.(562-564)GGC>GGT	p.G188G	RHCG_uc002bny.2_5'Flank|RHCG_uc002boa.2_RNA|RHCG_uc010bnq.1_Silent_p.G72G	NM_016321	NP_057405	Q9UBD6	RHCG_HUMAN	Rh family, C glycoprotein	188	Helical; (Potential).				amine transport|cellular ion homeostasis|epithelial cell differentiation|transepithelial ammonium transport	apical plasma membrane|basolateral plasma membrane|cytoplasmic vesicle|integral to plasma membrane	ammonia transmembrane transporter activity|ammonium transmembrane transporter activity|ankyrin binding			kidney(1)	1	Lung NSC(78;0.0237)|all_lung(78;0.0478)																	---	---	---	---
C15orf42	90381	broad.mit.edu	37	15	90170270	90170270	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90170270A>G	uc002boe.2	+	22	5686	c.5686A>G	c.(5686-5688)ACT>GCT	p.T1896A	C15orf42_uc010upv.1_RNA	NM_152259	NP_689472	Q7Z2Z1	TICRR_HUMAN	leucine-rich repeat kinase 1	1896					cell cycle|DNA repair|DNA replication|formation of translation preinitiation complex|G2/M transition checkpoint|mitotic cell cycle DNA replication checkpoint|regulation of DNA-dependent DNA replication initiation|response to ionizing radiation	nucleus	chromatin binding|protein binding			ovary(4)|central_nervous_system(2)|skin(1)	7	Lung NSC(78;0.0237)|all_lung(78;0.0478)		BRCA - Breast invasive adenocarcinoma(143;0.128)															---	---	---	---
ANPEP	290	broad.mit.edu	37	15	90348391	90348391	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90348391G>A	uc002bop.3	-	4	1107	c.815C>T	c.(814-816)ACG>ATG	p.T272M		NM_001150	NP_001141	P15144	AMPN_HUMAN	membrane alanine aminopeptidase precursor	272	Extracellular.|Interaction with HCoV-229E.|Metalloprotease.				angiogenesis|cell differentiation|interspecies interaction between organisms	cytosol|ER-Golgi intermediate compartment|integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|receptor activity|zinc ion binding			ovary(3)|skin(1)	4	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)													---	---	---	---
C15orf58	390637	broad.mit.edu	37	15	90784519	90784519	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90784519A>G	uc002bpc.2	+	4	558	c.379A>G	c.(379-381)AAC>GAC	p.N127D		NM_001013657	NP_001013679	Q6ZNW5	VTC2_HUMAN	hypothetical protein LOC390637	127					glucose metabolic process	cytoplasm	GDP-D-glucose phosphorylase activity				0																		---	---	---	---
IQGAP1	8826	broad.mit.edu	37	15	90982624	90982624	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90982624C>T	uc002bpl.1	+	6	629	c.528C>T	c.(526-528)GAC>GAT	p.D176D		NM_003870	NP_003861	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	176					energy reserve metabolic process|regulation of insulin secretion|small GTPase mediated signal transduction	actin filament|cytoplasm|midbody|nucleus|plasma membrane	calmodulin binding|GTPase inhibitor activity|protein phosphatase binding|Ras GTPase activator activity			ovary(2)|lung(2)|central_nervous_system(2)|pancreas(1)|skin(1)	8	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)															---	---	---	---
MAN2A2	4122	broad.mit.edu	37	15	91456935	91456935	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:91456935G>A	uc010bnz.2	+	19	2925	c.2810G>A	c.(2809-2811)CGC>CAC	p.R937H	MAN2A2_uc002bqc.2_Missense_Mutation_p.R937H|MAN2A2_uc010uql.1_Missense_Mutation_p.R599H|MAN2A2_uc010uqm.1_Missense_Mutation_p.R516H|MAN2A2_uc010uqn.1_RNA	NM_006122	NP_006113	P49641	MA2A2_HUMAN	mannosidase, alpha, class 2A, member 2	937					mannose metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-mannosidase activity|carbohydrate binding|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity|zinc ion binding			large_intestine(2)|ovary(1)	3	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)															---	---	---	---
SLCO3A1	28232	broad.mit.edu	37	15	92706350	92706350	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:92706350G>T	uc002bqx.2	+	10	2319	c.2118G>T	c.(2116-2118)ATG>ATT	p.M706I	SLCO3A1_uc002bqy.2_Intron	NM_013272	NP_037404	Q9UIG8	SO3A1_HUMAN	solute carrier organic anion transporter family,	706					sodium-independent organic anion transport	integral to membrane|plasma membrane	sodium-independent organic anion transmembrane transporter activity			skin(1)	1	Lung NSC(78;0.0158)|all_lung(78;0.0255)		BRCA - Breast invasive adenocarcinoma(143;0.0841)															---	---	---	---
IGF1R	3480	broad.mit.edu	37	15	99459996	99459996	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99459996C>T	uc002bul.2	+	10	2142	c.2092C>T	c.(2092-2094)CCT>TCT	p.P698S	IGF1R_uc010urq.1_Missense_Mutation_p.P698S|IGF1R_uc010bon.2_Missense_Mutation_p.P698S|IGF1R_uc010urr.1_Missense_Mutation_p.P148S	NM_000875	NP_000866	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor precursor	698					anti-apoptosis|immune response|insulin receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of DNA replication|protein autophosphorylation|protein tetramerization	microsome	ATP binding|identical protein binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor receptor activity|metal ion binding|phosphatidylinositol 3-kinase binding			lung(3)|kidney(3)|ovary(1)|central_nervous_system(1)	8	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Mecasermin(DB01277)													---	---	---	---
IGF1R	3480	broad.mit.edu	37	15	99491942	99491942	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99491942G>A	uc002bul.2	+						IGF1R_uc010bon.2_Intron	NM_000875	NP_000866			insulin-like growth factor 1 receptor precursor						anti-apoptosis|immune response|insulin receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of DNA replication|protein autophosphorylation|protein tetramerization	microsome	ATP binding|identical protein binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor receptor activity|metal ion binding|phosphatidylinositol 3-kinase binding			lung(3)|kidney(3)|ovary(1)|central_nervous_system(1)	8	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Mecasermin(DB01277)													---	---	---	---
TTC23	64927	broad.mit.edu	37	15	99761937	99761937	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99761937C>T	uc002bur.2	-						TTC23_uc002bus.2_Intron|TTC23_uc002but.2_Intron|TTC23_uc002buu.2_Intron|TTC23_uc002buv.2_Intron|TTC23_uc002bux.2_Intron|TTC23_uc002buw.2_Intron|TTC23_uc010boq.2_Intron|TTC23_uc002buy.2_Intron|TTC23_uc010bor.2_Intron|TTC23_uc002buz.2_Intron	NM_022905	NP_075056			tetratricopeptide repeat domain 23								binding				0	all_cancers(4;1.49e-13)|Lung NSC(78;0.000545)|all_lung(78;0.00121)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		all cancers(5;8.11e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00215)															---	---	---	---
ADAMTS17	170691	broad.mit.edu	37	15	100672316	100672316	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:100672316C>T	uc002bvv.1	-	12	1696	c.1617G>A	c.(1615-1617)CCG>CCA	p.P539P	ADAMTS17_uc002bvx.1_Silent_p.P296P	NM_139057	NP_620688	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1	539	Disintegrin.				proteolysis	intracellular|proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)												OREG0023513	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
LINS1	55180	broad.mit.edu	37	15	101114072	101114072	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101114072C>T	uc002bwe.2	-	6	1297	c.1006G>A	c.(1006-1008)GCT>ACT	p.A336T	LINS1_uc002bwd.2_5'Flank|LINS1_uc002bwf.2_Missense_Mutation_p.A336T|LINS1_uc002bwg.2_Missense_Mutation_p.A336T|LINS1_uc002bwh.2_Missense_Mutation_p.A336T|LINS1_uc010usa.1_Missense_Mutation_p.A217T|LINS1_uc002bwi.2_Missense_Mutation_p.A336T	NM_001040614	NP_001035704	Q8NG48	LINES_HUMAN	lines homolog 1	336											0	Lung NSC(78;0.0018)|all_lung(78;0.00223)|Melanoma(26;0.00852)		OV - Ovarian serous cystadenocarcinoma(32;0.00095)|LUSC - Lung squamous cell carcinoma(107;0.0766)|Lung(145;0.103)															---	---	---	---
ALDH1A3	220	broad.mit.edu	37	15	101447371	101447371	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101447371G>T	uc002bwn.3	+	11	1383	c.1279G>T	c.(1279-1281)GAA>TAA	p.E427*	ALDH1A3_uc010bpb.2_Nonsense_Mutation_p.E320*|uc002bwo.1_Intron	NM_000693	NP_000684	P47895	AL1A3_HUMAN	aldehyde dehydrogenase 1A3	427					retinal metabolic process	cytoplasm	aldehyde dehydrogenase|protein homodimerization activity			central_nervous_system(2)|lung(1)|pancreas(1)	4	Lung NSC(78;0.00144)|all_lung(78;0.0018)|Melanoma(26;0.00852)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.0766)|Lung(145;0.103)		NADH(DB00157)|Vitamin A(DB00162)													---	---	---	---
LRRK1	79705	broad.mit.edu	37	15	101566259	101566259	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:101566259G>A	uc002bwr.2	+	17	2641	c.2322G>A	c.(2320-2322)CTG>CTA	p.L774L	LRRK1_uc010usb.1_RNA|LRRK1_uc010usc.1_RNA	NM_024652	NP_078928	Q38SD2	LRRK1_HUMAN	leucine-rich repeat kinase 1	774	Roc.				small GTPase mediated signal transduction	mitochondrion	ATP binding|GTP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|lung(4)|central_nervous_system(3)|large_intestine(1)	12	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)															---	---	---	---
ITFG3	83986	broad.mit.edu	37	16	309593	309593	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:309593A>G	uc002cgf.2	+	4	575	c.380A>G	c.(379-381)GAC>GGC	p.D127G	ITFG3_uc010bqr.2_RNA|ITFG3_uc002cgg.2_Missense_Mutation_p.D127G|ITFG3_uc010uud.1_RNA|ITFG3_uc002cgh.2_Missense_Mutation_p.D127G	NM_032039	NP_114428	Q9H0X4	ITFG3_HUMAN	integrin alpha FG-GAP repeat containing 3	127	Extracellular (Potential).					integral to membrane				central_nervous_system(1)	1		all_cancers(16;0.000129)|all_epithelial(16;0.000206)|Hepatocellular(16;0.00264)|Lung NSC(18;0.0626)|all_lung(18;0.13)																---	---	---	---
RGS11	8786	broad.mit.edu	37	16	321411	321411	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:321411C>T	uc002cgj.1	-	11	739	c.736G>A	c.(736-738)GTC>ATC	p.V246I	RGS11_uc002cgi.1_Missense_Mutation_p.V225I|RGS11_uc010bqs.1_Missense_Mutation_p.V235I|RGS11_uc002cgk.1_Missense_Mutation_p.V62I	NM_183337	NP_899180	O94810	RGS11_HUMAN	regulator of G-protein signalling 11 isoform 1	246	G protein gamma.				G-protein coupled receptor protein signaling pathway|intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|signal transducer activity			lung(1)|pancreas(1)	2		all_cancers(16;6.71e-07)|all_epithelial(16;1.59e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00769)|all_lung(18;0.0186)																---	---	---	---
PIGQ	9091	broad.mit.edu	37	16	628808	628808	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:628808T>C	uc002cho.2	+	6	1195	c.1093T>C	c.(1093-1095)TTC>CTC	p.F365L	PIGQ_uc010bqw.2_Missense_Mutation_p.F365L|PIGQ_uc002chn.2_Missense_Mutation_p.F365L|PIGQ_uc010uui.1_Missense_Mutation_p.F379L|PIGQ_uc002chp.2_5'Flank	NM_148920	NP_683721	Q9BRB3	PIGQ_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	365	Helical; (Potential).|Leu-rich.				C-terminal protein lipidation|carbohydrate metabolic process|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	phosphatidylinositol N-acetylglucosaminyltransferase activity			central_nervous_system(1)	1		Hepatocellular(780;0.00335)																---	---	---	---
C16orf13	84326	broad.mit.edu	37	16	684616	684616	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:684616A>G	uc002chv.1	-	6	653	c.596T>C	c.(595-597)CTG>CCG	p.L199P	C16orf13_uc002chw.1_Silent_p.P176P|C16orf13_uc002chz.1_Silent_p.P156P|C16orf13_uc002cia.1_Missense_Mutation_p.L122P|C16orf13_uc002cib.1_Missense_Mutation_p.L102P|uc010uuk.1_5'Flank	NM_032366	NP_115742	Q96S19	CP013_HUMAN	hypothetical protein LOC84326 isoform a	199											0		Hepatocellular(780;0.00335)																---	---	---	---
STUB1	10273	broad.mit.edu	37	16	732217	732217	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:732217G>A	uc002cit.2	+	6	1133	c.722G>A	c.(721-723)CGG>CAG	p.R241Q	STUB1_uc002ciu.2_Missense_Mutation_p.R169Q|STUB1_uc010bqz.2_RNA|STUB1_uc002civ.2_RNA|JMJD8_uc002ciw.1_3'UTR|JMJD8_uc002cix.1_3'UTR|JMJD8_uc002ciy.1_3'UTR	NM_005861	NP_005852	Q9UNE7	CHIP_HUMAN	STIP1 homology and U-box containing protein 1	241	U-box.				cellular response to misfolded protein|DNA repair|misfolded or incompletely synthesized protein catabolic process|positive regulation of cellular chaperone-mediated protein complex assembly|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|proteasomal ubiquitin-dependent protein catabolic process|protein autoubiquitination|protein K63-linked ubiquitination|protein maturation|regulation of glucocorticoid metabolic process|ubiquitin-dependent SMAD protein catabolic process	cytoplasm|nuclear inclusion body|ubiquitin conjugating enzyme complex|ubiquitin ligase complex	Hsp70 protein binding|Hsp90 protein binding|kinase binding|misfolded protein binding|protein binding, bridging|protein homodimerization activity|SMAD binding|TPR domain binding|ubiquitin-ubiquitin ligase activity				0		Hepatocellular(780;0.00335)																---	---	---	---
WDR24	84219	broad.mit.edu	37	16	736929	736929	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:736929G>A	uc002ciz.1	-	3	1907	c.1147C>T	c.(1147-1149)CTG>TTG	p.L383L	JMJD8_uc002ciw.1_5'Flank|JMJD8_uc002cix.1_5'Flank|JMJD8_uc002ciy.1_5'Flank	NM_032259	NP_115635	Q96S15	WDR24_HUMAN	WD repeat domain 24	513										ovary(1)|central_nervous_system(1)	2		Hepatocellular(780;0.0218)																---	---	---	---
MSLNL	401827	broad.mit.edu	37	16	823205	823205	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:823205C>T	uc002cjz.1	-	10	2063	c.2063G>A	c.(2062-2064)AGA>AAA	p.R688K		NM_001025190	NP_001020361	Q96KJ4	MSLNL_HUMAN	mesothelin-like	337	Extracellular (Potential).				cell adhesion	integral to membrane				breast(3)|ovary(1)	4																		---	---	---	---
MSLNL	401827	broad.mit.edu	37	16	830388	830388	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:830388C>T	uc002cjz.1	-	3	613	c.613G>A	c.(613-615)GTG>ATG	p.V205M		NM_001025190	NP_001020361	Q96KJ4	MSLNL_HUMAN	mesothelin-like	Error:Variant_position_missing_in_Q96KJ4_after_alignment					cell adhesion	integral to membrane				breast(3)|ovary(1)	4																		---	---	---	---
CACNA1H	8912	broad.mit.edu	37	16	1262528	1262528	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1262528G>T	uc002cks.2	+	26	5025	c.4777G>T	c.(4777-4779)GAG>TAG	p.E1593*	CACNA1H_uc002ckt.2_Intron|CACNA1H_uc002cku.2_Nonsense_Mutation_p.E299*|CACNA1H_uc010brj.2_Intron|CACNA1H_uc002ckv.2_Intron	NM_021098	NP_066921	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type,	1593	Cytoplasmic (Potential).				aldosterone biosynthetic process|axon guidance|cellular response to hormone stimulus|cellular response to potassium ion|cortisol biosynthetic process|muscle contraction|myoblast fusion|positive regulation of acrosome reaction|regulation of heart contraction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(2)	2		Hepatocellular(780;0.00369)			Flunarizine(DB04841)|Mibefradil(DB01388)													---	---	---	---
UBE2I	7329	broad.mit.edu	37	16	1364357	1364357	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1364357G>A	uc002clc.1	+	3	234	c.130G>A	c.(130-132)GCC>ACC	p.A44T	UBE2I_uc002cld.1_Missense_Mutation_p.A44T|UBE2I_uc002cle.1_Missense_Mutation_p.A44T|UBE2I_uc002clf.1_Missense_Mutation_p.A44T|UBE2I_uc002clg.1_Missense_Mutation_p.A44T|UBE2I_uc002clh.1_Missense_Mutation_p.A44T|UBE2I_uc002cli.1_Missense_Mutation_p.A44T	NM_194261	NP_919237	P63279	UBC9_HUMAN	ubiquitin-conjugating enzyme E2I	44					cell division|chromosome segregation|interspecies interaction between organisms|mitosis|negative regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|protein sumoylation	cytoplasm|PML body|synaptonemal complex	ATP binding|enzyme binding|ubiquitin-protein ligase activity			breast(1)|skin(1)	2		Hepatocellular(780;0.00369)																---	---	---	---
UBE2I	7329	broad.mit.edu	37	16	1364387	1364387	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1364387G>A	uc002clc.1	+						UBE2I_uc002cld.1_Intron|UBE2I_uc002cle.1_Intron|UBE2I_uc002clf.1_Intron|UBE2I_uc002clg.1_Intron|UBE2I_uc002clh.1_Intron|UBE2I_uc002cli.1_Intron	NM_194261	NP_919237			ubiquitin-conjugating enzyme E2I						cell division|chromosome segregation|interspecies interaction between organisms|mitosis|negative regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|protein sumoylation	cytoplasm|PML body|synaptonemal complex	ATP binding|enzyme binding|ubiquitin-protein ligase activity			breast(1)|skin(1)	2		Hepatocellular(780;0.00369)																---	---	---	---
BAIAP3	8938	broad.mit.edu	37	16	1394649	1394649	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1394649C>T	uc002clk.1	+	19	1812	c.1812C>T	c.(1810-1812)GTC>GTT	p.V604V	BAIAP3_uc002clj.2_Silent_p.V586V|BAIAP3_uc010uuz.1_Silent_p.V569V|BAIAP3_uc010uva.1_Silent_p.V541V|BAIAP3_uc010uvc.1_Silent_p.V533V	NM_003933	NP_003924	O94812	BAIP3_HUMAN	BAI1-associated protein 3	604					G-protein coupled receptor protein signaling pathway|neurotransmitter secretion		protein C-terminus binding			pancreas(1)	1		Hepatocellular(780;0.0893)																---	---	---	---
C16orf42	115939	broad.mit.edu	37	16	1399558	1399558	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1399558G>A	uc002cll.2	-	6	887	c.819C>T	c.(817-819)GGC>GGT	p.G273G	GNPTG_uc002clm.2_5'Flank	NM_001001410	NP_001001410	Q9UJK0	TSR3_HUMAN	hypothetical protein LOC115939	273					rRNA processing						0		Hepatocellular(780;0.0893)																---	---	---	---
UNKL	64718	broad.mit.edu	37	16	1453292	1453292	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1453292C>T	uc010bro.1	-	3	349	c.341G>A	c.(340-342)CGT>CAT	p.R114H	UNKL_uc002clq.2_Missense_Mutation_p.R114H	NM_001037125	NP_001032202	Q9H9P5	UNKL_HUMAN	unkempt homolog (Drosophila)-like isoform 2	114						cytoplasm|nucleus	ligase activity|nucleic acid binding|zinc ion binding				0		Hepatocellular(780;0.0893)																---	---	---	---
C16orf91	283951	broad.mit.edu	37	16	1476347	1476347	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1476347G>A	uc010uvd.1	-	3	276	c.276C>T	c.(274-276)TGC>TGT	p.C92C		NM_001010878	NP_001010878	Q4G0I0	CSMT1_HUMAN	hypothetical protein LOC283951	Error:Variant_position_missing_in_Q4G0I0_after_alignment						integral to membrane					0																		---	---	---	---
TMEM204	79652	broad.mit.edu	37	16	1584500	1584500	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1584500C>T	uc002cmc.2	+	2	622	c.224C>T	c.(223-225)GCG>GTG	p.A75V	IFT140_uc002clz.2_Intron|IFT140_uc002cmb.2_Intron|TMEM204_uc002cmd.2_Missense_Mutation_p.A75V|TMEM204_uc010brr.1_Missense_Mutation_p.A75V	NM_024600	NP_078876	Q9BSN7	TM204_HUMAN	transmembrane protein 204	75	Extracellular (Potential).				response to stress	adherens junction|integral to membrane					0		Hepatocellular(780;0.219)																---	---	---	---
IFT140	9742	broad.mit.edu	37	16	1642550	1642550	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1642550G>A	uc002cmb.2	-	5	771	c.409C>T	c.(409-411)CGA>TGA	p.R137*		NM_014714	NP_055529	Q96RY7	IF140_HUMAN	intraflagellar transport 140	137	WD 3.									ovary(3)|pancreas(1)|skin(1)	5		Hepatocellular(780;0.219)																---	---	---	---
CRAMP1L	57585	broad.mit.edu	37	16	1723964	1723964	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1723964T>C	uc010uvh.1	+	20	3728	c.3728T>C	c.(3727-3729)CTG>CCG	p.L1243P	CRAMP1L_uc002cmf.2_RNA	NM_020825	NP_065876	Q96RY5	CRML_HUMAN	Crm, cramped-like	1243	Ser-rich.					nucleus	DNA binding				0																		---	---	---	---
MAPK8IP3	23162	broad.mit.edu	37	16	1817154	1817154	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1817154C>T	uc002cmk.2	+	26	3210	c.3090C>T	c.(3088-3090)GGC>GGT	p.G1030G	MAPK8IP3_uc002cml.2_Silent_p.G1024G|MAPK8IP3_uc010uvl.1_Silent_p.G1031G	NM_015133	NP_055948	Q9UPT6	JIP3_HUMAN	mitogen-activated protein kinase 8 interacting	1030					vesicle-mediated transport	Golgi membrane	kinesin binding|MAP-kinase scaffold activity|protein kinase binding			breast(2)|central_nervous_system(1)	3																		---	---	---	---
SPSB3	90864	broad.mit.edu	37	16	1828038	1828038	+	Silent	SNP	G	A	A	rs144730810		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:1828038G>A	uc002cmr.2	-	4	537	c.504C>T	c.(502-504)ATC>ATT	p.I168I	SPSB3_uc002cms.2_Silent_p.I40I|SPSB3_uc002cmt.2_Silent_p.I40I|SPSB3_uc002cmu.2_Silent_p.I168I|SPSB3_uc002cmv.2_Silent_p.I40I|SPSB3_uc010uvm.1_3'UTR	NM_080861	NP_543137	Q6PJ21	SPSB3_HUMAN	splA/ryanodine receptor domain and SOCS box	168	B30.2/SPRY.				intracellular signal transduction						0																		---	---	---	---
TBL3	10607	broad.mit.edu	37	16	2028568	2028568	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2028568G>A	uc002cnu.1	+	22	2411	c.2309G>A	c.(2308-2310)CGG>CAG	p.R770Q	TBL3_uc002cnv.1_Missense_Mutation_p.R656Q|TBL3_uc010bsc.1_Missense_Mutation_p.R637Q|TBL3_uc010uvt.1_Missense_Mutation_p.R239Q|TBL3_uc002cnw.1_RNA	NM_006453	NP_006444	Q12788	TBL3_HUMAN	transducin beta-like 3	770					G-protein signaling, coupled to cGMP nucleotide second messenger|rRNA processing	nucleolus|small-subunit processome	receptor signaling protein activity				0																		---	---	---	---
ABCA3	21	broad.mit.edu	37	16	2349463	2349463	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2349463A>T	uc002cpy.1	-	14	2394	c.1682T>A	c.(1681-1683)ATC>AAC	p.I561N	ABCA3_uc010bsk.1_Missense_Mutation_p.I503N|ABCA3_uc010bsl.1_Missense_Mutation_p.I561N	NM_001089	NP_001080	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A member 3	561	ABC transporter 1.				response to drug	integral to membrane|lamellar body|membrane fraction|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			breast(5)|ovary(5)|central_nervous_system(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	16		Ovarian(90;0.17)																---	---	---	---
ABCA3	21	broad.mit.edu	37	16	2374412	2374412	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2374412G>A	uc002cpy.1	-	6	1152	c.440C>T	c.(439-441)CCG>CTG	p.P147L	ABCA3_uc010bsk.1_Missense_Mutation_p.P147L|ABCA3_uc010bsl.1_Missense_Mutation_p.P147L|ABCA3_uc002cpz.1_Missense_Mutation_p.P147L	NM_001089	NP_001080	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A member 3	147					response to drug	integral to membrane|lamellar body|membrane fraction|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			breast(5)|ovary(5)|central_nervous_system(3)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	16		Ovarian(90;0.17)																---	---	---	---
CCNF	899	broad.mit.edu	37	16	2503260	2503260	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2503260G>A	uc002cqd.1	+	14	1625	c.1537G>A	c.(1537-1539)GTG>ATG	p.V513M	CCNF_uc002cqe.1_Missense_Mutation_p.V205M	NM_001761	NP_001752	P41002	CCNF_HUMAN	cyclin F	513					cell division|mitosis|negative regulation of centrosome duplication|protein ubiquitination|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	centriole|nucleus|SCF ubiquitin ligase complex	protein binding			central_nervous_system(1)|kidney(1)	2		Ovarian(90;0.17)																---	---	---	---
C16orf59	80178	broad.mit.edu	37	16	2512453	2512453	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2512453T>C	uc002cqh.2	+	7	819	c.788T>C	c.(787-789)GTG>GCG	p.V263A	C16orf59_uc002cqf.1_Missense_Mutation_p.V263A|C16orf59_uc002cqg.1_Missense_Mutation_p.V96A|C16orf59_uc002cqi.2_Missense_Mutation_p.V96A|C16orf59_uc010uwb.1_Missense_Mutation_p.V96A	NM_025108	NP_079384	Q7L2K0	CP059_HUMAN	hypothetical protein LOC80178	263											0		Ovarian(90;0.17)																---	---	---	---
SRRM2	23524	broad.mit.edu	37	16	2811736	2811736	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2811736C>T	uc002crk.2	+	11	1756	c.1207C>T	c.(1207-1209)CGT>TGT	p.R403C	SRRM2_uc002crj.1_Missense_Mutation_p.R307C|SRRM2_uc002crl.1_Missense_Mutation_p.R403C|SRRM2_uc010bsu.1_Missense_Mutation_p.R307C	NM_016333	NP_057417	Q9UQ35	SRRM2_HUMAN	splicing coactivator subunit SRm300	403	Pro-rich.|Ser-rich.					Cajal body|catalytic step 2 spliceosome|nuclear speck	C2H2 zinc finger domain binding|protein N-terminus binding|RNA binding			ovary(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
SRRM2	23524	broad.mit.edu	37	16	2812144	2812144	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2812144C>T	uc002crk.2	+	11	2164	c.1615C>T	c.(1615-1617)CGA>TGA	p.R539*	SRRM2_uc002crj.1_Nonsense_Mutation_p.R443*|SRRM2_uc002crl.1_Nonsense_Mutation_p.R539*|SRRM2_uc010bsu.1_Nonsense_Mutation_p.R443*	NM_016333	NP_057417	Q9UQ35	SRRM2_HUMAN	splicing coactivator subunit SRm300	539	Arg-rich.|Ser-rich.					Cajal body|catalytic step 2 spliceosome|nuclear speck	C2H2 zinc finger domain binding|protein N-terminus binding|RNA binding			ovary(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
PRSS21	10942	broad.mit.edu	37	16	2871500	2871500	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2871500G>A	uc002crt.2	+	6	945	c.839G>A	c.(838-840)TGG>TAG	p.W280*	PRSS21_uc002crs.2_Nonsense_Mutation_p.W278*|PRSS21_uc002crr.2_Nonsense_Mutation_p.W266*	NM_006799	NP_006790	Q9Y6M0	TEST_HUMAN	testisin isoform 1	280	Peptidase S1.				proteolysis	anchored to membrane|cytoplasm|membrane fraction|plasma membrane	serine-type endopeptidase activity			ovary(1)|skin(1)	2																		---	---	---	---
FLYWCH2	114984	broad.mit.edu	37	16	2946483	2946483	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2946483T>C	uc002csa.2	+	3	404	c.33T>C	c.(31-33)GGT>GGC	p.G11G	FLYWCH2_uc010uwj.1_Silent_p.G11G|FLYWCH2_uc010uwk.1_Silent_p.G11G	NM_138439	NP_612448	Q96CP2	FWCH2_HUMAN	FLYWCH family member 2	11											0																		---	---	---	---
ZSCAN10	84891	broad.mit.edu	37	16	3140226	3140226	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3140226C>T	uc002ctv.1	-	5	1132	c.1044G>A	c.(1042-1044)CCG>CCA	p.P348P	ZSCAN10_uc002cty.1_Silent_p.P9P|ZSCAN10_uc002ctw.1_Silent_p.P266P|ZSCAN10_uc002ctx.1_Silent_p.P276P	NM_032805	NP_116194	Q96SZ4	ZSC10_HUMAN	zinc finger and SCAN domain containing 10	348					negative regulation of transcription, DNA-dependent|viral reproduction	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1																		---	---	---	---
ZNF75A	7627	broad.mit.edu	37	16	3367750	3367750	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3367750T>C	uc002cut.3	+	6	1298	c.772T>C	c.(772-774)TCC>CCC	p.S258P	ZNF75A_uc002cuv.3_RNA	NM_153028	NP_694573	Q96N20	ZN75A_HUMAN	zinc finger protein 75a	258	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)	1																		---	---	---	---
ZNF434	54925	broad.mit.edu	37	16	3432986	3432986	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3432986T>G	uc002cuz.2	-	6	2126	c.1324A>C	c.(1324-1326)ACC>CCC	p.T442P	ZNF434_uc002cux.3_Missense_Mutation_p.T653P|ZNF434_uc010uwx.1_Missense_Mutation_p.T365P|ZNF434_uc002cuy.3_Missense_Mutation_p.T365P	NM_017810	NP_060280	Q9NX65	ZN434_HUMAN	zinc finger protein 434	442	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2																		---	---	---	---
BTBD12	84464	broad.mit.edu	37	16	3639766	3639766	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3639766C>T	uc002cvp.2	-	12	4500	c.3873G>A	c.(3871-3873)ACG>ACA	p.T1291T		NM_032444	NP_115820	Q8IY92	SLX4_HUMAN	BTB (POZ) domain containing 12	1291	Interaction with PLK1 and TERF2-TERF2IP.				DNA double-strand break processing involved in repair via single-strand annealing|double-strand break repair via homologous recombination|nucleotide-excision repair	Slx1-Slx4 complex	enzyme activator activity|protein binding				0													Direct_reversal_of_damage|Homologous_recombination	Fanconi_Anemia				---	---	---	---
BTBD12	84464	broad.mit.edu	37	16	3647857	3647857	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3647857G>A	uc002cvp.2	-	6	1934	c.1307C>T	c.(1306-1308)GCG>GTG	p.A436V		NM_032444	NP_115820	Q8IY92	SLX4_HUMAN	BTB (POZ) domain containing 12	436	Interaction with C20orf94, ERCC4 and MSH2.				DNA double-strand break processing involved in repair via single-strand annealing|double-strand break repair via homologous recombination|nucleotide-excision repair	Slx1-Slx4 complex	enzyme activator activity|protein binding				0													Direct_reversal_of_damage|Homologous_recombination	Fanconi_Anemia				---	---	---	---
CREBBP	1387	broad.mit.edu	37	16	3779420	3779420	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3779420G>A	uc002cvv.2	-	31	5832	c.5628C>T	c.(5626-5628)AAC>AAT	p.N1876N	CREBBP_uc002cvw.2_Silent_p.N1838N	NM_004380	NP_004371	Q92793	CBP_HUMAN	CREB binding protein isoform a	1876	Interaction with TRERF1.				cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia	cytoplasm|nuclear body	histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(97)|ovary(14)|lung(6)|skin(6)|breast(2)|NS(1)|pancreas(1)	127		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)				T|N|F|Mis|O	MLL|MORF|RUNXBP2	ALL|AML|DLBCL|B-NHL 		Rubinstein-Taybi syndrome		Rubinstein-Taybi_syndrome				---	---	---	---
PPL	5493	broad.mit.edu	37	16	4934449	4934449	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4934449G>A	uc002cyd.1	-	22	4297	c.4207C>T	c.(4207-4209)CTG>TTG	p.L1403L		NM_002705	NP_002696	O60437	PEPL_HUMAN	periplakin	1403	Potential.				keratinization	cytoskeleton|desmosome|mitochondrion|nucleus	protein binding|structural constituent of cytoskeleton			ovary(4)|central_nervous_system(1)|skin(1)	6																		---	---	---	---
A2BP1	54715	broad.mit.edu	37	16	7760686	7760686	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:7760686T>C	uc002cys.2	+	16	2121	c.1133T>C	c.(1132-1134)GTT>GCT	p.V378A	A2BP1_uc002cyt.2_Missense_Mutation_p.V351A|A2BP1_uc010uyb.1_Missense_Mutation_p.V378A|A2BP1_uc002cyw.2_3'UTR|A2BP1_uc002cyy.2_Missense_Mutation_p.V399A|A2BP1_uc002cyx.2_Intron|A2BP1_uc010uyc.1_Missense_Mutation_p.V372A	NM_018723	NP_061193	Q9NWB1	RFOX1_HUMAN	ataxin 2-binding protein 1 isoform 4	378					mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)														---	---	---	---
C16orf68	79091	broad.mit.edu	37	16	8729036	8729036	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8729036C>T	uc002cyz.2	+	5	843	c.567C>T	c.(565-567)GGC>GGT	p.G189G	C16orf68_uc002cza.2_Silent_p.G133G	NM_024109	NP_077014	Q9BUU2	MET22_HUMAN	hypothetical protein LOC79091	189							methyltransferase activity				0																		---	---	---	---
ABAT	18	broad.mit.edu	37	16	8857947	8857947	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8857947G>A	uc002czc.3	+	7	554	c.388G>A	c.(388-390)GCC>ACC	p.A130T	ABAT_uc002czd.3_Missense_Mutation_p.A130T|ABAT_uc010buh.2_Missense_Mutation_p.A72T|ABAT_uc010bui.2_Missense_Mutation_p.A130T	NM_020686	NP_065737	P80404	GABT_HUMAN	4-aminobutyrate aminotransferase precursor	130					behavioral response to cocaine|gamma-aminobutyric acid catabolic process|neurotransmitter catabolic process|neurotransmitter secretion	4-aminobutyrate transaminase complex|mitochondrial matrix	(S)-3-amino-2-methylpropionate transaminase activity|4-aminobutyrate transaminase activity|protein homodimerization activity|pyridoxal phosphate binding|succinate-semialdehyde dehydrogenase binding			upper_aerodigestive_tract(1)	1					Divalproex sodium(DB00510)|Isoniazid(DB00951)|L-Alanine(DB00160)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)|Pyruvic acid(DB00119)|Tiagabine(DB00906)|Valproic Acid(DB00313)|Vigabatrin(DB01080)													---	---	---	---
CARHSP1	23589	broad.mit.edu	37	16	8949043	8949043	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8949043G>T	uc002czh.1	-	4	772	c.422C>A	c.(421-423)TCT>TAT	p.S141Y	PMM2_uc002czg.1_RNA|CARHSP1_uc002czi.1_Missense_Mutation_p.S141Y	NM_001042476	NP_001035941	Q9Y2V2	CHSP1_HUMAN	calcium-regulated heat-stable protein 1	141					intracellular signal transduction|regulation of mRNA stability|regulation of transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|P granule	DNA binding|mRNA 3'-UTR binding|phosphatase binding				0																		---	---	---	---
USP7	7874	broad.mit.edu	37	16	8993580	8993580	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:8993580T>C	uc002czl.2	-	22	2543	c.2344A>G	c.(2344-2346)ACC>GCC	p.T782A	USP7_uc010uyk.1_Missense_Mutation_p.T683A|USP7_uc002czj.2_RNA|USP7_uc010uyj.1_Missense_Mutation_p.T683A|USP7_uc002czk.2_Missense_Mutation_p.T766A	NM_003470	NP_003461	Q93009	UBP7_HUMAN	ubiquitin specific peptidase 7	782	Interaction with ICP0/VMW110.				interspecies interaction between organisms|multicellular organismal development|protein deubiquitination|regulation of sequence-specific DNA binding transcription factor activity|ubiquitin-dependent protein catabolic process	cytoplasm|PML body	cysteine-type endopeptidase activity|p53 binding|protein C-terminus binding|transcription factor binding|ubiquitin protein ligase binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)	3																		---	---	---	---
GRIN2A	2903	broad.mit.edu	37	16	10274218	10274218	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10274218G>A	uc002czo.3	-	2	599	c.51C>T	c.(49-51)GTC>GTT	p.V17V	GRIN2A_uc010uym.1_Silent_p.V17V|GRIN2A_uc002czr.3_Silent_p.V17V|GRIN2A_uc010buk.2_Silent_p.V17V	NM_001134407	NP_001127879	Q12879	NMDE1_HUMAN	N-methyl-D-aspartate receptor subunit 2A isoform	17					response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			skin(32)|NS(5)|ovary(4)|large_intestine(1)|lung(1)|breast(1)|kidney(1)	45					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)													---	---	---	---
CIITA	4261	broad.mit.edu	37	16	11001246	11001246	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11001246C>T	uc002dai.3	+	11	2030	c.1897C>T	c.(1897-1899)CTG>TTG	p.L633L	CIITA_uc002daj.3_Silent_p.L634L|CIITA_uc002dak.3_Intron|CIITA_uc002dag.2_Silent_p.L633L|CIITA_uc002dah.2_Silent_p.L585L|CIITA_uc010bup.1_Intron	NM_000246	NP_000237	P33076	C2TA_HUMAN	class II transactivator	633	NACHT.				interferon-gamma-mediated signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of MHC class I biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|response to antibiotic|transcription, DNA-dependent	nucleus	activating transcription factor binding|ATP binding|protein C-terminus binding|protein complex binding|transcription coactivator activity|transcription regulatory region DNA binding			central_nervous_system(1)	1								T	FLJ27352|CD274|CD273|RALGDS|RUNDC2A|C16orf75	PMBL|Hodgkin Lymphona|								---	---	---	---
CIITA	4261	broad.mit.edu	37	16	11004056	11004056	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:11004056C>A	uc002dai.3	+	13	2961	c.2828C>A	c.(2827-2829)TCC>TAC	p.S943Y	CIITA_uc002daj.3_Missense_Mutation_p.S944Y|CIITA_uc002dak.3_Missense_Mutation_p.S359Y|CIITA_uc010bup.1_Missense_Mutation_p.P340T	NM_000246	NP_000237	P33076	C2TA_HUMAN	class II transactivator	943			Missing (in BLS2).		interferon-gamma-mediated signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of MHC class I biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|response to antibiotic|transcription, DNA-dependent	nucleus	activating transcription factor binding|ATP binding|protein C-terminus binding|protein complex binding|transcription coactivator activity|transcription regulatory region DNA binding			central_nervous_system(1)	1								T	FLJ27352|CD274|CD273|RALGDS|RUNDC2A|C16orf75	PMBL|Hodgkin Lymphona|								---	---	---	---
MKL2	57496	broad.mit.edu	37	16	14234480	14234480	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:14234480C>T	uc010uza.1	+	3	172	c.17C>T	c.(16-18)GCG>GTG	p.A6V	MKL2_uc002dcg.2_Missense_Mutation_p.A6V	NM_014048	NP_054767	Q9ULH7	MKL2_HUMAN	megakaryoblastic leukemia 2 protein	Error:Variant_position_missing_in_Q9ULH7_after_alignment					cell differentiation|muscle organ development|positive regulation of striated muscle tissue development|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		identical protein binding|nucleic acid binding|transcription coactivator activity			ovary(3)|kidney(1)|pancreas(1)	5																		---	---	---	---
KIAA0430	9665	broad.mit.edu	37	16	15718616	15718616	+	Intron	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15718616C>A	uc002ddr.2	-						KIAA0430_uc002ddq.2_Intron|KIAA0430_uc010uzv.1_Intron|KIAA0430_uc010uzw.1_Intron	NM_014647	NP_055462			limkain b1							peroxisome	nucleotide binding|RNA binding				0																		---	---	---	---
KIAA0430	9665	broad.mit.edu	37	16	15733099	15733099	+	5'UTR	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15733099G>A	uc002ddr.2	-	2					KIAA0430_uc002ddq.2_5'UTR|KIAA0430_uc010uzv.1_5'UTR|KIAA0430_uc010uzw.1_5'UTR|KIAA0430_uc010uzx.1_5'UTR	NM_014647	NP_055462			limkain b1							peroxisome	nucleotide binding|RNA binding				0																		---	---	---	---
NDE1	54820	broad.mit.edu	37	16	15761140	15761140	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15761140T>C	uc002ddt.1	+						NDE1_uc010uzy.1_Intron|NDE1_uc002dds.2_Intron	NM_017668	NP_060138			nuclear distribution gene E homolog 1						cell differentiation|cell division|centrosome duplication|establishment of chromosome localization|establishment of mitotic spindle orientation|G2/M transition of mitotic cell cycle|mitotic prometaphase|nervous system development	cleavage furrow|condensed chromosome kinetochore|cytosol|microtubule|spindle pole centrosome	microtubule binding			ovary(1)	1																		---	---	---	---
MYH11	4629	broad.mit.edu	37	16	15814772	15814772	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15814772A>C	uc002ddy.2	-	33	4822	c.4715T>G	c.(4714-4716)CTC>CGC	p.L1572R	MYH11_uc002ddv.2_Missense_Mutation_p.L1579R|MYH11_uc002ddw.2_Missense_Mutation_p.L1572R|MYH11_uc002ddx.2_Missense_Mutation_p.L1579R|MYH11_uc010bvg.2_Missense_Mutation_p.L1404R|NDE1_uc010uzy.1_Intron|NDE1_uc002dds.2_Intron|MYH11_uc010bvh.2_Missense_Mutation_p.L278R|NDE1_uc002ddz.1_5'Flank	NM_002474	NP_002465	P35749	MYH11_HUMAN	smooth muscle myosin heavy chain 11 isoform	1572	Potential.				axon guidance|cardiac muscle fiber development|elastic fiber assembly|skeletal muscle myosin thick filament assembly|smooth muscle contraction	cytosol|melanosome|muscle myosin complex|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			ovary(6)|skin(3)|lung(2)|breast(2)|upper_aerodigestive_tract(1)|pancreas(1)	15								T	CBFB	AML								---	---	---	---
MYH11	4629	broad.mit.edu	37	16	15917126	15917126	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15917126C>T	uc002ddy.2	-	3	595	c.488G>A	c.(487-489)CGG>CAG	p.R163Q	MYH11_uc002ddv.2_Missense_Mutation_p.R163Q|MYH11_uc002ddw.2_Missense_Mutation_p.R163Q|MYH11_uc002ddx.2_Missense_Mutation_p.R163Q|MYH11_uc010bvg.2_5'UTR|MYH11_uc002deb.3_Missense_Mutation_p.R163Q	NM_002474	NP_002465	P35749	MYH11_HUMAN	smooth muscle myosin heavy chain 11 isoform	163	Myosin head-like.				axon guidance|cardiac muscle fiber development|elastic fiber assembly|skeletal muscle myosin thick filament assembly|smooth muscle contraction	cytosol|melanosome|muscle myosin complex|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			ovary(6)|skin(3)|lung(2)|breast(2)|upper_aerodigestive_tract(1)|pancreas(1)	15								T	CBFB	AML								---	---	---	---
MYH11	4629	broad.mit.edu	37	16	15931787	15931787	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15931787C>T	uc002ddy.2	-	2	430	c.323G>A	c.(322-324)CGG>CAG	p.R108Q	MYH11_uc002ddv.2_Missense_Mutation_p.R108Q|MYH11_uc002ddw.2_Missense_Mutation_p.R108Q|MYH11_uc002ddx.2_Missense_Mutation_p.R108Q|MYH11_uc010bvg.2_5'UTR|MYH11_uc002deb.3_Missense_Mutation_p.R108Q	NM_002474	NP_002465	P35749	MYH11_HUMAN	smooth muscle myosin heavy chain 11 isoform	108	Myosin head-like.				axon guidance|cardiac muscle fiber development|elastic fiber assembly|skeletal muscle myosin thick filament assembly|smooth muscle contraction	cytosol|melanosome|muscle myosin complex|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			ovary(6)|skin(3)|lung(2)|breast(2)|upper_aerodigestive_tract(1)|pancreas(1)	15								T	CBFB	AML								---	---	---	---
MYH11	4629	broad.mit.edu	37	16	15931913	15931913	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15931913C>T	uc002ddy.2	-	2	304	c.197G>A	c.(196-198)GGC>GAC	p.G66D	MYH11_uc002ddv.2_Missense_Mutation_p.G66D|MYH11_uc002ddw.2_Missense_Mutation_p.G66D|MYH11_uc002ddx.2_Missense_Mutation_p.G66D|MYH11_uc010bvg.2_5'UTR|MYH11_uc002deb.3_Missense_Mutation_p.G66D	NM_002474	NP_002465	P35749	MYH11_HUMAN	smooth muscle myosin heavy chain 11 isoform	66	Myosin head-like.				axon guidance|cardiac muscle fiber development|elastic fiber assembly|skeletal muscle myosin thick filament assembly|smooth muscle contraction	cytosol|melanosome|muscle myosin complex|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			ovary(6)|skin(3)|lung(2)|breast(2)|upper_aerodigestive_tract(1)|pancreas(1)	15								T	CBFB	AML								---	---	---	---
ABCC1	4363	broad.mit.edu	37	16	16232222	16232222	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16232222G>A	uc010bvi.2	+	30	4469	c.4294G>A	c.(4294-4296)GTC>ATC	p.V1432I	ABCC1_uc010bvj.2_Missense_Mutation_p.V1373I|ABCC1_uc010bvk.2_Missense_Mutation_p.V1376I|ABCC1_uc010bvl.2_Intron|ABCC1_uc010bvm.2_Missense_Mutation_p.V1317I|ABCC1_uc002del.3_Missense_Mutation_p.V1326I	NM_004996	NP_004987	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C, member 1	1432	ABC transporter 2.|Cytoplasmic.				hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process|response to drug	Golgi apparatus|integral to plasma membrane|membrane fraction|nucleus	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)	4					Daunorubicin(DB00694)|Glibenclamide(DB01016)|Probenecid(DB01032)|Saquinavir(DB01232)|Sulfinpyrazone(DB01138)													---	---	---	---
ABCC6	368	broad.mit.edu	37	16	16259697	16259697	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16259697C>T	uc002den.3	-	23	3126	c.3089G>A	c.(3088-3090)CGA>CAA	p.R1030Q	ABCC6_uc010bvo.2_RNA	NM_001171	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C, member 6	1030	Cytoplasmic (By similarity).|ABC transmembrane type-1 2.				response to drug|visual perception	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			skin(2)|ovary(1)	3				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)														---	---	---	---
ITPRIPL2	162073	broad.mit.edu	37	16	19127180	19127180	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19127180G>A	uc002dfu.3	+	1	1927	c.1397G>A	c.(1396-1398)GGT>GAT	p.G466D	ITPRIPL2_uc002dft.2_Missense_Mutation_p.G162D	NM_001034841	NP_001030013	Q3MIP1	IPIL2_HUMAN	inositol 1,4,5-triphosphate receptor interacting	466	Cytoplasmic (Potential).					integral to membrane				skin(2)	2																		---	---	---	---
GDE1	51573	broad.mit.edu	37	16	19516332	19516332	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19516332C>T	uc002dgh.2	-	5	883	c.719G>A	c.(718-720)CGC>CAC	p.R240H	GDE1_uc002dgi.2_Missense_Mutation_p.R130H	NM_016641	NP_057725	Q9NZC3	GDE1_HUMAN	glycerophosphodiester phosphodiesterase 1	240	Lumenal (Potential).|GDPD.				glycerol metabolic process|lipid metabolic process	cytoplasm|integral to membrane	glycerophosphodiester phosphodiesterase activity|glycerophosphoinositol glycerophosphodiesterase activity|metal ion binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
C16orf62	57020	broad.mit.edu	37	16	19661787	19661787	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19661787T>C	uc002dgn.1	+						C16orf62_uc002dgo.1_Intron|C16orf62_uc002dgp.1_Intron	NM_020314	NP_064710			hypothetical protein LOC57020							integral to membrane				ovary(1)	1																		---	---	---	---
GP2	2813	broad.mit.edu	37	16	20331616	20331616	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20331616C>T	uc002dgv.2	-	6	918	c.835G>A	c.(835-837)GTC>ATC	p.V279I	GP2_uc002dgw.2_Missense_Mutation_p.V276I|GP2_uc002dgx.2_Missense_Mutation_p.V132I|GP2_uc002dgy.2_Missense_Mutation_p.V129I	NM_001007240	NP_001007241	P55259	GP2_HUMAN	zymogen granule membrane glycoprotein 2 isoform	279	ZP.					anchored to membrane|extracellular region|plasma membrane				ovary(3)|skin(1)	4																		---	---	---	---
UMOD	7369	broad.mit.edu	37	16	20348654	20348654	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20348654C>A	uc002dgz.2	-	8	1828	c.1699G>T	c.(1699-1701)GAA>TAA	p.E567*	UMOD_uc002dha.2_Nonsense_Mutation_p.E567*|UMOD_uc002dhb.2_Nonsense_Mutation_p.E600*	NM_003361	NP_003352	P07911	UROM_HUMAN	uromodulin precursor	567	ZP.				cellular defense response|negative regulation of cell proliferation	anchored to membrane|apical plasma membrane|basolateral plasma membrane|cilium membrane|extrinsic to membrane|primary cilium|spindle pole	calcium ion binding			ovary(1)|skin(1)	2																		---	---	---	---
UMOD	7369	broad.mit.edu	37	16	20359579	20359579	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20359579C>T	uc002dgz.2	-	4	1068	c.939G>A	c.(937-939)TGG>TGA	p.W313*	UMOD_uc002dha.2_Nonsense_Mutation_p.W313*|UMOD_uc002dhb.2_Nonsense_Mutation_p.W346*	NM_003361	NP_003352	P07911	UROM_HUMAN	uromodulin precursor	313					cellular defense response|negative regulation of cell proliferation	anchored to membrane|apical plasma membrane|basolateral plasma membrane|cilium membrane|extrinsic to membrane|primary cilium|spindle pole	calcium ion binding			ovary(1)|skin(1)	2																		---	---	---	---
ACSM5	54988	broad.mit.edu	37	16	20432718	20432718	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20432718C>T	uc002dhe.2	+	5	909	c.762C>T	c.(760-762)AGC>AGT	p.S254S		NM_017888	NP_060358	Q6NUN0	ACSM5_HUMAN	acyl-CoA synthetase medium-chain family member 5	254					fatty acid metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|GTP binding|metal ion binding			ovary(2)	2																		---	---	---	---
ACSM3	6296	broad.mit.edu	37	16	20802011	20802011	+	Splice_Site	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20802011G>A	uc002dhr.2	+	10	1513	c.1326_splice	c.e10+1	p.V442_splice	ACSM3_uc010vba.1_Splice_Site_p.V471_splice|ERI2_uc002dhs.2_Intron	NM_005622	NP_005613			SA hypertension-associated homolog isoform 1						regulation of blood pressure	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|metal ion binding			ovary(1)	1																		---	---	---	---
DNAH3	55567	broad.mit.edu	37	16	20981185	20981185	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20981185T>C	uc010vbe.1	-	52	8387	c.8387A>G	c.(8386-8388)AAA>AGA	p.K2796R	DNAH3_uc010vbd.1_Missense_Mutation_p.K231R	NM_017539	NP_060009	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	2796	Stalk (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)														---	---	---	---
DNAH3	55567	broad.mit.edu	37	16	20990861	20990861	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:20990861A>G	uc010vbe.1	-	50	7867	c.7867T>C	c.(7867-7869)TCC>CCC	p.S2623P	DNAH3_uc010vbd.1_Missense_Mutation_p.S58P	NM_017539	NP_060009	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	2623	AAA 4 (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)														---	---	---	---
DNAH3	55567	broad.mit.edu	37	16	21049096	21049096	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21049096A>G	uc010vbe.1	-	34	4937	c.4937T>C	c.(4936-4938)GTC>GCC	p.V1646A		NM_017539	NP_060009	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1646					ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)														---	---	---	---
ZP2	7783	broad.mit.edu	37	16	21217083	21217083	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21217083C>A	uc002dii.2	-	6	497	c.497G>T	c.(496-498)CGG>CTG	p.R166L	ZP2_uc010bwn.1_Missense_Mutation_p.R205L|ZP2_uc010bwo.2_Missense_Mutation_p.R205L	NM_003460	NP_003451	Q05996	ZP2_HUMAN	zona pellucida glycoprotein 2 preproprotein	166	Extracellular (Potential).				binding of sperm to zona pellucida|intracellular protein transport	endoplasmic reticulum|Golgi apparatus|integral to membrane|multivesicular body|plasma membrane|proteinaceous extracellular matrix|stored secretory granule	acrosin binding|coreceptor activity			central_nervous_system(2)|ovary(1)	3				GBM - Glioblastoma multiforme(48;0.0573)														---	---	---	---
CRYM	1428	broad.mit.edu	37	16	21288815	21288815	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21288815C>T	uc002dik.2	-	2	346	c.261G>A	c.(259-261)TCG>TCA	p.S87S	CRYM_uc010bwq.1_RNA|CRYM_uc002dil.2_Silent_p.S45S|CRYM_uc002dim.2_Silent_p.S87S	NM_001888	NP_001879	Q14894	CRYM_HUMAN	crystallin, mu isoform 1	87					negative regulation of transcription from RNA polymerase II promoter|sensory perception of sound|thyroid hormone transport	cytoplasm|nucleus|plasma membrane	NADP binding|protein homodimerization activity|thyroid hormone binding|transcription corepressor activity				0				GBM - Glioblastoma multiforme(48;0.0573)	Levothyroxine(DB00451)													---	---	---	---
OTOA	146183	broad.mit.edu	37	16	21726398	21726398	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21726398G>A	uc002djh.2	+	13	1414	c.1413G>A	c.(1411-1413)TCG>TCA	p.S471S	uc002diq.3_Intron|OTOA_uc010vbj.1_Silent_p.S392S|OTOA_uc002dji.2_Silent_p.S147S|OTOA_uc010vbk.1_Silent_p.S119S	NM_144672	NP_653273	Q7RTW8	OTOAN_HUMAN	otoancorin isoform 1	485					sensory perception of sound	anchored to membrane|apical plasma membrane|proteinaceous extracellular matrix				ovary(1)|central_nervous_system(1)|skin(1)	3				GBM - Glioblastoma multiforme(48;0.0414)														---	---	---	---
EEF2K	29904	broad.mit.edu	37	16	22268213	22268213	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22268213C>A	uc002dki.2	+	7	1248	c.763C>A	c.(763-765)CCG>ACG	p.P255T	EEF2K_uc002dkh.2_RNA	NM_013302	NP_037434	O00418	EF2K_HUMAN	elongation factor-2 kinase	255	Alpha-type protein kinase.				insulin receptor signaling pathway|translational elongation	cytosol	ATP binding|calcium ion binding|calmodulin binding|elongation factor-2 kinase activity|translation factor activity, nucleic acid binding			large_intestine(1)	1				GBM - Glioblastoma multiforme(48;0.0223)														---	---	---	---
EEF2K	29904	broad.mit.edu	37	16	22269945	22269945	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:22269945A>G	uc002dki.2	+	10	1645	c.1160A>G	c.(1159-1161)GAC>GGC	p.D387G	EEF2K_uc002dkh.2_RNA	NM_013302	NP_037434	O00418	EF2K_HUMAN	elongation factor-2 kinase	387					insulin receptor signaling pathway|translational elongation	cytosol	ATP binding|calcium ion binding|calmodulin binding|elongation factor-2 kinase activity|translation factor activity, nucleic acid binding			large_intestine(1)	1				GBM - Glioblastoma multiforme(48;0.0223)														---	---	---	---
COG7	91949	broad.mit.edu	37	16	23400377	23400377	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23400377C>T	uc002dlo.2	-	17	2365	c.2177G>A	c.(2176-2178)GGC>GAC	p.G726D		NM_153603	NP_705831	P83436	COG7_HUMAN	component of oligomeric golgi complex 7	726					intracellular protein transport|protein glycosylation|protein localization in Golgi apparatus|protein stabilization|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane|Golgi transport complex	protein binding				0				GBM - Glioblastoma multiforme(48;0.0401)														---	---	---	---
COG7	91949	broad.mit.edu	37	16	23409462	23409462	+	Intron	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23409462A>C	uc002dlo.2	-							NM_153603	NP_705831			component of oligomeric golgi complex 7						intracellular protein transport|protein glycosylation|protein localization in Golgi apparatus|protein stabilization|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane|Golgi transport complex	protein binding				0				GBM - Glioblastoma multiforme(48;0.0401)														---	---	---	---
EARS2	124454	broad.mit.edu	37	16	23535745	23535745	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23535745C>T	uc002dlt.3	-	9	1551	c.1519G>A	c.(1519-1521)GCC>ACC	p.A507T	EARS2_uc002dlr.3_RNA|EARS2_uc002dls.3_RNA	NM_001083614	NP_001077083	Q5JPH6	SYEM_HUMAN	glutamyl-tRNA synthetase 2 precursor	507					glutamyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|glutamate-tRNA ligase activity|RNA binding				0				GBM - Glioblastoma multiforme(48;0.0353)	L-Glutamic Acid(DB00142)													---	---	---	---
PLK1	5347	broad.mit.edu	37	16	23695261	23695261	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:23695261T>A	uc002dlz.1	+	5	940	c.887T>A	c.(886-888)ATT>AAT	p.I296N		NM_005030	NP_005021	P53350	PLK1_HUMAN	polo-like kinase 1	296	Protein kinase.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|G2/M transition DNA damage checkpoint|G2/M transition of mitotic cell cycle|mitotic metaphase/anaphase transition|mitotic prometaphase|mitotic prophase|negative regulation of cyclin-dependent protein kinase activity|peptidyl-serine phosphorylation|positive regulation of peptidyl-threonine phosphorylation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein destabilization|protein localization to chromatin|protein ubiquitination|regulation of mitotic anaphase|regulation of protein binding	centrosome|condensed nuclear chromosome outer kinetochore|cytosol|nucleoplasm|spindle microtubule|spindle midzone|spindle pole	anaphase-promoting complex binding|ATP binding|polo kinase kinase activity|protein kinase binding			lung(1)|skin(1)	2				GBM - Glioblastoma multiforme(48;0.0156)														---	---	---	---
PRKCB	5579	broad.mit.edu	37	16	24046806	24046806	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24046806C>T	uc002dmd.2	+	5	664	c.467C>T	c.(466-468)ACG>ATG	p.T156M	PRKCB_uc002dme.2_Missense_Mutation_p.T156M	NM_212535	NP_997700	P05771	KPCB_HUMAN	protein kinase C, beta isoform 1	156					apoptosis|B cell activation|B cell receptor signaling pathway|intracellular signal transduction|lipoprotein transport|platelet activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|synaptic transmission|transcription, DNA-dependent	cytosol|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|histone binding|histone kinase activity (H3-T6 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|zinc ion binding			ovary(3)|central_nervous_system(3)|lung(2)|large_intestine(1)	9					Vitamin E(DB00163)													---	---	---	---
RBBP6	5930	broad.mit.edu	37	16	24579196	24579196	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24579196G>A	uc002dmh.2	+	16	3076	c.2036G>A	c.(2035-2037)CGT>CAT	p.R679H	RBBP6_uc010vcb.1_Missense_Mutation_p.R546H|RBBP6_uc002dmi.2_Intron|RBBP6_uc010bxr.2_Intron|RBBP6_uc002dmk.2_Intron	NM_006910	NP_008841	Q7Z6E9	RBBP6_HUMAN	retinoblastoma-binding protein 6 isoform 1	679					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	chromosome|nucleolus|ubiquitin ligase complex	nucleic acid binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|pancreas(1)	4				GBM - Glioblastoma multiforme(48;0.0518)														---	---	---	---
ARHGAP17	55114	broad.mit.edu	37	16	24942329	24942329	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24942329G>T	uc002dnb.2	-	19	2384	c.2291C>A	c.(2290-2292)CCG>CAG	p.P764Q	ARHGAP17_uc002dmx.2_Missense_Mutation_p.P26Q|ARHGAP17_uc002dmw.2_Missense_Mutation_p.P26Q|ARHGAP17_uc002dmy.2_Missense_Mutation_p.P209Q|ARHGAP17_uc002dmz.2_Missense_Mutation_p.P288Q|ARHGAP17_uc002dna.2_Missense_Mutation_p.P491Q|ARHGAP17_uc002dnc.2_Missense_Mutation_p.P686Q|ARHGAP17_uc010vcf.1_Missense_Mutation_p.P507Q|ARHGAP17_uc002dne.1_Missense_Mutation_p.P26Q	NM_001006634	NP_001006635	Q68EM7	RHG17_HUMAN	nadrin isoform 1	764	SH3-binding (Potential).|Pro-rich.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|tight junction	GTPase activator activity|SH3 domain binding				0				GBM - Glioblastoma multiforme(48;0.0407)														---	---	---	---
ARHGAP17	55114	broad.mit.edu	37	16	24971233	24971233	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24971233G>A	uc002dnb.2	-	8	734	c.641C>T	c.(640-642)ACG>ATG	p.T214M	ARHGAP17_uc002dna.2_5'Flank|ARHGAP17_uc002dnc.2_Missense_Mutation_p.T214M|ARHGAP17_uc010vcf.1_Missense_Mutation_p.T35M|ARHGAP17_uc002dnf.2_Missense_Mutation_p.T122M|ARHGAP17_uc002dng.1_Missense_Mutation_p.T214M	NM_001006634	NP_001006635	Q68EM7	RHG17_HUMAN	nadrin isoform 1	214	BAR.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|tight junction	GTPase activator activity|SH3 domain binding				0				GBM - Glioblastoma multiforme(48;0.0407)														---	---	---	---
ARHGAP17	55114	broad.mit.edu	37	16	24980070	24980070	+	Missense_Mutation	SNP	T	C	C	rs149663874		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24980070T>C	uc002dnb.2	-	5	389	c.296A>G	c.(295-297)GAT>GGT	p.D99G	ARHGAP17_uc002dnc.2_Missense_Mutation_p.D99G|ARHGAP17_uc010vcf.1_Intron|ARHGAP17_uc002dnf.2_Missense_Mutation_p.D7G|ARHGAP17_uc002dng.1_Missense_Mutation_p.D99G	NM_001006634	NP_001006635	Q68EM7	RHG17_HUMAN	nadrin isoform 1	99	BAR.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|tight junction	GTPase activator activity|SH3 domain binding				0				GBM - Glioblastoma multiforme(48;0.0407)														---	---	---	---
LCMT1	51451	broad.mit.edu	37	16	25123324	25123324	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25123324G>A	uc002dnx.1	+						LCMT1_uc002dny.1_Intron|LCMT1_uc002dnz.1_Intron|LCMT1_uc002doa.1_Intron|LCMT1_uc002dnw.1_Intron	NM_016309	NP_057393			leucine carboxyl methyltransferase 1 isoform a								protein binding|protein C-terminal carboxyl O-methyltransferase activity|S-adenosylmethionine-dependent methyltransferase activity				0				GBM - Glioblastoma multiforme(48;0.0336)	L-Leucine(DB00149)													---	---	---	---
GTF3C1	2975	broad.mit.edu	37	16	27518336	27518336	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27518336G>A	uc002dov.1	-	9	1424	c.1384C>T	c.(1384-1386)CAG>TAG	p.Q462*	GTF3C1_uc002dou.2_Nonsense_Mutation_p.Q462*	NM_001520	NP_001511	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide	462						transcription factor TFIIIC complex	DNA binding|protein binding			ovary(2)|pancreas(1)|breast(1)|skin(1)	5																		---	---	---	---
GTF3C1	2975	broad.mit.edu	37	16	27523104	27523104	+	Silent	SNP	G	A	A	rs142782053	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27523104G>A	uc002dov.1	-	7	1132	c.1092C>T	c.(1090-1092)TTC>TTT	p.F364F	GTF3C1_uc002dou.2_Silent_p.F364F	NM_001520	NP_001511	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide	364						transcription factor TFIIIC complex	DNA binding|protein binding			ovary(2)|pancreas(1)|breast(1)|skin(1)	5																		---	---	---	---
GTF3C1	2975	broad.mit.edu	37	16	27549199	27549199	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27549199C>A	uc002dov.1	-	4	698	c.658G>T	c.(658-660)GGG>TGG	p.G220W	GTF3C1_uc002dou.2_Missense_Mutation_p.G220W	NM_001520	NP_001511	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide	220						transcription factor TFIIIC complex	DNA binding|protein binding			ovary(2)|pancreas(1)|breast(1)|skin(1)	5																		---	---	---	---
KIAA0556	23247	broad.mit.edu	37	16	27781217	27781217	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27781217C>T	uc002dow.2	+	21	4035	c.4011C>T	c.(4009-4011)TGC>TGT	p.C1337C		NM_015202	NP_056017	O60303	K0556_HUMAN	hypothetical protein LOC23247	1337										ovary(4)|large_intestine(2)|upper_aerodigestive_tract(1)|skin(1)	8																		---	---	---	---
SBK1	388228	broad.mit.edu	37	16	28331450	28331450	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28331450G>A	uc002dpd.2	+	4	1272	c.483G>A	c.(481-483)GCG>GCA	p.A161A		NM_001024401	NP_001019572	Q52WX2	SBK1_HUMAN	SH3-binding kinase 1	161	Protein kinase.					cytoplasm	ATP binding|protein serine/threonine kinase activity			ovary(1)|kidney(1)	2																		---	---	---	---
APOB48R	55911	broad.mit.edu	37	16	28509498	28509498	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28509498C>T	uc002dqb.1	+	4	3035	c.3025C>T	c.(3025-3027)CGT>TGT	p.R1009C	uc010vct.1_Intron|APOB48R_uc010byg.1_Missense_Mutation_p.R547C	NM_018690	NP_061160	Q0VD83	APOBR_HUMAN	apolipoprotein B48 receptor	1009					cholesterol metabolic process|lipid transport	chylomicron|low-density lipoprotein particle|plasma membrane|very-low-density lipoprotein particle					0																		---	---	---	---
CCDC101	112869	broad.mit.edu	37	16	28601436	28601436	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28601436C>A	uc002dqf.2	+	6	494	c.309C>A	c.(307-309)CTC>CTA	p.L103L	uc010vct.1_Intron	NM_138414	NP_612423	Q96ES7	SGF29_HUMAN	coiled-coil domain containing 101	103					establishment of protein localization to chromatin|histone H3 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	Ada2/Gcn5/Ada3 transcription activator complex|SAGA-type complex	methylated histone residue binding			central_nervous_system(1)	1																		---	---	---	---
CCDC101	112869	broad.mit.edu	37	16	28602230	28602230	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28602230G>A	uc002dqf.2	+	9	924	c.739G>A	c.(739-741)GCC>ACC	p.A247T	uc010vct.1_Intron	NM_138414	NP_612423	Q96ES7	SGF29_HUMAN	coiled-coil domain containing 101	247	SGF29 C-terminal.				establishment of protein localization to chromatin|histone H3 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	Ada2/Gcn5/Ada3 transcription activator complex|SAGA-type complex	methylated histone residue binding			central_nervous_system(1)	1																		---	---	---	---
SULT1A2	6799	broad.mit.edu	37	16	28603362	28603362	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28603362C>T	uc002dqg.1	-	8	1226	c.875G>A	c.(874-876)CGC>CAC	p.R292H	uc010vct.1_Intron|SULT1A2_uc002dqh.1_Missense_Mutation_p.R292H	NM_177528	NP_803564	P50226	ST1A2_HUMAN	sulfotransferase family, cytosolic, 1A,	292					3'-phosphoadenosine 5'-phosphosulfate metabolic process|amine biosynthetic process|catecholamine metabolic process|steroid metabolic process|sulfation|xenobiotic metabolic process	cytosol	aryl sulfotransferase activity|flavonol 3-sulfotransferase activity				0																		---	---	---	---
TUFM	7284	broad.mit.edu	37	16	28855330	28855330	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28855330G>A	uc002drh.2	-	8	1154	c.1015C>T	c.(1015-1017)CGG>TGG	p.R339W	uc010vct.1_Intron|SH2B1_uc002dri.2_5'Flank	NM_003321	NP_003312	P49411	EFTU_HUMAN	Tu translation elongation factor, mitochondrial	336			R -> Q (in COXPD4).			mitochondrial nucleoid	GTP binding|GTPase activity|protein binding|translation elongation factor activity			ovary(1)	1																		---	---	---	---
ATP2A1	487	broad.mit.edu	37	16	28912091	28912091	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28912091G>A	uc002dro.1	+	15	2138	c.1954G>A	c.(1954-1956)GCC>ACC	p.A652T	uc010vct.1_Intron|ATP2A1_uc002drn.1_Missense_Mutation_p.A652T|ATP2A1_uc002drp.1_Missense_Mutation_p.A527T	NM_173201	NP_775293	O14983	AT2A1_HUMAN	ATPase, Ca++ transporting, fast twitch 1 isoform	652	Cytoplasmic (By similarity).				apoptosis in response to endoplasmic reticulum stress|apoptotic mitochondrial changes|ATP biosynthetic process|calcium ion import|elevation of endoplasmic reticulum calcium ion concentration|elevation of mitochondrial calcium ion concentration|maintenance of mitochondrion location|negative regulation of striated muscle contraction|platelet activation|positive regulation of fast-twitch skeletal muscle fiber contraction|reduction of endoplasmic reticulum calcium ion concentration|relaxation of skeletal muscle|response to endoplasmic reticulum stress	endoplasmic reticulum membrane|ER-Golgi intermediate compartment|H zone|I band|microsome|perinuclear region of cytoplasm|platelet dense tubular network membrane|sarcoplasmic reticulum|sarcoplasmic reticulum membrane	ATP binding|ATP binding|calcium ion binding|calcium ion binding|calcium-transporting ATPase activity|protein homodimerization activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4																		---	---	---	---
RABEP2	79874	broad.mit.edu	37	16	28925659	28925659	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28925659G>T	uc002drq.2	-	5	840	c.792C>A	c.(790-792)GCC>GCA	p.A264A	uc010vct.1_Intron|RABEP2_uc010vdf.1_Silent_p.A193A|RABEP2_uc010byn.2_Silent_p.A264A|RABEP2_uc002drr.2_Silent_p.A264A	NM_024816	NP_079092	Q9H5N1	RABE2_HUMAN	rabaptin, RAB GTPase binding effector protein 2	264					endocytosis|protein transport	early endosome	growth factor activity|GTPase activator activity			ovary(1)|breast(1)|skin(1)	3																		---	---	---	---
NFATC2IP	84901	broad.mit.edu	37	16	28970371	28970371	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:28970371C>T	uc002dru.2	+	7	1066	c.1051C>T	c.(1051-1053)CGG>TGG	p.R351W	uc010vct.1_Intron|NFATC2IP_uc002drt.2_Missense_Mutation_p.R72W|NFATC2IP_uc002drv.2_Missense_Mutation_p.R70W|NFATC2IP_uc010vdh.1_Missense_Mutation_p.R59W	NM_032815	NP_116204	Q8NCF5	NF2IP_HUMAN	nuclear factor of activated T-cells,	351	Ubiquitin-like.					cytoplasm|nucleus				ovary(1)	1																		---	---	---	---
KCTD13	253980	broad.mit.edu	37	16	29934517	29934517	+	Silent	SNP	C	T	T	rs145620145		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29934517C>T	uc002duv.2	-	2	599	c.408G>A	c.(406-408)GCG>GCA	p.A136A	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|KCTD13_uc010vee.1_RNA	NM_178863	NP_849194	Q8WZ19	BACD1_HUMAN	potassium channel tetramerisation domain	136					cell migration|DNA replication|negative regulation of Rho protein signal transduction|proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination|stress fiber assembly	Cul3-RING ubiquitin ligase complex|nucleus|voltage-gated potassium channel complex	GTP-Rho binding|voltage-gated potassium channel activity				0																		---	---	---	---
SEPT1	1731	broad.mit.edu	37	16	30389975	30389975	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30389975G>A	uc002dxy.2	-	11	1160	c.973C>T	c.(973-975)CCT>TCT	p.P325S	SEPT1_uc002dxw.2_RNA|SEPT1_uc002dxx.2_Missense_Mutation_p.P150S	NM_052838	NP_443070	Q8WYJ6	SEPT1_HUMAN	septin 1	325					cell cycle|cell division	microtubule organizing center|septin complex	GTP binding|protein binding			ovary(1)	1			Colorectal(24;0.193)															---	---	---	---
SEPHS2	22928	broad.mit.edu	37	16	30455846	30455846	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30455846C>T	uc010ves.1	-	2	1379	c.1203G>A	c.(1201-1203)GCG>GCA	p.A401A	SEPHS2_uc002dyh.1_Silent_p.A344A|SEPHS2_uc010vet.1_Silent_p.A283A	NM_012248	NP_036380	Q99611	SPS2_HUMAN	selenophosphate synthetase 2	401					selenocysteine biosynthetic process		ATP binding|selenide, water dikinase activity			breast(2)	2																		---	---	---	---
ITGAL	3683	broad.mit.edu	37	16	30510648	30510648	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30510648G>A	uc002dyi.3	+						ITGAL_uc002dyj.3_Intron|ITGAL_uc010vev.1_Intron	NM_002209	NP_002200			integrin alpha L isoform a precursor						blood coagulation|heterophilic cell-cell adhesion|inflammatory response|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|leukocyte migration|regulation of immune response|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell	integrin complex	cell adhesion molecule binding|receptor activity			ovary(3)|lung(3)|central_nervous_system(3)|breast(1)	10					Efalizumab(DB00095)													---	---	---	---
ZNF768	79724	broad.mit.edu	37	16	30536495	30536495	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30536495G>A	uc002dyk.3	-	2	1142	c.966C>T	c.(964-966)TGC>TGT	p.C322C	ZNF768_uc010vex.1_Silent_p.C291C|uc002dyl.1_5'Flank|ZNF768_uc010vew.1_Silent_p.C291C	NM_024671	NP_078947	Q9H5H4	ZN768_HUMAN	zinc finger protein 768	322	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	DNA-directed RNA polymerase II, core complex	DNA binding|zinc ion binding				0																		---	---	---	---
ZNF785	146540	broad.mit.edu	37	16	30594225	30594225	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30594225G>A	uc002dyw.1	-	3	952	c.874C>T	c.(874-876)CGT>TGT	p.R292C	uc002dyu.2_RNA|ZNF785_uc002dyv.1_Missense_Mutation_p.R277C|ZNF785_uc010vez.1_Missense_Mutation_p.R257C	NM_152458	NP_689671	A8K8V0	ZN785_HUMAN	zinc finger protein 785	292	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1																		---	---	---	---
SRCAP	10847	broad.mit.edu	37	16	30735752	30735752	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30735752G>A	uc002dze.1	+	25	5392	c.5007G>A	c.(5005-5007)CCG>CCA	p.P1669P	SRCAP_uc002dzf.2_RNA|SRCAP_uc002dzg.1_Silent_p.P1464P|SRCAP_uc010bzz.1_Silent_p.P1239P	NM_006662	NP_006653	Q6ZRS2	SRCAP_HUMAN	Snf2-related CBP activator protein	1669	Pro-rich.				interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|nucleus|protein complex	ATP binding|DNA binding|helicase activity|histone acetyltransferase activity|transcription coactivator activity			ovary(3)|skin(1)	4			Colorectal(24;0.198)															---	---	---	---
SRCAP	10847	broad.mit.edu	37	16	30750774	30750774	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30750774G>A	uc002dze.1	+	34	9798	c.9413G>A	c.(9412-9414)CGC>CAC	p.R3138H	SRCAP_uc002dzf.2_RNA|SRCAP_uc002dzg.1_Missense_Mutation_p.R2933H	NM_006662	NP_006653	Q6ZRS2	SRCAP_HUMAN	Snf2-related CBP activator protein	3138					interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|nucleus|protein complex	ATP binding|DNA binding|helicase activity|histone acetyltransferase activity|transcription coactivator activity			ovary(3)|skin(1)	4			Colorectal(24;0.198)															---	---	---	---
RNF40	9810	broad.mit.edu	37	16	30785341	30785341	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30785341G>A	uc002dzq.2	+	20	3035	c.2912G>A	c.(2911-2913)TGC>TAC	p.C971Y	RNF40_uc010caa.2_Missense_Mutation_p.C970Y|RNF40_uc010cab.2_Missense_Mutation_p.C871Y|RNF40_uc010vfa.1_Missense_Mutation_p.C303Y|RNF40_uc002dzr.2_Missense_Mutation_p.C971Y|RNF40_uc010vfb.1_Missense_Mutation_p.C663Y	NM_014771	NP_055586	O75150	BRE1B_HUMAN	ring finger protein 40	971	RING-type.				histone H2B ubiquitination|histone monoubiquitination|ubiquitin-dependent protein catabolic process	nucleus|synaptosome|ubiquitin ligase complex	protein homodimerization activity|ubiquitin protein ligase binding|zinc ion binding			central_nervous_system(1)	1			Colorectal(24;0.198)															---	---	---	---
ZNF629	23361	broad.mit.edu	37	16	30794923	30794923	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30794923G>T	uc002dzs.1	-	3	934	c.726C>A	c.(724-726)GCC>GCA	p.A242A		NM_001080417	NP_001073886	Q9UEG4	ZN629_HUMAN	zinc finger protein 629	242	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0			Colorectal(24;0.198)															---	---	---	---
ZNF668	79759	broad.mit.edu	37	16	31073546	31073546	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31073546G>A	uc010caf.2	-	3	1060	c.703C>T	c.(703-705)CGC>TGC	p.R235C	ZNF668_uc002eao.2_Missense_Mutation_p.R235C	NM_024706	NP_078982	Q96K58	ZN668_HUMAN	zinc finger protein 668	235	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(4)	4																		---	---	---	---
ZNF646	9726	broad.mit.edu	37	16	31090419	31090419	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31090419C>T	uc002eap.2	+	2	3063	c.2774C>T	c.(2773-2775)GCA>GTA	p.A925V		NM_014699	NP_055514	O15015	ZN646_HUMAN	zinc finger protein 646	925					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			breast(2)	2																		---	---	---	---
ZNF646	9726	broad.mit.edu	37	16	31092576	31092576	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31092576C>T	uc002eap.2	+	2	5220	c.4931C>T	c.(4930-4932)GCC>GTC	p.A1644V		NM_014699	NP_055514	O15015	ZN646_HUMAN	zinc finger protein 646	1644					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			breast(2)	2																		---	---	---	---
VKORC1	79001	broad.mit.edu	37	16	31102461	31102461	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31102461C>T	uc002eas.2	-	3	712	c.486G>A	c.(484-486)AGG>AGA	p.R162R	PRSS53_uc002eaq.2_5'Flank|PRSS53_uc002ear.2_5'UTR|VKORC1_uc002eat.2_3'UTR|VKORC1_uc002eau.2_3'UTR	NM_024006	NP_076869	Q9BQB6	VKOR1_HUMAN	vitamin K epoxide reductase complex, subunit 1	162	Cytoplasmic (Potential).				peptidyl-glutamic acid carboxylation|post-translational protein modification	endoplasmic reticulum membrane|integral to membrane	vitamin-K-epoxide reductase (warfarin-sensitive) activity				0					Acenocoumarol(DB01418)|Dicumarol(DB00266)|Menadione(DB00170)|Phenindione(DB00498)|Phenprocoumon(DB00946)|Warfarin(DB00682)													---	---	---	---
PYCARD	29108	broad.mit.edu	37	16	31212911	31212911	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31212911T>C	uc010cak.2	-	3	823	c.583A>G	c.(583-585)AGC>GGC	p.S195G	PYCARD_uc002ebm.2_Missense_Mutation_p.S176G	NM_013258	NP_037390	Q9ULZ3	ASC_HUMAN	PYD and CARD domain containing isoform a	195	CARD.				induction of apoptosis|positive regulation of interleukin-1 beta secretion|positive regulation of NF-kappaB transcription factor activity|proteolysis|tumor necrosis factor-mediated signaling pathway	IkappaB kinase complex	caspase activator activity|cysteine-type endopeptidase activity|protein homodimerization activity|Pyrin domain binding				0																		---	---	---	---
ARMC5	79798	broad.mit.edu	37	16	31477419	31477419	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31477419C>T	uc002ecc.2	+	6	2546	c.2017C>T	c.(2017-2019)CGG>TGG	p.R673W	ARMC5_uc010vfn.1_Missense_Mutation_p.R768W|ARMC5_uc010vfo.1_Missense_Mutation_p.R705W|ARMC5_uc002eca.3_3'UTR|ARMC5_uc010vfp.1_Missense_Mutation_p.R481W|ARMC5_uc002ecb.2_3'UTR	NM_001105247	NP_001098717	Q96C12	ARMC5_HUMAN	armadillo repeat containing 5 isoform a	673							binding			pancreas(1)	1																		---	---	---	---
TGFB1I1	7041	broad.mit.edu	37	16	31485262	31485262	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31485262C>T	uc002ecd.1	+	4	315	c.289C>T	c.(289-291)CTT>TTT	p.L97F	TGFB1I1_uc002ece.1_Missense_Mutation_p.L80F|TGFB1I1_uc010caq.1_5'UTR	NM_001042454	NP_001035919	O43294	TGFI1_HUMAN	transforming growth factor beta 1 induced	97	Transcription activation (By similarity).|Interaction with PTK2 (By similarity).|Interaction with PTK2B.|LD motif 2.				androgen receptor signaling pathway|cell adhesion|negative regulation of cell proliferation|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent|positive regulation of transforming growth factor beta receptor signaling pathway|transcription from RNA polymerase II promoter|ubiquitin-dependent SMAD protein catabolic process|Wnt receptor signaling pathway	cytoplasm|cytoskeleton|focal adhesion|nuclear matrix	androgen receptor binding|I-SMAD binding|Roundabout binding|transcription coactivator activity|zinc ion binding				0																		---	---	---	---
ABCC12	94160	broad.mit.edu	37	16	48117992	48117992	+	Intron	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48117992G>T	uc002efc.1	-						ABCC12_uc002eey.1_Intron|ABCC12_uc002eez.1_Intron|ABCC12_uc002efa.1_Intron|ABCC12_uc002efb.1_Intron|ABCC12_uc002efd.1_Intron	NM_033226	NP_150229			ATP-binding cassette protein C12							integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)|skin(1)	3		all_cancers(37;0.0474)|all_lung(18;0.047)																---	---	---	---
ABCC12	94160	broad.mit.edu	37	16	48149368	48149368	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48149368C>T	uc002efc.1	-	13	2293	c.1947G>A	c.(1945-1947)ACG>ACA	p.T649T	ABCC12_uc002eey.1_RNA|ABCC12_uc002eez.1_RNA|ABCC12_uc002efa.1_RNA|ABCC12_uc002efb.1_RNA|ABCC12_uc002efd.1_RNA	NM_033226	NP_150229	Q96J65	MRP9_HUMAN	ATP-binding cassette protein C12	649	ABC transporter 1.					integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)|skin(1)	3		all_cancers(37;0.0474)|all_lung(18;0.047)																---	---	---	---
CBLN1	869	broad.mit.edu	37	16	49314826	49314826	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49314826C>T	uc002efq.2	-							NM_004352	NP_004343			cerebellin 1 precursor						nervous system development|synaptic transmission	cell junction|extracellular region|synapse					0		all_cancers(37;0.0766)|all_lung(18;0.24)																---	---	---	---
CBLN1	869	broad.mit.edu	37	16	49315236	49315236	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49315236C>A	uc002efq.2	-	1	480	c.141G>T	c.(139-141)ACG>ACT	p.T47T		NM_004352	NP_004343	P23435	CBLN1_HUMAN	cerebellin 1 precursor	47					nervous system development|synaptic transmission	cell junction|extracellular region|synapse					0		all_cancers(37;0.0766)|all_lung(18;0.24)																---	---	---	---
ZNF423	23090	broad.mit.edu	37	16	49671000	49671000	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:49671000G>A	uc002efs.2	-	5	2361	c.2063C>T	c.(2062-2064)ACG>ATG	p.T688M	ZNF423_uc010vgn.1_Missense_Mutation_p.T571M	NM_015069	NP_055884	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	688					cell differentiation|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(1)|lung(1)|kidney(1)|pancreas(1)	4		all_cancers(37;0.0155)																---	---	---	---
NOD2	64127	broad.mit.edu	37	16	50733414	50733414	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50733414C>T	uc002egm.1	+	2	194	c.89C>T	c.(88-90)TCG>TTG	p.S30L	NOD2_uc010cbj.1_Missense_Mutation_p.S3L|NOD2_uc010cbk.1_Missense_Mutation_p.S3L|NOD2_uc002egl.1_5'UTR	NM_022162	NP_071445	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain	30	CARD 1.				activation of MAPK activity involved in innate immune response|cytokine production involved in immune response|detection of bacterium|detection of muramyl dipeptide|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of macrophage apoptosis|nucleotide-binding oligomerization domain containing 2 signaling pathway|positive regulation of B cell activation|positive regulation of dendritic cell antigen processing and presentation|positive regulation of epithelial cell proliferation|positive regulation of ERK1 and ERK2 cascade|positive regulation of gamma-delta T cell activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-1 beta secretion|positive regulation of interleukin-10 production|positive regulation of interleukin-17 production|positive regulation of interleukin-6 production|positive regulation of JNK cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of Notch signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of prostaglandin-E synthase activity|positive regulation of prostaglandin-endoperoxide synthase activity|positive regulation of stress-activated MAPK cascade|positive regulation of tumor necrosis factor production|positive regulation of type 2 immune response|protein oligomerization|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cell surface|cytosol|plasma membrane|vesicle	ATP binding|CARD domain binding|muramyl dipeptide binding|protein kinase binding			ovary(3)|skin(1)	4		all_cancers(37;0.0156)																---	---	---	---
NOD2	64127	broad.mit.edu	37	16	50746202	50746202	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50746202G>A	uc002egm.1	+	4	2485	c.2380G>A	c.(2380-2382)GCC>ACC	p.A794T	NOD2_uc010cbk.1_Missense_Mutation_p.A767T|NOD2_uc002egl.1_Missense_Mutation_p.A572T|NOD2_uc010cbl.1_Missense_Mutation_p.A572T|NOD2_uc010cbm.1_Missense_Mutation_p.A572T|NOD2_uc010cbn.1_RNA|NOD2_uc010cbo.1_RNA|NOD2_uc010cbp.1_RNA|NOD2_uc010cbq.1_5'UTR|NOD2_uc010cbr.1_RNA	NM_022162	NP_071445	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain	794	LRR 1.				activation of MAPK activity involved in innate immune response|cytokine production involved in immune response|detection of bacterium|detection of muramyl dipeptide|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of macrophage apoptosis|nucleotide-binding oligomerization domain containing 2 signaling pathway|positive regulation of B cell activation|positive regulation of dendritic cell antigen processing and presentation|positive regulation of epithelial cell proliferation|positive regulation of ERK1 and ERK2 cascade|positive regulation of gamma-delta T cell activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-1 beta secretion|positive regulation of interleukin-10 production|positive regulation of interleukin-17 production|positive regulation of interleukin-6 production|positive regulation of JNK cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of Notch signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of prostaglandin-E synthase activity|positive regulation of prostaglandin-endoperoxide synthase activity|positive regulation of stress-activated MAPK cascade|positive regulation of tumor necrosis factor production|positive regulation of type 2 immune response|protein oligomerization|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cell surface|cytosol|plasma membrane|vesicle	ATP binding|CARD domain binding|muramyl dipeptide binding|protein kinase binding			ovary(3)|skin(1)	4		all_cancers(37;0.0156)																---	---	---	---
TOX3	27324	broad.mit.edu	37	16	52480005	52480005	+	Silent	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:52480005T>G	uc002egw.2	-	5	978	c.807A>C	c.(805-807)ACA>ACC	p.T269T	TOX3_uc010vgt.1_Silent_p.T264T|TOX3_uc010vgu.1_Silent_p.T269T	NM_001080430	NP_001073899	O15405	TOX3_HUMAN	TOX high mobility group box family member 3	269	HMG box.				apoptosis|negative regulation of neuron apoptosis|positive regulation of anti-apoptosis|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	chromatin binding|estrogen response element binding|phosphoprotein binding|protein homodimerization activity				0																		---	---	---	---
TOX3	27324	broad.mit.edu	37	16	52484376	52484376	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:52484376G>A	uc002egw.2	-	4	662	c.491C>T	c.(490-492)GCG>GTG	p.A164V	TOX3_uc010vgt.1_Missense_Mutation_p.A159V|TOX3_uc010vgu.1_Missense_Mutation_p.A164V	NM_001080430	NP_001073899	O15405	TOX3_HUMAN	TOX high mobility group box family member 3	164					apoptosis|negative regulation of neuron apoptosis|positive regulation of anti-apoptosis|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	chromatin binding|estrogen response element binding|phosphoprotein binding|protein homodimerization activity				0																		---	---	---	---
FTO	79068	broad.mit.edu	37	16	54145685	54145685	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:54145685G>A	uc002ehr.2	+	9	1598	c.1376G>A	c.(1375-1377)CGA>CAA	p.R459Q	FTO_uc010vha.1_Missense_Mutation_p.R163Q|FTO_uc010cbz.2_Missense_Mutation_p.R60Q|FTO_uc002ehs.2_RNA	NM_001080432	NP_001073901	Q9C0B1	FTO_HUMAN	fat mass and obesity associated	459					DNA dealkylation involved in DNA repair|oxidative single-stranded DNA demethylation|oxidative single-stranded RNA demethylation|RNA repair	nucleus	DNA-N1-methyladenine dioxygenase activity|ferrous iron binding|oxidative DNA demethylase activity|oxidative RNA demethylase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0																		---	---	---	---
CES7	221223	broad.mit.edu	37	16	55883550	55883550	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55883550T>C	uc002eip.2	-	11	1558	c.1409A>G	c.(1408-1410)GAC>GGC	p.D470G	CES7_uc002eio.2_Intron|CES7_uc002eiq.2_Missense_Mutation_p.D231G|CES7_uc002eir.2_Missense_Mutation_p.D364G	NM_001143685	NP_001137157	Q6NT32	EST5A_HUMAN	carboxylesterase 7 isoform 1	470						extracellular region	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity				0				all cancers(182;0.229)|Epithelial(162;0.231)														---	---	---	---
CES7	221223	broad.mit.edu	37	16	55883625	55883625	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55883625G>A	uc002eip.2	-	11	1483	c.1334C>T	c.(1333-1335)ACG>ATG	p.T445M	CES7_uc002eio.2_Intron|CES7_uc002eiq.2_Missense_Mutation_p.T206M|CES7_uc002eir.2_Missense_Mutation_p.T339M	NM_001143685	NP_001137157	Q6NT32	EST5A_HUMAN	carboxylesterase 7 isoform 1	445						extracellular region	carboxylesterase activity|methyl indole-3-acetate esterase activity|methyl jasmonate esterase activity|methyl salicylate esterase activity				0				all cancers(182;0.229)|Epithelial(162;0.231)														---	---	---	---
MT1E	4493	broad.mit.edu	37	16	56660394	56660394	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56660394C>T	uc002ejl.2	+	2	224	c.45C>T	c.(43-45)TGC>TGT	p.C15C	MT1A_uc002eji.2_Intron|MT1M_uc010vhe.1_Intron|MT1E_uc002ejm.2_Silent_p.C15C	NM_175617	NP_783316	P04732	MT1E_HUMAN	metallothionein 1E	15	Beta.	Divalent metal cation; cluster B.				cytoplasm	cadmium ion binding|copper ion binding|zinc ion binding				0																		---	---	---	---
HERPUD1	9709	broad.mit.edu	37	16	56976115	56976115	+	Missense_Mutation	SNP	A	G	G	rs141477337		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:56976115A>G	uc002eke.1	+	7	1386	c.977A>G	c.(976-978)GAC>GGC	p.D326G	HERPUD1_uc002ekf.1_Missense_Mutation_p.D325G|HERPUD1_uc002ekg.1_Missense_Mutation_p.D301G|HERPUD1_uc010cco.1_Missense_Mutation_p.T335A|HERPUD1_uc010ccp.1_Missense_Mutation_p.D228G|HERPUD1_uc002ekh.1_Missense_Mutation_p.D144G	NM_014685	NP_055500	Q15011	HERP1_HUMAN	homocysteine-inducible, endoplasmic reticulum	326	Cytoplasmic (Potential).					endoplasmic reticulum membrane|integral to membrane	protein binding				0								T	ERG	prostate								---	---	---	---
NLRC5	84166	broad.mit.edu	37	16	57060321	57060321	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57060321C>A	uc002ekk.1	+	6	1691	c.1466C>A	c.(1465-1467)GCC>GAC	p.A489D	NLRC5_uc010ccq.1_RNA|NLRC5_uc002ekn.2_Missense_Mutation_p.A294D|NLRC5_uc002ekl.2_Missense_Mutation_p.A294D|NLRC5_uc002ekm.2_Missense_Mutation_p.A294D|NLRC5_uc010ccr.1_RNA	NM_032206	NP_115582	Q86WI3	NLRC5_HUMAN	nucleotide-binding oligomerization domains 27	489	NACHT.				defense response to virus|innate immune response|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|negative regulation of type I interferon-mediated signaling pathway|positive regulation of interferon-gamma-mediated signaling pathway|positive regulation of MHC class I biosynthetic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of type I interferon-mediated signaling pathway|regulation of kinase activity	cytosol|nucleus	ATP binding|protein binding|RNA polymerase II core promoter sequence-specific DNA binding			ovary(4)|skin(2)|breast(1)	7		all_neural(199;0.225)																---	---	---	---
CX3CL1	6376	broad.mit.edu	37	16	57415947	57415947	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57415947A>G	uc002eli.2	+	3	264	c.197A>G	c.(196-198)GAG>GGG	p.E66G		NM_002996	NP_002987	P78423	X3CL1_HUMAN	chemokine (C-X3-C motif) ligand 1 precursor	66	Extracellular (Potential).|Chemokine.				cell adhesion|cytokine-mediated signaling pathway|defense response|immune response|leukocyte adhesive activation|positive regulation of calcium-independent cell-cell adhesion|positive regulation of inflammatory response	cell surface|extracellular space|integral to membrane|plasma membrane	chemokine activity				0																		---	---	---	---
COQ9	57017	broad.mit.edu	37	16	57492199	57492199	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57492199C>T	uc002elq.2	+	6	664	c.648C>T	c.(646-648)AGC>AGT	p.S216S	COQ9_uc002elr.2_Silent_p.S181S|COQ9_uc002els.2_Silent_p.S9S	NM_020312	NP_064708	O75208	COQ9_HUMAN	coenzyme Q9 homolog precursor	216					ubiquinone biosynthetic process	mitochondrion				breast(1)	1																		---	---	---	---
CCDC135	84229	broad.mit.edu	37	16	57738958	57738958	+	Intron	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57738958G>T	uc002emi.2	+						CCDC135_uc002emj.2_Intron|CCDC135_uc002emk.2_Intron	NM_032269	NP_115645			coiled-coil domain containing 135							cytoplasm				central_nervous_system(1)	1																		---	---	---	---
CCDC135	84229	broad.mit.edu	37	16	57761252	57761252	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57761252G>A	uc002emi.2	+	15	2216	c.2127G>A	c.(2125-2127)GCG>GCA	p.A709A	CCDC135_uc002emj.2_Silent_p.A709A|CCDC135_uc002emk.2_Silent_p.A644A	NM_032269	NP_115645	Q8IY82	CC135_HUMAN	coiled-coil domain containing 135	709	Potential.					cytoplasm				central_nervous_system(1)	1																		---	---	---	---
TEPP	374739	broad.mit.edu	37	16	58021297	58021297	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58021297C>T	uc002emw.3	+						TEPP_uc002emv.3_Intron	NM_199456	NP_955535			testis/prostate/placenta-expressed protein							extracellular region				kidney(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
GOT2	2806	broad.mit.edu	37	16	58750072	58750072	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:58750072C>A	uc002eof.1	-	8	979	c.865G>T	c.(865-867)GGA>TGA	p.G289*	GOT2_uc010vim.1_Nonsense_Mutation_p.G246*	NM_002080	NP_002071	P00505	AATM_HUMAN	aspartate aminotransferase 2 precursor	289					aspartate catabolic process|fatty acid transport|gluconeogenesis|response to ethanol	mitochondrial matrix|plasma membrane	L-aspartate:2-oxoglutarate aminotransferase activity|protein binding|pyridoxal phosphate binding			central_nervous_system(1)|skin(1)	2					L-Aspartic Acid(DB00128)|L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)													---	---	---	---
CDH8	1006	broad.mit.edu	37	16	62055290	62055290	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:62055290C>T	uc002eog.1	-	2	270	c.18G>A	c.(16-18)GCG>GCA	p.A6A		NM_001796	NP_001787	P55286	CADH8_HUMAN	cadherin 8, type 2 preproprotein	6					adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|skin(2)|breast(1)	9		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)														---	---	---	---
CDH5	1003	broad.mit.edu	37	16	66436802	66436802	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66436802G>A	uc002eom.3	+	12	2241	c.2085G>A	c.(2083-2085)GCG>GCA	p.A695A		NM_001795	NP_001786	P33151	CADH5_HUMAN	cadherin 5, type 2 preproprotein	695	Cytoplasmic (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion|regulation of establishment of cell polarity	integral to membrane|membrane fraction	beta-catenin binding|calcium ion binding|ion channel binding|receptor binding			ovary(2)|lung(2)|central_nervous_system(1)|skin(1)	6		Ovarian(137;0.0955)		OV - Ovarian serous cystadenocarcinoma(108;0.107)														---	---	---	---
PDP2	57546	broad.mit.edu	37	16	66919027	66919027	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66919027C>T	uc002eqk.1	+	2	1002	c.840C>T	c.(838-840)CAC>CAT	p.H280H		NM_020786	NP_065837	Q9P2J9	PDP2_HUMAN	pyruvate dehydrogenase phosphatase isoenzyme 2	280					pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix|protein serine/threonine phosphatase complex	[pyruvate dehydrogenase (lipoamide)] phosphatase activity|metal ion binding			ovary(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.088)|Epithelial(162;0.204)														---	---	---	---
PDP2	57546	broad.mit.edu	37	16	66919315	66919315	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66919315C>T	uc002eqk.1	+	2	1290	c.1128C>T	c.(1126-1128)TAC>TAT	p.Y376Y		NM_020786	NP_065837	Q9P2J9	PDP2_HUMAN	pyruvate dehydrogenase phosphatase isoenzyme 2	376					pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix|protein serine/threonine phosphatase complex	[pyruvate dehydrogenase (lipoamide)] phosphatase activity|metal ion binding			ovary(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.088)|Epithelial(162;0.204)														---	---	---	---
CES8	283848	broad.mit.edu	37	16	67037182	67037182	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67037182C>T	uc002eqv.2	+	7	862	c.819C>T	c.(817-819)TGC>TGT	p.C273C	CES8_uc010vix.1_Silent_p.C273C|CES8_uc002eqw.2_Silent_p.C273C|CES8_uc002eqy.2_Silent_p.C175C|CES8_uc002eqx.2_Silent_p.C79C|CES8_uc010viy.1_Silent_p.C179C|CES8_uc010viz.1_Silent_p.C175C|CES8_uc002eqz.2_5'Flank	NM_173815	NP_776176	Q5XG92	EST4A_HUMAN	carboxylesterase 8 (putative)	273						extracellular region	carboxylesterase activity				0																		---	---	---	---
C16orf70	80262	broad.mit.edu	37	16	67154060	67154060	+	Missense_Mutation	SNP	G	A	A	rs149407168		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67154060G>A	uc002erc.2	+	3	194	c.110G>A	c.(109-111)CGC>CAC	p.R37H	C16orf70_uc002erd.2_Missense_Mutation_p.R37H|C16orf70_uc002ere.1_Missense_Mutation_p.R15H	NM_025187	NP_079463	Q9BSU1	CP070_HUMAN	lin-10	37										ovary(2)	2		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0017)|Epithelial(162;0.00655)|all cancers(182;0.0579)														---	---	---	---
ELMO3	79767	broad.mit.edu	37	16	67234846	67234846	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67234846A>G	uc002esa.2	+	8	921	c.878A>G	c.(877-879)CAG>CGG	p.Q293R	ELMO3_uc002esb.2_Missense_Mutation_p.Q276R|ELMO3_uc002esc.2_Missense_Mutation_p.Q127R	NM_024712	NP_078988	Q96BJ8	ELMO3_HUMAN	engulfment and cell motility 3	240					apoptosis|phagocytosis	cytoplasm|cytoskeleton	SH3 domain binding				0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00067)|Epithelial(162;0.00442)|all cancers(182;0.0417)														---	---	---	---
ELMO3	79767	broad.mit.edu	37	16	67235728	67235728	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67235728C>T	uc002esa.2	+	11	1204	c.1161C>T	c.(1159-1161)GAC>GAT	p.D387D	ELMO3_uc002esb.2_Silent_p.D370D|ELMO3_uc002esc.2_Silent_p.D221D	NM_024712	NP_078988	Q96BJ8	ELMO3_HUMAN	engulfment and cell motility 3	334	ELMO.				apoptosis|phagocytosis	cytoplasm|cytoskeleton	SH3 domain binding				0		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00067)|Epithelial(162;0.00442)|all cancers(182;0.0417)														---	---	---	---
FHOD1	29109	broad.mit.edu	37	16	67263863	67263863	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67263863G>T	uc002esl.2	-	21	3357	c.3245C>A	c.(3244-3246)CCC>CAC	p.P1082H	LRRC29_uc002esf.2_5'Flank|LRRC29_uc002esg.2_5'Flank|LRRC29_uc010vjg.1_5'Flank|FHOD1_uc002esk.2_Missense_Mutation_p.P141H|FHOD1_uc010ced.2_Missense_Mutation_p.P889H	NM_013241	NP_037373	Q9Y613	FHOD1_HUMAN	formin homology 2 domain containing 1	1082					actin cytoskeleton organization	cytoplasm|cytoskeleton|nucleus	actin binding			breast(2)|ovary(1)	3		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000691)|Epithelial(162;0.00462)|all cancers(182;0.0434)														---	---	---	---
PLEKHG4	25894	broad.mit.edu	37	16	67319421	67319421	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67319421C>A	uc002eso.3	+	13	4959	c.2424C>A	c.(2422-2424)GCC>GCA	p.A808A	PLEKHG4_uc002esp.3_Silent_p.A615A|PLEKHG4_uc002esq.3_Silent_p.A808A|PLEKHG4_uc010cef.2_Silent_p.A808A|PLEKHG4_uc002ess.3_Silent_p.A808A|PLEKHG4_uc010ceg.2_Silent_p.A727A	NM_015432	NP_056247	Q58EX7	PKHG4_HUMAN	pleckstrin homology domain containing, family G	808	DH.				regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			skin(1)|pancreas(1)	2				OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)|Kidney(780;0.119)														---	---	---	---
PLEKHG4	25894	broad.mit.edu	37	16	67320198	67320198	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67320198G>A	uc002eso.3	+	14	4999	c.2464G>A	c.(2464-2466)GCG>ACG	p.A822T	PLEKHG4_uc002esp.3_Missense_Mutation_p.A629T|PLEKHG4_uc002esq.3_Missense_Mutation_p.A822T|PLEKHG4_uc010cef.2_Missense_Mutation_p.A822T|PLEKHG4_uc002ess.3_Missense_Mutation_p.A822T|PLEKHG4_uc010ceg.2_Missense_Mutation_p.A741T	NM_015432	NP_056247	Q58EX7	PKHG4_HUMAN	pleckstrin homology domain containing, family G	822	DH.				regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			skin(1)|pancreas(1)	2				OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)|Kidney(780;0.119)														---	---	---	---
LRRC36	55282	broad.mit.edu	37	16	67418933	67418933	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67418933G>A	uc002esv.2	+	14	2225	c.2206G>A	c.(2206-2208)GAG>AAG	p.E736K	LRRC36_uc002esw.2_RNA|LRRC36_uc002esx.2_Missense_Mutation_p.E615K|LRRC36_uc010vjk.1_Missense_Mutation_p.E511K|LRRC36_uc010vjl.1_Missense_Mutation_p.E208K|LRRC36_uc002esy.2_Missense_Mutation_p.E246K	NM_018296	NP_060766	Q1X8D7	LRC36_HUMAN	leucine rich repeat containing 36 isoform 1	736											0		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0669)|Epithelial(162;0.161)														---	---	---	---
C16orf48	84080	broad.mit.edu	37	16	67699032	67699032	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67699032C>T	uc002etw.1	-	3	603	c.320G>A	c.(319-321)CGG>CAG	p.R107Q	C16orf48_uc002etv.1_5'Flank|C16orf48_uc010cem.1_Missense_Mutation_p.R107Q|C16orf86_uc002etx.1_5'Flank|C16orf86_uc002ety.2_5'Flank|C16orf86_uc002etz.2_5'Flank	NM_032140	NP_115516	Q9H0I2	CP048_HUMAN	hypothetical protein LOC84080	107						microtubule cytoskeleton	protein binding				0		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.047)|all cancers(182;0.228)														---	---	---	---
TSNAXIP1	55815	broad.mit.edu	37	16	67859955	67859955	+	Missense_Mutation	SNP	C	T	T	rs61999337	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67859955C>T	uc002euj.2	+	9	1352	c.958C>T	c.(958-960)CGG>TGG	p.R320W	TSNAXIP1_uc010cep.2_3'UTR|TSNAXIP1_uc010vjz.1_Missense_Mutation_p.R197W|TSNAXIP1_uc002euf.3_Missense_Mutation_p.R28W|TSNAXIP1_uc010vka.1_Missense_Mutation_p.R374W|TSNAXIP1_uc010vkb.1_Missense_Mutation_p.R305W|TSNAXIP1_uc002eug.3_Missense_Mutation_p.R28W|TSNAXIP1_uc002euh.3_Missense_Mutation_p.R28W|TSNAXIP1_uc002eui.3_Missense_Mutation_p.R28W|TSNAXIP1_uc002euk.2_Missense_Mutation_p.R28W	NM_018430	NP_060900	Q2TAA8	TXIP1_HUMAN	translin-associated factor X interacting protein	320					cell differentiation|multicellular organismal development|spermatogenesis	perinuclear region of cytoplasm					0		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00432)|Epithelial(162;0.0192)|all cancers(182;0.125)														---	---	---	---
CTRL	1506	broad.mit.edu	37	16	67964673	67964673	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67964673G>A	uc002euw.2	-	4	284	c.274C>T	c.(274-276)CGA>TGA	p.R92*		NM_001907	NP_001898	P40313	CTRL_HUMAN	chymotrypsin-like precursor	92	Peptidase S1.				digestion|proteolysis	extracellular space	serine-type endopeptidase activity				0		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00412)|Epithelial(162;0.018)|all cancers(182;0.118)														---	---	---	---
NFATC3	4775	broad.mit.edu	37	16	68224734	68224734	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68224734C>A	uc002evo.1	+	9	2372	c.2162C>A	c.(2161-2163)CCT>CAT	p.P721H	NFATC3_uc010vkl.1_Missense_Mutation_p.P242H|NFATC3_uc010vkm.1_Missense_Mutation_p.P242H|NFATC3_uc010vkn.1_Missense_Mutation_p.P242H|NFATC3_uc010vko.1_Missense_Mutation_p.P242H|NFATC3_uc010vkp.1_Missense_Mutation_p.P242H|NFATC3_uc010vkq.1_Missense_Mutation_p.P242H|NFATC3_uc002evl.2_Missense_Mutation_p.P242H|NFATC3_uc002evk.2_Missense_Mutation_p.P721H|NFATC3_uc002evm.1_Missense_Mutation_p.P721H|NFATC3_uc002evn.1_Missense_Mutation_p.P721H|NFATC3_uc010vkr.1_Missense_Mutation_p.P242H|NFATC3_uc010vks.1_Missense_Mutation_p.P242H|NFATC3_uc010vkt.1_Missense_Mutation_p.P242H|NFATC3_uc010vku.1_Missense_Mutation_p.P242H|NFATC3_uc010vkv.1_Missense_Mutation_p.P242H|NFATC3_uc010vkw.1_Missense_Mutation_p.P242H|NFATC3_uc010vkx.1_Missense_Mutation_p.P242H|NFATC3_uc010vky.1_Missense_Mutation_p.P242H|NFATC3_uc010vkz.1_Missense_Mutation_p.P242H|NFATC3_uc010vla.1_Missense_Mutation_p.P242H|NFATC3_uc010vlb.1_Missense_Mutation_p.P242H|NFATC3_uc010vlc.1_Missense_Mutation_p.P242H	NM_173165	NP_775188	Q12968	NFAC3_HUMAN	nuclear factor of activated T-cells,	721					inflammatory response|transcription from RNA polymerase II promoter	nucleolus|plasma membrane	DNA binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	3		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0452)|all cancers(182;0.24)														---	---	---	---
ESRP2	80004	broad.mit.edu	37	16	68265793	68265793	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68265793A>C	uc010cfa.1	-	10	1429	c.1241T>G	c.(1240-1242)CTG>CGG	p.L414R	ESRP2_uc002evp.1_RNA|ESRP2_uc002evq.1_Missense_Mutation_p.L404R	NM_024939	NP_079215	Q9H6T0	ESRP2_HUMAN	RNA binding motif protein 35B	414	RRM 2.				mRNA processing|regulation of RNA splicing|RNA splicing	nucleus	mRNA binding|nucleotide binding			ovary(1)	1																		---	---	---	---
PLA2G15	23659	broad.mit.edu	37	16	68293369	68293369	+	Missense_Mutation	SNP	C	T	T	rs144572894		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68293369C>T	uc002evr.2	+	6	1131	c.1048C>T	c.(1048-1050)CGT>TGT	p.R350C	PLA2G15_uc010vld.1_3'UTR|PLA2G15_uc010vle.1_Missense_Mutation_p.R256C|PLA2G15_uc010vlf.1_Missense_Mutation_p.R150C|PLA2G15_uc002evs.2_Missense_Mutation_p.R171C	NM_012320	NP_036452	Q8NCC3	PAG15_HUMAN	lysophospholipase 3 (lysosomal phospholipase A2)	350					fatty acid catabolic process	extracellular region|lysosome	lysophospholipase activity|phosphatidylcholine-sterol O-acyltransferase activity|phospholipid binding			ovary(1)	1																		---	---	---	---
ZFP90	146198	broad.mit.edu	37	16	68597866	68597866	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68597866A>C	uc010cff.2	+	5	1468	c.1176A>C	c.(1174-1176)AAA>AAC	p.K392N	ZFP90_uc002ewb.2_Missense_Mutation_p.N198T|ZFP90_uc002ewc.2_Missense_Mutation_p.N198T|ZFP90_uc002ewd.2_Missense_Mutation_p.K392N|ZFP90_uc002ewe.2_Missense_Mutation_p.K392N	NM_133458	NP_597715	Q8TF47	ZFP90_HUMAN	zinc finger protein 90	392					positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00233)|Epithelial(162;0.0184)|all cancers(182;0.0946)														---	---	---	---
CDH3	1001	broad.mit.edu	37	16	68715004	68715004	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68715004T>C	uc002ewf.2	+						CDH3_uc010vli.1_Intron	NM_001793	NP_001784			cadherin 3, type 1 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion|response to stimulus|visual perception	integral to membrane	calcium ion binding	p.?(1)		ovary(3)|breast(1)|skin(1)	5		Ovarian(137;0.0564)		OV - Ovarian serous cystadenocarcinoma(108;0.000782)|Epithelial(162;0.0054)|all cancers(182;0.0384)														---	---	---	---
CDH3	1001	broad.mit.edu	37	16	68716251	68716251	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68716251G>T	uc002ewf.2	+	9	2175	c.1043G>T	c.(1042-1044)AGG>ATG	p.R348M	CDH3_uc010vli.1_Missense_Mutation_p.R293M	NM_001793	NP_001784	P22223	CADH3_HUMAN	cadherin 3, type 1 preproprotein	348	Extracellular (Potential).|Cadherin 3.				adherens junction organization|cell junction assembly|homophilic cell adhesion|response to stimulus|visual perception	integral to membrane	calcium ion binding	p.?(1)		ovary(3)|breast(1)|skin(1)	5		Ovarian(137;0.0564)		OV - Ovarian serous cystadenocarcinoma(108;0.000782)|Epithelial(162;0.0054)|all cancers(182;0.0384)														---	---	---	---
CDH1	999	broad.mit.edu	37	16	68845611	68845611	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68845611C>T	uc002ewg.1	+	7	981	c.857C>T	c.(856-858)GCC>GTC	p.A286V	CDH1_uc010vlj.1_RNA|CDH1_uc010cfg.1_Missense_Mutation_p.A286V	NM_004360	NP_004351	P12830	CADH1_HUMAN	cadherin 1, type 1 preproprotein	286	Cadherin 2.|Extracellular (Potential).				adherens junction organization|cellular component disassembly involved in apoptosis|cellular response to indole-3-methanol|cellular response to lithium ion|homophilic cell adhesion|negative regulation of cell-cell adhesion|positive regulation of transcription factor import into nucleus|positive regulation of transcription, DNA-dependent|regulation of immune response	actin cytoskeleton|aggresome|apical junction complex|catenin complex|cell-cell adherens junction|endosome|focal adhesion|Golgi apparatus|integral to membrane|internal side of plasma membrane|lateral plasma membrane|perinuclear region of cytoplasm	cell adhesion molecule binding|gamma-catenin binding	p.A286T(2)|p.E283fs*4(1)		breast(148)|stomach(71)|biliary_tract(8)|endometrium(3)|soft_tissue(2)|large_intestine(2)|urinary_tract(2)|oesophagus(2)|ovary(2)|thyroid(1)|central_nervous_system(1)|lung(1)	243		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)				Mis|N|F|S		lobular breast|gastric	gastric			Hereditary_Diffuse_Gastric_Cancer				---	---	---	---
WWP2	11060	broad.mit.edu	37	16	69964121	69964121	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69964121A>G	uc002exu.1	+	14	1494	c.1405A>G	c.(1405-1407)ACC>GCC	p.T469A	WWP2_uc002exv.1_Missense_Mutation_p.T469A|WWP2_uc010vlm.1_Missense_Mutation_p.T353A|WWP2_uc010vln.1_Missense_Mutation_p.T87A|WWP2_uc002exw.1_Missense_Mutation_p.T30A|uc002exx.1_5'Flank|MIR140_hsa-mir-140|MI0000456_5'Flank	NM_007014	NP_008945	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase	469	WW 4.				entry of virus into host cell|negative regulation of protein transport|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transporter activity|proteasomal ubiquitin-dependent protein catabolic process|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus|ubiquitin ligase complex	RNA polymerase II transcription factor binding|ubiquitin-protein ligase activity			lung(3)|ovary(1)|breast(1)|skin(1)	6																OREG0023910	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
PDPR	55066	broad.mit.edu	37	16	70176164	70176164	+	Missense_Mutation	SNP	G	A	A	rs137860192	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70176164G>A	uc002eyf.1	+	12	2300	c.1343G>A	c.(1342-1344)CGC>CAC	p.R448H	CLEC18C_uc002exy.2_Intron|PDPR_uc010vlr.1_Missense_Mutation_p.R348H|PDPR_uc002eyg.1_Missense_Mutation_p.R176H	NM_017990	NP_060460	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory	448					glycine catabolic process|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	aminomethyltransferase activity|oxidoreductase activity			breast(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.124)														---	---	---	---
PDPR	55066	broad.mit.edu	37	16	70180094	70180094	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70180094C>A	uc002eyf.1	+	16	2882	c.1925C>A	c.(1924-1926)CCT>CAT	p.P642H	CLEC18C_uc002exy.2_Intron|PDPR_uc010vlr.1_Missense_Mutation_p.P542H|PDPR_uc002eyg.1_Missense_Mutation_p.P370H|PDPR_uc002eyh.2_5'UTR|PDPR_uc010vls.1_5'UTR	NM_017990	NP_060460	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory	642					glycine catabolic process|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	aminomethyltransferase activity|oxidoreductase activity			breast(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.124)														---	---	---	---
DDX19A	55308	broad.mit.edu	37	16	70348830	70348830	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70348830T>C	uc002eys.2	+	3	261	c.132T>C	c.(130-132)AAT>AAC	p.N44N	DDX19B_uc010vly.1_Silent_p.N44N|DDX19B_uc010vlv.1_Silent_p.N49N|DDX19B_uc010vlw.1_5'UTR|DDX19B_uc002eyo.2_Silent_p.N44N|DDX19B_uc002eyp.2_Silent_p.N44N|DDX19B_uc002eyq.2_Intron|DDX19B_uc002eyr.2_5'UTR|DDX19B_uc010vlx.1_Intron	NM_007242	NP_009173	Q9NUU7	DD19A_HUMAN	DEAD (Asp-Glu-Ala-As) box polypeptide 19 isoform	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					mRNA transport|protein transport|transmembrane transport	cytoplasm|nuclear membrane|nuclear pore	ATP binding|ATP-dependent helicase activity|RNA binding				0		Ovarian(137;0.221)																---	---	---	---
FUK	197258	broad.mit.edu	37	16	70501860	70501860	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70501860G>A	uc002eyy.2	+	8	712	c.654G>A	c.(652-654)CGG>CGA	p.R218R	FUK_uc010cft.2_Silent_p.R250R|FUK_uc002eyz.2_Intron	NM_145059	NP_659496	Q8N0W3	FUK_HUMAN	fucokinase	218						cytoplasm	ATP binding|fucokinase activity			ovary(1)	1		Ovarian(137;0.0694)																---	---	---	---
MTSS1L	92154	broad.mit.edu	37	16	70708236	70708236	+	Silent	SNP	C	T	T	rs3813906		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70708236C>T	uc002ezj.2	-	11	1286	c.1026G>A	c.(1024-1026)TCG>TCA	p.S342S		NM_138383	NP_612392	Q765P7	MTSSL_HUMAN	metastasis suppressor 1-like	342	Ser-rich.				filopodium assembly|signal transduction		actin binding|cytoskeletal adaptor activity|SH3 domain binding			central_nervous_system(1)	1																		---	---	---	---
MTSS1L	92154	broad.mit.edu	37	16	70712237	70712237	+	Missense_Mutation	SNP	G	A	A	rs143995794		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70712237G>A	uc002ezj.2	-	8	802	c.542C>T	c.(541-543)ACG>ATG	p.T181M	MTSS1L_uc002ezk.1_Missense_Mutation_p.T98M	NM_138383	NP_612392	Q765P7	MTSSL_HUMAN	metastasis suppressor 1-like	181	IMD.				filopodium assembly|signal transduction		actin binding|cytoskeletal adaptor activity|SH3 domain binding			central_nervous_system(1)	1																		---	---	---	---
VAC14	55697	broad.mit.edu	37	16	70732653	70732653	+	Missense_Mutation	SNP	G	A	A	rs145938865	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70732653G>A	uc002ezm.2	-	15	1981	c.1723C>T	c.(1723-1725)CGG>TGG	p.R575W	VAC14_uc010cfw.2_Missense_Mutation_p.R341W|VAC14_uc002ezn.2_Missense_Mutation_p.R140W|VAC14_uc002ezl.2_Missense_Mutation_p.R7W|VAC14_uc010cfx.1_Missense_Mutation_p.R53W	NM_018052	NP_060522	Q08AM6	VAC14_HUMAN	Vac14 homolog	575	HEAT 6.				interspecies interaction between organisms	endoplasmic reticulum|endosome membrane|microsome	protein binding|receptor activity			pancreas(1)|skin(1)	2		Ovarian(137;0.0699)																---	---	---	---
HYDIN	54768	broad.mit.edu	37	16	70867932	70867932	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70867932G>A	uc002ezr.2	-	79	13662	c.13534C>T	c.(13534-13536)CGC>TGC	p.R4512C	HYDIN_uc010cfy.2_RNA	NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	4513										ovary(1)|skin(1)	2		Ovarian(137;0.0654)																---	---	---	---
HYDIN	54768	broad.mit.edu	37	16	70954518	70954518	+	Missense_Mutation	SNP	G	C	C	rs140107832	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70954518G>C	uc002ezr.2	-	46	7886	c.7758C>G	c.(7756-7758)AGC>AGG	p.S2586R		NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	2587										ovary(1)|skin(1)	2		Ovarian(137;0.0654)																---	---	---	---
HYDIN	54768	broad.mit.edu	37	16	70954686	70954686	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70954686C>T	uc002ezr.2	-	46	7718	c.7590G>A	c.(7588-7590)GCG>GCA	p.A2530A		NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	2531	Potential.									ovary(1)|skin(1)	2		Ovarian(137;0.0654)																---	---	---	---
FTSJD1	55783	broad.mit.edu	37	16	71319278	71319278	+	Silent	SNP	G	A	A	rs150475077		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71319278G>A	uc010cga.2	-	3	952	c.546C>T	c.(544-546)GAC>GAT	p.D182D	FTSJD1_uc002ezy.3_Silent_p.D182D|FTSJD1_uc002ezz.3_Silent_p.D182D	NM_001099642	NP_001093112	Q8IYT2	FTSJ1_HUMAN	FtsJ methyltransferase domain containing 1	182						integral to membrane	methyltransferase activity|nucleic acid binding			skin(1)	1																		---	---	---	---
FTSJD1	55783	broad.mit.edu	37	16	71319594	71319594	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71319594A>G	uc010cga.2	-	3	636	c.230T>C	c.(229-231)CTG>CCG	p.L77P	FTSJD1_uc002ezy.3_Missense_Mutation_p.L77P|FTSJD1_uc002ezz.3_Missense_Mutation_p.L77P	NM_001099642	NP_001093112	Q8IYT2	FTSJ1_HUMAN	FtsJ methyltransferase domain containing 1	77						integral to membrane	methyltransferase activity|nucleic acid binding			skin(1)	1																		---	---	---	---
MARVELD3	91862	broad.mit.edu	37	16	71674508	71674508	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:71674508G>A	uc002fau.2	+	3	874	c.811G>A	c.(811-813)GTG>ATG	p.V271M	PHLPP2_uc002fav.2_RNA|MARVELD3_uc010cge.2_3'UTR	NM_001017967	NP_001017967	Q96A59	MALD3_HUMAN	MARVEL domain containing 3 isoform 1	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment						integral to membrane				skin(1)	1		Ovarian(137;0.125)																---	---	---	---
TXNL4B	54957	broad.mit.edu	37	16	72122914	72122914	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72122914T>C	uc002fca.2	-	3	567	c.256A>G	c.(256-258)AAT>GAT	p.N86D	TXNL4B_uc010cgl.2_RNA|TXNL4B_uc010vmn.1_Missense_Mutation_p.N86D|TXNL4B_uc010vmo.1_Missense_Mutation_p.N86D	NM_017853	NP_060323	Q9NX01	TXN4B_HUMAN	thioredoxin-like 4B	86					mitosis|mRNA processing|RNA splicing	spliceosomal complex				ovary(1)	1																		---	---	---	---
ZFHX3	463	broad.mit.edu	37	16	72832241	72832241	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72832241T>C	uc002fck.2	-	9	5013	c.4340A>G	c.(4339-4341)CAC>CGC	p.H1447R	ZFHX3_uc002fcl.2_Missense_Mutation_p.H533R	NM_006885	NP_008816	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3 isoform A	1447	C2H2-type 14.				muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|positive regulation of myoblast differentiation	transcription factor complex	enzyme binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(2)|skin(2)	4		Ovarian(137;0.13)																---	---	---	---
ZFHX3	463	broad.mit.edu	37	16	72992679	72992679	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:72992679C>A	uc002fck.2	-	2	2039	c.1366G>T	c.(1366-1368)GTA>TTA	p.V456L	ZFHX3_uc002fcl.2_Intron	NM_006885	NP_008816	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3 isoform A	456					muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|positive regulation of myoblast differentiation	transcription factor complex	enzyme binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(2)|skin(2)	4		Ovarian(137;0.13)																---	---	---	---
RFWD3	55159	broad.mit.edu	37	16	74694895	74694895	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74694895T>C	uc002fda.2	-	2	551	c.453A>G	c.(451-453)ACA>ACG	p.T151T	RFWD3_uc010cgq.2_Silent_p.T151T	NM_018124	NP_060594	Q6PCD5	RFWD3_HUMAN	ring finger and WD repeat domain 3	151					DNA repair|mitotic cell cycle G1/S transition DNA damage checkpoint|response to ionizing radiation	nucleus	MDM2 binding|p53 binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)|breast(1)	3																		---	---	---	---
RFWD3	55159	broad.mit.edu	37	16	74694973	74694973	+	Silent	SNP	G	A	A	rs143577108	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74694973G>A	uc002fda.2	-	2	473	c.375C>T	c.(373-375)AGC>AGT	p.S125S	RFWD3_uc010cgq.2_Silent_p.S125S	NM_018124	NP_060594	Q6PCD5	RFWD3_HUMAN	ring finger and WD repeat domain 3	125					DNA repair|mitotic cell cycle G1/S transition DNA damage checkpoint|response to ionizing radiation	nucleus	MDM2 binding|p53 binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)|breast(1)	3																		---	---	---	---
WDR59	79726	broad.mit.edu	37	16	74926420	74926420	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74926420C>T	uc002fdh.1	-	20	2146	c.2044G>A	c.(2044-2046)GCC>ACC	p.A682T	WDR59_uc002fdf.1_Missense_Mutation_p.A127T|WDR59_uc002fdg.1_Missense_Mutation_p.A274T	NM_030581	NP_085058	Q6PJI9	WDR59_HUMAN	WD repeat domain 59	682	WD 8.									ovary(1)|breast(1)	2																		---	---	---	---
WDR59	79726	broad.mit.edu	37	16	74937958	74937958	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74937958C>T	uc002fdh.1	-	18	1855	c.1753G>A	c.(1753-1755)GCG>ACG	p.A585T	WDR59_uc002fdf.1_Missense_Mutation_p.A30T|WDR59_uc002fdg.1_Missense_Mutation_p.A177T	NM_030581	NP_085058	Q6PJI9	WDR59_HUMAN	WD repeat domain 59	585										ovary(1)|breast(1)	2																		---	---	---	---
WDR59	79726	broad.mit.edu	37	16	74972134	74972134	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74972134C>T	uc002fdh.1	-	8	667	c.565G>A	c.(565-567)GCC>ACC	p.A189T	WDR59_uc002fdi.2_Missense_Mutation_p.A189T|WDR59_uc002fdj.2_Missense_Mutation_p.A189T	NM_030581	NP_085058	Q6PJI9	WDR59_HUMAN	WD repeat domain 59	189	WD 4.									ovary(1)|breast(1)	2																		---	---	---	---
BCAR1	9564	broad.mit.edu	37	16	75263682	75263682	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75263682C>T	uc002fdv.2	-	7	2463	c.2340G>A	c.(2338-2340)GCG>GCA	p.A780A	BCAR1_uc002fdt.2_Silent_p.A233A|BCAR1_uc002fdu.2_Silent_p.A570A|BCAR1_uc010cgu.2_Silent_p.A769A|BCAR1_uc010vna.1_Silent_p.A778A|BCAR1_uc010vnb.1_Silent_p.A826A|BCAR1_uc002fdw.2_Silent_p.A780A|BCAR1_uc010vnc.1_Silent_p.A632A|BCAR1_uc010vnd.1_Silent_p.A798A|BCAR1_uc002fdx.2_Silent_p.A798A	NM_014567	NP_055382	P56945	BCAR1_HUMAN	breast cancer anti-estrogen resistance 1	780	Divergent helix-loop-helix motif.				actin filament organization|B cell receptor signaling pathway|blood coagulation|cell adhesion|cell division|cell migration|cell proliferation|epidermal growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|integrin-mediated signaling pathway|nerve growth factor receptor signaling pathway|platelet-derived growth factor receptor signaling pathway|positive regulation of cell migration|regulation of apoptosis|regulation of cell growth|T cell receptor signaling pathway	cytosol|focal adhesion|membrane fraction|ruffle	protein kinase binding|protein phosphatase binding|SH3 domain binding|signal transducer activity	p.A780V(1)		central_nervous_system(5)|breast(2)|prostate(1)	8				BRCA - Breast invasive adenocarcinoma(221;0.169)														---	---	---	---
CFDP1	10428	broad.mit.edu	37	16	75446574	75446574	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75446574A>G	uc002fdy.2	-	3	398	c.261T>C	c.(259-261)AGT>AGC	p.S87S	CFDP1_uc002fdz.2_Missense_Mutation_p.V11A|CFDP1_uc002fea.1_Silent_p.S87S	NM_006324	NP_006315	Q9UEE9	CFDP1_HUMAN	craniofacial development protein 1	87	Glu-rich.				multicellular organismal development					upper_aerodigestive_tract(1)	1																		---	---	---	---
CHST6	4166	broad.mit.edu	37	16	75512715	75512715	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75512715G>A	uc002fef.2	-	3	1192	c.1012C>T	c.(1012-1014)CCC>TCC	p.P338S	CHST6_uc002feg.1_RNA|CHST6_uc002feh.1_Missense_Mutation_p.P338S	NM_021615	NP_067628	Q9GZX3	CHST6_HUMAN	carbohydrate (N-acetylglucosamine 6-O)	338	Lumenal (Potential).				keratan sulfate biosynthetic process|N-acetylglucosamine metabolic process	Golgi membrane|integral to membrane	N-acetylglucosamine 6-O-sulfotransferase activity				0																		---	---	---	---
CHST6	4166	broad.mit.edu	37	16	75512915	75512915	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75512915A>C	uc002fef.2	-	3	992	c.812T>G	c.(811-813)GTG>GGG	p.V271G	CHST6_uc002feg.1_RNA|CHST6_uc002feh.1_Missense_Mutation_p.V271G	NM_021615	NP_067628	Q9GZX3	CHST6_HUMAN	carbohydrate (N-acetylglucosamine 6-O)	271	Lumenal (Potential).				keratan sulfate biosynthetic process|N-acetylglucosamine metabolic process	Golgi membrane|integral to membrane	N-acetylglucosamine 6-O-sulfotransferase activity				0																		---	---	---	---
TMEM231	79583	broad.mit.edu	37	16	75575304	75575304	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75575304G>A	uc002fem.2	-	6	777	c.714C>T	c.(712-714)GCC>GCT	p.A238A	CHST5_uc002fej.1_Intron|TMEM231_uc002fek.2_Silent_p.A267A|TMEM231_uc002fel.2_Silent_p.A122A|TMEM231_uc010vne.1_Silent_p.A91A|TMEM231_uc010cgx.1_Silent_p.A202A	NM_001077418	NP_001070886	Q9H6L2	TM231_HUMAN	transmembrane protein 231 isoform 2	238						integral to membrane					0																		---	---	---	---
MON1B	22879	broad.mit.edu	37	16	77229496	77229496	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77229496C>T	uc002fez.2	+	5	1690	c.1360C>T	c.(1360-1362)CGC>TGC	p.R454C	MON1B_uc010vnf.1_Missense_Mutation_p.R345C|MON1B_uc010vng.1_Missense_Mutation_p.R308C|MON1B_uc002ffa.2_Missense_Mutation_p.R334C	NM_014940	NP_055755	Q7L1V2	MON1B_HUMAN	MON1 homolog B	454							protein binding				0																		---	---	---	---
ADAMTS18	170692	broad.mit.edu	37	16	77328915	77328915	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77328915A>C	uc002ffc.3	-	19	3330	c.2911T>G	c.(2911-2913)TTG>GTG	p.L971V	ADAMTS18_uc010chc.1_Missense_Mutation_p.L559V	NM_199355	NP_955387	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1	971	TSP type-1 2.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(4)|lung(4)|kidney(4)|skin(3)|breast(1)|ovary(1)|pancreas(1)	18																		---	---	---	---
VAT1L	57687	broad.mit.edu	37	16	77850840	77850840	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:77850840A>G	uc002ffg.1	+	2	353	c.256A>G	c.(256-258)ATG>GTG	p.M86V		NM_020927	NP_065978	Q9HCJ6	VAT1L_HUMAN	vesicle amine transport protein 1 homolog (T.	86							oxidoreductase activity|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
ATMIN	23300	broad.mit.edu	37	16	81076008	81076008	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81076008C>T	uc002ffz.1	+	3	603	c.585C>T	c.(583-585)TGC>TGT	p.C195C	ATMIN_uc002fga.2_Silent_p.C37C|ATMIN_uc010vnn.1_Intron|ATMIN_uc002fgb.1_Silent_p.C37C	NM_015251	NP_056066	O43313	ATMIN_HUMAN	ATM interactor	195					response to DNA damage stimulus	nucleus	zinc ion binding				0																		---	---	---	---
ATMIN	23300	broad.mit.edu	37	16	81077122	81077122	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81077122C>T	uc002ffz.1	+	4	1037	c.1019C>T	c.(1018-1020)GCT>GTT	p.A340V	ATMIN_uc002fga.2_Missense_Mutation_p.A182V|ATMIN_uc010vnn.1_Missense_Mutation_p.A111V|ATMIN_uc002fgb.1_Missense_Mutation_p.A182V	NM_015251	NP_056066	O43313	ATMIN_HUMAN	ATM interactor	340	Required for formation of RAD51 foci.				response to DNA damage stimulus	nucleus	zinc ion binding				0																		---	---	---	---
PKD1L2	114780	broad.mit.edu	37	16	81248810	81248810	+	Intron	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81248810G>T	uc002fgh.1	-						PKD1L2_uc002fgj.2_Intron	NM_052892	NP_443124			polycystin 1-like 2 isoform a						neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3																OREG0023964	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
CDH13	1012	broad.mit.edu	37	16	83378482	83378482	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83378482A>G	uc002fgx.2	+	6	772	c.652A>G	c.(652-654)ACT>GCT	p.T218A	CDH13_uc010vns.1_Missense_Mutation_p.T265A|CDH13_uc010vnt.1_5'UTR|CDH13_uc010vnu.1_Missense_Mutation_p.T179A	NM_001257	NP_001248	P55290	CAD13_HUMAN	cadherin 13 preproprotein	218	Cadherin 1.				adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)														---	---	---	---
MBTPS1	8720	broad.mit.edu	37	16	84094331	84094331	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84094331C>T	uc002fhi.2	-	20	3162	c.2660G>A	c.(2659-2661)CGC>CAC	p.R887H	MBTPS1_uc002fhh.2_Missense_Mutation_p.R391H	NM_003791	NP_003782	Q14703	MBTP1_HUMAN	membrane-bound transcription factor site-1	887	Lumenal (Potential).				cholesterol metabolic process|proteolysis	endoplasmic reticulum lumen|endoplasmic reticulum membrane|Golgi membrane|integral to membrane	serine-type endopeptidase activity			ovary(2)	2																		---	---	---	---
MBTPS1	8720	broad.mit.edu	37	16	84103580	84103580	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84103580T>C	uc002fhi.2	-	14	2348	c.1846A>G	c.(1846-1848)ACT>GCT	p.T616A	MBTPS1_uc002fhh.2_Missense_Mutation_p.T120A	NM_003791	NP_003782	Q14703	MBTP1_HUMAN	membrane-bound transcription factor site-1	616	Lumenal (Potential).				cholesterol metabolic process|proteolysis	endoplasmic reticulum lumen|endoplasmic reticulum membrane|Golgi membrane|integral to membrane	serine-type endopeptidase activity			ovary(2)	2																		---	---	---	---
LRRC50	123872	broad.mit.edu	37	16	84203764	84203764	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84203764G>T	uc002fhl.3	+	8	1511	c.1330G>T	c.(1330-1332)GCT>TCT	p.A444S	LRRC50_uc010vnw.1_Missense_Mutation_p.A208S	NM_178452	NP_848547	Q8NEP3	DAAF1_HUMAN	leucine rich repeat containing 50	444	Pro-rich.				axonemal dynein complex assembly|cilium morphogenesis	cilium axoneme|cytoplasm|spindle pole	dynein binding				0														Kartagener_syndrome				---	---	---	---
ATP2C2	9914	broad.mit.edu	37	16	84476156	84476156	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84476156C>T	uc002fhx.2	+	15	1441	c.1352C>T	c.(1351-1353)GCC>GTC	p.A451V	ATP2C2_uc010chj.2_Missense_Mutation_p.A451V|ATP2C2_uc002fhy.2_Missense_Mutation_p.A468V|ATP2C2_uc002fhz.2_Missense_Mutation_p.A300V	NM_014861	NP_055676	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2	451	Extracellular (Potential).				ATP biosynthetic process	Golgi membrane|integral to membrane	ATP binding|calcium-transporting ATPase activity|metal ion binding|protein binding			breast(1)|central_nervous_system(1)	2																		---	---	---	---
ATP2C2	9914	broad.mit.edu	37	16	84494364	84494364	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84494364C>T	uc002fhx.2	+	24	2527	c.2438C>T	c.(2437-2439)GCG>GTG	p.A813V	ATP2C2_uc010chj.2_Missense_Mutation_p.A842V|ATP2C2_uc002fhy.2_Missense_Mutation_p.A830V|ATP2C2_uc002fhz.2_Missense_Mutation_p.A662V|ATP2C2_uc002fia.2_Missense_Mutation_p.A124V	NM_014861	NP_055676	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2	813	Helical; Name=7; (Potential).				ATP biosynthetic process	Golgi membrane|integral to membrane	ATP binding|calcium-transporting ATPase activity|metal ion binding|protein binding			breast(1)|central_nervous_system(1)	2																		---	---	---	---
KIAA0182	23199	broad.mit.edu	37	16	85688407	85688407	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85688407C>T	uc002fix.2	+	5	681	c.607C>T	c.(607-609)CGG>TGG	p.R203W	KIAA0182_uc002fiw.2_Missense_Mutation_p.R99W|KIAA0182_uc002fiy.2_Missense_Mutation_p.R130W	NM_014615	NP_055430	Q14687	GSE1_HUMAN	genetic suppressor element 1 isoform 1	203							protein binding			large_intestine(3)|ovary(1)|skin(1)	5																		---	---	---	---
KIAA0182	23199	broad.mit.edu	37	16	85701738	85701738	+	Intron	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85701738C>A	uc002fix.2	+						KIAA0182_uc002fiw.2_Intron|KIAA0182_uc002fiy.2_Intron|KIAA0182_uc002fiz.2_Intron|KIAA0182_uc010cho.2_Intron	NM_014615	NP_055430			genetic suppressor element 1 isoform 1								protein binding			large_intestine(3)|ovary(1)|skin(1)	5																		---	---	---	---
COX4I1	1327	broad.mit.edu	37	16	85839384	85839384	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85839384G>A	uc002fje.2	+	4	451	c.287G>A	c.(286-288)GGC>GAC	p.G96D	COX4I1_uc002fjf.2_3'UTR|COX4I1_uc002fjg.1_Missense_Mutation_p.G96D|COX4I1_uc010vom.1_Missense_Mutation_p.G63D	NM_001861	NP_001852	P13073	COX41_HUMAN	cytochrome c oxidase subunit IV isoform 1	96					respiratory electron transport chain	mitochondrial inner membrane|nucleus	cytochrome-c oxidase activity|protein binding			lung(1)	1		Renal(780;0.228)																---	---	---	---
FOXF1	2294	broad.mit.edu	37	16	86544353	86544353	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86544353G>A	uc002fjl.2	+	1	221	c.178G>A	c.(178-180)GCC>ACC	p.A60T	uc002fjk.1_5'Flank	NM_001451	NP_001442	Q12946	FOXF1_HUMAN	forkhead box F1	60	Fork-head.				branching involved in open tracheal system development|cardiac left ventricle morphogenesis|embryonic ectodermal digestive tract morphogenesis|endocardial cushion development|in utero embryonic development|lung vasculature development|midgut development|pancreas development|positive regulation of transcription, DNA-dependent|regulation of sequence-specific DNA binding transcription factor activity|ureter development|venous blood vessel development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding				0																		---	---	---	---
FBXO31	79791	broad.mit.edu	37	16	87367781	87367781	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:87367781C>T	uc002fjw.2	-	8	1152	c.1108G>A	c.(1108-1110)GTC>ATC	p.V370I	FBXO31_uc010vot.1_Missense_Mutation_p.V198I|FBXO31_uc002fjv.2_Missense_Mutation_p.V262I	NM_024735	NP_079011	Q5XUX0	FBX31_HUMAN	F-box protein 31	370					cell cycle|cyclin catabolic process|mitotic cell cycle G1/S transition DNA damage checkpoint|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	SCF ubiquitin ligase complex	cyclin binding			lung(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0272)														---	---	---	---
CDH15	1013	broad.mit.edu	37	16	89254647	89254647	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89254647T>C	uc002fmt.2	+	7	1009	c.932T>C	c.(931-933)ATC>ACC	p.I311T		NM_004933	NP_004924	P55291	CAD15_HUMAN	cadherin 15 preproprotein	311	Cadherin 3.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion|muscle cell differentiation|positive regulation of muscle cell differentiation	integral to membrane|plasma membrane	calcium ion binding			skin(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0261)														---	---	---	---
ANKRD11	29123	broad.mit.edu	37	16	89346308	89346308	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89346308G>A	uc002fmx.1	-	9	7103	c.6642C>T	c.(6640-6642)GAC>GAT	p.D2214D	ANKRD11_uc002fmy.1_Silent_p.D2214D|ANKRD11_uc002fnc.1_Silent_p.D2214D|ANKRD11_uc002fna.1_5'Flank|ANKRD11_uc002fnb.1_Silent_p.D2171D	NM_013275	NP_037407	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	2214	Pro-rich.					nucleus				ovary(4)|large_intestine(1)|central_nervous_system(1)	6		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)														---	---	---	---
ANKRD11	29123	broad.mit.edu	37	16	89349237	89349237	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89349237A>G	uc002fmx.1	-	9	4174	c.3713T>C	c.(3712-3714)CTC>CCC	p.L1238P	ANKRD11_uc002fmy.1_Missense_Mutation_p.L1238P|ANKRD11_uc002fnc.1_Missense_Mutation_p.L1238P|ANKRD11_uc002fnb.1_Missense_Mutation_p.L1195P	NM_013275	NP_037407	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	1238	Lys-rich.					nucleus				ovary(4)|large_intestine(1)|central_nervous_system(1)	6		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)														---	---	---	---
SPG7	6687	broad.mit.edu	37	16	89579441	89579441	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89579441C>T	uc002fnj.2	+	3	393	c.372C>T	c.(370-372)GAC>GAT	p.D124D	SPG7_uc002fni.2_Silent_p.D124D	NM_003119	NP_003110	Q9UQ90	SPG7_HUMAN	spastic paraplegia 7 isoform 1	124	Mitochondrial matrix (Potential).				cell death|nervous system development|protein catabolic process|proteolysis	integral to membrane|mitochondrial membrane	ATP binding|metalloendopeptidase activity|nucleoside-triphosphatase activity|unfolded protein binding|zinc ion binding				0		all_hematologic(23;0.00824)|Colorectal(91;0.102)		all cancers(4;1.39e-07)|OV - Ovarian serous cystadenocarcinoma(4;5.64e-06)|BRCA - Breast invasive adenocarcinoma(80;0.015)														---	---	---	---
ZNF276	92822	broad.mit.edu	37	16	89804227	89804227	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89804227T>C	uc002fos.3	+	10	1585	c.1488T>C	c.(1486-1488)TAT>TAC	p.Y496Y	ZNF276_uc010ciq.2_Silent_p.Y282Y|ZNF276_uc002fop.2_Silent_p.Y404Y|ZNF276_uc002foq.3_Silent_p.Y421Y|ZNF276_uc010cir.2_RNA|ZNF276_uc002for.3_Silent_p.Y282Y|ZNF276_uc010cis.2_Silent_p.Y255Y|ZNF276_uc002fot.3_RNA|ZNF276_uc010vpm.1_Silent_p.Y334Y|ZNF276_uc010cit.1_Silent_p.Y255Y|FANCA_uc002fou.1_3'UTR|FANCA_uc010vpn.1_3'UTR	NM_001113525	NP_001106997	Q8N554	ZN276_HUMAN	zinc finger protein 276 isoform a	496	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Lung NSC(15;2.19e-05)|all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.0278)														---	---	---	---
FANCA	2175	broad.mit.edu	37	16	89869684	89869684	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89869684G>T	uc002fou.1	-	8	817	c.775C>A	c.(775-777)CCT>ACT	p.P259T	FANCA_uc010vpn.1_Missense_Mutation_p.P259T|FANCA_uc002fov.1_Missense_Mutation_p.P242T|FANCA_uc002fow.1_Missense_Mutation_p.P259T|FANCA_uc002fox.1_Missense_Mutation_p.P259T|FANCA_uc010ciu.1_Missense_Mutation_p.P227T|FANCA_uc002foy.2_Missense_Mutation_p.P259T	NM_000135	NP_000126	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A isoform	259					DNA repair|protein complex assembly	cytoplasm|nucleoplasm	protein binding			ovary(2)|breast(2)|central_nervous_system(1)|skin(1)	6		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)				D|Mis|N|F|S			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
SPIRE2	84501	broad.mit.edu	37	16	89924878	89924878	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89924878C>A	uc002foz.1	+	8	1287	c.1235C>A	c.(1234-1236)CCT>CAT	p.P412H	SPIRE2_uc010civ.1_Missense_Mutation_p.P327H|SPIRE2_uc010ciw.1_Missense_Mutation_p.P412H|SPIRE2_uc002fpa.1_Missense_Mutation_p.P364H|SPIRE2_uc010cix.1_Missense_Mutation_p.P279H	NM_032451	NP_115827	Q8WWL2	SPIR2_HUMAN	spire homolog 2	412					transport	cytoplasm|cytoskeleton	actin binding			central_nervous_system(1)	1		Lung NSC(15;5.15e-06)|all_lung(18;8.38e-06)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0286)														---	---	---	---
TCF25	22980	broad.mit.edu	37	16	89967213	89967213	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89967213G>A	uc002fpb.2	+						TCF25_uc002fpc.2_Intron	NM_014972	NP_055787			NULP1						heart development|negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0		all_cancers(9;4.71e-08)|Lung NSC(15;0.000192)|all_lung(18;0.000319)|all_neural(9;0.0122)|all_hematologic(23;0.027)		BRCA - Breast invasive adenocarcinoma(80;0.0288)														---	---	---	---
RPH3AL	9501	broad.mit.edu	37	17	169217	169217	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:169217G>A	uc002frd.1	-	3	389	c.345C>T	c.(343-345)TGC>TGT	p.C115C	RPH3AL_uc010vpy.1_Silent_p.C115C|RPH3AL_uc002fre.1_Silent_p.C115C|RPH3AL_uc002frf.1_Silent_p.C115C|RPH3AL_uc010cjl.1_Silent_p.C115C	NM_006987	NP_008918	Q9UNE2	RPH3L_HUMAN	rabphilin 3A-like (without C2 domains)	115	RabBD.|FYVE-type.				exocytosis|intracellular protein transport	transport vesicle membrane	cytoskeletal protein binding|Rab GTPase binding|zinc ion binding			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.023)|all cancers(1;4.96e-06)|Epithelial(1;2.86e-05)|BRCA - Breast invasive adenocarcinoma(1;0.00453)|OV - Ovarian serous cystadenocarcinoma(1;0.0716)|LUAD - Lung adenocarcinoma(1115;0.102)|COAD - Colon adenocarcinoma(4;0.107)														---	---	---	---
GEMIN4	50628	broad.mit.edu	37	17	649698	649698	+	Missense_Mutation	SNP	T	C	C	rs35172207	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:649698T>C	uc002frs.1	-	2	1704	c.1585A>G	c.(1585-1587)ACT>GCT	p.T529A		NM_015721	NP_056536	P57678	GEMI4_HUMAN	gemin 4	529					rRNA processing|spliceosomal snRNP assembly	Cajal body|cytosol|nucleolus|small nuclear ribonucleoprotein complex|spliceosomal complex	protein binding			ovary(2)|kidney(1)|skin(1)	4		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.022)														---	---	---	---
GEMIN4	50628	broad.mit.edu	37	17	650285	650285	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:650285G>A	uc002frs.1	-	2	1117	c.998C>T	c.(997-999)GCC>GTC	p.A333V	GEMIN4_uc010vqa.1_3'UTR	NM_015721	NP_056536	P57678	GEMI4_HUMAN	gemin 4	333					rRNA processing|spliceosomal snRNP assembly	Cajal body|cytosol|nucleolus|small nuclear ribonucleoprotein complex|spliceosomal complex	protein binding			ovary(2)|kidney(1)|skin(1)	4		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.022)														---	---	---	---
RNMTL1	55178	broad.mit.edu	37	17	691343	691343	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:691343C>T	uc002frw.2	+	3	804	c.698C>T	c.(697-699)GCA>GTA	p.A233V		NM_018146	NP_060616	Q9HC36	RMTL1_HUMAN	RNA methyltransferase like 1	233					RNA processing		protein binding|RNA binding|RNA methyltransferase activity			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0219)														---	---	---	---
MYO1C	4641	broad.mit.edu	37	17	1370767	1370767	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1370767G>A	uc002fsp.2	-						MYO1C_uc002fsn.2_Intron|MYO1C_uc002fso.2_Intron	NM_001080779	NP_001074248			myosin IC isoform a						mRNA transport|protein transport|transmembrane transport	basal plasma membrane|cytoplasm|filamentous actin|lateral plasma membrane|nuclear pore|nucleolus|nucleoplasm|stereocilium membrane	actin binding|ATP binding|calmodulin binding|motor activity				0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)														---	---	---	---
MYO1C	4641	broad.mit.edu	37	17	1381748	1381748	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1381748G>A	uc002fsp.2	-	11	1471	c.1251C>T	c.(1249-1251)CTC>CTT	p.L417L	MYO1C_uc002fsn.2_Silent_p.L398L|MYO1C_uc002fso.2_Silent_p.L382L|MYO1C_uc010vqj.1_Silent_p.L382L|MYO1C_uc010vqk.1_Silent_p.L393L	NM_001080779	NP_001074248	O00159	MYO1C_HUMAN	myosin IC isoform a	417	Myosin head-like.				mRNA transport|protein transport|transmembrane transport	basal plasma membrane|cytoplasm|filamentous actin|lateral plasma membrane|nuclear pore|nucleolus|nucleoplasm|stereocilium membrane	actin binding|ATP binding|calmodulin binding|motor activity				0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)														---	---	---	---
PITPNA	5306	broad.mit.edu	37	17	1438733	1438733	+	Splice_Site	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1438733A>G	uc002fst.3	-	7	790	c.534_splice	c.e7+1	p.K178_splice	PITPNA_uc010cjt.2_Splice_Site_p.K62_splice|PITPNA_uc010cju.2_Splice_Site_p.K76_splice	NM_006224	NP_006215			phosphatidylinositol transfer protein, alpha						axon guidance|lipid metabolic process|visual perception	cytoplasm	phosphatidylcholine transmembrane transporter activity|phosphatidylinositol transporter activity|protein binding			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0845)														---	---	---	---
SCARF1	8578	broad.mit.edu	37	17	1538453	1538453	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1538453G>C	uc002fsz.1	-	11	2142	c.2092C>G	c.(2092-2094)CCC>GCC	p.P698A	SCARF1_uc002fsy.1_3'UTR|SCARF1_uc002fta.1_RNA|SCARF1_uc010cjv.1_Missense_Mutation_p.P612A	NM_003693	NP_003684	Q14162	SREC_HUMAN	scavenger receptor class F, member 1 isoform 1	698	Gly-rich.|Cytoplasmic (Potential).				cell adhesion|neuron remodeling|positive regulation of axon regeneration|receptor-mediated endocytosis	integral to membrane	low-density lipoprotein particle binding|scavenger receptor activity			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)														---	---	---	---
PRPF8	10594	broad.mit.edu	37	17	1577778	1577778	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1577778C>T	uc002fte.2	-	21	3371	c.3257G>A	c.(3256-3258)CGT>CAT	p.R1086H		NM_006445	NP_006436	Q6P2Q9	PRP8_HUMAN	U5 snRNP-specific protein	1086						catalytic step 2 spliceosome|nuclear speck|U5 snRNP	protein binding|RNA binding			lung(4)|ovary(2)	6				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)														---	---	---	---
SERPINF2	5345	broad.mit.edu	37	17	1649038	1649038	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1649038G>A	uc002ftk.1	+	5	279	c.202G>A	c.(202-204)GGA>AGA	p.G68R	SERPINF2_uc010vqr.1_Intron	NM_000934	NP_000925	P08697	A2AP_HUMAN	alpha-2-antiplasmin isoform a precursor	68					acute-phase response|fibrinolysis|platelet activation|platelet degranulation|regulation of proteolysis	extracellular space|platelet alpha granule lumen	protease binding|serine-type endopeptidase inhibitor activity				0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)	Streptokinase(DB00086)													---	---	---	---
SERPINF2	5345	broad.mit.edu	37	17	1657620	1657620	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1657620C>T	uc002ftk.1	+	10	1345	c.1268C>T	c.(1267-1269)ACC>ATC	p.T423I	SERPINF2_uc010vqr.1_Missense_Mutation_p.T359I	NM_000934	NP_000925	P08697	A2AP_HUMAN	alpha-2-antiplasmin isoform a precursor	423					acute-phase response|fibrinolysis|platelet activation|platelet degranulation|regulation of proteolysis	extracellular space|platelet alpha granule lumen	protease binding|serine-type endopeptidase inhibitor activity				0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)	Streptokinase(DB00086)													---	---	---	---
RPA1	6117	broad.mit.edu	37	17	1787232	1787232	+	Silent	SNP	C	T	T	rs112320339		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1787232C>T	uc002fto.2	+	13	1483	c.1368C>T	c.(1366-1368)GGC>GGT	p.G456G		NM_002945	NP_002936	P27694	RFA1_HUMAN	replication protein A1	456					cell cycle checkpoint|DNA recombinase assembly|DNA strand elongation involved in DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	actin cytoskeleton|cytoplasm|DNA replication factor A complex|PML body	metal ion binding|protein binding|single-stranded DNA binding				0													NER					---	---	---	---
SRR	63826	broad.mit.edu	37	17	2224592	2224592	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2224592A>G	uc002fue.1	+						SRR_uc002fui.1_Intron	NM_021947	NP_068766			serine racemase						D-serine biosynthetic process|L-serine metabolic process|protein homotetramerization|pyruvate biosynthetic process|response to lipopolysaccharide	cytoplasm|neuronal cell body|soluble fraction	ATP binding|calcium ion binding|D-serine ammonia-lyase activity|glycine binding|L-serine ammonia-lyase activity|magnesium ion binding|PDZ domain binding|protein homodimerization activity|pyridoxal phosphate binding|serine racemase activity|threonine racemase activity				0		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)		COAD - Colon adenocarcinoma(228;3.24e-06)|READ - Rectum adenocarcinoma(1115;0.0649)	L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)													---	---	---	---
METT10D	79066	broad.mit.edu	37	17	2323749	2323749	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2323749C>T	uc002fut.2	-	10	1352	c.1204G>A	c.(1204-1206)GTC>ATC	p.V402I	METT10D_uc002fuu.3_RNA|METT10D_uc010cka.2_RNA|METT10D_uc002fuv.2_Intron|METT10D_uc010vqx.1_RNA|METT10D_uc010vqy.1_Missense_Mutation_p.V184I	NM_024086	NP_076991	Q86W50	MET16_HUMAN	methyltransferase 10 domain containing	402							methyltransferase activity				0																		---	---	---	---
OR3A1	4994	broad.mit.edu	37	17	3195087	3195087	+	Nonsense_Mutation	SNP	G	A	A	rs138768418	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3195087G>A	uc002fvh.1	-	1	790	c.790C>T	c.(790-792)CGA>TGA	p.R264*		NM_002550	NP_002541	P47881	OR3A1_HUMAN	olfactory receptor, family 3, subfamily A,	264	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			kidney(2)|central_nervous_system(1)	3																		---	---	---	---
OR3A1	4994	broad.mit.edu	37	17	3195243	3195243	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3195243T>C	uc002fvh.1	-	1	634	c.634A>G	c.(634-636)ACC>GCC	p.T212A		NM_002550	NP_002541	P47881	OR3A1_HUMAN	olfactory receptor, family 3, subfamily A,	212	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			kidney(2)|central_nervous_system(1)	3																		---	---	---	---
OR1E2	8388	broad.mit.edu	37	17	3336211	3336211	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3336211C>T	uc010vre.1	-	1	925	c.925G>A	c.(925-927)GCC>ACC	p.A309T		NM_003554	NP_003545	P47887	OR1E2_HUMAN	olfactory receptor, family 1, subfamily E,	309	Cytoplasmic (Potential).				sensory perception of smell	integral to plasma membrane	olfactory receptor activity			large_intestine(1)	1																		---	---	---	---
SPATA22	84690	broad.mit.edu	37	17	3365814	3365814	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3365814T>C	uc002fvm.2	-	5	529	c.292A>G	c.(292-294)ATT>GTT	p.I98V	SPATA22_uc010vrg.1_Missense_Mutation_p.I82V|SPATA22_uc010vrf.1_Missense_Mutation_p.I98V|SPATA22_uc002fvn.2_Missense_Mutation_p.I98V|SPATA22_uc002fvo.2_Missense_Mutation_p.I98V|SPATA22_uc002fvp.2_Missense_Mutation_p.I98V|SPATA22_uc010ckf.2_Missense_Mutation_p.I55V	NM_032598	NP_115987	Q8NHS9	SPT22_HUMAN	spermatogenesis associated 22	98											0																		---	---	---	---
TRPV1	7442	broad.mit.edu	37	17	3474850	3474850	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3474850C>T	uc010vrr.1	-	14	2842	c.2315G>A	c.(2314-2316)CGC>CAC	p.R772H	TRPV1_uc010vro.1_Missense_Mutation_p.R783H|TRPV1_uc010vrp.1_Missense_Mutation_p.R712H|TRPV1_uc010vrq.1_Missense_Mutation_p.R770H|TRPV1_uc010vrs.1_Missense_Mutation_p.R772H|TRPV1_uc010vrt.1_Missense_Mutation_p.R772H|TRPV1_uc010vru.1_Missense_Mutation_p.R772H	NM_080706	NP_542437	Q8NER1	TRPV1_HUMAN	transient receptor potential cation channel,	772	Interaction with calmodulin (By similarity).|Cytoplasmic (Potential).				cell surface receptor linked signaling pathway|chemosensory behavior|thermoception	cell junction|dendritic spine membrane|integral to plasma membrane|postsynaptic membrane	ATP binding|calcium channel activity|calmodulin binding			ovary(1)	1				Lung(1;0.055)|COAD - Colon adenocarcinoma(5;0.0896)|LUAD - Lung adenocarcinoma(1115;0.131)	Alpha-Linolenic Acid(DB00132)|Aspartame(DB00168)|Icosapent(DB00159)													---	---	---	---
SHPK	23729	broad.mit.edu	37	17	3513977	3513977	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3513977G>A	uc002fvz.1	-	7	1417	c.1314C>T	c.(1312-1314)GAC>GAT	p.D438D	TRPV1_uc010vru.1_5'Flank	NM_013276	NP_037408	Q9UHJ6	SHPK_HUMAN	carbohydrate kinase-like	438					carbohydrate metabolic process	cytoplasm	ATP binding|sedoheptulokinase activity			ovary(1)	1				COAD - Colon adenocarcinoma(5;0.0828)														---	---	---	---
TAX1BP3	30851	broad.mit.edu	37	17	3567066	3567066	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3567066G>A	uc002fwc.2	-	4	504	c.351C>T	c.(349-351)GCC>GCT	p.A117A	P2RX5_uc002fwd.2_RNA|TAX1BP3_uc002fwe.1_3'UTR	NM_014604	NP_055419	O14907	TX1B3_HUMAN	Tax1 binding protein 3	117					activation of Cdc42 GTPase activity|negative regulation of protein localization at cell surface|negative regulation of Wnt receptor signaling pathway|Rho protein signal transduction|Wnt receptor signaling pathway	cytoplasm|nucleus	protein C-terminus binding				0				COAD - Colon adenocarcinoma(5;0.0761)														---	---	---	---
ITGAE	3682	broad.mit.edu	37	17	3662792	3662792	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3662792C>T	uc002fwo.3	-	8	869	c.770G>A	c.(769-771)CGG>CAG	p.R257Q		NM_002208	NP_002199	P38570	ITAE_HUMAN	integrin, alpha E precursor	257	VWFA.|Extracellular (Potential).				cell adhesion|integrin-mediated signaling pathway	integrin complex	receptor activity			large_intestine(2)|breast(1)|pancreas(1)	4				UCEC - Uterine corpus endometrioid carcinoma (3;0.0813)														---	---	---	---
CAMKK1	84254	broad.mit.edu	37	17	3779671	3779671	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:3779671A>T	uc002fwt.2	-	10	936	c.842T>A	c.(841-843)CTG>CAG	p.L281Q	CAMKK1_uc002fwu.2_Missense_Mutation_p.L281Q|CAMKK1_uc002fwv.2_Missense_Mutation_p.L319Q	NM_172206	NP_757343	Q8N5S9	KKCC1_HUMAN	calcium/calmodulin-dependent protein kinase 1	281	Protein kinase.				synaptic transmission	cytosol|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)	1				LUAD - Lung adenocarcinoma(2;2.11e-05)|Lung(3;0.0176)														---	---	---	---
ANKFY1	51479	broad.mit.edu	37	17	4120350	4120350	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4120350C>A	uc002fxq.1	-	4	424	c.386G>T	c.(385-387)AGA>ATA	p.R129I	ANKFY1_uc002fxn.2_Missense_Mutation_p.R171I|ANKFY1_uc002fxo.2_Missense_Mutation_p.R129I|ANKFY1_uc002fxp.2_Missense_Mutation_p.R129I|ANKFY1_uc010ckp.2_Missense_Mutation_p.R70I|ANKFY1_uc002fxr.2_Missense_Mutation_p.R129I|ANKFY1_uc010vrz.1_Missense_Mutation_p.R129I	NM_016376	NP_057460	Q9P2R3	ANFY1_HUMAN	ankyrin repeat and FYVE domain containing 1	129	BTB.					endosome membrane	metal ion binding|protein binding			ovary(2)|skin(1)	3																		---	---	---	---
GGT6	124975	broad.mit.edu	37	17	4461331	4461331	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4461331G>A	uc002fyd.3	-	4	1521	c.1461C>T	c.(1459-1461)TGC>TGT	p.C487C	MYBBP1A_uc002fxz.3_5'Flank|MYBBP1A_uc002fyb.3_5'Flank|GGT6_uc010vsb.1_Silent_p.C339C|GGT6_uc002fyc.3_Silent_p.C455C|GGT6_uc010vsc.1_Silent_p.C493C	NM_001122890	NP_001116362	Q6P531	GGT6_HUMAN	gamma-glutamyltransferase 6 isoform a	487	Extracellular (Potential).				glutathione biosynthetic process	integral to membrane	acyltransferase activity|gamma-glutamyltransferase activity			skin(1)	1																		---	---	---	---
PELP1	27043	broad.mit.edu	37	17	4586156	4586156	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4586156T>A	uc002fyi.3	-	4	738	c.512A>T	c.(511-513)GAC>GTC	p.D171V	PELP1_uc010vsf.1_Missense_Mutation_p.D24V	NM_014389	NP_055204	Q8IZL8	PELP1_HUMAN	proline, glutamic acid and leucine rich protein	171					transcription, DNA-dependent	cytoplasm|MLL1 complex	protein binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
TM4SF5	9032	broad.mit.edu	37	17	4684163	4684163	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4684163G>T	uc002fyw.1	+	2	288	c.257G>T	c.(256-258)AGG>ATG	p.R86M		NM_003963	NP_003954	O14894	T4S5_HUMAN	transmembrane 4 superfamily member 5	86	Cytoplasmic (Potential).					integral to plasma membrane				ovary(1)	1																		---	---	---	---
PLD2	5338	broad.mit.edu	37	17	4713051	4713051	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4713051A>G	uc002fzc.2	+	8	781	c.680A>G	c.(679-681)GAC>GGC	p.D227G	PLD2_uc010vsj.1_Missense_Mutation_p.D84G|PLD2_uc002fzd.2_Missense_Mutation_p.D227G	NM_002663	NP_002654	O14939	PLD2_HUMAN	phospholipase D2	227	PH.				cell communication|cytoskeleton organization|small GTPase mediated signal transduction		NAPE-specific phospholipase D activity|phosphatidylinositol binding|phospholipase D activity			breast(2)|upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	5					Choline(DB00122)													---	---	---	---
PLD2	5338	broad.mit.edu	37	17	4719240	4719240	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4719240T>C	uc002fzc.2	+						PLD2_uc010vsj.1_Intron|PLD2_uc002fzd.2_Intron	NM_002663	NP_002654			phospholipase D2						cell communication|cytoskeleton organization|small GTPase mediated signal transduction		NAPE-specific phospholipase D activity|phosphatidylinositol binding|phospholipase D activity			breast(2)|upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	5					Choline(DB00122)											OREG0024105	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
GPR172B	55065	broad.mit.edu	37	17	4936645	4936645	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4936645C>A	uc002gap.3	-	4	1758	c.1045G>T	c.(1045-1047)GGC>TGC	p.G349C	GPR172B_uc002gao.3_Missense_Mutation_p.G349C|GPR172B_uc010ckw.2_Missense_Mutation_p.G227C|GPR172B_uc010ckx.2_Intron	NM_001104577	NP_001098047	Q9NWF4	RFT_HUMAN	G protein-coupled receptor 172B precursor	349	Helical; (Potential).					integral to plasma membrane	receptor activity|riboflavin transporter activity				0																		---	---	---	---
GPR172B	55065	broad.mit.edu	37	17	4937501	4937501	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4937501G>A	uc002gap.3	-	3	996	c.283C>T	c.(283-285)CTG>TTG	p.L95L	GPR172B_uc002gao.3_Silent_p.L95L|GPR172B_uc010ckw.2_5'UTR|GPR172B_uc010ckx.2_Silent_p.L95L	NM_001104577	NP_001098047	Q9NWF4	RFT_HUMAN	G protein-coupled receptor 172B precursor	95	Helical; (Potential).					integral to plasma membrane	receptor activity|riboflavin transporter activity				0																		---	---	---	---
NLRP1	22861	broad.mit.edu	37	17	5485199	5485199	+	Missense_Mutation	SNP	G	A	A	rs149535960	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5485199G>A	uc002gci.2	-	3	1187	c.632C>T	c.(631-633)ACG>ATG	p.T211M	NLRP1_uc002gcg.1_Missense_Mutation_p.T211M|NLRP1_uc002gck.2_Missense_Mutation_p.T211M|NLRP1_uc002gcj.2_Missense_Mutation_p.T211M|NLRP1_uc002gcl.2_Missense_Mutation_p.T211M|NLRP1_uc002gch.3_Missense_Mutation_p.T211M|NLRP1_uc010clh.2_Missense_Mutation_p.T211M	NM_033004	NP_127497	Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1 isoform 1	211					defense response to bacterium|induction of apoptosis|neuron apoptosis|positive regulation of interleukin-1 beta secretion|response to muramyl dipeptide	cytoplasm|NALP1 inflammasome complex|nucleus	ATP binding|caspase activator activity|enzyme binding|protein domain specific binding			lung(4)|breast(2)|ovary(1)|central_nervous_system(1)|skin(1)	9		Colorectal(1115;3.48e-05)																---	---	---	---
WSCD1	23302	broad.mit.edu	37	17	6023893	6023893	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6023893A>C	uc010cli.2	+	9	2019	c.1640A>C	c.(1639-1641)GAC>GCC	p.D547A	WSCD1_uc002gcn.2_Missense_Mutation_p.D547A|WSCD1_uc002gco.2_Missense_Mutation_p.D547A|WSCD1_uc010clj.2_Missense_Mutation_p.D238A	NM_015253	NP_056068	Q658N2	WSCD1_HUMAN	WSC domain containing 1	547						integral to membrane	sulfotransferase activity				0																		---	---	---	---
AIPL1	23746	broad.mit.edu	37	17	6337282	6337282	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6337282G>T	uc002gcp.2	-	2	328	c.233C>A	c.(232-234)TCC>TAC	p.S78Y	AIPL1_uc002gcq.2_Intron|AIPL1_uc002gcr.2_Missense_Mutation_p.S78Y|AIPL1_uc010clk.2_Missense_Mutation_p.S56Y|AIPL1_uc010cll.2_Missense_Mutation_p.S78Y|AIPL1_uc002gcs.2_Missense_Mutation_p.S78Y	NM_014336	NP_055151	Q9NZN9	AIPL1_HUMAN	aryl hydrocarbon receptor interacting	78	PPIase FKBP-type.				protein farnesylation|protein folding|visual perception	cytoplasm|nucleus	farnesylated protein binding|unfolded protein binding				0				COAD - Colon adenocarcinoma(228;0.141)														---	---	---	---
KIAA0753	9851	broad.mit.edu	37	17	6532017	6532017	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6532017G>T	uc002gde.3	-	3	497	c.138C>A	c.(136-138)AAC>AAA	p.N46K	KIAA0753_uc010clo.2_5'UTR|KIAA0753_uc010vte.1_5'UTR	NM_014804	NP_055619	Q2KHM9	K0753_HUMAN	hypothetical protein LOC9851	46						centrosome					0				COAD - Colon adenocarcinoma(228;0.157)														---	---	---	---
TEKT1	83659	broad.mit.edu	37	17	6719250	6719250	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:6719250C>T	uc002gdt.2	-	4	498	c.388G>A	c.(388-390)GAC>AAC	p.D130N	TEKT1_uc010vth.1_5'UTR	NM_053285	NP_444515	Q969V4	TEKT1_HUMAN	tektin 1	130					microtubule cytoskeleton organization	cilium axoneme|flagellar axoneme|microtubule				ovary(1)|skin(1)	2		Myeloproliferative disorder(207;0.0255)																---	---	---	---
ASGR2	433	broad.mit.edu	37	17	7012084	7012084	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7012084C>T	uc002gep.3	-	3	513	c.248G>A	c.(247-249)GGT>GAT	p.G83D	ASGR2_uc010vtk.1_5'Flank|ASGR2_uc002gem.1_Intron|ASGR2_uc002gen.1_Missense_Mutation_p.G64D|ASGR2_uc002geo.1_Intron|ASGR2_uc002ger.3_Missense_Mutation_p.G83D|ASGR2_uc002geq.3_Intron|ASGR2_uc010clw.2_Intron|ASGR2_uc010vtl.1_Intron	NM_001181	NP_001172	P07307	ASGR2_HUMAN	asialoglycoprotein receptor 2 isoform a	83	Extracellular (Potential).				cell surface receptor linked signaling pathway|endocytosis	focal adhesion|integral to membrane|nucleolus	asialoglycoprotein receptor activity|protein binding|sugar binding			ovary(1)	1					Antihemophilic Factor(DB00025)													---	---	---	---
DLG4	1742	broad.mit.edu	37	17	7106814	7106814	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7106814C>T	uc002get.3	-	8	1764	c.563G>A	c.(562-564)CGC>CAC	p.R188H	DLG4_uc010vtm.1_RNA|DLG4_uc010vtn.1_Missense_Mutation_p.R85H|DLG4_uc010cly.2_Missense_Mutation_p.R142H|DLG4_uc010vto.1_Missense_Mutation_p.R185H|DLG4_uc002geu.2_Missense_Mutation_p.R142H	NM_001365	NP_001356	P78352	DLG4_HUMAN	post-synaptic density protein 95 isoform 1	145	PDZ 1.				axon guidance|learning|protein complex assembly|protein localization to synapse|signal transduction|synaptic transmission	cell junction|cortical cytoskeleton|endocytic vesicle membrane|neuron spine|postsynaptic density|postsynaptic membrane|synaptosome	protein binding|protein C-terminus binding			ovary(1)|breast(1)	2																		---	---	---	---
DVL2	1856	broad.mit.edu	37	17	7137558	7137558	+	Silent	SNP	G	A	A	rs146467021	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7137558G>A	uc002gez.1	-	1	306	c.24C>T	c.(22-24)GGC>GGT	p.G8G	DVL2_uc010vtr.1_Silent_p.G8G|DVL2_uc010clz.1_Silent_p.G8G	NM_004422	NP_004413	O14641	DVL2_HUMAN	dishevelled 2	8	Poly-Gly.				canonical Wnt receptor signaling pathway involved in regulation of cell proliferation|intracellular signal transduction|neural tube closure|positive regulation of JUN kinase activity|positive regulation of protein phosphorylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|segment specification|transcription from RNA polymerase II promoter	cytosol|nucleus|plasma membrane	frizzled binding|identical protein binding|signal transducer activity			lung(1)|kidney(1)	2																		---	---	---	---
NEURL4	84461	broad.mit.edu	37	17	7221256	7221256	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7221256G>A	uc002gga.1	-						GPS2_uc002gfv.1_5'Flank|GPS2_uc002gfw.1_5'Flank|GPS2_uc002gfx.1_5'Flank|NEURL4_uc002gfy.1_Intron|GPS2_uc002gfz.1_Intron|NEURL4_uc002ggb.1_Intron	NM_032442	NP_115818			neuralized homolog 4 isoform 1								protein binding			upper_aerodigestive_tract(1)|ovary(1)	2																		---	---	---	---
PLSCR3	57048	broad.mit.edu	37	17	7296236	7296236	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7296236G>A	uc002ggm.1	-	6	752	c.543C>T	c.(541-543)GGC>GGT	p.G181G	PLSCR3_uc002ggl.2_Intron|PLSCR3_uc002ggq.1_Silent_p.G12G|PLSCR3_uc002ggn.1_Silent_p.G181G|PLSCR3_uc002ggo.1_Silent_p.G181G|PLSCR3_uc002ggp.1_Silent_p.G12G|PLSCR3_uc002ggr.1_Silent_p.G181G|PLSCR3_uc010cmg.1_Silent_p.G181G	NM_020360	NP_065093	Q9NRY6	PLS3_HUMAN	phospholipid scramblase 3	181	Cytoplasmic (By similarity).				phospholipid scrambling	integral to membrane|plasma membrane	calcium ion binding|calcium-dependent protein binding|phospholipid scramblase activity|SH3 domain binding				0		Prostate(122;0.173)																---	---	---	---
FGF11	2256	broad.mit.edu	37	17	7345993	7345993	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7345993C>T	uc002ggz.2	+	4	740	c.489C>T	c.(487-489)CGC>CGT	p.R163R	FGF11_uc010vtw.1_3'UTR|FGF11_uc010cmi.2_Silent_p.R39R|FGF11_uc010vtx.1_Silent_p.R104R|FGF11_uc002gha.3_Silent_p.R39R|CHRNB1_uc002ghb.2_5'Flank|CHRNB1_uc010vty.1_5'Flank	NM_004112	NP_004103	Q92914	FGF11_HUMAN	fibroblast growth factor 11	163			R -> G.		cell-cell signaling|nervous system development|signal transduction		growth factor activity				0		Prostate(122;0.157)																---	---	---	---
ZBTB4	57659	broad.mit.edu	37	17	7369273	7369273	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7369273G>C	uc002ghc.3	-	3	1098	c.848C>G	c.(847-849)GCC>GGC	p.A283G	ZBTB4_uc002ghd.3_Missense_Mutation_p.A283G	NM_001128833	NP_001122305	Q9P1Z0	ZBTB4_HUMAN	zinc finger and BTB domain containing 4	283					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)|ovary(1)|central_nervous_system(1)	4		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)		COAD - Colon adenocarcinoma(228;4.1e-06)|READ - Rectum adenocarcinoma(115;0.0642)														---	---	---	---
ZBTB4	57659	broad.mit.edu	37	17	7369686	7369686	+	Silent	SNP	G	A	A	rs113782048		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7369686G>A	uc002ghc.3	-	3	685	c.435C>T	c.(433-435)AGC>AGT	p.S145S	ZBTB4_uc002ghd.3_Silent_p.S145S	NM_001128833	NP_001122305	Q9P1Z0	ZBTB4_HUMAN	zinc finger and BTB domain containing 4	145	BTB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)|ovary(1)|central_nervous_system(1)	4		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)		COAD - Colon adenocarcinoma(228;4.1e-06)|READ - Rectum adenocarcinoma(115;0.0642)														---	---	---	---
POLR2A	5430	broad.mit.edu	37	17	7402375	7402375	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7402375T>C	uc002ghf.3	+	9	1587	c.1353T>C	c.(1351-1353)TGT>TGC	p.C451C	POLR2A_uc002ghe.2_Silent_p.C451C	NM_000937	NP_000928	P24928	RPB1_HUMAN	DNA-directed RNA polymerase II A	451					mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|RNA-directed RNA polymerase activity|ubiquitin protein ligase binding			pancreas(1)	1		Prostate(122;0.173)																---	---	---	---
POLR2A	5430	broad.mit.edu	37	17	7414826	7414826	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7414826C>T	uc002ghf.3	+	24	4254	c.4020C>T	c.(4018-4020)GGC>GGT	p.G1340G		NM_000937	NP_000928	P24928	RPB1_HUMAN	DNA-directed RNA polymerase II A	1340					mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|RNA-directed RNA polymerase activity|ubiquitin protein ligase binding			pancreas(1)	1		Prostate(122;0.173)																---	---	---	---
CD68	968	broad.mit.edu	37	17	7484081	7484081	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7484081T>C	uc002ghv.2	+	4	931	c.740T>C	c.(739-741)GTG>GCG	p.V247A	CD68_uc002ghu.2_Missense_Mutation_p.V220A|MPDU1_uc010vub.1_5'Flank|MPDU1_uc002ghw.2_5'Flank|MPDU1_uc002ghx.2_5'Flank|MPDU1_uc010vuc.1_5'Flank	NM_001251	NP_001242	P34810	CD68_HUMAN	CD68 antigen isoform A	247	Extracellular (Potential).					endosome membrane|integral to membrane|lysosomal membrane|membrane fraction|plasma membrane					0																		---	---	---	---
SHBG	6462	broad.mit.edu	37	17	7536253	7536253	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7536253C>T	uc002gie.2	+	7	1074	c.1036C>T	c.(1036-1038)CGT>TGT	p.R346C	SHBG_uc010cmo.2_Missense_Mutation_p.R234C|SHBG_uc010cmp.2_Intron|SHBG_uc010cmq.2_Intron|SHBG_uc010cmr.2_Intron|SHBG_uc010cms.2_Intron|SHBG_uc010cmt.2_Missense_Mutation_p.R288C|SHBG_uc010cmu.2_Intron|SHBG_uc010cmz.2_Intron|SHBG_uc010cmv.2_Intron|SHBG_uc010cmw.2_Intron|SHBG_uc010cmx.2_Intron|SHBG_uc010cmy.2_Missense_Mutation_p.R288C|SHBG_uc002gid.3_Intron|SHBG_uc010cnd.2_Intron|SHBG_uc010cna.2_Intron|SHBG_uc010vue.1_Missense_Mutation_p.R328C|SHBG_uc010vuf.1_Intron|SHBG_uc010cnb.2_Intron|SHBG_uc010cnc.2_Intron	NM_001040	NP_001031	P04278	SHBG_HUMAN	sex hormone-binding globulin isoform 1	346	Laminin G-like 2.				hormone transport	extracellular region	androgen binding|protein homodimerization activity	p.0?(1)|p.?(1)			0		all_cancers(10;0.0867)		READ - Rectum adenocarcinoma(115;0.168)	Danazol(DB01406)|Dromostanolone(DB00858)|Estradiol(DB00783)|Estrone(DB00655)|Fluoxymesterone(DB01185)|Hydrocortisone(DB00741)|Mitotane(DB00648)|Norethindrone(DB00717)|Testosterone(DB00624)											OREG0024140	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
TP53	7157	broad.mit.edu	37	17	7578513	7578513	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7578513C>A	uc002gim.2	-	5	611	c.417G>T	c.(415-417)AAG>AAT	p.K139N	TP53_uc002gig.1_Missense_Mutation_p.K139N|TP53_uc002gih.2_Missense_Mutation_p.K139N|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.K7N|TP53_uc010cng.1_Missense_Mutation_p.K7N|TP53_uc002gii.1_Missense_Mutation_p.K7N|TP53_uc010cnh.1_Missense_Mutation_p.K139N|TP53_uc010cni.1_Missense_Mutation_p.K139N|TP53_uc002gij.2_Missense_Mutation_p.K139N|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Missense_Mutation_p.K46N|TP53_uc002gio.2_Missense_Mutation_p.K7N|TP53_uc010vug.1_Missense_Mutation_p.K100N	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	139	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		K -> N (in sporadic cancers; somatic mutation).|K -> T (in sporadic cancers; somatic mutation).|K -> Q (in sporadic cancers; somatic mutation).|K -> R (in sporadic cancers; somatic mutation).|K -> E (in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.K139N(8)|p.K139K(7)|p.0?(7)|p.K139fs*31(4)|p.K139fs*9(3)|p.K139Q(2)|p.K139R(2)|p.K139E(2)|p.N131fs*27(2)|p.K139*(2)|p.K139T(1)|p.L137_W146del10(1)|p.K139fs*4(1)|p.F134_T140>S(1)|p.A138_V143delAKTCPV(1)|p.K139fs*11(1)|p.K139fs*10(1)|p.A138_P142delAKTCP(1)|p.Q136_K139delQLAK(1)|p.K139_C141>N(1)|p.C135_T140delCQLAKT(1)|p.K139fs*29(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)			111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			---	---	---	---
DNAH2	146754	broad.mit.edu	37	17	7663158	7663158	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7663158T>C	uc002giu.1	+	16	2701	c.2687T>C	c.(2686-2688)ATT>ACT	p.I896T		NM_020877	NP_065928	Q9P225	DYH2_HUMAN	dynein heavy chain domain 3	896	Stem (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|skin(6)|central_nervous_system(1)	13		all_cancers(10;4.66e-07)|Prostate(122;0.081)																---	---	---	---
KDM6B	23135	broad.mit.edu	37	17	7750722	7750722	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7750722C>T	uc002giw.1	+	10	1585	c.1209C>T	c.(1207-1209)AGC>AGT	p.S403S	KDM6B_uc002gix.2_5'Flank	NM_001080424	NP_001073893	O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	403	Pro-rich.				inflammatory response	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			central_nervous_system(1)|pancreas(1)	2																		---	---	---	---
KDM6B	23135	broad.mit.edu	37	17	7751283	7751283	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7751283C>T	uc002giw.1	+	11	2053	c.1677C>T	c.(1675-1677)GGC>GGT	p.G559G	KDM6B_uc002gix.2_5'UTR	NM_001080424	NP_001073893	O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	559	Pro-rich.				inflammatory response	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			central_nervous_system(1)|pancreas(1)	2																		---	---	---	---
KDM6B	23135	broad.mit.edu	37	17	7751821	7751821	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7751821G>A	uc002giw.1	+	11	2591	c.2215G>A	c.(2215-2217)GAC>AAC	p.D739N	KDM6B_uc002gix.2_Missense_Mutation_p.D41N	NM_001080424	NP_001073893	O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	739	Pro-rich.|Thr-rich.				inflammatory response	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			central_nervous_system(1)|pancreas(1)	2																		---	---	---	---
LSMD1	84316	broad.mit.edu	37	17	7760658	7760658	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7760658T>C	uc002giz.2	-						LSMD1_uc002gja.2_Silent_p.A28A|CYB5D1_uc010cnn.1_5'Flank|CYB5D1_uc002gjb.3_5'Flank					RecName: Full=LSM domain-containing protein 1; AltName: Full=Phosphonoformate immuno-associated protein 2;							cytoplasm|nucleus				ovary(1)	1		all_cancers(10;0.11)|Prostate(122;0.219)																---	---	---	---
CNTROB	116840	broad.mit.edu	37	17	7837454	7837454	+	Splice_Site	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7837454A>G	uc002gjq.2	+	3	1190	c.271_splice	c.e3-2	p.D91_splice	TRAPPC1_uc002gjo.1_5'Flank|CNTROB_uc002gjp.2_Splice_Site_p.D91_splice|CNTROB_uc002gjr.2_5'Flank	NM_053051	NP_444279			centrobin, centrosomal BRCA2 interacting protein						centriole replication|centrosome separation|cytokinesis	centriole	protein domain specific binding			breast(1)|central_nervous_system(1)	2		Prostate(122;0.173)																---	---	---	---
CNTROB	116840	broad.mit.edu	37	17	7852000	7852000	+	Intron	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7852000G>T	uc002gjq.2	+						CNTROB_uc002gjp.2_Missense_Mutation_p.S859I|CNTROB_uc002gjr.2_Intron	NM_053051	NP_444279			centrobin, centrosomal BRCA2 interacting protein						centriole replication|centrosome separation|cytokinesis	centriole	protein domain specific binding			breast(1)|central_nervous_system(1)	2		Prostate(122;0.173)																---	---	---	---
ALOX15B	247	broad.mit.edu	37	17	7942624	7942624	+	Intron	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7942624A>C	uc002gju.2	+						ALOX15B_uc002gjv.2_Intron|ALOX15B_uc002gjw.2_Intron|ALOX15B_uc010vun.1_Intron|ALOX15B_uc010cnp.2_Intron	NM_001141	NP_001132			arachidonate 15-lipoxygenase, second type						induction of apoptosis|leukotriene biosynthetic process|negative regulation of cell cycle|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of growth|prostate gland development|regulation of epithelial cell differentiation	cytoplasm	arachidonate 15-lipoxygenase activity|iron ion binding|lipoxygenase activity			ovary(1)	1																		---	---	---	---
PER1	5187	broad.mit.edu	37	17	8045175	8045175	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8045175G>A	uc002gkd.2	-	22	3786	c.3548C>T	c.(3547-3549)GCT>GTT	p.A1183V	PER1_uc010cns.2_Missense_Mutation_p.A57V|PER1_uc010vuq.1_RNA	NM_002616	NP_002607	O15534	PER1_HUMAN	period 1	1183	CRY binding domain (By similarity).				circadian rhythm|entrainment of circadian clock|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	signal transducer activity			lung(2)|breast(2)|skin(2)|large_intestine(1)|ovary(1)|kidney(1)	9								T	ETV6	AML|CMML			Other_conserved_DNA_damage_response_genes					---	---	---	---
KRBA2	124751	broad.mit.edu	37	17	8273306	8273306	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8273306G>A	uc002glf.1	-	2	631	c.625C>T	c.(625-627)CGG>TGG	p.R209W	KRBA2_uc002glg.1_Missense_Mutation_p.R126W	NM_213597	NP_998762	Q6ZNG9	KRBA2_HUMAN	KRAB-A domain containing 2	209					DNA integration|regulation of transcription, DNA-dependent	intracellular	DNA binding				0																		---	---	---	---
MYH10	4628	broad.mit.edu	37	17	8417094	8417094	+	Intron	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8417094C>A	uc002gll.2	-						MYH10_uc002glm.2_Intron|MYH10_uc010cnx.2_Intron	NM_005964	NP_005955			myosin, heavy polypeptide 10, non-muscle						actin filament-based movement|axon guidance|cytokinesis after mitosis|regulation of cell shape	cell cortex|cleavage furrow|midbody|myosin complex|stress fiber	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(2)	2																		---	---	---	---
MFSD6L	162387	broad.mit.edu	37	17	8701920	8701920	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8701920C>T	uc002glp.1	-	1	667	c.519G>A	c.(517-519)GCG>GCA	p.A173A		NM_152599	NP_689812	Q8IWD5	MFS6L_HUMAN	major facilitator superfamily domain containing	173						integral to membrane				central_nervous_system(1)	1																		---	---	---	---
PIK3R6	146850	broad.mit.edu	37	17	8741934	8741934	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8741934C>A	uc002glq.1	-	4	376	c.136G>T	c.(136-138)GAT>TAT	p.D46Y	PIK3R6_uc002glr.1_RNA|PIK3R6_uc002gls.1_RNA	NM_001010855	NP_001010855	Q5UE93	PI3R6_HUMAN	phosphoinositide-3-kinase, regulatory subunit 6	46					platelet activation	cytosol					0																		---	---	---	---
PIK3R5	23533	broad.mit.edu	37	17	8791618	8791618	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8791618C>T	uc002glt.2	-	10	1553	c.1486G>A	c.(1486-1488)GCT>ACT	p.A496T	PIK3R5_uc010vuz.1_Missense_Mutation_p.A496T|PIK3R5_uc002glu.3_Missense_Mutation_p.A110T|PIK3R5_uc010coa.1_3'UTR|PIK3R5_uc010cob.1_Missense_Mutation_p.A110T	NM_014308	NP_055123	Q8WYR1	PI3R5_HUMAN	phosphoinositide-3-kinase, regulatory subunit 5	496					platelet activation	cytosol|membrane|nucleus				breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
GLP2R	9340	broad.mit.edu	37	17	9791238	9791238	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9791238T>C	uc002gmd.1	+							NM_004246	NP_004237			glucagon-like peptide 2 receptor precursor						G-protein signaling, coupled to cAMP nucleotide second messenger|positive regulation of cell proliferation	integral to membrane|plasma membrane				lung(2)|ovary(1)	3					Glucagon recombinant(DB00040)													---	---	---	---
GAS7	8522	broad.mit.edu	37	17	9821422	9821422	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9821422G>A	uc002gmg.1	-						GAS7_uc010vvc.1_Intron|GAS7_uc002gmh.1_Intron|GAS7_uc010vvd.1_Intron|GAS7_uc002gmi.2_Intron|GAS7_uc002gmj.1_Intron|GAS7_uc010coh.1_Intron	NM_201433	NP_958839			growth arrest-specific 7 isoform c						cell cycle arrest	cytoplasm	sequence-specific DNA binding transcription factor activity			lung(1)|pancreas(1)	2								T	MLL	AML*								---	---	---	---
MYH13	8735	broad.mit.edu	37	17	10210380	10210380	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10210380T>C	uc002gmk.1	-	36	5261	c.5171A>G	c.(5170-5172)AAC>AGC	p.N1724S		NM_003802	NP_003793	Q9UKX3	MYH13_HUMAN	myosin, heavy polypeptide 13, skeletal muscle	1724	Potential.				muscle contraction	muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)|skin(2)	6																		---	---	---	---
MYH8	4626	broad.mit.edu	37	17	10315817	10315817	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10315817G>A	uc002gmm.2	-	14	1381	c.1286C>T	c.(1285-1287)GCT>GTT	p.A429V	uc002gml.1_Intron	NM_002472	NP_002463	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle,	429	Myosin head-like.				muscle filament sliding	cytosol|muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			skin(6)|ovary(3)|breast(2)	11														Trismus-Pseudocamptodactyly_Syndrome_with_Cardiac_Myxoma_and_Freckling				---	---	---	---
MYH4	4622	broad.mit.edu	37	17	10354779	10354779	+	Intron	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10354779G>T	uc002gmn.2	-						uc002gml.1_Intron	NM_017533	NP_060003			myosin, heavy polypeptide 4, skeletal muscle						muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(10)|skin(2)|central_nervous_system(1)	13																		---	---	---	---
MYH1	4619	broad.mit.edu	37	17	10406172	10406172	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10406172C>A	uc002gmo.2	-	24	3088	c.2994G>T	c.(2992-2994)AAG>AAT	p.K998N	uc002gml.1_Intron	NM_005963	NP_005954	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	998	Potential.					muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(10)|skin(6)|breast(3)|upper_aerodigestive_tract(1)|kidney(1)	21																		---	---	---	---
MYH1	4619	broad.mit.edu	37	17	10419868	10419868	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10419868G>T	uc002gmo.2	-	3	186	c.92C>A	c.(91-93)CCT>CAT	p.P31H	uc002gml.1_Intron	NM_005963	NP_005954	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	31	Myosin head-like.					muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(10)|skin(6)|breast(3)|upper_aerodigestive_tract(1)|kidney(1)	21																		---	---	---	---
MYH2	4620	broad.mit.edu	37	17	10433061	10433061	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10433061C>T	uc010coi.2	-						uc002gml.1_Intron|MYH2_uc002gmp.3_Intron|MYH2_uc010coj.2_Intron	NM_001100112	NP_001093582			myosin heavy chain IIa						muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(5)|pancreas(4)|skin(3)|lung(1)|kidney(1)	14																		---	---	---	---
MYH3	4621	broad.mit.edu	37	17	10544484	10544484	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10544484G>A	uc002gmq.1	-	18	2160	c.2083C>T	c.(2083-2085)CGG>TGG	p.R695W		NM_002470	NP_002461	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle,	695	Myosin head-like.				muscle filament sliding|muscle organ development	cytosol|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)|central_nervous_system(2)|pancreas(1)	7																		---	---	---	---
MYH3	4621	broad.mit.edu	37	17	10546224	10546224	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10546224C>A	uc002gmq.1	-	14	1577	c.1500G>T	c.(1498-1500)GAG>GAT	p.E500D		NM_002470	NP_002461	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle,	500	Myosin head-like.				muscle filament sliding|muscle organ development	cytosol|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)|central_nervous_system(2)|pancreas(1)	7																		---	---	---	---
TMEM220	388335	broad.mit.edu	37	17	10628381	10628381	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10628381C>T	uc002gmx.2	-	4	712	c.234G>A	c.(232-234)GCG>GCA	p.A78A	TMEM220_uc002gmy.2_Silent_p.A68A	NM_001004313	NP_001004313	Q6QAJ8	TM220_HUMAN	transmembrane protein 220	78	Helical; (Potential).					integral to membrane					0																		---	---	---	---
DNAH9	1770	broad.mit.edu	37	17	11584077	11584077	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11584077C>T	uc002gne.2	+	19	3682	c.3614C>T	c.(3613-3615)GCC>GTC	p.A1205V	DNAH9_uc010coo.2_Missense_Mutation_p.A499V	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	1205	Stem (By similarity).				cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)														---	---	---	---
DNAH9	1770	broad.mit.edu	37	17	11845700	11845700	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:11845700G>A	uc002gne.2	+	67	12809	c.12741G>A	c.(12739-12741)GAG>GAA	p.E4247E	DNAH9_uc010coo.2_Silent_p.E3465E|DNAH9_uc002gnf.2_Silent_p.E559E	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	4247					cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)														---	---	---	---
RICH2	9912	broad.mit.edu	37	17	12847474	12847474	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:12847474G>A	uc002gnr.3	+	10	1149	c.822G>A	c.(820-822)GCG>GCA	p.A274A	RICH2_uc010vvk.1_Silent_p.A274A|RICH2_uc010vvl.1_Silent_p.A274A|RICH2_uc002gns.3_Silent_p.A74A|RICH2_uc010vvm.1_Silent_p.A274A|RICH2_uc010vvn.1_RNA|RICH2_uc002gnt.1_Translation_Start_Site	NM_014859	NP_055674	Q17R89	RHG44_HUMAN	Rho GTPase-activating protein RICH2	274	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0																		---	---	---	---
ZNF286A	57335	broad.mit.edu	37	17	15611458	15611458	+	Intron	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15611458T>A	uc010cot.2	+						ZNF286A_uc002goz.3_Intron|ZNF286A_uc010vwa.1_Intron|ZNF286A_uc002gpa.2_Intron	NM_001130842	NP_001124314			zinc finger protein 286						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.0781)														---	---	---	---
NCOR1	9611	broad.mit.edu	37	17	15983915	15983915	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15983915A>G	uc002gpo.2	-						NCOR1_uc002gpn.2_Intron|NCOR1_uc002gpp.1_Intron|NCOR1_uc010vwb.1_5'Flank|NCOR1_uc010coy.2_5'Flank|NCOR1_uc010vwc.1_5'Flank	NM_006311	NP_006302			nuclear receptor co-repressor 1						cellular lipid metabolic process|chromatin modification|negative regulation of JNK cascade|regulation of glycolysis by negative regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by negative regulation of transcription from an RNA polymerase II promoter|spindle assembly|transcription from RNA polymerase II promoter	nuclear chromatin|spindle microtubule|transcriptional repressor complex	histone deacetylase binding|transcription corepressor activity|transcription regulatory region DNA binding			upper_aerodigestive_tract(2)|ovary(1)|central_nervous_system(1)|kidney(1)	5				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)														---	---	---	---
ZNF287	57336	broad.mit.edu	37	17	16455518	16455518	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:16455518T>G	uc002gqi.2	-	6	2391	c.1938A>C	c.(1936-1938)AAA>AAC	p.K646N		NM_020653	NP_065704	Q9HBT7	ZN287_HUMAN	zinc finger protein 287	639					viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0				UCEC - Uterine corpus endometrioid carcinoma (92;0.083)														---	---	---	---
COPS3	8533	broad.mit.edu	37	17	17179363	17179363	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17179363G>A	uc002grd.2	-	2	262	c.171C>T	c.(169-171)GGC>GGT	p.G57G	COPS3_uc010vwv.1_Silent_p.G37G|COPS3_uc010vww.1_5'UTR	NM_003653	NP_003644	Q9UNS2	CSN3_HUMAN	COP9 constitutive photomorphogenic homolog	57					cullin deneddylation|response to light stimulus|signal transduction	cytoplasm|signalosome	protein binding			skin(1)	1																		---	---	---	---
TOM1L2	146691	broad.mit.edu	37	17	17766146	17766146	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17766146G>A	uc002grz.3	-	11	1258	c.1101C>T	c.(1099-1101)AGC>AGT	p.S367S	TOM1L2_uc002gry.3_Silent_p.S317S|TOM1L2_uc010vwy.1_Silent_p.S314S|TOM1L2_uc010cpr.2_Silent_p.S322S|TOM1L2_uc010vwz.1_Silent_p.S219S|TOM1L2_uc010vxa.1_Silent_p.S269S|TOM1L2_uc002grv.3_Silent_p.S100S	NM_001082968	NP_001076437	Q6ZVM7	TM1L2_HUMAN	target of myb1-like 2 isoform 3	367					intracellular protein transport	intracellular					0	all_neural(463;0.228)																	---	---	---	---
LRRC48	83450	broad.mit.edu	37	17	17880942	17880942	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17880942G>A	uc010vxd.1	+	4	409	c.30G>A	c.(28-30)CCG>CCA	p.P10P	LRRC48_uc002gsa.2_Silent_p.P10P|LRRC48_uc010vxc.1_Silent_p.P10P|LRRC48_uc002gsb.2_Silent_p.P10P	NM_001130090	NP_001123562	Q9H069	LRC48_HUMAN	leucine rich repeat containing 48 isoform a	10						cytoplasm				pancreas(1)	1	all_neural(463;0.228)																	---	---	---	---
ATPAF2	91647	broad.mit.edu	37	17	17931629	17931629	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:17931629C>T	uc002gse.1	-	3	394	c.241G>A	c.(241-243)GTC>ATC	p.V81I	ATPAF2_uc002gsd.1_Intron|ATPAF2_uc002gsf.1_RNA|ATPAF2_uc010cps.1_5'Flank|ATPAF2_uc010vxf.1_Missense_Mutation_p.V81I	NM_145691	NP_663729	Q8N5M1	ATPF2_HUMAN	ATP synthase mitochondrial F1 complex assembly	81					proton-transporting ATP synthase complex assembly	mitochondrion|nuclear speck	protein binding				0	all_neural(463;0.228)																	---	---	---	---
DRG2	1819	broad.mit.edu	37	17	18002994	18002994	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18002994G>A	uc002gsh.1	+	5	479	c.424G>A	c.(424-426)GTC>ATC	p.V142I	DRG2_uc010vxg.1_3'UTR|DRG2_uc002gsi.1_RNA|DRG2_uc002gsj.1_Missense_Mutation_p.V142I	NM_001388	NP_001379	P55039	DRG2_HUMAN	developmentally regulated GTP binding protein 2	142	G.				signal transduction		GTP binding			ovary(1)	1	all_neural(463;0.228)																	---	---	---	---
MYO15A	51168	broad.mit.edu	37	17	18027789	18027789	+	Intron	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18027789T>A	uc010vxh.1	+							NM_016239	NP_057323			myosin XV						sensory perception of sound	cytoplasm|myosin complex|stereocilium	actin binding|ATP binding|calmodulin binding|motor activity			skin(4)|ovary(2)|pancreas(1)|breast(1)|central_nervous_system(1)	9	all_neural(463;0.228)																	---	---	---	---
MYO15A	51168	broad.mit.edu	37	17	18069747	18069747	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18069747G>A	uc010vxh.1	+	60	10198	c.9860G>A	c.(9859-9861)GGC>GAC	p.G3287D	MYO15A_uc010vxi.1_Missense_Mutation_p.G551D|MYO15A_uc010vxk.1_Intron|MYO15A_uc010vxl.1_Missense_Mutation_p.G276D|MYO15A_uc002gsl.2_Missense_Mutation_p.G294D|MYO15A_uc010vxm.1_Intron|MYO15A_uc010cpv.2_Intron	NM_016239	NP_057323	Q9UKN7	MYO15_HUMAN	myosin XV	3287	Tail.|FERM.				sensory perception of sound	cytoplasm|myosin complex|stereocilium	actin binding|ATP binding|calmodulin binding|motor activity			skin(4)|ovary(2)|pancreas(1)|breast(1)|central_nervous_system(1)	9	all_neural(463;0.228)																	---	---	---	---
LLGL1	3996	broad.mit.edu	37	17	18140015	18140015	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18140015T>C	uc002gsp.2	+	12	1508	c.1447T>C	c.(1447-1449)TGT>CGT	p.C483R		NM_004140	NP_004131	Q15334	L2GL1_HUMAN	lethal giant larvae homolog 1	483					cortical actin cytoskeleton organization|exocytosis|protein complex assembly	cortical actin cytoskeleton	protein kinase binding|structural molecule activity			breast(2)|skin(2)|ovary(1)|haematopoietic_and_lymphoid_tissue(1)	6	all_neural(463;0.228)																	---	---	---	---
SMCR7	125170	broad.mit.edu	37	17	18168009	18168009	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18168009T>C	uc002gst.2	+	4	1507	c.1296T>C	c.(1294-1296)CGT>CGC	p.R432R	SMCR7_uc002gsu.2_3'UTR|SMCR7_uc010vxq.1_Silent_p.R443R	NM_139162	NP_631901	Q96C03	SMCR7_HUMAN	Smith-Magenis syndrome chromosome region,	432						integral to membrane	protein binding				0	all_neural(463;0.228)																	---	---	---	---
TRIM16L	147166	broad.mit.edu	37	17	18630970	18630970	+	Missense_Mutation	SNP	G	T	T	rs145703700	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18630970G>T	uc002gug.1	+	7	787	c.100G>T	c.(100-102)GGT>TGT	p.G34C	TRIM16L_uc010vyf.1_Missense_Mutation_p.G88C|TRIM16L_uc002guh.1_Missense_Mutation_p.G34C|TRIM16L_uc010cqg.1_Missense_Mutation_p.G136C|TRIM16L_uc002gui.1_Missense_Mutation_p.G34C|TRIM16L_uc010vyg.1_Missense_Mutation_p.G34C|TRIM16L_uc010vyh.1_Missense_Mutation_p.G34C	NM_001037330	NP_001032407	Q309B1	TR16L_HUMAN	tripartite motif-containing 16-like	34						cytoplasm					0																		---	---	---	---
TRIM16L	147166	broad.mit.edu	37	17	18638561	18638561	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18638561C>T	uc002gug.1	+	10	1522	c.835C>T	c.(835-837)CTC>TTC	p.L279F	TRIM16L_uc010vyf.1_Missense_Mutation_p.L333F|TRIM16L_uc002guh.1_Missense_Mutation_p.L279F|TRIM16L_uc010cqg.1_Missense_Mutation_p.L381F|TRIM16L_uc002gui.1_Missense_Mutation_p.L279F|TRIM16L_uc010vyg.1_Missense_Mutation_p.L279F|TRIM16L_uc010vyh.1_3'UTR	NM_001037330	NP_001032407	Q309B1	TR16L_HUMAN	tripartite motif-containing 16-like	279	B30.2/SPRY.					cytoplasm					0																		---	---	---	---
FAM83G	644815	broad.mit.edu	37	17	18874745	18874745	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:18874745G>A	uc002guw.2	-	6	2566	c.2399C>T	c.(2398-2400)ACG>ATG	p.T800M	SLC5A10_uc002gur.1_Intron|SLC5A10_uc002guu.1_Intron|SLC5A10_uc002gut.1_Intron|SLC5A10_uc002guv.1_Intron|SLC5A10_uc010vyl.1_Intron	NM_001039999	NP_001035088	A6ND36	FA83G_HUMAN	hypothetical protein LOC644815	800								p.T800T(1)		ovary(1)|central_nervous_system(1)	2																		---	---	---	---
SLC47A2	146802	broad.mit.edu	37	17	19608772	19608772	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19608772C>T	uc002gwe.3	-	10	1169	c.994G>A	c.(994-996)GAG>AAG	p.E332K	SLC47A2_uc002gwg.3_Missense_Mutation_p.E296K|SLC47A2_uc002gwf.3_Missense_Mutation_p.E296K|SLC47A2_uc002gwh.3_RNA|SLC47A2_uc002gwi.2_RNA|SLC47A2_uc010cqs.1_RNA|SLC47A2_uc010cqt.1_RNA	NM_152908	NP_690872	Q86VL8	S47A2_HUMAN	solute carrier family 47, member 2 isoform 1	332	Helical; (Potential).					integral to membrane|plasma membrane	drug:hydrogen antiporter activity				0	all_cancers(12;2.3e-05)|all_epithelial(12;0.0024)|Breast(13;0.245)																	---	---	---	---
ALDH3A1	218	broad.mit.edu	37	17	19642831	19642831	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19642831C>A	uc010cqu.2	-	7	1436	c.1106G>T	c.(1105-1107)AGC>ATC	p.S369I	ALDH3A1_uc010vzd.1_Missense_Mutation_p.S369I|ALDH3A1_uc002gwj.2_Missense_Mutation_p.S369I|ALDH3A1_uc010cqv.2_Missense_Mutation_p.S368I|ALDH3A1_uc002gwk.2_Missense_Mutation_p.S486I|ALDH3A1_uc002gwl.1_Missense_Mutation_p.S296I	NM_001135168	NP_001128640	P30838	AL3A1_HUMAN	aldehyde dehydrogenase 3A1	369					cellular aldehyde metabolic process	cytosol|endoplasmic reticulum	alcohol dehydrogenase (NADP+) activity|aldehyde dehydrogenase (NAD) activity|aldehyde dehydrogenase			ovary(1)|pancreas(1)	2	all_cancers(12;4.01e-05)|all_epithelial(12;0.00301)|Breast(13;0.186)			Colorectal(15;0.0829)	NADH(DB00157)													---	---	---	---
CYTSB	92521	broad.mit.edu	37	17	20109042	20109042	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20109042T>C	uc002gwq.2	+	4	1825	c.1680T>C	c.(1678-1680)GGT>GGC	p.G560G	CYTSB_uc010cqx.2_Silent_p.G560G|CYTSB_uc002gwr.2_Silent_p.G560G|CYTSB_uc002gws.2_Silent_p.G560G|CYTSB_uc002gwv.2_Silent_p.G479G|CYTSB_uc010vzf.1_Intron|CYTSB_uc002gww.2_Silent_p.G336G|CYTSB_uc002gwt.2_Silent_p.G479G|CYTSB_uc002gwu.2_Silent_p.G479G	NM_001033553	NP_001028725	Q5M775	CYTSB_HUMAN	spectrin domain with coiled-coils 1 NSP5b3b	560						nucleus					0																		---	---	---	---
USP22	23326	broad.mit.edu	37	17	20921354	20921354	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:20921354C>T	uc002gym.3	-	5	795	c.591G>A	c.(589-591)ACG>ACA	p.T197T	USP22_uc002gyn.3_Silent_p.T185T|USP22_uc002gyl.3_Silent_p.T92T	NM_015276	NP_056091	Q9UPT9	UBP22_HUMAN	ubiquitin thiolesterase 22	197					cell cycle|embryo development|histone deubiquitination|histone H4 acetylation|histone ubiquitination|positive regulation of mitotic cell cycle|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent|ubiquitin-dependent protein catabolic process	SAGA complex	ligand-dependent nuclear receptor transcription coactivator activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(1)	1																		---	---	---	---
KCNJ12	3768	broad.mit.edu	37	17	21319092	21319092	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21319092C>T	uc002gyv.1	+	3	1143	c.438C>T	c.(436-438)TAC>TAT	p.Y146Y		NM_021012	NP_066292	Q14500	IRK12_HUMAN	potassium inwardly-rectifying channel, subfamily	146	Selectivity filter (By similarity).				blood circulation|muscle contraction|regulation of heart contraction|synaptic transmission	integral to membrane	inward rectifier potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(3)|skin(1)	4				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)										Prostate(3;0.18)			---	---	---	---
KCNJ12	3768	broad.mit.edu	37	17	21319359	21319359	+	Silent	SNP	G	A	A	rs147653221	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21319359G>A	uc002gyv.1	+	3	1410	c.705G>A	c.(703-705)CCG>CCA	p.P235P		NM_021012	NP_066292	Q14500	IRK12_HUMAN	potassium inwardly-rectifying channel, subfamily	235	Cytoplasmic (By similarity).				blood circulation|muscle contraction|regulation of heart contraction|synaptic transmission	integral to membrane	inward rectifier potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(3)|skin(1)	4				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)										Prostate(3;0.18)			---	---	---	---
KCNJ12	3768	broad.mit.edu	37	17	21319540	21319540	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21319540G>A	uc002gyv.1	+	3	1591	c.886G>A	c.(886-888)GTG>ATG	p.V296M		NM_021012	NP_066292	Q14500	IRK12_HUMAN	potassium inwardly-rectifying channel, subfamily	296	Cytoplasmic (By similarity).				blood circulation|muscle contraction|regulation of heart contraction|synaptic transmission	integral to membrane	inward rectifier potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(3)|skin(1)	4				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)										Prostate(3;0.18)			---	---	---	---
TNFAIP1	7126	broad.mit.edu	37	17	26669407	26669407	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26669407G>A	uc002hax.1	+	6	672	c.653G>A	c.(652-654)CGT>CAT	p.R218H	TNFAIP1_uc002hay.2_Missense_Mutation_p.R218H|TNFAIP1_uc010waf.1_Missense_Mutation_p.R114H	NM_021137	NP_066960	Q13829	BACD2_HUMAN	tumor necrosis factor, alpha-induced protein 1	218					apoptosis|cell migration|DNA replication|embryo development|immune response|negative regulation of Rho protein signal transduction|proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination|stress fiber assembly	Cul3-RING ubiquitin ligase complex|endosome|nucleus|voltage-gated potassium channel complex	GTP-Rho binding|voltage-gated potassium channel activity				0	all_lung(13;0.000294)|Lung NSC(42;0.000964)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)														---	---	---	---
SLC13A2	9058	broad.mit.edu	37	17	26818618	26818618	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26818618G>A	uc002hbh.2	+	5	805	c.738G>A	c.(736-738)CTG>CTA	p.L246L	SLC13A2_uc010wal.1_Silent_p.L203L|SLC13A2_uc010wam.1_Silent_p.L202L|SLC13A2_uc010wan.1_Silent_p.L295L|SLC13A2_uc010wao.1_Silent_p.L203L|SLC13A2_uc002hbi.2_Silent_p.L175L	NM_003984	NP_003975	Q13183	S13A2_HUMAN	solute carrier family 13, member 2 isoform b	246						integral to plasma membrane|membrane fraction	low affinity sodium:dicarboxylate symporter activity				0	all_lung(13;0.000871)|Lung NSC(42;0.0027)			UCEC - Uterine corpus endometrioid carcinoma (53;0.154)	Succinic acid(DB00139)													---	---	---	---
FOXN1	8456	broad.mit.edu	37	17	26861535	26861535	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26861535C>T	uc010crm.2	+	7	1312	c.1114C>T	c.(1114-1116)CGC>TGC	p.R372C	FOXN1_uc002hbj.2_Missense_Mutation_p.R372C	NM_003593	NP_003584	O15353	FOXN1_HUMAN	forkhead box N1	372					defense response|embryo development|epithelial cell proliferation|keratinocyte differentiation|organ morphogenesis|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|regulation of transcription from RNA polymerase II promoter|thymus development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			skin(1)	1	Lung NSC(42;0.00431)																	---	---	---	---
ALDOC	230	broad.mit.edu	37	17	26902271	26902271	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26902271C>A	uc002hbp.2	-	3	339	c.194G>T	c.(193-195)AGT>ATT	p.S65I	ALDOC_uc010cro.2_Missense_Mutation_p.S65I	NM_005165	NP_005156	P09972	ALDOC_HUMAN	fructose-bisphosphate aldolase C	65					fructose 1,6-bisphosphate metabolic process|gluconeogenesis|glycolysis	cytosol	cytoskeletal protein binding|fructose-bisphosphate aldolase activity			ovary(1)	1	Lung NSC(42;0.00431)															OREG0024278	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SPAG5	10615	broad.mit.edu	37	17	26905515	26905515	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26905515C>T	uc002hbq.2	-	21	3322	c.3230G>A	c.(3229-3231)CGC>CAC	p.R1077H	ALDOC_uc002hbp.2_5'Flank|ALDOC_uc010cro.2_5'Flank	NM_006461	NP_006452	Q96R06	SPAG5_HUMAN	sperm associated antigen 5	1077	Potential.				cell division|mitosis|phosphatidylinositol-mediated signaling|spindle organization	condensed chromosome kinetochore|cytoplasm|spindle pole	protein binding			central_nervous_system(1)	1	Lung NSC(42;0.00431)																	---	---	---	---
SPAG5	10615	broad.mit.edu	37	17	26912628	26912628	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26912628C>T	uc002hbq.2	-	8	1876	c.1784G>A	c.(1783-1785)CGC>CAC	p.R595H	SGK494_uc010waq.1_Intron	NM_006461	NP_006452	Q96R06	SPAG5_HUMAN	sperm associated antigen 5	595	Potential.				cell division|mitosis|phosphatidylinositol-mediated signaling|spindle organization	condensed chromosome kinetochore|cytoplasm|spindle pole	protein binding			central_nervous_system(1)	1	Lung NSC(42;0.00431)																	---	---	---	---
SPAG5	10615	broad.mit.edu	37	17	26918993	26918993	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26918993C>T	uc002hbq.2	-						SGK494_uc010waq.1_Intron	NM_006461	NP_006452			sperm associated antigen 5						cell division|mitosis|phosphatidylinositol-mediated signaling|spindle organization	condensed chromosome kinetochore|cytoplasm|spindle pole	protein binding			central_nervous_system(1)	1	Lung NSC(42;0.00431)																	---	---	---	---
KIAA0100	9703	broad.mit.edu	37	17	26948132	26948132	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26948132G>A	uc002hbu.2	-	28	5215	c.5116C>T	c.(5116-5118)CGT>TGT	p.R1706C	KIAA0100_uc002hbt.2_Missense_Mutation_p.R35C	NM_014680	NP_055495	Q14667	K0100_HUMAN	hypothetical protein LOC9703 precursor	1706						extracellular region				ovary(2)|breast(1)|skin(1)	4	Lung NSC(42;0.00431)																	---	---	---	---
KIAA0100	9703	broad.mit.edu	37	17	26962029	26962029	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26962029G>A	uc002hbu.2	-	16	2675	c.2576C>T	c.(2575-2577)GCC>GTC	p.A859V		NM_014680	NP_055495	Q14667	K0100_HUMAN	hypothetical protein LOC9703 precursor	859						extracellular region				ovary(2)|breast(1)|skin(1)	4	Lung NSC(42;0.00431)																	---	---	---	---
KIAA0100	9703	broad.mit.edu	37	17	26962258	26962258	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26962258A>C	uc002hbu.2	-	16	2446	c.2347T>G	c.(2347-2349)TTC>GTC	p.F783V		NM_014680	NP_055495	Q14667	K0100_HUMAN	hypothetical protein LOC9703 precursor	783						extracellular region				ovary(2)|breast(1)|skin(1)	4	Lung NSC(42;0.00431)																	---	---	---	---
SUPT6H	6830	broad.mit.edu	37	17	27010800	27010800	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27010800A>C	uc002hby.2	+	17	2285	c.2195A>C	c.(2194-2196)AAG>ACG	p.K732T	SUPT6H_uc010crt.2_Missense_Mutation_p.K732T	NM_003170	NP_003161	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog	732					chromatin remodeling|regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter	nucleus	hydrolase activity, acting on ester bonds|RNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|skin(1)	3	Lung NSC(42;0.00431)																	---	---	---	---
SUPT6H	6830	broad.mit.edu	37	17	27024761	27024761	+	Intron	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27024761G>T	uc002hby.2	+						SUPT6H_uc010crt.2_Intron	NM_003170	NP_003161			suppressor of Ty 6 homolog						chromatin remodeling|regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter	nucleus	hydrolase activity, acting on ester bonds|RNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|skin(1)	3	Lung NSC(42;0.00431)																	---	---	---	---
NEK8	284086	broad.mit.edu	37	17	27064846	27064846	+	Missense_Mutation	SNP	G	A	A	rs140077709	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27064846G>A	uc002hcp.2	+	7	899	c.899G>A	c.(898-900)CGG>CAG	p.R300Q		NM_178170	NP_835464	Q86SG6	NEK8_HUMAN	NIMA-related kinase 8	300						cytoplasm|primary cilium	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			stomach(2)|ovary(1)|pancreas(1)|liver(1)|skin(1)	6	Lung NSC(42;0.0158)																	---	---	---	---
C17orf63	55731	broad.mit.edu	37	17	27086286	27086286	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27086286G>A	uc002hct.1	-	3	958	c.691C>T	c.(691-693)CGG>TGG	p.R231W	C17orf63_uc010wax.1_Missense_Mutation_p.R231W|C17orf63_uc010way.1_Missense_Mutation_p.R231W|C17orf63_uc002hcw.2_Missense_Mutation_p.R103W	NM_018182	NP_060652	Q8WU58	CQ063_HUMAN	hypothetical protein LOC55731	231										ovary(1)	1	all_epithelial(6;5.06e-20)|Lung NSC(42;0.01)		Epithelial(11;3.38e-06)|all cancers(11;2.46e-05)|OV - Ovarian serous cystadenocarcinoma(11;0.104)															---	---	---	---
FLOT2	2319	broad.mit.edu	37	17	27211255	27211255	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27211255C>T	uc002hdc.2	-	3	333	c.210G>A	c.(208-210)ACG>ACA	p.T70T		NM_004475	NP_004466	Q14254	FLOT2_HUMAN	flotillin 2	70					cell adhesion|epidermis development	cell surface|endocytic vesicle|endosome|membrane fraction					0	all_cancers(5;2.12e-15)|all_epithelial(6;3.44e-19)|Lung NSC(42;0.01)		Epithelial(11;3.26e-06)|all cancers(11;1.76e-05)|BRCA - Breast invasive adenocarcinoma(11;0.00015)|OV - Ovarian serous cystadenocarcinoma(11;0.0602)															---	---	---	---
SEZ6	124925	broad.mit.edu	37	17	27306729	27306729	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27306729G>T	uc002hdp.2	-	3	1021	c.827C>A	c.(826-828)TCT>TAT	p.S276Y	SEZ6_uc002hdm.2_RNA|SEZ6_uc010cry.1_Missense_Mutation_p.S276Y|SEZ6_uc002hdq.1_Missense_Mutation_p.S151Y|SEZ6_uc010crz.1_Missense_Mutation_p.S276Y	NM_178860	NP_849191	Q53EL9	SEZ6_HUMAN	seizure related 6 homolog isoform 1	276	Extracellular (Potential).					integral to membrane|plasma membrane				large_intestine(1)|central_nervous_system(1)	2	Lung NSC(42;0.0137)		Epithelial(11;4.73e-06)|all cancers(11;2.91e-05)|BRCA - Breast invasive adenocarcinoma(11;8.06e-05)|OV - Ovarian serous cystadenocarcinoma(11;0.111)															---	---	---	---
SSH2	85464	broad.mit.edu	37	17	27975166	27975166	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:27975166C>T	uc002heo.1	-	13	1342	c.1342G>A	c.(1342-1344)GCA>ACA	p.A448T	SSH2_uc010wbh.1_Missense_Mutation_p.A475T|SSH2_uc002hep.1_Missense_Mutation_p.A448T	NM_033389	NP_203747	Q76I76	SSH2_HUMAN	slingshot 2	448					actin cytoskeleton organization|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of lamellipodium assembly	cytoplasm|cytoskeleton	actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			skin(2)	2																		---	---	---	---
ATAD5	79915	broad.mit.edu	37	17	29163057	29163057	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29163057G>A	uc002hfs.1	+	2	2304	c.1958G>A	c.(1957-1959)AGC>AAC	p.S653N	ATAD5_uc002hft.1_Missense_Mutation_p.S550N	NM_024857	NP_079133	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	653					response to DNA damage stimulus	nucleus	ATP binding|nucleoside-triphosphatase activity			ovary(3)	3		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)																---	---	---	---
ADAP2	55803	broad.mit.edu	37	17	29250097	29250097	+	Intron	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29250097G>T	uc002hfx.2	+						ADAP2_uc010csk.2_Intron|ADAP2_uc002hfy.2_Intron|ADAP2_uc010csl.2_Intron	NM_018404	NP_060874			centaurin-alpha 2 protein						heart development|regulation of ARF GTPase activity	mitochondrial envelope|plasma membrane	ARF GTPase activator activity|inositol 1,3,4,5 tetrakisphosphate binding|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-4,5-bisphosphate binding|protein binding, bridging|zinc ion binding	p.?(1)		ovary(1)	1																		---	---	---	---
NF1	4763	broad.mit.edu	37	17	29556416	29556416	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29556416C>T	uc002hgg.2	+	21	3116	c.2783C>T	c.(2782-2784)GCT>GTT	p.A928V	NF1_uc002hgh.2_Missense_Mutation_p.A928V|NF1_uc010csn.1_Missense_Mutation_p.A788V|NF1_uc002hgi.1_5'UTR	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	928					actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.?(2)		soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)				D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			---	---	---	---
NF1	4763	broad.mit.edu	37	17	29653207	29653207	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29653207G>T	uc002hgg.2	+	37	5538	c.5205G>T	c.(5203-5205)GAG>GAT	p.E1735D	NF1_uc002hgh.2_Missense_Mutation_p.E1714D|NF1_uc002hgi.1_Missense_Mutation_p.E747D|NF1_uc010cso.2_Translation_Start_Site	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	1735	CRAL-TRIO.				actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity			soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)				D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			---	---	---	---
NF1	4763	broad.mit.edu	37	17	29654757	29654757	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29654757G>A	uc002hgg.2	+	38	5842	c.5509G>A	c.(5509-5511)GAC>AAC	p.D1837N	NF1_uc002hgh.2_Missense_Mutation_p.D1816N|NF1_uc002hgi.1_Missense_Mutation_p.D849N|NF1_uc010cso.2_Missense_Mutation_p.D25N	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	1837					actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity			soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)				D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			---	---	---	---
SUZ12	23512	broad.mit.edu	37	17	30322711	30322711	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30322711G>A	uc002hgs.2	+	14	1946	c.1724G>A	c.(1723-1725)CGT>CAT	p.R575H	SUZ12_uc002hgt.2_Missense_Mutation_p.R552H	NM_015355	NP_056170	Q15022	SUZ12_HUMAN	joined to JAZF1	575	VEFS-box.				negative regulation of cell differentiation|transcription, DNA-dependent	ESC/E(Z) complex	histone methyltransferase activity|methylated histone residue binding|zinc ion binding		JAZF1/SUZ12(131)	soft_tissue(98)|endometrium(33)	131		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.041)|Ovarian(249;0.182)|Breast(31;0.231)						T	JAZF1	endometrial stromal tumours								---	---	---	---
C17orf75	64149	broad.mit.edu	37	17	30658961	30658961	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30658961G>A	uc002hhg.2	-	10	1043	c.1012C>T	c.(1012-1014)CGA>TGA	p.R338*		NM_022344	NP_071739	Q9HAS0	NJMU_HUMAN	hypothetical protein LOC64149	338					spermatogenesis					ovary(1)	1		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)															---	---	---	---
CDK5R1	8851	broad.mit.edu	37	17	30815052	30815052	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:30815052G>A	uc002hhn.2	+	2	635	c.414G>A	c.(412-414)ACG>ACA	p.T138T	CDK5R1_uc010wca.1_Silent_p.T138T|CDK5R1_uc010ctc.2_5'UTR	NM_003885	NP_003876	Q15078	CD5R1_HUMAN	cyclin-dependent kinase 5, regulatory subunit 1	138					axon guidance|axonal fasciculation|brain development|cell proliferation|embryo development|ionotropic glutamate receptor signaling pathway|muscarinic acetylcholine receptor signaling pathway|negative regulation of transcription, DNA-dependent|neuron cell-cell adhesion|neuron migration|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of neuron apoptosis|regulation of cyclin-dependent protein kinase activity|regulation of neuron differentiation	axon|contractile fiber|cyclin-dependent protein kinase 5 holoenzyme complex|cytosol|dendritic spine|growth cone|neuromuscular junction|neuronal cell body|perinuclear region of cytoplasm|plasma membrane	cadherin binding|calcium ion binding|protein kinase binding			ovary(1)	1		Breast(31;0.159)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.0938)															---	---	---	---
LIG3	3980	broad.mit.edu	37	17	33310154	33310154	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33310154C>T	uc002hik.1	+	2	238	c.130C>T	c.(130-132)CTT>TTT	p.L44F	LIG3_uc002hii.2_Missense_Mutation_p.L44F|LIG3_uc002hij.2_Missense_Mutation_p.L44F|LIG3_uc010cth.1_Missense_Mutation_p.L53F	NM_013975	NP_039269	P49916	DNLI3_HUMAN	ligase III, DNA, ATP-dependent isoform alpha	44					base-excision repair|cell division|DNA ligation involved in DNA repair|DNA replication|reciprocal meiotic recombination|spermatogenesis	nucleoplasm	ATP binding|DNA binding|DNA ligase (ATP) activity|protein binding|zinc ion binding			skin(3)|lung(2)|ovary(2)|large_intestine(1)|pancreas(1)	9		Ovarian(249;0.17)			Bleomycin(DB00290)								Other_BER_factors					---	---	---	---
FNDC8	54752	broad.mit.edu	37	17	33457313	33457313	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33457313G>A	uc002hix.2	+	4	917	c.835G>A	c.(835-837)GCC>ACC	p.A279T		NM_017559	NP_060029	Q8TC99	FNDC8_HUMAN	fibronectin type III domain containing 8	279	Fibronectin type-III.									ovary(2)	2		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.022)														---	---	---	---
AMAC1	146861	broad.mit.edu	37	17	33520759	33520759	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33520759C>T	uc002hjd.2	-	1	654	c.568G>A	c.(568-570)GCC>ACC	p.A190T		NM_152462	NP_689675	Q8N808	AMAC1_HUMAN	acyl-malonyl condensing enzyme 1	190	Helical; (Potential).					integral to membrane					0				BRCA - Breast invasive adenocarcinoma(366;0.0917)														---	---	---	---
AMAC1	146861	broad.mit.edu	37	17	33521251	33521251	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33521251G>A	uc002hjd.2	-	1	162	c.76C>T	c.(76-78)CGC>TGC	p.R26C		NM_152462	NP_689675	Q8N808	AMAC1_HUMAN	acyl-malonyl condensing enzyme 1	26						integral to membrane					0				BRCA - Breast invasive adenocarcinoma(366;0.0917)														---	---	---	---
SLFN5	162394	broad.mit.edu	37	17	33586225	33586225	+	Silent	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:33586225T>G	uc002hjf.3	+	2	633	c.516T>G	c.(514-516)GCT>GCG	p.A172A	SLFN5_uc002hje.2_Silent_p.A172A|SLFN5_uc010wcg.1_Silent_p.A172A	NM_144975	NP_659412	Q08AF3	SLFN5_HUMAN	schlafen family member 5	172					cell differentiation		ATP binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0191)														---	---	---	---
GAS2L2	246176	broad.mit.edu	37	17	34072322	34072322	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34072322C>G	uc002hjv.1	-	6	2222	c.2194G>C	c.(2194-2196)GTG>CTG	p.V732L		NM_139285	NP_644814	Q8NHY3	GA2L2_HUMAN	growth arrest-specific 2 like 2	732					cell cycle arrest	cytoplasm|cytoskeleton				ovary(1)|skin(1)	2		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)														---	---	---	---
MYO19	80179	broad.mit.edu	37	17	34859015	34859015	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34859015G>A	uc010wcy.1	-	22	2994	c.2002C>T	c.(2002-2004)CGA>TGA	p.R668*	MYO19_uc002hmw.2_Nonsense_Mutation_p.R468*|MYO19_uc010cuu.2_RNA	NM_001163735	NP_001157207	Q96H55	MYO19_HUMAN	myosin XIX isoform 2	668	Myosin head-like.					mitochondrial outer membrane|myosin complex	actin binding|ATP binding|motor activity			ovary(1)	1		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)														---	---	---	---
MYO19	80179	broad.mit.edu	37	17	34861202	34861202	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34861202C>T	uc010wcy.1	-	20	2831	c.1839G>A	c.(1837-1839)ACG>ACA	p.T613T	MYO19_uc002hmw.2_Intron|MYO19_uc010cuu.2_RNA	NM_001163735	NP_001157207	Q96H55	MYO19_HUMAN	myosin XIX isoform 2	613	Myosin head-like.					mitochondrial outer membrane|myosin complex	actin binding|ATP binding|motor activity			ovary(1)	1		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)														---	---	---	---
MYO19	80179	broad.mit.edu	37	17	34871816	34871816	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:34871816G>A	uc010wcy.1	-	8	1424	c.432C>T	c.(430-432)TGC>TGT	p.C144C	MYO19_uc002hmw.2_Silent_p.C144C|MYO19_uc010cuu.2_RNA|MYO19_uc010wcz.1_RNA|MYO19_uc010wda.1_Silent_p.C10C|MYO19_uc002hmx.2_Silent_p.C144C	NM_001163735	NP_001157207	Q96H55	MYO19_HUMAN	myosin XIX isoform 2	144	Myosin head-like.					mitochondrial outer membrane|myosin complex	actin binding|ATP binding|motor activity			ovary(1)	1		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)														---	---	---	---
ACACA	31	broad.mit.edu	37	17	35620586	35620586	+	Splice_Site	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35620586A>G	uc002hnm.2	-	11	1409	c.1218_splice	c.e11+1	p.Q406_splice	ACACA_uc002hnk.2_Splice_Site_p.Q328_splice|ACACA_uc002hnl.2_Splice_Site_p.Q348_splice|ACACA_uc002hnn.2_Splice_Site_p.Q406_splice|ACACA_uc002hno.2_Splice_Site_p.Q443_splice|ACACA_uc010cuz.2_Splice_Site_p.Q406_splice	NM_198836	NP_942133			acetyl-Coenzyme A carboxylase alpha isoform 2						acetyl-CoA metabolic process|energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|triglyceride biosynthetic process	cytosol	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			large_intestine(1)|ovary(1)	2		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)													---	---	---	---
SYNRG	11276	broad.mit.edu	37	17	35946575	35946575	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:35946575C>T	uc002hoa.2	-	4	406	c.323G>A	c.(322-324)GGC>GAC	p.G108D	SYNRG_uc010wde.1_Missense_Mutation_p.G108D|SYNRG_uc010wdf.1_Missense_Mutation_p.G108D|SYNRG_uc002hoc.2_Missense_Mutation_p.G107D|SYNRG_uc002hoe.2_Missense_Mutation_p.G108D|SYNRG_uc002hod.2_Missense_Mutation_p.G108D|SYNRG_uc010wdg.1_Missense_Mutation_p.G108D|SYNRG_uc002hob.2_Missense_Mutation_p.G108D|SYNRG_uc002hog.1_Missense_Mutation_p.G141D|SYNRG_uc010wdh.1_Missense_Mutation_p.G108D	NM_007247	NP_009178	Q9UMZ2	SYNRG_HUMAN	synergin, gamma isoform 1	108					endocytosis|intracellular protein transport	AP-1 adaptor complex	calcium ion binding			ovary(2)	2																		---	---	---	---
HNF1B	6928	broad.mit.edu	37	17	36070610	36070610	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36070610A>G	uc002hok.3	-	5	1328	c.1107T>C	c.(1105-1107)CAT>CAC	p.H369H	HNF1B_uc010wdi.1_Silent_p.H343H	NM_000458	NP_000449	P35680	HNF1B_HUMAN	hepatocyte nuclear factor 1-beta isoform 1	369					endocrine pancreas development|genitalia development|kidney development|positive regulation of transcription initiation from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|pronephric nephron tubule development|regulation of pronephros size	nucleus	DNA binding|protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)	3		Breast(25;0.00765)|Ovarian(249;0.15)	STAD - Stomach adenocarcinoma(1;0.0142)											Hereditary_Prostate_Cancer				---	---	---	---
GPR179	440435	broad.mit.edu	37	17	36485145	36485145	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36485145C>T	uc002hpz.2	-	11	4328	c.4307G>A	c.(4306-4308)CGG>CAG	p.R1436Q		NM_001004334	NP_001004334	Q6PRD1	GP179_HUMAN	GPR158-like 1 precursor	1436	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(3)	3	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)																---	---	---	---
SOCS7	30837	broad.mit.edu	37	17	36517615	36517615	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36517615T>C	uc002hqa.2	+	2	933	c.810T>C	c.(808-810)ACT>ACC	p.T270T	SOCS7_uc010cvl.2_Silent_p.T270T|SOCS7_uc002hqb.2_RNA	NM_014598	NP_055413	O14512	SOCS7_HUMAN	suppressor of cytokine signaling 7	270	Mediates interaction with SORBS3.				intracellular signal transduction|negative regulation of signal transduction|regulation of growth	cytoplasm|nucleus|plasma membrane	protein binding|SH3 domain binding			skin(1)	1	Breast(7;3.47e-17)																	---	---	---	---
SOCS7	30837	broad.mit.edu	37	17	36521233	36521233	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36521233C>T	uc002hqa.2	+	4	1124	c.1001C>T	c.(1000-1002)CCG>CTG	p.P334L	SOCS7_uc010cvl.2_Intron|SOCS7_uc002hqb.2_RNA	NM_014598	NP_055413	O14512	SOCS7_HUMAN	suppressor of cytokine signaling 7	334	Mediates interaction with SORBS3.				intracellular signal transduction|negative regulation of signal transduction|regulation of growth	cytoplasm|nucleus|plasma membrane	protein binding|SH3 domain binding			skin(1)	1	Breast(7;3.47e-17)																	---	---	---	---
SRCIN1	80725	broad.mit.edu	37	17	36704872	36704872	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36704872C>T	uc002hqd.2	-	17	3416	c.3191G>A	c.(3190-3192)CGC>CAC	p.R1064H	SRCIN1_uc002hqf.1_Missense_Mutation_p.R936H|SRCIN1_uc002hqe.2_Missense_Mutation_p.R918H	NM_025248	NP_079524	Q9C0H9	SRCN1_HUMAN	SNAP25-interacting protein	936					exocytosis|negative regulation of protein tyrosine kinase activity|positive regulation of protein tyrosine kinase activity|regulation of cell migration|regulation of dendritic spine morphogenesis|substrate adhesion-dependent cell spreading	actin cytoskeleton|axon|cell junction|cytoplasm|dendrite|postsynaptic density|postsynaptic membrane	protein kinase binding				0																		---	---	---	---
MLLT6	4302	broad.mit.edu	37	17	36864102	36864102	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36864102G>A	uc002hqi.3	+	4	344	c.331G>A	c.(331-333)GTG>ATG	p.V111M	MLLT6_uc010wdr.1_Missense_Mutation_p.V111M|MLLT6_uc010cvm.1_Missense_Mutation_p.V111M	NM_005937	NP_005928	P55198	AF17_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	111					regulation of transcription, DNA-dependent	nucleus	protein binding|zinc ion binding			breast(3)|prostate(1)|lung(1)|skin(1)	6	Breast(7;4.43e-21)							T	MLL	AL								---	---	---	---
CWC25	54883	broad.mit.edu	37	17	36971151	36971151	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:36971151C>T	uc002hqu.2	-	3	544	c.391G>A	c.(391-393)GCC>ACC	p.A131T	CWC25_uc010wdv.1_Missense_Mutation_p.A68T|CWC25_uc010wdw.1_RNA|CWC25_uc010wdx.1_RNA	NM_017748	NP_060218	Q9NXE8	CWC25_HUMAN	coiled-coil domain containing 49	131											0																		---	---	---	---
FBXO47	494188	broad.mit.edu	37	17	37094820	37094820	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37094820A>G	uc002hrc.2	-							NM_001008777	NP_001008777			F-box protein 47												0																		---	---	---	---
MED1	5469	broad.mit.edu	37	17	37566708	37566708	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37566708A>G	uc002hrv.3	-	17	1978	c.1766T>C	c.(1765-1767)GTG>GCG	p.V589A	MED1_uc010wee.1_Missense_Mutation_p.V417A|MED1_uc002hru.2_Intron	NM_004774	NP_004765	Q15648	MED1_HUMAN	mediator complex subunit 1	589	Interaction with ESR1.|Interaction with THRA.|Interaction with VDR.|Interaction with the Mediator complex and THRA.				androgen biosynthetic process|androgen receptor signaling pathway|cellular lipid metabolic process|fat cell differentiation|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription initiation from RNA polymerase II promoter	mediator complex	DNA binding|estrogen receptor binding|ligand-dependent nuclear receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|peroxisome proliferator activated receptor binding|receptor activity|retinoic acid receptor binding|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			lung(2)|ovary(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	8		Ovarian(249;1.78e-06)|Lung SC(565;0.0262)	Lung(15;0.0178)|LUAD - Lung adenocarcinoma(14;0.146)	UCEC - Uterine corpus endometrioid carcinoma (308;6.64e-05)|BRCA - Breast invasive adenocarcinoma(366;0.00136)|READ - Rectum adenocarcinoma(1115;0.0649)											HNSCC(31;0.082)			---	---	---	---
CDK12	51755	broad.mit.edu	37	17	37665992	37665992	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37665992C>T	uc010cvv.2	+	7	3230	c.2644C>T	c.(2644-2646)CGG>TGG	p.R882W	CDK12_uc010wef.1_Missense_Mutation_p.R881W|CDK12_uc002hrw.3_Missense_Mutation_p.R882W	NM_016507	NP_057591	Q9NYV4	CDK12_HUMAN	Cdc2-related kinase, arginine/serine-rich	882	Protein kinase.				mRNA processing|phosphorylation of RNA polymerase II C-terminal domain|protein autophosphorylation|regulation of MAP kinase activity|RNA splicing	nuclear cyclin-dependent protein kinase holoenzyme complex|nuclear speck|nucleolus	ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity	p.R882L(1)		ovary(10)|lung(4)|breast(2)|skin(2)|large_intestine(1)	19															TCGA Ovarian(9;0.13)			---	---	---	---
CDK12	51755	broad.mit.edu	37	17	37672027	37672027	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37672027G>A	uc010cvv.2	+	9	3398	c.2812G>A	c.(2812-2814)GCC>ACC	p.A938T	CDK12_uc010wef.1_Missense_Mutation_p.A937T|CDK12_uc002hrw.3_Missense_Mutation_p.A938T	NM_016507	NP_057591	Q9NYV4	CDK12_HUMAN	Cdc2-related kinase, arginine/serine-rich	938	Protein kinase.				mRNA processing|phosphorylation of RNA polymerase II C-terminal domain|protein autophosphorylation|regulation of MAP kinase activity|RNA splicing	nuclear cyclin-dependent protein kinase holoenzyme complex|nuclear speck|nucleolus	ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity			ovary(10)|lung(4)|breast(2)|skin(2)|large_intestine(1)	19															TCGA Ovarian(9;0.13)			---	---	---	---
STARD3	10948	broad.mit.edu	37	17	37817127	37817127	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37817127G>A	uc002hsd.2	+	12	1143	c.1019G>A	c.(1018-1020)GGC>GAC	p.G340D	STARD3_uc010weh.1_RNA|STARD3_uc002hse.2_Missense_Mutation_p.G322D|STARD3_uc010wei.1_Missense_Mutation_p.G340D|STARD3_uc002hsf.2_Missense_Mutation_p.G206D|STARD3_uc002hsg.2_Missense_Mutation_p.G173D	NM_006804	NP_006795	Q14849	STAR3_HUMAN	StAR-related lipid transfer (START) domain	340	START.|Cytoplasmic (Potential).				cholesterol metabolic process|mitochondrial transport|steroid biosynthetic process	integral to membrane|late endosome membrane	cholesterol binding|cholesterol transporter activity				0	Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;1.04e-44)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)															---	---	---	---
TCAP	8557	broad.mit.edu	37	17	37822100	37822100	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37822100A>G	uc002hsh.2	+	2	256	c.242A>G	c.(241-243)TAC>TGC	p.Y81C	PNMT_uc002hsi.1_5'Flank	NM_003673	NP_003664	O15273	TELT_HUMAN	telethonin	81					adult heart development|cardiac muscle contraction|cardiac muscle fiber development|cardiac muscle tissue morphogenesis|detection of mechanical stimulus|muscle filament sliding|response to stress|sarcomere organization|skeletal muscle contraction|skeletal muscle myosin thick filament assembly|skeletal muscle thin filament assembly	cytosol|Z disc	structural constituent of muscle|titin binding|titin Z domain binding				0	all_cancers(6;6.59e-85)|all_epithelial(6;2.89e-103)|Breast(7;1.05e-86)|Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;3.87e-45)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)															---	---	---	---
GSDMB	55876	broad.mit.edu	37	17	38065251	38065251	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38065251A>G	uc010cwj.2	-	4	626	c.621T>C	c.(619-621)TAT>TAC	p.Y207Y	GSDMB_uc010cwi.2_5'Flank|GSDMB_uc010cwk.2_Intron|GSDMB_uc010cwl.2_Intron|GSDMB_uc010cwm.2_Intron|GSDMB_uc002htg.2_Silent_p.Y207Y|GSDMB_uc002hth.2_Silent_p.Y207Y|GSDMB_uc010wem.1_Silent_p.Y207Y	NM_001042471	NP_001035936	Q8TAX9	GSDMB_HUMAN	gasdermin B isoform 1	207						cytoplasm				breast(1)|pancreas(1)	2																		---	---	---	---
GSDMA	284110	broad.mit.edu	37	17	38130600	38130600	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38130600C>T	uc002htl.1	+	9	944	c.826C>T	c.(826-828)CGA>TGA	p.R276*	GSDMA_uc002htm.1_Nonsense_Mutation_p.R276*	NM_178171	NP_835465	Q96QA5	GSDMA_HUMAN	gasdermin 1	276					apoptosis|induction of apoptosis	perinuclear region of cytoplasm					0																		---	---	---	---
MED24	9862	broad.mit.edu	37	17	38178281	38178281	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38178281G>A	uc002htt.2	-	23	2863	c.2550C>T	c.(2548-2550)GAC>GAT	p.D850D	MED24_uc010weq.1_5'Flank|MED24_uc002htr.2_Translation_Start_Site|MED24_uc010wer.1_Silent_p.D185D|MED24_uc010wes.1_Silent_p.D710D|MED24_uc010wet.1_RNA|MED24_uc002hts.2_Silent_p.D875D|MED24_uc002htu.2_Silent_p.D837D|MED24_uc010cwn.2_Silent_p.D837D|MED24_uc010weu.1_Silent_p.D760D|MED24_uc010wev.1_Silent_p.D800D	NM_014815	NP_055630	O75448	MED24_HUMAN	mediator complex subunit 24 isoform 1	850					androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(1)	1	Colorectal(19;0.000442)																	---	---	---	---
THRA	7067	broad.mit.edu	37	17	38244733	38244733	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38244733C>T	uc002htw.2	+	8	1445	c.962C>T	c.(961-963)GCT>GTT	p.A321V	THRA_uc010cwp.1_Missense_Mutation_p.A321V|THRA_uc002htv.2_Missense_Mutation_p.A321V|THRA_uc002htx.2_Missense_Mutation_p.A321V	NM_003250	NP_003241	P10827	THA_HUMAN	thyroid hormone receptor, alpha isoform 2	321	Ligand-binding.				negative regulation of RNA polymerase II transcriptional preinitiation complex assembly|negative regulation of transcription initiation, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription from RNA polymerase II promoter	cytosol|nucleoplasm	protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|TBP-class protein binding|thyroid hormone binding|thyroid hormone receptor activity|transcription regulatory region DNA binding|zinc ion binding				0	Colorectal(19;0.000442)	Myeloproliferative disorder(1115;0.0255)			Levothyroxine(DB00451)|Liothyronine(DB00279)													---	---	---	---
NR1D1	9572	broad.mit.edu	37	17	38253335	38253335	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:38253335C>T	uc002htz.1	-	2	979	c.353G>A	c.(352-354)AGC>AAC	p.S118N	NR1D1_uc010cwq.1_RNA|NR1D1_uc010cwr.1_5'Flank	NM_021724	NP_068370	P20393	NR1D1_HUMAN	nuclear receptor subfamily 1, group D, member 1	118					cellular response to lipopolysaccharide|negative regulation of receptor biosynthetic process|negative regulation of toll-like receptor 4 signaling pathway|negative regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nuclear chromatin|nucleoplasm	sequence-specific DNA binding|steroid hormone receptor activity|transcription corepressor activity|transcription regulatory region DNA binding|zinc ion binding			skin(1)	1	Colorectal(19;0.000442)																	---	---	---	---
KRT39	390792	broad.mit.edu	37	17	39118660	39118660	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39118660G>A	uc002hvo.1	-	4	900	c.864C>T	c.(862-864)AAC>AAT	p.N288N	KRT39_uc010wfm.1_Silent_p.N21N	NM_213656	NP_998821	Q6A163	K1C39_HUMAN	type I hair keratin KA35	288	Coil 2.|Rod.					intermediate filament	structural molecule activity				0		Breast(137;0.00043)|Ovarian(249;0.15)																---	---	---	---
KRTAP1-3	81850	broad.mit.edu	37	17	39190660	39190660	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39190660G>A	uc002hvv.2	-	1	448	c.414C>T	c.(412-414)CAC>CAT	p.H138H		NM_030966	NP_112228	Q8IUG1	KRA13_HUMAN	keratin associated protein 1-3	148						extracellular region|keratin filament	structural constituent of epidermis				0		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)															---	---	---	---
KRT31	3881	broad.mit.edu	37	17	39551219	39551219	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39551219C>T	uc002hwn.2	-	6	1031	c.978G>A	c.(976-978)GCG>GCA	p.A326A	KRT31_uc010cxn.2_Silent_p.A326A	NM_002277	NP_002268	Q15323	K1H1_HUMAN	keratin 31	326	Coil 2.|Rod.				epidermis development	intermediate filament	protein binding|structural constituent of cytoskeleton				0		Breast(137;0.000496)																---	---	---	---
KRT31	3881	broad.mit.edu	37	17	39552772	39552772	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39552772C>T	uc002hwn.2	-	3	541	c.488G>A	c.(487-489)CGC>CAC	p.R163H	KRT31_uc010cxn.2_Missense_Mutation_p.R163H	NM_002277	NP_002268	Q15323	K1H1_HUMAN	keratin 31	163	Rod.|Coil 1B.				epidermis development	intermediate filament	protein binding|structural constituent of cytoskeleton				0		Breast(137;0.000496)																---	---	---	---
KRT37	8688	broad.mit.edu	37	17	39577629	39577629	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39577629C>T	uc002hwp.1	-	6	1278	c.1231G>A	c.(1231-1233)GAG>AAG	p.E411K	uc002hwo.1_Intron	NM_003770	NP_003761	O76014	KRT37_HUMAN	keratin 37	411	Coil 2.|Rod.					intermediate filament	structural molecule activity			skin(1)	1		Breast(137;0.000496)																---	---	---	---
KRT13	3860	broad.mit.edu	37	17	39659023	39659023	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39659023C>A	uc002hwu.1	-	5	1002	c.939G>T	c.(937-939)ATG>ATT	p.M313I	KRT13_uc002hwv.1_Missense_Mutation_p.M313I|KRT13_uc002hww.2_Missense_Mutation_p.M206I|KRT13_uc010wfr.1_Missense_Mutation_p.M206I|KRT13_uc010cxo.2_Missense_Mutation_p.M313I|KRT13_uc002hwx.1_Missense_Mutation_p.M301I	NM_153490	NP_705694	P13646	K1C13_HUMAN	keratin 13 isoform a	313	Rod.|Coil 2.				epidermis development	intermediate filament	structural molecule activity			ovary(2)|skin(2)|pancreas(1)	5		Breast(137;0.000286)																---	---	---	---
JUP	3728	broad.mit.edu	37	17	39767593	39767593	+	Intron	SNP	G	A	A	rs150555871	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39767593G>A	uc010wfs.1	-						KRT16_uc002hxg.3_Intron	NM_021991	NP_068831			junction plakoglobin						adherens junction organization|atrioventricular valve morphogenesis|cell migration|cell morphogenesis|cellular response to indole-3-methanol|cytoskeletal anchoring at plasma membrane|detection of mechanical stimulus|ectoderm development|endothelial cell-cell adhesion|gastrulation|morphogenesis of embryonic epithelium|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of Wnt receptor signaling pathway involved in heart development|nervous system development|oocyte development|positive regulation of protein import into nucleus|positive regulation of sequence-specific DNA binding transcription factor activity|skin development	actin cytoskeleton|Axin-APC-beta-catenin-GSK3B complex|basolateral plasma membrane|catenin complex|desmosome|fascia adherens|gamma-catenin-TCF7L2 complex|internal side of plasma membrane|nucleus|protein-DNA complex|Z disc|zonula adherens	alpha-catenin binding|cadherin binding|protein homodimerization activity|protein kinase binding|protein phosphatase binding|RPTP-like protein binding|specific RNA polymerase II transcription factor activity|transcription coactivator activity			ovary(2)|lung(2)|breast(1)	5		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)														---	---	---	---
ACLY	47	broad.mit.edu	37	17	40042448	40042448	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40042448G>A	uc002hyg.2	-	18	2152	c.1989C>T	c.(1987-1989)TCC>TCT	p.S663S	ACLY_uc002hyh.2_Silent_p.S653S|ACLY_uc002hyi.2_Silent_p.S717S|ACLY_uc010wfx.1_Silent_p.S707S|ACLY_uc010wfy.1_Silent_p.S392S	NM_001096	NP_001087	P53396	ACLY_HUMAN	ATP citrate lyase isoform 1	663					ATP catabolic process|cellular carbohydrate metabolic process|citrate metabolic process|coenzyme A metabolic process|energy reserve metabolic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|triglyceride biosynthetic process	citrate lyase complex|cytosol|nucleus	ATP binding|ATP citrate synthase activity|citrate (pro-3S)-lyase activity|metal ion binding|protein binding|succinate-CoA ligase (ADP-forming) activity			ovary(2)|central_nervous_system(1)	3		Breast(137;0.000143)																---	---	---	---
CNP	1267	broad.mit.edu	37	17	40125729	40125729	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40125729T>C	uc002hyl.1	+	4	1197	c.1053T>C	c.(1051-1053)ATT>ATC	p.I351I	CNP_uc010wfz.1_Silent_p.I228I|CNP_uc002hym.1_Silent_p.I331I|CNP_uc010wga.1_Silent_p.I116I|CNP_uc002hyn.1_Silent_p.I116I	NM_033133	NP_149124	P09543	CN37_HUMAN	2',3'-cyclic nucleotide 3' phosphodiesterase	351					cell killing|cyclic nucleotide catabolic process|RNA metabolic process|synaptic transmission	extracellular space|melanosome	2',3'-cyclic-nucleotide 3'-phosphodiesterase activity|ATP binding|protein binding				0		all_cancers(22;2.38e-06)|all_epithelial(22;6.79e-05)|Breast(137;0.000143)		UCEC - Uterine corpus endometrioid carcinoma (308;0.171)														---	---	---	---
RAB5C	5878	broad.mit.edu	37	17	40282496	40282496	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40282496G>A	uc002hyz.2	-	3	342	c.25C>T	c.(25-27)CGA>TGA	p.R9*	RAB5C_uc002hza.2_Nonsense_Mutation_p.R9*|RAB5C_uc010cxx.2_Nonsense_Mutation_p.R42*|RAB5C_uc010cxy.2_Intron	NM_201434	NP_958842	P51148	RAB5C_HUMAN	RAB5C, member RAS oncogene family isoform a	9					protein transport|small GTPase mediated signal transduction	early endosome membrane|melanosome|plasma membrane	GTP binding|GTPase activity|protein binding			large_intestine(1)|skin(1)	2		all_cancers(22;1.24e-06)|all_epithelial(22;4.33e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.128)														---	---	---	---
KCNH4	23415	broad.mit.edu	37	17	40321683	40321683	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40321683C>T	uc002hzb.2	-	9	1735	c.1402G>A	c.(1402-1404)GCT>ACT	p.A468T		NM_012285	NP_036417	Q9UQ05	KCNH4_HUMAN	potassium voltage-gated channel, subfamily H,	468	Extracellular (Potential).				regulation of transcription, DNA-dependent	voltage-gated potassium channel complex	two-component sensor activity|voltage-gated potassium channel activity			large_intestine(1)	1		all_cancers(22;1.24e-06)|all_epithelial(22;4.33e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.126)														---	---	---	---
KCNH4	23415	broad.mit.edu	37	17	40328120	40328120	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40328120G>A	uc002hzb.2	-	5	1114	c.781C>T	c.(781-783)CGA>TGA	p.R261*		NM_012285	NP_036417	Q9UQ05	KCNH4_HUMAN	potassium voltage-gated channel, subfamily H,	261	Helical; Name=Segment S2; (Potential).				regulation of transcription, DNA-dependent	voltage-gated potassium channel complex	two-component sensor activity|voltage-gated potassium channel activity			large_intestine(1)	1		all_cancers(22;1.24e-06)|all_epithelial(22;4.33e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.126)														---	---	---	---
STAT5B	6777	broad.mit.edu	37	17	40370281	40370281	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40370281G>A	uc002hzh.2	-	9	1226	c.1057C>T	c.(1057-1059)CGC>TGC	p.R353C	STAT5B_uc002hzi.3_Missense_Mutation_p.R353C	NM_012448	NP_036580	P51692	STA5B_HUMAN	signal transducer and activator of transcription	353					2-oxoglutarate metabolic process|allantoin metabolic process|citrate metabolic process|creatine metabolic process|creatinine metabolic process|fatty acid metabolic process|isoleucine metabolic process|JAK-STAT cascade involved in growth hormone signaling pathway|oxaloacetate metabolic process|response to estradiol stimulus|succinate metabolic process|taurine metabolic process|valine metabolic process	cytosol|nucleoplasm	calcium ion binding|glucocorticoid receptor binding|sequence-specific DNA binding transcription factor activity			ovary(3)|lung(2)|skin(1)	6		all_cancers(22;4.15e-07)|all_epithelial(22;2.83e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.135)	Dasatinib(DB01254)													---	---	---	---
STAT3	6774	broad.mit.edu	37	17	40468866	40468866	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40468866G>A	uc002hzl.1	-	23	2438	c.2198C>T	c.(2197-2199)TCA>TTA	p.S733L	STAT3_uc002hzk.1_Silent_p.F716F|STAT3_uc002hzm.1_Missense_Mutation_p.S732L|STAT3_uc010wgh.1_Missense_Mutation_p.S635L|STAT3_uc002hzn.1_Missense_Mutation_p.S733L|STAT3_uc010cyf.1_5'UTR	NM_139276	NP_644805	P40763	STAT3_HUMAN	signal transducer and activator of transcription	733					cellular component movement|eating behavior|eye photoreceptor cell differentiation|glucose homeostasis|interleukin-6-mediated signaling pathway|interspecies interaction between organisms|JAK-STAT cascade involved in growth hormone signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|protein import into nucleus|response to estradiol stimulus|sexual reproduction|temperature homeostasis	cytosol|nucleus|plasma membrane	calcium ion binding|ligand-regulated transcription factor activity|protein dimerization activity|protein kinase binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription factor binding|transcription regulatory region DNA binding			ovary(1)|lung(1)|breast(1)|central_nervous_system(1)	4		all_cancers(22;1.39e-06)|all_epithelial(22;2.95e-05)|Breast(137;0.000135)		BRCA - Breast invasive adenocarcinoma(366;0.139)										Hyperimmunoglobulin_E_Recurrent_Infection_Syndrome				---	---	---	---
STAT3	6774	broad.mit.edu	37	17	40485956	40485956	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40485956C>T	uc002hzl.1	-	9	1149	c.909G>A	c.(907-909)CCG>CCA	p.P303P	STAT3_uc002hzk.1_Silent_p.P303P|STAT3_uc002hzm.1_Silent_p.P303P|STAT3_uc010wgh.1_Silent_p.P205P|STAT3_uc002hzn.1_Silent_p.P303P	NM_139276	NP_644805	P40763	STAT3_HUMAN	signal transducer and activator of transcription	303					cellular component movement|eating behavior|eye photoreceptor cell differentiation|glucose homeostasis|interleukin-6-mediated signaling pathway|interspecies interaction between organisms|JAK-STAT cascade involved in growth hormone signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|protein import into nucleus|response to estradiol stimulus|sexual reproduction|temperature homeostasis	cytosol|nucleus|plasma membrane	calcium ion binding|ligand-regulated transcription factor activity|protein dimerization activity|protein kinase binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription factor binding|transcription regulatory region DNA binding			ovary(1)|lung(1)|breast(1)|central_nervous_system(1)	4		all_cancers(22;1.39e-06)|all_epithelial(22;2.95e-05)|Breast(137;0.000135)		BRCA - Breast invasive adenocarcinoma(366;0.139)										Hyperimmunoglobulin_E_Recurrent_Infection_Syndrome				---	---	---	---
NAGLU	4669	broad.mit.edu	37	17	40696170	40696170	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40696170C>A	uc002hzv.2	+	6	2486	c.2146C>A	c.(2146-2148)CCC>ACC	p.P716T		NM_000263	NP_000254	P54802	ANAG_HUMAN	alpha-N-acetylglucosaminidase precursor	716						lysosome	alpha-N-acetylglucosaminidase activity				0		all_cancers(22;1.58e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344)		BRCA - Breast invasive adenocarcinoma(366;0.13)	N-Acetyl-D-glucosamine(DB00141)													---	---	---	---
MLX	6945	broad.mit.edu	37	17	40723617	40723617	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40723617A>G	uc002iag.2	+	8	958	c.893A>G	c.(892-894)TAC>TGC	p.Y298C	MLX_uc002iaf.2_Missense_Mutation_p.Y244C|MLX_uc002iah.2_Missense_Mutation_p.Y214C	NM_170607	NP_733752	Q9UH92	MLX_HUMAN	transcription factor-like protein 4 isoform	298				Y -> C (in Ref. 3; BAA90977).	energy reserve metabolic process|negative regulation of transcription, DNA-dependent|positive regulation of cellular metabolic process	cytoplasm|nucleus	DNA binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding				0		all_cancers(22;4.26e-05)|Breast(137;0.000153)|all_epithelial(22;0.00148)		BRCA - Breast invasive adenocarcinoma(366;0.129)														---	---	---	---
TUBG2	27175	broad.mit.edu	37	17	40817684	40817684	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40817684G>A	uc010wgr.1	+						TUBG2_uc002iaq.2_Intron|TUBG2_uc002iar.2_Intron|TUBG2_uc002ias.2_Intron|TUBG2_uc002iap.2_Intron	NM_016437	NP_057521			tubulin, gamma 2						G2/M transition of mitotic cell cycle|microtubule-based process|protein polymerization	cytosol	GTP binding|GTPase activity|structural molecule activity			ovary(1)	1		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.141)														---	---	---	---
PLEKHH3	79990	broad.mit.edu	37	17	40821616	40821616	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40821616C>T	uc002iau.2	-	12	2504	c.2037G>A	c.(2035-2037)CAG>CAA	p.Q679Q	PLEKHH3_uc010cyl.1_Intron|PLEKHH3_uc002iat.1_RNA|PLEKHH3_uc002iav.2_RNA|PLEKHH3_uc010cym.1_Silent_p.Q40Q|PLEKHH3_uc002iaw.2_3'UTR	NM_024927	NP_079203	Q7Z736	PKHH3_HUMAN	pleckstrin homology domain containing, family H	679	FERM.				signal transduction	cytoskeleton				large_intestine(1)|ovary(1)	2		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.14)														---	---	---	---
CNTNAP1	8506	broad.mit.edu	37	17	40837450	40837450	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40837450G>A	uc002iay.2	+						CNTNAP1_uc010wgs.1_Intron	NM_003632	NP_003623			contactin associated protein 1 precursor						axon guidance|cell adhesion	paranode region of axon	receptor activity|receptor binding|SH3 domain binding|SH3/SH2 adaptor activity			ovary(3)|breast(3)|upper_aerodigestive_tract(1)|lung(1)	8		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.143)														---	---	---	---
CNTNAP1	8506	broad.mit.edu	37	17	40841571	40841571	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40841571G>A	uc002iay.2	+	11	1877	c.1661G>A	c.(1660-1662)CGC>CAC	p.R554H	CNTNAP1_uc010wgs.1_RNA	NM_003632	NP_003623	P78357	CNTP1_HUMAN	contactin associated protein 1 precursor	554	EGF-like 1.|Extracellular (Potential).				axon guidance|cell adhesion	paranode region of axon	receptor activity|receptor binding|SH3 domain binding|SH3/SH2 adaptor activity			ovary(3)|breast(3)|upper_aerodigestive_tract(1)|lung(1)	8		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.143)														---	---	---	---
EZH1	2145	broad.mit.edu	37	17	40859972	40859972	+	Intron	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40859972T>G	uc002iaz.2	-						EZH1_uc002iba.2_Intron|EZH1_uc010wgt.1_Intron|EZH1_uc010wgu.1_Intron|EZH1_uc010wgv.1_Intron|EZH1_uc010wgw.1_Intron|EZH1_uc010cyp.2_Intron|EZH1_uc010cyq.2_Intron|EZH1_uc010cyo.1_Intron	NM_001991	NP_001982			enhancer of zeste homolog 1						anatomical structure morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex	chromatin binding|DNA binding			ovary(3)	3		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0784)														---	---	---	---
WNK4	65266	broad.mit.edu	37	17	40933086	40933086	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40933086C>T	uc002ibj.2	+	1	391	c.370C>T	c.(370-372)CGT>TGT	p.R124C	WNK4_uc010wgx.1_5'UTR|WNK4_uc002ibk.1_5'Flank	NM_032387	NP_115763	Q96J92	WNK4_HUMAN	WNK lysine deficient protein kinase 4	124					intracellular protein kinase cascade	tight junction	ATP binding|protein serine/threonine kinase activity			ovary(3)|skin(3)|stomach(1)	7		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.0749)														---	---	---	---
WNK4	65266	broad.mit.edu	37	17	40937311	40937311	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40937311C>T	uc002ibj.2	+	6	1308	c.1287C>T	c.(1285-1287)CAC>CAT	p.H429H	WNK4_uc010wgx.1_Silent_p.H93H|WNK4_uc002ibk.1_Silent_p.H201H|WNK4_uc010wgy.1_Translation_Start_Site	NM_032387	NP_115763	Q96J92	WNK4_HUMAN	WNK lysine deficient protein kinase 4	429	Protein kinase.				intracellular protein kinase cascade	tight junction	ATP binding|protein serine/threonine kinase activity			ovary(3)|skin(3)|stomach(1)	7		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.0749)														---	---	---	---
PSME3	10197	broad.mit.edu	37	17	40993603	40993603	+	3'UTR	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:40993603G>A	uc002ibr.2	+	11					PSME3_uc002ibp.2_3'UTR|PSME3_uc002ibq.2_3'UTR|PSME3_uc002ibs.2_3'UTR|PSME3_uc010whd.1_3'UTR	NM_005789	NP_005780			proteasome activator subunit 3 isoform 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|regulation of proteasomal protein catabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome activator complex	endopeptidase activator activity|identical protein binding|MDM2 binding|p53 binding				0		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)														---	---	---	---
AOC3	8639	broad.mit.edu	37	17	41003924	41003924	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41003924G>A	uc002ibv.2	+	1	724	c.564G>A	c.(562-564)CTG>CTA	p.L188L		NM_003734	NP_003725	Q16853	AOC3_HUMAN	amine oxidase, copper containing 3 precursor	188	Extracellular (Potential).				amine metabolic process|cell adhesion|inflammatory response	cell surface|integral to membrane|plasma membrane	aliphatic-amine oxidase activity|aminoacetone:oxygen oxidoreductase(deaminating) activity|copper ion binding|phenethylamine:oxygen oxidoreductase (deaminating) activity|primary amine oxidase activity|protein homodimerization activity|quinone binding|tryptamine:oxygen oxidoreductase (deaminating) activity			central_nervous_system(2)|ovary(1)|skin(1)	4		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)	Hydralazine(DB01275)|Phenelzine(DB00780)													---	---	---	---
TMEM101	84336	broad.mit.edu	37	17	42089592	42089592	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42089592G>A	uc002ieu.2	-	4	503	c.478C>T	c.(478-480)CAG>TAG	p.Q160*	TMEM101_uc010wis.1_Nonsense_Mutation_p.Q102*	NM_032376	NP_115752	Q96IK0	TM101_HUMAN	transmembrane protein 101	160					positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to membrane	signal transducer activity			upper_aerodigestive_tract(1)|central_nervous_system(1)	2		Breast(137;0.0264)|Prostate(33;0.0861)		BRCA - Breast invasive adenocarcinoma(366;0.113)														---	---	---	---
C17orf53	78995	broad.mit.edu	37	17	42226267	42226267	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42226267C>A	uc002ifi.1	+	3	1281	c.1096C>A	c.(1096-1098)CCC>ACC	p.P366T	C17orf53_uc010czq.1_Missense_Mutation_p.P366T|C17orf53_uc002ifj.1_Missense_Mutation_p.P366T|C17orf53_uc002ifk.1_RNA	NM_024032	NP_076937	Q8N3J3	CQ053_HUMAN	hypothetical protein LOC78995	366											0		Breast(137;0.0364)|Prostate(33;0.0376)		BRCA - Breast invasive adenocarcinoma(366;0.114)														---	---	---	---
TMUB2	79089	broad.mit.edu	37	17	42266577	42266577	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42266577G>A	uc002ifo.2	+	3	380	c.223G>A	c.(223-225)GAC>AAC	p.D75N	C17orf65_uc002ifn.2_5'Flank|TMUB2_uc002ifp.2_Missense_Mutation_p.D55N|TMUB2_uc010wiu.1_Missense_Mutation_p.D55N|TMUB2_uc002ifq.2_Missense_Mutation_p.D75N|TMUB2_uc002ifr.2_Missense_Mutation_p.D55N|TMUB2_uc002ifs.2_Intron|TMUB2_uc002ift.2_Missense_Mutation_p.D55N|TMUB2_uc002ifu.2_Missense_Mutation_p.D55N|TMUB2_uc002ifv.2_Missense_Mutation_p.D55N|TMUB2_uc002ifw.1_Missense_Mutation_p.D55N|TMUB2_uc002ifx.2_Missense_Mutation_p.D55N|TMUB2_uc002ify.2_RNA	NM_001076674	NP_001070142	Q71RG4	TMUB2_HUMAN	transmembrane and ubiquitin-like domain	75						integral to membrane				lung(1)	1		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.113)														---	---	---	---
GPATCH8	23131	broad.mit.edu	37	17	42513890	42513890	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42513890C>T	uc002igw.1	-	4	281	c.217G>A	c.(217-219)GTT>ATT	p.V73I	GPATCH8_uc002igv.1_5'UTR|GPATCH8_uc010wiz.1_5'UTR	NM_001002909	NP_001002909	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8	73	G-patch.					intracellular	nucleic acid binding|zinc ion binding			ovary(2)|kidney(1)|skin(1)	4		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.206)														---	---	---	---
DBF4B	80174	broad.mit.edu	37	17	42828024	42828024	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:42828024A>G	uc002ihf.2	+	14	1464	c.1251A>G	c.(1249-1251)GGA>GGG	p.G417G	DBF4B_uc010wjc.1_Silent_p.G401G	NM_145663	NP_663696	Q8NFT6	DBF4B_HUMAN	DBF4 homolog B isoform 1	417					cell cycle	nucleus	nucleic acid binding|zinc ion binding				0		Prostate(33;0.0322)																---	---	---	---
KIF18B	146909	broad.mit.edu	37	17	43003519	43003519	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43003519T>C	uc010wji.1	-	16	2598	c.2497A>G	c.(2497-2499)AGG>GGG	p.R833G	KIF18B_uc002iht.2_3'UTR|KIF18B_uc010wjh.1_Missense_Mutation_p.R830G	NM_001080443	NP_001073912			kinesin family member 18B											ovary(2)	2		Prostate(33;0.155)																---	---	---	---
PLCD3	113026	broad.mit.edu	37	17	43195382	43195382	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43195382G>A	uc002iib.2	-	7	1353	c.1239C>T	c.(1237-1239)GCC>GCT	p.A413A		NM_133373	NP_588614	Q8N3E9	PLCD3_HUMAN	phospholipase C delta 3	413	PI-PLC X-box.				intracellular signal transduction|lipid catabolic process	cleavage furrow|cytoplasm|membrane	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			breast(2)|lung(1)	3					Phosphatidylserine(DB00144)													---	---	---	---
PLEKHM1	9842	broad.mit.edu	37	17	43555521	43555521	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43555521G>A	uc002ija.2	-						PLEKHM1_uc010wjm.1_Intron|PLEKHM1_uc002ijb.2_Intron|PLEKHM1_uc010wjn.1_Intron|hsa-mir-4315-1|MI0015844_5'Flank|PLEKHM1_uc002ijd.1_Intron	NM_014798	NP_055613			pleckstrin homology domain containing, family M						intracellular signal transduction	cytoplasm	metal ion binding				0	Renal(3;0.0405)																	---	---	---	---
IMP5	162540	broad.mit.edu	37	17	43923379	43923379	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43923379G>A	uc010wka.1	+	1	1107	c.1107G>A	c.(1105-1107)CTG>CTA	p.L369L	LOC100128977_uc010wjz.1_Intron	NM_175882	NP_787078	Q8IUH8	IMP5_HUMAN	intramembrane protease 5 precursor	369	Extracellular (Potential).					integral to membrane	aspartic-type endopeptidase activity			pancreas(2)	2	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.148)														---	---	---	---
KIAA1267	284058	broad.mit.edu	37	17	44248642	44248642	+	Nonsense_Mutation	SNP	G	A	A	rs149830411		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44248642G>A	uc002ikb.2	-	1	953	c.868C>T	c.(868-870)CGA>TGA	p.R290*	KIAA1267_uc002ikc.2_Nonsense_Mutation_p.R290*|KIAA1267_uc002ikd.2_Nonsense_Mutation_p.R290*|KIAA1267_uc010dav.2_Nonsense_Mutation_p.R290*	NM_015443	NP_056258	Q7Z3B3	K1267_HUMAN	hypothetical protein LOC284058	290	Potential.					MLL1 complex	protein binding			skin(2)	2		Melanoma(429;0.211)																---	---	---	---
ITGB3	3690	broad.mit.edu	37	17	45360719	45360719	+	Splice_Site	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45360719G>T	uc002ilj.2	+	3	186	c.166_splice	c.e3-1	p.A56_splice	ITGB3_uc002ili.1_Splice_Site_p.A56_splice|ITGB3_uc010wkr.1_Splice_Site	NM_000212	NP_000203			integrin beta chain, beta 3 precursor						activation of protein kinase activity|angiogenesis involved in wound healing|axon guidance|cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|leukocyte migration|negative regulation of lipid storage|negative regulation of lipid transport|negative regulation of lipoprotein metabolic process|negative regulation of low-density lipoprotein particle receptor biosynthetic process|negative regulation of macrophage derived foam cell differentiation|platelet activation|platelet degranulation|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of vascular endothelial growth factor receptor signaling pathway|regulation of bone resorption|smooth muscle cell migration|tube development	alphav-beta3 integrin-vitronectin complex|integrin complex|platelet alpha granule membrane	cell adhesion molecule binding|identical protein binding|platelet-derived growth factor receptor binding|receptor activity|vascular endothelial growth factor receptor 2 binding			central_nervous_system(5)|large_intestine(1)	6					Abciximab(DB00054)|Tirofiban(DB00775)													---	---	---	---
MRPL10	124995	broad.mit.edu	37	17	45904485	45904485	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45904485G>T	uc002ilz.2	-	3	334	c.308C>A	c.(307-309)GCT>GAT	p.A103D	MRPL10_uc010wky.1_Missense_Mutation_p.A64D|MRPL10_uc002ily.2_Missense_Mutation_p.A113D	NM_145255	NP_660298	Q7Z7H8	RM10_HUMAN	mitochondrial ribosomal protein L10 precursor	103					ribosome biogenesis|translation	mitochondrial large ribosomal subunit	structural constituent of ribosome			ovary(1)	1																		---	---	---	---
SP2	6668	broad.mit.edu	37	17	45994017	45994017	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45994017G>A	uc002imk.2	+	3	717	c.580G>A	c.(580-582)GTG>ATG	p.V194M	SP2_uc002iml.2_Missense_Mutation_p.V187M|uc002imm.2_Intron	NM_003110	NP_003101	Q02086	SP2_HUMAN	Sp2 transcription factor	194					immune response|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding|histone deacetylase binding|zinc ion binding				0																		---	---	---	---
HOXB8	3218	broad.mit.edu	37	17	46691798	46691798	+	Missense_Mutation	SNP	G	A	A	rs140795156	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46691798G>A	uc002inw.2	-	1	504	c.269C>T	c.(268-270)CCG>CTG	p.P90L		NM_024016	NP_076921	P17481	HXB8_HUMAN	homeobox B8	90						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
IGF2BP1	10642	broad.mit.edu	37	17	47117400	47117400	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47117400C>T	uc002iom.2	+	7	1099	c.765C>T	c.(763-765)TCC>TCT	p.S255S	IGF2BP1_uc010dbj.2_Intron	NM_006546	NP_006537	Q9NZI8	IF2B1_HUMAN	insulin-like growth factor 2 mRNA binding	255	KH 1.|Necessary for interaction with ELAVL4 and binding to TAU mRNA (By similarity).				CRD-mediated mRNA stabilization|negative regulation of translation|regulation of mRNA stability involved in response to stress	CRD-mediated mRNA stability complex|cytosol|dendritic spine|lamellipodium|nucleus|plasma membrane|stress granule	mRNA 3'-UTR binding|mRNA 5'-UTR binding|nucleotide binding|protein binding|translation regulator activity			kidney(1)	1																		---	---	---	---
PHB	5245	broad.mit.edu	37	17	47490598	47490598	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47490598C>A	uc002iox.1	-	2	102	c.29G>T	c.(28-30)GGC>GTC	p.G10V		NM_002634	NP_002625	P35232	PHB_HUMAN	prohibitin	10					cellular response to interleukin-6|DNA replication|glucocorticoid receptor signaling pathway|histone deacetylation|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of transcription by competitive promoter binding|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|progesterone receptor signaling pathway|regulation of apoptosis	integral to plasma membrane|mitochondrial inner membrane|nucleoplasm	histone deacetylase binding|transcription regulatory region DNA binding				0	all_cancers(4;2.62e-14)|Breast(4;4.21e-29)|all_epithelial(4;6.9e-18)		Epithelial(5;8.1e-06)|all cancers(6;7.71e-05)															---	---	---	---
NGFR	4804	broad.mit.edu	37	17	47579453	47579453	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47579453G>A	uc002ioz.3	+	2	220	c.95G>A	c.(94-96)TGC>TAC	p.C32Y		NM_002507	NP_002498	P08138	TNR16_HUMAN	nerve growth factor receptor precursor	32	TNFR-Cys 1.|Extracellular (Potential).				anti-apoptosis|apoptosis|induction of apoptosis by extracellular signals|membrane protein intracellular domain proteolysis|negative regulation of axonogenesis|negative regulation of cell cycle|nerve growth factor receptor signaling pathway|positive regulation of axonogenesis	cell surface|cytosol|endosome|extracellular region|integral to plasma membrane|nucleoplasm		p.C32*(1)		ovary(1)|lung(1)	2	all_cancers(4;1.45e-13)|Breast(4;6.34e-28)|all_epithelial(4;4.95e-17)																	---	---	---	---
NGFR	4804	broad.mit.edu	37	17	47583655	47583655	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47583655G>A	uc002ioz.3	+							NM_002507	NP_002498			nerve growth factor receptor precursor						anti-apoptosis|apoptosis|induction of apoptosis by extracellular signals|membrane protein intracellular domain proteolysis|negative regulation of axonogenesis|negative regulation of cell cycle|nerve growth factor receptor signaling pathway|positive regulation of axonogenesis	cell surface|cytosol|endosome|extracellular region|integral to plasma membrane|nucleoplasm				ovary(1)|lung(1)	2	all_cancers(4;1.45e-13)|Breast(4;6.34e-28)|all_epithelial(4;4.95e-17)																	---	---	---	---
MYST2	11143	broad.mit.edu	37	17	47874135	47874135	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47874135C>T	uc002ipm.2	+	3	313	c.187C>T	c.(187-189)CAG>TAG	p.Q63*	MYST2_uc002ipl.1_Nonsense_Mutation_p.Q63*|MYST2_uc010wma.1_Intron|MYST2_uc010wmb.1_Nonsense_Mutation_p.Q63*|MYST2_uc010wmc.1_Intron|MYST2_uc010wmd.1_5'UTR|MYST2_uc010wme.1_5'UTR	NM_007067	NP_008998	O95251	MYST2_HUMAN	MYST histone acetyltransferase 2	63					DNA replication|histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	histone acetyltransferase activity|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|lung(1)|skin(1)	3																		---	---	---	---
TAC4	255061	broad.mit.edu	37	17	47925364	47925364	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47925364C>T	uc002ipo.1	-	1	16	c.16G>A	c.(16-18)GCC>ACC	p.A6T	TAC4_uc002ipp.1_Missense_Mutation_p.A6T|TAC4_uc002ipq.1_Missense_Mutation_p.A6T|TAC4_uc002ipr.1_Missense_Mutation_p.A6T|TAC4_uc002ips.1_Missense_Mutation_p.A6T|TAC4_uc002ipt.2_RNA|TAC4_uc002ipu.2_RNA	NM_170685	NP_733786	Q86UU9	TKN4_HUMAN	tachykinin 4 isoform alpha	6					regulation of blood pressure	extracellular region				breast(1)	1																		---	---	---	---
DLX3	1747	broad.mit.edu	37	17	48068985	48068985	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48068985C>T	uc002ipy.2	-	3	986	c.760G>A	c.(760-762)GCA>ACA	p.A254T		NM_005220	NP_005211	O60479	DLX3_HUMAN	distal-less homeobox 3	254						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
SGCA	6442	broad.mit.edu	37	17	48244992	48244992	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48244992C>T	uc002iqi.2	+	3	243	c.207C>T	c.(205-207)CAC>CAT	p.H69H	SGCA_uc010wmh.1_Intron|SGCA_uc002iqj.2_Silent_p.H69H|SGCA_uc010wmi.1_RNA	NM_000023	NP_000014	Q16586	SGCA_HUMAN	sarcoglycan, alpha isoform 1 precursor	69	Extracellular (Potential).				muscle contraction|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma	calcium ion binding			ovary(2)	2																		---	---	---	---
COL1A1	1277	broad.mit.edu	37	17	48270026	48270026	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48270026C>T	uc002iqm.2	-	28	2030	c.1904G>A	c.(1903-1905)GGC>GAC	p.G635D		NM_000088	NP_000079	P02452	CO1A1_HUMAN	alpha 1 type I collagen preproprotein	635	Triple-helical region.				axon guidance|blood vessel development|collagen biosynthetic process|collagen fibril organization|embryonic skeletal system development|leukocyte migration|platelet activation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent|protein localization to nucleus|sensory perception of sound|skin morphogenesis|tooth mineralization|visual perception	collagen type I|extracellular space|plasma membrane	identical protein binding|platelet-derived growth factor binding		COL1A1/PDGFB(372)	soft_tissue(372)|central_nervous_system(7)|skin(1)|breast(1)|pancreas(1)	382					Collagenase(DB00048)|Palifermin(DB00039)			T	PDGFB|USP6	dermatofibrosarcoma protuberans|aneurysmal bone cyst 		Osteogenesis imperfecta						---	---	---	---
CHAD	1101	broad.mit.edu	37	17	48545630	48545630	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48545630G>A	uc010dbr.2	-	1	598	c.545C>T	c.(544-546)GCG>GTG	p.A182V	ACSF2_uc002iqu.2_Intron|ACSF2_uc010wml.1_Intron|ACSF2_uc010wmm.1_Intron|ACSF2_uc010wmn.1_Intron|ACSF2_uc010wmo.1_Intron|CHAD_uc010dbs.2_Missense_Mutation_p.A182V|ACSF2_uc010dbt.1_5'Flank	NM_001267	NP_001258	O15335	CHAD_HUMAN	chondroadherin precursor	182	LRR 5.				regulation of cell growth	proteinaceous extracellular matrix	extracellular matrix structural constituent			ovary(2)|central_nervous_system(1)	3	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)															---	---	---	---
CHAD	1101	broad.mit.edu	37	17	48545654	48545654	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48545654C>T	uc010dbr.2	-	1	574	c.521G>A	c.(520-522)CGC>CAC	p.R174H	ACSF2_uc002iqu.2_Intron|ACSF2_uc010wml.1_Intron|ACSF2_uc010wmm.1_Intron|ACSF2_uc010wmn.1_Intron|ACSF2_uc010wmo.1_Intron|CHAD_uc010dbs.2_Missense_Mutation_p.R174H|ACSF2_uc010dbt.1_5'Flank	NM_001267	NP_001258	O15335	CHAD_HUMAN	chondroadherin precursor	174	LRR 5.				regulation of cell growth	proteinaceous extracellular matrix	extracellular matrix structural constituent			ovary(2)|central_nervous_system(1)	3	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)															---	---	---	---
CHAD	1101	broad.mit.edu	37	17	48545885	48545885	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48545885C>T	uc010dbr.2	-	1	343	c.290G>A	c.(289-291)GGC>GAC	p.G97D	ACSF2_uc002iqu.2_Intron|ACSF2_uc010wml.1_Intron|ACSF2_uc010wmm.1_Intron|ACSF2_uc010wmn.1_Intron|ACSF2_uc010wmo.1_Intron|CHAD_uc010dbs.2_Missense_Mutation_p.G97D|ACSF2_uc010dbt.1_Intron	NM_001267	NP_001258	O15335	CHAD_HUMAN	chondroadherin precursor	97	LRR 1.				regulation of cell growth	proteinaceous extracellular matrix	extracellular matrix structural constituent			ovary(2)|central_nervous_system(1)	3	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)															---	---	---	---
CACNA1G	8913	broad.mit.edu	37	17	48697147	48697147	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48697147C>T	uc002irk.1	+	34	6257	c.5885C>T	c.(5884-5886)GCC>GTC	p.A1962V	CACNA1G_uc002irj.1_Intron|CACNA1G_uc002irl.1_Intron|CACNA1G_uc002irm.1_Missense_Mutation_p.A1928V|CACNA1G_uc002irn.1_Intron|CACNA1G_uc002iro.1_Intron|CACNA1G_uc002irp.1_Missense_Mutation_p.A1962V|CACNA1G_uc002irq.1_Missense_Mutation_p.A1939V|CACNA1G_uc002irr.1_Intron|CACNA1G_uc002irs.1_Missense_Mutation_p.A1951V|CACNA1G_uc002irt.1_Intron|CACNA1G_uc002irv.1_Intron|CACNA1G_uc002irw.1_Intron|CACNA1G_uc002iru.1_Missense_Mutation_p.A1928V|CACNA1G_uc002irx.1_Intron|CACNA1G_uc002iry.1_Intron|CACNA1G_uc002irz.1_Intron|CACNA1G_uc002isa.1_Intron|CACNA1G_uc002isb.1_Intron|CACNA1G_uc002isc.1_Missense_Mutation_p.A1864V|CACNA1G_uc002isd.1_Intron|CACNA1G_uc002ise.1_Missense_Mutation_p.A1830V|CACNA1G_uc002isf.1_Missense_Mutation_p.A1857V|CACNA1G_uc002isg.1_Intron|CACNA1G_uc002ish.1_Intron|CACNA1G_uc002isi.1_Intron	NM_018896	NP_061496	O43497	CAC1G_HUMAN	voltage-dependent calcium channel alpha 1G	1962	Cytoplasmic (Potential).				axon guidance	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(1)	1	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Ethosuximide(DB00593)|Flunarizine(DB04841)|Levetiracetam(DB01202)|Mibefradil(DB01388)|Pimozide(DB01100)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)													---	---	---	---
MBTD1	54799	broad.mit.edu	37	17	49280128	49280128	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49280128T>C	uc002itr.3	-	10	1341	c.997A>G	c.(997-999)ATG>GTG	p.M333V	MBTD1_uc002itp.3_Missense_Mutation_p.M169V|MBTD1_uc002itq.3_Missense_Mutation_p.M333V	NM_017643	NP_060113	Q05BQ5	MBTD1_HUMAN	mbt domain containing 1	333	MBT 2.				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(22;1.54e-08)															---	---	---	---
MBTD1	54799	broad.mit.edu	37	17	49284281	49284281	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49284281A>G	uc002itr.3	-	7	916	c.572T>C	c.(571-573)GTC>GCC	p.V191A	MBTD1_uc002itp.3_Missense_Mutation_p.V27A|MBTD1_uc002itq.3_Missense_Mutation_p.V191A	NM_017643	NP_060113	Q05BQ5	MBTD1_HUMAN	mbt domain containing 1	191	MBT 1.				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(22;1.54e-08)															---	---	---	---
ANKFN1	162282	broad.mit.edu	37	17	54535320	54535320	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54535320G>A	uc002iun.1	+	13	1581	c.1546G>A	c.(1546-1548)GCA>ACA	p.A516T		NM_153228	NP_694960	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain	516										large_intestine(1)|ovary(1)	2																		---	---	---	---
DGKE	8526	broad.mit.edu	37	17	54940084	54940084	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:54940084T>C	uc002iur.2	+	12	1816	c.1636T>C	c.(1636-1638)TCT>CCT	p.S546P	DGKE_uc002ius.1_3'UTR	NM_003647	NP_003638	P52429	DGKE_HUMAN	diacylglycerol kinase epsilon	546					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|phospholipid biosynthetic process|platelet activation	integral to membrane|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding|protein binding			breast(2)	2	Breast(9;3.59e-07)																	---	---	---	---
COIL	8161	broad.mit.edu	37	17	55027892	55027892	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55027892G>A	uc002iuu.2	-	2	742	c.711C>T	c.(709-711)AGC>AGT	p.S237S		NM_004645	NP_004636	P38432	COIL_HUMAN	coilin	237	2 X 4 AA repeats of A-R-N-S.					Cajal body|nucleolus	protein C-terminus binding			ovary(1)	1	Breast(9;6.15e-08)																	---	---	---	---
MSI2	124540	broad.mit.edu	37	17	55754397	55754397	+	3'UTR	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55754397C>A	uc002iuz.1	+	13					MSI2_uc010wnm.1_3'UTR	NM_138962	NP_620412			musashi 2 isoform a							cytoplasm	nucleotide binding|RNA binding			central_nervous_system(1)|pancreas(1)	2	Breast(9;1.78e-08)			GBM - Glioblastoma multiforme(1;0.0025)				T	HOXA9	CML								---	---	---	---
MKS1	54903	broad.mit.edu	37	17	56283688	56283688	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56283688C>T	uc002ivr.1	-	17	1619	c.1544G>A	c.(1543-1545)CGT>CAT	p.R515H	MKS1_uc010wnq.1_Missense_Mutation_p.R312H|MKS1_uc002ivs.1_Missense_Mutation_p.V443I	NM_017777	NP_060247	Q9NXB0	MKS1_HUMAN	Meckel syndrome type 1 protein isoform 1	515					cilium assembly	centrosome|cilium|microtubule basal body	protein binding			ovary(1)	1																		---	---	---	---
BZRAP1	9256	broad.mit.edu	37	17	56385226	56385226	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56385226A>C	uc002ivx.3	-	23	5679	c.4808T>G	c.(4807-4809)CTC>CGC	p.L1603R	BZRAP1_uc002ivv.2_5'Flank|BZRAP1_uc002ivw.2_5'Flank|BZRAP1_uc010dcs.2_Missense_Mutation_p.L1543R|BZRAP1_uc010wnt.1_Missense_Mutation_p.L1603R	NM_004758	NP_004749	O95153	RIMB1_HUMAN	peripheral benzodiazepine receptor-associated	1603						mitochondrion	benzodiazepine receptor binding			upper_aerodigestive_tract(2)|skin(1)	3	Medulloblastoma(34;0.127)|all_neural(34;0.237)																	---	---	---	---
TEX14	56155	broad.mit.edu	37	17	56699019	56699019	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56699019G>A	uc010dcz.1	-	5	664	c.546C>T	c.(544-546)CTC>CTT	p.L182L	TEX14_uc002iwr.1_Silent_p.L182L|TEX14_uc002iws.1_Silent_p.L182L|TEX14_uc010dda.1_5'UTR	NM_198393	NP_938207	Q8IWB6	TEX14_HUMAN	testis expressed sequence 14 isoform a	182						cytoplasm	ATP binding|protein kinase activity			stomach(4)|lung(3)|breast(3)|ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)|pancreas(1)	17	Medulloblastoma(34;0.127)|all_neural(34;0.237)																	---	---	---	---
TEX14	56155	broad.mit.edu	37	17	56738544	56738544	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:56738544G>A	uc010dcz.1	-						TEX14_uc002iwr.1_Intron|TEX14_uc002iws.1_Intron|TEX14_uc010dda.1_Intron|TEX14_uc010wnz.1_Silent_p.H139H	NM_198393	NP_938207			testis expressed sequence 14 isoform a							cytoplasm	ATP binding|protein kinase activity			stomach(4)|lung(3)|breast(3)|ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)|pancreas(1)	17	Medulloblastoma(34;0.127)|all_neural(34;0.237)																	---	---	---	---
PRR11	55771	broad.mit.edu	37	17	57247118	57247118	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57247118C>A	uc002ixf.1	+	2	84	c.5C>A	c.(4-6)CCC>CAC	p.P2H	PRR11_uc002ixg.1_RNA	NM_018304	NP_060774	Q96HE9	PRR11_HUMAN	proline rich 11	2										ovary(2)	2	Medulloblastoma(34;0.0922)|all_neural(34;0.101)																	---	---	---	---
GDPD1	284161	broad.mit.edu	37	17	57334600	57334600	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57334600A>C	uc002ixk.1	+	5	622	c.485A>C	c.(484-486)AAG>ACG	p.K162T	GDPD1_uc002ixj.2_Missense_Mutation_p.K162T	NM_182569	NP_872375	Q8N9F7	GDPD1_HUMAN	glycerophosphodiester phosphodiesterase domain	162	Cytoplasmic (Potential).|GDPD.				glycerol metabolic process|lipid metabolic process	cytoplasm|integral to membrane	glycerophosphodiester phosphodiesterase activity|metal ion binding				0	all_neural(34;0.0837)|Medulloblastoma(34;0.0922)																	---	---	---	---
TMEM49	81671	broad.mit.edu	37	17	57812763	57812763	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57812763G>T	uc002ixu.3	+	3	414	c.141G>T	c.(139-141)TGG>TGT	p.W47C	TMEM49_uc010wog.1_Intron|TMEM49_uc010woh.1_Missense_Mutation_p.W47C|TMEM49_uc010woi.1_5'UTR|TMEM49_uc010woj.1_5'UTR	NM_030938	NP_112200	Q96GC9	VMP1_HUMAN	transmembrane protein 49	47	Helical; (Potential).				autophagy|cell adhesion	endoplasmic reticulum|ER-Golgi intermediate compartment membrane|integral to membrane|plasma membrane|vacuolar membrane					0	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;1.15e-09)|all cancers(12;1.15e-08)															---	---	---	---
RPS6KB1	6198	broad.mit.edu	37	17	57987925	57987925	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:57987925T>C	uc002ixy.2	+	2	247	c.144T>C	c.(142-144)GGT>GGC	p.G48G	RPS6KB1_uc010ddj.1_Silent_p.G48G|RPS6KB1_uc010wom.1_5'UTR|RPS6KB1_uc010won.1_Silent_p.G48G|RPS6KB1_uc010woo.1_5'Flank	NM_003161	NP_003152	P23443	KS6B1_HUMAN	ribosomal protein S6 kinase, 70kDa, polypeptide	48					apoptosis|G1/S transition of mitotic cell cycle|insulin receptor signaling pathway|negative regulation of apoptosis|phosphatidylinositol-mediated signaling|positive regulation of mitotic cell cycle|positive regulation of translational initiation|TOR signaling cascade	cell junction|cytoplasm|cytosol|mitochondrial outer membrane|nucleus|nucleus|synapse|synaptosome	ATP binding|protein binding|protein kinase activity			large_intestine(1)	1	all_cancers(5;1.63e-13)|Breast(5;2.91e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;3.57e-12)|all cancers(12;6.41e-11)															---	---	---	---
MED13	9969	broad.mit.edu	37	17	60062167	60062167	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60062167C>T	uc002izo.2	-	14	2613	c.2536G>A	c.(2536-2538)GGA>AGA	p.G846R		NM_005121	NP_005112	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	846					androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			large_intestine(1)|ovary(1)	2																		---	---	---	---
TLK2	11011	broad.mit.edu	37	17	60689793	60689793	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60689793G>A	uc010ddp.2	+	23	2454	c.2186G>A	c.(2185-2187)CGC>CAC	p.R729H	TLK2_uc002izx.3_Missense_Mutation_p.R555H|TLK2_uc002izz.3_Missense_Mutation_p.R707H|TLK2_uc002jaa.3_Missense_Mutation_p.R675H|TLK2_uc010wpd.1_Missense_Mutation_p.R675H	NM_006852	NP_006843	Q86UE8	TLK2_HUMAN	tousled-like kinase 2 isoform A	729	Protein kinase.				cell cycle|chromatin modification|intracellular signal transduction|regulation of chromatin assembly or disassembly|response to DNA damage stimulus	nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			stomach(1)|kidney(1)	2																		---	---	---	---
MRC2	9902	broad.mit.edu	37	17	60759646	60759646	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60759646C>T	uc002jad.2	+	20	3256	c.2854C>T	c.(2854-2856)CGC>TGC	p.R952C	MRC2_uc002jae.2_Missense_Mutation_p.R23C|MRC2_uc002jaf.2_5'UTR	NM_006039	NP_006030	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	952	Extracellular (Potential).				endocytosis	integral to membrane	receptor activity|sugar binding			ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
STRADA	92335	broad.mit.edu	37	17	61781677	61781677	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61781677C>T	uc002jbm.2	-						STRADA_uc002jbn.2_Intron|STRADA_uc002jbo.2_Intron|STRADA_uc002jbp.2_Missense_Mutation_p.G338E|STRADA_uc002jbq.2_Intron|STRADA_uc010wpq.1_Intron|STRADA_uc010wpr.1_Intron|STRADA_uc010ddw.2_Intron|STRADA_uc002jbr.2_3'UTR	NM_001003787	NP_001003787			STE20-related kinase adaptor alpha isoform 1						activation of protein kinase activity|cell cycle arrest|insulin receptor signaling pathway|protein export from nucleus|regulation of fatty acid oxidation	cytosol|nucleus	ATP binding|kinase binding|protein kinase activity			ovary(1)	1																		---	---	---	---
DDX42	11325	broad.mit.edu	37	17	61895513	61895513	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61895513C>T	uc002jbu.2	+	19	2829	c.2572C>T	c.(2572-2574)CGG>TGG	p.R858W	DDX42_uc002jbv.2_Missense_Mutation_p.R858W|DDX42_uc002jbx.2_Missense_Mutation_p.R594W|DDX42_uc002jby.2_Missense_Mutation_p.R404W|DDX42_uc010wps.1_Missense_Mutation_p.R226W	NM_007372	NP_031398	Q86XP3	DDX42_HUMAN	DEAD box polypeptide 42 protein	858	Gly-rich.|His-rich.				protein localization|regulation of anti-apoptosis	Cajal body|cytoplasm|nuclear speck	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding	p.R858W(1)		ovary(2)|skin(2)|large_intestine(1)	5																		---	---	---	---
GH1	2688	broad.mit.edu	37	17	61994782	61994782	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61994782C>T	uc002jdj.2	-	5	603	c.541G>A	c.(541-543)GCA>ACA	p.A181T	GH1_uc002jdi.2_Missense_Mutation_p.A166T|GH1_uc002jdk.2_Missense_Mutation_p.A141T|GH1_uc002jdl.2_Missense_Mutation_p.A86T|GH1_uc002jdm.2_3'UTR|GH1_uc002jdn.2_Silent_p.T134T	NM_000515	NP_000506	P01241	SOMA_HUMAN	growth hormone 1 isoform 1	181					glucose transport|growth hormone receptor signaling pathway|JAK-STAT cascade|positive regulation of activation of JAK2 kinase activity|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of MAP kinase activity|positive regulation of multicellular organism growth|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of tyrosine phosphorylation of Stat5 protein|response to estradiol stimulus	extracellular space	growth factor activity|growth hormone receptor binding|hormone activity|metal ion binding|prolactin receptor binding				0																		---	---	---	---
CCDC46	201134	broad.mit.edu	37	17	64171179	64171179	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64171179C>T	uc002jfl.2	-	4	672	c.453G>A	c.(451-453)TCG>TCA	p.S151S	CCDC46_uc002jfm.2_Silent_p.S151S|CCDC46_uc010dep.2_Silent_p.S151S	NM_145036	NP_659473	Q8N8E3	CE112_HUMAN	coiled-coil domain containing 46 isoform a	151						centrosome					0			BRCA - Breast invasive adenocarcinoma(6;1.53e-06)															---	---	---	---
CACNG5	27091	broad.mit.edu	37	17	64873583	64873583	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:64873583A>C	uc010wqi.1	+	2	370	c.133A>C	c.(133-135)AAC>CAC	p.N45H	CACNG5_uc002jfr.2_Missense_Mutation_p.N45H|CACNG5_uc010wqj.1_Missense_Mutation_p.N45H	NM_145811	NP_665810	Q9UF02	CCG5_HUMAN	voltage-dependent calcium channel gamma-5	45					regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|postsynaptic density|postsynaptic membrane	voltage-gated calcium channel activity			pancreas(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(6;1.61e-08)															---	---	---	---
CACNG4	27092	broad.mit.edu	37	17	65026911	65026911	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65026911T>C	uc002jft.1	+	4	790	c.775T>C	c.(775-777)TCG>CCG	p.S259P		NM_014405	NP_055220	Q9UBN1	CCG4_HUMAN	voltage-dependent calcium channel gamma-4	259	Cytoplasmic (Potential).				membrane depolarization|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|endocytic vesicle membrane	voltage-gated calcium channel activity			central_nervous_system(1)	1	all_cancers(12;9.86e-11)		BRCA - Breast invasive adenocarcinoma(6;1.35e-07)															---	---	---	---
HELZ	9931	broad.mit.edu	37	17	65104694	65104694	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65104694C>T	uc010wqk.1	-	30	4828	c.4641G>A	c.(4639-4641)CCG>CCA	p.P1547P	HELZ_uc002jfv.3_RNA|HELZ_uc002jfx.3_Silent_p.P1546P|HELZ_uc010der.2_Silent_p.P90P	NM_014877	NP_055692			helicase with zinc finger domain											ovary(1)|pancreas(1)	2	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)																	---	---	---	---
HELZ	9931	broad.mit.edu	37	17	65105699	65105699	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65105699T>G	uc010wqk.1	-	29	4212	c.4025A>C	c.(4024-4026)CAC>CCC	p.H1342P	HELZ_uc002jfv.3_RNA|HELZ_uc002jfx.3_Missense_Mutation_p.H1341P|HELZ_uc010der.2_5'UTR	NM_014877	NP_055692			helicase with zinc finger domain											ovary(1)|pancreas(1)	2	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)																	---	---	---	---
HELZ	9931	broad.mit.edu	37	17	65132315	65132315	+	Splice_Site	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65132315C>T	uc010wqk.1	-	23	3144	c.2957_splice	c.e23-1	p.G986_splice	HELZ_uc002jfv.3_Splice_Site|HELZ_uc002jfx.3_Splice_Site_p.G985_splice	NM_014877	NP_055692			helicase with zinc finger domain											ovary(1)|pancreas(1)	2	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)																	---	---	---	---
HELZ	9931	broad.mit.edu	37	17	65147324	65147324	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65147324G>A	uc010wqk.1	-	18	2384	c.2197C>T	c.(2197-2199)CGC>TGC	p.R733C	HELZ_uc002jfv.3_RNA|HELZ_uc002jfx.3_Missense_Mutation_p.R732C	NM_014877	NP_055692			helicase with zinc finger domain											ovary(1)|pancreas(1)	2	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)																	---	---	---	---
ABCA9	10350	broad.mit.edu	37	17	67022598	67022598	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67022598C>T	uc002jhu.2	-	16	2204	c.2061G>A	c.(2059-2061)GTG>GTA	p.V687V	ABCA9_uc010dez.2_Silent_p.V687V	NM_080283	NP_525022	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A, member 9	687	ABC transporter 1.				transport	integral to membrane	ATP binding|ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)	6	Breast(10;1.47e-12)																	---	---	---	---
ABCA6	23460	broad.mit.edu	37	17	67084407	67084407	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67084407C>T	uc002jhw.1	-							NM_080284	NP_525023			ATP-binding cassette, sub-family A, member 6						transport	integral to membrane	ATP binding|ATPase activity			upper_aerodigestive_tract(2)|large_intestine(2)|ovary(2)|skin(1)	7	Breast(10;5.65e-12)																	---	---	---	---
ABCA10	10349	broad.mit.edu	37	17	67171631	67171631	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67171631A>G	uc010dfa.1	-	24	3672	c.2793T>C	c.(2791-2793)GGT>GGC	p.G931G	ABCA10_uc010wqs.1_5'UTR|ABCA10_uc010wqt.1_RNA	NM_080282	NP_525021	Q8WWZ4	ABCAA_HUMAN	ATP-binding cassette, sub-family A, member 10	931	Helical; (Potential).				transport	integral to membrane	ATP binding|ATPase activity			ovary(2)|central_nervous_system(1)|skin(1)	4	Breast(10;6.95e-12)																	---	---	---	---
ABCA10	10349	broad.mit.edu	37	17	67181721	67181721	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67181721A>G	uc010dfa.1	-	21	3273	c.2394T>C	c.(2392-2394)ACT>ACC	p.T798T	ABCA10_uc010wqt.1_RNA|ABCA10_uc010dfb.1_Silent_p.T399T	NM_080282	NP_525021	Q8WWZ4	ABCAA_HUMAN	ATP-binding cassette, sub-family A, member 10	798					transport	integral to membrane	ATP binding|ATPase activity			ovary(2)|central_nervous_system(1)|skin(1)	4	Breast(10;6.95e-12)																	---	---	---	---
ABCA5	23461	broad.mit.edu	37	17	67273772	67273772	+	Intron	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67273772T>A	uc002jif.2	-						ABCA5_uc002jic.2_Intron|ABCA5_uc002jid.2_Intron|ABCA5_uc002jie.2_Intron|ABCA5_uc002jig.2_Intron|ABCA5_uc002jih.2_Intron|ABCA5_uc010dfe.2_Intron	NM_018672	NP_061142			ATP-binding cassette, sub-family A , member 5						cholesterol efflux|high-density lipoprotein particle remodeling|negative regulation of macrophage derived foam cell differentiation	Golgi membrane|integral to membrane|late endosome membrane|lysosomal membrane	ATP binding|ATPase activity			ovary(2)|central_nervous_system(1)|skin(1)	4	Breast(10;3.72e-11)																	---	---	---	---
ABCA5	23461	broad.mit.edu	37	17	67309289	67309289	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67309289A>G	uc002jif.2	-	2	1469	c.251T>C	c.(250-252)GTG>GCG	p.V84A	ABCA5_uc002jig.2_Missense_Mutation_p.V84A|ABCA5_uc002jih.2_Missense_Mutation_p.V84A|ABCA5_uc010dfe.2_Missense_Mutation_p.V84A	NM_018672	NP_061142	Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A , member 5	84					cholesterol efflux|high-density lipoprotein particle remodeling|negative regulation of macrophage derived foam cell differentiation	Golgi membrane|integral to membrane|late endosome membrane|lysosomal membrane	ATP binding|ATPase activity			ovary(2)|central_nervous_system(1)|skin(1)	4	Breast(10;3.72e-11)																	---	---	---	---
KCNJ2	3759	broad.mit.edu	37	17	68171334	68171334	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:68171334G>A	uc010dfg.2	+	2	555	c.154G>A	c.(154-156)GGC>AGC	p.G52S	KCNJ2_uc002jir.2_Missense_Mutation_p.G52S	NM_000891	NP_000882	P63252	IRK2_HUMAN	potassium inwardly-rectifying channel J2	52	Cytoplasmic (By similarity).				synaptic transmission	integral to plasma membrane	inward rectifier potassium channel activity|protein binding				0	Breast(10;1.64e-08)																	---	---	---	---
SLC39A11	201266	broad.mit.edu	37	17	70943972	70943972	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:70943972C>T	uc002jjb.2	-	5	464	c.349G>A	c.(349-351)GGC>AGC	p.G117S	SLC39A11_uc002jja.2_Missense_Mutation_p.G117S|SLC39A11_uc002jjc.1_Missense_Mutation_p.G117S	NM_001159770	NP_001153242	Q8N1S5	S39AB_HUMAN	solute carrier family 39, member 11 isoform 1	117					zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			ovary(1)	1																		---	---	---	---
SDK2	54549	broad.mit.edu	37	17	71420161	71420161	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:71420161C>T	uc010dfm.2	-	13	1654	c.1654G>A	c.(1654-1656)GGC>AGC	p.G552S	SDK2_uc010dfn.2_Missense_Mutation_p.G231S	NM_001144952	NP_001138424	Q58EX2	SDK2_HUMAN	sidekick 2	552	Extracellular (Potential).|Ig-like C2-type 6.				cell adhesion	integral to membrane				ovary(2)	2																		---	---	---	---
CD300LB	124599	broad.mit.edu	37	17	72522097	72522097	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72522097G>A	uc002jkx.2	-	2	284	c.271C>T	c.(271-273)CGC>TGC	p.R91C	CD300LB_uc010wqz.1_Missense_Mutation_p.R91C	NM_174892	NP_777552	A8K4G0	CLM7_HUMAN	CD300 molecule-like family member b	54	Ig-like V-type.|Extracellular (Potential).					integral to membrane|plasma membrane	receptor activity			ovary(1)	1																		---	---	---	---
C17orf77	146723	broad.mit.edu	37	17	72588516	72588516	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72588516T>C	uc002jla.1	+	3	693	c.331T>C	c.(331-333)TGT>CGT	p.C111R	CD300LD_uc002jkz.2_5'Flank	NM_152460	NP_689673	Q96MU5	CQ077_HUMAN	hypothetical protein LOC146723	111	Cys-rich.					extracellular region					0																		---	---	---	---
MIF4GD	57409	broad.mit.edu	37	17	73263654	73263654	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73263654G>A	uc002jnr.2	-	5	535	c.406C>T	c.(406-408)CTG>TTG	p.L136L	MIF4GD_uc002jno.2_Silent_p.L177L|MIF4GD_uc002jnp.2_Silent_p.L170L|MIF4GD_uc002jnq.2_Silent_p.L177L			A9UHW6	MI4GD_HUMAN	RecName: Full=MIF4G domain-containing protein; AltName: Full=SLBP-interacting protein 1;          Short=hSLIP1;	136	MIF4G.				regulation of translation|RNA metabolic process	cytoplasm|nucleus	protein C-terminus binding			ovary(1)	1	all_cancers(13;1.25e-07)|all_epithelial(9;2.63e-08)|Breast(9;1.06e-07)		all cancers(21;3.02e-07)|Epithelial(20;2.92e-06)															---	---	---	---
SLC25A19	60386	broad.mit.edu	37	17	73269663	73269663	+	Missense_Mutation	SNP	C	T	T	rs142956040		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73269663C>T	uc002jns.3	-	6	1742	c.832G>A	c.(832-834)GCC>ACC	p.A278T	SLC25A19_uc010dge.2_Missense_Mutation_p.A221T|SLC25A19_uc002jnv.3_Missense_Mutation_p.A278T|SLC25A19_uc002jnu.3_Missense_Mutation_p.A278T|SLC25A19_uc002jnw.3_Missense_Mutation_p.A278T|SLC25A19_uc002jnt.3_Missense_Mutation_p.A278T	NM_021734	NP_068380	Q9HC21	TPC_HUMAN	solute carrier family 25, member 19	278	Solcar 3.					integral to membrane|mitochondrial inner membrane	binding|deoxynucleotide transmembrane transporter activity			ovary(1)	1	all_cancers(13;5.98e-08)|all_epithelial(9;1.16e-08)|Breast(9;3.1e-08)		all cancers(21;6.82e-07)|Epithelial(20;6.86e-06)															---	---	---	---
KIAA0195	9772	broad.mit.edu	37	17	73482463	73482463	+	Missense_Mutation	SNP	G	A	A	rs143448418	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73482463G>A	uc002jnz.3	+	5	640	c.365G>A	c.(364-366)CGG>CAG	p.R122Q	KIAA0195_uc010wsa.1_Missense_Mutation_p.R132Q	NM_014738	NP_055553	Q12767	K0195_HUMAN	hypothetical protein LOC9772	122					ATP biosynthetic process|cation transport	integral to membrane	ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism			ovary(1)	1	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)															---	---	---	---
KIAA0195	9772	broad.mit.edu	37	17	73487168	73487168	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73487168G>A	uc002jnz.3	+	12	1442	c.1167G>A	c.(1165-1167)GTG>GTA	p.V389V	KIAA0195_uc010wsa.1_Silent_p.V399V|KIAA0195_uc010wsb.1_Silent_p.V41V	NM_014738	NP_055553	Q12767	K0195_HUMAN	hypothetical protein LOC9772	389					ATP biosynthetic process|cation transport	integral to membrane	ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism			ovary(1)	1	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)															---	---	---	---
CASKIN2	57513	broad.mit.edu	37	17	73502880	73502880	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73502880C>A	uc002joc.2	-	6	1036	c.486G>T	c.(484-486)AAG>AAT	p.K162N	CASKIN2_uc010wsc.1_Missense_Mutation_p.K80N|CASKIN2_uc002jod.2_Missense_Mutation_p.K162N	NM_020753	NP_065804	Q8WXE0	CSKI2_HUMAN	cask-interacting protein 2 isoform a	162	ANK 4.					cytoplasm				pancreas(1)	1	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;4.57e-07)|Epithelial(20;2.92e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)															---	---	---	---
ITGB4	3691	broad.mit.edu	37	17	73732437	73732437	+	Silent	SNP	G	T	T	rs150965180	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73732437G>T	uc002jpg.2	+	15	2017	c.1830G>T	c.(1828-1830)ACG>ACT	p.T610T	ITGB4_uc002jph.2_Silent_p.T610T|ITGB4_uc010dgo.2_Silent_p.T610T|ITGB4_uc002jpi.3_Silent_p.T610T|ITGB4_uc010dgp.1_Silent_p.T610T|ITGB4_uc002jpj.2_Silent_p.T610T|ITGB4_uc010wsh.1_Silent_p.T165T	NM_000213	NP_000204	P16144	ITB4_HUMAN	integrin beta 4 isoform 1 precursor	610	Cysteine-rich tandem repeats.|Extracellular (Potential).|IV.				cell communication|cell motility|cell-matrix adhesion|hemidesmosome assembly|integrin-mediated signaling pathway|multicellular organismal development|response to wounding	cell leading edge|cell surface|hemidesmosome|integrin complex	protein binding|receptor activity			lung(4)	4	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)															---	---	---	---
ITGB4	3691	broad.mit.edu	37	17	73752689	73752689	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73752689C>T	uc002jpg.2	+	36	5075	c.4888C>T	c.(4888-4890)CCC>TCC	p.P1630S	ITGB4_uc002jph.2_Missense_Mutation_p.P1560S|ITGB4_uc002jpi.3_Missense_Mutation_p.P1560S|ITGB4_uc002jpj.2_Missense_Mutation_p.P1613S|GALK1_uc010wsi.1_Intron	NM_000213	NP_000204	P16144	ITB4_HUMAN	integrin beta 4 isoform 1 precursor	1630	Cytoplasmic (Potential).				cell communication|cell motility|cell-matrix adhesion|hemidesmosome assembly|integrin-mediated signaling pathway|multicellular organismal development|response to wounding	cell leading edge|cell surface|hemidesmosome|integrin complex	protein binding|receptor activity			lung(4)	4	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)															---	---	---	---
GALK1	2584	broad.mit.edu	37	17	73758878	73758878	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73758878T>C	uc010wsi.1	-	5	763	c.700A>G	c.(700-702)AGC>GGC	p.S234G	GALK1_uc002jpk.2_Missense_Mutation_p.S234G|GALK1_uc010wsj.1_3'UTR	NM_000154	NP_000145	P51570	GALK1_HUMAN	galactokinase 1	234					galactose catabolic process	cytosol	ATP binding|galactokinase activity|galactose binding				0	all_cancers(13;1.5e-07)		all cancers(21;1.03e-06)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)															---	---	---	---
SRP68	6730	broad.mit.edu	37	17	74057192	74057192	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74057192A>G	uc002jqk.1	-	6	788	c.753T>C	c.(751-753)ATT>ATC	p.I251I	SRP68_uc010wsu.1_Silent_p.I150I|SRP68_uc002jql.1_Silent_p.I213I	NM_014230	NP_055045	Q9UHB9	SRP68_HUMAN	signal recognition particle 68kDa	251					response to drug	cytosol|endoplasmic reticulum|nucleolus|ribosome|signal recognition particle, endoplasmic reticulum targeting	RNA binding|signal recognition particle binding			ovary(1)	1																		---	---	---	---
ZACN	353174	broad.mit.edu	37	17	74075598	74075598	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74075598C>A	uc002jqn.2	+	2	259	c.176C>A	c.(175-177)CCC>CAC	p.P59H	ZACN_uc002jqo.2_RNA|ZACN_uc010dgu.2_RNA	NM_180990	NP_851321	Q401N2	ZACN_HUMAN	zinc activated ligand-gated ion channel	59	Extracellular (Potential).				response to zinc ion	integral to membrane|membrane fraction|plasma membrane|postsynaptic membrane	extracellular ligand-gated ion channel activity|receptor activity				0																		---	---	---	---
SPHK1	8877	broad.mit.edu	37	17	74382931	74382931	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74382931T>C	uc002jrf.1	+	8	1228	c.419T>C	c.(418-420)CTA>CCA	p.L140P	SPHK1_uc002jrg.1_Missense_Mutation_p.L89P|SPHK1_uc002jrh.2_Missense_Mutation_p.L154P|SPHK1_uc002jrj.2_Missense_Mutation_p.L226P|SPHK1_uc002jri.2_Missense_Mutation_p.L140P|SPHK1_uc002jrk.3_Missense_Mutation_p.L140P|uc010wtd.1_RNA	NM_001142602	NP_001136074	Q9NYA1	SPHK1_HUMAN	sphingosine kinase 1 isoform 3	140	DAGKc.				'de novo' posttranslational protein folding|activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|anti-apoptosis|calcium-mediated signaling|positive regulation of angiogenesis|positive regulation of cell growth|positive regulation of cell migration|positive regulation of fibroblast proliferation|positive regulation of mitotic cell cycle|positive regulation of NF-kappaB import into nucleus|positive regulation of NF-kappaB transcription factor activity|positive regulation of protein ubiquitination|positive regulation of smooth muscle contraction|regulation of tumor necrosis factor-mediated signaling pathway|sphingoid catabolic process|sphingosine metabolic process	cytosol|membrane fraction|nucleus|plasma membrane|soluble fraction	ATP binding|calmodulin binding|D-erythro-sphingosine kinase activity|diacylglycerol kinase activity|DNA binding|magnesium ion binding|protein phosphatase 2A binding|sphinganine kinase activity			kidney(1)	1																		---	---	---	---
MGAT5B	146664	broad.mit.edu	37	17	74944855	74944855	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74944855C>T	uc002jti.2	+	16	2444	c.2341C>T	c.(2341-2343)CGC>TGC	p.R781C	MGAT5B_uc002jth.2_Missense_Mutation_p.R770C|MGAT5B_uc002jtj.2_Missense_Mutation_p.R177C	NM_198955	NP_945193	Q3V5L5	MGT5B_HUMAN	N-acetylglucosaminyltranferase VB isoform 2	772	Lumenal (Potential).					Golgi membrane|integral to membrane	alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase activity|metal ion binding			ovary(2)|skin(1)	3																		---	---	---	---
TNRC6C	57690	broad.mit.edu	37	17	76098572	76098572	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76098572G>A	uc002jud.2	+	19	5119	c.4519G>A	c.(4519-4521)GAC>AAC	p.D1507N	TNRC6C_uc002juf.2_Missense_Mutation_p.D1543N	NM_018996	NP_061869	Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C isoform 2	1507	Sufficient for translational repression when tethered to a target mRNA.				gene silencing by RNA|regulation of translation		nucleotide binding|RNA binding			ovary(1)|central_nervous_system(1)	2			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	76481646	76481646	+	IGR	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76481646G>T								DNAH17 (12790 upstream) : CYTH1 (188485 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	17	76482421	76482421	+	IGR	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76482421A>G								DNAH17 (13565 upstream) : CYTH1 (187710 downstream)																																			---	---	---	---
CANT1	124583	broad.mit.edu	37	17	76993130	76993130	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76993130C>T	uc002jwn.2	-	4	1014	c.575G>A	c.(574-576)GGC>GAC	p.G192D	CANT1_uc002jwk.2_Missense_Mutation_p.G192D|CANT1_uc002jwj.2_Missense_Mutation_p.G192D|CANT1_uc002jwl.2_RNA|CANT1_uc002jwm.1_5'Flank	NM_001159772	NP_001153244	Q8WVQ1	CANT1_HUMAN	calcium activated nucleotidase 1	192	Lumenal (Potential).				positive regulation of I-kappaB kinase/NF-kappaB cascade	endoplasmic reticulum membrane|Golgi cisterna membrane|integral to membrane	calcium ion binding|nucleoside-diphosphatase activity|signal transducer activity				0			BRCA - Breast invasive adenocarcinoma(99;0.0362)|OV - Ovarian serous cystadenocarcinoma(97;0.139)					T	ETV4	prostate								---	---	---	---
C1QTNF1	114897	broad.mit.edu	37	17	77040109	77040109	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77040109C>A	uc002jwp.2	+	2	399	c.59C>A	c.(58-60)TCT>TAT	p.S20Y	C1QTNF1_uc002jwq.2_Intron|C1QTNF1_uc002jwr.3_Missense_Mutation_p.S30Y|C1QTNF1_uc002jws.2_Missense_Mutation_p.S20Y|C1QTNF1_uc002jwt.2_Missense_Mutation_p.S118Y	NM_030968	NP_112230	Q9BXJ1	C1QT1_HUMAN	C1q and tumor necrosis factor related protein 1	20						collagen				ovary(1)	1			BRCA - Breast invasive adenocarcinoma(99;0.0294)|OV - Ovarian serous cystadenocarcinoma(97;0.201)															---	---	---	---
C1QTNF1	114897	broad.mit.edu	37	17	77044016	77044016	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77044016T>C	uc002jwp.2	+	4	1032	c.692T>C	c.(691-693)ATG>ACG	p.M231T	C1QTNF1_uc002jwq.2_Missense_Mutation_p.M149T|C1QTNF1_uc002jwr.3_Missense_Mutation_p.M241T|C1QTNF1_uc002jws.2_Missense_Mutation_p.M231T|C1QTNF1_uc002jwt.2_Missense_Mutation_p.M329T	NM_030968	NP_112230	Q9BXJ1	C1QT1_HUMAN	C1q and tumor necrosis factor related protein 1	231	C1q.					collagen				ovary(1)	1			BRCA - Breast invasive adenocarcinoma(99;0.0294)|OV - Ovarian serous cystadenocarcinoma(97;0.201)															---	---	---	---
ENPP7	339221	broad.mit.edu	37	17	77709367	77709367	+	Missense_Mutation	SNP	G	A	A	rs150460869		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77709367G>A	uc002jxa.2	+	3	945	c.925G>A	c.(925-927)GTC>ATC	p.V309I		NM_178543	NP_848638	Q6UWV6	ENPP7_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase	309					negative regulation of cell proliferation|negative regulation of DNA replication|sphingomyelin metabolic process	Golgi apparatus|integral to membrane|microvillus	sphingomyelin phosphodiesterase activity			central_nervous_system(2)|ovary(1)	3			OV - Ovarian serous cystadenocarcinoma(97;0.016)|BRCA - Breast invasive adenocarcinoma(99;0.0224)															---	---	---	---
CARD14	79092	broad.mit.edu	37	17	78176149	78176149	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78176149C>T	uc002jxw.1	+	15	2344	c.2149C>T	c.(2149-2151)CAT>TAT	p.H717Y	CARD14_uc002jxt.1_RNA|CARD14_uc002jxv.2_Missense_Mutation_p.H717Y|CARD14_uc010wud.1_RNA	NM_024110	NP_077015	Q9BXL6	CAR14_HUMAN	caspase recruitment domain protein 14 isoform 1	717					activation of NF-kappaB-inducing kinase activity|positive regulation of protein phosphorylation|regulation of apoptosis	aggresome|cytoplasm|plasma membrane	CARD domain binding			ovary(4)|skin(1)	5	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.017)|BRCA - Breast invasive adenocarcinoma(99;0.0908)															---	---	---	---
Unknown	0	broad.mit.edu	37	17	78280977	78280977	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78280977G>A	uc002jyf.2	+	13	2620	c.2477G>A	c.(2476-2478)CGA>CAA	p.R826Q	uc002jyg.1_Missense_Mutation_p.R557Q	NM_020954	NP_066005			hypothetical protein LOC57714																														---	---	---	---
RNF213	57674	broad.mit.edu	37	17	78321405	78321405	+	Silent	SNP	G	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78321405G>C	uc002jyh.1	+	4	3712	c.3489G>C	c.(3487-3489)GTG>GTC	p.V1163V		NM_020914	NP_065965	Q9HCF4	ALO17_HUMAN	ring finger protein 213	Error:Variant_position_missing_in_Q9HCF4_after_alignment										ovary(8)|lung(6)|breast(3)|large_intestine(2)|central_nervous_system(1)|pancreas(1)	21	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)															---	---	---	---
RNF213	57674	broad.mit.edu	37	17	78326838	78326838	+	Missense_Mutation	SNP	G	A	A	rs143778568		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78326838G>A	uc002jyh.1	+	8	4844	c.4621G>A	c.(4621-4623)GCG>ACG	p.A1541T	uc002jyi.1_RNA|RNF213_uc010dhw.1_5'Flank	NM_020914	NP_065965	Q9HCF4	ALO17_HUMAN	ring finger protein 213	Error:Variant_position_missing_in_Q9HCF4_after_alignment										ovary(8)|lung(6)|breast(3)|large_intestine(2)|central_nervous_system(1)|pancreas(1)	21	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)															---	---	---	---
RPTOR	57521	broad.mit.edu	37	17	78921083	78921083	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78921083G>A	uc002jyt.1	+	27	4002	c.3197G>A	c.(3196-3198)CGG>CAG	p.R1066Q	RPTOR_uc010wug.1_Missense_Mutation_p.R908Q|RPTOR_uc002jyu.1_5'Flank	NM_020761	NP_065812	Q8N122	RPTOR_HUMAN	raptor isoform 1	1066	WD 2.				cell cycle arrest|cell growth|cellular response to amino acid stimulus|cellular response to nutrient levels|insulin receptor signaling pathway|positive regulation of protein serine/threonine kinase activity|positive regulation of TOR signaling cascade|TOR signaling cascade	cytosol|lysosome|TORC1 complex	protein complex binding			lung(4)|urinary_tract(1)|ovary(1)	6																		---	---	---	---
C17orf56	146705	broad.mit.edu	37	17	79205370	79205370	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79205370G>A	uc002jzu.1	-						C17orf56_uc002jzr.1_5'Flank|C17orf56_uc002jzs.1_Intron|C17orf56_uc002jzt.1_Intron|C17orf56_uc002jzv.1_Intron|uc002jzw.1_RNA	NM_144679	NP_653280			hypothetical protein LOC146705							integral to membrane					0	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)															---	---	---	---
BAHCC1	57597	broad.mit.edu	37	17	79414083	79414083	+	Missense_Mutation	SNP	G	A	A	rs140605765	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79414083G>A	uc002kaf.2	+	9	3185	c.3185G>A	c.(3184-3186)CGC>CAC	p.R1062H	BAHCC1_uc002kae.2_Missense_Mutation_p.R292H	NM_001080519	NP_001073988	Q9P281	BAHC1_HUMAN	BAH domain and coiled-coil containing 1	1062							DNA binding			ovary(1)	1	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0224)|OV - Ovarian serous cystadenocarcinoma(97;0.116)															---	---	---	---
ACTG1	71	broad.mit.edu	37	17	79478559	79478559	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79478559T>C	uc002kaj.1	-	3	482	c.457A>G	c.(457-459)ATG>GTG	p.M153V	ACTG1_uc002kah.1_Missense_Mutation_p.M31V|ACTG1_uc002kai.1_Missense_Mutation_p.M110V|ACTG1_uc002kak.1_Missense_Mutation_p.M153V|ACTG1_uc010wun.1_Missense_Mutation_p.M153V|ACTG1_uc002kal.1_Missense_Mutation_p.M153V|ACTG1_uc002kag.2_RNA	NM_001614	NP_001605	P63261	ACTG_HUMAN	actin, gamma 1 propeptide	153					adherens junction organization|axon guidance|blood coagulation|cell junction assembly|cellular component movement	cytoskeleton|cytosol	ATP binding|identical protein binding			ovary(1)|central_nervous_system(1)	2	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0547)															---	---	---	---
NPLOC4	55666	broad.mit.edu	37	17	79564295	79564295	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79564295A>G	uc002kat.3	-	10	1151	c.969T>C	c.(967-969)GGT>GGC	p.G323G	NPLOC4_uc002kau.3_Silent_p.G323G|NPLOC4_uc010wur.1_Silent_p.G162G	NM_017921	NP_060391	Q8TAT6	NPL4_HUMAN	nuclear protein localization 4	323					cellular membrane fusion|ER-associated protein catabolic process|Golgi organization	cytosol|endoplasmic reticulum|nuclear outer membrane-endoplasmic reticulum membrane network|nucleus	zinc ion binding			ovary(1)|central_nervous_system(1)	2	all_neural(118;0.0878)|Melanoma(429;0.242)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)															---	---	---	---
NPLOC4	55666	broad.mit.edu	37	17	79571667	79571667	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79571667C>T	uc002kat.3	-	8	923	c.741G>A	c.(739-741)CAG>CAA	p.Q247Q	NPLOC4_uc002kau.3_Silent_p.Q247Q|NPLOC4_uc010wur.1_Silent_p.Q86Q	NM_017921	NP_060391	Q8TAT6	NPL4_HUMAN	nuclear protein localization 4	247					cellular membrane fusion|ER-associated protein catabolic process|Golgi organization	cytosol|endoplasmic reticulum|nuclear outer membrane-endoplasmic reticulum membrane network|nucleus	zinc ion binding			ovary(1)|central_nervous_system(1)	2	all_neural(118;0.0878)|Melanoma(429;0.242)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)															---	---	---	---
PDE6G	5148	broad.mit.edu	37	17	79620312	79620312	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79620312A>G	uc002kay.3	-	2	168	c.24T>C	c.(22-24)GCT>GCC	p.A8A	PDE6G_uc002kaz.3_Intron	NM_002602	NP_002593	P18545	CNRG_HUMAN	phosphodiesterase 6G	8					platelet activation|visual perception	cytosol	3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|enzyme inhibitor activity				0	all_neural(118;0.0878)|all_lung(278;0.175)|Lung NSC(278;0.192)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)															---	---	---	---
HGS	9146	broad.mit.edu	37	17	79662914	79662914	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79662914C>T	uc002kbg.2	+	15	1355	c.1278C>T	c.(1276-1278)AAC>AAT	p.N426N		NM_004712	NP_004703	O14964	HGS_HUMAN	hepatocyte growth factor-regulated tyrosine	426	Interaction with SNX1 (By similarity).				cellular membrane organization|endosome transport|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of cell proliferation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of JAK-STAT cascade|regulation of protein catabolic process	cytosol|early endosome membrane|multivesicular body membrane	metal ion binding|protein domain specific binding			ovary(1)	1	all_neural(118;0.0878)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)															---	---	---	---
ARHGDIA	396	broad.mit.edu	37	17	79827735	79827735	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79827735C>T	uc002kbp.2	-	1	111	c.72G>A	c.(70-72)TCG>TCA	p.S24S	ARHGDIA_uc002kjk.1_5'Flank|ARHGDIA_uc002kbq.2_Silent_p.S24S|ARHGDIA_uc002kbr.2_Silent_p.S24S|ARHGDIA_uc002kbs.1_Silent_p.S24S|ARHGDIA_uc002kbt.1_Silent_p.S24S|ARHGDIA_uc010dig.1_RNA	NM_004309	NP_004300	P52565	GDIR1_HUMAN	Rho GDP dissociation inhibitor (GDI) alpha	24					anti-apoptosis|cellular component movement|negative regulation of axonogenesis|negative regulation of cell adhesion|nerve growth factor receptor signaling pathway|positive regulation of axonogenesis|regulation of small GTPase mediated signal transduction|Rho protein signal transduction	cytoskeleton|cytosol	GTPase activator activity|identical protein binding|Rho GDP-dissociation inhibitor activity				0	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)															---	---	---	---
PCYT2	5833	broad.mit.edu	37	17	79862804	79862804	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79862804G>A	uc002kcf.1	-	13	1138	c.1075C>T	c.(1075-1077)CGA>TGA	p.R359*	PCYT2_uc010wva.1_Nonsense_Mutation_p.R327*|PCYT2_uc010wvb.1_Nonsense_Mutation_p.R327*|PCYT2_uc002kce.1_Nonsense_Mutation_p.R281*|PCYT2_uc002kcg.1_Nonsense_Mutation_p.R388*|PCYT2_uc002kch.1_Nonsense_Mutation_p.R377*|PCYT2_uc002kci.1_Nonsense_Mutation_p.R318*|PCYT2_uc010dii.1_Nonsense_Mutation_p.R337*|PCYT2_uc010wvc.1_Nonsense_Mutation_p.R281*	NM_002861	NP_002852	Q99447	PCY2_HUMAN	phosphate cytidylyltransferase 2, ethanolamine	359					phospholipid biosynthetic process		ethanolamine-phosphate cytidylyltransferase activity				0	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)															---	---	---	---
NOTUM	147111	broad.mit.edu	37	17	79914748	79914748	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79914748C>T	uc010wvg.1	-							NM_178493	NP_848588			notum pectinacetylesterase homolog precursor							extracellular region	hydrolase activity				0	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)															---	---	---	---
CCDC57	284001	broad.mit.edu	37	17	80129597	80129597	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80129597C>T	uc002kdz.1	-	13	2217	c.1862G>A	c.(1861-1863)CGC>CAC	p.R621H	CCDC57_uc002kdx.1_Missense_Mutation_p.R621H|CCDC57_uc010dik.1_Missense_Mutation_p.R129H	NM_198082	NP_932348	Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57	621										ovary(2)	2	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)															---	---	---	---
CCDC57	284001	broad.mit.edu	37	17	80159575	80159575	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80159575C>A	uc002kdz.1	-	3	601	c.246G>T	c.(244-246)AGG>AGT	p.R82S	CCDC57_uc002kdx.1_Missense_Mutation_p.R82S	NM_198082	NP_932348	Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57	82	Potential.									ovary(2)	2	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)															---	---	---	---
CSNK1D	1453	broad.mit.edu	37	17	80209275	80209275	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80209275C>T	uc002kej.2	-	6	1181	c.865G>A	c.(865-867)GAC>AAC	p.D289N	SLC16A3_uc002kee.2_Intron|CSNK1D_uc002kef.2_Missense_Mutation_p.D289N|CSNK1D_uc002kei.2_Missense_Mutation_p.D289N|CSNK1D_uc010wvj.1_Missense_Mutation_p.D86N|CSNK1D_uc010dil.2_RNA|CSNK1D_uc002keh.2_Missense_Mutation_p.D154N|CSNK1D_uc010dim.1_Missense_Mutation_p.D86N	NM_001893	NP_001884	P48730	KC1D_HUMAN	casein kinase 1, delta isoform 1	289					circadian regulation of gene expression|DNA repair|G2/M transition of mitotic cell cycle|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|regulation of circadian rhythm|Wnt receptor signaling pathway	centrosome|cytosol|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			breast(2)	2	Breast(20;0.00136)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.227)		OV - Ovarian serous cystadenocarcinoma(97;0.00463)|BRCA - Breast invasive adenocarcinoma(99;0.0155)															---	---	---	---
CSNK1D	1453	broad.mit.edu	37	17	80211059	80211059	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80211059T>C	uc002kej.2	-	4	714	c.398A>G	c.(397-399)AAC>AGC	p.N133S	SLC16A3_uc002kee.2_Intron|CSNK1D_uc002kef.2_Missense_Mutation_p.N133S|CSNK1D_uc002kei.2_Missense_Mutation_p.N133S|CSNK1D_uc010wvj.1_Intron|CSNK1D_uc010dil.2_5'Flank|CSNK1D_uc002keh.2_5'UTR|CSNK1D_uc010dim.1_5'Flank	NM_001893	NP_001884	P48730	KC1D_HUMAN	casein kinase 1, delta isoform 1	133	Protein kinase.				circadian regulation of gene expression|DNA repair|G2/M transition of mitotic cell cycle|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein phosphorylation|regulation of circadian rhythm|Wnt receptor signaling pathway	centrosome|cytosol|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			breast(2)	2	Breast(20;0.00136)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.227)		OV - Ovarian serous cystadenocarcinoma(97;0.00463)|BRCA - Breast invasive adenocarcinoma(99;0.0155)															---	---	---	---
CD7	924	broad.mit.edu	37	17	80273265	80273265	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80273265A>G	uc002kel.1	-	4	764	c.655T>C	c.(655-657)TGT>CGT	p.C219R		NM_006137	NP_006128	P09564	CD7_HUMAN	CD7 antigen precursor	219	Cytoplasmic (Probable).				immune response|T cell activation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to membrane|membrane fraction|plasma membrane	receptor activity				0	Breast(20;0.000675)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.249)		OV - Ovarian serous cystadenocarcinoma(97;0.00463)|BRCA - Breast invasive adenocarcinoma(99;0.0667)															---	---	---	---
CD7	924	broad.mit.edu	37	17	80274724	80274724	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80274724G>A	uc002kel.1	-	2	325	c.216C>T	c.(214-216)TAC>TAT	p.Y72Y	CD7_uc010din.2_Silent_p.Y72Y|CD7_uc002kem.2_Nonsense_Mutation_p.R54*|CD7_uc010wvk.1_Silent_p.Y72Y	NM_006137	NP_006128	P09564	CD7_HUMAN	CD7 antigen precursor	72	Ig-like.|Extracellular (Probable).				immune response|T cell activation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to membrane|membrane fraction|plasma membrane	receptor activity				0	Breast(20;0.000675)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.249)		OV - Ovarian serous cystadenocarcinoma(97;0.00463)|BRCA - Breast invasive adenocarcinoma(99;0.0667)															---	---	---	---
C17orf101	79701	broad.mit.edu	37	17	80373453	80373453	+	Missense_Mutation	SNP	G	A	A	rs61742456	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80373453G>A	uc002keu.1	-	2	226	c.125C>T	c.(124-126)CCG>CTG	p.P42L	C17orf101_uc002ket.1_Missense_Mutation_p.P42L|C17orf101_uc010dip.1_RNA|HEXDC_uc002kev.3_5'Flank|HEXDC_uc010diq.2_5'Flank	NM_024648	NP_078924	Q6PK18	CQ101_HUMAN	hypothetical protein LOC79701 isoform 1	42	Cytoplasmic (Potential).					integral to membrane	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			ovary(1)	1																		---	---	---	---
RAB40B	10966	broad.mit.edu	37	17	80656435	80656435	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80656435A>G	uc002kft.2	-	1	164	c.38T>C	c.(37-39)TTT>TCT	p.F13S	RAB40B_uc002kfs.2_5'Flank|RAB40B_uc010wvq.1_RNA	NM_006822	NP_006813	Q12829	RB40B_HUMAN	RAB40B, member RAS oncogene family	13					protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding			central_nervous_system(1)	1	Breast(20;0.00132)|all_neural(118;0.0952)	all_cancers(8;0.072)|all_epithelial(8;0.139)	BRCA - Breast invasive adenocarcinoma(99;0.0262)|OV - Ovarian serous cystadenocarcinoma(97;0.061)															---	---	---	---
TBCD	6904	broad.mit.edu	37	17	80772736	80772736	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80772736C>T	uc002kfz.2	+	13	1374	c.1244C>T	c.(1243-1245)GCG>GTG	p.A415V	TBCD_uc002kfx.1_Missense_Mutation_p.A398V|TBCD_uc002kfy.1_Missense_Mutation_p.A415V	NM_005993	NP_005984	Q9BTW9	TBCD_HUMAN	beta-tubulin cofactor D	415					'de novo' posttranslational protein folding|adherens junction assembly|negative regulation of cell-substrate adhesion|negative regulation of microtubule polymerization|post-chaperonin tubulin folding pathway|tight junction assembly	adherens junction|cytoplasm|lateral plasma membrane|microtubule|tight junction	beta-tubulin binding|chaperone binding|GTPase activator activity				0	Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)															---	---	---	---
THOC1	9984	broad.mit.edu	37	18	214899	214899	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:214899T>C	uc002kkj.3	-	21	1741	c.1701A>G	c.(1699-1701)AAA>AAG	p.K567K	THOC1_uc002kkk.3_RNA|THOC1_uc002kkh.3_Silent_p.K191K	NM_005131	NP_005122	Q96FV9	THOC1_HUMAN	THO complex 1	567					apoptosis|intronless viral mRNA export from host nucleus|mRNA processing|regulation of transcription elongation, DNA-dependent|RNA splicing|signal transduction|transcription, DNA-dependent	cytoplasm|nuclear matrix|nuclear speck|THO complex part of transcription export complex	DNA binding|protein binding|RNA binding			ovary(1)	1		all_cancers(4;0.0896)|Myeloproliferative disorder(11;0.0412)																---	---	---	---
SMCHD1	23347	broad.mit.edu	37	18	2718379	2718379	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2718379A>G	uc002klm.3	+	19	2594	c.2405A>G	c.(2404-2406)GAC>GGC	p.D802G	SMCHD1_uc002klk.3_RNA|SMCHD1_uc002kll.3_RNA	NM_015295	NP_056110	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible	802					chromosome organization		ATP binding				0																		---	---	---	---
SMCHD1	23347	broad.mit.edu	37	18	2802518	2802518	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:2802518T>C	uc002klm.3	+						SMCHD1_uc002klk.3_Intron|SMCHD1_uc002kll.3_Intron	NM_015295	NP_056110			structural maintenance of chromosomes flexible						chromosome organization		ATP binding				0																		---	---	---	---
EPB41L3	23136	broad.mit.edu	37	18	5630551	5630551	+	5'UTR	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:5630551C>T	uc002kmv.1	-	1					EPB41L3_uc010dkq.1_5'Flank					Homo sapiens mRNA for KIAA0987 protein, partial cds.						cortical actin cytoskeleton organization	cell-cell junction|cytoplasm|cytoskeleton|extrinsic to membrane	actin binding|structural molecule activity			ovary(5)	5																		---	---	---	---
LAMA1	284217	broad.mit.edu	37	18	6950818	6950818	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6950818G>A	uc002knm.2	-	58	8454	c.8360C>T	c.(8359-8361)TCT>TTT	p.S2787F	LAMA1_uc002knk.2_Missense_Mutation_p.S117F|LAMA1_uc002knl.2_Missense_Mutation_p.S240F|LAMA1_uc010wzj.1_Missense_Mutation_p.S2263F	NM_005559	NP_005550	P25391	LAMA1_HUMAN	laminin, alpha 1 precursor	2787	Laminin G-like 4.				axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|upper_aerodigestive_tract(2)|breast(2)|skin(2)|pancreas(2)|central_nervous_system(1)	21		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
LAMA1	284217	broad.mit.edu	37	18	6985263	6985263	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:6985263A>T	uc002knm.2	-	39	5727	c.5633T>A	c.(5632-5634)TTC>TAC	p.F1878Y	LAMA1_uc010wzj.1_Missense_Mutation_p.F1354Y	NM_005559	NP_005550	P25391	LAMA1_HUMAN	laminin, alpha 1 precursor	1878	Domain II and I.				axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|upper_aerodigestive_tract(2)|breast(2)|skin(2)|pancreas(2)|central_nervous_system(1)	21		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
LAMA1	284217	broad.mit.edu	37	18	7023236	7023236	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7023236G>A	uc002knm.2	-	19	2722	c.2628C>T	c.(2626-2628)AAC>AAT	p.N876N	LAMA1_uc010wzj.1_Silent_p.N352N	NM_005559	NP_005550	P25391	LAMA1_HUMAN	laminin, alpha 1 precursor	876	Laminin EGF-like 8.				axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|upper_aerodigestive_tract(2)|breast(2)|skin(2)|pancreas(2)|central_nervous_system(1)	21		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
LRRC30	339291	broad.mit.edu	37	18	7231156	7231156	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:7231156G>T	uc010wzk.1	+	1	20	c.20G>T	c.(19-21)AGG>ATG	p.R7M		NM_001105581	NP_001099051	A6NM36	LRC30_HUMAN	leucine rich repeat containing 30	7										ovary(1)|liver(1)	2																		---	---	---	---
PTPRM	5797	broad.mit.edu	37	18	8376470	8376470	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:8376470G>T	uc002knn.3	+	24	3801	c.3298G>T	c.(3298-3300)GGG>TGG	p.G1100W	PTPRM_uc010dkv.2_Missense_Mutation_p.G1113W|PTPRM_uc010wzl.1_Missense_Mutation_p.G887W	NM_002845	NP_002836	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	1100	Substrate binding (By similarity).|Tyrosine-protein phosphatase 1.|Cytoplasmic (Potential).				homophilic cell adhesion|negative regulation of angiogenesis|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|response to drug|retina layer formation|retinal ganglion cell axon guidance	cell-cell adherens junction|integral to plasma membrane|lamellipodium|perinuclear region of cytoplasm	cadherin binding|transmembrane receptor protein tyrosine phosphatase activity			lung(3)|ovary(2)|central_nervous_system(1)	6		Colorectal(10;0.234)																---	---	---	---
CHMP1B	57132	broad.mit.edu	37	18	11851713	11851713	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:11851713T>C	uc002kqe.2	+	1	325	c.203T>C	c.(202-204)ATG>ACG	p.M68T	GNAL_uc002kqc.2_Intron|GNAL_uc010dkz.2_Intron|GNAL_uc002kqd.2_Intron	NM_020412	NP_065145	Q7LBR1	CHM1B_HUMAN	chromatin modifying protein 1B	68					cell cycle|cell division|protein transport	cytosol|late endosome membrane	protein domain specific binding				0																		---	---	---	---
CEP192	55125	broad.mit.edu	37	18	13056189	13056189	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13056189T>C	uc010xac.1	+	19	3680	c.3600T>C	c.(3598-3600)AGT>AGC	p.S1200S	CEP192_uc010dlf.1_RNA|CEP192_uc010xad.1_Silent_p.S725S|CEP192_uc002kru.2_RNA|CEP192_uc002krv.2_5'UTR|CEP192_uc002krs.1_Silent_p.S941S	NM_032142	NP_115518	E9PF99	E9PF99_HUMAN	centrosomal protein 192kDa	1200										ovary(4)|pancreas(1)	5																		---	---	---	---
CEP192	55125	broad.mit.edu	37	18	13073070	13073070	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13073070A>G	uc010xac.1	+	30	5582	c.5502A>G	c.(5500-5502)CCA>CCG	p.P1834P	CEP192_uc010dlf.1_RNA|CEP192_uc010xad.1_Silent_p.P1359P|CEP192_uc002kru.2_RNA|CEP192_uc002krv.2_Silent_p.P256P|CEP192_uc002krw.2_5'UTR|CEP192_uc002krx.2_5'UTR	NM_032142	NP_115518	E9PF99	E9PF99_HUMAN	centrosomal protein 192kDa	1834										ovary(4)|pancreas(1)	5																		---	---	---	---
CEP192	55125	broad.mit.edu	37	18	13096260	13096260	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13096260G>T	uc010xac.1	+	36	6591	c.6511G>T	c.(6511-6513)GCG>TCG	p.A2171S	CEP192_uc010dlf.1_RNA|CEP192_uc010xad.1_Missense_Mutation_p.A1696S|CEP192_uc002kru.2_RNA|CEP192_uc002krv.2_Missense_Mutation_p.A593S|CEP192_uc002krw.2_Missense_Mutation_p.A320S|CEP192_uc002krx.2_Missense_Mutation_p.A175S|CEP192_uc002kry.2_RNA	NM_032142	NP_115518	E9PF99	E9PF99_HUMAN	centrosomal protein 192kDa	2171										ovary(4)|pancreas(1)	5																		---	---	---	---
C18orf19	125228	broad.mit.edu	37	18	13666696	13666696	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:13666696C>T	uc010dlh.2	-	5	1034	c.602G>A	c.(601-603)CGG>CAG	p.R201Q	C18orf19_uc010dlg.2_Missense_Mutation_p.G164S|C18orf19_uc010dli.2_Missense_Mutation_p.R201Q|C18orf19_uc002ksj.3_Missense_Mutation_p.R201Q|C18orf19_uc010dlj.2_RNA	NM_001098801	NP_001092271	Q96ND0	CR019_HUMAN	hypothetical protein LOC125228	201	DUF1279.					integral to membrane				breast(2)	2																		---	---	---	---
Unknown	0	broad.mit.edu	37	18	14183999	14183999	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:14183999T>C	uc010xag.1	+	3	688	c.390T>C	c.(388-390)GAT>GAC	p.D130D	uc002ksv.1_Missense_Mutation_p.I9T					RecName: Full=Putative ankyrin repeat domain-containing protein 20A5;																														---	---	---	---
SNRPD1	6632	broad.mit.edu	37	18	19209067	19209067	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19209067C>A	uc002ktj.1	+	4	459	c.328C>A	c.(328-330)CGT>AGT	p.R110S		NM_006938	NP_008869	P62314	SMD1_HUMAN	small nuclear ribonucleoprotein D1 polypeptide	110	Arg/Lys-rich (basic).				ncRNA metabolic process|spliceosomal snRNP assembly|spliceosome assembly	catalytic step 2 spliceosome|cytosol|nucleoplasm|small nuclear ribonucleoprotein complex|U12-type spliceosomal complex	protein binding|RNA binding				0																		---	---	---	---
CTAGE1	64693	broad.mit.edu	37	18	19995558	19995558	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:19995558G>A	uc002ktv.1	-	1	2321	c.2217C>T	c.(2215-2217)TTC>TTT	p.F739F		NM_172241	NP_758441	Q96RT6	CTGE2_HUMAN	cutaneous T-cell lymphoma-associated antigen 1	739	Pro-rich.					integral to membrane				ovary(1)	1	all_cancers(21;0.000361)|all_epithelial(16;9.61e-06)|Colorectal(14;0.0533)|Lung NSC(20;0.0605)|Ovarian(2;0.116)|all_lung(20;0.135)																	---	---	---	---
CABLES1	91768	broad.mit.edu	37	18	20815965	20815965	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:20815965G>A	uc002kuc.2	+	6	1292	c.1292G>A	c.(1291-1293)CGC>CAC	p.R431H	C18orf45_uc010xaq.1_Intron|CABLES1_uc002kub.2_Intron|CABLES1_uc002kud.2_Missense_Mutation_p.R166H	NM_001100619	NP_001094089	Q8TDN4	CABL1_HUMAN	Cdk5 and Abl enzyme substrate 1 isoform 2	431	Interacts with CDK3 (By similarity).				blood coagulation|cell cycle|cell division|regulation of cell cycle|regulation of cell division	cytosol|nucleus	cyclin-dependent protein kinase regulator activity|protein binding			breast(1)	1	all_cancers(21;0.000102)|all_epithelial(16;2.48e-06)|Lung NSC(20;0.00696)|all_lung(20;0.0197)|Colorectal(14;0.0202)|Ovarian(20;0.127)																	---	---	---	---
C18orf8	29919	broad.mit.edu	37	18	21089145	21089145	+	Intron	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:21089145A>C	uc010xax.1	+						C18orf8_uc010xau.1_Intron|C18orf8_uc010xav.1_Intron|C18orf8_uc010xaw.1_Intron|C18orf8_uc002kul.2_Intron	NM_013326	NP_037458			colon cancer-associated protein Mic1											ovary(1)	1	all_cancers(21;0.000122)|all_epithelial(16;8.08e-07)|Lung NSC(20;0.00206)|all_lung(20;0.00659)|Colorectal(14;0.0202)|Ovarian(20;0.127)																	---	---	---	---
ZNF521	25925	broad.mit.edu	37	18	22669538	22669538	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:22669538A>C	uc002kvk.2	-	7	4044	c.3797T>G	c.(3796-3798)GTT>GGT	p.V1266G	ZNF521_uc010xbe.1_RNA|ZNF521_uc010dly.2_Missense_Mutation_p.V1266G|ZNF521_uc002kvl.2_Missense_Mutation_p.V1046G	NM_015461	NP_056276	Q96K83	ZN521_HUMAN	zinc finger protein 521	1266	C2H2-type 29.				cell differentiation|multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein domain specific binding|zinc ion binding			ovary(4)|large_intestine(2)|lung(1)	7	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)							T	PAX5	ALL								---	---	---	---
DSG4	147409	broad.mit.edu	37	18	28992990	28992990	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28992990T>A	uc002kwq.2	+	16	2690	c.2555T>A	c.(2554-2556)ATT>AAT	p.I852N	DSG4_uc002kwr.2_Missense_Mutation_p.I871N	NM_177986	NP_817123	Q86SJ6	DSG4_HUMAN	desmoglein 4 isoform 2 preproprotein	852	Cytoplasmic (Potential).				homophilic cell adhesion	desmosome|integral to membrane	calcium ion binding			central_nervous_system(5)|ovary(3)	8			OV - Ovarian serous cystadenocarcinoma(10;0.00504)															---	---	---	---
MCART2	147407	broad.mit.edu	37	18	29339938	29339938	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29339938A>G	uc002kxa.2	-	1	906	c.687T>C	c.(685-687)TGT>TGC	p.C229C		NM_001034172	NP_001029344	Q3SY17	MCAR2_HUMAN	mitochondrial carrier triple repeat 2	229	Helical; Name=5; (Potential).|Solcar 3.				transport	integral to membrane|mitochondrial inner membrane				skin(1)	1			OV - Ovarian serous cystadenocarcinoma(10;0.0539)															---	---	---	---
MEP1B	4225	broad.mit.edu	37	18	29788206	29788206	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29788206T>C	uc002kxj.3	+	9	938	c.891T>C	c.(889-891)AGT>AGC	p.S297S		NM_005925	NP_005916	Q16820	MEP1B_HUMAN	meprin A beta precursor	297	Extracellular (Potential).|MAM.				digestion|proteolysis	extracellular space|integral to plasma membrane	metalloendopeptidase activity|zinc ion binding			ovary(2)	2																		---	---	---	---
FAM59A	64762	broad.mit.edu	37	18	29867701	29867701	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29867701G>A	uc002kxl.2	-	4	915	c.859C>T	c.(859-861)CTG>TTG	p.L287L	FAM59A_uc002kxk.1_Silent_p.L287L	NM_022751	NP_073588	Q9H706	FA59A_HUMAN	family with sequence similarity 59, member A	287	CABIT.									ovary(1)|skin(1)	2																		---	---	---	---
FAM59A	64762	broad.mit.edu	37	18	29867855	29867855	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:29867855G>A	uc002kxl.2	-	4	761	c.705C>T	c.(703-705)ACC>ACT	p.T235T	FAM59A_uc002kxk.1_Silent_p.T235T	NM_022751	NP_073588	Q9H706	FA59A_HUMAN	family with sequence similarity 59, member A	235	CABIT.									ovary(1)|skin(1)	2																		---	---	---	---
KLHL14	57565	broad.mit.edu	37	18	30260140	30260140	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:30260140T>A	uc002kxm.1	-	7	1968	c.1580A>T	c.(1579-1581)CAT>CTT	p.H527L	KLHL14_uc010dmd.1_Missense_Mutation_p.H76L	NM_020805	NP_065856	Q9P2G3	KLH14_HUMAN	kelch-like 14	527	Kelch 5.					cytosol|endoplasmic reticulum membrane				ovary(1)	1																		---	---	---	---
NOL4	8715	broad.mit.edu	37	18	31684084	31684084	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:31684084T>A	uc010dmi.2	-	4	795	c.566A>T	c.(565-567)GAC>GTC	p.D189V	NOL4_uc002kxr.3_Missense_Mutation_p.D25V|NOL4_uc010xbt.1_Missense_Mutation_p.D115V|NOL4_uc010dmh.2_Missense_Mutation_p.D115V|NOL4_uc010xbu.1_Missense_Mutation_p.D189V|NOL4_uc002kxt.3_Missense_Mutation_p.D189V|NOL4_uc010xbw.1_Missense_Mutation_p.D75V	NM_003787	NP_003778	O94818	NOL4_HUMAN	nucleolar protein 4	189						nucleolus	RNA binding			ovary(3)	3																		---	---	---	---
MOCOS	55034	broad.mit.edu	37	18	33795636	33795636	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:33795636T>C	uc002kzq.3	+	8	1516	c.1493T>C	c.(1492-1494)GTC>GCC	p.V498A		NM_017947	NP_060417	Q96EN8	MOCOS_HUMAN	molybdenum cofactor sulfurase	498					Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cytosol	lyase activity|Mo-molybdopterin cofactor sulfurase activity|molybdenum ion binding|pyridoxal phosphate binding			skin(1)	1					Pyridoxal Phosphate(DB00114)													---	---	---	---
FHOD3	80206	broad.mit.edu	37	18	34298375	34298375	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34298375G>A	uc002kzt.1	+	15	2635	c.2538G>A	c.(2536-2538)CCG>CCA	p.P846P	FHOD3_uc002kzs.1_Silent_p.P863P|FHOD3_uc010dmz.1_Silent_p.P578P|FHOD3_uc010dna.1_Silent_p.P166P	NM_025135	NP_079411	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	846	FH1.|Pro-rich.				actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding			skin(3)|large_intestine(2)|breast(2)|ovary(1)	8		all_epithelial(2;0.0181)|Colorectal(2;0.0195)																---	---	---	---
CELF4	56853	broad.mit.edu	37	18	34855120	34855120	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34855120C>T	uc002lae.2	-	4	931	c.535G>A	c.(535-537)GAG>AAG	p.E179K	CELF4_uc010dnd.1_Missense_Mutation_p.E178K|CELF4_uc002lag.2_Missense_Mutation_p.E169K|CELF4_uc002laf.2_Missense_Mutation_p.E174K|CELF4_uc002lai.2_Missense_Mutation_p.E164K|CELF4_uc002lah.1_5'Flank|CELF4_uc002laj.1_5'Flank	NM_020180	NP_064565	Q9BZC1	CELF4_HUMAN	bruno-like 4, RNA binding protein isoform 1	179	Sufficient for RNA-binding and MSE- dependent splicing activity.|RRM 2.				embryo development|germ cell development|regulation of alternative nuclear mRNA splicing, via spliceosome	cytoplasm|nucleus	BRE binding|nucleotide binding|translation repressor activity, nucleic acid binding			ovary(2)	2																		---	---	---	---
PSTPIP2	9050	broad.mit.edu	37	18	43568675	43568675	+	3'UTR	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:43568675T>C	uc002lbp.3	-	14					PSTPIP2_uc002lbq.3_Silent_p.K303K	NM_024430	NP_077748			proline-serine-threonine phosphatase interacting							membrane				ovary(1)	1																		---	---	---	---
ST8SIA5	29906	broad.mit.edu	37	18	44284567	44284567	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44284567C>T	uc002lcj.1	-	2	760	c.192G>A	c.(190-192)AGG>AGA	p.R64R	ST8SIA5_uc002lci.1_5'UTR|ST8SIA5_uc010xcy.1_Silent_p.R100R|ST8SIA5_uc010xcz.1_Intron|ST8SIA5_uc010dno.1_Silent_p.R100R	NM_013305	NP_037437	O15466	SIA8E_HUMAN	ST8 alpha-N-acetyl-neuraminide	64	Lumenal (Potential).				glycosphingolipid biosynthetic process|protein glycosylation	integral to Golgi membrane				upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)	3																		---	---	---	---
PIAS2	9063	broad.mit.edu	37	18	44407976	44407976	+	Missense_Mutation	SNP	G	A	A	rs148741759		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44407976G>A	uc002lck.2	-	11	1612	c.1454C>T	c.(1453-1455)CCT>CTT	p.P485L	PIAS2_uc010dnp.2_Missense_Mutation_p.P183L|PIAS2_uc002lcl.2_Missense_Mutation_p.P485L|PIAS2_uc010xda.1_Missense_Mutation_p.P183L|PIAS2_uc002lcm.2_Missense_Mutation_p.P485L	NM_004671	NP_004662	O75928	PIAS2_HUMAN	protein inhibitor of activated STAT X isoform	485	Nuclear localization signal (By similarity).				androgen receptor signaling pathway|negative regulation of androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck|PML body	androgen receptor binding|DNA binding|protein binding|SUMO ligase activity|transcription coactivator activity|zinc ion binding			ovary(2)|breast(1)|skin(1)	4																		---	---	---	---
PIAS2	9063	broad.mit.edu	37	18	44426780	44426780	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44426780C>T	uc002lck.2	-	6	909	c.751G>A	c.(751-753)GGG>AGG	p.G251R	PIAS2_uc010dnp.2_5'UTR|PIAS2_uc002lcl.2_Missense_Mutation_p.G251R|PIAS2_uc010xda.1_5'UTR|PIAS2_uc002lcm.2_Missense_Mutation_p.G251R|PIAS2_uc002lcn.1_Missense_Mutation_p.G255R	NM_004671	NP_004662	O75928	PIAS2_HUMAN	protein inhibitor of activated STAT X isoform	251	PINIT.				androgen receptor signaling pathway|negative regulation of androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck|PML body	androgen receptor binding|DNA binding|protein binding|SUMO ligase activity|transcription coactivator activity|zinc ion binding			ovary(2)|breast(1)|skin(1)	4																		---	---	---	---
TCEB3C	162699	broad.mit.edu	37	18	44554589	44554589	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44554589C>A	uc010xdb.1	-	1	1861	c.1625G>T	c.(1624-1626)AGA>ATA	p.R542I	KATNAL2_uc010dnq.1_Intron|KATNAL2_uc002lco.2_Intron|KATNAL2_uc002lcp.3_Intron	NM_145653	NP_663628	Q8NG57	ELOA3_HUMAN	transcription elongation factor B polypeptide	542					regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane|nucleus	DNA binding				0																		---	---	---	---
TCEB3C	162699	broad.mit.edu	37	18	44554644	44554644	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44554644C>T	uc010xdb.1	-	1	1806	c.1570G>A	c.(1570-1572)GCT>ACT	p.A524T	KATNAL2_uc010dnq.1_Intron|KATNAL2_uc002lco.2_Intron|KATNAL2_uc002lcp.3_Intron	NM_145653	NP_663628	Q8NG57	ELOA3_HUMAN	transcription elongation factor B polypeptide	524					regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane|nucleus	DNA binding				0																		---	---	---	---
TCEB3C	162699	broad.mit.edu	37	18	44554670	44554670	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:44554670G>A	uc010xdb.1	-	1	1780	c.1544C>T	c.(1543-1545)GCG>GTG	p.A515V	KATNAL2_uc010dnq.1_Intron|KATNAL2_uc002lco.2_Intron|KATNAL2_uc002lcp.3_Intron	NM_145653	NP_663628	Q8NG57	ELOA3_HUMAN	transcription elongation factor B polypeptide	515					regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane|nucleus	DNA binding				0																		---	---	---	---
SMAD2	4087	broad.mit.edu	37	18	45371711	45371711	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:45371711C>T	uc002lcy.2	-	10	1528	c.1280G>A	c.(1279-1281)CGA>CAA	p.R427Q	SMAD2_uc002lcz.2_Missense_Mutation_p.R427Q|SMAD2_uc010xdc.1_Missense_Mutation_p.R397Q|SMAD2_uc010xdd.1_Missense_Mutation_p.R397Q	NM_005901	NP_005892	Q15796	SMAD2_HUMAN	Sma- and Mad-related protein 2 isoform 1	427	MH2.				anterior/posterior pattern formation|cell fate commitment|common-partner SMAD protein phosphorylation|intracellular signal transduction|mesoderm formation|negative regulation of transcription, DNA-dependent|palate development|paraxial mesoderm morphogenesis|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription from RNA polymerase II promoter|primary miRNA processing|regulation of binding|regulation of transforming growth factor beta receptor signaling pathway|response to cholesterol|SMAD protein complex assembly|transforming growth factor beta receptor signaling pathway|zygotic specification of dorsal/ventral axis	activin responsive factor complex|cytosol	activating transcription factor binding|co-SMAD binding|double-stranded DNA binding|I-SMAD binding|R-SMAD binding|sequence-specific DNA binding transcription factor activity|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity|type I transforming growth factor beta receptor binding|ubiquitin protein ligase binding			large_intestine(3)|lung(1)|central_nervous_system(1)	5																		---	---	---	---
DYM	54808	broad.mit.edu	37	18	46808518	46808518	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46808518G>T	uc002ldi.1	-	10	1339	c.974C>A	c.(973-975)CCA>CAA	p.P325Q	DYM_uc010xdf.1_Missense_Mutation_p.P135Q|DYM_uc002ldj.3_Missense_Mutation_p.P147Q	NM_017653	NP_060123	Q7RTS9	DYM_HUMAN	dymeclin	325						Golgi apparatus					0																		---	---	---	---
DYM	54808	broad.mit.edu	37	18	46904948	46904948	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:46904948G>T	uc002ldi.1	-	5	775	c.410C>A	c.(409-411)CCT>CAT	p.P137H	DYM_uc010xdf.1_Intron	NM_017653	NP_060123	Q7RTS9	DYM_HUMAN	dymeclin	137						Golgi apparatus					0																		---	---	---	---
C18orf32	497661	broad.mit.edu	37	18	47017718	47017718	+	Intron	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47017718C>A	uc002ldm.1	-						RPL17_uc002ldn.2_5'Flank|RPL17_uc002ldo.2_Intron|RPL17_uc002ldp.2_Intron|RPL17_uc002ldq.2_Intron|RPL17_uc010xdg.1_Intron|SNORD58C_uc002ldr.2_5'Flank|SNORD58A_uc002lds.1_5'Flank	NM_001035006	NP_001030178			ribosomal protein L17						positive regulation of I-kappaB kinase/NF-kappaB cascade		signal transducer activity				0																		---	---	---	---
MYO5B	4645	broad.mit.edu	37	18	47462643	47462643	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47462643T>G	uc002leb.2	-	16	2270	c.1982A>C	c.(1981-1983)AAC>ACC	p.N661T	MYO5B_uc002lec.1_Missense_Mutation_p.N660T	NM_001080467	NP_001073936	Q9ULV0	MYO5B_HUMAN	myosin VB	661	Myosin head-like.|Actin-binding (Potential).				protein transport	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|skin(2)|central_nervous_system(1)	5				READ - Rectum adenocarcinoma(32;0.103)														---	---	---	---
ME2	4200	broad.mit.edu	37	18	48452240	48452240	+	Missense_Mutation	SNP	C	T	T	rs140281750		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48452240C>T	uc002ley.2	+	12	1542	c.1286C>T	c.(1285-1287)ACG>ATG	p.T429M	ME2_uc010dpd.2_Missense_Mutation_p.T429M	NM_002396	NP_002387	P23368	MAOM_HUMAN	malic enzyme 2, NAD(+)-dependent, mitochondrial	429					malate metabolic process	mitochondrial matrix	electron carrier activity|malate dehydrogenase (decarboxylating) activity|malate dehydrogenase (oxaloacetate-decarboxylating) activity|metal ion binding|NAD binding				0		Colorectal(6;0.0273)|all_epithelial(6;0.118)		Colorectal(21;0.0313)|READ - Rectum adenocarcinoma(32;0.105)|STAD - Stomach adenocarcinoma(97;0.184)	NADH(DB00157)													---	---	---	---
ELAC1	55520	broad.mit.edu	37	18	48510725	48510725	+	Silent	SNP	G	A	A	rs146406776	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:48510725G>A	uc002lez.2	+	3	523	c.417G>A	c.(415-417)GCG>GCA	p.A139A	ELAC1_uc010dpe.2_Silent_p.A139A|SMAD4_uc010xdo.1_Intron	NM_018696	NP_061166	Q9H777	RNZ1_HUMAN	elaC homolog 1	139					tRNA 3'-trailer cleavage	nucleus	endoribonuclease activity, producing 5'-phosphomonoesters|metal ion binding				0		Colorectal(6;0.0269)|all_epithelial(6;0.0729)		Colorectal(21;0.000943)|COAD - Colon adenocarcinoma(17;0.0398)|READ - Rectum adenocarcinoma(32;0.0894)|STAD - Stomach adenocarcinoma(97;0.18)														---	---	---	---
DCC	1630	broad.mit.edu	37	18	50985661	50985661	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50985661C>T	uc002lfe.1	+	24	4039	c.3452C>T	c.(3451-3453)CCT>CTT	p.P1151L	DCC_uc010dpf.1_Missense_Mutation_p.P786L	NM_005215	NP_005206	P43146	DCC_HUMAN	netrin receptor DCC precursor	1151	Cytoplasmic (Potential).				apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)														---	---	---	---
TCF4	6925	broad.mit.edu	37	18	53252529	53252529	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:53252529C>T	uc002lfz.2	-	3	739	c.127G>A	c.(127-129)GGA>AGA	p.G43R	TCF4_uc010xdx.1_Missense_Mutation_p.G19R|TCF4_uc010dph.1_Missense_Mutation_p.G43R|TCF4_uc010xdy.1_Missense_Mutation_p.G19R|TCF4_uc002lga.2_Missense_Mutation_p.G145R|TCF4_uc010dpi.2_Missense_Mutation_p.G43R	NM_003199	NP_003190	P15884	ITF2_HUMAN	transcription factor 4 isoform b	43	Essential for MYOD1 inhibition (By similarity).				positive regulation of neuron differentiation|protein-DNA complex assembly|transcription initiation from RNA polymerase II promoter	transcription factor complex	E-box binding|protein C-terminus binding|protein heterodimerization activity|RNA polymerase II core promoter proximal region sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|sequence-specific DNA binding RNA polymerase recruiting transcription factor activity|TFIIB-class binding transcription factor activity|TFIIB-class transcription factor binding			ovary(1)|lung(1)	2				Colorectal(16;0.00108)|READ - Rectum adenocarcinoma(59;0.0649)|COAD - Colon adenocarcinoma(17;0.0718)														---	---	---	---
ST8SIA3	51046	broad.mit.edu	37	18	55020138	55020138	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55020138G>A	uc002lgn.2	+	1	418	c.61G>A	c.(61-63)GCC>ACC	p.A21T		NM_015879	NP_056963	O43173	SIA8C_HUMAN	ST8 alpha-N-acetyl-neuraminide	21	Helical; Signal-anchor for type II membrane protein; (Potential).				glycosphingolipid biosynthetic process|N-glycan processing|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			breast(1)|skin(1)	2				READ - Rectum adenocarcinoma(59;0.19)|Colorectal(16;0.205)														---	---	---	---
ATP8B1	5205	broad.mit.edu	37	18	55315833	55315833	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:55315833G>A	uc002lgw.2	-	27	3643	c.3643C>T	c.(3643-3645)CGG>TGG	p.R1215W	uc002lgu.1_Intron|uc002lgv.1_Intron	NM_005603	NP_005594	O43520	AT8B1_HUMAN	ATPase, class I, type 8B, member 1	1215	Cytoplasmic (Potential).				ATP biosynthetic process|bile acid and bile salt transport|negative regulation of transcription, DNA-dependent	apical plasma membrane|integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			breast(5)|ovary(2)|central_nervous_system(2)|lung(1)	10		Colorectal(73;0.229)												Byler_disease				---	---	---	---
MALT1	10892	broad.mit.edu	37	18	56367746	56367746	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56367746G>A	uc002lhm.1	+	4	830	c.572G>A	c.(571-573)CGA>CAA	p.R191Q	MALT1_uc002lhn.1_Missense_Mutation_p.R191Q	NM_006785	NP_006776	Q9UDY8	MALT1_HUMAN	mucosa associated lymphoid tissue lymphoma	191	Ig-like C2-type 1.				activation of NF-kappaB-inducing kinase activity|anti-apoptosis|nuclear export|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-2 production|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphorylation|positive regulation of protein ubiquitination|positive regulation of T cell cytokine production|protein oligomerization|proteolysis|T cell receptor signaling pathway	CBM complex|cytosol|nucleus|perinuclear region of cytoplasm	cysteine-type endopeptidase activity|protein self-association|signal transducer activity|ubiquitin-protein ligase activity			ovary(2)|lung(1)|central_nervous_system(1)	4								T	BIRC3	MALT								---	---	---	---
RAX	30062	broad.mit.edu	37	18	56936315	56936315	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56936315C>T	uc002lhx.2	-	3	1149	c.962G>A	c.(961-963)CGC>CAC	p.R321H	RAX_uc010dpp.2_3'UTR	NM_013435	NP_038463	Q9Y2V3	RX_HUMAN	retina and anterior neural fold homeobox	321					visual perception	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1		Lung NSC(161;0.0804)|Colorectal(73;0.0946)		STAD - Stomach adenocarcinoma(84;0.18)														---	---	---	---
CDH20	28316	broad.mit.edu	37	18	59212279	59212279	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59212279C>T	uc010dps.1	+	9	1562	c.1550C>T	c.(1549-1551)GCG>GTG	p.A517V	CDH20_uc002lif.2_Missense_Mutation_p.A511V	NM_031891	NP_114097	Q9HBT6	CAD20_HUMAN	cadherin 20, type 2 preproprotein	517	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(3)|ovary(1)|pancreas(1)	5		Colorectal(73;0.186)																---	---	---	---
PHLPP1	23239	broad.mit.edu	37	18	60527752	60527752	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:60527752C>A	uc002lis.2	+	5	626	c.448C>A	c.(448-450)CTC>ATC	p.L150I		NM_194449	NP_919431	O60346	PHLP1_HUMAN	PH domain and leucine rich repeat protein	662	LRR 2.				apoptosis|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling	cytosol|membrane|nucleus	metal ion binding|protein serine/threonine phosphatase activity				0																		---	---	---	---
VPS4B	9525	broad.mit.edu	37	18	61077659	61077659	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61077659C>T	uc002lix.2	-	3	420	c.160G>A	c.(160-162)GCC>ACC	p.A54T	VPS4B_uc010dpx.2_Missense_Mutation_p.A54T|VPS4B_uc010dpy.2_5'UTR|VPS4B_uc010dpz.1_5'UTR	NM_004869	NP_004860	O75351	VPS4B_HUMAN	vacuolar protein sorting factor 4B	54	Potential.|MIT.				cell cycle|cell division|cellular membrane organization|endosome to lysosome transport via multivesicular body sorting pathway|intracellular cholesterol transport|protein transport|response to lipid	cytosol|early endosome|late endosome membrane|lysosome|nucleus|vacuolar membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding			ovary(1)	1																		---	---	---	---
SERPINB5	5268	broad.mit.edu	37	18	61154281	61154281	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61154281C>T	uc002liz.3	+	3	413	c.271C>T	c.(271-273)CGG>TGG	p.R91W	SERPINB5_uc002liy.2_Missense_Mutation_p.R91W	NM_002639	NP_002630	P36952	SPB5_HUMAN	serine (or cysteine) proteinase inhibitor, clade	91					cellular component movement|regulation of proteolysis	cytoplasm|extracellular space	protein binding|serine-type endopeptidase inhibitor activity			ovary(1)	1																		---	---	---	---
SERPINB13	5275	broad.mit.edu	37	18	61255916	61255916	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61255916C>T	uc002ljc.2	+	2	183	c.15C>T	c.(13-15)GGC>GGT	p.G5G	SERPINB13_uc002ljd.2_5'UTR|SERPINB13_uc010xep.1_Silent_p.G5G|SERPINB13_uc010xeq.1_5'UTR|SERPINB13_uc010xer.1_5'UTR	NM_012397	NP_036529	Q9UIV8	SPB13_HUMAN	serine (or cysteine) proteinase inhibitor, clade	5					regulation of proteolysis|response to UV	cytoplasm|extracellular region	serine-type endopeptidase inhibitor activity			ovary(1)	1																		---	---	---	---
HMSD	284293	broad.mit.edu	37	18	61620771	61620771	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61620771G>A	uc010dqj.2	+							NM_001123366	NP_001116838			histocompatibility (minor) serpin domain							extracellular region	serine-type endopeptidase inhibitor activity				0																		---	---	---	---
SERPINB8	5271	broad.mit.edu	37	18	61654383	61654383	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:61654383T>C	uc002ljv.2	+	7	1165	c.996T>C	c.(994-996)ACT>ACC	p.T332T	SERPINB8_uc002lju.2_Silent_p.T332T|SERPINB8_uc010xex.1_Silent_p.T150T	NM_198833	NP_942130	P50452	SPB8_HUMAN	serine (or cysteine) proteinase inhibitor, clade	332					regulation of proteolysis	cytosol	protein binding|serine-type endopeptidase inhibitor activity			skin(1)	1		Esophageal squamous(42;0.129)																---	---	---	---
RTTN	25914	broad.mit.edu	37	18	67809569	67809569	+	Missense_Mutation	SNP	C	T	T	rs113536228	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:67809569C>T	uc002lkp.2	-	19	2604	c.2536G>A	c.(2536-2538)GTT>ATT	p.V846I	RTTN_uc002lko.2_RNA|RTTN_uc010xfb.1_5'UTR	NM_173630	NP_775901	Q86VV8	RTTN_HUMAN	rotatin	846							binding			ovary(3)|pancreas(2)|skin(1)|breast(1)|central_nervous_system(1)	8		Esophageal squamous(42;0.129)																---	---	---	---
FBXO15	201456	broad.mit.edu	37	18	71790700	71790700	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:71790700G>A	uc002lle.2	-	8	1149	c.813C>T	c.(811-813)CCC>CCT	p.P271P	FBXO15_uc002llf.2_Silent_p.P347P	NM_152676	NP_689889	Q8NCQ5	FBX15_HUMAN	F-box protein 15 isoform 1	271										ovary(2)|pancreas(1)	3		Esophageal squamous(42;0.103)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.143)														---	---	---	---
TSHZ1	10194	broad.mit.edu	37	18	72998442	72998442	+	Silent	SNP	G	A	A	rs149658226	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72998442G>A	uc002lly.2	+	2	1508	c.945G>A	c.(943-945)GCG>GCA	p.A315A		NM_005786	NP_005777	Q6ZSZ6	TSH1_HUMAN	teashirt family zinc finger 1	360						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)														---	---	---	---
TSHZ1	10194	broad.mit.edu	37	18	72999411	72999411	+	Silent	SNP	G	A	A	rs146482929	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:72999411G>A	uc002lly.2	+	2	2477	c.1914G>A	c.(1912-1914)ACG>ACA	p.T638T		NM_005786	NP_005777	Q6ZSZ6	TSH1_HUMAN	teashirt family zinc finger 1	683						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)														---	---	---	---
MBP	4155	broad.mit.edu	37	18	74700859	74700859	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74700859G>A	uc010xfd.1	-	6	955	c.691C>T	c.(691-693)CGC>TGC	p.R231C	MBP_uc002lml.2_Missense_Mutation_p.R124C|MBP_uc002lmn.2_Missense_Mutation_p.R124C|MBP_uc002lmp.2_Missense_Mutation_p.R98C|MBP_uc010xfe.1_Missense_Mutation_p.R98C|MBP_uc010dqz.2_5'Flank	NM_001025101	NP_001020272	P02686	MBP_HUMAN	Golli-mbp isoform 1	231					central nervous system development|immune response|synaptic transmission	plasma membrane	structural constituent of myelin sheath			haematopoietic_and_lymphoid_tissue(1)	1		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.79e-06)|BRCA - Breast invasive adenocarcinoma(31;0.113)|READ - Rectum adenocarcinoma(1;0.188)														---	---	---	---
MBP	4155	broad.mit.edu	37	18	74728930	74728930	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74728930C>T	uc010xfd.1	-	4	698	c.434G>A	c.(433-435)GGA>GAA	p.G145E	MBP_uc002lml.2_Missense_Mutation_p.G12E|MBP_uc002lmn.2_Missense_Mutation_p.G12E|MBP_uc002lmp.2_Missense_Mutation_p.G12E|MBP_uc010xfe.1_Missense_Mutation_p.G12E|MBP_uc002lmr.2_Missense_Mutation_p.G145E	NM_001025101	NP_001020272	P02686	MBP_HUMAN	Golli-mbp isoform 1	145					central nervous system development|immune response|synaptic transmission	plasma membrane	structural constituent of myelin sheath			haematopoietic_and_lymphoid_tissue(1)	1		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.79e-06)|BRCA - Breast invasive adenocarcinoma(31;0.113)|READ - Rectum adenocarcinoma(1;0.188)														---	---	---	---
GALR1	2587	broad.mit.edu	37	18	74963043	74963043	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:74963043G>A	uc002lms.3	+	1	1036	c.539G>A	c.(538-540)CGC>CAC	p.R180H		NM_001480	NP_001471	P47211	GALR1_HUMAN	galanin receptor 1	180	Extracellular (Potential).				digestion|negative regulation of adenylate cyclase activity	integral to membrane|plasma membrane	galanin receptor activity			lung(1)	1		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.03e-06)|BRCA - Breast invasive adenocarcinoma(31;0.104)														---	---	---	---
PQLC1	80148	broad.mit.edu	37	18	77679231	77679231	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:77679231C>T	uc002lnl.2	-	5	733	c.561G>A	c.(559-561)GTG>GTA	p.V187V	PQLC1_uc010dre.2_Silent_p.V104V|PQLC1_uc002lnk.2_Silent_p.V169V|PQLC1_uc010xfm.1_Intron	NM_025078	NP_079354	Q8N2U9	PQLC1_HUMAN	PQ loop repeat containing 1 isoform 1	187	PQ-loop 2.|Helical; (Potential).					integral to membrane				large_intestine(1)|ovary(1)	2		Esophageal squamous(42;0.0212)|Melanoma(33;0.2)		OV - Ovarian serous cystadenocarcinoma(15;8.2e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0258)														---	---	---	---
RNF126	55658	broad.mit.edu	37	19	651781	651781	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:651781G>A	uc010drs.2	-	4	379	c.273C>T	c.(271-273)TTC>TTT	p.F91F	RNF126_uc002lpi.2_5'UTR	NM_194460	NP_919442	Q9BV68	RN126_HUMAN	ring finger protein 126	91							protein binding|zinc ion binding				0		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
C19orf21	126353	broad.mit.edu	37	19	757838	757838	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:757838C>T	uc002lpo.2	+	2	975	c.892C>T	c.(892-894)CGT>TGT	p.R298C		NM_173481	NP_775752	Q8IVT2	CS021_HUMAN	hypothetical protein LOC126353	298										upper_aerodigestive_tract(1)	1		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000145)|all_lung(49;0.000236)|Breast(49;0.0014)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
LPPR3	79948	broad.mit.edu	37	19	814946	814946	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:814946T>G	uc002lpx.1	-	5	603	c.539A>C	c.(538-540)AAC>ACC	p.N180T	LPPR3_uc010dru.1_Missense_Mutation_p.N92T|LPPR3_uc002lpw.1_Missense_Mutation_p.N180T|LPPR3_uc002lpy.1_5'UTR	NM_024888	NP_079164	Q6T4P5	LPPR3_HUMAN	plasticity-related protein 2	180						integral to membrane	phosphatidate phosphatase activity				0																		---	---	---	---
ABCA7	10347	broad.mit.edu	37	19	1041385	1041385	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1041385C>T	uc002lqw.3	+	2	256	c.25C>T	c.(25-27)CTG>TTG	p.L9L	ABCA7_uc010dsb.1_5'Flank|ABCA7_uc010dsa.2_Silent_p.L9L	NM_019112	NP_061985	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A, member 7	9					phagocytosis|transmembrane transport	ATP-binding cassette (ABC) transporter complex|endosome membrane|Golgi membrane|integral to membrane|plasma membrane	ATP binding|ATPase activity|transporter activity			pancreas(7)|ovary(1)|central_nervous_system(1)	9		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
HMHA1	23526	broad.mit.edu	37	19	1079813	1079813	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1079813C>T	uc002lqz.1	+	12	1717	c.1486C>T	c.(1486-1488)CGG>TGG	p.R496W	HMHA1_uc010xgd.1_Missense_Mutation_p.R512W|HMHA1_uc010xge.1_Missense_Mutation_p.R336W|HMHA1_uc002lra.1_Missense_Mutation_p.R336W|HMHA1_uc002lrb.1_Missense_Mutation_p.R379W|HMHA1_uc002lrc.1_Missense_Mutation_p.R131W|HMHA1_uc002lrd.1_5'Flank	NM_012292	NP_036424	Q92619	HMHA1_HUMAN	minor histocompatibility antigen HA-1	496	Potential.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding			lung(1)	1		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
GPX4	2879	broad.mit.edu	37	19	1105712	1105712	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1105712T>C	uc010xgg.1	+	5	487	c.380T>C	c.(379-381)TTC>TCC	p.F127S	GPX4_uc010xgh.1_Missense_Mutation_p.F127S|GPX4_uc010xgi.1_Missense_Mutation_p.F164S	NM_002085	NP_002076	P36969	GPX4_HUMAN	glutathione peroxidase 4 isoform A precursor	127					multicellular organismal development|phospholipid metabolic process		glutathione peroxidase activity|phospholipid-hydroperoxide glutathione peroxidase activity				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Glutathione(DB00143)													---	---	---	---
MUM1	84939	broad.mit.edu	37	19	1369333	1369333	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1369333C>T	uc010xgm.1	+	9	1561	c.1492C>T	c.(1492-1494)CGG>TGG	p.R498W	MUM1_uc010dsi.2_Missense_Mutation_p.R430W|MUM1_uc002lrz.2_Missense_Mutation_p.R499W|MUM1_uc002lsb.2_Missense_Mutation_p.R430W			Q2TAK8	MUM1_HUMAN	SubName: Full=MUM1 protein;	498					chromatin organization|DNA repair	nucleus	nucleosome binding|protein binding				0		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
TCF3	6929	broad.mit.edu	37	19	1611846	1611846	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1611846G>A	uc002ltr.2	-	19	1892	c.1825C>T	c.(1825-1827)CGG>TGG	p.R609W	TCF3_uc002ltn.2_Missense_Mutation_p.R58W|TCF3_uc002lto.2_Missense_Mutation_p.R370W|TCF3_uc002ltt.3_Missense_Mutation_p.R606W|TCF3_uc002ltq.2_Missense_Mutation_p.R613W|TCF3_uc002lts.1_Missense_Mutation_p.R521W	NM_003200	NP_003191	P15923	TFE2_HUMAN	transcription factor 3 isoform E12	609					B cell lineage commitment|B cell lineage commitment|G1 phase of mitotic cell cycle|immunoglobulin V(D)J recombination|muscle cell differentiation|positive regulation of B cell proliferation|positive regulation of cell cycle|positive regulation of muscle cell differentiation|positive regulation of neuron differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus|protein complex|transcription factor complex	bHLH transcription factor binding|DNA binding|E-box binding|identical protein binding|mitogen-activated protein kinase kinase kinase binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|vitamin D response element binding			lung(2)|breast(2)|ovary(1)|large_intestine(1)|skin(1)	7		Acute lymphoblastic leukemia(61;5.94e-12)|all_hematologic(61;1.27e-07)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)				T	PBX1|HLF|TFPT	pre B-ALL								---	---	---	---
ATP8B3	148229	broad.mit.edu	37	19	1785288	1785288	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1785288A>G	uc002ltw.2	-	27	3636	c.3402T>C	c.(3400-3402)CTT>CTC	p.L1134L	ATP8B3_uc002ltv.2_Silent_p.L1097L|ATP8B3_uc002ltx.2_RNA	NM_138813	NP_620168	O60423	AT8B3_HUMAN	ATPase, class I, type 8B, member 3	1134	Helical; (Potential).				ATP biosynthetic process		ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
KLF16	83855	broad.mit.edu	37	19	1854688	1854688	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1854688G>T	uc002luc.2	-	2	597	c.529C>A	c.(529-531)CAC>AAC	p.H177N	KLF16_uc010xgt.1_RNA	NM_031918	NP_114124	Q9BXK1	KLF16_HUMAN	BTE-binding protein 4	177	C2H2-type 2.					nucleus	DNA binding|zinc ion binding				0		Ovarian(11;1.78e-06)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
ADAT3	113179	broad.mit.edu	37	19	1912976	1912976	+	Silent	SNP	C	T	T	rs150936899		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1912976C>T	uc002luh.2	+	2	1110	c.882C>T	c.(880-882)TGC>TGT	p.C294C	SCAMP4_uc002lui.1_Intron|SCAMP4_uc002luj.2_Intron|SCAMP4_uc002luk.2_Intron|SCAMP4_uc010dss.2_Intron	NM_138422	NP_612431	Q96EY9	ADAT3_HUMAN	tRNA-specific adenosine deaminase 3	294		Zinc (By similarity).			tRNA processing		hydrolase activity|zinc ion binding			breast(1)|skin(1)	2		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
SCAMP4	113178	broad.mit.edu	37	19	1917712	1917712	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1917712G>A	uc002luj.2	+	3	134	c.27G>A	c.(25-27)CCG>CCA	p.P9P	SCAMP4_uc002lui.1_Silent_p.P9P|SCAMP4_uc002luk.2_Silent_p.P9P|SCAMP4_uc010dss.2_5'UTR	NM_079834	NP_524558	Q969E2	SCAM4_HUMAN	secretory carrier membrane protein 4	9	Cytoplasmic (Potential).				protein transport	integral to membrane					0		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
C19orf34	255193	broad.mit.edu	37	19	1953968	1953968	+	Silent	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1953968T>G	uc002lum.2	-	2	524	c.67A>C	c.(67-69)AGG>CGG	p.R23R	CSNK1G2_uc002lul.3_Intron	NM_152771	NP_689984			chromosome 19 open reading frame 34												0		Ovarian(11;0.000137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
BTBD2	55643	broad.mit.edu	37	19	1997450	1997450	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1997450G>A	uc002lup.1	-	2	420	c.420C>T	c.(418-420)GCC>GCT	p.A140A		NM_017797	NP_060267	Q9BX70	BTBD2_HUMAN	BTB (POZ) domain containing 2	140	BTB.					cytoplasmic mRNA processing body	protein binding			ovary(1)|skin(1)	2		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
AP3D1	8943	broad.mit.edu	37	19	2138621	2138621	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2138621C>T	uc002luz.2	-	2	412	c.189G>A	c.(187-189)ACG>ACA	p.T63T	AP3D1_uc002luy.2_Silent_p.T63T|AP3D1_uc002lva.2_Silent_p.T63T	NM_003938	NP_003929	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1	63	HEAT 1.				eye pigment biosynthetic process|intracellular protein transport|regulation of sequestering of zinc ion|vesicle-mediated transport	endosome membrane|Golgi membrane|membrane coat	binding|protein transporter activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
DOT1L	84444	broad.mit.edu	37	19	2194577	2194577	+	Splice_Site	SNP	G	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2194577G>C	uc002lvb.3	+	7	687	c.651_splice	c.e7+1	p.T217_splice		NM_032482	NP_115871			DOT1-like, histone H3 methyltransferase							nucleus	DNA binding|histone-lysine N-methyltransferase activity|protein binding			pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
DOT1L	84444	broad.mit.edu	37	19	2228241	2228241	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2228241G>A	uc002lvb.3	+						DOT1L_uc002lvc.1_Silent_p.A998A	NM_032482	NP_115871			DOT1-like, histone H3 methyltransferase							nucleus	DNA binding|histone-lysine N-methyltransferase activity|protein binding			pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	4		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
SPPL2B	56928	broad.mit.edu	37	19	2338765	2338765	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2338765T>C	uc002lvs.2	+	4	464	c.384T>C	c.(382-384)GGT>GGC	p.G128G	SPPL2B_uc010dsw.1_Silent_p.G100G|SPPL2B_uc010dsy.1_Silent_p.G100G|SPPL2B_uc010dsz.1_Silent_p.G128G|SPPL2B_uc002lvr.2_Silent_p.G128G|SPPL2B_uc010dta.1_5'UTR|SPPL2B_uc002lvu.2_5'Flank	NM_152988	NP_694533	Q8TCT7	PSL1_HUMAN	signal peptide peptidase-like 2B isoform 2	128	Cytoplasmic (Potential).|PA.					Golgi membrane|integral to membrane	aspartic-type endopeptidase activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
ZNF554	115196	broad.mit.edu	37	19	2834859	2834859	+	3'UTR	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2834859C>T	uc002lwm.2	+	5					ZNF554_uc002lwl.2_3'UTR	NM_001102651	NP_001096121			zinc finger protein 554						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
TLE6	79816	broad.mit.edu	37	19	2987202	2987202	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2987202C>T	uc002lwu.2	+	6	538	c.138C>T	c.(136-138)GGC>GGT	p.G46G	TLE6_uc002lwt.2_Silent_p.G169G|TLE6_uc010dtg.2_Silent_p.G169G|TLE6_uc002lwv.2_5'Flank	NM_024760	NP_079036	Q9H808	TLE6_HUMAN	transducin-like enhancer of split 6 isoform 2	46					regulation of transcription, DNA-dependent	nucleus				ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
TLE2	7089	broad.mit.edu	37	19	3013703	3013703	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3013703A>G	uc002lww.2	-	11	1100	c.837T>C	c.(835-837)CTT>CTC	p.L279L	TLE2_uc010xhb.1_5'UTR|TLE2_uc010dth.2_Silent_p.L280L|TLE2_uc010xhc.1_Silent_p.L157L|TLE2_uc010dti.2_Silent_p.L293L|TLE2_uc010xhd.1_Silent_p.L187L	NM_003260	NP_003251	Q04725	TLE2_HUMAN	transducin-like enhancer protein 2 isoform 1	279	Pro/Ser-rich.				negative regulation of canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|organ morphogenesis|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	protein binding|transcription corepressor activity				0				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
AES	166	broad.mit.edu	37	19	3053807	3053807	+	3'UTR	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3053807C>T	uc002lwy.1	-	7					AES_uc002lwx.1_3'UTR|AES_uc002lwz.1_3'UTR|AES_uc002lxa.1_3'UTR|AES_uc002lxb.1_3'UTR|AES_uc002lxc.2_3'UTR	NM_001130	NP_001121			amino-terminal enhancer of split isoform b						negative regulation of canonical Wnt receptor signaling pathway|negative regulation of protein binding|negative regulation of response to cytokine stimulus|negative regulation of transcription from RNA polymerase II promoter|organ morphogenesis|response to interleukin-1|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	protein binding|transcription corepressor activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
C19orf29	58509	broad.mit.edu	37	19	3624120	3624120	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3624120G>A	uc002lyh.2	-	2	261	c.208C>T	c.(208-210)CGA>TGA	p.R70*	C19orf29_uc002lyi.3_Nonsense_Mutation_p.R70*|C19orf29_uc010dto.2_RNA	NM_001080543	NP_001074012	Q8WUQ7	CS029_HUMAN	chromosome 19 open reading frame 29	70						catalytic step 2 spliceosome	protein binding				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00253)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
TJP3	27134	broad.mit.edu	37	19	3746068	3746068	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3746068A>T	uc010xhv.1	+	15	2098	c.2098A>T	c.(2098-2100)ATT>TTT	p.I700F	TJP3_uc010xhs.1_Missense_Mutation_p.I667F|TJP3_uc010xht.1_Missense_Mutation_p.I631F|TJP3_uc010xhu.1_Missense_Mutation_p.I676F|TJP3_uc010xhw.1_Missense_Mutation_p.I686F	NM_014428	NP_055243	O95049	ZO3_HUMAN	tight junction protein 3	681	Guanylate kinase-like.					tight junction	protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0118)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
TJP3	27134	broad.mit.edu	37	19	3747944	3747944	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3747944C>T	uc010xhv.1	+	18	2574	c.2574C>T	c.(2572-2574)GGC>GGT	p.G858G	TJP3_uc010xhs.1_Silent_p.G825G|TJP3_uc010xht.1_Silent_p.G789G|TJP3_uc010xhu.1_Silent_p.G834G|TJP3_uc010xhw.1_Silent_p.G844G	NM_014428	NP_055243	O95049	ZO3_HUMAN	tight junction protein 3	839						tight junction	protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0118)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
ITGB1BP3	27231	broad.mit.edu	37	19	3941177	3941177	+	Splice_Site	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3941177T>C	uc002lyz.3	+	7	792	c.502_splice	c.e7+2	p.V168_splice	ITGB1BP3_uc010xia.1_Splice_Site_p.V173_splice	NM_170678	NP_733778			integrin beta 1 binding protein 3						pyridine nucleotide biosynthetic process		ATP binding|metal ion binding|protein binding|ribosylnicotinamide kinase activity			skin(2)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00463)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
ITGB1BP3	27231	broad.mit.edu	37	19	3942152	3942152	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3942152C>T	uc002lyz.3	+	8	864	c.574C>T	c.(574-576)CTG>TTG	p.L192L	ITGB1BP3_uc010xia.1_Silent_p.L197L	NM_170678	NP_733778	Q9NPI5	NRK2_HUMAN	integrin beta 1 binding protein 3	192					pyridine nucleotide biosynthetic process		ATP binding|metal ion binding|protein binding|ribosylnicotinamide kinase activity			skin(2)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00463)|STAD - Stomach adenocarcinoma(1328;0.18)														---	---	---	---
SH3GL1	6455	broad.mit.edu	37	19	4365592	4365592	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4365592G>A	uc002maj.2	-	4	324	c.218C>T	c.(217-219)ACG>ATG	p.T73M	SH3GL1_uc002mak.2_Missense_Mutation_p.T73M|SH3GL1_uc010xig.1_Intron	NM_003025	NP_003016	Q99961	SH3G1_HUMAN	SH3-domain GRB2-like 1	73	Required for dimerization upon membrane association (By similarity).|BAR.				central nervous system development|endocytosis|signal transduction	early endosome membrane	lipid binding|protein binding			ovary(2)	2				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0152)|STAD - Stomach adenocarcinoma(1328;0.182)				T	MLL	AL								---	---	---	---
PLIN4	729359	broad.mit.edu	37	19	4511842	4511842	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4511842G>A	uc002mar.1	-	3	2088	c.2088C>T	c.(2086-2088)GTC>GTT	p.V696V	PLIN4_uc010dub.1_5'Flank	NM_001080400	NP_001073869	Q96Q06	PLIN4_HUMAN	plasma membrane associated protein, S3-12	696	19.|27 X 33 AA approximate tandem repeat.					lipid particle|plasma membrane					0																		---	---	---	---
PLIN5	440503	broad.mit.edu	37	19	4525675	4525675	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4525675G>T	uc002mas.2	-	6	743	c.690C>A	c.(688-690)ACC>ACA	p.T230T		NM_001013706	NP_001013728	Q00G26	PLIN5_HUMAN	lipid storage droplet protein 5	230						lipid particle					0																		---	---	---	---
DPP9	91039	broad.mit.edu	37	19	4688831	4688831	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4688831C>T	uc002mba.2	-	16	2081	c.1823G>A	c.(1822-1824)GGC>GAC	p.G608D		NM_139159	NP_631898	Q86TI2	DPP9_HUMAN	dipeptidylpeptidase 9	579					proteolysis	cytosol|membrane	aminopeptidase activity|serine-type peptidase activity			skin(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00884)														---	---	---	---
DPP9	91039	broad.mit.edu	37	19	4695417	4695417	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4695417G>A	uc002mba.2	-	12	1584	c.1326C>T	c.(1324-1326)TAC>TAT	p.Y442Y	DPP9_uc002mbb.2_Silent_p.Y442Y|DPP9_uc002mbc.2_Intron	NM_139159	NP_631898	Q86TI2	DPP9_HUMAN	dipeptidylpeptidase 9	413					proteolysis	cytosol|membrane	aminopeptidase activity|serine-type peptidase activity			skin(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00884)														---	---	---	---
ARRDC5	645432	broad.mit.edu	37	19	4902756	4902756	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:4902756T>C	uc002mbm.2	-	1	124	c.124A>G	c.(124-126)ATC>GTC	p.I42V		NM_001080523	NP_001073992	A6NEK1	ARRD5_HUMAN	arrestin domain containing 5	42					signal transduction						0				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0257)														---	---	---	---
KDM4B	23030	broad.mit.edu	37	19	5033029	5033029	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5033029C>T	uc002mbq.3	+	3	354	c.128C>T	c.(127-129)GCG>GTG	p.A43V	KDM4B_uc010xil.1_Missense_Mutation_p.A43V|KDM4B_uc010xim.1_Missense_Mutation_p.A43V	NM_015015	NP_055830	O94953	KDM4B_HUMAN	jumonji domain containing 2B	43	JmjN.				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			lung(1)	1																		---	---	---	---
PTPRS	5802	broad.mit.edu	37	19	5222149	5222149	+	Silent	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5222149T>A	uc002mbv.2	-	19	3420	c.3186A>T	c.(3184-3186)TCA>TCT	p.S1062S	PTPRS_uc002mbu.1_Silent_p.S631S|PTPRS_uc010xin.1_Silent_p.S631S|PTPRS_uc002mbw.2_Silent_p.S1040S|PTPRS_uc002mbx.2_Silent_p.S635S|PTPRS_uc002mby.2_Silent_p.S631S	NM_002850	NP_002841	Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type,	1062	Extracellular (Potential).|Fibronectin type-III 8.				cell adhesion	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			large_intestine(2)|ovary(1)|central_nervous_system(1)	4				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)														---	---	---	---
PTPRS	5802	broad.mit.edu	37	19	5231336	5231336	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5231336G>A	uc002mbv.2	-	14	2374	c.2140C>T	c.(2140-2142)CGC>TGC	p.R714C	PTPRS_uc002mbu.1_Intron|PTPRS_uc010xin.1_Intron|PTPRS_uc002mbw.2_Missense_Mutation_p.R701C|PTPRS_uc002mbx.2_Intron|PTPRS_uc002mby.2_Intron	NM_002850	NP_002841	Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type,	714	Extracellular (Potential).|Fibronectin type-III 4.				cell adhesion	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			large_intestine(2)|ovary(1)|central_nervous_system(1)	4				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)														---	---	---	---
ZNRF4	148066	broad.mit.edu	37	19	5455862	5455862	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5455862C>T	uc002mca.3	+	1	437	c.360C>T	c.(358-360)TTC>TTT	p.F120F		NM_181710	NP_859061	Q8WWF5	ZNRF4_HUMAN	zinc and ring finger 4 precursor	120	Extracellular (Potential).					integral to membrane	zinc ion binding			large_intestine(2)	2				UCEC - Uterine corpus endometrioid carcinoma (162;0.0002)														---	---	---	---
SAFB	6294	broad.mit.edu	37	19	5654190	5654190	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5654190C>T	uc002mcf.2	+	12	1698	c.1645C>T	c.(1645-1647)CGA>TGA	p.R549*	SAFB_uc002mcg.2_Nonsense_Mutation_p.R549*|SAFB_uc002mce.3_Nonsense_Mutation_p.R549*|SAFB_uc010xir.1_Nonsense_Mutation_p.R549*|SAFB_uc010xis.1_Nonsense_Mutation_p.R480*|SAFB_uc010xit.1_Nonsense_Mutation_p.R392*|SAFB_uc010xiu.1_Nonsense_Mutation_p.R348*	NM_002967	NP_002958	Q15424	SAFB1_HUMAN	scaffold attachment factor B	549	Interaction with POLR2A.				chromatin organization|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	double-stranded DNA binding|nucleotide binding|protein binding|RNA binding			ovary(1)|liver(1)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (162;0.000222)														---	---	---	---
SAFB	6294	broad.mit.edu	37	19	5657295	5657295	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5657295G>A	uc002mcf.2	+	14	1852	c.1799G>A	c.(1798-1800)CGG>CAG	p.R600Q	SAFB_uc002mcg.2_Missense_Mutation_p.R600Q|SAFB_uc002mce.3_Missense_Mutation_p.R600Q|SAFB_uc010xir.1_Missense_Mutation_p.R600Q|SAFB_uc010xis.1_Missense_Mutation_p.R531Q|SAFB_uc010xit.1_Missense_Mutation_p.R443Q|SAFB_uc010xiu.1_Missense_Mutation_p.R399Q	NM_002967	NP_002958	Q15424	SAFB1_HUMAN	scaffold attachment factor B	600	Interaction with SAFB2.|Interaction with POLR2A.|Nuclear localization signal (Potential).				chromatin organization|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	double-stranded DNA binding|nucleotide binding|protein binding|RNA binding			ovary(1)|liver(1)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (162;0.000222)														---	---	---	---
SAFB	6294	broad.mit.edu	37	19	5661653	5661653	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5661653C>T	uc002mcf.2	+	15	2040	c.1987C>T	c.(1987-1989)CGC>TGC	p.R663C	SAFB_uc002mcg.2_Missense_Mutation_p.R663C|SAFB_uc002mce.3_Missense_Mutation_p.R662C|SAFB_uc010xir.1_Missense_Mutation_p.R662C|SAFB_uc010xis.1_Missense_Mutation_p.R594C|SAFB_uc010xit.1_Missense_Mutation_p.R505C|SAFB_uc010xiu.1_Missense_Mutation_p.R462C	NM_002967	NP_002958	Q15424	SAFB1_HUMAN	scaffold attachment factor B	663	Interaction with SAFB2.|Interaction with POLR2A.|Arg-rich.|Glu-rich.				chromatin organization|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	double-stranded DNA binding|nucleotide binding|protein binding|RNA binding			ovary(1)|liver(1)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (162;0.000222)														---	---	---	---
TMEM146	257062	broad.mit.edu	37	19	5772974	5772974	+	Nonsense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5772974G>T	uc002mda.2	+	20	2000	c.1939G>T	c.(1939-1941)GAG>TAG	p.E647*		NM_152784	NP_689997	Q86XM0	TM146_HUMAN	transmembrane protein 146 precursor	647	Extracellular (Potential).					integral to membrane				ovary(1)|central_nervous_system(1)|pancreas(1)	3																		---	---	---	---
RFX2	5990	broad.mit.edu	37	19	5994881	5994881	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5994881G>A	uc002meb.2	-	18	2406	c.2137C>T	c.(2137-2139)CGC>TGC	p.R713C	RFX2_uc002mec.2_Missense_Mutation_p.R688C	NM_000635	NP_000626	P48378	RFX2_HUMAN	regulatory factor X2 isoform a	713					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			breast(4)|ovary(1)|skin(1)	6																		---	---	---	---
PSPN	5623	broad.mit.edu	37	19	6375606	6375606	+	Missense_Mutation	SNP	C	T	T	rs144043296		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6375606C>T	uc010xja.1	-	2	170	c.170G>A	c.(169-171)CGC>CAC	p.R57H		NM_004158	NP_004149	O60542	PSPN_HUMAN	persephin precursor	57					axon guidance|central nervous system development		growth factor activity			skin(1)	1																		---	---	---	---
GTF2F1	2962	broad.mit.edu	37	19	6383369	6383369	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6383369T>A	uc002meq.2	-	6	920	c.635A>T	c.(634-636)GAC>GTC	p.D212V	GTF2F1_uc010xjb.1_Missense_Mutation_p.D36V|GTF2F1_uc010xjc.1_Missense_Mutation_p.D127V	NM_002096	NP_002087	P35269	T2FA_HUMAN	general transcription factor IIF, polypeptide 1,	212					mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of transcription, DNA-dependent|positive regulation of viral transcription|response to virus|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cell junction|transcription factor TFIIF complex	catalytic activity|DNA binding|phosphatase activator activity|transcription coactivator activity|transcription factor binding				0																		---	---	---	---
KHSRP	8570	broad.mit.edu	37	19	6417776	6417776	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6417776G>A	uc002mer.3	-	11	1165	c.1055C>T	c.(1054-1056)GCT>GTT	p.A352V		NM_003685	NP_003676	Q92945	FUBP2_HUMAN	KH-type splicing regulatory protein	352	Gly-rich.|KH 3.				mRNA processing|mRNA transport|regulation of transcription, DNA-dependent|RNA splicing, via transesterification reactions|transcription, DNA-dependent	cytosol|nucleus	DNA binding|protein binding|RNA binding			skin(1)	1																OREG0025200	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
KHSRP	8570	broad.mit.edu	37	19	6418043	6418043	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6418043G>A	uc002mer.3	-	10	1037	c.927C>T	c.(925-927)GGC>GGT	p.G309G		NM_003685	NP_003676	Q92945	FUBP2_HUMAN	KH-type splicing regulatory protein	309	Gly-rich.				mRNA processing|mRNA transport|regulation of transcription, DNA-dependent|RNA splicing, via transesterification reactions|transcription, DNA-dependent	cytosol|nucleus	DNA binding|protein binding|RNA binding			skin(1)	1																OREG0025200	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
C3	718	broad.mit.edu	37	19	6690639	6690639	+	Splice_Site	SNP	C	T	T	rs113600381		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6690639C>T	uc002mfm.2	-	27	3551	c.3489_splice	c.e27+1	p.N1163_splice	C3_uc002mfl.2_Splice_Site	NM_000064	NP_000055			complement component 3 precursor						complement activation, alternative pathway|complement activation, classical pathway|G-protein coupled receptor protein signaling pathway|inflammatory response|positive regulation vascular endothelial growth factor production	extracellular space	endopeptidase inhibitor activity|receptor binding			skin(3)|ovary(1)|pancreas(1)	5				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)														---	---	---	---
TRIP10	9322	broad.mit.edu	37	19	6743070	6743070	+	Missense_Mutation	SNP	G	A	A	rs140280835		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6743070G>A	uc002mfs.2	+	4	356	c.290G>A	c.(289-291)CGT>CAT	p.R97H	TRIP10_uc010dux.1_Missense_Mutation_p.R97H|TRIP10_uc002mfr.2_Missense_Mutation_p.R97H|TRIP10_uc010duy.2_RNA|TRIP10_uc010duz.2_Intron	NM_004240	NP_004231	Q15642	CIP4_HUMAN	thyroid hormone receptor interactor 10	97	Required for podosome formation and interaction with AKAP9 and microtubules.|Induction of membrane tubulation.|Required for translocation to the plasma membrane in response to insulin (By similarity).				actin cytoskeleton organization|cell communication|endocytosis|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell cortex|cell projection|cytoskeleton|cytosol|Golgi apparatus|lysosome|perinuclear region of cytoplasm|phagocytic cup	GTPase activator activity|identical protein binding|lipid binding			ovary(1)	1																		---	---	---	---
TRIP10	9322	broad.mit.edu	37	19	6744821	6744821	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6744821T>C	uc002mfs.2	+	9	866	c.800T>C	c.(799-801)GTC>GCC	p.V267A	TRIP10_uc010dux.1_Missense_Mutation_p.V267A|TRIP10_uc002mfr.2_Missense_Mutation_p.V267A|TRIP10_uc010duy.2_RNA|TRIP10_uc010duz.2_Missense_Mutation_p.V86A	NM_004240	NP_004231	Q15642	CIP4_HUMAN	thyroid hormone receptor interactor 10	267	Induction of membrane tubulation.				actin cytoskeleton organization|cell communication|endocytosis|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell cortex|cell projection|cytoskeleton|cytosol|Golgi apparatus|lysosome|perinuclear region of cytoplasm|phagocytic cup	GTPase activator activity|identical protein binding|lipid binding			ovary(1)	1																		---	---	---	---
TRIP10	9322	broad.mit.edu	37	19	6750351	6750351	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6750351A>G	uc002mfs.2	+	13	1510	c.1444A>G	c.(1444-1446)AGC>GGC	p.S482G	TRIP10_uc010dux.1_Missense_Mutation_p.S426G|TRIP10_uc002mfr.2_Missense_Mutation_p.S426G|TRIP10_uc010duy.2_RNA|TRIP10_uc010duz.2_Missense_Mutation_p.S245G	NM_004240	NP_004231	Q15642	CIP4_HUMAN	thyroid hormone receptor interactor 10	482	Interaction with CDC42.|Interaction with PDE6G (By similarity).|Required for interaction with FASLG and localization to lysosomes.				actin cytoskeleton organization|cell communication|endocytosis|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cell cortex|cell projection|cytoskeleton|cytosol|Golgi apparatus|lysosome|perinuclear region of cytoplasm|phagocytic cup	GTPase activator activity|identical protein binding|lipid binding			ovary(1)	1																		---	---	---	---
ARHGEF18	23370	broad.mit.edu	37	19	7532014	7532014	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7532014C>T	uc002mgi.2	+						ARHGEF18_uc010xjm.1_Intron|ARHGEF18_uc002mgh.2_Intron|ARHGEF18_uc002mgj.1_Intron	NM_001130955	NP_001124427			Rho/Rac guanine nucleotide exchange factor 18						actin cytoskeleton organization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of cell shape|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(1)	1		Renal(5;0.0902)																---	---	---	---
ZNF358	140467	broad.mit.edu	37	19	7584279	7584279	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7584279A>G	uc002mgn.2	+	2	321	c.151A>G	c.(151-153)AAC>GAC	p.N51D		NM_018083	NP_060553	Q9NW07	ZN358_HUMAN	zinc finger protein 358	51					embryonic forelimb morphogenesis|neural tube development|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
KIAA1543	57662	broad.mit.edu	37	19	7677796	7677796	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7677796G>A	uc002mgv.3	+	11	2518	c.2417G>A	c.(2416-2418)AGC>AAC	p.S806N	KIAA1543_uc002mgu.3_Missense_Mutation_p.S833N|KIAA1543_uc002mgw.2_5'Flank	NM_020902	NP_065953	Q9P1Y5	CAMP3_HUMAN	NEZHA isoform 2	806	Pro-rich.				epithelial cell-cell adhesion|microtubule anchoring|regulation of microtubule cytoskeleton organization|zonula adherens maintenance	cytoplasm|microtubule|zonula adherens	microtubule minus-end binding			pancreas(1)	1																		---	---	---	---
KIAA1543	57662	broad.mit.edu	37	19	7681512	7681512	+	Intron	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7681512A>T	uc002mgv.3	+						KIAA1543_uc002mgu.3_Intron|KIAA1543_uc002mgw.2_Intron	NM_020902	NP_065953			NEZHA isoform 2						epithelial cell-cell adhesion|microtubule anchoring|regulation of microtubule cytoskeleton organization|zonula adherens maintenance	cytoplasm|microtubule|zonula adherens	microtubule minus-end binding			pancreas(1)	1																		---	---	---	---
SNAPC2	6618	broad.mit.edu	37	19	7986354	7986354	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7986354C>A	uc002miw.1	+	2	253	c.230C>A	c.(229-231)GCC>GAC	p.A77D	SNAPC2_uc002mix.1_RNA	NM_003083	NP_003074	Q13487	SNPC2_HUMAN	small nuclear RNA activating complex,	77					snRNA transcription|transcription from RNA polymerase II promoter|transcription from RNA polymerase III promoter	nucleoplasm	sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
FBN3	84467	broad.mit.edu	37	19	8175856	8175856	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8175856G>A	uc002mjf.2	-							NM_032447	NP_115823			fibrillin 3 precursor							proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(6)|skin(3)|pancreas(1)|central_nervous_system(1)	11																		---	---	---	---
FBN3	84467	broad.mit.edu	37	19	8190771	8190771	+	Intron	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8190771C>A	uc002mjf.2	-							NM_032447	NP_115823			fibrillin 3 precursor							proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(6)|skin(3)|pancreas(1)|central_nervous_system(1)	11																		---	---	---	---
KANK3	256949	broad.mit.edu	37	19	8399208	8399208	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8399208C>T	uc010dwa.2	-	4	1489	c.1423G>A	c.(1423-1425)GGA>AGA	p.G475R	KANK3_uc002mjp.1_5'UTR	NM_198471	NP_940873	Q6NY19	KANK3_HUMAN	ankyrin repeat domain 47	475											0																		---	---	---	---
HNRNPM	4670	broad.mit.edu	37	19	8550717	8550717	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8550717A>G	uc010dwe.2	+	14	1485	c.1405A>G	c.(1405-1407)ATT>GTT	p.I469V	HNRNPM_uc010xke.1_Missense_Mutation_p.I415V|HNRNPM_uc010dwd.2_Missense_Mutation_p.I430V|HNRNPM_uc002mka.2_Missense_Mutation_p.I334V|HNRNPM_uc002mkb.1_5'Flank	NM_005968	NP_005959	P52272	HNRPM_HUMAN	heterogeneous nuclear ribonucleoprotein M	469	10.|27 X 6 AA repeats of [GEVSTPAN]-[ILMV]- [DE]-[RH]-[MLVI]-[GAV].				alternative nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|integral to plasma membrane|nuclear matrix|nucleolus|paraspeckles	nucleotide binding|protein domain specific binding|RNA binding				0																		---	---	---	---
MYO1F	4542	broad.mit.edu	37	19	8587572	8587572	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8587572G>A	uc002mkg.2	-	26	3110	c.2996C>T	c.(2995-2997)CCG>CTG	p.P999L		NM_012335	NP_036467	O00160	MYO1F_HUMAN	myosin IF	999						unconventional myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|skin(1)	3																		---	---	---	---
MYO1F	4542	broad.mit.edu	37	19	8615552	8615552	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8615552C>T	uc002mkg.2	-	9	912	c.798G>A	c.(796-798)CCG>CCA	p.P266P	MYO1F_uc002mkh.2_Silent_p.P266P	NM_012335	NP_036467	O00160	MYO1F_HUMAN	myosin IF	266	Myosin head-like.					unconventional myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)|skin(1)	3																		---	---	---	---
ADAMTS10	81794	broad.mit.edu	37	19	8666009	8666009	+	Missense_Mutation	SNP	G	A	A	rs147270233		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8666009G>A	uc002mkj.1	-	6	887	c.613C>T	c.(613-615)CGG>TGG	p.R205W	ADAMTS10_uc002mkk.1_5'UTR	NM_030957	NP_112219	Q9H324	ATS10_HUMAN	ADAM metallopeptidase with thrombospondin type 1	205					proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			pancreas(2)|skin(2)	4																		---	---	---	---
ACTL9	284382	broad.mit.edu	37	19	8808937	8808937	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8808937C>T	uc002mkl.2	-	1	236	c.115G>A	c.(115-117)GGC>AGC	p.G39S		NM_178525	NP_848620	Q8TC94	ACTL9_HUMAN	actin-like 9	39						cytoplasm|cytoskeleton				large_intestine(2)|pancreas(1)	3																		---	---	---	---
OR2Z1	284383	broad.mit.edu	37	19	8841802	8841802	+	Missense_Mutation	SNP	C	T	T	rs58741481	byFrequency;by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8841802C>T	uc010xkg.1	+	1	412	c.412C>T	c.(412-414)CGC>TGC	p.R138C		NM_001004699	NP_001004699	Q8NG97	OR2Z1_HUMAN	olfactory receptor, family 2, subfamily Z,	138	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)|skin(1)	2																		---	---	---	---
MUC16	94025	broad.mit.edu	37	19	8976803	8976803	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:8976803T>C	uc002mkp.2	-	73	42467	c.42263A>G	c.(42262-42264)TAT>TGT	p.Y14088C	MUC16_uc010dwi.2_RNA|MUC16_uc010dwj.2_Missense_Mutation_p.Y888C|MUC16_uc010xki.1_Intron	NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	14118	SEA 14.|Extracellular (Potential).			Missing (in Ref. 3; AAK74120).	cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57																		---	---	---	---
MUC16	94025	broad.mit.edu	37	19	9069710	9069710	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9069710G>A	uc002mkp.2	-	3	17940	c.17736C>T	c.(17734-17736)GGC>GGT	p.G5912G		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	5914	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57																		---	---	---	---
ZNF317	57693	broad.mit.edu	37	19	9271056	9271056	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9271056C>T	uc002mku.2	+	7	1010	c.735C>T	c.(733-735)ACC>ACT	p.T245T	ZNF317_uc002mkv.2_Silent_p.T104T|ZNF317_uc002mkw.2_Silent_p.T213T|ZNF317_uc002mkx.2_Silent_p.T160T|ZNF317_uc002mky.2_Silent_p.T128T	NM_020933	NP_065984	Q96PQ6	ZN317_HUMAN	zinc finger protein 317	245					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
OR7D4	125958	broad.mit.edu	37	19	9324820	9324820	+	Missense_Mutation	SNP	T	C	C	rs145364350	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9324820T>C	uc002mla.1	-	1	694	c.694A>G	c.(694-696)AAG>GAG	p.K232E		NM_001005191	NP_001005191	Q8NG98	OR7D4_HUMAN	olfactory receptor, family 7, subfamily D,	232	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
OR7D4	125958	broad.mit.edu	37	19	9325102	9325102	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9325102G>T	uc002mla.1	-	1	412	c.412C>A	c.(412-414)CCC>ACC	p.P138T		NM_001005191	NP_001005191	Q8NG98	OR7D4_HUMAN	olfactory receptor, family 7, subfamily D,	138	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
ZNF560	147741	broad.mit.edu	37	19	9578800	9578800	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9578800G>A	uc002mlp.1	-	10	1033	c.823C>T	c.(823-825)CGC>TGC	p.R275C	ZNF560_uc010dwr.1_Missense_Mutation_p.R169C	NM_152476	NP_689689	Q96MR9	ZN560_HUMAN	zinc finger protein 560	275					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)|ovary(1)|large_intestine(1)|pancreas(1)|liver(1)	6																		---	---	---	---
COL5A3	50509	broad.mit.edu	37	19	10090719	10090719	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10090719A>T	uc002mmq.1	-	36	2695	c.2609T>A	c.(2608-2610)CTC>CAC	p.L870H		NM_015719	NP_056534	P25940	CO5A3_HUMAN	collagen, type V, alpha 3 preproprotein	870	Triple-helical region.				collagen fibril organization|skin development	collagen type V	collagen binding|extracellular matrix structural constituent			ovary(7)|lung(1)|central_nervous_system(1)|skin(1)	10			Epithelial(33;7.11e-05)															---	---	---	---
PPAN-P2RY11	692312	broad.mit.edu	37	19	10218652	10218652	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10218652C>T	uc002mna.2	+	5	355	c.355C>T	c.(355-357)CGT>TGT	p.R119C	PPAN-P2RY11_uc010xla.1_Missense_Mutation_p.R119C|PPAN_uc002mmz.1_Missense_Mutation_p.R119C|PPAN_uc002mnb.1_Missense_Mutation_p.R66C|SNORD105B_uc010dwz.1_5'Flank	NM_001040664	NP_001035754	Q9NQ55	SSF1_HUMAN	PPAN-P2RY11 protein	119	Brix.				RNA splicing	nucleolus	protein binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(20;2.19e-08)|Epithelial(33;1.76e-05)|all cancers(31;3.54e-05)															---	---	---	---
DNMT1	1786	broad.mit.edu	37	19	10252904	10252904	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10252904C>T	uc002mng.2	-						DNMT1_uc002mne.2_5'Flank|DNMT1_uc002mnf.2_Intron|DNMT1_uc010xlc.1_Intron|DNMT1_uc002mnh.2_Intron|DNMT1_uc010xld.1_Intron	NM_001379	NP_001370			DNA (cytosine-5-)-methyltransferase 1 isoform b						chromatin modification|maintenance of DNA methylation|negative regulation of histone H3-K9 methylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of gene expression|positive regulation of histone H3-K4 methylation|transcription, DNA-dependent	nucleus	DNA (cytosine-5-)-methyltransferase activity|DNA binding|transcription factor binding			ovary(2)|prostate(1)|lung(1)|breast(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Ifosfamide(DB01181)|Procainamide(DB01035)													---	---	---	---
DNMT1	1786	broad.mit.edu	37	19	10270717	10270717	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10270717C>T	uc002mng.2	-	14	1198	c.1018G>A	c.(1018-1020)GCC>ACC	p.A340T	DNMT1_uc010xlc.1_Missense_Mutation_p.A356T|DNMT1_uc002mnh.2_Missense_Mutation_p.A235T|DNMT1_uc010xld.1_Missense_Mutation_p.A340T|DNMT1_uc002mnk.2_RNA	NM_001379	NP_001370	P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1 isoform b	340	DNA replication foci-targeting sequence (By similarity).|Homodimerization.|Interaction with the PRC2/EED-EZH2 complex (By similarity).				chromatin modification|maintenance of DNA methylation|negative regulation of histone H3-K9 methylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of gene expression|positive regulation of histone H3-K4 methylation|transcription, DNA-dependent	nucleus	DNA (cytosine-5-)-methyltransferase activity|DNA binding|transcription factor binding			ovary(2)|prostate(1)|lung(1)|breast(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Ifosfamide(DB01181)|Procainamide(DB01035)													---	---	---	---
ICAM5	7087	broad.mit.edu	37	19	10403740	10403740	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10403740C>T	uc002mnu.3	+	6	1348	c.1283C>T	c.(1282-1284)ACG>ATG	p.T428M	ICAM5_uc002mnv.3_Missense_Mutation_p.T303M	NM_003259	NP_003250	Q9UMF0	ICAM5_HUMAN	intercellular adhesion molecule 5 precursor	428	Extracellular (Potential).|Ig-like C2-type 5.				cell-cell adhesion	integral to plasma membrane				breast(3)	3			OV - Ovarian serous cystadenocarcinoma(20;2.64e-09)|Epithelial(33;4.31e-06)|all cancers(31;9.75e-06)															---	---	---	---
ICAM5	7087	broad.mit.edu	37	19	10403882	10403882	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10403882T>A	uc002mnu.3	+	6	1490	c.1425T>A	c.(1423-1425)GAT>GAA	p.D475E	ICAM5_uc002mnv.3_Missense_Mutation_p.D350E	NM_003259	NP_003250	Q9UMF0	ICAM5_HUMAN	intercellular adhesion molecule 5 precursor	475	Extracellular (Potential).|Ig-like C2-type 5.				cell-cell adhesion	integral to plasma membrane				breast(3)	3			OV - Ovarian serous cystadenocarcinoma(20;2.64e-09)|Epithelial(33;4.31e-06)|all cancers(31;9.75e-06)															---	---	---	---
RAVER1	125950	broad.mit.edu	37	19	10431522	10431522	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10431522G>A	uc002moa.2	-	9	1710	c.1630C>T	c.(1630-1632)CGG>TGG	p.R544W	RAVER1_uc002mnz.2_5'Flank	NM_133452	NP_597709	Q8IY67	RAVR1_HUMAN	RAVER1	544						cytoplasm|nucleus	nucleotide binding|protein binding|RNA binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(20;1.81e-09)|Epithelial(33;3.65e-06)|all cancers(31;8.35e-06)															---	---	---	---
TYK2	7297	broad.mit.edu	37	19	10475403	10475403	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10475403C>T	uc002moc.3	-	9	1632	c.1254G>A	c.(1252-1254)TCG>TCA	p.S418S	TYK2_uc010dxe.2_Silent_p.S233S|TYK2_uc002mod.2_Silent_p.S418S	NM_003331	NP_003322	P29597	TYK2_HUMAN	tyrosine kinase 2	418	FERM.				intracellular protein kinase cascade|regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway	cytoskeleton|cytosol|membrane|nucleus	ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity			lung(5)|large_intestine(2)|ovary(1)|breast(1)	9			OV - Ovarian serous cystadenocarcinoma(20;1.77e-09)|Epithelial(33;3.92e-06)|all cancers(31;8.95e-06)															---	---	---	---
TYK2	7297	broad.mit.edu	37	19	10477105	10477105	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10477105G>A	uc002moc.3	-	6	995	c.617C>T	c.(616-618)GCC>GTC	p.A206V	TYK2_uc010dxe.2_Missense_Mutation_p.A21V|TYK2_uc002mod.2_Missense_Mutation_p.A206V	NM_003331	NP_003322	P29597	TYK2_HUMAN	tyrosine kinase 2	206	FERM.				intracellular protein kinase cascade|regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway	cytoskeleton|cytosol|membrane|nucleus	ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity			lung(5)|large_intestine(2)|ovary(1)|breast(1)	9			OV - Ovarian serous cystadenocarcinoma(20;1.77e-09)|Epithelial(33;3.92e-06)|all cancers(31;8.95e-06)															---	---	---	---
CDC37	11140	broad.mit.edu	37	19	10506796	10506796	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10506796G>A	uc002mof.1	-	2	302	c.186C>T	c.(184-186)GCC>GCT	p.A62A	CDC37_uc002moe.1_5'Flank|CDC37_uc010dxf.1_5'UTR|CDC37_uc002mog.1_Silent_p.A62A|CDC37_uc002moh.2_Silent_p.A62A	NM_007065	NP_008996	Q16543	CDC37_HUMAN	cell division cycle 37 protein	62					protein targeting|regulation of cyclin-dependent protein kinase activity|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway		unfolded protein binding				0			OV - Ovarian serous cystadenocarcinoma(20;4.65e-10)|Epithelial(33;6.48e-07)|all cancers(31;2.31e-06)	GBM - Glioblastoma multiforme(1328;0.0318)														---	---	---	---
PDE4A	5141	broad.mit.edu	37	19	10578219	10578219	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10578219C>A	uc002moj.2	+	15	2691	c.2583C>A	c.(2581-2583)GCC>GCA	p.A861A	PDE4A_uc002mok.2_Silent_p.A835A|PDE4A_uc002mol.2_Silent_p.A800A|PDE4A_uc002mom.2_Silent_p.A622A|PDE4A_uc002mon.2_Silent_p.A316A|PDE4A_uc002moo.2_3'UTR	NM_001111307	NP_001104777	P27815	PDE4A_HUMAN	phosphodiesterase 4A isoform 1	861					signal transduction	cytosol|membrane fraction|perinuclear region of cytoplasm|ruffle membrane|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|protein binding			ovary(1)|breast(1)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(20;5.8e-10)|Epithelial(33;7.58e-07)|all cancers(31;3.91e-06)		Cilostazol(DB01166)|Dipyridamole(DB00975)|Dyphylline(DB00651)|Enprofylline(DB00824)|Iloprost(DB01088)|Milrinone(DB00235)|Pentoxifylline(DB00806)|Phentolamine(DB00692)|Tadalafil(DB00820)|Theophylline(DB00277)													---	---	---	---
S1PR5	53637	broad.mit.edu	37	19	10624702	10624702	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10624702C>T	uc002mot.1	-	2	1043	c.986G>A	c.(985-987)GGC>GAC	p.G329D	S1PR5_uc002mou.1_Missense_Mutation_p.G329D	NM_030760	NP_110387	Q9H228	S1PR5_HUMAN	endothelial differentiation, sphingolipid	329	Cytoplasmic (By similarity).					integral to membrane|plasma membrane	lysosphingolipid and lysophosphatidic acid receptor activity			central_nervous_system(1)|pancreas(1)	2																		---	---	---	---
S1PR5	53637	broad.mit.edu	37	19	10624950	10624950	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10624950C>T	uc002mot.1	-	2	795	c.738G>A	c.(736-738)TCG>TCA	p.S246S	S1PR5_uc002mou.1_Silent_p.S246S	NM_030760	NP_110387	Q9H228	S1PR5_HUMAN	endothelial differentiation, sphingolipid	246	Cytoplasmic (By similarity).					integral to membrane|plasma membrane	lysosphingolipid and lysophosphatidic acid receptor activity			central_nervous_system(1)|pancreas(1)	2																		---	---	---	---
ILF3	3609	broad.mit.edu	37	19	10781739	10781739	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10781739C>T	uc002mpn.2	+	3	410	c.93C>T	c.(91-93)GTC>GTT	p.V31V	ILF3_uc002mpm.2_Silent_p.V31V|ILF3_uc002mpl.2_Silent_p.V31V|ILF3_uc002mpk.2_Silent_p.V31V|ILF3_uc010xli.1_Intron|ILF3_uc002mpo.2_Silent_p.V31V	NM_012218	NP_036350	Q12906	ILF3_HUMAN	interleukin enhancer binding factor 3 isoform a	31					M phase|negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrion|nucleolus|ribonucleoprotein complex	DNA binding|double-stranded RNA binding|protein binding|protein binding			ovary(3)	3			Epithelial(33;6.86e-06)|all cancers(31;1.65e-05)															---	---	---	---
DNM2	1785	broad.mit.edu	37	19	10893719	10893719	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10893719T>C	uc002mps.1	+	6	936	c.772T>C	c.(772-774)TTC>CTC	p.F258L	DNM2_uc010dxk.2_RNA|DNM2_uc002mpt.1_Missense_Mutation_p.F258L|DNM2_uc002mpv.1_Missense_Mutation_p.F258L|DNM2_uc002mpu.1_Missense_Mutation_p.F258L|DNM2_uc010dxl.1_Missense_Mutation_p.F258L|DNM2_uc002mpw.2_5'UTR	NM_001005361	NP_001005361	P50570	DYN2_HUMAN	dynamin 2 isoform 2	258					G2/M transition of mitotic cell cycle|positive regulation of apoptosis|positive regulation of transcription, DNA-dependent|post-Golgi vesicle-mediated transport|receptor internalization|signal transduction|synaptic vesicle transport|transferrin transport	cell junction|cytosol|Golgi membrane|microtubule|postsynaptic density|postsynaptic membrane	GTP binding|GTPase activity|microtubule binding			central_nervous_system(2)|skin(2)|ovary(1)|breast(1)	6			Epithelial(33;4.17e-05)|all cancers(31;8.48e-05)															---	---	---	---
SMARCA4	6597	broad.mit.edu	37	19	11143999	11143999	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11143999G>A	uc002mqf.3	+	26	3864	c.3580G>A	c.(3580-3582)GGG>AGG	p.G1194R	SMARCA4_uc010dxp.2_Missense_Mutation_p.G1194R|SMARCA4_uc010dxo.2_Missense_Mutation_p.G1194R|SMARCA4_uc010dxq.2_Missense_Mutation_p.G1194R|SMARCA4_uc010dxr.2_Missense_Mutation_p.G1194R|SMARCA4_uc002mqj.3_Missense_Mutation_p.G1194R|SMARCA4_uc010dxs.2_Missense_Mutation_p.G1194R|SMARCA4_uc010dxt.1_Missense_Mutation_p.G414R|SMARCA4_uc002mqh.3_Missense_Mutation_p.G317R|SMARCA4_uc002mqi.1_Missense_Mutation_p.G397R	NM_003072	NP_003063	P51532	SMCA4_HUMAN	SWI/SNF-related matrix-associated	1194	Helicase C-terminal.				chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex	androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity			lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1)	67		all_lung(6;0.0512)|Lung NSC(9;0.0568)						F|N|Mis		NSCLC				Rhabdoid_Predisposition_syndrome				---	---	---	---
DOCK6	57572	broad.mit.edu	37	19	11312743	11312743	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11312743C>T	uc002mqs.3	-	44	5551	c.5510G>A	c.(5509-5511)CGG>CAG	p.R1837Q	DOCK6_uc002mqr.3_Missense_Mutation_p.R237Q|DOCK6_uc010xlq.1_Missense_Mutation_p.R1176Q	NM_020812	NP_065863	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	1837	DHR-2.				blood coagulation	cytosol	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(2)|skin(1)	3																		---	---	---	---
LPPR2	64748	broad.mit.edu	37	19	11474490	11474490	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11474490C>T	uc002mre.1	+	8	1279	c.942C>T	c.(940-942)CTC>CTT	p.L314L	LPPR2_uc002mrf.1_Silent_p.L289L|LPPR2_uc010dxy.1_Silent_p.L121L	NM_022737	NP_073574	Q96GM1	LPPR2_HUMAN	lipid phosphate phosphatase-related protein type	314						integral to membrane	phosphatidate phosphatase activity			large_intestine(1)	1																		---	---	---	---
ZNF653	115950	broad.mit.edu	37	19	11598444	11598444	+	Silent	SNP	G	A	A	rs142746343		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11598444G>A	uc002mrz.1	-	4	887	c.834C>T	c.(832-834)TGC>TGT	p.C278C		NM_138783	NP_620138	Q96CK0	ZN653_HUMAN	zinc finger protein 653	278					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ACP5	54	broad.mit.edu	37	19	11685964	11685964	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11685964C>T	uc002msg.3	-	5	985	c.839G>A	c.(838-840)CGC>CAC	p.R280H	uc002msf.2_Intron|ACP5_uc002msh.3_Missense_Mutation_p.R280H|ACP5_uc002msi.3_Missense_Mutation_p.R280H|ACP5_uc002msj.3_Missense_Mutation_p.R280H	NM_001611	NP_001602	P13686	PPA5_HUMAN	acid phosphatase 5, tartrate resistant	280					water-soluble vitamin metabolic process	cytosol|integral to membrane|lysosome	acid phosphatase activity|ferric iron binding|ferrous iron binding			central_nervous_system(1)	1																		---	---	---	---
ACP5	54	broad.mit.edu	37	19	11686037	11686037	+	Missense_Mutation	SNP	C	T	T	rs146196342	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11686037C>T	uc002msg.3	-	5	912	c.766G>A	c.(766-768)GTG>ATG	p.V256M	uc002msf.2_Intron|ACP5_uc002msh.3_Missense_Mutation_p.V256M|ACP5_uc002msi.3_Missense_Mutation_p.V256M|ACP5_uc002msj.3_Missense_Mutation_p.V256M	NM_001611	NP_001602	P13686	PPA5_HUMAN	acid phosphatase 5, tartrate resistant	256					water-soluble vitamin metabolic process	cytosol|integral to membrane|lysosome	acid phosphatase activity|ferric iron binding|ferrous iron binding			central_nervous_system(1)	1																		---	---	---	---
ZNF823	55552	broad.mit.edu	37	19	11833260	11833260	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11833260C>A	uc002msm.2	-	4	1215	c.1089G>T	c.(1087-1089)AAG>AAT	p.K363N	ZNF823_uc010xmd.1_Missense_Mutation_p.K181N|ZNF823_uc010dyi.1_Missense_Mutation_p.K319N	NM_001080493	NP_001073962	P16415	ZN823_HUMAN	ZFP-36 for a zinc finger protein	363	C2H2-type 8.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2															HNSCC(68;0.2)			---	---	---	---
ZNF823	55552	broad.mit.edu	37	19	11833275	11833275	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11833275T>G	uc002msm.2	-	4	1200	c.1074A>C	c.(1072-1074)AAA>AAC	p.K358N	ZNF823_uc010xmd.1_Missense_Mutation_p.K176N|ZNF823_uc010dyi.1_Missense_Mutation_p.K314N	NM_001080493	NP_001073962	P16415	ZN823_HUMAN	ZFP-36 for a zinc finger protein	358					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2															HNSCC(68;0.2)			---	---	---	---
ZNF440	126070	broad.mit.edu	37	19	11942860	11942860	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11942860G>T	uc002msp.1	+	4	1025	c.869G>T	c.(868-870)GGA>GTA	p.G290V		NM_152357	NP_689570	Q8IYI8	ZN440_HUMAN	zinc finger protein 440	290	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
TNPO2	30000	broad.mit.edu	37	19	12817137	12817137	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12817137G>A	uc002muo.2	-	14	1726	c.1541C>T	c.(1540-1542)CCC>CTC	p.P514L	TNPO2_uc002mup.2_Missense_Mutation_p.P606L|TNPO2_uc002muq.2_Missense_Mutation_p.P514L|TNPO2_uc002mur.2_Missense_Mutation_p.P514L	NM_001136196	NP_001129668	O14787	TNPO2_HUMAN	transportin 2 (importin 3, karyopherin beta 2b)	514	HEAT 9.				intracellular protein transport	cytoplasm|nucleus	nuclear localization sequence binding|protein binding|protein transporter activity			ovary(1)	1																		---	---	---	---
RNASEH2A	10535	broad.mit.edu	37	19	12921005	12921005	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12921005G>A	uc002mvg.1	+	5	592	c.532G>A	c.(532-534)GCC>ACC	p.A178T	RNASEH2A_uc002mvf.1_Missense_Mutation_p.A96T	NM_006397	NP_006388	O75792	RNH2A_HUMAN	ribonuclease H2, large subunit	178					DNA replication|RNA catabolic process	nucleus|ribonuclease H2 complex	metal ion binding|ribonuclease H activity|RNA binding			breast(2)|central_nervous_system(1)	3																		---	---	---	---
MAST1	22983	broad.mit.edu	37	19	12984861	12984861	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12984861A>G	uc002mvm.2	+	26	4018	c.3890A>G	c.(3889-3891)GAC>GGC	p.D1297G		NM_014975	NP_055790	Q9Y2H9	MAST1_HUMAN	microtubule associated serine/threonine kinase	1297					cytoskeleton organization|intracellular protein kinase cascade	cytoplasm|cytoskeleton|plasma membrane	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|large_intestine(1)|skin(1)	7																		---	---	---	---
FARSA	2193	broad.mit.edu	37	19	13035938	13035938	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13035938G>A	uc002mvs.2	-	8	940	c.892C>T	c.(892-894)CGG>TGG	p.R298W	FARSA_uc002mvt.2_RNA|FARSA_uc010xmv.1_Missense_Mutation_p.R267W|FARSA_uc010dyy.1_Missense_Mutation_p.R219W	NM_004461	NP_004452	Q9Y285	SYFA_HUMAN	phenylalanyl-tRNA synthetase, alpha subunit	298					phenylalanyl-tRNA aminoacylation	cytosol|soluble fraction	ATP binding|phenylalanine-tRNA ligase activity|protein binding|tRNA binding			ovary(1)	1					L-Phenylalanine(DB00120)													---	---	---	---
CALR	811	broad.mit.edu	37	19	13054445	13054445	+	Splice_Site	SNP	T	C	C	rs112182567		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13054445T>C	uc002mvu.2	+	8	1133	c.1053_splice	c.e8+2	p.K351_splice	CALR_uc002mvv.2_5'Flank|RAD23A_uc002mvw.1_5'Flank|RAD23A_uc002mvx.1_5'Flank|RAD23A_uc002mvz.1_5'Flank|RAD23A_uc002mwa.1_5'Flank|RAD23A_uc002mvy.1_5'Flank|RAD23A_uc010xmw.1_5'Flank	NM_004343	NP_004334			calreticulin precursor						cell cycle arrest|cellular senescence|glucocorticoid receptor signaling pathway|negative regulation of neuron differentiation|negative regulation of retinoic acid receptor signaling pathway|negative regulation of steroid hormone receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative regulation of translation|peptide antigen assembly with MHC class I protein complex|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of DNA replication|positive regulation of phagocytosis|post-translational protein modification|protein export from nucleus|protein maturation by protein folding|protein N-linked glycosylation via asparagine|protein stabilization|regulation of apoptosis|sequestering of calcium ion	cytosol|endoplasmic reticulum lumen|extracellular space|MHC class I peptide loading complex|nucleus|perinuclear region of cytoplasm|polysome|proteinaceous extracellular matrix	androgen receptor binding|calcium ion binding|chaperone binding|complement component C1q binding|DNA binding|integrin binding|mRNA binding|protein binding involved in protein folding|sugar binding|ubiquitin protein ligase binding|unfolded protein binding|zinc ion binding			ovary(1)	1					Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
CACNA1A	773	broad.mit.edu	37	19	13372399	13372399	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13372399G>A	uc010dze.2	-	26	4354	c.4118C>T	c.(4117-4119)TCA>TTA	p.S1373L	CACNA1A_uc010xnd.1_Missense_Mutation_p.S78L|CACNA1A_uc002mwx.3_Missense_Mutation_p.S78L|CACNA1A_uc010dzc.2_Missense_Mutation_p.S898L|CACNA1A_uc002mwy.3_Missense_Mutation_p.S1372L|CACNA1A_uc010xne.1_Missense_Mutation_p.S901L	NM_001127221	NP_001120693	O00555	CAC1A_HUMAN	calcium channel, alpha 1A subunit isoform 3	1373	III.|Cytoplasmic (Potential).				cell death|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|membrane depolarization|regulation of insulin secretion	cytoplasm|nucleus	syntaxin binding			large_intestine(2)	2			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Cinnarizine(DB00568)|Loperamide(DB00836)|Nisoldipine(DB00401)|Pregabalin(DB00230)													---	---	---	---
CACNA1A	773	broad.mit.edu	37	19	13411460	13411460	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13411460T>C	uc010dze.2	-	18	2422	c.2186A>G	c.(2185-2187)GAG>GGG	p.E729G	CACNA1A_uc010dzc.2_Missense_Mutation_p.E254G|CACNA1A_uc002mwy.3_Missense_Mutation_p.E728G|CACNA1A_uc010xne.1_Missense_Mutation_p.E257G	NM_001127221	NP_001120693	O00555	CAC1A_HUMAN	calcium channel, alpha 1A subunit isoform 3	729	Cytoplasmic (Potential).|Poly-Glu.				cell death|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|membrane depolarization|regulation of insulin secretion	cytoplasm|nucleus	syntaxin binding			large_intestine(2)	2			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Cinnarizine(DB00568)|Loperamide(DB00836)|Nisoldipine(DB00401)|Pregabalin(DB00230)													---	---	---	---
IL27RA	9466	broad.mit.edu	37	19	14153568	14153568	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14153568G>A	uc002mxx.2	+	6	1158	c.735G>A	c.(733-735)ACG>ACA	p.T245T		NM_004843	NP_004834	Q6UWB1	I27RA_HUMAN	class I cytokine receptor precursor	245	Extracellular (Potential).				cell surface receptor linked signaling pathway|immune response	integral to plasma membrane	transmembrane receptor activity				0																OREG0025302	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
LPHN1	22859	broad.mit.edu	37	19	14273545	14273545	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14273545G>T	uc010xnn.1	-	6	1379	c.1083C>A	c.(1081-1083)ACC>ACA	p.T361T	LPHN1_uc010xno.1_Silent_p.T356T|uc002myf.2_Intron	NM_001008701	NP_001008701	O94910	LPHN1_HUMAN	latrophilin 1 isoform 1 precursor	361	Olfactomedin-like.|Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			ovary(2)|lung(2)|central_nervous_system(1)	5																		---	---	---	---
CD97	976	broad.mit.edu	37	19	14517769	14517769	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14517769C>T	uc002myl.2	+	17	2327	c.2204C>T	c.(2203-2205)GCG>GTG	p.A735V	CD97_uc002mym.2_Missense_Mutation_p.A686V|CD97_uc002myn.2_Missense_Mutation_p.A642V	NM_078481	NP_510966	P48960	CD97_HUMAN	CD97 antigen isoform 1 precursor	735	Cytoplasmic (Potential).				cell adhesion|cell-cell signaling|cellular component movement|immune response|inflammatory response|neuropeptide signaling pathway	extracellular space|integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(3)|breast(1)	4																OREG0025312	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
PKN1	5585	broad.mit.edu	37	19	14561174	14561174	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14561174C>T	uc002myp.2	+	5	823	c.655C>T	c.(655-657)CGG>TGG	p.R219W	PKN1_uc002myq.2_Missense_Mutation_p.R225W	NM_002741	NP_002732	Q16512	PKN1_HUMAN	protein kinase N1 isoform 2	219	REM 3.				activation of JUN kinase activity|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	endosome|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|GTP-Rho binding|histone binding|histone deacetylase binding|histone kinase activity (H3-T11 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|Rac GTPase binding			ovary(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)	8																		---	---	---	---
PKN1	5585	broad.mit.edu	37	19	14569089	14569089	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14569089C>A	uc002myp.2	+	9	1489	c.1321C>A	c.(1321-1323)CTG>ATG	p.L441M	PKN1_uc002myq.2_Missense_Mutation_p.L447M	NM_002741	NP_002732	Q16512	PKN1_HUMAN	protein kinase N1 isoform 2	441	C2.				activation of JUN kinase activity|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	endosome|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|GTP-Rho binding|histone binding|histone deacetylase binding|histone kinase activity (H3-T11 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|Rac GTPase binding			ovary(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)	8																		---	---	---	---
EMR3	84658	broad.mit.edu	37	19	14765914	14765914	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14765914C>A	uc002mzi.3	-	6	605	c.457G>T	c.(457-459)GGG>TGG	p.G153W	EMR3_uc010dzp.2_Missense_Mutation_p.G101W|EMR3_uc010xnv.1_Intron	NM_032571	NP_115960	Q9BY15	EMR3_HUMAN	egf-like module-containing mucin-like receptor	153	Extracellular (Potential).				neuropeptide signaling pathway	extracellular space|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(5)|skin(1)	6																		---	---	---	---
EMR2	30817	broad.mit.edu	37	19	14854312	14854312	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14854312C>A	uc002mzp.1	-	20	2839	c.2383G>T	c.(2383-2385)GGG>TGG	p.G795W	EMR2_uc010dzs.1_Missense_Mutation_p.G254W|EMR2_uc010xnw.1_Missense_Mutation_p.G737W|EMR2_uc002mzo.1_Missense_Mutation_p.G784W|EMR2_uc002mzq.1_Missense_Mutation_p.G735W|EMR2_uc002mzr.1_Missense_Mutation_p.G746W|EMR2_uc002mzs.1_Missense_Mutation_p.G653W|EMR2_uc002mzt.1_Missense_Mutation_p.G691W|EMR2_uc002mzu.1_Missense_Mutation_p.G702W	NM_013447	NP_038475	Q9UHX3	EMR2_HUMAN	egf-like module containing, mucin-like, hormone	795	Cytoplasmic (Potential).				cell adhesion|neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			lung(2)|ovary(1)|skin(1)	4																		---	---	---	---
EMR2	30817	broad.mit.edu	37	19	14866516	14866516	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14866516T>C	uc002mzp.1	-	13	1822	c.1366A>G	c.(1366-1368)AAC>GAC	p.N456D	EMR2_uc010dzs.1_Intron|EMR2_uc010xnw.1_Missense_Mutation_p.N456D|EMR2_uc002mzo.1_Missense_Mutation_p.N445D|EMR2_uc002mzq.1_Missense_Mutation_p.N396D|EMR2_uc002mzr.1_Missense_Mutation_p.N407D|EMR2_uc002mzs.1_Missense_Mutation_p.N314D|EMR2_uc002mzt.1_Missense_Mutation_p.N352D|EMR2_uc002mzu.1_Missense_Mutation_p.N363D|EMR2_uc010xnx.1_Intron|EMR2_uc010xny.1_Intron	NM_013447	NP_038475	Q9UHX3	EMR2_HUMAN	egf-like module containing, mucin-like, hormone	456	Extracellular (Potential).				cell adhesion|neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			lung(2)|ovary(1)|skin(1)	4																		---	---	---	---
OR7C1	26664	broad.mit.edu	37	19	14910188	14910188	+	Missense_Mutation	SNP	G	A	A	rs141077779		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14910188G>A	uc010xnz.1	-	1	761	c.761C>T	c.(760-762)ACG>ATG	p.T254M		NM_198944	NP_945182	O76099	OR7C1_HUMAN	olfactory receptor, family 7, subfamily C,	254	Helical; Name=6; (Potential).				sensory perception of smell|spermatogenesis	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2																		---	---	---	---
CCDC105	126402	broad.mit.edu	37	19	15133859	15133859	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15133859G>A	uc002nae.2	+	7	1527	c.1428G>A	c.(1426-1428)CAG>CAA	p.Q476Q		NM_173482	NP_775753	Q8IYK2	CC105_HUMAN	coiled-coil domain containing 105	476					microtubule cytoskeleton organization	microtubule				ovary(1)	1																		---	---	---	---
SYDE1	85360	broad.mit.edu	37	19	15222137	15222137	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15222137A>G	uc002nah.1	+	5	1335	c.1304A>G	c.(1303-1305)TAC>TGC	p.Y435C	SYDE1_uc002nai.1_Missense_Mutation_p.Y368C|SYDE1_uc002naj.1_Missense_Mutation_p.Y92C	NM_033025	NP_149014	Q6ZW31	SYDE1_HUMAN	synapse defective 1, Rho GTPase, homolog 1	435	Rho-GAP.				activation of Rho GTPase activity|small GTPase mediated signal transduction	cytosol	Rho GTPase activator activity			ovary(1)|pancreas(1)	2																		---	---	---	---
NOTCH3	4854	broad.mit.edu	37	19	15272414	15272414	+	Missense_Mutation	SNP	G	A	A	rs151322770		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15272414G>A	uc002nan.2	-	33	6101	c.6025C>T	c.(6025-6027)CGG>TGG	p.R2009W		NM_000435	NP_000426	Q9UM47	NOTC3_HUMAN	Notch homolog 3 precursor	2009	Cytoplasmic (Potential).				Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity			lung(8)|ovary(5)|skin(4)|prostate(2)|central_nervous_system(1)|breast(1)	21			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)															---	---	---	---
NOTCH3	4854	broad.mit.edu	37	19	15289721	15289721	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15289721G>A	uc002nan.2	-	23	3826	c.3750C>T	c.(3748-3750)TGC>TGT	p.C1250C	NOTCH3_uc002nao.1_Silent_p.C1198C	NM_000435	NP_000426	Q9UM47	NOTC3_HUMAN	Notch homolog 3 precursor	1250	Extracellular (Potential).|EGF-like 32.				Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity			lung(8)|ovary(5)|skin(4)|prostate(2)|central_nervous_system(1)|breast(1)	21			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)															---	---	---	---
NOTCH3	4854	broad.mit.edu	37	19	15289829	15289829	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15289829C>T	uc002nan.2	-						NOTCH3_uc002nao.1_Intron	NM_000435	NP_000426			Notch homolog 3 precursor						Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity			lung(8)|ovary(5)|skin(4)|prostate(2)|central_nervous_system(1)|breast(1)	21			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)															---	---	---	---
NOTCH3	4854	broad.mit.edu	37	19	15290989	15290989	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15290989T>C	uc002nan.2	-	20	3297	c.3221A>G	c.(3220-3222)GAG>GGG	p.E1074G	NOTCH3_uc002nao.1_Missense_Mutation_p.E1022G	NM_000435	NP_000426	Q9UM47	NOTC3_HUMAN	Notch homolog 3 precursor	1074	Extracellular (Potential).|EGF-like 27.				Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity			lung(8)|ovary(5)|skin(4)|prostate(2)|central_nervous_system(1)|breast(1)	21			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)															---	---	---	---
NOTCH3	4854	broad.mit.edu	37	19	15295143	15295143	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15295143G>A	uc002nan.2	-	16	2605	c.2529C>T	c.(2527-2529)GGC>GGT	p.G843G	NOTCH3_uc002nao.1_Intron	NM_000435	NP_000426	Q9UM47	NOTC3_HUMAN	Notch homolog 3 precursor	843	Extracellular (Potential).|EGF-like 21; calcium-binding (Potential).				Notch receptor processing|Notch signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity			lung(8)|ovary(5)|skin(4)|prostate(2)|central_nervous_system(1)|breast(1)	21			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)															---	---	---	---
AKAP8	10270	broad.mit.edu	37	19	15484787	15484787	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15484787C>T	uc002nav.2	-	4	242	c.181G>A	c.(181-183)GCC>ACC	p.A61T	AKAP8_uc010dzy.2_5'Flank|AKAP8_uc010dzz.1_RNA|AKAP8_uc010xog.1_Intron	NM_005858	NP_005849	O43823	AKAP8_HUMAN	A-kinase anchor protein 8	61					signal transduction	nuclear matrix				ovary(1)|breast(1)	2																		---	---	---	---
RASAL3	64926	broad.mit.edu	37	19	15569226	15569226	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15569226C>T	uc002nbe.2	-	8	887	c.801G>A	c.(799-801)ACG>ACA	p.T267T	RASAL3_uc010eaa.1_5'Flank	NM_022904	NP_075055	Q86YV0	RASL3_HUMAN	RAS protein activator like 3	267	PH.				negative regulation of Ras protein signal transduction|signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	Ras GTPase activator activity				0																		---	---	---	---
TPM4	7171	broad.mit.edu	37	19	16197334	16197334	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16197334A>G	uc002ndj.2	+	3	609	c.368A>G	c.(367-369)GAC>GGC	p.D123G	TPM4_uc002ndi.2_Missense_Mutation_p.D159G|TPM4_uc002ndk.1_Missense_Mutation_p.D33G	NM_003290	NP_003281	P67936	TPM4_HUMAN	tropomyosin 4 isoform 2	123	By similarity.				cellular component movement|muscle filament sliding|response to oxidative stress	cytosol|muscle thin filament tropomyosin|stress fiber	actin binding|calcium ion binding|structural constituent of muscle		TPM4/ALK(12)	soft_tissue(10)|haematopoietic_and_lymphoid_tissue(2)|breast(1)	13								T	ALK	ALCL								---	---	---	---
TMEM38A	79041	broad.mit.edu	37	19	16791337	16791337	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:16791337C>T	uc002nes.2	+	3	502	c.411C>T	c.(409-411)GCC>GCT	p.A137A		NM_024074	NP_076979	Q9H6F2	TM38A_HUMAN	transmembrane protein 38A	137	Cytoplasmic (Potential).|His-rich.					integral to membrane|nuclear membrane|sarcoplasmic reticulum membrane	potassium channel activity			central_nervous_system(2)|ovary(1)	3																		---	---	---	---
CPAMD8	27151	broad.mit.edu	37	19	17057905	17057905	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17057905G>T	uc002nfb.2	-	21	2814	c.2782C>A	c.(2782-2784)CTG>ATG	p.L928M		NM_015692	NP_056507	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain	881						extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1)	13																		---	---	---	---
CPAMD8	27151	broad.mit.edu	37	19	17132952	17132952	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17132952G>A	uc002nfb.2	-	2	305	c.273C>T	c.(271-273)GGC>GGT	p.G91G		NM_015692	NP_056507	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain	44						extracellular space|plasma membrane	serine-type endopeptidase inhibitor activity			ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1)	13																		---	---	---	---
MYO9B	4650	broad.mit.edu	37	19	17303576	17303576	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17303576C>T	uc010eak.2	+	21	2985	c.2833C>T	c.(2833-2835)CGG>TGG	p.R945W	MYO9B_uc002nfi.2_Missense_Mutation_p.R945W|MYO9B_uc002nfj.1_Missense_Mutation_p.R945W	NM_004145	NP_004136	Q13459	MYO9B_HUMAN	myosin IXB isoform 1	945	Neck or regulatory domain.				actin filament-based movement	cell cortex|cytosol|filamentous actin|myosin complex|perinuclear region of cytoplasm	actin binding|ADP binding|ATP binding|ATPase activity|calmodulin binding|metal ion binding|microfilament motor activity|Rho GTPase activator activity			breast(1)	1																		---	---	---	---
C19orf62	29086	broad.mit.edu	37	19	17387325	17387325	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17387325G>A	uc002nfu.2	+	7	709	c.591G>A	c.(589-591)CCG>CCA	p.P197P	C19orf62_uc010xpl.1_Silent_p.P122P|C19orf62_uc002nfv.2_Silent_p.P197P|C19orf62_uc010ean.2_RNA|C19orf62_uc002nfw.2_Silent_p.P197P	NM_014173	NP_054892	Q9NWV8	BABA1_HUMAN	mediator of Rap80 interactions and targeting 40	197	VWFA-like.				chromatin modification|double-strand break repair|G2/M transition DNA damage checkpoint|positive regulation of DNA repair|protein K63-linked deubiquitination|response to ionizing radiation	BRCA1-A complex|BRISC complex|cytoplasm	protein binding			ovary(1)|haematopoietic_and_lymphoid_tissue(1)	2																		---	---	---	---
ANKLE1	126549	broad.mit.edu	37	19	17394487	17394487	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17394487G>A	uc002nga.2	+	5	1190	c.914G>A	c.(913-915)AGC>AAC	p.S305N	ANKLE1_uc010xpm.1_RNA|ANKLE1_uc010eao.1_Missense_Mutation_p.S327N|ANKLE1_uc010xpn.1_Missense_Mutation_p.S359N|ANKLE1_uc002nfy.2_Missense_Mutation_p.S294N|ANKLE1_uc002nfz.2_Missense_Mutation_p.S11N	NM_152363	NP_689576	Q8NAG6	ANKL1_HUMAN	ankyrin repeat domain 41	305						nuclear envelope					0																		---	---	---	---
ANO8	57719	broad.mit.edu	37	19	17440803	17440803	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17440803C>T	uc002ngf.2	-	11	1453	c.1294G>A	c.(1294-1296)GCC>ACC	p.A432T	ANO8_uc010eap.2_RNA	NM_020959	NP_066010	Q9HCE9	ANO8_HUMAN	anoctamin 8	432	Extracellular (Potential).|Leu-rich.					chloride channel complex	chloride channel activity			ovary(3)	3																		---	---	---	---
GTPBP3	84705	broad.mit.edu	37	19	17452077	17452077	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17452077C>T	uc010eas.2	+	8	1264	c.1199C>T	c.(1198-1200)ACG>ATG	p.T400M	GTPBP3_uc010xpo.1_Missense_Mutation_p.T422M|GTPBP3_uc002ngh.3_Missense_Mutation_p.T379M|GTPBP3_uc002ngg.3_Missense_Mutation_p.T432M|GTPBP3_uc002ngi.3_Missense_Mutation_p.T66M	NM_032620	NP_116009	Q969Y2	GTPB3_HUMAN	GTP binding protein 3 (mitochondrial) isoform V	400					tRNA modification	mitochondrion	GTP binding|GTPase activity			skin(1)	1																		---	---	---	---
PLVAP	83483	broad.mit.edu	37	19	17476457	17476457	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17476457C>T	uc002ngk.1	-	3	867	c.817G>A	c.(817-819)GAC>AAC	p.D273N		NM_031310	NP_112600	Q9BX97	PLVAP_HUMAN	plasmalemma vesicle associated protein	273	Extracellular (Potential).					caveola|integral to membrane|perinuclear region of cytoplasm					0																		---	---	---	---
SLC27A1	376497	broad.mit.edu	37	19	17615329	17615329	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17615329C>T	uc002ngu.1	+	12	1899	c.1849C>T	c.(1849-1851)CGG>TGG	p.R617W	SLC27A1_uc010xpp.1_Missense_Mutation_p.R438W|SLC27A1_uc002ngv.1_Missense_Mutation_p.R219W	NM_198580	NP_940982	Q6PCB7	S27A1_HUMAN	solute carrier family 27, member 1	617	Cytoplasmic (Potential).				cardiolipin biosynthetic process|fatty acid metabolic process|long-chain fatty acid transport|negative regulation of phospholipid biosynthetic process|phosphatidic acid biosynthetic process|phosphatidylcholine biosynthetic process|phosphatidylethanolamine biosynthetic process|phosphatidylinositol biosynthetic process|phosphatidylserine biosynthetic process|transmembrane transport	endomembrane system|integral to membrane	fatty acid transporter activity|nucleotide binding				0																		---	---	---	---
GLT25D1	79709	broad.mit.edu	37	19	17678226	17678226	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17678226G>A	uc002nhc.1	+	4	513	c.501G>A	c.(499-501)GCG>GCA	p.A167A	GLT25D1_uc010eax.1_5'Flank	NM_024656	NP_078932	Q8NBJ5	GT251_HUMAN	glycosyltransferase 25 domain containing 1	167					lipopolysaccharide biosynthetic process	endoplasmic reticulum lumen	procollagen galactosyltransferase activity				0																		---	---	---	---
MAP1S	55201	broad.mit.edu	37	19	17834940	17834940	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17834940C>T	uc002nhe.1	+	3	235	c.226C>T	c.(226-228)CGG>TGG	p.R76W	MAP1S_uc010eaz.1_RNA|MAP1S_uc010eba.1_Missense_Mutation_p.R76W|MAP1S_uc002nhf.1_Intron|MAP1S_uc010xpv.1_Missense_Mutation_p.R50W	NM_018174	NP_060644	Q66K74	MAP1S_HUMAN	BPY2 interacting protein 1	76	Necessary for the microtubule-organizing center localization.				apoptosis|brain development|microtubule bundle formation|mitochondrion transport along microtubule|neuron projection morphogenesis	cytosol|dendrite|microtubule|neuronal cell body|nucleus|perinuclear region of cytoplasm|spindle|synapse	actin filament binding|beta-tubulin binding|DNA binding|microtubule binding			central_nervous_system(1)	1																		---	---	---	---
JAK3	3718	broad.mit.edu	37	19	17937672	17937672	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17937672C>T	uc002nhn.3	-	24	3355	c.3255G>A	c.(3253-3255)CGG>CGA	p.R1085R	JAK3_uc010ebh.2_Intron	NM_000215	NP_000206	P52333	JAK3_HUMAN	Janus kinase 3	1085	Protein kinase 2.				B cell differentiation|cytokine-mediated signaling pathway|enzyme linked receptor protein signaling pathway|intracellular protein kinase cascade|negative regulation of dendritic cell cytokine production|negative regulation of FasL biosynthetic process|negative regulation of interleukin-10 production|negative regulation of interleukin-12 production|negative regulation of T-helper 1 cell differentiation|negative regulation of thymocyte apoptosis|peptidyl-tyrosine phosphorylation|positive regulation of anti-apoptosis|response to interleukin-15|response to interleukin-2|response to interleukin-4|response to interleukin-9|T cell homeostasis	cytoskeleton|cytosol|endomembrane system|membrane	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding			haematopoietic_and_lymphoid_tissue(40)|lung(5)|breast(5)|ovary(3)|stomach(2)|upper_aerodigestive_tract(1)	56							2	Mis		acute megakaryocytic leukemia|								---	---	---	---
ISYNA1	51477	broad.mit.edu	37	19	18548682	18548682	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18548682A>G	uc002njd.1	-	2	158	c.108T>C	c.(106-108)GGT>GGC	p.G36G	ISYNA1_uc002nja.1_5'Flank|ISYNA1_uc002njb.1_5'Flank|ISYNA1_uc002njc.1_5'UTR|ISYNA1_uc010xqh.1_5'UTR|ISYNA1_uc002nje.1_Silent_p.G36G|ISYNA1_uc002njf.1_5'UTR	NM_016368	NP_057452	Q9NPH2	INO1_HUMAN	inositol-3-phosphate synthase 1	36					inositol biosynthetic process|phospholipid biosynthetic process	cytoplasm	binding|inositol-3-phosphate synthase activity			ovary(1)|pancreas(1)	2																		---	---	---	---
ELL	8178	broad.mit.edu	37	19	18555559	18555559	+	3'UTR	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18555559C>T	uc002njh.2	-	12					ELL_uc010ebq.2_3'UTR|ELL_uc002njg.2_3'UTR	NM_006532	NP_006523			elongation factor RNA polymerase II						positive regulation of transcription elongation, DNA-dependent|positive regulation of viral transcription|transcription elongation from RNA polymerase II promoter|viral reproduction	Cajal body|nuclear speck|transcription elongation factor complex	protein binding			lung(1)	1				GBM - Glioblastoma multiforme(1328;7.81e-07)				T	MLL	AL								---	---	---	---
KLHL26	55295	broad.mit.edu	37	19	18778551	18778551	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18778551G>A	uc002njz.1	+	3	371	c.344G>A	c.(343-345)CGG>CAG	p.R115Q		NM_018316	NP_060786	Q53HC5	KLH26_HUMAN	kelch-like 26	115	BTB.									ovary(1)	1																		---	---	---	---
CRTC1	23373	broad.mit.edu	37	19	18888114	18888114	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18888114A>G	uc002nkb.3	+	14	1915	c.1827A>G	c.(1825-1827)GGA>GGG	p.G609G	CRTC1_uc010ebv.2_Silent_p.G625G|CRTC1_uc010ebw.2_Silent_p.G445G|CRTC1_uc002nkc.3_Silent_p.G307G	NM_015321	NP_056136	Q6UUV9	CRTC1_HUMAN	mucoepidermoid carcinoma translocated 1 isoform	609					interspecies interaction between organisms|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	cAMP response element binding protein binding|protein binding		CRTC1/MAML2(516)	salivary_gland(474)|lung(35)|thyroid(4)|breast(3)|skin(2)|ovary(1)	519																		---	---	---	---
COMP	1311	broad.mit.edu	37	19	18893873	18893873	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18893873G>A	uc002nke.2	-	18	2254	c.2218C>T	c.(2218-2220)CGC>TGC	p.R740C	COMP_uc002nkd.2_Missense_Mutation_p.R707C|COMP_uc010xqj.1_Missense_Mutation_p.R687C	NM_000095	NP_000086	P49747	COMP_HUMAN	cartilage oligomeric matrix protein precursor	740	Mediates cell survival and induction of the IAP family of survival proteins.|TSP C-terminal.				anti-apoptosis|apoptosis|cell adhesion|limb development	extracellular space|proteinaceous extracellular matrix	calcium ion binding|collagen binding|extracellular matrix structural constituent|heparan sulfate proteoglycan binding|heparin binding				0																		---	---	---	---
COMP	1311	broad.mit.edu	37	19	18895845	18895845	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:18895845G>A	uc002nke.2	-	16	1811	c.1775C>T	c.(1774-1776)ACG>ATG	p.T592M	COMP_uc002nkd.2_Missense_Mutation_p.T559M|COMP_uc010xqj.1_Missense_Mutation_p.T539M	NM_000095	NP_000086	P49747	COMP_HUMAN	cartilage oligomeric matrix protein precursor	592	Mediates cell survival and induction of the IAP family of survival proteins.|TSP C-terminal.				anti-apoptosis|apoptosis|cell adhesion|limb development	extracellular space|proteinaceous extracellular matrix	calcium ion binding|collagen binding|extracellular matrix structural constituent|heparan sulfate proteoglycan binding|heparin binding				0																		---	---	---	---
SF4	57794	broad.mit.edu	37	19	19413144	19413144	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19413144A>C	uc002nmh.2	-	7	819	c.817T>G	c.(817-819)TTC>GTC	p.F273V	SF4_uc002nmf.2_5'UTR|SF4_uc002nmg.2_5'UTR|SF4_uc002nmi.2_Missense_Mutation_p.F63V|SF4_uc002nmj.2_Missense_Mutation_p.F63V|SF4_uc010xqr.1_RNA|SF4_uc010xqs.1_RNA	NM_172231	NP_757386	Q8IWZ8	SUGP1_HUMAN	splicing factor 4	273	SURP motif 2.				nuclear mRNA splicing, via spliceosome	nucleoplasm|spliceosomal complex	RNA binding				0																		---	---	---	---
GMIP	51291	broad.mit.edu	37	19	19745507	19745507	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19745507G>A	uc002nnd.2	-	18	2010	c.1893C>T	c.(1891-1893)ACC>ACT	p.T631T	GMIP_uc010xrb.1_Silent_p.T605T|GMIP_uc010xrc.1_Silent_p.T602T	NM_016573	NP_057657	Q9P107	GMIP_HUMAN	GEM interacting protein	631	Rho-GAP.				negative regulation of Rho GTPase activity|small GTPase mediated signal transduction	cytosol	metal ion binding|protein binding|Rho GTPase activator activity			ovary(1)	1																		---	---	---	---
ZNF14	7561	broad.mit.edu	37	19	19822782	19822782	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19822782T>C	uc002nnk.1	-	4	1462	c.1308A>G	c.(1306-1308)AGA>AGG	p.R436R		NM_021030	NP_066358	P17017	ZNF14_HUMAN	zinc finger protein 14	436	C2H2-type 12.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)	3		Renal(1328;0.0474)																---	---	---	---
ZNF253	56242	broad.mit.edu	37	19	20003166	20003166	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:20003166T>C	uc002noj.2	+	4	1202	c.1110T>C	c.(1108-1110)TGT>TGC	p.C370C	ZNF253_uc002nok.2_Silent_p.C294C|ZNF253_uc002nol.2_RNA	NM_021047	NP_066385	O75346	ZN253_HUMAN	zinc finger protein 253	370	C2H2-type 8.			Missing (in Ref. 1; AAC26844).	negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ZNF429	353088	broad.mit.edu	37	19	21712464	21712464	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21712464C>T	uc002nqd.1	+	2	145	c.8C>T	c.(7-9)CCA>CTA	p.P3L	ZNF429_uc010ecu.1_Missense_Mutation_p.P3L	NM_001001415	NP_001001415	Q86V71	ZN429_HUMAN	zinc finger protein 429	3					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2																		---	---	---	---
ZNF208	7757	broad.mit.edu	37	19	22155502	22155502	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22155502T>C	uc002nqp.2	-	5	2183	c.2034A>G	c.(2032-2034)AAA>AAG	p.K678K	ZNF208_uc002nqo.1_Intron	NM_007153	NP_009084			zinc finger protein 208											ovary(5)|skin(2)	7		all_lung(12;0.0961)|Lung NSC(12;0.103)																---	---	---	---
ZNF676	163223	broad.mit.edu	37	19	22363020	22363020	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22363020G>T	uc002nqs.1	-	3	1817	c.1499C>A	c.(1498-1500)ACT>AAT	p.T500N		NM_001001411	NP_001001411	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	500					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)																---	---	---	---
ZNF98	148198	broad.mit.edu	37	19	22605022	22605022	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:22605022G>T	uc002nqt.2	-	1	127	c.5C>A	c.(4-6)CCA>CAA	p.P2Q		NM_001098626	NP_001092096	A6NK75	ZNF98_HUMAN	zinc finger protein 98	2					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)																---	---	---	---
POP4	10775	broad.mit.edu	37	19	30106243	30106243	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30106243C>T	uc002nsf.2	+	7	675	c.619C>T	c.(619-621)CGG>TGG	p.R207W	POP4_uc002nsg.2_Missense_Mutation_p.R126W	NM_006627	NP_006618	O95707	RPP29_HUMAN	processing of precursor 4	207					mRNA cleavage|rRNA processing|tRNA processing	nucleolar ribonuclease P complex|ribonuclease MRP complex	identical protein binding|ribonuclease P activity|RNA binding				0	Ovarian(5;0.000567)|Breast(6;0.0602)|Esophageal squamous(110;0.239)		UCEC - Uterine corpus endometrioid carcinoma (4;2.65e-06)|STAD - Stomach adenocarcinoma(5;1.7e-06)|Lung(7;0.0623)|LUAD - Lung adenocarcinoma(5;0.0989)|BRCA - Breast invasive adenocarcinoma(6;0.225)															---	---	---	---
CCNE1	898	broad.mit.edu	37	19	30313453	30313453	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30313453C>T	uc002nsn.2	+	11	1236	c.1053C>T	c.(1051-1053)GGC>GGT	p.G351G	CCNE1_uc002nso.2_Silent_p.G336G|CCNE1_uc002nsp.2_Silent_p.G98G	NM_001238	NP_001229	P24864	CCNE1_HUMAN	cyclin E1 isoform 1	351					androgen receptor signaling pathway|cell division|positive regulation of transcription, DNA-dependent|regulation of cyclin-dependent protein kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle	cytosol|nucleoplasm	androgen receptor binding|protein kinase binding|transcription coactivator activity			lung(2)	2	all_cancers(1;2.19e-31)|all_epithelial(1;1.49e-30)|all_lung(1;1.37e-11)|Lung NSC(1;2.35e-11)|Ovarian(5;0.000902)|Breast(6;0.0203)|Esophageal squamous(110;0.195)		UCEC - Uterine corpus endometrioid carcinoma (4;2.65e-06)|Epithelial(1;6.85e-98)|all cancers(1;1.38e-94)|OV - Ovarian serous cystadenocarcinoma(1;1.38e-90)|STAD - Stomach adenocarcinoma(5;5.8e-07)|GBM - Glioblastoma multiforme(4;0.0394)|Lung(7;0.092)|LUAD - Lung adenocarcinoma(5;0.115)|BRCA - Breast invasive adenocarcinoma(6;0.183)|COAD - Colon adenocarcinoma(1;0.188)|Colorectal(1;0.202)															---	---	---	---
CCNE1	898	broad.mit.edu	37	19	30314672	30314672	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30314672G>A	uc002nsn.2	+	12	1404	c.1221G>A	c.(1219-1221)CCG>CCA	p.P407P	CCNE1_uc002nso.2_Silent_p.P392P|CCNE1_uc002nsp.2_Silent_p.P154P	NM_001238	NP_001229	P24864	CCNE1_HUMAN	cyclin E1 isoform 1	407					androgen receptor signaling pathway|cell division|positive regulation of transcription, DNA-dependent|regulation of cyclin-dependent protein kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle	cytosol|nucleoplasm	androgen receptor binding|protein kinase binding|transcription coactivator activity			lung(2)	2	all_cancers(1;2.19e-31)|all_epithelial(1;1.49e-30)|all_lung(1;1.37e-11)|Lung NSC(1;2.35e-11)|Ovarian(5;0.000902)|Breast(6;0.0203)|Esophageal squamous(110;0.195)		UCEC - Uterine corpus endometrioid carcinoma (4;2.65e-06)|Epithelial(1;6.85e-98)|all cancers(1;1.38e-94)|OV - Ovarian serous cystadenocarcinoma(1;1.38e-90)|STAD - Stomach adenocarcinoma(5;5.8e-07)|GBM - Glioblastoma multiforme(4;0.0394)|Lung(7;0.092)|LUAD - Lung adenocarcinoma(5;0.115)|BRCA - Breast invasive adenocarcinoma(6;0.183)|COAD - Colon adenocarcinoma(1;0.188)|Colorectal(1;0.202)															---	---	---	---
ZNF536	9745	broad.mit.edu	37	19	31039985	31039985	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31039985G>A	uc002nsu.1	+	4	3597	c.3459G>A	c.(3457-3459)ACG>ACA	p.T1153T	ZNF536_uc010edd.1_Silent_p.T1153T	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536	1153					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(7)|large_intestine(2)|skin(2)	11	Esophageal squamous(110;0.0834)																	---	---	---	---
TSHZ3	57616	broad.mit.edu	37	19	31767694	31767694	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31767694C>T	uc002nsy.3	-	2	3070	c.3005G>A	c.(3004-3006)CGG>CAG	p.R1002Q		NM_020856	NP_065907	Q63HK5	TSH3_HUMAN	zinc finger protein 537	1002					negative regulation of transcription, DNA-dependent|regulation of respiratory gaseous exchange by neurological system process	growth cone|nucleus	chromatin binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|skin(2)|pancreas(1)|lung(1)	8	Esophageal squamous(110;0.226)																	---	---	---	---
TSHZ3	57616	broad.mit.edu	37	19	31769996	31769996	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:31769996C>T	uc002nsy.3	-	2	768	c.703G>A	c.(703-705)GAG>AAG	p.E235K		NM_020856	NP_065907	Q63HK5	TSH3_HUMAN	zinc finger protein 537	235	C2H2-type 1.				negative regulation of transcription, DNA-dependent|regulation of respiratory gaseous exchange by neurological system process	growth cone|nucleus	chromatin binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)|skin(2)|pancreas(1)|lung(1)	8	Esophageal squamous(110;0.226)																	---	---	---	---
DPY19L3	147991	broad.mit.edu	37	19	32949259	32949259	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32949259A>G	uc002ntg.2	+	12	1342	c.1166A>G	c.(1165-1167)GAT>GGT	p.D389G	DPY19L3_uc002nth.1_Missense_Mutation_p.D389G|DPY19L3_uc002nti.1_RNA	NM_207325	NP_997208	Q6ZPD9	D19L3_HUMAN	dpy-19-like 3	389						integral to membrane				ovary(4)	4	Esophageal squamous(110;0.162)																	---	---	---	---
GPATCH1	55094	broad.mit.edu	37	19	33600822	33600822	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33600822G>T	uc002nug.1	+	11	1799	c.1485G>T	c.(1483-1485)ACG>ACT	p.T495T		NM_018025	NP_060495	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1	495						catalytic step 2 spliceosome	nucleic acid binding			skin(1)	1	Esophageal squamous(110;0.137)																	---	---	---	---
WDR88	126248	broad.mit.edu	37	19	33623197	33623197	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33623197C>T	uc002nui.2	+	1	200	c.122C>T	c.(121-123)GCC>GTC	p.A41V		NM_173479	NP_775750	Q6ZMY6	WDR88_HUMAN	PQQ repeat and WD repeat domain containing	41										ovary(1)|breast(1)|central_nervous_system(1)	3	Esophageal squamous(110;0.137)																	---	---	---	---
WDR88	126248	broad.mit.edu	37	19	33635754	33635754	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33635754C>T	uc002nui.2	+	3	470	c.392C>T	c.(391-393)CCG>CTG	p.P131L		NM_173479	NP_775750	Q6ZMY6	WDR88_HUMAN	PQQ repeat and WD repeat domain containing	131	WD 1.									ovary(1)|breast(1)|central_nervous_system(1)	3	Esophageal squamous(110;0.137)																	---	---	---	---
CHST8	64377	broad.mit.edu	37	19	34263870	34263870	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34263870G>A	uc002nus.3	+	5	1682	c.1177G>A	c.(1177-1179)GCC>ACC	p.A393T	CHST8_uc002nut.3_Missense_Mutation_p.A393T|CHST8_uc002nuu.2_Missense_Mutation_p.A393T	NM_001127895	NP_001121367	Q9H2A9	CHST8_HUMAN	carbohydrate (N-acetylgalactosamine 4-0)	393	Lumenal (Potential).				carbohydrate biosynthetic process|central nervous system development|hormone biosynthetic process|proteoglycan biosynthetic process|sulfur compound metabolic process	Golgi membrane|integral to membrane	N-acetylgalactosamine 4-O-sulfotransferase activity			skin(2)|large_intestine(1)|ovary(1)	4	Esophageal squamous(110;0.162)																	---	---	---	---
KCTD15	79047	broad.mit.edu	37	19	34297881	34297881	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34297881C>T	uc002nuy.3	+	5	624	c.356C>T	c.(355-357)ACG>ATG	p.T119M	KCTD15_uc002nuv.2_Missense_Mutation_p.T119M|KCTD15_uc002nuw.3_Missense_Mutation_p.T119M|KCTD15_uc010xrt.1_Missense_Mutation_p.T119M|KCTD15_uc002nux.3_Missense_Mutation_p.T119M	NM_001129994	NP_001123466	Q96SI1	KCD15_HUMAN	potassium channel tetramerisation domain	119	BTB.					voltage-gated potassium channel complex	voltage-gated potassium channel activity			pancreas(1)	1	Esophageal squamous(110;0.162)																	---	---	---	---
KIAA0355	9710	broad.mit.edu	37	19	34842451	34842451	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34842451C>T	uc002nvd.3	+	13	3717	c.2858C>T	c.(2857-2859)ACG>ATG	p.T953M		NM_014686	NP_055501	O15063	K0355_HUMAN	hypothetical protein LOC9710	953										ovary(1)	1	Esophageal squamous(110;0.162)																	---	---	---	---
UBA2	10054	broad.mit.edu	37	19	34960033	34960033	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34960033C>T	uc002nvk.2	+	17	1900	c.1830C>T	c.(1828-1830)CGC>CGT	p.R610R	UBA2_uc002nvl.2_Silent_p.R514R	NM_005499	NP_005490	Q9UBT2	SAE2_HUMAN	SUMO-1 activating enzyme subunit 2	610					protein sumoylation	nucleus	ATP binding|enzyme activator activity|ligase activity|metal ion binding|protein heterodimerization activity|SUMO activating enzyme activity			ovary(1)	1	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)															---	---	---	---
GRAMD1A	57655	broad.mit.edu	37	19	35506831	35506831	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35506831G>A	uc010xse.1	+	11	1310	c.1173G>A	c.(1171-1173)TCG>TCA	p.S391S	GRAMD1A_uc002nxk.2_Silent_p.S384S|GRAMD1A_uc002nxl.2_Silent_p.S157S|GRAMD1A_uc010xsf.1_Silent_p.S396S|GRAMD1A_uc002nxm.1_RNA|GRAMD1A_uc002nxn.1_Silent_p.S6S	NM_020895	NP_065946	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A isoform 1	391						integral to membrane					0	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)															---	---	---	---
GRAMD1A	57655	broad.mit.edu	37	19	35506881	35506881	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35506881C>T	uc010xse.1	+						GRAMD1A_uc002nxk.2_Intron|GRAMD1A_uc002nxl.2_Intron|GRAMD1A_uc010xsf.1_Intron|GRAMD1A_uc002nxm.1_Intron|GRAMD1A_uc002nxn.1_Intron	NM_020895	NP_065946			GRAM domain containing 1A isoform 1							integral to membrane					0	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)															---	---	---	---
GRAMD1A	57655	broad.mit.edu	37	19	35510388	35510388	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35510388G>A	uc010xse.1	+	13	1563	c.1426G>A	c.(1426-1428)GCC>ACC	p.A476T	GRAMD1A_uc002nxk.2_Missense_Mutation_p.A469T|GRAMD1A_uc002nxl.2_Missense_Mutation_p.A242T|GRAMD1A_uc010xsf.1_Missense_Mutation_p.A481T|GRAMD1A_uc002nxm.1_RNA|GRAMD1A_uc002nxn.1_Missense_Mutation_p.A91T	NM_020895	NP_065946	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A isoform 1	476						integral to membrane					0	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)															---	---	---	---
FXYD5	53827	broad.mit.edu	37	19	35648331	35648331	+	Silent	SNP	G	A	A	rs149367243	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35648331G>A	uc002nyg.1	+	3	155	c.69G>A	c.(67-69)ACG>ACA	p.T23T	FXYD5_uc010xsq.1_Silent_p.T23T|FXYD5_uc002nyh.1_Silent_p.T23T	NM_014164	NP_054883	Q96DB9	FXYD5_HUMAN	FXYD domain-containing ion transport regulator 5	23	Extracellular (Potential).				microvillus assembly|negative regulation of calcium-dependent cell-cell adhesion	integral to membrane	actin binding|cadherin binding|ion channel activity				0	all_lung(56;9.4e-09)|Lung NSC(56;1.4e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.75e-22)|OV - Ovarian serous cystadenocarcinoma(14;3.17e-20)|all cancers(14;7.07e-19)|LUSC - Lung squamous cell carcinoma(66;0.0221)															---	---	---	---
FAM187B	148109	broad.mit.edu	37	19	35718977	35718977	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35718977C>T	uc002nyk.1	-	1	652	c.607G>A	c.(607-609)GTC>ATC	p.V203I		NM_152481	NP_689694	Q17R55	F187B_HUMAN	family with sequence similarity 187, member B	203	Extracellular (Potential).					integral to membrane				ovary(2)	2																		---	---	---	---
USF2	7392	broad.mit.edu	37	19	35769607	35769607	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35769607G>A	uc002nyq.1	+	8	843	c.734G>A	c.(733-735)CGG>CAG	p.R245Q	USF2_uc010xss.1_Missense_Mutation_p.R245Q|USF2_uc002nyr.1_Missense_Mutation_p.R178Q|USF2_uc002nys.1_Missense_Mutation_p.R47Q|USF2_uc002nyt.1_Missense_Mutation_p.R114Q|USF2_uc002nyu.1_Missense_Mutation_p.R47Q|USF2_uc002nyv.1_Missense_Mutation_p.R47Q	NM_003367	NP_003358	Q15853	USF2_HUMAN	upstream stimulatory factor 2 isoform 1	245	Poly-Arg.|Basic motif.				lipid homeostasis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter by glucose	nucleus	bHLH transcription factor binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity				0	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)		Epithelial(14;7.4e-20)|OV - Ovarian serous cystadenocarcinoma(14;6.47e-19)|all cancers(14;4.17e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)															---	---	---	---
CD22	933	broad.mit.edu	37	19	35829297	35829297	+	Silent	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35829297T>G	uc010edt.2	+	6	1289	c.1212T>G	c.(1210-1212)ACT>ACG	p.T404T	CD22_uc010xst.1_Silent_p.T232T|CD22_uc010edu.2_Intron|CD22_uc010edv.2_Silent_p.T404T|CD22_uc002nzb.3_Intron|CD22_uc010edx.2_RNA	NM_001771	NP_001762	P20273	CD22_HUMAN	CD22 molecule precursor	404	Extracellular (Potential).|Ig-like C2-type 3.				cell adhesion		protein binding|sugar binding			ovary(5)|lung(3)|breast(1)	9	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.83e-19)|OV - Ovarian serous cystadenocarcinoma(14;3.19e-18)|all cancers(14;3.41e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)		OspA lipoprotein(DB00045)													---	---	---	---
FFAR2	2867	broad.mit.edu	37	19	35941193	35941193	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:35941193G>A	uc002nzg.2	+	2	657	c.577G>A	c.(577-579)GCA>ACA	p.A193T	FFAR2_uc010eea.2_Missense_Mutation_p.A193T	NM_005306	NP_005297	O15552	FFAR2_HUMAN	free fatty acid receptor 2	193	Helical; Name=5; (Potential).					integral to plasma membrane	G-protein coupled receptor activity|lipid binding			central_nervous_system(1)	1	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)															---	---	---	---
MLL4	9757	broad.mit.edu	37	19	36229049	36229049	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36229049G>A	uc010eei.2	+	37	7829	c.7829G>A	c.(7828-7830)CGC>CAC	p.R2610H		NM_014727	NP_055542	Q9UMN6	MLL4_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 4	2610	SET.				chromatin-mediated maintenance of transcription		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(6)|breast(2)|ovary(1)|kidney(1)|skin(1)	11	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)															---	---	---	---
U2AF1L4	199746	broad.mit.edu	37	19	36234764	36234764	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36234764C>T	uc002obg.2	-	6	539	c.230G>A	c.(229-231)CGG>CAG	p.R77Q	TMEM149_uc002obb.2_5'Flank|TMEM149_uc002obc.2_5'Flank|TMEM149_uc002obd.3_5'Flank|TMEM149_uc010xsy.1_5'Flank|TMEM149_uc010eej.2_5'UTR|U2AF1L4_uc002obh.1_Silent_p.A34A|U2AF1L4_uc002obe.2_Missense_Mutation_p.R136Q|U2AF1L4_uc002obf.2_Missense_Mutation_p.G117S|PSENEN_uc002obi.1_5'Flank|PSENEN_uc002obj.1_5'Flank|PSENEN_uc002obk.1_5'Flank			Q8WU68	U2AF4_HUMAN	Homo sapiens cDNA FLJ35525 fis, clone SPLEN2001650.	175	C3H1-type 2.				mRNA processing|RNA splicing	nuclear speck|spliceosomal complex	nucleotide binding|RNA binding|zinc ion binding				0	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)															---	---	---	---
WDR62	284403	broad.mit.edu	37	19	36574062	36574062	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36574062A>G	uc002odc.2	+	11	1560	c.1469A>G	c.(1468-1470)GAC>GGC	p.D490G	WDR62_uc002odd.2_Missense_Mutation_p.D490G	NM_173636	NP_775907	O43379	WDR62_HUMAN	WD repeat domain 62 isoform 2	490	WD 7.				cerebral cortex development	nucleus					0	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)															---	---	---	---
CAPNS1	826	broad.mit.edu	37	19	36636731	36636731	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36636731C>A	uc002odj.2	+	7	637	c.480C>A	c.(478-480)GGC>GGA	p.G160G	CAPNS1_uc002odi.1_Silent_p.G160G|CAPNS1_uc002odk.2_Silent_p.G160G|CAPNS1_uc002odl.2_Silent_p.G160G	NM_001749	NP_001740	P04632	CPNS1_HUMAN	calpain, small subunit 1	160	2 (By similarity).|EF-hand 2.				positive regulation of cell proliferation	cytoplasm|plasma membrane	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity				0	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)															---	---	---	---
ZNF565	147929	broad.mit.edu	37	19	36674439	36674439	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36674439T>C	uc002odn.2	-	5	537	c.429A>G	c.(427-429)GGA>GGG	p.G143G	ZNF565_uc010ees.2_Silent_p.G78G|ZNF565_uc002odo.2_Silent_p.G143G	NM_152477	NP_689690	Q8N9K5	ZN565_HUMAN	zinc finger protein 565	143					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.206)															---	---	---	---
ZNF382	84911	broad.mit.edu	37	19	37118100	37118100	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37118100A>C	uc002oek.2	+	5	1414	c.1301A>C	c.(1300-1302)AAA>ACA	p.K434T	ZNF382_uc010efa.2_Missense_Mutation_p.K385T|ZNF382_uc010efb.2_Missense_Mutation_p.K433T|ZNF382_uc002oel.2_Missense_Mutation_p.K433T	NM_032825	NP_116214	Q96SR6	ZN382_HUMAN	zinc finger protein 382	434	Required for transcriptional repression activity; probably mediates sequence- specific DNA-binding (By similarity).				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)															---	---	---	---
ZNF568	374900	broad.mit.edu	37	19	37441303	37441303	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37441303A>C	uc002ofc.2	+	7	1763	c.1248A>C	c.(1246-1248)AAA>AAC	p.K416N	ZNF568_uc010efg.2_Intron|ZNF568_uc010xtn.1_Intron|ZNF568_uc002ofd.2_Missense_Mutation_p.K340N|ZNF568_uc010efe.2_Missense_Mutation_p.K340N|ZNF568_uc010eff.1_Intron	NM_198539	NP_940941	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	416					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)															---	---	---	---
ZNF585A	199704	broad.mit.edu	37	19	37647166	37647166	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37647166A>C	uc002ofo.1	-	3	395	c.164T>G	c.(163-165)GTG>GGG	p.V55G	ZNF585A_uc002ofm.1_5'UTR|ZNF585A_uc002ofn.1_5'UTR	NM_199126	NP_954577	Q6P3V2	Z585A_HUMAN	zinc finger protein 585A	55	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)															---	---	---	---
ZNF585B	92285	broad.mit.edu	37	19	37677371	37677371	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:37677371A>G	uc002ofq.2	-	5	1322	c.1068T>C	c.(1066-1068)TGT>TGC	p.C356C	uc002ofp.1_5'Flank|ZNF585B_uc002ofr.1_Silent_p.C170C	NM_152279	NP_689492	Q52M93	Z585B_HUMAN	zinc finger protein 585B	356	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			ovary(1)	1			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)															---	---	---	---
ZNF571	51276	broad.mit.edu	37	19	38056713	38056713	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38056713C>T	uc002ogt.2	-	4	718	c.617G>A	c.(616-618)CGT>CAT	p.R206H	uc002ogm.2_Intron|uc002ogn.2_Intron|ZNF540_uc002ogo.2_Intron|ZNF540_uc002ogp.2_Intron|ZNF540_uc002ogq.2_Intron|ZNF571_uc002ogr.1_Intron|uc002ogs.1_5'Flank|ZNF571_uc010efp.2_Missense_Mutation_p.R206H	NM_016536	NP_057620	Q7Z3V5	ZN571_HUMAN	zinc finger protein 571	206	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)															---	---	---	---
ZNF540	163255	broad.mit.edu	37	19	38090660	38090660	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38090660T>C	uc002ogq.2	+						ZNF540_uc002ogu.2_Intron|ZNF540_uc010efq.2_Intron	NM_152606	NP_689819			zinc finger protein 540						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)	1			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)															---	---	---	---
SIPA1L3	23094	broad.mit.edu	37	19	38572899	38572899	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38572899G>A	uc002ohk.2	+	3	1203	c.694G>A	c.(694-696)GCC>ACC	p.A232T		NM_015073	NP_055888	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like	232					regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(1)|central_nervous_system(1)	2			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)															---	---	---	---
SIPA1L3	23094	broad.mit.edu	37	19	38610383	38610383	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38610383A>C	uc002ohk.2	+	9	3238	c.2729A>C	c.(2728-2730)AAC>ACC	p.N910T		NM_015073	NP_055888	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like	910					regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(1)|central_nervous_system(1)	2			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)															---	---	---	---
SIPA1L3	23094	broad.mit.edu	37	19	38631909	38631909	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38631909C>T	uc002ohk.2	+	11	3738	c.3229C>T	c.(3229-3231)CGC>TGC	p.R1077C		NM_015073	NP_055888	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like	1077					regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(1)|central_nervous_system(1)	2			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)															---	---	---	---
DPF1	8193	broad.mit.edu	37	19	38702952	38702952	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38702952C>T	uc002ohl.2	-	10	1067	c.1040G>A	c.(1039-1041)TGC>TAC	p.C347Y	DPF1_uc002ohm.2_Missense_Mutation_p.C381Y|DPF1_uc002ohn.2_Missense_Mutation_p.C299Y|DPF1_uc010xtu.1_Missense_Mutation_p.C355Y|DPF1_uc010xtv.1_Missense_Mutation_p.C365Y	NM_004647	NP_004638	Q92782	DPF1_HUMAN	D4, zinc and double PHD fingers family 1 isoform	347	PHD-type 2.				induction of apoptosis|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nBAF complex	zinc ion binding				0	all_cancers(60;1.24e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)															---	---	---	---
CATSPERG	57828	broad.mit.edu	37	19	38855605	38855605	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38855605G>A	uc002oih.3	+	21	2637	c.2550G>A	c.(2548-2550)ACG>ACA	p.T850T	CATSPERG_uc002oig.3_Silent_p.T810T|CATSPERG_uc002oif.3_Silent_p.T490T|CATSPERG_uc010efw.2_RNA	NM_021185	NP_067008	Q6ZRH7	CTSRG_HUMAN	cation channel, sperm-associated, gamma	850	Extracellular (Potential).				cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane				ovary(1)|skin(1)	2																		---	---	---	---
GGN	199720	broad.mit.edu	37	19	38876891	38876891	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38876891C>T	uc002oij.1	-	3	1146	c.1011G>A	c.(1009-1011)CCG>CCA	p.P337P	GGN_uc002oik.1_Intron|GGN_uc010efy.1_Silent_p.P254P	NM_152657	NP_689870	Q86UU5	GGN_HUMAN	gametogenetin	337	Interaction with GGNBP1 (By similarity).|Pro-rich.				cell differentiation|multicellular organismal development|spermatogenesis						0	all_cancers(60;3.4e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)															---	---	---	---
RYR1	6261	broad.mit.edu	37	19	38958422	38958422	+	Silent	SNP	C	T	T	rs151182947		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38958422C>T	uc002oit.2	+	25	3481	c.3351C>T	c.(3349-3351)GAC>GAT	p.D1117D	RYR1_uc002oiu.2_Silent_p.D1117D	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	1117	6 X approximate repeats.|Cytoplasmic.|B30.2/SPRY 2.				muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)													---	---	---	---
RYR1	6261	broad.mit.edu	37	19	38964072	38964072	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38964072G>A	uc002oit.2	+	28	3951	c.3821G>A	c.(3820-3822)CGC>CAC	p.R1274H	RYR1_uc002oiu.2_Missense_Mutation_p.R1274H	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	1274	Cytoplasmic.|6 X approximate repeats.				muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)													---	---	---	---
RYR1	6261	broad.mit.edu	37	19	39008131	39008131	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39008131C>T	uc002oit.2	+	66	9948	c.9818C>T	c.(9817-9819)ACG>ATG	p.T3273M	RYR1_uc002oiu.2_Missense_Mutation_p.T3273M|RYR1_uc002oiv.1_Missense_Mutation_p.T193M|RYR1_uc010xuf.1_Missense_Mutation_p.T193M	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	3273					muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)													---	---	---	---
RYR1	6261	broad.mit.edu	37	19	39062650	39062650	+	Intron	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39062650C>A	uc002oit.2	+						RYR1_uc002oiu.2_Intron	NM_000540	NP_000531			skeletal muscle ryanodine receptor isoform 1						muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)													---	---	---	---
MAP4K1	11184	broad.mit.edu	37	19	39087976	39087976	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39087976C>T	uc002oix.1	-	24	1935	c.1827G>A	c.(1825-1827)GCG>GCA	p.A609A	MAP4K1_uc002oiw.1_Silent_p.A196A|MAP4K1_uc002oiy.1_Silent_p.A609A	NM_007181	NP_009112	Q92918	M4K1_HUMAN	mitogen-activated protein kinase kinase kinase	609	CNH.				activation of JUN kinase activity|peptidyl-serine phosphorylation		ATP binding|MAP kinase kinase kinase kinase activity|protein binding|small GTPase regulator activity			skin(4)|lung(3)|ovary(1)	8	all_cancers(60;6.42e-06)|Ovarian(47;0.103)		Lung(45;0.000751)|LUSC - Lung squamous cell carcinoma(53;0.00272)															---	---	---	---
HNRNPL	3191	broad.mit.edu	37	19	39336341	39336341	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39336341G>T	uc010xul.1	-	4	670	c.659C>A	c.(658-660)CCT>CAT	p.P220H	HNRNPL_uc010xum.1_Missense_Mutation_p.P87H|HNRNPL_uc010xun.1_5'Flank	NM_001533	NP_001524	P14866	HNRPL_HUMAN	heterogeneous nuclear ribonucleoprotein L	220	RRM 2.				nuclear mRNA splicing, via spliceosome	cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|RNA binding|transcription regulatory region DNA binding				0	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)															---	---	---	---
RINL	126432	broad.mit.edu	37	19	39361497	39361497	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39361497C>A	uc002ojq.2	-	8	783	c.395G>T	c.(394-396)AGG>ATG	p.R132M	RINL_uc002ojr.1_5'Flank|RINL_uc010xuo.1_Missense_Mutation_p.R246M	NM_198445	NP_940847	Q6ZS11	RINL_HUMAN	Ras and Rab interactor-like	132							GTPase activator activity			pancreas(1)	1																		---	---	---	---
PAPL	390928	broad.mit.edu	37	19	39575932	39575932	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39575932G>T	uc002oki.2	+	2	297	c.23G>T	c.(22-24)TGG>TTG	p.W8L	PAPL_uc010egl.2_Missense_Mutation_p.W8L	NM_001004318	NP_001004318	Q6ZNF0	PAPL_HUMAN	iron/zinc purple acid phosphatase-like protein	8						extracellular region	acid phosphatase activity|metal ion binding				0																		---	---	---	---
PAK4	10298	broad.mit.edu	37	19	39665676	39665676	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39665676G>A	uc002okj.1	+	7	1665	c.1204G>A	c.(1204-1206)GCC>ACC	p.A402T	PAK4_uc002okl.1_Missense_Mutation_p.A402T|PAK4_uc002okn.1_Missense_Mutation_p.A402T|PAK4_uc002okm.1_Missense_Mutation_p.A249T|PAK4_uc002oko.1_Missense_Mutation_p.A249T|PAK4_uc002okp.1_Missense_Mutation_p.A312T	NM_001014831	NP_001014831	O96013	PAK4_HUMAN	p21-activated kinase 4 isoform 1	402	Protein kinase.				cellular component movement|signal transduction	Golgi apparatus	ATP binding|protein binding|protein serine/threonine kinase activity			lung(3)|ovary(1)	4	all_cancers(60;1.03e-07)|all_epithelial(25;9.66e-08)|all_lung(34;1.58e-07)|Lung NSC(34;1.88e-07)|Ovarian(47;0.0454)		Epithelial(26;4.82e-25)|all cancers(26;2.94e-22)|Lung(45;0.000797)|LUSC - Lung squamous cell carcinoma(53;0.00113)															---	---	---	---
PLEKHG2	64857	broad.mit.edu	37	19	39905866	39905866	+	Missense_Mutation	SNP	G	A	A	rs149780650		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39905866G>A	uc010xuz.1	+	3	669	c.344G>A	c.(343-345)CGG>CAG	p.R115Q	PLEKHG2_uc010xuy.1_Missense_Mutation_p.R56Q|PLEKHG2_uc002olj.2_Missense_Mutation_p.R115Q|PLEKHG2_uc010xva.1_5'UTR	NM_022835	NP_073746	Q9H7P9	PKHG2_HUMAN	common-site lymphoma/leukemia guanine nucleotide	115	DH.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			skin(2)|pancreas(1)|breast(1)	4	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)															---	---	---	---
ZNF780B	163131	broad.mit.edu	37	19	40541695	40541695	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40541695A>G	uc002omu.2	-	5	1136	c.1071T>C	c.(1069-1071)GGT>GGC	p.G357G	ZNF780B_uc002omv.2_Silent_p.G209G	NM_001005851	NP_001005851	Q9Y6R6	Z780B_HUMAN	zinc finger protein 780B	357					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	p.G357G(1)		ovary(1)|pancreas(1)	2	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)																	---	---	---	---
MAP3K10	4294	broad.mit.edu	37	19	40715068	40715068	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40715068C>T	uc002ona.2	+	6	1782	c.1494C>T	c.(1492-1494)TCC>TCT	p.S498S	MAP3K10_uc002onb.2_5'UTR	NM_002446	NP_002437	Q02779	M3K10_HUMAN	mitogen-activated protein kinase kinase kinase	498					activation of JUN kinase activity|induction of apoptosis|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of JNK cascade|protein autophosphorylation|smoothened signaling pathway	cytoplasm	ATP binding|bHLH transcription factor binding|JUN kinase kinase kinase activity|protein homodimerization activity|transcription corepressor activity			ovary(2)|lung(2)|skin(1)|pancreas(1)	6																		---	---	---	---
HIPK4	147746	broad.mit.edu	37	19	40886603	40886603	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40886603A>G	uc002onp.2	-	3	1580	c.1295T>C	c.(1294-1296)CTG>CCG	p.L432P		NM_144685	NP_653286	Q8NE63	HIPK4_HUMAN	homeodomain interacting protein kinase 4	432						cytoplasm	ATP binding|protein serine/threonine kinase activity			ovary(1)|stomach(1)	2			Lung(22;4.95e-05)|LUSC - Lung squamous cell carcinoma(20;0.000292)															---	---	---	---
PRX	57716	broad.mit.edu	37	19	40904650	40904650	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40904650G>A	uc002onr.2	-	6	527	c.258C>T	c.(256-258)TGC>TGT	p.C86C	PRX_uc002onq.2_5'UTR|PRX_uc002ons.2_Silent_p.C86C	NM_181882	NP_870998	Q9BXM0	PRAX_HUMAN	periaxin isoform 2	86	PDZ.				axon ensheathment	cytoplasm|nucleus|plasma membrane	protein binding			ovary(2)	2			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)															---	---	---	---
SHKBP1	92799	broad.mit.edu	37	19	41083492	41083492	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41083492C>T	uc002oob.2	+	4	265	c.216C>T	c.(214-216)TTC>TTT	p.F72F	SHKBP1_uc002ooc.2_Silent_p.F72F|SHKBP1_uc002ood.2_Silent_p.F72F|SHKBP1_uc010xvl.1_Missense_Mutation_p.S15L|SHKBP1_uc002ooe.2_5'UTR|SHKBP1_uc002oof.2_5'UTR|SHKBP1_uc010xvm.1_5'Flank|SHKBP1_uc010xvn.1_5'Flank	NM_138392	NP_612401	Q8TBC3	SHKB1_HUMAN	SH3KBP1 binding protein 1	72	BTB.					voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)|pancreas(1)	2			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)															---	---	---	---
SHKBP1	92799	broad.mit.edu	37	19	41094995	41094995	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41094995C>T	uc002oob.2	+	15	1549	c.1500C>T	c.(1498-1500)TAC>TAT	p.Y500Y	SHKBP1_uc002ooc.2_Silent_p.Y475Y|SHKBP1_uc002ood.2_Intron|SHKBP1_uc010xvl.1_Silent_p.Y423Y|SHKBP1_uc002ooe.2_Silent_p.Y337Y|SHKBP1_uc002oof.2_Silent_p.Y337Y|SHKBP1_uc010xvm.1_Silent_p.Y280Y|SHKBP1_uc010xvn.1_Silent_p.Y378Y	NM_138392	NP_612401	Q8TBC3	SHKB1_HUMAN	SH3KBP1 binding protein 1	500						voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)|pancreas(1)	2			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)															---	---	---	---
NUMBL	9253	broad.mit.edu	37	19	41175859	41175859	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41175859C>T	uc002oon.2	-	9	1271	c.1103G>A	c.(1102-1104)AGT>AAT	p.S368N	NUMBL_uc010xvq.1_Missense_Mutation_p.S327N|NUMBL_uc002ooo.2_Missense_Mutation_p.S367N|NUMBL_uc010xvr.1_Missense_Mutation_p.S327N	NM_004756	NP_004747	Q9Y6R0	NUMBL_HUMAN	numb homolog (Drosophila)-like	368					cytokine-mediated signaling pathway|lateral ventricle development|neuroblast division in subventricular zone|protein metabolic process	cytoplasm	protein binding			lung(3)|ovary(1)|breast(1)	5			Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105)															---	---	---	---
CYP2A7	1549	broad.mit.edu	37	19	41384662	41384662	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41384662T>C	uc002opm.2	-						CYP2A7_uc002opo.2_Intron|CYP2A7_uc002opn.2_Intron	NM_000764	NP_000755			cytochrome P450, family 2, subfamily A,							endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding			ovary(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	3			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)															---	---	---	---
CYP2A13	1553	broad.mit.edu	37	19	41596019	41596019	+	Silent	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41596019T>G	uc002opt.2	+	3	420	c.411T>G	c.(409-411)GGT>GGG	p.G137G		NM_000766	NP_000757	Q16696	CP2AD_HUMAN	cytochrome P450, family 2, subfamily A,	137					xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|coumarin 7-hydroxylase activity|electron carrier activity|heme binding			ovary(2)|skin(1)	3					Clomipramine(DB01242)|Nicotine(DB00184)													---	---	---	---
CYP2S1	29785	broad.mit.edu	37	19	41703708	41703708	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41703708G>A	uc002opw.2	+	3	423	c.368G>A	c.(367-369)CGG>CAG	p.R123Q	CYP2F1_uc010xvw.1_Intron|CYP2S1_uc010xvx.1_Intron	NM_030622	NP_085125	Q96SQ9	CP2S1_HUMAN	cytochrome P450, family 2, subfamily S,	123					xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|retinoic acid 4-hydroxylase activity			skin(1)	1																		---	---	---	---
CD79A	973	broad.mit.edu	37	19	42383170	42383170	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42383170G>A	uc002orv.2	+	2	375	c.190G>A	c.(190-192)GTC>ATC	p.V64I	CD79A_uc002oru.2_Missense_Mutation_p.V64I	NM_001783	NP_001774	P11912	CD79A_HUMAN	CD79A antigen isoform 1 precursor	64	Ig-like C2-type.|Extracellular (Potential).				B cell differentiation|B cell proliferation|B cell receptor signaling pathway	B cell receptor complex|external side of plasma membrane|integral to membrane|membrane raft|multivesicular body	transmembrane receptor activity			ovary(2)|pancreas(1)	3								O|S		DLBCL								---	---	---	---
DEDD2	162989	broad.mit.edu	37	19	42713966	42713966	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42713966G>A	uc002osu.1	-	4	543	c.475C>T	c.(475-477)CGG>TGG	p.R159W	DEDD2_uc002osv.1_RNA|DEDD2_uc002osw.1_Missense_Mutation_p.R154W|DEDD2_uc002osx.1_Silent_p.G42G|DEDD2_uc002osy.1_Missense_Mutation_p.R159W|DEDD2_uc010eid.2_RNA	NM_133328	NP_579874	Q8WXF8	DEDD2_HUMAN	death effector domain-containing  DNA binding	159	Bipartite nuclear localization signal (Potential).				activation of pro-apoptotic gene products|apoptotic nuclear change|cellular homeostasis|induction of apoptosis via death domain receptors|intracellular signal transduction|negative regulation of transcription, DNA-dependent|RNA processing|rRNA catabolic process|transcription, DNA-dependent	nucleolus	DNA binding|receptor signaling complex scaffold activity				0		Prostate(69;0.0704)																---	---	---	---
ERF	2077	broad.mit.edu	37	19	42754575	42754575	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42754575G>A	uc002ote.3	-	2	323	c.165C>T	c.(163-165)TTC>TTT	p.F55F	ERF_uc002otd.3_5'UTR	NM_006494	NP_006485	P50548	ERF_HUMAN	Ets2 repressor factor	55	ETS.				cell proliferation|regulation of transcription from RNA polymerase II promoter	nucleus	ligand-regulated transcription factor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			lung(1)|kidney(1)|central_nervous_system(1)|skin(1)	4		Prostate(69;0.00682)																---	---	---	---
CIC	23152	broad.mit.edu	37	19	42791392	42791392	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42791392C>T	uc002otf.1	+	3	492	c.452C>T	c.(451-453)GCC>GTC	p.A151V		NM_015125	NP_055940	Q96RK0	CIC_HUMAN	capicua homolog	151					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			ovary(4)|breast(4)|lung(1)|central_nervous_system(1)|skin(1)	11		Prostate(69;0.00682)						T	DUX4	soft tissue sarcoma								---	---	---	---
CIC	23152	broad.mit.edu	37	19	42793400	42793400	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42793400T>C	uc002otf.1	+	8	1242	c.1202T>C	c.(1201-1203)TTT>TCT	p.F401S		NM_015125	NP_055940	Q96RK0	CIC_HUMAN	capicua homolog	401					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			ovary(4)|breast(4)|lung(1)|central_nervous_system(1)|skin(1)	11		Prostate(69;0.00682)						T	DUX4	soft tissue sarcoma								---	---	---	---
MEGF8	1954	broad.mit.edu	37	19	42840314	42840314	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42840314A>G	uc002otl.3	+	6	1695	c.1060A>G	c.(1060-1062)ACC>GCC	p.T354A	MEGF8_uc002otm.3_5'Flank	NM_001410	NP_001401	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	354	Extracellular (Potential).|Kelch 3.					integral to membrane	calcium ion binding|structural molecule activity			ovary(1)	1		Prostate(69;0.00682)																---	---	---	---
MEGF8	1954	broad.mit.edu	37	19	42847714	42847714	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42847714C>T	uc002otl.3	+	9	2234	c.1599C>T	c.(1597-1599)AGC>AGT	p.S533S	MEGF8_uc002otm.3_Silent_p.S74S	NM_001410	NP_001401	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	533	Extracellular (Potential).|Kelch 6.					integral to membrane	calcium ion binding|structural molecule activity			ovary(1)	1		Prostate(69;0.00682)																---	---	---	---
LIPE	3991	broad.mit.edu	37	19	42909670	42909670	+	Silent	SNP	G	A	A	rs2229615		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42909670G>A	uc002otr.2	-	8	2686	c.2409C>T	c.(2407-2409)CTC>CTT	p.L803L	uc010eif.1_Intron	NM_005357	NP_005348	Q05469	LIPS_HUMAN	hormone-sensitive lipase	803					cholesterol metabolic process|protein phosphorylation|triglyceride catabolic process	caveola|cytosol	hormone-sensitive lipase activity|protein binding			ovary(1)|breast(1)	2		Prostate(69;0.00682)																---	---	---	---
PSG3	5671	broad.mit.edu	37	19	43243014	43243014	+	Nonsense_Mutation	SNP	G	A	A	rs145970990		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43243014G>A	uc002oue.2	-	2	424	c.292C>T	c.(292-294)CGA>TGA	p.R98*	PSG3_uc002ouf.2_RNA|PSG1_uc002oug.1_Intron|PSG3_uc010eil.2_Nonsense_Mutation_p.R120*	NM_021016	NP_066296	Q16557	PSG3_HUMAN	pregnancy specific beta-1-glycoprotein 3	98	Ig-like V-type.				defense response|female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00682)																---	---	---	---
PSG8	440533	broad.mit.edu	37	19	43258572	43258572	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43258572T>C	uc002ouo.2	-	5	1254	c.1156A>G	c.(1156-1158)ACA>GCA	p.T386A	PSG3_uc002ouf.2_Intron|PSG1_uc002oug.1_Intron|PSG8_uc010eim.2_RNA|PSG8_uc002oui.2_Missense_Mutation_p.T225A|PSG8_uc002ouh.2_Missense_Mutation_p.T386A|PSG8_uc010ein.2_Missense_Mutation_p.T264A|PSG8_uc002ouj.3_Missense_Mutation_p.T168A|PSG8_uc002ouk.3_Missense_Mutation_p.T225A|PSG8_uc002oul.3_Missense_Mutation_p.T386A|PSG8_uc002oum.3_Missense_Mutation_p.T293A|PSG1_uc002oun.2_Intron|PSG8_uc002oup.3_Missense_Mutation_p.T293A	NM_182707	NP_874366	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8 isoform	386	Ig-like C2-type 3.					extracellular region					0		Prostate(69;0.00899)																---	---	---	---
PSG7	5676	broad.mit.edu	37	19	43439854	43439854	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43439854T>G	uc002ovl.3	-	2	234	c.132A>C	c.(130-132)AAA>AAC	p.K44N	PSG3_uc002ouf.2_Intron|PSG11_uc002ouw.2_Intron|PSG10_uc002ouv.1_Intron|PSG6_uc002ovh.1_Intron|PSG6_uc002ovi.2_Intron|PSG6_uc010xwk.1_Intron|PSG11_uc002ovk.1_Intron|PSG7_uc010xwl.1_Intron	NM_002783	NP_002774	Q13046	PSG7_HUMAN	pregnancy specific beta-1-glycoprotein 7	44	Ig-like V-type.				female pregnancy	extracellular region					0		Prostate(69;0.00682)																---	---	---	---
PSG6	5675	broad.mit.edu	37	19	43579495	43579495	+	Intron	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43579495A>C	uc002ovi.2	-						PSG6_uc010xwk.1_Intron|PSG2_uc002ovr.2_Intron|PSG2_uc002ovq.3_Intron|PSG2_uc010eiq.1_Intron|PSG2_uc002ovs.3_Intron|PSG2_uc002ovt.3_Intron					SubName: Full=Putative uncharacterized protein PSG6;						female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00899)																---	---	---	---
PSG2	5670	broad.mit.edu	37	19	43579557	43579557	+	Missense_Mutation	SNP	G	A	A	rs146901045	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43579557G>A	uc002ovr.2	-	3	751	c.658C>T	c.(658-660)CGG>TGG	p.R220W	PSG6_uc002ovi.2_Intron|PSG6_uc010xwk.1_Intron|PSG2_uc002ovq.3_Missense_Mutation_p.R220W|PSG2_uc010eiq.1_Missense_Mutation_p.R220W|PSG2_uc002ovs.3_Missense_Mutation_p.R220W|PSG2_uc002ovt.3_Missense_Mutation_p.R220W	NM_031246	NP_112536	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	220	Ig-like C2-type 1.				cell migration|female pregnancy	extracellular region					0		Prostate(69;0.00682)																---	---	---	---
PSG2	5670	broad.mit.edu	37	19	43579689	43579689	+	Missense_Mutation	SNP	T	C	C	rs16976431		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43579689T>C	uc002ovr.2	-	3	619	c.526A>G	c.(526-528)ACA>GCA	p.T176A	PSG6_uc002ovi.2_Intron|PSG6_uc010xwk.1_Intron|PSG2_uc002ovq.3_Missense_Mutation_p.T176A|PSG2_uc010eiq.1_Missense_Mutation_p.T176A|PSG2_uc002ovs.3_Missense_Mutation_p.T176A|PSG2_uc002ovt.3_Missense_Mutation_p.T176A	NM_031246	NP_112536	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	176	Ig-like C2-type 1.				cell migration|female pregnancy	extracellular region					0		Prostate(69;0.00682)																---	---	---	---
PSG9	5678	broad.mit.edu	37	19	43766296	43766296	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43766296C>T	uc002owd.3	-						PSG9_uc002owe.3_Intron|PSG9_uc010xwm.1_Intron|PSG9_uc002owf.3_Intron|PSG9_uc002owg.2_Intron|PSG9_uc002owh.2_Intron	NM_002784	NP_002775			pregnancy specific beta-1-glycoprotein 9						female pregnancy	extracellular region				ovary(1)|skin(1)	2		Prostate(69;0.00682)																---	---	---	---
PHLDB3	653583	broad.mit.edu	37	19	43990810	43990810	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:43990810C>T	uc002own.3	-	12	1638	c.1379G>A	c.(1378-1380)CGG>CAG	p.R460Q	PHLDB3_uc010eit.2_Missense_Mutation_p.R164Q	NM_198850	NP_942147	Q6NSJ2	PHLB3_HUMAN	pleckstrin homology-like domain, family B,	460	Potential.										0		Prostate(69;0.0153)																---	---	---	---
ETHE1	23474	broad.mit.edu	37	19	44012128	44012128	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44012128C>T	uc002owp.2	-	6	747	c.680G>A	c.(679-681)GGC>GAC	p.G227D	ETHE1_uc010eiu.1_Missense_Mutation_p.G227D	NM_014297	NP_055112	O95571	ETHE1_HUMAN	ETHE1 protein precursor	227						mitochondrial matrix|nucleus	hydrolase activity|metal ion binding				0		Prostate(69;0.0153)																---	---	---	---
XRCC1	7515	broad.mit.edu	37	19	44058891	44058891	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44058891G>A	uc002owt.2	-	4	441	c.321C>T	c.(319-321)CGC>CGT	p.R107R	XRCC1_uc010xwp.1_Silent_p.R76R	NM_006297	NP_006288	P18887	XRCC1_HUMAN	X-ray repair cross complementing protein 1	107					base-excision repair|single strand break repair	nucleoplasm	damaged DNA binding|protein binding			ovary(2)|lung(2)|large_intestine(1)|prostate(1)|breast(1)	7		Prostate(69;0.0153)											Other_BER_factors					---	---	---	---
IRGC	56269	broad.mit.edu	37	19	44223252	44223252	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44223252G>A	uc002oxh.2	+	2	689	c.542G>A	c.(541-543)CGG>CAG	p.R181Q		NM_019612	NP_062558	Q6NXR0	IIGP5_HUMAN	immunity-related GTPase family, cinema	181						membrane	GTP binding|hydrolase activity, acting on acid anhydrides			ovary(1)|central_nervous_system(1)|skin(1)	3		Prostate(69;0.0435)																---	---	---	---
KCNN4	3783	broad.mit.edu	37	19	44273605	44273605	+	Silent	SNP	G	A	A	rs144044337		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44273605G>A	uc002oxl.2	-	6	1434	c.1038C>T	c.(1036-1038)GCC>GCT	p.A346A	KCNN4_uc010eiz.2_Missense_Mutation_p.R239C	NM_002250	NP_002241	O15554	KCNN4_HUMAN	intermediate conductance calcium-activated	346	Calmodulin-binding.				defense response	voltage-gated potassium channel complex	calcium-activated potassium channel activity|calmodulin binding			ovary(2)	2		Prostate(69;0.0352)			Clotrimazole(DB00257)|Halothane(DB01159)|Quinine(DB00468)													---	---	---	---
Unknown	0	broad.mit.edu	37	19	44388108	44388108	+	IGR	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44388108C>A								ZNF404 (3820 upstream) : ZNF45 (28673 downstream)																																			---	---	---	---
ZNF230	7773	broad.mit.edu	37	19	44515214	44515214	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44515214T>C	uc002oyb.1	+	5	1274	c.1023T>C	c.(1021-1023)TGT>TGC	p.C341C		NM_006300	NP_006291	Q9UIE0	ZN230_HUMAN	zinc finger protein 230	341	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0352)																---	---	---	---
ZNF230	7773	broad.mit.edu	37	19	44515476	44515476	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44515476C>A	uc002oyb.1	+	5	1536	c.1285C>A	c.(1285-1287)CTT>ATT	p.L429I		NM_006300	NP_006291	Q9UIE0	ZN230_HUMAN	zinc finger protein 230	429	C2H2-type 10; atypical.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0352)																---	---	---	---
ZNF222	7673	broad.mit.edu	37	19	44536387	44536387	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44536387G>A	uc002oyc.2	+	4	743	c.560G>A	c.(559-561)CGT>CAT	p.R187H	ZNF284_uc010ejd.2_Intron|ZNF222_uc002oye.2_Missense_Mutation_p.R227H|ZNF222_uc002oyd.2_Missense_Mutation_p.R133H	NM_013360	NP_037492	Q9UK12	ZN222_HUMAN	zinc finger protein 222 isoform 2	187	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)	3		Prostate(69;0.0435)																---	---	---	---
ZNF234	10780	broad.mit.edu	37	19	44661744	44661744	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44661744G>A	uc002oym.2	+	6	1882	c.1575G>A	c.(1573-1575)TCG>TCA	p.S525S	ZNF234_uc002oyl.3_Silent_p.S525S	NM_006630	NP_006621	Q14588	ZN234_HUMAN	zinc finger protein 234	525	C2H2-type 14.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0435)																---	---	---	---
ZNF285	26974	broad.mit.edu	37	19	44891059	44891059	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44891059G>T	uc002ozd.3	-	4	1435	c.1348C>A	c.(1348-1350)CAC>AAC	p.H450N	ZFP112_uc010xwz.1_Intron|ZNF285_uc010xxa.1_Missense_Mutation_p.H457N	NM_152354	NP_689567	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	450	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|skin(2)	4																		---	---	---	---
APOC2	344	broad.mit.edu	37	19	45452066	45452066	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45452066C>T	uc002pah.2	+	3	267	c.164C>T	c.(163-165)GCC>GTC	p.A55V		NM_000483	NP_000474	P02655	APOC2_HUMAN	apolipoprotein C-II precursor	55	Lipoprotein lipase cofactor.				cholesterol efflux|chylomicron remnant clearance|high-density lipoprotein particle clearance|lipid catabolic process|lipoprotein metabolic process|negative regulation of cholesterol transport|negative regulation of lipid metabolic process|negative regulation of receptor-mediated endocytosis|negative regulation of very-low-density lipoprotein particle clearance|phospholipid efflux|positive regulation of fatty acid biosynthetic process|positive regulation of lipoprotein lipase activity|positive regulation of phospholipase activity|positive regulation of phospholipid catabolic process|positive regulation of triglyceride catabolic process|triglyceride homeostasis|very-low-density lipoprotein particle remodeling	chylomicron|intermediate-density lipoprotein particle|low-density lipoprotein particle|spherical high-density lipoprotein particle|very-low-density lipoprotein particle	lipase inhibitor activity|lipid binding|lipoprotein lipase activator activity|phospholipase activator activity|phospholipase binding|protein homodimerization activity			kidney(1)	1	Lung NSC(12;0.00858)|all_lung(12;0.0197)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00327)|Epithelial(262;0.174)														---	---	---	---
MARK4	57787	broad.mit.edu	37	19	45783751	45783751	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45783751C>T	uc002pbb.1	+						MARK4_uc002paz.1_Intron|MARK4_uc002pba.1_Intron|MARK4_uc002pbc.1_Intron					RecName: Full=MAP/microtubule affinity-regulating kinase 4;          EC=2.7.11.1; AltName: Full=MAP/microtubule affinity-regulating kinase-like 1;						microtubule bundle formation|nervous system development|positive regulation of programmed cell death	centrosome|neuron projection	ATP binding|gamma-tubulin binding|microtubule binding|protein serine/threonine kinase activity|tau-protein kinase activity|ubiquitin binding			central_nervous_system(2)|large_intestine(1)	3		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0102)														---	---	---	---
CD3EAP	10849	broad.mit.edu	37	19	45911809	45911809	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45911809G>A	uc002pbq.1	+	3	1071	c.583G>A	c.(583-585)GGG>AGG	p.G195R	PPP1R13L_uc002pbo.2_5'Flank|PPP1R13L_uc002pbp.2_5'Flank|CD3EAP_uc002pbr.1_Missense_Mutation_p.G197R	NM_012099	NP_036231	O15446	RPA34_HUMAN	CD3E antigen, epsilon polypeptide associated	195					rRNA transcription|transmembrane receptor protein tyrosine kinase signaling pathway	chromosome|RNA polymerase I transcription factor complex	DNA-directed RNA polymerase activity			large_intestine(2)|ovary(2)	4		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0251)														---	---	---	---
FOSB	2354	broad.mit.edu	37	19	45974168	45974168	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45974168C>T	uc002pbx.3	+	2	1000	c.408C>T	c.(406-408)CGC>CGT	p.R136R	ERCC1_uc002pbu.1_Intron|FOSB_uc002pbw.2_Silent_p.R136R|FOSB_uc010eke.2_Silent_p.R97R|FOSB_uc002pby.3_Silent_p.R136R|FOSB_uc010eka.1_Silent_p.R97R|FOSB_uc010ekb.1_Silent_p.R136R|FOSB_uc010ekc.1_Intron|FOSB_uc010ekf.2_Silent_p.R97R|FOSB_uc010ekd.1_Silent_p.R136R|FOSB_uc010ekg.2_Intron|FOSB_uc002pca.3_Silent_p.R87R	NM_006732	NP_006723	P53539	FOSB_HUMAN	FBJ murine osteosarcoma viral oncogene homolog B	136					behavior|multicellular organismal development|negative regulation of transcription from RNA polymerase II promoter	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			ovary(2)|lung(1)	3		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00814)|Epithelial(262;0.18)|GBM - Glioblastoma multiforme(486;0.242)														---	---	---	---
SYMPK	8189	broad.mit.edu	37	19	46355761	46355761	+	Silent	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46355761T>G	uc002pdn.2	-	4	449	c.204A>C	c.(202-204)ACA>ACC	p.T68T	SYMPK_uc002pdo.1_Silent_p.T68T|SYMPK_uc002pdp.1_Silent_p.T68T|SYMPK_uc002pdq.1_Silent_p.T68T	NM_004819	NP_004810	Q92797	SYMPK_HUMAN	symplekin	68	Interaction with HSF1.				cell adhesion|mRNA processing	cytoplasm|cytoskeleton|nucleoplasm|tight junction	protein binding			ovary(1)	1		all_neural(266;0.0299)|Ovarian(192;0.0308)		OV - Ovarian serous cystadenocarcinoma(262;0.00509)|GBM - Glioblastoma multiforme(486;0.0593)														---	---	---	---
PNMAL2	57469	broad.mit.edu	37	19	46997216	46997216	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46997216A>C	uc002pes.2	-	1	1954	c.1507T>G	c.(1507-1509)TCG>GCG	p.S503A	uc002peu.1_5'Flank	NM_020709	NP_065760	Q9ULN7	PNML2_HUMAN	PNMA-like 2	503										central_nervous_system(1)	1		Ovarian(192;0.00965)|all_neural(266;0.0459)		OV - Ovarian serous cystadenocarcinoma(262;0.000322)|all cancers(93;0.00233)|GBM - Glioblastoma multiforme(486;0.0421)|Epithelial(262;0.0427)														---	---	---	---
PRKD2	25865	broad.mit.edu	37	19	47197228	47197228	+	Missense_Mutation	SNP	C	T	T	rs140899472		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47197228C>T	uc002pfh.2	-	11	1822	c.1480G>A	c.(1480-1482)GCT>ACT	p.A494T	PRKD2_uc010ekt.2_5'Flank|PRKD2_uc002pfe.2_Missense_Mutation_p.A14T|PRKD2_uc002pff.2_Missense_Mutation_p.A14T|PRKD2_uc002pfg.2_Missense_Mutation_p.A337T|PRKD2_uc002pfi.2_Missense_Mutation_p.A494T|PRKD2_uc002pfj.2_Missense_Mutation_p.A494T|PRKD2_uc010xye.1_Missense_Mutation_p.A494T|PRKD2_uc002pfk.2_Missense_Mutation_p.A337T	NM_001079881	NP_001073350	Q9BZL6	KPCD2_HUMAN	protein kinase D2 isoform A	494	PH.				cell death|intracellular signal transduction|positive regulation of transcription from RNA polymerase II promoter|protein autophosphorylation|T cell receptor signaling pathway	cytoplasm|membrane|nucleus	ATP binding|metal ion binding|protein kinase C activity			ovary(2)|central_nervous_system(2)|stomach(1)|large_intestine(1)|lung(1)	7		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000189)|all cancers(93;0.000545)|Epithelial(262;0.0219)|GBM - Glioblastoma multiforme(486;0.0353)														---	---	---	---
PRKD2	25865	broad.mit.edu	37	19	47204162	47204162	+	Missense_Mutation	SNP	C	T	T	rs10402397	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47204162C>T	uc002pfh.2	-	8	1357	c.1015G>A	c.(1015-1017)GCC>ACC	p.A339T	PRKD2_uc002pfg.2_Missense_Mutation_p.A182T|PRKD2_uc002pfi.2_Missense_Mutation_p.A339T|PRKD2_uc002pfj.2_Missense_Mutation_p.A339T|PRKD2_uc010xye.1_Missense_Mutation_p.A339T|PRKD2_uc002pfk.2_Missense_Mutation_p.A182T	NM_001079881	NP_001073350	Q9BZL6	KPCD2_HUMAN	protein kinase D2 isoform A	339					cell death|intracellular signal transduction|positive regulation of transcription from RNA polymerase II promoter|protein autophosphorylation|T cell receptor signaling pathway	cytoplasm|membrane|nucleus	ATP binding|metal ion binding|protein kinase C activity			ovary(2)|central_nervous_system(2)|stomach(1)|large_intestine(1)|lung(1)	7		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000189)|all cancers(93;0.000545)|Epithelial(262;0.0219)|GBM - Glioblastoma multiforme(486;0.0353)														---	---	---	---
STRN4	29888	broad.mit.edu	37	19	47228065	47228065	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47228065G>A	uc002pfl.2	-	12	1626	c.1593C>T	c.(1591-1593)TAC>TAT	p.Y531Y	STRN4_uc002pfm.2_Silent_p.Y538Y|STRN4_uc010xyf.1_RNA	NM_013403	NP_037535	Q9NRL3	STRN4_HUMAN	zinedin isoform 1	531						cytoplasm|membrane	armadillo repeat domain binding|calmodulin binding|protein complex binding|protein phosphatase 2A binding				0		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000563)|all cancers(93;0.00138)|Epithelial(262;0.0217)|GBM - Glioblastoma multiforme(486;0.035)														---	---	---	---
GRLF1	2909	broad.mit.edu	37	19	47492844	47492844	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47492844C>A	uc010ekv.2	+	4	3948	c.3948C>A	c.(3946-3948)ACC>ACA	p.T1316T		NM_004491	NP_004482	Q9NRY4	RHG35_HUMAN	glucocorticoid receptor DNA binding factor 1	1316	Rho-GAP.				axon guidance|negative regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|transcription, DNA-dependent	cytosol	DNA binding|Rho GTPase activator activity|transcription corepressor activity			central_nervous_system(1)	1		all_cancers(25;1.51e-09)|all_epithelial(76;1.87e-07)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|Ovarian(192;0.0129)|all_neural(266;0.026)|Breast(70;0.077)		all cancers(93;2.03e-05)|OV - Ovarian serous cystadenocarcinoma(262;2.57e-05)|Epithelial(262;0.00135)|GBM - Glioblastoma multiforme(486;0.0289)														---	---	---	---
NPAS1	4861	broad.mit.edu	37	19	47548488	47548488	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47548488C>T	uc002pfw.2	+	12	1548	c.1352C>T	c.(1351-1353)GCG>GTG	p.A451V	NPAS1_uc002pfx.2_Missense_Mutation_p.A276V|NPAS1_uc002pfy.2_Missense_Mutation_p.A451V|NPAS1_uc010xyj.1_3'UTR	NM_002517	NP_002508	Q99742	NPAS1_HUMAN	neuronal PAS domain protein 1	451					central nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity				0		all_cancers(25;4.31e-08)|all_epithelial(76;2.96e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.102)		all cancers(93;6.02e-05)|OV - Ovarian serous cystadenocarcinoma(262;7.35e-05)|Epithelial(262;0.00389)|GBM - Glioblastoma multiforme(486;0.0252)														---	---	---	---
SAE1	10055	broad.mit.edu	37	19	47712471	47712471	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47712471A>C	uc002pgc.2	+	9	1060	c.1004A>C	c.(1003-1005)AAG>ACG	p.K335T	SAE1_uc002pgd.2_3'UTR|SAE1_uc010ekx.2_Missense_Mutation_p.E263D|SAE1_uc010ekw.2_RNA|SAE1_uc010xyk.1_Missense_Mutation_p.K161T|SAE1_uc002pge.2_Missense_Mutation_p.K271T	NM_016402	NP_057486	Q9UBE0	SAE1_HUMAN	SubName: Full=SUMO-1 activating enzyme subunit 1, isoform CRA_b; SubName: Full=cDNA, FLJ96708, Homo sapiens SUMO-1 activating enzyme subunit 1 (SAE1), mRNA;	335					protein sumoylation|protein ubiquitination	nucleus	ATP-dependent protein binding|enzyme activator activity|ligase activity|protein C-terminus binding|protein heterodimerization activity|ubiquitin activating enzyme activity			ovary(1)	1		all_cancers(25;1.13e-05)|all_lung(116;0.000192)|all_epithelial(76;0.000274)|Lung NSC(112;0.000446)|all_neural(266;0.0652)|Ovarian(192;0.15)		all cancers(93;0.00013)|OV - Ovarian serous cystadenocarcinoma(262;0.000146)|Epithelial(262;0.00697)|GBM - Glioblastoma multiforme(486;0.0278)														---	---	---	---
DHX34	9704	broad.mit.edu	37	19	47884214	47884214	+	Missense_Mutation	SNP	G	A	A	rs148368794		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47884214G>A	uc010xyn.1	+	15	3465	c.3124G>A	c.(3124-3126)GCA>ACA	p.A1042T	DHX34_uc010xyo.1_Missense_Mutation_p.A171T	NM_014681	NP_055496	Q14147	DHX34_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 34	1042						intracellular	ATP binding|ATP-dependent helicase activity|RNA binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)	5		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;7.16e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000489)|GBM - Glioblastoma multiforme(486;0.00413)|Epithelial(262;0.0132)														---	---	---	---
SLC8A2	6543	broad.mit.edu	37	19	47951106	47951106	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47951106C>T	uc002pgx.2	-	4	2001	c.1723G>A	c.(1723-1725)GAC>AAC	p.D575N	SLC8A2_uc010xyq.1_Missense_Mutation_p.D331N|SLC8A2_uc010xyr.1_Missense_Mutation_p.D38N|SLC8A2_uc010ele.2_Missense_Mutation_p.D575N	NM_015063	NP_055878	Q9UPR5	NAC2_HUMAN	solute carrier family 8 member 2 precursor	575	Calx-beta 2.|Cytoplasmic (Potential).				cell communication|platelet activation	integral to membrane|plasma membrane	calcium:sodium antiporter activity|calmodulin binding			skin(3)|ovary(1)	4		all_cancers(25;3.05e-07)|all_lung(116;4.19e-06)|Lung NSC(112;7.16e-06)|all_epithelial(76;7.65e-06)|all_neural(266;0.0652)|Ovarian(192;0.086)|Breast(70;0.173)		OV - Ovarian serous cystadenocarcinoma(262;0.000501)|all cancers(93;0.00058)|Epithelial(262;0.0181)|GBM - Glioblastoma multiforme(486;0.0457)														---	---	---	---
NAPA	8775	broad.mit.edu	37	19	47996443	47996443	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47996443C>T	uc002pha.1	-						uc002pgz.1_Intron|NAPA_uc002phb.1_Intron|NAPA_uc002phc.1_Intron|NAPA_uc002phd.1_Intron|NAPA_uc010elf.1_Intron	NM_003827	NP_003818			N-ethylmaleimide-sensitive factor attachment						cellular membrane fusion|intra-Golgi vesicle-mediated transport|post-Golgi vesicle-mediated transport	cytosol					0		all_cancers(25;1.55e-10)|all_epithelial(76;3.4e-08)|all_lung(116;1.73e-07)|Lung NSC(112;3.95e-07)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		OV - Ovarian serous cystadenocarcinoma(262;0.000466)|all cancers(93;0.000739)|Epithelial(262;0.0168)|GBM - Glioblastoma multiforme(486;0.049)														---	---	---	---
GLTSCR2	29997	broad.mit.edu	37	19	48253479	48253479	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48253479C>A	uc002phm.2	+	3	358	c.334C>A	c.(334-336)CTC>ATC	p.L112I	GLTSCR2_uc002phk.2_Missense_Mutation_p.L112I|GLTSCR2_uc002phl.2_Missense_Mutation_p.L112I|GLTSCR2_uc010elj.2_Missense_Mutation_p.L112I|GLTSCR2_uc010elk.1_5'Flank	NM_015710	NP_056525	Q9NZM5	GSCR2_HUMAN	glioma tumor suppressor candidate region gene 2	112						nucleolus				central_nervous_system(1)	1		all_cancers(25;1.47e-06)|all_lung(116;6.89e-05)|all_epithelial(76;0.000108)|Lung NSC(112;0.000117)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000301)|OV - Ovarian serous cystadenocarcinoma(262;0.00031)|Epithelial(262;0.0149)|GBM - Glioblastoma multiforme(486;0.0278)														---	---	---	---
SULT2A1	6822	broad.mit.edu	37	19	48389507	48389507	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48389507T>C	uc002phr.2	-	1	148	c.8A>G	c.(7-9)GAC>GGC	p.D3G		NM_003167	NP_003158	Q06520	ST2A1_HUMAN	bile-salt sulfotransferase 2A1	3					3'-phosphoadenosine 5'-phosphosulfate metabolic process|bile acid catabolic process|cellular lipid metabolic process|digestion|sulfation|xenobiotic metabolic process	cytosol	bile-salt sulfotransferase activity			ovary(1)|pancreas(1)	2		all_cancers(25;3.02e-09)|all_lung(116;6.48e-07)|all_epithelial(76;7.35e-07)|Lung NSC(112;1.56e-06)|all_neural(266;0.0146)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000254)|all cancers(93;0.000545)|Epithelial(262;0.0217)|GBM - Glioblastoma multiforme(486;0.0552)														---	---	---	---
LIG1	3978	broad.mit.edu	37	19	48664643	48664643	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48664643G>A	uc002pia.1	-	4	349	c.229C>T	c.(229-231)CCT>TCT	p.P77S	LIG1_uc002phz.1_RNA|LIG1_uc002pib.1_RNA|LIG1_uc010xzf.1_Missense_Mutation_p.P77S|LIG1_uc010xzg.1_Missense_Mutation_p.P47S|LIG1_uc010xzh.1_RNA	NM_000234	NP_000225	P18858	DNLI1_HUMAN	DNA ligase I	77					anatomical structure morphogenesis|base-excision repair|cell division|DNA ligation involved in DNA repair|DNA strand elongation involved in DNA replication|double-strand break repair via homologous recombination|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	ATP binding|DNA binding|DNA ligase (ATP) activity|metal ion binding			large_intestine(2)|lung(1)	3		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)								NER					---	---	---	---
KCNJ14	3770	broad.mit.edu	37	19	48965276	48965276	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48965276G>A	uc002pje.1	+	2	700	c.295G>A	c.(295-297)GCC>ACC	p.A99T	KCNJ14_uc002pjf.1_Missense_Mutation_p.A99T	NM_013348	NP_037480	Q9UNX9	IRK14_HUMAN	potassium inwardly-rectifying channel J14	99	Helical; Name=M1; (By similarity).					voltage-gated potassium channel complex	inward rectifier potassium channel activity			skin(1)	1		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000109)|all cancers(93;0.000129)|Epithelial(262;0.0081)|GBM - Glioblastoma multiforme(486;0.0222)														---	---	---	---
RASIP1	54922	broad.mit.edu	37	19	49238493	49238493	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49238493C>T	uc002pki.2	-	4	1336	c.1139G>A	c.(1138-1140)CGC>CAC	p.R380H		NM_017805	NP_060275	Q5U651	RAIN_HUMAN	Ras-interacting protein 1	380					signal transduction	Golgi stack|perinuclear region of cytoplasm				pancreas(1)	1		all_lung(116;4.89e-06)|all_epithelial(76;7.04e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;9.98e-05)|all cancers(93;0.000272)|Epithelial(262;0.0155)|GBM - Glioblastoma multiforme(486;0.0222)														---	---	---	---
PPP1R15A	23645	broad.mit.edu	37	19	49377756	49377756	+	Silent	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49377756A>C	uc002pky.3	+	2	1535	c.1266A>C	c.(1264-1266)ACA>ACC	p.T422T		NM_014330	NP_055145	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	422	4 X 34 AA approximate repeats.|Glu-rich.|Interaction with SMAD7.				apoptosis|cell cycle arrest|regulation of translation|response to DNA damage stimulus	endoplasmic reticulum	protein binding			lung(1)	1		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)														---	---	---	---
PPFIA3	8541	broad.mit.edu	37	19	49643281	49643281	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49643281C>A	uc002pmr.2	+	18	2636	c.2304C>A	c.(2302-2304)GGC>GGA	p.G768G	PPFIA3_uc010yai.1_RNA|PPFIA3_uc010yaj.1_RNA|PPFIA3_uc002pms.2_Silent_p.G636G|PPFIA3_uc002pmt.2_5'Flank	NM_003660	NP_003651	O75145	LIPA3_HUMAN	PTPRF interacting protein alpha 3	768						cell surface|cytoplasm	protein binding			lung(1)	1		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.36e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000203)|GBM - Glioblastoma multiforme(486;0.00307)|Epithelial(262;0.00677)														---	---	---	---
CD37	951	broad.mit.edu	37	19	49839009	49839009	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49839009C>A	uc002pnd.2	+	2	229	c.108C>A	c.(106-108)ATC>ATA	p.I36I	uc002pnb.1_Intron|CD37_uc002pnc.2_RNA|CD37_uc010yam.1_Silent_p.I36I|CD37_uc010yan.1_5'UTR|CD37_uc002pnf.3_5'UTR|CD37_uc002pne.2_5'UTR	NM_001774	NP_001765	P11049	CD37_HUMAN	CD37 antigen isoform A	36	Helical; (Potential).					integral to membrane					0		all_lung(116;2.81e-06)|Lung NSC(112;5.89e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00088)|GBM - Glioblastoma multiforme(486;0.0443)														---	---	---	---
PIH1D1	55011	broad.mit.edu	37	19	49952722	49952722	+	Intron	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49952722G>T	uc002pns.2	-						PIH1D1_uc010yap.1_Intron|PIH1D1_uc010yaq.1_Missense_Mutation_p.P116H	NM_017916	NP_060386			NOP17						box C/D snoRNP assembly	pre-snoRNP complex					0		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00152)|GBM - Glioblastoma multiforme(486;0.0244)														---	---	---	---
ALDH16A1	126133	broad.mit.edu	37	19	49967725	49967725	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49967725G>A	uc002pnt.2	+	11	1499	c.1383G>A	c.(1381-1383)TCG>TCA	p.S461S	ALDH16A1_uc010yar.1_Silent_p.S410S|ALDH16A1_uc010yas.1_Silent_p.S296S|ALDH16A1_uc010yat.1_Silent_p.S298S	NM_153329	NP_699160	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	461							oxidoreductase activity|protein binding			skin(1)	1		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0251)														---	---	---	---
FCGRT	2217	broad.mit.edu	37	19	50027966	50027966	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50027966C>T	uc002poe.2	+	5	1290	c.804C>T	c.(802-804)GGC>GGT	p.G268G	FCGRT_uc002pod.2_RNA|FCGRT_uc002pog.2_Silent_p.G268G|FCGRT_uc002pof.1_Silent_p.G173G|FCGRT_uc010yax.1_3'UTR|FCGRT_uc002poh.1_Silent_p.G128G|FCGRT_uc002poi.2_5'Flank|RCN3_uc002poj.2_5'Flank	NM_001136019	NP_001129491	P55899	FCGRN_HUMAN	Fc fragment of IgG, receptor, transporter, alpha	268	Extracellular (Potential).|Alpha-3.				antigen processing and presentation|female pregnancy|immune response	integral to membrane|MHC class I protein complex	IgG binding|receptor activity			ovary(1)	1		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.0966)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00291)|GBM - Glioblastoma multiforme(134;0.0156)														---	---	---	---
NOSIP	51070	broad.mit.edu	37	19	50059900	50059900	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50059900G>A	uc002pok.2	-	8	783	c.631C>T	c.(631-633)CGC>TGC	p.R211C	NOSIP_uc002pol.2_Missense_Mutation_p.R211C	NM_015953	NP_057037	Q9Y314	NOSIP_HUMAN	nitric oxide synthase interacting protein	211					negative regulation of nitric-oxide synthase activity|nitric oxide metabolic process	cytosol|nucleus	protein binding			skin(1)	1		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.0966)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00321)|GBM - Glioblastoma multiforme(134;0.0133)														---	---	---	---
IRF3	3661	broad.mit.edu	37	19	50165555	50165555	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50165555C>T	uc010end.1	-	6	1014	c.632G>A	c.(631-633)CGG>CAG	p.R211Q	IRF3_uc002pos.1_5'Flank|IRF3_uc002pot.1_Intron|IRF3_uc002pox.1_Missense_Mutation_p.R211Q|IRF3_uc002poy.1_Missense_Mutation_p.R211Q|IRF3_uc002pou.2_Missense_Mutation_p.R211Q|IRF3_uc002pov.2_Missense_Mutation_p.R65Q|IRF3_uc002pow.2_Missense_Mutation_p.R211Q|IRF3_uc002poz.1_Missense_Mutation_p.R211Q|BCL2L12_uc002ppa.2_5'Flank|BCL2L12_uc002ppb.2_5'Flank	NM_001571	NP_001562	Q14653	IRF3_HUMAN	interferon regulatory factor 3	211	Involved in HERC5 binding.				interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|MyD88-independent toll-like receptor signaling pathway|negative regulation of type I interferon production|response to virus|Toll signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	cytosol|endosome membrane|nucleoplasm|plasma membrane	DNA binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription cofactor activity			ovary(2)	2		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.0011)|GBM - Glioblastoma multiforme(134;0.02)														---	---	---	---
IRF3	3661	broad.mit.edu	37	19	50168016	50168016	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50168016A>G	uc010end.1	-	2	462	c.80T>C	c.(79-81)GTG>GCG	p.V27A	IRF3_uc002pos.1_5'Flank|IRF3_uc002pot.1_Missense_Mutation_p.V27A|IRF3_uc002pox.1_Missense_Mutation_p.V27A|IRF3_uc002poy.1_Missense_Mutation_p.V27A|IRF3_uc002pou.2_Missense_Mutation_p.V27A|IRF3_uc002pov.2_Intron|IRF3_uc002pow.2_Missense_Mutation_p.V27A|IRF3_uc002poz.1_Missense_Mutation_p.V27A|IRF3_uc010ene.1_Missense_Mutation_p.V27A|BCL2L12_uc002ppa.2_5'Flank|BCL2L12_uc002ppb.2_5'Flank	NM_001571	NP_001562	Q14653	IRF3_HUMAN	interferon regulatory factor 3	27	IRF tryptophan pentad repeat.				interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|MyD88-independent toll-like receptor signaling pathway|negative regulation of type I interferon production|response to virus|Toll signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	cytosol|endosome membrane|nucleoplasm|plasma membrane	DNA binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription cofactor activity			ovary(2)	2		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.0011)|GBM - Glioblastoma multiforme(134;0.02)														---	---	---	---
PRMT1	3276	broad.mit.edu	37	19	50189488	50189488	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50189488G>A	uc010enf.1	+	9	940	c.898G>A	c.(898-900)GGC>AGC	p.G300S	PRMT1_uc002ppc.1_RNA|PRMT1_uc002ppd.2_Missense_Mutation_p.G276S|PRMT1_uc002ppe.2_Missense_Mutation_p.G282S|PRMT1_uc002ppf.2_RNA|PRMT1_uc002ppg.2_Missense_Mutation_p.G247S|PRMT1_uc010yba.1_RNA|PRMT1_uc010ybb.1_5'Flank|C19orf76_uc002pph.2_5'Flank	NM_001536	NP_001527	Q8WUW5	Q8WUW5_HUMAN	HMT1 hnRNP methyltransferase-like 2 isoform 1	281						cytoplasm	protein methyltransferase activity			ovary(1)	1		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00103)|GBM - Glioblastoma multiforme(134;0.012)														---	---	---	---
CPT1C	126129	broad.mit.edu	37	19	50216816	50216816	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50216816G>A	uc002ppj.2	+	19	2571	c.2366G>A	c.(2365-2367)CGC>CAC	p.R789H	CPT1C_uc002ppk.2_Missense_Mutation_p.R778H|CPT1C_uc010eng.2_Missense_Mutation_p.R789H|CPT1C_uc010enh.2_Missense_Mutation_p.R789H|CPT1C_uc010eni.1_Missense_Mutation_p.R357H	NM_152359	NP_689572	Q8TCG5	CPT1C_HUMAN	carnitine palmitoyltransferase 1C isoform 2	789	Cytoplasmic (Potential).				fatty acid metabolic process	integral to membrane|mitochondrial outer membrane	carnitine O-palmitoyltransferase activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0011)|GBM - Glioblastoma multiforme(134;0.00786)														---	---	---	---
MED25	81857	broad.mit.edu	37	19	50333067	50333067	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50333067T>C	uc002ppw.1	+	6	603	c.550T>C	c.(550-552)TCT>CCT	p.S184P	MED25_uc010ybe.1_Intron|MED25_uc002ppx.1_5'UTR	NM_030973	NP_112235	Q71SY5	MED25_HUMAN	mediator complex subunit 25	184	Interaction with the Mediator complex.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm				ovary(1)	1		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00822)|GBM - Glioblastoma multiforme(134;0.0122)														---	---	---	---
IL4I1	259307	broad.mit.edu	37	19	50393070	50393070	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50393070C>T	uc002pqt.1	-	8	1639	c.1561G>A	c.(1561-1563)GCA>ACA	p.A521T	IL4I1_uc002pqv.1_Missense_Mutation_p.A530T|IL4I1_uc010eno.1_Missense_Mutation_p.A529T|IL4I1_uc002pqw.1_Missense_Mutation_p.A529T|IL4I1_uc002pqu.1_Missense_Mutation_p.A543T	NM_152899	NP_690863	Q96RQ9	OXLA_HUMAN	interleukin 4 induced 1 isoform 1 precursor	521						lysosome	L-amino-acid oxidase activity			lung(1)|ovary(1)|prostate(1)	3		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00245)|OV - Ovarian serous cystadenocarcinoma(262;0.0169)														---	---	---	---
MYH14	79784	broad.mit.edu	37	19	50794154	50794154	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50794154C>T	uc002prr.1	+	34	4900	c.4853C>T	c.(4852-4854)GCA>GTA	p.A1618V	MYH14_uc010enu.1_Missense_Mutation_p.A1659V|MYH14_uc002prq.1_Missense_Mutation_p.A1626V|MYH14_uc010ycb.1_5'UTR|MYH14_uc002prs.1_5'UTR	NM_024729	NP_079005	Q7Z406	MYH14_HUMAN	myosin, heavy chain 14 isoform 2	1618	Potential.				axon guidance|regulation of cell shape	myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			central_nervous_system(1)	1		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)														---	---	---	---
LRRC4B	94030	broad.mit.edu	37	19	51022624	51022624	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51022624G>A	uc002pss.2	-	3	483	c.346C>T	c.(346-348)CAG>TAG	p.Q116*		NM_001080457	NP_001073926	Q9NT99	LRC4B_HUMAN	leucine rich repeat containing 4B precursor	116	Extracellular (Potential).|LRR 2.					cell junction|integral to membrane|presynaptic membrane				central_nervous_system(1)|skin(1)	2		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00284)|GBM - Glioblastoma multiforme(134;0.0188)														---	---	---	---
SYT3	84258	broad.mit.edu	37	19	51135928	51135928	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51135928G>A	uc002pst.2	-	2	923	c.289C>T	c.(289-291)CGC>TGC	p.R97C	SYT3_uc002psv.2_Missense_Mutation_p.R97C|SYT3_uc010ycd.1_Missense_Mutation_p.R97C	NM_032298	NP_115674	Q9BQG1	SYT3_HUMAN	synaptotagmin III	97	Cytoplasmic (Potential).					cell junction|endosome|integral to membrane|synaptic vesicle membrane	metal ion binding|transporter activity			ovary(2)|breast(1)	3		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00462)|GBM - Glioblastoma multiforme(134;0.0188)														---	---	---	---
KLK6	5653	broad.mit.edu	37	19	51466574	51466574	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51466574C>T	uc002pui.2	-	5	689	c.429G>A	c.(427-429)TGG>TGA	p.W143*	KLK6_uc010eoj.2_Intron|KLK6_uc002puh.2_Nonsense_Mutation_p.W152*|KLK6_uc002puj.2_Nonsense_Mutation_p.W36*|KLK6_uc010ycn.1_Nonsense_Mutation_p.W36*|KLK6_uc002pul.2_Nonsense_Mutation_p.W143*|KLK6_uc002pum.2_Nonsense_Mutation_p.W36*	NM_001012964	NP_001012982	Q92876	KLK6_HUMAN	kallikrein-related peptidase 6 isoform A	143	Peptidase S1.				amyloid precursor protein metabolic process|central nervous system development|collagen catabolic process|hormone metabolic process|myelination|positive regulation of G-protein coupled receptor protein signaling pathway|protein autoprocessing|proteolysis|regulation of cell differentiation|tissue regeneration	endoplasmic reticulum|extracellular region|microsome|mitochondrion|nucleolus	protein binding|serine-type endopeptidase activity				0		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00372)|GBM - Glioblastoma multiforme(134;0.00871)														---	---	---	---
KLK12	43849	broad.mit.edu	37	19	51534093	51534093	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51534093G>A	uc002pvg.1	-	4	662	c.542C>T	c.(541-543)ACG>ATG	p.T181M	KLK11_uc002pvf.1_5'Flank|KLK12_uc010ycp.1_RNA|KLK12_uc010ycq.1_Missense_Mutation_p.T71M|KLK12_uc010ycr.1_Missense_Mutation_p.T71M|KLK12_uc010ycs.1_Missense_Mutation_p.T71M|KLK12_uc002pvh.1_Missense_Mutation_p.T181M|KLK12_uc002pvi.1_Missense_Mutation_p.T181M|KLK12_uc002pvj.1_Silent_p.H94H	NM_145894	NP_665901	Q9UKR0	KLK12_HUMAN	kallikrein 12 isoform 2	181	Peptidase S1.				proteolysis	extracellular region|soluble fraction	serine-type endopeptidase activity			ovary(1)	1		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00399)														---	---	---	---
SIGLEC7	27036	broad.mit.edu	37	19	51650058	51650058	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51650058G>A	uc002pvv.1	+	5	1144	c.1075G>A	c.(1075-1077)GCT>ACT	p.A359T	SIGLEC7_uc002pvw.1_Missense_Mutation_p.A266T|SIGLEC7_uc010eoq.1_Intron|SIGLEC7_uc010eor.1_Intron	NM_014385	NP_055200	Q9Y286	SIGL7_HUMAN	sialic acid binding Ig-like lectin 7 isoform 1	359	Helical; (Potential).				cell adhesion	integral to plasma membrane	receptor activity|sugar binding			large_intestine(1)	1		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000836)|OV - Ovarian serous cystadenocarcinoma(262;0.00297)														---	---	---	---
IGLON5	402665	broad.mit.edu	37	19	51827069	51827069	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51827069C>T	uc002pwc.2	+	3	312	c.312C>T	c.(310-312)CTC>CTT	p.L104L		NM_001101372	NP_001094842	A6NGN9	IGLO5_HUMAN	IgLON family member 5 precursor	104	Ig-like C2-type 1.					extracellular region					0																		---	---	---	---
SIGLEC8	27181	broad.mit.edu	37	19	51955720	51955720	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51955720C>T	uc002pwt.2	-	7	1480	c.1413G>A	c.(1411-1413)TCG>TCA	p.S471S	SIGLEC8_uc010yda.1_Silent_p.S362S|SIGLEC8_uc002pwu.2_Intron|SIGLEC8_uc010eox.2_Silent_p.S378S	NM_014442	NP_055257	Q9NYZ4	SIGL8_HUMAN	sialic acid binding Ig-like lectin 8 precursor	471	Cytoplasmic (Potential).|SLAM-like motif.				cell adhesion	integral to membrane	sugar binding|transmembrane receptor activity			ovary(2)|kidney(1)|central_nervous_system(1)|skin(1)	5		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000627)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)														---	---	---	---
SIGLEC6	946	broad.mit.edu	37	19	52034755	52034755	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52034755C>T	uc002pwy.2	-	2	248	c.86G>A	c.(85-87)CGG>CAG	p.R29Q	SIGLEC6_uc002pwz.2_Missense_Mutation_p.R29Q|SIGLEC6_uc002pxa.2_Missense_Mutation_p.R29Q|SIGLEC6_uc010ydb.1_Intron|SIGLEC6_uc010ydc.1_Missense_Mutation_p.R18Q|SIGLEC6_uc010eoz.1_Missense_Mutation_p.R18Q|SIGLEC6_uc010epb.1_Intron|SIGLEC6_uc010epa.1_Missense_Mutation_p.R18Q	NM_001245	NP_001236	O43699	SIGL6_HUMAN	sialic acid binding Ig-like lectin 6 isoform 1	29	Extracellular (Potential).|Ig-like V-type.				cell adhesion|cell-cell signaling	cytoplasm|extracellular region|integral to plasma membrane|membrane fraction|nucleus				ovary(1)	1		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00115)|OV - Ovarian serous cystadenocarcinoma(262;0.0165)														---	---	---	---
ZNF613	79898	broad.mit.edu	37	19	52443538	52443538	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52443538A>G	uc002pxz.1	+	4	515	c.92A>G	c.(91-93)GAC>GGC	p.D31G	ZNF613_uc002pya.1_5'UTR	NM_001031721	NP_001026891	Q6PF04	ZN613_HUMAN	zinc finger protein 613 isoform 1	31	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.0183)														---	---	---	---
ZNF613	79898	broad.mit.edu	37	19	52447789	52447789	+	Missense_Mutation	SNP	G	A	A	rs145019318		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52447789G>A	uc002pxz.1	+	6	1076	c.653G>A	c.(652-654)CGC>CAC	p.R218H	ZNF613_uc002pya.1_Missense_Mutation_p.R182H	NM_001031721	NP_001026891	Q6PF04	ZN613_HUMAN	zinc finger protein 613 isoform 1	218	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.0183)														---	---	---	---
ZNF614	80110	broad.mit.edu	37	19	52519343	52519343	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52519343C>T	uc002pyj.2	-	5	1910	c.1508G>A	c.(1507-1509)AGA>AAA	p.R503K	ZNF614_uc002pyi.3_Intron|ZNF614_uc010epj.2_Missense_Mutation_p.R206K	NM_025040	NP_079316	Q8N883	ZN614_HUMAN	zinc finger protein 614	503	C2H2-type 10.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	5		all_neural(266;0.0505)		GBM - Glioblastoma multiforme(134;0.00513)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)														---	---	---	---
PPP2R1A	5518	broad.mit.edu	37	19	52716328	52716328	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52716328C>T	uc002pyp.2	+	6	931	c.772C>T	c.(772-774)CGC>TGC	p.R258C	PPP2R1A_uc010ydk.1_Missense_Mutation_p.R203C|PPP2R1A_uc010epm.1_Missense_Mutation_p.R298C|PPP2R1A_uc002pyq.2_Missense_Mutation_p.R79C	NM_014225	NP_055040	P30153	2AAA_HUMAN	alpha isoform of regulatory subunit A, protein	258	HEAT 7.|PP2A subunit B binding.|Polyoma small and medium T antigens Binding.			R -> A (in Ref. 2; AAA36399).	ceramide metabolic process|chromosome segregation|G2/M transition of mitotic cell cycle|inactivation of MAPK activity|induction of apoptosis|negative regulation of cell growth|negative regulation of tyrosine phosphorylation of Stat3 protein|protein complex assembly|protein dephosphorylation|regulation of cell adhesion|regulation of cell differentiation|regulation of DNA replication|regulation of transcription, DNA-dependent|regulation of Wnt receptor signaling pathway|response to organic substance|RNA splicing|second-messenger-mediated signaling	chromosome, centromeric region|cytosol|membrane|microtubule cytoskeleton|mitochondrion|nucleus|protein phosphatase type 2A complex|soluble fraction	antigen binding|protein heterodimerization activity|protein phosphatase type 2A regulator activity	p.R258C(1)		endometrium(31)|ovary(28)|lung(2)|breast(2)|skin(1)|kidney(1)|pancreas(1)	66				GBM - Glioblastoma multiforme(134;0.00456)|OV - Ovarian serous cystadenocarcinoma(262;0.015)				Mis		clear cell ovarian carcinoma								---	---	---	---
ZNF578	147660	broad.mit.edu	37	19	53014063	53014063	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53014063T>C	uc002pzp.3	+	6	673	c.429T>C	c.(427-429)GAT>GAC	p.D143D		NM_001099694	NP_001093164	Q96N58	ZN578_HUMAN	zinc finger protein 578	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)														---	---	---	---
ZNF578	147660	broad.mit.edu	37	19	53014508	53014508	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53014508T>C	uc002pzp.3	+	6	1118	c.874T>C	c.(874-876)TGT>CGT	p.C292R		NM_001099694	NP_001093164	Q96N58	ZN578_HUMAN	zinc finger protein 578	67	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)														---	---	---	---
ZNF611	81856	broad.mit.edu	37	19	53209757	53209757	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53209757G>A	uc002pzz.2	-	7	868	c.551C>T	c.(550-552)ACT>ATT	p.T184I	ZNF611_uc010eqc.2_Missense_Mutation_p.T114I|ZNF611_uc010ydo.1_Missense_Mutation_p.T114I|ZNF611_uc010ydr.1_Missense_Mutation_p.T115I|ZNF611_uc010ydp.1_Missense_Mutation_p.T184I|ZNF611_uc010ydq.1_Missense_Mutation_p.T184I|ZNF611_uc002qaa.3_Missense_Mutation_p.T114I	NM_030972	NP_112234	Q8N823	ZN611_HUMAN	zinc finger protein 611 isoform a	184					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(262;0.0233)|GBM - Glioblastoma multiforme(134;0.04)														---	---	---	---
ZNF816A	125893	broad.mit.edu	37	19	53456031	53456031	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:53456031C>T	uc002qal.1	-	4	464	c.163G>A	c.(163-165)GAG>AAG	p.E55K	ZNF321_uc010eqj.2_Missense_Mutation_p.E39K|ZNF321_uc002qak.1_Missense_Mutation_p.E39K|ZNF816A_uc002qam.1_Missense_Mutation_p.E39K	NM_001031665	NP_001026835	Q0VGE8	ZN816_HUMAN	zinc finger protein 816A	55	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.0313)														---	---	---	---
MIR520F	574464	broad.mit.edu	37	19	54185469	54185469	+	RNA	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54185469G>A	hsa-mir-520f|MI0003146	+			c.57G>A			uc010yea.1_5'Flank|MIR515-2_hsa-mir-515-2|MI0003147_5'Flank																	0																		---	---	---	---
CACNG7	59284	broad.mit.edu	37	19	54416107	54416107	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54416107G>A	uc002qcr.1	+	1	37	c.22G>A	c.(22-24)GCC>ACC	p.A8T	CACNG7_uc010era.1_Missense_Mutation_p.A8T	NM_031896	NP_114102	P62955	CCG7_HUMAN	voltage-dependent calcium channel gamma-7	8	Helical; (Potential).				regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(1)	1	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0711)														---	---	---	---
LENG8	114823	broad.mit.edu	37	19	54967856	54967856	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54967856C>T	uc002qfv.1	+	10	1520	c.1376C>T	c.(1375-1377)GCG>GTG	p.A459V	LENG8_uc002qfw.2_Missense_Mutation_p.A496V			Q96PV6	LENG8_HUMAN	RecName: Full=Leukocyte receptor cluster member 8;	459							protein binding			central_nervous_system(1)|pancreas(1)	2	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.139)														---	---	---	---
LENG9	94059	broad.mit.edu	37	19	54973555	54973555	+	Silent	SNP	G	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54973555G>C	uc010yez.1	-	1	1340	c.1221C>G	c.(1219-1221)GGC>GGG	p.G407G		NM_198988	NP_945339	Q96B70	LENG9_HUMAN	leukocyte receptor cluster (LRC) member 9	407					RNA metabolic process	intracellular	catalytic activity|nucleic acid binding|zinc ion binding				0	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.134)														---	---	---	---
LILRA1	11024	broad.mit.edu	37	19	55106736	55106736	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55106736G>C	uc002qgh.1	+	5	712	c.530G>C	c.(529-531)TGG>TCG	p.W177S	LILRA2_uc010yfg.1_Intron|LILRA1_uc010yfh.1_Missense_Mutation_p.W177S	NM_006863	NP_006854	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor,	177	Ig-like C2-type 2.|Extracellular (Potential).				cell surface receptor linked signaling pathway|defense response|regulation of immune response	integral to membrane|plasma membrane	antigen binding|transmembrane receptor activity			skin(2)|ovary(1)	3				GBM - Glioblastoma multiforme(193;0.0348)														---	---	---	---
LILRA1	11024	broad.mit.edu	37	19	55106743	55106743	+	Silent	SNP	G	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55106743G>C	uc002qgh.1	+	5	719	c.537G>C	c.(535-537)CGG>CGC	p.R179R	LILRA2_uc010yfg.1_Intron|LILRA1_uc010yfh.1_Silent_p.R179R	NM_006863	NP_006854	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor,	179	Ig-like C2-type 2.|Extracellular (Potential).				cell surface receptor linked signaling pathway|defense response|regulation of immune response	integral to membrane|plasma membrane	antigen binding|transmembrane receptor activity			skin(2)|ovary(1)	3				GBM - Glioblastoma multiforme(193;0.0348)														---	---	---	---
LILRA1	11024	broad.mit.edu	37	19	55106755	55106755	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55106755T>C	uc002qgh.1	+	5	731	c.549T>C	c.(547-549)TCT>TCC	p.S183S	LILRA2_uc010yfg.1_Intron|LILRA1_uc010yfh.1_Silent_p.S183S	NM_006863	NP_006854	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor,	183	Ig-like C2-type 2.|Extracellular (Potential).				cell surface receptor linked signaling pathway|defense response|regulation of immune response	integral to membrane|plasma membrane	antigen binding|transmembrane receptor activity			skin(2)|ovary(1)	3				GBM - Glioblastoma multiforme(193;0.0348)														---	---	---	---
LILRA1	11024	broad.mit.edu	37	19	55106787	55106787	+	Missense_Mutation	SNP	C	G	G	rs151320443		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55106787C>G	uc002qgh.1	+	5	763	c.581C>G	c.(580-582)TCG>TGG	p.S194W	LILRA2_uc010yfg.1_Intron|LILRA1_uc010yfh.1_Missense_Mutation_p.S194W	NM_006863	NP_006854	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor,	194	Ig-like C2-type 2.|Extracellular (Potential).				cell surface receptor linked signaling pathway|defense response|regulation of immune response	integral to membrane|plasma membrane	antigen binding|transmembrane receptor activity			skin(2)|ovary(1)	3				GBM - Glioblastoma multiforme(193;0.0348)														---	---	---	---
KIR2DL3	3804	broad.mit.edu	37	19	55250017	55250017	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55250017C>T	uc002qgv.2	+						KIR2DL3_uc002qgx.2_Missense_Mutation_p.L3F|KIR2DL3_uc002qgy.2_Missense_Mutation_p.L3F|KIR2DL3_uc010erw.1_Missense_Mutation_p.L3F|KIR2DL1_uc002qgz.1_5'Flank	NM_015868	NP_056952			killer cell immunoglobulin-like receptor, two						immune response|regulation of immune response	integral to plasma membrane	antigen binding|protein binding|receptor activity			ovary(2)	2				GBM - Glioblastoma multiforme(193;0.0192)												OREG0003673	type=REGULATORY REGION|Gene=KIR2DL3|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	---	---	---	---
KIR2DL1	3802	broad.mit.edu	37	19	55286697	55286697	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55286697T>A	uc002qhb.1	+	4	489	c.451T>A	c.(451-453)TCC>ACC	p.S151T	KIR2DS4_uc010yfj.1_Intron|KIR2DS4_uc010yfk.1_Intron|KIR2DL3_uc010erw.1_Intron|KIR2DL1_uc002qgz.1_Intron|KIR2DL3_uc002qha.1_RNA|KIR3DP1_uc010yfi.1_Intron|KIR2DL1_uc010erz.1_Missense_Mutation_p.S151T	NM_014218	NP_055033	P43626	KI2L1_HUMAN	killer cell immunoglobulin-like receptor, two	151	Extracellular (Potential).|Ig-like C2-type 2.				immune response|natural killer cell inhibitory signaling pathway	integral to plasma membrane	protein binding|receptor activity				0				GBM - Glioblastoma multiforme(193;0.0192)														---	---	---	---
FCAR	2204	broad.mit.edu	37	19	55401039	55401039	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55401039C>T	uc002qhr.1	+	5	871	c.674C>T	c.(673-675)ACG>ATG	p.T225M	FCAR_uc002qhs.1_RNA|FCAR_uc002qht.1_Missense_Mutation_p.T176M|FCAR_uc010esi.1_Missense_Mutation_p.T102M|FCAR_uc002qhu.1_Missense_Mutation_p.T129M|FCAR_uc002qhv.1_Missense_Mutation_p.T203M|FCAR_uc002qhw.1_Missense_Mutation_p.T213M|FCAR_uc002qhx.1_Missense_Mutation_p.T117M|FCAR_uc002qhy.1_Missense_Mutation_p.T191M|FCAR_uc002qhz.1_Silent_p.D188D|FCAR_uc002qia.1_Missense_Mutation_p.T116M	NM_002000	NP_001991	P24071	FCAR_HUMAN	Fc alpha receptor isoform a precursor	225	Extracellular (Potential).				immune response	extracellular region|integral to plasma membrane	IgA binding|receptor activity			ovary(1)|skin(1)	2				GBM - Glioblastoma multiforme(193;0.0443)														---	---	---	---
NLRP2	55655	broad.mit.edu	37	19	55494426	55494426	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55494426G>A	uc002qij.2	+	6	1446	c.1360G>A	c.(1360-1362)GCC>ACC	p.A454T	NLRP2_uc010yfp.1_Missense_Mutation_p.A431T|NLRP2_uc010esn.2_Missense_Mutation_p.A430T|NLRP2_uc010eso.2_Missense_Mutation_p.A451T|NLRP2_uc010esp.2_Missense_Mutation_p.A432T	NM_017852	NP_060322	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	454	NACHT.				apoptosis|positive regulation of caspase activity|positive regulation of interleukin-1 beta secretion	cytoplasm	ATP binding|Pyrin domain binding			ovary(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)														---	---	---	---
NLRP2	55655	broad.mit.edu	37	19	55501468	55501468	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55501468C>T	uc002qij.2	+	9	2531	c.2445C>T	c.(2443-2445)TGC>TGT	p.C815C	NLRP2_uc010yfp.1_Silent_p.C792C|NLRP2_uc010esn.2_Silent_p.C791C|NLRP2_uc010eso.2_Silent_p.C812C|NLRP2_uc010esp.2_Silent_p.C793C	NM_017852	NP_060322	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	815	LRR 1.				apoptosis|positive regulation of caspase activity|positive regulation of interleukin-1 beta secretion	cytoplasm	ATP binding|Pyrin domain binding			ovary(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)														---	---	---	---
GP6	51206	broad.mit.edu	37	19	55543656	55543656	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:55543656A>G	uc002qik.2	-	3	204	c.176T>C	c.(175-177)CTG>CCG	p.L59P	GP6_uc002qil.2_Missense_Mutation_p.L59P|GP6_uc010esq.2_Missense_Mutation_p.L59P|RDH13_uc010esr.1_Intron	NM_016363	NP_057447	Q9HCN6	GPVI_HUMAN	glycoprotein VI (platelet) isoform 2	59	Ig-like C2-type 1.|Extracellular (Potential).				enzyme linked receptor protein signaling pathway|leukocyte migration|platelet activation	integral to plasma membrane	collagen binding|transmembrane receptor activity			ovary(1)|central_nervous_system(1)	2			BRCA - Breast invasive adenocarcinoma(297;0.156)	GBM - Glioblastoma multiforme(193;0.0515)														---	---	---	---
SBK2	646643	broad.mit.edu	37	19	56047577	56047577	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56047577A>G	uc010ygc.1	-	1	85	c.85T>C	c.(85-87)TTA>CTA	p.L29L		NM_001101401	NP_001094871	P0C263	SBK2_HUMAN	SH3-binding domain kinase family, member 2	29							ATP binding|protein serine/threonine kinase activity				0																		---	---	---	---
CCDC106	29903	broad.mit.edu	37	19	56160437	56160437	+	Missense_Mutation	SNP	C	T	T	rs11558497		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56160437C>T	uc002qlr.2	+	2	760	c.25C>T	c.(25-27)CGG>TGG	p.R9W	CCDC106_uc002qls.2_Missense_Mutation_p.R9W	NM_013301	NP_037433	Q9BWC9	CC106_HUMAN	coiled-coil domain containing 106	9						nucleus					0		Colorectal(82;0.00403)|Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.105)														---	---	---	---
U2AF2	11338	broad.mit.edu	37	19	56180878	56180878	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56180878C>T	uc002qlu.2	+	11	2168	c.1113C>T	c.(1111-1113)GGC>GGT	p.G371G	U2AF2_uc002qlt.2_Silent_p.G367G	NM_007279	NP_009210	P26368	U2AF2_HUMAN	U2 (RNU2) small nuclear RNA auxiliary factor 2	371					mRNA 3'-end processing|mRNA export from nucleus|termination of RNA polymerase II transcription	nucleoplasm|spliceosomal complex	enzyme binding|nucleotide binding|RNA binding			ovary(1)	1		Colorectal(82;0.00244)|Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.107)														---	---	---	---
EPN1	29924	broad.mit.edu	37	19	56189998	56189998	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56189998C>T	uc002qlw.2	+	2	347	c.5C>T	c.(4-6)TCG>TTG	p.S2L	EPN1_uc002qlv.2_Missense_Mutation_p.S2L|EPN1_uc010etd.2_Missense_Mutation_p.S2L|EPN1_uc002qlx.2_Missense_Mutation_p.S113L	NM_001130072	NP_001123544	Q9Y6I3	EPN1_HUMAN	epsin 1 isoform b	2					endocytosis|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway	coated pit|cytoplasm|nucleus|plasma membrane	lipid binding				0		Colorectal(82;0.00244)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.112)														---	---	---	---
NLRP8	126205	broad.mit.edu	37	19	56473560	56473560	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56473560G>A	uc002qmh.2	+	4	2241	c.2170G>A	c.(2170-2172)GCG>ACG	p.A724T	NLRP8_uc010etg.2_Missense_Mutation_p.A724T	NM_176811	NP_789781	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	724						cytoplasm	ATP binding			ovary(4)|breast(3)|central_nervous_system(2)|skin(2)|large_intestine(1)|kidney(1)	13		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)														---	---	---	---
ZNF787	126208	broad.mit.edu	37	19	56600295	56600295	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56600295C>T	uc010eth.1	-	3	365	c.246G>A	c.(244-246)ACG>ACA	p.T82T		NM_001002836	NP_001002836	Q6DD87	ZN787_HUMAN	zinc finger protein 787	82	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1		Colorectal(82;3.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0559)														---	---	---	---
ZSCAN5B	342933	broad.mit.edu	37	19	56702357	56702357	+	Splice_Site	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56702357C>A	uc010ygh.1	-	3	589	c.589_splice	c.e3-1	p.G197_splice		NM_001080456	NP_001073925			zinc finger and SCAN domain containing 5B						viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2																		---	---	---	---
ZNF582	147948	broad.mit.edu	37	19	56901826	56901826	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56901826T>G	uc002qmz.1	-	3	213	c.54A>C	c.(52-54)GAA>GAC	p.E18D	ZNF582_uc002qmy.2_Missense_Mutation_p.E49D	NM_144690	NP_653291	Q96NG8	ZN582_HUMAN	zinc finger protein 582	18	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|large_intestine(1)	4		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0547)														---	---	---	---
ZNF583	147949	broad.mit.edu	37	19	56935118	56935118	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56935118G>A	uc010ygl.1	+	5	1256	c.1091G>A	c.(1090-1092)CGT>CAT	p.R364H	ZNF583_uc002qnc.2_Missense_Mutation_p.R364H|ZNF583_uc010ygm.1_Missense_Mutation_p.R364H	NM_001159860	NP_001153332	Q96ND8	ZN583_HUMAN	zinc finger protein 583	364	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0564)														---	---	---	---
ZNF583	147949	broad.mit.edu	37	19	56935173	56935173	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:56935173T>C	uc010ygl.1	+	5	1311	c.1146T>C	c.(1144-1146)TGT>TGC	p.C382C	ZNF583_uc002qnc.2_Silent_p.C382C|ZNF583_uc010ygm.1_Silent_p.C382C	NM_001159860	NP_001153332	Q96ND8	ZN583_HUMAN	zinc finger protein 583	382	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0564)														---	---	---	---
ZNF471	57573	broad.mit.edu	37	19	57035890	57035890	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57035890A>G	uc002qnh.2	+	5	587	c.454A>G	c.(454-456)ACC>GCC	p.T152A		NM_020813	NP_065864	Q9BX82	ZN471_HUMAN	zinc finger protein 471	152					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0307)														---	---	---	---
ZFP28	140612	broad.mit.edu	37	19	57061537	57061537	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57061537C>T	uc002qnj.2	+	6	860	c.789C>T	c.(787-789)GAC>GAT	p.D263D	ZFP28_uc002qni.2_Silent_p.D263D|uc002qnk.1_Intron	NM_020828	NP_065879	Q8NHY6	ZFP28_HUMAN	zinc finger protein 28	263	KRAB 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0302)														---	---	---	---
USP29	57663	broad.mit.edu	37	19	57641635	57641635	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57641635T>C	uc002qny.2	+	4	1948	c.1592T>C	c.(1591-1593)ATT>ACT	p.I531T		NM_020903	NP_065954	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	531					protein modification process|ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|protein binding|ubiquitin thiolesterase activity			lung(6)|ovary(2)|breast(2)|pancreas(1)	11		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)														---	---	---	---
DUXA	503835	broad.mit.edu	37	19	57669815	57669815	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57669815T>C	uc002qoa.1	-	4	364	c.319A>G	c.(319-321)ACC>GCC	p.T107A		NM_001012729	NP_001012747	A6NLW8	DUXA_HUMAN	double homeobox A	107	Homeobox 2.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0123)														---	---	---	---
ZNF460	10794	broad.mit.edu	37	19	57803352	57803352	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57803352C>T	uc002qog.2	+	3	1765	c.1443C>T	c.(1441-1443)TGC>TGT	p.C481C	ZNF460_uc010ygv.1_Silent_p.C440C	NM_006635	NP_006626	Q14592	ZN460_HUMAN	zinc finger protein 460	481	C2H2-type 11.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)														---	---	---	---
ZNF552	79818	broad.mit.edu	37	19	58319467	58319467	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58319467A>T	uc002qqg.2	-	3	1335	c.1165T>A	c.(1165-1167)TTT>ATT	p.F389I	ZNF587_uc002qqb.2_Intron|ZNF552_uc010yhg.1_Missense_Mutation_p.F385I	NM_024762	NP_079038	Q9H707	ZN552_HUMAN	zinc finger protein 552	389	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0259)														---	---	---	---
A1BG	1	broad.mit.edu	37	19	58863010	58863010	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58863010G>T	uc002qsd.3	-	5	719	c.657C>A	c.(655-657)TCC>TCA	p.S219S	NCRNA00181_uc002qse.2_Intron|A1BG_uc002qsf.1_RNA|NCRNA00181_uc002qsg.2_5'Flank	NM_130786	NP_570602	P04217	A1BG_HUMAN	alpha 1B-glycoprotein precursor	219	Ig-like V-type 3.					extracellular region					0		all_cancers(17;3.04e-16)|all_epithelial(17;7.77e-12)|Lung NSC(17;3.25e-05)|Colorectal(82;5.46e-05)|all_lung(17;0.000129)|all_neural(62;0.0182)|Ovarian(87;0.0443)|Breast(46;0.0889)|Renal(17;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0269)														---	---	---	---
RPS5	6193	broad.mit.edu	37	19	58904732	58904732	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58904732C>T	uc002qsn.2	+	4	397	c.325C>T	c.(325-327)CTG>TTG	p.L109L	RPS5_uc002qso.2_Silent_p.L109L	NM_001009	NP_001000	P46782	RS5_HUMAN	ribosomal protein S5	109					endocrine pancreas development|regulation of translational fidelity|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit	mRNA binding|structural constituent of ribosome				0		all_cancers(17;1.71e-22)|all_epithelial(17;1.69e-16)|Lung NSC(17;2.25e-06)|all_lung(17;9.97e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Breast(46;0.0194)|Ovarian(87;0.0443)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.171)|GBM - Glioblastoma multiforme(193;0.0323)|Lung(386;0.0543)|LUSC - Lung squamous cell carcinoma(496;0.176)														---	---	---	---
ZNF324	25799	broad.mit.edu	37	19	58982642	58982642	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58982642G>A	uc002qsw.1	+	4	877	c.783G>A	c.(781-783)GCG>GCA	p.A261A	ZNF324_uc002qsx.1_Silent_p.A38A	NM_014347	NP_055162	O75467	Z324A_HUMAN	zinc finger protein 324	261	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)														---	---	---	---
SLC27A5	10998	broad.mit.edu	37	19	59009928	59009928	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:59009928G>A	uc002qtc.2	-	10	2137	c.2027C>T	c.(2026-2028)ACG>ATG	p.T676M	SLC27A5_uc002qtb.2_RNA	NM_012254	NP_036386	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid	676	Cytoplasmic (Probable).				bile acid and bile salt transport|bile acid biosynthetic process|very long-chain fatty acid metabolic process	endoplasmic reticulum membrane|integral to membrane	ATP binding|cholate-CoA ligase activity|long-chain fatty acid-CoA ligase activity				0		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.181)														---	---	---	---
SLC27A5	10998	broad.mit.edu	37	19	59010056	59010056	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:59010056G>A	uc002qtc.2	-	10	2009	c.1899C>T	c.(1897-1899)GAC>GAT	p.D633D	SLC27A5_uc002qtb.2_RNA	NM_012254	NP_036386	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid	633	Cytoplasmic (Probable).				bile acid and bile salt transport|bile acid biosynthetic process|very long-chain fatty acid metabolic process	endoplasmic reticulum membrane|integral to membrane	ATP binding|cholate-CoA ligase activity|long-chain fatty acid-CoA ligase activity				0		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.181)														---	---	---	---
ZBTB45	84878	broad.mit.edu	37	19	59028198	59028198	+	Silent	SNP	G	A	A	rs148034788		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:59028198G>A	uc002qtd.2	-	2	1135	c.843C>T	c.(841-843)GAC>GAT	p.D281D	ZBTB45_uc002qte.2_Silent_p.D281D|ZBTB45_uc002qtf.2_Silent_p.D281D	NM_032792	NP_116181	Q96K62	ZBT45_HUMAN	zinc finger and BTB domain containing 45	281					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0165)|Lung(386;0.18)												OREG0025700	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
NRSN2	80023	broad.mit.edu	37	20	330364	330364	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:330364G>A	uc002wdi.3	+	3	615	c.77G>A	c.(76-78)CGC>CAC	p.R26H	NRSN2_uc002wdj.2_Intron|NRSN2_uc002wdl.2_Missense_Mutation_p.R25H	NM_024958	NP_079234	Q9GZP1	NRSN2_HUMAN	neurensin 2	26						integral to membrane|plasma membrane|transport vesicle					0		all_cancers(10;0.0834)																---	---	---	---
NRSN2	80023	broad.mit.edu	37	20	333852	333852	+	Splice_Site	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:333852A>G	uc002wdi.3	+	4	728	c.190_splice	c.e4-2	p.I64_splice	NRSN2_uc002wdj.2_Splice_Site|NRSN2_uc002wdl.2_Intron	NM_024958	NP_079234			neurensin 2							integral to membrane|plasma membrane|transport vesicle					0		all_cancers(10;0.0834)																---	---	---	---
SCRT2	85508	broad.mit.edu	37	20	644456	644456	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:644456C>T	uc002wec.2	-	2	1361	c.783G>A	c.(781-783)ACG>ACA	p.T261T	SRXN1_uc002web.2_Intron	NM_033129	NP_149120	Q9NQ03	SCRT2_HUMAN	scratch 2 protein	261	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0																		---	---	---	---
ANGPT4	51378	broad.mit.edu	37	20	853641	853641	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:853641G>A	uc002wei.2	-	9	1577	c.1474C>T	c.(1474-1476)CGT>TGT	p.R492C	ANGPT4_uc010zpn.1_3'UTR	NM_015985	NP_057069	Q9Y264	ANGP4_HUMAN	angiopoietin 4 precursor	492	Fibrinogen C-terminal.				anti-apoptosis|blood coagulation|cellular response to hypoxia|leukocyte migration|negative regulation of angiogenesis|negative regulation of blood vessel endothelial cell migration|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of peptidyl-tyrosine phosphorylation|signal transduction	extracellular space	receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity			ovary(2)	2																		---	---	---	---
NSFL1C	55968	broad.mit.edu	37	20	1424423	1424423	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:1424423T>C	uc002wfc.2	-	9	2032	c.1084A>G	c.(1084-1086)AAT>GAT	p.N362D	NSFL1C_uc002wfd.2_Missense_Mutation_p.N251D|NSFL1C_uc002wfe.2_Missense_Mutation_p.N331D|NSFL1C_uc002wff.2_RNA|NSFL1C_uc010gag.2_Missense_Mutation_p.N128D	NM_016143	NP_057227	Q9UNZ2	NSF1C_HUMAN	p47 protein isoform a	362	UBX.					chromosome|Golgi stack|nucleus	lipid binding|protein binding				0																		---	---	---	---
ZNF343	79175	broad.mit.edu	37	20	2464065	2464065	+	Silent	SNP	C	T	T	rs145914187	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2464065C>T	uc002wge.1	-	6	2030	c.1542G>A	c.(1540-1542)ACG>ACA	p.T514T	ZNF343_uc010gao.1_Silent_p.T514T|ZNF343_uc002wgd.1_Silent_p.T424T	NM_024325	NP_077301	Q6P1L6	ZN343_HUMAN	zinc finger protein 343	514	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
TMC2	117532	broad.mit.edu	37	20	2621932	2621932	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2621932G>A	uc002wgf.1	+	20	2671	c.2656G>A	c.(2656-2658)GCC>ACC	p.A886T	TMC2_uc002wgg.1_Missense_Mutation_p.A870T	NM_080751	NP_542789	Q8TDI7	TMC2_HUMAN	transmembrane cochlear-expressed protein 2	886	Cytoplasmic (Potential).					integral to membrane				ovary(3)	3																		---	---	---	---
CPXM1	56265	broad.mit.edu	37	20	2776418	2776418	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2776418G>A	uc002wgu.2	-	11	1611	c.1547C>T	c.(1546-1548)GCT>GTT	p.A516V	CPXM1_uc010gas.2_Intron	NM_019609	NP_062555	Q96SM3	CPXM1_HUMAN	carboxypeptidase X, member 1 precursor	516					cell adhesion|proteolysis		metallocarboxypeptidase activity|zinc ion binding			ovary(2)|skin(2)	4																		---	---	---	---
C20orf141	128653	broad.mit.edu	37	20	2796209	2796209	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2796209C>T	uc010gat.2	+	3	369	c.286C>T	c.(286-288)CGC>TGC	p.R96C	C20orf141_uc002wgv.1_Intron|C20orf141_uc002wgw.2_Missense_Mutation_p.R96C|uc002wgx.1_5'Flank|uc002wgy.1_5'Flank	NM_080739	NP_542777	Q9NUB4	CT141_HUMAN	hypothetical protein LOC128653	96	Leu-rich.					integral to membrane					0																		---	---	---	---
ProSAPiP1	9762	broad.mit.edu	37	20	3147448	3147448	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3147448C>T	uc002wia.1	-	1	1760	c.362G>A	c.(361-363)GGC>GAC	p.G121D	ProSAPiP1_uc002wib.1_Missense_Mutation_p.G121D	NM_014731	NP_055546	O60299	PRIP1_HUMAN	ProSAPiP1 protein	121						cell junction|cytoplasm|postsynaptic density|postsynaptic membrane				pancreas(1)	1																		---	---	---	---
ITPA	3704	broad.mit.edu	37	20	3199170	3199170	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3199170C>T	uc002wid.2	+	6	445	c.303C>T	c.(301-303)CAC>CAT	p.H101H	ITPA_uc002wie.2_Silent_p.H84H|ITPA_uc002wif.2_RNA	NM_033453	NP_258412	Q9BY32	ITPA_HUMAN	inosine triphosphatase isoform a	101					nucleotide metabolic process	cytoplasm	metal ion binding|nucleoside-triphosphate diphosphatase activity|nucleotide binding			ovary(1)	1																OREG0025730	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SLC4A11	83959	broad.mit.edu	37	20	3210887	3210887	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3210887C>T	uc002wig.2	-	12	1531	c.1483G>A	c.(1483-1485)GCC>ACC	p.A495T	SLC4A11_uc010zqe.1_Missense_Mutation_p.A522T|SLC4A11_uc002wih.2_RNA|SLC4A11_uc010zqf.1_Missense_Mutation_p.A479T	NM_032034	NP_114423	Q8NBS3	S4A11_HUMAN	solute carrier family 4 member 11	495	Helical; (Potential).|Membrane (bicarbonate transporter).				cellular cation homeostasis|fluid transport|phosphoenolpyruvate-dependent sugar phosphotransferase system	basolateral plasma membrane|integral to membrane	bicarbonate transmembrane transporter activity|borate transmembrane transporter activity|hydrogen ion channel activity|inorganic anion exchanger activity|sodium channel activity|sugar:hydrogen symporter activity			ovary(1)	1																		---	---	---	---
ATRN	8455	broad.mit.edu	37	20	3540039	3540039	+	Splice_Site	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:3540039G>T	uc002wim.2	+	7	1203	c.1113_splice	c.e7-1	p.A371_splice	ATRN_uc002wil.2_Splice_Site_p.A371_splice	NM_139321	NP_647537			attractin isoform 1						inflammatory response	extracellular space|integral to plasma membrane	receptor activity|sugar binding			ovary(1)|breast(1)	2																		---	---	---	---
RASSF2	9770	broad.mit.edu	37	20	4766954	4766954	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4766954G>A	uc002wld.2	-	10	888	c.834C>T	c.(832-834)TTC>TTT	p.F278F	RASSF2_uc002wlc.2_RNA|RASSF2_uc002wle.2_RNA|RASSF2_uc002wlf.2_Silent_p.F278F|RASSF2_uc010gbh.2_Intron	NM_170774	NP_739580	P50749	RASF2_HUMAN	Ras association domain family 2	278	SARAH.				cell cycle|signal transduction	nucleus	protein binding			ovary(3)|lung(2)|large_intestine(1)	6																		---	---	---	---
RASSF2	9770	broad.mit.edu	37	20	4770317	4770317	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:4770317G>A	uc002wld.2	-	7	618	c.564C>T	c.(562-564)GGC>GGT	p.G188G	RASSF2_uc002wlc.2_RNA|RASSF2_uc002wle.2_RNA|RASSF2_uc002wlf.2_Silent_p.G188G|RASSF2_uc010gbh.2_5'Flank	NM_170774	NP_739580	P50749	RASF2_HUMAN	Ras association domain family 2	188	Ras-associating.				cell cycle|signal transduction	nucleus	protein binding			ovary(3)|lung(2)|large_intestine(1)	6																		---	---	---	---
PLCB4	5332	broad.mit.edu	37	20	9319541	9319541	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9319541G>A	uc002wnf.2	+	6	362	c.226G>A	c.(226-228)GAT>AAT	p.D76N	PLCB4_uc010gbw.1_Missense_Mutation_p.D76N|PLCB4_uc010gbx.2_Missense_Mutation_p.D76N|PLCB4_uc002wne.2_Missense_Mutation_p.D76N	NM_182797	NP_877949	Q15147	PLCB4_HUMAN	phospholipase C beta 4 isoform b	76					intracellular signal transduction|lipid catabolic process	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			skin(11)|ovary(3)|pancreas(1)	15																		---	---	---	---
PLCB4	5332	broad.mit.edu	37	20	9457375	9457375	+	Intron	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:9457375C>A	uc002wnf.2	+						PLCB4_uc010gbx.2_Intron|PLCB4_uc002wne.2_Silent_p.S1157S|PLCB4_uc002wnh.2_Intron	NM_182797	NP_877949			phospholipase C beta 4 isoform b						intracellular signal transduction|lipid catabolic process	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			skin(11)|ovary(3)|pancreas(1)	15																		---	---	---	---
JAG1	182	broad.mit.edu	37	20	10621869	10621869	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10621869G>A	uc002wnw.2	-	24	3456	c.2940C>T	c.(2938-2940)TGC>TGT	p.C980C		NM_000214	NP_000205	P78504	JAG1_HUMAN	jagged 1 precursor	980	Extracellular (Potential).				angiogenesis|cell communication|cell fate determination|endothelial cell differentiation|hemopoiesis|keratinocyte differentiation|myoblast differentiation|Notch receptor processing|Notch signaling pathway|regulation of cell migration|regulation of cell proliferation	extracellular region|integral to plasma membrane	calcium ion binding|growth factor activity|Notch binding|structural molecule activity			lung(3)|ovary(2)|central_nervous_system(2)|breast(1)|pancreas(1)	9														Alagille_Syndrome				---	---	---	---
JAG1	182	broad.mit.edu	37	20	10633110	10633110	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:10633110C>T	uc002wnw.2	-						JAG1_uc010gcd.1_5'Flank	NM_000214	NP_000205			jagged 1 precursor						angiogenesis|cell communication|cell fate determination|endothelial cell differentiation|hemopoiesis|keratinocyte differentiation|myoblast differentiation|Notch receptor processing|Notch signaling pathway|regulation of cell migration|regulation of cell proliferation	extracellular region|integral to plasma membrane	calcium ion binding|growth factor activity|Notch binding|structural molecule activity			lung(3)|ovary(2)|central_nervous_system(2)|breast(1)|pancreas(1)	9														Alagille_Syndrome				---	---	---	---
BTBD3	22903	broad.mit.edu	37	20	11904042	11904042	+	Missense_Mutation	SNP	G	A	A	rs149470256		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:11904042G>A	uc002wnz.2	+	4	1656	c.1297G>A	c.(1297-1299)GTT>ATT	p.V433I	BTBD3_uc002wny.2_Missense_Mutation_p.V372I|BTBD3_uc002woa.2_Missense_Mutation_p.V372I|BTBD3_uc010zrf.1_Missense_Mutation_p.V282I|BTBD3_uc010zrg.1_Missense_Mutation_p.V282I|BTBD3_uc010zrh.1_Missense_Mutation_p.V282I	NM_014962	NP_055777	Q9Y2F9	BTBD3_HUMAN	BTB/POZ domain containing protein 3 isoform a	433										ovary(2)|central_nervous_system(1)	3																		---	---	---	---
ISM1	140862	broad.mit.edu	37	20	13279917	13279917	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13279917G>A	uc010gce.1	+	6	1212	c.1206G>A	c.(1204-1206)ACG>ACA	p.T402T	TASP1_uc010zri.1_Intron	NM_080826	NP_543016	B1AKI9	ISM1_HUMAN	isthmin 1 homolog precursor	402	AMOP.					extracellular region					0																		---	---	---	---
MACROD2	140733	broad.mit.edu	37	20	13982967	13982967	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:13982967G>A	uc002wou.2	+	2	344	c.80G>A	c.(79-81)CGC>CAC	p.R27H	MACROD2_uc002wot.2_Missense_Mutation_p.R27H|MACROD2_uc002wos.2_RNA	NM_080676	NP_542407	A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2 isoform 1	27											0		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)																---	---	---	---
FLRT3	23767	broad.mit.edu	37	20	14306867	14306867	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:14306867A>C	uc002wov.1	-	3	1753	c.1286T>G	c.(1285-1287)CTT>CGT	p.L429R	MACROD2_uc002wot.2_Intron|MACROD2_uc002wou.2_Intron|FLRT3_uc002wow.1_Missense_Mutation_p.L429R	NM_198391	NP_938205	Q9NZU0	FLRT3_HUMAN	fibronectin leucine rich transmembrane protein 3	429	Extracellular (Potential).|Fibronectin type-III.				cell adhesion	integral to plasma membrane|proteinaceous extracellular matrix	protein binding, bridging|receptor signaling protein activity			kidney(1)	1		Colorectal(1;0.0464)	COAD - Colon adenocarcinoma(2;0.129)	Colorectal(1;0.0393)														---	---	---	---
SLC24A3	57419	broad.mit.edu	37	20	19698220	19698220	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19698220G>A	uc002wrl.2	+	16	1965	c.1768G>A	c.(1768-1770)GCC>ACC	p.A590T		NM_020689	NP_065740	Q9HC58	NCKX3_HUMAN	solute carrier family 24	590	Helical; (Potential).					integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			ovary(1)	1																		---	---	---	---
RIN2	54453	broad.mit.edu	37	20	19972820	19972820	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19972820T>C	uc002wro.1	+	9	2113	c.2077T>C	c.(2077-2079)TAT>CAT	p.Y693H	RIN2_uc010gcu.1_Missense_Mutation_p.Y260H|RIN2_uc010gcv.1_Missense_Mutation_p.Y487H	NM_018993	NP_061866	Q8WYP3	RIN2_HUMAN	Ras and Rab interactor 2	693	VPS9.				endocytosis|small GTPase mediated signal transduction	cytoplasm	GTPase activator activity|Rab guanyl-nucleotide exchange factor activity			lung(4)|ovary(1)	5																		---	---	---	---
CRNKL1	51340	broad.mit.edu	37	20	20032930	20032930	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:20032930G>A	uc002wrs.2	-						C20orf26_uc010gcw.1_5'Flank|C20orf26_uc010zse.1_5'Flank|C20orf26_uc002wru.2_5'Flank|CRNKL1_uc002wrt.1_Intron	NM_016652	NP_057736			crooked neck-like 1 protein						spliceosome assembly	catalytic step 2 spliceosome|cytoplasm|nuclear speck	RNA binding			ovary(2)|large_intestine(1)	3																		---	---	---	---
PLK1S1	55857	broad.mit.edu	37	20	21195317	21195317	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21195317A>G	uc002wsb.2	+	9	1724	c.1591A>G	c.(1591-1593)AGT>GGT	p.S531G	PLK1S1_uc010zsh.1_Missense_Mutation_p.S428G|PLK1S1_uc010zsi.1_Missense_Mutation_p.S398G|PLK1S1_uc010zsj.1_RNA|uc002wsc.2_Intron|PLK1S1_uc002wsd.2_RNA|uc002wse.2_Intron	NM_018474	NP_060944	Q2M2Z5	KIZ_HUMAN	polo-like kinase 1 substrate 1 isoform 1	531					spindle organization	centrosome	protein kinase binding				0																		---	---	---	---
XRN2	22803	broad.mit.edu	37	20	21327078	21327078	+	Missense_Mutation	SNP	C	T	T	rs147104098		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21327078C>T	uc002wsf.1	+	17	1650	c.1555C>T	c.(1555-1557)CGG>TGG	p.R519W	XRN2_uc002wsg.1_Missense_Mutation_p.R443W|XRN2_uc010zsk.1_Missense_Mutation_p.R465W	NM_012255	NP_036387	Q9H0D6	XRN2_HUMAN	5'-3' exoribonuclease 2	519					cell growth|DNA catabolic process, exonucleolytic|mRNA processing|regulation of transcription, DNA-dependent|RNA catabolic process|spermatogenesis|transcription termination, DNA-dependent	nucleolus	5'-3' exoribonuclease activity|nucleic acid binding|protein binding|zinc ion binding			skin(1)	1																		---	---	---	---
NKX2-4	644524	broad.mit.edu	37	20	21377979	21377979	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:21377979A>G	uc010gcz.2	-	1	69	c.59T>C	c.(58-60)ATC>ACC	p.I20T		NM_033176	NP_149416	Q9H2Z4	NKX24_HUMAN	NK2 homeobox 4	20					multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
CD93	22918	broad.mit.edu	37	20	23066041	23066041	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23066041G>A	uc002wsv.2	-	1	937	c.789C>T	c.(787-789)GGC>GGT	p.G263G		NM_012072	NP_036204	Q9NPY3	C1QR1_HUMAN	CD93 antigen precursor	263	EGF-like 1.|Extracellular (Potential).				cell-cell adhesion|interspecies interaction between organisms|macrophage activation|phagocytosis	plasma membrane	calcium ion binding|complement component C1q binding|receptor activity|sugar binding			large_intestine(2)	2	Colorectal(13;0.0352)|Lung NSC(19;0.0542)|all_lung(19;0.118)																	---	---	---	---
NXT1	29107	broad.mit.edu	37	20	23334874	23334874	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23334874C>T	uc002wsx.1	+	2	583	c.196C>T	c.(196-198)CCT>TCT	p.P66S		NM_013248	NP_037380	Q9UKK6	NXT1_HUMAN	NTF2-like export factor 1	66	NTF2.					cytoplasm|nuclear pore				ovary(1)	1	Lung NSC(19;0.0605)|Colorectal(13;0.0993)|all_lung(19;0.135)																	---	---	---	---
GZF1	64412	broad.mit.edu	37	20	23345951	23345951	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23345951G>A	uc010gdb.2	+	3	1105	c.931G>A	c.(931-933)GAG>AAG	p.E311K	GZF1_uc002wsy.2_Missense_Mutation_p.E311K|GZF1_uc010zsq.1_Intron|GZF1_uc010zsr.1_Intron|GZF1_uc002wsz.2_Missense_Mutation_p.E311K	NM_022482	NP_071927	Q9H116	GZF1_HUMAN	GDNF-inducible zinc finger protein 1	311					transcription, DNA-dependent	nucleolus|nucleoplasm	sequence-specific DNA binding|zinc ion binding			kidney(1)	1	Lung NSC(19;0.0605)|Colorectal(13;0.0993)|all_lung(19;0.135)																	---	---	---	---
CST8	10047	broad.mit.edu	37	20	23473681	23473681	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:23473681C>A	uc002wth.1	+	3	675	c.318C>A	c.(316-318)GCC>GCA	p.A106A		NM_005492	NP_005483	O60676	CST8_HUMAN	cystatin 8 precursor	106						extracellular region	cysteine-type endopeptidase inhibitor activity				0	Colorectal(13;0.0431)|Lung NSC(19;0.235)																	---	---	---	---
C20orf3	57136	broad.mit.edu	37	20	24954301	24954301	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:24954301C>T	uc002wty.2	-	4	502	c.401G>A	c.(400-402)CGG>CAG	p.R134Q	C20orf3_uc002wtz.2_Missense_Mutation_p.R134Q|C20orf3_uc010zsw.1_Missense_Mutation_p.R134Q	NM_020531	NP_065392	Q9HDC9	APMAP_HUMAN	chromosome 20 open reading frame 3	134	Extracellular (Potential).				biosynthetic process	cell surface|integral to membrane	arylesterase activity|strictosidine synthase activity			ovary(1)	1																		---	---	---	---
ACSS1	84532	broad.mit.edu	37	20	25000733	25000733	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25000733C>T	uc002wub.2	-	7	2037	c.1159G>A	c.(1159-1161)GCC>ACC	p.A387T	ACSS1_uc002wuc.2_Missense_Mutation_p.A387T|ACSS1_uc010gdc.2_Intron|ACSS1_uc002wud.1_RNA|ACSS1_uc002wua.2_Missense_Mutation_p.A304T	NM_032501	NP_115890	Q9NUB1	ACS2L_HUMAN	acyl-CoA synthetase short-chain family member 1	387					acetyl-CoA biosynthetic process|ethanol oxidation|xenobiotic metabolic process	mitochondrial matrix	acetate-CoA ligase activity|AMP binding|ATP binding|protein binding			ovary(1)|skin(1)	2					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)													---	---	---	---
NINL	22981	broad.mit.edu	37	20	25485593	25485593	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:25485593G>A	uc002wux.1	-	6	713	c.639C>T	c.(637-639)AGC>AGT	p.S213S	NINL_uc010gdn.1_Silent_p.S213S|NINL_uc010gdo.1_Silent_p.S53S|NINL_uc010ztf.1_Silent_p.S229S	NM_025176	NP_079452	Q9Y2I6	NINL_HUMAN	ninein-like	213	EF-hand 3.				G2/M transition of mitotic cell cycle	cytosol|microtubule|microtubule organizing center	calcium ion binding			ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5																		---	---	---	---
HM13	81502	broad.mit.edu	37	20	30136897	30136897	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30136897G>A	uc002wwe.2	+	5	634	c.520G>A	c.(520-522)GTC>ATC	p.V174I	HM13_uc002wwc.2_Missense_Mutation_p.V174I|HM13_uc002wwd.2_Missense_Mutation_p.V174I|HM13_uc002wwf.2_Missense_Mutation_p.V50I|HM13_uc010gdu.2_Missense_Mutation_p.V50I	NM_030789	NP_110416	Q8TCT9	HM13_HUMAN	minor histocompatibility antigen 13 isoform 1	174	Cytoplasmic (Potential).				membrane protein proteolysis	cell surface|endoplasmic reticulum membrane|integral to membrane|plasma membrane	aspartic-type endopeptidase activity|protein binding			breast(1)	1	all_cancers(5;3.44e-05)|Lung NSC(7;4.38e-06)|all_lung(7;7.65e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		all cancers(5;0.000479)|Colorectal(19;0.00202)|COAD - Colon adenocarcinoma(19;0.0264)															---	---	---	---
TPX2	22974	broad.mit.edu	37	20	30354354	30354354	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30354354C>T	uc002wwp.1	+						TPX2_uc010gdv.1_Intron	NM_012112	NP_036244			TPX2, microtubule-associated protein homolog						activation of protein kinase activity|apoptosis|cell division|cell proliferation|mitosis|regulation of mitotic spindle organization	cytoplasm|microtubule|nucleus|spindle pole	ATP binding|GTP binding|protein kinase binding			large_intestine(1)|ovary(1)	2			Epithelial(4;0.000771)|Colorectal(19;0.00306)|all cancers(5;0.004)|COAD - Colon adenocarcinoma(19;0.0347)|OV - Ovarian serous cystadenocarcinoma(3;0.0656)															---	---	---	---
FOXS1	2307	broad.mit.edu	37	20	30432637	30432637	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30432637C>T	uc002wwt.1	-	1	784	c.709G>A	c.(709-711)GTC>ATC	p.V237I		NM_004118	NP_004109	O43638	FOXS1_HUMAN	forkhead box S1	237					anti-apoptosis|artery morphogenesis|blood vessel remodeling|camera-type eye development|cardiac muscle cell proliferation|collagen fibril organization|embryonic heart tube development|insulin receptor signaling pathway|lymphangiogenesis|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|neural crest cell fate commitment|neuromuscular process controlling balance|Notch signaling pathway|ossification|paraxial mesodermal cell fate commitment|patterning of blood vessels|positive regulation of multicellular organism growth|positive regulation of transcription from RNA polymerase II promoter|regulation of blood vessel size|regulation of organ growth|somitogenesis|vascular endothelial growth factor receptor signaling pathway|vasculogenesis|ventricular cardiac muscle tissue morphogenesis	transcription factor complex	chromatin DNA binding|DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			ovary(1)	1																		---	---	---	---
FOXS1	2307	broad.mit.edu	37	20	30432760	30432760	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30432760A>T	uc002wwt.1	-	1	661	c.586T>A	c.(586-588)TCC>ACC	p.S196T		NM_004118	NP_004109	O43638	FOXS1_HUMAN	forkhead box S1	196					anti-apoptosis|artery morphogenesis|blood vessel remodeling|camera-type eye development|cardiac muscle cell proliferation|collagen fibril organization|embryonic heart tube development|insulin receptor signaling pathway|lymphangiogenesis|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription, DNA-dependent|neural crest cell fate commitment|neuromuscular process controlling balance|Notch signaling pathway|ossification|paraxial mesodermal cell fate commitment|patterning of blood vessels|positive regulation of multicellular organism growth|positive regulation of transcription from RNA polymerase II promoter|regulation of blood vessel size|regulation of organ growth|somitogenesis|vascular endothelial growth factor receptor signaling pathway|vasculogenesis|ventricular cardiac muscle tissue morphogenesis	transcription factor complex	chromatin DNA binding|DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			ovary(1)	1																		---	---	---	---
XKR7	343702	broad.mit.edu	37	20	30584347	30584347	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30584347C>T	uc002wxe.2	+	3	1001	c.827C>T	c.(826-828)ACG>ATG	p.T276M		NM_001011718	NP_001011718	Q5GH72	XKR7_HUMAN	XK, Kell blood group complex subunit-related	276	Helical; (Potential).					integral to membrane				ovary(1)|breast(1)|skin(1)	3			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)															---	---	---	---
TM9SF4	9777	broad.mit.edu	37	20	30720867	30720867	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30720867G>A	uc002wxj.2	+	2	302	c.67G>A	c.(67-69)GCC>ACC	p.A23T	TM9SF4_uc010ztr.1_5'UTR|TM9SF4_uc010zts.1_5'UTR|TM9SF4_uc002wxk.2_Missense_Mutation_p.A6T	NM_014742	NP_055557	Q92544	TM9S4_HUMAN	transmembrane 9 superfamily protein member 4	23						integral to membrane				central_nervous_system(1)|pancreas(1)	2			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)															---	---	---	---
ASXL1	171023	broad.mit.edu	37	20	31024560	31024560	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31024560G>A	uc002wxs.2	+	12	4471	c.4045G>A	c.(4045-4047)GTA>ATA	p.V1349I	ASXL1_uc010geb.2_Missense_Mutation_p.V1240I	NM_015338	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like 1 isoform 1	1349					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	PR-DUB complex	metal ion binding|protein binding			haematopoietic_and_lymphoid_tissue(239)|large_intestine(6)|central_nervous_system(2)|ovary(1)	248								F|N|Mis		MDS|CMML								---	---	---	---
DNMT3B	1789	broad.mit.edu	37	20	31372633	31372633	+	Missense_Mutation	SNP	C	T	T	rs149520896		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31372633C>T	uc002wyc.2	+	4	595	c.274C>T	c.(274-276)CGG>TGG	p.R92W	DNMT3B_uc010ztx.1_RNA|DNMT3B_uc010zty.1_RNA|DNMT3B_uc002wyd.2_Missense_Mutation_p.R92W|DNMT3B_uc002wye.2_Missense_Mutation_p.R92W|DNMT3B_uc010gee.2_RNA|DNMT3B_uc010gef.2_RNA|DNMT3B_uc010ztz.1_Missense_Mutation_p.R92W|DNMT3B_uc010zua.1_Intron|DNMT3B_uc002wyf.2_Missense_Mutation_p.R104W	NM_006892	NP_008823	Q9UBC3	DNM3B_HUMAN	DNA cytosine-5 methyltransferase 3 beta isoform	92	Interaction with DNMT1 and DNMT3A.				negative regulation of histone H3-K9 methylation|positive regulation of gene expression|positive regulation of histone H3-K4 methylation		metal ion binding|protein binding|transcription corepressor activity			lung(3)|ovary(2)	5																		---	---	---	---
BPIL1	80341	broad.mit.edu	37	20	31606521	31606521	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31606521A>G	uc002wyj.2	+	9	942	c.748A>G	c.(748-750)ACC>GCC	p.T250A		NM_025227	NP_079503	Q8N4F0	BPIL1_HUMAN	bactericidal/permeability-increasing	250						extracellular region	lipid binding			skin(2)|large_intestine(1)|ovary(1)	4																		---	---	---	---
BPIL1	80341	broad.mit.edu	37	20	31609114	31609114	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31609114A>G	uc002wyj.2	+	14	1416	c.1222A>G	c.(1222-1224)ACC>GCC	p.T408A		NM_025227	NP_079503	Q8N4F0	BPIL1_HUMAN	bactericidal/permeability-increasing	408						extracellular region	lipid binding			skin(2)|large_intestine(1)|ovary(1)	4																		---	---	---	---
C20orf186	149954	broad.mit.edu	37	20	31671197	31671197	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31671197A>G	uc010zue.1	+	3	209	c.194A>G	c.(193-195)GAC>GGC	p.D65G		NM_182519	NP_872325	P59827	LPLC4_HUMAN	antimicrobial peptide RY2G5 precursor	65						cytoplasm|extracellular region	lipid binding				0																		---	---	---	---
CBFA2T2	9139	broad.mit.edu	37	20	32228349	32228349	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32228349G>A	uc002wzg.1	+						CBFA2T2_uc010zug.1_Intron|CBFA2T2_uc002wze.1_Intron|CBFA2T2_uc002wzf.1_Intron|CBFA2T2_uc002wzh.1_Intron|CBFA2T2_uc002wzi.1_Intron|CBFA2T2_uc002wzj.1_Intron|CBFA2T2_uc002wzk.1_Intron	NM_005093	NP_005084			core-binding factor, runt domain, alpha subunit							nucleus	protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			pancreas(1)|skin(1)	2																		---	---	---	---
E2F1	1869	broad.mit.edu	37	20	32267689	32267689	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32267689G>A	uc002wzu.3	-	3	584	c.444C>T	c.(442-444)GAC>GAT	p.D148D		NM_005225	NP_005216	Q01094	E2F1_HUMAN	E2F transcription factor 1	148	Potential.				apoptosis|cell proliferation|G1 phase of mitotic cell cycle|G2 phase of mitotic cell cycle|mRNA stabilization|negative regulation of transcription involved in G1/S phase of mitotic cell cycle|positive regulation of fibroblast proliferation|positive regulation of transcription from RNA polymerase II promoter|regulation of G1/S transition of mitotic cell cycle	mitochondrion|Rb-E2F complex	sequence-specific DNA binding transcription factor activity|transcription corepressor activity|transcription factor binding				0																		---	---	---	---
ZNF341	84905	broad.mit.edu	37	20	32345012	32345012	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32345012G>A	uc002wzy.2	+	6	820	c.800G>A	c.(799-801)GGC>GAC	p.G267D	ZNF341_uc002wzx.2_Missense_Mutation_p.G267D|ZNF341_uc010geq.2_Missense_Mutation_p.G177D|ZNF341_uc010ger.2_RNA	NM_032819	NP_116208	Q9BYN7	ZN341_HUMAN	zinc finger protein 341	267					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2																		---	---	---	---
GGT7	2686	broad.mit.edu	37	20	33444645	33444645	+	Missense_Mutation	SNP	C	A	A	rs140535819		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33444645C>A	uc002xay.2	-	8	1109	c.1066G>T	c.(1066-1068)GCC>TCC	p.A356S	GGT7_uc002xaz.1_Missense_Mutation_p.A373S	NM_178026	NP_821158	Q9UJ14	GGT7_HUMAN	gamma-glutamyltransferase 7	356	Extracellular (Potential).				glutathione biosynthetic process	integral to membrane	acyltransferase activity|gamma-glutamyltransferase activity			ovary(1)	1																		---	---	---	---
TRPC4AP	26133	broad.mit.edu	37	20	33609007	33609007	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:33609007G>A	uc002xbk.2	-	9	1238	c.1204C>T	c.(1204-1206)CGT>TGT	p.R402C	TRPC4AP_uc010zuq.1_Intron|TRPC4AP_uc002xbl.2_Missense_Mutation_p.R394C|TRPC4AP_uc010zur.1_Missense_Mutation_p.R363C|TRPC4AP_uc002xbm.1_Missense_Mutation_p.R402C	NM_015638	NP_056453	Q8TEL6	TP4AP_HUMAN	TRPC4-associated protein isoform a	402					protein ubiquitination|ubiquitin-dependent protein catabolic process	Cul4A-RING ubiquitin ligase complex	protein binding			central_nervous_system(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(18;0.00936)															---	---	---	---
CEP250	11190	broad.mit.edu	37	20	34061354	34061354	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34061354G>T	uc002xcm.2	+	14	2036	c.1365G>T	c.(1363-1365)CAG>CAT	p.Q455H	CEP250_uc010zve.1_Translation_Start_Site|CEP250_uc010zvd.1_RNA	NM_007186	NP_009117	Q9BV73	CP250_HUMAN	centrosomal protein 2	455	Potential.				centriole-centriole cohesion|G2/M transition of mitotic cell cycle|protein localization|regulation of centriole-centriole cohesion	centriole|cilium|cytosol|microtubule basal body|perinuclear region of cytoplasm|protein complex	protein C-terminus binding|protein kinase binding			ovary(4)|central_nervous_system(1)	5	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)															---	---	---	---
CEP250	11190	broad.mit.edu	37	20	34097836	34097836	+	Nonsense_Mutation	SNP	G	T	T	rs144859303		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34097836G>T	uc002xcm.2	+	35	7689	c.7018G>T	c.(7018-7020)GGA>TGA	p.G2340*	CEP250_uc010zve.1_Nonsense_Mutation_p.G1708*	NM_007186	NP_009117	Q9BV73	CP250_HUMAN	centrosomal protein 2	2340	Potential.				centriole-centriole cohesion|G2/M transition of mitotic cell cycle|protein localization|regulation of centriole-centriole cohesion	centriole|cilium|cytosol|microtubule basal body|perinuclear region of cytoplasm|protein complex	protein C-terminus binding|protein kinase binding			ovary(4)|central_nervous_system(1)	5	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)															---	---	---	---
RBM12	10137	broad.mit.edu	37	20	34240525	34240525	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34240525C>T	uc002xdq.2	-	3	2952	c.2720G>A	c.(2719-2721)CGG>CAG	p.R907Q	CPNE1_uc010zvj.1_Intron|CPNE1_uc002xde.2_Intron|CPNE1_uc002xdf.2_Intron|CPNE1_uc002xdg.2_Intron|CPNE1_uc010gfi.2_Intron|CPNE1_uc010gfj.2_Intron|CPNE1_uc002xdh.2_Intron|CPNE1_uc002xdi.2_Intron|CPNE1_uc002xdj.2_Intron|CPNE1_uc002xdk.2_Intron|CPNE1_uc002xdl.2_Intron|CPNE1_uc002xdm.2_Intron|CPNE1_uc010gfk.1_Intron|CPNE1_uc002xdn.1_Intron|CPNE1_uc002xdo.1_Intron|CPNE1_uc002xdp.1_Intron|RBM12_uc002xdr.2_Missense_Mutation_p.R907Q|RBM12_uc002xds.2_Missense_Mutation_p.R907Q	NM_152838	NP_690051	Q9NTZ6	RBM12_HUMAN	RNA binding motif protein 12	907	RRM 3.					nucleus	nucleotide binding|protein binding|RNA binding			ovary(3)	3	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.00953)															---	---	---	---
NFS1	9054	broad.mit.edu	37	20	34262293	34262293	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34262293T>C	uc002xdw.1	-	10	1179	c.1115A>G	c.(1114-1116)GAC>GGC	p.D372G	CPNE1_uc002xdn.1_RNA|CPNE1_uc002xdo.1_RNA|CPNE1_uc002xdp.1_RNA|NFS1_uc002xdt.1_Missense_Mutation_p.D312G|NFS1_uc002xdu.1_Missense_Mutation_p.D312G|NFS1_uc002xdv.1_RNA|NFS1_uc010zvk.1_Missense_Mutation_p.D170G|NFS1_uc010zvl.1_Missense_Mutation_p.D321G	NM_021100	NP_066923	Q9Y697	NFS1_HUMAN	NFS1 nitrogen fixation 1 precursor	372					cysteine metabolic process|iron incorporation into metallo-sulfur cluster|Mo-molybdopterin cofactor biosynthetic process|protein complex assembly|water-soluble vitamin metabolic process	cytosol|mitochondrial matrix|nucleus	cysteine desulfurase activity|protein homodimerization activity|pyridoxal phosphate binding			ovary(1)|skin(1)	2	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.0886)		L-Alanine(DB00160)|L-Cysteine(DB00151)|Pyridoxal Phosphate(DB00114)													---	---	---	---
PHF20	51230	broad.mit.edu	37	20	34501982	34501982	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34501982A>C	uc002xek.1	+	12	1799	c.1688A>C	c.(1687-1689)GAC>GCC	p.D563A		NM_016436	NP_057520	Q9BVI0	PHF20_HUMAN	PHD finger protein 20	563					regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex	DNA binding|zinc ion binding			ovary(1)	1	Breast(12;0.00631)|all_lung(11;0.0145)																	---	---	---	---
PHF20	51230	broad.mit.edu	37	20	34519260	34519260	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34519260T>G	uc002xek.1	+	15	2305	c.2194T>G	c.(2194-2196)TCC>GCC	p.S732A		NM_016436	NP_057520	Q9BVI0	PHF20_HUMAN	PHD finger protein 20	732					regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex	DNA binding|zinc ion binding			ovary(1)	1	Breast(12;0.00631)|all_lung(11;0.0145)																	---	---	---	---
PHF20	51230	broad.mit.edu	37	20	34535454	34535454	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34535454C>T	uc002xek.1	+	18	3055	c.2944C>T	c.(2944-2946)CCG>TCG	p.P982S		NM_016436	NP_057520	Q9BVI0	PHF20_HUMAN	PHD finger protein 20	982					regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex	DNA binding|zinc ion binding			ovary(1)	1	Breast(12;0.00631)|all_lung(11;0.0145)																	---	---	---	---
C20orf152	140894	broad.mit.edu	37	20	34611564	34611564	+	Intron	SNP	C	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34611564C>G	uc002xes.1	+						C20orf152_uc002xer.1_Missense_Mutation_p.T433R|C20orf152_uc010gfp.1_Intron					SubName: Full=C20orf152 protein;												0	Breast(12;0.00631)																	---	---	---	---
EPB41L1	2036	broad.mit.edu	37	20	34763532	34763532	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34763532G>A	uc002xfb.2	+	3	408	c.237G>A	c.(235-237)ACG>ACA	p.T79T	EPB41L1_uc002xeu.2_Silent_p.T17T|EPB41L1_uc010zvo.1_Silent_p.T79T|EPB41L1_uc002xev.2_Silent_p.T79T|EPB41L1_uc002xew.2_Silent_p.T17T|EPB41L1_uc002xex.2_Silent_p.T48T|EPB41L1_uc002xey.2_Silent_p.T79T|EPB41L1_uc002xez.2_Silent_p.T17T	NM_012156	NP_036288	Q9H4G0	E41L1_HUMAN	erythrocyte membrane protein band 4.1-like 1	79					cortical actin cytoskeleton organization|synaptic transmission	cytoskeleton|cytosol|extrinsic to membrane|plasma membrane	actin binding|structural molecule activity			ovary(2)|pancreas(1)	3	Breast(12;0.0239)																	---	---	---	---
EPB41L1	2036	broad.mit.edu	37	20	34776321	34776321	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:34776321T>C	uc002xfb.2	+	9	1097	c.926T>C	c.(925-927)ATC>ACC	p.I309T	EPB41L1_uc002xeu.2_Missense_Mutation_p.I247T|EPB41L1_uc010zvo.1_Missense_Mutation_p.I309T|EPB41L1_uc002xev.2_Missense_Mutation_p.I309T|EPB41L1_uc002xew.2_Missense_Mutation_p.I212T|EPB41L1_uc002xex.2_Missense_Mutation_p.I278T|EPB41L1_uc002xey.2_Missense_Mutation_p.I236T|EPB41L1_uc002xez.2_Missense_Mutation_p.I247T	NM_012156	NP_036288	Q9H4G0	E41L1_HUMAN	erythrocyte membrane protein band 4.1-like 1	309	FERM.				cortical actin cytoskeleton organization|synaptic transmission	cytoskeleton|cytosol|extrinsic to membrane|plasma membrane	actin binding|structural molecule activity			ovary(2)|pancreas(1)	3	Breast(12;0.0239)																	---	---	---	---
SLA2	84174	broad.mit.edu	37	20	35262919	35262919	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35262919G>A	uc002xfv.2	-	3	527	c.165C>T	c.(163-165)CTC>CTT	p.L55L	SLA2_uc002xfu.2_Silent_p.L55L	NM_032214	NP_115590	Q9H6Q3	SLAP2_HUMAN	Src-like-adaptor 2 isoform a	55	SH3.				antigen receptor-mediated signaling pathway|B cell mediated immunity|intracellular receptor mediated signaling pathway|negative regulation of B cell activation|negative regulation of calcium-mediated signaling|negative regulation of transcription from RNA polymerase II promoter|T cell activation	cytoplasmic membrane-bounded vesicle|endosome membrane|plasma membrane	protein N-terminus binding|SH3/SH2 adaptor activity				0	Breast(12;0.114)	Myeloproliferative disorder(115;0.00878)																---	---	---	---
C20orf117	140710	broad.mit.edu	37	20	35423006	35423006	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35423006C>T	uc002xgd.1	-						C20orf117_uc002xge.1_Intron	NM_199181	NP_954650			hypothetical protein LOC140710 isoform 2												0		Myeloproliferative disorder(115;0.00874)																---	---	---	---
C20orf132	140699	broad.mit.edu	37	20	35788534	35788534	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:35788534G>A	uc010zvu.1	-	8	815	c.724C>T	c.(724-726)CGC>TGC	p.R242C	C20orf132_uc002xgk.2_5'Flank|C20orf132_uc002xgm.2_Missense_Mutation_p.R242C|C20orf132_uc002xgn.2_Missense_Mutation_p.R242C	NM_152503	NP_689716	Q9H579	CT132_HUMAN	hypothetical protein LOC140699 isoform 1	152											0		Myeloproliferative disorder(115;0.00878)																---	---	---	---
VSTM2L	128434	broad.mit.edu	37	20	36572399	36572399	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36572399G>A	uc002xhk.3	+	4	613	c.359G>A	c.(358-360)GGC>GAC	p.G120D		NM_080607	NP_542174	Q96N03	VTM2L_HUMAN	V-set and transmembrane domain containing 2 like	120	Ig-like.									ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(115;0.00878)																---	---	---	---
KIAA1755	85449	broad.mit.edu	37	20	36848109	36848109	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36848109C>T	uc002xhy.1	-	11	2751	c.2479G>A	c.(2479-2481)GTC>ATC	p.V827I	KIAA1755_uc002xhv.1_5'Flank|KIAA1755_uc002xhw.1_5'Flank|KIAA1755_uc002xhx.1_Missense_Mutation_p.V105I	NM_001029864	NP_001025035	Q5JYT7	K1755_HUMAN	hypothetical protein LOC85449	827										ovary(4)|pancreas(1)	5		Myeloproliferative disorder(115;0.00874)																---	---	---	---
ADIG	149685	broad.mit.edu	37	20	37210000	37210000	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37210000G>A	uc002xjb.1	+	1	163	c.107G>A	c.(106-108)CGC>CAC	p.R36H		NM_001018082	NP_001018092	Q0VDE8	ADIG_HUMAN	small adipocyte factor 1	36					brown fat cell differentiation|positive regulation of fat cell differentiation|white fat cell differentiation	cytoplasm|integral to membrane|nucleus					0		Myeloproliferative disorder(115;0.00878)																---	---	---	---
SLC32A1	140679	broad.mit.edu	37	20	37353590	37353590	+	Missense_Mutation	SNP	G	A	A	rs148951877		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37353590G>A	uc002xjc.2	+	1	486	c.223G>A	c.(223-225)GCT>ACT	p.A75T		NM_080552	NP_542119	Q9H598	VIAAT_HUMAN	solute carrier family 32, member 1	75	Cytoplasmic (Potential).				neurotransmitter secretion	clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|integral to membrane|plasma membrane|synaptic vesicle membrane	vesicular hydrogen:amino acid antiporter activity				0		Myeloproliferative disorder(115;0.00878)			Glycine(DB00145)													---	---	---	---
SLC32A1	140679	broad.mit.edu	37	20	37356262	37356262	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37356262C>T	uc002xjc.2	+	2	821	c.558C>T	c.(556-558)TAC>TAT	p.Y186Y		NM_080552	NP_542119	Q9H598	VIAAT_HUMAN	solute carrier family 32, member 1	186	Lumenal, vesicle (Potential).				neurotransmitter secretion	clathrin sculpted gamma-aminobutyric acid transport vesicle membrane|integral to membrane|plasma membrane|synaptic vesicle membrane	vesicular hydrogen:amino acid antiporter activity				0		Myeloproliferative disorder(115;0.00878)			Glycine(DB00145)													---	---	---	---
ACTR5	79913	broad.mit.edu	37	20	37400368	37400368	+	Missense_Mutation	SNP	G	A	A	rs78656585		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37400368G>A	uc002xjd.2	+	9	1758	c.1733G>A	c.(1732-1734)CGC>CAC	p.R578H		NM_024855	NP_079131	Q9H9F9	ARP5_HUMAN	ARP5 actin-related protein 5 homolog	578					DNA recombination|double-strand break repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent|UV-damage excision repair	cytoplasm|Ino80 complex	ATP binding|protein binding				0		Myeloproliferative disorder(115;0.00878)																---	---	---	---
ZHX3	23051	broad.mit.edu	37	20	39830874	39830874	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39830874C>T	uc002xjs.1	-	3	3061	c.2683G>A	c.(2683-2685)GCA>ACA	p.A895T	ZHX3_uc002xjq.1_Intron|ZHX3_uc002xjr.1_Intron|ZHX3_uc002xjt.1_Missense_Mutation_p.A895T|ZHX3_uc002xju.1_Missense_Mutation_p.A895T|ZHX3_uc010ggg.1_Missense_Mutation_p.A895T	NM_015035	NP_055850	Q9H4I2	ZHX3_HUMAN	zinc fingers and homeoboxes 3	895					negative regulation of transcription, DNA-dependent	cytoplasm|nucleolus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3		Myeloproliferative disorder(115;0.00425)																---	---	---	---
LPIN3	64900	broad.mit.edu	37	20	39978860	39978860	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39978860C>A	uc002xjx.2	+	7	1016	c.925C>A	c.(925-927)CCT>ACT	p.P309T	LPIN3_uc010ggh.2_Missense_Mutation_p.P310T|LPIN3_uc010zwf.1_RNA	NM_022896	NP_075047	Q9BQK8	LPIN3_HUMAN	lipin 3	309					fatty acid metabolic process	nucleus	phosphatidate phosphatase activity			ovary(3)|central_nervous_system(1)	4		Myeloproliferative disorder(115;0.000739)																---	---	---	---
LPIN3	64900	broad.mit.edu	37	20	39983468	39983468	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39983468C>T	uc002xjx.2	+	13	1720	c.1629C>T	c.(1627-1629)GCC>GCT	p.A543A	LPIN3_uc010ggh.2_Silent_p.A544A|LPIN3_uc010zwf.1_RNA	NM_022896	NP_075047	Q9BQK8	LPIN3_HUMAN	lipin 3	543					fatty acid metabolic process	nucleus	phosphatidate phosphatase activity			ovary(3)|central_nervous_system(1)	4		Myeloproliferative disorder(115;0.000739)																---	---	---	---
LPIN3	64900	broad.mit.edu	37	20	39985753	39985753	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39985753G>A	uc002xjx.2	+	15	1968	c.1877G>A	c.(1876-1878)CGC>CAC	p.R626H	LPIN3_uc010ggh.2_Missense_Mutation_p.R627H|LPIN3_uc010zwf.1_RNA	NM_022896	NP_075047	Q9BQK8	LPIN3_HUMAN	lipin 3	626	C-LIP.				fatty acid metabolic process	nucleus	phosphatidate phosphatase activity			ovary(3)|central_nervous_system(1)	4		Myeloproliferative disorder(115;0.000739)																---	---	---	---
LPIN3	64900	broad.mit.edu	37	20	39986568	39986568	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39986568G>A	uc002xjx.2	+	17	2177	c.2086G>A	c.(2086-2088)GCG>ACG	p.A696T	LPIN3_uc010ggh.2_Missense_Mutation_p.A697T|LPIN3_uc010zwf.1_RNA	NM_022896	NP_075047	Q9BQK8	LPIN3_HUMAN	lipin 3	696	C-LIP.				fatty acid metabolic process	nucleus	phosphatidate phosphatase activity			ovary(3)|central_nervous_system(1)	4		Myeloproliferative disorder(115;0.000739)																---	---	---	---
EMILIN3	90187	broad.mit.edu	37	20	39990765	39990765	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:39990765C>A	uc002xjy.1	-	4	1668	c.1444G>T	c.(1444-1446)GCA>TCA	p.A482S		NM_052846	NP_443078	Q9NT22	EMIL3_HUMAN	elastin microfibril interfacer 3	482	Potential.					proteinaceous extracellular matrix				ovary(1)	1		Myeloproliferative disorder(115;0.00425)																---	---	---	---
CHD6	84181	broad.mit.edu	37	20	40042028	40042028	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40042028T>G	uc002xka.1	-	35	7245	c.7067A>C	c.(7066-7068)AAG>ACG	p.K2356T	CHD6_uc002xjz.1_5'UTR	NM_032221	NP_115597	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	2356					chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding			ovary(6)|skin(5)|lung(2)|central_nervous_system(1)	14		Myeloproliferative disorder(115;0.00425)																---	---	---	---
CHD6	84181	broad.mit.edu	37	20	40122585	40122585	+	Splice_Site	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:40122585C>T	uc002xka.1	-	9	1271	c.1093_splice	c.e9-1	p.P365_splice	CHD6_uc002xkd.2_Splice_Site_p.P343_splice	NM_032221	NP_115597			chromodomain helicase DNA binding protein 6						chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding			ovary(6)|skin(5)|lung(2)|central_nervous_system(1)	14		Myeloproliferative disorder(115;0.00425)																---	---	---	---
SFRS6	6431	broad.mit.edu	37	20	42087851	42087851	+	Intron	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42087851G>T	uc010zwg.1	+						SFRS6_uc002xki.2_5'UTR|SFRS6_uc002xkk.2_Intron	NM_006275	NP_006266			arginine/serine-rich splicing factor 6						mRNA 3'-end processing|mRNA export from nucleus|mRNA splice site selection|termination of RNA polymerase II transcription	nucleoplasm	nucleotide binding|protein binding|RNA binding				0		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)															---	---	---	---
JPH2	57158	broad.mit.edu	37	20	42747165	42747165	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42747165G>T	uc002xli.1	-	3	2141	c.1268C>A	c.(1267-1269)GCT>GAT	p.A423D		NM_020433	NP_065166	Q9BR39	JPH2_HUMAN	junctophilin 2 isoform 1	423	Cytoplasmic (Potential).				calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional sarcoplasmic reticulum membrane|plasma membrane					0		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)															---	---	---	---
JPH2	57158	broad.mit.edu	37	20	42815111	42815111	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42815111G>A	uc002xli.1	-	1	1108	c.235C>T	c.(235-237)CGC>TGC	p.R79C	JPH2_uc002xlj.2_Missense_Mutation_p.R79C	NM_020433	NP_065166	Q9BR39	JPH2_HUMAN	junctophilin 2 isoform 1	79	Gly-rich.|MORN 3.|Cytoplasmic (Potential).				calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional sarcoplasmic reticulum membrane|plasma membrane					0		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)															---	---	---	---
FITM2	128486	broad.mit.edu	37	20	42935372	42935372	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42935372G>T	uc002xlr.1	-	2	783	c.682C>A	c.(682-684)CTG>ATG	p.L228M		NM_001080472	NP_001073941	Q8N6M3	FITM2_HUMAN	fat storage-inducing transmembrane protein 2	228	Helical; (Potential).				cellular triglyceride homeostasis|lipid particle organization|positive regulation of sequestering of triglyceride|regulation of triglyceride biosynthetic process	integral to endoplasmic reticulum membrane				skin(2)	2																		---	---	---	---
SERINC3	10955	broad.mit.edu	37	20	43135484	43135484	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43135484A>T	uc002xme.2	-	6	901	c.767T>A	c.(766-768)ATC>AAC	p.I256N	SERINC3_uc002xmf.1_Missense_Mutation_p.I256N|SERINC3_uc010ggs.1_Missense_Mutation_p.I249N|SERINC3_uc010zwp.1_Missense_Mutation_p.I201N	NM_198941	NP_945179	Q13530	SERC3_HUMAN	tumor differentially expressed protein 1	256	Helical; (Potential).					integral to membrane|plasma membrane	protein binding			skin(3)	3		Myeloproliferative disorder(115;0.0122)	Colorectal(3;0.000291)|COAD - Colon adenocarcinoma(18;0.00189)															---	---	---	---
PI3	5266	broad.mit.edu	37	20	43804666	43804666	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43804666C>T	uc002xng.2	+	2	268	c.244C>T	c.(244-246)CGG>TGG	p.R82W		NM_002638	NP_002629	P19957	ELAF_HUMAN	elafin preproprotein	82	WAP.				copulation	proteinaceous extracellular matrix	serine-type endopeptidase inhibitor activity				0		Myeloproliferative disorder(115;0.0122)																---	---	---	---
SEMG1	6406	broad.mit.edu	37	20	43836613	43836613	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43836613A>C	uc002xni.2	+	2	732	c.675A>C	c.(673-675)GAA>GAC	p.E225D	SEMG1_uc002xnj.2_Missense_Mutation_p.E225D|SEMG2_uc010ggz.2_Intron|SEMG1_uc002xnh.2_Missense_Mutation_p.E225D	NM_003007	NP_002998	P04279	SEMG1_HUMAN	semenogelin I preproprotein	225					insemination|sexual reproduction	extracellular space|stored secretory granule	structural molecule activity			skin(2)	2		Myeloproliferative disorder(115;0.0122)																---	---	---	---
SYS1-DBNDD2	767557	broad.mit.edu	37	20	43995503	43995503	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43995503C>T	uc002xnx.2	+						SYS1_uc010gha.2_Intron|SYS1_uc002xnv.2_Intron|SYS1_uc002xnw.1_Intron	NM_001048225	NP_001041690			SCF apoptosis response protein 1 isoform a												0																		---	---	---	---
WFDC10B	280664	broad.mit.edu	37	20	44333640	44333640	+	5'UTR	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44333640A>C	uc002xpb.2	-	1					WFDC10B_uc002xpc.2_5'UTR|WFDC13_uc002xpd.2_Intron	NM_172006	NP_742003			WAP four-disulfide core domain 10B isoform a							extracellular region	peptidase inhibitor activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)																---	---	---	---
PLTP	5360	broad.mit.edu	37	20	44538707	44538707	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44538707A>G	uc002xqn.1	-	4	283	c.203T>C	c.(202-204)GTG>GCG	p.V68A	PLTP_uc002xql.1_5'UTR|PLTP_uc002xqm.1_Missense_Mutation_p.V88A|PLTP_uc002xqo.1_Missense_Mutation_p.V68A|PLTP_uc002xqp.1_Missense_Mutation_p.V68A|PLTP_uc002xqq.1_Missense_Mutation_p.V37A|PLTP_uc010zxj.1_Intron|PLTP_uc010ghj.1_Missense_Mutation_p.V68A	NM_006227	NP_006218	P55058	PLTP_HUMAN	phospholipid transfer protein isoform a	68					cellular lipid metabolic process|lipid transport	extracellular region	lipid binding			ovary(1)	1		Myeloproliferative disorder(115;0.0122)																---	---	---	---
PLTP	5360	broad.mit.edu	37	20	44540049	44540049	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44540049C>T	uc002xqn.1	-	2	123	c.43G>A	c.(43-45)GCA>ACA	p.A15T	PLTP_uc002xql.1_5'Flank|PLTP_uc002xqm.1_Missense_Mutation_p.A35T|PLTP_uc002xqo.1_Missense_Mutation_p.A15T|PLTP_uc002xqp.1_Missense_Mutation_p.A15T|PLTP_uc002xqq.1_5'UTR|PLTP_uc010zxj.1_Missense_Mutation_p.A15T|PLTP_uc010ghj.1_Missense_Mutation_p.A15T	NM_006227	NP_006218	P55058	PLTP_HUMAN	phospholipid transfer protein isoform a	15					cellular lipid metabolic process|lipid transport	extracellular region	lipid binding			ovary(1)	1		Myeloproliferative disorder(115;0.0122)																---	---	---	---
PCIF1	63935	broad.mit.edu	37	20	44576377	44576377	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44576377G>A	uc002xqs.2	+	17	2412	c.2098G>A	c.(2098-2100)GAG>AAG	p.E700K	PCIF1_uc002xqt.2_3'UTR|PCIF1_uc002xqu.2_Missense_Mutation_p.E169K	NM_022104	NP_071387	Q9H4Z3	PCIF1_HUMAN	phosphorylated CTD interacting factor 1	700						nucleus				skin(1)	1																		---	---	---	---
ZNF335	63925	broad.mit.edu	37	20	44578880	44578880	+	Silent	SNP	G	A	A	rs142739306	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44578880G>A	uc002xqw.2	-	22	3588	c.3465C>T	c.(3463-3465)GAC>GAT	p.D1155D	ZNF335_uc002xqv.2_Silent_p.D267D|ZNF335_uc010zxk.1_Silent_p.D1000D	NM_022095	NP_071378	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	1155					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(3)|ovary(1)	4		Myeloproliferative disorder(115;0.0122)																---	---	---	---
SLC12A5	57468	broad.mit.edu	37	20	44664442	44664442	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44664442C>T	uc010zxl.1	+	4	451	c.375C>T	c.(373-375)GGC>GGT	p.G125G	SLC12A5_uc002xra.2_Silent_p.G102G|SLC12A5_uc010zxm.1_RNA|SLC12A5_uc002xrb.2_Silent_p.G102G	NM_001134771	NP_001128243	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium-chloride	125	Cytoplasmic (Potential).				potassium ion transport|sodium ion transport	integral to membrane	potassium:chloride symporter activity			ovary(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)													---	---	---	---
SLC12A5	57468	broad.mit.edu	37	20	44676089	44676089	+	Intron	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44676089C>A	uc010zxl.1	+						SLC12A5_uc010zxm.1_Intron|SLC12A5_uc002xrb.2_Intron	NM_001134771	NP_001128243			solute carrier family 12 (potassium-chloride						potassium ion transport|sodium ion transport	integral to membrane	potassium:chloride symporter activity			ovary(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)													---	---	---	---
SLC12A5	57468	broad.mit.edu	37	20	44682290	44682290	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44682290A>G	uc010zxl.1	+	20	2766	c.2690A>G	c.(2689-2691)GAT>GGT	p.D897G	SLC12A5_uc002xrb.2_Missense_Mutation_p.D874G	NM_001134771	NP_001128243	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium-chloride	897	Cytoplasmic (Potential).				potassium ion transport|sodium ion transport	integral to membrane	potassium:chloride symporter activity			ovary(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)													---	---	---	---
NCOA5	57727	broad.mit.edu	37	20	44699079	44699079	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:44699079G>A	uc002xrd.2	-	2	663	c.135C>T	c.(133-135)GGC>GGT	p.G45G	NCOA5_uc002xrc.2_5'UTR|NCOA5_uc002xre.2_Silent_p.G45G	NM_020967	NP_066018	Q9HCD5	NCOA5_HUMAN	nuclear receptor coactivator 5	45	Arg/Asp-rich (mixed charge).|Transcription repression.				regulation of transcription, DNA-dependent|transcription, DNA-dependent|translation	nucleus	aminoacyl-tRNA ligase activity|ATP binding			central_nervous_system(1)|skin(1)	2		Myeloproliferative disorder(115;0.0122)																---	---	---	---
ZMYND8	23613	broad.mit.edu	37	20	45850036	45850036	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45850036C>T	uc002xta.1	-	20	3540	c.3286G>A	c.(3286-3288)GCA>ACA	p.A1096T	ZMYND8_uc010ghq.1_Missense_Mutation_p.A727T|ZMYND8_uc010ghr.1_Missense_Mutation_p.A998T|ZMYND8_uc002xst.1_Missense_Mutation_p.A978T|ZMYND8_uc002xsu.1_Missense_Mutation_p.A969T|ZMYND8_uc002xsv.1_Missense_Mutation_p.A1024T|ZMYND8_uc002xsw.1_Missense_Mutation_p.A802T|ZMYND8_uc002xsx.1_Missense_Mutation_p.A802T|ZMYND8_uc002xsy.1_Missense_Mutation_p.A1025T|ZMYND8_uc002xsz.1_Missense_Mutation_p.A987T|ZMYND8_uc010zxy.1_Missense_Mutation_p.A1123T|ZMYND8_uc002xtb.1_Missense_Mutation_p.A1070T|ZMYND8_uc002xss.2_Missense_Mutation_p.A1096T|ZMYND8_uc010zxz.1_Missense_Mutation_p.A964T|ZMYND8_uc002xtc.1_Missense_Mutation_p.A1070T|ZMYND8_uc002xtd.1_Missense_Mutation_p.A1045T|ZMYND8_uc002xte.1_Missense_Mutation_p.A1050T|ZMYND8_uc010zya.1_Missense_Mutation_p.A1096T|ZMYND8_uc002xtf.1_Missense_Mutation_p.A1116T|ZMYND8_uc002xsr.1_Missense_Mutation_p.A195T	NM_012408	NP_036540	Q9ULU4	PKCB1_HUMAN	zinc finger, MYND-type containing 8 isoform b	1096							protein binding|zinc ion binding			central_nervous_system(2)|urinary_tract(1)|ovary(1)|skin(1)	5			Epithelial(1;0.0289)|all cancers(1;0.0962)|OV - Ovarian serous cystadenocarcinoma(1;0.154)															---	---	---	---
SULF2	55959	broad.mit.edu	37	20	46295135	46295135	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:46295135C>T	uc002xto.2	-	12	2004	c.1674G>A	c.(1672-1674)CAG>CAA	p.Q558Q	SULF2_uc002xtr.2_Silent_p.Q558Q|SULF2_uc002xtq.2_Silent_p.Q558Q|SULF2_uc010zyd.1_5'Flank	NM_018837	NP_061325	Q8IWU5	SULF2_HUMAN	sulfatase 2 isoform a precursor	558					bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding			ovary(2)|breast(2)|pancreas(1)|skin(1)	6																		---	---	---	---
ARFGEF2	10564	broad.mit.edu	37	20	47587742	47587742	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47587742G>A	uc002xtx.3	+	10	1428	c.1276G>A	c.(1276-1278)GAG>AAG	p.E426K		NM_006420	NP_006411	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine	426					exocytosis|intracellular signal transduction|regulation of ARF protein signal transduction	cytosol|Golgi membrane	ARF guanyl-nucleotide exchange factor activity			breast(3)|upper_aerodigestive_tract(1)	4			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)															---	---	---	---
CSE1L	1434	broad.mit.edu	37	20	47688880	47688880	+	Missense_Mutation	SNP	G	A	A	rs149344844		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47688880G>A	uc002xty.2	+	9	960	c.826G>A	c.(826-828)GCA>ACA	p.A276T	CSE1L_uc010zyg.1_Missense_Mutation_p.A59T|CSE1L_uc010ghx.2_Intron|CSE1L_uc010ghy.2_5'UTR|CSE1L_uc010zyh.1_5'Flank	NM_001316	NP_001307	P55060	XPO2_HUMAN	CSE1 chromosome segregation 1-like protein	276					apoptosis|cell proliferation|intracellular protein transport	cytoplasm|nucleus	importin-alpha export receptor activity			large_intestine(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(12;0.000491)|Colorectal(8;0.198)															---	---	---	---
KCNB1	3745	broad.mit.edu	37	20	47989713	47989713	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47989713T>G	uc002xur.1	-	2	2548	c.2384A>C	c.(2383-2385)AAC>ACC	p.N795T	KCNB1_uc002xus.1_Missense_Mutation_p.N795T	NM_004975	NP_004966	Q14721	KCNB1_HUMAN	potassium voltage-gated channel, Shab-related	795	Cytoplasmic (Potential).				energy reserve metabolic process|regulation of insulin secretion	voltage-gated potassium channel complex	protein binding|voltage-gated potassium channel activity			pancreas(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(12;0.000405)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)															---	---	---	---
RNF114	55905	broad.mit.edu	37	20	48561937	48561937	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48561937C>T	uc002xux.2	+	3	346	c.310C>T	c.(310-312)CGG>TGG	p.R104W	RNF114_uc010zyo.1_Missense_Mutation_p.R104W|RNF114_uc002xuy.2_RNA	NM_018683	NP_061153	Q9Y508	RN114_HUMAN	zinc finger protein 313	104					cell differentiation|multicellular organismal development|spermatogenesis	intracellular	zinc ion binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
RNF114	55905	broad.mit.edu	37	20	48565796	48565796	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:48565796A>G	uc002xux.2	+	5	561	c.525A>G	c.(523-525)ATA>ATG	p.I175M	RNF114_uc010zyo.1_Intron|RNF114_uc002xuy.2_RNA	NM_018683	NP_061153	Q9Y508	RN114_HUMAN	zinc finger protein 313	175					cell differentiation|multicellular organismal development|spermatogenesis	intracellular	zinc ion binding			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
FAM65C	140876	broad.mit.edu	37	20	49247309	49247309	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49247309C>T	uc002xvm.2	-	2	394	c.76G>A	c.(76-78)GCA>ACA	p.A26T	FAM65C_uc010zyt.1_Missense_Mutation_p.A30T|FAM65C_uc010zyu.1_RNA|FAM65C_uc002xvn.1_Missense_Mutation_p.A26T	NM_080829	NP_543019	Q96MK2	FA65C_HUMAN	hypothetical protein LOC140876	26										ovary(2)	2																		---	---	---	---
MOCS3	27304	broad.mit.edu	37	20	49576575	49576575	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49576575G>A	uc002xvy.1	+	1	1213	c.1196G>A	c.(1195-1197)GGC>GAC	p.G399D	DPM1_uc002xvw.1_5'Flank|DPM1_uc002xvx.1_5'Flank	NM_014484	NP_055299	O95396	MOCS3_HUMAN	molybdenum cofactor synthesis 3	399	Rhodanese.				enzyme active site formation via L-cysteine persulfide|Mo-molybdopterin cofactor biosynthetic process|tRNA thio-modification|tRNA wobble uridine modification|water-soluble vitamin metabolic process	cytosol	ATP binding|metal ion binding|nucleotidyltransferase activity|protein binding|thiosulfate sulfurtransferase activity|URM1 activating enzyme activity			skin(2)|ovary(1)	3																		---	---	---	---
MOCS3	27304	broad.mit.edu	37	20	49576721	49576721	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49576721G>A	uc002xvy.1	+	1	1359	c.1342G>A	c.(1342-1344)GCC>ACC	p.A448T	DPM1_uc002xvw.1_5'Flank|DPM1_uc002xvx.1_5'Flank	NM_014484	NP_055299	O95396	MOCS3_HUMAN	molybdenum cofactor synthesis 3	448	Rhodanese.				enzyme active site formation via L-cysteine persulfide|Mo-molybdopterin cofactor biosynthetic process|tRNA thio-modification|tRNA wobble uridine modification|water-soluble vitamin metabolic process	cytosol	ATP binding|metal ion binding|nucleotidyltransferase activity|protein binding|thiosulfate sulfurtransferase activity|URM1 activating enzyme activity			skin(2)|ovary(1)	3																		---	---	---	---
KCNG1	3755	broad.mit.edu	37	20	49620904	49620904	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:49620904C>T	uc002xwa.3	-	3	1509	c.1214G>A	c.(1213-1215)AGC>AAC	p.S405N		NM_002237	NP_002228	Q9UIX4	KCNG1_HUMAN	potassium voltage-gated channel, subfamily G,	405						voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)|central_nervous_system(1)	2																		---	---	---	---
NFATC2	4773	broad.mit.edu	37	20	50048666	50048666	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50048666A>C	uc002xwd.2	-	9	2880	c.2660T>G	c.(2659-2661)GTA>GGA	p.V887G	NFATC2_uc002xwc.2_Missense_Mutation_p.V887G|NFATC2_uc010zyv.1_Missense_Mutation_p.V668G|NFATC2_uc010zyw.1_Missense_Mutation_p.V668G|NFATC2_uc010zyx.1_Missense_Mutation_p.V867G|NFATC2_uc010zyy.1_Missense_Mutation_p.V668G|NFATC2_uc010zyz.1_Missense_Mutation_p.V668G|NFATC2_uc002xwe.2_Missense_Mutation_p.V867G	NM_173091	NP_775114	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells,	887					B cell receptor signaling pathway|positive regulation of B cell proliferation|response to DNA damage stimulus|response to drug	actin cytoskeleton|nucleus|plasma membrane	protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2	Hepatocellular(150;0.248)																	---	---	---	---
NFATC2	4773	broad.mit.edu	37	20	50140129	50140129	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50140129C>T	uc002xwd.2	-	2	871	c.651G>A	c.(649-651)TCG>TCA	p.S217S	NFATC2_uc002xwc.2_Silent_p.S217S|NFATC2_uc010zyv.1_5'UTR|NFATC2_uc010zyw.1_5'UTR|NFATC2_uc010zyx.1_Silent_p.S197S|NFATC2_uc010zyy.1_5'UTR|NFATC2_uc010zyz.1_5'UTR|NFATC2_uc002xwe.2_Silent_p.S197S	NM_173091	NP_775114	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells,	217	3 X approximate SP repeats.|2.				B cell receptor signaling pathway|positive regulation of B cell proliferation|response to DNA damage stimulus|response to drug	actin cytoskeleton|nucleus|plasma membrane	protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2	Hepatocellular(150;0.248)																	---	---	---	---
ATP9A	10079	broad.mit.edu	37	20	50241766	50241766	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50241766G>A	uc002xwg.1	-	18	1981	c.1981C>T	c.(1981-1983)CCC>TCC	p.P661S	ATP9A_uc010gih.1_Missense_Mutation_p.P525S|ATP9A_uc002xwf.1_Intron	NM_006045	NP_006036	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	661	Cytoplasmic (Potential).				ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(4)	4																		---	---	---	---
ATP9A	10079	broad.mit.edu	37	20	50290773	50290773	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50290773A>G	uc002xwg.1	-	11	956	c.956T>C	c.(955-957)GTT>GCT	p.V319A	ATP9A_uc010gih.1_Missense_Mutation_p.V183A|ATP9A_uc002xwf.1_Intron	NM_006045	NP_006036	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	319	Helical; (Potential).				ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(4)	4																		---	---	---	---
ATP9A	10079	broad.mit.edu	37	20	50290852	50290852	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50290852T>G	uc002xwg.1	-	11	877	c.877A>C	c.(877-879)ATC>CTC	p.I293L	ATP9A_uc010gih.1_Missense_Mutation_p.I157L|ATP9A_uc002xwf.1_Intron	NM_006045	NP_006036	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	293	Cytoplasmic (Potential).				ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(4)	4																		---	---	---	---
SALL4	57167	broad.mit.edu	37	20	50401131	50401131	+	Silent	SNP	G	A	A	rs143702441		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:50401131G>A	uc002xwh.3	-	4	2936	c.2835C>T	c.(2833-2835)GAC>GAT	p.D945D	SALL4_uc010gii.2_Silent_p.D508D|SALL4_uc002xwi.3_Silent_p.D168D	NM_020436	NP_065169	Q9UJQ4	SALL4_HUMAN	sal-like 4	945					transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2																		---	---	---	---
TSHZ2	128553	broad.mit.edu	37	20	51872527	51872527	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:51872527C>A	uc002xwo.2	+	2	3486	c.2530C>A	c.(2530-2532)CGG>AGG	p.R844R		NM_173485	NP_775756	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	844	Homeobox; atypical.				multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|haematopoietic_and_lymphoid_tissue(1)	6			STAD - Stomach adenocarcinoma(23;0.1)															---	---	---	---
PCK1	5105	broad.mit.edu	37	20	56140412	56140412	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56140412T>C	uc002xyn.3	+	10	1584	c.1421T>C	c.(1420-1422)ATC>ACC	p.I474T	PCK1_uc010zzm.1_Missense_Mutation_p.I157T	NM_002591	NP_002582	P35558	PCKGC_HUMAN	cytosolic phosphoenolpyruvate carboxykinase 1	474					gluconeogenesis|glucose homeostasis|glycerol biosynthetic process from pyruvate|response to insulin stimulus	cytosol|nucleus	carboxylic acid binding|GTP binding|magnesium ion binding|manganese ion binding|phosphoenolpyruvate carboxykinase (GTP) activity			skin(1)	1	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)															---	---	---	---
GNAS	2778	broad.mit.edu	37	20	57430146	57430146	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57430146G>A	uc002xzw.2	+	1	2111	c.1826G>A	c.(1825-1827)CGC>CAC	p.R609H	GNAS_uc002xzt.2_Intron|GNAS_uc002xzu.3_Intron|GNAS_uc010gjq.2_Intron|GNAS_uc002xzv.2_RNA	NM_080425	NP_536350	P63092	GNAS2_HUMAN	GNAS complex locus XLas	Error:Variant_position_missing_in_P63092_after_alignment					activation of adenylate cyclase activity|cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|intracellular transport|platelet activation|regulation of insulin secretion|sensory perception of smell|transmembrane transport|water transport	heterotrimeric G-protein complex|intrinsic to membrane|trans-Golgi network membrane	adenylate cyclase activity|GTP binding|GTPase activity|guanyl-nucleotide exchange factor activity|identical protein binding|signal transducer activity			pituitary(201)|thyroid(35)|ovary(15)|adrenal_gland(9)|liver(7)|large_intestine(5)|parathyroid(5)|kidney(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|testis(1)|stomach(1)|small_intestine(1)|autonomic_ganglia(1)|pancreas(1)	292	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)					Mis		pituitary adenoma		McCune-Albright syndrome; pseudohypoparathyroidism|type IA		3-Methylglutaconic_Aciduria_and_Myelodysplasia|McCune-Albright_syndrome|Mazabraud_syndrome	TSP Lung(22;0.16)			---	---	---	---
GNAS	2778	broad.mit.edu	37	20	57430208	57430208	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57430208G>T	uc002xzw.2	+	1	2173	c.1888G>T	c.(1888-1890)GCC>TCC	p.A630S	GNAS_uc002xzt.2_Intron|GNAS_uc002xzu.3_Intron|GNAS_uc010gjq.2_Intron|GNAS_uc002xzv.2_RNA	NM_080425	NP_536350	P63092	GNAS2_HUMAN	GNAS complex locus XLas	Error:Variant_position_missing_in_P63092_after_alignment					activation of adenylate cyclase activity|cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|intracellular transport|platelet activation|regulation of insulin secretion|sensory perception of smell|transmembrane transport|water transport	heterotrimeric G-protein complex|intrinsic to membrane|trans-Golgi network membrane	adenylate cyclase activity|GTP binding|GTPase activity|guanyl-nucleotide exchange factor activity|identical protein binding|signal transducer activity			pituitary(201)|thyroid(35)|ovary(15)|adrenal_gland(9)|liver(7)|large_intestine(5)|parathyroid(5)|kidney(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|testis(1)|stomach(1)|small_intestine(1)|autonomic_ganglia(1)|pancreas(1)	292	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)					Mis		pituitary adenoma		McCune-Albright syndrome; pseudohypoparathyroidism|type IA		3-Methylglutaconic_Aciduria_and_Myelodysplasia|McCune-Albright_syndrome|Mazabraud_syndrome	TSP Lung(22;0.16)			---	---	---	---
GNAS	2778	broad.mit.edu	37	20	57484421	57484421	+	Missense_Mutation	SNP	G	A	A	rs121913495		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57484421G>A	uc002xzw.2	+	8	2816	c.2531G>A	c.(2530-2532)CGT>CAT	p.R844H	GNAS_uc002xzt.2_3'UTR|GNAS_uc010gjq.2_Missense_Mutation_p.R142H|GNAS_uc002xzx.2_Missense_Mutation_p.R142H|GNAS_uc010gjr.2_Missense_Mutation_p.R92H|GNAS_uc002xzy.2_Missense_Mutation_p.R127H|GNAS_uc002yaa.2_Missense_Mutation_p.R187H|GNAS_uc010zzt.1_Missense_Mutation_p.R202H|GNAS_uc002yab.2_Intron|GNAS_uc002yad.2_Missense_Mutation_p.R92H|GNAS_uc002yae.2_Missense_Mutation_p.R126H	NM_080425	NP_536350	P63092	GNAS2_HUMAN	GNAS complex locus XLas	201	GTP (By similarity).		R -> L (in non-MAS endocrine tumors).|R -> S (in AIMAH, pituitary tumor and polyostotic fibrous dysplasia).|R -> H (in MAS, somatotrophinoma and AIMAH).|R -> G (in MAS).		activation of adenylate cyclase activity|cellular response to glucagon stimulus|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|intracellular transport|platelet activation|regulation of insulin secretion|sensory perception of smell|transmembrane transport|water transport	heterotrimeric G-protein complex|intrinsic to membrane|trans-Golgi network membrane	adenylate cyclase activity|GTP binding|GTPase activity|guanyl-nucleotide exchange factor activity|identical protein binding|signal transducer activity	p.R201H(37)|p.R201L(1)|p.R844H(1)		pituitary(201)|thyroid(35)|ovary(15)|adrenal_gland(9)|liver(7)|large_intestine(5)|parathyroid(5)|kidney(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|testis(1)|stomach(1)|small_intestine(1)|autonomic_ganglia(1)|pancreas(1)	292	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)					Mis		pituitary adenoma		McCune-Albright syndrome; pseudohypoparathyroidism|type IA		3-Methylglutaconic_Aciduria_and_Myelodysplasia|McCune-Albright_syndrome|Mazabraud_syndrome	TSP Lung(22;0.16)			---	---	---	---
ZNF831	128611	broad.mit.edu	37	20	57768122	57768122	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57768122A>G	uc002yan.2	+	1	2048	c.2048A>G	c.(2047-2049)GAC>GGC	p.D683G		NM_178457	NP_848552	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	683						intracellular	nucleic acid binding|zinc ion binding			skin(13)|ovary(1)	14	all_lung(29;0.0085)																	---	---	---	---
SYCP2	10388	broad.mit.edu	37	20	58450383	58450383	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58450383G>T	uc002yaz.2	-	33	3431	c.3292C>A	c.(3292-3294)CTT>ATT	p.L1098I		NM_014258	NP_055073	Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	1098					cell division|meiotic prophase I|synaptonemal complex assembly		DNA binding			ovary(3)|lung(2)	5	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)															---	---	---	---
PPP1R3D	5509	broad.mit.edu	37	20	58514433	58514433	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58514433G>A	uc002ybb.2	-	1	920	c.554C>T	c.(553-555)TCG>TTG	p.S185L	C20orf177_uc002yba.2_Intron|C20orf177_uc010zzx.1_5'Flank|C20orf177_uc002ybc.2_5'Flank	NM_006242	NP_006233	O95685	PPR3D_HUMAN	protein phosphatase 1, regulatory subunit 3D	185	CBM21.				glycogen metabolic process		protein binding|protein serine/threonine phosphatase activity				0	all_lung(29;0.00391)		BRCA - Breast invasive adenocarcinoma(7;5.12e-09)															---	---	---	---
C20orf177	63939	broad.mit.edu	37	20	58519690	58519690	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58519690T>C	uc002yba.2	+	5	1107	c.692T>C	c.(691-693)CTG>CCG	p.L231P	C20orf177_uc010zzx.1_Missense_Mutation_p.L74P|C20orf177_uc002ybc.2_Missense_Mutation_p.L231P	NM_022106	NP_071389	Q9NTX9	CT177_HUMAN	hypothetical protein LOC63939	231										ovary(2)|breast(1)	3	all_lung(29;0.00693)		BRCA - Breast invasive adenocarcinoma(7;1.22e-08)															---	---	---	---
CDH4	1002	broad.mit.edu	37	20	60348123	60348123	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60348123C>T	uc002ybn.1	+	4	475	c.461C>T	c.(460-462)CCG>CTG	p.P154L	CDH4_uc002ybp.1_Missense_Mutation_p.P80L	NM_001794	NP_001785	P55283	CADH4_HUMAN	cadherin 4, type 1 preproprotein	154					adherens junction organization|cell junction assembly		calcium ion binding	p.W155fs*46(1)		lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)															---	---	---	---
HRH3	11255	broad.mit.edu	37	20	60791286	60791286	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60791286C>G	uc002ycf.2	-	3	1411	c.1114G>C	c.(1114-1116)GCC>CCC	p.A372P	HRH3_uc002ycg.2_Missense_Mutation_p.A292P|HRH3_uc002ych.2_Intron|HRH3_uc002yci.2_Missense_Mutation_p.A372P	NM_007232	NP_009163	Q9Y5N1	HRH3_HUMAN	histamine receptor H3	372	Helical; Name=6; (Potential).				G-protein signaling, coupled to cyclic nucleotide second messenger|neurotransmitter secretion	integral to plasma membrane	histamine receptor activity				0	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;7.08e-07)		Histamine Phosphate(DB00667)													---	---	---	---
OSBPL2	9885	broad.mit.edu	37	20	60861748	60861748	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60861748G>A	uc002yck.1	+	11	1308	c.1106G>A	c.(1105-1107)CGG>CAG	p.R369Q	OSBPL2_uc002ycl.1_Missense_Mutation_p.R357Q|OSBPL2_uc011aah.1_Missense_Mutation_p.R277Q	NM_144498	NP_653081	Q9H1P3	OSBL2_HUMAN	oxysterol-binding protein-like protein 2 isoform	369					lipid transport		lipid binding			ovary(1)|central_nervous_system(1)	2	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;1.33e-06)															---	---	---	---
LAMA5	3911	broad.mit.edu	37	20	60913518	60913518	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60913518A>G	uc002ycq.2	-							NM_005560	NP_005551			laminin alpha 5 precursor						angiogenesis|cell proliferation|cell recognition|cytoskeleton organization|endothelial cell differentiation|focal adhesion assembly|integrin-mediated signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	integrin binding			ovary(1)|pancreas(1)|skin(1)	3	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)		Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
CABLES2	81928	broad.mit.edu	37	20	60966496	60966496	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:60966496T>A	uc002ycv.2	-	9	1112	c.1105A>T	c.(1105-1107)ATG>TTG	p.M369L		NM_031215	NP_112492	Q9BTV7	CABL2_HUMAN	Cdk5 and Abl enzyme substrate 2	369					cell cycle|cell division|regulation of cell cycle|regulation of cell division		cyclin-dependent protein kinase regulator activity			pancreas(1)	1	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)															---	---	---	---
DIDO1	11083	broad.mit.edu	37	20	61542723	61542723	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61542723G>A	uc002ydr.1	-	3	506	c.242C>T	c.(241-243)GCG>GTG	p.A81V	DIDO1_uc002yds.1_Missense_Mutation_p.A81V|DIDO1_uc002ydt.1_Missense_Mutation_p.A81V|DIDO1_uc002ydu.1_Missense_Mutation_p.A81V|DIDO1_uc002ydv.1_Missense_Mutation_p.A81V|DIDO1_uc002ydw.1_Missense_Mutation_p.A81V|DIDO1_uc002ydx.1_Missense_Mutation_p.A81V|DIDO1_uc011aao.1_Missense_Mutation_p.A81V	NM_033081	NP_149072	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1 isoform c	81					apoptosis|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(3)|skin(3)	6	Breast(26;5.68e-08)																	---	---	---	---
BIRC7	79444	broad.mit.edu	37	20	61870593	61870593	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61870593C>T	uc002yej.2	+						BIRC7_uc010gkc.1_Silent_p.G219G|BIRC7_uc002yei.2_Intron	NM_139317	NP_647478			livin inhibitor of apoptosis isoform alpha						activation of JUN kinase activity|anti-apoptosis|DNA fragmentation involved in apoptotic nuclear change	cytoplasm|nucleus	enzyme binding|zinc ion binding			ovary(1)|lung(1)|kidney(1)	3	all_cancers(38;2.72e-09)																	---	---	---	---
BIRC7	79444	broad.mit.edu	37	20	61870799	61870799	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61870799C>T	uc002yej.2	+	6	912	c.739C>T	c.(739-741)CAG>TAG	p.Q247*	BIRC7_uc010gkc.1_3'UTR|BIRC7_uc002yei.2_Nonsense_Mutation_p.Q229*	NM_139317	NP_647478	Q96CA5	BIRC7_HUMAN	livin inhibitor of apoptosis isoform alpha	247					activation of JUN kinase activity|anti-apoptosis|DNA fragmentation involved in apoptotic nuclear change	cytoplasm|nucleus	enzyme binding|zinc ion binding			ovary(1)|lung(1)|kidney(1)	3	all_cancers(38;2.72e-09)																	---	---	---	---
C20orf195	79025	broad.mit.edu	37	20	62187508	62187508	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62187508G>A	uc002yfj.2	+	2	584	c.492G>A	c.(490-492)GCG>GCA	p.A164A	C20orf195_uc002yfk.2_Silent_p.A164A	NM_024059	NP_076964	Q9BVV2	CT195_HUMAN	hypothetical protein LOC79025	164											0	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;9.69e-09)|all cancers(9;5.84e-08)|BRCA - Breast invasive adenocarcinoma(10;3.63e-06)															---	---	---	---
PRIC285	85441	broad.mit.edu	37	20	62192636	62192636	+	Intron	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62192636G>T	uc002yfm.2	-						PRIC285_uc002yfl.1_Intron	NM_001037335	NP_001032412			PPAR-alpha interacting complex protein 285						cellular lipid metabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	ATP binding|DNA binding|helicase activity|ribonuclease activity|RNA binding|transcription coactivator activity|zinc ion binding			central_nervous_system(2)	2	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;1.27e-08)|all cancers(9;7.32e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)															---	---	---	---
PRIC285	85441	broad.mit.edu	37	20	62197197	62197197	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62197197G>A	uc002yfm.2	-	9	3870	c.2978C>T	c.(2977-2979)ACG>ATG	p.T993M	PRIC285_uc002yfl.1_Missense_Mutation_p.T424M	NM_001037335	NP_001032412	Q9BYK8	PR285_HUMAN	PPAR-alpha interacting complex protein 285	993	Ala-rich.				cellular lipid metabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	ATP binding|DNA binding|helicase activity|ribonuclease activity|RNA binding|transcription coactivator activity|zinc ion binding			central_nervous_system(2)	2	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;1.27e-08)|all cancers(9;7.32e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)															---	---	---	---
NPBWR2	2832	broad.mit.edu	37	20	62737684	62737684	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62737684G>A	uc011abt.1	-	1	501	c.501C>T	c.(499-501)AGC>AGT	p.S167S		NM_005286	NP_005277	P48146	NPBW2_HUMAN	neuropeptides B/W receptor 2	167	Helical; Name=4; (Potential).					plasma membrane	opioid receptor activity|protein binding			large_intestine(1)	1	all_cancers(38;2.58e-11)|all_epithelial(29;6.4e-13)|Lung NSC(23;1.25e-09)|all_lung(23;4.21e-09)																	---	---	---	---
MYT1	4661	broad.mit.edu	37	20	62848487	62848487	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62848487G>A	uc002yii.2	+	11	2063	c.1699G>A	c.(1699-1701)GCC>ACC	p.A567T	MYT1_uc002yih.2_Missense_Mutation_p.A269T|MYT1_uc002yij.2_Missense_Mutation_p.A199T	NM_004535	NP_004526	Q01538	MYT1_HUMAN	myelin transcription factor 1	567				ATPRANLA -> RHTQGQLG (in Ref. 5; AAA59897).	cell differentiation|nervous system development	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)																	---	---	---	---
TMPRSS15	5651	broad.mit.edu	37	21	19725301	19725301	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19725301T>C	uc002ykw.2	-	10	1121	c.1090A>G	c.(1090-1092)AAT>GAT	p.N364D		NM_002772	NP_002763	P98073	ENTK_HUMAN	enterokinase precursor	364	Extracellular (Potential).|MAM.				proteolysis	brush border|integral to membrane	scavenger receptor activity|serine-type endopeptidase activity			ovary(5)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	8																		---	---	---	---
ADAMTS5	11096	broad.mit.edu	37	21	28306805	28306805	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:28306805T>G	uc002ymg.2	-	4	2398	c.1669A>C	c.(1669-1671)ACC>CCC	p.T557P		NM_007038	NP_008969	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1	557	Disintegrin.				proteolysis	proteinaceous extracellular matrix	integrin binding|metalloendopeptidase activity|zinc ion binding			upper_aerodigestive_tract(2)|ovary(1)|pancreas(1)	4																		---	---	---	---
RNF160	26046	broad.mit.edu	37	21	30329763	30329763	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30329763A>G	uc002ymr.2	-	15	2934	c.2921T>C	c.(2920-2922)CTA>CCA	p.L974P		NM_015565	NP_056380	O94822	LTN1_HUMAN	zinc finger protein 294	928							ligase activity|zinc ion binding				0																		---	---	---	---
RNF160	26046	broad.mit.edu	37	21	30358520	30358520	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:30358520G>C	uc002ymr.2	-	3	436	c.423C>G	c.(421-423)GAC>GAG	p.D141E	RNF160_uc010gll.1_RNA	NM_015565	NP_056380	O94822	LTN1_HUMAN	zinc finger protein 294	95							ligase activity|zinc ion binding				0																		---	---	---	---
KRTAP26-1	388818	broad.mit.edu	37	21	31692151	31692151	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31692151G>A	uc002ynw.2	-	1	457	c.203C>T	c.(202-204)CCG>CTG	p.P68L		NM_203405	NP_981950	Q6PEX3	KR261_HUMAN	keratin associated protein 26-1	68						intermediate filament				ovary(1)	1																		---	---	---	---
KRTAP13-4	284827	broad.mit.edu	37	21	31802665	31802665	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:31802665C>A	uc011acw.1	+	1	72	c.72C>A	c.(70-72)TCC>TCA	p.S24S		NM_181600	NP_853631	Q3LI77	KR134_HUMAN	keratin associated protein 13-4	24						intermediate filament					0																		---	---	---	---
TIAM1	7074	broad.mit.edu	37	21	32590005	32590005	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:32590005C>T	uc002yow.1	-	10	2478	c.2006G>A	c.(2005-2007)CGC>CAC	p.R669H	TIAM1_uc011adk.1_Missense_Mutation_p.R669H|TIAM1_uc011adl.1_Missense_Mutation_p.R669H|TIAM1_uc002yox.1_Missense_Mutation_p.R277H	NM_003253	NP_003244	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	669					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cell-cell junction|cytosol	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|breast(3)|ovary(2)|large_intestine(2)	10																		---	---	---	---
SYNJ1	8867	broad.mit.edu	37	21	34003362	34003362	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34003362A>T	uc002yqh.2	-	32	4782	c.4782T>A	c.(4780-4782)GAT>GAA	p.D1594E	SYNJ1_uc011ads.1_3'UTR|SYNJ1_uc002yqf.2_3'UTR|SYNJ1_uc002yqg.2_Missense_Mutation_p.D1508E|SYNJ1_uc002yqi.2_3'UTR|SYNJ1_uc002yqe.3_Missense_Mutation_p.D180E	NM_003895	NP_003886	O43426	SYNJ1_HUMAN	synaptojanin 1 isoform a	1555	Pro-rich.						inositol-polyphosphate 5-phosphatase activity|nucleotide binding|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|RNA binding			ovary(4)|skin(1)	5																		---	---	---	---
SYNJ1	8867	broad.mit.edu	37	21	34003846	34003846	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34003846T>G	uc002yqh.2	-	32	4298	c.4298A>C	c.(4297-4299)AAC>ACC	p.N1433T	SYNJ1_uc011ads.1_3'UTR|SYNJ1_uc002yqf.2_3'UTR|SYNJ1_uc002yqg.2_Missense_Mutation_p.N1347T|SYNJ1_uc002yqi.2_3'UTR|SYNJ1_uc002yqe.3_Missense_Mutation_p.N19T	NM_003895	NP_003886	O43426	SYNJ1_HUMAN	synaptojanin 1 isoform a	1394	Pro-rich.						inositol-polyphosphate 5-phosphatase activity|nucleotide binding|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|RNA binding			ovary(4)|skin(1)	5																		---	---	---	---
SYNJ1	8867	broad.mit.edu	37	21	34038860	34038860	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34038860G>T	uc002yqh.2	-	16	1952	c.1952C>A	c.(1951-1953)GCT>GAT	p.A651D	SYNJ1_uc011ads.1_Missense_Mutation_p.A607D|SYNJ1_uc002yqf.2_Missense_Mutation_p.A612D|SYNJ1_uc002yqg.2_Missense_Mutation_p.A607D|SYNJ1_uc002yqi.2_Missense_Mutation_p.A651D	NM_003895	NP_003886	O43426	SYNJ1_HUMAN	synaptojanin 1 isoform a	612	Catalytic (Potential).						inositol-polyphosphate 5-phosphatase activity|nucleotide binding|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|RNA binding			ovary(4)|skin(1)	5																		---	---	---	---
DNAJC28	54943	broad.mit.edu	37	21	34860605	34860605	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:34860605T>C	uc002yrv.2	-	2	1545	c.1096A>G	c.(1096-1098)ACA>GCA	p.T366A	DNAJC28_uc002yrw.2_Missense_Mutation_p.T366A	NM_017833	NP_060303	Q9NX36	DJC28_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 28	366				LIVPILTRQKVHFDAQKEIVRAQKIYETLIKTKEVTDRNPN NLDQGEGEKTPEIKKGFLNWMNLWKFIKIRSF -> CSHPD QAKSPF (in Ref. 2; BAA91185).			heat shock protein binding				0																		---	---	---	---
ITSN1	6453	broad.mit.edu	37	21	35169850	35169850	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35169850G>A	uc002yta.1	+	18	2388	c.2120G>A	c.(2119-2121)CGG>CAG	p.R707Q	DONSON_uc002ysn.1_Intron|ITSN1_uc002yth.3_RNA|ITSN1_uc002ysz.2_Missense_Mutation_p.R707Q|ITSN1_uc010gmg.2_Missense_Mutation_p.R670Q|ITSN1_uc010gmh.2_RNA|ITSN1_uc002ysw.2_Missense_Mutation_p.R707Q|ITSN1_uc010gmi.2_Missense_Mutation_p.R670Q|ITSN1_uc010gmj.2_Missense_Mutation_p.R591Q|ITSN1_uc002ysy.2_Missense_Mutation_p.R707Q|ITSN1_uc002ysx.2_Missense_Mutation_p.R670Q|ITSN1_uc002ytb.1_Missense_Mutation_p.R707Q|ITSN1_uc002ytc.1_Missense_Mutation_p.R707Q|ITSN1_uc002ytd.2_RNA|ITSN1_uc010gmk.2_Missense_Mutation_p.R670Q|ITSN1_uc010gml.2_RNA|ITSN1_uc002ytj.2_Missense_Mutation_p.R707Q|ITSN1_uc010gmm.1_RNA|ITSN1_uc002yte.2_Missense_Mutation_p.R641Q	NM_003024	NP_003015	Q15811	ITSN1_HUMAN	intersectin 1 isoform ITSN-l	707					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic vesicle endocytosis	cell junction|coated pit|cytosol|lamellipodium|synapse|synaptosome	calcium ion binding|proline-rich region binding|protein complex scaffold|Rho guanyl-nucleotide exchange factor activity			ovary(3)|skin(1)	4																		---	---	---	---
SLC5A3	6526	broad.mit.edu	37	21	35468344	35468344	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:35468344G>A	uc002yto.2	+	2	1359	c.847G>A	c.(847-849)GTG>ATG	p.V283M	MRPS6_uc002ytp.2_Intron	NM_006933	NP_008864	P53794	SC5A3_HUMAN	solute carrier family 5 (inositol transporters),	283	Cytoplasmic (Potential).					integral to plasma membrane	myo-inositol:sodium symporter activity			ovary(2)	2																		---	---	---	---
CBR1	873	broad.mit.edu	37	21	37443284	37443284	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37443284T>C	uc002yvb.1	+	2	455	c.326T>C	c.(325-327)GTG>GCG	p.V109A	uc011aea.1_Intron|SETD4_uc002yva.2_Intron|CBR1_uc010gmx.1_Missense_Mutation_p.V109A|CBR1_uc010gmy.1_Missense_Mutation_p.V109A	NM_001757	NP_001748	P16152	CBR1_HUMAN	carbonyl reductase 1	109					drug metabolic process|vitamin K metabolic process	cytoplasm	15-hydroxyprostaglandin dehydrogenase (NADP+) activity|carbonyl reductase (NADPH) activity|prostaglandin-E2 9-reductase activity|protein binding				0					Acetohexamide(DB00414)|Lubiprostone(DB01046)													---	---	---	---
DOPEY2	9980	broad.mit.edu	37	21	37650362	37650362	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37650362T>C	uc002yvg.2	+	29	5881	c.5802T>C	c.(5800-5802)TTT>TTC	p.F1934F	DOPEY2_uc011aeb.1_Silent_p.F1883F	NM_005128	NP_005119	Q9Y3R5	DOP2_HUMAN	pad-1-like	1934					endoplasmic reticulum organization|Golgi to endosome transport|multicellular organismal development|protein transport	Golgi membrane				ovary(1)|central_nervous_system(1)	2																		---	---	---	---
CLDN14	23562	broad.mit.edu	37	21	37833865	37833865	+	Silent	SNP	G	A	A	rs150731625	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:37833865G>A	uc002yvk.1	-	2	271	c.129C>T	c.(127-129)GCC>GCT	p.A43A	CLDN14_uc002yvn.1_Silent_p.A43A|CLDN14_uc002yvo.1_Silent_p.A43A|CLDN14_uc002yvl.1_Silent_p.A43A|CLDN14_uc002yvm.1_Silent_p.A43A	NM_012130	NP_036262	O95500	CLD14_HUMAN	claudin 14	43	Extracellular (Potential).				calcium-independent cell-cell adhesion|protein complex assembly|tight junction assembly	endoplasmic reticulum|integral to membrane|tight junction	identical protein binding|structural molecule activity				0																		---	---	---	---
TTC3	7267	broad.mit.edu	37	21	38537990	38537990	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38537990A>G	uc002yvz.2	+	33	3579	c.3474A>G	c.(3472-3474)GGA>GGG	p.G1158G	TTC3_uc011aee.1_Silent_p.G848G|TTC3_uc002ywa.2_Silent_p.G1158G|TTC3_uc002ywb.2_Silent_p.G1158G|TTC3_uc010gnf.2_Silent_p.G923G|TTC3_uc002ywc.2_Silent_p.G848G|TTC3_uc002ywd.1_Silent_p.G222G	NM_001001894	NP_001001894	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1158					protein K48-linked ubiquitination|ubiquitin-dependent protein catabolic process	nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			skin(3)|ovary(2)|lung(2)|breast(2)	9		Myeloproliferative disorder(46;0.0412)																---	---	---	---
DSCR3	10311	broad.mit.edu	37	21	38612925	38612925	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38612925C>T	uc002ywf.1	-	3	312	c.73G>A	c.(73-75)GTG>ATG	p.V25M	DSCR3_uc010gnm.1_RNA|DSCR3_uc010gnn.1_Translation_Start_Site|DSCR3_uc010gnl.2_Missense_Mutation_p.V25M|DSCR3_uc011aeg.1_Missense_Mutation_p.V25M|DSCR3_uc011aeh.1_Intron	NM_006052	NP_006043	O14972	DSCR3_HUMAN	Down syndrome critical region protein 3	25					vacuolar transport	nucleus|retromer complex					0																		---	---	---	---
KCNJ6	3763	broad.mit.edu	37	21	39086687	39086687	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39086687G>A	uc011aej.1	-	3	826	c.773C>T	c.(772-774)ACG>ATG	p.T258M	KCNJ6_uc002ywo.2_Missense_Mutation_p.T258M	NM_002240	NP_002231	P48051	IRK6_HUMAN	potassium inwardly-rectifying channel J6	258	Cytoplasmic (By similarity).				synaptic transmission	Golgi apparatus|voltage-gated potassium channel complex	G-protein activated inward rectifier potassium channel activity|protein binding			skin(1)	1					Halothane(DB01159)													---	---	---	---
DSCR4	10281	broad.mit.edu	37	21	39493258	39493258	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39493258G>A	uc002ywp.2	-	1	197	c.92C>T	c.(91-93)CCG>CTG	p.P31L	DSCR8_uc002ywt.3_5'Flank|DSCR8_uc010gnp.2_5'Flank|DSCR8_uc010gnq.2_5'Flank|DSCR8_uc010gnr.2_5'Flank|DSCR8_uc010gns.2_5'Flank	NM_005867	NP_005858	P56555	DSCR4_HUMAN	Down syndrome critical region protein 4	31										ovary(1)	1																		---	---	---	---
KCNJ15	3772	broad.mit.edu	37	21	39671266	39671266	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39671266G>A	uc002ywv.2	+	4	385	c.83G>A	c.(82-84)CGC>CAC	p.R28H	KCNJ15_uc002yww.2_Missense_Mutation_p.R28H|KCNJ15_uc002ywx.2_Missense_Mutation_p.R28H	NM_002243	NP_002234	Q99712	IRK15_HUMAN	potassium inwardly-rectifying channel J15	28	Cytoplasmic (By similarity).				synaptic transmission	integral to plasma membrane	inward rectifier potassium channel activity			ovary(2)|skin(2)|breast(1)|central_nervous_system(1)	6																		---	---	---	---
ERG	2078	broad.mit.edu	37	21	39947607	39947607	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:39947607C>T	uc010gnw.2	-	3	313	c.18G>A	c.(16-18)CCG>CCA	p.P6P	ERG_uc010gnv.2_5'UTR|ERG_uc010gnx.2_Silent_p.P6P|ERG_uc011ael.1_Silent_p.P6P|ERG_uc002yxb.2_Silent_p.P6P|ERG_uc002yxc.3_Silent_p.P6P|ERG_uc010gnz.2_RNA	NM_001136155	NP_001129627	P11308	ERG_HUMAN	ets-related isoform 4	6					cell proliferation|multicellular organismal development|protein phosphorylation	cytoplasm|nucleus|ribonucleoprotein complex	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity		TMPRSS2/ERG(2499)|FUS/ERG(163)|EWSR1/ERG(162)	prostate(2499)|bone(167)|haematopoietic_and_lymphoid_tissue(153)|soft_tissue(5)|lung(2)|skin(1)|ovary(1)	2828		Prostate(19;3.6e-06)																---	---	---	---
BRWD1	54014	broad.mit.edu	37	21	40568602	40568602	+	Silent	SNP	C	T	T	rs147384341		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:40568602C>T	uc002yxk.1	-	41	6532	c.6393G>A	c.(6391-6393)TCG>TCA	p.S2131S	BRWD1_uc010goc.1_Silent_p.S774S|BRWD1_uc002yxl.2_Silent_p.S2131S	NM_018963	NP_061836	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	2131					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				skin(3)|ovary(1)	4		Prostate(19;8.44e-08)|all_epithelial(19;0.223)																---	---	---	---
IGSF5	150084	broad.mit.edu	37	21	41137583	41137583	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41137583T>C	uc002yyo.2	+	3	325	c.222T>C	c.(220-222)AGT>AGC	p.S74S		NM_001080444	NP_001073913	Q9NSI5	IGSF5_HUMAN	immunoglobulin superfamily 5 like	74	Ig-like V-type 1.|Extracellular (Potential).					integral to membrane|tight junction					0		Prostate(19;5.35e-06)																---	---	---	---
DSCAM	1826	broad.mit.edu	37	21	41496266	41496266	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:41496266C>T	uc002yyq.1	-						DSCAM_uc002yyr.1_Intron	NM_001389	NP_001380			Down syndrome cell adhesion molecule isoform						cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)|skin(4)|upper_aerodigestive_tract(1)	11		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)																---	---	---	---
TMPRSS2	7113	broad.mit.edu	37	21	42843873	42843873	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42843873G>A	uc002yzj.2	-	10	1069	c.935C>T	c.(934-936)GCG>GTG	p.A312V	TMPRSS2_uc010gor.2_Missense_Mutation_p.A349V|TMPRSS2_uc010gos.1_Missense_Mutation_p.A312V	NM_005656	NP_005647	O15393	TMPS2_HUMAN	transmembrane protease, serine 2 isoform 2	312	Peptidase S1.|Extracellular (Potential).				proteolysis	cytoplasm|extracellular region|integral to plasma membrane	scavenger receptor activity|serine-type endopeptidase activity		TMPRSS2/ERG(2499)|TMPRSS2/ETV1(24)	prostate(2523)|central_nervous_system(1)	2524		Prostate(19;4.48e-07)|all_epithelial(19;0.031)						T	ERG|ETV1|ETV4|ETV5	prostate 								---	---	---	---
RIPK4	54101	broad.mit.edu	37	21	43162074	43162074	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43162074G>A	uc002yzn.1	-	8	1327	c.1279C>T	c.(1279-1281)CAG>TAG	p.Q427*		NM_020639	NP_065690	P57078	RIPK4_HUMAN	ankyrin repeat domain 3	427						cytoplasm|nucleus	ATP binding|protein serine/threonine kinase activity			ovary(2)|central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)	7																		---	---	---	---
ZNF295	49854	broad.mit.edu	37	21	43411698	43411698	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43411698T>G	uc002zab.3	-	3	2721	c.2507A>C	c.(2506-2508)AAC>ACC	p.N836T	ZNF295_uc002yzz.3_Missense_Mutation_p.N635T|ZNF295_uc002yzy.3_Missense_Mutation_p.N836T|ZNF295_uc002zaa.3_Missense_Mutation_p.N836T	NM_001098402	NP_001091872	Q9ULJ3	ZN295_HUMAN	zinc finger protein 295 isoform L	836					negative regulation of transcription, DNA-dependent|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|nucleus	methyl-CpG binding|protein binding|zinc ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3																		---	---	---	---
UMODL1	89766	broad.mit.edu	37	21	43557730	43557730	+	Nonstop_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43557730G>T	uc002zaf.1	+	22	3957	c.3957G>T	c.(3955-3957)TAG>TAT	p.*1319Y	UMODL1_uc002zad.1_Nonstop_Mutation_p.*1247Y|UMODL1_uc002zae.1_Nonstop_Mutation_p.*1375Y|UMODL1_uc002zag.1_Nonstop_Mutation_p.*1447Y|UMODL1_uc002zal.1_Nonstop_Mutation_p.*269Y|UMODL1_uc010gpa.1_RNA	NM_001004416	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1 isoform 1 precursor	1319						cytoplasm|extracellular region|integral to membrane|plasma membrane	calcium ion binding|peptidase inhibitor activity			ovary(2)|skin(1)	3																		---	---	---	---
ABCG1	9619	broad.mit.edu	37	21	43645809	43645809	+	Missense_Mutation	SNP	C	T	T	rs144780823	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43645809C>T	uc002zaq.2	+	2	177	c.71C>T	c.(70-72)ACG>ATG	p.T24M	ABCG1_uc002zan.2_Missense_Mutation_p.T26M|ABCG1_uc002zam.2_Missense_Mutation_p.T2M|ABCG1_uc002zao.2_Missense_Mutation_p.T21M|ABCG1_uc002zap.2_Missense_Mutation_p.T24M|ABCG1_uc002zar.2_Missense_Mutation_p.T35M|ABCG1_uc011aev.1_Missense_Mutation_p.T35M	NM_004915	NP_004906	P45844	ABCG1_HUMAN	ATP-binding cassette sub-family G member 1	24	Cytoplasmic (Potential).				amyloid precursor protein catabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|detection of hormone stimulus|high-density lipoprotein particle remodeling|intracellular cholesterol transport|lipoprotein metabolic process|low-density lipoprotein particle remodeling|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|positive regulation of cholesterol biosynthetic process|regulation of cholesterol esterification|regulation of transcription, DNA-dependent|response to lipid|reverse cholesterol transport	endoplasmic reticulum membrane|external side of plasma membrane|Golgi membrane|recycling endosome	ADP binding|ATP binding|cholesterol transporter activity|glycoprotein transporter activity|phospholipid transporter activity|protein heterodimerization activity|protein homodimerization activity|sterol-transporting ATPase activity|toxin transporter activity			ovary(2)|central_nervous_system(1)	3					Adenosine triphosphate(DB00171)													---	---	---	---
PDE9A	5152	broad.mit.edu	37	21	44182222	44182222	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44182222C>T	uc002zbm.2	+	14	1178	c.1115C>T	c.(1114-1116)GCG>GTG	p.A372V	PDE9A_uc002zbn.2_Missense_Mutation_p.A245V|PDE9A_uc002zbo.2_Missense_Mutation_p.A319V|PDE9A_uc002zbp.2_Missense_Mutation_p.A165V|PDE9A_uc002zbq.2_Missense_Mutation_p.A270V|PDE9A_uc002zbs.2_Missense_Mutation_p.A165V|PDE9A_uc002zbr.2_Missense_Mutation_p.A165V|PDE9A_uc002zbt.2_Missense_Mutation_p.A244V|PDE9A_uc002zbu.2_Missense_Mutation_p.A238V|PDE9A_uc002zbv.2_Missense_Mutation_p.A212V|PDE9A_uc002zbw.2_Missense_Mutation_p.A155V|PDE9A_uc002zbx.2_Missense_Mutation_p.A312V|PDE9A_uc002zby.2_Missense_Mutation_p.A155V|PDE9A_uc002zbz.2_Missense_Mutation_p.A264V|PDE9A_uc002zca.2_Missense_Mutation_p.A331V|PDE9A_uc002zcb.2_Missense_Mutation_p.A346V|PDE9A_uc002zcc.2_Missense_Mutation_p.A271V|PDE9A_uc002zcd.2_Missense_Mutation_p.A286V|PDE9A_uc002zce.2_Missense_Mutation_p.A305V|PDE9A_uc002zcf.2_Missense_Mutation_p.A165V|PDE9A_uc002zcg.2_Missense_Mutation_p.A165V|PDE9A_uc002zch.2_Missense_Mutation_p.A155V|PDE9A_uc010gpf.1_Missense_Mutation_p.A165V	NM_002606	NP_002597	O76083	PDE9A_HUMAN	phosphodiesterase 9A isoform a	372	Catalytic (By similarity).				platelet activation|signal transduction	cytosol|endoplasmic reticulum|Golgi apparatus|perinuclear region of cytoplasm|ruffle membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding|protein binding			ovary(1)|skin(1)	2																		---	---	---	---
PDE9A	5152	broad.mit.edu	37	21	44189215	44189215	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44189215A>T	uc002zbm.2	+	17	1603	c.1540A>T	c.(1540-1542)ATT>TTT	p.I514F	PDE9A_uc002zbn.2_Missense_Mutation_p.I387F|PDE9A_uc002zbo.2_Missense_Mutation_p.I461F|PDE9A_uc002zbp.2_Missense_Mutation_p.I307F|PDE9A_uc002zbq.2_Missense_Mutation_p.I412F|PDE9A_uc002zbs.2_Missense_Mutation_p.I307F|PDE9A_uc002zbr.2_Missense_Mutation_p.I307F|PDE9A_uc002zbt.2_Missense_Mutation_p.I386F|PDE9A_uc002zbu.2_Missense_Mutation_p.I380F|PDE9A_uc002zbv.2_Missense_Mutation_p.I354F|PDE9A_uc002zbw.2_Missense_Mutation_p.I297F|PDE9A_uc002zbx.2_Missense_Mutation_p.I454F|PDE9A_uc002zby.2_Missense_Mutation_p.I297F|PDE9A_uc002zbz.2_Missense_Mutation_p.I406F|PDE9A_uc002zca.2_Missense_Mutation_p.I473F|PDE9A_uc002zcb.2_Missense_Mutation_p.I488F|PDE9A_uc002zcc.2_Missense_Mutation_p.I413F|PDE9A_uc002zcd.2_Missense_Mutation_p.I428F|PDE9A_uc002zce.2_Missense_Mutation_p.I447F|PDE9A_uc002zcf.2_Missense_Mutation_p.I307F|PDE9A_uc002zcg.2_Missense_Mutation_p.I307F|PDE9A_uc002zch.2_Missense_Mutation_p.I297F	NM_002606	NP_002597	O76083	PDE9A_HUMAN	phosphodiesterase 9A isoform a	514	Catalytic (By similarity).				platelet activation|signal transduction	cytosol|endoplasmic reticulum|Golgi apparatus|perinuclear region of cytoplasm|ruffle membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding|protein binding			ovary(1)|skin(1)	2																		---	---	---	---
NDUFV3	4731	broad.mit.edu	37	21	44329047	44329047	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44329047G>A	uc002zcn.2	+	3	309	c.243G>A	c.(241-243)ACG>ACA	p.T81T	NDUFV3_uc002zcm.2_Silent_p.T446T	NM_001001503	NP_001001503	P56181	NDUV3_HUMAN	NADH-ubiquinone oxidoreductase flavoprotein 3	81					mitochondrial electron transport, NADH to ubiquinone|transport	mitochondrial respiratory chain complex I|nucleus	NADH dehydrogenase (ubiquinone) activity			ovary(2)	2				STAD - Stomach adenocarcinoma(101;0.0606)	NADH(DB00157)													---	---	---	---
CRYAA	1409	broad.mit.edu	37	21	44589279	44589279	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44589279G>A	uc002zdd.1	+	1	139	c.70G>A	c.(70-72)GAC>AAC	p.D24N		NM_000394	NP_000385	P02489	CRYAA_HUMAN	crystallin, alpha A	24					anti-apoptosis|negative regulation of intracellular transport|protein homooligomerization|response to heat|visual perception	cytoplasm|nucleus	structural constituent of eye lens|unfolded protein binding			breast(1)|central_nervous_system(1)	2																		---	---	---	---
SIK1	150094	broad.mit.edu	37	21	44840168	44840168	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:44840168C>T	uc002zdf.2	-	8	1045	c.918G>A	c.(916-918)GAG>GAA	p.E306E		NM_173354	NP_775490	P57059	SIK1_HUMAN	salt-inducible kinase 1	306	UBA.				anoikis|cell cycle|cell differentiation|intracellular protein kinase cascade|multicellular organismal development|regulation of cell differentiation|regulation of mitotic cell cycle	nucleus	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			lung(2)|testis(2)|ovary(1)|central_nervous_system(1)|skin(1)	7																		---	---	---	---
TRAPPC10	7109	broad.mit.edu	37	21	45522763	45522763	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45522763C>T	uc002zea.2	+	22	3620	c.3451C>T	c.(3451-3453)CCG>TCG	p.P1151S	TRAPPC10_uc010gpo.2_Missense_Mutation_p.P862S|TRAPPC10_uc011afa.1_Missense_Mutation_p.P529S	NM_003274	NP_003265	P48553	TPC10_HUMAN	trafficking protein particle complex 10	1151					vesicle-mediated transport	Golgi apparatus|integral to membrane	binding|sodium ion transmembrane transporter activity			ovary(1)|skin(1)	2																		---	---	---	---
PFKL	5211	broad.mit.edu	37	21	45740004	45740004	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45740004G>A	uc002zel.2	+	12	1224	c.1165G>A	c.(1165-1167)GCC>ACC	p.A389T	PFKL_uc002zek.2_Missense_Mutation_p.A436T|PFKL_uc002zem.2_5'UTR|PFKL_uc002zen.2_5'UTR	NM_002626	NP_002617	P17858	K6PL_HUMAN	liver phosphofructokinase	389				A -> T (in Ref. 1; CAA33597 and 2; CAB46744).	fructose 6-phosphate metabolic process|glycolysis|protein oligomerization	6-phosphofructokinase complex	6-phosphofructokinase activity|ATP binding|fructose-6-phosphate binding|identical protein binding|kinase binding|metal ion binding				0				Colorectal(79;0.0811)														---	---	---	---
KRTAP10-11	386678	broad.mit.edu	37	21	46066753	46066753	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46066753C>A	uc002zfr.3	+	1	423	c.378C>A	c.(376-378)TGC>TGA	p.C126*	C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_198692	NP_941965	P60412	KR10B_HUMAN	keratin associated protein 10-11	126	25 X 5 AA repeats of C-C-X(3).|11.					keratin filament				ovary(1)	1																		---	---	---	---
KRTAP10-12	386685	broad.mit.edu	37	21	46117348	46117348	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46117348A>C	uc002zfw.1	+	1	262	c.232A>C	c.(232-234)AGC>CGC	p.S78R	C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_198699	NP_941972	P60413	KR10C_HUMAN	keratin associated protein 10-12	78	19 X 5 AA repeats of C-C-X(3).					keratin filament					0																		---	---	---	---
SUMO3	6612	broad.mit.edu	37	21	46226955	46226955	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46226955G>A	uc002zfz.1	-	4	384	c.223C>T	c.(223-225)CTG>TTG	p.L75L	SUMO3_uc011afi.1_Silent_p.L113L|SUMO3_uc002zga.1_Silent_p.G91G	NM_006936	NP_008867	P55854	SUMO3_HUMAN	small ubiquitin-like modifier protein 3	75	Ubiquitin-like.				protein sumoylation	cytoplasm|kinetochore	protein binding				0				Colorectal(79;0.058)														---	---	---	---
PTTG1IP	754	broad.mit.edu	37	21	46276177	46276177	+	Missense_Mutation	SNP	C	T	T	rs141726521	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46276177C>T	uc002zgb.1	-	4	590	c.380G>A	c.(379-381)CGG>CAG	p.R127Q	PTTG1IP_uc011afj.1_RNA|PTTG1IP_uc011afk.1_Intron	NM_004339	NP_004330	P53801	PTTG_HUMAN	pituitary tumor-transforming gene 1	127	Cytoplasmic (Potential).				protein import into nucleus	cytoplasm|integral to membrane|nucleus				ovary(1)	1				Colorectal(79;0.0659)														---	---	---	---
ITGB2	3689	broad.mit.edu	37	21	46323287	46323287	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46323287G>A	uc002zgd.2	-	4	536	c.492C>T	c.(490-492)GGC>GGT	p.G164G	ITGB2_uc002zge.2_Silent_p.G164G|ITGB2_uc002zgf.3_Silent_p.G164G|ITGB2_uc011afl.1_Silent_p.G86G|ITGB2_uc010gpw.2_Intron|ITGB2_uc002zgg.2_Silent_p.G164G	NM_001127491	NP_001120963	P05107	ITB2_HUMAN	integrin, beta 2 precursor	164	Extracellular (Potential).|VWFA.				apoptosis|blood coagulation|cell-cell signaling|cell-matrix adhesion|inflammatory response|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|multicellular organismal development|neutrophil chemotaxis|regulation of cell shape|regulation of immune response|regulation of peptidyl-tyrosine phosphorylation	integrin complex	glycoprotein binding|protein kinase binding|receptor activity			ovary(4)|central_nervous_system(3)|breast(2)	9				Colorectal(79;0.0669)	Simvastatin(DB00641)													---	---	---	---
ITGB2	3689	broad.mit.edu	37	21	46330684	46330684	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46330684C>T	uc002zgd.2	-	1	58	c.14G>A	c.(13-15)CGC>CAC	p.R5H	ITGB2_uc002zge.2_Missense_Mutation_p.R5H|ITGB2_uc002zgf.3_Missense_Mutation_p.R5H|ITGB2_uc011afl.1_5'UTR|ITGB2_uc010gpw.2_Missense_Mutation_p.R5H|ITGB2_uc002zgg.2_Missense_Mutation_p.R5H	NM_001127491	NP_001120963	P05107	ITB2_HUMAN	integrin, beta 2 precursor	5					apoptosis|blood coagulation|cell-cell signaling|cell-matrix adhesion|inflammatory response|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|multicellular organismal development|neutrophil chemotaxis|regulation of cell shape|regulation of immune response|regulation of peptidyl-tyrosine phosphorylation	integrin complex	glycoprotein binding|protein kinase binding|receptor activity			ovary(4)|central_nervous_system(3)|breast(2)	9				Colorectal(79;0.0669)	Simvastatin(DB00641)													---	---	---	---
ADARB1	104	broad.mit.edu	37	21	46591591	46591591	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46591591A>G	uc002zgy.2	+	3	455	c.20A>G	c.(19-21)GAA>GGA	p.E7G	ADARB1_uc002zgr.2_Missense_Mutation_p.E7G|ADARB1_uc002zgs.2_RNA|ADARB1_uc002zgw.2_Missense_Mutation_p.E7G|ADARB1_uc002zgv.2_RNA|ADARB1_uc002zgt.2_Missense_Mutation_p.E7G|ADARB1_uc010gpx.2_RNA|ADARB1_uc002zgq.2_RNA|ADARB1_uc002zgu.2_RNA|ADARB1_uc011afo.1_Missense_Mutation_p.E56G	NM_015833	NP_056648	P78563	RED1_HUMAN	RNA-specific adenosine deaminase B1 isoform 2	7					adenosine to inosine editing|mRNA modification|mRNA processing|RNA processing	nucleoplasm|nucleus	double-stranded RNA adenosine deaminase activity|double-stranded RNA adenosine deaminase activity|double-stranded RNA binding|double-stranded RNA binding|metal ion binding|mRNA binding|RNA binding			skin(1)	1				Colorectal(79;0.115)														---	---	---	---
ADARB1	104	broad.mit.edu	37	21	46600267	46600267	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46600267G>A	uc002zgy.2	+	5	1421	c.986G>A	c.(985-987)CGC>CAC	p.R329H	ADARB1_uc002zgr.2_Missense_Mutation_p.R329H|ADARB1_uc002zgs.2_RNA|ADARB1_uc002zgw.2_Missense_Mutation_p.R329H|ADARB1_uc002zgv.2_RNA|ADARB1_uc002zgt.2_Missense_Mutation_p.R329H|ADARB1_uc010gpx.2_RNA|ADARB1_uc002zgq.2_RNA|ADARB1_uc002zgu.2_RNA	NM_015833	NP_056648	P78563	RED1_HUMAN	RNA-specific adenosine deaminase B1 isoform 2	329					adenosine to inosine editing|mRNA modification|mRNA processing|RNA processing	nucleoplasm|nucleus	double-stranded RNA adenosine deaminase activity|double-stranded RNA adenosine deaminase activity|double-stranded RNA binding|double-stranded RNA binding|metal ion binding|mRNA binding|RNA binding			skin(1)	1				Colorectal(79;0.115)														---	---	---	---
ADARB1	104	broad.mit.edu	37	21	46641938	46641938	+	Silent	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46641938C>A	uc002zgy.2	+	12	2487	c.2052C>A	c.(2050-2052)CCC>CCA	p.P684P	ADARB1_uc002zgr.2_Silent_p.P684P|ADARB1_uc002zgs.2_RNA|ADARB1_uc002zgw.2_Silent_p.P644P|ADARB1_uc002zgv.2_RNA|ADARB1_uc002zgt.2_Silent_p.P644P|ADARB1_uc010gpx.2_RNA|ADARB1_uc002zgq.2_RNA|ADARB1_uc002zgu.2_RNA	NM_015833	NP_056648	P78563	RED1_HUMAN	RNA-specific adenosine deaminase B1 isoform 2	684	A to I editase.				adenosine to inosine editing|mRNA modification|mRNA processing|RNA processing	nucleoplasm|nucleus	double-stranded RNA adenosine deaminase activity|double-stranded RNA adenosine deaminase activity|double-stranded RNA binding|double-stranded RNA binding|metal ion binding|mRNA binding|RNA binding			skin(1)	1				Colorectal(79;0.115)														---	---	---	---
COL18A1	80781	broad.mit.edu	37	21	46875562	46875562	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46875562C>A	uc011afs.1	+	1	139	c.118C>A	c.(118-120)CAT>AAT	p.H40N	COL18A1_uc002zhg.2_Intron|COL18A1_uc002zhi.2_Missense_Mutation_p.H40N	NM_130444	NP_569711	P39060	COIA1_HUMAN	alpha 1 type XVIII collagen isoform 3 precursor	40					cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception	collagen|extracellular space	extracellular matrix structural constituent|metal ion binding|protein binding			central_nervous_system(1)	1				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)														---	---	---	---
COL18A1	80781	broad.mit.edu	37	21	46888526	46888526	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46888526C>T	uc011afs.1	+	2	1743	c.1722C>T	c.(1720-1722)GTC>GTT	p.V574V	COL18A1_uc002zhg.2_Silent_p.V159V|COL18A1_uc002zhi.2_Silent_p.V339V	NM_130444	NP_569711	P39060	COIA1_HUMAN	alpha 1 type XVIII collagen isoform 3 precursor	574	TSP N-terminal.				cell adhesion|negative regulation of cell proliferation|organ morphogenesis|visual perception	collagen|extracellular space	extracellular matrix structural constituent|metal ion binding|protein binding			central_nervous_system(1)	1				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)														---	---	---	---
SLC19A1	6573	broad.mit.edu	37	21	46951629	46951629	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46951629C>T	uc002zhl.1	-	3	742	c.623G>A	c.(622-624)CGC>CAC	p.R208H	SLC19A1_uc010gpy.1_Missense_Mutation_p.R208H|SLC19A1_uc011aft.1_Missense_Mutation_p.R168H|SLC19A1_uc002zhm.1_Missense_Mutation_p.R208H|SLC19A1_uc010gpz.1_Missense_Mutation_p.R87H	NM_194255	NP_919231	P41440	S19A1_HUMAN	solute carrier family 19 member 1	208	Cytoplasmic (Probable).				folic acid metabolic process	integral to plasma membrane|membrane fraction	folic acid binding|folic acid transporter activity|methotrexate transporter activity|reduced folate carrier activity				0				Colorectal(79;0.0569)|READ - Rectum adenocarcinoma(84;0.172)														---	---	---	---
SLC19A1	6573	broad.mit.edu	37	21	46951891	46951891	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:46951891G>A	uc002zhl.1	-	3	480	c.361C>T	c.(361-363)CTC>TTC	p.L121F	SLC19A1_uc010gpy.1_Missense_Mutation_p.L121F|SLC19A1_uc011aft.1_Missense_Mutation_p.L81F|SLC19A1_uc002zhm.1_Missense_Mutation_p.L121F|SLC19A1_uc010gpz.1_5'UTR	NM_194255	NP_919231	P41440	S19A1_HUMAN	solute carrier family 19 member 1	121	Extracellular (Probable).				folic acid metabolic process	integral to plasma membrane|membrane fraction	folic acid binding|folic acid transporter activity|methotrexate transporter activity|reduced folate carrier activity				0				Colorectal(79;0.0569)|READ - Rectum adenocarcinoma(84;0.172)														---	---	---	---
C21orf57	54059	broad.mit.edu	37	21	47711306	47711306	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:47711306A>G	uc002ziv.2	+	3	698	c.269A>G	c.(268-270)GAC>GGC	p.D90G	C21orf57_uc002zit.1_Missense_Mutation_p.D90G|C21orf57_uc002ziu.1_Missense_Mutation_p.D90G|C21orf57_uc002ziw.2_Missense_Mutation_p.D45G|C21orf57_uc002zix.2_Missense_Mutation_p.D90G|C21orf57_uc010gqh.2_Intron|C21orf57_uc002ziy.2_Intron|uc010gqi.1_5'Flank	NM_058181	NP_478061	P58557	YBEY_HUMAN	hypothetical protein LOC54059 isoform 1	90							metal ion binding|metalloendopeptidase activity				0	Breast(49;0.112)			Colorectal(79;0.236)														---	---	---	---
CECR5	27440	broad.mit.edu	37	22	17619184	17619184	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17619184C>T	uc002zmf.2	-	8	1027	c.999G>A	c.(997-999)ACG>ACA	p.T333T	CECR5_uc002zmd.2_Silent_p.T144T|CECR5_uc002zme.2_Silent_p.T125T|CECR5_uc002zmg.2_Silent_p.T133T|CECR5_uc002zmh.2_Silent_p.T303T	NM_033070	NP_149061	Q9BXW7	CECR5_HUMAN	cat eye syndrome chromosome region, candidate 5	333							hydrolase activity				0		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)																---	---	---	---
CECR5	27440	broad.mit.edu	37	22	17619556	17619556	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17619556G>A	uc002zmf.2	-	7	847	c.819C>T	c.(817-819)TAC>TAT	p.Y273Y	CECR5_uc002zmd.2_Silent_p.Y84Y|CECR5_uc002zme.2_Silent_p.Y65Y|CECR5_uc002zmg.2_Intron|CECR5_uc002zmh.2_Silent_p.Y243Y	NM_033070	NP_149061	Q9BXW7	CECR5_HUMAN	cat eye syndrome chromosome region, candidate 5	273							hydrolase activity				0		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)																---	---	---	---
MICAL3	57553	broad.mit.edu	37	22	18383756	18383756	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:18383756A>G	uc002zng.3	-	6	1052	c.699T>C	c.(697-699)CGT>CGC	p.R233R	MICAL3_uc011agl.1_Silent_p.R233R|MICAL3_uc002znh.2_Silent_p.R233R|MICAL3_uc002znj.1_5'UTR|MICAL3_uc002znk.1_Silent_p.R233R|MICAL3_uc002znl.1_5'UTR|MICAL3_uc010grf.2_Silent_p.R233R|MICAL3_uc011agm.1_Silent_p.R233R	NM_015241	NP_056056	Q7RTP6	MICA3_HUMAN	microtubule associated monoxygenase, calponin	233						cytoplasm|cytoskeleton	monooxygenase activity|zinc ion binding				0		all_epithelial(15;0.198)		Lung(27;0.0427)														---	---	---	---
TSSK2	23617	broad.mit.edu	37	22	19119562	19119562	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19119562A>G	uc002zow.2	+	1	1242	c.650A>G	c.(649-651)GAC>GGC	p.D217G	DGCR14_uc002zot.2_3'UTR|DGCR14_uc002zou.2_3'UTR|DGCR14_uc002zov.2_RNA	NM_053006	NP_443732	Q96PF2	TSSK2_HUMAN	testis-specific serine kinase 2	217	Protein kinase.				cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			stomach(1)	1	Colorectal(54;0.0993)																	---	---	---	---
HIRA	7290	broad.mit.edu	37	22	19340889	19340889	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19340889G>A	uc002zpf.1	-	23	3058	c.2838C>T	c.(2836-2838)CTC>CTT	p.L946L	HIRA_uc011agx.1_Silent_p.L812L|HIRA_uc010grn.1_Silent_p.L739L|HIRA_uc010gro.1_Silent_p.L902L|HIRA_uc010grp.2_RNA	NM_003325	NP_003316	P54198	HIRA_HUMAN	HIR histone cell cycle regulation defective	946	Interaction with histone H4.				chromatin modification|regulation of transcription from RNA polymerase II promoter	PML body	chromatin binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(1)	1	Colorectal(54;0.0993)																	---	---	---	---
CDC45	8318	broad.mit.edu	37	22	19492925	19492925	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19492925G>A	uc002zpr.2	+	10	821	c.745G>A	c.(745-747)GTT>ATT	p.V249I	CDC45_uc011agz.1_Missense_Mutation_p.V244I|CDC45_uc011aha.1_Missense_Mutation_p.V281I|CDC45_uc002zps.2_Missense_Mutation_p.V249I|CDC45_uc002zpt.2_Missense_Mutation_p.V203I	NM_003504	NP_003495	O75419	CDC45_HUMAN	CDC45-like	249					DNA replication checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle	centrosome|nucleoplasm	protein binding			lung(1)	1																		---	---	---	---
TBX1	6899	broad.mit.edu	37	22	19752648	19752648	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19752648T>C	uc002zqb.2	+						TBX1_uc002zqa.1_Intron|TBX1_uc002zqc.2_Intron	NM_080646	NP_542377			T-box 1 isoform A						embryonic viscerocranium morphogenesis|heart development|parathyroid gland development|pharyngeal system development|regulation of transcription from RNA polymerase II promoter|soft palate development|thymus development	nucleus	protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|breast(1)	2	Colorectal(54;0.0993)	all_lung(157;3.05e-06)																---	---	---	---
C22orf29	79680	broad.mit.edu	37	22	19839203	19839203	+	Nonsense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19839203A>T	uc002zqg.2	-	2	1181	c.582T>A	c.(580-582)TGT>TGA	p.C194*	GNB1L_uc002zqd.1_Intron|GNB1L_uc002zqe.1_Intron|GNB1L_uc002zqf.1_Intron|C22orf29_uc002zqh.2_Nonsense_Mutation_p.C194*|C22orf29_uc002zqi.2_Nonsense_Mutation_p.C194*|C22orf29_uc010grt.1_Intron	NM_024627	NP_078903	Q7L3V2	CV029_HUMAN	hypothetical protein LOC79680	194											0	Colorectal(54;0.0993)																	---	---	---	---
C22orf29	79680	broad.mit.edu	37	22	19839482	19839482	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19839482G>T	uc002zqg.2	-	2	902	c.303C>A	c.(301-303)GGC>GGA	p.G101G	GNB1L_uc002zqd.1_Intron|GNB1L_uc002zqe.1_Intron|GNB1L_uc002zqf.1_Intron|C22orf29_uc002zqh.2_Silent_p.G101G|C22orf29_uc002zqi.2_Silent_p.G101G|C22orf29_uc010grt.1_Intron	NM_024627	NP_078903	Q7L3V2	CV029_HUMAN	hypothetical protein LOC79680	101											0	Colorectal(54;0.0993)																	---	---	---	---
TXNRD2	10587	broad.mit.edu	37	22	19918573	19918573	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19918573C>T	uc011ahc.1	-	2	185	c.152G>A	c.(151-153)GGC>GAC	p.G51D	TXNRD2_uc002zql.1_5'UTR|TXNRD2_uc002zqm.1_RNA|TXNRD2_uc002zqn.1_RNA|TXNRD2_uc002zqo.1_RNA|TXNRD2_uc002zqp.1_RNA|TXNRD2_uc002zqr.1_Missense_Mutation_p.G50D|TXNRD2_uc010grv.1_Missense_Mutation_p.G51D|TXNRD2_uc002zqj.1_RNA|TXNRD2_uc002zqs.2_Missense_Mutation_p.G19D	NM_006440	NP_006431	Q9NNW7	TRXR2_HUMAN	thioredoxin reductase 2 precursor	51	FAD (By similarity).				cell redox homeostasis|response to oxygen radical	mitochondrion	flavin adenine dinucleotide binding|NADP binding|thioredoxin-disulfide reductase activity			ovary(2)	2	Colorectal(54;0.0993)																	---	---	---	---
ZNF74	7625	broad.mit.edu	37	22	20760073	20760073	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:20760073C>T	uc010gsm.2	+	6	962	c.750C>T	c.(748-750)TGC>TGT	p.C250C	ZNF74_uc002zsg.2_Silent_p.C179C|ZNF74_uc002zsh.2_Silent_p.C250C|ZNF74_uc002zsi.2_Silent_p.C179C|ZNF74_uc010gsn.2_Silent_p.C179C	NM_003426	NP_003417	Q16587	ZNF74_HUMAN	zinc finger protein 74	250	C2H2-type 1.				multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	actin cytoskeleton|nucleus	DNA binding|RNA binding|zinc ion binding			ovary(1)	1	Melanoma(16;0.000465)|Ovarian(15;0.0025)|Colorectal(54;0.0221)|all_neural(72;0.219)	Lung SC(17;0.0262)|all_lung(157;0.248)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)															---	---	---	---
PI4KA	5297	broad.mit.edu	37	22	21068910	21068910	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21068910G>A	uc002zsz.3	-						PI4KA_uc010gsp.2_Intron|PI4KA_uc002zsy.3_Intron	NM_058004	NP_477352			phosphatidylinositol 4-kinase type 3 alpha						phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling|synaptic transmission	Golgi-associated vesicle	1-phosphatidylinositol 4-kinase activity|ATP binding|protein binding			lung(2)|upper_aerodigestive_tract(1)|salivary_gland(1)	4	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)															---	---	---	---
SERPIND1	3053	broad.mit.edu	37	22	21138398	21138398	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21138398A>C	uc002ztb.1	+	3	1095	c.1028A>C	c.(1027-1029)GAC>GCC	p.D343A	PI4KA_uc002zsz.3_Intron|SERPIND1_uc002ztc.2_Missense_Mutation_p.D371A	NM_000185	NP_000176	P05546	HEP2_HUMAN	heparin cofactor II precursor	343					blood coagulation|chemotaxis|regulation of proteolysis	extracellular region	heparin binding|serine-type endopeptidase inhibitor activity				0	all_cancers(11;6.16e-25)|all_epithelial(7;1.02e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)		Ardeparin(DB00407)											OREG0026325	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SNAP29	9342	broad.mit.edu	37	22	21224775	21224775	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21224775A>G	uc011ahw.1	+	2	495	c.388A>G	c.(388-390)ACC>GCC	p.T130A		NM_004782	NP_004773	O95721	SNP29_HUMAN	synaptosomal-associated protein 29	130					cellular membrane fusion|exocytosis|protein transport|vesicle targeting	cell junction|cytoplasm|nucleus|synapse|synaptosome	SNAP receptor activity				0	all_cancers(11;2.77e-25)|all_epithelial(7;8.92e-24)|Lung NSC(8;1.49e-15)|all_lung(8;2.54e-14)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000592)|Lung(15;0.0117)															---	---	---	---
SLC7A4	6545	broad.mit.edu	37	22	21385168	21385168	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:21385168G>A	uc002zud.2	-	2	1002	c.934C>T	c.(934-936)CGG>TGG	p.R312W	SLC7A4_uc002zue.2_Missense_Mutation_p.R312W	NM_004173	NP_004164	O43246	CTR4_HUMAN	solute carrier family 7 (cationic amino acid	312					cellular amino acid metabolic process	integral to membrane	basic amino acid transmembrane transporter activity			ovary(1)|lung(1)	2	all_cancers(11;2.85e-22)|Lung NSC(8;4.21e-14)|all_lung(8;6.08e-13)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0968)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)		L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)													---	---	---	---
TOP3B	8940	broad.mit.edu	37	22	22311699	22311699	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22311699G>A	uc002zvs.2	-	18	2811	c.2376C>T	c.(2374-2376)GGC>GGT	p.G792G	TOP3B_uc010gtm.1_3'UTR|TOP3B_uc002zvr.2_3'UTR|TOP3B_uc010gtl.2_Silent_p.G792G|TOP3B_uc002zvt.3_Silent_p.G792G	NM_003935	NP_003926	O95985	TOP3B_HUMAN	topoisomerase (DNA) III beta	792					DNA topological change	nucleus	ATP binding|DNA topoisomerase type I activity|protein binding			kidney(1)	1	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.145)														---	---	---	---
TOP3B	8940	broad.mit.edu	37	22	22318365	22318365	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22318365C>T	uc002zvs.2	-	11	1569	c.1134G>A	c.(1132-1134)CCG>CCA	p.P378P	TOP3B_uc010gtm.1_5'UTR|TOP3B_uc002zvr.2_Silent_p.P103P|TOP3B_uc010gtl.2_Silent_p.P378P|TOP3B_uc002zvt.3_Silent_p.P378P	NM_003935	NP_003926	O95985	TOP3B_HUMAN	topoisomerase (DNA) III beta	378					DNA topological change	nucleus	ATP binding|DNA topoisomerase type I activity|protein binding			kidney(1)	1	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.145)														---	---	---	---
LOC96610	96610	broad.mit.edu	37	22	22681967	22681967	+	RNA	SNP	C	T	T	rs140594791	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22681967C>T	uc011aim.1	+	37		c.3458C>T								Parts of antibodies, mostly variable regions.												0																		---	---	---	---
GGTLC2	91227	broad.mit.edu	37	22	22988849	22988849	+	Missense_Mutation	SNP	G	A	A	rs149057858	byFrequency	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:22988849G>A	uc010gtt.2	+	1	68	c.34G>A	c.(34-36)GCC>ACC	p.A12T	LOC96610_uc011aim.1_Intron|POM121L1P_uc011ait.1_5'Flank|GGTLC2_uc010gts.2_Missense_Mutation_p.A12T	NM_199127	NP_954578	Q14390	GGTL2_HUMAN	gamma-glutamyltransferase-like 4 isoform 1	12					glutathione biosynthetic process		gamma-glutamyltransferase activity			ovary(1)	1	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.3e-31)|Acute lymphoblastic leukemia(6;5.54e-23)		READ - Rectum adenocarcinoma(21;0.145)														---	---	---	---
RAB36	9609	broad.mit.edu	37	22	23492314	23492314	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23492314G>A	uc002zwv.1	+	3	372	c.332G>A	c.(331-333)TGC>TAC	p.C111Y	RAB36_uc010gtw.1_Missense_Mutation_p.C111Y	NM_004914	NP_004905	O95755	RAB36_HUMAN	RAB36, member RAS oncogene family	111					protein transport|small GTPase mediated signal transduction	Golgi membrane	GTP binding			ovary(1)|central_nervous_system(1)	2	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.155)														---	---	---	---
BCR	613	broad.mit.edu	37	22	23540509	23540509	+	Intron	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:23540509C>T	uc002zww.2	+						BCR_uc002zwx.2_Intron	NM_004327	NP_004318			breakpoint cluster region isoform 1						regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	ATP binding|GTPase activator activity|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity		BCR/JAK2(6)	haematopoietic_and_lymphoid_tissue(6)|central_nervous_system(3)|urinary_tract(1)|lung(1)|skin(1)	12								T	ABL1| FGFR1|JAK2 	CML|ALL|AML								---	---	---	---
MMP11	4320	broad.mit.edu	37	22	24121421	24121421	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24121421T>C	uc002zxx.2	+	2	178	c.156T>C	c.(154-156)CAT>CAC	p.H52H	MMP11_uc002zxy.2_RNA|MMP11_uc002zxz.2_5'Flank	NM_005940	NP_005931	P24347	MMP11_HUMAN	matrix metalloproteinase 11 preproprotein	52					collagen catabolic process|multicellular organismal development|proteolysis	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding			skin(2)|large_intestine(1)	3		Medulloblastoma(6;9.86e-08)|all_neural(6;0.000318)																---	---	---	---
MMP11	4320	broad.mit.edu	37	22	24122630	24122630	+	Silent	SNP	G	A	A	rs144331076		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24122630G>A	uc002zxx.2	+	3	445	c.423G>A	c.(421-423)ACG>ACA	p.T141T	MMP11_uc002zxy.2_RNA|MMP11_uc002zxz.2_5'Flank	NM_005940	NP_005931	P24347	MMP11_HUMAN	matrix metalloproteinase 11 preproprotein	141					collagen catabolic process|multicellular organismal development|proteolysis	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding			skin(2)|large_intestine(1)	3		Medulloblastoma(6;9.86e-08)|all_neural(6;0.000318)																---	---	---	---
MMP11	4320	broad.mit.edu	37	22	24123153	24123153	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24123153C>A	uc002zxx.2	+	5	746	c.724C>A	c.(724-726)CCA>ACA	p.P242T	MMP11_uc002zxy.2_RNA|MMP11_uc002zxz.2_5'Flank	NM_005940	NP_005931	P24347	MMP11_HUMAN	matrix metalloproteinase 11 preproprotein	242					collagen catabolic process|multicellular organismal development|proteolysis	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding			skin(2)|large_intestine(1)	3		Medulloblastoma(6;9.86e-08)|all_neural(6;0.000318)																---	---	---	---
GSTT1	2952	broad.mit.edu	37	22	24384180	24384180	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24384180A>G	uc002zze.3	-	1	105	c.52T>C	c.(52-54)TAC>CAC	p.Y18H	GSTT1_uc002zzf.3_RNA|GSTT1_uc010gug.2_RNA|GSTT1_uc011ajl.1_5'UTR|GSTT1_uc010guh.2_RNA|GSTT1_uc010gui.1_RNA	NM_000853	NP_000844	P30711	GSTT1_HUMAN	glutathione S-transferase theta 1	18	GST N-terminal.				glutathione metabolic process	cytosol|soluble fraction	glutathione peroxidase activity|glutathione transferase activity			ovary(1)	1					Glutathione(DB00143)									Myelodysplasia_and_Acute_Myeloid_Leukemia_(AML)_Familial				---	---	---	---
CABIN1	23523	broad.mit.edu	37	22	24456456	24456456	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24456456G>A	uc002zzi.1	+	12	1596	c.1469G>A	c.(1468-1470)CGC>CAC	p.R490H	CABIN1_uc002zzj.1_Missense_Mutation_p.R440H|CABIN1_uc002zzl.1_Missense_Mutation_p.R490H	NM_012295	NP_036427	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	490					cell surface receptor linked signaling pathway|chromatin modification	nucleus	protein phosphatase inhibitor activity			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	5																		---	---	---	---
CABIN1	23523	broad.mit.edu	37	22	24459538	24459538	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24459538C>A	uc002zzi.1	+	14	1940	c.1813C>A	c.(1813-1815)CTG>ATG	p.L605M	CABIN1_uc002zzj.1_Missense_Mutation_p.L555M|CABIN1_uc002zzl.1_Missense_Mutation_p.L605M	NM_012295	NP_036427	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	605					cell surface receptor linked signaling pathway|chromatin modification	nucleus	protein phosphatase inhibitor activity			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	5																		---	---	---	---
CABIN1	23523	broad.mit.edu	37	22	24460544	24460544	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24460544T>C	uc002zzi.1	+	15	2058	c.1931T>C	c.(1930-1932)ATG>ACG	p.M644T	CABIN1_uc002zzj.1_Missense_Mutation_p.M594T|CABIN1_uc002zzl.1_Missense_Mutation_p.M644T	NM_012295	NP_036427	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	644	TPR 4.				cell surface receptor linked signaling pathway|chromatin modification	nucleus	protein phosphatase inhibitor activity			ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	5																		---	---	---	---
SUSD2	56241	broad.mit.edu	37	22	24584195	24584195	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24584195C>T	uc002zzn.1	+	14	2388	c.2344C>T	c.(2344-2346)CGC>TGC	p.R782C		NM_019601	NP_062547	Q9UGT4	SUSD2_HUMAN	sushi domain containing 2 precursor	782	Extracellular (Potential).				immune response	integral to membrane	polysaccharide binding|protein binding|scavenger receptor activity			skin(1)	1																		---	---	---	---
SUSD2	56241	broad.mit.edu	37	22	24584205	24584205	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24584205C>T	uc002zzn.1	+	14	2398	c.2354C>T	c.(2353-2355)GCG>GTG	p.A785V		NM_019601	NP_062547	Q9UGT4	SUSD2_HUMAN	sushi domain containing 2 precursor	785	Extracellular (Potential).				immune response	integral to membrane	polysaccharide binding|protein binding|scavenger receptor activity			skin(1)	1																		---	---	---	---
GGT5	2687	broad.mit.edu	37	22	24621267	24621267	+	Silent	SNP	C	T	T	rs139383582		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24621267C>T	uc002zzo.3	-	10	1866	c.1449G>A	c.(1447-1449)TCG>TCA	p.S483S	GGT5_uc002zzp.3_Silent_p.S484S|GGT5_uc002zzr.3_Silent_p.S451S|GGT5_uc002zzq.3_Silent_p.S451S|GGT5_uc011ajm.1_Silent_p.S407S	NM_004121	NP_004112	P36269	GGT5_HUMAN	gamma-glutamyltransferase 5 isoform b	483	Extracellular (Potential).				glutathione biosynthetic process|hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process	integral to membrane|plasma membrane	acyltransferase activity|gamma-glutamyltransferase activity			ovary(2)|skin(1)	3																		---	---	---	---
GGT5	2687	broad.mit.edu	37	22	24622188	24622188	+	Missense_Mutation	SNP	C	T	T	rs149456868		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24622188C>T	uc002zzo.3	-	8	1502	c.1085G>A	c.(1084-1086)CGC>CAC	p.R362H	GGT5_uc002zzp.3_Missense_Mutation_p.R362H|GGT5_uc002zzr.3_Missense_Mutation_p.R330H|GGT5_uc002zzq.3_Missense_Mutation_p.R330H|GGT5_uc011ajm.1_Missense_Mutation_p.R285H|GGT5_uc011ajn.1_RNA	NM_004121	NP_004112	P36269	GGT5_HUMAN	gamma-glutamyltransferase 5 isoform b	362	Extracellular (Potential).				glutathione biosynthetic process|hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process	integral to membrane|plasma membrane	acyltransferase activity|gamma-glutamyltransferase activity			ovary(2)|skin(1)	3																		---	---	---	---
PIWIL3	440822	broad.mit.edu	37	22	25131777	25131777	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25131777A>G	uc003abd.1	-	13	1949	c.1532T>C	c.(1531-1533)CTC>CCC	p.L511P	PIWIL3_uc011ajx.1_Missense_Mutation_p.L402P|PIWIL3_uc011ajy.1_Missense_Mutation_p.L402P|PIWIL3_uc010gut.1_Missense_Mutation_p.L511P	NM_001008496	NP_001008496	Q7Z3Z3	PIWL3_HUMAN	piwi-like 3	511					cell differentiation|gene silencing by RNA|meiosis|multicellular organismal development|regulation of translation|spermatogenesis	cytoplasm	RNA binding			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
MYO18B	84700	broad.mit.edu	37	22	26423303	26423303	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:26423303A>G	uc003abz.1	+	43	7613	c.7363A>G	c.(7363-7365)ACC>GCC	p.T2455A	MYO18B_uc003aca.1_Missense_Mutation_p.T2336A|MYO18B_uc010guy.1_Missense_Mutation_p.T2337A|MYO18B_uc010guz.1_Missense_Mutation_p.T2335A|MYO18B_uc011aka.1_Missense_Mutation_p.T1609A|MYO18B_uc011akb.1_Missense_Mutation_p.T1968A|MYO18B_uc010gva.1_Missense_Mutation_p.T438A|MYO18B_uc010gvb.1_RNA	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2455						nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity	p.P2455S(1)		ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12																		---	---	---	---
CHEK2	11200	broad.mit.edu	37	22	29130437	29130437	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29130437G>T	uc003adu.1	-	2	345	c.273C>A	c.(271-273)GCC>GCA	p.A91A	CHEK2_uc003ads.1_5'UTR|CHEK2_uc010gvh.1_Silent_p.A91A|CHEK2_uc010gvi.1_Silent_p.A91A|CHEK2_uc010gvj.1_RNA|CHEK2_uc003adr.1_RNA|CHEK2_uc010gvk.1_RNA|CHEK2_uc003adt.1_Silent_p.A91A|CHEK2_uc003adv.1_Silent_p.A91A|CHEK2_uc003adw.1_Silent_p.A91A|CHEK2_uc003adx.1_5'UTR|CHEK2_uc003ady.1_Silent_p.A91A|CHEK2_uc003adz.1_5'UTR	NM_007194	NP_009125	O96017	CHK2_HUMAN	protein kinase CHK2 isoform a	91					cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			central_nervous_system(17)|stomach(1)|ovary(1)|lung(1)	20								F			breast 		Direct_reversal_of_damage|Other_conserved_DNA_damage_response_genes	Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|CHEK2-associated_cancer				---	---	---	---
EMID1	129080	broad.mit.edu	37	22	29630164	29630164	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29630164C>T	uc003aen.2	+	11	1074	c.999C>T	c.(997-999)GGC>GGT	p.G333G	EMID1_uc003aem.2_Silent_p.G335G|EMID1_uc003aeo.2_Silent_p.G335G|EMID1_uc003aep.2_Intron	NM_133455	NP_597712	Q96A84	EMID1_HUMAN	EMI domain containing 1	333	Collagen-like.					collagen					0																		---	---	---	---
EWSR1	2130	broad.mit.edu	37	22	29674091	29674091	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29674091C>T	uc003aet.2	+	5	627	c.299C>T	c.(298-300)ACC>ATC	p.T100I	EWSR1_uc003aes.3_Missense_Mutation_p.T100I|EWSR1_uc003aev.2_Missense_Mutation_p.T106I|EWSR1_uc003aew.2_Missense_Mutation_p.T100I|EWSR1_uc003aex.2_Missense_Mutation_p.T100I|EWSR1_uc003aey.2_5'UTR	NM_005243	NP_005234	Q01844	EWS_HUMAN	Ewing sarcoma breakpoint region 1 isoform 2	100	11.|EAD (Gln/Pro/Thr-rich).|31 X approximate tandem repeats.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	calmodulin binding|nucleotide binding|RNA binding|zinc ion binding		EWSR1/FLI1(2266)|EWSR1/ATF1(323)|EWSR1/WT1(231)|EWSR1/ERG(162)|EWSR1/NR4A3(140)|EWSR1/DDIT3(43)|EWSR1/CREB1(42)|EWSR1/FEV(10)|EWSR1/POU5F1(10)|EWSR1/ETV1(7)|EWSR1/ETV4(6)|EWSR1/ZNF384(4)|EWSR1/PBX1(3)|EWSR1/SP3(3)|EWSR1/PATZ1(2)	bone(2526)|soft_tissue(702)|skin(8)|autonomic_ganglia(4)|haematopoietic_and_lymphoid_tissue(4)|salivary_gland(2)|central_nervous_system(2)|NS(2)|pancreas(2)|lung(1)|ovary(1)	3254								T	FLI1|ERG|ZNF278|NR4A3|FEV|ATF1|ETV1|ETV4|WT1|ZNF384|CREB1|POU5F1| PBX1	Ewing sarcoma| desmoplastic small round cell tumor |ALL|clear cell sarcoma|sarcoma|myoepithelioma								---	---	---	---
EWSR1	2130	broad.mit.edu	37	22	29692343	29692343	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29692343G>A	uc003aet.2	+	12	1607	c.1279G>A	c.(1279-1281)GTG>ATG	p.V427M	EWSR1_uc003aev.2_Missense_Mutation_p.V432M|EWSR1_uc003aew.2_Missense_Mutation_p.V371M|EWSR1_uc003aex.2_Missense_Mutation_p.V426M|EWSR1_uc003aey.2_Missense_Mutation_p.V222M|EWSR1_uc003aez.2_Missense_Mutation_p.V88M	NM_005243	NP_005234	Q01844	EWS_HUMAN	Ewing sarcoma breakpoint region 1 isoform 2	427	RRM.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	calmodulin binding|nucleotide binding|RNA binding|zinc ion binding		EWSR1/FLI1(2266)|EWSR1/ATF1(323)|EWSR1/WT1(231)|EWSR1/ERG(162)|EWSR1/NR4A3(140)|EWSR1/DDIT3(43)|EWSR1/CREB1(42)|EWSR1/FEV(10)|EWSR1/POU5F1(10)|EWSR1/ETV1(7)|EWSR1/ETV4(6)|EWSR1/ZNF384(4)|EWSR1/PBX1(3)|EWSR1/SP3(3)|EWSR1/PATZ1(2)	bone(2526)|soft_tissue(702)|skin(8)|autonomic_ganglia(4)|haematopoietic_and_lymphoid_tissue(4)|salivary_gland(2)|central_nervous_system(2)|NS(2)|pancreas(2)|lung(1)|ovary(1)	3254								T	FLI1|ERG|ZNF278|NR4A3|FEV|ATF1|ETV1|ETV4|WT1|ZNF384|CREB1|POU5F1| PBX1	Ewing sarcoma| desmoplastic small round cell tumor |ALL|clear cell sarcoma|sarcoma|myoepithelioma								---	---	---	---
THOC5	8563	broad.mit.edu	37	22	29907096	29907096	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:29907096T>C	uc003afr.2	-	20	2322	c.1987A>G	c.(1987-1989)AGG>GGG	p.R663G	THOC5_uc003afq.2_Missense_Mutation_p.R324G|THOC5_uc003afs.2_Missense_Mutation_p.R663G|THOC5_uc003aft.2_Missense_Mutation_p.R663G|THOC5_uc003afu.2_Missense_Mutation_p.R663G|THOC5_uc010gvo.2_Missense_Mutation_p.R407G	NM_001002878	NP_001002878	Q13769	THOC5_HUMAN	THO complex 5	663					intronless viral mRNA export from host nucleus|monocyte differentiation|mRNA processing|primitive hemopoiesis|RNA splicing	cytoplasm|intermediate filament cytoskeleton|THO complex part of transcription export complex	protein binding|RNA binding			breast(3)	3																		---	---	---	---
LIF	3976	broad.mit.edu	37	22	30640779	30640779	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30640779G>A	uc003agz.2	-	2	275	c.163C>T	c.(163-165)CTC>TTC	p.L55F	LIF_uc011aks.1_Intron|uc003aha.2_5'Flank	NM_002309	NP_002300	P15018	LIF_HUMAN	leukemia inhibitory factor (cholinergic	55					immune response|leukemia inhibitory factor signaling pathway|negative regulation of hormone secretion|positive regulation of cell proliferation|positive regulation of macrophage differentiation|positive regulation of MAPKKK cascade|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis|positive regulation of peptidyl-serine phosphorylation of STAT protein|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tyrosine phosphorylation of Stat1 protein|positive regulation of tyrosine phosphorylation of Stat3 protein|regulation of metanephric nephron tubule epithelial cell differentiation		cytokine activity|growth factor activity|leukemia inhibitory factor receptor binding				0			Epithelial(10;0.171)															---	---	---	---
OSM	5008	broad.mit.edu	37	22	30660107	30660107	+	Missense_Mutation	SNP	G	A	A	rs145296302		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30660107G>A	uc003ahb.2	-	3	576	c.524C>T	c.(523-525)CCG>CTG	p.P175L		NM_020530	NP_065391	P13725	ONCM_HUMAN	oncostatin M precursor	175					cell proliferation|immune response|negative regulation of cell proliferation|negative regulation of hormone secretion|positive regulation of cell division|positive regulation of cell proliferation|positive regulation of MAPKKK cascade|positive regulation of peptidyl-serine phosphorylation|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of transcription from RNA polymerase II promoter|regulation of growth	extracellular space|oncostatin-M receptor complex	cytokine activity|growth factor activity|oncostatin-M receptor binding			skin(1)	1			Epithelial(10;0.206)															---	---	---	---
SEC14L2	23541	broad.mit.edu	37	22	30803546	30803546	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30803546G>A	uc003ahr.2	+	5	550	c.377G>A	c.(376-378)CGG>CAG	p.R126Q	SEC14L2_uc003ahq.2_Missense_Mutation_p.R126Q|SEC14L2_uc011akx.1_Missense_Mutation_p.R72Q|SEC14L2_uc003ahs.2_Missense_Mutation_p.R52Q|SEC14L2_uc011aky.1_Intron|SEC14L2_uc003aht.2_5'Flank|SEC14L2_uc003ahu.3_5'Flank|SEC14L2_uc010gvv.2_5'Flank|SEC14L2_uc010gvw.1_5'Flank|MTP18_uc010gvx.1_5'Flank|MTP18_uc003ahv.1_5'Flank|MTP18_uc010gvy.1_5'Flank	NM_012429	NP_036561	O76054	S14L2_HUMAN	SEC14-like 2 isoform 1	126	CRAL-TRIO.				positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane|nucleus	phospholipid binding|transporter activity|vitamin E binding				0					Vitamin E(DB00163)													---	---	---	---
SEC14L3	266629	broad.mit.edu	37	22	30864639	30864639	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:30864639A>G	uc003ahy.2	-	5	368	c.279T>C	c.(277-279)CGT>CGC	p.R93R	SEC14L3_uc003ahz.2_Silent_p.R16R|SEC14L3_uc003aia.2_Silent_p.R34R|SEC14L3_uc003aib.2_Silent_p.R34R	NM_174975	NP_777635	Q9UDX4	S14L3_HUMAN	SEC14-like 3	93	CRAL-TRIO.					integral to membrane|intracellular	lipid binding|transporter activity			ovary(3)|pancreas(1)|skin(1)	5					Vitamin E(DB00163)													---	---	---	---
DEPDC5	9681	broad.mit.edu	37	22	32194580	32194580	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32194580A>G	uc003als.2	+	14	1026	c.884A>G	c.(883-885)CAA>CGA	p.Q295R	DEPDC5_uc011als.1_Missense_Mutation_p.Q295R|DEPDC5_uc011alu.1_Missense_Mutation_p.Q295R|DEPDC5_uc011alv.1_RNA|DEPDC5_uc003alt.2_Missense_Mutation_p.Q295R|DEPDC5_uc003alr.1_Missense_Mutation_p.Q295R|DEPDC5_uc011alt.1_Missense_Mutation_p.Q267R	NM_014662	NP_055477	O75140	DEPD5_HUMAN	DEP domain containing 5 isoform 1	295					intracellular signal transduction					ovary(4)|central_nervous_system(3)|pancreas(1)	8																		---	---	---	---
DEPDC5	9681	broad.mit.edu	37	22	32275554	32275554	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32275554G>T	uc003als.2	+	37	3898	c.3756G>T	c.(3754-3756)GTG>GTT	p.V1252V	DEPDC5_uc011als.1_Silent_p.V1183V|DEPDC5_uc011alu.1_Silent_p.V1283V|DEPDC5_uc011alv.1_RNA|DEPDC5_uc003alt.2_Silent_p.V1274V|DEPDC5_uc003alu.2_Silent_p.V701V|DEPDC5_uc003alv.2_RNA|DEPDC5_uc003alw.2_Silent_p.V550V|DEPDC5_uc011alx.1_Silent_p.V100V|DEPDC5_uc010gwk.2_Silent_p.V278V|DEPDC5_uc011aly.1_Silent_p.V100V	NM_014662	NP_055477	O75140	DEPD5_HUMAN	DEP domain containing 5 isoform 1	1252					intracellular signal transduction					ovary(4)|central_nervous_system(3)|pancreas(1)	8																		---	---	---	---
Unknown	0	broad.mit.edu	37	22	32435615	32435615	+	IGR	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32435615G>A								YWHAH (82026 upstream) : SLC5A1 (3422 downstream)																																			---	---	---	---
LARGE	9215	broad.mit.edu	37	22	33960906	33960906	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:33960906T>C	uc003and.3	-	7	1294	c.715A>G	c.(715-717)ATC>GTC	p.I239V	LARGE_uc011amd.1_Missense_Mutation_p.I38V|LARGE_uc003ane.3_Missense_Mutation_p.I239V|LARGE_uc010gwp.2_Missense_Mutation_p.I239V|LARGE_uc011ame.1_Missense_Mutation_p.I171V|LARGE_uc011amf.1_Missense_Mutation_p.I239V|LARGE_uc010gwq.1_RNA	NM_004737	NP_004728	O95461	LARGE_HUMAN	like-glycosyltransferase	239	Lumenal (Potential).				glycosphingolipid biosynthetic process|muscle cell homeostasis|N-acetylglucosamine metabolic process|protein glycosylation	integral to Golgi membrane	acetylglucosaminyltransferase activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(1;0.219)																---	---	---	---
LARGE	9215	broad.mit.edu	37	22	34046425	34046425	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:34046425C>T	uc003and.3	-	4	915	c.336G>A	c.(334-336)GAG>GAA	p.E112E	LARGE_uc003ane.3_Silent_p.E112E|LARGE_uc010gwp.2_Silent_p.E112E|LARGE_uc011ame.1_Silent_p.E44E|LARGE_uc011amf.1_Silent_p.E112E	NM_004737	NP_004728	O95461	LARGE_HUMAN	like-glycosyltransferase	112	Lumenal (Potential).				glycosphingolipid biosynthetic process|muscle cell homeostasis|N-acetylglucosamine metabolic process|protein glycosylation	integral to Golgi membrane	acetylglucosaminyltransferase activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(1;0.219)																---	---	---	---
MCM5	4174	broad.mit.edu	37	22	35808601	35808601	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35808601G>A	uc003anu.3	+	8	1112	c.1018G>A	c.(1018-1020)GCC>ACC	p.A340T	MCM5_uc010gwr.2_Missense_Mutation_p.A149T|MCM5_uc003anv.3_Missense_Mutation_p.A297T|MCM5_uc010gws.1_RNA|MCM5_uc003anw.1_Missense_Mutation_p.A124T	NM_006739	NP_006730	P33992	MCM5_HUMAN	minichromosome maintenance complex component 5	340	MCM.				cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	MCM complex	ATP binding|DNA binding|helicase activity|protein binding			ovary(1)	1																		---	---	---	---
APOL5	80831	broad.mit.edu	37	22	36122795	36122795	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36122795G>A	uc003aof.2	+	3	680	c.680G>A	c.(679-681)GGC>GAC	p.G227D		NM_030642	NP_085145	Q9BWW9	APOL5_HUMAN	apolipoprotein L5	227					lipid metabolic process|lipid transport|lipoprotein metabolic process	cytoplasm|extracellular region	high-density lipoprotein particle binding|lipid binding|protein binding				0																		---	---	---	---
APOL1	8542	broad.mit.edu	37	22	36661851	36661851	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36661851A>G	uc003apf.2	+	6	1137	c.969A>G	c.(967-969)GAA>GAG	p.E323E	APOL1_uc011amn.1_Silent_p.E200E|APOL1_uc003apc.2_RNA|APOL1_uc003ape.2_Silent_p.E339E|APOL1_uc011amo.1_Silent_p.E200E|APOL1_uc011amp.1_Silent_p.E323E|APOL1_uc011amq.1_Silent_p.E305E|APOL1_uc010gwx.2_Silent_p.E200E	NM_003661	NP_003652	O14791	APOL1_HUMAN	apolipoprotein L1 isoform a precursor	323					cholesterol metabolic process|cytolysis|innate immune response|killing of cells of other organism|lipid transport|lipoprotein metabolic process	high-density lipoprotein particle|very-low-density lipoprotein particle	chloride channel activity|lipid binding|protein binding			breast(2)|ovary(1)	3																		---	---	---	---
EIF3D	8664	broad.mit.edu	37	22	36907587	36907587	+	Missense_Mutation	SNP	A	C	C	rs142855354		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36907587A>C	uc003apq.2	-	14	1712	c.1596T>G	c.(1594-1596)GAT>GAG	p.D532E	EIF3D_uc011amr.1_Missense_Mutation_p.D359E|EIF3D_uc003apr.2_Missense_Mutation_p.D532E|EIF3D_uc011ams.1_Missense_Mutation_p.D435E|EIF3D_uc011amt.1_Missense_Mutation_p.D483E	NM_003753	NP_003744	O15371	EIF3D_HUMAN	eukaryotic translation initiation factor 3	532	Asp/Glu-rich (highly acidic).					cytosol|eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			pancreas(1)	1																OREG0026522	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
EIF3D	8664	broad.mit.edu	37	22	36907593	36907593	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36907593A>C	uc003apq.2	-	14	1706	c.1590T>G	c.(1588-1590)GAT>GAG	p.D530E	EIF3D_uc011amr.1_Missense_Mutation_p.D357E|EIF3D_uc003apr.2_Missense_Mutation_p.D530E|EIF3D_uc011ams.1_Missense_Mutation_p.D433E|EIF3D_uc011amt.1_Missense_Mutation_p.D481E	NM_003753	NP_003744	O15371	EIF3D_HUMAN	eukaryotic translation initiation factor 3	530	Asp/Glu-rich (highly acidic).					cytosol|eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			pancreas(1)	1																OREG0026522	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
EIF3D	8664	broad.mit.edu	37	22	36912644	36912644	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36912644A>G	uc003apq.2	-	12	1203	c.1087T>C	c.(1087-1089)TGG>CGG	p.W363R	EIF3D_uc011amr.1_Missense_Mutation_p.W190R|EIF3D_uc003apr.2_Missense_Mutation_p.W363R|EIF3D_uc011ams.1_Missense_Mutation_p.W266R|EIF3D_uc011amt.1_Missense_Mutation_p.W314R	NM_003753	NP_003744	O15371	EIF3D_HUMAN	eukaryotic translation initiation factor 3	363						cytosol|eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			pancreas(1)	1																		---	---	---	---
CSF2RB	1439	broad.mit.edu	37	22	37331710	37331710	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37331710G>T	uc003aqa.3	+	12	1662	c.1445G>T	c.(1444-1446)AGC>ATC	p.S482I	CSF2RB_uc003aqc.3_Missense_Mutation_p.S488I	NM_000395	NP_000386	P32927	IL3RB_HUMAN	colony stimulating factor 2 receptor, beta	482	Box 1 motif.|Cytoplasmic (Potential).				respiratory gaseous exchange	granulocyte macrophage colony-stimulating factor receptor complex	cytokine receptor activity			skin(2)|pancreas(1)	3					Sargramostim(DB00020)													---	---	---	---
SSTR3	6753	broad.mit.edu	37	22	37602945	37602945	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37602945C>T	uc003ara.2	-	2	960	c.898G>A	c.(898-900)GCG>ACG	p.A300T	SSTR3_uc003arb.2_Missense_Mutation_p.A300T	NM_001051	NP_001042	P32745	SSR3_HUMAN	somatostatin receptor 3	300	Helical; Name=7; (Potential).				G-protein signaling, coupled to cyclic nucleotide second messenger|induction of apoptosis by hormones|negative regulation of cell proliferation	integral to plasma membrane|nonmotile primary cilium	somatostatin receptor activity			lung(1)	1																		---	---	---	---
CARD10	29775	broad.mit.edu	37	22	37888489	37888489	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37888489G>A	uc003asx.1	-	18	2707	c.2704C>T	c.(2704-2706)CCT>TCT	p.P902S	CARD10_uc003ast.1_RNA|CARD10_uc003asu.1_5'UTR|CARD10_uc003asv.1_5'UTR|CARD10_uc011ank.1_Missense_Mutation_p.P220S|CARD10_uc003asw.1_Missense_Mutation_p.P616S|CARD10_uc003asy.1_Missense_Mutation_p.P902S	NM_014550	NP_055365	Q9BWT7	CAR10_HUMAN	caspase recruitment domain protein 10	902					activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis	CBM complex	receptor signaling complex scaffold activity			upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1)	6	Melanoma(58;0.0574)																	---	---	---	---
CARD10	29775	broad.mit.edu	37	22	37914112	37914112	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37914112C>T	uc003asx.1	-	2	242	c.239G>A	c.(238-240)CGC>CAC	p.R80H	CARD10_uc003ast.1_RNA|CARD10_uc003asy.1_Missense_Mutation_p.R80H	NM_014550	NP_055365	Q9BWT7	CAR10_HUMAN	caspase recruitment domain protein 10	80	CARD.				activation of NF-kappaB-inducing kinase activity|protein complex assembly|regulation of apoptosis	CBM complex	receptor signaling complex scaffold activity			upper_aerodigestive_tract(1)|lung(1)|breast(1)|ovary(1)|prostate(1)|kidney(1)	6	Melanoma(58;0.0574)																	---	---	---	---
LGALS2	3957	broad.mit.edu	37	22	37966581	37966581	+	Splice_Site	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37966581A>G	uc003ata.2	-	3	361	c.249_splice	c.e3+1	p.K83_splice		NM_006498	NP_006489			lectin, galactoside-binding, soluble, 2											breast(1)|skin(1)	2	Melanoma(58;0.0574)																	---	---	---	---
MICALL1	85377	broad.mit.edu	37	22	38321893	38321893	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38321893A>T	uc003aui.2	+	8	1392	c.1308A>T	c.(1306-1308)GAA>GAT	p.E436D		NM_033386	NP_203744	Q8N3F8	MILK1_HUMAN	molecule interacting with Rab13	436	Pro-rich.|Poly-Glu.					cytoplasm|cytoskeleton	protein binding|zinc ion binding			breast(1)	1	Melanoma(58;0.045)																	---	---	---	---
MICALL1	85377	broad.mit.edu	37	22	38328677	38328677	+	Missense_Mutation	SNP	G	A	A	rs146567866		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38328677G>A	uc003aui.2	+	11	2218	c.2134G>A	c.(2134-2136)GGC>AGC	p.G712S		NM_033386	NP_203744	Q8N3F8	MILK1_HUMAN	molecule interacting with Rab13	712						cytoplasm|cytoskeleton	protein binding|zinc ion binding			breast(1)	1	Melanoma(58;0.045)																	---	---	---	---
PLA2G6	8398	broad.mit.edu	37	22	38565395	38565395	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38565395G>A	uc003auy.1	-	2	175	c.39C>T	c.(37-39)GGC>GGT	p.G13G	PLA2G6_uc003auz.1_Silent_p.G13G|PLA2G6_uc003ava.1_Silent_p.G13G|PLA2G6_uc003avb.2_Silent_p.G13G|PLA2G6_uc010gxk.1_RNA|PLA2G6_uc011ano.1_Silent_p.G13G	NM_003560	NP_003551	O60733	PA2G6_HUMAN	phospholipase A2, group VI isoform a	13					cardiolipin biosynthetic process|cell death|lipid catabolic process	centrosome|membrane				ovary(1)	1	Melanoma(58;0.045)				Quinacrine(DB01103)													---	---	---	---
GTPBP1	9567	broad.mit.edu	37	22	39112978	39112978	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39112978C>T	uc003awg.2	+	4	961	c.807C>T	c.(805-807)GGC>GGT	p.G269G		NM_004286	NP_004277	O00178	GTPB1_HUMAN	GTP binding protein 1	269					immune response|positive regulation of mRNA catabolic process|signal transduction	cytoplasmic exosome (RNase complex)|cytosol	GTP binding|GTPase activity			ovary(1)	1	Melanoma(58;0.04)																	---	---	---	---
APOBEC3B	9582	broad.mit.edu	37	22	39380219	39380219	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39380219G>T	uc003awo.1	+	2	211	c.157G>T	c.(157-159)GGG>TGG	p.G53W	APOBEC3A_uc011aoc.1_Intron|APOBEC3B_uc003awp.1_Missense_Mutation_p.G53W|APOBEC3B_uc003awq.1_RNA|APOBEC3D_uc011aod.1_Intron|APOBEC3D_uc011aoe.1_Intron|APOBEC3D_uc011aof.1_Intron	NM_004900	NP_004891	Q9UH17	ABC3B_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic	53					negative regulation of transposition		hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines|RNA binding|zinc ion binding			ovary(1)	1	Melanoma(58;0.04)																	---	---	---	---
CACNA1I	8911	broad.mit.edu	37	22	40054262	40054262	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40054262C>A	uc003ayc.2	+	11	2098	c.2098C>A	c.(2098-2100)CTG>ATG	p.L700M	CACNA1I_uc003ayd.2_Missense_Mutation_p.L665M|CACNA1I_uc003aye.2_Missense_Mutation_p.L615M|CACNA1I_uc003ayf.2_Missense_Mutation_p.L580M	NM_021096	NP_066919	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type,	700	Cytoplasmic (Potential).|II.				axon guidance|signal transduction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity|protein binding			breast(1)|central_nervous_system(1)	2	Melanoma(58;0.0749)				Flunarizine(DB04841)|Paramethadione(DB00617)|Verapamil(DB00661)													---	---	---	---
CACNA1I	8911	broad.mit.edu	37	22	40054286	40054286	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40054286G>A	uc003ayc.2	+	11	2122	c.2122G>A	c.(2122-2124)GAC>AAC	p.D708N	CACNA1I_uc003ayd.2_Missense_Mutation_p.D673N|CACNA1I_uc003aye.2_Missense_Mutation_p.D623N|CACNA1I_uc003ayf.2_Missense_Mutation_p.D588N	NM_021096	NP_066919	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type,	708	Helical; Name=S3 of repeat II; (Potential).|II.				axon guidance|signal transduction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity|protein binding			breast(1)|central_nervous_system(1)	2	Melanoma(58;0.0749)				Flunarizine(DB04841)|Paramethadione(DB00617)|Verapamil(DB00661)													---	---	---	---
TNRC6B	23112	broad.mit.edu	37	22	40662535	40662535	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40662535A>C	uc011aor.1	+	5	2512	c.2301A>C	c.(2299-2301)AAA>AAC	p.K767N	TNRC6B_uc003aym.2_Intron|TNRC6B_uc003ayn.3_Missense_Mutation_p.K767N|TNRC6B_uc003ayo.2_Missense_Mutation_p.K571N	NM_001162501	NP_001155973	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B isoform 1	767					gene silencing by RNA|regulation of translation	cytoplasmic mRNA processing body	nucleotide binding|RNA binding				0																		---	---	---	---
ADSL	158	broad.mit.edu	37	22	40745896	40745896	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40745896A>G	uc003ayp.3	+	2	273	c.214A>G	c.(214-216)ATC>GTC	p.I72V	ADSL_uc003ays.3_Missense_Mutation_p.I72V|ADSL_uc003ayq.3_Missense_Mutation_p.I72V|ADSL_uc003ayr.3_5'UTR|ADSL_uc003ayt.3_Missense_Mutation_p.I72V	NM_000026	NP_000017	P30566	PUR8_HUMAN	adenylosuccinate lyase isoform a	72			I -> V (in ADSL deficiency; severe).		AMP biosynthetic process|protein tetramerization|purine base metabolic process	cytosol	(S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate AMP-lyase (fumarate-forming) activity|N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity			ovary(1)	1																		---	---	---	---
SGSM3	27352	broad.mit.edu	37	22	40803496	40803496	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:40803496G>A	uc003ayu.1	+	13	1657	c.1448G>A	c.(1447-1449)CGC>CAC	p.R483H	SGSM3_uc011aos.1_Missense_Mutation_p.R416H|SGSM3_uc011aot.1_Missense_Mutation_p.R420H|SGSM3_uc010gyd.1_Missense_Mutation_p.R554H	NM_015705	NP_056520	Q96HU1	SGSM3_HUMAN	small G protein signaling modulator 3	483	SH3.				cell cycle arrest|Rap protein signal transduction	cytoplasm	Rab GTPase activator activity|Rab GTPase binding			ovary(2)	2																		---	---	---	---
MCHR1	2847	broad.mit.edu	37	22	41077648	41077648	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41077648G>A	uc003ayz.2	+	2	1253	c.985G>A	c.(985-987)GCC>ACC	p.A329T	MCHR1_uc003aza.2_Missense_Mutation_p.A218T|uc003azb.1_RNA	NM_005297	NP_005288	Q99705	MCHR1_HUMAN	G protein-coupled receptor 24	329	Helical; Name=6; (Potential).				elevation of cytosolic calcium ion concentration|feeding behavior|generation of precursor metabolites and energy|inhibition of adenylate cyclase activity by G-protein signaling pathway	integral to plasma membrane|nonmotile primary cilium	neuropeptide receptor activity				0																		---	---	---	---
EP300	2033	broad.mit.edu	37	22	41560056	41560056	+	Splice_Site	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41560056G>T	uc003azl.3	+	22	4124	c.3729_splice	c.e22-1	p.L1243_splice		NM_001429	NP_001420			E1A binding protein p300						apoptosis|cell cycle|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|histone H4 acetylation|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of androgen receptor signaling pathway|response to estrogen stimulus|response to hypoxia	centrosome|histone acetyltransferase complex	androgen receptor binding|beta-catenin binding|DNA binding|histone acetyltransferase activity|RNA polymerase II activating transcription factor binding|transcription coactivator activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(22)|large_intestine(13)|breast(9)|central_nervous_system(5)|upper_aerodigestive_tract(4)|pancreas(4)|lung(3)|ovary(2)|stomach(1)|skin(1)	64								T| N|F|Mis|O	MLL|RUNXBP2	colorectal|breast|pancreatic|AML|ALL|DLBCL				Rubinstein-Taybi_syndrome				---	---	---	---
L3MBTL2	83746	broad.mit.edu	37	22	41626162	41626162	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41626162G>T	uc003azo.2	+	17	2079	c.2025G>T	c.(2023-2025)AAG>AAT	p.K675N	L3MBTL2_uc003azn.2_RNA|CHADL_uc003azq.3_Intron|CHADL_uc010gyj.2_Intron	NM_031488	NP_113676	Q969R5	LMBL2_HUMAN	l(3)mbt-like 2	675					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	methylated histone residue binding|transcription corepressor activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
ACO2	50	broad.mit.edu	37	22	41920873	41920873	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41920873G>A	uc003bac.2	+	13	1528	c.1506G>A	c.(1504-1506)GCG>GCA	p.A502A	ACO2_uc003bad.2_Silent_p.A527A	NM_001098	NP_001089	Q99798	ACON_HUMAN	aconitase 2, mitochondrial precursor	502					citrate metabolic process|tricarboxylic acid cycle	mitochondrial matrix|nucleus	4 iron, 4 sulfur cluster binding|aconitate hydratase activity|citrate hydro-lyase (cis-aconitate-forming) activity|iron ion binding|isocitrate hydro-lyase (cis-aconitate-forming) activity			breast(2)|ovary(1)|lung(1)	4																		---	---	---	---
TCF20	6942	broad.mit.edu	37	22	42605766	42605766	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42605766C>A	uc003bcj.1	-	1	5680	c.5546G>T	c.(5545-5547)AGC>ATC	p.S1849I	TCF20_uc003bck.1_Missense_Mutation_p.S1849I|TCF20_uc003bnt.2_Missense_Mutation_p.S1849I	NM_005650	NP_005641	Q9UGU0	TCF20_HUMAN	transcription factor 20 isoform 1	1849					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription coactivator activity|zinc ion binding			ovary(4)|skin(1)	5																		---	---	---	---
TCF20	6942	broad.mit.edu	37	22	42607709	42607709	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42607709G>A	uc003bcj.1	-	1	3737	c.3603C>T	c.(3601-3603)AGC>AGT	p.S1201S	TCF20_uc003bck.1_Silent_p.S1201S|TCF20_uc003bnt.2_Silent_p.S1201S	NM_005650	NP_005641	Q9UGU0	TCF20_HUMAN	transcription factor 20 isoform 1	1201					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription coactivator activity|zinc ion binding			ovary(4)|skin(1)	5																		---	---	---	---
TTLL1	25809	broad.mit.edu	37	22	43459836	43459836	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43459836C>T	uc003bdi.2	-	7	971	c.730G>A	c.(730-732)GCC>ACC	p.A244T	TTLL1_uc010gzh.2_Missense_Mutation_p.A244T|TTLL1_uc003bdj.2_Missense_Mutation_p.A130T|TTLL1_uc003bdh.2_Missense_Mutation_p.A206T	NM_012263	NP_036395	O95922	TTLL1_HUMAN	tubulin tyrosine ligase-like family, member 1	244	TTL.				protein polyglutamylation	cytoplasm|microtubule	ATP binding|tubulin-glutamic acid ligase activity|tubulin-tyrosine ligase activity			skin(1)	1		Ovarian(80;0.0694)		BRCA - Breast invasive adenocarcinoma(115;0.00461)														---	---	---	---
TTLL12	23170	broad.mit.edu	37	22	43563183	43563183	+	3'UTR	SNP	G	A	A	rs151316744	by1000genomes	TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43563183G>A	uc003bdq.2	-	14					TTLL12_uc003bdp.2_3'UTR|TTLL12_uc003bdr.1_3'UTR	NM_015140	NP_055955			tubulin tyrosine ligase-like family, member 12						protein modification process		tubulin-tyrosine ligase activity			central_nervous_system(1)	1		Ovarian(80;0.221)|Glioma(61;0.222)																---	---	---	---
TTLL12	23170	broad.mit.edu	37	22	43570575	43570575	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43570575G>A	uc003bdq.2	-	7	996	c.964C>T	c.(964-966)CGC>TGC	p.R322C	TTLL12_uc003bdr.1_Missense_Mutation_p.R322C	NM_015140	NP_055955	Q14166	TTL12_HUMAN	tubulin tyrosine ligase-like family, member 12	322	TTL.				protein modification process		tubulin-tyrosine ligase activity			central_nervous_system(1)	1		Ovarian(80;0.221)|Glioma(61;0.222)																---	---	---	---
SCUBE1	80274	broad.mit.edu	37	22	43614342	43614342	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43614342C>T	uc003bdt.1	-	15	1898	c.1810G>A	c.(1810-1812)GAG>AAG	p.E604K		NM_173050	NP_766638	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1	604					adult heart development|blood coagulation|endothelial cell differentiation|inflammatory response|post-embryonic development|protein homooligomerization	external side of plasma membrane|extracellular space|extrinsic to plasma membrane	calcium ion binding|identical protein binding|protein heterodimerization activity			central_nervous_system(2)|ovary(1)|lung(1)|skin(1)	5		all_neural(38;0.0414)|Ovarian(80;0.07)																---	---	---	---
EFCAB6	64800	broad.mit.edu	37	22	44022459	44022459	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44022459T>C	uc003bdy.1	-	20	2548	c.2333A>G	c.(2332-2334)AAA>AGA	p.K778R	EFCAB6_uc003bdz.1_Missense_Mutation_p.K626R|EFCAB6_uc010gzi.1_Missense_Mutation_p.K626R|EFCAB6_uc010gzj.1_Missense_Mutation_p.K76R|EFCAB6_uc010gzk.1_RNA	NM_022785	NP_073622	Q5THR3	EFCB6_HUMAN	CAP-binding protein complex interacting protein	778					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	calcium ion binding			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	7		Ovarian(80;0.0247)|all_neural(38;0.025)																---	---	---	---
PARVG	64098	broad.mit.edu	37	22	44594549	44594549	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:44594549T>C	uc011aqe.1	+	12	1184	c.760T>C	c.(760-762)TTC>CTC	p.F254L	PARVG_uc003bep.2_Missense_Mutation_p.F254L|PARVG_uc011aqf.1_Missense_Mutation_p.F254L|PARVG_uc003beq.2_RNA|PARVG_uc003ber.2_RNA	NM_001137605	NP_001131077	Q9HBI0	PARVG_HUMAN	parvin, gamma	254	CH 2.				cell-matrix adhesion	cytoplasm|cytoskeleton|focal adhesion	actin binding				0		Ovarian(80;0.024)|all_neural(38;0.0299)																---	---	---	---
GTSE1	51512	broad.mit.edu	37	22	46704680	46704680	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46704680G>A	uc011aqy.1	+	4	814	c.602G>A	c.(601-603)CGG>CAG	p.R201Q	GTSE1_uc011aqz.1_Missense_Mutation_p.R48Q	NM_016426	NP_057510	Q9NYZ3	GTSE1_HUMAN	G-2 and S-phase expressed 1	182					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G2 phase of mitotic cell cycle|microtubule-based process	cytoplasmic microtubule				ovary(1)	1		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00462)														---	---	---	---
CELSR1	9620	broad.mit.edu	37	22	46765103	46765103	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:46765103T>A	uc003bhw.1	-	27	7925	c.7925A>T	c.(7924-7926)CAC>CTC	p.H2642L	CELSR1_uc011arc.1_Silent_p.A1107A	NM_014246	NP_055061	Q9NYQ6	CELR1_HUMAN	cadherin EGF LAG seven-pass G-type receptor 1	2642	Cytoplasmic (Potential).				central nervous system development|homophilic cell adhesion|neural tube closure|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein dimerization activity			lung(4)|breast(4)|pancreas(2)|skin(1)	11		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)														---	---	---	---
BRD1	23774	broad.mit.edu	37	22	50191596	50191596	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50191596G>A	uc003biv.2	-	5	2442	c.1955C>T	c.(1954-1956)GCG>GTG	p.A652V	BRD1_uc011arf.1_Missense_Mutation_p.A247V|BRD1_uc011arg.1_Missense_Mutation_p.A701V|BRD1_uc011arh.1_Missense_Mutation_p.A652V|BRD1_uc003biu.3_Missense_Mutation_p.A652V	NM_014577	NP_055392	O95696	BRD1_HUMAN	bromodomain containing protein 1	652					histone H3 acetylation	MOZ/MORF histone acetyltransferase complex	zinc ion binding			pancreas(1)	1		all_cancers(38;6.11e-10)|all_epithelial(38;8.06e-09)|all_lung(38;6.64e-05)|Lung NSC(38;0.0011)|Breast(42;0.00235)|Ovarian(80;0.0139)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0369)|BRCA - Breast invasive adenocarcinoma(115;0.21)														---	---	---	---
BRD1	23774	broad.mit.edu	37	22	50217576	50217576	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50217576C>T	uc003biv.2	-	1	877	c.390G>A	c.(388-390)CCG>CCA	p.P130P	BRD1_uc011arf.1_5'UTR|BRD1_uc011arg.1_Silent_p.P130P|BRD1_uc011arh.1_Silent_p.P130P|BRD1_uc003biu.3_Silent_p.P130P	NM_014577	NP_055392	O95696	BRD1_HUMAN	bromodomain containing protein 1	130					histone H3 acetylation	MOZ/MORF histone acetyltransferase complex	zinc ion binding			pancreas(1)	1		all_cancers(38;6.11e-10)|all_epithelial(38;8.06e-09)|all_lung(38;6.64e-05)|Lung NSC(38;0.0011)|Breast(42;0.00235)|Ovarian(80;0.0139)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0369)|BRCA - Breast invasive adenocarcinoma(115;0.21)														---	---	---	---
ALG12	79087	broad.mit.edu	37	22	50304233	50304233	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50304233G>A	uc003biy.2	-	4	592	c.318C>T	c.(316-318)GGC>GGT	p.G106G		NM_024105	NP_077010	Q9BV10	ALG12_HUMAN	alpha-1,6-mannosyltransferase ALG12	106	Helical; (Potential).				dolichol-linked oligosaccharide biosynthetic process|GPI anchor biosynthetic process|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	integral to membrane|intrinsic to endoplasmic reticulum membrane					0		all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164)		BRCA - Breast invasive adenocarcinoma(115;0.199)|LUAD - Lung adenocarcinoma(64;0.247)														---	---	---	---
IL17REL	400935	broad.mit.edu	37	22	50438940	50438940	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50438940C>T	uc003bje.1	-	6	533	c.301G>A	c.(301-303)GGG>AGG	p.G101R		NM_001001694	NP_001001694	Q6ZVW7	I17EL_HUMAN	interleukin 17 receptor E-like	101										pancreas(1)	1		all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)														---	---	---	---
MOV10L1	54456	broad.mit.edu	37	22	50580617	50580617	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50580617G>T	uc003bjj.2	+	16	2261	c.2178G>T	c.(2176-2178)TGG>TGT	p.W726C	MOV10L1_uc003bjk.3_Missense_Mutation_p.W726C|MOV10L1_uc011arp.1_Missense_Mutation_p.W706C|MOV10L1_uc011arq.1_Missense_Mutation_p.W487C|MOV10L1_uc010hao.1_RNA	NM_018995	NP_061868	Q9BXT6	M10L1_HUMAN	MOV10-like 1 isoform 1	726					germ cell development|multicellular organismal development|spermatogenesis		ATP binding|ATP-dependent RNA helicase activity|magnesium ion binding|RNA binding			ovary(2)|skin(1)	3		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)												OREG0026672	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
MOV10L1	54456	broad.mit.edu	37	22	50599434	50599434	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50599434C>T	uc003bjj.2	+	26	3587	c.3504C>T	c.(3502-3504)AAC>AAT	p.N1168N	MOV10L1_uc003bjk.3_Silent_p.N1122N|MOV10L1_uc011arp.1_Intron|MOV10L1_uc003bjl.2_Silent_p.N295N	NM_018995	NP_061868	Q9BXT6	M10L1_HUMAN	MOV10-like 1 isoform 1	1168					germ cell development|multicellular organismal development|spermatogenesis		ATP binding|ATP-dependent RNA helicase activity|magnesium ion binding|RNA binding			ovary(2)|skin(1)	3		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)														---	---	---	---
TUBGCP6	85378	broad.mit.edu	37	22	50656233	50656233	+	Missense_Mutation	SNP	C	A	A	rs150137904		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50656233C>A	uc003bkb.1	-	25	5904	c.5392G>T	c.(5392-5394)GGC>TGC	p.G1798C	TUBGCP6_uc003bka.1_Missense_Mutation_p.G868C|TUBGCP6_uc010har.1_Missense_Mutation_p.G1790C|TUBGCP6_uc010has.1_RNA	NM_020461	NP_065194	Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	1798					G2/M transition of mitotic cell cycle|microtubule nucleation	centrosome|cytosol|gamma-tubulin ring complex|microtubule|spindle pole	microtubule binding			ovary(2)|central_nervous_system(2)	4		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)														---	---	---	---
TUBGCP6	85378	broad.mit.edu	37	22	50656953	50656953	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50656953C>T	uc003bkb.1	-	22	5430	c.4918G>A	c.(4918-4920)GCG>ACG	p.A1640T	TUBGCP6_uc003bka.1_Missense_Mutation_p.A727T|TUBGCP6_uc010har.1_Missense_Mutation_p.A1632T|TUBGCP6_uc010has.1_RNA	NM_020461	NP_065194	Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	1640					G2/M transition of mitotic cell cycle|microtubule nucleation	centrosome|cytosol|gamma-tubulin ring complex|microtubule|spindle pole	microtubule binding			ovary(2)|central_nervous_system(2)	4		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)														---	---	---	---
TUBGCP6	85378	broad.mit.edu	37	22	50659376	50659376	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50659376A>G	uc003bkb.1	-	16	3924	c.3412T>C	c.(3412-3414)TCC>CCC	p.S1138P	TUBGCP6_uc003bka.1_Missense_Mutation_p.S225P|TUBGCP6_uc010har.1_Missense_Mutation_p.S1130P|TUBGCP6_uc010has.1_RNA	NM_020461	NP_065194	Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	1138	9 X 27 AA tandem repeats.|5.				G2/M transition of mitotic cell cycle|microtubule nucleation	centrosome|cytosol|gamma-tubulin ring complex|microtubule|spindle pole	microtubule binding			ovary(2)|central_nervous_system(2)	4		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)														---	---	---	---
TUBGCP6	85378	broad.mit.edu	37	22	50682196	50682196	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50682196G>A	uc003bkb.1	-	1	1205	c.693C>T	c.(691-693)GGC>GGT	p.G231G	TUBGCP6_uc010har.1_Silent_p.G231G|TUBGCP6_uc010has.1_RNA|TUBGCP6_uc010hau.1_Silent_p.G231G	NM_020461	NP_065194	Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	231					G2/M transition of mitotic cell cycle|microtubule nucleation	centrosome|cytosol|gamma-tubulin ring complex|microtubule|spindle pole	microtubule binding			ovary(2)|central_nervous_system(2)	4		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)														---	---	---	---
HDAC10	83933	broad.mit.edu	37	22	50687192	50687192	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50687192G>A	uc003bkg.2	-						HDAC10_uc003bke.2_Intron|HDAC10_uc003bkf.2_Intron|HDAC10_uc010hav.2_Intron|HDAC10_uc003bkh.2_Intron|HDAC10_uc003bki.2_Intron|HDAC10_uc003bkj.2_Intron|HDAC10_uc003bkk.1_5'Flank	NM_032019	NP_114408			histone deacetylase 10 isoform 1						negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|nucleus	histone deacetylase activity|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)				0		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)														---	---	---	---
PLXNB2	23654	broad.mit.edu	37	22	50716090	50716090	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50716090T>C	uc003bkv.3	-	33	5232	c.5126A>G	c.(5125-5127)GAC>GGC	p.D1709G	PLXNB2_uc003bkt.1_Missense_Mutation_p.D501G|PLXNB2_uc003bku.1_Missense_Mutation_p.D694G	NM_012401	NP_036533	O15031	PLXB2_HUMAN	plexin B2 precursor	1709	Cytoplasmic (Potential).				regulation of small GTPase mediated signal transduction	integral to membrane|intracellular	GTPase activator activity|protein binding|receptor activity			ovary(4)|central_nervous_system(1)|skin(1)	6		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)														---	---	---	---
FAM116B	414918	broad.mit.edu	37	22	50752265	50752265	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50752265G>A	uc011aru.1	-	15	1253	c.1181C>T	c.(1180-1182)GCG>GTG	p.A394V	FAM116B_uc011arv.1_Missense_Mutation_p.A394V	NM_001001794	NP_001001794	Q8NEG7	F116B_HUMAN	family with sequence similarity 116, member B	394											0		all_cancers(38;4.34e-09)|all_epithelial(38;3.03e-08)|all_lung(38;0.00141)|Breast(42;0.00387)|Lung NSC(38;0.0199)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)														---	---	---	---
SAPS2	9701	broad.mit.edu	37	22	50873444	50873444	+	Missense_Mutation	SNP	G	A	A	rs140951188		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50873444G>A	uc003blb.1	+	14	1872	c.1450G>A	c.(1450-1452)GCC>ACC	p.A484T	SAPS2_uc003bky.1_Missense_Mutation_p.A484T|SAPS2_uc003bkz.1_Missense_Mutation_p.A484T|SAPS2_uc003blc.2_Missense_Mutation_p.A484T|SAPS2_uc003bla.1_Missense_Mutation_p.A485T|SAPS2_uc003bld.1_Missense_Mutation_p.A43T	NM_014678	NP_055493	O75170	PP6R2_HUMAN	SAPS domain family, member 2	484						cytoplasm|intracellular membrane-bounded organelle	protein binding				0		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.222)														---	---	---	---
SBF1	6305	broad.mit.edu	37	22	50900243	50900243	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50900243C>T	uc003blh.2	-	21	2820	c.2625G>A	c.(2623-2625)AGG>AGA	p.R875R	SBF1_uc011arx.1_Silent_p.R539R|SBF1_uc003bli.2_Silent_p.R876R	NM_002972	NP_002963	O95248	MTMR5_HUMAN	SET binding factor 1	875					protein dephosphorylation	integral to membrane|nucleus	protein tyrosine/serine/threonine phosphatase activity				0		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)														---	---	---	---
SBF1	6305	broad.mit.edu	37	22	50902823	50902823	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50902823G>A	uc003blh.2	-	15	1879	c.1684C>T	c.(1684-1686)CGG>TGG	p.R562W	SBF1_uc011arx.1_Missense_Mutation_p.R226W|SBF1_uc003bli.2_Missense_Mutation_p.R563W	NM_002972	NP_002963	O95248	MTMR5_HUMAN	SET binding factor 1	562					protein dephosphorylation	integral to membrane|nucleus	protein tyrosine/serine/threonine phosphatase activity				0		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)														---	---	---	---
MIOX	55586	broad.mit.edu	37	22	50928232	50928232	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50928232C>T	uc003bll.1	+	10	919	c.805C>T	c.(805-807)CCC>TCC	p.P269S	MIOX_uc003blm.1_Missense_Mutation_p.A264V|MIOX_uc003bln.1_Missense_Mutation_p.A225V	NM_017584	NP_060054	Q9UGB7	MIOX_HUMAN	myo-inositol oxygenase	269					inositol catabolic process	cytoplasm|inclusion body	aldo-keto reductase (NADP) activity|ferric iron binding|inositol oxygenase activity				0		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)														---	---	---	---
TYMP	1890	broad.mit.edu	37	22	50966137	50966137	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:50966137G>A	uc003bmb.3	-	4	646	c.526C>T	c.(526-528)CTG>TTG	p.L176L	SCO2_uc003bma.2_5'Flank|SCO2_uc003blz.3_5'Flank|TYMP_uc003bmc.3_Silent_p.L176L|TYMP_uc003bmd.3_Silent_p.L176L|TYMP_uc010hbd.2_Silent_p.L176L|TYMP_uc003bme.3_Silent_p.L176L|TYMP_uc003bmf.3_Silent_p.L143L|TYMP_uc011arz.1_Silent_p.L176L	NM_001113756	NP_001107228	P19971	TYPH_HUMAN	endothelial cell growth factor 1	176					angiogenesis|cell differentiation|chemotaxis|DNA replication|mitochondrial genome maintenance|pyrimidine base metabolic process|pyrimidine nucleoside catabolic process|pyrimidine nucleoside salvage|pyrimidine nucleotide metabolic process	cytosol	growth factor activity|platelet-derived growth factor receptor binding|pyrimidine-nucleoside phosphorylase activity|thymidine phosphorylase activity			ovary(1)	1		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)	Capecitabine(DB01101)|Docetaxel(DB01248)|Floxuridine(DB00322)|Fluorouracil(DB00544)|Sulfasalazine(DB00795)|Tamoxifen(DB00675)													---	---	---	---
MAPK8IP2	23542	broad.mit.edu	37	22	51049186	51049186	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:51049186G>A	uc003bmx.2	+	13	2571	c.2454G>A	c.(2452-2454)ACG>ACA	p.T818T	MAPK8IP2_uc003bmy.2_Silent_p.T791T|MAPK8IP2_uc011asc.1_Silent_p.T172T	NM_012324	NP_036456	Q13387	JIP2_HUMAN	mitogen-activated protein kinase 8 interacting	818					behavioral fear response|dendrite morphogenesis|MAPKKK cascade|nonassociative learning|positive regulation of anti-apoptosis|regulation of excitatory postsynaptic membrane potential|regulation of JNK cascade|regulation of receptor activity|regulation of synaptic transmission, glutamatergic|signal complex assembly|social behavior	cytoplasm|postsynaptic density	beta-amyloid binding|kinesin binding|MAP-kinase scaffold activity|protein kinase activator activity|protein kinase binding			large_intestine(2)|central_nervous_system(1)	3		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		OV - Ovarian serous cystadenocarcinoma(4;1.28e-70)|Epithelial(4;3.46e-65)|GBM - Glioblastoma multiforme(4;4.83e-06)|Lung(4;0.125)|BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)														---	---	---	---
ARSA	410	broad.mit.edu	37	22	51063681	51063681	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:51063681G>A	uc003bnb.3	-	9	1669	c.1416C>T	c.(1414-1416)TTC>TTT	p.F472F	ARSA_uc003bna.3_Silent_p.F388F|ARSA_uc003bnc.3_Silent_p.F472F|ARSA_uc003bnd.3_Silent_p.F472F|ARSA_uc003bmz.3_Silent_p.F472F	NM_001085426	NP_001078895	P15289	ARSA_HUMAN	arylsulfatase A isoform a precursor	472						lysosome	arylsulfatase activity|calcium ion binding|cerebroside-sulfatase activity			pancreas(1)|skin(1)	2		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)	Micafungin(DB01141)													---	---	---	---
PLCXD1	55344	broad.mit.edu	37	X	215966	215966	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:215966C>T	uc004cpc.2	+	7	1248	c.936C>T	c.(934-936)GAC>GAT	p.D312D	PLCXD1_uc011mgx.1_RNA	NM_018390	NP_060860	Q9NUJ7	PLCX1_HUMAN	phosphatidylinositol-specific phospholipase C, X	312					intracellular signal transduction|lipid metabolic process		phospholipase C activity				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)																---	---	---	---
SHOX	6473	broad.mit.edu	37	X	601751	601751	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:601751G>A	uc004cph.1	+	5	1253	c.562G>A	c.(562-564)GCC>ACC	p.A188T	SHOX_uc004cpi.2_Missense_Mutation_p.A188T	NM_000451	NP_000442	O15266	SHOX_HUMAN	short stature homeobox isoform SHOXa	188					skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)																---	---	---	---
ZBED1	9189	broad.mit.edu	37	X	2406834	2406834	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:2406834C>T	uc004cqg.2	-	2	2128	c.1927G>A	c.(1927-1929)GAG>AAG	p.E643K	DHRSX_uc004cqf.3_Intron|ZBED1_uc004cqh.1_Missense_Mutation_p.E643K	NM_004729	NP_004720	O96006	ZBED1_HUMAN	zinc finger, BED-type containing 1	643						nuclear chromosome	DNA binding|metal ion binding|protein dimerization activity|transposase activity				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)																---	---	---	---
MXRA5	25878	broad.mit.edu	37	X	3240253	3240253	+	Missense_Mutation	SNP	C	T	T	rs112514198		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:3240253C>T	uc004crg.3	-	5	3630	c.3473G>A	c.(3472-3474)CGC>CAC	p.R1158H		NM_015419	NP_056234	Q9NR99	MXRA5_HUMAN	adlican precursor	1158						extracellular region				ovary(5)|lung(1)|central_nervous_system(1)|skin(1)	8		all_lung(23;0.00031)|Lung NSC(23;0.000946)																---	---	---	---
STS	412	broad.mit.edu	37	X	7177509	7177509	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:7177509G>A	uc004cry.3	+	5	762	c.517G>A	c.(517-519)GGA>AGA	p.G173R		NM_000351	NP_000342	P08842	STS_HUMAN	steryl-sulfatase precursor	173	Lumenal.				female pregnancy|steroid catabolic process	endoplasmic reticulum membrane|endosome|Golgi apparatus|integral to membrane|lysosome|microsome|plasma membrane	metal ion binding|steryl-sulfatase activity			central_nervous_system(1)	1		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)			Estrone(DB00655)									Ichthyosis				---	---	---	---
VCX3B	425054	broad.mit.edu	37	X	8433555	8433555	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:8433555T>C	uc010ndo.2	+	2	371	c.64T>C	c.(64-66)TCC>CCC	p.S22P	VCX3B_uc011mht.1_Missense_Mutation_p.S22P|VCX3B_uc004csd.1_Missense_Mutation_p.S22P	NM_001001888	NP_001001888	Q9H321	VCX3B_HUMAN	variable charge, X-linked 3B	22						nucleolus					0																		---	---	---	---
PRPS2	5634	broad.mit.edu	37	X	12827408	12827408	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:12827408C>T	uc004cvb.2	+	3	486	c.362C>T	c.(361-363)GCG>GTG	p.A121V	PRPS2_uc004cva.2_Missense_Mutation_p.A124V|PRPS2_uc010nec.2_Missense_Mutation_p.A57V	NM_002765	NP_002756	P11908	PRPS2_HUMAN	phosphoribosyl pyrophosphate synthetase 2	121					nucleoside metabolic process|ribonucleoside monophosphate biosynthetic process		ATP binding|kinase activity|magnesium ion binding|protein homodimerization activity|ribose phosphate diphosphokinase activity				0																		---	---	---	---
FANCB	2187	broad.mit.edu	37	X	14862683	14862683	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:14862683T>C	uc004cwg.1	-	9	2375	c.2107A>G	c.(2107-2109)ACA>GCA	p.T703A	FANCB_uc004cwh.1_Missense_Mutation_p.T703A	NM_001018113	NP_001018123	Q8NB91	FANCB_HUMAN	Fanconi anemia complementation group B	703					DNA repair	nucleoplasm				lung(1)	1	Hepatocellular(33;0.183)												Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
GRPR	2925	broad.mit.edu	37	X	16170603	16170603	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:16170603G>A	uc004cxj.2	+	3	1643	c.990G>A	c.(988-990)AGG>AGA	p.R330R		NM_005314	NP_005305	P30550	GRPR_HUMAN	gastrin-releasing peptide receptor	330	Cytoplasmic (Potential).				cell proliferation	integral to plasma membrane	bombesin receptor activity			ovary(3)|lung(1)	4	Hepatocellular(33;0.183)																	---	---	---	---
TXLNG	55787	broad.mit.edu	37	X	16859573	16859573	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:16859573A>G	uc004cxq.1	+	10	1322	c.1271A>G	c.(1270-1272)TAC>TGC	p.Y424C	TXLNG_uc010ney.1_Missense_Mutation_p.Y292C	NM_018360	NP_060830	Q9NUQ3	TXLNG_HUMAN	gamma-taxilin	424	Potential.				cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nuclear membrane				lung(1)	1																		---	---	---	---
CDKL5	6792	broad.mit.edu	37	X	18528952	18528952	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18528952T>G	uc004cym.2	+	3	330	c.77T>G	c.(76-78)GTT>GGT	p.V26G	CDKL5_uc004cyn.2_Missense_Mutation_p.V26G	NM_003159	NP_003150	O76039	CDKL5_HUMAN	cyclin-dependent kinase-like 5	26	ATP (By similarity).|Protein kinase.				neuron migration|positive regulation of axon extension|positive regulation of dendrite morphogenesis|positive regulation of Rac GTPase activity|protein autophosphorylation	dendrite cytoplasm|dendritic growth cone|nucleus	ATP binding|cyclin-dependent protein kinase activity|Rac GTPase binding			ovary(2)|large_intestine(1)|stomach(1)|central_nervous_system(1)|skin(1)	6	Hepatocellular(33;0.183)																	---	---	---	---
CDKL5	6792	broad.mit.edu	37	X	18668525	18668525	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:18668525T>C	uc004cym.2	+						CDKL5_uc004cyn.2_Intron|RS1_uc004cyo.2_Intron	NM_003159	NP_003150			cyclin-dependent kinase-like 5						neuron migration|positive regulation of axon extension|positive regulation of dendrite morphogenesis|positive regulation of Rac GTPase activity|protein autophosphorylation	dendrite cytoplasm|dendritic growth cone|nucleus	ATP binding|cyclin-dependent protein kinase activity|Rac GTPase binding			ovary(2)|large_intestine(1)|stomach(1)|central_nervous_system(1)|skin(1)	6	Hepatocellular(33;0.183)																	---	---	---	---
MAP7D2	256714	broad.mit.edu	37	X	20073944	20073944	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:20073944G>A	uc004czr.1	-						MAP7D2_uc004czq.1_Intron|MAP7D2_uc011mji.1_Intron|MAP7D2_uc010nfo.1_Intron|MAP7D2_uc011mjj.1_Intron|MAP7D2_uc004czs.1_Missense_Mutation_p.S120L	NM_152780	NP_689993			MAP7 domain containing 2											ovary(2)|breast(1)	3																		---	---	---	---
CNKSR2	22866	broad.mit.edu	37	X	21550166	21550166	+	Silent	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:21550166A>C	uc004czx.1	+	11	1320	c.1284A>C	c.(1282-1284)CGA>CGC	p.R428R	CNKSR2_uc004czw.2_Silent_p.R428R|CNKSR2_uc011mjn.1_Silent_p.R379R|CNKSR2_uc011mjo.1_Silent_p.R428R|CNKSR2_uc004czy.2_Silent_p.R50R	NM_014927	NP_055742	Q8WXI2	CNKR2_HUMAN	connector enhancer of kinase suppressor of Ras	428	DUF1170.				regulation of signal transduction	cytoplasm|membrane	protein binding			large_intestine(1)|lung(1)	2																		---	---	---	---
DCAF8L1	139425	broad.mit.edu	37	X	27998658	27998658	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:27998658A>G	uc004dbx.1	-	1	909	c.794T>C	c.(793-795)GTA>GCA	p.V265A		NM_001017930	NP_001017930	A6NGE4	DC8L1_HUMAN	DDB1 and CUL4 associated factor 8-like 1	265	WD 2.									ovary(3)|skin(1)	4																		---	---	---	---
FAM47B	170062	broad.mit.edu	37	X	34962141	34962141	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:34962141G>A	uc004ddi.1	+	1	1211	c.1193G>A	c.(1192-1194)CGC>CAC	p.R398H		NM_152631	NP_689844	Q8NA70	FA47B_HUMAN	hypothetical protein LOC170062	398										ovary(3)|breast(1)	4																		---	---	---	---
DDX3X	1654	broad.mit.edu	37	X	41203521	41203521	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:41203521C>T	uc004dfe.2	+	10	1749	c.894C>T	c.(892-894)TGC>TGT	p.C298C	DDX3X_uc010nhf.1_Silent_p.C282C|DDX3X_uc004dff.2_Silent_p.C298C|DDX3X_uc011mkq.1_Silent_p.C282C|DDX3X_uc011mkr.1_Silent_p.C298C|DDX3X_uc011mks.1_Intron|DDX3X_uc004dfg.2_RNA|DDX3X_uc011mkt.1_RNA	NM_001356	NP_001347	O00571	DDX3X_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3	298	Necessary for interaction with XPO1.|Helicase ATP-binding.				interspecies interaction between organisms	cytoplasm|nuclear speck	ATP binding|ATP-dependent RNA helicase activity|DNA binding|protein binding|RNA binding			ovary(2)|breast(2)|central_nervous_system(1)|skin(1)	6															HNSCC(61;0.18)			---	---	---	---
SLC9A7	84679	broad.mit.edu	37	X	46480450	46480450	+	Silent	SNP	G	A	A	rs141094938		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46480450G>A	uc004dgu.1	-	15	1790	c.1782C>T	c.(1780-1782)AGC>AGT	p.S594S		NM_032591	NP_115980	Q96T83	SL9A7_HUMAN	solute carrier family 9, member 7	594					regulation of pH	Golgi membrane|integral to membrane|recycling endosome membrane|trans-Golgi network	potassium:hydrogen antiporter activity|protein homodimerization activity|sodium:hydrogen antiporter activity			ovary(2)	2																		---	---	---	---
SLC9A7	84679	broad.mit.edu	37	X	46491045	46491045	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:46491045G>A	uc004dgu.1	-	14	1721	c.1713C>T	c.(1711-1713)AAC>AAT	p.N571N		NM_032591	NP_115980	Q96T83	SL9A7_HUMAN	solute carrier family 9, member 7	571					regulation of pH	Golgi membrane|integral to membrane|recycling endosome membrane|trans-Golgi network	potassium:hydrogen antiporter activity|protein homodimerization activity|sodium:hydrogen antiporter activity			ovary(2)	2																		---	---	---	---
RBM10	8241	broad.mit.edu	37	X	47044609	47044609	+	Intron	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:47044609T>G	uc004dhf.2	+						RBM10_uc004dhg.2_Intron|RBM10_uc004dhh.2_Intron|RBM10_uc010nhq.2_Intron|RBM10_uc004dhi.2_Intron	NM_005676	NP_005667			RNA binding motif protein 10 isoform 1						mRNA processing|RNA splicing	chromatin remodeling complex	nucleotide binding|RNA binding|zinc ion binding			ovary(1)|large_intestine(1)|prostate(1)|breast(1)|pancreas(1)	5																		---	---	---	---
Unknown	0	broad.mit.edu	37	X	48074052	48074052	+	IGR	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48074052C>A								SSX5 (17853 upstream) : SSX1 (40745 downstream)																																			---	---	---	---
PORCN	64840	broad.mit.edu	37	X	48368225	48368225	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48368225G>A	uc010nie.1	+	2	175	c.17G>A	c.(16-18)CGC>CAC	p.R6H	PORCN_uc004djq.1_Missense_Mutation_p.R119H|PORCN_uc004djr.1_Missense_Mutation_p.R6H|PORCN_uc004djs.1_Missense_Mutation_p.R6H|PORCN_uc004djt.1_5'UTR|PORCN_uc011mlx.1_5'UTR|PORCN_uc004dju.1_5'UTR|PORCN_uc004djv.1_Missense_Mutation_p.R6H|PORCN_uc004djw.1_Missense_Mutation_p.R6H	NM_203475	NP_982301	Q9H237	PORCN_HUMAN	porcupine isoform D	6	Cytoplasmic (Potential).				Wnt receptor signaling pathway	endoplasmic reticulum membrane|integral to membrane	acyltransferase activity			ovary(2)|central_nervous_system(1)	3																		---	---	---	---
GATA1	2623	broad.mit.edu	37	X	48650563	48650563	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48650563G>A	uc004dkq.3	+	3	624	c.533G>A	c.(532-534)AGC>AAC	p.S178N		NM_002049	NP_002040	P15976	GATA1_HUMAN	GATA binding protein 1	178					basophil differentiation|eosinophil differentiation|erythrocyte development|megakaryocyte differentiation|platelet aggregation|platelet formation|positive regulation of anti-apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|regulation of glycoprotein biosynthetic process|transcription from RNA polymerase II promoter	nuclear membrane|nucleolus|nucleoplasm	C2H2 zinc finger domain binding|RNA polymerase II regulatory region sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	p.?(2)|p.V74_C199del(1)		haematopoietic_and_lymphoid_tissue(246)|lung(2)	248								Mis|F		megakaryoblastic leukemia of Downs Syndrome								---	---	---	---
GRIPAP1	56850	broad.mit.edu	37	X	48837687	48837687	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48837687G>A	uc004dly.1	-	21	1905	c.1870C>T	c.(1870-1872)CGG>TGG	p.R624W	GRIPAP1_uc004dlz.2_Missense_Mutation_p.R514W|GRIPAP1_uc004dma.2_Missense_Mutation_p.R545W	NM_020137	NP_064522	Q4V328	GRAP1_HUMAN	GRIP1 associated protein 1 isoform 1	624	Potential.					early endosome		p.R267R(2)		breast(2)|kidney(1)	3																		---	---	---	---
CACNA1F	778	broad.mit.edu	37	X	49065114	49065114	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49065114G>A	uc004dnb.2	-	43	5079	c.5017C>T	c.(5017-5019)CGG>TGG	p.R1673W	CACNA1F_uc010nip.2_Missense_Mutation_p.R1662W	NM_005183	NP_005174	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type,	1673	Cytoplasmic (Potential).				axon guidance|detection of light stimulus involved in visual perception	voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity			breast(3)|ovary(1)|kidney(1)|skin(1)	6					Verapamil(DB00661)													---	---	---	---
MIR188	406964	broad.mit.edu	37	X	49768114	49768114	+	RNA	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49768114C>A	hsa-mir-188|MI0000484	+			c.6C>A			CLCN5_uc004dor.1_Intron|CLCN5_uc004doq.1_Intron|uc011mnv.1_RNA																	0																		---	---	---	---
CLCN5	1184	broad.mit.edu	37	X	49853395	49853395	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49853395C>A	uc004dos.1	+	9	1636	c.1388C>A	c.(1387-1389)GCT>GAT	p.A463D	CLCN5_uc004dor.1_Missense_Mutation_p.A533D|CLCN5_uc004doq.1_Missense_Mutation_p.A533D|CLCN5_uc004dot.1_Missense_Mutation_p.A463D	NM_000084	NP_000075	P51795	CLCN5_HUMAN	chloride channel 5 isoform b	463	Helical; (By similarity).				excretion	apical part of cell|endosome membrane|Golgi membrane|integral to plasma membrane	antiporter activity|ATP binding			ovary(2)|lung(1)|central_nervous_system(1)	4	Ovarian(276;0.236)																	---	---	---	---
AKAP4	8852	broad.mit.edu	37	X	49961604	49961604	+	Nonsense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:49961604C>A	uc004dow.1	-	4	338	c.214G>T	c.(214-216)GGA>TGA	p.G72*	AKAP4_uc004dov.1_Nonsense_Mutation_p.G63*|AKAP4_uc010njp.1_5'UTR|AKAP4_uc004dou.1_Nonsense_Mutation_p.G63*	NM_003886	NP_003877	Q5JQC9	AKAP4_HUMAN	A-kinase anchor protein 4 isoform 1	72					cell projection organization|single fertilization|sperm motility	cAMP-dependent protein kinase complex|cilium|cytoskeleton|microtubule-based flagellum	protein kinase A binding			kidney(3)|central_nervous_system(2)|ovary(1)|lung(1)|skin(1)	8	Ovarian(276;0.236)																	---	---	---	---
SMC1A	8243	broad.mit.edu	37	X	53423400	53423400	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53423400G>A	uc004dsg.2	-	17	2769	c.2700C>T	c.(2698-2700)GGC>GGT	p.G900G	SMC1A_uc011moe.1_Silent_p.G878G	NM_006306	NP_006297	Q14683	SMC1A_HUMAN	structural maintenance of chromosomes 1A	900	Potential.				cell cycle checkpoint|cell division|DNA repair|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|mitotic sister chromatid cohesion|mitotic spindle organization|negative regulation of DNA endoreduplication|nuclear mRNA splicing, via spliceosome|response to radiation|signal transduction in response to DNA damage	cohesin core heterodimer|condensed chromosome kinetochore|condensed nuclear chromosome|cytoplasm|meiotic cohesin complex|nucleoplasm	ATP binding|chromatin binding|microtubule motor activity|protein heterodimerization activity			ovary(5)|central_nervous_system(1)	6																		---	---	---	---
RIBC1	158787	broad.mit.edu	37	X	53457908	53457908	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53457908A>G	uc004dsk.2	+	8	1265	c.1112A>G	c.(1111-1113)CAC>CGC	p.H371R		NM_001031745	NP_001026915	Q8N443	RIBC1_HUMAN	RIB43A domain with coiled-coils 1 isoform 1	371											0																		---	---	---	---
HUWE1	10075	broad.mit.edu	37	X	53577661	53577661	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53577661T>G	uc004dsp.2	-	66	9856	c.9454A>C	c.(9454-9456)ACC>CCC	p.T3152P	HUWE1_uc004dsn.2_Missense_Mutation_p.T1960P	NM_031407	NP_113584	Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1	3152					base-excision repair|cell differentiation|histone ubiquitination|protein monoubiquitination|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	DNA binding|protein binding|ubiquitin-protein ligase activity			ovary(8)|large_intestine(4)|breast(4)|kidney(1)	17																		---	---	---	---
WNK3	65267	broad.mit.edu	37	X	54275285	54275285	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54275285A>C	uc004dtd.1	-	17	3935	c.3496T>G	c.(3496-3498)TGT>GGT	p.C1166G	WNK3_uc004dtc.1_Missense_Mutation_p.C1166G	NM_001002838	NP_001002838	Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3 isoform 2	1166					intracellular protein kinase cascade|positive regulation of establishment of protein localization in plasma membrane|positive regulation of peptidyl-threonine phosphorylation|positive regulation of rubidium ion transmembrane transporter activity|positive regulation of rubidium ion transport|positive regulation of sodium ion transmembrane transporter activity|positive regulation of sodium ion transport|protein autophosphorylation	adherens junction|tight junction	ATP binding|protein binding|protein serine/threonine kinase activity|rubidium ion transmembrane transporter activity|sodium ion transmembrane transporter activity			lung(4)|ovary(3)|kidney(2)|central_nervous_system(2)	11																		---	---	---	---
FGD1	2245	broad.mit.edu	37	X	54482933	54482933	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54482933G>A	uc004dtg.2	-						FGD1_uc011moi.1_Intron	NM_004463	NP_004454			faciogenital dysplasia protein						actin cytoskeleton organization|apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|organ morphogenesis|regulation of Cdc42 GTPase activity|regulation of cell shape|small GTPase mediated signal transduction	cytoskeleton|cytosol|Golgi apparatus|lamellipodium|nucleus|plasma membrane|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(3)|skin(2)|central_nervous_system(1)	6																		---	---	---	---
GNL3L	54552	broad.mit.edu	37	X	54581076	54581076	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54581076C>A	uc004dth.1	+	14	1536	c.1397C>A	c.(1396-1398)CCG>CAG	p.P466Q	GNL3L_uc004dti.2_RNA	NM_019067	NP_061940	Q9NVN8	GNL3L_HUMAN	guanine nucleotide binding protein-like 3	466					ribosome biogenesis	nucleolus	GTP binding			ovary(1)	1																		---	---	---	---
ALAS2	212	broad.mit.edu	37	X	55047538	55047538	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:55047538A>G	uc004dua.3	-	5	723	c.585T>C	c.(583-585)TGT>TGC	p.C195C	ALAS2_uc004dub.3_Silent_p.C182C|ALAS2_uc004dud.3_Silent_p.C158C	NM_000032	NP_000023	P22557	HEM0_HUMAN	5-aminolevulinate synthase 2 isoform a	195					cellular iron ion homeostasis|erythrocyte differentiation|heme biosynthetic process|hemoglobin biosynthetic process|oxygen homeostasis|response to hypoxia	mitochondrial inner membrane|mitochondrial matrix	5-aminolevulinate synthase activity|coenzyme binding|glycine binding|protein binding|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups			ovary(1)	1					Glycine(DB00145)													---	---	---	---
MAGEH1	28986	broad.mit.edu	37	X	55478831	55478831	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:55478831G>T	uc004dum.2	+	1	294	c.24G>T	c.(22-24)CGG>CGT	p.R8R		NM_014061	NP_054780	Q9H213	MAGH1_HUMAN	melanoma antigen, family H, 1 protein	8	MAGE.				apoptosis					ovary(1)|lung(1)|central_nervous_system(1)|skin(1)	4																		---	---	---	---
ZXDA	7789	broad.mit.edu	37	X	57935414	57935414	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:57935414T>C	uc004dve.2	-	1	1654	c.1441A>G	c.(1441-1443)ATG>GTG	p.M481V		NM_007156	NP_009087	P98168	ZXDA_HUMAN	zinc finger, X-linked, duplicated A	481	C2H2-type 8.|Required for interaction with ZXDC.				positive regulation of transcription, DNA-dependent	nucleus	C2H2 zinc finger domain binding|identical protein binding|nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1																		---	---	---	---
ARHGEF9	23229	broad.mit.edu	37	X	62944542	62944542	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:62944542A>G	uc004dvl.2	-	2	898	c.59T>C	c.(58-60)GTC>GCC	p.V20A	ARHGEF9_uc004dvj.1_Intron|ARHGEF9_uc004dvk.1_5'UTR|ARHGEF9_uc011mos.1_5'UTR|ARHGEF9_uc004dvm.1_5'UTR|ARHGEF9_uc011mot.1_Intron|ARHGEF9_uc004dvn.2_Missense_Mutation_p.V27A	NM_015185	NP_056000	O43307	ARHG9_HUMAN	Cdc42 guanine exchange factor 9	20	SH3.				apoptosis|induction of apoptosis by extracellular signals|ion transmembrane transport|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(5)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	8																		---	---	---	---
LAS1L	81887	broad.mit.edu	37	X	64738290	64738290	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:64738290G>A	uc004dwa.1	-	12	1576	c.1504C>T	c.(1504-1506)CGC>TGC	p.R502C	LAS1L_uc004dwc.1_Missense_Mutation_p.R485C|LAS1L_uc004dwd.1_Missense_Mutation_p.R443C|LAS1L_uc004dvy.1_Missense_Mutation_p.R15C|LAS1L_uc004dvz.1_Missense_Mutation_p.R15C	NM_031206	NP_112483	Q9Y4W2	LAS1L_HUMAN	LAS1-like	502						MLL1 complex|nucleolus	protein binding			ovary(3)|large_intestine(1)	4																		---	---	---	---
EFNB1	1947	broad.mit.edu	37	X	68058478	68058478	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:68058478C>T	uc004dxd.3	+	2	927	c.147C>T	c.(145-147)GGC>GGT	p.G49G	EFNB1_uc004dxe.2_Silent_p.G49G	NM_004429	NP_004420	P98172	EFNB1_HUMAN	ephrin-B1 precursor	49	Extracellular (Potential).				cell adhesion|cell-cell signaling	integral to plasma membrane|soluble fraction|synapse	ephrin receptor binding				0																		---	---	---	---
DGAT2L6	347516	broad.mit.edu	37	X	69421746	69421746	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69421746G>A	uc004dxx.1	+	5	576	c.479G>A	c.(478-480)TGC>TAC	p.C160Y		NM_198512	NP_940914	Q6ZPD8	DG2L6_HUMAN	diacylglycerol O-acyltransferase 2-like 6	160					lipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	acyltransferase activity			ovary(1)	1																		---	---	---	---
KIF4A	24137	broad.mit.edu	37	X	69623781	69623781	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69623781C>T	uc004dyg.2	+	24	2814	c.2687C>T	c.(2686-2688)GCT>GTT	p.A896V	KIF4A_uc010nkw.2_Missense_Mutation_p.A896V	NM_012310	NP_036442	O95239	KIF4A_HUMAN	kinesin family member 4	896	Potential.|Interaction with PRC1.				anterograde axon cargo transport|axon guidance|blood coagulation|organelle organization	chromosome|cytosol|midbody|nuclear matrix|spindle microtubule	ATP binding|DNA binding|microtubule motor activity|protein binding			ovary(4)	4																		---	---	---	---
DLG3	1741	broad.mit.edu	37	X	69719077	69719077	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:69719077A>G	uc004dyi.1	+	15	2250	c.1922A>G	c.(1921-1923)AAT>AGT	p.N641S	DLG3_uc004dyj.1_Missense_Mutation_p.N336S|DLG3_uc011mpn.1_Missense_Mutation_p.N189S	NM_021120	NP_066943	Q92796	DLG3_HUMAN	synapse-associated protein 102 isoform a	641	Guanylate kinase-like.				axon guidance|negative regulation of cell proliferation|synaptic transmission	plasma membrane	guanylate kinase activity			large_intestine(1)|pancreas(1)	2	Renal(35;0.156)																	---	---	---	---
MED12	9968	broad.mit.edu	37	X	70345242	70345242	+	Silent	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70345242A>G	uc004dyy.2	+	16	2467	c.2268A>G	c.(2266-2268)GTA>GTG	p.V756V	MED12_uc011mpq.1_Silent_p.V756V|MED12_uc004dyz.2_Silent_p.V756V|MED12_uc004dza.2_Silent_p.V603V	NM_005120	NP_005111	Q93074	MED12_HUMAN	mediator complex subunit 12	756					androgen receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|protein domain specific binding|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4	Renal(35;0.156)																	---	---	---	---
OGT	8473	broad.mit.edu	37	X	70776938	70776938	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:70776938C>A	uc004eaa.1	+	10	1520	c.1303C>A	c.(1303-1305)CTG>ATG	p.L435M	BCYRN1_uc011mpt.1_Intron|OGT_uc004eab.1_Missense_Mutation_p.L425M|OGT_uc004eac.2_Missense_Mutation_p.L296M|OGT_uc004ead.2_Missense_Mutation_p.L54M	NM_181672	NP_858058	O15294	OGT1_HUMAN	O-linked GlcNAc transferase isoform 1	435	TPR 12.				cellular response to retinoic acid|positive regulation of granulocyte differentiation|positive regulation of histone H3-K4 methylation|positive regulation of proteolysis|protein O-linked glycosylation|signal transduction	cytosol|MLL5-L complex	enzyme activator activity|protein binding|protein N-acetylglucosaminyltransferase activity			ovary(3)|kidney(1)|pancreas(1)	5	Renal(35;0.156)																	---	---	---	---
TSIX	9383	broad.mit.edu	37	X	73040777	73040777	+	RNA	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73040777A>G	uc004ebn.2	+	1		c.28738A>G			XIST_uc004ebm.1_RNA	NR_003255				Homo sapiens XIST antisense RNA (non-protein coding) (TSIX), non-coding RNA.												0																		---	---	---	---
XIST	7503	broad.mit.edu	37	X	73069603	73069603	+	RNA	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73069603A>G	uc004ebm.1	-	1		c.2986T>C				NR_001564				Homo sapiens cDNA: FLJ21545 fis, clone COL06195.												0																		---	---	---	---
XIST	7503	broad.mit.edu	37	X	73071177	73071177	+	RNA	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73071177C>T	uc004ebm.1	-	1		c.1412G>A				NR_001564				Homo sapiens cDNA: FLJ21545 fis, clone COL06195.												0																		---	---	---	---
KIAA2022	340533	broad.mit.edu	37	X	73963628	73963628	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:73963628T>C	uc004eby.2	-	3	1381	c.764A>G	c.(763-765)AAT>AGT	p.N255S		NM_001008537	NP_001008537	Q5QGS0	K2022_HUMAN	hypothetical protein LOC340533	255					base-excision repair, gap-filling|DNA replication proofreading|DNA replication, removal of RNA primer|nucleotide-excision repair, DNA gap filling|regulation of mitotic cell cycle|S phase of mitotic cell cycle	delta DNA polymerase complex	3'-5'-exodeoxyribonuclease activity|DNA-directed DNA polymerase activity			ovary(7)|large_intestine(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	15																		---	---	---	---
ZDHHC15	158866	broad.mit.edu	37	X	74698760	74698760	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:74698760G>A	uc004ecg.2	-	3	702	c.224C>T	c.(223-225)TCT>TTT	p.S75F	ZDHHC15_uc004ech.2_Missense_Mutation_p.S66F|ZDHHC15_uc011mqo.1_RNA|ZDHHC15_uc004eci.2_Missense_Mutation_p.S66F	NM_144969	NP_659406	Q96MV8	ZDH15_HUMAN	zinc finger, DHHC-type containing 15 isoform 1	75						integral to membrane	zinc ion binding			ovary(2)	2																		---	---	---	---
ATRX	546	broad.mit.edu	37	X	76937085	76937085	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:76937085G>A	uc004ecp.3	-	9	3895	c.3663C>T	c.(3661-3663)AGC>AGT	p.S1221S	ATRX_uc004ecq.3_Silent_p.S1183S|ATRX_uc004eco.3_Silent_p.S1006S|ATRX_uc004ecr.2_Silent_p.S1153S|ATRX_uc010nlx.1_Silent_p.S1192S|ATRX_uc010nly.1_Silent_p.S1166S	NM_000489	NP_000480	P46100	ATRX_HUMAN	transcriptional regulator ATRX isoform 1	1221					DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30					Phosphatidylserine(DB00144)			Mis|F|N		Pancreatic neuroendocrine tumors		ATR-X (alpha thalassemia/mental retardation) syndrome						---	---	---	---
FAM46D	169966	broad.mit.edu	37	X	79699014	79699014	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:79699014A>G	uc004edl.1	+	5	1310	c.976A>G	c.(976-978)ACC>GCC	p.T326A	FAM46D_uc004edm.1_Missense_Mutation_p.T326A	NM_152630	NP_689843	Q8NEK8	FA46D_HUMAN	hypothetical protein LOC169966	326										lung(2)	2																		---	---	---	---
POU3F4	5456	broad.mit.edu	37	X	82763323	82763323	+	5'UTR	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:82763323C>A	uc004eeg.2	+	1						NM_000307	NP_000298			POU domain, class 3, transcription factor 4						sensory perception of sound	nucleus	sequence-specific DNA binding transcription factor activity			ovary(1)	1																		---	---	---	---
SATL1	340562	broad.mit.edu	37	X	84362915	84362915	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:84362915G>A	uc011mqx.1	-	1	1060	c.1060C>T	c.(1060-1062)CGA>TGA	p.R354*	SATL1_uc004een.2_Nonsense_Mutation_p.R354*	NM_001163541	NP_001157013	Q86VE3	SATL1_HUMAN	spermidine/spermine N1-acetyl transferase-like 1	167	Gln-rich.						N-acetyltransferase activity			breast(2)	2																		---	---	---	---
KLHL4	56062	broad.mit.edu	37	X	86869479	86869479	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:86869479T>C	uc004efb.2	+	3	815	c.633T>C	c.(631-633)TTT>TTC	p.F211F	KLHL4_uc004efa.2_Silent_p.F211F	NM_019117	NP_061990	Q9C0H6	KLHL4_HUMAN	kelch-like 4 isoform 1	211	BTB.					cytoplasm|microtubule cytoskeleton|nucleolus	actin binding			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5																		---	---	---	---
PCDH19	57526	broad.mit.edu	37	X	99662990	99662990	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:99662990C>T	uc010nmz.2	-	1	2282	c.606G>A	c.(604-606)TCG>TCA	p.S202S	PCDH19_uc004efw.3_Silent_p.S202S|PCDH19_uc004efx.3_Silent_p.S202S	NM_020766	NP_001098713	Q8TAB3	PCD19_HUMAN	protocadherin 19 isoform b	202	Cadherin 2.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|breast(2)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	7																		---	---	---	---
SRPX2	27286	broad.mit.edu	37	X	99921851	99921851	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:99921851C>T	uc004egb.2	+	8	1362	c.882C>T	c.(880-882)GGC>GGT	p.G294G		NM_014467	NP_055282	O60687	SRPX2_HUMAN	sushi-repeat-containing protein, X-linked 2	294	Sushi 3.				angiogenesis|cell motility|cell-cell adhesion|positive regulation of cell migration involved in sprouting angiogenesis|regulation of phosphorylation	cytoplasm|extracellular region	receptor binding			ovary(2)	2																		---	---	---	---
SYTL4	94121	broad.mit.edu	37	X	99944870	99944870	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:99944870C>A	uc004egd.3	-	11	1251	c.895G>T	c.(895-897)GGC>TGC	p.G299C	SYTL4_uc010nnb.2_Translation_Start_Site|SYTL4_uc010nnc.2_Missense_Mutation_p.G299C|SYTL4_uc004ege.3_Missense_Mutation_p.G299C|SYTL4_uc004egf.3_Missense_Mutation_p.G299C|SYTL4_uc004egg.3_Missense_Mutation_p.G299C	NM_080737	NP_542775	Q96C24	SYTL4_HUMAN	synaptotagmin-like 4	299					exocytosis|intracellular protein transport	extrinsic to membrane|plasma membrane|synaptic vesicle|transport vesicle membrane	neurexin binding|phospholipid binding|Rab GTPase binding|transporter activity|zinc ion binding			ovary(2)	2					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)													---	---	---	---
ARL13A	392509	broad.mit.edu	37	X	100242381	100242381	+	Silent	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100242381G>A	uc004ego.2	+	6	605	c.489G>A	c.(487-489)GAG>GAA	p.E163E	ARL13A_uc011mrf.1_Silent_p.E163E|ARL13A_uc010nng.2_Silent_p.E163E	NM_001012990	NP_001013008	Q5H913	AR13A_HUMAN	ADP-ribosylation factor-like 13 isoform a	163							GTP binding			ovary(1)	1																		---	---	---	---
DRP2	1821	broad.mit.edu	37	X	100502130	100502130	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100502130G>A	uc004egz.2	+	12	1598	c.1229G>A	c.(1228-1230)CGC>CAC	p.R410H	DRP2_uc011mrh.1_Missense_Mutation_p.R332H	NM_001939	NP_001930	Q13474	DRP2_HUMAN	dystrophin related protein 2	410					central nervous system development	cytoplasm|cytoskeleton	zinc ion binding			ovary(2)	2																		---	---	---	---
DRP2	1821	broad.mit.edu	37	X	100505903	100505903	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100505903T>C	uc004egz.2	+						DRP2_uc011mrh.1_Intron	NM_001939	NP_001930			dystrophin related protein 2						central nervous system development	cytoplasm|cytoskeleton	zinc ion binding			ovary(2)	2																		---	---	---	---
ARMCX2	9823	broad.mit.edu	37	X	100911457	100911457	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:100911457C>T	uc004eid.2	-	3	1473	c.1118G>A	c.(1117-1119)CGC>CAC	p.R373H	ARMCX2_uc004eie.3_Missense_Mutation_p.R373H|ARMCX2_uc004eif.3_Missense_Mutation_p.R373H|ARMCX2_uc004eig.3_Missense_Mutation_p.R373H|ARMCX2_uc010nnt.2_Missense_Mutation_p.R373H	NM_177949	NP_808818	Q7L311	ARMX2_HUMAN	ALEX2 protein	373						integral to membrane	binding			ovary(6)	6																		---	---	---	---
GPRASP1	9737	broad.mit.edu	37	X	101912007	101912007	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:101912007C>T	uc004ejj.3	+	5	3967	c.3166C>T	c.(3166-3168)CCA>TCA	p.P1056S	GPRASP1_uc004eji.3_Missense_Mutation_p.P1056S|GPRASP1_uc010nod.2_Missense_Mutation_p.P1056S	NM_014710	NP_055525	Q5JY77	GASP1_HUMAN	G protein-coupled receptor associated sorting	1056	OPRD1-binding.					cytoplasm	protein binding			ovary(1)|lung(1)	2																		---	---	---	---
RAB40AL	282808	broad.mit.edu	37	X	102192850	102192850	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102192850T>C	uc004ejs.2	+	1	651	c.604T>C	c.(604-606)TCC>CCC	p.S202P		NM_001031834	NP_001027004	P0C0E4	RB40L_HUMAN	RAB40A, member RAS oncogene family-like	202	SOCS box.				protein transport|small GTPase mediated signal transduction	mitochondrion|plasma membrane	GTP binding			ovary(2)	2																		---	---	---	---
TCEAL4	79921	broad.mit.edu	37	X	102841974	102841974	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:102841974G>T	uc004ekl.2	+	3	664	c.371G>T	c.(370-372)AGG>ATG	p.R124M	TCEAL4_uc004ekn.2_Missense_Mutation_p.R124M|TCEAL4_uc004ekm.2_Missense_Mutation_p.R124M|TCEAL4_uc004eko.2_Missense_Mutation_p.R124M	NM_024863	NP_079139	Q96EI5	TCAL4_HUMAN	transcription elongation factor A (SII)-like 4	124					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0																		---	---	---	---
TEX13A	56157	broad.mit.edu	37	X	104465051	104465051	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:104465051C>T	uc004ema.2	-	2	143	c.31G>A	c.(31-33)GGG>AGG	p.G11R	IL1RAPL2_uc004elz.1_Intron|TEX13A_uc004emb.2_Missense_Mutation_p.G11R	NM_031274	NP_112564	Q9BXU3	TX13A_HUMAN	testis expressed sequence 13A	11						intracellular	zinc ion binding			ovary(2)	2																		---	---	---	---
IRS4	8471	broad.mit.edu	37	X	107978530	107978530	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:107978530C>T	uc004eoc.2	-	1	1078	c.1045G>A	c.(1045-1047)GCC>ACC	p.A349T		NM_003604	NP_003595	O14654	IRS4_HUMAN	insulin receptor substrate 4	349						plasma membrane	insulin receptor binding|SH3/SH2 adaptor activity|signal transducer activity			ovary(4)|large_intestine(2)|lung(1)|breast(1)|skin(1)|pancreas(1)	10																		---	---	---	---
KIAA1210	57481	broad.mit.edu	37	X	118220541	118220541	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:118220541A>G	uc004era.3	-	11	4652	c.4652T>C	c.(4651-4653)ATG>ACG	p.M1551T		NM_020721	NP_065772	Q9ULL0	K1210_HUMAN	hypothetical protein LOC57481	1551										ovary(4)|skin(1)	5																		---	---	---	---
CUL4B	8450	broad.mit.edu	37	X	119693927	119693927	+	Intron	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119693927G>A	uc004esw.2	-						CUL4B_uc004esv.2_Intron	NM_003588	NP_003579			cullin 4B isoform 1						cell cycle|DNA repair|ubiquitin-dependent protein catabolic process	Cul4B-RING ubiquitin ligase complex|nucleus	protein binding|ubiquitin protein ligase binding			lung(1)|central_nervous_system(1)|pancreas(1)	3																		---	---	---	---
C1GALT1C1	29071	broad.mit.edu	37	X	119760846	119760846	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:119760846T>G	uc004esy.2	-	3	523	c.176A>C	c.(175-177)GAG>GCG	p.E59A	C1GALT1C1_uc004esz.2_Missense_Mutation_p.E59A	NM_152692	NP_689905	Q96EU7	C1GLC_HUMAN	C1GALT1-specific chaperone 1	59	Lumenal (Potential).					integral to membrane					0																		---	---	---	---
OCRL	4952	broad.mit.edu	37	X	128682529	128682529	+	Intron	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128682529T>C	uc004euq.2	+						OCRL_uc004eur.2_Intron	NM_000276	NP_000267			phosphatidylinositol polyphosphate 5-phosphatase						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	clathrin-coated vesicle|cytosol|early endosome|Golgi stack|Golgi-associated vesicle	GTPase activator activity|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|protein binding			lung(2)|ovary(1)|kidney(1)	4																		---	---	---	---
ELF4	2000	broad.mit.edu	37	X	129201185	129201185	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129201185T>C	uc004evd.3	-	9	1888	c.1503A>G	c.(1501-1503)CCA>CCG	p.P501P	ELF4_uc004eve.3_Silent_p.P501P	NM_001421	NP_001412	Q99607	ELF4_HUMAN	E74-like factor 4	501					natural killer cell proliferation|NK T cell proliferation|positive regulation of transcription from RNA polymerase II promoter	PML body	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1								T	ERG	AML								---	---	---	---
FHL1	2273	broad.mit.edu	37	X	135290746	135290746	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135290746T>C	uc004ezo.2	+	5	734	c.634T>C	c.(634-636)TGC>CGC	p.C212R	FHL1_uc010nrz.2_Missense_Mutation_p.C212R|FHL1_uc004ezm.2_RNA|FHL1_uc004ezl.2_Missense_Mutation_p.C212R|FHL1_uc004ezq.2_Intron|FHL1_uc011mvy.1_Missense_Mutation_p.C212R|FHL1_uc011mvz.1_Missense_Mutation_p.C212R|FHL1_uc004ezn.2_Missense_Mutation_p.C212R|FHL1_uc011mwa.1_Missense_Mutation_p.C241R|FHL1_uc011mwb.1_RNA|FHL1_uc004ezp.2_Missense_Mutation_p.C228R|FHL1_uc004ezr.2_Silent_p.I30I	NM_001159702	NP_001153174	Q13642	FHL1_HUMAN	four and a half LIM domains 1 isoform 1	212	LIM zinc-binding 3.				cell differentiation|cell growth|muscle organ development|organ morphogenesis	cytosol|nucleus|plasma membrane	protein binding|zinc ion binding				0	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
ARHGEF6	9459	broad.mit.edu	37	X	135758805	135758805	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135758805C>A	uc004fab.2	-	18	2385	c.1923G>T	c.(1921-1923)GAG>GAT	p.E641D	ARHGEF6_uc011mwd.1_Missense_Mutation_p.E514D|ARHGEF6_uc011mwe.1_Missense_Mutation_p.E487D	NM_004840	NP_004831	Q15052	ARHG6_HUMAN	Rac/Cdc42 guanine nucleotide exchange factor 6	641					apoptosis|cell junction assembly|induction of apoptosis by extracellular signals|JNK cascade|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|Rho guanyl-nucleotide exchange factor activity				0	Acute lymphoblastic leukemia(192;0.000127)																	---	---	---	---
MAGEC3	139081	broad.mit.edu	37	X	140983303	140983303	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:140983303C>T	uc011mwp.1	+	6	1081	c.1081C>T	c.(1081-1083)CGA>TGA	p.R361*	MAGEC3_uc004fbs.2_Intron|MAGEC3_uc010nsj.2_5'Flank	NM_138702	NP_619647	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3 isoform 1	361	MAGE 1.									skin(2)|central_nervous_system(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
MAMLD1	10046	broad.mit.edu	37	X	149671649	149671649	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:149671649C>T	uc004fee.1	+	5	2222	c.2146C>T	c.(2146-2148)CCC>TCC	p.P716S	MAMLD1_uc011mxu.1_Intron|MAMLD1_uc011mxv.1_Missense_Mutation_p.P691S|MAMLD1_uc011mxw.1_Missense_Mutation_p.P602S	NM_005491	NP_005482	Q13495	MAMD1_HUMAN	mastermind-like domain containing 1	716					male gonad development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
FATE1	89885	broad.mit.edu	37	X	150889940	150889940	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150889940G>A	uc004fex.2	+	3	392	c.308G>A	c.(307-309)GGC>GAC	p.G103D		NM_033085	NP_149076	Q969F0	FATE1_HUMAN	fetal and adult testis expressed transcript	103						endoplasmic reticulum|integral to membrane				ovary(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
GABRQ	55879	broad.mit.edu	37	X	151820127	151820127	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:151820127T>C	uc004ffp.1	+	8	1060	c.1040T>C	c.(1039-1041)GTC>GCC	p.V347A		NM_018558	NP_061028	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) receptor, theta	347	Helical; (Potential).					cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity|neurotransmitter transporter activity			ovary(2)|pancreas(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
ATP2B3	492	broad.mit.edu	37	X	152806925	152806925	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152806925T>C	uc004fht.1	+	2	443	c.317T>C	c.(316-318)CTG>CCG	p.L106P	ATP2B3_uc004fhs.1_Missense_Mutation_p.L106P	NM_001001344	NP_001001344	Q16720	AT2B3_HUMAN	plasma membrane calcium ATPase 3 isoform 3b	106	Helical; (Potential).				ATP biosynthetic process|platelet activation	integral to membrane|plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding			pancreas(1)	1	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
ATP2B3	492	broad.mit.edu	37	X	152818719	152818719	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:152818719C>T	uc004fht.1	+	11	2176	c.2050C>T	c.(2050-2052)CGG>TGG	p.R684W	ATP2B3_uc004fhs.1_Missense_Mutation_p.R684W	NM_001001344	NP_001001344	Q16720	AT2B3_HUMAN	plasma membrane calcium ATPase 3 isoform 3b	684	Cytoplasmic (Potential).				ATP biosynthetic process|platelet activation	integral to membrane|plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding			pancreas(1)	1	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
ABCD1	215	broad.mit.edu	37	X	153006102	153006102	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153006102G>A	uc004fif.2	+	7	2108	c.1709G>A	c.(1708-1710)GGC>GAC	p.G570D	ABCD1_uc004fig.2_Missense_Mutation_p.G70D|ABCD1_uc004fih.2_5'Flank	NM_000033	NP_000024	P33897	ABCD1_HUMAN	ATP-binding cassette, sub-family D (ALD), member	570	ABC transporter.				fatty acid beta-oxidation using acyl-CoA oxidase|peroxisomal membrane transport|peroxisome organization	cytosol|integral to peroxisomal membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|identical protein binding|peroxisomal fatty-acyl-CoA transporter activity				0	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
HCFC1	3054	broad.mit.edu	37	X	153216354	153216354	+	Silent	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153216354G>T	uc004fjp.2	-	23	6141	c.5613C>A	c.(5611-5613)GCC>GCA	p.A1871A		NM_005334	NP_005325	P51610	HCFC1_HUMAN	host cell factor 1	1871					cell cycle|interspecies interaction between organisms|positive regulation of cell cycle|positive regulation of gene expression|protein stabilization|reactivation of latent virus|regulation of protein complex assembly|transcription from RNA polymerase II promoter	mitochondrion|MLL1 complex|MLL5-L complex|Set1C/COMPASS complex	chromatin binding|identical protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)	2	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
TMEM187	8269	broad.mit.edu	37	X	153247781	153247781	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153247781G>T	uc004fjq.2	+	2	802	c.268G>T	c.(268-270)GCA>TCA	p.A90S	hsa-mir-3202-2|MI0014253_5'Flank	NM_003492	NP_003483	Q14656	TM187_HUMAN	transmembrane protein 187	90	Helical; (Potential).					integral to membrane|transport vesicle					0	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
FLNA	2316	broad.mit.edu	37	X	153593070	153593070	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153593070G>A	uc004fkk.2	-	13	2095	c.1846C>T	c.(1846-1848)CCA>TCA	p.P616S	FLNA_uc010nuu.1_Missense_Mutation_p.P616S	NM_001110556	NP_001104026	P21333	FLNA_HUMAN	filamin A, alpha isoform 2	616	Filamin 4.				actin crosslink formation|actin cytoskeleton reorganization|cell junction assembly|cytoplasmic sequestering of protein|establishment of protein localization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|negative regulation of protein catabolic process|negative regulation of sequence-specific DNA binding transcription factor activity|platelet activation|platelet degranulation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of transcription factor import into nucleus|protein localization at cell surface|protein stabilization|receptor clustering	cell cortex|cytosol|extracellular region|nucleus|plasma membrane	actin filament binding|Fc-gamma receptor I complex binding|glycoprotein binding|GTP-Ral binding|protein homodimerization activity|Rac GTPase binding|signal transducer activity|transcription factor binding			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)																	---	---	---	---
TAZ	6901	broad.mit.edu	37	X	153641810	153641810	+	Intron	SNP	C	A	A			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153641810C>A	uc004fkx.2	+						DNASE1L1_uc004fku.1_5'Flank|DNASE1L1_uc004fkv.1_5'Flank|DNASE1L1_uc004fkw.1_5'Flank|TAZ_uc004fky.2_Intron|TAZ_uc004fkz.2_Intron|TAZ_uc004fla.2_Intron|TAZ_uc004flb.2_Intron|TAZ_uc010nuy.2_Intron|TAZ_uc004flc.3_Intron	NM_000116	NP_000107			tafazzin isoform 1						cardiac muscle contraction|cardiac muscle tissue development|cardiolipin biosynthetic process|cristae formation|hemopoiesis|mitochondrial ATP synthesis coupled electron transport|mitochondrial respiratory chain complex I assembly|skeletal muscle tissue development	integral to membrane|mitochondrion	1-acylglycerophosphocholine O-acyltransferase activity				0	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)																	---	---	---	---
ATP6AP1	537	broad.mit.edu	37	X	153664070	153664070	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153664070A>G	uc004flf.1	+	10	1307	c.1246A>G	c.(1246-1248)AGC>GGC	p.S416G	ATP6AP1_uc004flg.1_RNA|ATP6AP1_uc004flh.1_Missense_Mutation_p.S376G|GDI1_uc011mzo.1_5'Flank|GDI1_uc004fli.3_5'Flank	NM_001183	NP_001174	Q15904	VAS1_HUMAN	ATPase, H+ transporting, lysosomal accessory	416					ATP hydrolysis coupled proton transport	integral to membrane|proton-transporting V-type ATPase, V1 domain|vacuolar membrane	ATP binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|proton-transporting ATPase activity, rotational mechanism			ovary(3)|breast(1)	4	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)																	---	---	---	---
PLXNA3	55558	broad.mit.edu	37	X	153693480	153693480	+	Silent	SNP	C	T	T	rs138065609		TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153693480C>T	uc004flm.2	+	11	2336	c.2163C>T	c.(2161-2163)TGC>TGT	p.C721C		NM_017514	NP_059984	P51805	PLXA3_HUMAN	plexin A3 precursor	721	Extracellular (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane	transmembrane receptor activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)																	---	---	---	---
SLC10A3	8273	broad.mit.edu	37	X	153715964	153715964	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153715964C>T	uc004flq.2	-	3	1580	c.1316G>A	c.(1315-1317)CGC>CAC	p.R439H	UBL4A_uc004flo.2_5'Flank|SLC10A3_uc004flr.2_Missense_Mutation_p.R410H|SLC10A3_uc004flp.2_Missense_Mutation_p.R439H	NM_001142392	NP_001135864	P09131	P3_HUMAN	solute carrier family 10, member 3 isoform 1	439					organic anion transport	integral to membrane	bile acid:sodium symporter activity			ovary(1)|skin(1)	2	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)																	---	---	---	---
F8	2157	broad.mit.edu	37	X	154130402	154130402	+	Silent	SNP	T	C	C			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154130402T>C	uc004fmt.2	-	19	6210	c.6039A>G	c.(6037-6039)GGA>GGG	p.G2013G	F8_uc010nvi.1_Intron	NM_000132	NP_000123	P00451	FA8_HUMAN	coagulation factor VIII isoform a precursor	2013	F5/8 type A 3.|Plastocyanin-like 6.		G -> R (in HEMA).		acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation	extracellular space|plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity|protein binding			ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	11	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)													---	---	---	---
CLIC2	1193	broad.mit.edu	37	X	154563692	154563692	+	Silent	SNP	C	T	T			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:154563692C>T	uc004fnf.2	-	1	295	c.45G>A	c.(43-45)GAG>GAA	p.E15E	CLIC2_uc010nvj.1_Silent_p.E15E	NM_001289	NP_001280	O15247	CLIC2_HUMAN	chloride intracellular channel 2	15	N-terminal.|Required for insertion into the membrane (By similarity).				signal transduction	chloride channel complex|cytoplasm|nucleus	voltage-gated chloride channel activity			large_intestine(1)|ovary(1)|skin(1)	3	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)																	---	---	---	---
UTY	7404	broad.mit.edu	37	Y	15362891	15362891	+	Intron	SNP	A	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:15362891A>G	uc004fsx.1	-						UTY_uc004fsw.1_Intron|UTY_uc010nwx.1_Intron	NM_007125	NP_009056			tetratricopeptide repeat protein isoform 3						chromatin modification	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0																		---	---	---	---
UTY	7404	broad.mit.edu	37	Y	15447586	15447586	+	Silent	SNP	T	G	G			TCGA-BR-4298-01A-01D-1126-08	TCGA-BR-4298-11A-01D-1126-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:15447586T>G	uc004fsx.1	-	16	3405	c.2400A>C	c.(2398-2400)ACA>ACC	p.T800T	UTY_uc004fsw.1_Silent_p.T463T|UTY_uc010nwx.1_Intron|UTY_uc004fsy.2_Silent_p.T800T|UTY_uc004fsz.2_Silent_p.T800T	NM_007125	NP_009056	O14607	UTY_HUMAN	tetratricopeptide repeat protein isoform 3	800					chromatin modification	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0																		---	---	---	---
